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?

How scientists see each other ?

You are more than welcome to share your views ;)

Zanclus samples from Anse des Cascades - 19 July 2011

Because the sea was very rough during the two weeks in Reunion and because we could not be sampling in the marine reserve, this was the only site where we could go to search for the Moorish idol: Anse des Cascades.

And here are the 15 samples we collected with my brother ...

Sampling trip July - Reunion

The past two weeks, Emilie and I have been in holidays in Reunion. But as everyone knows, none of us as biologist can be in real holidays. So, we kept this statement true and we went snorkeling to see cucumber ;). Anyway, here are some pictures we took while "working".

Here is the culprit sea cucumber, Synapta maculata (on right hand side), with its nice tentacles around its mouth. The urchin Diadema setosum with its five characteristic white dots and peacock worm in the top left.

Then we saw some fish like this trumpet fish and this Picasso trigger fish.

This puffer fish that Emilie hunted for a while to get this nice picture!

Also some beautiful fish and others not very nice.

Emilie picked up some ophiuroids also. This one was probably Ophionereis porrecta as you can see.

Who's who? who can say which one is moorish idol and which one is the bannerfish?

And then when we left, we got a very nice surprise (thanks to Emilie's piercing eyes!). Look in the water close to the fishing boat, there are two dark roundish shapes. Who guessed?

Two juveniles of rays at only 3m from the beach!

That was our snorkeling in the reserve area at Etang Sale

Golden Mole field trip

Just a quick update on my field trip:

I have been to Shongweni, Illovo beach and Umkomaas. Tim joined me for the first week at Shongweni and Illovo (thanks Tim!), and Sarita will be joining me next week at Vernon Crookes. Tomorrow I'm headed for Scottburgh.

Mole-catching has proven to be far trickier than I ever imagined! But I can't say I wasn't warned...

I will be back on Saturday 18th if all goes according to plan, so should see you all the following Monday.

Skinks phylogeography in southern Africa

Last monday, Catherine presented an interesting paper presenting phylogeographic data on rock skinks distributed from south Angola to the west part of South Africa. They used an impressive data set representing <1Kb of mitochondrial region and >2.5Kb of nuclear region. Using samples from different regions they could propose a scenario for the colonization history (from north to south) and found some geographical breaks. Moreover, they found signs of hybridization between the lineages. The paper is a good example of phylogeographic studies in the region. Thanks Catherine and sorry for being late!

From PORTIK DM, BAUER AM & JACKMAN TR. Molecular Ecology, 2011, 20: 1744–1748

Title: Bridging the gap: western rock skinks (Trachylepis sulcata) have a short history in South Africa

Abstract

Phylogeographic patterns in wide-ranging species in southern Africa remain largely unexplored, especially in areas north of South Africa. Here, we investigate population structuring, demographic history, and the colonization pattern of the western rock skink (Trachylepis sulcata), a rock-dwelling species with a range extending from southwestern South Africa into Angola. Using 1056 bp from the mitochondrial marker ND2 and > 2.5 kb from three nuclear genes (EXPH5, KIF24, RAG-1), we constructed allele networks, generated extended Bayesian skyline plots and performed population clustering analyses. Analyses of historical demographic patterns show an overall southward range expansion from Northern Namibia into Southern Namibia and South Africa, although we find contrasting genetic breaks across these geographic regions using nuclear and mitochondrial data. We suggest that mtDNA has introgressed across a nuclear break corresponding to the Knersvlakte region of South Africa, a previously proposed biogeographic barrier for rupicolous species. This pattern of mitochondrial variation contrasts sharply to that of other South African taxa previously investigated, which all show significant mtDNA differentiation across the Knersvlakte region. Additionally, while other taxa show divergences dating to the Pliocene, T. sulcata appears to be a recent arrival in southern Africa, having crossed this barrier and colonized South Africa in the mid-Pleistocene. The complex phylogeographic history of T. sulcata corroborates the intricate patterns of genetic variation found in South African taxa and provides novel insight into historical processes affecting species distributed across Namibia.

