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ARS Home » Pacific West Area » Hilo, Hawaii » Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center » Tropical Pest Genetics and Molecular Biology Research Unit » Research » Publications at this Location » Publication #394673
Research Project: Advancing Molecular Pest Management, Diagnostics, and Eradication of Fruit Flies and Invasive Species

Location: Tropical Pest Genetics and Molecular Biology Research Unit

Title: Whole genomes reveal evolutionary relationships and mechanisms underlying gene-tree discordance in Neodiprion sawflies

Author
item HERRIG, DANIELLE - University Of Kentucky
item RIDENBAUGH, RYAN - University Of Kentucky
item VERTACNIK, KIM - Columbia River Intertribal Fish Commission
item EVERSON, KATHRYN - University Of Kentucky
item Sim, Sheina
item Geib, Scott
item WEISROCK, DAVID - University Of Kentucky
item LINNEN, CATHERINE - University Of Kentucky

Submitted to: Systematic Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/5/2024
Publication Date: 7/6/2024
Citation: Herrig, D.K., Ridenbaugh, R.D., Vertacnik, K.L., Everson, K.M., Sim, S.B., Geib, S.M., Weisrock, D.W., Linnen, C.R. 2024. Whole genomes reveal evolutionary relationships and mechanisms underlying gene-tree discordance in Neodiprion sawflies. Systematic Biology. 73(5):839-860. https://doi.org/10.1093/sysbio/syae036.
DOI: https://doi.org/10.1093/sysbio/syae036

Interpretive Summary: Scientists at the University of Kentucky and their collaborators at USDA-ARS demonstrate how different genome sub-sampling strategies can be used to reconstruct a species-level phylogeny for the genus Neodiprion. The study found that using all genome-wide SNPs, genes, and window sizes resulted in same or similar tree topologies, but sub-sampling SNPs resulted in differences in topologies of some taxa as sampling became increasingly sparse. The results of this study reveal that multiple phylogenetic tree-reconstruction methods should be applied to identify phylogenetically informative loci and regions that reveal the phylogenetic history of a species complex, and a window-based approach at subsampling the genome is particularly informative for recently diverged taxa.

Technical Abstract: With the evolution of sequencing technologies comes the question of how best to use whole genome sequences to answer evolutionary questions. Here, we use a pseudo-reference approach to produce whole genomes of 18 eastern North American species of Neodiprion sawflies along with a western outgroup species. Using these genomes, we investigate the phylogenetic histories of these species and how subdividing these genomes may influence our results. Specifically, we divided the genomes by SNPs, genes, and chromosomal windows to determine if we would reach the same phylogenetic relationships and overarching species tree regardless of the approach used. We find a highly-supported and fully resolved phylogeny when using all SNP data across the entire genome. However, different topologies were recovered with subsampling SNPs at different distances. Very similar trees were obtained when creating a coalescent-based species tree using different window sizes or genes. In addition to exploring the overall phylogenetic tree, we also asked if specific regions of the genome showed variation in tree topology. These trees revealed additional heterogeneous topologies and one region of interest revealing that the phylogenetic history of these species is complex. Additional studies are needed to investigate why different subsampling strategies and regions of the genome produce different topologies. The methods used to come to these conclusions present a way for future phylogenetic studies using whole genome datasets to query the robustness of their species trees using different subsampling strategies and identify potential regions of interest.