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Marius Roesti
University of Basel
Zoological Institute

A novel genomic signature of adaptation from standing variation revealed in threespine stickleback


Author(s): Roesti, M, Gavrilets, S, Hendry, AP, Salzburger, W, Berner, D


Understanding how natural selection shapes the genome is becoming a major endeavor in evolutionary biology. Selection will often target pre-existing (standing) genetic variation. Nevertheless, theory has generally been developed for selection on novel variants. We here use extensive modeling tailored to adaptive divergence in threespine stickleback to characterize the genomic footprints of adaption from shared standing variation. The emerging predictions are then examined using genome-wide markers and targeted sequencing across many natural populations. Combined, our findings offer a novel explanation for heterogeneous genomic differentiation between diverging populations, challenge the widely held view that genomic regions of high and low population differentiation reliably point to loci under divergent and balancing selection, and allow us to propose a novel methodological framework for searching adaptation genes in natural populations.

Janice Britton-Davidian
University of Montpellier 2
Institut des Sciences de l'Evolution

Are Robertsonian fusions barriers to introgression in a house mouse hybrid zone?


Author(s): Britton-Davidian, J, Villafan de la Torre, E, Smadja, C, Caminade, P, Boursot, P


Genomic regions of low recombination are expected to contribute to the accumulation of incompatibilities allowing speciation with gene flow to occur. While chromosomal inversions are well documented in such processes, the role of Robertsonian (Rb) fusions (that join two acrocentric chromosomes by their centromere to form a metacentric one) is less clear. The house mouse is an emblematic model of Rb variation since one subspecies, M. m. domesticus, displays >80 Rb races. Previous cytogenetic studies demonstrated a decrease in recombination rates along the proximal 50% of Rb chromosomes in both homozygotes and heterozygotes. This study explores the role of Rb fusions in reducing gene flow by investigating their effect on genome admixture between two subspecies of the house mouse. In Denmark where the two taxa form a tension zone, M. m. domesticus carries 3 Rb fusions while M. m. musculus has an all-acrocentric karyotype. Genome admixture was assessed using 127 SNPs diagnostic of the two subspecies and covering the proximal 25% of 3 chromosomal arms involved in Rb fusions and 2 acrocentrics. We compared patterns of genomic admixture in the proximal regions to those at 86 diagnostic loci randomly distributed in the genome by fitting a genomic cline model with 3 parameters (centre and slope in each subspecific context). In the domesticus genomic context, Rb clines were much steeper than that of the average reference loci. Their centre was displaced in favour of musculus, however, due to introgression of large chromosomal blocks, and both of these patterns were stronger for the most proximal loci. This is compatible with the predicted effects of reduced recombination in Rb fusions coupled with incompatibilities in these genomic regions. In addition, clines for acrocentrics were smoother than average in the musculus genomic context, suggesting that other undescribed effects are acting, such as a possible advantage of domesticus acrocentric centromeres.

Camille Roux
Université de Lausanne
Département d'écologie et d'évolution

Crossing the species barrier: genomic islands of introgression between two extremely divergent Ciona intestinalis species


Author(s): Roux, C, Tsagkogeorga, G, Bierne, N, Galtier, N


Inferring a realistic demographic model from genetic data is an important challenge to gain insights into the historical events during the speciation process and to detect the molecular signature of selection along genomes. Recent advances in divergence population genetics have reported that speciation in face of gene flow occurred more frequently than theoretically expected, but the approaches used rarely account for genome wide heterogeneity (GWH) in introgression rates. However, GWH is expected as a consequence of variation in effects of natural selection on migrant alleles. We investigated the impact of GWH on the inference of divergence with gene flow between two cryptic species of the marine model Ciona intestinalis. These morphologically indistinguishable entities are highly diverged molecular-wise, but evidence of hybridisation has been reported in both laboratory and field studies. We examined polymorphism and divergence patterns across 852 genes scattered throughout the C. intestinalis genome. We compared various speciation models and statistically tested for GWH under the ABC framework. Our results demonstrate the presence of significant extents of gene flow resulting from a recent secondary contact between the two gene pools, after more than 3My of divergence in isolation. The inferred rates of introgression are relatively low, highly variable across loci and mostly unidirectional, which is consistent with the idea that numerous genetic incompatibilities have accumulated over time throughout the genomes of these highly-diverged species and that introgression could be adaptive. A genomic map of the level of gene flow identified two islands of introgression, i.e. large genome regions of unidirectional introgression. This study clarifies the history and degree of isolation of two cryptic and partially sympatric model species, and provides a methodological framework for the study of GWH in introgression rates at various stages of the speciation process.