Panmixia of european eels

Next monday, Emilie will present a very interesting paper assessing the level of panmixia in the European eel. From samples of both larvae in the spawning area of the Sargasso Sea and glass eels recruiting in European rivers, they used an impressive body of population genetics methods to assess the demographic status of the European eels. The paper is well written and probably represents one of the best recent examples of population genetic studies. Thanks Emilie

From ALS TD, HANSEN M, MAES GE, CASTONGUAY M, RIEMANN L, AARESTRUP K, MUNK P, SPARHOLT H, HANEL R & BERNATCHEZ L, Molecular Ecology, 2011, 20: 1333–1346

Title: All roads lead to home: panmixia of European eel in the Sargasso Sea

Abstract

European eels (Anguilla anguilla) spawn in the remote Sargasso Sea in partial sympatry with American eels (Anguilla rostrata), and juveniles are transported more than 5000 km back to the European and North African coasts. The two species have been regarded as classic textbook examples of panmixia, each comprising a single, randomly mating population. However, several recent studies based on continental samples have found subtle, but significant, genetic differentiation, interpreted as geographical or temporal heterogeneity between samples. Moreover, European and American eels can hybridize, but hybrids have been observed almost exclusively in Iceland, suggesting hybridization in a specific region of the Sargasso Sea and subsequent nonrandom dispersal of larvae. Here, we report the first molecular population genetics study based on analysis of 21 microsatellite loci in larvae of both Atlantic eel species sampled directly in the spawning area, supplemented by analysis of European glass eel samples. Despite a clear East–West gradient in the overlapping distribution of the two species in the Sargasso Sea, we only observed a single putative hybrid, providing evidence against the hypothesis of a wide marine hybrid zone. Analyses of genetic differentiation, isolation by distance, isolation by time and assignment tests provided strong evidence for panmixia in both the Sargasso Sea and across all continental samples of European eel after accounting for the presence of sibs among newly hatched larvae. European eel has declined catastrophically, and our findings call for management of the species as a single unit, necessitating coordinated international conservation efforts.

Journal club sessions (April-August 2011)

Date            Speaker    Field
18th April     Amanda     Phylogeny
9th May       Catherine    Phylogeography
16th May     Emilie         Population genetics
23rd May     Ilkser         Phylogeny
30th May     Mpho         Phylogeography
6th June       Tim             Population genetics
13th June     Paulette       Phylogeny
20th June    Amanda       Population genetics
27th June    Carel           Phylogeography
4th July       Kerry          Phylogeny
25th July     Miekie         Phylogeography
1st August     Sam          Population genetics
8th August  Sarita           Phylogeography

The speciation genes

Today, Amanda will present an opinion paper discussing about the need for the definition of the speciation genes, i.e. genes involve in reproductive isolation prior to the actual speciation event. They propose a definition for these genes based on several assumptions. Then they present some examples of such genes. Thanks Amanda.

From Nosil P & Schluter D, Trends in Ecology and Evolution, April 2011, Vol. 26, No. 4: 160-167

Title: The genes underlying the process of speciation

Abstract

The long-standing goal of finding genes causing reproductive isolation is being achieved. To better link the genetics with the process of speciation, we propose that ‘speciation gene’ be defined as any gene contributing to the evolution of reproductive isolation. Characterizing a speciation gene involves establishing that the gene affects a component of reproductive isolation; demonstrating that divergence at the locus occurred before completion of speciation; and quantifying the effect size of the gene (i.e. the increase in total reproductive isolation caused by its divergence). Review of a sample of candidate speciation genes found that few meet these criteria. Improved characterization of speciation genes will clarify how numerous they are, their properties and how they affect genome-wide patterns of divergence.

