Evaluating UCE Data Adequacy and Integrating Uncertainty in a Comprehensive Phylogeny of Ants

Systematic Biology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 8, 2025

Abstract While some relationships in phylogenomic studies have remained stable since the Sanger sequencing era, many challenging nodes remain, even with genome-scale data. Incongruence or lack of resolution era is frequently attributed to inadequate data modeling and analytical issues that lead systematic biases. However, few investigate potential for random error establish expectations level achievable a given empirical dataset integrate uncertainties across methods when faced conflicting results. Ants are most species-rich lineage social insects one ecologically important terrestrial animals. Consequently, ants garnered significant research attention, including their systematics. Despite this, there has been no comprehensive genus-level phylogeny inferred using genomic thoroughly evaluates both signal strength incongruence. In this study, we provide insight into quantify uncertainty ant tree life by utilizing taxonomically Ultraconserved Elements date, 277 (81%) recognized genera from all 16 extant subfamilies, representing over 98% described species. We use simulations resolution, identify branches less-than-expected concordance, dissect effects model selection on recalcitrant nodes. Simulations show hundreds loci needed resolve our phylogeny. This demonstrates continued role studies. Our analyses picture support incongruence phylogeny, while offering more nuanced depiction significantly expanding generic sampling. consensus approach different find assumptions about root age exert substantial influence divergence dating. results suggest advancing understanding will require not only but also refined phylogenetic models. workflow identifying under-supported concatenation analyses, outline pragmatic way reconcile phylogenomics, introduce user-friendly locus tool

Language: Английский

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Evaluating UCE data adequacy and integrating uncertainty in a comprehensive phylogeny of ants

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

Published: July 5, 2024

Abstract While some relationships in phylogenomic studies have remained stable since the era of Sanger sequencing, many challenging nodes elude resolution, even with genome-scale data. As early grappled random error and insufficient information, incongruence or lack resolution phylogenomics is generally associated inadequate modeling biological phenomena combined analytical issues leading to systematic biases. Few studies, however, explore potential for establish an expectation what level should be expected from a given empirical dataset. In presenting incongruent results, phylogeneticists face choice providing diverse array results different approaches single preferred tree, few attempting integrate uncertainties across methods. Recent phylogenetic work has uncovered well-supported often novel relationships, as well more contentious findings, phylogeny ants. Ants are most species-rich lineage social insects among ecologically important terrestrial animals. result, they attracted much research, including regarding systematics. To date, there been no comprehensive genus-level ants inferred using genomic data effort evaluate signal throughout. Here we provide deeper insight into quantify uncertainty ant tree life. We accomplish this taxonomically Ultraconserved Elements dataset 277 (81%) recognized genera all 16 extant subfamilies, representing over 98% described species-level diversity. use simulations expectations identify branches less-than-expected concordance, dissect effects model selection on recalcitrant nodes. also construct consensus integrating multiple analyses. Simulations show that hundreds loci needed resolve our phylogeny, under best-case scenario known parameters without bias. This demonstrates continues play role phylogenomics. Our analyses picture support topology congruent recent study subfamily-level, while rendering realistic significantly expanding generic sampling. divergence dating find assumptions about root age significant impact dates inferred. suggest improved understanding will require both better models. workflow under-supported concatenation analyses, outline pragmatic way reconcile conflicting phylogenomics, introduce user-friendly locus tool dating.

Language: Английский

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Bee Systematics and Conservation

Sociobiology, Journal Year: 2025, Volume and Issue: 72(2), P. e11416 - e11416

Published: May 15, 2025

Diversity can be examined and interpreted from various perspectives, including species richness, genetic phenotypic differences, variation in behaviors natural history, phylogenetic history. Centuries of taxonomic research have revealed approximately 21,000 bee worldwide. These subdivided into a hierarchy subgroups that reflects their evolutionary thanks to the increasingly more comprehensive hypotheses available. Advances systematics enhanced our understanding how diversity has evolved, origin Cretaceous, shifts geographical distribution, evolution social parasitic behaviors, changes relationships between bees plants they visit throughout 120-million-year shared An important outcome enduring relationship with flowering is vital role play pollination both agricultural ecosystems. Habitat loss, climate change, other anthropogenic environmental alterations led declines populations, which sparked concerns about conservation highlighted importance complementary aspects diversity, components this variation. The availability reliable significant advancements, enabling assessments communities predictions regarding vulnerability habitat change ecological functions. This review explores perspectives documenting interpreting changing world summarizes current classification while discussing advances contemporary research.

Language: Английский

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Evolutionary History and Ecology of Andrena (Foveoandrena) androfovea: A New Nearctic Mining Bee (Hymenoptera, Andrenidae) Species and Subgenus

Ecology and Evolution, Journal Year: 2024, Volume and Issue: 14(11)

Published: Nov. 1, 2024

ABSTRACT With about 1700 described species, the mining bee genus Andrena is a rapidly diversifying lineage and one of most species‐rich groups bees. Recent phylogenomic advances have greatly improved our understanding phylogeny genus, yet many species still await description, subgeneric assignments that are in line with their evolutionary history, as well study morphology behavior. Here we provide comprehensive account newly discovered androfovea n. sp. We sequence genome new include it presently analysis using ultraconserved element (UCE) data, comprising 264 samples 249 species. Given recovered phylogenetic position establish subgenus, Foveoandrena , detailed morphological discuss antiquity historical biogeography light molecular divergence time estimates. Lastly, document foraging behavior photos video footage, species' unusual host plant associations Chamaesaracha Quincula both Solanaceae. Being likely oligolectic on these plants, present first documented case an being narrowly associated members this family. By integrating multiple lines documentation, provides particularly discovery description.

Language: Английский

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Phylogeny, antiquity, and niche occupancy of Trinomia (Hymenoptera: Halictidae), an Afrotropical endemic genus of Nomiinae

Molecular Phylogenetics and Evolution, Journal Year: 2024, Volume and Issue: unknown, P. 108273 - 108273

Published: Dec. 1, 2024

Language: Английский

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