Shannon Corrigan

Capturing protein-coding genes across highly divergent species

DNA hybridization capture combined with next generation sequencing can be used to determine the sequences of hundreds of target genes across hundreds of individuals in a single experiment. However, the approach has thus far only been successfully applied to capture targets that are highly similar in sequence to the bait molecules. Here we introduce modifications that extend the reach of the method to allow efficient capture of highly divergent homologous target sequences using a single set of baits. These modifications have important implications for comparative biology.

DNA capture reveals transoceanic gene flow in endangered river sharks

Significance The river sharks of the genus Glyphis, widely feared as man-eaters throughout India, remain very poorly known to science. The group constitutes five described species, all of which are considered highly endangered and restricted to freshwater systems in Australasia and Southeast Asia. DNA sequence data derived from 19th-century dried museum material augmented with contemporary samples indicates that only three of the five currently described species are valid; that there is a genetically distinct, but as-yet-undescribed, species recorded in Bangladesh and Sarawak in Malaysian Borneo; and that these iconic and mysterious sharks are not restricted to freshwater at all but rather appear to be adapted to both marine and freshwater habitats. For over a hundred years, the “river sharks” of the genus Glyphis were only known from the type specimens of species that had been collected in the 19th century. They were widely considered extinct until populations of Glyphis-like sharks were rediscovered in remote regions of Borneo and Northern Australia at the end of the 20th century. However, the genetic affinities between the newly discovered Glyphis-like populations and the poorly preserved, original museum-type specimens have never been established. Here, we present the first (to our knowledge) fully resolved, complete phylogeny of Glyphis that includes both archival-type specimens and modern material. We used a sensitive DNA hybridization capture method to obtain complete mitochondrial genomes from all of our samples and show that three of the five described river shark species are probably conspecific and widely distributed in Southeast Asia. Furthermore we show that there has been recent gene flow between locations that are separated by large oceanic expanses. Our data strongly suggest marine dispersal in these species, overturning the widely held notion that river sharks are restricted to freshwater. It seems that species in the genus Glyphis are euryhaline with an ecology similar to the bull shark, in which adult individuals live in the ocean while the young grow up in river habitats with reduced predation pressure. Finally, we discovered a previously unidentified species within the genus Glyphis that is deeply divergent from all other lineages, underscoring the current lack of knowledge about the biodiversity and ecology of these mysterious sharks.

Rediscovery of the Threatened River Sharks, Glyphis garricki and G. glyphis, in Papua New Guinea

Recent surveys of the shark and ray catches of artisanal fishers in the Western Province of Papua New Guinea (PNG) resulted in the rediscovery of the threatened river sharks, Glyphis garricki and Glyphis glyphis. These represent the first records of both species in PNG since the 1960s and 1970s and highlight the lack of studies of shark biodiversity in PNG. Two individuals of G. garricki and three individuals of G. glyphis were recorded from coastal marine waters of the Daru region of PNG in October and November 2014. The two G. garricki specimens were small individuals estimated to be 100–105 cm and ~113 cm total length (TL). The three G. glyphis specimens were all mature, one a pregnant female and two adult males. These are the first adults of G. glyphis recorded to date providing a more accurate maximum size for this species, i.e. ~260 cm TL. A single pup which was released from the pregnant female G. glyphis, was estimated to be ~65 cm TL. Anecdotal information from the fishers of pregnant females of G. glyphis containing 6 or 7 pups provides the first estimate of litter size for this species. The jaws of the pregnant female G. glyphis were retained and a detailed description of the dentition is provided, since adult dentition has not been previously documented for this species. Genetic analyses confirmed the two species cluster well within samples from these species collected in northern Australia.

Population genomics of C. melanopterus using target gene capture data: demographic inferences and conservation perspectives

Population genetics studies on non-model organisms typically involve sampling few markers from multiple individuals. Next-generation sequencing approaches open up the possibility of sampling many more markers from fewer individuals to address the same questions. Here, we applied a target gene capture method to deep sequence ~1000 independent autosomal regions of a non-model organism, the blacktip reef shark (Carcharhinus melanopterus). We devised a sampling scheme based on the predictions of theoretical studies of metapopulations to show that sampling few individuals, but many loci, can be extremely informative to reconstruct the evolutionary history of species. We collected data from a single deme (SID) from Northern Australia and from a scattered sampling representing various locations throughout the Indian Ocean (SCD). We explored the genealogical signature of population dynamics detected from both sampling schemes using an ABC algorithm. We then contrasted these results with those obtained by fitting the data to a non-equilibrium finite island model. Both approaches supported an Nm value ~40, consistent with philopatry in this species. Finally, we demonstrate through simulation that metapopulations exhibit greater resilience to recent changes in effective size compared to unstructured populations. We propose an empirical approach to detect recent bottlenecks based on our sampling scheme.

Historical introgression drives pervasive mitochondrial admixture between two species of pelagic sharks

We use a genomic sampling of both nuclear and mitochondrial DNA markers to examine a pattern of genetic admixture between Carcharhinus galapagensis (Galapagos sharks) and Carcharhinus obscurus (dusky sharks), two well-known and closely related sharks that have been recognized as valid species for more than 100years. We describe widespread mitochondrial-nuclear discordance in which these species are readily distinguishable based on 2152 nuclear single nucleotide polymorphisms from 910 independent autosomal regions, but show pervasive mitochondrial admixture. The species are superficially morphologically cryptic as adults but show marked differences in internal anatomy, as well as niche separation. There was no indication of ongoing hybridization between the species. We conclude that the observed mitochondrial-nuclear discordance is likely due to historical mitochondrial introgression following a range expansion.

Redescription of the eagle rays Myliobatis hamlyni Ogilby, 1911 and M. tobijei Bleeker, 1854 (Myliobatiformes: Myliobatidae) from the East Indo-West Pacific

The eagle rays Myliobatis hamlyni Ogilby, 1911 and Myliobatis tobijei Bleeker, 1854 are redescribed based on museum specimens and new material from Australia, Indonesia, the Philippines, Taiwan and Japan. These two species are closely related to Myliobatis aquila (L.) from the eastern Atlantic and can be distinguished from each other by a combination of their coloration, meristics, depth preferences and subtle morphometric characters. Myliobatis hamlyni was previously considered to be an Australian endemic, but its distribution is herein extended northward to Taiwan and Okinawa. Myliobatis tobijei was considered to occur southwards from Japan to Indonesia, but its distribution is herein restricted to the western North Pacific, primarily Japan.

Rhinobatos whitei, a new shovelnose ray (Batoidea: Rhinobatidae) from the Philippine Archipelago

A new shovelnose ray, Rhinobatos whitei sp. nov., is described from material collected at fish markets of the southern Philippines. This ray was first formally indentified as an undescribed species more than a decade ago as part of a WWF funded survey of sharks and rays of the Philippines. It was considered to be most closely related to another shovelnose ray found nearby in the western North Pacific, R. schlegelii, but differs from that species in body shape and aspects of coloration, meristics and morphometry. It differs from all other shovelnose rays of the region in its NADH2 sequence, clustering together with an Indonesian species R. jimbaranensis, and another undescribed species from Borneo.

A description of the mitogenome of the Endangered Taiwanese angelshark, Squatina formosa.

Abstract Squatinid sharks are among the most threatened of cartilaginous fishes. Here we describe the complete mitochondrial genome sequence (16,690 bp) of the Endangered Taiwanese angelshark, Squatina formosa. It has 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region in the typical vertebrate arrangement.