Abstracts & Links to Past Webinars
SASSB Youtube Channel is available HERE.
You can find videos for past webinars on the YouTube channel and links to specific webinars are below.
1 August 2024, Prof Alex Pyron, The George Washington University
Unsupervised machine learning for species delimitation, integrative taxonomy, and biodiversity conservation
Integrative taxonomy, combining data from multiple axes of biologically relevant variation, is a major goal of systematics. Ideally, such taxonomies will derive from similarly integrative species-delimitation analyses. Yet, most current methods rely solely or primarily on molecular data, with other layers often incorporated only in a post hoc qualitative or comparative manner. A major limitation is the difficulty of devising quantitative parametric models linking different datasets in a unified ecological and evolutionary framework. Machine Learning (ML) methods offer flexibility in this arena by easily learning high-dimensional associations between observations (e.g., individual specimens) across a wide array of input features (e.g., genetics, geography, environment, and phenotype) to delimit statistically meaningful clusters. Here, I implement an unsupervised method using Self-Organizing (or “Kohonen”) Maps (SOMs) for such purposes. Recent extensions called “SuperSOMs” can integrate multiple layers, each of which exerts independent influence on a two-dimensional output grid via empirically estimated weights. The grid cells are then delimited into K distinct units that can be interpreted as species or other entities. I show empirical examples in salamanders (Desmognathus) and snakes (Storeria) with layers representing alleles, space, climate, and traits. Simulations reveal that the SuperSOM approach can detect K = 1, tends not to over-split, reflects contributions from all layers, and limits large layers (e.g., genetic matrices) from overwhelming other datasets, desirable properties addressing major concerns from previous studies. Finally, I suggest that these and similar methods could integrate conservation-relevant layers such as population trends and human encroachment to delimit management units from an explicitly quantitative framework grounded in the ecology and evolution of species limits and boundaries.
6 June 2024 Dr Lucas Czech, Global Institute, University of Copenhagen
Leveraging phylogenetic placement to understand the environmental drivers of microbial community composition
In recent years, phylogenetic placement has emerged as a powerful tool for investigating the evolutionary relationships and dynamics of microbial communities. By assigning (microbial) sequences to their most likely positions within a phylogenetic reference tree, phylogenetic placement enables us to gain valuable insights, for instance, into the origins, transmission, and evolution of infectious agents. This talk explores several methods for the analysis and visualization of phylogenetic placements, specifically focusing on microbial and meta-genomic samples, and highlighting potential applications to several contexts.
In particular, this talk will go beyond employing phylogenetic placement for traditional sequence classification. Various placement-based methodologies have been developed to infer the influential factors driving the composition of microbial communities within a phylogenetic framework, such as Edge PCA, Edge Correlation, and Placement-Factorization. These methods enable us to identify key branches in the tree, thus shedding light on the evolutionary dynamics and traits associated with a set of microbial samples. This approach allows us to unravel the interplay between the microbial abundances, host factors, and environmental variables, and can potentially facilitate an understanding of microbial communities in their evolutionary context. This talk aims to provide an overview of these advancements in phylogenetic placement methods and their applications.
3 August Speaker: Dr Simon Martin, University of Ediburgh
Chromosomal rearrangements and species boundaries
Chromosomal rearrangements – changes to the physical structure of the genome – can alter inheritance patterns, with important evolutionary consequences. In this presentation, I will describe three examples of these consequences from our work on butterflies. First, I will show how ten chromosomal fusion events in the genus Heliconius created ten long chromosomes which, curiously, are more reliable for inferring species relationships than the ten short chromosomes. This is due to an interaction between recombination, gene flow (through hybridization) and selection. Second, I will present evidence that chromosome fusions that differentiate species in the genus Brenthis contributed directly to promoting speciation, probably by causing reduced fitness in hybrids. Third, and finally, I will present ongoing work dissecting a complex rearrangement in the genus Danaus. This genomic region differentiates subspecies by driving adaptation to local environments, but it also confounds species relationships due to persistence of an ancient polymorphism. In summary, our work shows that chromosome rearrangements not only contribute to speciation, but also affect how we interpret species relationships and species boundaries.
Additional Speaker:
Juanita Avontuur, University of Pretoria: Synteny patterns within and between Bradyrhizobium supergroups: order or chaos
4 May Speaker Information: Dr Susan Perkins, City College of New York
Malaria’s Many Mates: The Systematics of Haemosporidian Parasites
While five (or possibly more) species of Plasmodium are those typically associated with causing the disease malaria in humans, they belong to a very diverse order known as Haemosporida. In this talk, I will summarize my almost thirty years of working on the systematics of these parasites. The evolutionary relationships of the lineages within the Order Haemosporida have been contentious throughout the entire history of their study. Earliest attempts at reconstructing a phylogeny used simple, non-cladistic depictions that largely relied on host use patterns and life history traits, but for the past two decades, the sequencing of parasite genes for phylogenetic analyses has become ubiquitous. Many of these molecular phylogenetic studies have had their own problems, however, due to issues of locus paralogy, biases in nucleotide composition, and evolutionary rate variation. Others have suffered from problems due to limited taxon sampling. We have recently attempted to vastly improve our confidence in the phylogenetic relationships of the haemosporidians through increasing the taxonomic breadth of lineages as well as generating massive amounts of data via transcriptomic approaches. Guidelines for future work in the systematics of haemosporidians will be shared.
