Admixture, the mixing of genetically distinct populations, is increasingly recognized as a fundamental biological process. One major goal of admixture analyses is to estimate the timing of admixture events. Whereas most methods today can only detect the most recent admixture event, here, we present coalescent theory and associated software that can be used to estimate the timing of multiple admixture events in an admixed population. We extensively validate this approach and evaluate the conditions under which it can successfully distinguish one-from two-pulse admixture models. We apply our approach to real and simulated data of Drosophila melanogaster. We find evidence of a single very recent pulse of cosmopolitan ancestry contributing to African populations, as well as evidence for more ancient admixture among genetically differentiated populations in sub-Saharan Africa. These results suggest our method can quantify complex admixture histories involving genetic material introduced by multiple discrete admixture pulses. The new method facilitates the exploration of admixture and its contribution to adaptation, ecological divergence, and speciation.

Admixture is increasingly being recognized as an important factor in evolutionary genetics. The distribution of genomic admixture tracts, and the resulting effects on admixture linkage disequilibrium, can be used to date the timing of admixture between species or populations. However, the theory used for such prediction assumes selective neutrality despite the fact that many famous examples of admixture involve natural selection acting for or against admixture. In this paper, we investigate the effects of positive selection on the distribution of tract lengths. We develop a theoretical framework that relies on approximating the trajectory of the selected allele using a logistic function. By numerically calculating the expected allele trajectory, we also show that the approach can be extended to cases where the logistic approximation is poor due to the effects of genetic drift. Using simulations, we show that the model is highly accurate under most scenarios. We use the model to show that positive selection on average will tend to increase the admixture tract length. However, perhaps counter-intuitively, conditional on the allele frequency at the time of sampling, positive selection will actually produce shorter expected tract lengths. We discuss the consequences of our results in interpreting the timing of the introgression of EPAS1 from Denisovans into the ancestors of Tibetans.

Genes that do not segregate in heterozygotes at Mendelian ratios are a potentially important evolutionary force in natural populations. Although the impacts of segregation distortion are widely appreciated, we have little quantitative understanding about how often these loci arise and fix within lineages. Here, we develop a statistical approach for detecting segregation distorting genes from the comprehensive comparison of whole genome sequence data obtained from bulk gamete versus somatic tissues. Our approach enables estimation of map positions and confidence intervals, and quantification of effect sizes of segregation distorters. We apply our method to the pollen of two interspecific F1 hybrids of Arabidopsis lyrata and A. halleri and we identify three loci across eight chromosomes showing significant evidence of segregation distortion in both pollen samples. Based on this, we estimate that novel segregation distortion elements evolve and achieve high frequencies within lineages at a rate of approximately one per 244,000 years. Furthermore, we estimate that haploid‐acting segregation distortion may contribute between 10% and 30% of reduced pollen viability in F1 individuals. Our results indicate haploid acting factors evolve rapidly and dramatically influence segregation in F1 hybrid individuals.

Admixture, the mixing of genetically distinct populations, is increasingly recognized as a fundamental biological process. One major goal of admixture analyses is to estimate the timing of admixture events. Whereas most methods today can only detect the most recent admixture event, here we present coalescent theory and associated software that can be used to estimate the timing of multiple admixture events in an admixed population. We extensively validate this approach and evaluate the conditions under which it can succesfully distinguish one from two-pulse admixture models. We apply our approach to real and simulated data of Drosophila melanogaster. We find evidence of a single very recent pulse of cosmopolitan ancestry contributing to African populations as well as evidence for more ancient admixture among genetically differentiated populations in sub-Saharan Africa. These results suggest our method can quantify complex admixture histories involving genetic material introduced by multiple discrete admixture pulses. The new method facilitates the exploration of admixture and its contribution to adaptation, ecological divergence, and speciation.

Bacterial symbionts that manipulate the reproduction of their hosts to increase their successful transmission are important factors in invertebrate ecology and evolution. In light of their use as a biological control agent, studying the genomic and phenotypic diversity of reproductive manipulators can improve efforts to control infectious diseases and contribute to our understanding of host-symbiont evolution. Despite the vast genomic and phenotypic diversity of reproductive manipulators, only a handful of Wolbachia strains are used as biological control agents because little is known about the broad scale infection frequencies of these bacteria in nature. Here we develop a data mining approach to quantify the number of arthropod and nematode host species available on the Sequence Read Archive (SRA) that are infected with Wolbachia and other reproductive manipulators such as Rickettsia and Spiroplasma. Across the entire database, we found reproductive manipulators infected 1733 arthropod and 103 nematode samples, representing 121 and 10 species, respectively. We estimated that Wolbachia infects approximately 24% of all arthropod species and 20% of all nematode species. In contrast, we estimated other reproductive manipulators infect 0-8% of arthropod and nematode species. We show that relative Wolbachia density within hosts, titer, is significantly lower than the titer of the other reproductive manipulators. Considering the fitness costs of high titers, low titer may contribute to enabling Wolbachia's high prevalence across hosts species and mitigate impacts on host biology compared with other reproductive manipulator taxa. Our study demonstrates that data mining is a powerful tool for understanding host-symbiont coevolution and opens an array of previously inaccessible questions for further analysis. IntroductionBacterial symbionts of eukaryotic hosts exhibit an impressive array of phenotypes that interact with host biology. Included among these symbionts are bacteria that alter host reproduction in order to increase their likelihood of transmission to the next host generation [1-4], a strategy termed reproductive manipulation. Depending on the nature of host reproduction, reproductive manipulators are generally transmitted vertically by associating with either the oocyte or developing embryos [5]. Manipulative phenotypes range from strategies that prevent the survival of uninfected offspring, such as cytoplasmic incompatibility, to strategies such as feminization, male killing, and parthenogenesis, that actually change the sex ratio to favor females for overall increased infection rates [1][2][3][4]. These drastic manipulations to normal host biology mean that reproductive manipulators can induce reproductive isolation, drive changes in sexuality, and alter reproductive ecology in their hosts [6][7][8].