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SDG 15

Navigating tissue banking regulation: conceptual frameworks for researchers, administrators, regulators and policy-makers.
19 November 2014
University of Sydney

Lipworth, W

In the “post-genomic” age of biomedical research, researchers often wish to utilise collections of human tissue. This type of research raises many ethical and legal issues and anyone wishing to use such collections is faced with an enormously complex set of regulatory requirements, many of which are still ambiguous, reflecting ongoing ethical and legal debate. Whilst there is no way of entirely avoiding such regulatory complexity and ambiguity, conceptual frameworks can assist those who wish to use, administer, authorise and generate policy on tissue banking research. Two conceptual frameworks are described here: a taxonomy of tissue banking practices, aimed at assisting those who need to ensure that tissue banks meet ethical and legal requirements; and a “syncretic” approach to policy-making, for those who wish to generate new policy,or streamline existing policy relating to tissue banking research
Cladobotryum spp. Nees emend. (syn. Dactylium Nees)
28 April 2020
University of Sydney

Perrine-Walker, Francine;Thai, Meghann

Historically, the soil habiting fungus Cladobotryum dendroides (Teleopmorh- Hypomyces rosellus) is the main causal agent of cobweb disease of the cultivated mushroom Agaricus bisporus. However, there are several Cladobotryum species that cause cobweb disease in commercially cultivated white button mushroom and other economically and wild edible mushrooms .The Cladobotryum protrusum genome is the first complete genome to be sequenced in the genus Cladobotryum (39.09 Mb).
From reference genomes to population genomics: comparing three reference aligned reduced-representation sequencing pipelines in two wildlife species
18 August 2020
University of Sydney

Wright, Belinda;Farquharson, Katherine A.;McLennan, Elspeth A.;Belov, Katherine;Hogg, Carolyn J.;Grueber, Catherine E.

Background: Recent advances in genomics have greatly increased research opportunities for non-model species. For wildlife, a growing availability of reference genomes means that population genetics is no longer restricted to a small set of anonymous loci. When used in conjunction with a reference genome, reduced-representation sequencing (RRS) provides a cost-effective method for obtaining reliable diversity information for population genetics. Many software tools have been developed to process RRS data, though few studies of non-model species incorporate genome alignment in calling loci. A commonly-used RRS analysis pipeline, Stacks, has this capacity and so it is timely to compare its utility with existing software originally designed for alignment and analysis of whole genome sequencing data. Here we examine population genetic inferences from two species for which reference-aligned reduced-representation data have been collected. Our two study species are a threatened Australian marsupial (Tasmanian devil Sarcophilus harrisii; declining population) and an Arctic-circle migrant bird (pink-footed goose Anser brachyrhynchus; expanding population). Analyses of these data are compared using Stacks versus two widely-used genomics packages, SAM tools and GATK. We also introduce a custom R script to improve the reliability of single nucleotide polymorphism (SNP) calls in all pipelines and conduct population genetic inferences for non-model species with reference genomes. Results: Although we identified orders of magnitude fewer SNPs in our devil data set than for goose, we found remarkable symmetry between the two species in our assessment of software performance. For both datasets, all three methods were able to delineate population structure, even with varying numbers of loci. For both species, population structure inferences were influenced by the percent of missing data. Conclusions: For studies of non-model species with a reference genome, we recommend combining Stacks output with further filtering (as included in our R pipeline) for population genetic studies, paying particular attention to potential impact of missing data thresholds. We recognise SAM tools as a viable alternative for researchers more familiar with this software. We caution against the use of GATK in studies with limited computational resources or time. Keywords: Population genomics, DArTseq, Reference genome, Tasmanian devil, Pink-footed goose, Population differentiation, Stacks, SAM tools, GATK
Genetic analysis of scat samples to inform conservation of the Tasmanian devil
18 August 2020
University of Sydney

Grueber, Catherine E.;Chong, Rowena;Gooley, Rebecca M.;McLennan, Elspeth A.;Barrs, Vanessa R.;Belov, Katherine;Hogg, Carolyn J.

Recent advances in molecular genetics have enabled a great deal of information about species to be obtained from analysis of non-invasively collected samples such as scat. Scat provides genetic information via residual host DNA on the outside of the scat, via characterising the genetic makeup of intestinal microbes that are present in the scat, or by examining the DNA remnants of prey items that have passed through the animal’s digestive tract. In this review, we provide a case study to demonstrate how these approaches are being used to better understand the threatened Tasmanian devil in the landscape, and to support the species’ conservation. Scat analysis enables us to quantify the genetic diversity of remote populations, where trapping is logistically challenging. We are beginning to learn how conservation management impacts the microbiome of threatened species, and investigate how various management strategies may be impacting the diverse array of bacteria and viruses that devils, like all animal species, are host to. We are using scat samples to better understand the interaction between devils and other animals in their environment by learning more about what they eat. We explore the strengths and challenges of these approaches by comparing our work to that conducted in other species. Finally, we provide specific examples of how our results are being integrated into conservation strategy for the devil.
“Devil Tools & Tech”: A Synergy of Conservation Research and Management Practice
18 August 2020
University of Sydney

Hogg, Carolyn J.;Grueber, Catherine E.;Pemberton, David;Fox, Samantha;Lee, Andrew V.;Ivy, Jamie A.;Belov, Katherine

Biodiversity conservation continually presents new challenges, yet conservation resources are limited, and funding for applied conservation re-search projects more so. Recently, many have reported on the “research–implementation gap,” whereby conservation research ﬁndings are infrequently translated into conservation actions. In this perspective, we describe our experiences working in a large multi-institutional, multi-disciplinary team as we attempt to bridge the research–implementation gap by developing conservation tools needed to address the conservation challenges faced by Tasmanian devils (Sarcophilus harrisii). We discuss our project’s history, lessons learnt,outcomes, and future plans to provide insights that may help others develop multi-institutional projects, designed to target rapid and direct implementation of conservation research into management action. Key to our success is the needs-based prioritization of research measured against the management team’s questions, recognition of the different needs of academia, industry and government, a collegiate approach, and willingness to embrace adaptive management. Challenges include developing a project which meets all strategictargets of different institutions, in addition to sourcing funds. Overall, our goal has been to establish an enduring research-management framework, to facilitate improved integration of scientiﬁc research into the management needs of Tasmanian devil conservation, and serve as a template for other species management project
The Tasmanian devil microbiome— implications for conservation and management
18 August 2020
University of Sydney

Cheng, Yuanyuan;Fox, Samantha;Pemberton, David;Hogg, Carolyn;Papenfuss, Anthony T.;Belov, Katherine

Background: The Tasmanian devil, the world’s largest carnivorous marsupial, is at risk of extinction due to devil facial tumour disease (DFTD), a fatal contagious cancer. The Save the Tasmanian Devil Program has established an insurance population, which currently holds over 600 devils in captive facilities across Australia. Microbes are known to play a crucial role in the health and well-being of humans and other animals, and increasing evidence suggests that changes in the microbiota can influence various aspects of host physiology and development. To improve our understanding of devils and facilitate management and conservation of the species, we characterised the microbiome of wild devils and investigated differences in the composition of microbial community between captive and wild individuals. Results: A total of 1,223,550 bacterial 16S ribosomal RNA (rRNA) sequences were generated via Roche 454 sequencing from 56 samples, including 17 gut, 15 skin, 18 pouch and 6 oral samples. The devil’s gut microbiome was dominated by Firmicutes and showed a high Firmicutes-to-Bacteroidetes ratio, which appears to be a common feature of many carnivorous mammals. Metabolisms of carbohydrates, amino acids, energy, cofactors and vitamins, nucleotides and lipids were predicted as the most prominent metabolic pathways that the devil's gut flora contributed to. The microbiota inside the female’s pouch outside lactation was highly similar to that of the skin, both co-dominated by Firmicutes and Proteobacteria. The oral microbiome had similar proportions of Proteobacteria, Bacteroidetes, Firmicutes and Fusobacteria. Conclusions: Compositional differences were observed in all four types of microbiota between devils from captive and wild populations. Certain captive devils had significantly lower levels of gut bacterial diversity than wild individuals, and the two groups differed in the proportion of gut bacteria accounting for the metabolism of glycan, amino acids and cofactors and vitamins. Further studies are underway to investigate whether alterations in the microbiome of captive devils can have impacts on their ability to adapt and survive following re-introduction to the wild. Keywords: Tasmanian devil, Marsupial, Carnivore, Microbiota, Endangered species, Conservation and management
Marsupial Gut Microbiome
19 August 2020
University of Sydney

Chong, Rowena;Cheng, Yuanyuan;Hogg, Carolyn J.;Belov, Katherine

The study of the gut microbiome in threatened wildlife species has enormous potential to improve conservation efforts and gain insights into host-microbe coevolution. Threatened species are often housed in captivity, and during this process undergo considerable changes to their gut microbiome. Studying the gut microbiome of captive animals therefore allows identification of dysbiosis and opportunities for improving management practices in captivity and for subsequent translocations. Manipulation of the gut microbiome through methods such as fecal transplant may offer an innovative means of restoring dysbiotic microbiomes in threatened species to provide health benefits. Finally, characterization of the gut microbiome (including the viral components, or virome) provides important baseline health information and may lead to discovery of significant microbial pathogens. Here we summarize our current understanding of microbiomes in Australian marsupial species.
Preserving the demographic and genetic integrity of a single source population during multiple translocations
19 August 2020
University of Sydney

Hogg, C.J.;McLennan, E.A.;Wise, P.;Lee, A.V.;Pemberton, D.;Fox, S.;Belov, Katherine;Grueber, C.E.

Globally, conservation translocations are common often using island, or‘virtual island’populations as a source site. We investigated demographic and genetic consequences of using a single source island population for multiple translocations. Our harvest selection protocol preserves the source population whilst providing individuals that are representative of the source population. Our study species, Tasmanian devils, are endangered due to an infectious cancer with an 80 % reduction in population size across their range. In 2012, an island population was established to protect the species. The island population was harvested three times with devils translocated to wild location across Tasmania (2016, N = 16; 2017, N = 33; 2018, N = 30). Efforts to harvest individuals demographically representative of the source population was achievable in 2017 and 2018, with a large male bias occurring in 2016 due to logistic constraints. Using internal relatedness (IR; proxy for hetero-zygosity), we showed that harvesting animals in equal-sized groups of high, medium and low IR, succeeded in maintaining genetic profiles of the source population over repeated harvests. There was little within-year variation in observed heterozygosity pre- and post-harvest compared to the harvest group, and only a small reduction (0.001) in heterozygosity across years. We used simulations to show that using a random selection would likely have eroded diversity relative to our structured approach (86.6% of iterations showed greater loss). Our method maintained a viable source population over multiple harvests, providing conservation managers with a tool for conserving single source populations used in threatened species translocation
Metapopulation management of an Endangered species with limited genetic diversity in the presence of disease: the Tasmanian devil Sarcophilus harrisii
19 August 2020
University of Sydney

Hogg, Carolyn

There has been much discussion relating to the current biodiversity crisis, with the loss of species now at an unprecedented rate. Using augmentation and/or reintroduction to minimize the loss of species in the wild is becoming more prominent. Zoological institutions have been traditionally involved in the management of insurance populations providing a range of species for release to the wild. Insurance populations can be costly, both in resources and behavioural changes, and so should aim to be maintained for as short a time as possible, with a maximum of 40 years. A Tasmanian devil Sarcophilus harrisii insurance population was established in 2006 with the arrival of devil facial tumour disease, and was founded with 120 individuals sourced predominantly from the west coast of Tasmania. Here the challenges of establishing and managing an insurance population in an already genetically depauperate species in the presence of a contagious cancer are discussed. The Tasmanian devil insurance metapopulation now includes a continuum of management scenarios (from intensive zoo-based facilities, through free-range enclosures, to an island and fenced peninsula) and consists of over 700 devils representing at least 180 founders. The lessons learned in regard to this programme are presented, including the issues surrounding reduced genetic diversity and how we are striving to improve the long-term management of the insurance metapopulation through a combination of molecular genetics, modelling and on-the-ground management. The tools and technologies that have been developed in this programme are directly applicable to the recovery and management of a suite of other threatened fauna.
Comparative genomics for biodiversity conservation
19 August 2020
University of Sydney

Grueber, Catherine

Genomic approaches are gathering momentum in biology and emerging opportunities lie in the creative use of comparative molecular methods for revealing the processes that influence diversity of wildlife. However, few comparative genomic studies are performed with explicit and specific objectives to aid conservation of wild populations. Here I provide a brief overview of comparative genomic approaches that offer specific benefits to biodiversity conservation. Because conservation examples are few, I draw on research from other areas to demonstrate how comparing genomic data across taxa may be used to inform the characterisation of conservation units and studies of hybridisation, as well as studies that provide conservation outcomes from a better understanding of the drivers of divergence. A comparative approach can also provide valuable insight into the threatening processes that impact rare species, such as emerging diseases and their management in conservation. In addition to these opportunities, I note areas where additional research is warranted. Overall, comparing and contrasting the genomic composition of threatened and other species provide several useful tools for helping to preserve the molecular biodiversity of the global ecosystem.
Carbon farming for resilient rangelands: people, paddocks and policy
14 September 2020
University of Sydney

Baumber, Alex;Waters, Cathy;Cross, Rebecca;Metternicht, Graciela;Simpson, Marja

Carbon farming is a new land use option over extensive areas of the Australian rangelands. This land use change has been promoted by government incentives to mitigate climate change, with most of Australia’s land sector abatement to date being delivered in rangelands. Aside from these mitigation benefits, carbon farming has also demonstrated potential co-benefits that enhance socio-ecological resilience by diversifying land uses and income streams, providing opportunities for sustainable land management to enhance soil and vegetation and creating opportunities for self-organisation and collaboration. However, factors such as policy uncertainty, perceived loss of future land use flexibility and the potential for carbon farming eligibility to create social divisions may negatively affect resilience. In this paper we weigh up these risks, opportunities and co-benefits and propose indicators for measuring the impact of carbon farming on the resilience of rangeland systems. A set of land policy principles for enhancing resilience through carbon farming are also identified.
Comparison of three methods of estimating the population size of an arboreal mammal in a fragmented rural landscape
21 December 2020
University of Sydney

Crowther, Mathew S.;Dargan, Jessica R.;Madani, George;Rus, Adrian I.;Krockenberger, Mark B.;McArthur, Clare;Moore, Ben D.;Lunne, Daniel;Mella, Valentina S. A.

Context. Precise and accurate estimates of animal numbers are often essential for population and epidemiological models, as well as for guidance for population management and conservation. This is particularly true for threatened species in landscapes facing multiple threats. Estimates can be derived by different methods, but the question remains as to whether these estimates are comparable. Aims. We compared three methods to estimate population numbers, namely, distance sampling, mark–recapture analysis, and home-range overlap analysis, for a population of the iconic threatened species, the koala (Phascolarctos cinereus). This population occupies a heavily fragmented forest and woodland habitat on the Liverpool Plains, northwestern New South Wales, Australia, on a mosaic of agricultural and mining lands. Key results. All three methods produced similar estimates, with overlapping confidence intervals. Distance sampling required less expertise and time and had less impact on animals, but also had less precision; however, future estimates using the method could be improved by increasing both the number and expertise of the observers. Conclusions. When less intrusive methods are preferred, or fewer specialised practitioners are available, we recommend distance sampling to obtain reliable estimates of koala numbers. Although its precision is lower with a low number of sightings, it does produce estimates of numbers similar to those from the other methods. However, combining multiple methods can be useful when other material (genetic, health and demographic) is also needed, or when decisions based on estimates are for high-profile threatened species requiring greater confidence. We recommend that all estimates of population numbers, and their precision or variation, be recorded and reported so that future studies can use them as prior information, increasing the precision of future surveys through Bayesian analyses.
Habitat fragmentation affects movement and space use of a specialist folivore, the koala
21 December 2020
University of Sydney

Rus, Adrian I.;McArthur, Clare;Mella, Valentina S. A.;Crowther, Mathew S.