Additional Speakers:
Dr Shúné Oliver, Wits Institute for Malaria Research
Anthropogenic pollution as a driver of the evolution of insecticide resistance in the major malaria vector Anopheles arabiensis (Diptera: Culicidae)
Malaria case numbers had plateaued until the advent of the COVID-19 pandemic. The interruption of intervention efforts lead to the first substantial increase in malaria infections and deaths. A significant reason for this increase is related to challenges with vector control. The major malaria vector Anopheles arabiensis is one of the challenges. This species, which is responsible for transmitting malaria in Southern Africa and is the primary vector in South Africa. This species represents a particular challenge in malaria control. It is an extremely adaptable vector that primarily bites and rests outdoors. As such, conventional control methods targeting indoor biting and resting mosquitoes, such as indoor residual spraying and insecticide treated nets, poorly control this species. Furthermore, it has also been demonstrated to exhibit behavioural avoidance, and will avoid entering sprayed houses and will shift to increased outdoor biting. This adaptability is a particular challenge and is leading to various evolutionary changes. One of the most significant is the adaptation to breeding in polluted water. Anopheles arabiensis, like all members of the An. gambiae complex, breed in temporary bodies of water. These sites are typically clean, clear, and sunlit. Adaptation to breeding in polluted water, which typically only housed non-anopheline mosquitoes, has meant that this species has increased its breeding range. Anopheles mosquitoes that have adapted to breeding in polluted water, like An. arabiensis, are adapting to urban environments. Furthermore, larval exposure to anthropogenic pollution has various pleiotropic effects. One of the most significant is the effects is acting as a driver for insecticide resistance. In this presentation, we will cover the various ways that a range of larval pollutant exposures affects the biology of this adaptable species and discuss whether it is a potential challenge to vector control efforts in a South African context.
Dr Mamohale Chaisi, SANBI & UP
Genetic diversity and host-parasite relations of haemosporidia in Afrotropical birds
The Afrotropical region has one of the highest avian diversity in the world and related to this is a high diversity of haemosporidian parasites. Over 200 species of Plasmodium, Haemoproteus and Leucocytozoon spp. have been described globally based on morphology. Molecular studies suggest a much higher diversity, however this diversity has not been fully explored in South African birds and knowledge gaps still exist in haemosporidian diversity and ecology, and their effect on avian health and conservation. Parasite burdens affect avian community structure, immunity, survivorship, growth, fecundity and health; and differ between host taxa, captive and wild populations, and migratory and resident birds. Disease transmission is affected by host-vector-parasite interactions and may increase due to climate warming. Climate change may also alter vector reproductive cycles, creating increased risk of infection or parasite burden. We conducted a molecular survey of haemosporidian parasites from selected areas in South and western Africa in order to elucidate their prevalence, biodiversity, distribution, host-parasite and evolutionary relationships, host switching potential, differential diagnosis and pathogenicity. Some of these lineages have been associated with mortalities in populations of captive and wild birds in other parts of the world. The study provides baseline data that contribute to our understanding on aspects of the biogeography, pathogenicity and evolutionary relationships of hemosporidian parasites of Afrotropical birds.
3 November Speaker Information: Dr Marike Palmer
SeqCode: Empowering prokaryotic taxonomists to use resources that are appropriate for naming the organisms they study
With the enormous advances in molecular sequence data generation, microbial taxonomy has progressively evolved towards a hierarchical system strongly rooted in phylogenetics and evolutionary cohesion. As a result of this, genomics has become fully integrated into prokaryotic systematics, which provides the opportunity to start assessing the extent of our exploration efforts into biodiversity space. The genomes of most type strains have been sequenced, genome sequence similarity is widely used for delineation of species, and phylogenomic methods are commonly used for classification of higher taxonomic ranks. As such, microbial taxa identified from environmental metagenomics can be as robustly delineated as their cultivated counterparts. In response to these developments, a new code of nomenclature, SeqCode (The Code of Nomenclature of Prokaryotes Described from Sequence Data), has been developed to allow naming of Archaea and Bacteria using DNA sequences as nomenclatural types. This code is considered a living document, with the goal of serving the broader microbiological community. The SeqCode will allow naming of the enormous uncultivated biodiversity discovered through the aid of metagenomic sequencing and single-cell genomics, fastidious prokaryotes that cannot reasonably be maintained and distributed by culture collections, as well as organisms that cannot be legally transferred between countries, thus facilitating the naming of taxa in every biome on Earth. This will promote synergies between the field and laboratory disciplines of microbiology and stabilize the working language, i.e., nomenclature, of prokaryotic systematists.
