Widespread gene flow following range expansion in Anna's Hummingbird

Adams, Nicole; Bandivadekar, Ruta R.; Battey, C. J.; Clark, Michael W; Epperly, Kevin; Ruegg, Kristen; Tell, Lisa A.; Bay, Rachael A.

doi:10.1111/mec.16928

Cited by 5 publications

(6 citation statements)

References 124 publications

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“…These patterns do not align with expected gradients of genetic diversity if contemporary genetic patterns reflect northward postglacial expansion as the glaciers retreated (Miller et al 2020;Adams et al 2023). However, comparable or higher genetic diversity has also been observed at the leading expansion front (Vandepitte et al 2017;Wang et al 2017;Bors et al 2019) likely due to continued high gene flow with the core population (Miller et al 2020;Adams et al 2023). Expansions that occur at a rapid pace are also likely to retain higher heterozygosity at the expansion front (Goodsman et al 2014).…”

Section: Discussionmentioning

confidence: 82%

“…Population-level differences in genetic diversity can also show signatures of range expansion dynamics (Provan and Bennett 2008;Peter and Slatkin 2015;Adams et al 2023). Due to founder effects and greater geographic isolation, the expansion front is expected to have lower levels of genetic diversity compared to the core of the range (García-Ramos and Kirkpatrick 1997;Excoffier 2004;Eckert et al 2008;Excoffier et al 2009).…”

Section: Discussionmentioning

confidence: 99%

“…Finally, the directionality index was low (ψ < 0.03) for all pairwise comparisons: ψ = 0.002 (z = 0.01) between the southern Appalachian and western populations, ψ = -0.03 (z = -1.04) between the boreal and western population, and ψ = 0.02 (z = 0.95) between the southern Appalachian and boreal populations. The direction of ψ might indicate that the boreal population has been a source population for expansion; however, these values were not significantly different from zero, supporting an isolation by distance model or a population expansion model in which populations are equidistant from the origin of expansion and are exhibiting comparable levels of gene flow between populations (Peter and Slatkin 2013;Adams et al 2023).…”

Section: (A) Population Structurementioning

confidence: 90%

“…Finally, to assess the direction of gene flow between the three populations, we calculated a directionality index (ψ) from the 2D SFS with a custom script from (Adams et al 2023) using equation 1b from (Peter and Slatkin 2013). Balanced sample sizes are necessary to calculate ψ (Peter and Slatkin 2013), such that we randomly selected 22 individuals from both the southern Appalachian and the boreal populations to created new SAF and 2D SFS files between each population pair.…”

Section: (C) Population Structurementioning

confidence: 99%

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How Veeries vary: Whole genome sequencing resolves fine-scale genetic structure in a long-distance migratory bird,Catharus fuscescens

Kimmitt

Pegan

Jones

et al. 2023

Preprint

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Fine-scale resolution of spatial genetic structure is important for understanding a species' evolutionary history and contemporary genetic diversity. For high-latitude species with high dispersal ability, such as long-distance migratory birds, populations typically exhibit little genetic structure due to high gene flow and recent postglacial expansion. Some migratory birds, however, show high breeding site fidelity, which might reduce gene flow such that population genetic structure could be detectable with sufficient genomic data. We sequenced over 120 low-coverage whole genomes from across the breeding range of a long-distance migratory bird, the Veery (Catharus fuscescens). As this species' breeding range extends across both historically glaciated and unglaciated regions in North America, we evaluated whether contemporary patterns of structure and genetic diversity are consistent with historical population isolation in glacial refugia. We found strong evidence for isolation by distance across the breeding range, as well as significant population structure between southern Appalachian and northern populations. However, patterns of genetic diversity did not support southern Appalachia as a glacial refugium. Resolution of isolation by distance across the breeding range was sufficient to assign likely breeding origins of individuals sampled in this species' poorly understood South American nonbreeding range, demonstrating the potential to assess migratory connectivity in this species using genomic data. Overall, our findings suggest that isolation by distance yields subtle associations between genetic structure and geography across the breeding range even in the absence of obvious historical vicariance or contemporary barriers to dispersal.

