- University of Johannesburg, Auckland Park 2009, South Africa
Peter Teske
University of Johannesburg, South Africa, Zoology, Faculty Member
- My research focuses on discovering how near-contemporary and historical environmental factors have generated genetic ... moreMy research focuses on discovering how near-contemporary and historical environmental factors have generated genetic structure in marine animals. My main focus areas are southern Africa and temperate Australia.edit
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Understanding the dietary preferences of endangered species can be useful in implementing conservation strategies, including habitat restoration, translocation, and captive breeding. Environmental DNA (eDNA) from feces provides a... more
Understanding the dietary preferences of endangered species can be useful in implementing conservation strategies, including habitat restoration, translocation, and captive breeding. Environmental DNA (eDNA) from feces provides a non-invasive method for analysing animal diets. Currently, metabarcoding, a PCR-based approach, is the method of choice for analysing such data. However, this method has limitations, specifically PCR bias, which can result in the overestimation of the importance of certain taxa and failure to detect other taxa because they do not amplify. The present study compared metabarcoding with metagenomics, a PCR-free method, to assess the diversity of prey items in the feces of a critically endangered South African estuarine pipefish, Syngnathus watermeyeri, and its widely distributed congener S. temminckii to investigate potential dietary competition. The metabarcoding results showed a distinct difference between the diets of S. watermeyeri and S. temminckii, with ...
The reconstruction of complete mitochondrial genomes (mitogenomes) has considerable potential to clarify species relationships in cases where morphological analysis and DNA sequencing of individual genes are inconclusive. However, the... more
The reconstruction of complete mitochondrial genomes (mitogenomes) has considerable potential to clarify species relationships in cases where morphological analysis and DNA sequencing of individual genes are inconclusive. However, the trend to use only mitogenomes for the phylogenies presented in mitogenome announcements carries the inherent risk that the study species’ taxonomy is incorrect because no mitogenomes have yet been reconstructed for its sister species. Here, I illustrate this problem using the mitogenomes of two seahorses, Hippocampus capensis and H. queenslandicus. Both specimens used for mitogenome reconstruction originated from traditional Chinese medicine markets rather than native habitats. Although mitogenome phylogenies placed these specimens correctly among the seahorses from which mitogenomes were available at the time, incorporating single-marker sequence from closely related species into the phylogenies revealed that both mitogenomes are problematic. The mito...
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Upwelling triggers a mass migration of sardines into an ecological trap.
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The estuarine pipefish, Syngnathus watermeyeri, is one of the rarest animals in Africa and occurs in only two South African estuaries. The species was declared provisionally extinct in 1994, but was later rediscovered and is currently... more
The estuarine pipefish, Syngnathus watermeyeri, is one of the rarest animals in Africa and occurs in only two South African estuaries. The species was declared provisionally extinct in 1994, but was later rediscovered and is currently listed by the IUCN as Critically Endangered. A conservation programme was launched in 2017, with the re-introduction of captive-bred individuals into estuaries where this species was recorded historically was the main aims. Successful captive breeding requires knowledge of the species’ dietary requirements. In the present study, we used metabarcoding of faecal DNA to identify prey species consumed by wild-captured S. watermeyeri from one of the two surviving populations. We compared the diet of the estuarine pipefish with that of the longsnout pipefish, S. temminckii, in the same estuary, to determine whether these two species compete for the same prey items. Both species occupy similar estuarine habitats, but S. temminckii has a much wider distributio...
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Seahorses and pipefishes are heavily exploited for use in Traditional Chinese Medicine (TCM), and less frequently for curio markets or as aquarium fish. A number of recent studies have used DNA barcoding to identify species sold at TCM... more
Seahorses and pipefishes are heavily exploited for use in Traditional Chinese Medicine (TCM), and less frequently for curio markets or as aquarium fish. A number of recent studies have used DNA barcoding to identify species sold at TCM markets in East Asia, but the usefulness of this approach in determining the region of origin remains poorly explored. Here, we generated DNA barcodes of dried seahorses and pipefishes destined for TCM that were confiscated at South Africa’s largest airport because they lacked the export permits required for the CITES-listed seahorses. These were compared with published sequences and new sequences generated for Mozambican seahorses, with the aim of determining whether it is possible to identify their country of origin. All pipefishes were identified as Syngnathoides biaculeatus, a widespread Indo-Pacific species, but the published sequence data did not provide sufficient resolution to identify the region of origin. The same was true of the majority of...
