A New Lineage‐Based Tribal Classification of the Family Caryophyllaceae
21 Dec 2010-International Journal of Plant Sciences (The University of Chicago Press)-Vol. 171, Iss: 2, pp 185-198
TL;DR: The phylogenies reveal that the closest relatives to Schiedea are a pair of widespread, largely Arctic taxa, Honckenya peploides and Wilhelmsia physodes, and are not reflective of natural groups; this study proposes abandoning this classification in favor of a new system that recognizes major lineages of the molecular phylogeny at the tribal level.
Abstract: Understanding the relationships within the Caryophyllaceae has been difficult, in part because of arbitrarily and poorly defined genera and difficulty in determining phylogenetically useful morphological characters. This study represents the most complete phylogenetic analysis of the family to date, with particular focus on the genera and relationships within the large subfamily Alsinoideae, using molecular characters to examine the monophyly of taxa and the validity of the current taxonomy as well as to resolve the obscure origins of divergent taxa such as the endemic Hawaiian Schiedea. Maximum parsimony and maximum likelihood analyses of three chloroplast gene regions (matK, trnL‐F, and rps16) from 81 newly sampled and 65 GenBank specimens reveal that several tribes and genera, especially within the Alsinoideae, are not monophyletic. Large genera such as Arenaria and Minuartia are polyphyletic, as are several smaller genera. The phylogenies reveal that the closest relatives to Schiedea are a pair of wid...
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University of Florida1, Brown University2, Florida Museum of Natural History3, National Museum of Natural History4, University of Idaho5, University of Cambridge6, University of Washington7, University of Wisconsin-Madison8, Oberlin College9, Eastern Illinois University10, University of New Orleans11, Virginia Tech12, Harvard University13, University of Michigan14, University of Arizona15, Yale University16
TL;DR: It is confirmed that with large amounts of sequence data, most deep-level relationships within the angiosperms can be resolved and will be of broad utility for many areas of biology, including physiology, ecology, paleobiology, and genomics.
Abstract: PREMISE OF THE STUDY Recent analyses employing up to five genes have provided numerous insights into angiosperm phylogeny, but many relationships have remained unresolved or poorly supported. In the hope of improving our understanding of angiosperm phylogeny, we expanded sampling of taxa and genes beyond previous analyses. METHODS We conducted two primary analyses based on 640 species representing 330 families. The first included 25260 aligned base pairs (bp) from 17 genes (representing all three plant genomes, i.e., nucleus, plastid, and mitochondrion). The second included 19846 aligned bp from 13 genes (representing only the nucleus and plastid). KEY RESULTS Many important questions of deep-level relationships in the nonmonocot angiosperms have now been resolved with strong support. Amborellaceae, Nymphaeales, and Austrobaileyales are successive sisters to the remaining angiosperms (Mesangiospermae), which are resolved into Chloranthales + Magnoliidae as sister to Monocotyledoneae + [Ceratophyllaceae + Eudicotyledoneae]. Eudicotyledoneae contains a basal grade subtending Gunneridae. Within Gunneridae, Gunnerales are sister to the remainder (Pentapetalae), which comprises (1) Superrosidae, consisting of Rosidae (including Vitaceae) and Saxifragales; and (2) Superasteridae, comprising Berberidopsidales, Santalales, Caryophyllales, Asteridae, and, based on this study, Dilleniaceae (although other recent analyses disagree with this placement). Within the major subclades of Pentapetalae, most deep-level relationships are resolved with strong support. CONCLUSIONS Our analyses confirm that with large amounts of sequence data, most deep-level relationships within the angiosperms can be resolved. We anticipate that this well-resolved angiosperm tree will be of broad utility for many areas of biology, including physiology, ecology, paleobiology, and genomics.
606 citations
TL;DR: This paper reviews some exciting new insights into the role of ecology in speciation in plants, focusing on the angiosperms and the role and limits of adaptive radiation.
