Loquat ( Eriobotrya japonica (Thunb . ) Lindl) population genomics suggests a two‐staged domestication and identifies genes showing convergence/parallel selective sweeps with apple or peach

Population genomics of rapid adaptation by soft selective sweeps

Trends in Ecology & Evolution ◽

10.1016/j.tree.2013.08.003 ◽

2013 ◽

Vol 28 (11) ◽

pp. 659-669 ◽

Cited By ~ 305

Author(s):

Philipp W. Messer ◽

Dmitri A. Petrov

Keyword(s):

Population Genomics ◽

Selective Sweeps ◽

Rapid Adaptation ◽

Soft Selective Sweeps

Download Full-text

Comparative and population genomics approaches reveal the basis of adaptation to deserts in a small rodent

10.1101/856310 ◽

2019 ◽

Author(s):

Anna Tigano ◽

Jocelyn P. Colella ◽

Matthew D. MacManes

Keyword(s):

North America ◽

Population Genomics ◽

Protein Denaturation ◽

Gene Families ◽

Small Rodent ◽

Selective Sweeps ◽

Cellular Mechanisms ◽

Dietary Shift ◽

Recent Emergence ◽

Signature Of Selection

AbstractOrganisms that live in deserts offer the opportunity to investigate how species adapt to environmental conditions that are lethal to most plants and animals. In the hot deserts of North America, high temperatures and lack of water are conspicuous challenges for organisms living there. The cactus mouse (Peromyscus eremicus) displays several adaptations to these conditions, including low metabolic rate, heat tolerance, and the ability to maintain homeostasis under extreme dehydration. To investigate the genomic basis of desert adaptation in cactus mice, we built a chromosome-level genome assembly and resequenced 26 additional cactus mouse genomes from two locations in southern California (USA). Using these data, we integrated comparative, population, and functional genomic approaches. We identified 16 gene families exhibiting significant contractions or expansions in the cactus mouse compared to 17 other Myodontine rodent genomes, and found 232 sites across the genome associated with selective sweeps. Functional annotations of candidate gene families and selective sweeps revealed a pervasive signature of selection at genes involved in the synthesis and degradation of proteins, consistent with the evolution of cellular mechanisms to cope with protein denaturation caused by thermal and hyperosmotic stress. Other strong candidate genes included receptors for bitter taste, suggesting a dietary shift towards chemically defended desert plants and insects, and a growth factor involved in lipid metabolism, potentially involved in prevention of dehydration. Understanding how species adapted to the recent emergence of deserts in North America will provide an important foundation for predicting future evolutionary responses to increasing temperatures, droughts and desertification in the cactus mouse and other species.

Download Full-text

Fine-mapping the Favored Mutation in a Positive Selective Sweep

10.1101/139055 ◽

2017 ◽

Cited By ~ 5

Author(s):

Ali Akbari ◽

Joseph J. Vitti ◽

Arya Iranmehr ◽

Mehrdad Bakhtiari ◽

Pardis C. Sabeti ◽

...

Keyword(s):

Selective Sweep ◽

Population Genomics ◽

Simulated Data ◽

Human Populations ◽

Selective Sweeps ◽

1000 Genomes ◽

Candidate Mutation ◽

African Populations ◽

Signature Of Selection ◽

Out Of Africa

AbstractMethods to identify signatures of selective sweeps in population genomics data have been actively developed, but mostly do not identify the specific mutation favored by the selective sweep. We present a method, iSAFE, that uses a statistic derived solely from population genetics signals to pinpoint the favored mutation even when the signature of selection extends to 5Mbp. iSAFE was tested extensively on simulated data and in human populations from the 1000 Genomes Project, at 22 loci with previously characterized selective sweeps. For 14 of the 22 loci, iSAFE ranked the previously characterized candidate mutation among the 13 highest scoring (out of ∼ 21, 000 variants). Three loci did not show a strong signal. For the remaining loci, iSAFE identified previously unreported mutations as being favored. In these regions, all of which involve pigmentation related genes, iSAFE identified identical selected mutations in multiple non-African populations suggesting an out-of-Africa onset of selection. The iSAFE software can be downloaded from https://github.com/alek0991/iSAFE.

Download Full-text