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The validity of morphology-based species boundaries between the southern African representatives of the genus Tricolia Risso, 1826 was assessed using mitochondrial COI and 16S rRNA sequence data. Most phylogenies obtained from individual and combined genetic datasets recovered 10 of the southern African members of the genus as a monophyletic clade. No COI sequences of the 11th species (T. adusta) were available, but this species clustered among the other African species in the 16S rRNA phylogeny. Discrepancies between morphology and genetics were identified in two clades within which there was limited genetic variation and no differentiation between two groups of nominal species, comprising respectively T. africana (Bartsch, 1915) and T. capensis (Dunker, 1846), and T. bicarinata (Dunker, 1846), T. insignis (Turton, 1932) and T. kraussi (Smith, 1911). In both cases the distributions of the nominal taxa coincide with well-known biogeographic disjunctions, and there is evidence of overlapping and intergrading shell characters. We propose that both of these unresolved clades be recognized as single, phenotypically plastic species, for which the oldest available names are respectively T. capensis and T. bicarinata. Despite the resultant reduction in number of recognized species, the phasianellid fauna of southern Africa remains the most diverse in the world, with 10 endemic species and 3 tropical species extending south into KwaZulu-Natal. [ABSTRACT FROM AUTHOR]

The genus Nyctiphanes (Malacostraca, Euphausiacea) comprises four neritic species that display antitropical geographic distribution in the Pacific ( N. simplex and N. australis) and Atlantic ( N. couchii and N. capensis) Oceans. We studied the origin of this distribution applying methods for phylogenetic reconstruction and molecular dating of nodes using a Bayesian MCMC analysis and the DNA sequence information contained in mtDNA 16S rDNA and cytochrome oxidase (COI). We tested hypotheses of vicariance by contrasting the time estimates of cladogenesis with the onset of the major barriers to ocean circulation. It was estimated that Nyctiphanes originated in the Pacific Ocean during the Miocene, with a lower limit of 18 miilion years ago (Mya). An Atlantic–Pacific cladogenic event (95% HPD 3.2–9.6) took place after the closure of the Tethyan Sea, suggesting that dispersal occurred from the Indo-Pacific, most likely via southern Africa. Similarly, the antitropical distribution pattern observed in the eastern Atlantic Ocean likely resulted from recent Pliocene–Pleistocene (95% HPD 1.0–4.97) northward dispersal from the southern hemisphere. Our results imply that dispersal appears to have had a significant role to play in the evolution of this group. [ABSTRACT FROM AUTHOR]

Eleven polymorphic microsatellite loci were developed from an enrichment library of the roman, Chrysoblephus laticeps, and characterized for 40 individuals collected in Africa's largest and oldest Marine Protected Area (MPA), the Tsitsikamma National Park. The number of alleles per locus ranged from three to 19, and heterozygosities ranged from 0.20 to 0.85. A significant departure from Hardy–Weinberg equilibrium was detected for one locus, and linkage disequilibrium was identified among three pairs of loci. The markers will be useful to detect whether populations resident in MPAs along the South African coast are genetically connected, and whether there is spillover of recruits into adjacent exploited areas. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Explaining why some species are widespread, while others are not, is fundamental to biogeography, ecology, and evolutionary biology. A unique way to study evolutionary and ecological mechanisms that either limit species’ spread or facilitate range expansions is to conduct research on species that have restricted distributions. Nonindigenous species, particularly those that are highly invasive but have not yet spread beyond the introduced site, represent ideal systems to study range size changes. Here, we used species distribution modeling and genomic data to study the restricted range of a highly invasive Australian marine species, the ascidian Pyura praeputialis. This species is an aggressive space occupier in its introduced range (Chile), where it has fundamentally altered the coastal community. We found high genomic diversity in Chile, indicating high adaptive potential. In addition, genomic data clearly showed that a single region from Australia was the only donor of genotypes to the introduced range. We identified over 3,500 km of suitable habitat adjacent to its current introduced range that has so far not been occupied, and importantly species distribution models were only accurate when genomic data were considered. Our results suggest that a slight change in currents, or a change in shipping routes, may lead to an expansion of the species’ introduced range that will encompass a vast portion of the South American coast. Our study shows how the use of population genomics and species distribution modeling in combination can unravel mechanisms shaping range sizes and forecast future range shifts of invasive species. [ABSTRACT FROM AUTHOR]

