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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.

Craig Primmer
University of Turku
Department of Biology
Finland

Annotated genes and non-annotated genomes: use of model organism gene annotation information for understanding the molecular basis of traits of ecological and evolutionary importance

poster 

Author(s): Primmer, CR, Papakostas, S, Leder, EH, Davis, MJ, Ragan, MA

Summary:

Recent advances in molecular technologies have opened up unprecedented opportunities for evolutionary biologists and ecologists to better understand the molecular basis of traits of ecological and evolutionary importance in almost any organism. Nevertheless, reliable and systematic inference of functionally relevant information from these masses of data remains challenging. In my poster, I will highlight how the Gene Ontology (GO) database can be of use in meeting this challenge. The GO provides a largely species-neutral source of information on the molecular function, biological role and cellular location of tens of thousands of gene products. As it is designed to be species neutral, the GO is well suited for cross-species use i.e. functional annotation derived from model organisms can be transferred to inferred orthologs in newly sequenced species. In other words, the GO can provide gene annotation information for species with non-annotated genomes. I will highlight the both the strengths and the current weaknesses of using GO for enhancing the understanding of molecular function in ecologically relevant species and present some examples of its use for evolutionary contexts

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.

Sverre Lundemo
Uppsala university
Department of ecology and genetics
Sweden

Genetic basis of leaf trichome density in natural populations of Arabidopsis thaliana

poster 

Author(s): Lundemo, S, Breed, MF, Ågren, J

Summary:

Trichomes are hair-like epidermal structures on plant surfaces that may contribute to herbivore deterrence, UV protection, and tolerance to drought. In the annual plant Arabidopsis thaliana, leaf trichome density varies considerably among populations. We examined the genetic basis of differences in trichome density between two populations located close to the northern (Sweden) and southern (Italy) margin of the native range. We planted parental lines and 400 recombinant inbred lines (RILs) derived from a cross between the two populations at the sites of both source populations. Seedlings were planted at the time of natural seedling establishment in the autumn, and trichome density was scored on leaves before flowering in spring. We mapped QTL for trichome density using a linkage map based on 360 SNPs spaced at ca. 1 cM intervals. We asked how many QTL contribute to differences in trichome density and what is the magnitude of their effects? Do QTL for trichome density co-locate with candidate genes known to influence trichome density? Can QTL effects be linked to mutations in these genes? Preliminary analyses detected 11 QTL influencing trichome density. Of these, one QTL on chromosome 2 was consistently detected across years and at both study sites, and explained between 19% and 44% of the variation in RIL means. This QTL was located in a genomic region harbouring two genes known to influence trichome density: ETC2 and TCL1. Sequence differences between the two parental lines in these two candidate genes corresponded to four and one amino acid, respectively. We will present an analysis of the functional significance of the sequence differences detected and of their geographic distribution. In ongoing work, we explore the adaptive significance of trichome density by connecting variation in trichome density to variation in other putatively adaptive traits and to fitness in the field.

Pawel Rosikiewicz
University of Lausanne
Department of Ecology and Evolution
Switzerland

Genetic exchange in a multigenomic fungus; Rhisophagus irregularis

poster 

Author(s): Rosikiewicz, P, Sanders, IR

Summary:

Rhizophagus irregularis is a model species of an arbuscular mycorrhizal fungi (AMF). The AMF forms symbiotic relationship with roots of land plants, improving plant growth and protecting plants against parasites. R. irregularis is a particularly important species of AMF because it colonizes roots of most of crop plants such as rice, potato and wheat. However, different isolates of this fungus can affect plant phenotype differently. Moreover, it recently has been shown that two isolates of AMF can exchange genetic material, a process that can alter both, plant and fungal phenotypes. R. irregularis, is a coenocytic organism, which means that many nuclei coexist and can move in the common cytoplasm. The genetic exchange between two AMF isolates occurs via vegetative hyphal fusion. However, unlike in most fungi AMF produces multinucleate spores and it has been shown that each isolate of R. irregularis carries genetically different nuclei, which are maintained in successive AMF generations. What is unknown is the fate of parental nuclei after the genetic exchange, how many parental nuclei are exchanged and whether the mix of nuclei is random. In addition the nuclei are exchange with the surrounding cytoplasm. This lead to a question whether mitochondria from both parental isolates are transmitted to the offspring and how can it influence the fungal and plant phenotypes.

Stéphanie Thépot
UMR de génétique végétale
France

Genome-wide analysis of the genetic architecture of flowering time and fitness in wheat experimental populations

poster 

Author(s): Thépot, S, Goldringer, I, Mackay, I, Enjalbert, J

Summary:

Flowering time is a major adaptive trait, as it allows plants to synchronize their vegetative cycle with optimal environmental conditions and thus to maximize their fitness. This trait has been studied over 20 generations in different experimental wheat populations, relying on three gene pools: two selfing pools obtained by pyramid crosses of two sets of 16 parents. The third is an outcrossing pool obtained by random crossing of 61 parents by the use of male sterility. These three pools have been dispatched over 12 sites in France, and then cultivated year after year in isolation, without migration or human selection. Fast evolution, both over time and in space, was noticed for flowering time. Using both shifts in allelic, or association genetics, these adaptations were in part explained by polymorphisms at key genes controlling vernalisation or photoperiod sensitivity (Rhoné et al. 2008, 2010). We recently developed an extended study of the outcrossing population, genotyping about 400 SSD lines with a 9k SNPs array (Chao et al. 2010), and performing an extended phenotyping of flowering time, under contrasted environmental conditions (variations in vernalization and photoperiod). With this highly recombinant and highly diverse population we describe the distribution of effects over detected QTNs, the major QTNs corresponding to previously described candidate genes. The detected QTNs x environment interactions highlight the genetics of local adaptation. Comparing major genes handled by plant breeders, and results obtained on wheat experimental populations, we will show how the genetic architecture of flowering time and its strong interaction with environment can explain the genetic architecture of fitness traits in natural populations.

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.

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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