Widespread introgression across a phylogeny of 155 Drosophila genomes

Current Biology, Journal Year: 2021, Volume and Issue: 32(1), P. 111 - 123.e5

Published: Nov. 16, 2021

Language: Английский

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Highly contiguous assemblies of 101 drosophilid genomes

eLife, Journal Year: 2021, Volume and Issue: 10

Published: July 19, 2021

Over 100 years of studies in Drosophila melanogaster and related species the genus have facilitated key discoveries genetics, genomics, evolution. While high-quality genome assemblies exist for several this group, they only encompass a small fraction genus. Recent advances long-read sequencing allow tens or even hundreds to be efficiently generated. Here, we utilize Oxford Nanopore build an open community resource 101 lines 93 drosophilid encompassing 14 groups 35 sub-groups. The genomes are highly contiguous complete, with average contig N50 10.5 Mb greater than 97% BUSCO completeness 97/101 assemblies. We show that Nanopore-based accurate coding regions, particularly respect insertions deletions. These assemblies, along detailed laboratory protocol assembly pipelines, released as public will serve starting point addressing broad questions ecology, evolution at scale species.

Language: Английский

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Highly Contiguous Genome Assemblies of 15 Drosophila Species Generated Using Nanopore Sequencing

G3 Genes Genomes Genetics, Journal Year: 2018, Volume and Issue: 8(10), P. 3131 - 3141

Published: Oct. 1, 2018

Abstract The Drosophila genus is a unique group containing wide range of species that occupy diverse ecosystems. In addition to the most widely studied species, melanogaster, many other members in this also possess well-developed set genetic tools. Indeed, high-quality genomes exist for several within genus, facilitating studies function and evolution cis-regulatory regions proteins by allowing comparisons across at least 50 million years evolution. Yet, available still fail capture much substantial diversity genus. We have therefore tested protocols rapidly inexpensively sequence assemble genome from any using single-molecule sequencing technology Oxford Nanopore. Here, we use present highly contiguous assemblies 15 species: 10 12 originally sequenced (ananassae, erecta, mojavensis, persimilis, pseudoobscura, sechellia, simulans, virilis, willistoni, yakuba), four additional had previously reported (biarmipes, bipectinata, eugracilis, mauritiana), one novel assembly (triauraria). Genomes were generated an average 29x depth-of-coverage data after resulted contig N50 4.4 Mb. Subsequent alignment contigs published reference demonstrates our could be used close over 60% gaps currently genomes. Importantly, materials reagents cost each was approximately $1,000 (USD). This study power cost-effectiveness long-read provides framework affordable

Language: Английский

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Large-scale characterization of sex pheromone communication systems in Drosophila

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: July 6, 2021

Abstract Insects use sex pheromones as a reproductive isolating mechanism to attract conspecifics and repel heterospecifics. Despite the profound knowledge of pheromones, little is known about coevolutionary mechanisms constraints on their production detection. Using whole-genome sequences infer kinship among 99 drosophilids, we investigate how phylogenetic chemical traits have interacted at wide evolutionary timescale. Through series syntheses electrophysiological recordings, identify 52 sex-specific compounds, many which are detected via olfaction. Behavioral analyses reveal that 43 male-specific compounds transferred female during copulation mediate receptivity and/or male courtship inhibition. Measurement signals demonstrates cognate olfactory channels evolve rapidly independently over time guarantee efficient intra- inter-specific communication systems. Our results show sexual isolation barriers between species can be reinforced by species-specific signals.

Language: Английский

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Sky islands of the Cameroon Volcanic Line support the westernmost clade of five new Typoderus weevils (Coleoptera: Curculionidae: Molytinae)

Arthropod Systematics & Phylogeny, Journal Year: 2021, Volume and Issue: 79, P. 57 - 74

Published: April 20, 2021

Abstract The weevil genus Typoderus is for the first time reported west of Congo basin. Analysis 2,136 aligned positions from one mitochondrial and two nuclear fragments revealed a moderately supported clade five new Cameroonian species: T. amphion sp. nov. (Mt. Oku), canthus nov . clytius Cameroon), iphitus Kupe) telamon Kupe). Molecular clock analysis 20 DNA barcode using fixed substitution rate estimated divergences within this to be during Middle Late Miocene (10.5–5.4 million years ago, MYA), which pre-dates onset Pliocene-Pleistocene global climatic fluctuations corresponding cycles African forest size fluctuation. Such relatively old dates are unexpected might reflect four unavoidable shortcomings temporal analysis: 1. undersampled ingroup, 2. scarcity comparative data other animal clades Cameroon Volcanic Line, 3. oversimplification fixed-rate molecular approach single maternally-inherited protein-coding marker 4. possible overestimation comparatively ages when largely saturated sequences. Two obscure species Republic hypothesized belong : distinctus (Hoffmann, 1968) comb. (from Anchonidium subgenus Neoanchonidium) baloghi Subanchonidium). Three genus-group names newly synonymized under Entypoderus Voss, 1965 syn. (the only non-nominative ), Neoanchonidium Hoffmann, 1968 (subgenus ) Subanchonidium ). Habitus images supplementary information all sequenced specimens available online at dx.doi.org/10.5883/DS-VGDS005 dx.doi.org/10.5883/DS-VGDS006.

