Category Archives: theory

Is equilibrium out of reach or are there some sneaky bouts of sex?

Posted on 30 Aug, 2016 by Stacy Krueger-Hadfield

Reproductive systems impact the evolution of genetic diversity at the population level. Yet, we don’t know a lot about organisms that are partially clonal, despite the large component of biodiversity that dabbles in asexual reproduction to varying degrees. Clonal dynamics are … Continue reading →

Posted in bioinformatics, evolution, genomics, natural history, next generation sequencing, theory | Tagged , , , | 1 Comment

Opening Pandora's box: PSMC and population structure

Posted on 18 May, 2016 by Patrícia Chrzanová Pečnerová

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 →

Posted in bioinformatics, methods, Paleogenomics, population genetics, theory | Tagged , , , , | 6 Comments

RADseq and missing data: some considerations

Posted on 10 May, 2016 by Ethan Linck

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 , , , | 6 Comments

Sweeps and Demographic Inference

Posted on 25 Apr, 2016 by Arun Sethuraman

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 →

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What makes a range?

Posted on 1 Apr, 2016 by Stacy Krueger-Hadfield

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

Posted on 25 Mar, 2016 by Arun Sethuraman

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?

Posted on 14 Mar, 2016 by Patrícia Chrzanová Pečnerová

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

Posted on 1 Mar, 2016 by Reid Brennan

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

The Carnivorous Rodents of Southeast Asia

Posted on 15 Feb, 2016 by Bryan McLean

Whoa, Wallace. There be carnivorous rats on those islands. Sixty-two species, to be exact, across the broader Indo-Australian Archipelago. Among them are small- and large-bodied rats, worm-eaters with elongated snouts (“vermivores”), and even amphibious forms (Fig. 1), and they are … Continue reading →

Posted in adaptation, evolution, natural history, phylogenetics, theory | Leave a comment

Genomics of Hybridization – Part II, Top three of 2015

Posted on 28 Jan, 2016 by Arun Sethuraman

Death Valley pupfishes (Cyprinodon) are among the most endangered vertebrates on earth, with small inbred populations, with heavy risks of extinction in extreme environments. Martin et al. (2016) in a recent publication quantify diversity and adaptability in a very small population … Continue reading →

Posted in bioinformatics, conservation, genomics, methods, natural history, next generation sequencing, population genetics, R, software, speciation, STRUCTURE, theory | Tagged , , , , | Leave a comment