Reconstruction of the complete mitogenomes of predator and prey from a faecal metagenomic dataset.

The application of faecal DNA in genetic studies of wild populations minimises disturbances to their normal behaviours and body integrity. Here, I present an analysis of a metagenomic dataset generated from the faecal DNA of several specimens of the estuarine pipefish, Syngnathus watermeyeri, to simultaneously assemble the mitogenomes of the predator and its main prey species, the copepod Pseudodiaptomus hessei. The mitogenomes of the pipefish and the copepod were successfully reconstructed using a combination of short seed extension and denovo metagenomic assembly. Nucleotide blast searches of the circular contigs, mitogenome annotations, and Bayesian phylogenetic analyses confirm the completeness and correct taxonomic placements of the two mitogenomes. In addition, heteroplasmy detection and Pool-Seq variant calling quantified the level of genetic diversity in the sequences that formed these assemblies. These can be used as a first step to non-invasively survey genetic diversity in these populations.

The complete mitogenome dataset of the Critically Endangered estuarine pipefish, Syngnathus watermeyeri.

The Critically Endangered South African estuarine pipefish, Syngnathus watermeyeri, is one of the rarest teleost fish on the planet. In this analysed dataset, the complete mitochondrial genome of this species was assembled, annotated, and described. In addition, its evolutionary history was reconstructed in a Maximum Likelihood and a Bayesian framework. A circular mitochondrial contig 16 449 bp in length was assembled. A total of 13 protein-coding genes, 22 tRNAs and two rRNAs were annotated. The mitochondrial phylogenetic analysis showed that S. watermeyeri diverged from its widely distributed southern African sister species S. temminckii approximately 1.5 million years ago, and the ancestor of these two southern Afican pipefish species diverged from a clade of northern hemisphere pipefishes comprising S. acus, S. rostellatus, and S. typhle approximately 5.3 million years ago. The dataset presented here serves as the first step in understanding the evolutionary history of Africa's rarest pipefish.

The complete mitochondrial genome of Octopus vulgaris.

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.

Mitogenome selection in the evolution of key ecological strategies in the ancient hexapod class Collembola.

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.

The sardine run in southeastern Africa is a mass migration into an ecological trap.

The KwaZulu-Natal sardine run, popularly known as the "greatest shoal on Earth," is a mass migration of South African sardines from their temperate core range into the subtropical Indian Ocean. It has been suggested that this represents the spawning migration of a distinct subtropical stock. Using genomic and transcriptomic data from sardines collected around the South African coast, we identified two stocks, one cool temperate (Atlantic) and the other warm temperate (Indian Ocean). Unexpectedly, we found that sardines participating in the sardine run are primarily of Atlantic origin and thus prefer colder water. These sardines separate from the warm-temperate stock and move into temporarily favorable Indian Ocean habitat during brief cold-water upwelling periods. Once the upwelling ends, they find themselves trapped in physiologically challenging subtropical habitat and subject to intense predation pressure. This makes the sardine run a rare example of a mass migration that has no apparent fitness benefits.

MORPHOLOGICAL AND MOLECULAR CHARACTERIZATION OF THE PLAGUE VECTOR XENOPSYLLA BRASILIENSIS.

Members of the flea family Pulicidae have been the focus of many studies due to their significance as diseases vectors of medical and veterinary importance and their cosmopolitan distribution. They often exhibit variation in morphological features that can make correct species identification and management challenging. This may also apply to Xenopsylla brasiliensis (Baker, 1904), an important plague vector. In the current study, we aimed to provide genetic tools for reliable species identification using a DNA barcoding approach. A total of 73 flea specimens was collected from a native host (Namaqua rock mouse, Micaelamys namaquensis) in South Africa and identified morphologically. In addition, we took measurements of 7 morphological characteristics. Subsequently, we successfully generated barcodes of the mitochondrial cytochrome c oxidase subunit I (COI) gene for X. brasiliensis. We validated this approach by comparing our data to COI sequences from Rwandan X. brasiliensis. While sequences from both regions suggested a close relationship between the 2 X. brasiliensis populations, both haplotype and nucleotide diversity were substantially larger for the South African specimens. This may be attributed to human-assisted spread, differences in habitat, and/or host species sampled and merits further study in the future.

Transcriptomic Diversity in the Livers of South African Sardines Participating in the Annual Sardine Run.

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 transcriptome from six individuals that participated in the 2019 sardine run demonstrated heterogeneous levels of variation. Data presented in the current study provide new insights into the complex function of the liver transcriptome in South African sardines.

The complete mitogenome of Leptestheria brevirostris Barnard, 1924, a rock pool clam shrimp (Branchiopoda: Spinicaudata) from Central District, Botswana.

Spinicaudatan clam shrimp are a widespread and diverse group of branchiopod crustaceans, yet few mitochondrial genomes have been published for this taxonomic group. Here, we present the mitogenome of Leptestheria brevirostris from a rock pool ecosystem in Botswana. Massively parallel sequencing of a single specimen facilitated the reconstruction of the species' 15,579 bp circularized mitogenome. The reconstructed phylogenetic tree confirms that L. brevirostris forms a monophyletic group with other diplostracan branchiopods, and that these are the sister taxon to Notostraca. The mitogenome reconstructed here is the first to be reported from a leptestherid clam shrimp.

