Seeing the whole picture: What molecular ecology is gaining from whole genomes

Taylor, Rebecca S.; Jensen, Evelyn L.; Coltman, David W.; Foote, Andrew D.

doi:10.1111/mec.16282

Cited by 12 publications

(9 citation statements)

References 45 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Furthermore, identifying the genes associated with genomic differentiation can provide key insights into the biotic or abiotic factors that are the actual sources of selection (Poelstra et al, 2014; Todesco et al, 2022), which are often not well understood. Finally, studying the patterns of diversity and differentiation across the genome can inform us on the relative roles of evolutionary forces other than selection involved in the origin and maintenance of phenotypic differences between diverging taxa, including gene flow, mutation, genetic drift, and recombination (Taylor et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

The genomic basis of reproductive and migratory behaviour in a polymorphic salmonid

Tigano

Russello

2022

Molecular Ecology

View full text Add to dashboard Cite

Recent ecotypic differentiation provides unique opportunities to investigate the genomic basis and architecture of local adaptation, while offering insights into how species form and persist. Sockeye salmon (Oncorhynchus nerka) exhibit migratory and resident (“kokanee”) ecotypes, which are further distinguished into shore‐spawning and stream‐spawning reproductive ecotypes. Here, we analysed 36 sockeye (stream‐spawning) and kokanee (stream‐ and shore‐spawning) genomes from a system where they co‐occur and have recent common ancestry (Okanagan Lake/River in British Columbia, Canada) to investigate the genomic basis of reproductive and migratory behaviour. Examination of the genomic landscape of differentiation, differences in allele frequencies and genotype–phenotype associations revealed three main blocks of sequence differentiation on chromosomes 7, 12 and 20, associated with migratory behaviour, spawning location and spawning timing. Structural variants identified in these same areas suggest they could contribute to ecotypic differentiation directly as causal variants or via maintenance of their genomic architecture through recombination suppression mechanisms. Genes in these regions were related to spatial memory and swimming endurance (SYNGAP, TPM3), as well as eye and brain development (including SIX6), potentially associated with differences in migratory behaviour and visual habitats across spawning locations, respectively. Additional genes (GREB1L, ROCK1) identified here have been associated with timing of migration in other salmonids and could explain variation in timing of O. nerka spawning. Together, these results based on the joint analysis of sequence and structural variation represent a significant advance in our understanding of the genomic landscape of ecotypic differentiation at different stages in the speciation continuum.

show abstract

Section: Introductionmentioning

confidence: 99%

The genomic basis of reproductive and migratory behaviour in a polymorphic salmonid

Tigano

Russello

2022

Molecular Ecology

View full text Add to dashboard Cite

show abstract

“…Modern DNA sequencing technologies and analytical methods, especially simulation-based approaches, enable detailed molecular inferences on population-level processes and demographic history in human and wildlife populations (Foote et al, 2021; Hoban et al, 2012; Taylor et al, 2021; Vilaça et al, 2021). However, there are limits as to what can be deduced from present-day genetic data.…”

Section: Introductionmentioning

confidence: 99%

Museum specimens of a landlocked pinniped reveal recent loss of genetic diversity and unexpected population connections

Heino

Nyman

Palo

et al. 2022

Preprint

View full text Add to dashboard Cite

Aim: The Saimaa ringed seal (Pusa hispida saimensis) is endemic to Lake Saimaa in Finland. The subspecies is thought to have originated when parts of the ringed seal population of the Baltic region were trapped in lakes emerging due to post-glacial bedrock rebound around 9,000 years ago. During the 20th century, the population experienced a drastic human-induced bottleneck. Today encompassing a little over 400 seals with extremely low genetic diversity, it is classified as endangered. Our main aim was to evaluate the role of the 20th century bottleneck in the erosion of genetic diversity in the Saimaa seal population. We also evaluated connections with other ringed seals from the Baltic Sea, Lake Ladoga, North America, Svalbard and the White Sea. Location: Lake Saimaa, Finland, together with the Baltic Sea and the Arctic Ocean. Methods: We sequenced sections of the mitochondrial control region from 60 up to 125 years old museum specimens of the Saimaa ringed seal. The generated dataset was combined with publicly available sequences. We studied how genetic variation has changed through time in this subspecies, and how it is phylogenetically related to other ringed seal populations. Results: We observed temporal fluctuations in haplotype frequencies and loss of haplotypes accompanied by a recent reduction in female effective population size. In apparent contrast with the traditionally held view of the Baltic origin of the population, the Saimaa ringed seal mtDNA variation shows also affinities to North American ringed seals. Main conclusions: Our results suggest that the Saimaa ringed seal has experienced recent genetic drift associated with small population size. The results further suggest that extant Baltic ringed seals do not represent well the ancestral population of the Saimaa ringed seal, which calls for re-evaluation of the deep history of this subspecies.

show abstract

“…Multiple studies take advantage of the comprehensive genomic data to examine polygenic adaptations (Montejo‐Kovacevich et al, 2021; Pereira et al, 2021), while others use WGS to conduct genotype environment association (GEA) analysis, revealing a fine‐scale look at genomic regions involved in adaptation to particular environmental variables (Colicchio et al, 2021; DeRaad et al, 2021). As the editors write in their conclusion, “the contributions presented in this special issue herald a new era in molecular ecology, as we anticipate that a burgeoning and widespread application of WGS will provide unprecedented insights into consequential questions in ecology and evolution,” (Taylor, Jensen, et al, 2021).…”

Section: Highlights Of 2021mentioning

confidence: 99%

“…The final special issue of 2021, “Whole genome sequencing in molecular ecology”, was edited by Rebecca Taylor, Evelyn Jensen, David Coltman, Andrew Foote, and Sangeet Lamichhaney. This timely special issue showcases “an array of studies that leverage the resolution of whole genome sequencing (WGS) to provide new insights into the molecular ecology of a range of species and ecosystems” (Taylor, Jensen, et al, 2021). One theme among the papers within the special issue centers on methodological approaches and advances in whole genome sequencing (WGS) and includes manuscripts highlighting the role of WGS in producing improved genome assemblies that allow a clearer picture of diversity at intra‐ and infra‐organismal levels (Blom, 2021; Wold et al, 2021; Yamaguchi et al, 2021).…”

Section: Highlights Of 2021mentioning

confidence: 99%

“…A final manuscript on this topic provides a comprehensive review of how the particular advantages of WGS compared to RRL allow for a fine‐scale picture of the evolutionary history of invasive species (North et al, 2021). As noted in the editorial, “WGS is assisting conservation by providing conclusive assessments of population structure, which when coupled with analyses of demographic history is providing deeper understanding into how populations arrived at their present states” (Taylor, Jensen, et al, 2021). A collection of papers in this special issue demonstrate the implications of such advances across charismatic study systems including Southern White Rhinos (Sánchez‐Barreiro et al, 2021), Komodo dragons (Iannucci et al, 2021), Galapagos tortoises (Jensen et al, 2021), Mexican wolves (Taron et al, 2021), and New Zealand's alpine parrots (Martini et al, 2021).…”

Section: Highlights Of 2021mentioning

confidence: 99%

See 1 more Smart Citation