HENRY

Nick Thieberger, who runs the wonderful PARADISEC project talks about what happened at The Puliima National Indigenous Languages Information Communication Technology Forum, including new software for linguists, and some new language preservation projects.

Pete Lockhart reviews some new phylogenetic methods for detecting and resolving rapid radiation events (abstract only):

A deeper phylogenetic understanding of ancient patterns of diversification would contribute to solving many problems in evolutionary biology, yet many of these phylogenies remain poorly resolved. Ancient rapid radiations pose a major challenge for phylogenetic analysis for two main reasons. First, the pattern to be deciphered, the order of divergence among lineages, tends to be supported by small amounts of data. Second, the time since divergence is large and, thus, the potential for misinterpreting phylogenetic information is great. Here, we review the underlying causes of difficulty in determining the branching patterns of diversification in ancient rapid radiations, and review novel data exploration tools that can facilitate understanding of these radiations.

The paper that had been causing all the noise about differential rates of gene selection in humans and chimps has finally been released:

Observations of numerous dramatic and presumably adaptive phenotypic modifications during human evolution prompt the common belief that more genes have undergone positive Darwinian selection in the human lineage than in the chimpanzee lineage since their evolutionary divergence 6–7 million years ago. Here, we test this hypothesis by analyzing nearly 14,000 genes of humans and chimps. To ensure an accurate and unbiased comparison, we select a proper outgroup, avoid sequencing errors, and verify statistical methods. Our results show that the number of positively selected genes is substantially smaller in humans than in chimps, despite a generally higher nonsynonymous substitution rate in humans. These observations are explainable by the reduced efficacy of natural selection in humans because of their smaller long-term effective population size but refute the anthropocentric view that a grand enhancement in Darwinian selection underlies human origins.

Although human and chimp positively selected genes have different molecular functions and participate in different biological processes, the differences do not ostensibly correspond to the widely assumed adaptations of these species, suggesting how little is currently known about which traits have been under positive selection. Our analysis of the identified positively selected genes lends support to the association between human Mendelian diseases and past adaptations but provides no evidence for either the chromosomal speciation hypothesis or the widespread brain-gene acceleration hypothesis of human origins.

Abstract is here

Language Description, History and Development: Linguistic indulgence in memory of Terry Crowley, contains a who’s who of Austronesian (and otherwise!) linguists all showing their respect for the late Terry Crowley (Bonus link)

Selten and Warglien in P.N.A.S. try to experimentally evolve a new language:

We investigate in a series of laboratory experiments how costs and benefits of linguistic communication affect the emergence of simple languages in a coordination task when no common language is available in the beginning. The experiment involved pairwise computerized communication between 152 subjects involved in at least 60 rounds. The subjects had to develop a common code referring to items in varying lists of geometrical figures distinguished by up to three features. A code had to be made of a limited repertoire of letters. Using letters had a cost (…) Our experiments show that a too small repertoire of letters causes coordination failures. Cost efficiency and role asymmetry are important factors enhancing communicative success. In stable environments, grammars do not seem to matter much, and instead efficient arbitrary codes often do better. However, in an environment with novelty, compositional grammars offer considerable coordination advantages and therefore are more likely to arise.

Update: John Hawks goes into more detail

….Mursi Tribeswoman with iPod and AK-47 ?

Obviously staged (note the pile of cash in her hand), but beautiful none the less.

The BlindScientist interviews Joe Felsenstein one of the founders of modern phylogenetics:

The maximum likelihood method for phylogenies was introduced by Edwards and Cavalli-Sforza in 1964, and for molecular sequences it was first done by the great statistician Jerzy Neyman in 1971. My 1981 paper did cite Neyman (it didn’t credit Edwards and Cavalli-Sforza but at least I have cited their pioneering work on this many times before and since). What I did that was new was to make it practical to do multi-species cases by introducing the pruning algorithm. I also promoted and explained ML for years. In the 1980s I gave many talks at universities. I usually had to explain what likelihood was because the statistics courses that biologists took didn’t bother to teach them this.

I also wrote a number of review articles and made programs available to do ML. Of my papers, the 1981 ML paper is the third most cited so far (after the 1985 bootstrap paper, a paper in 1989 in Cladistics describing PHYLIP, and just ahead of my 1985 paper on phylogenetic comparative methods). Basically they are all part of the process of promoting a statistical modelling approach to phylogenies, so it is hard to label one as more important. Possibly my most important paper in the long run will be my 1978 paper on a model of macroevolution, which has had no citations in the past 22 years.