Genomic divergence and differential gene expression between crustacean ecotypes across a marine thermal gradient.

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.

The complete mitogenome of the fairy shrimp Streptocephalus cafer (Lovén, 1847) (Crustacea: Branchiopoda: Anostraca) from an ephemeral pond in Botswana, southern Africa.

Fairy shrimps (Anostraca) constitute an important component of seasonally aquatic habitats, but few complete mitochondrial genomes have been published for this group. Here, we report the mitogenome of a common southern African species, Streptocephalus cafer, from Botswana (accession number: MN720104). Low-coverage shotgun sequencing recovered two contigs 15653 bp and 1347 bp in length that are separated by a repetitive region of unknown length within the non-coding control region. The mitogenome's GC content is 31.80%. Phylogenetic analysis using protein-coding genes confirms the sister taxon relationship of S. cafer with the only other congener whose mitogenome has been reconstructed to date, the Asian S. sirindhornae.

The complete mitogenome of an undescribed clam shrimp of the genus Gondwanalimnadia (Branchiopoda: Spinicaudata), from a temporary wetland in Central District, Botswana.

Clam shrimps (Spinicaudata) are a widespread and diverse crustacean group that frequent temporary aquatic habitats, but few complete mitochondrial genomes have been published for this group. Here, we report the mitogenome of an undescribed Gondwanalimnadia species from Botswana. Raw sequences were assembled into a single circular genome with a total length of 15,663 bp. Thirteen protein-coding genes, 22 tRNAs, and 2 rRNAs were identified using the MITOS pipeline. The mitogenome's GC content is 33.52%. Phylogenetic analysis using protein-coding genes confirmed that Gondwanalimnadia sp. is closely related to another member of the Limnadiidae, Limnadia lenticularis.

Environmental DNA Metabarcoding as a Means of Estimating Species Diversity in an Urban Aquatic Ecosystem.

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.

A globally threatened shark, Carcharias taurus, shows no population decline in South Africa.

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.

De Novo Transcriptome Assembly and Annotation of Liver and Brain Tissues of Common Brushtail Possums (Trichosurus vulpecula) in New Zealand: Transcriptome Diversity after Decades of Population Control.

The common brushtail possum (Trichosurus vulpecula), introduced from Australia in the mid-nineteenth century, is an invasive species in New Zealand where it is widespread and forms the largest self-sustained reservoir of bovine tuberculosis (Mycobacterium bovis) among wild populations. 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. 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 respectively. Functional annotation and polymorphism assignment of the assembled transcripts demonstrated a considerable level of variation in the core metabolic pathways that represent potential targets for selection pressure exerted by chemical toxicants. This study suggests that the brushtail possum population in New Zealand harbours considerable variation in metabolic pathways that could potentially promote the development of tolerance against chemical toxicants.

Thermal selection as a driver of marine ecological speciation.

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.

Mitochondrial DNA is unsuitable to test for isolation by distance.

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 the lack of IBD in the four species studied, and support for IBD was particularly strong for the SNP data. We conclude that mtDNA sequence data are often not suitable to test for IBD, and can be misleading about species' true dispersal potential. The observed failure of mtDNA to reliably detect IBD, in addition to being a single-locus marker, is likely a result of a selection-driven reduction in genetic diversity obscuring spatial genetic differentiation.

Mitogenomics data reveal effective population size, historical bottlenecks, and the effects of hunting on New Zealand fur seals (Arctocephalus forsteri).

The New Zealand fur seal (Arctocephalus forsteri) passed through a population bottleneck due to commercial sealing during the eighteenth to nineteenth centuries. To facilitate future management options, we reconstructed the demographic history of New Zealand fur seals in a Bayesian framework using maternally inherited, mitochondrial DNA sequences. Mitogenomic data suggested two separate clades (most recent common ancestor 5000 years ago) of New Zealand fur seals that survived large-scale human harvest. Mitochondrial haplotype diversity was high, with 45 singletons identified from 46 individuals although mean nucleotide diversity was low (0.012 ± 0.0061). Variation was not constrained geographically. Analyses of mitogenomes support the hypothesis for a population bottleneck approximately 35 generations ago, which coincides with the peak of commercial sealing. Mitogenomic data are consistent with a pre-human effective population size of approximately 30,000 that first declined to around 10,000 (due to the impact of Polynesian colonization, particularly in the first 100 years of their arrival into New Zealand), and then to 100-200 breeding individuals during peak of commercial sealing.

Complete mitochondrial genome of the stoat (Mustela erminea) and New Zealand fur seal (Arctocephalus forsteri) and their significance for mammalian phylogeny.

The complete mitochondrial genome of three mustelid species, stoats (Mustela erminea), weasels (Mustela nivalis) and ferrets (Mustela furo), and the New Zealand fur seal (Arctocephalus forsteri) were sequenced using direct mitochondrial DNA extraction and overlapping long PCRs. The usual 37 mammalian mitochondrial genes (13 protein coding genes, 22 t-RNA and 2 r-RNA) were identified in all four mitogenomes. The divergence of stoats from other members of the sub-family Mustelinae was dated 4.5 million years ago. The mitogenomic data were consistent with a bear-like origin of seals.