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Mitochondrial DNA (mtDNA) has long been used to date the divergence between species, and to explore the time when species’ effective population sizes changed. The idea that mitochondrial DNA is useful for molecular dating rests on the... more
Mitochondrial DNA (mtDNA) has long been used to date the divergence between species, and to explore the time when species’ effective population sizes changed. The idea that mitochondrial DNA is useful for molecular dating rests on the premise that its evolution is neutral. This premise was questionable to begin with, and even though it has long been challenged, the evidence against clock-like evolution of mtDNA is usually ignored. Here, we present a particularly clear and simple example to illustrate the implications of violations of the assumption of selective neutrality. DNA sequences were generated for the mtDNA COI gene and the nuclear 28S rRNA of two closely related and widely distributed rocky shore snails whose geographical ranges are defined by different thermal preferences. To our knowledge, this is the first study to use nuclear rRNA sequence for studying species-level genealogies instead of phylogenetics, presumably because this marker is considered to be uninformative at...
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Intraspecific genetic structure in widely distributed marine species often mirrors the boundaries between temperature-defined bioregions. This suggests that the same thermal gradients that maintain distinct species assemblages also drive... more
Intraspecific genetic structure in widely distributed marine species often mirrors the boundaries between temperature-defined bioregions. This suggests that the same thermal gradients that maintain distinct species assemblages also drive the evolution of new biodiversity. Ecological speciation scenarios are often invoked to explain such patterns, but the fact that adaptation is usually only identified when phylogenetic splits are already evident makes it impossible to rule out the alternative scenario of allopatric speciation with subsequent adaptation. We integrated large-scale genomic and environmental datasets along one of the world's best-defined marine thermal gradients (the South African coastline) to test the hypothesis that incipient ecological speciation is a result of divergence linked to the thermal environment. We identified temperature-associated gene regions in a coastal fish species that is spatially homogeneous throughout several temperature-defined biogeographic...
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The cosmopolitan lamniform shark Carcharias taurus (commonly known as the ragged-tooth, grey nurse or sand tiger shark) is threatened by overexploitation in parts of its range. Return migrations of females to specific nursery areas... more
The cosmopolitan lamniform shark Carcharias taurus (commonly known as the ragged-tooth, grey nurse or sand tiger shark) is threatened by overexploitation in parts of its range. Return migrations of females to specific nursery areas suggest that females exhibit reproductive philopatry, a behaviour that over time might lead to genetically isolated subpopulations over various spatial scales. To investigate genetic evidence for reproductive philopatry, genetic data from mitochondrial and microsatellite markers were generated for 104 young-of-the-year and juvenile sharks. Comparing the smallest versus the largest young sharks revealed a pattern of size-related differentiation between nurseries that was only found in the smaller size class. This not only confirms reproductive philopatry of their mothers, but is also in line with previous observations of larger juvenile sharks increasing their migration range and moving between sites. Our results highlight the need to target young-of-the-year sharks when investigating reproductive philopatry to exclude roaming individuals that obscure size-related signals of genetic differentiation. Given the species’ high susceptibility to overexploitation, the evidence for reproductive philopatry is of direct importance to the management and conservation of C. taurus worldwide. As many nursery areas as possible should be protected to ensure that the number of locally resident juveniles and the pool of the returning females remain stable in the long term. This may warrant protected areas, or time-area closures, prohibiting exploitation in the nursery areas during pupping season.
