Small mammalian genomics of adaptation

While large mammals have had their day on our blog, two recent studies on small mammals reveal the genetics of size evolution in island mice, and differential introgression of mitochondrial and nuclear genomes in chipmunks – steps towards understanding the process of adaptive evolution to new environments post divergence.
Gray et al. (2015) study of the adaptation genetics through a common-garden cross-breeding experiment of the largest species of wild house mice – variants of Mus musculus domesticus on Gough Island (GI), a volcanic island in the Atlantic Ocean. These mice were introduced to the island within the last two centuries, and weigh almost twice as much as their common mice relatives. After creating inbred lines from cross-bred Gough Island mice and mainland common mice, all mice were phenotyped over 16 weeks, and genotyped with SNP arrays for QTL studies. Analyses of growth trajectories revealed significant weight differences between wild and lab-reared GI mice, and between GI and wild mice raised in similar environments. F1 hybrids from GI and wild mice indicate similarities in growth up until 3 weeks, and closer to mid-parent values beyond, with F2’s varying widely in weight at all ages, apart from evidence of sex related, maternal, and line effects. They identify 8 QTL for weight differences, and 11 for growth rate differences, with variance in timing of their greatest effects across crosses, and offer hypotheses for the evolution of body size in newly isolated populations of mice.

This research is a first, necessary, and foundational step toward pinpointing the genetic variants responsible for increased size in GI mice. Identifying the causative genes and mutations will allow several intriguing evolutionary questions to be answered. Did selection on Gough Island target standing variants or new mutations? Do the causative loci show signatures of adaptive evolution predicted by strong selection on individual loci or by selection spread across many genes?

Smart adaptation to food availability…

Good et al. (2015) in a study of introgression during “secondary contact” in two species of chipmunks – yellow-tailed Tamias amoenus, and red-tailed Tamias ruficaudus, attempt to characterize the frequency and importance of hybridization during speciation. Via genome-wide targeted re-sequencing of over 10,000 exonic regions, characterization of the species super-trees for autosomal and X chromosome loci, the authors report discordance of up to a 20 times lower potential introgression in the X. With further analyses using an ABBA-BABA framework, indicated less than 1% of total nuclear loci to have introgressed from either species, a stark contrast to mitochondrial work previously suggested.
"The Essence of the Yellow Pine Chipmunk" - Image courtesy Alex Badyaev -

“The Essence of the Yellow Pine Chipmunk” – Image courtesy Alex Badyaev –

With respect to the overall importance of hybridization, we must ultimately understand what the contribution of introgressed alleles has been to adaptive evolution…However, to understand the broader importance of hybridization to adaptation we must ultimately understand what proportion of adaptive variants derive from introgression versus mutation and standing genetic variation within species.

Gray, Melissa M., et al. “Genetics of Rapid and Extreme Size Evolution in Island Mice.” Genetics (2015): genetics-115. DOI: 10.1534/genetics.115.177790
Good, Jeffrey M., et al. “Negligible nuclear introgression despite complete mitochondrial capture between two species of chipmunks.” Evolution (2015). DOI: 10.1111/evo.12712

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