2 June Speaker Information: Dr Vinita Gowda
Understanding generation, evolution, and maintenance of plant biodiversity in India.
Abstract:
Biodiversity refers to the biological diversity in any region, which is often measured using different ecological metrics such as species diversity or abundance. The measuring entity in any of these metric is a “taxa”. The origin, maintenance and extinction of these taxa, therefore, are key to our understanding of how biodiversity is generated and maintained in any region. India is known for its two megadiverse regions: Western Ghats and Eastern Himalayas. I will present one case study from each of these regions that will highlight evolutionary and ecological mechanisms that may be used by plants to create as well as maintain taxonomic diversity. The Eastern Himalayan region is represented by taxa from the NE Indian states, which has a continuous distribution with flora from SE Asia, while the Western Ghats is different because it forms an isolated floristic region (from the NE or SE Asia), although it is historically connected to African flora. Our studies reveal that many diverse plant taxa from these regions may be very young (~7-10 mya), lack clear reproductive isolation boundaries, as well as have a high propensity for polyploidization. Further, abiotic and biotic factors such as the availability of hyper-diverse niches, monsoon intensification, and generalist pollinators also mean that local hybridization events may be common in both these regions and outcrossing may be very common. Our study provides us with an opportunity to understand how incipient speciation may look like in many of these taxa, which may allow us to see how species evolve and create biodiversity in hyperdiverse regions around the world.
Additional Speakers:
Jessica Minnaar, Wits University
Drivers of species diversification in Galtonia (Hyacinthaceae): a Drakensberg near-endemic genus
The Drakensberg Mountain Centre (DMC) is recognised as a major centre of species diversity and endemism, with climatic, topographic, and edaphic variation across the region promoting the significant levels of biodiversity observed today. However, unlike other major centres of endemism, such as the Cape Floristic Region, few studies have explored the patterns and processes of species diversification in the region. Therefore, investigating the drivers of speciation in Galtonia, a Drakensberg near-endemic genus, contributes to our understanding of the evolutionary processes that have resulted in such a remarkably diverse region. In addition to mapping distribution data from 148 herbarium specimens and field collections of five species, we investigated the likely drivers of speciation in Galtonia by measuring floral and vegetative features and undertook a Principal Components Analysis to infer whether adaptation occurred in response to abiotic or biotic factors. Variation in vegetative habit, leaf shape, and leaf size among Galtonia species is evident, with relatively minor distinctions in floral form, suggesting they evolved in response to abiotic rather than biotic factors. Therefore, climatic and topographical variation along the Drakensberg escarpment appear to play an important role in species diversification in this genus. Additionally, microhabitat specialization to different soils and habitats of the escarpment are likely to have promoted ecological speciation within Galtonia. The disjunct geographic and altitudinal distribution of Galtonia species and differences in habitat indicate that ecological speciation in allopatry and parapatry possibly promoted divergence of its species across the DMC. Galtonia species are characterized by slightly different tepal colours (viz., pale creamy yellow, pale green, and pure white). With regards to biotic factors, relatively few floral differences among Galtonia species suggest that pollinators may not have played an important role in reproductively isolating species. However, the pollinators of Galtonia species, and their role in species diversification has not been formally investigated. No scent was observed in G. regalis or G. candicans during the day, a characteristic associated with a bird pollination syndrome. Malachite sunbirds have been observed visiting G. regalis and G. princeps during the day, and night observations are yet to be conducted. Therefore, the main floral visitors, and potential pollinators, and functional floral traits (nectar properties) of Galtonia species are being investigated to see whether they differ between sister species and are correlated with the main floral visitors respectively. Preliminary results from an investigation during the 2021/2022 summer flowering season will be presented.
Kamil Frankiewicz
Big travels of small herbs: what drives diversification of celery and its cousins
Diversification rates may be affected by extrinsic (e.g. availability of ecological niches) and intrinsic factors. Among them, life form may be instrumental because herbaceous plants have shorter generation times and more pronounced r reproductive strategy than their woody relatives. Tribe Apieae (Apioideae, Apiaceae) – to which celery, dill or parsley belong – are well-suited to study the effects of life form on diversification as it represents a considerable variation of life spans, growth forms, and reproductive strategies. Combining the analysis of diversification rates with reconstruction of ancestral traits and estimation of biogeographic scenarios, we studied what drives the speciation (and extinction) in this group of high culinary (and economic) significance.
Please note starting time 15h30 on 5 May 2022!