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Pyura stolonifera is a large solitary ascidian found in Africa, Australasia and South America. The taxonomic status of different populations of this species is disputed, especially since there is evidence for several distinct... more
Pyura stolonifera is a large solitary ascidian found in Africa, Australasia and South America. The taxonomic status of different populations of this species is disputed, especially since there is evidence for several distinct morphological and genetic units that point towards the existence of multiple cryptic species. While some researchers still recognize P. stolonifera as a single species, others treat the different populations as distinct species. Here, we present a revision of the P. stolonifera species complex based on the examination of samples from all regions where there are reliable reports of this taxon. We recognize four species that are both morphologically and genetically distinct, one of which is new to science and is formally described here. This species is morphologically distinct from the other three members of the species complex in terms of the colour and texture of the tunic, the arrangement of the gonads within the gut and the shape of the dorsal tubercle, among...
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Abstract Two endemic southern African pipefish species (Teleostei: Syngnathidae) co-occur in estuaries on the southeast coast of South Africa. The larger longsnout pipefish, Syngnathus temminckii , is abundant and has a wide range that... more
Abstract Two endemic southern African pipefish species (Teleostei: Syngnathidae) co-occur in estuaries on the southeast coast of South Africa. The larger longsnout pipefish, Syngnathus temminckii , is abundant and has a wide range that comprises coastal and estuarine habitats in all three of the region's marine biogeographic provinces. In contrast, the smaller estuarine pipefish S . watermeyeri is critically endangered, and confined to a few warm-temperate estuaries. Here, we explore reasons for these considerable differences in conservation status. Fecundity is related to fish size, with large live-bearing S . temminckii males carrying up to 486 developing eggs/embryos, compared to a maximum of only 44 recorded for S . watermeyeri . Loss of submerged seagrass habitats due to episodic river flooding appears to be correlated with the temporary absence of both species from such systems. Prolonged cessation in river flow to estuaries can cause a collapse in estuarine zooplankton stocks, a food resource that is important to pipefish species. The greater success of S . temminckii when compared to S . watermeyeri can be attributed to the former species' wider geographic distribution, fecundity, habitat selection and ability to use both estuaries and the marine environment as nursery areas. Genetic data indicate that this has resulted in a much smaller long-term effective population size of S . watermeyeri , a situation that has persisted since the beginning of the present interglacial period. Syngnathus watermeyeri is thus naturally more susceptible to anthropogenic disturbances, which have resulted in an alarming reduction in its contemporary population size. Possible measures to promote the conservation of S . watermeyeri are presented.
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Southern Africa is a biodiversity hotspot of patellid limpets, with three genera (Helcion, Cymbula and Scutellastra) identified and described in the region. Scutellastra is the most diverse and most frequently studied of these and, along... more
Southern Africa is a biodiversity hotspot of patellid limpets, with three genera (Helcion, Cymbula and Scutellastra) identified and described in the region. Scutellastra is the most diverse and most frequently studied of these and, along with Cymbula, includes species with territorial and non-territorial foraging behaviours. We used three mitochondrial markers (12S rRNA, 16S rRNA and COI) and one nuclear marker (ATPSβ intron) to assess evolutionary relationships among species of Cymbula and Scutellastra with these two foraging behaviours and to identify which foraging mode is the more ancient. Maximum Likelihood and Bayesian Inference phylogenetic analyses revealed that the species sharing a foraging type are monophyletic in both genera. Territoriality is a derived character, as the clades with this foraging type are nested within a tree that otherwise comprises non-territorial taxa. These include Helcion, which was recovered as sister to the Cymbula/Scutellastra clade, and the next...
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Aim We provide an overview of the location and ages of coastal phylogeographical breaks in southern Australian planktonic dispersers, and test the hypothesis that the absence of such breaks in some species is an artefact of insufficient... more
Aim We provide an overview of the location and ages of coastal phylogeographical breaks in southern Australian planktonic dispersers, and test the hypothesis that the absence of such breaks in some species is an artefact of insufficient resolution of genetic markers when such breaks evolved comparatively recently. Location Temperate coastal Australia. Methods We generated a large (> 1500 individuals) data set from rapidly evolving microsatellite markers for two codistributed Australian coastal gastropods, and compared it with mitochondrial DNA data. Both study species, the snail Nerita atramentosa and the limpet Siphonaria diemenensis, have long planktonic dispersal phases, and neither taxon exhibits substantial regional genetic structure on the basis of mitochondrial DNA. We tested for the presence of genetic structure by means of AMOVA, Bayesian clustering (structure) and iterated realloction (flock). Results There was no compelling evidence for the existence of more than one evolutionary lineage in either species. Main conclusions Discrepancies in the phylogeographical structuring of co-distributed intertidal taxa cannot be attributed to insufficient marker resolution for the two species considered here, and likely reflect a combination of abiotic and biotic factors that include porous dispersal barriers, life history and species age/history. It appears that contemporary oceanography does not explain the presence of phylogeographical breaks, but may serve to maintain breaks that evolved earlier. Deep genetic divergence in some of the previously studied coastal invertebrates suggests that these could be cryptic species, in which case competitive exclusion may play a role in constraining species biogeography.
