Seminar Series
Every semester, EES organise a seminar series, which takes place on Mondays at 16:00 at Biozentrum, Großhaderner Str. 2, 82152 Planegg-Martinsried, Lecture Hall B 01.027
External speakers are invited across all three areas (Evolution, Ecology and Systematics), leading to a wide-range of presented research topics.
Winter Semester 2023/24
30.10.2023
Jonna Kulmuni -Semipermeable species boundaries and adaptive potential of hybridization
University of Amsterdam
Abstract: Hybridization is widespread across the Tree of Life, and it is predicted to increase due to climate change and human action, which bring previously isolated populations into contact. Increased rate of hybridization can lead to erosion of species barriers and biological diversity, but it can also provide the raw material for adaptation via introgression or increased genetic diversity. Using mound-building wood ants I show both deleterious and beneficial consequences of hybridization. Moreover, evolution of hybrid populations is repeatable at the genomic level, suggesting some outcomes of hybridization could be predictable. With on-going climate change semipermeable species boundaries may provide an advantage and allow persistence of populations in the new environmental conditions.
Host: Richard Merrill (merrill@bio.lmu.de)
06.11.2023
Claudia Bank - Epistasis and adaptation on fitness landscapes
University of Bern
Abstract: Epistasis occurs when the effect of a mutation depends on its carrier's genetic background. Although increasing evidence indicates ubiquitous epistasis for fitness, its role during evolution is debated. Fitness landscapes are mappings of genotype or phenotype to fitness, which capture the full extent and complexity of epistasis. Theoretical studies of fitness landscapes have shown how epistasis affects the path and the outcome of evolution. In addition, empirical fitness landscapes, in which the competitive fitness of sets of tens to thousands of connected genotypes was measured, have shown that epistasis is common and depends on the measure of fitness, the choice of mutations for the fitness landscape, and the environment in which fitness was assessed. Here, I present an overview of the field of evolutionary fitness landscape research and highlight ongoing work in my research group that aims at bridging the gap between fitness landscape theory and the role of epistasis in nature.
Host: Dirk Metzler (metzler@bio.lmu.de)
13.11.2023
Jordan Martin - Social drive explains rapid adaptation and eco-evolutionary feedback in small-scale human societies
University of Zurich
Abstract: Social interactions play a crucial role in generating feedback between ecological and evolutionary dynamics, due to their joint effects on the expression and selection of functional traits. Developing generalizable models of eco-evolutionary feedback in social environments is, therefore, crucial for understanding convergent social evolution across the natural world, as well as for predicting population growth or decline in response to ongoing environmental change. In this talk, I will present a novel eco-evolutionary feedback model developed during my PhD research, which attempts to explain otherwise paradoxical patterns of rapid adaptation in small-scale human societies. This ‘social drive’ model demonstrates how phenotypic plasticity among group members can generate and maintain feedback between the quantitative genetic causes and ecological effects of social interactions in fluctuating environments. Using extensive long-term data on the indigenous Tsimane people of Bolivia, I then provide strong empirical support for the predictions of this social drive model. Results show how (i) indirect genetic effects due to plasticity among Tsimane neighbors are accelerating the contemporary adaptation of fertility, and also how (ii) density- and frequency-dependent selection among Tsimane neighbors is acting to maintain these accelerating effects across generations.
Host: Niels Dingemanse (n.dingemanse@bio.lmu.de)
20.11.2023
Stefan Prost - The use of genomics for applied conservation.
University of Oulu
Abstract: Global change is impacting wildlife around the world, making conservation of threatened species and environments paramount. State-of-the-art genomic methods can be used to better understand threatened species and to inform conservation management strategies (both in situ and ex situ). However, efficient conservation can only be achieved when science, policy and society work together. In this talk, I will highlight different modern genomic techniques and how they are being used for applied conservation and to inform policy. I will also show how some methods can be used for local capacity building, education and citizen-science to support conservation of threatened species and environments around the world.
