A fast, reproducible, high-throughput variant calling workflow for population genomics

CD Mirchandani, AJ Shultz… - Molecular Biology …, 2024 - academic.oup.com
The increasing availability of genomic resequencing data sets and high-quality reference
genomes across the tree of life present exciting opportunities for comparative population …

Revisiting the role of genetic variation in adaptation

D Agashe, M Sane, S Singhal - The American Naturalist, 2023 - journals.uchicago.edu
Evolutionary biologists have thought about the role of genetic variation during adaptation for
a very long time—before we understood the organization of the genetic code, the …

Origin matters: Using a local reference genome improves measures in population genomics

DMJ Thorburn, K Sagonas… - Molecular ecology …, 2023 - Wiley Online Library
Genome sequencing enables answering fundamental questions about the genetic basis of
adaptation, population structure and epigenetic mechanisms. Yet, we usually need a …

Investigating diadromy in fishes and its loss in an-omics era

ML Delgado, DE Ruzzante - Iscience, 2020 - cell.com
Diadromy, the predictable movements of individuals between marine and freshwater
environments, is biogeographically and phylogenetically widespread across fishes. Thus …

Genomic basis of parallel adaptation varies with divergence in Arabidopsis and its relatives

M Bohutínská, J Vlček, S Yair… - Proceedings of the …, 2021 - National Acad Sciences
Parallel adaptation provides valuable insight into the predictability of evolutionary change
through replicated natural experiments. A steadily increasing number of studies have …

Parallel genetic evolution and speciation from standing variation

KA Thompson, MM Osmond, D Schluter - Evolution Letters, 2019 - academic.oup.com
Adaptation often proceeds from standing variation, and natural selection acting on pairs of
populations is a quantitative continuum ranging from parallel to divergent. Yet, it is unclear …

Shared ancestral polymorphisms and chromosomal rearrangements as potential drivers of local adaptation in a marine fish

H Cayuela, Q Rougemont, M Laporte… - Molecular …, 2020 - Wiley Online Library
Gene flow has tremendous importance for local adaptation, by influencing the fate of de
novo mutations, maintaining standing genetic variation and driving adaptive introgression …

Reinventing the wheel? Reassessing the roles of gene flow, sorting and convergence in repeated evolution

JM Waters, GA McCulloch - Molecular Ecology, 2021 - Wiley Online Library
Biologists have long been intrigued by apparently predictable and repetitive evolutionary
trajectories inferred across a variety of lineages and systems. In recent years, high …

Ecological diversification in an adaptive radiation of plants: the role of de novo mutation and introgression

BW Stone, CA Wessinger - Molecular Biology and Evolution, 2024 - academic.oup.com
Adaptive radiations are characterized by rapid ecological diversification and speciation
events, leading to fuzzy species boundaries between ecologically differentiated species …

Selection on standing genetic variation mediates convergent evolution in extremophile fish

K Ryan, R Greenway, J Landers… - Molecular …, 2023 - Wiley Online Library
Hydrogen sulfide is a toxic gas that disrupts numerous biological processes, including
energy production in the mitochondria, yet fish in the Poecilia mexicana species complex …