Using and navigating the plant tree of life

Soltis, Douglas E.; Moore, Michael J.; Sessa, Emily B.; Smith, Stephen A.; Soltis, Pamela S.

doi:10.1002/ajb2.1071

Cited by 16 publications

(14 citation statements)

References 28 publications

(33 reference statements)

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“…An important corollary of the points above is that the widely used framework of angiosperm phylogeny, based largely on the plastid genome (e.g., APG IV, ; Soltis et al., , b), may not reflect the true species tree and/or may be incomplete as a result of evolutionary processes leading to cytonuclear discordance. More broad‐scale phylogenomic studies of angiosperms and green plants in general, explicitly comparing results from both the nuclear and plastid genomes, are clearly needed to evaluate the plastid‐based phylogenetic framework and to elucidate the extent of cytonuclear discordance at deep phylogenetic levels.…”

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confidence: 99%

Nuclear phylogenomic analyses of asterids conflict with plastome trees and support novel relationships among major lineages

Stull

Soltis

et al. 2020

American J of Botany

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Premise Discordance between nuclear and organellar phylogenies (cytonuclear discordance) is a well‐documented phenomenon at shallow evolutionary levels but has been poorly investigated at deep levels of plant phylogeny. Determining the extent of cytonuclear discordance across major plant lineages is essential not only for elucidating evolutionary processes, but also for evaluating the currently used framework of plant phylogeny, which is largely based on the plastid genome. Methods We present a phylogenomic examination of a major angiosperm clade (Asteridae) based on sequence data from the nuclear, plastid, and mitochondrial genomes as a means of evaluating currently accepted relationships inferred from the plastome and exploring potential sources of genomic conflict in this group. Results We recovered at least five instances of well‐supported cytonuclear discordance concerning the placements of major asterid lineages (i.e., Ericales, Oncothecaceae, Aquifoliales, Cassinopsis, and Icacinaceae). We attribute this conflict to a combination of incomplete lineage sorting and hybridization, the latter supported in part by previously inferred whole‐genome duplications. Conclusions Our results challenge several long‐standing hypotheses of asterid relationships and have implications for morphological character evolution and for the importance of ancient whole‐genome duplications in early asterid evolution. These findings also highlight the value of reevaluating broad‐scale angiosperm and green‐plant phylogeny with nuclear genomic data.

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confidence: 99%

Nuclear phylogenomic analyses of asterids conflict with plastome trees and support novel relationships among major lineages

Stull

Soltis

et al. 2020

American J of Botany

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“…Subsequent advancements in molecular technology, phylogenetic methodologies, and comparative methods have led to an explosion of molecular systematics and phylogeny-based comparative studies. The results have led to a better understanding of relationships and evolution of the organisms with which we share our planet (Chase et al, 1993;San Mauro & Agorreta, 2010;Losos et al, 2013;Hinchliff et al, 2015;Soltis et al, 2018;Bakker et al, 2020). Moreover, recent efforts in reconstructing the tree of life, integrating methods and sharing data across disciplines, digitizing biological collections, harvesting big data from high-throughput DNA sequencing, and development of analytical and genetic tools (Wen et al, 2015(Wen et al, , 2017Soltis et al, 2018;Leebens-Mack et al, 2019;Bakker et al, 2020) have empowered systematic and evolutionary biology to undertake novel and integrative studies from perspectives that were previously impossible (e.g., Chanderbali et al, 2017;Ma et al, 2017aMa et al, , 2017bEllwood et al, 2018;Hodel et al, 2018;Landis et al, 2018;Lewin et al, 2018;Lu et al, 2018;Dong et al, 2019).…”

Section: Editorialmentioning

confidence: 99%

In memory of Professor Tang Yan‐Cheng: New perspectives in systematic and evolutionary biology

Xiang

Chen

Song

et al. 2020

J of Sytematics Evolution

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“…Whereas the ToL has obvious connotation to the entirety of life, its use is often confined to a subset of the living world: expressions such as the "prokaryotic tree of life" (McInerney et al 2008), "plant tree of life" (Soltis et al 2018), "fungal tree of life", "tree of life of birds" or "amphibian tree of life" ( Supplementary Table S1) are not uncommon. This is unfortunate, because in this way the ToL may end up with the same fate as the infamous "family tree", for example, which in most publications had nothing to do with actual families (understood either in the everyday sense of the word or as a rank in systematics).…”

Section: Scope Taxon Sampling and Diversitymentioning

confidence: 99%

The Coral of Life

Podani

2019

Evol Biol

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The Tree of Life (ToL) has been of central importance in the biological sciences, usually understood as a model or a metaphor, and portrayed in various graphical forms to summarize the history of life as a single diagram. If it is seen as a mathematical construct-a rooted graph theoretical tree or, as more recently viewed, a directed network [Network of Life (NoL)]-then its proper visualization is not feasible, for both epistemological and technical reasons. As an overview included in this study demonstrates, published ToLs and NoLs are extremely diverse in appearance and content, and they suffer from inevitable bias towards particular groups, or are restricted to a single major taxon. Metaphorical trees are even less useful for the purpose, because ramification is the only property of botanical trees that may be interpreted in an evolutionary or phylogenetic context. This paper argues that corals, as suggested by Darwin in his early notebooks, are superior to trees as metaphors, and may also be used as mathematical models. A coral diagram is useful for portraying past and present life because it is suitable: (1) to illustrate bifurcations and anastomoses, (2) to depict species richness of taxa proportionately, (3) to show chronology, extinct taxa and major evolutionary innovations, (4) to express taxonomic continuity, (5) to expand particulars due to its self-similarity, and (6) to accommodate a genealogy-based, rank-free classification. This paper is supplemented with a figure, The Coral of Life (CoL), which is, to the author's knowledge, the first attempt to combine all of the above features in a single diagram for the entirety of life, thus serving as a prototype for further analysis and improvement. The discussion is partly historical: references to classical and modern writings help the reader to understand how biological thinking and methods of visualization have evolved to reach this achievement.

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Using and navigating the plant tree of life

Cited by 16 publications

References 28 publications

Nuclear phylogenomic analyses of asterids conflict with plastome trees and support novel relationships among major lineages

Nuclear phylogenomic analyses of asterids conflict with plastome trees and support novel relationships among major lineages

In memory of Professor Tang Yan‐Cheng: New perspectives in systematic and evolutionary biology

The Coral of Life

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