Habitat fragmentation changes landscape patterns and can disrupt many important ecological processes. Movement allows individuals to find resource patches to maintain their fitness and habitat fragmentation can disrupt this process. We explored the ecological impact of habitat fragmentation on movement and space use of a specialist folivore, the koala Phascolarctos cinereus. We GPS tracked koala movements within a fragmented agricultural landscape. We calculated the total distance moved across four months and the number of core patches by each koala. We used four metrics (proximity, functional connectivity, clumpiness, perimeter-to-area fractal dimension) to quantify landscape fragmentation within koala home ranges and determine its effects on movement and space use. Functional connectivity had the greatest effect on individual movement and space use. Decreasing connectivity led to longer and more direct movements by koalas and more core patches within an individual home range. Our study provides insight into the effects of habitat fragmentation on animal movement and space use, which can be used by wildlife managers to plan and manage landscapes more effectively.We conclude that restoring or protecting resource patches to promote greater functional connectivity will reduce the costs associated with the isolation of resource patches for species occupying fragmented landscapes. By providing a quantitative relationship between habitat connectivity and movement and space use costs, our results enable managers to set restoration targets, by identifying the most effective way to provide the functional connectivity minimizing the negative impact on focal species.
Foxes in trees: a threat for Australian arboreal fauna?
21 December 2020
University of Sydney

Mella, Valentina S. A.;McArthur, Clare;Frend, Robert;Crowther, Mathew S.

We document the first evidence of tree climbing by red foxes (Vulpes vulpes) in Australia. Camera traps recorded foxes in trees on the Liverpool Plains, New South Wales. This finding prompts a reassessment of the impact that this invasive predator has on Australian fauna: from purely terrestrial to also potentially arboreal.
Austropuccinia psidii, causing myrtle rust, has a gigabase-sized genome shaped by transposable elements
10 June 2021
University of Sydney

Tobias, P.A.;Schwessinger, B.;Deng, C.H.;Wu, C.;Dong, C.;Sperschneider, J.;Jones, A.;Lou, Z.;Zhang, P.;Sandhu, K.;Smith, G.R.;Tibbits, J.;Chagn�, D.;Park, R.F.

Austropuccinia psidii, originating in South America, is a globally invasive fungal plant pathogen that causes rust disease on Myrtaceae. Several biotypes are recognized, with the most widely distributed pandemic biotype spreading throughout the Asia-Pacific and Oceania regions over the last decade. Austropuccinia psidii has a broad host range with more than 480 myrtaceous species. Since first detected in Australia in 2010, the pathogen has caused the near extinction of at least three species and negatively affected commercial production of several Myrtaceae. To enable molecular and evolutionary studies into A. psidii pathogenicity, we assembled a highly contiguous genome for the pandemic biotype. With an estimated haploid genome size of just over 1?Gb (gigabases), it is the largest assembled fungal genome to date. The genome has undergone massive expansion via distinct transposable element (TE) bursts. Over 90% of the genome is covered by TEs predominantly belonging to the Gypsy superfamily. These TE bursts have likely been followed by deamination events of methylated cytosines to silence the repetitive elements. This in turn led to the depletion of CpG sites in TEs and a very low overall GC content of 33.8%. Compared to other Pucciniales, the intergenic distances are increased by an order of magnitude indicating a general insertion of TEs between genes. Overall, we show how TEs shaped the genome evolution of A. psidii and provide a greatly needed resource for strategic approaches to combat disease spread.
Policing the pedal rebels: A case study of environmental activism under covid-19
25 June 2021
University of Sydney

Lee, Murray

Australia, along with nation-states internationally, has entered a new phase of environmentally focused activism, with globalised, coordinated and social media–enabled environmental social movements seeking to address human-induced climate change and related issues such as the mass extinction of species and land clearing. Some environmental protest groups such as Extinction Rebellion (XR) have attracted significant political, media and popular commentary for their sometimes theatrical and disruptive forms of nonviolent protest and civil disobedience. Drawing on green and cultural criminology, this article constitutes an autoethnographic account of environmental protest during the final stages of the initial COVID-19 lockdown in NSW, Australia. It takes as a case study a small protest by an XR subgroup called the Pedal Rebels. The article explores the policing of environmental protest from an activist standpoint, highlighting the extraordinary police resources and powers mobilised to regulate a small peaceful group of ‘socially distanced’ protesters operating within the existing public health orders. It places an autoethnographic description of this protest in the context of policing practice and green and cultural criminology. Additionally, it outlines the way in which such policing is emboldened by changes to laws affecting environmental protest, making activism an increasingly risky activity.
Environmental and public health co-benefits of consumer switches to immunity-supporting food
28 April 2022
University of Sydney

Tulloch, Ayesha I. T.;Oh, Rachel R. Y.;Gallegos, Danielle

During COVID-19, there has been a surge in public interest for information on immunity-boosting foods. There is little scientific support for immunity-supporting properties of specific foods, but strong evidence for food choice impacts on other health outcomes (e.g. risk of non-communicable disease) and environmental sustainability. Here, we relate online recommendations for "immunity-boosting" foods across five continents to their environmental and human health impacts. More frequently recommended food items and groups are plant based and have lower land use and greenhouse gas emission impacts plus more positive health outcomes (reducing relative risks of mortality or chronic diet-related diseases) per serving of food. We identify trade-offs between environmental outcomes of increasing consumption of recommended food items, with aquatic environment impacts increasing with food recommendation frequency. People's reliance on the Internet for health information creates an opportunity to consolidate behaviour change towards consuming foods with multiple co-benefits. Our study identifies win-win options for nudging online information-seeking behaviour towards more sustainable choices for terrestrial biodiversity conservation and human health.
Factors influencing the success of hand-reared juvenile brushtail possums (Trichosurus vulpecula) released into the wild
27 July 2022
University of Sydney

Mella, Valentina S. A.;Gillies, Callum;McArthur, Clare;Webb, Elliot;Herbert, Catherine

Context: Wildlife is ubiquitous in urban environments, resulting in frequent interactions with humans and human infrastructure. The result of these interactions is often negative, in the form of road injury, orphaning of dependent young or eviction from natural home ranges. Wildlife rehabilitation programmes are devised to counter these negative interactions. However, the success of current management strategies is rarely assessed. Aims: We aimed to determine whether short-term survival of juvenile hand-reared common brushtail possums (Trichosurus vulpecula) released in the wild was a function of (1) intrinsic factors such as sex, individual personality and level of human habituation, and (2) extrinsic factors such as release practice (soft vs hard-release) or location (urban vs rural). We also evaluated the relationship between habituation to humans and time spent in care by possums, if presence of conspecifics during the rehabilitation process influenced the development of individual personality, and if this differed in hand-raised animals compared with wild individuals. Methods: We radio-tracked and monitored 20 hand-reared juvenile possums (10 females and 10 males) for up to 40 days after release in the wild. Key results: Eight possums (40%) survived until the end of the study, nine possums (45%) were killed by foxes or had to be returned into care and three possums (15%) had unknown fates (i.e. lost VHF signal). We found that more exploratory individuals and those less human-habituated were more likely to be successful in the wild in both rural and urban areas, whether or not they were hard or soft released. Conclusions: Our results suggest that personality is a key criterion to consider when evaluating the success of rehabilitation programmes. Behavioural traits of hand-reared brushtail possums differed significantly from those of wild individuals, showing that captive conditions can affect the development of personality. Hand-reared possums that spent more time in care were also more likely to display highly human-habituated behaviours. Implications: By demonstrating which factors influence success of hand-reared wildlife after release in the wild, our results help in evaluating current rearing and release practices, and improve the evidence base for developing best practice wildlife rehabilitation guidelines.
Monitoring changes in global soil organic carbon stocks from space
15 September 2022
University of Sydney

Padarian, José;Stockmann, Uta;Minasny, Budiman;McBratney, Alex

Soils are under threat globally, with declining soil productivity and soil health in many places. As a key indicator of soil functioning, soil organic carbon (SOC) is crucial for ensuring food, soil, water and energy security, together with biodiversity protection. While there is a global effort to map SOC stock and status, SOC is a dynamic soil property and can change rapidly as a function of land management and land use. Here, we introduce a semi-mechanistic model to monitor SOC stocks at a global scale, underpinned by one of the largest worldwide soil database to date. Our model generates a SOC stock baseline for the year 2001, which is then propagated through time by keeping track of annual landcover changes obtained from remote sensing products with loss and gain dynamics dependent on temperature and precipitation, which finally define the magnitude, rate and direction of the SOC changes. We estimated a global SOC stock in the top 30~cm of around 793 Pg with annual losses due to landcover change of 1.9 Pg SOC/yr from 2001 to 2020, 20% larger than the annual production-based emissions of the United States in 2018. The biggest losses were found in the tropic and sub-tropical regions, accounting for almost 50% of the total global loss. This is a considerable contribution to greenhouse gas emissions but it also has a direct impact on agricultural production with more than 16 million hectares per year falling below critical SOC limits. The proposed modelling framework is flexible, allowing it to be updated as more remote sensing and soil data becomes available, offering a first-of-its-kind global spatio-temporal SOC stock assessment and monitoring system.
Turning the Endangered Species Act inside Out
01 January 2004
University of Pennsylvania

Mathews, Jud

Within a week, both the Fifth and D.C. Circuits upheld the takings prohibitions of the Endangered Species Act (ESA) of 1973, as applied to species found only in single states, against Commerce Clause challenges. Both cases reach the same result, but the legal analysis used to get there could hardly be more different. In GDF Realty, the Fifth Circuit found the requisite "substantial impact" on commerce by treating the species themselves as commodities and aggregating the economic impact of all endangered species "takings". The D.C. Circuit, by contrast, held in Rancho Viejo that the true object of ESA regulation is not endangered species, but the commercial development that threatens them, which plainly falls within Congress's powers to regulate under the Commerce Clause. The two courts saved the threatened arroyo toads and subterranean invertebrates, but they read the Endangered Species Act as if it were two different statutes.This curious divergence can only be understood in light of the unsettled state of Commerce Clause jurisprudence following United States v. Lopez and United States v. Morrison. Those two decisions upended fifty years of conventional wisdom about the limits on Congress's power under the Commerce Clause – namely, that there were effectively none – and left lower courts with an uncertain new framework to apply. Of the two cases considered here, Rancho Viejo represents the abler attempt to square the ESA with the new Commerce Clause doctrine, because its analysis is more objective than GDF Realty's and more clearly satisfies the strictures of Lopez and Morrison. But like GDF Realty, Rancho Viejo must present the ESA's impact on commerce, which is peripheral in the statutory design, as the Act's core object – must turn the ESA "inside out," so to speak – in order to justify it under the Commerce Clause. This cramped conception of the statute does not convincingly justify all of its applications. The shortcomings of Rancho Viejo do not represent sloppiness on the part of the D.C. Circuit, however. Instead, they reflect the failure of the Lopez and Morrison framework to meet the Supreme Court's stated aspiration to distinguish "between what is truly national and what is truly local".
Qualitative, Quantitative, and Integrative Conservation
01 January 2010
University of Pennsylvania

Colburn, Jamison E.

In this essay for a symposium on new directions in environmental law, I reflect back on the last 35 years of Endangered Species Act (ESA) practice and offer several modest reforms. My claim is that conservation has been growing increasingly quantitative and risk-based, much like other fields of regulation, but that big problems lie ahead if this trend continues with the ESA as currently structured. In my view, the quantitative demands of listing species, designing recovery objectives, and designating so-called 'critical habitat' are depleting the resources we have put into the ESA because it is an expression of fundamentally qualitative hopes. Thus, the statute is not structured to guide much of the decision-making that is now required, leaving its agents to interpret and implement an Act that diverges substantially from the actual contexts in which it is implemented. If the Fish & Wildlife Service and the NOAA Fisheries Service are to bring these two divergent approaches to conservation into a more productive relationship, they must start by reorganizing themselves to reflect the informational environments in which they operate. This means adapting institutionally to carry out only those conservation actions that are best carried out centrally while distributing the rest of their workload to more localized or non-centralized partners.
Traditional Knowledge, Genetic Resources, Patent Law and its Protection: A Legal Analysis of Africa, Latin America, and India. How India Can Protect it Fiercely
01 June 2021
University of Pennsylvania

Bhandari, Avantika

Traditional knowledge (TK) is comprised of the know-how, skills, and innovations that are practiced by Indigenous and local communities; these are passed down form generation to generation and form a part of the communities' cultural and spiritual identity. The concept and scope of TK are vast; therefore, it has been a subject of heated debate in international forums for decades. TK includes both traditional and cultural expressions and genetic resources; however, this dissertation covers only TK associated with genetic resources. TK has proven to be helpful as an input in modern industries. For instance, many pharmaceutical companies have utilized traditional medicinal knowledge as a cure and, at times, to develop drugs quickly. The dissertation is chiefly oriented towards formulating a sui-generis mechanism tailored specifically for Indian order to grant protection to the country's rich and diverse repository of TK. India, which is considered one of the world's mega-biodiversity hot spots and is home to different schools of medicine, has a lot to offer through its TK. However, the country has made little progress when it comes to a comprehensive TK protection policy. The present dissertation explores various instances of TK misappropriation both within India and other countries. The second chapter establishes the need for an international legal framework to ensure comprehensive TK protection. The third and fourth chapters specifically mention the laws and regulations adopted by countries in Latin America and Africa at national and regional levels, with the aim of studying their efforts and suggesting provisions in the Indian context. The chapters examine those nations' sui-generis legislations, which are primarily based on customary laws. The proposed Indian sui-generis law takes inspiration from South Africa's new legislation and Article 82 of Costa Rica's Biodiversity Law. Chapter 5 focuses on the current national legislation of India that provides protection to TK. It also examines the defensive protection offered to TK through TKDL. The concluding chapter offers suggestions and recommends steps that India could take to protect its TK, focusing primarily on the role of customary law.
Composition Over Division: The Statutes of the National Forest System
01 September 2021
University of Pennsylvania

Colburn, Jamison

Most crises like those facing the National Forest System (NFS) have complex origins. But few of them result from as vast or as tangled a range of causes as do those facing the NFS. Appropriations to fight the wildfires now consuming our forests and choking the West have steadily grown, far outpacing inflation for a generation now. Timber and other commodity production has remained at historic lows for as long. And biodiversity conservation measures cannot gain the acquiescence of different constituencies long enough to withstand the inevitable lawsuits or turnover in administrative personnel. If Congress originally expected that judicial oversight would keep the Forest Service managing the NFS consistent with its own intent, that assumption has long since been buried. This study puts the NFS statutes' distinct facets in a truer light, though, offering what it calls a compositional interpretation. It shows how Congress's reiterations of research, reporting, and analysis requirements, combined with its multi-level planning mandates and varied oversight mechanisms, should fit together to enable continuous, deliberate improvements within the Forest Service.
Adaptation Limits Diversification of Experimental Bacterial Populations
29 March 2004
University of Edinburgh