Allopatric speciation in reef fish

A while ago, Kerry presented a paper presenting a study aiming to evaluate the mode of speciation in an Indo-Pacific reef fish species complex: Dascyllus trimaculatus. From both mt DNA sequences and a set of 16 microsatellites, they defined the population/species boundaries between the different groups morphologically distinct. From their results, they found that the mode of speciation in this taxon fit well with allopatry, but found some support for additional factors such as ecological factors. Thanks Kerry.

From Leray M, Beldade R, Holbrook SJ, Schmitt RJ, Planes S and Bernardi G. Evolution, 2009, 64-5: 1218–1230

Title: Allopatric divergence and speciation in coral reef fish: the three-spot dascilllus, Dascillus trimaculatus, species complex

Abstract

Long pelagic larval phases and the absence of physical barriers impede rapid speciation and contrast the high diversity observed in marine ecosystems such as coral reefs. In this study, we used the three-spot dascyllus (Dascyllus trimaculatus) species complex to evaluate speciation modes at the spatial scale of the Indo-Pacific. The complex includes four recognized species and four main color morphs that differ in distribution. Previous studies of the group using mitochondrial DNA revealed a non congruence between color morphs and genetic groupings; with two of the color morphs grouped together and one color morph separated into three clades. Using extensive geographic sampling of 563 individuals and a combination of mitochondrial DNA sequences and 13 nuclear microsatellites, we defined population/species boundaries and inferred different speciation modes. The complex is composed of seven genetically distinct entities, some of which are distinct morphologically. Despite extensive dispersal abilities and an apparent lack of barriers, observed genetic partitions are consistent with allopatric speciation. However, ecological pressure, assortative mating, and sexual selection, were likely important during periods of geographical isolation. This study therefore suggests that primarily historical factors later followed by ecological factors caused divergence and speciation in this group of coral reef fish.

Retracing an insect pest invasion route

Next Monday, Emilie will present a paper presenting a study aiming to search for the most likely invasion route of an insect pest species: the aphid Myzus persicae nicotianae. They used seven microsatellites and various methods combining traditional (F-statistics, genetic diversity parameters), Bayesian-based (Structure) and coalescent-based (DiyABC) approaches. These methods helped them first to identify the genetic subdivisions of the species between the potential sources in Europe and North America and the newly colonized areas (South America). Then, the program DiyABC was used to test different colonization scenarios. Thanks Emilie.

From Zepeda-Paulo FA, Simon JC, Ramirez CC, Fuentes-Contreras E, Margaritopoulos JT, Wilson ACC, Sorenson CE, Briones LM, Azevedo R, Ohashi DV, Lacroix C, Glais L, Figueroa CC (2010) Molecular Ecology 19, 4738–4752

Title: The invasion route for an insect pest species: the tobacco aphid in the New World

Abstract

Background. Biological invasions are rapid evolutionary events in which populations are usually subject to a founder event during introduction followed by rapid adaptation to the new environment. Molecular tools and Bayesian approaches have shown their utility in exploring different evolutionary scenarios regarding the invasion routes of introduced species.

Aims. We examined the situation for the tobacco aphid, Myzus persicae nicotianae, a recently introduced aphid species in Chile. Using seven microsatellite loci and approximate Bayesian computation, we studied populations of the tobacco aphid sampled from several American and European countries, identifying the most likely source populations and tracking the route of introduction to Chile.

Major results and conclusions. Our population genetic data are consistent with available historical information, pointing to an introduction route of the tobacco aphid from Europe and ⁄ or from other putative populations (e.g. Asia) with subsequent introduction through North America to South America. Evidence of multiple introductions to North America from different genetic pools, with successive loss of genetic diversity from Europe towards North America and a strong bottleneck during the southward introduction to South America, was also found. Additionally, we examined the special case of a widespread multilocus genotype that was found in all American countries examined. This case provides further evidence for the existence of highly successful genotypes or ‘superclones’ in asexually reproducing organisms.

