Anchored phylogenomics improves the resolution of evolutionary relationships in the rapid radiation of<i>Protea</i>L.

Mitchell, Nora; Lewis, Paul O.; Lemmon, Emily Moriarty; Lemmon, Alan R.; Holsinger, Kent E.

doi:10.3732/ajb.1600227

Cited by 78 publications

(67 citation statements)

References 68 publications

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“…The application of the NGS techniques has enabled access to large amounts of data and has helped resolve the basal polytomies in certain groups of organisms where traditional Sanger approaches using analyses of multiple‐genes failed (e.g., Graminoids, Leseber & Duvall, ; Rhinoceroses, Willerslev et al, ; Pentapetaleae, Moore et al, ; Paserida, Nabholz et al, ; Neoaves, Pacheco et al, ; Malpighiales, Xi et al, ; Commelinids, Barrett et al, ; Guenons, Guschanski et al, ; Zingiberales, Barrett et al, , Sass et al, ; Ipomeeae, Eserman et al, ; Arundinarieae, Ma et al, ; Apocynaceae, Straub et al, ; Asteraceae, Mandel et al, ; Goodeniaceae, Gardner et al, ; Columbiforms, Soares et al, ; Vitales, Zhang et al, , Wen et al, ; Eupolypod II Ferns, Wei et al, ; Hippeastreae, García et al, ; Protea , Mitchell et al, ). Most of these studies concluded in favor of the radiation hypothesis, since the NGS analysis of complete chloroplast genomes and large nuclear data sets yielded short deep branches (Leseber & Duvall, ; Moore et al, ; Nabholz et al, ; Xi et al, ; Guschanski et al, ; Straub et al, ; Mandel et al, ; Gardner et al, ; Sass et al, ; Soares et al, ; Zhang et al, ; García et al, ; Mitchell et al, ) or non‐fully resolved trees (Willerslev et al, ; Barrett et al, , ; Ma et al, ; Wei et al, ). A previous phylogenetic study based on seven DNA regions proposed a burst of diversification for the origin of the Asian Palmate group (Valcárcel et al, ).…”

Section: Discussionmentioning

confidence: 99%

Chloroplast phylogenomic data support Eocene amphi‐Pacific early radiation for the Asian Palmate core Araliaceae

Valcárcel

Wen

2019

J of Sytematics Evolution

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Traditional phylogenies based on analysis of multiple genes have failed to obtain a well‐resolved evolutionary history for the backbone of the Asian Palmate group of Araliaceae, the largest clade of the family. In this study, we applied the genome skimming approach of next‐generation sequencing to address whether the lack of resolution at the base of the Asian Palmate tree is due to molecular sampling error or the footprint of ancient radiation. Twenty‐nine complete plastid genomes of Araliaceae (17 newly sequenced) were analyzed (RAxML, Beast, Lagrange, and BioGeoBears) to provide the first phylogenomic reconstruction of the group (95% of genera included). As a result, the early divergences of the Asian Palmate group have been clarified but the backbone of its core is not totally resolved, with short internal branches pointing to an ancient radiation scenario. East Asia is inferred as the most likely ancestral area for the Asian Palmate group (from late Paleocene to Eocene) from which early colonization of the Neotropics is inferred during the Eocene. The radiation of the core Palmate group took place during the late Eocene, most likely in the context of the Boreotropical hypothesis. Recurrent episodes of southward migration (to the tropics) coupled with northern latitude local extinctions (promoting geographic isolation of lineages) followed by northward expansion (promoting contact of lineages that erased the trace of preceding geographic isolation) are hypothesized to have linked to the alternation of the cold and warm periods of the Eocene.

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Section: Discussionmentioning

confidence: 99%

Chloroplast phylogenomic data support Eocene amphi‐Pacific early radiation for the Asian Palmate core Araliaceae

Valcárcel

Wen

2019

J of Sytematics Evolution

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“…It is often difficult to estimate phylogenetic relationships in rapid radiations (Knowles & Chan, ). In earlier work, we used an anchored phylogenomics approach (Lemmon, Emme, & Lemmon, ) to sequence almost 500 nuclear genes conserved across all angiosperms (Buddenhagen et al., In Review) and built a robust and highly resolved phylogeny for 59 Protea species (Mitchell, Lewis, Moriarty Lemmon, Lemmon, & Holsinger, ; Buddenhagen et al. In Review).…”

Section: Methodsmentioning

confidence: 99%

“…To ensure that our results are robust in the face of both phylogenetic and trait/climate uncertainty, we compared results of analyses using the “best” tree from the program ASTRAL‐II (Figure ; Mirarab & Warnow, ) or 100 bootstrap replicates from the ASTRAL‐II analysis of Mitchell et al. () with either the posterior mean of the trait/climate distribution or 100 random samples from the HPD distribution. We thus have a two‐by‐two table comparing one measure (mean trait on the best tree), 100 measures (mean trait on 100 bootstrap trees; 100 observations of traits on best tree), or 10,000 measures (100 observations of traits on 100 bootstrap trees).…”

