Inferring phylogenies with incomplete data sets: a 5-gene, 567-taxon analysis of angiosperms

Burleigh, J. Gordon; Hilu, Khidir W.; Soltis, Douglas E.

doi:10.1186/1471-2148-9-61

Cited by 75 publications

(96 citation statements)

References 61 publications

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“…This finding differs from previous molecular phylogenetic analyses in providing strong support for these clades. Although Berberidopsidales, Santalales, and Caryophyllales have often been placed with Asteridae, and Saxifragales with Rosidae and Vitaceae, these relationships were only weakly supported (3,5,6,8,9,17,18).…”

Section: Discussionmentioning

confidence: 99%

“…More than 90% of eudicot species diversity is found within the clade Pentapetalae (1), which includes major clades such as Rosidae, Caryophyllales, Saxifragales, Asteridae, and Santalales, as well as smaller lineages such as Berberidopsidales and Dilleniaceae (3)(4)(5)(6)(7)(8). Previous analyses of multigene data sets have failed to resolve relationships among the major clades of Pentapetalae (6,9). The inability to resolve these relationships suggests that the major lineages of Pentapetalae diverged rapidly, a hypothesis supported by the fossil record (10,11).…”

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confidence: 99%

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Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots

Moore

Soltis

Bell

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

630

644

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Although Pentapetalae (comprising all core eudicots except Gunnerales) include ≈70% of all angiosperms, the origin of and relationships among the major lineages of this clade have remained largely unresolved. Phylogenetic analyses of 83 protein-coding and rRNA genes from the plastid genome for 86 species of seed plants, including new sequences from 25 eudicots, indicate that soon after its origin, Pentapetalae diverged into three clades: (i) a "superrosid" clade consisting of Rosidae, Vitaceae, and Saxifragales; (ii) a "superasterid" clade consisting of Berberidopsidales, Santalales, Caryophyllales, and Asteridae; and (iii) Dilleniaceae. Maximum-likelihood analyses support the position of Dilleniaceae as sister to superrosids, but topology tests did not reject alternative positions of Dilleniaceae as sister to Asteridae or all remaining Pentapetalae. Molecular dating analyses suggest that the major lineages within both superrosids and superasterids arose in as little as 5 million years. This phylogenetic hypothesis provides a crucial historical framework for future studies aimed at elucidating the underlying causes of the morphological and species diversity in Pentapetalae.Angiosperm Tree of Life | Pentapetalae | plastid genome T he Eudicotyledoneae (sensu) (1), or eudicots, comprise ≈75% of all angiosperm species (2) and encompass enormous morphological, biochemical, and ecological diversity. More than 90% of eudicot species diversity is found within the clade Pentapetalae (1), which includes major clades such as Rosidae, Caryophyllales, Saxifragales, Asteridae, and Santalales, as well as smaller lineages such as Berberidopsidales and Dilleniaceae (3-8). Previous analyses of multigene data sets have failed to resolve relationships among the major clades of Pentapetalae (6, 9). The inability to resolve these relationships suggests that the major lineages of Pentapetalae diverged rapidly, a hypothesis supported by the fossil record (10, 11). However, our understanding of the origins and evolution of Pentapetalae diversity, and consequently much of angiosperm diversity, is hindered by the lack of a well-supported phylogenetic hypothesis.Phylogenetic analyses based on complete plastid genome sequences have resolved several enigmatic relationships within angiosperms (12, 13). However, these analyses have not included data for many crucial eudicot clades. To resolve relationships among the major clades of Eudicotyledoneae (with a focus on Pentapetalae), we performed phylogenetic analyses using a data set composed of 83 genes derived from 86 complete plastid genome sequences, 25 of which were eudicot sequences generated for this study. To date, this is the largest plastid genome data set used for phylogenetic inference and includes representatives of nearly all (37 of 42) orders of eudicots sensu Angiosperm Phylogeny Group (APG) III (14). The resulting phylogenetic hypothesis helps to clarify the diversification of Pentapetalae and provides an improved framework for investigating evolutionary processes that accompanie...

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Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots

Moore

Soltis

Bell

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

630

644

View full text Add to dashboard Cite

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“…We estimated a phylogenetic tree of flowering plants using the DNA data set of Burleigh et al 12 , comprising 567 species and 10,552 base pairs. We refined their alignments 12 , then partitioned the data set into MatK (which is often a pseudogene), 1st þ 2nd codon positions, 3rd codon positions, RNA stems and RNA loops. We estimated a maximum-likelihood topology using RaxML 38 , applying an independent GTR þ I þ G model to each data partition.…”

Section: Methodsmentioning

confidence: 99%

“…For each family, we estimated the amount of genetic change for the chloroplast and nuclear genomes from a large DNA sequence data set 12 . We estimated molecular branch lengths in substitutions per site, and absolute rates of molecular evolution in substitutions per site per million years.…”

Section: Data Setsmentioning

confidence: 99%

Taller plants have lower rates of molecular evolution

et al. 2013

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Rates of molecular evolution have a central role in our understanding of many aspects of species' biology. However, the causes of variation in rates of molecular evolution remain poorly understood, particularly in plants. Here we show that height accounts for about onefifth of the among-lineage rate variation in the chloroplast and nuclear genomes of plants. This relationship holds across 138 families of flowering plants, and when accounting for variation in species richness, temperature, ultraviolet radiation, latitude and growth form. Our observations can be explained by a link between height and rates of genome copying in plants, and we propose a mechanistic hypothesis to account for this-the 'rate of mitosis' hypothesis. This hypothesis has the potential to explain many disparate observations about rates of molecular evolution across the tree of life. Our results have implications for understanding the evolutionary history and future of plant lineages in a changing world.

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“…These include studies that addressed the impact of including incomplete taxa, the impact of incomplete characters, and the impacts of missing data on branch-length estimation and support values (e.g. Wiens, 2003Wiens, , 2005Driskell et al, 2004;Philippe et al, 2004;Wiens and Moen, 2008;Burleigh et al, 2009;Lemmon et al, 2009;Sanderson et al, 2010Sanderson et al, , 2011Cho et al, 2011;Pyron et al, 2011;Wiens and Morrill, 2011;Crawley and Hilu, 2012;Simmons, 2012Simmons, , 2014Wiens and Tiu, 2012;Hovmöller et al, 2013;Roure et al, 2013;Jiang et al, 2014). However, an important and largely unresolved question is how missing data impact divergence-time estimation.…”

Section: Introductionmentioning

confidence: 99%

Do missing data influence the accuracy of divergence-time estimation with BEAST?

Wiens

2015

Molecular Phylogenetics and Evolution

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Inferring phylogenies with incomplete data sets: a 5-gene, 567-taxon analysis of angiosperms

Cited by 75 publications

References 61 publications

Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots

Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots

Taller plants have lower rates of molecular evolution

Do missing data influence the accuracy of divergence-time estimation with BEAST?

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