Biology subjects

Ferreira, E. A.

Publications and source records attributed to Ferreira, E. A..

4 recordsLinked to original sources

bioRxiv2024

Divergence and parallelism in two tropical drosophilids simultaneously invading a desert environment

Invasive species have once been called a grand experiment in evolution but natural replicates of such experiments are often scarce. In particular, whether the rapid adaptation to the new environment involves genetic predisposition in the ancestral range or mainly occurs via post-introductory selection on a genetically variable propagule remains unknown. Here, we investigate the parallel adaptation of two drosophilid species of the genus Zaprionus, Z. indianus (the African fig fly) and Z. tuberculatus, to contrasting agrarian and desert environments following their introduction in Egypt during the last four decades. Field collection unraveled distinct spatial distribution of the two species. Population genomics analyses showed correlated differentiation levels at orthologous genes before and after introduction in both species. Nonetheless, phenotypic analyses revealed distinct fruit preference and desiccation resistance between both species as well as between introduced and native Z. tuberculatus populations. Hence, despite signals of genomic parallelism, ecological divergence between the two species likely facilitates their co-existence in the introduced regions. Our results provide a significant step towards understanding the mechanisms underlying the simultaneous invasive success of both species, which have also recently invaded the Americas and Europe, and of which one at least is a notorious pest.

evolutionary biology↗

bioRxiv2023

Saltational episodes of reticulate evolution in the jumping pomace fly Drosophila saltans species group

Phylogenomics reveals reticulate evolution to be widespread across taxa, but whether reticulation is due to low statistical power or it is a true evolutionary pattern remains a field of investigation. Here, we investigate the phylogeny and quantify reticulation in the Drosophila saltans species group, a Neotropical clade of the subgenus Sophophora comprising 23 species whose relationships have long been problematic. Phylogenetic analyses revealed conflicting topologies between the X chromosome, autosomes and the mitochondria. We extended the ABBA-BABA test of asymmetry in phylogenetic discordance to cases where no "true" species tree could be inferred, and applied our new test (called 2A2B) to whole genome data and to individual loci. We used four strategies, two of which consisted of windows from pseudo-reference genomes aligned to either an outgroup or ingroup species, and two based on our new assemblies using either conserved genes or [≥]50 kb-long syntenic blocks with conserved collinearity across Neotropical Sophophora. Evidence for reticulation varied among the strategies, being lowest in the synteny-based approach, where it did not exceed [~]7% of the blocks in the most conflicting species quartets. High incidences of low phylogenetic resolution (polytomy) were restricted to three nodes on the tree, that coincided with major paleogeographical events in South America. Our results identify possible technical biases in quantifying reticulate evolution and indicate that episodic rapid radiations have played a major role in the evolution of a largely understudied Neotropical clade.

evolutionary biology↗

bioRxiv2022

Genomic islands of divergence between Drosophila yakuba subspecies predominantly overlap with chromosomal inversions

During the early stages of local adaptation and speciation, genetic differences tend to accumulate at certain regions of the genome leading to the formation of genomic islands of divergence (GIDs). This pattern may be due to selection and/or difference in the rate of recombination. Here, we investigate the possible causes of GIDs in Drosophila yakuba mayottensis, and reconfirm using field collection its association with toxic noni (Morinda citrifolia) fruits on the Mayotte island. Population genomics revealed lack of genetic structure on the island and identified 20 GIDs distinguishing D. y. mayottensis from generalist mainland populations of D. y. yakuba. The GIDs were enriched with gene families involved in the metabolism of lipids, sugars, peptides and xenobiotics, suggesting a role in host shift. We assembled a new genome for D. y. mayottensis and identified five novel chromosomal inversions. Twelve GIDs ([~]72% of outlier windows) fell close to or within subspecies-specific inversions. However, three GIDs were in collinear, high recombining regions indicating strong signal of hard selective sweeps. Unlike D. y. mayottensis, D. sechellia, the only other noni-specialist, is homosequential with its generalist relatives. Thus, both selection and rearrangements shape GIDs and striking convergences can occur between species with distinct genomic architectures.

evolutionary biology↗

bioRxiv2022

Evolution of assortative mating following selective introgression of pigmentation genes between two Drosophila species

Adaptive introgression is ubiquitous in animals but experimental support for its role in driving speciation remains scarce. In the absence of conscious selection, admixed laboratory strains of Drosophila asymmetrically and progressively lose alleles from one parental species and reproductive isolation against the predominant parent ceases after 10 generations. Here, we selectively introgressed during one year light pigmentation genes of D. santomea into the genome of its dark sibling D. yakuba, and vice versa. We found that the pace of phenotypic change differed between the species and the sexes, and identified through genome sequencing common as well as distinct introgressed loci in each species. Mating assays showed that assortative mating between introgressed flies and both parental species persisted even after four years ([~] 60 generations) from the end of the selection. Those results indicate that selective introgression of as low as 0.5% of the genome can beget morphologically-distinct and reproductively-isolated strains, two prerequisites for the delimitation of new species. Our findings hence represent a significant step towards understanding the genome-wide dynamics of speciation-through-introgression.

evolutionary biology↗