DFG FOR 1078 Natural Selection in Structured Populations
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Seminars 2012

26/03/12 - John Pool - "Population genomics of sub-Saharan Drosophila melanogaster: African diversity and non-African admixture"

University of Wisconsin, USA

poolAbstract: Drosophila melanogaster has played a pivotal role in the development of modern population genetics. However, many basic questions regarding the demographic and adaptive history of this species remain unresolved. We report the genome sequencing of 139 wild-derived strains of D. melanogaster, representing 22 population samples from the sub-Saharan ancestral range of this species, along with one European sample. The bulk of these genomes were sequenced at >25X depth from haploid embryos. Results indicated a pervasive influence of non-African admixture in many African populations, motivating the development and application of a novel admixture detection algorithm. Most inferred admixture tracts were on the scale of megabases/centiMorgans, suggesting very recent introgression. Admixture proportions were found to vary greatly among population samples (with higher levels occurring in larger towns) and even among genomes from the same population (with some collections containing a mixture of non-admixed and highly admixed individuals). Across all African genomes, admixture levels differed between chromosomes, with local regions of sharply increased or decreased admixture also apparent. After filtering putatively admixed regions, the greatest genetic diversity was observed in southern Africa (e.g. Zambia), while diversity in other populations was consistent with a recent geographic expansion from this region. The European population showed fundamentally different levels of diversity reduction on each major chromosome, retaining 41% of an African sample’s nucleotide diversity on the X chromosome, 62% on chromosome 2, and 80% on chromosome 3. Some African populations displayed diversity reductions specific to one or two chromosome arms, potentially reflecting a strong influence of inversion-related selection on genome-scale diversity. Finally, genomic scans were conducted to illuminate the genetic basis of directional selection (1) within an African population, (2) differentiating African populations, and (3) differentiating European and African populations. Unique sets of gene functions were observed to be enriched for each set of genomic outliers.

23/04/2012 - Magnus Nordborg - "Elucidating the genotype-phenotype map using Arabidopsis"

Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria

nordborgAbstract: Making sense of natural variation remains one of the greatest challenges in biology. Understanding how genetic variation translates into phenotypic variation, and how this translation depends on the environment is fundamental to our understanding of evolution, and has enormous practical implications for medicine, agriculture and energy production. We are attempting to tackle this problem using Arabidopsis thaliana as a model. Because it is highly self-fertilizing and naturally exists as inbred lines, A. thaliana can be brought into the laboratory and grown, in replicate, under different environmental conditions, in order to explore how the genotype-phenotype map works and has been molded by evolution. The presence of inbred lines, coupled with its compact, 120 Mb genome, also makes A. thaliana useful as a model for genomic approaches that will soon be possible in others organisms. As part of the 1,001 Genomes Project, we are sequencing well over 1,000 inbred lines, and are complementing these data with other kinds of “-omic” information, such as DNA methylation patterns and transcriptome measurements in large numbers of lines under multiple environmental conditions. For example, we are currently analyzing the data from a study that involved flowering time and multiple other phenotypes in a sample of 200 Swedish lines grown at two different temperatures. These data have been complemented with transcriptome (via mRNA-seq) and DNA methylation (via bisulfite sequencing) measurements of all lines under both temperatures. By supplementing the genome-wide associations between genotype and phenotype with the “in-between-ome”, we hope to gain insight not only in which genetic polymorphisms are associated with phenotypic variation, but why. By carrying out these kinds of studies in A. thaliana, which can be grown in replicate under controlled conditions, we also hope to gain insight into the limitations of these “brute force” genomic approaches, which are rapidly becoming economically feasible for a broad range of species, but may not be practicable from a biological point of view. In particular, we have learned much about the difficulties involved in identifying causal genetic polymorphisms through genome-wide association studies.