5 May Speaker Information: Dr Luis Miguel Rodrequez-R
Indexing the Genomic Diversity of Archaea and Bacteria with MiGA, the Microbial Genomes Atlas.
Abstract:
During the past decade the number of publicly available sequenced prokaryotic genomes has grown at an unprecedented rate. Yet, the information behind this trove of data remains difficult to access, and genome-based comparisons against comprehensive databases remain technically cumbersome and computationally intensive. To address these issues, we have developed MiGA, the Microbial Genomes Atlas, a genomic data analysis framework integrating best practices in genome processing and quality evaluation, fast genome-based querying of reference databases, and robust statistical tests of taxonomic classification and novelty. In order to democratize access to the MiGA framework, we have also implemented user-friendly interfaces including web-based browsing and administration for all users, a complete command-line interface for intermediate users, and a fully documented Ruby API for advanced users. In addition, we have deployed MiGA to a variety of environments that users can access freely including MiGA Online for detailed manual curation of individual entries and MiGA @ XSEDE for high-throughput genome processing. In addition, we use the various MiGA features to curate and maintain reference genome collections including all determined genomes from type material of named species (TypeMat), a dereplicated set of genomes determined by culture-independent techniques such as single cell genomics and genome-resolved metagenomics (Uncultivated), 8 environment-specific genome collections, and over 700 collections for specific taxonomic groups, allowing the accurate, precise, and comprehensive taxonomic classification of query genomes. To date, MiGA has processed over 50 thousand jobs from users around the globe (including 1500 registered users), the MiGA Online webserver has been used in over 250 publications, and the framework is actively being ported to additional environments including high-performance computing centers and cloud computing platforms. The MiGA codebase, its interfaces, and the online deployments are available at http://microbial-genomes.org/.
Additional speakers: TBA
7 April Speaker Information: Prof Jonah Choiniere
Dinosaurs of darkness: how owl-like senses independently evolved in the ancestors of birds
Living owls are the quintessential night hunters, using visual and auditory adaptations to catch prey even in complete darkness. These traits are rare in living birds, but could they have evolved in their ancestors - theropod dinosaurs? Understanding sensory evolution is challenging in the fossil record, however, and doing so requires novel means of data collection. To examine this question, we CT scanned the skulls of more than 100 birds and non-avian dinosaurs, and used these scans to reconstruct the inner ear, parts of which reflect auditory capabilities. We also collected information on the maximum size of the pupil using small bones of the reptile eye known as scleral ossicles. When combined, these two proxies allowed us to confidently infer that alvarezsaurs, a bizarre group of non-avian dinosaurs, had hearing and vision that were well-suited for nocturnal habits. We hypothesized that these adaptations would have served them well in the sandy desert environments of the Cretaceous of Mongolia, where harsh conditions and cryptic prey posed challenges for survival.
Additional speakers:
Viktor Radermacher, University of Minnesota
A new Heterodontosaurus specimen elucidates the unique ventilatory macroevolution of ornithischian dinosaurs
Ornithischia is one of the three major clades of dinosaurs and includes well-known and cherished taxa like the horned Triceratops, spiked Stegosaurus, and crested duck-billed Parasaurolophus. The last half a century has seen considerable strides in elucidating the biology of dinosaurs, elevating fossils from interesting rocks into living breathing animals. However, much of this research effort has been concentrated on the long-necked sauropodomorphs and carnivorous theropods – the precursors to modern birds – rendering Ornithischia neglected by comparison; a fate exacerbated by a scant early fossil record for the clade. Furthermore, while we know many ancillary aspects of ornithischian life history like dietary preferences and social behaviours, a satisfying understanding of their ventilatory anatomy remains elusive – an area of study pivotal in bringing other dinosaurian lineages into the modern paradigm as dynamic, energetically demanding animals. We present a new specimen of the early-branching South African ornithischian Heterodontosaurus tucki that preserves a suite of new and unexpected postcranial material. Visualised using phase-contrast enhanced synchrotron microCT data, this new anatomy is pertinent in providing a high-resolution glimpse into the early evolution of this group, allow us to posit a step-wise hypothesis for their ventilatory evolution, and better understand the macroevolutionary constraints imposed on the lineage’s subsequent 130 Million year radiation.
Dr Kimi Chapelle, American Museum of Natural History
A quantitative method for inferring locomotory shifts in amniotes during ontogeny and its application to dinosaurs
Evolutionary transitions between quadrupedal and bipedal postures are pivotal to the diversification of amniotes on land. Within Dinosauria there are at least four instances of lineages evolving quadrupedality from bipedality. Similarly, developmental, or ontogenetic postural shifts from quadrupedality to bipedality have been hypothesized in several dinosaur taxa, including the iconic southern African basal sauropodomorph dinosaur Massospondylus carinatus Owen (1854). However both non-destructive and quantitative methods for testing this in extinct species have been lacking. We extend such a method for reliably inferring posture in tetrapods to the study of ontogenetic postural transitions using measurements of proportional limb robusticity. We apply this to the ontogenetic series of living and extinct amniotes, focusing on dinosaurs. Our method correctly predicts the general pattern of ontogenetic conservation of quadrupedal and bipedal postures in many living amniote species and infers the same pattern in most dinosaurs. We infer a transition from early-ontogenetic quadrupedality to late-ontogenetic bipedality in only two dinosaur taxa. The phylogenetic positions of these shifts suggest that heterochrony may play a role in the macroevolution of posture, at least in dinosaurs.