Host: Sarah Mueller (s.mueller@bio.lmu.de)
27.11.2023
Melanie Dammhahn - Patterns and consequences of individual variation in landscapes of fear: who takes the risk and does it matter?
University of Münster
Abstract: To eat or to feed others - that is one of the most fundamental problems governing animal behaviour. Besides direct predation risk, the mere presence of predators might change prey foraging behaviour. This perceived predation risk varies in space and time creating a landscape of fear. Hitherto, landscapes of fear have been studied as species-specific layers, assuming that each individual of a species perceives the same risk. However, individuals differ in risk-taking behaviour. In this talk, I will present results of empirical studies in which we illuminated patterns and consequences of individualised landscapes of fear.
Host: Niels Dingemanse (n.dingemanse@bio.lmu.de)
4.12.2023
Linda Weiss - Molecular Mechanisms of phenotypic plasticity: Environment perception, signal transmission and the development of adaptive phenotypes in the freshwater crustacean Daphnia
Ruhr University Bochum
Abstract: Phenotypic plasticity describes the ability of an organism to respond to changing environmental conditions by the adaptation of its phenotype. Thereby, organisms can conquer environments with fluctuating conditions as their genotype is geared with adaptive strategies increasing the individual’s fitness. The freshwater crustacean Daphnia reacts highly plastic to a wide variety of environmental cues, by developing adaptive context-dependent phenotypes.
I will present the progress that has been made in deciphering mechanistic underpinnings underlying adaptive strategies in Daphnia. I focus on inducible defence expression as well as environmentally induced diapause. These strategies allow Daphnia to overcome harsh environmental conditions. In this context, causes of climate change negatively affect these adaptive strategies, makig Daphnia susceptible to anthropogenic environmental challenges.
Host: Maria Stockenreiter (stockenreiter@bio.lmu.de)
29.01.2024
Nico Posnian - Georg-August-University Göttingen (postponed to the next semester)
Host: Richard Merrill (merrill@bio.lmu.de)
05.02.2024
Nathan Baker - The spatio-temporal patterns of European riverine biodiversity
Nature Research Centre, Lithuania
Abstract: Like a fingerprint, no two riverine communities are alike. Then again, since riverine communities are in a constant state of flux shifting and changing both spatially and temporally, a community’s uniqueness is only but a snapshot representing an exact moment in time, the moment in which it was sampled. By collecting enough of these ‘snapshots’ we can derive broader ecological patterns and, with coupled snapshots of environmental conditions, explore their potential drivers. Accordingly, my research addresses two simple questions: HOW and WHY freshwater biodiversity is changing. Using an ecological and statistical approach, I explore the spatio-temporal patterns of a changing freshwater landscape, first at a very localized scale, then at a supraregional scale, and lastly at the pan-European scale. Findings show that freshwater biodiversity is context dependent, with local and regional factors playing key roles in shaping the observed patterns. In a nutshell, European freshwater biodiversity is changing, with some parts showing improvements, while others showing deterioration. This makes monitoring and mitigation efforts challenging, since the “blanket” approach is not as effective as once thought. So, where to from here? The short answer: it’s complicated. The long answer: After some initial recovery, European freshwater biodiversity is entering a new era of challenges. It is up to us to mitigate these challenges, beginning with better predictive tools, conscious planning, and improved monitoring.
Host: Sarah Mueller (s.mueller@bio.lmu.de)
Summer Semester 2023
08.05.2023
Hannah Rowland - How toxins mediate ecological interactions - C A N C E L L E D
MPI for Chemical Ecology, Jena, Germany
Abstract: My research examines how toxins mediate ecological interactions between plants, herbivores, and predators. My primary study system is centred around toxic steroidal heart poisons produced by milkweed plants. I also have major projects on poison frogs, tiger moths, and snakes. My goal is to understand how multi-trophic interactions lead to evolutionary innovation and diversification. To achieve this I integrate research across different biological levels of organisation, and use multidisciplinary tools from small molecule chemistry, to molecular and cell biology, to whole animal behaviour. I will present my research examining the evolution of – and new adaptations to – toxicity, that has broad implications for the evolutionary dynamics of signalling systems and animal behaviour. My talk will addresses specific evolutionary questions such as the role of epistasis and contingency in molecular evolution, and how novel protein functions arise.
