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.