High-Quality Genome Assemblies Reveal Evolutionary Dynamics of Repetitive DNA and Structural Rearrangements in the Drosophila virilis Subgroup

Genome Biology and Evolution, Journal Year: 2023, Volume and Issue: 16(1)

Published: Dec. 30, 2023

High-quality genome assemblies across a range of nontraditional model organisms can accelerate the discovery novel aspects evolution. The Drosophila virilis group has several attributes that distinguish it from more highly studied species in genus, such as an unusual abundance repetitive elements and extensive karyotype evolution, addition to being attractive for speciation genetics. Here, we used long-read sequencing assemble five genomes three characterized sequence structural divergence DNA We find our contiguous allow characterization chromosomal arrangements with ease facilitate analysis inversion breakpoints. also leverage small panel resequenced strains explore genomic pattern polymorphism this show known demographic histories largely predicts extent genome-wide segregating polymorphism. further neo-X chromosome americana displays X-like levels nucleotide diversity. found were responsible much composition among species. Helitron-derived tandem repeats tripled on Y D. compared novamexicana, accounting most difference repeat content between these sister Repeats characteristics both transposable satellite DNAs expanded by 3-fold, mostly euchromatin, novamexicana virilis. Our results represent major advance understanding biology emerging clade.

Language: Английский

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Temperature affects conspecific and heterospecific mating rates inDrosophila

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 28, 2024

ABSTRACT Behavioral mating choices and success are important factors in the development of reproductive isolation during speciation. Environmental conditions, especially temperature, can affect these key traits. conditions vary across, frequently delimit species’ geographic ranges. Pairing suboptimal with relative rarity conspecifics at range margins may set stage for hybridization. Despite importance behaviors as a barrier, general understanding interaction between behavioral environment is lacking, part because systematic studies rare. With this report, we begin to bridge that gap by providing evidence temperature has significant - but not consistent influence on success, thus Drosophila . We studied propensity four different temperatures among 14 species non-choice conspecific trials heterospecific two triads known regularly hybridize wild. show frequency varies significantly across 10°C (from 18ºC 28ºC), both 1:1 high-density en-masse trials, effect highly species-specific. also consistently low moderate some crosses. As decreases outside optimal thermal range, while matings remain constant, proportion relatively high. This result indicates modulate impose barriers rate More broadly, our results demonstrate truly understand how choice occur nature, they need be an environmental context.

Language: Английский

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High quality genome assemblies reveal evolutionary dynamics of repetitive DNA and structural rearrangements in theDrosophila virilissub-group

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Aug. 14, 2023

ABSTRACT High-quality genome assemblies across a range of non-traditional model organisms can accelerate the discovery novel aspects evolution. The Drosophila virilis group has several attributes that distinguish it from more highly studied species in genus, such as an unusual abundance repetitive elements and extensive karyotype evolution, addition to being attractive for speciation genetics. Here we used long-read sequencing assemble five genomes three characterized sequence structural divergence DNA We find our contiguous allow characterization chromosomal arrangements with ease facilitate analysis inversion breakpoints. also leverage small panel resequenced strains explore genomic pattern polymorphism this show known demographic histories largely predicts extent genome-wide segregating polymorphism. further neo-X chromosome D. americana displays X-like levels nucleotide diversity. found were responsible much composition among species. Helitron-derived tandem repeats tripled on Y compared novamexicana , accounting most difference repeat content between these sister Repeats characteristics both transposable satellite DNAs expanded by three-fold, mostly euchromatin, . Our results represent major advance understanding biology emerging clade. Significance statement sub-group is enticing combination attributes, including abundant diverse content, rearrangements, hybridization capability. lack high-quality have prevented detailed Here, present new along analyses variants, polymorphisms, DNAs, genes repeats. expansion mobilization non-canonical accounts assembled species, especially striking takeover single type element one Overall, study positions variety future studies.

Language: Английский

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Saltational episodes of reticulate evolution in theDrosophila saltansspecies group

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Oct. 10, 2023

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

Language: Английский

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