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Southern Africa is a marine biodiversity hotspot that not only comprises faunal elements from the Atlantic and Indian Oceans, but also large numbers of endemic species. Using mitochondrial and nuclear DNA sequence data, we explored... more
Southern Africa is a marine biodiversity hotspot that not only comprises faunal elements from the Atlantic and Indian Oceans, but also large numbers of endemic species. Using mitochondrial and nuclear DNA sequence data, we explored whether genetic structure in the endemic coastal goby Psammogobius knysnaensis, a species whose range straddles both biomes, is linked to the boundary between the two oceans. Subtle genetic structure was identified between Atlantic and Indian Ocean populations, with genetic diversity being lower in the Atlantic, and particularly on the west coast. Our results point to partial isolation between the populations associated with each biome that is most likely driven by the region’s oceanography, but unlike in other species, there is no evidence for distinct regional evolutionary lineages that are likely adapted to the environmental conditions prevalent in each region. The exclusive presence of P. knysnaensis in sheltered habitats (estuaries and lagoons) may protect this species from the severe impacts of cold water upwelling on the west coast.
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The Wild Coast in south-eastern South Africa is strongly influenced by the warm, southward-flowing Agulhas Current. This current has a significant impact on dispersal in the coastal biota of the region, and facilitates high levels of... more
The Wild Coast in south-eastern South Africa is strongly influenced by the warm, southward-flowing Agulhas Current. This current has a significant impact on dispersal in the coastal biota of the region, and facilitates high levels of connectivity among populations. However, it is not known how the region's high-velocity hydrology affects genetic population structure in endemic estuarine species, populations of which are frequently isolated from the sea. Here, we compared genetic structure in two estuarine crabs of the family Hymenosomatidae. Both are presumed to have low dispersal potential, but they differ in terms of their life histories. Hymenosoma longicrure has abbreviated larval development and can complete its entire life cycle within estuaries, whereas Neorhynchoplax bovis is a direct developer that lacks planktonic larvae. Using DNA sequence data from the mitochondrial COI gene and the intron of the nuclear ANT gene, we found that levels of genetic structure differ considerably between the species. Depending on the genetic marker used, H. longicrure is genetically homogeneous (COI) or displays low levels of genetic structure and minor evidence of recruitment near natal sites (ANT). In contrast, connectivity in N. bovis is much lower, as this species has a unique combination of alleles at each site, indicating that recruitment is mostly local. These results support previous findings suggesting that even a short larval dispersal phase is sufficient to maintain high levels of connectivity and prevent genetic divergence among populations.
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ABSTRACT Global climatic oscillations have shaped the contemporary genetic structure of marine taxa in different ways. Previous demographic studies have indicated that various intertidal marine species display genetic signatures of... more
ABSTRACT Global climatic oscillations have shaped the contemporary genetic structure of marine taxa in different ways. Previous demographic studies have indicated that various intertidal marine species display genetic signatures of demographic expansion that either pre- or postdate the Last Glacial Maximum. Such expansions and the ability of species to colonise new habitats will influence their genetic structure, but the link between scales of larval dispersal and the strength of phylogeographic structure is not always clear. We analysed a fragment of the mitochondrial COI gene of 11 sympatric species of intertidal southern African patellid limpets to investigate how ancient oceanographic dynamics have shaped and maintained their contemporary spatial genetic variation. Our data show that the patellid limpets investigated display congruent evidence of spatial expansion during the Late Pleistocene or Early Holocene, which corresponds with the establishment of the contemporary southern African shoreline. We argue that closely related and co-distributed southern African intertidal invertebrates responded to ancient climatic oscillations as a cohesive group. In contrast, contemporary oceanographic circulation has shaped the phylogeographic patterns of these limpets in different ways. We show close relationships between phylogeography and biogeography for some species, but not for others, despite the similarities in their life histories and exposure to the same climatic changes.