17 November Speaker Information: Prof Philippe Lemey
Evolutionary origins of SARS-CoV-2 and tracking its spread using phylodynamic data integration.
I will describe a collaborative effort to address evolutionary questions on the recent emergence of human coronavirus SARS-CoV-2 including the role of reservoir species, the role of recombination, and its time of divergence from animal viruses. Our findings indicate that sarbecoviruses – the viral subgenus containing SARS-CoV and SARS-CoV-2 – undergo frequent recombination and exhibit spatially structured genetic diversity on a regional scale in China. Contrary to other analyses, we find that SARS-CoV-2 itself is not a recombinant of any sarbecoviruses detected to date, and its receptor binding motif, important for specificity to human ACE2 receptors, appears to be an ancestral trait shared with bat viruses, not one acquired recently via recombination. Divergence dates between SARS-CoV-2 and the bat sarbecovirus reservoir indicates that the lineage giving rise to SARS-CoV-2 has been circulating unnoticed in bats for decades.
Following the emergence of the virus, unprecedented sequencing efforts have resulted in the accumulation of more than 100,000 genome sequences sampled globally. Despite this rich source of information, evolutionary reconstructions are hindered by the slow accumulation of sequence divergence over its relatively short history of transmission and by the spatiotemporal bias in genome sampling. I will describe a phylodynamic data integration approach in a Bayesian framework and demonstrate how it helps addressing questions about SARS-CoV-2 molecular epidemiology.
SASSB AGM to accompany webinar
14 October Speaker Information: Donat Agosti, Ronell Klopper & Thembile Khoza
Plenary: Donat Agosti, Plazi, Bern, Switzerland
(Re)discovering known biodiversity imprisoned in scientific publications
Scholarly knowledge about biodiversity is documented in hundreds of millions of pages of scientific literature. This includes original descriptions of all species on earth, and the chain of taxonomic treatments that might follow them, linked by citation. These treatments include statements about species distribution, behaviour, life forms, ecology, conservation status, and changes to species limits through splitting or synonymy. Each taxonomic name has at least one taxonomic treatment, a well delimited section in a scholarly publication. In the digital age, linking a taxonomic name to the respective treatment allows a potential entry point to all other knowledge about that species within the digital realm. This not only provides immediate online access, but it can save tremendous time and effort for researchers. Plazi is a Swiss NGO with the mission to liberate data from taxonomic publications and make it openly and immediately accessible. It is a virtual organization with a production facility in Porto Alegre, Brazil. It maintains two research infrastructures, TreatmentBank and the Biodiversity Literature Repository, which liberate data and provide long term access respectively. Currently, Plazi has liberated over 600,000 taxonomic treatments and 400,000 figures from over 65,000 articles. Data can be analysed and assessed for article and treatment level data. Quality controlled data is available permanently on the Biodiversity Literature Repository or via applications providing a general image (Ocellus) or taxonomic names (Synospecies) based access. These data are increasingly reused. Plazi provides over 55% of datasets to the Global Biodiversity Information Facility (GBIF), making it the largest single dataset provider, and is the sole source of over 80,000 species names from its publications mediated data. Over 489 publications have been based on these data to date. Plazi has developed tools to liberate data that are openly accessible, and is opening up courses to allow partners to make use of these tools and infrastructure to process their specific publications, such as those covering a particular taxon or geographic region, or published by a natural history institution. This presentation will provide an overview of Plazi, it’s data and processing and thoughts on how to involve the community.
Additional Speakers:
Ronell R Klopper, Foundational Research & Services Directorate, SANBI
The South African National Plant Checklist and e-Flora of South Africa projects
The South African National Plant Checklist forms the taxonomic backbone to which all other data on our unique plant diversity are linked. The e-Flora of South Africa builds on the checklist and provides descriptive data for every species. Together these two resources deliver the foundational data required for plant diversity research and projects in South Africa. This presentation will give a brief overview of the SA National Plant Checklist and the e-Flora of South Africa projects, their history, aspects around their compilation, and outputs from these initiatives.
