Evolutionary dynamics of genome size and content during the adaptive radiation of Heliconiini butterflies

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Сен. 12, 2023

Heliconius butterflies, a speciose genus of Müllerian mimics, represent classic example an adaptive radiation that includes range derived dietary, life history, physiological and neural traits. However, key lineages within the genus, across broader Heliconiini tribe, lack genomic resources, limiting our understanding how neutral processes shaped genome evolution during their radiation. Here, we generate highly contiguous assemblies for nine Heliconiini, 29 additional reference-assembled genomes, improve 10 existing assemblies. Altogether, provide dataset annotated genomes total 63 species, including 58 species tribe. We use this extensive to robust dated heliconiine phylogeny, describe major patterns introgression, explore architecture, basis innovations in enigmatic group, assessment putative regulatory regions at stem. Our work illustrates increased resolution provided by such dense sampling improves power test gene-phenotype hypotheses, precisely characterize evolve.

Язык: Английский

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Opportunities and challenges in Asian bee research and conservation

Biological Conservation, Год журнала: 2023, Номер 285, С. 110173 - 110173

Опубликована: Авг. 7, 2023

The challenges of bee research in Asia are unique and severe, reflecting different cultures, landscapes, faunas. Strategies frameworks developed North America or Europe may not prove applicable. Virtually none these species have been assessed by the IUCN there is a paucity public data on even basics distribution. If we do know present, their distribution threats, cannot protect them, but our knowledge base vanishingly small compared to rest world. To better understand meet challenges, this perspective conveys ideas accumulated over hundreds years cumulative study Asian bees authors, including academic, governmental, other researchers from 13 countries beyond. We outline special circumstances current state affairs, highlight importance highly social as flagships for lesser-known solitary bees, dire need further food security, identify target areas study. Finally, framework via which will catalyze future region, especially governmental partnerships necessary effectively conserve species.

Язык: Английский

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Phylogenomic Discordance in the Eared Seals is best explained by Incomplete Lineage Sorting following Explosive Radiation in the Southern Hemisphere

Systematic Biology, Год журнала: 2020, Номер 70(4), С. 786 - 802

Опубликована: Дек. 10, 2020

Abstract The phylogeny and systematics of fur seals sea lions (Otariidae) have long been studied with diverse data types, including an increasing amount molecular data. However, only a few phylogenetic relationships reached acceptance because strong gene-tree species tree discordance. Divergence times estimates in the group also vary largely between studies. These uncertainties impeded understanding biogeographical history group, such as when how trans-equatorial dispersal subsequent speciation events occurred. Here, we used high-coverage genome-wide sequencing for 14 15 Otariidae to elucidate family its bearing on taxonomy history. Despite extreme topological discordance among gene trees, found fully supported that agrees well-accepted establishes monophyly genus Arctocephalus. Our support relatively recent trans-hemispheric at base southern clade, which rapidly diversified into six major lineages 3 2.5 Ma. Otaria diverged first, followed by Phocarctos then four within Zalophus be nonmonophyletic, California (Zalophus californianus) Steller (Eumetopias jubatus) grouping closer than Galapagos lion wollebaeki) evidence introgression two genera. Overall, high degree genealogical was best explained incomplete lineage sorting resulting from quasi-simultaneous clade introgresssion playing subordinate role explaining incongruence prior studies family. [Hybridization; ILS; phylogenomics; Pleistocene; Pliocene; monophyly.]

Язык: Английский

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Honey Bees Can Taste Amino and Fatty Acids in Pollen, but Not Sterols

Frontiers in Ecology and Evolution, Год журнала: 2021, Номер 9

Опубликована: Июнь 25, 2021

The nutritional composition of food is often complex as resources contain a plethora different chemical compounds, some them more, less meaningful to consumers. Plant pollen, major source for bees, particular importance it comprises nearly all macro- and micronutrients required by bees successful development reproduction. However, perceiving evaluating nutrients may be tedious impair quick foraging decisions. It therefore likely that nutrient perception restricted specific or groups. To better understand the role taste in pollen quality assessment we investigated Western honey bee, Apis mellifera . We tested if were able perceive concentration differences amino acids, fatty sterols, three highly important groups via antennal reception. By means proboscis extension response (PER) experiments with chemotactile stimulation, could show can distinguish between differing acid concentration, but not sterol concentration. Bees also sterols when presented alone. Our finding suggests protein lipid content prioritized over content.