21/05/2012 - Eva Stukenbrock - "Unravelling patterns of speciation and specialization in fungal plant pathogens using comparative population genomics"

MPI for Terrestrial Microbiology, Marburg, Germany

stutenbrockAbstract: The fungus Mycosphaerella graminicola emerged as a new pathogen of cultivated wheat during its domestication about 11000 years ago. We assembled 12 high quality full genome sequences to investigate the genetic footprints of selection in this wheat pathogen and closely related species that infect wild grasses. Current levels of genetic diversity measured through statistics such as PN / PS and π were not significantly different in M. graminicola relative to its wild sister species. Furthermore M. graminicola still contains a significant amount of “ancestral” polymorphisms shared with its wild sister species suggesting that the loss of variation in M. graminicola was not severe during its specialization to wheat. Recent divergence between pathogen sister species is attested by the high degree of incomplete lineage sorting (ILS) in their genomes. We exploit ILS to generate an ancestral recombination map of the species without any crossing data, document recent times of species divergence relative to genome divergence and show that gene rich regions or regions with low recombination experiences stronger effects of natural selection on neutral diversity. It is clear that while domesticated plant species have become restricted in their evolutionary potential through loss of variation, “domesticated” pathogens such as M. graminicola seem readily able to maintain ancestral variation, regenerate lost diversity and evolve new specificities.top

11/06/2012 - Dan Graur - "The compositional architecture of mammalian genomes"

graurTheoretical Molecular Evolution and Bioinformatics, University of Houston

02/07/2012 - Stephan Greiner - "Oenothera - A model for cytoplasmic speciation barriers and functional asexuality"

MPI for Molecular Plant Physiology, Potsdam, Germany

greinerAbstract:  The genus Oenothera Oenothera displays a unique combination of non-Mendelian genetic features, like permanent translocation heterozygosity and biparental transmission of plastids. They allow the exchange of plastids between species, which often results in plastome-genome incompatibility (PGI) - a hybridization barrier according to the Dobzhansky-Muller model. In turn, PGI provides molecular access to speciation forces acting on photosynthesis. Furthermore, Oenothera exhibits over 20 transitions between sexual and functionally asexual reproduction, caused by chromosomal translocations. Both features make Oenothera an ideal model for examining hypotheses regarding the evolutionary advantages of sex, as well as of speciation. To address these questions we established Oenothera as a molecular model over the past decade. We could indentify two plastid candidate loci for PGI, both involved in plastid gene regulation. Moreover, the first genetic map of sexual Oenothera species has been generated assigning more than 1,700 dominant and co-dominant molecular markers to seven coupling groups. Remarkably, homologous recombination (HR) was almost completely suppressed in F2 segregants and, if it occurred at all, was restricted to the telomeric regions of the chromosomes. These data shade a new light on the role of HR in sexual reproduction.

30/07/12  -   Haipeng Li  -  "A New Test for Detecting Recent Positive Selection that is Free from the Confounding Impacts of Demography."

CAS-MPG Partner Institute for Computational Biology, Shanghai, China

li_haipengAbstract: It has been a long-standing interest in evolutionary biology to search for the traces of recent positive Darwinian selection in organisms. However, such efforts have been severely hindered by the confounding signatures of demography. As a consequence neutrality tests often lead to false inference of positive selection since they detect the deviation from the standard neutral model. Here, using the maximum frequency of derived mutations (MFDM) to examine the unbalanceness of the tree of a locus, I propose a statistical test that is analytically free from the confounding effects of varying population size and has a high statistical power (up to 90.5%) to detect recent positive selection. When compared with five well-known neutrality tests for detecting selection (i.e., Tajima’s D-test, Fu & Li’s D-test, Fay & Wu’s H-test, the E-test and the joint DH test), the MFDM test is indeed the only one free from the confounding impacts of bottlenecks and size expansions. Simulations based on wide-range parameters demonstrated that the MFDM test is robust to background selection, population subdivision and admixture (including hidden population structure). Moreover, when two high-frequency mutations are introduced, the MFDM test is robust to the misinference of derived and ancestral variants of segregating sites due to multiple hits. Finally, the sensitivity of the MFDM test in detecting balancing selection is also discussed. In summary, it is demonstrated that summary statistics based on tree topology can be used to detect selection, and this work provides a reliable method that can distinguish selection from demography even when DNA polymorphism data from only one locus is available. The software is available at www.picb.ac.cn/evolgen/softwarestop

19/10/2012 - Daven Presgraves - "Evolutionary genetics of speciation and recombination in Drosophila."