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Abstract Five to seven subspecies of Antarctic Tern (Sterna vittata) are recognised, with at least three (S. v. vittata, S. v. tristanensis and S. v. sanctipauli) wintering in South Africa. Morphological characters used to define these... more
Abstract Five to seven subspecies of Antarctic Tern (Sterna vittata) are recognised, with at least three (S. v. vittata, S. v. tristanensis and S. v. sanctipauli) wintering in South Africa. Morphological characters used to define these subspecies are not perfectly reliable, but fidelity to nesting site suggests they could be genetically distinct. We used morphological data and DNA to investigate the validity of subspecies. We further used stable isotope analysis of feather samples collected from the non-breeding grounds in South Africa to attempt to ascertain the population of origin. Nuclear and mitochondrial DNA sequence data identified two major genetic clades: one mostly comprised individuals partially or completely matching the morphological description of S. v. tristanensis, the other included individuals from S. v. vittata and S. v. sanctipauli. Stable isotope values indicated that juveniles originated from at least three populations. Irrespective of their morphological and genetic characteristics, most immatures moulted in Antarctic waters, and adults moulted in various habitats. Their colony of origin could not therefore be inferred from stable isotope values from feathers. Results indicate that morphological groupings may reflect a north-south cline across the Indian Ocean. Adequate conservation strategies require rigorous reassessment of the currently accepted subspecies, including DNA analyses of samples from the breeding grounds, particularly on Amsterdam and St Paul Islands.
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Unusually low genetic diversity can be a warning of an urgent need to mitigate causative anthropogenic activities. However, current low levels of genetic diversity in a population could also be due to natural historical events, including... more
Unusually low genetic diversity can be a warning of an urgent need to mitigate causative anthropogenic activities. However, current low levels of genetic diversity in a population could also be due to natural historical events, including recent evolutionary divergence, or long-term persistence at a small population size. Here, we determine whether the relatively low genetic diversity of pygmy blue whales (Balaenoptera musculus brevicauda) in Australia is due to natural causes or overexploitation. We apply recently developed analytical approaches in the largest genetic dataset ever compiled to study blue whales (297 samples collected after whaling and representing lineages from Australia, Antarctica and Chile). We find that low levels of genetic diversity in Australia are due to a natural founder event from Antarctic blue whales (Balaenoptera musculus intermedia) that occurred around the Last Glacial Maximum, followed by evolutionary divergence. Historical climate change has therefor...
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Genetic divergence among populations of marine broadcast spawners in the absence of past geological barriers presents an intriguing challenge to understanding speciation in the sea. To determine how differences in life history affect... more
Genetic divergence among populations of marine broadcast spawners in the absence of past geological barriers presents an intriguing challenge to understanding speciation in the sea. To determine how differences in life history affect genetic divergence and demographic histories across incomplete dispersal barriers, we conducted a comparative phylogeographic study of three intertidal limpets (Siphonaria spp.) represented on either side of a biogeographic disjunction separating tropical and subtropical marine provinces in southeastern Africa. Using a combination of mitochondrial and nuclear sequence data, we identified two distinct evolutionary lineages each in both Siphonaria concinna (a planktonic disperser) and S. nigerrima (a direct developer), and panmixia in a second planktonic disperser, S. capensis. Although phylogeographic breaks were present in two species, how these became established differed depending on their life histories. In the direct developer, lack of gene flow following divergence, and demographic expansion from a small initial size in the species' subtropical population, point to a single colonisation event. In contrast, the evolutionary lineages of the planktonic disperser split into two genetic lineages with much larger initial population sizes and southward gene flow continued at least periodically, indicating that divergence in this species may have been driven by a combination of reduced larval dispersal and divergent selection. These findings help explain why the presence or absence of phylogeographic breaks often appears to be independent of species' dispersal potential.