Colegrave, Nick;Wills, Matthew A;Buckling, Angus

Adaptation to a specific niche theoretically constrains a population's ability to subsequently diversify into other niches. We tested this theory using the bacterium Pseudomonas fluorescens, which diversifies into niche specialists when propagated in laboratory microcosms. Numerically dominant genotypes were allowed to diversify in isolation. As predicted, populations increased in fitness through time but showed a greatly decreased ability to diversify. Subsequent experiments demonstrated that niche generalists and reductions in intrinsic evolvability were not responsible for our data. These results show that niche specialization may come with a cost of reduced potential to diversify.
Pollination and parasitism in functionally dioecious figs
12 April 2004
University of Edinburgh

Weiblen, George D;Yu, Douglas W;West, Stuart A

Fig wasps (Agaonidae: Hymenoptera) are seed predators and their interactions with Ficus species (Moraceae) range from mutualism to parasitism. Recently, considerable attention has been paid to conflicts of interest between the mutualists and how they are resolved in monoecious fig species. However, despite the fact that different conflicts can arise, little is known about the factors that influence the persistence of the mutualism in functionally dioecious Ficus.We studied the fig pollinator mutualism in 14 functionally dioecious fig species and one monoecious species from tropical lowland rainforests near Madang, Papua New Guinea. Observations and experiments suggest that (i) pollinating wasps are monophagous and attracted to a particular host species; (ii) pollinating and non-pollinating wasps are equally attracted to gall (male) figs and seed (female) figs in functionally dioecious species; (iii) di¡ering style lengths between gall figs and seed figs may explain why pollinators do not develop in the latter ; (iv) negative density dependence may stabilize the interaction between pollinating wasps and their parasitoids; and (v) seed figs may reduce the search efficiency of non-pollinators. This increased pollinator production without a corresponding decrease in seed production could provide an advantage for dioecy in conditions where pollinators are limiting.
Conflict of interest in a mutualism: documenting the elusive fig wasp seed trade-off
12 April 2004
University of Edinburgh

Herre, E Allen

The generally accepted view that mutualisms represent reciprocal exploitations implies a greater or lesser degree of inherent tension between the partners. This view emphasizes the importance of identifying conflicts of interest between the partners, and then attempting to quantify the effects of factors that influence costs and benefits to each. The natural history of the speciose fig-fig wasp pollination mutualisms permits such measurements. However, previous attempts to document the presumed tensions, which are expected to result in a negative relationship between the production of viable seeds and pollinator wasp offspring, have met with mixed results, casting doubt on the existence of the conflict. Here, we present hierarchical analyses of 929 fruits sampled from 30 crops representing nine species of monoecious New World figs. These analyses control for the confounding influences of variation in (1) pollination intensity (numbers of foundress pollinators); (2) flower number per fruit; and (3) the proportion of those flowers that develop, on seed and wasp production, both among and within crops. We thereby show that a negative relationship between the production of viable seeds and wasps is, in fact, ubiquitous, thus documenting this underlying tension inherent in the mutualism. We suggest that complex interactions of variables that influence costs and benefits are likely to be a general property of most mutualistic systems.
Asymmetric leaves1 mediates leaf patterning and stem cell function in Arabidopsis
08 February 2005
University of Edinburgh

Byrne, Mary E;Barley, Ross;Curtis, Mark;Arroyo, Juana Maria;Dunham, Maitreya;Hudson, Andrew;Martienssen, Robert A

Meristem function in plants requires both the maintenance of stem cells and the specification of founder cells from which lateral organs arise. Lateral organs are patterned along proximodistal, dorsoventral and mediolateral axes (1,2). Here we show that the Arabidopsis mutant asymmetric leaves1 (as1) disrupts this process. AS1 encodes a myb domain protein, closely related to PHANTASTICA in Antirrhinum and ROUGH SHEATH2 in maize, both of which negatively regulate knotted-class homeobox genes. AS1 negatively regulates the homeobox genes KNAT1 and KNAT2 and is, in turn, negatively regulated by the meristematic homeobox gene SHOOT MERISTEMLESS. This genetic pathway defines a mechanism for differentiating between stem cells and organ founder cells within the shoot apical meristem and demonstrates that genes expressed in organ primordia interact with meristematic genes to regulate shoot morphogenesis
The methylated component of the Neurospora crassa genome
09 February 2005
University of Edinburgh

Selker, Eric U;Tountas, Nikolaos A;Cross, Sally H;Margolin, Brian S;Murphy, Jonathan G;Bird, Adrian P;Freitag, Michael

Cytosine methylation is common, but not ubiquitous, in eukaryotes. Mammals (1) and the fungus Neurospora crassa (2,3) have about 2–3% of cytosines methylated. In mammals, methylation is almost exclusively in the under-represented CpG dinucleotides, and most CpGs are methylated (1) whereas in Neurospora, methylation is not preferentially in CpG dinucleotides and the bulk of the genome is unmethylated (4). DNA methylation is essential in mammals (5) but is dispensable in Neurospora (3,6) making this simple eukaryote a favoured organism in which to study methylation. Recent studies indicate that DNA methylation in Neurospora depends on one DNA methyltransferase, DIM-2 (ref. 6), directed by a histone H3 methyltransferase, DIM-5 (ref. 7), but little is known about its cellular and evolutionary functions. As only four methylated sequences have been reported previously in N. crassa, we used methyl-binding-domain agarose chromatography (8) to isolate the methylated component of the genome. DNA sequence analysis shows that the methylated component of the genome consists almost exclusively of relics of transposons that were subject to repeat-induced point mutation—a genome defence system that mutates duplicated sequences (9).
The genome sequence of the filamentous fungus Neurospora crassa
09 February 2005
University of Edinburgh

Read, Nick D;et al

Neurospora crassa is a central organism in the history of twentieth-century genetics, biochemistry and molecular biology. Here, we report a high-quality draft sequence of the N. crassa genome. The approximately 40-megabase genome encodes about 10,000 protein-coding genes—more than twice as many as in the fission yeast Schizosaccharomyces pombe and only about 25% fewer than in the fruitfly Drosophila melanogaster. Analysis of the gene set yields insights into unexpected aspects of Neurospora biology including the identification of genes potentially associated with red light photobiology, genes implicated in secondary metabolism, and important differences in Ca21 signalling as compared with plants and animals. Neurospora possesses the widest array of genome defence mechanisms known for any eukaryotic organism, including a process unique to fungi called repeat-induced point mutation (RIP). Genome analysis suggests that RIP has had a profound impact on genome evolution, greatly slowing the creation of new genes through genomic duplication and resulting in a genome with an unusually low proportion of closely related genes.
An everlasting pioneer: the story of Antirrhinum research
16 February 2005
University of Edinburgh

Schwarz-Sommer, Zsuzsanna;Davies, Brendan;Hudson, Andrew

Despite the tremendous success of Arabidopsis thaliana, no single model can represent the vast range of form that is seen in the ~250,000 existing species of flowering plants (angiosperms). Here, we consider the history and future of an alternative angiosperm model — the snapdragon Antirrhinum majus. We ask what made Antirrhinum attractive to the earliest students of variation and inheritance, and how its use led to landmark advances in plant genetics and to our present understanding of plant development. Finally, we show how the wide diversity of Antirrhinum species, combined with classical and molecular genetics — the two traditional strengths of Antirrhinum — provide an opportunity for developmental, evolutionary and ecological approaches. These factors make A. majus an ideal comparative angiosperm.
Proximity signal and shade avoidance differences between early and late successional trees
23 February 2005
University of Edinburgh

Gilbert, Ian R;Jarvis, Paul G;Smith, Harry

Competitive interactions between plants determine the success of individuals and species. In developing forests, competition for light is the predominant factor. Shade tolerators acclimate photosynthetically to low light1±3 and are capable of long-term survival under the shade cast by others, whereas shade avoiders rapidly dominate gaps but are overtaken in due course by shade-tolerant, later successional species. Shade avoidance4±6 results from the phytochrome-mediated perception of far-red radiation (700± 800 nm) scattered from the leaves of neighbours, provides early warning of shading7, and induces developmental responses that, when successful, result in the overgrowth of those neighbours8. Shade tolerators cast a deep shade, whereas less-tolerant species cast light shade9, and saplings tend to have high survivorship in shade cast by conspecific adults, but high rates of mortality when shaded by more-tolerant species9. Here we report a parallel relationship in which the shade-avoidance responses of three tree species are inversely proportional to proximity signals generated by those species. On this basis, early successional species generate small proximity signals but react strongly to them, whereas late successional species react weakly but generate strong signals.
Trichloroacetic acid cycling in Sitka spruce (Picea sitchensis) saplings and the effects on tree health following long term exposure.
05 October 2005
University of Edinburgh

Dickey, Catherine A;Heal, Kate V;Stidson, R T;Koren, R;Cape, Neil;Schröder, V;Heal, Mathew R

Trichloroacetic acid (TCA, CCl3COOH) has been associated with forest damage but the source of TCA to trees is poorly characterised. To investigate the routes and effects of TCA uptake in conifers, 120 Sitka spruce (Picea sitchensis (Bong.) Carr) saplings were exposed to control, 10 or 100 μg l−1 solutions of TCA applied twice weekly to foliage only or soil only over two consecutive 5-month growing seasons. At the end of each growing season similar elevated TCA concentrations (approximate range 200–300 ng g−1 dwt) were detected in both foliage and soil-dosed saplings exposed to 100 μg l−1 TCA solutions showing that TCA uptake can occur from both exposure routes. Higher TCA concentrations in branchwood of foliage-dosed saplings suggest that atmospheric TCA in solution is taken up indirectly into conifer needles via branch and stemwood. TCA concentrations in needles declined slowly by only 25–30% over 6 months of winter without dosing. No effect of TCA exposure on sapling growth was measured during the experiment. However at the end of the first growing season needles of saplings exposed to 10 or 100 μg l−1 foliage-applied TCA showed significantly more visible damage, higher activities of some detoxifying enzymes, lower protein contents and poorer water control than needles of saplings dosed with the same TCA concentrations to the soil. At the end of each growing season the combined TCA storage in needles, stemwood, branchwood and soil of each sapling was <6% of TCA applied. Even with an estimated half-life of tens of days for within-sapling elimination of TCA during the growing season, this indicates that TCA is eliminated rapidly before uptake or accumulates in another compartment. Although TCA stored in sapling needles accounted for only a small proportion of TCA stored in the sapling/soil system it appears to significantly affect some measures of sapling health.
Behaviour of the babirusa (Babyrousa babyrussa) with suggestions for husbandry.
11 May 2006
University of Edinburgh

Leus, Kristin;Bowles, D;Bell, J;Macdonald, Alastair A

The babirusa is a remarkable pig, endemic on the Indonesian islands of Sulawesi, Buru and the smaller Sula and Togian islands. The single species of the genus is divisable into three living subspecies: Babyrousa babyrussa babyrussa (Sula Islands and Buru), B.b. togeanensis (Togian islands) and B.b. celebenesis (Sulawesi) (Groves, 1980), of which only the latter is currently represented in captivity. The species is listed in the IUCN Red Data Book as vulnerable and can be considered a marker animal for the disturbance of the primary rainforest. The Indonesian Department of Forest Protection and nature Conservation (Perlindungan Hutan dan Pelestarian Alam: PHPA) has given it the second most important priority after the Indonesian rhinos. This present paper reports the results of studies carried out on a large number of babirussa. Observations were made in Antwerp Zoo in Belgium and in the Zoos at Surabaya and Jakarta in Indonesia. These institutions represent 3 different ways in which the babirusa are currently kept in captivity. In Antwerp Zoo, each animal has its own enclosure; Surabaya Zoo keeps animals in large groups and Jakarta Zoo houses them in pairs. Each of these different housing techniques had its own implications on the behaviour shown by the animals and this allowed us to make suggestions for their future husbandry.
A Feminist in the Forest: Situated Knowledges and Mixing Methods in Natural Resource Management
25 August 2006
University of Edinburgh

Nightingale, Andrea J

Donna Haraway’s (1991) concept of partial or situated knowledges has been a major influence on feminist methodological debates within geography. In this paper, I argue that geographers can interrogate the partiality of knowledge by developing research designs that incorporate methods derived from different epistemological traditions. The silences and gaps between data sets can be explored to interrogate the partiality of knowledge produced in different theoretical and methodological contexts. Also, advocates of interpretive methodologies can add substantially to theoretical debates over epistemology by demonstrating how the results from all methods are incomplete and subject to power – and positionality – laden interpretations. Using different methods is one way to highlight this issue and to challenge the hegemony of positivist science within mainstream academic and policy circles.
The routes and kinetics of trichloroacetic acid uptake and elimination in Sitka spruce (Picea sitchensis) saplings via atmospheric deposition pathways
05 October 2006
University of Edinburgh

Heal, Mathew R;Dickey, Catherine A;Cape, Neil;Heal, Kate V

A major flux of trichloroacetic acid (TCA) to forests is via wet deposition, but the transfer of TCA into tree foliage may occur by an above- or below-ground pathway. To investigate the routes and kinetics of TCA uptake, two groups of 10 Sitka spruce saplings (with an equivalent number of controls) were exposed to a single application of 200 μg TCA in solution, either to the soil only, or sprayed as a mist to the foliage only. The needle foliage was subsequently analysed regularly for TCA for 3 months during the growing season. Significant uptake into current year (C) needles was observed from both routes just a few days after application, providing direct evidence of an above-ground uptake route. Uptake of TCA was also observed in the previous year needle class (C+1). Kinetic modelling of the data indicated that the half-life for within-needle elimination (during the growing season) was 50±30 days. Most of the applied TCA appeared to be degraded before uptake, either in the soil, or externally on the sapling foliage.
Experiments and Observation of Peat Smouldering Fires
14 February 2007
University of Edinburgh

Ashton, Clare;Rein, Guillermo;Dios, JD;Torero, Jose L;Legg, C;Davies, M;Gray, A

If a subsurface layer of peat is ignited, it smoulders (flameless combustion) slowly but steadily. These fires propagate for long periods of time (days, weeks, even years), are particularly difficult to extinguish and can spread over very extensive areas. Smouldering fires have an impact on the soil since the fuel burning is the combustible portion of the soil itself. An example of a peat fire is the recent wildfire that occurred this summer in Rothiemurchus, near Aviemore (Scotland). A 40 year old plantation of lodgepole pine of about 15 ha was burned accidentally. The main fire was extinguished within three days, but the peat underneath the forest continued to smoulder for more than thirty days, destroying the tree roots. Peat combustion processes remain mostly unknown to the fire community and more experimental and theoretical studies are needed. It is known that the smouldering of underground fuels is governed by the diffusion of heat and oxygen through the soil layers between the reaction site and the surface. It is highly desired to conduct more experiments on smouldering (aka glowing) combustion of peat to allow derivation of fire maps for forecast from information in the weather maps. The main factor controlling factor ignition is moisture content. This paper reports the measurements and observations from smouldering box experiments using peat from the UK. The smouldering box is a simple procedure which captures the essentials of peat ignition and burning. The test is conducted in a small box (side of ~20 cm) made of insulating side-walls and open on the top. The sample is ignited using an electrically heated coil running along one side of the peat. A successful ignition is followed by sustained smouldering combustion that consumes the sample. Temperature and spread rates are measured, and the residue is weighed and described. In our series of experiments we have found that the critical moisture content below which ignition is highly probable is 120 % ± 10 % (in dry basis). We found that this value compare well with that reported by researcher in Canada (~110%) and Indonesia (>120%), which suggests that critical moisture content depends weakly on peat origin.
Assessment of Expert Opinion: Seasonal Sheep Preference and Plant Response to Grazing
15 May 2007
University of Edinburgh

