Widespread introgression across a phylogeny of 155 Drosophila genomes

Suvorov, Anton; Kim, Bernard; Wang, Jeremy; Armstrong, Ellie E.; Peede, David; D'Agostino, Emmanuel R. R.; Price, Daniel O.; Waddell, Peter J.; Lang, Michael; Courtier‐Orgogozo, Virginie; David, Jean R.; Petrov, Dmitri A.; Matute, Daniel R.; Schrider, Daniel R.; Comeault, Aaron A.

doi:10.1016/j.cub.2021.10.052

Cited by 179 publications

(238 citation statements)

References 141 publications

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“…The rate variation model allowed some sites to be evolutionarily invariable [(+I), 19.28% sites]. The structure of the resulting phylogenetic tree is generally consistent with the species tree obtained for 155 genomes of Drosophila species ( Suvorov et al, 2021 ) excluding D. willistoni , for which the position on the species tree is indicated by a dashed line. The callouts specify the transposable element and insertion events on the branches of the evolutionary tree.…”

Section: Resultssupporting

confidence: 62%

Episodes of Rapid Recovery of the Functional Activity of the ras85D Gene in the Evolutionary History of Phylogenetically Distant Drosophila Species

et al. 2022

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As assemblies of genomes of new species with varying degrees of relationship appear, it becomes obvious that structural rearrangements of the genome, such as inversions, translocations, and transposon movements, are an essential and often the main source of evolutionary variation. In this regard, the following questions arise. How conserved are the regulatory regions of genes? Do they have a common evolutionary origin? And how and at what rate is the functional activity of genes restored during structural changes in the promoter region? In this article, we analyze the evolutionary history of the formation of the regulatory region of the ras85D gene in different lineages of the genus Drosophila, as well as the participation of mobile elements in structural rearrangements and in the replacement of specific areas of the promoter region with those of independent evolutionary origin. In the process, we substantiate hypotheses about the selection of promoter elements from a number of frequently repeated motifs with different degrees of degeneracy in the ancestral sequence, as well as about the restoration of the minimum required set of regulatory sequences using a conversion mechanism or similar.

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Section: Resultssupporting

confidence: 62%

Episodes of Rapid Recovery of the Functional Activity of the ras85D Gene in the Evolutionary History of Phylogenetically Distant Drosophila Species

et al. 2022

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“…1). The Lordiphosa genus is the sister lineage to the New-World Sophophora (Gao et al, 2011; Kim et al, 2021; Suvorov et al, 2022). Within Lordiphosa , sex combs are found in all described members of the miki species group and all members of the denticeps species group except L. medogensis Katoh and Gao, 2018 (Fartyal et al, 2017; Gao et al, 2011; Katoh et al, 2018) (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…For the estimated ASTRAL tree we calculated the support of each node using local posterior probabilities (LPP) (Sayyari and Mirarab, 2016). We implemented the Bayesian algorithm of MCMCTree v4.9h (Yang, 2007) with approximate likelihood computation to estimate divergence times using five fossils for age prior construction, analogous to the calibration scheme A described in (Suvorov et al, 2021). First, we divided our 250 loci into five equal datasets and generated five supermatrices consisting of 50 MSAs each.…”

Section: Phylogenetic Tree Reconstructionmentioning

confidence: 99%

Secondary reversion to sexual monomorphism associated with tissue-specific loss of doublesex expression

Gao

Barmina

Thompson

et al. 2022

Preprint

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Animal evolution is characterized by frequent turnover of sexually dimorphic traits – new sex- specific characters are gained, and some ancestral sex-specific characters are lost, in many lineages. In insects, sexual differentiation is predominantly cell-autonomous and depends on the expression of the doublesex (dsx) transcription factor. In most cases, cells that transcribe dsx have the potential to undergo sex-specific differentiation, while those that lack dsx expression do not. Consistent with this mode of development, comparative research has shown that the origin of new sex-specific traits can be associated with the origin of new spatial domains of dsx expression. In this report, we examine the opposite situation – a secondary loss of the sex comb, a male-specific grasping structure that develops on the front legs of some drosophilid species. We show that, while the origin of the sex comb is linked to an evolutionary gain of dsx expression in the leg, sex comb loss in a newly identified species of Lordiphosa (Drosophilidae) is associated with a secondary loss of dsx expression. We discuss how the developmental control of sexual dimorphism affects the mechanisms by which sex-specific traits can evolve.

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“…In the second approach, we followed the procedure outlined in Suvorov et al (2021) to generate a node age-calibrated phylogeny using MCMCTREE software, which is part of the PAML package ver. 4.9 package (Yang 1997(Yang , 2007.…”

Section: Divergence Timesmentioning

confidence: 99%

Phylogenomics provides insights into the evolution of cactophily and host plant shifts inDrosophila

Moreyra

Almeida

Allan

et al. 2022

Preprint

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Cactophilic species of the Drosophila buzzatii cluster (repleta group) comprise an excellent model group to investigate genomic changes underlying adaptation to extreme climate conditions and host plants. In particular, these species offer a subject to study the transition from chemically simpler breeding sites (like prickly pears of the genus Opuntia) to chemically more complex hosts (columnar cacti). Here, we report four highly contiguous genome assemblies of three species of the buzzatii cluster. Based on this genomic data and inferred phylogenetic relationships, we identified candidate taxonomically restricted genes (TRGs) likely involved in the evolution of cactophily and cactus host specialization in internal branches of the subgenus Drosophila. Functional enrichment analyses of TRGs within the buzzatii cluster identified genes involved in detoxification, water preservation, immune system response, anatomical structure development, and morphogenesis. In contrast, processes that regulate responses to stress, as well as the metabolism of nitrogen compounds, transport, and secretion were found in the set of species that are columnar cacti dwellers. These findings are in line with the hypothesis that those genomic innovations brought about instrumental mechanisms underlying adaptation in a group of species that speciated in the arid regions of South America.

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Widespread introgression across a phylogeny of 155 Drosophila genomes

Cited by 179 publications

References 141 publications

Episodes of Rapid Recovery of the Functional Activity of the ras85D Gene in the Evolutionary History of Phylogenetically Distant Drosophila Species

Episodes of Rapid Recovery of the Functional Activity of the ras85D Gene in the Evolutionary History of Phylogenetically Distant Drosophila Species

Secondary reversion to sexual monomorphism associated with tissue-specific loss of doublesex expression

Phylogenomics provides insights into the evolution of cactophily and host plant shifts inDrosophila

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