Journal Club Sessions (Semester 1)

Date	Name	Venue
12 Mar	Kerry	Tea room
19 Mar	Sarita	Tea room
26 Mar	Sam	Tea room
2 Apr	Arrie	Tea room
16 Apr	Thierry	Tea room
23 Apr	Emilie	Tea room
7 May	Ilkser	Tea room
14 May	Catherine	Tea room
21 May	Amanda	Tea room
28 May	Paulette	Tea room
4 June	Bianca	Tea room
11 June	Michael	Tea room
18 June	Angelika	Tea room
25 June	Carel	Tea room

The historical Biogeography of Mammalia

Today, Sarita will present a paper on historical biogeography of mammals. The authors proposed to identify the origins of the different groups of mammals by comparing nine different methods for reconstructing ancestral areas including data on phylogenies, divergence times and ancestral areas reconstructions. This approach shows that both dispersal and vicariance triggered diversification of mammals. Thanks Sarita.

From MS Springer, RW Meredith, JE Janecka and WJ Murphy, Philosophical Transactions of the Royale Society B, (2011) 366, 2478–2502 [doi:10.1098/rstb.2011.0023]


Title: The historical biogeography of Mammalia

Abstract. Palaeobiogeographic reconstructions are underpinned by phylogenies, divergence times and ancestral area reconstructions, which together yield ancestral area chronograms that provide a basis for proposing and testing hypotheses of dispersal and vicariance. Methods for area coding include multi-state coding with a single character, binary coding with multiple characters and string coding. Ancestral reconstruction methods are divided into parsimony versus Bayesian/likelihood approaches. We compared nine methods for reconstructing ancestral areas for placental mammals. Ambiguous reconstructions were a problem for all methods. Important differences resulted from coding areas based on the geographical ranges of extant species versus the geographical provenance of the oldest fossil for each lineage. Africa and South America were reconstructed as the ancestral areas for Afrotheria and Xenarthra, respectively. Most methods reconstructed Eurasia as the ancestral area for Boreoeutheria, Euarchontoglires and Laurasiatheria. The coincidence of molecular dates for the separation of Afrotheria and Xenarthra at approximately 100 Ma with the plate tectonic sundering of Africa and South America hints at the importance of vicariance in the early history of Placentalia. Dispersal has also been important including the origins of Madagascar’s endemic mammal fauna. Further studies will benefit from increased taxon sampling and the application of new ancestral area reconstruction methods.

Journal Club Sessions (Semester 1)

Date	Name	Venue
16 Jan	Arrie	7-34
23 Jan	Thierry	7-34
30 Jan	Emilie	7-34
6 Feb	Ilkser	7-34
13 Feb	Catherine	7-34
20 Feb	Amanda	Tea room / Office
27 Feb	Paulette	Tea room / Office
5 Mar	Carel	Tea room / Office
12 Mar	Kerry	Tea room / Office
19 Mar	Sarita	7-34
26 Mar	Sam	7-34
2 Apr	Arrie	7-34
16 Apr	Thierry	7-34
23 Apr	Emilie	7-34
7 May	Ilkser	7-34
14 May	Catherine	7-34
21 May	Angelika	7-34
28 May	Paulette	7-34

Microsatellite development in the Moorish Idol

Congratulation to Miekie for her nice poster on development of microsatellites in the Moorish Idol (Zanclus cornutus)! Good job!

Design of hybrid primers

Failures in PCR amplification is very common in a molecular lab as multiple factors can affect it (DNA quality,  parameter of the PCR program, use of non-specific primers etc.). So, we have to limit these issues as much as we can. One way is to design good primers. The problem is that often it is not possible to have 25bp of conserved region of interest for the studied taxon. A previous paper that focused on protein evolution got around this issue by showing that 3 to 4 conserved codons were enough to design a good primer (Rose et al. 1998). More recently, adapting this approach to nucleotide sequences, we developed a set of conserved (and efficient) COI primers for the echinoderm phylum (sea-urchins, sea-cucumbers, sea-lilies or crinoids, sea-stars and brittle-stars; Hoareau & Boissin 2010). I used the same approach to design the ND2 primers for the whole vertebrates. I think this is very worthy as the same set of primers can be used by everyone in the lab. See below the graph that shows a conserved 3' region for each primer.