Host: Richard Merrill (merrill@bio.lmu.de)
15.05.2023
Stuart Baird- Genome Polarisation
IVB, Czech Academy of Sciences, Czech Republic
Abstract: Incomplete barriers to geneflow allow admixed inheritance across, not down the tree of life. This may change the rate of adaptation in times of rapid environmental shifts such as the current climate crisis.To understand this potential requires knowledge of the prevalence of barriers in nature and their barrier strength. Genome polarisation paints genomes with respect to the sides of barriers, and so may help in building this knowledge base.
Host: Jochen Wolf (j.wolf@bio.lmu.de)
22.05.2023
Sean Stankowski - Selection on many loci drove the origin and spread of a key innovation
IST, Austria
Abstract: Key innovations are fundamental to biological diversification, but their genetic architecture is poorly understood. A recent transition from egg-laying to live-bearing in Littorina snails provides the opportunity to study the architecture of a young innovation. Samples do not cluster by reproductive mode in a genome-wide phylogeny, but local genealogical analysis revealed numerous genomic regions where all live-bearers carry the same core haplotype. Associated regions show evidence for live-bearer-specific positive selection, and are enriched for genes that are differentially expressed between egg-laying and live-bearing reproductive systems. Ages of selective sweeps suggest live-bearing alleles accumulated gradually, involving selection at different times in the past. Our results suggest that innovation can have a polygenic basis, and that novel functions can evolve gradually, rather than in a single step.
Host: Jochen Wolf (j.wolf@bio.lmu.de)
05.06.2023
Ivan Kolidarov - Evolution of Functionally Novel Genes: Insights From the Animal Venoms
(TUM, Germany)
Abstract: In this talk, we will explore the evolution of novel functions in animals, with a focus on toxins in venomous bees and snakes. We will base our discussion on a combination of genomic and proteomic data, as well as tools such as synteny, phylogenetic and protein space AI analyses that were used to investigate the origin and diversification of toxin-encoding genes. We will delve into the mechanisms of gene duplication and its relationship to the emergence of novel biological functions, illustrating it by the evolution of g2 family of phospholipase A2 in Vertebrata and the 3-finger toxins in caenophidian snakes. Our reconstruction of evolutionary history suggests that duplication events and the resulting functional redundancy have played a significant role in the evolution of these gene families. However, our research also highlights that the evolution of functionally diverse genes is a complex process that is shaped by a variety of historical, genomic, and ecological factors, and that neofunctionalization may not always be the best model to explain the evolution of genetic novelty
Host: Andrea Pozzi (pozzi@bio.lmu.de)
19.06.2023
Daven Presgraves - The roles of selfish genes during complex speciation in Drosophila
University of Rochester, USA and Wissenschaftskolleg zu Berlin, Germany
Abstract: Eukaryotic genomes contain a diversity of evolutionarily “selfish” genetic elements (SGEs) that obtain transmission advantages at the expense of their host carriers. SGEs tend to use one of two broad strategies: over-replicate relative to the host genome (e.g., transposable elements) or distort Mendelian transmission (e.g., meiotic drive elements). Sex chromosomes, it turns out, are especially susceptible to the accumulation of meiotic drive elements that, by distorting X versus Y chromosome transmission, bias progeny sex ratios. Such “sex-ratio drive” potentiates evolutionary conflicts of interest between drivers and drive-suppressors at X-linked, Y-linked, and autosomal loci. Molecular arms races arising from recurrent bouts of sex-ratio drive and suppression can have far reaching consequences for genome evolution and for speciation. In this talk, I will show how a system of sex-ratio drivers & suppressors evolved recently and then rapidly amplified and diversified among three closely related species of Drosophila— D. simulans, D. mauritiana, and D. sechellia. I will discuss how this drive system contributed to the evolution of genetic incompatibility and to the history of gene flow among between species.
