Genome Patterns of Selection and Introgression of Haplotypes in Natural Populations of the House Mouse (Mus musculus)

Staubach, Fabian; Lorenc, Anna; Messer, Philipp W.; Tang, Kun; Petrov, Dmitri A.; Tautz, Diethard

doi:10.1371/journal.pgen.1002891

Cited by 140 publications

(187 citation statements)

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“…Our analysis of house mouse genomes produces an evolutionary history that differs from that reported by Staubach et al (7) not only in terms of the number of populations involved but also by accounting for the evolutionary history of the populations involved. We consider the percentages of the genome with introgressed origin reported by Staubach et al (7) to be overestimates, because introgression involving an ancestral population that later split into more than one extant population would be multiply reported for each extant population in the case of the study by Staubach et al (7).…”

Section: Resultsmentioning

confidence: 68%

“…Our study included all of the samples in the study of Staubach et al (7). Furthermore, our study included additional samples from an M. m. musculus population from China (25) that were not used in the study of Staubach et al (7).…”

Section: Resultsmentioning

confidence: 99%

“…Furthermore, our study included additional samples from an M. m. musculus population from China (25) that were not used in the study of Staubach et al (7). In this analysis, we used estimated gene tree topologies alone.…”

Section: Resultsmentioning

confidence: 99%

“…A serious limitation of these methods is that they would grossly overestimate the amount of reticulation in a dataset when other causes of incongruence are at play. Indeed, several recent studies (5)(6)(7)(8)(9) have shown that detecting hybridization in practice can be complicated by the presence of incomplete lineage sorting (ILS) (Fig. 1).…”

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confidence: 99%

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Maximum likelihood inference of reticulate evolutionary histories

Yu¹,

Dong²,

Liu

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

264

389

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Hybridization plays an important role in the evolution of certain groups of organisms, adaptation to their environments, and diversification of their genomes. The evolutionary histories of such groups are reticulate, and methods for reconstructing them are still in their infancy and have limited applicability. We present a maximum likelihood method for inferring reticulate evolutionary histories while accounting simultaneously for incomplete lineage sorting. Additionally, we propose methods for assessing confidence in the amount of reticulation and the topology of the inferred evolutionary history. Our method obtains accurate estimates of reticulate evolutionary histories on simulated datasets. Furthermore, our method provides support for a hypothesis of a reticulate evolutionary history inferred from a set of house mouse (Mus musculus) genomes. As evidence of hybridization in eukaryotic groups accumulates, it is essential to have methods that infer reticulate evolutionary histories. The work we present here allows for such inference and provides a significant step toward putting phylogenetic networks on par with phylogenetic trees as a model of capturing evolutionary relationships. reticulate evolution | incomplete lineage sorting | phylogenetic networks | maximum likelihood P hylogenetic trees have long been a mainstay of biology, providing an interpretive model of the evolution of molecules and characters and a backdrop against which comparative genomics and phenomics are conducted. Nevertheless, some evolutionary events, most notably horizontal gene transfer in prokaryotes and hybridization in eukaryotes, necessitate going beyond trees (1). These events result in reticulate evolutionary histories, which are best modeled by phylogenetic networks (2). The topology of a phylogenetic network is given by a rooted, directed, acyclic graph (rDAG) that is leaf-labeled by a set of taxa ( Fig. 1; more details are provided in Model and SI Appendix). Reticulation events result in genomic regions with local genealogies that are incongruent with the speciation pattern. Several methods and heuristics use this incongruence as a signal for inferring reticulation events and reconstructing phylogenetic networks from local genealogies. These methods, which are surveyed elsewhere (2-4), assume that reticulation events are the sole cause of all incongruence among the gene trees and seek phylogenetic networks to explain all of the incongruence. A serious limitation of these methods is that they would grossly overestimate the amount of reticulation in a dataset when other causes of incongruence are at play. Indeed, several recent studies (5-9) have shown that detecting hybridization in practice can be complicated by the presence of incomplete lineage sorting (ILS) (Fig. 1).Recently, a set of methods was devised to analyze data where reticulation and ILS might both be simultaneously at play (10-15). However, these methods are all applicable to simple scenarios of species evolution and mostly assume a known hypothesis about the topol...