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... of the species status of one recently described species the 'Queensland sea-horse', Hippocampus queenslandicus ... to SL, an NSERC Discovery grant to DG, Project Seahorse, the National ... Pacific Syngnathidae... more
... of the species status of one recently described species the 'Queensland sea-horse', Hippocampus queenslandicus ... to SL, an NSERC Discovery grant to DG, Project Seahorse, the National ... Pacific Syngnathidae (Pisces: Syngnathiformes), including both recent and fossil forms. ...
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Tests for isolation by distance (IBD) are the most commonly used method of assessing spatial genetic structure. Many studies have exclusively used mitochondrial DNA (mtDNA) sequences to test for IBD, but this marker is often in conflict... more
Tests for isolation by distance (IBD) are the most commonly used method of assessing spatial genetic structure. Many studies have exclusively used mitochondrial DNA (mtDNA) sequences to test for IBD, but this marker is often in conflict with multilocus markers. Here, we report a review of the literature on IBD, with the aims of determining (a) whether significant IBD is primarily a result of lumping spatially discrete populations, and (b) whether microsatellite datasets are more likely to detect IBD when mtDNA does not. We also provide empirical data from four species in which mtDNA failed to detect IBD by comparing these with microsatellite and SNP data. Our results confirm that IBD is mostly found when distinct regional populations are pooled, and this trend disappears when each is analysed separately. Discrepancies between markers were found in almost half of the studies reviewed, and microsatellites were more likely to detect IBD when mtDNA did not. Our empirical data rejected t...
Research Interests: Marine Biology, Population Genetics, Biology, Single Nucleotide Polymorphisms (SNPs), Medicine, and 12 moreNext generation sequencing, mtDNA, Mitochondrial DNA, Microsatellites, SARDINE, Marine invertebrates, Divergent Selection, RAD Seq, Neutral Theory, mtDNA diversity, Goby Fish, and Isolation by distance
A molecular phylogenetic analysis based on mitochondrial 16S ribosomal DNA and Control Region sequences from native and introduced populations was undertaken, in order to characterize the introduction of Cichla (peacock bass or tucunaré)... more
A molecular phylogenetic analysis based on mitochondrial 16S ribosomal DNA and Control Region sequences from native and introduced populations was undertaken, in order to characterize the introduction of Cichla (peacock bass or tucunaré) species in Brazil. Mitochondrial DNA haplotypes found in introduced fish from Minas Gerais state (southeastern Brazil) clustered only with those from native species of the Tocantins River (Cichla piquiti and C. kelberi), thereby suggesting a single or, at most, few translocation acts in this area, even though with fish from the same source-population. Our study contributes to an understanding of the introduction of Cichla in regions of Brazil outside the Amazon basin, and adds phylogenetic data to the recently describe Cichla species, endemic from the Tocantins-Araguaia basin.
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The critically endangered estuarine pipefish, Syngnathus watermeyeri, is one of Africa’s rarest fish species and currently faces a significant risk of extinction. A combination of anthropogenic and natural factors threaten submerged... more
The critically endangered estuarine pipefish, Syngnathus watermeyeri, is one of Africa’s rarest fish species and currently faces a significant risk of extinction. A combination of anthropogenic and natural factors threaten submerged macrophyte beds in the two South African estuaries (Bushmans and Kariega) in which the species’ only two known remaining populations reside. Here, we genotyped 34 pipefish from both populations using genome-wide data to determine whether the two estuaries harbour distinct genetic diversity, such that translocating individuals between them might improve the genetic health of both. Our results show that both populations are highly inbred, and no statistically significant genetic structure was found between them. Moreover, individuals both within and between estuaries were very closely related to each other. These results indicate that the remaining populations of the estuarine pipefish suffer from the adverse genetic effects of small population sizes. Even...
