Tuesday, March 31, 2009

One More Reason to Love Geneious

We at the AMNH have been adopting Geneious as well and after we recently purchased several copies, they donated licenses on our behalf to Diponegoro University in Indonesia, the International Centre of Insect Physiology in Kenya and the University of the Philippines Marine Science Institute, places which some of our postdocs have been collaborating. The press release that the company just released about this states that they have developed a general practice of providing discounts to researchers in low GDP countries to help promote bioinformatics around the world. Broader impacts included the box!

Hey R Users! Time to Update ape

The ape package written by Emmanuel Paradis is the foundation for phylogenetic analyses in R. Yesterday, Paradis and his coauthors posted a new version (3.2) on the CRAN archive yesterday. There don't seem to be too many new functions, but there are some important bug fixes. One these - preventing calculation of negative state probabilities when reconstructing discrete character states - solves one of the more vexing problems I've had with the ace function. You should definitely get the update if you're doing ancestral reconstruction of discretely coded traits! Now we just need to hope the April 17th upgrade to R 2.9 goes smoothly...

Sunday, March 29, 2009

Speciation with gene flow?

Liam’s post on nested clade analysis (below) reminded me of this very recent paper by Becquet and Przeworski (Evolution, online accepted). Many of us are interested in understanding whether speciation typically entails an abrupt cessation of gene flow between populations, or whether the process is “leaky”, with continued exchange of migrants after the initial population split. These are typically referred to as the “isolation” and “isolation-migration” models, and several computational tools have been developed to estimate parameters relevant to the isolation-migration model (IM, MIMAR).

Becquet and Przeworski look at both of these programs (and MIMAR is one of their own) and ask the simple question of how they perform when some of their underlying assumptions are violated. Their answer: not as well as one might like. When ancestral populations are structured, both IM and MIMAR can lead to rejections of a true allopatry (isolation only) model, even when there is no post-separation gene-flow. Moreover, parameter estimates – including divergence time and ancestral population sizes – become unreliable when there is ancestral population structure or when gene-flow rates change through time. Real population histories likely involve both time-varying levels of gene flow and complex current and historical population structure and it is not clear how to develop methods that are robust to a broad range of potential splitting scenarios. Approximate Bayesian methods, anyone?

Friday, March 27, 2009

A method that fails . . . or why can’t we all just get along?

Nested Clade Phylogeographic Analysis (NCPA) ranks among the mostly widely used methods in the gene-genealogy based analysis of intraspecific phylogeography. The method was originally described more than 13 years ago (Templeton et al. 1995), and has by some accounts (e.g., Knowles 2008) been used over 1700 times. Certainly, the original description of the method has been cited over 600 times, a number that continues to grow (with 8 citations already reported for 2009 at the time of writing). The method has also been described elsewhere, including in Alan Templeton’s recent book. The primary innovation of the method when introduced (as purported in Templeton et al. 1995 and Templeton 2006) is that by incorporating the temporal information of gene trees, the procedure extends our phylogeographic inference capabilities beyond the traditional FSTs and Nms of classical population genetics.

Nielsen and Beaumont (2009; pp. 1037-1038) provide a wonderfully succinct description of NCPA. Given a sample of haplotypes at a given genetic locus, the user first identifies an estimate of the haplotype network for the sample. He or she then hierarchically agglomerates sets of haplotypes separated by 1, 2, 3, . . ., etc. mutational steps. Next, the user calculates statistics describing the geographic dispersion within clades and between nested clades, and compares these statistics to those obtained by permuting geographical information among samples - retaining the distances from the clades with significant statistics for comparison to an inference key. Inferences liable to result from the procedure include such things as range expansion, long distance migration, and geographic fragmentation.

However, the method has received some pointed criticism as well, most notably from Lacey Knowles at the University of Michigan. Recently, Knowles and Templeton exchanged vitriolic attacks in the pages of the journal Evolution (Knowles 2008; Templeton 2009). Earlier, Knowles and Maddison (2002; maybe someone can tell me why the article, pp. 2623-2635, is missing from the online journal issue here) published a simulation study sharply critical of the method in Molecular Ecology, and Templeton (2004) responded in kind. Criticized shortcomings of the method include an exceedingly high type I error rate in simulation studies (estimated to be ~20% by Templeton 2008, but as high as 75% in other analyses), and subjectivity in the agglomeration of nested clades and in the application of the method's inference key. Other detailed critiques of NCPA can be found in Beaumont and Panchal (2008) and in Nielsen and Beaumont (2009) (the latter even includes a fascinating discussion of the 'Forer effect' as it might pertain to this method).

