A5039602318- Evolution and Genetic Dynamics
- Genetic diversity and population structure
- Genomics and Phylogenetic Studies
- Plant and animal studies
- Genetic and phenotypic traits in livestock
- Epigenetics and DNA Methylation
- Genetic Mapping and Diversity in Plants and Animals
- Evolutionary Game Theory and Cooperation
- Evolutionary Algorithms and Applications
- Plant Reproductive Biology
- Nutrition, Genetics, and Disease
- Mathematical and Theoretical Epidemiology and Ecology Models
- Algorithms and Data Compression
- Ecology and Vegetation Dynamics Studies
- Animal Behavior and Reproduction
Technical University of Munich
2019-2024
University of Salzburg
2022-2024
Abstract Stochastic simulation is a key tool in population genetics, since the models involved are often analytically intractable and usually only way of obtaining ground-truth data to evaluate inferences. Because this, large number specialized programs have been developed, each filling particular niche, but with largely overlapping functionality substantial duplication effort. Here, we introduce msprime version 1.0, which efficiently implements ancestry mutation simulations based on...
The reproductive mechanism of a species is key driver genome evolution. standard Wright-Fisher model for the reproduction individuals in population assumes that each individual produces number offspring negligible compared to total size. Yet many plants, invertebrates, prokaryotes or fish exhibit neutrally skewed distribution strong selection events yielding few produce up same magnitude as As result, genealogy sample characterized by multiple (more than two) coalescing simultaneously common...
Abstract Several methods based on the sequentially Markovian coalescent (SMC) make use of full genome sequence data from samples to infer population demographic history including past changes in size, admixture, migration events and structure. More recently, original theoretical framework has been extended allow simultaneous estimation size along with other life traits such as selfing or seed banking. The latter developments enhance applicability SMC nonmodel species. Although convergence...
Several methods based on the Sequential Markovian coalescence (SMC) have been developed that make use of genome sequence data to uncover population demographic history, which is interest in its own right and a key requirement generate null model for selection tests. While these can be applied all possible kind species, underlying assumptions are sexual reproduction each generation non-overlapping generations. However, many plants, invertebrates, fungi other taxa, those often violated due...
The evolution from outcrossing to selfing occurred recently across the eukaryote tree of life in plants, animals, fungi, and algae. Despite short-term advantages, is hypothetically an evolutionary dead-end reproductive strategy. tippy distribution on phylogenies suggests that most species are recent origin. However, dating such transitions challenging yet central for testing this hypothesis. We build previous theories disentangle differential effect past changes rate or population size...
Abstract The reproductive mechanism of a species is key driver genome evolution. standard Wright-Fisher model for the reproduction individuals in population assumes that each individual produces number offspring negligible compared to total size. Yet many plants, invertebrates, prokaryotes or fish exhibit neutrally skewed distribution strong selection events yielding few produce up same magnitude as As result, genealogy sample characterized by multiple (more than two) coalescing...
With the availability of high-quality full genome polymorphism (SNPs) data, it becomes feasible to study past demographic and selective history populations in exquisite detail. However, such inferences still suffer from a lack statistical resolution for recent, example bottlenecks, events, and/or with small nucleotide diversity. Additional heritable (epi)genetic markers, as indels, transposable elements, microsatellites, or cytosine methylation, may provide further, yet untapped, information...
Abstract The speed of population adaptation to changing biotic and abiotic environments is determined by the interaction between genetic drift, positive selection linkage effects. Many marine species (fish, crustaceans), invertebrates pathogens humans crops, exhibit sweepstakes reproduction characterized production a very large amount offspring (fecundity phase) from which only small fraction may survive next generation (viability phase). Using stochastic simulations, we investigate whether...
Abstract Many methods based on the Sequentially Markovian Coalescent (SMC) have been and are being developed. These make use of genome sequence data to uncover population demographic history. More recently, new extended original theoretical framework, allowing simultaneous estimation history other biological variables. can be applied many different species, under model assumptions, in hopes unlocking population/species evolutionary Although convergence proofs particular cases given using...
With the availability of high-quality full genome polymorphism (SNPs) data, it becomes feasible to study past demographic and selective history populations in exquisite detail. However, such inferences still suffer from a lack statistical resolution for recent, example bottlenecks, events, and/or with small nucleotide diversity. Additional heritable (epi)genetic markers, as indels, transposable elements, microsatellites, or cytosine methylation, may provide further, yet untapped, information...
Abstract Several methods based on the Sequential Markovian Coalescent (SMC) have been developed to use full genome sequence data uncover population demographic history, which is of interest in its own right and a key requirement generate null model for selection tests. While these can be applied all possible species, underlying assumptions are sexual reproduction at each generation no overlap generations. However, many plant, invertebrate, fungi other those often violated due different...
Abstract The evolution from outcrossing to selfing is a transition that occurred recurrently throughout the eukaryote tree of life, in plants, animals, fungi and algae. Despite some short-term advantages, supposed be an evolutionary dead-end reproductive strategy on long-term its tippy distribution phylogenies suggests most species are recent origin. However, dating such transitions challenging while it central for this hypothesis. We develop two methods making use full genome polymorphism...
With the availability of high quality full genome polymorphism (SNPs) data, it becomes feasible to study past demographic and selective history populations in exquisite detail. However, such inferences still suffer from a lack statistical resolution for recent, e.g. bottlenecks, events, and/or with small nucleotide diversity. Additional heritable (epi)genetic markers, as indels, transposable elements, microsatellites or cytosine methylation, may provide further, yet untapped, information on...
With the availability of high quality full genome polymorphism (SNPs) data, it becomes feasible to study past demographic and selective history populations in exquisite detail. However, such inferences still suffer from a lack statistical resolution for recent, e.g. bottlenecks, events, and/or with small nucleotide diversity. Additional heritable (epi)genetic markers, as indels, transposable elements, microsatellites or cytosine methylation, may provide further, yet untapped, information on...
Abstract With the availability of high quality full genome polymorphism (SNPs) data, it becomes feasible to study past demographic and selective history populations in exquisite detail. However, such inferences still suffer from a lack statistical resolution for recent, e.g. bottlenecks, events, and/or with small nucleotide diversity. Additional heritable (epi)genetic markers, as indels, transposable elements, microsatellites or cytosine methylation, may provide further, yet untapped,...
With the availability of high quality full genome polymorphism (SNPs) data, it becomes feasible to study past demographic and selective history populations in exquisite detail. However, such inferences still suffer from a lack statistical resolution for recent, e.g. bottlenecks, events, and/or with small nucleotide diversity. Additional heritable (epi)genetic markers, as indels, transposable elements, microsatellites or cytosine methylation, may provide further, yet untapped, information on...
Abstract Stochastic simulation is a key tool in population genetics, since the models involved are often analytically intractable and usually only way of obtaining ground-truth data to evaluate inferences. Because this necessity, large number specialised programs have been developed, each filling particular niche, but with largely overlapping functionality substantial duplication effort. Here, we introduce msprime version 1.0, which efficiently implements ancestry mutation simulations based...