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Dominic Wright
Linköping University
IFM Dept of Biology
Sweden

A sexual ornament in chickens is determined by large-effect pleiotropic alleles at HAO1 and BMP2, selected during domestication

talk 

Author(s): Wright, D, Johnsson, M, Andersson, L, Jensen, P

Summary:

The genetic analysis of phenotypes and the identification of the causative underlying genes remains central to molecular and evolutionary biology. By utilizing the domestication process it is possible to exploit the large differences between domesticated animals and their wild counterparts to study both this and the mechanism of domestication itself. Domestication itself is characterized by strong directional selection, which can leave putative signatures of this selection present in the genome in the form of reduced heterozygosity (referred to as selective sweeps). We have generated multiple intercrosses and advanced intercrosses based on wild-derived and domestic chickens to fine-map genomic regions (or QTL) affecting a sexual ornament (one to less than 400kb in size). These regions have been over-laid with putative selective sweeps identified in domestic chickens (each approximately 40kb in length), and found to be significantly associated with them. By using expression QTL analysis, we show that two genes in the 400kb region, HAO1 and BMP2, are controlling multiple aspects of the domestication phenotype, from a sexual ornament to multiple life-history traits. Resequencing of these animals reveals four differentially-fixed polymorphisms between the parental lines exist in strongly conserved regions within the selective sweep present within this region, which are candidate causative QTN. This study demonstrates the potential for large-effect mutations in domestication, as well as the use of selective sweeps to identify putative QTN in such instances.

Luisa Pallares
Max Plank Institute for Evolutionary Biology
Department of Evolutionary Genetics
Germany

Finding QTNs in genes affecting craniofacial morphology in wild house mice

talk 

Author(s): Pallares, LF, Harr, B, Turner, LM, Tautz, D

Summary:

The understanding of the evolution of complex phenotypes, as for example, biological shape, depends on the identification of the genetic variants responsible for between-individual variation, being this the variation over which natural selection would act. For that reason, we used a natural-occurring hybrid system with the aim of identify genetic variants involved in craniofacial bone morphology. Hybrid mice from the Bavarian contact zone between Mus musculus musculus and M.m.domesticus were used in this study. Skull and mandible shape were measured with 3D landmarks and analyzed using Geometric morphometrics. The shape coordinates were reduced to principal component (PC) scores, which were used as phenotypes for the genome wide association mapping. With the aim of detect genes affecting specific regions of the bones, which are not detected by the complex shape changes represented by principal components, 3D pairwise distances between landmarks were also included in the mapping. 14 genetic regions, containing 24 genes were associated with PC axis and 11 regions with 32 genes were associated with pairwise distances. Several of the genes identified are known to be involved in bone morphogenesis suggesting that the association mapping recovers credible candidate regions. One region was identified as having general (association with PC1-16.5%) as well as specific effects in skull shape. We are now associating allelic differences in the candidate regions with shape differences across the hybrid zone to identify QTN candidates. Our results not only identified new genes possibly involved in skull morphogenesis, but also indicate that they are responsible for some of the morphological differences between two closely related species, and therefore are relevant for understanding the evolution of morphological divergence. Besides, we show that performing association studies with wild populations from a hybrid zone is a very promising tool for studying complex phenotypes.

William Cresko
University of Oregon
Department of Biology
United States

Genomic architecture facilitates and frustrates the identification of adaptive mutations in stickleback

talk 

Author(s): Cresko, WA

Summary:

Is adaptive evolution defined by numerous small mutations, few large mutations, or some combination of both? This deceptively simple question has bedeviled geneticists for years. A simple model is the sequential fixation of adaptive mutations in a single population subject to directional selection. Adaptive evolution is in reality a complex and dynamic process. Populations are structured geographically, and mutations are often subject to gene flow as well as temporally and spatially variable selection. Under such a mutation-migration-selection schema a variety of mutation types can occur, such as single nucleotide changes, insertion-deletions, and large chromosomal rearrangements. Thus, both the genetic and genomic architecture of traits can evolve in a metapopulation context. A consequence is that the present effect sizes of adaptive alleles are the outcome of an evolutionary process, not a description of the entire path. More practically, the genomic localization of large effect loci may be enhanced at the expense of understanding the order of mutational changes. Only recently have we acquired the requisite genomic tools to fully tackle this problem in natural populations. I will discuss our recent findings of the genetic and genomic architecture of adaptive mutations in threespine stickleback, including recent discoveries of significant structural variation and its role in very recent (<60 year) and rapid parallel evolution. I will show how this genomic architecture can facilitate the hunt for adaptive loci using GWAS in natural polymorphic populations, but then pose significant challenges for the identification of the evolutionary history of the precise mutational changes. Lastly, I will argue that fully understanding the genetic basis of adaptation would require a complete description of the entire adaptive process, and the answer to ‘what are the sizes of mutational changes’ may often be ‘all of the above’.