Thembile Khoza, Zoological Research, Foundational Research and Services, South African National Biodiversity Institute
Compiling and dissemination of Animal Checklist for South African species
The South African National Biodiversity Institute (SANBI) is mandated through National Environmental Management: Biodiversity Act (2004) to co-ordinate and promote the taxonomy of South Africa’s biodiversity. In partial fulfillment of the mandate, SANBI embarked on an initiative to develop and regularly update the checklist of animals in the country. The checklist is to list the estimated 65000 animal species described from South Africa, their distribution and conservation status. In collaboration with partner institutions and taxon experts, a checklist of South African animal taxa is compiled and systematically updated based on literature and expert consultations. Up-to-date lists are shared as an open, freely accessible and trusted digital resource through National Biodiversity Information System (NBIS). To date, progress has been made on most of the major groups with taxon experts working on them, these include arachnids, butterflies, mammals, birds, fishes, frogs and reptiles. The National Animal Checklist is guided by the animal checklist policy, which provides standard guidelines for the compilation, updating, verification and curation.
2 September Speaker Information: Dr Isabel Sanmartín, Joanne Bentley, & Seth Musker
Plenary: Dr Isabel Sanmartín, Royal Botanic Garden, CSIC
The Rand Flora Revisited: New approaches for bridging the micro and macroevolutionary levels in biogeography and evolution
Evolutionary biologists and biogeographers, in their efforts to determine which factors govern biodiversity dynamics, have used two approaches that differ primarily in the taxonomy level they focus on: microevolutionary processes (genetic drift, mutation, migration) act mostly on individuals and populations, while macroevolutionary processes (extinction, dispersal, speciation) focuses on diversification at and above species level in relation to environments and over longer time scales. These two levels are difficult to bridge because they often imply different analytical techniques (population genetics vs. phylogenetics) and data sources (multicopy DNA vs nucleotide substitutions in protein-coding genes). The advent of Next Generation Sequencing techniques has made this feasible by scaling up the numbers of genes, individuals, populations, and species sampled in a cost-effective way. Techniques like target sequencing permit to obtain large datasets of DNA sequences for hundreds or thousand of markers across different phylogenetic levels. This molecular revolution has gone in hand in hand with new advances in the development of analytical approaches, and the exponential growth of bioinformatics. In this conference, I will review advances in the fields of statistical phylogenetics and machine learning, and show with examples how their integration with NGS molecular techniques and external sources of evidence (e.g., paleoclimatic reconstructions, ecological traits) allow us to explore patterns and processes of biotic assembly at different spatio-temporal scales, from extinction and adaptation of species to climate change to population decline and demographic expansion in more recent times. For this, I will use a continental floristic riddle, the Rand Flora, where sister-taxa at various taxonomic levels (populations, species, clades) occur on opposite sides of the African continent; the pattern has been explained by the effects of ancient and ongoing climate-driven extinction.
Additional Speakers:
Joanne Bentley, UCT
Lineage origin, historical migration patterns, and the contributions of geographic proximity and ecological filtering to dispersal in an African-centred paper daisy lineage
Background: Long-distance dispersal and range expansion were explored in the “Relhania clade”, a diverse (ca. 120 species) and morphologically-disparate lineage of “paper daisies” (Gnaphalieae: Asteraceae) that associates with cool-growing season habitats in southern and East Africa, and in the greater Mediterranean region. A model-based biogeographic approach was used to explore historical range movements in the Relhania clade by inferring the centre of origin and the directionality and timing of range expansion. The relative importance of geographical distance and ecological filtering as determinants of dispersal was also explored.
Results: Multiple northwards migrations from a centre of origin in southern Africa were inferred since the Miocene, with geographic proximity being a strong determinant of dispersal. Ecological filtering was also found to shape dispersal in this clade, with members selecting to migrate within a moderate temperature and rainfall range, avoiding extreme niches.
Seth Musker, University of Bayreuth, Germany
The genomics of dynamic diversification on a continental archipelago: the case of Erica abietina from the Cape Floristic Region: Or ‘What to call the things that I’m calling things’.
There is an increasing recognition that understanding the process of speciation requires detailed investigation of systems in which species limits are ‘fuzzy’ and factors such as divergence, convergence, gene flow and selection are at play. With close to 700 species, Erica L. (heathers; Ericaceae) is by far the largest plant genus in the Cape Floristic Region, and yet the reasons for its diversity remain obscure. One remarkable characteristic is the apparent lability of floral trait evolution, as indicated by a phylogenetic hypothesis of roughly 60% of Cape Erica (Pirie et al., 2016). Erica abietina L. s.l. (Pirie et al., 2017) shows clear variation in floral length and colour: of its four subspecies, two (E. a. abietina and E. a. atrorosea) have long flowers (18-26 mm) and two (E. a. constantiana and E. a. diabolis) have short flowers (8-14 mm), while one (E. a. abietina) has red flowers, and the rest are pink (Oliver & Oliver, 2002). The species is confined to the Cape Peninsula, an isolated mountain range separated from the rest of the Cape Fold mountains by an extensive plain of mostly unsuitable habitat. These factors make E. abietina an excellent subject for speciation research at the interface of micro- and macroevolution. Using reduced-representation sequencing (GBS; (Elshire et al., 2011)) data from 61 E. abietina samples representing all subspecies and several putative hybrids, we uncovered several interesting and sometimes unexpected patterns:
1. The four subspecies are genetically distinct, but absolute divergence varies considerably;
2. the short- and long-flowered subspecies are not each other’s closest relatives, suggesting convergent evolution of floral traits;
3. there are two previously unrecognized genetic groups within E. a. atrorosea that are geographically isolated and associate with different geological substrates;
4. both between and within floral types, individuals with mixed ancestry are common and occur in geographical contact zones, in one case forming a hybrid swarm; and
5. networks including two reticulations involving both E. a. atrorosea lineages are strongly favored over the best-supported strictly bifurcating species tree.
