Global Phylogeography of Angel sharks

Next Monday, Madonna will present a paper on phylogeny and global phylogeography of Angel sharks: 17 (out of 22) species in the genus Squatina. In this paper, the authors first obtained a comprehensive phylogenetic reconstruction and tested biogeographic patterns using a molecular clock. The genus was found to be monophyletic and composed of four main clades. The authors found supports for the effect of both the Thetys Sea closure and the rise of the Panamian isthmus on the diversification of the genus. Thanks Madonna.

From Stelbrink B, vonRintelen T, Cliff G, Kriwet J; Molecular Phylogenetic and Evolution (2010) 54:395-404

Title: Molecular systematics and global phylogeography of angel sharks (genus Squatina)

Abstract.

Angel sharks of the genus Squatina represent a group comprising 22 extant benthic species inhabiting continental shelves and upper slopes. In the present study, a comprehensive phylogenetic reconstruction of 17 Squatina species based on two mitochondrial markers (COI and 16S rRNA) is provided. The phylogenetic reconstructions are used to test biogeographic patterns. In addition, a molecular clock analysis is conducted to estimate divergence times of the emerged clades. All analyses show Squatina to be monophyletic. Four geographic clades are recognized, of which the Europe–North Africa–Asia clade is probably a result of the Tethys Sea closure. A second sister group relationship emerged in the analyses, including S. californica (eastern North Pacific) and S. dumeril (western North Atlantic), probably related to the rise of the Panamanian isthmus. The molecular clock analysis show that both lineage divergences coincide with the estimated time of these two geological events.

Phylogeography of Dalton's Mouse (West Africa)

Next Monday, Catherine will present a paper on phylogeography of a small rodent: the Dalton's Mouse in West Africa. In this paper, the authors (1) found discrepancies between recognized morphospecies and phylogenetic results, (2) found evidence of refuges in the region, (3) found an effect of biogeographic barriers, (4) discussed the taxonomic status (biological species) of the different lineages and (5) found support for historic introgression events between lineages. Thanks Catherine.

From J. BRYJA, L. GRANJON, G. DOBIGNY, H. PATZENHAUEROVA, A. KONECNY, J.M. DUPLANTIER, P. GAUTHIER, M. COLYN, L. DURNEZ, A. LALIS and V. NICOLAS; Molecular Ecology (2010) doi: 10.1111/j.1365-294X.2010.04847.x

Title: Plio-Pleistocene history of West African Sudanian savanna and the phylogeography of the Praomys daltoni complex (Rodentia): the environment/geography/genetic interplay

Abstract.

Rodents of the Praomys daltoni complex are typical inhabitants of the Sudanian savanna ecosystem in western Africa and represent a suitable model for testing the effect s of Quaternary climatic oscillations on extant genetic variation patterns. Phylogeographical analyses of mitochondrial DNA sequences (cytochrome b) across the distribution range of the complex revealed several well-defined clades that do not support the division of the clade into the two species currently recognized on the basis of morphology, i.e. P. daltoni (Thomas, 1892) and Praomys derooi (Van der Straeten & Verheyen 1978). The observed genetic structure fits the refuge hypothesis, suggesting that only a small number of populations repeatedly survived in distinct forest-savanna mosaic blocks during the arid phases of the Pleistocene, and then expanded again during moister periods. West African rivers may also have contributed to genetic differentiation, especially by forming barriers after secondary contact of expanding populations. The combination of three types of genetic markers (mtDNA sequences, microsatellite loci, cytogenetic data) provides evidence for the presence of up to three lineages, which most probably represent distinct biological species. Furthermore, incongruence between nuclear and mtDNA markers in some individuals unambiguously points towards a past introgression event. Our results highlight the importance of combining different molecular markers for an accurate interpretation of genetic data.

