New insights into the phylogeny and infrageneric taxonomy of Saussurea based on hybrid capture phylogenomics (Hyb-Seq) DOI Creative Commons

LIAN-SHENG XU,

Zhuqiu Song, Tian Li

et al.

Plant Diversity, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 1, 2024

Saussurea is one of the largest and most rapidly evolving genera within Asteraceae, comprising approximately 520 species from Northern Hemisphere. A comprehensive infrageneric classification, supported by robust phylogenetic trees corroborated morphological other data, has not yet been published. For first time, we recovered a well-resolved nuclear phylogeny consisting four main clades, which was also data. Our analyses show that ancient hybridization likely source deep cytoplasmic-nuclear conflict in Saussurea, based on data more suitable than chloroplast for exploring classification Saussurea. Based obtained characters, proposed revised taxonomy includes subgenera 13 sections. Specifically, 1) S. sect. Cincta, Gymnocline, Lagurostemon, Strictae were moved subg. to Amphilaena, 2) Pseudoeriocoryne Eriocoryne 3) Laguranthera Theodorea.

Language: Английский

Phylogenomics and morphology of Celmisiinae (Asteraceae: Astereae): Taxonomic and evolutionary implications DOI Creative Commons
D A V I D Nicol, Patricio Saldivia, Tina C. Summerfield

et al.

Molecular Phylogenetics and Evolution, Journal Year: 2024, Volume and Issue: 195, P. 108064 - 108064

Published: March 19, 2024

The tribe Astereae (Asteraceae) includes 36 subtribes and 252 genera, is distributed worldwide in temperate tropical regions. One of the subtribes, Celmisiinae Saldivia, has been recently circumscribed to include six genera ca. 160 species, restricted eastern Australia, New Zealand, Guinea. species show an impressive range growth habit, from small herbs ericoid subshrubs medium-sized trees. They live a wide habitats are often dominant subalpine alpine vegetation. Despite well-supported circumscription Celmisiinae, uncertainties have remained about their internal relationships classification at genus levels. This study exploited recent advances high-throughput sequencing build robust multi-gene phylogeny for subtribe Celmisiinae. target enrichment Angiosperms353 bait set hybpiper-nf paragone-nf pipelines were used retrieve, infer, assemble orthologous loci 75 taxa representing all main putative clades within subtribe. Because diploidised ploidy level as well missing data assemblies, uncertainty remains surrounding inference orthology detection. However, based on variety gene-family sets, coalescent concatenation-based phylogenetic reconstructions recovered similar topologies. Paralogy gene-families caused some problems, but estimated phylogenies well-resolved. phylogenomic evidence supported three clades: Pleurophyllum clade (Pleurophyllum, Macrolearia Damnamenia), mostly Zealand Subantarctic Islands, Celmisia mainland Shawia (including 'Olearia pro parte' Pachystegia) Australia results presented here add accumulating support efficient method documenting plant diversity.

Language: Английский

Citations

5
A thorny tale: The origin and diversification of Cirsium (Compositae) DOI
Lucía D. Moreyra, Alfonso Susanna, Juan Antonio Calleja

et al.

Molecular Phylogenetics and Evolution, Journal Year: 2025, Volume and Issue: 204, P. 108285 - 108285

Published: Jan. 11, 2025

Language: Английский

Citations

0
Target capture sequencing clarifies key relationships in the Eriostemon group (Rutaceae: Zanthoxyloideae) and supports a reclassification of Philotheca, including the recognition of two new genera DOI Creative Commons
Harvey K. Orel, Todd G. B. McLay,

Paul I. Forster

et al.

Taxon, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 6, 2025

Abstract The Eriostemon group (Rutaceae) is a clade of 16 genera and ~ 209 species endemic to Australia, New Zealand Caledonia. Recent efforts address taxonomic phylogenetic uncertainty in the using plastome nuclear ribosomal DNA sequences have made some progress but also highlighted problematic areas that require further research. In particular, current circumscription Philotheca known be non‐monophyletic, unclear relationships prevented reclassification group. We generated target capture data Angiosperms353 universal bait kit conducted analyses on with aims resolving uncertain backbone clarifying . Our results uncovered extensive cytonuclear discordance group, conflict between our phylogenies previous observed several key tree. Despite this, positions polyphyletic lineages were consistent enough across enable confident genus, which presented herein. Two sections , P. sect. Corynonema Erionema are raised generic rank under names Erioseira respectively. Cyanochlamys transferred into genus Muiriantha type section retained becomes entirety genus. Appropriate nomenclatural changes transfer all currently recognised subspecies their respective this new classification.