Pollock, Meg L;Legg, Colin J;Holland, John P;Theobald, Chris M

Expert opinion was sought on two issues relating to herbivory: seasonal sheep preferences for plant species and seasonal plant response to grazing. Expert opinion is commonly used to parameterize models: it is therefore important to assess its quality. Understanding the limitations of expert knowledge can allow prioritization of future research. Nine experts in plant or grazing ecology from Scotland/Northern England were individually interviewed. The experts ranked sheep preferences for species in four rangeland vegetation types and provided categorical information on plant response to grazing. For both issues, seasonal information was collected. Uncertainty (unanswered questions) on plant responses was much higher than uncertainty on sheep preferences. Uncertainty on sheep preference was significantly negatively correlated with plant species commonness, but not with quantity of scientific literature. Uncertainty on plant responses was significantly negatively correlated with both plant commonness and literature. There was agreement between experts on sheep preferences; standardized seasonal information for selected plant species is presented. In general, experts considered graminoids to be preferred over dwarf shrubs, with forbs and other species groups intermediate. Seasonal variation in sheep preference was greater for heath and mire than for grasslands. There was limited agreement between experts on seasonal plant responses. Some experts considered grazing in summer to affect growth more than grazing in winter, while others thought season had little effect. Sufficient agreement was found at the species level to present results on plant responses. Experts considered graminoids more resilient to grazing than dwarf shrubs. Experts agreed on sheep preference at different times of year, and on the overall resilience of plant species to grazing. However, the experts held two paradigms on the impact of seasonal grazing. Further research is required to explore this, since seasonal grazing regimes are currently promoted as conservation management tools.
Should There Be An Obligation of Disclosure of Origin of Genetic Resources in Patent Applications? Learning Lessons from Developing Countries
18 August 2008
University of Edinburgh

Laurie, Graeme

The article discusses whether there should be an obligation of disclosure of origin of genetic resources in patent applications. In particular, Laurie comments on the evolving relations of the intellectual property world and the role of the World Intellectual Property Organisation (WIPO) in the international policy debate on such matters. The difficulties of the interconnectedness of the patent system and the Convention on Biological Diversity are considered, with the possible implications of an obligation of disclosure for the future of patent law, and international laws and policy.
Detecting Recombination in 4-Taxa DNA Sequence Alignments with Bayesian Hidden Markov Models and Markov Chain Monte Carlo
27 November 2008
University of Edinburgh

McGuire, Graine;Husmeier, Dirk

This article presents a statistical method for detecting recombination in DNA sequence alignments, which is based on combining two probabilistic graphical models: (1) a taxon graph (phylogenetic tree) representing the relationship between the taxa, and (2) a site graph (hidden Markov model) representing interactions between different sites in the DNA sequence alignments. We adopt a Bayesian approach and sample the parameters of the model from the posterior distribution with Markov chain Monte Carlo, using a Metropolis-Hastings and Gibbs-within-Gibbs scheme. The proposed method is tested on various synthetic and real-world DNA sequence alignments, and we compare its performance with the established detection methods RECPARS, PLATO, and TOPAL, as well as with two alternative parameter estimation schemes.
Methyl bromide and methyl chloride fluxes from temperate forest litter
03 March 2011
University of Edinburgh

Blei, Emanuel;Heal, Mathew R

Methyl halide fluxes were measured from fine (nonwoody) litter samples in a temperate deciduous forest site in Scotland on 16 occasions over more than a year and from a coniferous forest site. The resulting mean (+/-1 sd) CH3Br and CH3Cl fluxes were 4.1 +/- 3.7 ng kg-1 h-1 and 0.98 +/- 0.62 µg kg-1 h-1, respectively, for dry mass leaf litter and 5.7 +/- 6.3 ng kg-1 h-1 and 0.47 +/- 0.14 µg kg-1 h-1 for dry mass needle litter. Temporal variations of net fluxes from leaf litter were significantly greater than spatial variations suggesting seasonality in the fluxes. The mean CH3Cl/CH3Br mass ratio of fluxes was ~200, an order of magnitude larger than the ratio of their estimated global turnovers. Temperate forest litter may be a moderate net source of CH3Cl globally but a negligible source of CH3Br. These statements refer to the nonwoody litter component only.
Twenty + Futures
27 February 2013
University of Edinburgh

Jamieson, Lynn;Cunningham-Burley, Sarah;Rawlins, Emma

In a period of heightened awareness of global threats to orderly and predictable futures for people and planet – recession, climate change, peak oil, loss of biodiversity, terrorism – does this uncertainty impact on how young adults in their twenties think about their futures, particularly partnering and parenting? Exploratory interviews with childless young men and women in their twenties sought to investigate.
SEED-BEARING GLOSSOPTERIS LEAVES
19 December 2014
University of the Witwatersrand

Kovacs-Endrody, E.

Seeds are commonly known elements of Glossopteris floras. The connection of these seeds to any definite elements in the floras and their systematic position with it has always been uncertain, and they are usually referred to as a group "incertae sedis". Several of these seeds have been described and placed in the genera Cardiocarpus Brongniart, Cordiocarpus Geinitz and Samaropsis Goeppert, specially erected for them. Arber (1905, p . 206) noticed the common occurrence of seeds with Glossopteris leaves, and refers to them without any further conclusion as "A few seeds .. . in association with fronds of Glossopteris broumiana. The seeds are possibly referable to Cardiocarpus".
On tile anatomy of Dadoxylon arberi Seward with some remarks on the phylogenetical tendencies of its tracheid pits
07 January 2015
University of the Witwatersrand

Erasmus, T.

A well preserved specimen of Dadoxylon arberi Seward has been discovered in the Beaufort Series (Upper Karroo System) of the Empangeni district in Natal, South Africa. The species is characterized by the tracheid pits which are araucaroid in the multiseriate condition, but which are more often circular and separately arranged or appear in stellate groups. The cross field pits tend to be aligned in horizontal pairs. Dadoxylon arberi shows a relationship with several species of the recent Araucariaceae. Its resemblance to other Gondwana woods from other Southern Hemisphere countries suggests a great uniformity in the elements of the coniferous flora of that time. It is suggested that Dadoxylon arberi represents an intermediate form between the Araucariaceae and Podocarpaceae. The reduction in the seriation of the tracheid pits and a drifting thereof seems to stand in close correlation with the formation of annual rings.
Notes on some Glossopteris species from Hammanskraal (Transvaal)
07 January 2015
University of the Witwatersrand

Kovacs- Endrody, E.

The study of Glossopteris began with the mistake that two half fronds were glued together as one and that specimen was chosen as the holotype of one of the first Glossopteris ever described, Glossopteris browniana var. indica Bngn. The mistake led to confusion and even to distrust of the possibility of identifying Glossopteris species on frond impressions only. As most of the GIossopteris remains are such, and the literature from Brongniart onwards is mainly based on them, the frond morphography is bound to be the starting point of the classification. The present paper shows that (a) with the examination of greater numbers of specimens, it is possible to select the specific characters and to learn the individual variations and (b) identifications can only be based on the original descriptions and figures of the taxa.
The biodiversity heritage library and African digital libraries in the global context.
02 September 2015
University of the Witwatersrand

Kalfatovic, Martin R.;Fourie, Anne-Lise

The Biodiversity Heritage Library (BHL) was created in 2006 as a direct response to the needs of the taxonomic community for access to early literature. Designed with meeting these needs, the BHL was grant-funded and quickly proved its value to its target users. The original BHL organizational model, based on US and UK partners, provided a template for, first, BHL Europe, and then a series of global nodes, most recently, BHL Africa and BHL Singapore. As the BHL moved from project to a cornerstone of biodiversity infrastructure, sustainability, appropriate expansion, collaboration with national and pan-national digital libraries (Europeana, the Digital Public Library of America) became more important. Working within the unique and often challenging environments of Sub-Saharan Africa, BHL assisted in the creation of BHL Africa is an inclusive network of African libraries and institutions in Western, Eastern, Central and Southern Africa. The short term goals of BHL/BHL Africa are surveying the biodiversity content of Sub-Saharan partners, defining digitization and aggregation capacity, and delivering African content to the BHL portal. This presentation will cover principles of pan-institutional digital library development, working across multiple African institutions, address areas of growth, and formulate lessons learned through global BHL growth.
Farmers’ and Breeders’ Rights: Bridging Access to, and IP Protection of, Plant Varieties in Africa
18 January 2016
University of the Witwatersrand

Munyi, Peter;De Jonge, Bram

Studies in Africa have shown that saving, using, exchanging and selling farm-saved seed is the main channel through which farmers access seed and planting material. Moreover, these saving and related practices are recognised in international law, mainly through the International Treaty on Plant Genetic Resources for Food and Agriculture (Plant Treaty), which many African countries have ratified. These practices are also recognised by, inter alia, obligations at the national level to protect traditional knowledge relevant to seeds and planting material. The standard being employed in developing plant variety protection (PVP) mechanisms in Africa, as with elsewhere in the world, is the 1991 revision of the Convention of the International Union for the Protection of New Varieties of Plants (UPOV, 1991). This Convention has, since its inception, been developed with reference to developed-world farming practices. This article looks at how farmers’ rights are enshrined in Africa’s legal frameworks, and the extent to which the current process of developing regional PVP systems on the continent is taking farmers’ rights into account. The article then makes recommendations on how a balance can be struck between farmers’ and breeders’ rights, while still complying with the UPOV 1991 framework.
GENETIC DIVERSITY AND GENE FLOW IN THE MORPHOLOGICALLY VARIABLE, RARE ENDEMICS BEGONIA DREGEI AND BEGONIA HOMONYMA (BEGONIACEAE)
31 March 2016
University of the Witwatersrand

MATOLWENI, LUZUKO ORLYN;BALKWILL, KEVIN;MCLELLAN, TRACY

Excellent models for the study of evolutionary pro¬cesses are often provided by taxa that pose the greatest problems in systematics (Wolf, Soltis, and Soltis, 1991). Endemic plants provide a superb tool for studying the dynamic processes of speciation and evolution, particu¬larly island endemic plants (Ito and Ono, 1990; Aradya, Mueller-Dombois, and Ranker, 1991; Barrett, 1996). Ev¬idence of most evolutionary events that formed continen¬tal biota has been lost because such biota are so ancient (Carson, 1987). Complex patterns of variation may blur species boundaries and lead to taxonomic complexity.
Nested species- rich networks of scavenging vertebrates support high levels of interspecific competition.
24 May 2016
University of the Witwatersrand

Sebastián-González, E.;Moleón, M.;Gibert, J.P.;Guimarães, P.R.;Sánchez-Zapata, J.A.;Botella, F.;Mateo-Tomás, P.;Olea, P.P.

Disentangling the processes that shape the organization of ecological assemblages and its implications for species coexistence is one of the foremost challenges of ecology. Although insightful advances have recently related community composition and structure with species coexistence in mutualistic and antagonistic networks, little is known regarding other species assemblages, such as those of scavengers exploiting carrion. Here we studied seven assemblages of scavengers feeding on ungulate carcasses in mainland Spain. We used dynamical models to investigate if community composition, species richness and structure (nestedness) affect species coexistence at carcasses. Scavenging networks showed a nested pattern in sites where highly efficient, obligate scavengers (i.e., vultures) were present and a non- nested pattern everywhere else. Griffon Vulture ( Gyps fulvus ) and certain meso- facultative mammalian scavengers (i.e., red fox, Vulpes vulpes, and stone marten, Martes foina ) were the main species contributing to nestedness. Assemblages with vultures were also the richest ones in species. Nested species- rich assemblages with vulture presence were associated with high carcass consumption rates, indicating higher interspecific competition at the local scale. However, the proportion of species stopping the consumption of carrion (as derived from the competitive dynamic model) stabilized at high richness and nestedness levels. This suggests that high species richness and nestedness may characterize scavenging networks that are robust to high levels of interspecific competition for carrion. Some facilitative interactions driven by vultures and major facultative scavengers could be behind these observations. Our findings are relevant for understanding species' coexistence in highly competitive systems.
Space use variation in Co-occurring sister species: Response to environmental variation or competition?
03 June 2016
University of the Witwatersrand

Dufour, C.M.S.;Meynard, C.;Watson, J.;Pillay, N.;Ganem, G.;Rioux, C.;Benhamou, S.;Perez, J.;Du Plessis, J.J.;Avenant, N.

Coexistence often involves niche differentiation either as the result of environmental divergence, or in response to competition. Disentangling the causes of such divergence requires that environmental variation across space is taken into account, which is rarely done in empirical studies. We address the role of environmental variation versus competition in coexistence between two rodent species: Rhabdomys bechuanae (bechuanae) and Rhabdomys dilectus dilectus (dilectus) comparing their habitat preference and home range (HR) size in areas with similar climates, where their distributions abut (allopatry) or overlap (sympatry). Using Outlying Mean Index analyses, we test whether habitat characteristics of the species deviate significantly from a random sample of available habitats. In allopatry, results suggest habitat selection: dilectus preferring grasslands with little bare soil while bechuanae occurring in open shrublands. In sympatry, shrubland type habitats dominate and differences are less marked, yet dilectus selects habitats with more cover than bechuanae. Interestingly, bechuanae shows larger HRs than dilectus, and both species display larger HRs in sympatry. Further, HR overlaps between species are lower than expected. We discuss our results in light of data on the phylogeography of the genus and propose that evolution in allopatry resulted in adaptation leading to different habitat preferences, even at their distribution margins, a divergence expected to facilitate coexistence. However, since sympatry occurs in sites where environmental characteristics do not allow complete species separation, competition may explain reduced inter-species overlap and character displacement in HR size. This study reveals that both environmental variation and competition may shape species coexistence.
Biomass increases go under cover: Woody vegetation dynamics in South African rangelands.
03 June 2016
University of the Witwatersrand

Mograbi, P.J.;Erasmus, B.F.N.;Witkowski, E.T.F.;Martin, R.E.;Main, R.;Asner, G.P.;Wessels, K.J.;Mathieu, R.;Knapp, D.E.

