Implementing Large Genomic Single Nucleotide Polymorphism Data Sets in Phylogenetic Network Reconstructions : A Case Study of Particularly Rapid Radiations of Cichlid Fish

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2020
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European Union (EU): 293700
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Comparative genomics of parallel in repeated adaptive radiations (GenAdap)
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Systematic Biology. Oxford University Press (OUP). 2020, 69(5), pp. 848-862. ISSN 1063-5157. eISSN 1076-836X. Available under: doi: 10.1093/sysbio/syaa005
Zusammenfassung

The Midas cichlids of the Amphilophus citrinellus spp. species complex from Nicaragua (13 species) are an extraordinary example of adaptive and rapid radiation (< 24,000 years old). These cichlids are a very challenging group to infer its evolutionary history in phylogenetic analyses, due to the apparent prevalence of incomplete lineage sorting (ILS), as well as past and current gene flow. Assuming solely a vertical transfer of genetic material from an ancestral lineage to new lineages is not appropriate in many cases of genes transferred horizontally in nature. Recently developed methods to infer phylogenetic networks under such circumstances might be able to circumvent these problems. These models accommodate not just ILS, but also gene flow, under the multispecies network coalescent model (MSNC), processes that are at work in young, hybridizing, and/or rapidly diversifying lineages. There are currently only a few programs available that implement MSNC for estimating phylogenetic networks. Here, we present a novel way to incorporate single nucleotide polymorphism (SNP) data into the currently available PhyloNetworks program. Based on simulations, we demonstrate that SNPs can provide enough power to recover the true phylogenetic network. We also show that it can accurately infer the true network more often than other similar SNP-based programs (PhyloNet and HyDe). Moreover, our approach results in a faster algorithm compared to the original pipeline in PhyloNetworks, without losing power. We also applied our new approach to infer the phylogenetic network of Midas cichlid radiation. We implemented the most comprehensive genomic dataset to date (RADseq dataset of 679 individuals and >37K SNPs from 19 ingroup lineages) and present estimated phylogenetic networks for this extremely young and fast-evolving radiation of cichlid fish. We demonstrate that the MSNC is more appropriate than the multispecies coalescent alone for the analysis of this rapid radiation.

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570 Biowissenschaften, Biologie
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Phylogenetic networks, multispecies network coalescent, phylogenomics, SNPs, genomics, RADseq
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ISO 690OLAVE, Melisa, Axel MEYER, 2020. Implementing Large Genomic Single Nucleotide Polymorphism Data Sets in Phylogenetic Network Reconstructions : A Case Study of Particularly Rapid Radiations of Cichlid Fish. In: Systematic Biology. Oxford University Press (OUP). 2020, 69(5), pp. 848-862. ISSN 1063-5157. eISSN 1076-836X. Available under: doi: 10.1093/sysbio/syaa005
BibTex
@article{Olave2020-09-01Imple-48603,
  year={2020},
  doi={10.1093/sysbio/syaa005},
  title={Implementing Large Genomic Single Nucleotide Polymorphism Data Sets in Phylogenetic Network Reconstructions : A Case Study of Particularly Rapid Radiations of Cichlid Fish},
  number={5},
  volume={69},
  issn={1063-5157},
  journal={Systematic Biology},
  pages={848--862},
  author={Olave, Melisa and Meyer, Axel}
}
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