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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

A Target Enrichment Bait Set for Studying Relationships among Ostariophysan Fishes

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Author(s):
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Faircloth, Brant C. [1, 2] ; Alda, Fernando [3] ; Hoekzema, Kendra [4] ; Burns, Michael D. [4, 5] ; Oliveira, Claudio [6] ; Albert, James S. [7] ; Melo, Bruno F. [6] ; Ochoa, Luz E. [6] ; Roxo, Fabio F. [8] ; Chakrabarty, Prosanta [1, 2] ; Sidlauskas, Brian L. [4] ; Alfaro, Michael E. [9]
Total Authors: 12
Affiliation:
[1] Louisiana State Univ, Museum Nat Sci, Baton Rouge, LA 70803 - USA
[2] Louisiana State Univ, Dept Biol Sci, Baton Rouge, LA 70803 - USA
[3] Univ Tennessee, Dept Biol Geol & Environm Sci, Chattanooga, TN 37403 - USA
[4] Oregon State Univ, Dept Fisheries & Wildlife, Corvallis, OR 97331 - USA
[5] Cornell Univ, Cornell Lab Ornithol, Museum Vertebrates, Ithaca, NY 14850 - USA
[6] Univ Estadual Paulista, Inst Biociencias, Dept Morfol, BR-18618689 Botucatu, SP - Brazil
[7] Univ Louisiana Lafayette, Dept Biol, Lafayette, LA 70503 - USA
[8] Univ Estadual Paulista, Inst Biociencias, Dept Zool, Botucatu, SP - Brazil
[9] Univ Calif Los Angeles, Dept Ecol & Evolutionary Biol, Los Angeles, CA 90095 - USA
Total Affiliations: 9
Document type: Journal article
Source: Copeia; v. 108, n. 1, p. 47-60, MAR 2020.
Web of Science Citations: 0
Abstract

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 (>1,000 loci) of ultraconserved nuclear loci from ostariophysans, the second largest actinopterygian superorder. In this study, we describe how we designed a bait set to enrich 2,708 ultracon served nuclear loci from ostariophysan fishes by combining an existing genome assembly with low coverage sequence data collected from two ostariophysan lineages. 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 Ma) to more recent divergence events that have occurred during the last 50 million years. 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. (AU)

FAPESP's process: 16/11313-8 - Phylogeny of the Order Characiformes (Teleostei: Ostariophysi) using ultraconserved elements
Grantee:Bruno Francelino de Melo
Support type: Scholarships in Brazil - Post-Doctorate
FAPESP's process: 14/26508-3 - Phylogeny of the hyperdiverse order Characiformes (Teleostei: Ostariophysi) using ultraconserved elements
Grantee:Claudio de Oliveira
Support type: Research Projects - Thematic Grants
FAPESP's process: 14/06853-8 - Phylogenetic analysis of the relationships and diversification patterns of Trichomycteridae (Teleostei, Siluriformes) using DNA sequences
Grantee:Luz Eneida Ochoa Orrego
Support type: Scholarships in Brazil - Doctorate
FAPESP's process: 14/05051-5 - Harnessing phylogenomic comparative methods to understand the diversification of fishes of the superfamily Loricarioidea
Grantee:Fábio Fernandes Roxo
Support type: Scholarships in Brazil - Post-Doctorate