Woody biomass dynamics are an expression of ecosystem function, yet biomass estimates do not provide information on the spatial distribution of woody vegetation within the vertical vegetation subcanopy. We demonstrate the ability of airborne light detection and ranging (LiDAR) to measure aboveground biomass and subcanopy structure, as an explanatory tool to unravel vegetation dynamics in structurally heterogeneous landscapes. We sampled three communal rangelands in Bushbuckridge, South Africa, utilised by rural communities for fuelwood harvesting. Woody biomass estimates ranged between 9 Mg ha-1 on gabbro geology sites to 27 Mg ha-1 on granitic geology sites. Despite predictions of woodland depletion due to unsustainable fuelwood extraction in previous studies, biomass in all the communal rangelands increased between 2008 and 2012. Annual biomass productivity estimates (10-14% p.a.) were higher than previous estimates of 4% and likely a significant contributor to the previous underestimations of modelled biomass supply. We show that biomass increases are attributable to growth of vegetation <5 m in height, and that, in the high wood extraction rangeland, 79% of the changes in the vertical vegetation subcanopy are gains in the 1-3m height class. The higher the wood extraction pressure on the rangelands, the greater the biomass increases in the low height classes within the subcanopy, likely a strong resprouting response to intensive harvesting. Yet, fuelwood shortages are still occurring, as evidenced by the losses in the tall tree height class in the high extraction rangeland. Loss of large trees and gain in subcanopy shrubs could result in a structurally simple landscape with reduced functional capacity. This research demonstrates that intensive harvesting can, paradoxically, increase biomass and this has implications for the sustainability of ecosystem service provision. The structural implications of biomass increases in communal rangelands could be misinterpreted as woodland recovery in the absence of three-dimensional, subcanopy information.
Biogeochemical cycles and biodiversity as key drivers of ecosystem services provided by soils.
16 July 2016
University of the Witwatersrand

Smith, P.;Cotrufo, M. F.;Rumpel, C.;Paustian, K.;Kuikman, P.J.;Elliott, J.A.;McDowell, R.;Griffiths, R.I.;Asakawa, S.;Bustamante, M.;House, J.I.;Sobocká, J.;Harper, R.;Pan, G.;West, P.C.;Gerber, J.S.;Clark, J.M.;Adhya, T.;Scholes, R.J.;Scholes, M.C.

Soils play a pivotal role in major global biogeochemical cycles (carbon, nutrient, and water), while hosting the largest diversity of organisms on land. Because of this, soils deliver fundamental ecosystem services, and management to change a soil process in support of one ecosystem service can either provide co-benefits to other services or result in trade-offs. In this critical review, we report the state-of-the-art understanding concerning the biogeochemical cycles and biodiversity in soil, and relate these to the provisioning, regulating, supporting, and cultural ecosystem services which they underpin. We then outline key knowledge gaps and research challenges, before providing recommendations for management activities to support the continued delivery of ecosystem services from soils. We conclude that, although soils are complex, there are still knowledge gaps, and fundamental research is still needed to better understand the relationships between different facets of soils and the array of ecosystem services they underpin, enough is known to implement best practices now. There is a tendency among soil scientists to dwell on the complexity and knowledge gaps rather than to focus on what we do know and how this knowledge can be put to use to improve the delivery of ecosystem services. A significant challenge is to find effective ways to share knowledge with soil managers and policy makers so that best management can be implemented. A key element of this knowledge exchange must be to raise awareness of the ecosystems services underpinned by soils and thus the natural capital they provide. We know enough to start moving in the right direction while we conduct research to fill in our knowledge gaps. The lasting legacy of the International Year of Soils in 2015 should be for soil scientists to work together with policy makers and land managers to put soils at the centre of environmental policy making and land management decisions.
Unveiling the micronome of cassava (manihot esculenta crantz).
16 September 2016
University of the Witwatersrand

Rogans, S.J.;Rey, C.

MicroRNAs (miRNAs) are an important class of endogenous non-coding single-stranded small RNAs (21-24 nt in length), which serve as post-transcriptional negative regulators of gene expression in plants. Despite the economic importance of Manihot esculenta Crantz (cassava) only 153 putative cassava miRNAs (from multiple germplasm) are available to date in miRBase (Version 21), and identification of a number of miRNAs from the cassava EST database have been limited to comparisons with Arabidopsis. In this study, mature sequences of all known plant miRNAs were used as a query for homologous searches against cassava EST and GSS databases, and additional identification of novel and conserved miRNAs were gleaned from next generation sequencing (NGS) of two cassava landraces (T200 from southern Africa and TME3 from West Africa) at three different stages post explant transplantation and acclimatization. EST and GSS derived data revealed 259 and 32 miRNAs in cassava, and one of the miRNA families (miR2118) from previous studies has not been reported in cassava. NGS data collectively displayed expression of 289 conserved miRNAs in leaf tissue, of which 230 had not been reported previously. Of the 289 conserved miRNAs identified in T200 and TME3, 208 were isomiRs. Thirty-nine novel cassava-specific miRNAs of low abundance, belonging to 29 families, were identified. Thirtyeight (98.6%) of the putative new miRNAs identified by NGS have not been previously reported in cassava. Several miRNA targets were identified in T200 and TME3, highlighting differential temporal miRNA expression between the two cassava landraces. This study contributes to the expanding knowledge base of the micronome of this important crop.
Systematic land-cover change in KwaZulu-Natal, South Africa: Implications for biodiversity.
22 September 2016
University of the Witwatersrand

Jewitt, D.;Goodman, P.S.;Erasmus, B.F.N.;O'Connor, T.G.;Witkowski, E.T.F.

Land-cover change and habitat loss are widely recognised as the major drivers of biodiversity loss in the world. Land-cover maps derived from satellite imagery provide useful tools for monitoring land-use and land-cover change. KwaZulu-Natal, a populous yet biodiversity-rich province in South Africa, is one of the first provinces to produce a set of three directly comparable land-cover maps (2005, 2008 and 2011). These maps were used to investigate systematic land-cover changes occurring in the province with a focus on biodiversity conservation. The Intensity Analysis framework was used for the analysis as this quantitative hierarchical method addresses shortcomings of other established land-cover change analyses. In only 6 years (2005-2011), a massive 7.6% of the natural habitat of the province was lost to anthropogenic transformation of the landscape. The major drivers of habitat loss were agriculture, timber plantations, the built environment, dams and mines. Categorical swapping formed a significant part of landscape change, including a return from anthropogenic categories to secondary vegetation, which we suggest should be tracked in analyses. Longer-term rates of habitat loss were determined using additional land-cover maps (1994, 2000). An average of 1.2% of the natural landscape has been transformed per annum since 1994. Apart from the direct loss of natural habitat, the anthropogenically transformed land covers all pose additional negative impacts for biodiversity remaining in these or surrounding areas. A target of no more than 50% of habitat loss should be adopted to adequately conserve biodiversity in the province. Our analysis provides the first provincial assessment of the rate of loss of natural habitat and may be used to fulfil incomplete criteria used in the identification of Threatened Terrestrial Ecosystems, and to report on the Convention on Biological Diversity targets on rates of natural habitat loss.
Land-cover change in the Kruger to Canyons Biosphere Reserve 1993-2006): A first step towards creating a conservation plan for the subregion.
22 September 2016
University of the Witwatersrand

Coetzer, K.L.;Erasmus, B.F.N.;Witkowski, E.T.F.;Bachoo, A.K.

This paper is a first step towards a conservation plan for the Kruger to Canyons Biosphere Reserve K2C) on the South African Central Lowveld, quantifying the historical land-cover trends 1993-2006). During the analysis period, 36% of the biosphere reserve BR) underwent land-cover change. Settlement areas increased by 39.7%, mainly in rural areas, becoming denser, particularly along roadways. Human-Impacted Vegetation increased by 6.8% and Intact Vegetation declined by 7.3%, predominantly around settlement areas, which is testament to the interdependency between rural communities and the local environment. However, settlement expansion exceeded the rate of rangeland growth; in the long term, this may raise questions for sustainable resource extraction. Similarly, the block losses of intact vegetation are of concern; issues of fragmentation arise, with knock-on effects for ecosystem functioning. In the economic sector, agriculture increased by 51.9%, while forestry and mining declined by 7.1% and 6.3%, respectively. The future of these three sectors may also have significant repercussions for land-cover change in the BR. The identification of historical drivers, along with the chance that existing trends may continue, will have important implications for biodiversity protection in this landscape. Applied within a conservation-planning framework, these land-cover data, together with economic and biodiversity data, will help reconcile the spatial requirements of socio-economic development with those of conservation.
Effects of water and nutrient addition on the coppice growth response of cut Terminalia sericea.
22 September 2016
University of the Witwatersrand

Moyo, H.;Scholes, M.C.;Twine, W.

The ability of a woody plant to coppice and remain vigorous largely depends on the severity of disturbances, resource availability and the mobilisation of stored reserves. There is limited information about the role played by resource limitation on the recovery of cut trees. This study investigated the effects of water and nutrient supplementation on coppice growth responses of resprouting cut trees in a semi-arid savannah in South Africa. Cut trees were exposed to different levels of water and nutrient (nitrogen and phosphorus) supplementation over a period of 2 years in a factorial experimental design. We hypothesised that adding water and nutrients would result in an increased coppice growth response and replenishment of stored structural reserves. Adding water and nutrients significantly increased shoot diameter, shoot length and resprouting ratio for the initial 12 months after cutting but not stored structural reserves. Such a response pattern suggests that the initial growth of resprouting shoots may be strongly resource-limited, while resources are concentrated on supporting fewer resprouting shoots compared to a higher number. Conservation implications: If practicing rotational tree harvesting, trees resprouting in resource-poor locations need a longer resting period to recover stored reserves and to also recover lost height after cutting.
Towards Citizen–Expert Knowledge Exchange for Biodiversity Informatics: A Conceptual Architecture
26 January 2017
University of the Witwatersrand

Kiptoo, Caroline Chepkoech;Gerber, Aurona;Van der Merwe, Alta

This article proposes a conceptual architecture for citizen–expert knowledge exchange in biodiversity management. Expert services, such as taxonomic identification, are required in many biodiversity management activities, yet these services remain inaccessible to poor communities, such as small-scale farmers. The aim of this research was to combine ontology and crowdsourcing technologies to provide taxonomic services to such communities. The study used a design science research (DSR) approach to develop the conceptual architecture. The DSR approach generates knowledge through building and evaluation of novel artefacts. The research instantiated the architecture through the development of a platform for experts and farmers to share knowledge on fruit flies. The platform is intended to support rural fruit farmers in Kenya with control and management of fruit flies. Expert knowledge about fruit flies is captured in an ontology that is integrated into the platform. The non-expert citizen participation includes harnessing crowdsourcing technologies to assist with organism identification. An evaluation of the architecture was done through an experiment of fruit fly identification using the platform. The results showed that the crowds, supported by an ontology of expert knowledge, could identify most samples to species level and in some cases to sub-family level. The conceptual architecture may guide and enable creation of citizen–expert knowledge exchange applications, which may alleviate the taxonomic impediment, as well as allow poor citizens access to expert knowledge. Such a conceptual architecture may also enable the implementation of systems that allow non-experts to participate in sharing of knowledge, thus providing opportunity for the evolution of comprehensive biodiversity knowledge systems.
Bridging the knowing–doing gap in South Africa and the role of environmental volunteer groups
13 April 2017
University of the Witwatersrand

Dzerefos, C.M.;Witkowski, E.T.F.

The implementation gap between science, policy and practice has led to loss of biodiversity and ecosystem services throughout Africa and is described in a case study from Limpopo Province, South Africa. In 2006, the South African National Biodiversity Institute first highlighted the Woodbush Granite Grassland (WGG) in the Greater Tzaneen Local Municipality as the only Critically Endangered ecosystem in Limpopo Province. Five years later (2011), the Critically Endangered listing was published in the Government Gazette No. 34809. After repeated and sustained efforts for many years from volunteers of a local environmental group - currently known as the Friends of the Haenertsburg Grassland (FroHG) - in 2015 the intent to formally protect 126 ha was published in the Government Gazette No. 2609. Unfortunately, the proposed protected area accounts for only 66% of the largest remaining fragment of WGG, which excludes an important colony of medicinal plants. Considering that only 6% of the original extent of WGG remains in an untransformed state the whole fragment should be conserved. Non-alignment of municipal spatial priorities, as in the Haenertsburg town plan from 1896, to provincial and national environmental priorities has resulted in numerous incidents that have degraded what little remains of the WGG ecosystem. Failure of the provincial authorities to act timeously to enforce environmental regulations resulted in the FroHG successfully involving national authorities to stop illegal land occupation while another incident involving an illegal fence was resolved 9 years after erection. A strengthened relationship with Lepelle Northern Water has resulted in better planning of activities in relation to an existing pipeline. This case study shows various avenues available to environmental volunteer groups in South Africa and suggests that long-term lobbying can yield positive results. Conservation implications: Formal conservation of WGG through the intended nature reserve proclamation represents application of environmental legislation (notably Listing Notice 3, National Environmental Management Act 107 of 1998: Environmental Impact Assessment Regulations, 2014), scientific recommendations and policy. Better cooperation between provincial administration and FroHG will benefit the protection and management of WGG.
The sixth World Flora Online Council meeting held in South Africa
19 September 2019
University of the Witwatersrand

le Roux, M.;Klopper, R.;Jackson, P.S.W.;Loizeau, P.;Victor, J.E.;Sebola, J.R.

Biannual Council meetings are held with the aim of developing a World Flora Online (WFO) in response to Target 1 of the Global Strategy for Plant Conservation (2011-2020). Objectives: To report on the sixth WFO Council meeting held in Pretoria, South Africa, on November 2016. Method: A WFO Council meeting (preceded by Taxonomic and Technical Working Group meetings) was hosted by the South African National Biodiversity Institute in Pretoria. Results: Significant progress with the development of the WFO portal was made. Conclusion: The WFO portal will be launched at the International Botanical Congress in China in 2017.
Notes on the flowering and pollination of the endemic grassland Aloe reitzii var. reitzii (Asphodelaceae)
19 September 2019
University of the Witwatersrand

Symes, C.T.

Aloe reitzii var. reitzii is a succulent with a restricted distribution in the montane grassland of eastern South Africa. It is a summer (late January-March) flowering succulent that grows on rocky outcrops at 1000 m-1600 m, and the conspicuous inflorescences suggest a pollination system focused towards birds. Objectives: To understand more about the pollination biology of A. reitzii var. reitzii. Methods: Nectar standing crop (flower volume and concentration) and the proportion of plants flowering were recorded. Camera traps and observations were used to record visitors to A. reitzii var. reitzii inflorescences. Results: Nectar volume was 36 μL ± 27 μL per flower (range 6 μL-93 μL; n = 27) and concentration was 16.5% ± 1.7% (range 13.5% - 19.5%). Camera trap observations, where 18.9% of all plants were observed flowering, recorded the three bird species Cape Weaver, Ploceus capensis, Malachite Sunbird, Nectarinia famosa and Greater Double-collared Sunbird, Cinnyris afer (60.4%, 27.1% and 12.5% of plant visits, respectively) visiting inflorescences. Conclusion: Because birds are important pollinators for many Aloe species, it is assumed that the bird species detected visiting A. reitzii var. reitzii are similarly important pollinators. At least 10 invertebrate species and sengi (Elephantulus sp.) were also recorded as visitors to flowers, but they may be less important pollinators than specialist and generalist avian nectarivores. This study provides further insight into the pollination biology of a diverse, and ecologically important, succulent genus in Africa.
A review of biodiversity reporting by the South African seafood industry
14 July 2020
University of the Witwatersrand

Usher, K;Maroun, W

Background: Biodiversity reporting is an area of sustainability accounting research that has received comparatively little attention from the academic community. This is despite the growing scientific concern about climate change, habitat destruction and extinction of species and mounting evidence on the implications of these environmental issues for our current way of life. This necessitates additional research on biodiversity reporting, especially in a South African context given that the country is home to some of the richest biodiversity regions on earth. Aim: This research examines what information companies in the South African seafood industry are reporting on biodiversity. This includes the development and application of an easy-to-use disclosure scorecard to track the quality of biodiversity-related disclosures. Setting: The study focuses on South African biodiversity reporting. The choice of region is informed by the country’s significant marine resources and mature corporate reporting environment, where non-financial disclosures are expected to be well developed. Methods: Content analysis was used to collect data from a sample of companies’ integrated and sustainability reports. The data were analysed interpretively to determine what biodiversity disclosures companies provide and the quality of those disclosures. Conclusion: The study shows that while the quantum of biodiversity reporting is relatively low, some companies are starting to provide more detailed accounts of their biodiversity impact, pointing to higher levels of reporting quality. There is still room for improvement, but these findings suggest that reporting on non-financial sustainability issues is maturing and that companies are beginning to appreciate the importance of preserving biodiversity for ensuring long-term sustainability. © 2018. The Authors.
A stylistic analysis of a wildlife conservation of a prologue and visual narrative documentary, “From brutal poacher to delicate pastry chef”
01 April 2022
University of the Witwatersrand

Moodley, V.