Язык: Английский

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Expanding the Repertoire of the Plant-Infecting Ophioviruses through Metatranscriptomics Data

Viruses, Год журнала: 2023, Номер 15(4), С. 840 - 840

Опубликована: Март 25, 2023

Ophioviruses (genus Ophiovirus, family Aspiviridae) are plant-infecting viruses with non-enveloped, filamentous, naked nucleocapsid virions. Members of the genus Ophiovirus have a segmented single-stranded negative-sense RNA genome (ca. 11.3-12.5 kb), encompassing three or four linear segments. In total, these segments encode to seven proteins in sense and antisense orientation, both viral complementary strands. The includes species infecting monocots dicots, mostly trees, shrubs some ornamentals. From genomic perspective, as today, there complete genomes available for only species. Here, by exploring large publicly metatranscriptomics datasets, we report identification molecular characterization 33 novel genetic evolutionary cues ophioviruses. Genetic distance insights suggest that all detected could correspond members species, which expand current diversity ophioviruses ca. 4.5-fold. increase tentative host range first time mosses, liverwort ferns. addition, were linked several Asteraceae, Orchidaceae Poaceae crops/ornamental plants. Phylogenetic analyses showed clade liverworts fern ophioviruses, characterized long branches, suggesting is still plenty unsampled hidden within genus. This study represents significant expansion genomics opening door future works on peculiarity this virus

Язык: Английский

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PhyloAcc-GT: A Bayesian Method for Inferring Patterns of Substitution Rate Shifts on Targeted Lineages Accounting for Gene Tree Discordance

Molecular Biology and Evolution, Год журнала: 2023, Номер 40(9)

Опубликована: Сен. 1, 2023

An important goal of evolutionary genomics is to identify genomic regions whose substitution rates differ among lineages. For example, experiencing accelerated molecular evolution in some lineages may provide insight into links between genotype and phenotype. Several comparative methods have been developed accelerations species, including a Bayesian method called PhyloAcc, which models shifts rate multiple target on phylogeny. However, few consider the possibility discordance trees individual loci species tree due incomplete lineage sorting, might cause false positives. Here, we present PhyloAcc-GT, extends PhyloAcc by modeling gene heterogeneity. Given tree, adopt multispecies coalescent model as prior distribution trees, use Markov chain Monte Carlo (MCMC) for inference, design novel MCMC moves sample efficiently. Through extensive simulations, show that PhyloAcc-GT outperforms other identifying lineage-specific detecting complex patterns shifts, robust specification population size parameters. usually more conservative than calling convergent because it identifies ancestral terminal branches. We apply two examples evolution: flightlessness ratites marine mammal adaptations, tool associated with specific while accounting sorting.

Язык: Английский

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The meaning and measure of concordance factors in phylogenomics

Molecular Biology and Evolution, Год журнала: 2024, Номер 41(11)

Опубликована: Окт. 17, 2024

Abstract As phylogenomic datasets have grown in size, researchers developed new ways to measure biological variation and assess statistical support for specific branches. Larger more sites loci therefore less sampling variance. While we can accurately the mean signal these datasets, lower variance is often reflected uniformly high measures of branch support—such as bootstrap posterior probability—limiting their utility. also revealed substantial topologies found across individual loci, such that single species tree inferred by most phylogenetic methods represents a limited summary data many purposes. In contrast support, degree underlying topological among should be approximately constant regardless size dataset. “Concordance factors” (CFs) similar statistics become increasingly important tools phylogenetics. this review, explain why CFs thought descriptors rather than argue they provide information about predictive power not contained support. We review growing suite measuring concordance, compare them common framework reveals interrelationships, demonstrate how calculate using an example from birds. discuss might change future move beyond estimating “tree life” toward myriad evolutionary histories genomic variation.

