No abstract

Cryptic species represent a substantial fraction of the diversity of Drosophilidae, hampering studies on species ecologies and their evolution. Anthophilous species within the Drosophila lutzii group encompass some of the most widely distributed Neotropical lineages. Nevertheless, their ranges, ecologies, divergence times, and phylogenetic relationships are largely unknown. In this study, we analyzed the cryptic diversity of the lutzii species complex occurring in Southern Brazil and shed light on the ecological and evolutionary processes underlying their current patterns of coexistence. We used an integrative approach, evaluating molecular, ecological, and morphological traits under an evolutionary ecology framework. We documented the unexpected occurrence of D. alei in Southern Brazil, whose range was only known for the Andean region. Our phylogenetic analysis indicated that despite morphological similarities, D. alei is more closely related to D. denieri than to D. lutzii, and that divergence among these three species dates back to the Neogene (7.3 Mya). Niche modeling suggests that D. denieri and D. lutzii populations expanded their ranges and were established in Southern Brazil during the Quaternary (150 kya), being affected by similar paleoclimatic events. On the other hand, D. alei shows distinct abiotic requirements than D. denieri and D. lutzii, and environmental distribution models suggested a significant reduction in its suitable areas during the Quaternary, especially in Southern Brazil. This suggests that the current sympatry observed in this region likely reflects a secondary contact between the three species resulting from niche divergence processes. Altogether, these results advance the understanding of the distribution and phylogenetic relationships of Neotropical anthophilous Drosophila, revealing the interplay between ecological and historical factors in their speciation.

Understanding the mechanisms that shape the architecture, diversity and adaptations of genomes and their ecological and genetic interfaces is of utmost importance to understand biological evolution. Transposable elements (TEs) play an important role in genome evolution, due to their ability to transpose within and between genomes, providing sites of non-allelic recombination. Here we investigate patterns and processes of TE driven genome evolution associated with niche diversification. Specifically, we compared TE content, TE landscapes, and frequency of horizontal transposon transfers (HTTs) across genomes of flower-breeding Drosophila (FBD) with different levels of specialization on flowers. Further, we investigated whether niche breadth, and ecological and geographical overlaps are associated with potential for HTT rates. Landscape analysis evidenced a general phylogenetic pattern, in which species of the D. bromeliae group presented L-shaped curves, indicating recent transposition bursts, whereas D. lutzii showed a bimodal pattern. The great frequency of highly similar sequences recovered for all FBD suggests that these species probably experienced similar ecological pressures and evolutionary histories that contributed to the diversification of their mobilomes. Likewise, the richness of TEs superfamilies also appear to be associated with ecological traits. Furthermore, the two more widespread species, the specialist D. incompta and the generalist D. lutzii, presented the highest frequency of HTT events. Our analyses also revealed that HTT opportunities are positively influenced by abiotic niche overlap but are not associated with phylogenetic relationships or niche breadth. This suggests the existence of intermediate vectors promoting HTTs between species that do not necessarily present overlapping biotic niches.

Transposable elements (TEs) have the main role in shaping the evolution of genomes and host species, contributing to the creation of new genes and promoting rearrangements frequently associated with new regulatory networks. Support for these hypotheses frequently results from studies with model species, and Drosophila provides a great model organism to the study of TEs. Micropia belongs to the Ty3/Gypsy group of long terminal repeats (LTR) retroelements and comprises one of the least studied Drosophila transposable elements. In this study, we assessed the evolutionary history of Micropia within Drosophilidae, while trying to assist in the classification of this TE. At first, we performed searches of Micropia presence in the genome of natural populations from several species. Then, based on searches within online genomic databases, we retrieved Micropia-like sequences from the genomes of distinct Drosophilidae species. We expanded the knowledge of Micropia distribution within Drosophila species. The Micropia retroelements we detected consist of an array of divergent sequences, which we subdivided into 20 subfamilies. Even so, a patchy distribution of Micropia sequences within the Drosophilidae phylogeny could be identified, with incongruences between the species phylogeny and the Micropia phylogeny. Comparing the pairwise synonymous distance (dS) values between Micropia and three host nuclear sequences, we found several cases of unexpectedly high levels of similarity between Micropia sequences in divergent species. All these findings provide a hypothesis to the evolution of Micropia within Drosophilidae, which include several events of vertical and horizontal transposon transmission, associated with ancestral polymorphisms and recurrent Micropia sequences diversification.