To dive deeper, we investigated the role of selection in divergence of the very closely related and parapatric E. a. abietina and E. a. diabolis by scanning for highly divergent loci. BLAST searches of candidate loci uncovered two interesting cases: 1) a locus near a probable flavonol synthase gene which could be involved in flower colour variation, and 2) a locus near a probable microtubule-associated protein coding gene, which might regulate petal cell growth and thus control flower length. We hypothesize that strong divergent selection acting on flower-trait genes is responsible for the maintenance of these distinct forms despite ongoing gene flow, and that these subspecies could be in the very early stages of speciation.
5 August Speaker Information: Dr Sandra Knapp, Bianca Ferreira, Frederik Bekker
Plenary: Dr Sandra Knapp, Department of Life Sciences, Natural History Museum
Solanaceae – more than potatoes and tomatoes!
The nightshade family – Solanaceae – is the source of many products used by people all over the world, way more than just the origin of chips and ketchup. For only a medium-sized plant family, the nightshades really pack a punch, both in terms of commercially important foods and medicines, but also in terms of underutilised crops important for local agriculture. For understanding the potential utility of these species, both taxonomy – species recognition and identification – and phylogenetics – species relationships – are vitally important. One without the other only gives us half the power. I will briefly review the diversity of the family, then focus on the megadiverse genus Solanum. With more than 1,200 species and distributed worldwide, Solanum is most diverse in the Neotropics, but recent work has shown that diversification is fastest in Africa and Australia, counter to expectations. Africa has also been crucial in the evolution of several crops – some globally, some locally important. I will explore the nexus between taxonomy and phylogeny in Solanum, and finally suggest areas for further research into both that will aid our understanding of both biology and conservation of these plants both ex situ and in their native ranges.
Additional Speakers:
Bianca Ferreira, Wits
Morphometric and molecular analysis of the Senecio achilleifolius complex (Senecioneae, Asteraceae) in South Africa
Roughly 300 species of Senecio L. occur in South Africa. There are three currently recognised species within Senecio sensu lato, viz., S. tanacetopsis, S. seminiveus and S. achilleifolius, that require clearer delimitation. The species boundaries of these three species need to be re-assessed as they appear morphologically similar and may in fact be a single species. This study aimed to understand whether this species complex contains three distinct species, or simply three different growth forms or morphs of the same species that vary according to diverse environmental pressures and habitats over different altitudinal ranges. The Senecio achilleifolius species complex was revised and delimited using morphometric (quantitative and qualitative morphological data), ecological (altitudinal and distribution data), molecular AFLP data, and DNA sequence data to determine if one or more species should be recognised. Multivariate and molecular analyses of the S. achilleifolius complex do not support the three currently recognised species. The results support the description of a new taxon incorrectly included in the S. achilleifolius species group and the combination and reassignments of two defined species, S. seminiveus and S. tanacetopsis, as varieties of a single species. Altitudinal factors and other environmental stresses appear to affect some morphological features of the populations (e.g. capitula size, distance between leaves), resulting in considerable morphological variation between and within populations of the same species. A high number of individuals from the S. seminiveus and S. tanacetopsis populations showed admixture, which is likely due to the retention of ancestral polymorphisms between species groups (not hybridisation). Collectively, these data indicate that there is potentially a unique taxon within the complex, and that the complex comprises a S. achilleifolius and S. seminiveus with two varieties.
