Distinguishing migration from isolation using genes with intragenic recombination: detecting introgression in the Drosophila simulans species complex

Inferring the Demographic History and Inheritance Mode of Tetraploid Species Using ABC

Genomic patterns of diversity and divergence are impacted by certain life history traits, reproductive systems, and demographic history. The latter is characterized by fluctuations in population sizes over time, as well as by temporal patterns of introgression. For a given organism, identifying a demographic history that deviates from the standard neutral model allows a better understanding of its evolution but also helps to reduce the risk of false positives when screening for molecular targets of natural selection. Tetraploid organisms and beyond have demographic histories that are complicated by the mode of polyploidization, the mode of inheritance, and different scenarios of gene flow between sub-genomes and diploid parental species. Here we provide guidelines for experimenters wishing to address these issues through a flexible statistical framework: approximate Bayesian computation (ABC). The emphasis is on the general philosophy of the approach to encourage future users to exploit the enormous flexibility of ABC beyond the limitations imposed by generalist data analysis pipelines.

Hybrid Sterility, Genetic Conflict and Complex Speciation: Lessons From the Drosophila simulans Clade Species

The three fruitfly species of the Drosophila simulans clade- D. simulans, D. mauritiana, and D. sechellia- have served as important models in speciation genetics for over 40 years. These species are reproductively isolated by geography, ecology, sexual signals, postmating-prezygotic interactions, and postzygotic genetic incompatibilities. All pairwise crosses between these species conform to Haldane's rule, producing fertile F1 hybrid females and sterile F1 hybrid males. The close phylogenetic proximity of the D. simulans clade species to the model organism, D. melanogaster, has empowered genetic analyses of their species differences, including reproductive incompatibilities. But perhaps no phenotype has been subject to more continuous and intensive genetic scrutiny than hybrid male sterility. Here we review the history, progress, and current state of our understanding of hybrid male sterility among the D. simulans clade species. Our aim is to integrate the available information from experimental and population genetics analyses bearing on the causes and consequences of hybrid male sterility. We highlight numerous conclusions that have emerged as well as issues that remain unresolved. We focus on the special role of sex chromosomes, the fine-scale genetic architecture of hybrid male sterility, and the history of gene flow between species. The biggest surprises to emerge from this work are that (i) genetic conflicts may be an important general force in the evolution of hybrid incompatibility, (ii) hybrid male sterility is polygenic with contributions of complex epistasis, and (iii) speciation, even among these geographically allopatric taxa, has involved the interplay of gene flow, negative selection, and positive selection. These three conclusions are marked departures from the classical views of speciation that emerged from the modern evolutionary synthesis.

Supervised machine learning reveals introgressed loci in the genomes of Drosophila simulans and D. sechellia

Hybridization and gene flow between species appears to be common. Even though it is clear that hybridization is widespread across all surveyed taxonomic groups, the magnitude and consequences of introgression are still largely unknown. Thus it is crucial to develop the statistical machinery required to uncover which genomic regions have recently acquired haplotypes via introgression from a sister population. We developed a novel machine learning framework, called FILET (Finding Introgressed Loci via Extra-Trees) capable of revealing genomic introgression with far greater power than competing methods. FILET works by combining information from a number of population genetic summary statistics, including several new statistics that we introduce, that capture patterns of variation across two populations. We show that FILET is able to identify loci that have experienced gene flow between related species with high accuracy, and in most situations can correctly infer which population was the donor and which was the recipient. Here we describe a data set of outbred diploid Drosophila sechellia genomes, and combine them with data from D. simulans to examine recent introgression between these species using FILET. Although we find that these populations may have split more recently than previously appreciated, FILET confirms that there has indeed been appreciable recent introgression (some of which might have been adaptive) between these species, and reveals that this gene flow is primarily in the direction of D. simulans to D. sechellia.

Understanding the extent to which species or diverged populations hybridize in nature is crucially important if we are to understand the speciation process. Accordingly numerous research groups have developed methodology for finding the genetic evidence of such introgression. In this report we develop a supervised machine learning approach for uncovering loci which have introgressed across species boundaries. We show that our method, FILET, has greater accuracy and power than competing methods in discovering introgression, and in addition can detect the directionality associated with the gene flow between species. Using whole genome sequences from Drosophila simulans and Drosophila sechellia we show that FILET discovers quite extensive introgression between these species that has occurred mostly from D. simulans to D. sechellia. Our work highlights the complex process of speciation even within a well-studied system and points to the growing importance of supervised machine learning in population genetics.

Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence

Speciation results from the progressive accumulation of mutations that decrease the probability of mating between parental populations or reduce the fitness of hybrids—the so-called species barriers. The speciation genomic literature, however, is mainly a collection of case studies, each with its own approach and specificities, such that a global view of the gradual process of evolution from one to two species is currently lacking. Of primary importance is the prevalence of gene flow between diverging entities, which is central in most species concepts and has been widely discussed in recent years. Here, we explore the continuum of speciation thanks to a comparative analysis of genomic data from 61 pairs of populations/species of animals with variable levels of divergence. Gene flow between diverging gene pools is assessed under an approximate Bayesian computation (ABC) framework. We show that the intermediate "grey zone" of speciation, in which taxonomy is often controversial, spans from 0.5% to 2% of net synonymous divergence, irrespective of species life history traits or ecology. Thanks to appropriate modeling of among-locus variation in genetic drift and introgression rate, we clarify the status of the majority of ambiguous cases and uncover a number of cryptic species. Our analysis also reveals the high incidence in animals of semi-isolated species (when some but not all loci are affected by barriers to gene flow) and highlights the intrinsic difficulty, both statistical and conceptual, of delineating species in the grey zone of speciation.

Isolated populations accumulate genetic differences across their genomes as they diverge, whereas gene flow between populations counteracts divergence and tends to restore genetic homogeneity. Speciation proceeds by the accumulation at specific loci of mutations that reduce the fitness of hybrids, therefore preventing gene flow—the so-called species barriers. Importantly, species barriers are expected to act locally within the genome, leading to the prediction of a mosaic pattern of genetic differentiation between populations at intermediate levels of divergence—the genic view of speciation. At the same time, linked selection also contributes to speed up differentiation in low-recombining and gene-dense regions. We used a modelling approach that accounts for both sources of genomic heterogeneity and explored a wide continuum of genomic divergence made by 61 pairs of species/populations in animals. Our analysis provides a unifying picture of the relationship between molecular divergence and ability to exchange genes. We show that the "grey zone" of speciation—the intermediate state in which species definition is controversial—spans from 0.5% to 2% of molecular divergence, with these thresholds being independent of species life history traits and ecology. Semi-isolated species, between which alleles can be exchanged at some but not all loci, are numerous, with the earliest species barriers being detected at divergences as low as 0.075%. These results have important implications regarding taxonomy, conservation biology, and the management of biodiversity.

A Natural Population Derived from Species Hybridizationin the Drosophila ananassae Species Complexon Penang Island, Malaysia

We surveyed natural population of the Drosophila ananassae species complex on Penang Island, Malaysia. Analyses of phenotypic traits, chromosome arrangements, molecular markers, and reproductive isolation suggest the existence of two species: D. ananassae and D. cf. parapallidosa. Molecular marker analysis indicates that D. cf. parapallidosa carries chromosome Y and 4 introgressions from D. ananassae. Thus, D. cf. parapallidosa seems to be a hybrid descendant that recently originated from a natural D. parapallidosa♀× D. ananassae♂ cross. Furthermore, D. cf. parapallidosa behaves differently from authentic D. parapallidosa with respect to its reproductive isolation from D. ananassae. Premating isolation is usually seen in only the D. ananassae♀× D. parapallidosa♂ cross, but we observed it in crosses of both directions between D. ananassae and D. cf. parapallidosa. In addition, hybrid males from the D. ananassae♀× D. parapallidosa♂ cross are usually sterile, but they were fertile when D. ananassae♀ were mated with D. cf. parapallidosa ♂. We attempted an artificial reconstruction of the hybrid species to simulate the evolutionary process(es) that produced D. cf. parapallidosa. This is a rare case of natural hybrid population in Drosophila and may be a useful system for elucidating speciation with gene flow.

Fission and fusion in island taxa--serendipity, or something to be expected?

A well-used metaphor for oceanic islands is that they act as 'natural laboratories' for the study of evolution. But how can islands or archipelagos be considered analogues of laboratories for understanding the evolutionary process itself? It is not necessarily the case that just because two or more related species occur on an island or archipelago, somehow, this can help us understand more about their evolutionary history. But in some cases, it can. In this issue of Molecular Ecology, Garrick et al. () use population-level sampling within closely related taxa of Galapagos giant tortoises to reveal a complex demographic history of the species Chelonoidis becki - a species endemic to Isabela Island, and geographically restricted to Wolf Volcano. Using microsatellite genotyping and mitochondrial DNA sequencing, they provide a strong case for C. becki being derived from C. darwini from the neighbouring island of Santiago. But the interest here is that colonization did not happen only once. Garrick et al. () reveal C. becki to be the product of a double colonization event, and their data reveal these two founding lineages to be now fusing back into one. Their results are compelling and add to a limited literature describing the evolutionary consequences of double colonization events. Here, we look at the broader implications of the findings of Garrick et al. () and suggest genomic admixture among multiple founding populations may be a characteristic feature within insular taxa.