Documentaries, like other genres, are being increasingly used by wildlife conservationists for creating awareness and influencing viewers to become active backers of wildlife protection. While there have been analyses of documentaries that focus on cinematic techniques, stylistic analyses of the language used in them have been limited. This paper analyses the prologue to the documentary, “The journey from brutal poacher to delicate pastry chef”, and the visual monologue narrative, “The Pastry Chef”, to show how the scriptwriter uses language as rhetoric to raise social consciousness amongst its audience. The paper adopts the stylistic pluralism approach which blends literary criticism, linguistic analysis and stylistic description. Leech and Short’s (2007) broad framework of linguistic and stylistic categories (i.e. lexical items, grammatical features, figures of speech and other rhetoric features and cohesiveness) is used to show how the scriptwriter creates awareness of wildlife conservation and positions people as active backers of wildlife protection. It argues that linguistic choices – such as lexical items, grammatical features and cohesive devices – and rhetoric are critical features of documentary design. Keywords: documentary; rhetoric; stylistics; wildlife conservation
Northern NGOs, southern NGOs and international environmental law: The common interest of humankind is the interest of northern mankind!
31 August 2009
North West University

Scholtz, Werner

States need to address global environmental problems that threaten humankind. Sovereign states, however, seem ill equipped to find solutions to counter global environmental degradation. It is in this regard important to take cognisance of the proliferation of non-governmental organisations (NGOs), which actively participate in the field of global environmental matters. International NGOs are not constrained by sovereignty and state interest. The question that accordingly arises is whether international NGOs present a solution to global environmental problems. Are NGOs the hope of humankind in this regard? Can they pursue solutions to ensure the survival of mankind? It is the main aim of this article to present answers to the above questions. Thus, the first part of this article examines the challenges that global environmental problems in a state centred system pose. The second part of this article briefly defines NGOs, introduces the different types of NGOs as well as the roles that they fulfil in international environmental law. The third part follows a critical southern approach in order to determine whether NGOs can truly pursue a global agenda. The last part of this article generates proposals to the problems presented in this article.
Trichloroacetic acid of different origin in Norway spruce needles and chloroplasts
24 May 2010
North West University

Forczek, S.T.;Schröder, P.;Weissflog, L.;Krüger, Gert;Rohlenová, J.;Matucha, M.

Trichloroacetic acid (TCA), a secondary atmospheric pollutant, is also formed in forest soil and thus ranked among natural organohalogens. The observed biooxidation of atmospheric tetrachloroethene (PER) to TCA in chloroplasts has led to the investigation of the mode of action of TCA in spruce needles, since TCA is also accumulated in the needles after its rapid uptake from soil by roots. Being phytotoxic, TCA considerably influences conifers by affecting their photosynthetic apparatus. We examined the transport of TCA from soil into chloroplasts in order to compare the effects of TCA on conifers from both sources, i.e. endogenously produced within chloroplasts or taken up by roots. The influence of TCA formed in chloroplasts was found to be much more adverse than that of “soil” TCA.
The world of spirits and the respect for nature: towards a new appreciation of animism
10 January 2011
North West University

Kimmerle, Heinz

The belief in spirits has diminished in Western thought since Enlightenment. But it has not disappeared totally. In the subconscious of people and in different subcultures and also in literature and art it is still alive. Derrida, before his death, worked out a new spectrology in which the status of reality of spirits is interpreted as absently present. In Sub-Saharan African thought this belief is broadly present and deeply rooted. It is the core of traditional African religions. Also intellectuals, although they may have taken over Christian or Islamic convictions, mostly stick to this belief. An important aspect of the African belief in spirits is that they also dwell in nature. In principle they can choose for all natural things to dwell in them, and there is a special inclination for trees. The spiritual conception of reality as a whole is called animism. This important religion has been devaluated in connection with colonialism. Recently the respect for nature which comes forth from this religion is highly appreciated by ecological philosophy.
A practical exploration of the feasibility of integrative multidisciplinary research from a broad ecohealth perspective in South Africa.
19 January 2012
North West University

Van Eeden, Elize S

This discussion is a deliberation on the progress towards the possibility of carrying out feasible research according to an Integrative Multidisciplinary (IMD) research methodology (theoretically and practically). To explore the IMD research methodology, a group of researchers from several disciplines started discussions in early February 2011 to plan a pilot research process in the Bekkersdal Township of the municipal region of Westonaria (Gauteng, South Africa). It was decided that the focus of research would be on exploring a broad definition of ecohealth to accommodate several disciplines and to attempt to produce a “package” of research results from many disciplinary angles. These results will eventually be discussed and refined through interdisciplinary (ID) and transdisciplinary (TD) research phases to “contain” consolidated reflections of the status of the well-being of the Bekkersdal community. However, the primary research question remains: whether it is possible to do research using IMD methodology, and whether this proposed methodology is more promising and constructive as an aid to understanding and disseminating research from various disciplinary angles than other methodologies.
Kirstenbosch: the final victory of botanical nationalism.
26 January 2012
North West University

McCracken, Donal P

• Opsomming: Alhoewel die Nasionale Botaniese Tuine by Kirstenbosch eers in 1913 tot stand gekom het, was Botaniese tuine reeds vir 60 jaar ŉ kenmerk van die Kaapse stedelike gemeenskap. Die ou tuine van die Duits-Oos Indiese Kompanjie in Kaapstad het by verskeie geleenthede botaniese elemente gehad. Hierdie tuine het daartoe bygedra om belangstelling in die Kaapse flora in beide Europa en die Kaap te bevorder. Die vestiging van Kirstenbosch het die belofte vir die oorwinning van Suid-Afrikaanse botaniese nasionalisme ingehou. Laasgenoemde is egter vir 76 jaar vertraag weens die kloof tussen die Kaapse en Pretoriase botaniese ondernemings.
The history of nature conservation in Sandton.
06 February 2012
North West University

Carruthers, E J

• Opsomming: Hierdie artikel word gewy aan 'n baanbrekerspoging om stedelike natuurbewaring in Suid-Afrika toe te pas. Die dorp Sandton het in 1969 tot stand gekom toe aan voorstedelike gebiede en kleinhoewes noord van Johannesburg plaaslike selfbestuur toegeken is. Uit die staanspoor het die Stadsraad die regte verhouding tussen stads- en natuurgebiede probeer bewerkstellig ten einde die lewensgehalte van die inwoners te bestendig en om dele van die hoëveld in die dorpsgrond te bewaar. Hoewel die Stadsraad destyds geloof is vir sy versiendheid en onverskrokke optrede, geniet bewaring nie meer voorkeur sover dit Sandton se plaaslike bestuur aanbetref nie. Die Sentrale regering tree nou egter op om te voorkom dat die natuurlike omgewing heeltemal deur stedelike ontwikkeling vernietig word.
Rhodes Fruit Farms: a small beginning in the Paarl valley.
13 February 2012
North West University

Aucamp, Chris

• Opsomming: Rhodes Fruit Farms, geleë in die Groot Drakenstein vallei het in 1897 o.l.v. Harry Pickstone met die finansiële steun van Cecil John Rhodes tot stand gekom. Pickstone het die moontlikhede om sagtevrugte aan die Kaap op groot skaal vir die plaaslike en uitvoermark te verbou ingesien en onder sy leiding is 'n maatskappy gestig, grond aangekoop, en die bedryf op 'n wetenskaplike en winsgewende basis geplaas. Rhodes Fruit Farms het sedert sy nederige begin 'n uiters belangrike bydrae gelewer tot die vooruitgang van die sagtevrugtebedryf in Suid-Afrika.
Resistance to Bt Maize in Busseola fusca (Lepidoptera: Noctuidae) from Vaalharts, South Africa
03 October 2012
North West University

Kruger, Marlene;Van den Berg, Johann;Van Rensburg, J.B.J.

The first report of resistance of the maize stem borer [Busseola fusca (Fuller)] to Bt maize (MON810) was made in the Christiana area of South Africa during 2007. The objective of this study was to evaluate the status of resistance of other populations of B. fusca to Bt maize. One greenhouse and two laboratory studies were conducted. B. fusca populations were collected on Bt maize as well as the adjacent refugia (conventional maize and non-Bt maize) in the Vaalharts area, 50 km from the Christiana site. Control populations were collected from sites where Bt maize was not planted. In the greenhouse study 720 potted plants were each artificially infested with 10 neonate larvae of the F1-generation after the field collected populations were reared through to adults. Numbers of live larvae and larval mass per plant were determined at regular intervals over a 35-d period. Larvae of the Christiana conventional population (Bt-susceptible) on Bt maize (CHR08ConBt) and Bethal conventional population (Bt-susceptible) on Bt maize (BET08Con-Bt) did not survive on Bt maize for longer than 12 d. The populations collected from both Bt (VAA08Bt-Bt) maize and refuges (VAA08Ref-Bt) at Vaalharts were resistant and the subsequent generation of larvae completed their life cycle on Bt maize. Similar results were observed in the laboratory experiments. This study confirmed resistance of B. fusca to the Cry1Ab toxin (MON810). The geographical distribution of resistance was shown to include at least the Vaalharts area, in addition to the original report for the Christiana area. These observations that larvae collected from refugia at Vaalharts was resistant, show that the efficacy of the refuge strategy is compromised in this area because the contribution of refugia did not produce large enough numbers of susceptible individuals to mate with moths of which larvae survived inside Bt maize fields.
Myth as a biodiversity conservation strategy for the Vhavenda, South Africa
17 October 2012
North West University

Siebert, Stefan John;Mutshinyalo, T.T.

The use of myth and superstition is an integral part of indigenous communities in Africa. It is used as a traditional approach for sustainable use and management of natural resources. The use of myths has significantly played a role in preserving biodiversity in the traditional Vhavenda community. Certain trees are forbidden for use as firewood, which has indirectly contributed towards the conservation of associated biodiversity and ecosystems services. The article is based on a study that investigates the role played by traditional Vhavenda myths in conserving biodiversity and associated ecosystems, including reasons behind the use of myths in prohibiting unsustainable use of biodiversity. Different techniques were used to collect data, namely interviews, observations, personal experience and a literature review. Results suggest that workable indigenous approaches exist to deal with biodiversity conservation
Revegetation of a uranium mine dump by using fertilizer treated sessile oaks
22 October 2012
North West University

Katzur, Joachim;Lange, Christian Albert;Böcker, Lutz

The rehabilitation of contaminated sites and the establishment of suitable trees for revegetation purposes is often problematic due to the mostly suboptimal nutrient supply and the poor humus reservoir. For these reasons hydrogels (Stockosorb®) and novel humus substitutes (NOVIHUM®), serving as long lasting fertilizer (LLF), were recently tested successfully. At the beginning of this multiyear study, those LLFs were administered to the root zone of young sessile oaks (Quercus petraea (Mattuschka) Liebl.), growing in test trials on a uranium mine dump in Schlema (Germany). To quantify the effect of LLFs on plant vitality, chlorophyll a fluorescence measurements and JIP test analyses were used. The results revealed up to 49% higher average photosynthetic vitality (PIABS) of the LLF treated plants compared to controls. Particularly in the first test year, the efficiency of photosynthetic electron transport was strongly increased. This stimulation of photosynthetic activity was supported by direct measurements showing up to 129% increased diameter growth of the treated plants after a four year experimental period.Furthermore an increase of the maximum water holding capacity of the dump soil was attained by using LLFs. Overall, the findings reported here represent a feasible, ecologically justifiable reforestation method with a low environmental hazard potential.
Towards sustainable land management in the drylands: scientific connections in monitoring and assessing dryland degradation, climate change and biodiversity
05 November 2012
North West University

Kellner, Klaus;Cowie, A.L.;Penman, T.D.;Gorissen, L.;Winslow, M.D.

The United Nations Convention to Combat Desertification and its sister conventions, the United Nations Framework Convention on Climate Change and the Convention on Biological Diversity, all aim to halt or mitigate the deterioration of the ecological processes on which life depends. Sustainable land management (SLM) is fundamental to achieving the goals of all three Conventions. Changes in land management undertaken to address dryland degradation and desertification can simultaneously reduce net greenhouse gas emissions and contribute to conservation of biodiversity. Management to protect and enhance terrestrial carbon stocks, both in vegetation and soil, is of central importance to all three conventions. Protection of biodiversity conveys stability and resilience to agro-ecosystems and increases carbon storage potential of dryland systems. SLM improves livelihoods of communities dependent on the land. Despite these complementarities between the three environmental goals, tradeoffs often arise in their pursuit. The importance of human–environment interactions to the condition of land compels attention to adaptive management. In order to reconcile concerns and agendas at a higher strategic level, identification of synergies, conflicts, trade-offs, interconnections, feedbacks and spillover effects among multiple objectives, drivers, actions, policies and time horizons are crucial. Once these issues are transparent, coordinated action can be put into place across the three multilateral environmental agreements in the development of strategies and policy measures to support SLM.
Differential responses of resistant and susceptible groundnut genotypes at cellular level to Ditylenchus africanus
13 November 2012
North West University

Jordaan, Anine;Steenkamp, Sonia;McDonald, Alexander Henrique;De Waele, Dirk Gaby Marthe Albert

Ditylenchus africanus causes cellular breakdown in pod tissue of susceptible groundnut cultivars. The histopathology of this nematode on a resistant genotype was studied using light microscopy and compared with the histopathology of D. africanus on a susceptible genotype. Plants of breeding line PC254K1 and cv. Sellie were propagated in a glasshouse, inoculated with D. africanus at inoculum levels of 2000, 5000 and 7000 nematodes per plant and the pods were collected at 90, 120 and 150 days after planting. In contrast to the susceptible genotype, only a small number of nematodes were observed in restricted areas of the pod tissue of the resistant genotype. Furthermore, the resistant genotype showed neither external symptoms nor cellular breakdown in reaction to D. africanus. According to results of this study, the mechanism of resistance involved may be the inhibition of proper development, migration and reproduction of this nematode, thus preventing it building up to damaging population levels.
Multiple emergences of genetically diverse amphibian-infecting chytrids include a globalized hypervirulent recombinant lineage
29 November 2012
North West University

Farrer, Rhys A.;Weinert, Lucy A.;Bielby, Jon;Garner, Trenton W.J.;Balloux, Francois;Du Preez, Louis Heyns;Weldon, Ché

Batrachochytrium dendrobatidis (Bd) is a globally ubiquitous fungal infection that has emerged to become a primary driver of amphibian biodiversity loss. Despite widespread effort to understand the emergence of this panzootic, the origins of the infection, its patterns of global spread, and principle mode of evolution remain largely unknown. Using comparative population genomics, we discovered three deeply diverged lineages of Bd associated with amphibians. Two of these lineages were found in multiple continents and are associated with known introductions by the amphibian trade. We found that isolates belonging to one clade, the global panzootic lineage (BdGPL) have emerged across at least five continents during the 20th century and are associated with the onset of epizootics in North America, Central America, the Caribbean, Australia, and Europe. The two newly identified divergent lineages, Cape lineage (BdCAPE) and Swiss lineage (BdCH), were found to differ in morphological traits when compared against one another and BdGPL, and we show that BdGPL is hypervirulent. BdGPL uniquely bears the hallmarks of genomic recombination, manifested as extensive intergenomic phylogenetic conflict and patchily distributed heterozygosity. We postulate that contact between previously genetically isolated allopatric populations of Bd may have allowed recombination to occur, resulting in the generation, spread, and invasion of the hypervirulent BdGPL leading to contemporary disease-driven losses in amphibian biodiversity.
Host suitability of selected South African maize genotypes to the root-knot nematode species Meloidogyne incognita race 2 and Meloidogynejavanica: a preliminary study
22 January 2013
North West University

Fourie, Hendrika;Ngobeni, G.L.;McDonald, Alexander Henrique;Mashela, P.W.