Frederik Bekker, Stellenbosch University
The gigas effect: A reliable predictor of ploidy? Case studies in Oxalis
Whole genome duplication (i.e. polyploidy) is an important evolutionary process. Its long-term evolutionary potential to generate diversity and lead to lineage divergence remains a mystery. Polyploidy often causes major phenotypic changes in polyploids of which the most prominent is termed the "gigas" effect. This enlargement of plant traits (gigas effect) has been associated with fitness advantages in polyploids. Using Oxalis as a study system, we examine whether Oxalis polyploids exhibit the gigas effect using 24 species across the genus from the Oxalis living research collection in the Stellenbosch University Botanical Gardens. We also tested for phenotypic and ecological differences between diploids and polyploids in a globally invasive and local weedy species, Oxalis purpurea. Using known correlates of the gigas effect, we show that Oxalis polyploids display a very small and inconsistent gigas effect. This is contrary to predictions from literature. Oxalis purpurea polyploids, however, produced significantly more and larger clone bulbs than diploids did. Polyploid success and persistence in Oxalis could be as a result of a temporary initial gigas effect - upon polyploid formation. This effect can later become diluted through local adaptation. The tendency of Oxalis purpurea polyploids to produce more and larger clone bulbs could potentially explain how Oxalis polyploids persist and become widespread after successful establishment.
1 July Speaker Information: Dr David Hibbett, Wilma Nel & Aiden Visagie
Phylogenomic analyses resolve taxonomic ambiguity for two new genera in the Ophiostomatales
Wilma Nel, Wilhelm de Beer, Michael J. Wingfield, Tuan Duong
Continued discovery and description of fungal species has meant that currently available DNA barcodes often fail to conclusively delineate many genera and species. Consequently, the increasing availably of whole genome sequence data is emerging as an important tool to clarify these ambiguous taxonomic relationships. The Ophiostomatales (Ascomycota) accommodates more than 300 species characterized by similar morphological adaptations to arthropod dispersal. We investigated the occurrence and taxonomic novelty of ophiostomatalean-like fungi from the Termitomyces fungus combs of fungus-farming termites. Morphological characteristics and DNA sequence data revealed that the studied isolates reside in three well-supported lineages representing three novel species. However, the generic placement of these species could not be clarified using conventional DNA markers. A phylogenomic approach was consequently utilized to resolve this question. The results provided sufficient evidence to introduce two new genera (Intubia and Chrysosphaeria) residing in a broadly defined Ophiostomatales. Three new species, Intubia macrotermitinae, Intubia oerlemansii and Chrysosphaeria jan-nelii were described in these genera.
Isolation and identification of Penicillium from wheat associated agricultural soils
Aiden Visagie, Karin Jacobs & Cobus M Visagie
Department of Microbiology, Stellenbosch University and Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria
South Africa is a fungal biodiversity hotspot and contains many undescribed fungi. This is especially true considering Penicillium, a genus characterized by branched conidiophores that resembles a tiny brush. Penicillium occurs worldwide and affects humans and animals in many ways. Their importance necessitates a stable taxonomy that allows researchers to easily identify strains to species level. The systematics and classification of species in this genus are well established and represents one of the most modern taxonomies for all fungi. The widely used consilient concept of species considers morphological, physiological, and phylogenetic characters to delineate species. This modern approach led to working on these difficult fungi becoming easier than ever, including finding missing diversity and describing new species. In this study, isolations from wheat growing agricultural soils resulted in 633 Penicillium strains. These were identified using mainly beta-tubulin sequences. These strains were screened for potential PGP (Plant Growth Promoting) properties, in the form of Phosphate solubilization (PS) activity, as well as Indole acetic acid (IAA) production. The five best performing strains were used in potting trials, to test their ability to affect wheat plants development (IAA) and available soil phosphorus (PS) and therefore assist plant growth. In this presentation, we discuss the modern taxonomy of Penicillium and summarize the main results obtained during our survey, including the description of some new species, and the PGP potential of these fungi.
SASSB 3 June YouTube Recording
3 June Abstracts
A phylogenetic assessment of parasitoid wasps (Ichneumonidae; Banchinae) in the Afrotropical region using total evidence
Terry Reynolds Berry, Conrad A. Matthee & Simon van Noort
A comprehensive higher level revision of the subfamily Banchinae in the Afrotropical region is provided, including an investigation of evolutionary relationships. Morphological data were combined with molecular sequence data from two nuclear genes, 18S and 28S, and one mitochondrial gene, COI, for 76 taxa representing all three tribes and 10 of the 12 currently recognized Afrotropical genera. Divergence dates and historical biogeography were estimated on the inferred phylogeny. The most important results of the study suggest that (1) the tribes, as represented in the Afrotropical region, form separate clades, with monophyly well-supported for Glyptini and Banchini; (2) the endemic genus Sjostedtiella, along with other “forest-associated” lineages, was found to be the oldest banchine genus within the Afrotropical region; and (3) the dating of the temperate-associated genus Cryptopimpla refutes the hypothesis that banchine lineages found within the Cape region of South Africa are more derived because of their association with the Cape Floristic Region. Most of the genera were found to be monophyletic, while paraphyly was found for Lissonota. In addition, certain genera appear more speciose in tropical savanna or forested regions, whiles others were only found in temperate regions, supporting relative affinities of these genera to specific biogeographical areas defined by habitat and climate. The results presented here illustrate the need for a reassessment of the generic status of Lissonota.