@article{LiCorriganYangetal.2015,
  author    = {Li, Chenhong and Corrigan, Shannon and Yang, Lei and Straube, Nicolas and Harris, Mark and Hofreiter, Michael and White, William T. and Naylor, Gavin J. P.},
  title     = {DNA capture reveals transoceanic gene flow in endangered river sharks},
  series = {Proceedings of the National Academy of Sciences of the United States of America},
  volume    = {112},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  number    = {43},
  publisher = {National Acad. of Sciences},
  address   = {Washington},
  issn      = {0027-8424},
  doi       = {10.1073/pnas.1508735112},
  pages     = {13302 -- 13307},
  year      = {2015},
  abstract  = {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.},
  language  = {en}
}
@article{StraubePreickNayloretal.2021,
  author    = {Straube, Nicolas and Preick, Michaela and Naylor, Gavin J. P. and Hofreiter, Michael},
  title     = {Mitochondrial DNA sequencing of a wet-collection syntype demonstrates the importance of type material as genetic resource for lantern shark taxonomy (Chondrichthyes: Etmopteridae)},
  series = {Royal Society Open Science},
  volume    = {8},
  journal   = {Royal Society Open Science},
  number    = {9},
  publisher = {Royal Society},
  address   = {London},
  issn      = {2054-5703},
  doi       = {10.1098/rsos.210474},
  pages     = {13},
  year      = {2021},
  abstract  = {After initial detection of target archival DNA of a 116-year-old syntype specimen of the smooth lantern shark, Etmopterus pusillus, in a single-stranded DNA library, we shotgun-sequenced additional 9 million reads from this same DNA library. Sequencing reads were used for extracting mitochondrial sequence information for analyses of mitochondrial DNA characteristics and reconstruction of the mitochondrial genome. The archival DNA is highly fragmented. A total of 4599 mitochondrial reads were available for the genome reconstruction using an iterative mapping approach. The resulting genome sequence has 12 times coverage and a length of 16 741 bp. All 37 vertebrate mitochondrial loci plus the control region were identified and annotated. The mitochondrial NADH2 gene was subsequently used to place the syntype haplotype in a network comprising multiple E. pusillus samples from various distant localities as well as sequences from a morphological similar species, the shortfin smooth lantern shark Etmopterus joungi. Results confirm the almost global distribution of E. pusillus and suggest E. joungi to be a junior synonym of E. pusillus. As mitochondrial DNA often represents the only available reference information in non-model organisms, this study illustrates the importance of mitochondrial DNA from an aged, wet collection type specimen for taxonomy.},
  language  = {en}
}
@article{AgneNaylorPreicketal.2022,
  author    = {Agne, Stefanie and Naylor, Gavin J. P. and Preick, Michaela and Yang, Lei and Thiel, Ralf and Weigmann, Simon and Paijmans, Johanna L. A. and Barlow, Axel and Hofreiter, Michael and Straube, Nicolas},
  title     = {Taxonomic identification of two poorly known lantern shark species based on mitochondrial DNA from wet-collection paratypes},
  series = {Frontiers in Ecology and Evolution},
  volume    = {10},
  journal   = {Frontiers in Ecology and Evolution},
  publisher = {Frontiers Media},
  address   = {Lausanne},
  issn      = {2296-701X},
  doi       = {10.3389/fevo.2022.910009},
  pages     = {10},
  year      = {2022},
  abstract  = {Etmopteridae (lantern sharks) is the most species-rich family of sharks, comprising more than 50 species. Many species are described from few individuals, and re-collection of specimens is often hindered by the remoteness of their sampling sites. For taxonomic studies, comparative morphological analysis of type specimens housed in natural history collections has been the main source of evidence. In contrast, DNA sequence information has rarely been used. Most lantern shark collection specimens, including the types, were formalin fixed before long-term storage in ethanol solutions. The DNA damage caused by both fixation and preservation of specimens has excluded these specimens from DNA sequence-based phylogenetic analyses so far. However, recent advances in the field of ancient DNA have allowed recovery of wet-collection specimen DNA sequence data. Here we analyse archival mitochondrial DNA sequences, obtained using ancient DNA approaches, of two wet-collection lantern shark paratype specimens, namely Etmopterus litvinovi and E. pycnolepis, for which the type series represent the only known individuals. Target capture of mitochondrial markers from single-stranded DNA libraries allows for phylogenetic placement of both species. Our results suggest synonymy of E. benchleyi with E. litvinovi but support the species status of E. pycnolepis. This revised taxonomy is helpful for future conservation and management efforts, as our results indicate a larger distribution range of E. litvinovi. This study further demonstrates the importance of wet-collection type specimens as genetic resource for taxonomic research.},
  language  = {en}
}