Thirty-one commercial maize (Zea mays L.) hybrids and open-pollinated varieties (OPV's) were screened in separate greenhouse trials with a resistant inbred line MP712W as reference genotype for host suitability to Meloidogyne incognita race 2 and Meloidogyne javanica. Approximately 10 000 eggs and second-stage juveniles (J2) of the appropriate root-knot nematode species were inoculated on roots of each maize seedling 10 days after plant emergence. The numbers of eggs and J2 per root system were counted, while it was also calculated g-1 root. In addition, percentage resistance in relation to the most susceptible genotype and nematode reproduction factors (Rf) were calculated for the maize genotypes screened. Substantial variation existed among the maize hybrids and OPV's with regard to the nematode parameters evaluated. A number of genotypes could be regarded as highly resistant to M. incognita race 2 based on the fact that they supported less than 10% of the population of this root-knot nematode species, compared to that supported by the most susceptible genotype. Several hybrids and OPV's were identified with Rf values less than one for M. incognita race 2 and M. javanica respectively, indicating antibiosis resistance to these parasites. Screenings of maize genotypes in this study have provided a clear indication of the genetic variability within the maize genome, also with regard to susceptibility of the crop to root-knot nematodes. This substantiates the fact that maize could not be regarded as a non-host to root-knot nematodes on a generic basis, particularly in terms of commercial hybrids. It is suggested that commercial maize hybrids are screened on a continuous basis against root-knot nematodes, which would facilitate selection of hybrids that are less susceptible to both nematode species but that would perform optimally in soils conducive to root-knot-nematode infestation.
Payment for ecosystem services
14 August 2013
North West University

Benjamin, Antonio Herman

This address focuses on the legislative design for payment or ecosystem services (PES) since most countries do not have specific legislation that addresses the subject. Brazil is in the process of drafting national legislation on ecosystem services and there are several important issues that can be learnt from this experience.
Law, the laws of nature and ecosystem energy services: a case of wilful blindness
14 August 2013
North West University

Hodas, David R

Ecosystems services include the collection, concentration, and storage of solar energy as fossil fuels (e.g., coal, petroleum, and natural gas). These concentrated forms of energy were produced by ancient ecosystem services. However, our legal and economic systems fail to recognise the value of the ecosystem service subsidies embedded in fossil fuels. This ecosystem services price subsidy causes overuse and waste of fossil fuels in the free market: fossil fuels are consumed more quickly than they can be replaced by ecosystem services and in far larger quantities than they would be if the price of fossil fuels included the cost of solar energy collection, concentration and manufacturing of raw fossil fuels. Moreover, burning fossil fuels produces enormous environmental, human health and welfare costs and damage. Virtually no legal literature on ecosystem services, sustainable development, or sustainable energy, considers fossil fuels in this context. Without understanding stored energy as an ecosystem service, we cannot reasonably expect to manage our fossil fuel energy resources sustainably. International and domestic energy law and policy systems generally ignore this feature of fossil fuel energy, a blind spot that explains why reducing greenhouse gas emissions from fossil fuels is fundamentally a political challenge. This paper will use new understandings emerging from the field of complex systems to critique existing legal decision-making models that do not adequately account for energy ecosystem services in policy design, resource allocation and project approvals. The paper proposes a new "least-social-cost" decision-making legal structure that includes ecosystem energy services.
Towards the legal recognition and governance of forest ecosystem services in Mozambique
14 August 2013
North West University

Norfolk, Simon;Cosijn, Michaela

Within the context of Mozambique, this paper examines the state of forest ecosystem services, the dependency of the population on these systems for their well-being, if an adaptive governance regime is being created which will ensure the resilience of the forest ecosystem services including the legal framework, the institutions operating within this framework, the tools available and their functioning, and how cooperative governance is operating.
Confirming the pest status of Trimen’s false tiger, Agoma trimenii (Felder) (Lepidoptera: Agaristidae), on grapevines in South Africa
23 September 2013
North West University

Pretorius, J.D.;Zaayman, J.L.;Van den Berg, J.

Various lepidopteran pests attack grapevines in South Africa, but they are mostly regarded as sporadic pests that seldom cause economic damage. The leaf-feeding silver-striped hawk moth, Hippotion celerio (Linneaus) (Sphingidae), is common in the Western Cape Province and occasionally causes economic damage to young vines. Theretra capensis (Linneaus) (Sphingidae) (grapevine hawk moth) and Heraclia superba (Butler) (Agaristidae) (superb false tiger) have also been reported on vines, but are rarely of economic importance (Annecke & Moran, 1982).
Hydration state of the Moss Hylocomium splendens and the Lichen Cladina stellaris governs uptake and revolatilization of airborne α- and γ‑Hexachlorocyclohexane
22 January 2014
North West University

Kylin, H.;Bouwman, Henk

The partitioning of α- and γ-hexachlorocyclohexane between air and the moss Hylocomium splendens and the lichen Cladina stellaris were studied under laboratory conditions. After cultivation of the sample material to obtain a common starting point free from outside influence, the material was divided into four different treatment categories with different hydration/desiccation regimes. The concentrations of the analytes were 3–5 times higher in the hydrated moss or lichen than in the desiccated material. The results are in contrast to how these compounds are taken up by pine needles in which there is a continuous accumulation, more rapid during periods with high temperatures and dry weather. In general, the different adaptations to water economy is a more important explanatory factor for the concentration of airborne hydrophobic pollutants in mosses, lichens, and vascular plants than their designation as “plants” in a broad sense. It is, therefore, not advisible to mix data from different organism groups for monitoring or modeling purposes.
Sustainable rural learning ecologies- a prolegomenon traversing transcendence of discursive notions of sustainability, social justice, development and food sovereignty
26 February 2014
North West University

Hlalele, Dipane

This paper contributes, through traversing contested notions of sustainability, social justice, development and food sovereignty, to discourses around creation of sustainable rural learning ecologies. There has always been at least in the realm of scientific discourse, an attempt to dissociate the natural or physical environment from the social and human environment. This trend did not only affect the two spheres of existence only. It is further imbued and spawned fragmented and pervasive terminology, practices and human thought. Drawing from the ‘creating sustainable rural learning ecologies’ research project that commenced in 2011, I challenge and contest the use of such discourses and argue for the transcendence of such. This would, in my opinion, create space for harmonious and fluid co-existence between nature and humanity, such that the contribution of learning practices exudes and expedites sustainability in rural ecologies.
The power of praise psalms to encourage awareness of ecological issues amongst worshippers
21 May 2014
North West University

De Klerk, Barend J.

The liturgy ought to sensitise believers anew to glorifying God as the Creator and the Recreator of the universe. The Book of Psalms may be used to great effect to sharpen the ecological awareness of believers. The topic is investigated on the basis of three creation psalms, namely Psalm 19, 104 and 148. In particular, it asks how the praise of the so-called creation psalms serves to alert believers not only to conserve nature in their own context, but also, together with nature, to praise God in word and deed? The fact that the ecological crisis directly concerns our earth, air and water, that is, our basic sustenance ought to lead worshippers in the worship service to serious reflection. The destruction of ecological systems has a direct effect on every other problem faced by plant, human and animal. The focus of Psalm 19 on the heavens puts air pollution, global warming and damage to the ozone layer on the agenda of every worship-service participant. In the songs of praise in Psalm 104 and 148, humans are seen as part of the artistic creation web which ought to be conserved.
Stigmaeus maraghehiensis, a new species of the genus Stigmaeus Koch (Acari: Stigmaeidae) from northwest Iran
24 June 2014
North West University

Bagheri, Mohammad;Ghorbani, Hamed;Saber, Moosa;Navaei-Bonab, Reza;Ueckermann, Edward A.;Mehrvar, Ali

A new species of Stigmaeus Koch (Acari: Stigmaeidae), Stigmaeus maraghehiensis sp. nov., is described and illustrated from the soil in apple orchards in Maragheh, East Azerbaijan Province, Iran. A key to all known Iranian species of the genus is provided.
Writing and contextualising local history. A historical narrative of the Wellington Horticultural Society (Coloured).
28 July 2014
North West University

Cleophas, Francois J

The purpose of this study was to enhance local history as a focus area in a Higher Education (HE) teaching context. This article documented a case study of the practice of flower growing as a recreational-competitive activity. A historical narrative was thus constructed around the Wellington Horticulture Society (Coloured), henceforth referred to as the (WHS). The founding of the WHS coincided with the emergence of cultural organisations in Wellington. Furthermore, it was part of a social development, known as garden culture. By using documentary evidence, previous research material and an oral historical account, a narrative of the WHS was created, emphasising aspects, such as competition, family history and garden culture. This research identified social and political dilemmas associated with the WHS.
Transboundary movements of genetically modified organisms and the Cartagena protocol: key issues and concerns
04 February 2015
North West University

Lim Tung, Odile J

Biotechnology or the engineering of the genetic material of species can give way to avenues of possibilities for the benefit of people, fauna and flora but also has the potential of posing untold and undiscovered threats to human beings and other living organisms. One of the first attempts to legislate on international rules on biotechnology can be traced back to article 19 of the Convention on Biological Diversity (CBD) in 1992. The CBD is indeed the first international legal instrument apart from the then European Community’s relevant directives to suggest that biotechnology is a matter of concern for the international community while providing a basis upon which more detailed procedures would be elaborated in the field of biosafety. While the CBD includes international rules on access to genetic resources, access to and the transfer of technology, the handling of biotechnology and the distribution of its benefits, it does not include a detailed regulation on genetically modified organisms (GMOs) and their possible adverse effects on the environment, human and animal health. It was only with the coming into existence of the Cartagena Protocol on Biosafety (Cartagena Protocol) to the CBD in 2000 that the safe transfer, handling and use of living modified organisms (LMOs) such as genetically engineered plants, animals, and microbes were at last being catered for, albeit leaving aside the broader categories of GMOs. Due to the need for the negotiators of this protocol to make compromises, there were still key issues on the international biosafety framework pertaining mainly to the scope of the GMOs to be covered by this protocol and by the Advanced Informed Agreement procedure; identification and traceability issues; and liability and redress issues. Nine years after the entry into force of the Cartagena Protocol the transboundary movements of GMOs have clearly increased with new categories of GMOs and genetically modified products to regulate. The debate on the safety of GMOs used for food and feed as well as the effects of GMOs on the receiving environment is still very lively throughout the world, amidst a lack of traceability of GMOs or epidemiological studies in the GMO-producing countries. However, there has been some progress on liability and redress with regard to damage resulting from the transboundary movement of LMOs with the adoption of rules and procedures for liability and redress in 2010 with the Nagoya-Kuala Lumpur Supplementary Protocol "(hereafter the Nagoya SP)" to the Cartagena Protocol, which is yet to enter into force. There are also concerns on the harmonisation of national biosafety regulation, risk assessment and risk management standards, the interpretation of socio-economic considerations, and the monitoring of compliance with the provisions of the Cartagena The scope of the GMOs covered by the Cartagena Protocol is discussed first, which discussion is followed by the discussion of identification and traceability issues, the harmonisation of national biosafety regulation, the harmonisation of risk assessment and risk management standards, the scope of the relevant socio-economic considerations, implementation, and concerns about the settlement of disputes.
The legal status of the Spanish Imperial Eagle in Spain and thoughts on environmental law and policy as contributing factors in the conservation of species
04 February 2015
North West University

Knobel, Johann C

This contribution reflects on the contributory role of environmental law and policy in the successful conservation interventions on behalf of the rare Spanish Imperial Eagle (Aquila Adalberti), with the aim of gaining insights that may be more universally applicable, including in jurisdictions such as South Africa. An overview of applicable international, European and Spanish laws and policies is given, and the role played by these instruments is considered together with successes attained with diverse conservation goals in respect of the Spanish Imperial Eagle. The exceptionally comprehensive character of the legal protection of the Spanish Imperial Eagle is highlighted, in conjunction with some extra-legal factors that have contributed to successful outcomes. While quantification of the role of the law in the conservation of a species remains elusive, it is probably safe to conclude that environmental law and policy have played a vital and central role in the improvement of the conservation status of the Spanish Imperial Eagle. It is submitted that the conservation interventions on behalf of the Spanish Imperial Eagle show that concerted legal and other conservation interventions can effectively halt and reverse the decline of an endangered species. However, such interventions are onerous and expensive and ideally, effective conservation measures should be in place before populations have declined to a critical level. Birds of prey face similar threats in South Africa and Spain, and a number of South African raptor species will soon be classified as endangered. While South African biodiversity laws and policy are similar to the European and Spanish laws in general import and methodology, the South African laws and policy are more restricted in scope, less detailed and less prescriptive. When comparing the use of Spanish and South African legislation in the conservation of birds of prey, sight must not be lost of the varying conservation needs of different species and the unequal resources available to different jurisdictions.
Pest resistance to Cry1Ab Bt maize: field resistance, contributing factors and lessons from South Africa
11 May 2015
North West University

Van den Berg, Johnnie;Hilbeck, Angelika;Bøhn, Thomas

This paper documents the historical development of resistance of the African maize stem borer, Busseola fusca (Fuller) (Lepidoptera: Noctuidae) to Bt maize (Zea mays L.). This pest was one of the first to evolve resistance to Bt maize expressing Cry1Ab protein. A time-line of events and contributing factors are presented, from the commencement of efficacy testing through to the present situation, where the Cry1Ab toxin has lost its efficacy against B. fusca at many localities throughout the maize producing region, and single-gene Bt maize events often require insecticide treatments for which farmers are compensated. Significant levels of pest survival on Bt maize was observed in the first season after commercial release in 1998 and confirmed seven years later. Reduced selection pressure on the target pest is the objective of insect resistance management (IRM), and strategies to accomplish this should receive highest priority. Where resistance is prevalent, the only viable options to reduce selection pressure are withdrawal of the product and/or enforcement of high-dose/refuge requirements. The latter action may however be of no value under conditions where resistance is prevalent, since the value of refugia to an IRM strategy may be compromised. Remedial actions taken in South Africa included the propagation and enforcement of refuge compliance followed by the release of pyramided maize hybrids in 2011. These pyramids combine Cry1A.105 and Cry2Ab2 toxin-producing transgenes, replacing the ineffective single-transgene. However, it remains uncertain if cross-resistance occurs between Cry1A.105/Cry2Ab2 and the closely related Cry1Ab toxin, and for how long this pyramided event will endure. Cultivation of Cry1Ab-expressing hybrids continues in areas where resistance levels have been confirmed to be high. In retrospect, this case provides lessons regarding IRM, not only in South Africa, but wherever Bt crops are being introduced.
Leveraging Traditional Knowledge on the Medicinal Uses of Plants within the Patent System: The Digitisation and Disclosure of Knowledge in South Africa
24 June 2015
North West University

Amechi, Emeka Polycarp

Traditional knowledge (TK) plays an important role in the global economy and is valuable not only to those who traditionally depend on it in their daily lives, but also to modern industry, especially the global biotechnology, pharmaceutical and agribusiness corporations. Yet the exploitation of TK by these industries does not usually lead to corresponding benefits to indigenous communities either in the form of attribution or compensation. Such misappropriations of TK are aided by the fact that the global intellectual property (IP) regime as presently structured is based entirely on the traditionally western or conventional description of knowledge, as are its conceptions of individual intellectual property ownership. In response to the fact that their calls for the reform of the global patent system have not be heeded, most developing countries, including South Africa, have resorted to the adoption of a radically different strategy in their approach to intellectual property, particularly as it concerns the protection of their TK from misappropriation. This is evident in the adoption of strategic measures in South Africa for the protection of various aspects of its TK forms from misappropriation, such as the National Recordal System (NRS) and Disclosure of Origins (DRs). This paper seeks to explore the implications of these measures in leveraging TK within the structure, content and conceptual framework of the patent system in South Africa. The focus is on TK associated with the medicinal uses of plants (TKMUP).
Herbaceous species diversity patterns across various treatments of herbivory and fire along the sodic zone of the Nkuhlu exclosures, Kruger National Park
17 September 2015
North West University

Van Coller, Helga;Siebert, Frances;Siebert, Stefan J.

