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Category Archives: genomics
Anti-predatory adaptations in sticklebacks and butterflies
Two recent studies analyze character shifts in response to different selection regimes – (1) Mullerian mimicry wing patterns in Heliconius butterflies, and (2) anti-intraguild-predator adaptations in armor and shape of threespine sticklebacks. Hoyal Cuthill and Charleston 2015 Wing patterning genes … Continue reading
Clinal genomic variation in Drosophila species
Two recent manuscripts describe adaptive evolutions to clinal/latitudinal variations in Drosophila species to supplement a growing wealth of recent studies on geographic variation and adaptive evolution in natural populations of fruitflies (eg. see Kao et al. 2015, Zhao et al. … Continue reading
A Nice opinion on confronting uncertainty and modeling it for GBS data
Just over a week ago, I had the opportunity to work in Chris Nice‘s lab at Texas State University. I was accompanied by one of our MS students, Ben, and my colleague, Erik Sotka, to prep libraries for a genomic … Continue reading
Genomics of domestication in chicken and cattle
Two recent studies attempt to understand the process of adaptive evolution in domestication and artificial selection by characterizing (a) sweeps, and their association with phenotypes in extant hybrid lines (Sheng et al. 2015), and (b) phylogenomic position of an extinct … Continue reading
Posted in adaptation, bioinformatics, domestication, evolution, genomics, natural history, Paleogenomics, phylogeography, population genetics, selection, speciation, STRUCTURE
Tagged domestication, ecological speciation, Evolution, hybridization, natural selection, population genetics, population structure
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On false positives in Isolation with Migration analyses
The IM suite of tools (IM, IMa, IMa2, IMa2p, etc.) are used widely by molecular ecologists at large for the analyses and estimation of ancestral demography under an Isolation with Migration (IM) model. However, these tools come with fundamental assumptions … Continue reading
Posted in evolution, genomics, howto, IMa2, methods, Molecular Ecology views, natural history, population genetics, software, theory
Tagged Evolution, gene flow, genomics, IM, isolation with migration, methods, migration, population genetics
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On background selection in Ficedula flycatchers
Several recent studies (including those I wrote about last week) use genome-wide scans of differentiation to understand evolutionary mechanisms behind high or low divergence. However, there has been contentious support for and against these differentiation islands being due to differential … Continue reading
Introgression history in sticklebacks and oaks
Speciation theory has many monikers for differential gene flow – migration, introgression, admixture, hybridization, secondary contact. As a homogenizing process, gene flow at large acts to reduce differentiation between populations post-divergence. However, selection and demography affect the rates of gene … Continue reading
Sweptaway – Part 3 – Adaptation genomics of White Sands Lizards
Recent colonization events offer juicy insights into the adaptive evolution of species in response to natural selection of novel habitats – however, they are confounded by demographic changes (eg. bottlenecks, differential migration). In a recent study, Laurent et al. (2015) … Continue reading
Sweptaway – Part 2
Numerous methods have been developed over the last few years for the detection of selective sweeps (hard and soft – see my previous post). This week, we look at three new studies that (a) compare existing methods to detect sweeps … Continue reading
Posted in adaptation, bioinformatics, evolution, genomics, methods, population genetics, selection, software, theory
Tagged genomics, methods, natural selection, population structure
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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 … Continue reading
Posted in adaptation, domestication, evolution, genomics, natural history, pedigree, phylogenetics, population genetics, selection
Tagged Evolution, gene flow, genomics, natural selection
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