Sometimes, it will not work if we cannot find a conserved region long enough to design the primers. But I suggest that if you have to design primers (other than microsatellites!) you should try this method. Soon enough, we will have only a small set of primers for all the species in the lab.

Alignment of ND2 sequences (+ flanking regions) of various vertebrates showing the regions where I designed the primers

Vicariance and adaptation in a common temperate ophiuroids

Congratulations to Emilie (and her colleagues) for their new paper in Molecular Ecology. It has just been accepted. Find below the details of this nice paper.


Title: Did vicariance and adaptation drive cryptic speciation and evolution of brooding in Ophioderma longicauda (Echinodermata: Ophiuroidea), a common atlanto-mediterranean ophiuroid?


Authors: Emilie Boissin, Sabine Stohr and Anne Chenuil

Abstract: Over the last decade, cryptic speciation has been discovered in an increasing number of taxa. Species complexes are useful models for the understanding of speciation processes. Motivated by the discovery of brooding specimens in the common Atlanto-Mediterranean broadcast spawning brittle star, Ophioderma longicauda, a recent study revealed the occurrence of divergent mitochondrial lineages. We analysed 218 specimens from 23 locations spread over the geographic range of the species with partial Cytochrome c Oxidase subunit I (COI) sequences. A subset of this sample was also surveyed with the internal transcribed spacer of the ribosomal DNA cluster (nuclear ITS-1). Our study revealed six highly divergent mitochondrial lineages and the ITS-1 data confirmed that they most likely represent a species complex. Geographic ranges, abundances and genetic structures are contrasted among the putative cryptic species. Lineages in which brooding specimens have been found form a monophyletic group and are restricted to the Eastern Mediterranean basin, an oligotrophic zone. A phylogeny-trait association analysis revealed a phylogenetic signal for low  ‘chlorophyll a’ values (our proxy for oligotrophy). An ecological shift related to the hyper oligotrophy of the Eastern Mediterranean region is therefore likely to have played a role in the evolution of brooding. This study revealed that a complex mixture of vicariance, population expansion, adaptive divergence and possibly high local diversification rates resulting from brooding has shaped the evolution of this species complex. The dating analysis showed that these events probably occurred in the Pleistocene epoch.

Brooded juvenile (SEM image) and adult (picture) of Ophioderma longicauda 

JC_29.08.11_minutes

In our journal club from last Monday, we discussed an interesting paper by McGovern and co-workers: “Divergence genetics analysis reveal historical population processes leading to contrasting phylogeographic patterns in co-distributed species” (Molecular Ecology, 2010, 19, 5043–5060).

The paper emphasizes the importance of taking into consideration the historical perspective when studying any spatial genetic pattern. A phylogeographic break does not necessarily means that the gene flow is currently restricted (that’s what is happening in the bat star across QCS). The contrary is also true a more subtle differentiation at this break is not equals to a greater contemporaneous gene flow (instead it can be due to a more recent divergence time, this is what is happening in the snail).

Contrary to the extrapolation of gene flow from traditional Fst, the software IMa does not make assumptions of equilibrium (genetic drift/mutation/migration) and allows disentangling between ancestral polymorphism and ongoing gene flow. A good paper to read about this topic is the paper accessible in the September edition of TREE from Marko & Hart (The complex analytical landscape of gene flow inference, Trends in Ecology and Evolution September 2011, Vol. 26, No. 9).

We also discussed the extirpation of the snail and the recolonization range. Why was the snail extirpated if it is the cold species of the two? And when did it recolonize this entire range? Indeed, the date of divergence between north and south populations does not approximate the recolonization but just the population split. The recolonization of the north by the snails could have happened any time between 282000 and 11000-17000 years ago.

We discussed the possible causes explaining the fact that the older event in the bat star (282000) was visible by AMOVA but not the more recent one (100000). Maybe a difference in the duration of the separation is the explanation, given that gene flow seems homogeneous across the range of the bat star.

We also discussed the problems of using a single gene. We talked about selection and the difference of informativeness/variability between nuclear and mitochondrial markers.

We discussed about the choice of the markers, particularly tRNAs, and the importance of the calibration in the dating of divergence time.