Host: John Parsch (parsch@bio.lmu.de)
26.06.2023
Rahel Sollman- Hierarchical statistical models in wildlife ecology
Leibniz Institute for Zoo and Wildlife Research
Abstract: Hierarchical statistical models (HSM) are multi-level models in which one level is conditional on another. These models are used in a myriad ways, for example, to account for nested sampling designs, to model processes on multiple scales (e.g., spatial or temporal), or to disentangle ecological from observation processes. The latter is particularly important in wildlife research, as animals are notoriously difficult to observe. As a result, ecological state variables of interest, such as species presence or abundance, are observed imperfectly, e.g., a species may be present but never detected by sampling; or a population may consist of more individuals than are counted. In my talk, I will provide an overview over HSM that address this form of observation bias, also called imperfect detection, by describing an observation model that is conditioned on the true, but latent, underlying ecological state. I will present occupancy models, in which repeated species-level detection/non-detection data collected across multiple sites (observation) are used to estimate species occurrence (ecological state) while accounting for imperfect species detection, and which are often fit to joint data from multiple species (i.e., community occupancy models). I will touch on count-based models to estimate abundance, with a focus on distance sampling, in which individual detection probability is described as a declining function of distance from the observer, allowing for estimation of abundance (ecological state) from counts (observations). Finally, I will discuss traditional and spatial capture-recapture, the gold standard of abundance estimation, based on repeated detection data of animals that can be identified individually, through natural or artificial marks. I illustrate all approaches with case studies that also showcase extensions to the basic models. Overall, HSM is a flexible framework that can be tailored to specific sampling circumstances to investigate spatio-temporal processes in wildlife ecology while addressing imperfect detection.
Host: Richard Merrill (merrill@bio.lmu.de)
03.07.2023
Andreas Fleischmann - Food, sex and crime: interactions between carnivorous plants and insects
Botanische Staatssammlung München
Abstract: Carnivorous plants are generally considered deadly traps for insects and small animals. However all of the currently known ca. 860 species of carnivorous plants have flowers that are pollinated by insects. How do they avoid eating their pollinators? Modes of prey attraction and pollinator "protection" are presented. Moreover, several insects have adapted to live in or on the traps of carnivorous plants, as herbivores (feeding on the carnivorous plants), kleptoparasites (feeding on the prey of carnivorous plants) or mutualists (in a symbiotic relationship with carnivorous plants). These specialized insect associates will also be illustrated in the talk, including their adaptions to survive in the deadly habitat they live in.
Host: Gundrun Kadereit (G.Kadereit@biologie.uni-muenchen.de)
10.07.2023
Markus Möst - The multifarious outcomes of hybridization and the consequences of life cycle variation
University of Innsbruck
Abstract: Hybridization and introgression are now recognized as important evolutionary processes that can facilitate speciation and rapid adaptation to new environments. However, a hybridization event may have various outcomes and may range from a collapse of species into a hybrid swarm, over hybrid speciation and adaptive introgression to a complete removal of hybrids and purging of introgressed alleles via intrinsic or extrinsic forces that may eradicate the traces of a hybridization event and contribute to the maintenance of stable specie boundaries. The results of a secondary contact may even differ within the same pair of species, for example along an extended contact zone or among multiple contact zones. Factors affecting the outcome and dynamics of hybridization include spatial heterogeneity and – often underappreciated – features of species’ life cycles, such as cyclical parthenogenesis or propagule banks. I will contrast different outcomes of hybridization and the role of life cycle in the Heliconius butterflies and a hybridizing Daphnia water flea species complex. I will highlight a few intriguing cases of adaptive introgression in Heliconius butterflies and continue with recent work leveraging whole-genome time series obtained from Daphnia resting eggs deposited in lake sediments reconstructing recent cases of secondary contact and interspecific hybridization following anthropogenic habitat disturbance through cultural eutrophication in European peri-Alpine lakes. Despite periods of extensive hybridization and extended backcrossing during ecological transitions, the parental species still exist as distinct units alongside hybrid lineages. I will discuss possible mechanisms reducing the impact of hybridization and highlight the role and interaction of life cycle features and spatio-temporal ecological heterogeneity in maintaining species boundaries in this hybridizing species complex. To conclude, I will discuss ongoing work studying the consequences of hybridization in a keystone species for its community and ecosystem.