Evolutionary Genetics in Drosophila, University of Rochester, USA

presgravesAbstract: The three species of the Drosophila simulans clade — the cosmopolitan species, D. simulans, and the two island endemic species, D. mauritiana and D. sechellia — are important models in speciation genetics, but some details of their phylogenetic and speciation history remain unresolved. In the first part of the talk, I will present findings from ongoing genomic and genetic analyses of the evolution of reproductive isolation among these three species. Our fine-scale genome-wide genetic analysis of the numbers and kinds of hybrid incompatibilities between species reveals a strikingly high density of hybrid male sterility factors on the X chromosome. Our evolutionary genomics analyses show that despite geographic, ecological, and reproductive barriers between the D. simulans clade species, speciation has nevertheless involved low levels of recurrent gene flow, including quite recently. In the second part of the talk, I will present findings from our genetic analysis of an evolved species difference in the rate of recombination. The total genetic map of D. mauritiana is ~1.7-fold longer than that of the model species D. melanogaster. I will show that evolutionary change at a single gene is sufficient to account for the observed phenotypic difference in crossover frequency between these species.

29/10/2012 - Katja Nowick - "Changes in Transcription Factor Genes and Gene Regulatory Networks during Primate Evolution."

Bioinformatics, University of Leipzig

nowick Abstract: The molecular changes underlying major phenotypic differences between humans and other primates are not well understood, but alterations in gene regulatory networks are likely to play a major role. We therefore analyzed evolutionary changes in the largest family of transcription factors (TFs), the Krüppel-type zinc finger (KZNF) gene family, between primates. We revealed that the evolutionary history of this family is very complex, characterized by many lineage-specific gene duplications and gene losses. Orthologs and paralogs rapidly diverge in sequence and domain composition in ways that predict functional divergence. Furthermore, members of the KZNF family also rapidly acquire differences in expression patterns. Between humans and chimpanzees, KZNF genes are largely enriched among the genes with changed brain expression. By analyzing co-expression patterns of TF genes we revealed that KZNFs are tightly embedded in a network that regulates the expression of genes important for energy metabolism and protein transport in the brain. The structure of this network has considerably changed between humans and chimpanzees, which has potentially played an important role during the evolution of the human brain. I will discuss how different types of evolutionary changes, such as duplications, sequence and expression changes, altered the gene regulatory networks between primates and might have opened the door to the evolution of phenotypic differences.

19/11/2012 - Aurelien Tellier - "Ecological and evolutionary importance of soil seed banks for plant species."

Center of Life and Food Sciences Weihenstephan, Technische Universität München

tellierAbstract: Seed and egg dormancy is a prevalent life-history trait in plants and invertebrates whose storage effect buffers against environmental variability, modulates species extinction in fragmented habitats, and increases genetic variation. Experimental evidence for reliable differences in dormancy over evolutionary is scarce because complex ecological experiments in the field are needed to measure them. To cope with these difficulties, we developed in a first study a new Approximate Bayesian Computation (ABC) framework that integrates ecological information on population census sizes in the priors of the parameters, along with a coalescent model accounting simultaneously for seed banks and spatial genetic structuring of populations. We provide evidence for the existence of a seed bank in two wild tomato species (Solanum chilense and S. peruvianum) found in western South America. The inferred difference in germination rate between these species may reflect divergent seed dormancy adaptations, in agreement with previous population genetic analyses and the ecology of these two sister species: seeds spend on average a shorter time in the soil in the specialist species (S. chilense) than in the generalist species (S. peruvianum). We then further extended our coalescent model with seed bank to population with varying effective size in time. We demonstrate theoretically, and confirm by simulations followed by ABC inference, that the rescaling of the coalescent process due to the seed bank can lead to misestimates of the time and magnitude of past demographic events such as population expansion or crash. Our results highlight the necessity to take into account the existence of seed banks for inference of the time and magnitude of past demographic events with SNPs sequence data and coalescent models.