Historical demographic events shape genetic diversity that remains evident in the genomes of contemporary populations. In the case of species that are of conservation concern, this information helps to unravel evolutionary histories that can be critical in guiding conservation efforts. The Knysna seahorse, Hippocampus capensis, is the world's most endangered seahorse species, and it presently survives in only three estuaries on the South African south coast. Factors that contributed to the species becoming endangered are unclear; additionally, the lack of information on whether the three populations should be managed separately because of potential long-term isolation hampers effective management efforts. In the present study, we reconstructed the seahorses' demographic history using a suite of microsatellite loci. We found that the largest population (Knysna Estuary) has colonised the other estuaries relatively recently (< 450 years ago), and that its population size is comparatively large and stable. Neither of the other two populations shows signs of long-term reductions in population size. The high conservation status of the species is thus a result of its limited range rather than historical population declines. Our findings indicate that the long-term survival of H. capensis depends primarily on the successful management of the Knysna population, although the other estuaries may serve as reservoirs of genetic diversity. [ABSTRACT FROM AUTHOR]

Temporary wetland ecosystems are common in arid and semi‐arid environments, and are inhabited by diverse invertebrate communities. Little is known about the dynamics of genetic connectivity in the geographically scattered populations of these wetland specialists.The current study investigated the spatial genetic structure and dispersal history of a recently described calanoid copepod, Lovenula raynerae, reported from temporary wetlands in the Eastern Cape province of South Africa. We tested whether the species represents a single, well‐connected population or comprises different regional genetic groups, some of which may be rare or endangered.Mitochondrial COI sequences were generated for 365 specimens from 46 temporary wetlands spread across the species' known distribution range. Isolation‐by‐distance and isolation‐by‐environment patterns of partitioning genetic variations across the landscape were evaluated. In addition, the presence of historical impediments to gene flow between contemporary populations was investigated using a combination of Monmonier's algorithm and Bayesian reconstruction of phylogeographical diffusion in continuous space.The wetland populations were highly structured across the landscape and could be assigned to six distinct evolutionary lineages, potentially representing some level of cryptic speciation. Two distinct phases were identified in the dispersal history of these lineages. Initially, dispersal only occurred inland of a postulated barrier, but eventually the barrier disappeared and the species extended its range by spreading into regions close to the coastline. Molecular dating shows that the barrier represents the upper limit of the coastline during the Pliocene, and that its crossing was facilitated by Pliocene sea regression in southern Africa.Our finding shows that complex demographic histories can be preserved in the mitochondrial DNA of temporary wetland crustaceans because of limited effective gene flow after initial colonisation events. This makes them an interesting study system to explore the long‐term effects of climate change on arid ecosystem communities. [ABSTRACT FROM AUTHOR]

A longstanding question in evolutionary biology is how natural selection and environmental pressures shape the mitochondrial genomic architectures of organisms. Mitochondria play a pivotal role in cellular respiration and aerobic metabolism, making their genomes functionally highly constrained. Evaluating selective pressures on mitochondrial genes can provide functional and ecological insights into the evolution of organisms. Collembola (springtails) are an ancient hexapod group that includes the oldest terrestrial arthropods in the fossil record, and that are closely associated with soil environments. Of interest is the diversity of habitat stratification preferences (life forms) exhibited by different species within the group. To understand whether signals of positive selection are linked to the evolution of life forms, we analysed 32 published Collembola mitogenomes in a phylomitogenomic framework. We found no evidence that signatures of selection are correlated with the evolution of novel life forms, but rather that mutations have accumulated as a function of time. Our results highlight the importance of nuclear-mitochondrial interactions in the evolution of collembolan life forms and that mitochondrial genomic data should be interpreted with caution, as complex selection signals may complicate evolutionary inferences. [ABSTRACT FROM AUTHOR]

