An ultraconserved element probe set for velvet worms (Onychophora)

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  • Sato, Shoyo
  • Shahan Derkarabetian
  • Arianna Lord
  • Gonzalo Giribet
Onychophora are cryptic, soil-dwelling invertebrates known for their biogeographic affinities, diversity of reproductive modes, close phylogenetic relationship to arthropods, and peculiar prey capture mechanism. The 216 valid species of Onychophora are grouped into two families – Peripatopsidae and Peripatidae – and apart from a few relationships among major lineages within these two families, a stable phylogenetic backbone for the phylum has yet to be resolved. This has hindered our understanding of onychophoran biogeographic patterns, evolutionary history, and systematics. Neopatida, the Neotropical clade of peripatids, has proved particularly difficult, with recalcitrant nodes and low resolution, potentially due to rapid radiation of the group during the Cretaceous. Previous studies have had to compromise between number of loci and number of taxa due to limitations of Sanger sequencing and phylotranscriptomics, respectively. Additionally, aspects of their genome size and structure have made molecular phylogenetics difficult and data matrices have been affected by missing data. To address these issues, we leveraged recent, published transcriptomes and the first high quality genome for the phylum and designed a high affinity ultraconserved element (UCE) probe set for Onychophora. This new probe set, consisting of ∼ 20,000 probes that target 1,465 loci across both families, has high locus recovery and phylogenetic utility. Phylogenetic analyses recovered the monophyly of major clades of Onychophora and revealed a novel lineage from the Neotropics that challenges our current understanding of onychophoran biogeographic endemicity. This new resource could drastically increase the power of molecular datasets and potentially allow access to genomic scale data from archival museum specimens to further tackle the issues exasperating onychophoran systematics.
OriginalsprogEngelsk
Artikelnummer108115
TidsskriftMolecular Phylogenetics and Evolution
Vol/bind197
Antal sider11
ISSN1055-7903
DOI
StatusUdgivet - 2024

Bibliografisk note

Funding Information:
Adam Baldinger provided collections support at the MCZ. Computations for this project were done on the Cannon cluster, supported by the FAS Division of Science at Harvard University. SEM was conducted at the Center for Nanoscale Systems. For field companionship, we are indebted to Gregory D. Edgecombe, Michele K. Nishiguchi & Y.-Y. Zhen (Australia, 2000); Stephanie Aktipis & Michele K. Nishiguchi (Australia, 2004); Gregory D. Edgecombe (Australia, 2006); Ligia R. Benavides & J\u00EArome Y. Murienne (Gabon, 2009); Savel R. Daniels and Benjamin L. de Bivort (South Africa, 2011); Gustavo Hormiga (Brazil, 2012); Gustavo Hormiga & Abel P\u00E9rez-Gonz\u00E1lez (Chile, 2014); Scott Bartlam & Rosa M. Fern\u00E1ndez (New Zealand, 2014); Savel R. Daniels & Christine D. Palmer (South Africa, 2014); Miquel A. Arnedo, Caitlin M. Baker & Rosa M. Fern\u00E1ndez (New Zealand, 2016); Ligia R. Benavides, Julia G. Cosgrove & Gustavo Hormiga (Trinidad & Tobago, 2017). Additional specimens were provided by numerous colleagues, without whose help, this work would have not been possible: Ligia R. Benavides (Colombia and Ecuador), Michael G. Branstetter (Costa Rica, Guyana), Rebecca Buckman-Young & Julia G. Cosgrove (Puerto Rico), J.E. Cadle (Peru), C.A. Car (Australia), Roberto Carrera Mart\u00EDnez (Puerto Rico), Gerardo Contreras & Griselda Montiel (Mexico), Savel R. Daniels (Australia and South Africa), Luis Espinasa (Ecuador), Jeremy Huff (Dominican Republic), Milan Janda (Papua New Guinea), John T. Longino from the LLAMA project (Mexico), Diego Luna (Colombia), Luke Mahler (Dominican Republic), Georg Mayer (Australia, Chile, and Costa Rica), Igor V. Muratov (Jamaica), J\u00EArome Y. Murienne (French Guiana), J. Ochoa Camara (Colombia), Mandy Read (Australia, E. Realpe (Colombia), Gary Rosenberg (Jamaica), Carlos J. Santos (Puerto Rico), Tedd Shultz, U. Meller & John S. Lapolla (French Guiana), Peter J. Schwendinger (Malaysia), D. Seaborg (Jamaica), Diana Tamariz (Puerto Rico), Ana L. Tourinho (Brazil), Sebasti\u00E1n V\u00E9lez (New Zealand), Hannah Wood (Australia and New Zealand), M. Zumbado & J.F. Corrales (Costa Rica). Editor-in-chief Guillermo Ort\u00ED and two anonymous reviewers provided comments that greatly improved the manuscript. All specimens acquired by the authors for this project were collected under valid permits (New Zealand multiple permits [38002-RES]; Australia [QLD #WITK00845202; WA Permits #OF000190, #CE000648, #SF004565]; Chile [Autorizaci\u00F3n #026/2014]; South Africa [Eastern Cape permits #CRO 108/ 11CR and CRO 109/11CR; KZN #OP 4085/2011; Western Cape Permit #AAA007-00344-0035]; Puerto Rico [#2015-IC-056]; Trinidad & Tobago [Trinidad permit A No. 1176; B No. 000573; Tobago Special Game License without number]. Additional specimens were obtained from Museum loans or from colleagues with additional permits. New sequences are deposited in the Sequence Read Archive (BioProject PRJNA1076361, SRA Accession Numbers SRR28030502\u2013SRR23080567, SRR28385900). Probe file, individual locus statistics, final matrices, and tree files can be found online at Harvard Dataverse (https://doi.org/10.7910/DVN/MTYWIX).

Funding Information:
This work was supported by the National Science Foundation (grant number 2154245) \u201CCollaborative Research: PurSUiT: Understanding the Neotropical Velvet Worms (Onychophora, Peripatidae, Neopatida), a Cretaceous Radiation of Terrestrial Panarthropods\u201D; MCZ Putnam Expedition Grants to Gabon, Puerto Rico, South Africa and Trinidad & Tobago; and National Geographic Society [9043-11] to Brazil. Published by a grant from the Wetmore Colles fund.

Publisher Copyright:
© 2024 The Authors

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