Abstract: Ecology affects each of the three principal processes leading to speciation: genetic differentiation among populations within species, acquisition of reproductive isolation among populations, and the rise of ecological differentiation among such populations, allowing them to coexist. Until recently, however, the ties between ecology and speciation in plants have received relatively little attention. This paper reviews some exciting new insights into the role of ecology in speciation, focusing on the angiosperms. I consider five main topics, including (1) the determinants of the spatial scale of genetic differentiation within species ; (2) the role and limits of adaptive radiation in increasing net rates of plant diversification; (3) the potential role of ecological speciation; (4) the contributions of hybridization to speciation, adaptive radiation, and the ecological breadth of clades; and (5) the ecological determinants of net diversification rate for individual lineages, and of the species richness for regional floras. Limited dispersal, especially of seeds, favors genetic differentiation at small spatial scales and is likely to foster rapid speciation and narrow endemism. Meta-analyses show that the minimum area required for in situ speciation on islands increases with the spatial scale of gene flow in various organisms. In angiosperms, fleshy fruits dispersed by vertebrates often increase the distance over which seeds are dispersed, but can decrease it in forest understories. Nutrient-poor soils should work against the evolution of fleshy fruits and promote speciation and narrow endemism. Selection for adaptation to different conditions drives adaptive radiation, the rise of a diversity of ecological roles and attendant adaptations within a lineage. On islands, adaptive radiation often leads to woodiness, monocarpy, developmental heterophylly, and sexual dimorphism, as well as differences in habitat, growth form, and floral morphology. Adaptive radiation appears to accelerate speciation in only some plant clades. Extensive radiation in some lineages has been ascribed to early colonization, large amounts of heritable genetic variation, "genetic lines of least resistance" upon which selection could act, absence of potential competitors, and possession of "key innovations" that provide access to novel resources. To these should be added large island area, organismal abundance, saturation of ecological space, and the synergism action of limited dispersal and divergent selection producing parallel radiations in isolated regions. Data for Hawaiian lobeliads suggest that within-island species richness of Cyanea-involving divergence in elevation and flower tube length-saturates within 0.6 and 1.5 Ma. Adaptive radiation in pollinators is an important mechanism of ecological speciation: adaptation to different pollinators leads to pollinator partitioning and reproductive isolation. Selection for longer nectar spurs and pollinator mouth parts led to increased speciation in Aquilegia and other groups. A similar process may work once tubular flowers evolve from cup-shaped blossoms. Selection for floral divergence may be limited in forest understories illuminated by dim, greenish light, which may account for the predominance of small, visually inconspicuous flowers in temperate and tropical understory species. Hybridization can stimulate speciation by forming transgressive phenotypes that exceed the range seen in parental taxa, and by introgressing adaptive gene combinations. The likelihood of transgressive phenotypes increases with the genetic divergence between parental taxa, so speciation via transgressive hybridization may be most likely among taxa with intermediate amounts of divergence. Several large adaptive radiations appear to have occurred after hybridization, suggesting a special role for the extensive amount of genetic variation that can be supplied and refreshed by syngameons. Rates of net species diversification are greater in herbs (especially annuals) vs. woody plants; in animal- vs. wind-pollinated species; in plants with poorly dispersed seeds; in families with a greater diversity of growth forms, pollination and seed dispersal mechanisms, and species distributions; in families at lower latitudes; in families with higher rates of genetic evolution; in hermaphroditic or monoecious vs. dioecious clades; in earlier-maturing woody plants; in plants with bilateral vs. radial flowers; in plants with hummingbird-pollinated flowers; in epiphytic vs. terrestrial bromeliads and orchids; in bromeliads differentiating along geographically extensive cordilleras; and in young vs. old clades. Evidence for the last pattern may, however, be an artifact of (auto)regressing (In N) / t vs. t. High rates of diversification in epiphytic orchids are tied to small effective population sizes, suggesting a role for intermittent genetic drift alternating with strong selection on floral traits. Across angiosperms, a massive increase in diversification rates was preceded by a major increase in leaf vein density and hydraulic conductance between 140 and 110 Ma ago, leading to higher photosynthetic rates than coexisting ferns and gymnosperms. Based on the economic theory of plant defense, this should have led to lower allocation to anti-herbivore defenses, selecting for low-cost qualitative toxins ratherthan all-purpose but highly expensive qualitative defenses, triggering an arms' race between angiosperm and their herbivores. Finally, regional plant species richness increases with regional area and proxies for latitude, rainfall, topographic heterogeneity, and vegetation stratification. The Cape Floristic Province has roughly twice as many species as expected from its area and environmental conditions, most likely reflecting the predominance of short-distance dispersal associated with poor soils and myrmecochory in the Cape Province, as well as low rates of regeneration and competitive exclusion following fire.
