The Traveler’s Restaurant Process — A Better Description of the Dirichlet Process for Partitioning Sets

[latexpage] I. "Have Any of These People Ever Been to a Chinese Restaurant?" The Dirichlet process is a stochastic process that can be used to partition a set of elements into a set of subsets. In biological modeling, it is commonly used to assign elements into groups, such as molecular sequence sites into distinct rate categories. Very often, an intuitive explanation as to how it works invokes the "Chinese Restaurant Process" analogy. I have always found this analogy very jarring and confusing, Read more [...]

“Pre-Columbian Mycobacterial Genomes Reveal Seals As A Source Of New World Human Tuberculosis”

When, in 1994, definitive evidence of tuberculosis in humans was reported from pre-Columbian America, it was a startling. Conventional understanding had pegged tuberculosis as part of the new, exotic, and (to immunologically-naive populaces) deadly menagerie of pathogens brought by Europeans over to the Americas. While there were suggestions of pre-Columbian tuberculosis in the Americans, these were based on lesions on bones, which were ambiguous. Unlike previous cases, however, the Chiribaya mummy Read more [...]

Multispecies Coalescent Species Delimitation: Conflating Populations with Species in the Grey Zone (Evolution 2017 Talk)

Folks! The always fantastic Evolution meetings were a blast. So many great talks, and, perhaps more importantly, great catching up with so many friends, collaborators, and colleagues! I presented a talk on our PNAS paper showing how the Multispecies Coalescent model, when used for "species" delimitation, actually delimits Wright-Fisher populations. Titled "Multispecies Coalescent Species Delimitation: Conflating Populations with Species in the Grey Zone", the entire talk can Read more [...]

“Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous–Paleogene boundary”

Some nice work that ties the timing of the radiation of three independent lineages of frogs, constituting the majority of modern living frogs, to about the time the major groups of dinosaurs took a hit (literally and figuratively!). Compelling and interesting story, with lots of intriguing follow-up questions. A more general article covering the findings is available here. Yan-Jie Feng, David C. Blackburn, Dan Liang, David M. Hillis, David B. Wake, David C. Cannatella, and Peng Zhang. Read more [...]

Evolution of Bioluminescence in Millipedes

Walk deep into a rainforest at night. Switch off your headlamps. And wait with open eyes. At first, it is so pitch black that you cannot see your own hand if you wave it in front of nose (as Bilbo might have said). As your eyes get accustomed to the darkness, you will realize one thing. Everything glows. Everything. There is fine fuzzy layer of bioluminescent fungus covering dead leaves and the bark of trees, so you can almost make out the forest like some one has traced it out in ghostly yellow-green Read more [...]