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Abstract Understanding the genetics of adaptation and speciation is critical for a complete picture of how biodiversity is generated and maintained. Heterogeneous genomic differentiation between diverging taxa is commonly documented, with genomic regions of high differentiation interpreted as resulting from differential gene flow, linked selection and reduced recombination rates. Disentangling the roles of each of these non‐exclusive processes in shaping genome‐wide patterns of divergence is challenging but will enhance our knowledge of the repeatability of genomic landscapes across taxa. Here, we combine whole‐genome resequencing and genome feature data to investigate the processes shaping the genomic landscape of differentiation for a sister‐species pair of haplodiploid pine sawflies,Neodiprion leconteiandNeodiprion pinetum. We find genome‐wide correlations between genome features and summary statistics are consistent with pervasive linked selection, with patterns of diversity and divergence more consistently predicted by exon density and recombination rate than the neutral mutation rate (approximated by dS). We also find that both global and local patterns ofFST,dXYandπprovide strong support for recurrent selection as the primary selective process shaping variation across pine sawfly genomes, with some contribution from balancing selection and lineage‐specific linked selection. Because inheritance patterns for haplodiploid genomes are analogous to those of sex chromosomes, we hypothesize that haplodiploids may be especially prone to recurrent selection, even if gene flow occurred throughout divergence. Overall, our study helps fill an important taxonomic gap in the genomic landscape literature and contributes to our understanding of the processes that shape genome‐wide patterns of genetic variation.
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Contrasting continental patterns of adaptive population divergence in the holarctic ectomycorrhizal fungus Boletus edulis
Summary In the hyperdiverse fungi, the process of speciation is virtually unknown, including for the > 20 000 species of ectomycorrhizal mutualists. To understand this process, we investigated patterns of genome‐wide differentiation in the ectomycorrhizal porcini mushroom, Boletus edulis , a globally distributed species complex with broad ecological amplitude. By whole‐genome sequencing 160 individuals from across the Northern Hemisphere, we genotyped 792 923 single nucleotide polymorphisms to characterize patterns of genome‐wide differentiation and to identify the adaptive processes shaping global population structure. We show that B. edulis exhibits contrasting patterns of genomic divergence between continents, with multiple lineages present across North America, while a single lineage dominates Europe. These geographical lineages are inferred to have diverged 1.62–2.66 million years ago, during a period of climatic upheaval and the onset of glaciation in the Pliocene–Pleistocene boundary. High levels of genomic differentiation were observed among lineages despite evidence of substantial and ongoing introgression. Genome scans, demographic inference, and ecological niche models suggest that genomic differentiation is maintained by environmental adaptation, not physical isolation. Our study uncovers striking patterns of genome‐wide differentiation on a global scale and emphasizes the importance of local adaptation and ecologically mediated divergence, rather than prezygotic barriers such as allopatry or genomic incompatibility, in fungal population differentiation.
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- Award ID(s):
- 2114785
- PAR ID:
- 10465837
- Date Published:
- Journal Name:
- New Phytologist
- Volume:
- 237
- Issue:
- 1
- ISSN:
- 0028-646X
- Page Range / eLocation ID:
- 295 to 309
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1111/nph.18521
