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Visions, needs and requirements for (future) research environments: An exploration with ERC Grantee Stephan Schiffels [article]

Katharina Flicker, Bernd Saurugger, Stephan Schiffels
2021 Zenodo  
Let's see what Stephan Schiffels - group leader for population genetics at the Department for Archeogenetics of the Max Planck Institute for the Science of Human History in Jena - has to say.  ...  Schiffels received his PhD in 2012 from the University of Cologne. He worked as a Postdoc at the Wellcome Sanger Institute in Hinxton (UK).  ...  Stephan "I would love to see more credits and value given to other forms of publishing, also to public outreach, when it comes to evaluating scientists for grants and jobs" TU Wien : Wien Finally, considering  ... 
doi:10.5281/zenodo.4541283 fatcat:nf2kanu7znajrofrny2kvljhmm

The asexual genome of Drosophila [article]

Stephan Schiffels, Ville Mustonen, Michael Lässig
2017 arXiv   pre-print
The rate of recombination affects the mode of molecular evolution. In high-recombining sequence, the targets of selection are individual genetic loci; under low recombination, selection collectively acts on large, genetically linked genomic segments. Selection under linkage can induce clonal interference, a specific mode of evolution by competition of genetic clades within a population. This mode is well known in asexually evolving microbes, but has not been traced systematically in an obligate
more » ... sexual organism. Here we show that the Drosophila genome is partitioned into two modes of evolution: a local interference regime with limited effects of genetic linkage, and an interference condensate with clonal competition. We map these modes by differences in mutation frequency spectra, and we show that the transition between them occurs at a threshold recombination rate that is predictable from genomic summary statistics. We find the interference condensate in segments of low-recombining sequence that are located primarily in chromosomal regions flanking the centromeres and cover about 20% of the Drosophila genome. Condensate regions have characteristics of asexual evolution that impact gene function: the efficacy of selection and the speed of evolution are lower and the genetic load is higher than in regions of local interference. Our results suggest that multicellular eukaryotes can harbor heterogeneous modes and tempi of evolution within one genome. We argue that this variation generates selection on genome architecture.
arXiv:1711.10849v1 fatcat:v5zp5ltjuvectadznr3m7wzmyy

The asexual genome of Drosophila [article]

Stephan Schiffels, Ville Mustonen, Michael Lässig
2017 bioRxiv   pre-print
The rate of recombination affects the mode of molecular evolution. In high-recombining sequence, the targets of selection are individual genetic loci; under low recombination, selection collectively acts on large, genetically linked genomic segments. Selection under linkage can induce clonal interference, a specific mode of evolution by competition of genetic clades within a population. This mode is well known in asexually evolving microbes, but has not been traced systematically in an obligate
more » ... sexual organism. Here we show that the Drosophila genome is partitioned into two modes of evolution: a local interference regime with limited effects of genetic linkage, and an interference condensate with clonal competition. We map these modes by differences in mutation frequency spectra, and we show that the transition between them occurs at a threshold recombination rate that is predictable from genomic summary statistics. We find the interference condensate in segments of low-recombining sequence that are located primarily in chromosomal regions flanking the centromeres and cover about 20% of the Drosophila genome. Condensate regions have characteristics of asexual evolution that impact gene function: the efficacy of selection and the speed of evolution are lower and the genetic load is higher than in regions of local interference. Our results suggest that multicellular eukaryotes can harbour heterogeneous modes and tempi of evolution within one genome. We argue that this variation generates selection on genome architecture.
doi:10.1101/226670 fatcat:lqhnpri4onc7dlprylgu4vuroq

Heuristic Function Evaluation Framework [chapter]

Nera Nešić, Stephan Schiffel
2016 Lecture Notes in Computer Science  
Here's to the future, for the dreams of youth. vii Acknowledgements I would like to thank my advisor, Stephan Schiffel, for his patience and guidance through this project, for the time he spent discussing  ...  The action heuristic study done by Schiffel and Trutman looks into possibility of generating such simulation guiding heuristics for GGP players [20] .  ... 
doi:10.1007/978-3-319-50935-8_7 fatcat:nqrfktcksrfibmkjlzcibrimxe

Rate and cost of adaptation in the Drosophila genome [article]

