Category Archives: genomics

Genomic diversity and secondary contact

Under a divergence, or isolation model, the genomes of individuals in a daughter-population are expected to harbor greater differentiation relative to its sister-population, and lower differentiation within the population (after sufficient time since divergence). Divergence thus is a mechanism of … Continue reading

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Another lesson in genomics experimental design and avoiding batch effects

Twitter has been abuzz with Orna Man and Yoav Gilad’s (re)analysis of the data from a recent PNAS paper: “Comparison of the transcriptional landscapes between human and mouse tissues”. The PNAS paper concluded that the gene expression profiles of different … Continue reading

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When genomes duplicate

Whole genome duplication events have played an important role in the evolutionary history of plants. Vallejo-Marín et al. (2015) describe origins of a new polyploid species, Mimulus peregrines, found on the Scottish mainland as well as the Orkney Islands. It was formed within … Continue reading

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Gene flow and Population Fitness

Fitness effects of gene flow (both advantageous and deleterious) have garnered plenty of recent press and scientific exploration. At the population level, the concepts and consequences are notoriously familiar. In the context of immigration, they reduce to existing genetic variation, … Continue reading

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Sous les mers: cradles or museums of biodiversity?

While thinking about environmental genomics and writing this post on a recent article in Heredity, I interviewed Eric Pante.

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Grasping gorgonians

A recent issue of Heredity focused on the brave new world of environmental genomics. After highlighting the special issue, I started chatting to one of the contributors, Eric Pante and became interested in his work on gorgonians. Eric and his co-authors explored the … Continue reading

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Quantifying risks of consanguineous mating in humans

The efficacy of selection in purging a deleterious mutation from a randomly mating population depends on numerous factors, including dominance effects of alleles – see my previous posts. Simplistically, most new mutations are expected to be heterozygotic, and be purged … Continue reading

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A mammoth bottleneck prior to extinction

Here’s to back-to-back posts on extinct mammalian genomes! Woolly mammoth genomes are all the rage. How do I know? Just check out the new book, pre-print, and paper that were recently published.

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Extinct and extant Equus genomes reveal speciation with gene flow despite chromosome number variation

In their recent PNAS paper*, Hákon et al. generate full genome sequence data for each living species of asses and zebras, thus completing the set of genomes available for all extant species in the genus Equus (genomes for the donkey and … Continue reading

Posted in genomics, speciation | 1 Comment

Procrustes Analyses in R

Procrustes transformations (i.e. a form of multidimensional scaling that allows the comparison of two data sets) have been used extensively in recent literature to assess the similarity of geographical and genetic distributions of species, following the lead of Wang et … Continue reading

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