Development of microsatellite markers in the Sparidae and their application in population genetics of the hottentot seabream around South Africa

By defining the degree of genetic spatial variation of populations, inferences can be made about what biological and environmental factors influence the genetic divergence and biogeography of marine species (Cowen et al. 2006). The marine environment is extensive, covering over 70 percent of the earth’s surface and contain highly diverse habitats (Avise 1998; Chopelet et al. 2009). These habitats are not always continuous and may be patchy (e.g. kelp beds) and variable (Gratwicke & Speight 2005). The interactions of individuals (life-history traits) of a species within and between patchy habitats leads to a specific degree of genetic diversity and population structure that can be identified (Chopelet et al. 2009). Marine species are often characterised by specific life-history traits such as high fecundity, numerous pelagic eggs and larvae, mobility and longevity which contribute to high levels of gene flow counterbalancing spatial heterogeneity of habitats (Avise 1998; Hauser & Carvalho 2008). These life-history traits coupled with homogenous transient habitats (allowing dispersal between habitats) that have limited physical barriers lead to a general lack of highly divergent populations at a regional scale. This is however not always the case for all organisms with several marine fish having been identified with population structure on local and regional scales (González et al. 2008; Narum et al. 2008; Nielsen et al. 2009). Population genetics plays a major role in the management and the conservation of commercial marine fish as the statistical approaches allow for the identification of the number of stocks that may need to be conserved separately. Marine fish are harvested in large quantities and this has led to overexploitation (Carvalho & Hauser 1998). By over-harvesting, genetic diversity may be lost which has wider implications as this decreases the ability of the species to adapt (Fenberg & Roy 2008). Also marine fish are one of the last wild sources of protein and as the stocks become depleted it has far reaching implications on the people who rely on it as a food source and income (Ryman et al. 1995). The correct management and conservation required to maintain the sustainability of this resource starts with the improvement of knowledge of the population biology of the targeted species.

South Africa has a wide range of marine fish species due to the diverse geological and oceanographic features which provide a number of habitats along the coast. One of the most prevalent and diverse fish families along the South African coast is the Sparidae. This family is of economic importance to the line fishery and many of these species are considered vulnerable or endangered due to a combination of overfishing and life-history traits. Two species of particular interest are the hottentot seabream (Pachymetopon blochii) and white steenbras (Lithognathus lithognathus). Both species are endemic to southern Africa and are considered vulnerable to overexploitation.

This study reports the development of microsatellite markers for both the above mentioned species using the Fast Isolation by AFLP of Sequences Containing Repeats (FIASCO) developed by Zane et al. (2002). Nine polymorphic markers were identified in each of these species. Nineteen markers (fifteen newly developed and four from other sparids) were used as a panel on eleven economically important sparids, to test microsatellite cross-species amplification. From this study twelve adequate polymorphic loci were identified for the white steenbras (applied in a population genetic study by a PhD student associated with SAIAB) and fourteen in the hottentot seabream which were applied in this dissertation. We were also able to identify a number of polymorphic loci for the other sparids (Fig. 1). It was concluded that the sparids do not show a negative correlation between genetic distance and microsatellite amplification success and polymorphism.

Fig. 1 Summary of the number of microsatellites that amplification (A) and were polymorphic (P) in the different sparid species included in this study.

The study further investigated the population genetic structure of the hottentot seabream. Pachymetopon blochii is an endemic, demersal sparid occurring along the west coast of southern Africa, found mainly in kelp beds and rocky outcrops (Heemstra & Heemstra 2004). This species is targeted by line fisheries and is considered vulnerable due to its slow growth and sedentary adults. Two hypotheses are considered in this study, the first being that the eggs and larvae remain in the habitats where the adults are found and this would lead to less gene flow between geographically separated habitats (hypothesis of isolation). Alternatively the eggs and larvae could be transported by the inshore currents which would lead to a single population identified along the west coast of South Africa (hypothesis of panmixia). The main aim of this study was to investigate which of these two hypotheses best explains the population connectivity in the hottentot seabream.

