Biology subjects

Matute, D. R.

Publications and source records attributed to Matute, D. R..

6 recordsLinked to original sources

bioRxiv2018

Recent invasion of P transposable element into Drosophila yakuba

Transposable elements (TEs) are self-replicating genetic units that are common across prokaryotes and eukaryotes. They have been implicated in the origin of new molecular functions and in some cases, new phenotypes. Yet, the processes that lead to their evolution and how they enter the genome of their hosts remain largely underexplored. The P-element is one of the most well-known TEs in Eukaryotes, due to its rapid expansion in Drosophila melanogaster in the 1960s and its faster invasion of D. simulans, despite its fitness consequences in both species. Here, we describe a recent invasion of P-elements into Drosophila yakuba. Overall, PEs were found in D. yakuba with no PEs detected across its sister species, D. teissieri and D. santomea. These findings are surprising due the lack of a genetic bridge between D. yakuba and other Drosophila that harbor PEs, implicating a horizontal gene transfer mechanism similar to the one that gave rise to the invasion of PEs in D. melanogaster and D. simulans. We also report that the presence of these PEs causes a mild hybrid dysgenesis phenomenon; namely they cause a reduction in female reproductive potential (lower number of ovaries and ovarioles), but only at 29{degrees}C and not at 23{degrees}C. Given the ability of PEs to cross species boundaries and the fact that both D. santomea and D. teissieri have the ability to produce fertile progeny with D. yakuba, the yakuba species complex provides an opportunity to study PE spread through vertical transmission.\n\nARTICLE SUMMARYP-elements (PEs) are transposons found in Neotropical Drosophila species. PEs have previously invaded two African Drosophila species where they rapidly increased in population frequency and fixed. We found that PEs invaded the genome of D. yakuba, an African species. In just 8 years, the frequency of the PEs increased from 0% to 18% but then decreased to 2%. This turnover shows that PE invasions can be transient. We found no evidence of full PEs in D. yakuba sister species, D. santomea and D. teissieri. PEs in this species complex can reveal the interplay between transposable elements and hybridization in nature.

evolutionary biology↗

bioRxiv2017

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.\n\nAUTHOR SUMMARYUnderstanding 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.

evolutionary biology↗

bioRxiv2017

Fine scale mapping of genomic introgressions within the Drosophila yakuba clade

The process of speciation involves populations diverging over time until they are genetically and reproductively isolated. Hybridization between nascent species was long thought to directly oppose speciation. However, the amount of interspecific genetic exchange (introgression) mediated by hybridization remains largely unknown, although recent progress in genome sequencing has made measuring introgression more tractable. A natural place to look for individuals with admixed ancestry (indicative of introgression) is in regions where species co-occur. In west Africa, D. santomea and D. yakuba hybridize on the island of Sao Tome, while D. yakuba and D. teissieri hybridize on the nearby island of Bioko. In this report, we quantify the genomic extent of introgression between the three species of the Drosophila yakuba clade (D. yakuba, D. santomea), D. teissieri). We sequenced the genomes of 86 individuals from all three species. We also developed and applied a new statistical framework, using a hidden Markov approach, to identify introgression. We found that introgression has occurred between both species pairs but most introgressed segments are small (on the order of a few kilobases). After ruling out the retention of ancestral polymorphism as an explanation for these similar regions, we find that the sizes of introgressed haplotypes indicate that genetic exchange is not recent (>1,000 generations ago). We additionally show that in both cases, introgression was rarer on X chromosomes than on autosomes which is consistent with sex chromosomes playing a large role in reproductive isolation. Even though the two species pairs have stable contemporary hybrid zones, providing the opportunity for ongoing gene flow, our results indicate that genetic exchange between these species is currently rare.\n\nAUTHOR SUMMARYEven though hybridization is thought to be pervasive among animal species, the frequency of introgression, the transfer of genetic material between species, remains largely unknown. In this report we quantify the magnitude and genomic distribution of introgression among three species of Drosophila that encompass the two known stable hybrid zones in this genetic model genus. We obtained whole genome sequences for individuals of the three species across their geographic range (including their hybrid zones) and developed a hidden Markov model-based method to identify patterns of genomic introgression between species. We found that nuclear introgression is rare between both species pairs, suggesting hybrids in nature rarely successfully backcross with parental species. Nevertheless, some D. santomea alleles introgressed into D. yakuba have spread from Sao Tome to other islands in the Gulf of Guinea where D. santomea is not found. Our results indicate that in spite of contemporary hybridization between species that produces fertile hybrids, the rates of gene exchange between species are low.