26/11/2012 Felicity Jones - "The genetics and genomics of stickleback adaptive diversity"

Max Planck Institute for Developmental Biology, Tuebingen, Germany

jonesAbstract: The adaptive radiation of sticklebacks, coupled with a rapidly increasing number of genetic and genomic tools, provides an outstanding opportunity to characterize evolutionary processes underlying phenotypic diversity, adaptation, and speciation. Previous studies have shown that parallel evolution of lateral plate morphology occurred on a global scale via the repeated reuse of genetic variation at the EDA locus (Colosimo et al., 2005). To search for other loci contributing to repeated adaptation, we sequenced 21 marine and freshwater sticklebacks from globally diverse populations (Jones et al., 2012). We identified with high resolution a set of 81 shared adaptive loci, including chromosomal inversions, that are consistently associated with marine–freshwater divergence. We used this genome-wide set of loci to address a long-standing debate about the relative contribution of coding and regulatory changes underlying adaptive evolution in natural populations. We find that both coding and regulatory changes occur, but regulatory changes predominate in this classic example of repeated adaptive evolution in nature. We also identified chromosomal inversions with ecotype-specific orientation that provide a mechanism for the spread of co-adapted suites of alleles. Consistent with theoretical predictions of divergence-with-gene flow we find adaptive loci fall within genomic regions of low recombination rate suggesting that the recombination landscape shapes genetic variation used in parallel adaptive divergence. We have previously shown that adaptation does not always proceed by reuse of globally shared genetic variation: for example, parallel evolution of pelvic reduction occurs via population-specific mutations at the Pitx1 locus (Chan et al., 2010). Ongoing analyses of additional benthic–limnetic and marine–freshwater populations should make it possible to estimate the relative proportion of both shared and locally-restricted adaptive variants contributing to recent diversification and reproductive isolation of sticklebacks. Collecting and analyzing billions of base pairs of DNA sequence creates many challenges for data analysis and visualization. We have generated an interactive gateway to both browse and download predicted stickleback genes, sequence variants, and adaptive loci (http://sticklebrowser.stanford.edu). We hope this will facilitate additional studies in many laboratories, adding to an already solid foundation that makes stickleback a powerful model system for studying fundamental problems in evolutionary biology.

Jones et al (2012) The genomic basis of adaptive evolution in threespine sticklebacks. Nature 484:55-61.

10/12/2012 - Julien Dutheil - "Ancestral population genomics: sequencing the present to infer the past."

Institut des Sciences de L'Evolution de Montpellier, France

dutheilAbstract: The genome of a single individual is a mosaic of regions with distinct histories generated by recombination of parental genomes. The footprints of recombination leave a record of the genetical ancestry of the ancient populations the genome once belonged to. Comparing at least two genomes has hence great potential to infer the history of these populations. Genome data from closely related species mostly exist as one sequence per species, from one individual or as a consensus of several ones. Nevertheless, the comparison of genomes from different species conveys insights into the history of their common ancestors, providing the species are close enough for recombination and other rearrangements not to have entirely shuffled the underlying sequence genealogies. I will introduce the coalescent hidden Markov model (coalHMM) methodology, which builds on coalescent theory and hidden Markov chains to reconstruct the ancestral recombination graph of two or more genomes from distinct species. We used this methodology to infer the patterns of incomplete lineage sorting along the genome alignment, together with the recombination map, of the Human-Chimpanzee ancestor. From the inferred patterns, we examine signatures of ancient selection and provide new insights on the long-standing observation of the reduced divergence on the X chromosome.