Stephan Schiffels, Michael Lässig, Ville Mustonen
2014 bioRxiv   pre-print
Recent studies have consistently inferred high rates of adaptive molecular evolution between Drosophila species. At the same time, the Drosophila genome evolves under different rates of recombination, which results in partial genetic linkage between alleles at neighboring genomic loci. Here we analyze how linkage correlations affect adaptive evolution. We develop a new inference method for adaptation that takes into account the effect on an allele at a focal site caused by neighboring
more » ... s alleles (background selection) and by neighboring adaptive substitutions (hitchhiking). Using complete genome sequence data and fine-scale recombination maps, we infer a highly heterogeneous scenario of adaptation in Drosophila. In high-recombining regions, about 50% of all amino acid substitutions are adaptive, together with about 20% of all substitutions in proximal intergenic regions. In low-recombining regions, only a small fraction of the amino acid substitutions are adaptive, while hitchhiking accounts for the majority of these changes. Hitchhiking of deleterious alleles generates a substantial collateral cost of adaptation, leading to a fitness decline of about 30/2N per gene and per million years in the lowest-recombining regions. Our results show how recombination shapes rate and efficacy of the adaptive dynamics in eukaryotic genomes.
doi:10.1101/008680 fatcat:jyibgva7cnf3bnudbhqed3tmfe

MSMC and MSMC2: The Multiple Sequentially Markovian Coalescent [chapter]

Stephan Schiffels, Ke Wang
2020 Msphere  
As introduced in Schiffels and Durbin [1] , to simplify interpretation of the three inferred rates, we can plot a simple summary by taking the ratio of the across-rate and the mean within-rate, which  ... 
doi:10.1007/978-1-0716-0199-0_7 pmid:31975167 fatcat:2ahf4psvzndbvkieqv2sgvw6pm

Rate and cost of adaptation in the Drosophila Genome [article]

Stephan Schiffels, Michael Lässig, Ville Mustonen
2014 arXiv   pre-print
Nourmohammad A, Schiffels S, Lässig M (2013) Evolution of molecular phenotypes under stabilizing selection. J Stat Mech 2013: P01012. doi:10.1088/1742--5468/2013/01/P01012. 52.  ... 
arXiv:1409.1946v1 fatcat:lyx7drmgbfhotnj5ckxjkdrhsu

Inferring human population size and separation history from multiple genome sequences [article]

Stephan Schiffels, Richard Durbin
2014 bioRxiv   pre-print
The availability of complete human genome sequences from populations across the world has given rise to new population genetic inference methods that explicitly model their ancestral relationship under recombination and mutation. So far, application of these methods to evolutionary history more recent than 20-30 thousand years ago and to population separations has been limited. Here we present a new method that overcomes these shortcomings. The Multiple Sequentially Markovian Coalescent (MSMC)
more » ... nalyses the observed pattern of mutations in multiple individuals, focusing on the first coalescence between any two individuals. Results from applying MSMC to genome sequences from nine populations across the world suggest that the genetic separation of non-African ancestors from African Yoruban ancestors started long before 50,000 years ago, and give information about human population history as recently as 2,000 years ago, including the bottleneck in the peopling of the Americas, and separations within Africa, East Asia and Europe.
doi:10.1101/005348 fatcat:qztdn3sfijcj7n4ihkyn6t4vb4

Knowledge-Based General Game Playing

Sebastian Haufe, Daniel Michulke, Stephan Schiffel, Michael Thielscher
2011 Künstliche Intelligenz  
General Game Playing (GGP) is concerned with the development of systems that can play well an arbitrary game solely by being given the rules of the game. This problem is considerably harder than traditional artificial intelligence (AI) game playing. Writing a player for a particular game allows to focus on the design of elaborate strategies and libraries that are specific to this game. Systems able to play arbitrary, previously unknown games cannot be given game-specific knowledge. They rather
more » ... eed to be endowed with high-level cognitive abilities such as general strategic thinking and abstract reasoning. This makes General Game Playing a good example of a challenge problem, which encompasses a variety of AI research areas including knowledge representation and reasoning, heuristic search, planning, and learning. 10.2
doi:10.1007/s13218-010-0073-8 fatcat:ylia7hhcnjbtnobn7j4li5qhpm

Decomposition of Multi-player Games [chapter]

Dengji Zhao, Stephan Schiffel, Michael Thielscher
2009 Lecture Notes in Computer Science  
Acknowledgments I would like to acknowledge and extend my heartfelt gratitude to Michael Thielscher and Stephan Schiffel who were abundantly helpful and offered undivided support and guidance.  ... 
doi:10.1007/978-3-642-10439-8_48 fatcat:afaoun55ufbgfhlrzyzj2b4cxy

Emergent Neutrality in Adaptive Asexual Evolution

Stephan Schiffels, Gergely J. Szöllősi, Ville Mustonen, Michael Lässig
2011 Genetics  
Schiffels et al. SI hitchhiking.  ...  Schiffels et al. This Figure shows simulation and theory results for an approach to equilibrium, starting from an initially poorly adapted state (see main Text).  ... 
doi:10.1534/genetics.111.132027 pmid:21926305 pmcid:PMC3241435 fatcat:fmkqxxlfgzagpfr6a746n76qvm

Tracking human population structure through time from whole genome sequences [article]

