Biology subjects

D'Agostino, E. R. R.

Publications and source records attributed to D'Agostino, E. R. R..

4 recordsLinked to original sources

bioRxiv2021

15 years of introgression studies: quantifying gene flow across Eukaryotes

With the rise of affordable next generation sequencing technology, introgression -- or the exchange of genetic materials between taxa -- is widely perceived to be a ubiquitous phenomenon in nature. Although this claim is supported by several keystone studies, no thorough assessment on the frequency of introgression in nature has been performed to date. In this manuscript, we aim to address this knowledge gap by providing a meta-analysis of the most comprehensive survey of introgression studies in Eukaryotes to date (724 papers with claims of introgression). We first examined the evidence given to support introgression, and if/how the lines of evidence have changed across time. We then collated a single statistic, Pattersons D, that quantifies the strength of introgression across 123 studies to further assess how taxonomic group, divergence time, and aspects of life history influence introgression. We find three main results. Studies on introgression are much more frequent in plants and mammals than any other taxonomic group. The study of introgression has shifted from a largely qualitative assessment of whether introgression happens, to a focus on when and how much introgression has occurred across taxa. The most often used introgression statistic, Pattersons D, shows several intriguing patterns suggesting introgression reports may be biased by both differences in reporting criteria and sequencing technology, but may also differ across taxonomic systems and throughout the process of speciation. Together, these results suggest the need for a unified approach to quantifying introgression in natural communities, and highlight important areas of future research that can be better assessed once this unified approach is met.

evolutionary biology↗

bioRxiv2020

Widespread introgression across a phylogeny of 155 Drosophila genomes

Genome-scale sequence data have invigorated the study of hybridization and introgression, particularly in animals. However, outside of a few notable cases, we lack systematic tests for introgression at a larger phylogenetic scale across entire clades. Here we leverage 155 genome assemblies, from 149 species, to generate a fossil-calibrated phylogeny and conduct multilocus tests for introgression across nine monophyletic radiations within the genus Drosophila. Using complementary phylogenomic approaches, we identify widespread introgression across the evolutionary history of Drosophila. Mapping gene-tree discordance onto the phylogeny revealed that both ancient and recent introgression has occurred across most of the nine clades that we examined. Our results provide the first evidence of introgression occurring across the evolutionary history of Drosophila and highlight the need to continue to study the evolutionary consequences of hybridization and introgression in this genus and across the Tree of Life.

evolutionary biology↗

bioRxiv2020

Highly contiguous assemblies of 101 drosophilid genomes

Over 100 years of studies in Drosophila melanogaster and related species in the genus Drosophila have facilitated key discoveries in genetics, genomics, and evolution. While high-quality genome assemblies exist for several species in this group, they only encompass a small fraction of the genus. Recent advances in long read sequencing allow high quality genome assemblies for tens or even hundreds of species to be generated. Here, we utilize Oxford Nanopore sequencing to build an open community resource of high-quality assemblies for 101 lines of 95 drosophilid species encompassing 14 species groups and 35 sub-groups with an average contig N50 of 10.5 Mb and greater than 97% BUSCO completeness in 97/101 assemblies. These assemblies, along with detailed wet lab protocol and assembly pipelines, are released as a public resource and will serve as a starting point for addressing broad questions of genetics, ecology, and evolution within this key group.

evolutionary biology↗

bioRxiv2020

P-elements strengthen reproductive isolation within the Drosophila simulans species complex

Determining mechanisms that underlie reproductive isolation is key to understanding how species boundaries are maintained in nature. Transposable elements (TEs) are ubiquitous across eukaryotic genomes. However, the role of TEs in modulating the strength of reproductive isolation between species is poorly understood. Several species of Drosophila have been found to harbor P-elements (PEs), yet only D. simulans is known to be polymorphic for their presence in wild populations. PEs can cause reproductive isolation between PE-containing (P) and PE-lacking (M) lineages of the same species. However, it is unclear whether they also contribute to the magnitude of reproductive isolation between species. Here, we use the simulans species complex to assess whether differences in PE status between D. simulans and its sister species, which do not harbor PEs, contribute to multiple barriers to gene flow between species. We show that crosses involving a P D. simulans father and an M mother from a sister species exhibit lower F1 female fecundity than crosses involving an M D. simulans father and an M sister-species mother. Our results suggest that the presence of PEs in a species can strengthen isolation from its sister species, providing evidence that transposable elements can play a role in reproductive isolation and facilitate the process of speciation. IMPACT SUMMARYTransposable elements (TEs) are repetitive genetic units found across the tree of life. They play a fundamental role on the evolution of each species genome. TEs have been implicated in diversification, extinction, and the origin of novelty. However, their potential role in contributing to the maintenance of species boundaries remains largely understudied. Using whole genome sequences, we compared the relative content of TEs across the three species of the Drosophila simulans complex. We find that the presence of one TE, P-element, in D. simulans, and its absence in the sister taxa, differentiates the three species. P-elements (PEs) cause a suite of fitness defects in Drosophila pure-species individuals if their father has PEs but their mother does not, a phenomenon known as hybrid dysgenesis (HD). We thus studied the possibility that PEs enhance isolation between recently-diverged species. In particular, we studied whether the progeny from interspecific crosses were more prone to suffer from HD than pure species. We found that the presence of paternal PEs reduces hybrid female fecundity, mirroring observations of HD described within species. The effect of PEs is stronger in the interspecific hybrids than in pure species. Our results suggest that PEs can strengthen reproductive isolation in well-formed sister species that still hybridize in nature and pose the question of whether other TEs are involved in the formation of species or in their persistence over time.

evolutionary biology↗