Language: Английский

Citations

0
A phylogenomic approach to disentangling the evolution of the large and diverse daisy tribe Anthemideae (Asteraceae) DOI Creative Commons

David Criado‐Ruiz,

Joan Vallès, Randall J. Bayer

et al.

Journal of Systematics and Evolution, Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 7, 2024

Abstract The daisy tribe Anthemideae Cass. is one of the largest and most diverse tribes within Asteraceae. We analyzed a data set including 61 out 111 genera, all but four 19 currently recognized subtribes (Inulantherinae, Lapidophorinae, Lonadinae, Vogtiinae) using targeted high‐throughput sequencing approach, first focused on tribe. followed different phylogenomic approaches, nuclear plastid data, as well additional analytical methods to estimate divergence times diversification rates, unravel evolutionary history classification this Our results reinforce phylogenetic backbone advanced in previous studies further reveal possible occurrence ancient hybridization events, capture, and/or incomplete lineage sorting (ILS), suggesting that complex processes have played an important role evolution also support merging subtribe Physmasperminae into Athanasiinae Matricariinae Anthemidinae clarify previously unresolved relationships. Furthermore, study provides insights biogeographic patterns by identifying three main groups: Southern African Grade, Asian Clade, circum‐Mediterranean Clade. These groups partially coincide with identified ones. Overall, research more detailed understanding improves its classification. emphasizes importance approaches for deciphering dynamics large plant lineages.

Language: Английский

Citations

2
Truly the best of both worlds: Merging lineage‐specific and universal probe kits to maximize phylogenomic inference DOI Creative Commons
Luiz Henrique M. Fonseca, Pieter Asselman, Katherine R. Goodrich

et al.

Applications in Plant Sciences, Journal Year: 2024, Volume and Issue: 12(6)

Published: Sept. 25, 2024

Abstract Premise Hybridization capture kits are now commonly used for reduced representation approaches in genomic sequencing, with both universal and clade‐specific available. Here, we present a probe kit targeting 799 low‐copy genes the plant family Annonaceae. Methods This new version of combines original 469 from previous Annonaceae 334 Angiosperms353 kit. We also compare results obtained using our custom approach subset specimens. Parsimony‐informative sites maximum likelihood phylogenetic inference were assessed combined matrices genera Asimina Deeringothamnus . Results The Annonaceae799 derived have extremely high recovery rates. Off‐target reads detected. When evaluating size, proportion on‐ off‐target regions, number parsimony‐informative sites, incorporated panel generally outperformed Discussion demonstrated that sequences set variable relevant future studies on species‐level phylogenomics within‐species integration establishes connection between projects makes available population studies.

Language: Английский

Citations

1
New insights into the phylogeny and infrageneric taxonomy of Saussurea based on hybrid capture phylogenomics (Hyb-Seq) DOI Creative Commons

LIAN-SHENG XU,

Zhuqiu Song, Tian Li

et al.

Plant Diversity, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 1, 2024

Saussurea is one of the largest and most rapidly evolving genera within Asteraceae, comprising approximately 520 species from Northern Hemisphere. A comprehensive infrageneric classification, supported by robust phylogenetic trees corroborated morphological other data, has not yet been published. For first time, we recovered a well-resolved nuclear phylogeny consisting four main clades, which was also data. Our analyses show that ancient hybridization likely source deep cytoplasmic-nuclear conflict in Saussurea, based on data more suitable than chloroplast for exploring classification Saussurea. Based obtained characters, proposed revised taxonomy includes subgenera 13 sections. Specifically, 1) S. sect. Cincta, Gymnocline, Lagurostemon, Strictae were moved subg. to Amphilaena, 2) Pseudoeriocoryne Eriocoryne 3) Laguranthera Theodorea.

Language: Английский

Citations

0