Patrik Nosil
University of Sheffield
Department of Animal and Plant Sciences
United Kingdom

Experimental insights into the processes driving genome evolution


Author(s): Nosil, P, Gompert, Z, Parchman, T, Buerkle, A, Comeault, A, Farkas, T, Feder, J


Understanding the processes driving patterns of genome variation is a major goal in biology. Although observational genome scans have usefully quantified heterogeneity in levels of genetic differentiation across the genome, it can be problematic to infer evolutionary process and causation from such genome scans alone because a particular pattern of genomic divergence could arise via various combinations of selection, recombination, drift, gene flow, mutation, and demographic history. In this regard, experiments have the potential to isolate the contributions of specific evolutionary processes to patterns of genome variation. In this talk, I describe the processes driving and constraining genome evolution in experimental populations of stick insects that were transplanted to novel host-plant and climatic environments in the wild. I contrast the experimental results with genome variation among long-established natural populations and discuss the collective empirical results in light of theory. The talk will illustrate how combined experimental and genomic approaches can move the field of genomics towards becoming a more predictive science.

Philine Feulner
Max Planck Institute for Evolutionary Biology
Evolutionary Ecology

Genomic islands of divergence: a comparison of five parapatric lake-river population pairs of three-spined sticklebacks


Author(s): Feulner, PGD, Chain, FJJ, Panchal, M, Huang, Y, Eizaguirre, C, Kalbe, M, Lenz, T, Samonte, I, Stoll, M, Bornberg-Bauer, E, Reusch, T, Milinski, M


Sticklebacks have recently colonized various freshwater habitats and have since undergone recurrent phenotypic divergence. Here, we sample five geographically distinct lake-river population pairs of the three-spined stickleback for investigating patterns of population divergence at varying stages of ecological speciation. Using 60 whole genome sequences (15x coverage each) we identify genomic islands of divergence between parapatric lake-river ecotypes. This allows us to evaluate the number, size and distribution of genomic islands of divergence between several population pairs and to assess the extent of population differentiation across our samples. We identify different genes and genomic regions potentially associated with ecological differentiation in the five lake-river comparisons. This suggests that divergence patterns between lakes and rivers can involve multiple molecular pathways. Interestingly, we find some associations between genomic structural variations and islands of divergence. This is based on our extensive set of structural variations including deletions, copy-number variations, inversions, and translocations. Combined with estimates of the recombination rates across the genomes, we provide insights into the relevance of the genomic architecture and the role of genomic islands during adaptive divergence.

Qixin He
University of Michigan
Ecology and Evolutionary Biology
United States

Genomic tests of whether chromosomal rearrangements facilitated local adaptation in Anopheles gambiae based on coalescent expectations


Author(s): He, Q, Knowles, LL


As the primary malaria vector that is widely distributed in sub-Sahara, Anopheles gambiae s. str. utilizes many different microhabitats where human reside. Its fast adaptation is partly attributed to polymorphic inversions within or between populations in the species. Theory predicts that large paracentric inversions, which do not directly affect individual fitness, can facilitate local adaptation by suppressing recombination among co-adapted genes captured by inversions. Clines and associations between inversions and specific environmental factors are suggestive of causal relationships, but do not demonstrate that the inversions facilitated the local adaptation. Here, by comparing the time to coalescence of genomic regions within inversions and among collinear regions, we can estimate the age of inversions, selective strength acting on inversions in local populations, and how selection varies depending on the connectivity among populations. Genomic regions inside inversions where co-adapted genes can be identified as well. In this study, wild mosquito samples were collected from five populations in transitional ecozones between forest and savanna in Cameroon. Karyotypes for two major inversions, 2La and 2Rb, were determined molecularly and genome-wide SNPs were identified for each individual from barcoded Illumina sequencing. Genetic data, together with spatial information on the sampled individuals, are then analyzed with a coalescent modeling framework to test whether inversions contributed to genomic divergence among ecologically dissimilar populations under gene flow. The approach provides new insights into genomic profiles when population divergence (or speciation) is promoted by structural genomic variants.

Alexandre Blanckaert
University of Vienna
Department for Mathematics

How Dobzhansky-Muller Incompatibilities accumulate in presence of gene flow?


Author(s): Blanckaert, A, Hermisson, J


Interest in speciation research has experienced a recent shift from the classical problem of “When does it happen?” to more process-oriented questions: “How does it happen?” This is of relevance, in particular, for parapatric speciation, where the build-up of pre- or postzygotic barriers to gene-flow is a gradual process. The standard mechanism for the evolution of postzygotic isolation is the accumulation of Dobzhansky-Muller incompatibilities (DMI). While this process is reasonably well understood for allopatric speciation, one can ask how it unfolds in the face of gene flow. In a recent paper, Bank et al. (2012) have studied the very first step of this process and described the conditions for a first two-locus DMI to appear and be maintained. Here, we extend this model to study more than one DMI. In particular, we are interested in the influence of the presence of a first DMI on the fate of a second one and in predictions about the genetic architecture of the growing barrier. Using a combination of analytical and numerical methods, we analyze a migration-selection model with unidirectional gene flow from a continent to an island. As expected, we generally find that the presence of a first DMI makes it easier for further DMI's to be stably maintained – once it is established. However, the picture is much more complex for the establishment process of the second DMI itself. Depending on linkage patterns and the strength of the incompatibilities, the presence of the first DMI may either facilitate the origination of a second one or impede it. We interpret our results in the light of recent ideas of “islands of speciation” or “genome hitch-hiking.”

