DFG FOR 1078 Natural Selection in Structured Populations

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Abstracts PhD students - FOR 1078 Meeting 2013

P1: Inferring the demography of Drosophila melanogaster by approximate bayesian methods

Pablo Duchén
Evolutionary Biology, LMU BioCenter
Projectleader: Prof. Dr. Wolfgang Stephan

Drosophila melanogaster spread from sub-Saharan Africa to the rest of the world colonizing new environments. Here, we modeled the joint demography of African (Zimbabwe), European (The Netherlands), and North American (North Carolina) populations using an approximate Bayesian computation (ABC) approach. By testing different models (including scenarios with continuous migration), we found that admixture between Africa and Europe most likely generated the North American population, with an estimated proportion of African ancestry of 15%. We also revisited the demography of the ancestral population (Africa) and found-in contrast to previous work-that a bottleneck fits the history of the population of Zimbabwe better than expansion. Finally, we compared the site-frequency spectrum of the ancestral population to analytical predictions under the estimated bottleneck model.

P1: Evidence for positive selection in the php-pgd region of Drosophila melanogaster

Susanne Voigt
Evolutionary Biology, LMU BioCenter
Projectleader: Prof. Dr. Wolfgang Stephan

The region around the two tandemly duplicated genes ph-d and ph-p seems to have a complex molecular evolutionary history. Before Drosophila melanogaster migrated out of Africa to become a cosmopolitan species, the locus was a target of positive selection in the ancestral population. This left the molecular signature of a selective sweep in this region of the X chromosome, and likely caused the functional divergence of two ph genes. The patterns of this sweep can still be observed in the derived non-African populations from Europe and Asia. It appears, however, that successfully settling in a temperate environment went in hand with a second adaptive event in this genomic region. The target of that selection in the European populations appears to be of a regulatory nature and selection likely caused the fixation of derived variants in the intergenic region of the two genes ph-p and CG3835. These derived variants are very rare in Africa and probably went not to fixation due to the out-of-Africa bottleneck experienced by the non-African populations, since they are found in intermediate frequency in the Asian populations. Via reporter gene assays using the site-specific ΦC31 integration system, it is clarified whether these derived variants confer changes in the expression of the two aforementioned genes.top

P2: A putative case for adaptive post-transcriptional gene regulation in Drosophila melanogaster

Ana Catalán
Evolutionary Biology, LMU BioCenter
Projectleader: Prof. John Parsch

Changes in gene regulation are thought to be crucial for the adaptation of organisms to their environment. Transcriptome analyses can be used to identify candidate genes for ecological adaptation, but can be complicated by variation in gene expression between tissues, sexes, or individuals. Here we use high-throughput RNA sequencing of a single Drosophila melanogaster tissue to detect brain-specific differences in gene expression between the sexes and between two populations, one from the ancestral species range in sub-Saharan Africa and one from the recently colonized species range in Europe. Relatively few genes (<40) displayed sexually dimorphic expression in the brain, but there was an enrichment of sex-biased genes, especially male-biased genes, on the X chromosome. Over 230 genes differed in brain expression between flies from the African and European populations, with the between-population divergence being highly correlated between males and females. Candidate genes for ecological adaptation include those involved in sensory perception (heat, UV light), mating behavior, and detoxification. Expression differences were associated with transposable element insertions at two genes implicated in insecticide resistance (Cyp6g1 and CHKov1). Also, a 49 bp indel in the 3’UTR of MtnA, a gene that has been associated with heavy metal tolerance, is a candidate example for adaptive post-transcriptional gene expression regulation. Analysis of the brain transcriptome revealed many candidates for ecological adaptation that were not detected in previous studies using whole flies. There was little evidence for sex-specific regulatory adaptation in the brain, as most expression differences between populations were observed in both males and females.