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During austral winter, the southern and eastern coastlines of South Africa witness one of the largest animal migrations on the planet, the KwaZulu-Natal sardine run. Hundreds of millions of temperate sardines, Sardinops sagax, form large... more
During austral winter, the southern and eastern coastlines of South Africa witness one of the largest animal migrations on the planet, the KwaZulu-Natal sardine run. Hundreds of millions of temperate sardines, Sardinops sagax, form large shoals that migrate north-east towards the subtropical Indian Ocean. Recent studies have highlighted the role that genetic and environmental factors play in sardine run formation. In the present study, we used massively parallel sequencing to assemble and annotate the first reference transcriptome from the liver cells of South African sardines, and to investigate the functional content and transcriptomic diversity. A total of 1,310,530 transcripts with an N50 of 1578 bp were assembled de novo. Several genes and core biochemical pathways that modulate energy production, energy storage, digestion, secretory processes, immune responses, signaling, regulatory processes, and detoxification were identified. The functional content of the liver transcriptom...
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All multicellular organisms host a wide diversity of microorganisms in and on their bodies, which are collectively known as their microbiome. Characterising microbial communities that inhabit different body niches in wild animals is... more
All multicellular organisms host a wide diversity of microorganisms in and on their bodies, which are collectively known as their microbiome. Characterising microbial communities that inhabit different body niches in wild animals is critical to better understand the dynamics of microbiome diversityand its functional significance. The current study is the first to apply massively parallel sequencing of 16S rRNA to characterise the microbial diversity and functional content of oral microbiota in two of New Zealand’s most important invasive mammals, the omnivorous common brushtail possum (Trichosurus vulpecula) and the carnivorous stoat (Mustela erminea). In total, strains of bacteria belonging to 19 different phyla, 27 classes, 52 orders, 103 families, 163 genera and 51 known species were identified from the oral cavities of the study species. Strains of the phyla Proteobacteria, Firmicutes, Bacteroidetes, Fusobacteria, and Actinobacteria dominated the core oral microbial diversity in...
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AimBiogeographical transition zones are areas of overlap between the faunas of adjacent biogeographical entities. Particularly, the well-defined transition zones along linear coastlines are interesting natural laboratories to study... more
AimBiogeographical transition zones are areas of overlap between the faunas of adjacent biogeographical entities. Particularly, the well-defined transition zones along linear coastlines are interesting natural laboratories to study dispersal and incipient speciation. Few studies have explored whether marine biogeographical transition zones harbour biodiversity that is distinct from that of the biogeographical entities they separate. The Wild Coast in eastern South Africa is a poorly-studied transition zone between region’s warm-temperate and subtropical faunas, and is generally considered to be an area of faunal overlap.LocationThe South African portion of the Western Indian OceanMethodsSequences of the DNA barcoding marker COI were generated from 306 estuarine sandprawns (Callichirus kraussi) collected at 13 sites. Genetic structure and evolutionary history were assessed using a haplotype network and a Bayesian discrete phylogeographic analysis.ResultTwo populations were identified...
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Adaptation to environments that are changing as a result of human activities is critical to species’ survival. A large number of species are adapting to, and even thriving in, urban green spaces, but this diversity remains largely... more
Adaptation to environments that are changing as a result of human activities is critical to species’ survival. A large number of species are adapting to, and even thriving in, urban green spaces, but this diversity remains largely undocumented. In the current study, we explored the potential of environmental DNA (eDNA) to document species diversity in one of the largest green spaces in Johannesburg, South Africa. Using a novel metabarcoding approach that assembles short DNA fragments suitable for massively parallel sequencing platforms to the approximate standard ~710 bp COI barcoding fragment, we document the presence of 26 phyla, 52 classes, 134 orders, 289 families, 380 genera and 522 known species from the study site. Our results highlight the critical role that urban areas play in protecting the world’s declining biodiversity.