Aim: Biogeographical 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 the region's warm‐temperate and subtropical faunas, and is generally considered to be an area of faunal overlap. Location: The South African portion of the Western Indian Ocean. Methods: Sequences of the DNA barcoding marker COI were generated from 306 estuarine sandprawns (Kraussillichirus kraussi) collected at 13 sites. Genetic structure and evolutionary history were assessed using a haplotype network and a Bayesian discrete phylogeographic analysis. Result: Two populations were identified whose ranges are centred on the Wild Coast, a rare one in the northern portion and a more common one in the central and southern portion of this biogeographical transition zone. These populations are not closely related to each other, but descend from subtropical and warm‐temperate sister populations, respectively. Although genetic distances between populations were low, they exceeded within‐population distances, indicating the presence of a "barcoding gap." Conclusions: This is the first study to indicate that the Wild Coast marine biogeographical transition zone is not merely an area of faunal overlap, and one of very few studies to have discovered genetically unique populations within a marine biogeographical transition zone. The Wild Coast may harbour additional unique biodiversity that remains to be discovered, including rare species that require protection. More research is required to understand how this environmentally dynamic marine biogeographical transition zone differs from the adjacent biogeographical provinces. [ABSTRACT FROM AUTHOR]

Background: The Octopus vulgaris species complex consists of numerous morphologically similar but genetically distinct species. The current publicly available mitogenome of this species has been generated from a specimen collected from Tsukiji Fish Market, Tokyo, Japan. Octopus from the northwestern Pacific Ocean are now considered to be a separate species, Octopus sinensis. For this reason, we hypothesised that the current record of O. vulgaris was sequenced from a specimen of O. sinensis. Here, we sequenced the first complete mitogenome of a specimen of Octopus vulgaris sensu stricto that was collected from the species' confirmed distribution areas in northeastern Atlantic., Methods and Results: The complete mitogenome was assembled de novo and annotated using 250 bp paired-end sequences. A single circular contig 15,655 bp in length with a mean read coverage of 1089 reads was reconstructed. The annotation pipeline identified 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNA) and two ribosomal RNAs. A maximum likelihood phylogenetic tree recovered the assembled mitogenome as the sister taxon of a monophyletic group comprising O. sinensis and the previously published mitogenome of "O. vulgaris" from Japan. This confirms that the latter was a Japanese specimen of O. sinensis., Conclusion: The mitogenome sequenced here is the first to be published for Octopus vulgaris sensu stricto. It represents an important first step in genetics-informed research on the evolution, conservation, and management of this commercially important species., (© 2023. The Author(s).)

