Pleistocene glacial cycles drastically changed the distributions of taxa endemic to temperate rainforests in the Pacific Northwest, with many experiencing reduced habitat suitability during glacial periods. In this study, we investigate whether glacial cycles promoted intraspecific divergence and whether subsequent range changes led to secondary contact and gene flow. For seven invertebrate species endemic to the PNW, we estimated species distribution models (SDMs) and projected them onto current and historical climate conditions to assess how habitat suitability changed during glacial cycles. Using single nucleotide polymorphism (SNP) data from these species, we assessed population genetic structure and used a machine‐learning approach to compare models with and without gene flow between populations upon secondary contact after the last glacial maximum (LGM). Finally, we estimated divergence times and rates of gene flow between populations. SDMs suggest that there was less suitable habitat in the North Cascades and Northern Rocky Mountains during glacial compared to interglacial periods, resulting in reduced habitat suitability and increased habitat fragmentation during the LGM. Our genomic data identify population structure in all taxa, and support gene flow upon secondary contact in five of the seven taxa. Parameter estimates suggest that population divergences date to the later Pleistocene for most populations. Our results support a role of refugial dynamics in driving intraspecific divergence in the Cascades Range. In these invertebrates, population structure often does not correspond to current biogeographic or environmental barriers. Rather, population structure may reflect refugial lineages that have since expanded their ranges, often leading to secondary contact between once isolated lineages.
Understanding the processes that shape genetic diversity by either promoting or preventing population divergence can help identify geographic areas that either facilitate or limit gene flow. Furthermore, broadly distributed species allow us to understand how biogeographic and ecogeographic transitions affect gene flow. We investigated these processes using genomic data in the Northern Alligator Lizard (Elgaria coerulea), which is widely distributed in Western North America across diverse ecoregions (California Floristic Province and Pacific Northwest) and mountain ranges (Sierra Nevada, Coastal Ranges, and Cascades). We collected single-nucleotide polymorphism data from 120 samples of E. coerulea. Biogeographic analyses of squamate reptiles with similar distributions have identified several shared diversification patterns that provide testable predictions for E. coerulea, including deep genetic divisions in the Sierra Nevada, demographic stability of southern populations, and recent post-Pleistocene expansion into the Pacific Northwest. We use genomic data to test these predictions by estimating the structure, connectivity, and phylogenetic history of populations. At least 10 distinct populations are supported, with mixed-ancestry individuals situated at most population boundaries. A species tree analysis provides strong support for the early divergence of populations in the Sierra Nevada Mountains and recent diversification into the Pacific Northwest. Admixture and migration analyses detect gene flow among populations in the Lower Cascades and Northern California, and a spatial analysis of gene flow identified significant barriers to gene flow across both the Sierra Nevada and Coast Ranges. The distribution of genetic diversity in E. coerulea is uneven, patchy, and interconnected at population boundaries. The biogeographic patterns seen in E. coerulea are consistent with predictions from co-distributed species.
more » « less- NSF-PAR ID:
- 10489275
- Publisher / Repository:
- Oxford University Press
- Date Published:
- Journal Name:
- Journal of Heredity
- Volume:
- 115
- Issue:
- 1
- ISSN:
- 0022-1503
- Format(s):
- Medium: X Size: p. 57-71
- Size(s):
- ["p. 57-71"]
- Sponsoring Org:
- National Science Foundation
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Abstract Aim A central aim of biogeography is to understand how biodiversity is generated and maintained across landscapes. Here, we establish phylogenetic and population genetic patterns in a widespread reptile to quantify the influence of historical biogeography and current environmental variation on patterns of genetic diversity.
Location Western North America.
Taxon Western terrestrial garter snake,
Thamnophis elegans .Methods We used double‐digest RADseq to estimate phylogenetic relationships and characterize population genetic structure across the three widespread subspecies of
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T .e .elegans displayed a latitudinal gradient in genetic variation across the Sierra Nevada and northern California, while populations ofT .e .terrestris show discrete genetic breaks consistent with well‐known biogeographic barriers. Lastly, GEA analyses identified allele frequency shifts at loci associated with a common set of environmental variables in bothT .e .elegans andT .e .terrestris .Main Conclusion T .elegans is composed of distinct evolutionary lineages, each with its own geographic range and history of diversification.T .e .elegans andT .e .terrestris show unique patterns of diversification as populations dispersed from east to west and while adapting to the new environments they colonized. Historical events, landscape features and environmental variation have all contributed to patterns of differentiation inT .elegans . -
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Abstract Background Distributional responses by alpine taxa to repeated, glacial-interglacial cycles throughout the last two million years have significantly influenced the spatial genetic structure of populations. These effects have been exacerbated for the American pika (
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