Mateusz Konczal
Faculty of Biology and Earth Sciences, Jagiellonian University in Krakow
Institute of Environmental Sciences
Poland

Genomic pattern of selection for ecologically important trait - transcriptome analyses of the bank vole artificial selection experiment

talk 

Author(s): Konczal, MS, Babik, W, Orlowska, P, Radwan, J, Rudolf, A, Sadowska, ET, Koteja, P

Summary:

Although, a response to selection at the genomic level has been investigated for some traits, little is known about the genomics of adaptation in ecologically important traits in vertebrates. Here we compared transcriptomes of the bank voles (Myodes glareolus) selected for high swim-induced aerobic metabolism (A) with unselected controls (C). In 13th generation of selection, voles from 4 replicate A lines achieved 48% higher max rates of oxygen consumption than those from 4 C lines (means±SD; A:5.32±0.64, C:3.59±0.57 mlO2/min) and differed in several other morphophysiological and behavioral traits. Our aim was to characterize the differences in allele frequencies and the differences in expression level between A and C lines, and thus pinpoint genes contributing to phenotypic diversification. Using Illumina paired-end sequencing and de novo transcriptome assembling we constructed reference liver and heart transcriptomes. Sequences obtained for each line from pools of liver and heart RNA were mapped to the reference transcriptomes to detect SNPs and measure the expression level. On average 33.5 and 29.3 mln 100 bp reads per line were obtained for liver and heart respectively, which allowed reliable polymorphism detection in over 7 000 genes resulting in more than 80 000 SNPs. About 1 600 of these SNPs showed allele frequency ranges which did not overlap between A and C lines, about 15% more than obtained from simulations assuming the differentiation purely by drift. However, the average differences in frequencies were similar for simulations and the experiment. We also identified a modest number (10 in heart and 45 in liver) of genes that showed more than two-fold differences in expression between A and C lines. Our results show that the rapid phenotypic diversification is accompanied by only minor changes in allele frequencies or expression level making the presence of genes of large effect unlikely and indicating a highly polygenic basis of the selected trait.

Mathieu Joron
Muséum National d'Histoire Naturelle
CNRS UMR 7205, Institut Systématique Evolution et Biodiversité
France

Inversions, supergenes and the genomic evolution of loci of large effect

talk 

Author(s): Joron, M

Summary:

Supergenes are defined as clusters of genetic elements maintaining fitness-related traits maintained in high linkage disequilibrium in response to selection for specific combinations of those traits. Recent studies have uncovered that supergenes may be maintained by structural variation presumed to help avoid recombination and the deleterious effects of maladaptive trait combinations. Chromosomal inversions are well-known for their suppressing effect on recombination, and can lock together multiple beneficial gene variants controlling specific trait combinations. There are historical examples, as well as numerous new cases of structural variation associated with the maintenance of well-differentiated morphotypes, ecotypes, or species in sympatry in diverse taxa. Chromosomal rearrangements are therefore important mechanisms of genomic architecture evolution, which merge the control of multiple beneficial traits under a simple inheritance. Thus they provide a way of building up loci of large phenotypic effect, often found to be associated with adaptive variation and radiations. But exactly how multiple beneficial traits become recruited within inversions at the population level is still unclear. In this talk, I will discuss the origins of rearrangement-associated adaptations from plant and animal taxa. I will highlight the role of the ecology of each individual trait and their different combinations, the role of the selection regimes underlying the fitness benefits of tight linkage, and the role of introgression. A continuum of genomic architectures underlies adaptive variation from stable polymorphisms within populations to ecotypes and to ecological speciation. Inversions and supergenes are therefore excellent genomic microcosms to improve our understanding of the process of adaptation and the ecology and tempo of the build-up of linkage disequilibrium between multiple traits.

Matt Rockman
New York University
Department of Biology
United States

QTNs of no effect

talk 

Author(s): Rockman, M

Summary:

The effect-size distribution of QTNs is at the heart of much debate in the evolutionary genetics community. An important complication is that effect sizes are not intrinsic properties of alleles. They depend on environment and genetic background in complicated ways. Using C. elegans as a model, we have found that populations harbor extensive genetic variation with no effect on phenotype under ordinary conditions but with life-or-death consequences in perturbed conditions. Alleles with no phenotypic effect at all may contribute to adaptive evolution when background or environment changes. Given that alleles of all effect sizes clearly contribute to evolution, our research program should shift to identifying the biological circumstances that favor adaptation by specific genetic architectures.

