Historical specimens and the limits of subspecies phylogenomics in the New World quails (Odontophoridae)
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As phylogenomics focuses on comprehensive taxon sampling at the species and population/subspecies levels, incorporating genomic data from historical specimens has become increasingly common. While historical samples can fill critical gaps in our understanding of the evolutionary history of diverse groups, they also introduce additional sources of phylogenomic uncertainty, making it difficult to discern novel evolutionary relationships from artifacts caused by sample quality issues. These problems highlight the need for improved strategies to disentangle artifactual patterns from true biological signal as historical specimens become more prevalent in phylogenomic datasets. Here, we tested the limits of historical specimen-driven phylogenomics to resolve subspecies-level relationships within a highly polytypic family, the New World quails (Odontophoridae), using thousands of ultraconserved elements (UCEs). We found that relationships at and above the species-level were well-resolved and highly supported across all analyses, with the exception of discordant relationships within the two most polytypic genera which included many historical specimens. We examined the causes of discordance and found that inferring phylogenies from subsets of taxa resolved the disagreements, suggesting that analyzing subclades can help remove artifactual causes of discordance in datasets that include historical samples. At the subspecies-level, we found well-resolved geographic structure within the two most polytypic genera, including the most polytypic species in this family, Northern Bobwhites (Colinus virginianus), demonstrating that variable sites within UCEs are capable of resolving phylogenetic structure below the species level. Our results highlight the importance of complete taxonomic sampling for resolving relationships among polytypic species, often through the inclusion of historical specimens, and we propose an integrative strategy for understanding and addressing the uncertainty that historical samples sometimes introduce to phylogenetic analyses.
| Originalsprog | Engelsk |
|---|---|
| Artikelnummer | 107559 |
| Tidsskrift | Molecular Phylogenetics and Evolution |
| Vol/bind | 175 |
| Antal sider | 14 |
| ISSN | 1055-7903 |
| DOI | |
| Status | Udgivet - 2022 |
Bibliografisk note
Funding Information:
We thank the following institutions and people who provided tissue and toepad loans to make this work possible: American Museum of Natural History (AMNH - Paul Sweet & Tom Trombone); Academy of Natural Sciences of Drexel University (ANSP - Nate Rice); Florida Museum of Natural History (FLMNH - Andy Kratter); Field Museum of Natural History (FMNH - Ben Marks, Shannon Hackett, & John Bates); University of Kansas Biodiversity Research Institute (KU - Mark Robbins); Natural History Museum of Los Angeles County (LACM - Kimball Garrett); Louisiana State University Museum of Natural Science (LSU - Donna Dittmann, Van Remsen, & Fred Sheldon); Moore Laboratory of Zoology (MLZ - James Maley); Museo de Zoología ‘Alfonso L. Herrera’ (UNAM - Adolfo Navarro Sigüenza); National Museum of Natural History (USNM - Christopher Milensky); University of Washington Burke Museum (UWBM - Sharon Birks); Western Foundation of Vertebrate Zoology (WFVZ - René Corado); and the Yale Peabody Museum (YPM - Kristof Zyskowski). Marguerite Poché provided assistance with the lab work. We also thank Shahan Derkarabetian, an anonymous reviewer, and the editors for their helpful comments on the manuscript. This research was supported by startup funds from LSU to B.C.F. and by National Science Foundation (NSF) DEB-1655624 to B.C.F and R.T.B. R.T.K. and E.L.B. were supported by NSF DEB-1118823 and DEB-1655683. J.F.S. was supported by a Carrie Lynn Yoder Superior Graduate Student Scholarship from the Louisiana State University Department of Biological Sciences and NSF DBI-2109361. P.A.H. acknowledges support from Villum Fonden research grant no. 25925. Portions of this research were conducted with high performance computational resources provided by Louisiana State University (http://www.hpc.lsu.edu). Funders had no role in creating or approving manuscript content. Animal tissues used in this research were collected from museum specimens and are not subject to Institutional Animal Care and Use Committee approval. Raw sequencing reads are available from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (BioProject PRJNA 777908). The PHYLUCE computer code used in this study is available from https://github.com/faircloth-lab/phyluce. Other custom computer code, DNA alignments, analysis inputs, and analysis outputs are available from Dryad at https://doi.org/10.5061/dryad.bcc2fqzg6.
Funding Information:
This research was supported by startup funds from LSU to B.C.F. and by National Science Foundation (NSF) DEB-1655624 to B.C.F and R.T.B. R.T.K. and E.L.B. were supported by NSF DEB-1118823 and DEB-1655683. J.F.S. was supported by a Carrie Lynn Yoder Superior Graduate Student Scholarship from the Louisiana State University Department of Biological Sciences and NSF DBI-2109361. P.A.H. acknowledges support from Villum Fonden research grant no. 25925. Portions of this research were conducted with high performance computational resources provided by Louisiana State University ( http://www.hpc.lsu.edu ). Funders had no role in creating or approving manuscript content.
Funding Information:
We thank the following institutions and people who provided tissue and toepad loans to make this work possible: American Museum of Natural History (AMNH - Paul Sweet & Tom Trombone); Academy of Natural Sciences of Drexel University (ANSP - Nate Rice); Florida Museum of Natural History (FLMNH - Andy Kratter); Field Museum of Natural History (FMNH - Ben Marks, Shannon Hackett, & John Bates); University of Kansas Biodiversity Research Institute (KU - Mark Robbins); Natural History Museum of Los Angeles County (LACM - Kimball Garrett); Louisiana State University Museum of Natural Science (LSU - Donna Dittmann, Van Remsen, & Fred Sheldon); Moore Laboratory of Zoology (MLZ - James Maley); Museo de Zoología ‘Alfonso L. Herrera’ (UNAM - Adolfo Navarro Sigüenza); National Museum of Natural History (USNM - Christopher Milensky); University of Washington Burke Museum (UWBM - Sharon Birks); Western Foundation of Vertebrate Zoology (WFVZ - René Corado); and the Yale Peabody Museum (YPM - Kristof Zyskowski). Marguerite Poché provided assistance with the lab work. We also thank Shahan Derkarabetian, an anonymous reviewer, and the editors for their helpful comments on the manuscript.
Publisher Copyright:
© 2022 Elsevier Inc.
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