Язык: Английский

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Building a reliable 16S mini-barcode library of wild bees from Occitania, south-west of France

Biodiversity Data Journal, Год журнала: 2025, Номер 13

Опубликована: Янв. 7, 2025

DNA barcoding and metabarcoding are now powerful tools for studying biodiversity especially the accurate identification of large sample collections belonging to diverse taxonomic groups. Their success depends largely on resolution sequences used as barcodes reliability reference databases. For wild bees, barcode coverage is consistently growing in volume, but some incorrect species annotations need be cared for. The COI (Cytochrome Oxydase subunit 1) gene, most barcoding/metabarcoding arthropods, suffers from primer bias difficulties covering all bee using classical Folmer primers. We present here a curated database 250 bp mini-barcode region 16S rRNA suitable low-cost bees applications, such eDNA analysis or sequencing ancient degraded DNA. Sequenced specimens were captured Occitania (south-west France) morphologically identified by entomologists, with total 530 individuals 171 19 genera. A customised workflow including distance-tree inferences second round entomologist observations, when necessary, was validation 348 mini-barcodes 148 species. Amongst them, 93 did not have any available before our contribution. This high-quality library data freely scientific community, aim facilitating future large-scale characterisation communities context pollinators' decline.

Язык: Английский

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Bumble bee gut microbial community structure differs between species and commercial suppliers, but metabolic potential remains largely consistent

Applied and Environmental Microbiology, Год журнала: 2025, Номер unknown

Опубликована: Фев. 6, 2025

ABSTRACT Bumble bees are key pollinators for natural and agricultural plant communities. Their health performance supported by a core gut microbiota composed of few bacterial taxa. However, the taxonomic composition community structure bumble bee microbiotas can vary with species, environment, origin (i.e., whether colonies come from wild or commercial rearing facility), it is unclear metabolic capabilities therefore as well. Here we used metagenomic sequencing to examine composition, structure, potential across two different Bombus impatiens suppliers, B. , three other species sampled sites within native range all four species. We found that varied between populations origins suppliers. Notably, Apibacter consistently present in some species—suggesting may be previously unrecognized phylotype bees—and lack phylotypes populations. despite variation high-level was largely consistent hosts, including related host performance, though activity remains investigated. IMPORTANCE Our study first compare genome-level whole suppliers In addition, profiled full time. Overall, our results provide new insight into function will help researchers evaluate how well studies conducted one population translate Research on increasing relevance continue discover ways social influence health, decline abundance.

Язык: Английский

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Cytogenetics of insects in the era of chromosome-level genome assemblies

Vavilov Journal of Genetics and Breeding, Год журнала: 2025, Номер 29(2), С. 230 - 237

Опубликована: Апрель 10, 2025

Over the past few years, a revolution has occurred in cytogenetics, driven by emergence and spread of methods for obtaining high-quality chromosome-level genome assemblies. In fact, this led to new tool studying chromosomes chromosomal rearrangements, is thousands times more powerful than light microscopy. This revolutionized cytogenetics many groups insects which previously karyotype information, if available at all, was limited chromosome number. Even impressive are achievements genomic approach general patterns organization evolution insects. Thus, it been shown that rapid transformations numbers, often found order Lepidoptera, most carried out parsimonious way, as result simple fusions fissions chromosomes. It established these not random occur independently different phylogenetic lineages due reuse same ancestral breakpoints. tendency correlated with presence so-called interstitial telomeres, i.e. telomere-like structures located ends chromosomes, but inside them. revealed that, insects, telomeric DNA just set short repeats, very long sequence consisting (TTAGG) n (or other motifs), regularly specifically interrupted retrotransposons, motifs diverse terms their length nucleotide composition. The number assemblies GenBank database growing exponentially now exceeds thousand species. Therefore, exceptional prospects using data analysis beyond doubt.

Язык: Английский

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