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Section: Resultsmentioning

confidence: 68%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

See 2 more Smart Citations

Maximum likelihood inference of reticulate evolutionary histories

Yu¹,

Dong²,

Liu

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

264

389

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“…appealing because it explains the high level of divergence between the two haplogroups. The term 'comet allele' has been proposed to describe haplotypes that have introgressed across species or sub-species boundaries-similar to comets, they have 'dipped' into this system from another lineage (Staubach et al, 2012). There are precedents for such events in other species such as that described by Brand et al (2013) where D. simulans alleles have entered the D. sechellia genome in an adaptive process.…”

Section: A Footprint Of a Selective Sweep?mentioning

confidence: 99%

High nucleotide diversity and limited linkage disequilibrium in Helicoverpa armigera facilitates the detection of a selective sweep

Song¹,

Downes²,

Parker³

et al. 2015

Heredity

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Insecticides impose extreme selective pressures on populations of target pests and so insecticide resistance loci of these species may provide the footprints of 'selective sweeps'. To lay the foundation for future genome-wide scans for selective sweeps and inform genome-wide association study designs, we set out to characterize some of the baseline population genomic parameters of one of the most damaging insect pests in agriculture worldwide, Helicoverpa armigera. To this end, we surveyed nine Z-linked loci in three Australian H. armigera populations. We find that estimates of π are in the higher range among other insects and linkage disequilibrium decays over short distances. One of the surveyed loci, a cytochrome P450, shows an unusual haplotype configuration with a divergent allele at high frequency that led us to investigate the possibility of an adaptive introgression around this locus.

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Genomic Studies of Adaptation in Natural Populations

Martin

Jiggins

2013

Encyclopedia of Life Sciences

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Understanding the genetic basis of adaptive evolution is a problem almost as old as evolutionary biology itself. Recent advances in genome sequencing and the ability to generate genomic samples from natural populations promises to provide answers to many long‐standing questions. The recent surge in genomic studies of adaptation has been accompanied by the development of numerous powerful techniques to analyse these enormous data sets. The state of the field is reviewed in this article, with an emphasis on the various approaches used. This article covers both ‘top‐down’, used to identify the genetic basis of a known trait, and ‘bottom‐up’ approaches, used to identify the footprints of selection on the genome. It shows how recent studies highlight the benefits of combining multiple methods and also discusses important goals for the future of the field. Key Concepts: Association mapping is used to identify genomic loci that control a trait of interest, by identifying molecular markers that display genotype‐by‐phenotype associations. Either offspring from controlled crosses or population samples can be used as the recombinant ‘mapping population’. Numerous loci underlying important adaptive traits have been identified using association mapping; however, this approach is biased towards loci of large effect and may not accurately capture the true genetic architecture of a trait. Genome‐wide scans for the footprints of selection are less sensitive to effect‐size biases but are naive with regard to the trait(s) under selection. Selective sweeps can be identified by the presence of reduced variation, enhanced linkage disequilibrium and a shift in the ‘site frequency spectrum’. Loci under divergent selection between populations can be identified as outliers displaying greater differentiation between populations than expected under neutral evolution. By comparing between‐species divergence with within‐species polymorphism at synonymous and nonsynonymous sites, it has been estimated that a large proportion of the genome is involved in adaptive evolution.

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Genome Patterns of Selection and Introgression of Haplotypes in Natural Populations of the House Mouse (Mus musculus)

Cited by 140 publications

References 63 publications

Maximum likelihood inference of reticulate evolutionary histories

Maximum likelihood inference of reticulate evolutionary histories

High nucleotide diversity and limited linkage disequilibrium in Helicoverpa armigera facilitates the detection of a selective sweep

Genomic Studies of Adaptation in Natural Populations

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