Phylogeography of poison frog

Next Monday, Samantha will present a paper on phylogeography of poison frog in Costa Rica and Panama. In this paper, the authors try to identify the level of mitochondrial polyphyly within the species (though I don’t really understand what that means). The second aim is to identify the phylogeographic pattern of this species on its distribution range and compare it to other frogs in the same region. Find below the details of the study. Thanks Samantha.

From J. Susanne Hauswaldt, Ann-Kathrin Ludewig, Miguel Vences and Heike Prohl, Journal of Biogeography (2010) doi:10.1111/j.1365-2699.2010.02438.x

Title: Widespread co-occurrence of divergent mitochondrial haplotype lineages in a Central American species of poison frog (Oophaga pumilio)

Abstract.

Aim To analyse the phylogeographic structure of the strawberry poison frog, Oophaga pumilio (Dendrobatidae), across a large part of its range using a combination of mitochondrial and nuclear markers.

Location Costa Rica and Panama.

Methods Sequence analyses of a mitochondrial (cytochrome b) and a nuclear (RAG-1) gene fragment as well as analyses of seven microsatellite loci were carried out on 269 individuals of O. pumilio sampled from 24 localities and on two individuals of O. vicentei.

Results Two main mitochondrial haplotype lineages, corresponding to a northern (north Costa Rica) and a southern (south Costa Rica and eastern Panama) lineage, were identified. They differed by up to 7% uncorrected distance. We observed co-occurrence of both lineages in seven populations in Costa Rica and Panama, indicating a pattern of extensive admixture. The two main mitochondrial lineages of O. pumilio roughly corresponded to a previously described phylogeographic pattern. Microsatellites indicate admixture spanning over a wide geographic area, but significant variation between the northern and southern groups was also found with microsatellite data. While microsatellite data reconstructed a separation south of an assumed Caribbean valley barrier, mitochondrial haplotypes of the ‘southern lineage’ shifted this barrier towards the

north.

Main conclusions Despite admixture, all three markers showed significant variation between the northern and southern groups. Phylogeographical breaks known from other anuran species in the study region could not be verified for O. pumilio. The unexpected clustering of the population from Escudo de Veraguas and the individuals of O. vincentei with the northern O. pumilio lineage indicates the need for a fundamental and careful taxonomic revision, including an interspecific phylogeography of the entire genus.

What is a species tree?

Because I maybe expected a lot from the last journal club (Brunes et al. 2010) for us to understand the concept of Species tree, I was a bit disappointed. So, I googled this morning to search for some answers. I found some, though not many. So, you can find below the two sources where I found definitions for "Species tree". Then, I propose a tentative definition and try to cover all the implications I could find when attempting to resolve a species tree. Hope it will help!

Sources:

www.encyclopedia.com

species tree: A phylogenetic tree which depicts the evolutionary relationships of a set of species. Inferred trees, based on gene trees or other character trees, are often presented as estimates of the true species tree.

www.nature.com/nrmicro/journal/v1/n2/glossary/nrmicro751_glossary.html

A phylogenetic tree that represents evolutionary relationships between species as a whole, as opposed to phylogenetic trees for individual genes

A tentative definition of Species tree:

“Species tree” is the conceptual view of the real evolutionary relationships between species. It is opposed to the phylogenetic trees drew from individual genes that give potentially different evolutionary relationships between species.

What does it mean:

I think that the basis of this concept reside in the fact that the evolutionary relationships constructed from individual genes are false in general, maybe very false compared to the species tree. To resolve a species tree, the alternative is to use several or numerous genes (depending on the model), expecting to find a great improvement in the resolution of the tree. I think one can find an ultimate resolution of the species tree if and only if one can find concordant evolutionary relationships between species using different sets of genes. Probably, sometimes it is possible, sometimes not. So, as we saw in this paper of Brunes et al. (2010), finding supports for the different nodes using several genes allowed them to reach the species tree of these tree frogs. I guess the worse cases would be those involving radiations where no support could be found because the relationships between the species represent a polytomy (all lineages diverged at the same time). In such cases, I guess people would keep trying to add more and more genes without getting any concordant resolution.

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.