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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 #414118
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: Recurrent selection shapes the genomic landscape of differentiation between a pair of host-specialized haplodiploids that diverged with gene flow

Author
item GLOVER, ASHLEIGH - University Of Kentucky
item SOUSA, VITOR - University Of Kentucky
item RIDENBAUGH, RYAN - University Of Kentucky
item Sim, Sheina
item Geib, Scott
item LINNEN, CATHERINE - University Of Kentucky

Submitted to: Molecular Ecology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/2/2024
Publication Date: 8/20/2024
Citation: Glover, A.N., Sousa, V.C., Ridenbaugh, R.D., Sim, S.B., Geib, S.M., Linnen, C.R. 2024. Recurrent selection shapes the genomic landscape of differentiation between a pair of host-specialized haplodiploids that diverged with gene flow. Molecular Ecology. 33(18). Article e17509. https://doi.org/10.1111/mec.17509.
DOI: https://doi.org/10.1111/mec.17509

Interpretive Summary: Scientists from the University of Kentucky and USDA-ARS Tropical Pest Genetics and Molecular Biology Research Unit present research on genome-wide patterns of diversity, differentiation, and divergence between sister taxa in the genus Neodiprion, the haplodiploid sawflies, N. lecontei and N. pinetum. Chromosome-scale assemblies for both species enabled the detection of patterns associated with lowered recombination in centromeric regions and suggests that divergence is primarily driven by recurrent selection pressures. This study contributes to our foundational understanding of species formation and maintenance.

Technical Abstract: Understanding the genetics of adaptation and speciation is critical for a complete picture of how biodiversity is generated and maintained. Heterogeneous genomic differentiation (henceforth genomic landscapes) between diverging taxa is commonly documented, with genomic regions of high differentiation interpreted as resulting from differential gene flow, linked selection, and a reduction in recombination rate. Disentangling the roles of each of these non-exclusive processes in shaping genomic divergence is challenging but will enhance our knowledge of the repeatability of genomic landscapes across taxa. Here, we use whole-genome resequencing and genome feature data to investigate the processes shaping the genomic landscape of a sister-species pair of haplodiploid pine sawflies, Neodiprion lecontei and Neodiprion pinetum. Genome-wide correlations among measures of diversity (p), differentiation (FST), absolute divergence (dXY), and genome features as well as multiple linear regression provide evidence for widespread linked selection across the genome. We find that estimates of dXY tend to be lower in FST outlier windows compared to non-outlier windows, suggesting recurrent selection is the primary driver of genomic divergence. Because haplodiploidy is analogous to sex chromosomes, we hypothesize that haplodiploids may be especially prone to recurrent selection. By examining local patterns of FST, dXY, and p we find that maintenance of ancestral polymorphism and lineage-specific linked selection has also contributed to the formation of the genomic landscape. Overall, our study contributes to our understanding of the processes that shape genomic divergence and highlights the importance of sufficient knowledge of the study system to allow for more informed hypotheses and data interpretation.