Gondwanan relic or recent arrival? The biogeographic origins and systematics of Australian tarantulas DOI Creative Commons
Ethan Briggs, Saoirse Foley, Lyn G. Cook

et al.

Molecular Phylogenetics and Evolution, Journal Year: 2024, Volume and Issue: unknown, P. 108246 - 108246

Published: Nov. 1, 2024

The composition of Australia's fauna and flora has been largely assembled by two biogeographic processes, vicariance long-distance dispersal establishment. These patterns can be observed today through the survival Gondwanan lineages contrasted with relatively recent colonization from south-east Asia, respectively. In general, post-Gondwanan immigrant Asia are taxa traits that facilitate dispersal. Consequently, like tarantulas (Araneae, Theraphosidae) pan-tropical but also have a low propensity for dispersal, thought to in origin. However, Australian unsampled phylogenomic studies and, as such, their classification origins long debated unresolved. Here we test if current, morphology-based Selenocosmiinae is accurate assess whether were present Australia while it was part Gondwana. We sample 369 tarantula specimens across Australia, greatly expanding geographic sampling previous studies, develop first continent-wide phylogeny tarantulas. To resolve 'back bone' generate 20 new transcriptomes species representing distinct uncovered using mitochondrial sequence data combine these published transcriptomic data. Through recovery ultra-conserved element (UCE) loci testing multiple occupancy matrices, find clade monophyletic nested inside Asian Selenocosmiinae. young radiation crown age 8.3-18.8 Ma therefore reject hypothesis origin animals instead, infer Asia. Our findings indicate they underwent rapid radiation, possibly coinciding arrival into Australia. refute monophyly Selenocosmia Coremiocnemis currently recognised, remove stalkeri synonymy stirlingi.

Language: Английский

Evaluating UCE Data Adequacy and Integrating Uncertainty in a Comprehensive Phylogeny of Ants DOI Creative Commons
Marek L. Borowiec, Y. Miles Zhang, Karen Neves

et al.

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

Citations

1
Disentangling a genome-wide mosaic of conflicting phylogenetic signals in Western Rattlesnakes DOI
Justin M. Bernstein, Yannick Francioli, Drew R. Schield

et al.

Molecular Phylogenetics and Evolution, Journal Year: 2025, Volume and Issue: unknown, P. 108309 - 108309

Published: Feb. 1, 2025

Language: Английский

Citations

1
An ultraconserved element probe set for velvet worms (Onychophora) DOI Creative Commons
Shoyo Sato, Shahan Derkarabetian, Arianna Lord

et al.

Molecular Phylogenetics and Evolution, Journal Year: 2024, Volume and Issue: 197, P. 108115 - 108115

Published: May 27, 2024

Onychophora are cryptic, soil-dwelling invertebrates known for their biogeographic affinities, diversity of reproductive modes, close phylogenetic relationship to arthropods, and peculiar prey capture mechanism. The 216 valid species grouped into two families - Peripatopsidae Peripatidae apart from a few relationships among major lineages within these families, stable backbone the phylum has yet be resolved. This hindered our understanding onychophoran patterns, evolutionary history, systematics. Neopatida, Neotropical clade peripatids, proved particularly difficult, with recalcitrant nodes low resolution, potentially due rapid radiation group during Cretaceous. Previous studies have had compromise between number loci taxa limitations Sanger sequencing phylotranscriptomics, respectively. Additionally, aspects genome size structure made molecular phylogenetics difficult data matrices been affected by missing data. To address issues, we leveraged recent, published transcriptomes first high quality designed affinity ultraconserved element (UCE) probe set Onychophora. new set, consisting ∼ 20,000 probes that target 1,465 across both locus recovery utility. Phylogenetic analyses recovered monophyly clades revealed novel lineage Neotropics challenges current endemicity. resource could drastically increase power datasets allow access genomic scale archival museum specimens further tackle issues exasperating

Language: Английский

Citations

6
Broken Ring Speciation in California Mygalomorph Spiders (Nemesiidae, Calisoga) DOI
Rodrigo Monjaraz‐Ruedas, James Starrett,

Dean H. Leavitt

et al.

The American Naturalist, Journal Year: 2024, Volume and Issue: 204(1), P. 55 - 72

Published: March 5, 2024

Language: Английский

Citations

4
Navigating phylogenetic conflict and evolutionary inference in plants with target capture data DOI Creative Commons
Elizabeth Joyce, Alexander N. Schmidt‐Lebuhn, Harvey K. Orel

et al.

Published: May 27, 2024

Target capture has quickly become a preferred approach for plant systematic and evolutionary research, marking step-change in the generation of data phylogenetic inference. While this advancement facilitated resolution many relationships, conflict continues to be reported, often attributed genome duplication, reticulation, deep coalescence or rapid speciation – processes that are particularly common evolution. The proliferation methods designed analyse target presence these can overwhelming researchers, especially students. In review, we guide researchers through bioinformatic workflow, with particular focus on robust inference conflict. Through highlight key considerations reducing artefactual conflict, synthesise strategies managing paralogs, explain causes measurement summarise current investigating biological underlying draw from examples Australian flora, review is broadly relevant any researcher working data. We conclude inherent inevitable but when properly managed, provide unprecedented insight into extraordinary complex histories plants.

Language: Английский

Citations

4
Evaluating UCE data adequacy and integrating uncertainty in a comprehensive phylogeny of ants DOI
Marek L. Borowiec, Y. Miles Zhang, Karen Neves

et al.

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

Citations

4
Gondwanan relic or recent arrival? The biogeographic origins and systematics of Australian tarantulas DOI Creative Commons
Ethan Briggs, Saoirse Foley, Lyn G. Cook

et al.

Molecular Phylogenetics and Evolution, Journal Year: 2024, Volume and Issue: unknown, P. 108246 - 108246

Published: Nov. 1, 2024

The composition of Australia's fauna and flora has been largely assembled by two biogeographic processes, vicariance long-distance dispersal establishment. These patterns can be observed today through the survival Gondwanan lineages contrasted with relatively recent colonization from south-east Asia, respectively. In general, post-Gondwanan immigrant Asia are taxa traits that facilitate dispersal. Consequently, like tarantulas (Araneae, Theraphosidae) pan-tropical but also have a low propensity for dispersal, thought to in origin. However, Australian unsampled phylogenomic studies and, as such, their classification origins long debated unresolved. Here we test if current, morphology-based Selenocosmiinae is accurate assess whether were present Australia while it was part Gondwana. We sample 369 tarantula specimens across Australia, greatly expanding geographic sampling previous studies, develop first continent-wide phylogeny tarantulas. To resolve 'back bone' generate 20 new transcriptomes species representing distinct uncovered using mitochondrial sequence data combine these published transcriptomic data. Through recovery ultra-conserved element (UCE) loci testing multiple occupancy matrices, find clade monophyletic nested inside Asian Selenocosmiinae. young radiation crown age 8.3-18.8 Ma therefore reject hypothesis origin animals instead, infer Asia. Our findings indicate they underwent rapid radiation, possibly coinciding arrival into Australia. refute monophyly Selenocosmia Coremiocnemis currently recognised, remove stalkeri synonymy stirlingi.

Language: Английский

Citations

0