Host: Richard Merrill (merrill@bio.lmu.de)
Winter Semester 2022/23
21.11.2022
Cristina Tuni -Reproductive trait evolution: unravelling the effects of pre- and post-copulatory sexual
selection. (ONLINE ONLY)
University of Torino, Italy
Abstract: Sexual selection operates both before and after mating, with evolutionary theory predicting that traits involved in mate acquisition, namely pre-copulatory traits, covary with those involved in fertilization success, namely post-copulatory traits. Based on the nature of these associations, selection acting on traits, such as male ornaments and/or armaments, can potentially constrain or facilitate the evolution of other traits, such as testes and/or sperm phenotype, and vice-versa. Using the field cricket Gryllus bimaculatus as a model system, my research aims at understanding how pre- and post-copulatory sexual selection shape complex reproductive phenotypes. I will
discuss findings from studies uncovering both, phenotypic and genetic correlations among behaviour, morphology, and ejaculate traits, suggesting that traits are integrated at the genetic level. I will further report on a long-
term experimental evolution study designed to disentangle the effects of pre-and post-copulatory selective pressures on a range of reproductive traits. The study of male courtship singing, aggressiveness and weaponry (mandibles), testes and sperm traits, will allow understanding whether and which traits diverge in response to altered pre- or post-mating selective pressures, potentially shedding light on correlated evolution and/or evolutionary trade-offs between reproductive traits.
05.12.2022
R. Brian Langerhans - Predictability and parallelism of multi-trait adaptation and speciation.
North Carolina State University, United States of America
Abstract: Environments shape the traits of organisms and appear to ultimately cause the majority of speciation on Earth. While the deterministic action of selection on organismal phenotypes is widespread, the degree to which evolutionary change might be predicted (from theory) and the magnitude of parallelism (consistent occurrences) during evolution is not yet well understood. Using the post-Pleistocene radiation of Bahamas mosquitofish (Gambusia hubbsi) inhabiting blue holes, I assess the predictability, parallelism, and magnitude of evolutionary divergence in nearly 100 traits and six reproductive isolating barriers. Natural selection clearly drives a non-trivial amount of
predictable and repeatable evolution, directly influencing the evolution of multiple isolating barriers during speciation. But just how predictable and consistent are these patterns, how generalizable are the results, and what explains all of the “unexplained” phenotypic evolution and reproductive isolation?
19.12.2022
Carolin Haug -Quantifying convergent evolution: examples from “flying crustaceans”
LMU Munich, Germany
Abstract: Animal life appears almost unlimited in overall form variation,yet we see repetitively the same shapes evolving independently. This phenomenon is generally addressed as convergence. Besides the fact that convergence is widely recognised as “similar morphologies in distantly related lineages”, the question often remains: how similar is similar? I present several cases of convergence within the group Insecta
using quantifiable characteristics of specimens from the modern fauna and the fossil record. Especially apparent are
similar morphologies due to similar selective pressures for grasping and holding prey items. I demonstrate that using
fossil and extant representatives of numerous distantly related lineages in a frame of quantifiable traits offers the detection of cases of convergent evolution and evolutionary processes behind it.
