Saltational episodes of reticulate evolution in theDrosophila saltansspecies group DOI Creative Commons
Carolina Prediger, Erina A. Ferreira, Samara Videira Zorzato

et al.

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

Temperature affects conspecific and heterospecific mating rates in Drosophila DOI
Jonathan A. Rader, Daniel R. Matute

Animal Behaviour, Journal Year: 2025, Volume and Issue: unknown, P. 123168 - 123168

Published: April 1, 2025

Language: Английский

Citations

0
Recurrent duplication and diversification of a vital DNA repair gene family across Drosophila DOI Creative Commons
Cara L. Brand,

G. Oliver,

Isabella Z. Farkas

et al.

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(6)

Published: June 1, 2024

Abstract Maintaining genome integrity is vital for organismal survival and reproduction. Essential, broadly conserved DNA repair pathways actively preserve integrity. However, many proteins evolve adaptively. Ecological forces like UV exposure are classically cited drivers of evolution. Intrinsic repetitive DNA, which also imperil integrity, have received less attention. We recently reported that a Drosophila melanogaster-specific satellite array triggered species-specific, adaptive evolution protein called Spartan/MH. The Spartan family proteases cleave hazardous, covalent crosslinks form between (“DNA–protein crosslink repair”). Appreciating satellites both ubiquitous universally fast-evolving, we hypothesized turnover spurs DNA–protein beyond single gene the D. melanogaster lineage. This hypothesis predicts pervasive diversification across species. To study evolutionary history family, conducted population genetic, molecular evolution, phylogenomic, tissue-specific expression analyses. uncovered widespread signals positive selection multiple genes timescales. detected recurrent duplication, divergence, loss. Finally, found ovary-enriched parent consistently birthed functionally diverged, testis-enriched daughter genes. account diversification, introduce novel mechanistic model antagonistic coevolution links regulation protease activity. framework promises to accelerate our understanding how repeats drive innovation

Language: Английский

Citations

3
Chromosomal Inversions and the Demography of Speciation in Drosophila montana and Drosophila flavomontana DOI Creative Commons
Noora Poikela, Dominik R. Laetsch, Ville Hoikkala

et al.

Genome Biology and Evolution, Journal Year: 2024, Volume and Issue: 16(3)

Published: March 1, 2024

Abstract Chromosomal inversions may play a central role in speciation given their ability to locally reduce recombination and therefore genetic exchange between diverging populations. We analyzed long- short-read whole-genome data from sympatric allopatric populations of 2 Drosophila virilis group species, montana flavomontana, understand if have contributed divergence. identified 3 large alternatively fixed on the X chromosome one each autosomes 4 5. A comparison demographic models estimated for inverted noninverted (colinear) chromosomal regions suggests that these arose before time species split. detected low rate interspecific gene flow (introgression) D. which was further reduced inside lower than Together, results suggest were already present common ancestral population sister taxa within both after onset Such ancestrally polymorphic foster by allowing accumulation divergence loci involved adaptation reproductive isolation early process, while at colinear continues until evolving barriers complete speciation. The overlapping are particularly good candidates driving process since they harbor strong incompatibilities recent study experimental introgression.

Language: Английский

Citations

3
Characterization of clock‐related proteins and neuropeptides in Drosophila littoralis and their putative role in diapause DOI Creative Commons
Giulia Manoli, Meet Zandawala, Taishi Yoshii

et al.

The Journal of Comparative Neurology, Journal Year: 2023, Volume and Issue: 531(15), P. 1525 - 1549

Published: July 26, 2023

Insects from high latitudes spend the winter in a state of overwintering diapause, which is characterized by arrested reproduction, reduced food intake and metabolism, increased life span. The main trigger to enter diapause decreasing day length summer-autumn. It thus assumed that circadian clock acts as an internal sensor for measuring photoperiod orchestrates appropriate seasonal changes physiology metabolism through various neurohormones. However, little known about neuronal organization network neurosecretory system controls high-latitude insects. We addressed this here mapping expression proteins neuropeptides/neurohormones fly Drosophila littoralis. found principal both systems similar melanogaster, but with some striking differences neuropeptide levels patterns. small ventrolateral neurons express pigment-dispersing factor (PDF) short F (sNPF) are most important robust rhythmicity D. melanogaster virtually lack PDF sNPF In contrast, dorsolateral ion transport peptide additionally allatostatin-C appear suited transfer day-length information lateral cells littoralis contain more neuropeptides than melanogaster. Among them, coexpress corazonin, PDF, diuretic hormone 44 control diapause. Our work sets stage investigate roles these diverse regulating insect

Language: Английский

Citations

6
Chromosomal inversions and their impact on insect evolution DOI

Igor V. Sharakhov,

Maria V. Sharakhova

Current Opinion in Insect Science, Journal Year: 2024, Volume and Issue: 66, P. 101280 - 101280

