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

Molecular Ecology
Anna TiganoMatthew D MacManes

Abstract

Organisms 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 ...Continue Reading

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Citations

Mar 11, 2020·Molecular Ecology Resources·Jocelyn P ColellaMatthew D MacManes
Jan 19, 2021·Evolution; International Journal of Organic Evolution·Noëlle K J BittnerMichael W Nachman
Mar 10, 2021·The Journal of Heredity·Jocelyn P ColellaMatthew D MacManes
Apr 18, 2021·Trends in Ecology & Evolution·Joana L RochaRasmus Nielsen
May 29, 2021·The Journal of Animal Ecology·Raúl Araya-DonosoDavid Véliz
Jul 27, 2021·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Nicolás LichilínAstrid Böhne
Jul 10, 2021·Molecular Biology and Evolution·Hengwu JiaoHuabin Zhao
Sep 9, 2021·The Journal of Experimental Biology·Jocelyn P ColellaMatthew D MacManes

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Datasets Mentioned

BETA
PRJNA494228

Methods Mentioned

BETA
Genome Sequencing
PCA
MDS
Hi‐C

Software Mentioned

samblaster
mummer4
ngsCovar
ANGSD
ngstools
busco
pilon
Juicebox
juicer
longranger

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