P2: Linking function with adaptive cis-regulatory divergence

Amanda Glaser-Schmitt
Evolutionary Biology, LMU BioCenter
Projectleader: Prof. John Parsch

Although it is decades since biologists first predicted the importance of regulatory mutations in adaptive evolution, examples of adaptive regulatory changes are still somewhat rare, especially in comparison to the numerous examples of adaptive structural changes. Drosophila melanogaster originated in sub-Saharan Africa and expanded its range to more temperate regions ~15,000 years ago; thus, divergence in gene regulation between the ancestral population and derived populations may reflect adaptation associated with environmental factors. I will focus on CG9509, a gene of unknown function that shows evidence for adaptive regulatory divergence between cosmopolitan (non-sub-Saharan African) and sub-Saharan African populations of D. melanogaster. A1.2-kb enhancer region upstream of CG9509 which shows evidence for a selective sweep in Europe has previously been identified as being responsible for 2-3 times greater expression in European populations in comparison to sub-Saharan Africa. In this talk, I will extend the analysis of sequence and expression variation in CG9509 to other cosmopolitan and sub-Saharan African populations. I will then present the various methods we are using to link genotype with expression variation in this gene. Last, I will discuss the possible functions of CG9509 and how we are attempting to correlate phenotype with expression variation and determine how an increase in CG9509 expression outside sub-Saharan Africa may be adaptive.top

P3: Cold tolerance and phenotypic plasticity in different populations of D. melanogaster

Korbinian von Heckel
Evolutionary Biology, LMU BioCenter
Projectleader: Dr. Stephan Hutter

Drosophila melanogaster - nowadays a cosmopolitan human commensal - is of afro-tropical origin and colonised temperate habitats only after the last glaciation event about 15,000 years ago. An increase in cold resistance has likely been one of the major adaptations facilitating this range expansion. My PhD project aims at uncovering genes that are responsible for the increased cold tolerance of European flies, with particular regard to adaptive changes in gene expression. To this end, I will compare the genome wide expression response to a cold shock via RNAseq in a cold-tolerant European and a cold-sensitive African strain.

As a first step, I have analysed the cold tolerance of several populations on the basis of their chill coma recovery time (CCRT). Chill coma recovery is a widely used laboratory assay to estimate cold tolerance in insects. In D. melanogaster it has been shown that CCRT follows a latitudinal cline, i.e. decreases with latitude. Apart from the geographical origin, CCRT is heavily influenced by plastic changes. In fact, environmental variations affect CCRT to a much greater extent than genetic differences between populations.

I will present the results of chill coma recovery experiments conducted with flies from Zambia, Rwanda, Denmark and Sweden. Furthermore, I will show the impact of cold rearing and acclimation on CCRT in the Zambian and Swedish population and discuss the degree of plasticity and consequences for experimental design.

T2: The frequency spectra after a selective sweep

Sebastian Bossert
Faculty of Mathematics and Physics, University of Freiburg
Projectleader: Prof. Dr. Peter Pfaffelhuber

The frequency spectrum provides a means of investigating DNA-sequence data. In order to understand different patterns theoretical results can be consulted. While the expected frequency spectrum of a sample under a neutral Wright-Fisher model is a well known result, the situation under selection is different. Approximations for the expected frequency spectrum after a selective sweep (including recombinations) are rare, due to the difficulty of determining approximations for the genealogy under selection.

For neutral loci linked to the selective site, Etheridge et al. (2006) have derived a good approximation using a Yule process. This result can be applied in order to get a new approximation formula, called Yule formula, for the expected frequency spectrum of a sample after a selective sweep. This Yule formula will be presented and compared with other theoretical approximation formulas by simulation.top

T1: Population genetics of Cape Verde Arabidopsis

Andrea Fulgione
Structural & Computational Biology, University of Vienna
Projectleader: Prof. Dr. Joachim Hermisson

Arabidopsis thaliana is a plant model organism for molecular biology and genetics. Distributed over a wide geographic and environmental range, it is a useful model to clarify how populations adapt to their environment.

