Diversification of Treefrogs

Thanks Tim to send the paper early this week. Next Monday, Tim proposes to present a paper talking about phylogenetics of treefrogs. I went through it quickly and it sounds like a good paper. It presents the diversification of a group of treefrogs species (Phyllomedusa burmeisteri) that occurs in one of the most diverse terrestrial hotspot on earth: The Brazilian Atlantic forest. We’ll probably learn more about the origin and evolution of polyploid taxa and hopefully, we will finally find out about the difference between gene trees and species trees.

From Brunes et al. Molecular Phylogenetics and Evolution (2010) 57:1120–1133.

Title: Gene and species trees of a Neotropical group of treefrogs: Genetic diversification in the Brazilian Atlantic Forest and the origin of a polyploid species

Abstract. The Neotropical Phyllomedusa burmeisteri treefrog group includes four diploid (P. bahiana, P. burmeisteri, P. distincta and P. iheringii) and one tetraploid (P. tetraploidea) forms. Here we use mitochondrial and nuclear sequence variation from across its range to verify if recognized morphospecies correspond to phylogenetic clades, examine the origin of the polyploid P. tetraploidea, and compare range wide patterns of diversification to those of other BAF organisms. We compared single gene trees with one Bayesian multi-gene tree, and one Bayesian species tree inferred under a coalescent framework. Our mtDNA phylogenetic analyses showed that P. bahiana, P. burmeisteri and P. iheringii correspond to monophyletic clades, while P. distincta and P. tetraploidea were paraphyletic. The nuclear gene trees were concordant in revealing two moderately supported groups including (i) P. bahiana and P. burmeisteri (northern species) and (ii) P. distincta, P. tetraploidea and P. iheringii (southern species). The multi-gene tree and the species tree retrieved similar topologies, giving high support to the northern and southern clades, and to the sister-taxa relationship between P. tetraploidea and P. distincta. Estimates of tMRCA suggest a major split within the P. burmeisteri group at ~5 Myr (between northern and southern groups), while the main clades were originated between ~0.4 and 2.5 Myr, spanning the late Pliocene and Pleistocene. Patterns of geographic and temporal diversification within the group were congruent with those uncovered for other co-distributed organisms. Independent paleoecological and geological data suggest that vicariance associated with climatic oscillations and neotectonic activity may have driven lineage divergence within the P. burmeisteri group. P. tetraploidea probably originated from polyploidization of P. distincta or from a common ancestor.

Journal club sessions (Jan-March 2011)

Hi all,
Today, we discussed the next sessions of journal club (January to March 2011). Everyone was randomly assigned to a slot (even the absent). Find below the list




Date Speaker Field
31st January   Tim Phylogeny
7th February Samantha Phylogeography
14th February Mpho Phylogeny
21st February Catherine Population genetics
28th February Madonna Phylogeography
7th March Alex Phylogeny
14th March Emilie Population genetics
21st March Kerry Phylogeography
28th March Amanda Phylogeny

IAA as source or sink?

On Monday, I will present the Journal Club. I chose the paper Carel mistakenly sent to us last week. It would be fine if each of us can choose one of the two hypotheses (IAA as source or sink of new species). Find below the details of the study.

From Fitzpatrick et al. Molecular Ecology (2011) 20, 219–234.

Title: The West Pacific diversity hotspot as a source or sink for new species? Population genetic insights from the Indo-Pacific parrotfish Scarus rubroviolaceus

Abstract. We used a population genetic approach to quantify major population subdivisions and patterns of migration within a broadly distributed Indo-Pacific parrotfish. We genotyped 15 microsatellite loci in Scarus rubroviolaceus collected from 20 localities between Africa and the Americas. A STRUCTURE model indicates the presence of four major populations: Eastern Pacific, Hawaii, Central-West Pacific and a less well-differentiated Indian Ocean. We used the isolation and migration model to estimate splitting times, population sizes and migration patterns between sister population pairs. To eliminate loci under selection, we used BayeScan to select loci for three isolation and migration models: Eastern Pacific and Central-West Pacific, Hawaii and the Central-West Pacific, and Indian Ocean and the Central-West Pacific. To test the assumption of a stepwise mutation model (SMM), we used likelihood to test the SMM against a two-phase model that allowed mutational complexity. A posteriori, minor departures from SMM were estimated to affect ≤2% of the alleles in the data. The data were informative about the contemporary and ancestral population sizes, migration rates and the splitting time in the eastern Pacific ⁄ Central-West Pacific comparison. The model revealed a splitting time -17 000 BP, a larger contemporary Ne in the Central-West Pacific than in the eastern Pacific and a strong bias of east to west migration. These characteristics support the Center of Accumulation model of peripatric diversification in low-diversity peripheral sites and perhaps migration from those sites to the western Pacific diversity hotspot.

Welcome to MEEP Lab

Dear Meepers,
Welcome to this blog that will allow us to exchange ideas and tips, discuss our journal club and whatever you want to share. This is your blog, so make it alive!!