For this purpose, the spatial and temporal genetic variation of this species along the South African west coast was assessed. Fourteen highly polymorphic loci were genotyped for 288 individuals across nine locations sampled in 2001 and in 189 samples from six locations in 2009 (Fig. 2). Individual-based statistical analyses suggested the presence of one population along the coast. The effective population size was estimated to be relatively small (~ 9989 individuals). Weak spatial structure was identified between the sampling locations from 2009 using Factorial Correspondence Analysis (FCA), Analysis of Molecular Variance (AMOVA) and Spatial Autocorrelation (SAC). Between the 2001 sampling locations no significant spatial structure was identified. Temporal variation was identified between the two sampling years. This was likely due to “larval genetic patchiness” which led to variations in the observed population structure across different years. In conclusion, one population of the hottentot seabream was identified along the coast of South Africa with weak spatial and temporal variation between years, which is likely due to the larval dispersal and mortality mediated through the oceanographic features along the west coast.

Fig. 2 Map of the locations sampled along the coast of South Africa in 2001 and 2009. The 2001 sampling locations are indicated in blue and the 2009 sampling locations in red. The inset shows a map of Africa (google maps; orange line indicates the west coast of southern Africa where the hottentot is distributed) and an image of the hottentot seabream.

Introgressive hybridization in herring gulls

Next Monday, Paulette will present a paper on the evolutionary history of three closely related species of Herring Gull: Larus argenteus, L. hyperboreus, L. marinus. A previous study showed that each of these species presented a biphyletic pattern based on mitochondrial markers, suggesting introgression events provoked by recent hybridization. In this paper, the authors studied the evolutionary history of these species, specifically analyzing the introgression events using both mtDNA and RLFP. Thanks Paulette.

From Sternkopf V, Liebers-Helbig D, Ritz MS, Zhang J, Helbig AJ, de Knijff P (2010) BMC Evolutionary Biology 10:348

Title: Introgressive hybridization and the evolutionary history of the herring gull complex revealed by mitochondrial and nuclear DNA

Abstract

Background: Based on extensive mitochondrial DNA (mtDNA) sequence data, we previously showed that the model of speciation among species of herring gull (Larus argentatus) complex was not that of a ring species, but most likely due more complex speciation scenario’s. We also found that two species, herring gull and glaucous gull (L. hyperboreus) displayed an unexpected biphyletic distribution of their mtDNA haplotypes. It was evident that mtDNA sequence data alone were far from sufficient to obtain a more accurate and detailed insight into the demographic processes that underlie speciation of this complex, and that extensive autosomal genetic analysis was warranted.

Results: For this reason, the present study focuses on the reconstruction of the phylogeographic history of a limited number of gull species by means of a combined approach of mtDNA sequence data and 230 autosomal amplified fragment length polymorphism (AFLP) loci. At the species level, the mtDNA and AFLP genetic data were largely congruent. Not only for argentatus and  hyperboreus, but also among a third species, great black-backed gull (L. marinus) we observed two distinct groups of mtDNA sequence haplotypes. Based on the AFLP data we were also able to detect distinct genetic subgroups among the various argentatus, hyperboreus, and marinus populations, supporting our initial hypothesis that complex demographic scenario’s underlie speciation in the herring gull complex.

Conclusions: We present evidence that for each of these three biphyletic gull species, extensive mtDNA introgression could have taken place among the various geographically distinct subpopulations, or even among current species. Moreover, based on a large number of autosomal AFLP loci, we found evidence for distinct and complex demographic scenario’s for each of the three species we studied. A more refined insight into the exact phylogeographic history within the herring gull complex is still impossible, and requires detailed autosomal sequence information, a topic of our future studies.

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.

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!!