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Background: Mitochondrial DNA (mtDNA) has long been used to date historical demographic events. The idea that it is useful for molecular dating rests on the premise that its evolution is neutral. Even though this idea has long been... more
Background: Mitochondrial DNA (mtDNA) has long been used to date historical demographic events. The idea that it is useful for molecular dating rests on the premise that its evolution is neutral. Even though this idea has long been challenged, the evidence against clock-like evolution of mtDNA is often ignored. Here, we present a particularly clear and simple example to illustrate the implications of violations of the assumption of selective neutrality. Methods: DNA sequences were generated for the mtDNA COI gene and the nuclear 28S rRNA of two closely related rocky shore snails, and species-level variation was compared. Nuclear rRNA is not usually used to study intraspecific variation in species that are not spatially structured, presumably because this marker is assumed to evolve so slowly that it is more suitable for phylogenetics. Results: Even though high inter-specific divergence reflected the faster evolutionary rate of COI, intraspecific genetic variation was similar for bo...
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The New Zealand brushtail possum (Trichosurus vulpecula), introduced from Australia in the 1850s, is an invasive species that is widespread throughout New Zealand and forms the largest self-sustained reservoir of bovine tuberculosis... more
The New Zealand brushtail possum (Trichosurus vulpecula), introduced from Australia in the 1850s, is an invasive species that is widespread throughout New Zealand and forms the largest self-sustained reservoir of bovine tuberculosis (Mycobacterium bovis) in the wild. Conservation and agricultural authorities regularly apply a series of population control measures to suppress brushtail possum populations. The evolutionary consequence of more than half a century of intensive population control operations on the species genomic diversity and population structure is hindered by a paucity of available genomic resources for the species. This study is the first to characterise the functional content and diversity of brushtail possum liver and brain cerebral cortex transcriptomes. Raw sequences from hepatic cells and cerebral cortex were assembled into 58,001 and 64,735 transcripts in hepatic cells and cerebral cortex, respectively. Functional annotation and polymorphism assignment of the a...
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Intraspecific genetic structure in widely distributed marine species often mirrors the boundaries between temperature-defined bioregions. This suggests that the same thermal gradients that maintain distinct species assemblages also drive... more
Intraspecific genetic structure in widely distributed marine species often mirrors
the boundaries between temperature-defined bioregions. This suggests
that the same thermal gradients that maintain distinct species assemblages
also drive the evolution of new biodiversity. Ecological speciation scenarios
are often invoked to explain such patterns, but the fact that adaptation is
usually only identified when phylogenetic splits are already evident makes
it impossible to rule out the alternative scenario of allopatric speciation with
subsequent adaptation.We integrated large-scale genomic and environmental
datasets along one of the world’s best-defined marine thermal gradients
(the South African coastline) to test the hypothesis that incipient ecological
speciation is a result of divergence linked to the thermal environment. We
identified temperature-associated gene regions in a coastal fish species that
is spatially homogeneous throughout several temperature-defined biogeographic
regions based on selectively neutral markers. Based on these gene
regions, the species is divided into geographically distinct regional populations.
Importantly, the ranges of these populations are delimited by the
same ecological boundaries that define distinct infraspecific genetic lineages
in co-distributed marine species, and biogeographic disjunctions in species
assemblages. Our results indicate that temperature-mediated selection represents
an early stage of marine ecological speciation in coastal regions that
lack physical dispersal barriers.
the boundaries between temperature-defined bioregions. This suggests
that the same thermal gradients that maintain distinct species assemblages
also drive the evolution of new biodiversity. Ecological speciation scenarios
are often invoked to explain such patterns, but the fact that adaptation is
usually only identified when phylogenetic splits are already evident makes
it impossible to rule out the alternative scenario of allopatric speciation with
subsequent adaptation.We integrated large-scale genomic and environmental
datasets along one of the world’s best-defined marine thermal gradients
(the South African coastline) to test the hypothesis that incipient ecological
speciation is a result of divergence linked to the thermal environment. We
identified temperature-associated gene regions in a coastal fish species that
is spatially homogeneous throughout several temperature-defined biogeographic
regions based on selectively neutral markers. Based on these gene
regions, the species is divided into geographically distinct regional populations.
Importantly, the ranges of these populations are delimited by the
same ecological boundaries that define distinct infraspecific genetic lineages
in co-distributed marine species, and biogeographic disjunctions in species
assemblages. Our results indicate that temperature-mediated selection represents
an early stage of marine ecological speciation in coastal regions that
lack physical dispersal barriers.