VolcanoFinder:Genomic scans for adaptive introgression

Recent research shows that introgression between closely-related species is an important source of adaptive alleles for a wide range of taxa. Typically, detection of adaptive introgression from genomic data relies on comparative analyses that require sequence data from both the recipient and the donor species. However, in many cases, the donor is unknown or the data is not currently available. Here, we introduce a genome-scan method-VolcanoFinder-to detect recent events of adaptive introgression using polymorphism data from the recipient species only. VolcanoFinder detects adaptive introgression sweeps from the pattern of excess intermediate-frequency polymorphism they produce in the flanking region of the genome, a pattern which appears as a volcano-shape in pairwise genetic diversity. Using coalescent theory, we derive analytical predictions for these patterns. Based on these results, we develop a composite-likelihood test to detect signatures of adaptive introgression relative to the genomic background. Simulation results show that VolcanoFinder has high statistical power to detect these signatures, even for older sweeps and for soft sweeps initiated by multiple migrant haplotypes. Finally, we implement VolcanoFinder to detect archaic introgression in European and sub-Saharan African human populations, and uncovered interesting candidates in both populations, such as TSHR in Europeans and TCHH-RPTN in Africans. We discuss their biological implications and provide guidelines for identifying and circumventing artifactual signals during empirical applications of VolcanoFinder

Rapid De Novo Evolution of X Chromosome Dosage Compensation in Silene latifolia, a Plant with Young Sex Chromosomes

Evidence for dosage compensation in Silene latifolia, a plant with 10-million-year-old sex chromosomes, reveals that dosage compensation can evolve rapidly in young XY systems and is not an animal-specific phenomenon

scc_examples

Examples of the resampling test for sister clade comparison. Needs data files from the archive data.tar.gz

Data from: Standard sister clade comparison fails when testing derived character states

Comparing species richness in sister clades that differ in a character is one of the ways to study factors influencing diversification. While most of its applications focused on traits that increase diversification, some were used to study the association of a trait with less species richness, e.g. the occurrence of dioecy in flowering plants. We show here, using simulations and an analytical model, that the null expectation of equal species richness that is generally used in sister clade comparisons is wrong in the case of a derived trait occurring independently from speciation: one should expect less species in the clade with the derived character when there is no difference in diversification rates. This is due to the waiting time for the derived state to appear, which causes it to occur more often on longer branches. This has the important implication that the probability for a clade to possess the derived state depends on the tree geometry, and thus on species richness: less species-rich clades are more likely to possess the derived state. A test for differences in species richness should be based upon observed tree imbalance. We present a method to do this, and find that we cannot confirm earlier work that concluded that dioecy decreases diversification; on the contrary, it seems to be associated to higher species richness than expected

Data from: Standard sister clade comparison fails when testing derived character states

Comparing species richness in sister clades that differ in a character is one of the ways to study factors influencing diversification. While most of its applications focused on traits that increase diversification, some were used to study the association of a trait with less species richness, e.g. the occurrence of dioecy in flowering plants. We show here, using simulations and an analytical model, that the null expectation of equal species richness that is generally used in sister clade comparisons is wrong in the case of a derived trait occurring independently from speciation: one should expect less species in the clade with the derived character when there is no difference in diversification rates. This is due to the waiting time for the derived state to appear, which causes it to occur more often on longer branches. This has the important implication that the probability for a clade to possess the derived state depends on the tree geometry, and thus on species richness: less species-rich clades are more likely to possess the derived state. A test for differences in species richness should be based upon observed tree imbalance. We present a method to do this, and find that we cannot confirm earlier work that concluded that dioecy decreases diversification; on the contrary, it seems to be associated to higher species richness than expected

Labile sex expression in angiosperm species with sex chromosomes

International audienceHere, we review the literature on sexual lability in dioecious angiosperm species with well-studied sex chromosomes. We distinguish three types of departures from strict dioecy, concerning either a minority of flowers in some individuals (leakiness) or the entire individual, which can constantly be bisexual or change sex. We found that for only four of the 22 species studied, reports of lability are lacking. The occurrence of lability is only weakly related to sex chromosome characteristics (number of sex-linked genes, age of the non-recombining region). These results contradict the naive idea that lability is an indication of the absence or the recent evolution of sex chromosomes, and thereby contribute to a growing consensus that sex chromosomes do not necessarily fix sex determination once and for all. We discuss some implications of these findings for the evolution of sex chromosomes, and suggest that more species with well-characterized lability should be studied with genomic data and tools. This article is part of the theme issue ‘Sex determination and sex chromosome evolution in land plants’

scc_test

R source code for the resampling test for sister clade comparisons proposed in the manuscrip