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.

Journal Club Sessions (Aug-Nov)

Date	Speaker	Field
29-Aug	Emilie	Phylogeography
05-Sep	Tim	Phylogeny
12-Sep	Ilkser	Population genetics
19-Sep	Catherine	Phylogeny
26-Sep
03-Oct	Amanda	Phylogeography
10-Oct	Carel	Population genetics
17-Oct	Kerry	Phylogeography
24-Oct	Sarita	Population genetics
31-Oct	Miekie	Phylogeny
07-Nov	Paulette	Phylogeography
14-Nov	Sam	Population genetics
21-Nov	Thierry	Phylogeny

Does the geography alone can trigger life history adaptation?

Here the geography represent vicariance events that correspond to a rupture of gene flow of an ancestral single population/species. Does anyone can think of any processes by which such vicariance event alone (without change in habitats or ecology) can induce changes in life history traits such as reproductive startegy, dispersal ability etc.
Any ideas?