251 citations
TL;DR: A taxonomic backbone at the genus level is provided that reflects the current state of knowledge and accepts 749 genera for the Caryophyllales, a major lineage of flowering plants with approximately 12500 species in 39 families.
Abstract: The Caryophyllales constitute a major lineage of flowering plants with approximately 12500 species in 39 families. A taxonomic backbone at the genus level is provided that reflects the current state of knowledge and accepts 749 genera for the order. A detailed review of the literature of the past two decades shows that enormous progress has been made in understanding overall phylogenetic relationships in Caryophyllales. The process of re-circumscribing families in order to be monophyletic appears to be largely complete and has led to the recognition of eight new families (Anacampserotaceae, Kewaceae, Limeaceae, Lophiocarpaceae, Macarthuriaceae, Microteaceae, Montiaceae and Talinaceae), while the phylogenetic evaluation of generic concepts is still well underway. As a result of this, the number of genera has increased by more than ten percent in comparison to the last complete treatments in the Families and genera of vascular plants” series. A checklist with all currently accepted genus names in Caryophyllales, as well as nomenclatural references, type names and synonymy is presented. Notes indicate how extensively the respective genera have been studied in a phylogenetic context. The most diverse families at the generic level are Cactaceae and Aizoaceae, but 28 families comprise only one to six genera. This synopsis represents a first step towards the aim of creating a global synthesis of the species diversity in the angiosperm order Caryophyllales integrating the work of numerous specialists around the world.
198 citations
Cites background from "A New Lineage‐Based Tribal Classifi..."
...– Phytokeys 50: 35 – 42. rabeler r. k., Wagner W. L. & Hartman r. L. 2014: Are naria and Minuartia (Caryophyllaceae): an update since Harbaugh et al. (2010)....
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TL;DR: The aim of the present study was to infer a substantially larger, more evenly sampled, phylogenetic tree for Caryophyllaceae in order to more confidently resolve relationships within this clade, and to propose the name Plurcaryphyllaceae for thisClade and provide a phylogenetic definition.
Abstract: The aim of the present study was to infer a substantially larger, more evenly sampled, phylogenetic tree for Caryophyllaceae in order to more confidently resolve relationships within this clade. This would allow us to evaluate previous classification schemes and to infer the evolution of a number of characters that have figured prominently in higher-level taxonomic treatments. We have inferred a 630-tip phylogeny (ca. 30% of the 2200 species) using maximum likelihood analyses of data from the nuclear ribosomal ITS region and five chloroplast genes and intergenic spacers: matK, ndhF, trnL-trnF, trnQ-rps16, and trnS-trnfM. Our results confirm that subfamily Paronychioideae is paraphyletic at the base of Caryophyllaceae. Alsinoideae and Caryophylloideae together form a clade, within which neither subfamily is monophyletic. With only a few exceptions, our results support the tribal classification presented by Harbaugh & al. (2010). In agreement with other recent studies, it appears that many of the larger genera are not strictly monophyletic. Our results imply that the first Caryophyllaceae had stipules, free sepals, small apetalous flowers with few stamens, and single-seeded indehiscent or irregularly dehiscing utricles. Stipules were lost along the branch to the Alsinoideae-Caryophylloideae clade, and the evolution of a tubular calyx marks Caryophylloideae. The evolution of petals, 10 stamens, and capsule fruits is inferred to have taken place along the branch subtending a clade that includes Sperguleae (mostly containing former members of Paronychioideae) and the remainder of Caryophyllaceae. As this previously unnamed major group is both well-supported in molecular phylogenetic studies and marked by clear-cut apomorphies, we propose the name Plurcaryophyllaceae for this clade and provide a phylogenetic definition.
150 citations
TL;DR: Temperate and boreal North America is a much more important source of Hawaiian flora than suggested by most 20th century authorities on Pacific plant life and molecular phylogenetic evidence for North American ancestry of Hawaiian plant radiations underlines the potential of long-distance dispersal to shape floras.
111 citations
Cites background from "A New Lineage‐Based Tribal Classifi..."
...…as well as North America, the founder of Schiedea appears most likely to have dispersed from North America, where three of the four taxa (subspecies) of Honckenya are restricted and where the most closely related continental relatives of Honckenya and Wilhelmsia are endemic (Harbaugh et al., 2010)....
