TY - JOUR
T1 - Gauging ages of tiger swallowtail butterflies using alternate SNP analyses
AU - Vernygora, Oksana V.
AU - Campbell, Erin O.
AU - Grishin, Nick V.
AU - Sperling, Felix A.H.
AU - Dupuis, Julian R.
N1 - Funding Information:
We thank C. Davis, C. Nargang, E. Chapman, K. Yakimovich, J. Sperling, and S. Dang for their assistance with sample preparation and sequencing and two anonymous reviewers for comments on an earlier draft. We also thank M. Ayres, A. Book, B. Brunet, M. Carter, M. Evans, P. Feeny, S. Ferguson, C. Duckett, M. Furr, D. McCorkle, M. Peterson, L. Rosenberry, D. Rubinoff, B. Sperling, T. Sperling, J. Wells and C. Yoon for their assistance in collecting specimens. This research was enabled in part by support provided by WestGrid (www.westgrid.ca) and Compute Canada (www.computecanada.ca). We also thank the University of Kentucky Center for Computational Sciences and Information Technology Services Research Computing for their support and use of the Lipscomb Compute Cluster and associated research computing resources. This research was supported by the National Science and Engineering Council of Canada Discovery Grant to FAHS (RGPIN-2018-04920) and USDA-NIFA HATCH (Project KY008091). We are grateful to J. Brock, A. Warren, K. Davis, and M. Strangeland for the permission to use their photos in our figures. We also thank L. Jackson and V. Shegelski for their help with imaging and accessioning voucher specimens in the E.H. Strickland Entomological Museum at the University of Alberta.
Funding Information:
This research was enabled in part by support provided by WestGrid ( www.westgrid.ca ) and Compute Canada (www.computecanada.ca). We also thank the University of Kentucky Center for Computational Sciences and Information Technology Services Research Computing for their support and use of the Lipscomb Compute Cluster and associated research computing resources. This research was supported by the National Science and Engineering Council of Canada Discovery Grant to FAHS (RGPIN-2018-04920) and USDA-NIFA HATCH (Project KY008091). We are grateful to J. Brock, A. Warren, K. Davis, and M. Strangeland for the permission to use their photos in our figures. We also thank L. Jackson and V. Shegelski for their help with imaging and accessioning voucher specimens in the E.H. Strickland Entomological Museum at the University of Alberta.
Publisher Copyright:
© 2022 Elsevier Inc.
PY - 2022/6
Y1 - 2022/6
N2 - Divergence times underpin diverse evolutionary hypotheses, but conflicting age estimates across studies diminish the validity of such hypotheses. These conflicts have continued to grow as large genomics datasets become commonplace and analytical approaches proliferate. To provide more stable temporal intervals, age estimations should be interpreted in the context of both the type of data and analysis being used. Here, we use multispecies coalescent (MSC), concatenation-based, and categorical data transformation approaches on genome-wide SNP data to infer divergence ages within the Papilio glaucus group of tiger swallowtail butterflies in North America. While the SNP data supported previously recognized relationships within the group (P. multicaudata, ((P. eurymedon, P. rutulus), (P. appalachiensis, P. canadensis, P. glaucus))), estimated ages of divergence between the major lineages varied substantially among analyses. MSC produced wide credibility intervals particularly for deeper nodes, reflecting uncertainty in the coalescence times as a possible result of conflicting signal across gene trees. Concatenation, in contrast, gave narrower and more well-defined posterior distributions for the node ages; however, the higher precision of these time estimates is a likely artefact due to more simplistic underlying assumptions of this approach that do not account for conflict among gene trees. Transformed categorical data analysis gave the least precise and the most variable results, with its simple substitution model coupled with a relaxed clock tending to produce spurious results from large genome-wide datasets. While median node ages differed considerably between analyses (∼2 Mya between MSC and concatenation-based results), their corresponding credibility intervals nonetheless highlight common temporal patterns for deeper divergences in the group as well as finer-scale phylogeography. Age distributions across analyses support an origin of the group during the warm period of the early to mid-Pliocene. Late Pliocene climate aridification and cooling drove divergence between eastern and western groups that further diversified during the period of repeated Pleistocene glaciations. Our results provide a structured comparative assessment of divergence time estimates and evolutionary relationships in a well-studied group of butterflies, and support better understanding of analytical biases in divergence time estimation.
AB - Divergence times underpin diverse evolutionary hypotheses, but conflicting age estimates across studies diminish the validity of such hypotheses. These conflicts have continued to grow as large genomics datasets become commonplace and analytical approaches proliferate. To provide more stable temporal intervals, age estimations should be interpreted in the context of both the type of data and analysis being used. Here, we use multispecies coalescent (MSC), concatenation-based, and categorical data transformation approaches on genome-wide SNP data to infer divergence ages within the Papilio glaucus group of tiger swallowtail butterflies in North America. While the SNP data supported previously recognized relationships within the group (P. multicaudata, ((P. eurymedon, P. rutulus), (P. appalachiensis, P. canadensis, P. glaucus))), estimated ages of divergence between the major lineages varied substantially among analyses. MSC produced wide credibility intervals particularly for deeper nodes, reflecting uncertainty in the coalescence times as a possible result of conflicting signal across gene trees. Concatenation, in contrast, gave narrower and more well-defined posterior distributions for the node ages; however, the higher precision of these time estimates is a likely artefact due to more simplistic underlying assumptions of this approach that do not account for conflict among gene trees. Transformed categorical data analysis gave the least precise and the most variable results, with its simple substitution model coupled with a relaxed clock tending to produce spurious results from large genome-wide datasets. While median node ages differed considerably between analyses (∼2 Mya between MSC and concatenation-based results), their corresponding credibility intervals nonetheless highlight common temporal patterns for deeper divergences in the group as well as finer-scale phylogeography. Age distributions across analyses support an origin of the group during the warm period of the early to mid-Pliocene. Late Pliocene climate aridification and cooling drove divergence between eastern and western groups that further diversified during the period of repeated Pleistocene glaciations. Our results provide a structured comparative assessment of divergence time estimates and evolutionary relationships in a well-studied group of butterflies, and support better understanding of analytical biases in divergence time estimation.
KW - Concatenation
KW - Divergence times
KW - Molecular dating
KW - Multispecies coalescent
KW - Papilio glaucus
KW - Phylogenetics
UR - http://www.scopus.com/inward/record.url?scp=85127487848&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85127487848&partnerID=8YFLogxK
U2 - 10.1016/j.ympev.2022.107465
DO - 10.1016/j.ympev.2022.107465
M3 - Article
C2 - 35351633
AN - SCOPUS:85127487848
SN - 1055-7903
VL - 171
JO - Molecular Phylogenetics and Evolution
JF - Molecular Phylogenetics and Evolution
M1 - 107465
ER -