With this intent, an almost completely unstudied population of Arabidopsis has been extensively sampled in the Cape Verde Islands. The only studied individual from this population (Cvi-0) is both genetically and phenotypically divergent from other studied individuals for many traits, which are likely to be ecologically important in the Cape Verde Islands. Previous research in Cvi-0 will provide hypotheses about the alleles that underlie complex trait divergence in this population. We will elucidate the demographic history of Cape Verde Arabidopsis using sequence data from this population together with data from the Arabidopsis 1001 Genomes Project. Then, we will identify regions of the genome that contain signatures of positive selection using genome scans. Finally, we will reconstruct the adaptive histories of functional variants that are known from previous research in Cvi-0. This project provides a novel opportunity to clarify the details of quantitative trait adaptation in an interesting and divergent population of A. thaliana.

E1: Geographic mosaic of host defenses

Isabelle Kleeberg
Evolutionary Biology, University of Mainz
Projectleader: Prof. Dr. Susanne Foitzik

Social parasites such as slave-making ants exhibit strong selection pressures on their host species leading to the expression of co-adaptations and the evolution of novel traits as described in the ‘arms race’ and ‘Red Queen’ theories. The dulotic ant Protomognathus americanus exploits the brood care behavior of its hosts Temnothorax longispinosus and T. curvispinosus, thereby reducing host colony´s fitness. Due to the geographic mosaic theory of coevolution the expression of behavioral traits can differ between separate regions due to different selection pressures. We collected 17 populations of the hosts T. longispinosus and T. curvispinosus and estimated the parasitation rate of the slavemaking ant P. americanus. We hypothesized that different parasitation rates are correlated with the expression of defense traits, such as aggression, enemy recognition and evacuation probability. We found that host colony aggression increases with parasitation rate whereas all populations showed enemy recognition irrespective of parasitation rate. Furthermore we found differences between species. Temnothorax curvispinosus showed high aggression when confronted with a living slavemaker and choose to fight over flight whereas T. longispinosus choose to evacuate more often. These results indicate a geographic mosaic of defense mechanisms due to different parasite pressures and different defense strategies in the two host species.top

E1: The genetic basis of reproductive division of labor in Temnothorax ants: First results of a gene expression study

Barbara Feldmeyer
Evolutionary Biology, University of Mainz
Projectleader: Prof. Dr. Susanne Foitzik

Reproductive division of labor is a key feature of social Hymenoptera. Although queens and workers share the same set of genes, they strongly differ in morphology, physiology, behavior and longevity. Following queen removal, young brood tending workers of the facultative polygynous ant Temnothorax longispinosus start to develop ovaries and engage in dominance interactions. Here we report the results of an RNA-seq approach to identify caste specific genes and gene expression patterns along a reproductive gradient with the queen resembling the main reproductive phenotype, followed by reproductive nest-workers, none-reproductive nest-workers and foragers as the non-reproductive extreme.

E2: The role of hybridization in the colonization of newly opened habitats

Johanna Griebel, Monika Poxleitner, Amanda Navas Fara, Sabine Giessler, and Justyna Wolinska
Evolutionary Ecology, LMU BioCenter
Projectleader: Dr. Justyna Wolinska

The role of hybridization has been underestimated for a long time. For example, hybrids were often considered less fit then their parental species, due to genetic incompatibility. However, hybridization occurs frequently in plants and in animals. In the Daphnia longispina complex hybridization has been shown to be common and in some lakes hybrids have even been able to outcompete their parental species. Here I will present a study examining how hybrid-specific traits facilitate the colonization of novel habitats. Communities of the D. longispina complex in ten quarry lakes in and around Munich have been screened at 15 microsatellite loci over the last five years. Analysis of communities and populations structure will be presented. These quarry lakes are considered to be “novel habitats” for two reasons: they have been created only 15-80 years ago, and they are re-opened for colonization every spring (Daphnia do not survive winter in these shallow lakes; population needs to be re-established from sexually produced diapauses eggs). Analysis of communities and populations structure will be presented. Furthermore, we observed that one of the studied lakes (Feldmochinger See) has become dominated by a single hybrid clone - the “super clone”. Using laboratory experiments we examined the competitive strength and fitness parameters of the “super clone”. Uncovering the pattern that makes the “super clone” so special will contribute to a general knowledge about hybrid-specific traits and their contribution to evolutionary processes.top