Thomas Mitchell-Olds
Duke University
Department of Biology
United States

Selection on the genes that control complex traits

talk 

Author(s): Mitchell-Olds, T, Olson-Manning, C, Anderson, J, Lee, C, Prasad, K, Song, B

Summary:

How does environmental heterogeneity influence growth, reproduction, and fitness in genetically variable plant populations? In Boechera, a wild relative of Arabidopsis, we used genome-wide markers to quantify selection coefficients at polymorphic loci throughout the life cycle, across multiple sites and years. We found strong natural selection that varied among environments, with stronger selection on reproduction than on survival components of fitness.

Next, we cloned a QTL that controls defensive chemistry, damage by herbivores, and fitness in nature. This gene encodes the first enzyme in the glucosinolate biosynthetic pathway, causing variation in chemical defense and herbivore damage, with subsequent effects on fitness. These ecological effects are driven by functional changes following gene duplication, and by two selectively favored amino acid changes in the proteins that they encode. These changes cause a gain of novel enzyme function, modulated by allelic differences in catalytic rate and gene copy number, which control survival and reproduction in nature.

Finally, to understand biochemical control of complex trait variation, we examined the relationship between pathway flux and protein polymorphism in the enzymes responsible for glucosinolate biosynthesis. We perturbed the enzymes in the glucosinolate pathway, and showed that flux control is focused in the first enzymatic step, and that flux control of these defensive phenotypes is robust across environmental treatments. Furthermore, signatures of selection showed that this enzyme is the only one in the pathway that shows evidence of selection. Our results support the hypothesis that natural selection preferentially acts on enzymes with high control over flux and phenotype.

Carmelo Fruciano
University of Konstanz
Department of Biology
Germany

The genetic bases of body shape architecture of two sympatric Mesoamerican cichlid species: a RAD-QTL approach

talk 

Author(s): Fruciano, C, Franchini, P, Jones, JC, Spreitzer, ML, Elmer, KR, Henning, F, Meyer, A

Summary:

Determining the genetic bases of phenotypic adaptation and ultimately speciation is one of the major quests in evolutionary biology. Cichlid fish species flocks are a prime example of recent rapid radiations often associated with adaptive phenotypic divergence from a common ancestor in a short period of time. In these fishes divergence in eco-morphological traits, including body shape, colour, lips and jaws, are thought to underpin their diversification. The Midas cichlid species complex (Amphilophus) of Nicaragua provides one of the few known examples of sympatric speciation, where species have rapidly evolved different eco-morphologies in young crater lakes. In this study we use SNP marker genotypes generated using ddRAD sequencing and a combination of morphometric analyses to identify significant QTLs in ecologically divergent cichlid species with different body morphs: an elongated limnetic species (A. zaliosus) and a high-bodied benthic species (A. astorquii) inhabiting lake Apoyo. A total of 453 informative RAD markers were identified in 240 F2 hybrids. These markers were used to construct a genetic map for which 25 linkage groups were resolved. We found 27 segregating SNPs linked to QTLs. The QTL-linked genomic regions were annotated to identify genes that likely contribute to divergence in body shape in benthic and limnetic Midas cichlid sympatric species. These results underline the effectiveness of RAD-Seq as a tool for rapid and efficient generation of QTL-targeted and genome-wide marker data and a promising method for investigating the genomic bases of divergence in ecologically relevant traits.

Anna Santure
University of Sheffield
Department of Animal and Plant Sciences
United Kingdom

The genomic architecture of morphological, life history and fitness traits in two long term wild populations of great tits (Parus major) - can we find evidence for genes of major effect?

talk 

Author(s): Santure, A, DeCauwer, I, Poissant, J, Robinson, MR, Visser, ME, VanOers, K, Groenen, MAM, Sheldon, BC, Slate, J

Summary:

Currently there is much debate, yet relatively little empirical data, on the nature of genetic architecture of quantitative traits in wild populations. Where is additive genetic variation located in the genome? Is trait variation influenced by many genes of small effect distributed throughout the genome, or by a few genes of major effect? Do the same loci cause phenotypic variation in different populations? Great tits (Parus major) have been studied extensively in long-term studies across Europe, and are consequently considered an ecological 'model organism'. Recently, a large number of genomic resources have been developed for the great tit, including a genetic linkage map with 5,500 SNPs. In this study, we use three different marker-based approaches (partitioning of additive genetic variance across genomic regions, pedigree-based quantitative trait locus mapping and genome wide association scans) to investigate the genetic architecture of morphological, life history and fitness traits in two long-term study populations of great tit - one in The Netherlands, and the other in the United Kingdom. We demonstrate that for most quantitative traits there is little evidence of genes of major effect, and that the two populations share very similar genomic architectures.

Contacts

Chairman: Octávio S. Paulo
Tel: 00 351 217500614 direct
Tel: 00 351 217500000 ext22359
Fax: 00 351 217500028
email: mail@eseb2013.com

Address

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
Portugal

Website

Computational Biology & Population Genomics Group 
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