Category Archives: methods

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

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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

Posted in conservation, methods, population genetics | Tagged | 1 Comment

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 , , , | Leave a comment

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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Environmental association analyses: a practical guide for a practical guide

Obtaining extensive SNP data for your organism of choice isn’t such a feat these days, but actually matching that breadth of data with appropriate analyses is still a challenge. Fortunately, there has been an avalanche of new methods to make … Continue reading

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Models matter when linking genetic diversity to niche model predictions

Ecological niche models and the methods to create them continue to evolve. These techniques provide a tidy way to relate the distributions of taxa to environmental variables from the present, past, or future. Oh, and they are pretty too: Those pretty … Continue reading

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Mixed modeling of methylation measures (increase your power by 60%)

Do you want to increase your power to detect differentially methylated CpG sites by 60%*? Yes?! Then do I have the pre-print for you.

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Conversation starter: common mistakes in population genetics

When interpreting the results, it is important to focus more on biological relevance than on statistical significance. That does not mean that significance is unimportant; results that have a straightforward interpretation but are not significant should not be considered. On the … Continue reading

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