Category Archives: methods

Genomics of Hybridization – Part II, Top three of 2015

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

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

Genomics of Hybridization – Part 1

In a series of articles, I will discuss recent advances in hybridization genomics – the fundamentals of adaptive introgression, “islands of speciation”, differential gene flow, and linked selection have been discussed in my previous posts (here, here, and also at … Continue reading

Posted in adaptation, evolution, genomics, methods, natural history, next generation sequencing, pedigree, phylogenetics, plants, population genetics, RNAseq, software, speciation, species delimitation, STRUCTURE, theory, transcriptomics | Tagged , , , , , , | Leave a comment

Comparing your options for phylogenomic data

The choices for current-generation (last generation?) molecular markers are grouped in two primary camps. First, the “reduced representation” methods: take some DNA, cut it up with specific enzymes, tag those pieces, read the sequences. These methods produce lots and lots of … Continue reading

Posted in methods, next generation sequencing, phylogenetics | Tagged , , | 2 Comments

The biggest problem in landscape genetics and how to fix it

Landscape genetics is a field that has expanded rapidly in recent years, but that doesn’t mean that it hasn’t gone without criticism. Perhaps the largest problem with landscape genetics (LG) studies is one of timing. If you observe genetic differentiation … Continue reading

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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 , , , , , , , | Leave a comment

Measuring dispersal rate in Neotropical fishes in units of ‘wallace’

Alfred Russel Wallace often gets second billing compared to Charles Darwin but in a paper recently accepted at Systematic Biology, Tagliacollo et al.  define a new term for their analyses (dispersal rate, D) and measure D in units of ‘wallaces‘ (wa) to honor the contributions of Alfred … Continue reading

Posted in methods, phylogenetics, phylogeography, Uncategorized | 1 Comment

Landscape genetics shows that Tanzanian forest monkeys feel the heat of human influence

A new publication appearing in Heredity applies new methods for associating population genetic data with landscape resistance to an tropical, endangered species. The authors utilize multiple measurements of landscape resistance, like forest cover and distance from the nearest village, to select the … Continue reading

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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

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The Goldilocks zone of missing data

Reduced representation sequencing approaches, such as RADseq and UCEs, have provided some fascinating inferences in recent years, but something has always been missing in these analyses: data. As sampled taxa become more divergent, the price paid for more loci is … Continue reading

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Picking the ripest model with PHRAPL

To study patterns of genetic variation is to consider scale. The choices an investigator makes when designing a study can produce such a beautiful breadth of evolutionary patterns: from populations to species, from local to continental, from ancient to contemporary. The fields that … Continue reading

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