Environmental gradients between marine biogeographical provinces separate distinct faunal communities. However, the absence of absolute dispersal barriers allows numerous species to occur on both sides of such boundaries. While the regional populations of such widespread species are often morphologically indistinguishable from each other, genetic evidence suggests that they represent unique ecotypes, and likely even cryptic species, that may be uniquely adapted to their local environment. Here, we explored genomic divergence in four sympatric southern African decapod crustaceans whose ranges span the boundary between the cool-temperate west coast (south-eastern Atlantic) and the warm-temperate south coast (south-western Indian Ocean) near the southern tip of the African continent. Using genome-wide data, we found that all four species comprise distinct west coast and south coast ecotypes, with molecular dating suggesting divergence during the Pleistocene. Transcriptomic data from the hepatopancreas of twelve specimens of one of these species, the mudprawn Upogebia africana, which were exposed to either 10 °C or 20 °C, showed a clear difference in gene expression profiles between the west- and south coast ecotypes. This difference was particularly clear at 10 °C, where individuals from the south coast experienced a 'transcriptomic shock'. This low temperature is more typical of the west coast during upwelling events, and the physiological stress experienced by the south coast ecotype under such conditions may explain its absence from that coastline. Our results shed new light on the processes involved in driving genomic divergence and incipient speciation along coastlines with porous dispersal barriers., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Knowledge about the demographic histories of natural populations helps to evaluate their conservation status, and potential impacts of natural and anthropogenic pressures. In particular, estimates of effective population size obtained through molecular data can provide useful information to guide management decisions for vulnerable populations. The spotted ragged-tooth shark, Carcharias taurus (also known as the sandtiger or grey nurse shark), is widely distributed in warm-temperate and subtropical waters, but has suffered severe population declines across much of its range as a result of overexploitation. Here, we used multilocus genotype data to investigate the demographic history of the South African C. taurus population. Using approximate Bayesian computation and likelihood-based importance sampling, we found that the population underwent a historical range expansion that may have been linked to climatic changes during the late Pleistocene. There was no evidence for a recent anthropogenic decline. Together with census data suggesting a stable population, these results support the idea that fishing pressure and other threats have so far not been detrimental to the local C. taurus population. The results reported here indicate that South Africa could possibly harbour the last remaining, relatively pristine population of this widespread but vulnerable top predator.

The 'Abundant-Centre Hypothesis' is a well-established but controversial hypothesis stating that the abundance of a species is highest at the centre of its range and decreases towards the edges, where conditions are unfavourable. As genetic diversity depends on population size, edge populations are expected to show lower intra-population genetic diversity than core populations, while showing high inter-population genetic divergence. Here, the genetic implications of the Abundant-Centre Hypothesis were tested on two coastal mussels from South Africa that disperse by means of planktonic larvae, the native Perna perna and the invasive Mytilus galloprovincialis. Genetic structure was found within P. perna, which, together with evidence from Lagrangian particle simulations, points to significant reductions in gene flow between sites. Despite this, the expected diversity pattern between centre and edge populations was not found for either species. We conclude that the genetic predictions of the Abundant-Centre Hypothesis are unlikely to be met by high-dispersal species with large population sizes, and may only become evident in species with much lower levels of connectivity.

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.

Background: Ecosystem engineers facilitate habitat formation and enhance biodiversity, but when they become invasive, they present a critical threat to native communities because they can drastically alter the receiving habitat. Management of such species thus needs to be a priority, but the poorly resolved taxonomy of many ecosystem engineers represents a major obstacle to correctly identifying them as being either native or introduced. We address this dilemma by studying the sea squirt Pyura stolonifera, an important ecosystem engineer that dominates coastal communities particularly in the southern hemisphere. Using DNA sequence data from four independently evolving loci, we aimed to determine levels of cryptic diversity, the invasive or native status of each regional population, and the most appropriate sampling design for identifying the geographic ranges of each evolutionary unit., Results: Extensive sampling in Africa, Australasia and South America revealed the existence of "nested" levels of cryptic diversity, in which at least five distinct species can be further subdivided into smaller-scale genetic lineages. The ranges of several evolutionary units are limited by well-documented biogeographic disjunctions. Evidence for both cryptic native diversity and the existence of invasive populations allows us to considerably refine our view of the native versus introduced status of the evolutionary units within Pyura stolonifera in the different coastal communities they dominate., Conclusions: This study illustrates the degree of taxonomic complexity that can exist within widespread species for which there is little taxonomic expertise, and it highlights the challenges involved in distinguishing between indigenous and introduced populations. The fact that multiple genetic lineages can be native to a single geographic region indicates that it is imperative to obtain samples from as many different habitat types and biotic zones as possible when attempting to identify the source region of a putative invader. "Nested" cryptic diversity, and the difficulties in correctly identifying invasive species that arise from it, represent a major challenge for managing biodiversity.