evolutionary biology↗

bioRxiv2017

The Rate Of Evolution Of Postmating-Prezygotic Reproductive Isolation In Drosophila

Reproductive isolation (RI) is an intrinsic aspect of species, as described in the Biological Species Concept. For that reason, the identification of the precise traits and mechanisms of RI, and the rates at which they evolve, is crucial to understanding how species originate and persist. Nonetheless, precise measurements of the magnitude of reproductive isolation are rare. Previous work has measured the rates of evolution of prezygotic and postzygotic barriers to gene flow, yet no systematic analysis has carried out the study of the rates of evolution of postmating-prezygotic (PMPZ) barriers. We systematically measured the magnitude of two barriers to gene flow that act after mating occurs but before zygotic fertilization and also measured a premating (female mating rate in nonchoice experiments) and two postzygotic barriers (hybrid inviability and hybrid sterility) for all pairwise crosses of species within the Drosophila melanogaster subgroup. Our results indicate that PMPZ isolation evolves faster than hybrid inviability but slower than premating isolation. We also describe seven new interspecific hybrids in the group. Our findings open up a large repertoire of tools that will enable researchers to manipulate hybrids and explore the genetic basis of interspecific differentiation, reproductive isolation, and speciation.

evolutionary biology↗

bioRxiv2017

A Maladaptive Combination Of Traits Contributes To The Maintenance Of A Stable Hybrid Zone Between Two Divergent Species Of Drosophila

Geographical areas where two species come into contact and hybridize serve as natural laboratories for assessing mechanisms that limit gene flow between species. The ranges of about half of all closely related Drosophila species overlap, and the genomes of several pairs reveal signatures of past introgression. However, only two contemporary hybrid zones have been characterized in the genus, and both are recently diverged sister species (D. simulans-D. sechellia, Ks = 0.05; D. yakuba-D. santomea, Ks = 0.048). Here we present evidence of a new hybrid zone, and the ecological mechanisms that maintain it, between two highly divergent Drosophila species (Ks = 0.11). On the island of Bioko in west Africa, D. teissieri occupies mostly forests, D. yakuba occupies mostly open agricultural areas, and recently, we discovered that hybrids between these species occur near the interface of these habitats. Genome sequencing revealed that all field-sampled hybrids are F1 progeny of D. yakuba females and D. teissieri males. We found no evidence for either advanced-generation hybrids or F1 hybrids produced by D. teissieri females and D.yakuba males. The lack of advanced-generation hybrids on Bioko is consistent with mark-recapture and laboratory experiments that we conducted, which indicate hybrids have a maladaptive combination of traits. Like D. yakuba, hybrids behaviorally prefer open habitat that is relatively warm and dry, but like D. teissieri, hybrids have low desiccation tolerance, which we predict leaves them physiologically ill-equipped to cope with their preferred habitat. These observations are consistent with recent findings of limited introgression in the D. yakuba clade and identify an ecological mechanism for limiting gene flow between D. yakuba and D. teissieri; namely, selection against hybrids that we have documented, in combination with hybrid male sterility, contributes to the maintenance of this narrow (~30m), stable hybrid zone centered on the forest-open habitat ecotone. Our results show how a deleterious combination of parental traits can result in unfit or maladapted hybrids.

evolutionary biology↗

bioRxiv2016

Ecological speciation within the Phytophthora group

Over the past few years, symptoms akin to late blight disease have been reported on a variety of crop plants in South America. Despite the economic importance of these crops, the causal agents of the diseases belonging to the genus Phytophthora have not been completely characterized. In this study, we used an integrative approach that leveraged morphological, ecological, and genetic approaches to explore cryptic speciation within P. infestans sensu lato. We described a new Phytophthora species collected in Colombia from tree tomato (Solanum betaceum), a semi-domesticated fruit. All morphological traits and population genetic analyses, using microsatellite data and a reduced representation of single nucleotide polymorphism (SNP) data, support the description of the new species, Phytophthora betacei sp. nov. We have demonstrated that ecological differences are important in the persistence of P. infestans and P. betacei as genetically isolated units across an overlapping area in the northern Andes.

evolutionary biology↗