Category Archives: theory

Opening Pandora’s box: PSMC and population structure

Essentially, all models are wrong, but some are useful. — George Box Publication of the Li and Durbin’s 2011 paper titled “Inference of human population history from individual whole-genome sequences” was a milestone in the inference of demography. By allowing … Continue reading

RedditDiggMendeleyPocketShare and Enjoy
Posted in bioinformatics, methods, Paleogenomics, population genetics, theory | Tagged , , , , | 3 Comments

RADseq and missing data: some considerations

Unlike Sanger sequencing, where loci are directly targeted for each individual and sequencing errors are relatively rare, massively multilocus datasets from next generation sequencing platforms are characterized by large amounts of missing data. This is particularly true for restriction digest … Continue reading

Posted in bioinformatics, genomics, methods, Molecular Ecology, the journal, next generation sequencing, phylogenetics, population genetics, theory | Tagged , , , | 5 Comments

Sweeps and Demographic Inference

Population genetics presents us with numerous conundrums – several of which have to do with how the same genomic disposition can be “reached” over evolutionary time with multiple alternate demographic or selective processes. I have discussed several of these issues … Continue reading

Posted in bioinformatics, evolution, genomics, population genetics, selection, theory | Tagged , , , | Leave a comment

What makes a range?

Why do species have restricted geographic distributions? Classic ecological perspectives tell us distribution limits occur where ecological parameters coincide with the boundaries of ecological niches. Evolutionary perspectives, on the other hand, surmise distribution boundaries reflect a failure of niche evolution. Though small … Continue reading

Posted in adaptation, evolution, plants, selection, theory | Tagged , , , , , | Leave a comment

The why’s of sex

Sex isn’t quite what it seems – while superficially wasteful in an evolutionary sense (why inherit on only one half of your genes, when you can inherit all of them asexually, or why waste resources in mating when you don’t … Continue reading

Posted in adaptation, evolution, genomics, mutation, natural history, next generation sequencing, population genetics, selection, theory, yeast | Tagged , , , , | Leave a comment

Are genetic drift and inbreeding the same thing?

Does it ever happen to you that the more you try to understand something, the more difficult to understand it turns out to be? Recently, I’ve had such a problem with two of the very basic microevolutionary phenomena – genetic … Continue reading

Posted in conservation, evolution, population genetics, quantitative genetics, theory, Uncategorized | Tagged , , , , , | Leave a comment

A different perspective on genetic architecture

As an ecological geneticist, I’m constantly reminded how much we don’t understand about the genetic nature of adaptive variation. Sure, we have lots of examples of genes/pathways/regions that seem to be responsible for adaptation, but we don’t really know if … Continue reading

Posted in association genetics, evolution, genomics, mutation, quantitative genetics, theory | Leave a comment