09.01.2023
Anja Hörger -Constraint or opportunity? How trade-offs in stress adaptation may facilitate the evolution of heavy metal hyperaccumulation in plants
Paris-Lodron-University Salzburg, Austria
Abstract: Metal hyperaccumulating plants are able to accumulate exceptionally high concentrations of heavy metals in their shoots to levels that would be toxic to most other plant species. This trait has evolved independently multiple times in the plant kingdom. Although our understanding of the molecular mechanisms involved in metal uptake and tolerance has improved, not much is known about the processes that have led to the evolution of metal hyperaccumulation in plants. Recent studies have provided new insight into the ecological
and evolutionary significance of this trait by showing that the metal hyperaccumulatingplant Noccaea caerulescens can use high concentrations of accumulated metals to defend itself against attack by pathogenic microorganisms and/or herbivores. Interestingly, attacked N. caerulescens plants seem compromised in the inducible defence responses that are used by most plants to provide protection against antagonists, which suggests that it
relies on accumulated metal for resistance. The fact that these plants have evolved the ability to uptake and store metals in their shoot tissue, but have in turn lost defences common to most plants suggests a trade-off in expressing both traits. We studied physiological, molecular and ecological processes involved in the gain of metal
hyperaccumulation and loss of other defensive traits in N. caerulescens. Genes involved in the trade-off were identified and analysed using a combined phenotyping and transcriptomics strategy. Our results provide new insights into the evolution and ecology of metal hyperaccumulation and contribute to the understanding of how plant adaptation to biotic and abiotic stress may be connected.
06.02.2023
Aurélien Tellier - Inference of ecological and life-history traits from full genome polymorphism data: tales of success and limitations
Technical University of Munich, Germany
Abstract: While most inference methods using full-genome data can be applied to all possible kind of species, the underlying assumptions are often sexual reproduction in each generation and non-overlapping generations. However, in many plants, invertebrates, fungi and other taxa, those assumptions are often violated due to different ecological and life history traits, such as self-fertilization, long term dormant structures (seed or egg-banking) or large
variance in offspring production. Furthermore, the resolution of past inference decreases when there is a lack of SNPs in the data. I will present here three new developments of the Sequentially Markovian Coalescent (SMC) and Deep Learning (DL) methods based on Graph Neural Networks (GNN) allowing us to 1) infer seed banking / dormancy or selfing rates and their change in time, 2) infer the variance in offspring production and regions under positive selection along the genome, and 3) integrate epigenetic (methylation) markers to improve the inference of past events.
07.02.2023
Krushnamegh Kunte - The Evolution and Genetics of Butterfly Wing Colour Patterns
National Center for Biological Sciences, Bangalore, India
Abstract: Butterflies use colours in many aspects of their lives: from keeping warm in cold climates to evading predators and impressing potential mates. In this talk, Dr. Kunte will narrate scientific discoveries on how butterfly colour patterns have diversified under natural and sexual selection, how genetic variation and genomic architecture facilitate colour pattern diversification, and how the patterns are regulated during development through co-option and other means. Thus, this talk will bring to the audience a unique appreciation of the evolutionary patterns and genetic mechanisms by which butterflies get their brilliant colours.
Summer Semester 2020
20.01.2020
Björn Benning - Bryozoa in a nutshell: evolution, ecology, systematics
Oberösterreichisches Landmuseum Linz, Austria
27.04.2020
Virginie Courtier-Orgogozo - Evolution of Drosophila Bristles
CNRS, Paris, France
08.06.2020
Douglas Sheil - Forests and Water: Advances and Controversies
Norwegian University of Life Sciences
13.07.2020
Joana Meier
University of Cambridge, UK
Winter Semester 2019/20
18.11.2019
Alistair McGregor - Investigating the Evolution of Developmental Regulation in Spiders and Flies
Oxford Brookes University, UK
Abstract: Research in my lab focuses on questions that are key to understanding animal evolution: How does the genetic regulation of development evolve and what is the genetic and developmental bases for morphological variation within and between species. To address these questions we study the genomics and genetics of the development of the spider Parasteatoda tepidariorum, and gene regulation and morphological evolution among flies of the Drosophila melanogaster species subgroup. In this talk I will present our recent work on the regulation of segmentation in Parasteatoda, and on investigating cis-regulatory logic and morphology evolution among Drosophila species. Research in my lab focuses on questions that are key to understanding animal evolution: How does the genetic regulation of development evolve and what is the genetic and developmental bases for morphological variation within and between species. To address these questions we study the genomics and genetics of the development of the spider Parasteatoda tepidariorum, and gene regulation and morphological evolution among flies of the Drosophila melanogaster species subgroup. In this talk I will present our recent work on the regulation of segmentation in Parasteatoda, and on investigating cis-regulatory logic and morphology evolution among Drosophila species.
