Historical specimens and the limits of subspecies phylogenomics in the New World quails (Odontophoridae)
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Historical specimens and the limits of subspecies phylogenomics in the New World quails (Odontophoridae). / Salter, Jessie F.; Hosner, Peter A.; Tsai, Whitney L. E.; McCormack, John E.; Braun, Edward L.; Kimball, Rebecca T.; Brumfield, Robb T.; Faircloth, Brant C.
In: Molecular Phylogenetics and Evolution, Vol. 175, 107559, 2022.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Historical specimens and the limits of subspecies phylogenomics in the New World quails (Odontophoridae)
AU - Salter, Jessie F.
AU - Hosner, Peter A.
AU - Tsai, Whitney L. E.
AU - McCormack, John E.
AU - Braun, Edward L.
AU - Kimball, Rebecca T.
AU - Brumfield, Robb T.
AU - Faircloth, Brant C.
N1 - Publisher Copyright: © 2022 Elsevier Inc.
PY - 2022
Y1 - 2022
N2 - 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.
AB - 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.
KW - Galliformes
KW - Historical DNA
KW - Phylogenetics
KW - Systematics
KW - Taxonomy
KW - UCEs
U2 - 10.1016/j.ympev.2022.107559
DO - 10.1016/j.ympev.2022.107559
M3 - Journal article
C2 - 35803448
AN - SCOPUS:85134589213
VL - 175
JO - Molecular Phylogenetics and Evolution
JF - Molecular Phylogenetics and Evolution
SN - 1055-7903
M1 - 107559
ER -
ID: 318812326