Published: Oct. 5, 2024

Language: Английский

Citations

1
Evolutionary Quantitative Proteomics of Reproductive Protein Divergence in Drosophila DOI Creative Commons
Martin D. Garlovsky, Yasir H. Ahmed-Braimah

Molecular & Cellular Proteomics, Journal Year: 2023, Volume and Issue: 22(8), P. 100610 - 100610

Published: June 29, 2023

Reproductive traits often evolve rapidly between species. Understanding the causes and consequences of this rapid divergence requires characterization female male reproductive proteins their effect on fertilization success. Species in Drosophila virilis clade exhibit rampant interspecific incompatibilities, making them ideal for studies diversification role speciation. Importantly, intraejaculate protein abundance allocation is poorly understood. Here, we identify quantify transferred ejaculate proteome using multiplexed isobaric labeling lower tract before immediately after mating three species group. We identified over 200 putative proteins, many which show differential species, suggesting that males transfer a species-specific seminal fluid during copulation. also 2000 contain female-specific serine-type endopeptidases showed elevated rates molecular evolution, similar to some proteins. Our findings suggest can manifest terms patterns.

Language: Английский

Citations

2
Transposable elements in a cold-tolerant fly species,Drosophila montana: a link to adaptation to the harsh cold environments DOI Creative Commons
Mohadeseh Sadat Tahami, Carlos Vargas-Chávez, Noora Poikela

et al.

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

Published: April 22, 2024

Abstract Background Substantial discoveries during the past century have revealed that transposable elements (TEs) can play a crucial role in genome evolution by affecting gene expression and inducing genetic rearrangements, among other molecular structural effects. Yet, our knowledge on of TEs adaptation to extreme climates is still at its infancy. The availability long-read sequencing has opened up possibility identify study potential functional effects with higher precision. In this work, we used Drosophila montana as model for cold-adapted organisms association between harsh climates. Results Using PacBio technique, de novo identified manually curated TE sequences five genomes from eco-geographical distinct populations. We 489 new consensus which represented 92% total D. . Overall, 11-13% occupied TEs, expected are non-randomly distributed across genome. potentially active families, most them retrotransposon class TEs. Additionally, found present analyzed were located nearby previously cold tolerant genes. Some these contain promoter transcription binding sites. Finally, detected fixed polymorphic inversion breakpoints. Conclusions Our research significant number newly , suggesting non-model species should be studied get comprehensive view repertoire beyond. Genome annotations library allowed us genes, high population frequencies, regulatory regions thus good candidates stress response. also allow first time breakpoints three inversions.

Language: Английский

Citations

0
Transposable elements in Drosophila montana from harsh cold environments DOI Creative Commons
Mohadeseh Sadat Tahami, Carlos Vargas-Chávez, Noora Poikela

et al.

Mobile DNA, Journal Year: 2024, Volume and Issue: 15(1)

Published: Oct. 1, 2024

Language: Английский

Citations

0
Landmark-based estimates of genomic disparity DOI Open Access
Ashwini V. Mohan, Anjali Goswami, Jeffrey W. Streicher

et al.

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

Published: Oct. 31, 2024

Abstract Genomic architecture has played a key role in the evolution of biodiversity. Structural comparisons genome sequences have informed study supergenes, sex chromosomes, and some earliest divergences tree life. However, multi-species whole still many computational analytical limitations. Here we present computationally non-intensive approach, based on geometric morphometrics, that generates disparity scores using conserved as landmarks. This ‘geno-metric’ method captures structural differences homologous chromosomal regions can be applied at micro- macroevolutionary scales. Using ultraconserved elements (UCEs) landmarks, provide empirical demonstrations with chromosome 5 from Drosophila virilis group 40 placental mammal genomes. These examples identify rearrangements while also confirming UCE landmark placement strong parallels morphometrics regarding size, orientation, phylogenetic signal availability. simulations, show UCE-inferred is correlated overall levels which further studied models continuous trait evolution. Landmark-based estimates are valuable addition to comparative genomic toolkit they offer an intuitive, rapid mechanism for detecting expansions, contractions, rearrangements. We highlight potential this approach translocations duplications. Significance Statement The increased throughput sequencing outpaced development tools extract information these big data, creating urgent need novel methodological perspectives genomics. describe validate morphometric landmarks effectively variation structure. principles morphological disparity, genomics greatly increased, syntenic organization chromosomes placed quantitative contexts.

Language: Английский

Citations

0
Saltational episodes of reticulate evolution in the Drosophila saltans species group DOI Creative Commons
Carolina Prediger, Erina A. Ferreira, Samara Videira Zorzato

et al.

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(12)

Published: Dec. 1, 2024

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 study. 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 based on assemblies using either conserved genes ≥50 kb-long syntenic blocks with collinearity Sophophora, consisted windows from pseudo-reference genomes aligned an ingroup outgroup species. Evidence for varied among being lowest synteny-based approach, did not exceed ∼7% most quartets. High incidences were restricted three nodes 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

Citations

0