Category Archives: phylogenetics

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

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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

Pre-adapted algal ancestors colonized land

The colonization of land by plants 450 Mya marked a major transition on Earth and was one of the critical events that led to the emergence of extant terrestrial ecosystems. Chief among the challenges the terrestrial environment presented for these … Continue reading

Posted in adaptation, bioinformatics, Coevolution, evolution, genomics, haploid-diploid, next generation sequencing, phylogenetics, plants, transcriptomics | Tagged | Leave a comment

The scent of home

We decided to divide and conquere the west coast of North America in search of more populations of Gracilaria vermiculophylla, as if we didn’t already have enough by Midsummer’s Eve! I headed to my home state – California. I was able to sneak … Continue reading

Posted in adaptation, DNA barcoding, evolution, haploid-diploid, natural history, phylogenetics | Tagged , , , , , | Leave a comment

Anti-predatory adaptations in sticklebacks and butterflies

Two recent studies analyze character shifts in response to different selection regimes – (1) Mullerian mimicry wing patterns in Heliconius butterflies, and (2) anti-intraguild-predator adaptations in armor and shape of threespine sticklebacks. Hoyal Cuthill and Charleston 2015 Wing patterning genes … Continue reading

Posted in adaptation, Coevolution, evolution, genomics, natural history, phylogenetics, phylogeography, population genetics, selection, speciation | Tagged , , , | Leave a comment

Introgression history in sticklebacks and oaks

Speciation theory has many monikers for differential gene flow – migration, introgression, admixture, hybridization, secondary contact. As a homogenizing process, gene flow at large acts to reduce differentiation between populations post-divergence. However, selection and demography affect the rates of gene … Continue reading

Posted in adaptation, evolution, genomics, natural history, phylogenetics, population genetics, selection, speciation, species delimitation | Tagged , , , , , | 1 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

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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Small mammalian genomics of adaptation

While large mammals have had their day on our blog, two recent studies on small mammals reveal the genetics of size evolution in island mice, and differential introgression of mitochondrial and nuclear genomes in chipmunks – steps towards understanding the … Continue reading

Posted in adaptation, domestication, evolution, genomics, natural history, pedigree, phylogenetics, population genetics, selection | Tagged , , , | Leave a comment

And who made your beer?

In the spirit of it being almost Friday, and while we’re on the topic of your favorite beverages – perhaps wine puts you to sleep, couldn’t care less where it came from, but prefer the bitterness of lager beers at your … Continue reading

Posted in adaptation, evolution, genomics, natural history, next generation sequencing, phylogenetics, population genetics, selection, speciation, yeast | Tagged , , , , | 2 Comments