Language: Английский

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DrosoPhyla: Resources for Drosophilid Phylogeny and Systematics

Genome Biology and Evolution, Journal Year: 2021, Volume and Issue: 13(8)

Published: Aug. 1, 2021

Abstract The vinegar fly Drosophila melanogaster is a pivotal model for invertebrate development, genetics, physiology, neuroscience, and disease. whole family Drosophilidae, which contains over 4,400 species, offers plethora of cases comparative evolutionary studies. Despite long history phylogenetic inference, many relationships remain unresolved among the genera, subgenera, species groups in Drosophilidae. To clarify these relationships, we first developed set new genomic markers assembled multilocus data 17 genes from 704 We then inferred tree with highly supported this family. Additionally, were able to determine position some previously unplaced species. These results establish framework investigating evolution traits fruit flies, as well valuable resources systematics.

Language: Английский

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A comprehensive phylogeny and revised taxonomy illuminate the origin and diversification of the global radiation of Papilio (Lepidoptera: Papilionidae)

Molecular Phylogenetics and Evolution, Journal Year: 2023, Volume and Issue: 183, P. 107758 - 107758

Published: March 11, 2023

Language: Английский

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Single-fly genome assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life

PLoS Biology, Journal Year: 2024, Volume and Issue: 22(7), P. e3002697 - e3002697

Published: July 18, 2024

Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. We previously developed cost-effective hybrid Oxford Nanopore (ONT) long-read Illumina short-read approach used it to assemble 101 drosophilid genomes from laboratory cultures, greatly increasing number assemblies this taxonomic group. The next challenge address culture bias taxon sampling by that cannot easily be reared lab. Here, we build upon our previous methods perform amplification-free ONT single wild flies obtained either directly field or ethanol-preserved specimens museum collections, improving representation lesser studied taxa whole-genome data. Using Novaseq X Plus P2 sequencers with R10.4.1 chemistry, set new benchmark inexpensive at US $150 per while assembling as little 35 ng genomic DNA fly. present 183 179 resource systematics, phylogenetics, comparative genomics. Of these genomes, 62 are pooled lab strains 121 adult flies. Despite sample limitations working small insects, most single-fly diploid comparable contiguity (>1 Mb contig N50), completeness (>98% complete dipteran BUSCOs), accuracy (>QV40 genome-wide R10.4.1) inbred lines. well-resolved multi-locus phylogeny 360 4 outgroup encompassing publicly available (as August 2023) Finally, Progressive Cactus whole-genome, reference-free alignment built subset 298 suitably high-quality genomes. alignment, along updated protocols computational pipelines, released an open tool studying evolution scale entire insect family.

Language: Английский

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Evolution of Reproductive Behavior

Genetics, Journal Year: 2020, Volume and Issue: 214(1), P. 49 - 73

Published: Jan. 1, 2020

Abstract Behaviors associated with reproduction are major contributors to the evolutionary success of organisms and subject many forces, including natural sexual selection, conflict. Successful involves a range behaviors, from finding an appropriate mate, courting, copulation, successful production (in oviparous animals) deposition eggs following mating. As consequence, behaviors genes often under strong selection evolve rapidly. Courtship rituals in flies follow multimodal pattern, mediated through visual, chemical, tactile, auditory signals. Premating allow males females assess species identity, reproductive state, condition their partners. Conflicts between “interests” individual males, and/or strategies females, drive evolution behaviors. For example, seminal proteins transmitted by show evidence rapid evolution, positive selection. Postmating oviposition sites, highly variable Drosophila span spectrum generalists obligate specialists. Chemical recognition features prominently adaptation host plants for feeding oviposition. Selection acting on variation pre-, peri-, postmating can lead isolation incipient speciation. Response at genetic level include expansion gene families, such as those detecting pheromonal cues mating, or changes expression leading visual wing spots that assessed during Here, we consider behavior two distinct, yet complementary, scales. Some studies take microevolutionary approach, identifying networks involved reproduction, then dissecting genetics underlying complex D. melanogaster. Other macroevolutionary comparing across genus how these might correlate environmental cues. A full synthesis this field will require unification levels.

Language: Английский

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The Drosophila‐parasitizing wasp Leptopilina heterotoma: A comprehensive model system in ecology and evolution

Ecology and Evolution, Journal Year: 2023, Volume and Issue: 13(1)

Published: Jan. 1, 2023

Abstract The parasitoid Leptopilina heterotoma has been used as a model system for more than 70 years, contributing greatly to diverse research areas in ecology and evolution. Here, we synthesized the large body of work on L. with aim identify new avenues that could be interest also researchers studying other parasitoids insects. We start our review description typical characteristics, well higher taxonomic groups which this species belongs. then continue discussing host suitability immunity, foraging behaviors, fat accumulation life histories. subsequently shift focus towards parasitoid‐parasitoid interactions, including coexistence within larger guild Drosophila parasitoids, chemical communication, mating population structuring. conclude by highlighting assets system, its intermediate history syndromes, ease observing collecting natural hosts wasps, recent genomic advances.

Language: Английский

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