Ke Wang, Iain Mathieson, Jared O'Connell, Stephan Schiffels
2019 bioRxiv   pre-print
AbstractThe genetic diversity of humans, like many species, has been shaped by a complex pattern of population separations followed by isolation and subsequent admixture. This pattern, reaching at least as far back as the appearance of our species in the paleontological record, has left its traces in our genomes. Reconstructing a population's history from these traces is a challenging problem. Here we present a novel approach based on the Multiple Sequentially Markovian Coalescent (MSMC) to
more » ... yse the population separation history. Our approach, called MSMC-IM, uses an improved implementation of the MSMC (MSMC2) to estimate coalescence rates within and across pairs of populations, and then fits a continuous Isolation-Migration model to these rates to obtain a time-dependent estimate of gene flow. We show, using simulations, that our method can identify complex demographic scenarios involving post-split admixture or archaic introgression. We apply MSMC-IM to whole genome sequences from 15 worldwide populations, tracking the process of human genetic diversification. We detect traces of extremely deep ancestry between some African populations, with around 1% of ancestry dating to divergences older than a million years ago.Author SummaryHuman demographic history is reflected in specific patterns of shared mutations between the genomes from different populations. Here we aim to unravel this pattern to infer population structure through time with a new approach, called MSMC-IM. Based on estimates of coalescence rates within and across populations, MSMC-IM fits a time-dependent migration model to the pairwise rate of coalescences. We implemented this approach as an extension to existing software (MSMC2), and tested it with simulations exhibiting different histories of admixture and gene flow. We then applied it to the genomes from 15 worldwide populations to reveal their pairwise separation history ranging from a few thousand up to several million years ago. Among other results, we find evidence for remarkably deep population structure in some African population pairs, suggesting that deep ancestry dating to one million years ago and older is still present in human populations in small amounts today.
doi:10.1101/585265 fatcat:j3f25iysfffjhpu4vzjpyljbfi

Estimating human mobility in Holocene Western Eurasia with large-scale ancient genomic data [article]

Clemens Schmid, Stephan Schiffels
2021 bioRxiv   pre-print
The recent increase in openly available ancient human DNA samples allows for new, large-scale meta analysis applications. Trans-generational past human mobility is one of the key aspects that ancient genomics can contribute to, since changes in ancestry -- unlike cultural changes seen in the archaeological record -- necessarily reflect movements of people. Here we present a new algorithm to quantify past human mobility from large ancient genomic datasets. The key idea of the method is for each
more » ... ndividual to compare a hypothetical genetic "origin" point with its actual burial point in space. This is achieved by first creating an interpolated ancestry field through space and time based on Multidimensional scaling and Gaussian process regression, and then using this field to map the ancient individuals into space according to their genetic profile. We apply this new algorithm to a dataset of 3191 aDNA samples with genome-wide data from Western Eurasia in the last 10,000 years and derive a diachronic measure of mobility for subregions in Western, Central, Southern and Eastern Europe. For regions and periods with sufficient data coverage, our mobility estimates show general concordance with previous results, but also reveal new signals of movements beyond the well-known key events.
doi:10.1101/2021.12.20.473345 fatcat:lvwk4g2szbca5ip2taub2kqkem

A Multiagent Semantics for the Game Description Language [chapter]

Stephan Schiffel, Michael Thielscher
2010 Communications in Computer and Information Science  
The Game Description Language (GDL) has been developed for the purpose of formalizing game rules. It serves as the input language for general game players, which are systems that learn to play previously unknown games without human intervention. In this paper, we show how GDL descriptions can be intepreted as multiagent domains and, conversely, how a large class of multiagent environments can be specified in GDL. The resulting specifications are declarative, compact, and easy to understand and
more » ... aintain. At the same time they can be fully automatically understood and used by autonomous agents who intend to participate in these environments. Our main result is a formal characterization of the class of multiagent domains that serve as formal semantics for-and can be described in-the Game Description Language.
doi:10.1007/978-3-642-11819-7_4 fatcat:hqosf5jqdrf3bgxierhu5eeq5q

Automated verification of state sequence invariants in general game playing

Sebastian Haufe, Stephan Schiffel, Michael Thielscher
2012 Artificial Intelligence  
A general game player is a system that can play previously unknown games given nothing but their rules. Many of the existing successful approaches to general game playing require to generate some form of game-specific knowledge, but when current systems establish knowledge they rely on the approximate method of playing random sample matches rather than formally proving knowledge. In this paper, we present a theoretically founded and practically viable method for automatically verifying
more » ... s of games whose rules are given in the general Game Description Language (GDL). We introduce a simple formal language to describe game-specific knowledge as state sequence invariants, and we provide a proof theory for verifying these invariants with the help of Answer Set Programming. We prove the correctness of this method against the formal semantics for GDL, and we report on extensive experiments with a practical implementation of this proof system, which show that our method of formally proving knowledge is viable for the practice of general game playing.
doi:10.1016/j.artint.2012.04.003 fatcat:hljbzt7ixfdrxeicyarq7yha54
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