Vitor Sousa
University of Bern
Institute of Ecology and Evolution

Identifying loci under selection against gene flow in isolation with migration models


Author(s): Sousa, VC, Carneiro, M, Ferrand, N, Hey, J


When divergence occurs in the presence of gene flow there can arise an interesting dynamic in which selection against gene flow, at sites associated with population specific adaptations or genetic incompatibilities, can cause net gene flow to vary across the genome. Loci linked to sites under selection may experience reduced gene flow and may experience genetic bottlenecks by the action of nearby selective sweeps. Data from histories such as these may be poorly fit by conventional neutral model approaches to demographic inference which treat all loci as equally subject to forces of genetic drift and gene flow. To allow for demographic inference in the face of such histories, as well as the identification of loci affected by selection, we developed an isolation with migration model that explicitly provides for variation among genomic regions in migration rates and/or rates of genetic drift. The method allows for loci to fall into any of multiple groups, each characterized by a different set of parameters, thus relaxing the assumption that all loci share the same demography. By grouping loci, the method can be applied to data with multiple loci and still have tractable dimensionality and statistical power. We studied the performance of the method using simulated data, and we applied the method to study the divergence of two subspecies of European rabbits (Oryctolagus cuniculus).

Christen Bossu
Uppsala Universitet, Uppsala, Sweden
Ecology and Genetics

Islands of genomic divergence across the hooded and carrion crow hybrid zone: linking genes and ‘magic traits’


Author(s): Bossu, CM, Baglione, V, Grabherr, M, Kruszewicz, A, Lantz, H, Müller, I, Poelstra, J, Vijay, N, Wikelski, M, Wolf, J


A comprehensive understanding of the speciation process at a genomic level requires investigation at different stages in the evolutionary continuum from onset to completion and hybrid zones provide such opportunities. The European crow hybrid zone between the all black carrion crow (Corvus [c.] corone) and grey coated hooded crow (C. [c.] cornix) is a classic example of early stage speciation characterized by a lack of neutral genetic divergence, limited evidence of postzygotic reproductive isolation, and the rapid divergence of distinct plumage characteristics that mediate strong assortative mating. Here we took a population genomic approach to characterize genomic divergence between color morphs to identify genes with major effect on speciation and potential ”magic traits” involved in the earliest stages of divergence. Initial analyses of 66 re-sequenced genomes reveal a heterogeneous landscape of genome divergence with 4 narrow regions of the genome that show significant differentiation between the grey hooded crow populations from Sweden and Poland with respect to black carrion crow populations from Germany and Spain. These regions are potentially associated with structural variants (i.e. a pericentric inversion on chromosome 18), as well as differentially expressed candidate genes within the melanogenic pathway. However, fixed differences detected in these genomic regions in contrast to no divergence of the coding sequence of MC1R or intron regions linked to primary candidate genes points to potential cis-regulatory elements driving the initial divergence of expression profiles and plumage characteristics. Comparison of outlier regions with both a white coated and all black outgroup species (C. torquatus & C. brachyrhynchos, respectively) will determine whether the divergence is the result of standing genetic variation or derived mutations.

Tanja Pyhäjärvi
University of Oulu
Department of Biology

Local adaptation, inversions and non-genic variation in teosinte


Author(s): Pyhäjärvi, T, Hufford, MB, Mezmouk, S, Ross-Ibarra, J


Populations of widely distributed plant species have to adapt to local environmental conditions. Locally adapted plant populations are often observed, but the genetic basis of adaptation is rarely known. We used high-density genotype data and a wide set of environmental variables to identify adaptive genetic variation in teosinte, a wild relative of maize. Overall, population structure in teosinte was strong and was affected by altitude, dispersal events and admixture between subspecies. Patterns of linkage disequilibrium revealed four megabase-scale inversions that were polymorphic in teosinte populations. Inversions segregated in clinal patterns, were associated with environmental variation and were extremely differentiated among subspecies and populations. In addition, we found that non-genic variation plays a role in local adaptation of teosinte. These results suggest that large structural rearrangements and variation outside coding regions can be important for adaptation, especially in large plant genomes in which the gene space constitutes a small fraction of the entire genome.


Chairman: Octávio S. Paulo
Tel: 00 351 217500614 direct
Tel: 00 351 217500000 ext22359
Fax: 00 351 217500028


XIV Congress of the European Society for Evolutionary Biology

Organization Team
Department of Animal Biology (DBA)
Faculty of Sciences of the University of Lisbon
P-1749-016 Lisbon


Computational Biology & Population Genomics Group