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...Extensive molecular phylogenetic sampling across Alsinoideae by Wagner et al. (2005b) and Harbaugh et al. (2010) led to the discovery that Schiedea is sister to two monotypic genera, Honckenya and Wilhelmsia (Fig....
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...…chain immediately prior to formation of the oldest, modern high-elevation island, Kaua‘i. Key words: Angiosperms, adaptive radiation, disjunctions, flora, island biogeography, long-distance dispersal, ecological opportunity, Hawaiian Islands, North America, Pacific, phytogeography, sky islands....
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...The most diverse lineage of Hawaiian Caryophyllaceae also appears to have probably descended from a North American founder, based on recent molecular results (Wagner et al., 2005b; Harbaugh et al., 2010)....
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18,553 citations
"A New Lineage‐Based Tribal Classifi..." refers methods in this paper
...All MP analyses were performed in PAUP* 4.0b10 (Swofford 2002)....
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...Sequences were aligned manually by eye in PAUP* 4.0b10 (Swofford 2002)....
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TL;DR: This work developed, implemented, and thoroughly tested rapid bootstrap heuristics in RAxML (Randomized Axelerated Maximum Likelihood) that are more than an order of magnitude faster than current algorithms and can contribute to resolving the computational bottleneck and improve current methodology in phylogenetic analyses.
Abstract: Despite recent advances achieved by application of high-performance computing methods and novel algorithmic techniques to maximum likelihood (ML)-based inference programs, the major computational bottleneck still consists in the computation of bootstrap support values. Conducting a probably insufficient number of 100 bootstrap (BS) analyses with current ML programs on large datasets—either with respect to the number of taxa or base pairs—can easily require a month of run time. Therefore, we have developed, implemented, and thoroughly tested rapid bootstrap heuristics in RAxML (Randomized Axelerated Maximum Likelihood) that are more than an order of magnitude faster than current algorithms. These new heuristics can contribute to resolving the computational bottleneck and improve current methodology in phylogenetic analyses. Computational experiments to assess the performance and relative accuracy of these heuristics were conducted on 22 diverse DNA and AA (amino acid), single gene as well as multigene, real-world alignments containing 125 up to 7764 sequences. The standard BS (SBS) and rapid BS (RBS) values drawn on the best-scoring ML tree are highly correlated and show almost identical average support values. The weighted RF (Robinson-Foulds) distance between SBS- and RBS-based consensus trees was smaller than 6% in all cases (average 4%). More importantly, RBS inferences are between 8 and 20 times faster (average 14.73) than SBS analyses with RAxML and between 18 and 495 times faster than BS analyses with competing programs, such as PHYML or GARLI. Moreover, this performance improvement increases with alignment size. Finally, we have set up two freely accessible Web servers for this significantly improved version of RAxML that provide access to the 200-CPU cluster of the Vital-IT unit at the Swiss Institute of Bioinformatics and the 128-CPU cluster of the CIPRES project at the San Diego Supercomputer Center. These Web servers offer the possibility to conduct large-scale phylogenetic inferences to a large part of the community that does not have access to, or the expertise to use, high-performance computing resources. (Maximum likelihood; phylogenetic inference; rapid bootstrap; RAxML; support values.)
6,585 citations
"A New Lineage‐Based Tribal Classifi..." refers methods in this paper
...…performed for all three chloroplast regions separately and combined with the Webbased program RAxML (Stamatakis et al. 2005) using the GTR model with 1000 bootstrap replicates (Stamatakis et al. 2008); they were performed at least twice for each data set to ensure the stability of the topology....
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TL;DR: Six primers for the amplification of three non-coding regions of chloroplast DNA via the polymerase chain reaction (PCR) have been designed and worked for most species tested, which means that they may be used to study the population biology and evolution of plants.
Abstract: Six primers for the amplification of three non-coding regions of chloroplast DNA via the polymerase chain reaction (PCR) have been designed. In order to find out whether these primers were universal, we used them in an attempt to amplify DNA from various plant species. The primers worked for most species tested including algae, bryophytes, pteridophytes, gymnosperms and angiosperms. The fact that they amplify chloroplast DNA non-coding regions over a wide taxonomic range means that these primers may be used to study the population biology (in supplying markers) and evolution (inter- and probably intraspecific phylogenies) of plants.
5,212 citations
01 Jan 1998
3,650 citations