Phylogenomics and morphology of Celmisiinae (Asteraceae: Astereae): Taxonomic and evolutionary implications

Nicol, Duncan A.; Saldivia, Patricio; Summerfield, Tina C.; Heads, Michael; Lord, Janice M.; Khaing, Ei P.; Larcombe, Matthew J.

doi:10.1016/j.ympev.2024.108064

Cited by 2 publications

(1 citation statement)

References 98 publications

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“…Now, target capture datasets indicate that these processes are pervasive in plants, manifesting as conflict. In the Australian flora, conflict has been attributed to likely WGD events in target capture datasets of Adenanthos , Pomaderris (Nge, Kellermann, et al 2021), Calytrix (Nge et al 2022), Cryptandra (Nge et al 2024), Senecio , Celmisiinae (Nicol et al 2024) and many lineages in Sapindales (Joyce et al 2023). Conflict due to reticulation has been detected in Adansonia (Karimi et al 2020) and Thelypteridaceae (Bloesch et al 2022), and reticulation in concert with deep coalescence in Adenanthos and Eucalyptus (McLay et al 2023).…”

Section: Introductionmentioning

confidence: 99%

Navigating phylogenetic conflict and evolutionary inference in plants with target capture data

Joyce,

Schmidt-Lebuhn,

Orel

et al. 2024

Preprint

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

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Section: Introductionmentioning

confidence: 99%

Navigating phylogenetic conflict and evolutionary inference in plants with target capture data

Joyce,

Schmidt-Lebuhn,

Orel

et al. 2024

Preprint

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

Criado‐Ruiz,

Vallès,

Bayer

et al. 2024

J of Systematics Evolution

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

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Phylogenomics and morphology of Celmisiinae (Asteraceae: Astereae): Taxonomic and evolutionary implications

Cited by 2 publications

References 98 publications

Navigating phylogenetic conflict and evolutionary inference in plants with target capture data

Navigating phylogenetic conflict and evolutionary inference in plants with target capture data

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

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