NewtCap : An Efficient Target Capture Approach to Boost Genomic Studies in Salamandridae (True Salamanders and Newts)
Ecology and Evolution, vol. 15, pp. e71835
Abstract
ABSTRACT Salamanders have large and complex genomes, hampering whole genome sequencing. However, reduced representation sequencing provides a feasible alternative to obtain genome‐wide data. We present NewtCap: a sequence capture bait set that targets c . 7 k coding regions across the genomes of all true salamanders and newts (the family Salamandridae, also known as “salamandrids”). We test the efficacy of NewtCap, originally designed for the Eurasian Triturus newts, in 30 species, belonging to 17 different genera that cover all main Salamandridae lineages. We also test NewtCap in two other salamander families. We discover that NewtCap performs well across all Salamandridae lineages (but not in the salamander families Ambystomatidae and Hynobiidae). As expected, the amount of genetic divergence from the genus Triturus correlates negatively to capture efficacy and mapping success. However, this does not impede our downstream analyses. We showcase the potential of NewtCap in the contexts of; (1) phylogenomics, by reconstructing the phylogeny of Salamandridae, (2) phylogeography, by sequencing the four closely related species comprising the genus Taricha , (3) hybrid zone analysis, by genotyping two Lissotriton species and different classes of interspecific hybrids, and (4) conservation genetics, by comparing Triturus ivanbureschi samples from several wild populations and one captive‐bred population. Overall, NewtCap has the potential to boost straightforward, reproducible, and affordable genomic studies, tackling both fundamental and applied research questions across salamandrids.
Authors 7
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Manon Chantal de Visser corresponding Aachen Faculty of Science Institute of Biology Leiden Leiden University Leiden the Netherlands Understanding Evolution Naturalis Biodiversity Center Leiden the Netherlands
Leiden University · Naturalis Biodiversity Center
Affiliation as printed
Blijdorp Conservation & Science Center, Royal Rotterdam Zoological & Botanical Gardens Rotterdam the Netherlands
Faculty of Science, Institute of Biology Leiden Leiden University Leiden the Netherlands
Understanding Evolution Naturalis Biodiversity Center Leiden the Netherlands
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James France Aachen Faculty of Science Institute of Biology Leiden Leiden University Leiden the Netherlands Understanding Evolution Naturalis Biodiversity Center Leiden the Netherlands
Leiden University · Naturalis Biodiversity Center
Affiliation as printed
Faculty of Science, Institute of Biology Leiden Leiden University Leiden the Netherlands
Understanding Evolution Naturalis Biodiversity Center Leiden the Netherlands
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University of California, Los Angeles
Affiliation as printed
Department of Ecology and Evolutionary Biology University of California, Los Angeles Los Angeles California USA
La Kretz Center for California Conservation Science Institute of the Environment and Sustainability, University of California, Los Angeles Los Angeles California USA
Nutcracker Therapeutics Emeryville California USA
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University of California, Davis · University of California, Los Angeles
Affiliation as printed
Department of Ecology and Evolutionary Biology University of California, Los Angeles Los Angeles California USA
Department of Wildlife, Fish, and Conservation Biology University of California Davis California USA
La Kretz Center for California Conservation Science Institute of the Environment and Sustainability, University of California, Los Angeles Los Angeles California USA
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Anagnostis Theodoropoulos Aachen Faculty of Science Institute of Biology Leiden Leiden University Leiden the Netherlands Understanding Evolution Naturalis Biodiversity Center Leiden the Netherlands
Leiden University · Naturalis Biodiversity Center
Affiliation as printed
Faculty of Science, Institute of Biology Leiden Leiden University Leiden the Netherlands
Understanding Evolution Naturalis Biodiversity Center Leiden the Netherlands
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University of California, Los Angeles
Affiliation as printed
Department of Ecology and Evolutionary Biology University of California, Los Angeles Los Angeles California USA
La Kretz Center for California Conservation Science Institute of the Environment and Sustainability, University of California, Los Angeles Los Angeles California USA
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Ben Wielstra Aachen Faculty of Science Institute of Biology Leiden Leiden University Leiden the Netherlands Understanding Evolution Naturalis Biodiversity Center Leiden the Netherlands
Leiden University · Naturalis Biodiversity Center
Affiliation as printed
Faculty of Science, Institute of Biology Leiden Leiden University Leiden the Netherlands
Understanding Evolution Naturalis Biodiversity Center Leiden the Netherlands
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