Understanding relationships between large herbivores and plant species diversity in dynamic riparian zones is critical to biodiversity conservation. The Nkuhlu exclosures in the Kruger National Park (KNP) provided opportunity to investigate spatial heterogeneity patterns within riparian zones, as well as how these patterns are affected by fire and herbivory. A monitoring project was initiated to answer questions about the dynamics of the herbaceous layer and was aimed at determining, (1) whether there exists meaningful variance in herbaceous plant species richness and diversity across different treatments in the ecologically sensitive sodic zone and (2) whether an increase in herbaceous biomass, an artefact of herbivory and fire exclusion, suppresses herbaceous plant species diversity and richness. Herbaceous vegetation was sampled in two 1 m2 circular sub-plots in the eastern and western corners of 81 fixed plots. The biomass of each plot was estimated with a disc pasture meter (DPM) diagonally with the plot. DPM-readings were converted to kg/ha, according to the latest conversions for the Lowveld Savanna. Species richness and biomass showed significant variance across treatments, whereas no significant variation in herbaceous species diversity was perceived. Combined treatment of fire absence and herbivore presence contributed to higher forb species richness in the sodic zone. Biomass is significantly higher in fully fenced areas where herbivores are excluded, as opposed to the open and partially fenced areas. Although no significant variation was recorded for diversity across treatments, lowest diversity was recorded in the absence of all herbivores, especially in combination with fire treatment. Therefore herbivores are essential in sustaining herbaceous plant species richness in the sodic zone, whilst no significant results were found with regard to their effect on species diversity. Although statistically non-significant, fire seems to suppress species richness.
A new species of Pavetta (Rubiaceae) from South Africa
17 November 2015
North West University

Siebert, Stefan John;Retief, Elizabeth;Van Wyk, Abraham E.

Pavetta glaucophylla Retief, S. J. Siebert & A. E. van Wyk, a new species of the Rubiaceae (Ixoroideae) from South Africa, is described and illustrated. A member of Pavetta L. subg. Pavetta, it has a restricted range and is near endemic to the Sekhukhuneland Centre of Endemism. Hitherto P. glaucophylla has mainly been confused with P. zeyheri Sond., from which it differs in being a taller plant with larger, blue-green leaves in living condition instead of dark green to gray-green leaves and flowers in which the calyx lobes are 0.5–0.75 mm long and triangular-ovate, and 1.25–2 mm long and not triangular-lanceolate, as in P. zeyheri
Mycorrhiza–induced resistance against the root-knot nematode Meloidogyne incognita involves priming of defense gene responses in tomato
12 February 2016
North West University

Vos, C.;De Waele, D.;Van Tuinen, D.;Chatagnier, O.;Schouteden, N.

Arbuscular mycorrhizal fungi (AMF) have great potential as biocontrol organisms against the rooteknot nematode Meloidogyne incognita which causes severe gall formation in plants, but knowledge about the underlying molecular mechanisms involved in the biocontrol of nematodes is scarce. In the present study, suppression subtractive hybridization (SSH) was used to investigate plant genes that are specifically up-regulated in tomato roots (Solanum lycopersicum cv. Marmande) pre-colonized by the AMF Glomus mosseae (BEG 12) and 12 days after soil inoculation with M. incognita juveniles. Nematode infection was significantly lower in the mycorrhizal roots as compared to the non-mycorrhizal roots, and identified genes were classified mainly in the categories of defense, signal transduction and protein synthesis and modification. The higher expression of a selection of defense-related plant genes specifically in the biocontrol interaction compared to in plants that were only mycorrhizal or only nematodeinfected was confirmed, which pleads for the existence of mycorrhiza-induced priming of plant defense responses. In conclusion, by focusing on up-regulated gene expression in the biocontrol interaction between mycorrhizal tomato and M. incognita, new insights were found into the molecular mechanisms underlying the mycorrhiza-induced resistance against rooteknot nematodes. In particular, the involvement of the phenylpropanoid pathway and reactive oxygen species (ROS) metabolism could explain the reduced rooteknot nematode infection in mycorrhizal tomato roots, processes that have also been reported to play a pivotal role in plant resistance to nematodes
An updated plant checklist for Tankwa Karoo National Park, South Africa
01 March 2016
North West University

Steyn, H.M.;Bester, S.P.;Bezuidenhout, H.

An updated checklist is provided for the flora of Tankwa Karoo National Park, which occupies an area of 143,600 ha. A total of 730 species and 780 plant taxa (species, subspecies and varieties), representing 267 genera in 73 families, are recorded for the park. This comprises 30 bryophytes, 7 pteridophytes, 189monocotyledons and 554 dicotyledons. Sixteen species are endemic or near-endemic to the Hantam-Tanqua-Roggeveld subregion. Twenty-eight species are of conservation concern and six species have been declared as alien invasives
Agistemus aimogastaensis sp. n. (Acari, Actinedida, Stigmaeidae), a recently discovered predator of eriophyid mites Aceria oleae and Oxycenus maxwelli, in olive orchards in Argentina
05 April 2016
North West University

Leiva, Sergio;Theron, Pieter;Fernandez, Nestor;Rollard, Christine

A new species, Agistemus aimogastaensis, is described with the aid of optical and Scanning Electron Microscopy. This mite is an important predator of two eriophyid mites (Aceria oleae and Oxycenus maxwelli) in olive orchards (Olea europaea, variety Arauco) in La Rioja Province. The problems related to eriophyids in olive orchards in Argentina are highlighted and photos of the damage on leaves and fruit are included
National Herbarium Plant Collecting Programme reveals new country and provincial distribution records from South African National Parks (Apocynaceae, Asteraceae & Xanthorrhoeaceae : Asphodeloideae)
30 May 2016
North West University

Bester, Stoffel P.;Herman, Paul P.J.;Klopper, Ronell R.

New country and provincial distribution records for South Africa of specimens collected mainly in various South African National Parks are reported on here. The taxa included in this contribution are of Orthanthera albida (Apocynaceae), Doellia cafra (Asteraceae), Bulbine ophiophylla (Xanthorrhoeaceae: Asphodeloideae) and Trachyandra asperata var. basutoensis (Xanthorrhoeaceae: Asphodeloideae).
Commicarpus pentandrus
15 June 2016
North West University

Struwig, M.;Siebert, S.;Condy, G.

This is the first species of the Nyctaginaceae to be illustrated in Flowering Plants of Africa. It is commonly known as the four o’clock family, as most members have flowers that open in the late afternoon to early evening. The family is renowned for its genera Mirabilis (commonly known as four o’clocks) and Bougainvillea (commonly known as Bougainvilla) for their brightly coloured and profuse flowering. These and most other genera are mainly distributed in the Neotropics and western North America, and globally the family consists of 30 genera with 300–400 species. In southern Africa, the family is represented by five genera with 20 species. Commicarpus Standl. is the genus in southern Africa with the largest and most spectacular flowers.
The plights of African resource patenting through the lenses of the World Trade Organization: an assessment of South Africa's rooibos tea's labyrinth journey
03 August 2016
North West University

Amusan, Samuel Olalere

Background Just as developing states are blessed with natural resources capable of transforming their economies into a positive direction, the imposed World Trade Organisation's (WTO) mores continue to relegate them to the status of underdevelopment. The consequences of this on investment, trade and finance in Third World States (TWSs), especially Africa, are disarticulation of the economy, exploitation, disinvestment, unemployment, political instability and unavailability of relevant technology to move TWSs forward, among others. This gives rise to the politics behind Rooibos (Aspalathus linearis) patenting (a medicinal plant found only in South Africa) by various multinational corporations (MNCs). Materials and methods This study adopted political economy approach with emphasis on both primary and secondary sources of data collection using content analysis. Result There is need to adhere strictly to the issues of intellectual property rights (IPRs), geographical indications (GIs), prior informed consent (PIC), and access and sharing benefits (ASB). These have not been observed by the western states because of their economic of neo-imperialism to the disadvantage of developing states. Conclusion This paper recommends that there is need for a regional regime such as African Regional Intellectual Property Organisation (ARIPO), on indigenous knowledge (IK) to patent the continental biodiversity resources.
Amphibian symbiotic bacteria do not show a universal ability to inhibit growth of the global panzootic lineage of Batrachochytrium dendrobatidis
09 September 2016
North West University

Antwis, Rachael E.;Garner, Trenton W.J.;Preziosi, Richard F.;Harrison, Xavier A.

Microbiomes associated with multicellular organisms influence the disease susceptibility of hosts. The potential exists for such bacteria to protect wildlife from infectious diseases, particularly in the case of the globally distributed and highly virulent fungal pathogen Batrachochytrium dendrobatidis of the global panzootic lineage (B. dendrobatidis GPL), responsible for mass extinctions and population declines of amphibians. B. dendrobatidis GPL exhibits wide genotypic and virulence variation, and the ability of candidate probiotics to restrict growth across B. dendrobatidis isolates has not previously been considered. Here we show that only a small proportion of candidate probiotics exhibited broad-spectrum inhibition across B. dendrobatidis GPL isolates. Moreover, some bacterial genera showed significantly greater inhibition than others, but overall, genus and species were not particularly reliable predictors of inhibitory capabilities. These findings indicate that bacterial consortia are likely to offer a more stable and effective approach to probiotics, particularly if related bacteria are selected from genera with greater antimicrobial capabilities. Together these results highlight a complex interaction between pathogens and host-associated symbiotic bacteria that will require consideration in the development of bacterial probiotics for wildlife conservation. Future efforts to construct protective microbiomes should incorporate bacteria that exhibit broad-spectrum inhibition of B. dendrobatidis GPL isolates
Ecological genetics and host range expansion by Busseola fusca (Lepidoptera: Noctuidae)
12 September 2016
North West University

Assefa, Y.;Van den Berg, J.;Conlong, D.E.;Martin, L. A.

The host plant range of pests can have important consequences for its evolution, and plays a critical role in the emergence and spread of a new pest outbreak. This study addresses the ecological genetics of the indigenous African maize stem borer, Busseola fusca (Fuller) (Lepidoptera: Noctuidae), in an attempt to investigate the evolutionary forces that may be involved in the recent host range expansion and establishment of this species in Ethiopian and southern African sugarcane. We used populations from Ethiopia, Zimbabwe, and South Africa to examine whether the host range expansion patterns shared by the Ethiopian and the southern African populations of B. fusca have evolved independently. Base-pair differences in the cytochrome oxidase I (COI) gene were used to characterize haplotype diversity and phylogenetic relationships. There were seven haplotypes among the 30 sequenced individuals collected on four host plant species from 17 localities in the four countries. Of the seven COI haplotypes identified, the two major ones occurred in both sugarcane and maize. Genetic analyses revealed no detectable genetic differentiation between southern African B. fusca populations from maize and sugarcane (FST = 0.019; P = 0.24). However, there was strong evidence of variation in genetic composition between populations of the pest from different geographic regions (FST = 0.948; P < 0.001). The main implication of these findings is that the B. fusca populations in maize in southern Africa are more likely to shift to sugarcane, suggesting that ecological opportunity is an important factor in host plant range expansion by a pest
The first records of Polygala westii (Polygalaceae) for South Africa (North-West Province) and a key to the southern African Polygala species in the Section Tetrasepalae
12 September 2016
North West University

Bester, Stoffel Petrus;Paiva, Jorge

The first record of Polygala westii (Polygalaceae) from the North-West Province (South Africa) is reported on here. The species is very rare and has previously only been collected in two separate gatherings. This species is characterised by having bracts and bracteoles caducous, the anterior sepals connate at least as much as half of their length and seeds pubescent and carunculate. It grows in a habitat that are severely impacted by agriculture and mining. A preliminary assessment of its conservation status is given. A key to the South African species in the subsection (Tetrasepalae) to which P. westii belong is provided. The aim of this paper is to highlight the species in order to stimulate the lookout for more material of this species
Widespread presence of the pathogenic fungus Batrachochytrium dendrobatidis in wild amphibian communities in Madagascar
12 September 2016
North West University

Bletz, Molly C.;Weldon, Ché;Rosa, Gonçalo M.;Andreone, Franco;Courtois, Elodie A.

Amphibian chytridiomycosis, an emerging infectious disease caused by the fungus Batrachochytrium dendrobatidis (Bd), has been a significant driver of amphibian declines. While globally widespread, Bd had not yet been reported from within Madagascar.Wedocument surveys conducted across the country between 2005 and 2014, showing Bd ’s first record in 2010. Subsequently, Bd was detected in multiple areas, with prevalence reaching up to 100%. Detection of Bd appears to be associated with mid to high elevation sites and to have a seasonal pattern, with greater detectability during the dry season. Lineage-based PCR was performed on a subset of samples. While some did not amplify with any lineage probe, when a positive signal was observed, samples were most similar to the Global Panzootic Lineage (BdGPL). These results may suggest that Bd arrived recently, but do not exclude the existence of a previously undetected endemic Bd genotype. Representatives of all native anuran families have tested Bd-positive, and exposure trials confirm infection by Bd is possible. Bd’s presence could pose significant threats to Madagascar’s unique ‘‘megadiverse’’ amphibians.

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