P5: Transcriptome sequencing in wild tomatoes

Aparna Reddy
Institute of Population Genetics, University of Düsseldorf
Projectleader: Prof. Dr. Laura Rose

Wild tomato species are native to diverse habitats in South America and have become a model system for evolutionary biology studies because of their recent divergence, distinctive morphological characters and difference in mating systems. Our project aims to study the patterns of population structure, demography, speciation history and natural selection of two closely related species (i.e, S. peruvianum and S. chilense) of 20 individuals of each species. RNA was isolated from young leaves. In our pilot study we sequenced four RNA libraries using the Illumina / Solexa Genome Analyzer II. Samples were multiplexed and had an average of ~4 million reads per library.

The quality of the sequences was analyzed and trimmed to get rid of some low quality bases at the start of each read (9 bases). Filtered reads were mapped to the available tomato reference genome. Currently we are working to identify putative SNPs and genes to investigate questions about species history and natural selection.

P5: Inferring Demography from Next-Generation-Sequencing Data

Paul Staab
Evolutionary Biology, LMU BioCenter
Projectleader: Prof. Dr. Dirk Metzler

Selection and demographic forces can create similar patters in the genome. Disentangling both effects is a major challenge when reconstructing the evolutionary history of one or more species from genomic data. Current approaches for analyzing demographic effects often require known neutral loci, while the ones for identifying selection usually compare the loci against a neutral background. When strong a priori information about both selection and demographic forces is not available, this creates a chicken-and-egg problem.

We aim solve this dilemma by adapting our algorithm Jaatha to analyze selection and demography at the same time. As a prerequisite, we need to utilize the informational benefit that huge Next-Generation-Sequencing dataset offer. I will shortly introduce Jaatha and talk about the challenges that arise from computational aspects as well as from modeling approaches when dealing with those datasets.top

P4: The role of biogeography in shaping diversity of the intestinal microbiota in house mice

Jun Wang
Evolutionary Genomics, University of Kiel
Projectleader: Prof. Dr. John Baines

The microbial communities inhabiting the mammalian intestinal tract play an important role in diverse aspects of host biology, and may also serve as an importance force of selection. One of the examples is the B4glnt2 gene which are shown to be under balancing selection (Linnenbrink et al. 2010), and the knockout study perform in lab mouse have demonstrated that the gene indeed regulates the gut microbiota (Staubach et al. 2012). However, little is known regarding the forces shaping variation in these communities in natural conditions. To shed light on the contributions of host genetics, transmission and geography to diversity in microbial communities between individuals, we performed a survey of intestinal microbial communities in a panel of 121 house mice derived from eight locations across western Europe using pyrosequencing of the bacterial 16S rRNA gene (Linnenbrink et al. in press). The host factors studied included population structure estimated by microsatellite loci and mitochondrial DNA, genetic distance and geography. To determine whether host tissue (mucosa)-associated communities display properties distinct from those of the lumen, both the cecal mucosa and contents were examined. We identified Bacteroides, Robinsoniella and Helicobacter as the most abundant genera in both the cecal content and mucosa-associated communities of wild house mice. Overall we found geography to be the most significant factor explaining patterns of diversity in the intestinal microbiota, with a comparatively weaker influence of host population structure and genetic distance. Furthermore, the influence of host genetic distance was limited to the mucosa communities, consistent with this environment being more intimately coupled to the host. The follow up work will focus on the candidate genera of bacteria to investigate the genomic basis of adaption/interaction to host genotypes; and future field works will search for signatures of microbiota-driven selection in the wild, after identifying important bacterial members in the lab.