How do the readers of this blog perceive the current standing of NCPA? Furthermore, but on a much more philosophical note, how do readers view the kind of heated exchange partaken of by Knowles (2008) and Templeton (2009)? Is it true (to paraphrase A. N. Whitehead) that the clash of ideas is more of an opportunity than a calamity?

Note: For other fun exchanges in the recent literature among people I know, please check out: Downhower et al. (2009) and the response by Langerhans and Gifford (2009); or Bokma (2008), and the reply by Rabosky and Lovette (2008).

Tuesday, March 24, 2009

Real Life Muppets

I just returned from some fieldwork in Tanzania along with Luke Mahler, a grad student in the Losos Lab at Harvard. We were collecting chameleons and other herps for his work on ecological and morphological evolution and my work on lizard malaria parasites. It was a pretty successful trip (just surviving the immigration office in Dar es Salaam was a huge accomplishment!) with some really cool species found - including this Rhampholeon species from near the Udzungwe Mountains. This tiny creature (about 4 cm long) has to have inspired a Muppet or two.

Monday, March 23, 2009

PAUP GUI is Back

The folks at the Woods Hole Workshop on Molecular Evolution have posted a new version of the PAUP* GUI for Mac OSX. This link replaces one to an expired version of this GUI that was posted last year. If last year's version is any indication, it seems likely that this new version will expire at some point a few months from now. The new version of the GUI remains only partly functional and very buggy. Nevertheless, you may find it useful for some basic fuctions if you haven't yet learned how to use the fully-functional command line version of PAUP*. The link and the GUI executable itself are unsecured, though a line appears when you run the application saying "This version prepared for exclusive use fo authorized course participants." I'll start feeling guilty about using it as soon as I get the PAUP* manual I bought from Sinauer years ago.

Sunday, March 22, 2009

Best short Darwin biography?

I just finished “The Reluctant Mr Darwin” by David Quammen. This book is an absolute gem, and I had a hard time putting it down. At ~200 pages, even those with the shortest of attention spans will find this an enthralling read. This is a refreshing look at Darwin the mortal, Darwin the ever-curious naturalist with – even by Victorian standards – rather curious social habits. This may inspire me to give the original Desmond and Moore biography a second try, though it has sat on my shelf for a good number of years gathering dust….

My favorite passage in Quammen’s book is when he is giving a very strong endorsement for a reading of the Origin in the original: “Ignore the paperback reprints of the sixth edition. Trust no one; before you buy, before you read, check the small print in front under ‘Notes on the Text’ or the discrete line of dating opposite the title page…do yourself and Charles Darwin a favor: Find a reprint of the first edition. That’s the book with all its courageous freshness and its flaws, that provoked the most cataclysmic shift in human thinking within the past four hundred years.” I just loved that! I think my next reading project might be a facsimile of the 1859 edition…

Thursday, March 19, 2009

The New Geneious Pro Beta (v4.6): A Sweet Upgrade

You may already be familiar with my shameless love for the Geneious Pro software. My lab uses this software to view and annotate trace files, assemble contigs, and make alignments. For these purposes, Geneious is superior to Sequencher and available for only a fraction of the price ($249 for students/$495 for other academics). What's more, the folks at Geneious are constantly making improvements. Some really cool ones are making their debut in the latest beta release (v 4.6). My personal favorite is the automated assembly function, which can be used to automatically generate contigs from sequences that share some common motif in their file names (e.g., species1_forward & species1_reverse). We're using this function to put together forward and reverse reads from short DNA fragments. Another major shortcoming of Geneious bites the dust... Of course, there are still some bugs to be worked out (we are, for example, having problems automating end trimming and assembly of sets of sequences >40), but the folks at Geneious are actively working to solve these problems.

Bodega Phylogenetics Wiki - Major Revisions

The 10th annual Applied Phylogenetics Workshop took place last week at the Bodega Bay Marine Lab. If you didn't make it to the workshop, but are interested in learning about the latest methods in applied phylogenetics I have good news: we've wikified the workshop! Recent upgrades to the Wiki include new tutorials on how to conduct basic phylogenetic analyses, analyze morphological evolution using the program Brownie, and assesss patterns of community assembly and evolution. We've also expanded our coverage of phylogenetic comparative methods and made progress toward completion of a comprehensive BEAST tutorial. Check it out and don't be shy about signing up as a contributor yourself!