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Section: Discussionmentioning

confidence: 82%

Section: Discussionmentioning

confidence: 99%

Section: (A) Population Structurementioning

confidence: 90%

Section: (C) Population Structurementioning

confidence: 99%

See 2 more Smart Citations

How Veeries vary: Whole genome sequencing resolves fine-scale genetic structure in a long-distance migratory bird,Catharus fuscescens

Kimmitt

Pegan

Jones

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…We then used realSFS to create folded site frequency spectra for each population, followed by realSFS's command saf2theta, and finally thetaStat do_stat to estimate various population genetic parameters. From this output, we estimated p by dividing the global estimate for pairwise q (tP) by the total number of sites (nSites), following Adams et al (2023) and https://github.com/nt246/lcwgs-guidetutorial/blob/main/tutorial4_summary_stats/markdowns/03_diversity.md.…”

Section: Genetic Diversitymentioning

confidence: 99%

Genomic and physiological adaptation to temperature in the invasive golden star runicate (Botryllus schlosseri)

Tobias

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Because non-indigenous species (NIS) often encounter novel environments during colonization and expansion, species invasions present useful opportunities to investigate the mode and pace of adaptive change in natural populations. In this dissertation, I use the range expansion of the invasive golden star tunicate, Botryllus schlosseri, as a natural experiment to study how a pernicious NIS adapts its thermal physiology on contemporary time scales. In Chapter 2, I applied low-coverage whole genome sequencing (lcWGS) to investigate patterns of population genetic structure and signatures of local adaptation to temperature. In addition to illustrating the potential for rapid adaptation of thermal tolerance at the genomic level, this chapter demonstrated that the molecular basis of thermal adaptation on either coast is distinct, providing valuable evidence for parallel adaptation being driven by divergent molecular means. In Chapter 3, I performed a physiological study to investigate differentiation of post-larval heat tolerance across five populations across a major biogeographic break on the east coast of North America. I found that northern populations are more susceptible to heat stress than their southern, warm-exposed counterparts, providing evidence for adaptive shifts of thermal tolerance. Further, by taking advantage of natural temporal variability in temperature, I demonstrated that temperature during development positively affects heat tolerance at later life stages, establishing developmental plasticity of thermal tolerance. In Chapter 4, I extended my physiological investigation to the west coast of North America, comparing post-larval heat tolerance across three populations spanning a 24.3° latitudinal gradient while expanding to include differentiation of cold tolerance in adults. Similar to the east coast, I observed that the two northern populations were more susceptible to heat stress than their southern counterpart. For cold tolerance, I observed a pattern of countergradient variation whereby northern populations were better able to maintain cardiac function in the cold than southern populations. This suggests compensatory genetic adaptation to the colder water temperatures at higher latitudes. Overall, my work furthers our understanding of how NIS are able to rapidly shift their thermal physiology in response to novel environments, shedding light on the potential of species more generally to adapt to environmental change on contemporary timescales.

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How Veeries vary: Whole genome sequencing resolves genetic structure in a long-distance migratory bird

Kimmitt,

Pegan,

Jones

et al. 2023

Ornithology

View full text Add to dashboard Cite

In high-latitude species with high dispersal ability, such as long-distance migratory birds, populations are often assumed to exhibit little genetic structure due to high gene flow or recent postglacial expansion. We sequenced over 120 low-coverage whole genomes from across the breeding range of a long-distance migratory bird, the Veery (Catharus fuscescens), revealing strong evidence for isolation by distance. Additionally, we found distinct genetic structure between boreal, western montane U.S., and southern Appalachian sampling regions. We suggest that population genetic structure in this highly migratory species is detectable with the high resolution afforded by whole-genomic data because, similar to many migratory birds, the Veery exhibits high breeding-site fidelity, which likely limits gene flow. Resolution of isolation by distance across the breeding range was sufficient to assign likely breeding origins of individuals sampled in this species’ poorly understood South American nonbreeding range, demonstrating the potential to assess migratory connectivity in this species using genomic data. As the Veery’s breeding range extends across both historically glaciated and unglaciated regions in North America, we also evaluated whether contemporary patterns of structure and genetic diversity are consistent with historical population isolation in glacial refugia. We found that patterns of genetic diversity did not support southern montane regions (southern Appalachians or western U.S. mountains) as glacial refugia. Overall, our findings suggest that isolation by distance yields subtle associations between genetic structure and geography across the breeding range of this highly vagile species even in the absence of obvious historical vicariance or contemporary barriers to dispersal.

show abstract

Widespread gene flow following range expansion in Anna's Hummingbird

Cited by 5 publications

References 124 publications

How Veeries vary: Whole genome sequencing resolves fine-scale genetic structure in a long-distance migratory bird,Catharus fuscescens

How Veeries vary: Whole genome sequencing resolves fine-scale genetic structure in a long-distance migratory bird,Catharus fuscescens

Genomic and physiological adaptation to temperature in the invasive golden star runicate (Botryllus schlosseri)

How Veeries vary: Whole genome sequencing resolves genetic structure in a long-distance migratory bird

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