25.11.2019
Marie Herbestein - Unlocking the paradox of imperfect mimicry using ant mimicking spiders
Macquarie University, Australia
Abstract: Batesian mimics are deliciously palatable species that gain protection from a predator by resembling a defended or unpalatable model. Theory predicts that mimics that closely resemble their model should have the greatest advantage, while inaccurate mimics should be recognised and attacked by predators. This is all fine and good, but in reality, we find that mimics are highly variable, some are excellent in mimicking their model and others are rubbish at it. There are many different hypotheses that try to explain the persistence of inaccurate mimics, and we have a research project at Macquarie University that tests these ideas using ant mimicking spiders. In this seminar, I will illustrate the range of mimic fidelity in ant mimicking spiders and present the evaluation of some of the common hypotheses. If time and technology permits we will even play an online game.
09.12.2019
Julien Gagneur - Modelling the regulatory code: From basic biology to clinical research
Technical University of Munich, Germany
My lab is interested in understanding how gene expression is encoded in genomes, and how to leverage this knowledge for medical application. To this end, we employ statistical modeling of ‘omics data and work in close collaboration with experimentalists. I will provide an overview of recent studies on RNA metabolism and protein expression control and on deep learning based models of cis-regulatory elements. I will also report on methodologies for using RNA-sequencing as a powerful companion tool to genome sequencing for pinpointing causes of rare genetic disorders.
16.12.2019
Aurelien Tellier -Inference of past demography and life history traits from whole genome genetic and epigenetic data
Technical University of Munich, Germany
Several methods based on the Sequential Markovian coalescence (SMC) have been developed to use full genome sequence data to uncover population demographic history, which is of interest in its own right and is a key requirement to generate a null model for selection tests. While these methods can be applied in principle to all possible species, they have two main limitations: 1) the underlying assumptions are sexual reproduction at each generation and no overlap of generations, and 2) the inference accuracy depends on the ratio of recombination to mutation. However, in many plants, invertebrates, fungi and other taxa, these assumptions are often violated due to different ecological and life history traits, such as self-fertilization, long term dormant structures (seed or egg-banking) or large variance in offspring production. In this presentation I will first describe a novel SMC-based method which we developed to infer 1) the rates of seed/egg-bank and of self-fertilization, and 2) the populations' past demographic history. Using simulated data sets, we demonstrate the accuracy of our method for a wide range of demographic scenarios and for sequence lengths from one to 30 Mb using four sampled genomes. As a test, we apply our method to a Swedish and a German population of Arabidopsis thaliana demonstrating a selfing rate of ca. 0:87 and the absence of any detectable seed-bank. In contrast, we show that the water flea Daphnia pulex exhibits a long lived egg-bank of three to 18 generations. Second, I will provide recommendations for the use of SMC-based methods for non-model organisms, highlighting the importance of the per site and the effective ratios of recombination over mutation. Third, I will show some preliminary results on the effect and estimation of a violation of the Wright-Fisher model assumption, namely the large variance in offspring production which is common to fish, invertebrates and fungal species. Finally, if time permits, I will show some preliminary results on the use of methylation patterns to enhance the power of inference under an SMC model using both genetic and epigenetic markers.