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A target enrichment bait set for studying relationships among ostariophysan fishes

View ORCID ProfileBrant C. Faircloth, Fernando Alda, Kendra Hoekzema, Michael D. Burns, Claudio Oliveira, James S. Albert, Bruno F. Melo, Luz E. Ochoa, Fábio F. Roxo, Prosanta Chakrabarty, Brian L. Sidlauskas, Michael E. Alfaro
doi: https://doi.org/10.1101/432583
Brant C. Faircloth
1Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
2Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
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  • ORCID record for Brant C. Faircloth
  • For correspondence: brant@faircloth-lab.org
Fernando Alda
2Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
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Kendra Hoekzema
3Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, USA
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Michael D. Burns
3Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, USA
4Department of Biological Sciences, Western Michigan University, Kalamazoo, MI, USA
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Claudio Oliveira
5Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, Brazil
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James S. Albert
6Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, USA
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Bruno F. Melo
5Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, Brazil
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Luz E. Ochoa
5Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, Brazil
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Fábio F. Roxo
7Departamento de Zoologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, Brazil
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Prosanta Chakrabarty
1Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
2Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
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Brian L. Sidlauskas
3Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, USA
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Michael E. Alfaro
8Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
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  • Abstract
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Summary

  1. Target enrichment of conserved nuclear loci has helped reconstruct evolutionary relationships among a wide variety of species. While there are preexisting bait sets to enrich a few hundred loci across all fishes or a thousand loci from acanthomorph fishes, no bait set exists to enrich large numbers (>1000 loci) of ultraconserved nuclear loci from ostariophysans, the second largest actinopterygian superorder.

  2. In this manuscript, we describe how we designed a bait set to enrich 2,708 ultraconserved nuclear loci from ostariophysan fishes by combining an existing genome assembly with low coverage sequence data collected from two ostariophysan lineages.

  3. We perform a series of enrichment experiments using this bait set across the ostariophysan Tree of Life, from the deepest splits among the major groups (>150 MYA) to more recent divergence events that have occured during the last 50 million years.

  4. Our results demonstrate that the bait set we designed is useful for addressing phylogenetic questions from the origin of crown ostariophysans to more recent divergence events, and our in silico results suggest that this bait set may be useful for addressing evolutionary questions in closely related groups of fishes, like Clupeiformes.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted October 02, 2018.
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A target enrichment bait set for studying relationships among ostariophysan fishes
Brant C. Faircloth, Fernando Alda, Kendra Hoekzema, Michael D. Burns, Claudio Oliveira, James S. Albert, Bruno F. Melo, Luz E. Ochoa, Fábio F. Roxo, Prosanta Chakrabarty, Brian L. Sidlauskas, Michael E. Alfaro
bioRxiv 432583; doi: https://doi.org/10.1101/432583
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A target enrichment bait set for studying relationships among ostariophysan fishes
Brant C. Faircloth, Fernando Alda, Kendra Hoekzema, Michael D. Burns, Claudio Oliveira, James S. Albert, Bruno F. Melo, Luz E. Ochoa, Fábio F. Roxo, Prosanta Chakrabarty, Brian L. Sidlauskas, Michael E. Alfaro
bioRxiv 432583; doi: https://doi.org/10.1101/432583

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