Section: Methodsmentioning

confidence: 99%

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Correlated evolution between climate and suites of traits along a fast–slow continuum in the radiation ofProtea

Mitchell

Carlson

Holsinger

2018

Ecology and Evolution

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Evolutionary radiations are responsible for much of Earth's diversity, yet the causes of these radiations are often elusive. Determining the relative roles of adaptation and geographic isolation in diversification is vital to understanding the causes of any radiation, and whether a radiation may be labeled as “adaptive” or not. Across many groups of plants, trait–climate relationships suggest that traits are an important indicator of how plants adapt to different climates. In particular, analyses of plant functional traits in global databases suggest that there is an “economics spectrum” along which combinations of functional traits covary along a fast–slow continuum. We examine evolutionary associations among traits and between trait and climate variables on a strongly supported phylogeny in the iconic plant genus Protea to identify correlated evolution of functional traits and the climatic‐niches that species occupy. Results indicate that trait diversification in Protea has climate associations along two axes of variation: correlated evolution of plant size with temperature and leaf investment with rainfall. Evidence suggests that traits and climatic‐niches evolve in similar ways, although some of these associations are inconsistent with global patterns on a broader phylogenetic scale. When combined with previous experimental work suggesting that trait–climate associations are adaptive in Protea, the results presented here suggest that trait diversification in this radiation is adaptive.

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“…A well‐resolved phylogeny is essential for understanding the evolution and biogeography of maples in the world and has been made possible by the development of anchored phylogenomics (Lemmon et al, ) that enabled orthologous data to be collected efficiently across broad taxonomic groups. The DNA sequence data from multiple nuclear loci have been used successfully in constructing solid phylogenetic frameworks for large plant genera (Buddenhagen et al, ; Mitchell et al, ; Wanke et al, ). Therefore, the main objectives of the study were to generate a robust phylogeny of Acer for the first time using the anchored phylogenomics data and to explore implications of the well‐resolved phylogeny for the previous biogeographic hypotheses.…”

Section: Introductionmentioning

confidence: 99%

Maple phylogeny and biogeography inferred from phylogenomic data

Stukel

Bussies

et al. 2019

J of Sytematics Evolution

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Acer (the maple genus) is one of the diverse tree genera in the Northern Hemisphere with about 152 species, most of which are in eastern Asia. There are roughly a dozen species in Europe/western Asia and a dozen in North America. Several phylogenetic studies of Acer have been conducted since 1998, but none have provided a satisfactory resolution for basal relationships among sections of Acer. Here we report the first well‐resolved phylogeny of Acer based on DNA sequences of over 500 nuclear loci generated using the anchored hybrid enrichment method and explore the implications of the robust phylogeny for Acer systematics and biogeography. Our phylogenetic results support the most recent taxonomic treatment of Acer by de Jong with some modifications; section Pentaphylla may be expanded to include section Trifoliata, and A. yangbiense may be included in section Lithocarpa. Sections Spicata, Negundo, Arguta, and Palmata form a clade sister to the rest of the genus where sections Glabra and Parviflora comprise the first clade followed by section Macrantha, sections Ginnala, Lithocarpa, Indivisa, sections Platanoidea and Macrophylla, section Rubra, section Acer, and section Pentaphylla. Monotypic sections Glabra and Macrophylla in North America are sister to the Japanese section Parviflora and Eurasian section Platanoidea, respectively. Ancestral area inferences using statistical dispersal and vicariance analysis (S‐DIVA) and dispersal and extinction cladogenesis (DEC) methods suggest that Asia might be the most likely ancestral area of Acer as proposed by Wolfe and Tanai and molecular dating using Bayesian evolutionary analysis by sampling trees (BEAST) indicate that section diversifications of Acer might have completed largely in the late Eocene and the intercontinental disjunctions of Acer between eastern Asia and eastern North America formed mostly in the Miocene.

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Anchored phylogenomics improves the resolution of evolutionary relationships in the rapid radiation ofProteaL.

Cited by 78 publications

References 68 publications

Chloroplast phylogenomic data support Eocene amphi‐Pacific early radiation for the Asian Palmate core Araliaceae

Chloroplast phylogenomic data support Eocene amphi‐Pacific early radiation for the Asian Palmate core Araliaceae

Correlated evolution between climate and suites of traits along a fast–slow continuum in the radiation ofProtea

Maple phylogeny and biogeography inferred from phylogenomic data

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