Capturing Protein-Coding Genes Across Highly Divergent Species

Li, Chenhong; Hofreiter, Michael; Straube, Nicolas; Corrigan, Shannon; Naylor, Gavin J. P.

doi:10.2144/000114039

Cited by 191 publications

(257 citation statements)

References 29 publications

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“…In addition, a subset of the samples was also successfully subjected to a nuclear gene capture protocol (13). The inferred relationships among the four major clades based on a concatenated maximum-likelihood analysis of 100 single-copy nuclear genes was identical to the inference derived from the mitochondrial data (SI Appendix, Fig.…”

Section: Resultsmentioning

confidence: 78%

“…We prepared the target libraries following the methods of Li et al (13). For the subsequent target capture, we used "homemade baits," see SI Appendix, Detailed Protocol for Target Capture.…”

Section: Methodsmentioning

confidence: 99%

“…The mitochondrial sequence of one G. fowlerae (GN1363) specimen was also determined using PCR with overlapping primers and Sanger sequencing following the method of Aschliman et al (34) to validate the accuracy of sequence collected by our target capture method. To compare with the mitochondrial data, we also collected sequences of nuclear protein-coding genes for representatives of the major Glyphis lineages following the targeted nuclear gene capture protocol of Li et al (13).…”

Section: Methodsmentioning

confidence: 99%

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DNA capture reveals transoceanic gene flow in endangered river sharks

Corrigan

Yang

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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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.freshwater sharks | DNA | museum specimens

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Section: Resultsmentioning

confidence: 78%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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DNA capture reveals transoceanic gene flow in endangered river sharks

Corrigan

Yang

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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“…Genomic DNA (0.5-3 μg per sample) was sheared to c. 500 bp using acoustic ultrasonication on a Covaris M220 Focused-ultrasonicator (Covaris, Inc., Massachusetts, USA) to form a target library for each specimen. Illumina sequencing libraries (Meyer & Kircher, 2010) were then prepared using the 'with-bead' method (Fisher et al, 2011), following Li et al (2013). Two custom biotinylated RNA bait libraries (MYbaits MYcroarray, Ann Arbor, MI, USA) were used in two separate DNA hybridization experiments per sample.…”

Section: Taxon Samplingmentioning

confidence: 99%

Phylogeny of the manta and devilrays (Chondrichthyes: mobulidae), with an updated taxonomic arrangement for the family

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Corrigan

Yang

et al. 2017

Zoological Journal of the Linnean Society

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DNA sequence data from mitochondrial genomes and c. 1000 nuclear exons were analysed for a complete taxon sampling of manta and devilrays (Mobulidae) to estimate a current molecular phylogeny for the family. The resulting inferences were combined with morphological information to adopt an integrated approach to resolving the taxonomic arrangement of the family. The members of the genus Manta were found to consistently nest within the Mobula species and consequently the genus Manta is placed into the synonymy of Mobula. Mobula eregoodootenkee, M. japanica and M. rochebrunei were each found to be junior synonyms of M. kuhlii, M. mobular and M. hypostoma, respectively. The mitochondrial and nuclear tree topologies were in agreement except for the placement of M. tarapacana which was basal to all other mobulids in the nuclear exon analysis, but as the sister group to the M. alfredi-M. birostris-M. mobular clade in the mitochondrial genome analysis. Results from this study are used to a revise the taxonomy for the family Mobulidae. A single genus is now recognized (where there were previously two) and eight nominal species (where there were previously 11).

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“…We sampled 19 species and 48 individuals ( Table 1, the DNA capture kit (MyBaits), which is able to support differences larger than 5% between 181 probe sequences and target sequences (e.g., Li et al, 2013). The complete sequence of the 182 chloroplast genome of Phalaenopsis aphrodite subsp.…”

Section: Sampling and Dna Extraction 152mentioning

confidence: 99%