Diversification of land plants: insights from a family-level phylogenetic analysis

<p>Abstract</p> <p>Background</p> <p>Some of the evolutionary history of land plants has been documented based on the fossil record and a few broad-scale phylogenetic analyses, especially focusing on angiosperms and ferns. Here, we reconstructed phylogenetic relationships among all 706 families of land plants using molecular data. We dated the phylogeny using multiple fossils and a molecular clock technique. Applying various tests of diversification that take into account topology, branch length, numbers of extant species as well as extinction, we evaluated diversification rates through time. We also compared these diversification profiles against the distribution of the climate modes of the Phanerozoic.</p> <p>Results</p> <p>We found evidence for the radiations of ferns and mosses in the shadow of angiosperms coinciding with the rather warm Cretaceous global climate. In contrast, gymnosperms and liverworts show a signature of declining diversification rates during geological time periods of cool global climate.</p> <p>Conclusions</p> <p>This broad-scale phylogenetic analysis helps to reveal the successive waves of diversification that made up the diversity of land plants we see today. Both warm temperatures and wet climate may have been necessary for the rise of the diversity under a successive lineage replacement scenario.</p

Reconsidering the generation time hypothesis based on nuclear ribosomal ITS sequence comparisons in annual and perennial angiosperms

17 pages, 3 figures, 5 tables.-- PMID: 19113991 [PubMed].[Background] Differences in plant annual/perennial habit are hypothesized to cause a generation time effect on divergence rates. Previous studies that compared rates of divergence for internal transcribed spacer (ITS1 and ITS2) sequences of nuclear ribosomal DNA (nrDNA) in angiosperms have reached contradictory conclusions about whether differences in generation times (or other life history features) are associated with divergence rate heterogeneity. We compared annual/perennial ITS divergence rates using published sequence data, employing sampling criteria to control for possible artifacts that might obscure any actual rate variation caused by annual/perennial differences.[Results] Relative rate tests employing ITS sequences from 16 phylogenetically-independent annual/perennial species pairs rejected rate homogeneity in only a few comparisons, with annuals more frequently exhibiting faster substitution rates. Treating branch length differences categorically (annual faster or perennial faster regardless of magnitude) with a sign test often indicated an excess of annuals with faster substitution rates. Annuals showed an approximately 1.6-fold rate acceleration in nucleotide substitution models for ITS. Relative rates of three nuclear loci and two chloroplast regions for the annual Arabidopsis thaliana compared with two closely related Arabidopsis perennials indicated that divergence was faster for the annual. In contrast, A. thaliana ITS divergence rates were sometimes faster and sometimes slower than the perennial. In simulations, divergence rate differences of at least 3.5-fold were required to reject rate constancy in > 80 % of replicates using a nucleotide substitution model observed for the combination of ITS1 and ITS2. Simulations also showed that categorical treatment of branch length differences detected rate heterogeneity > 80% of the time with a 1.5-fold or greater rate difference.[Conclusion] Although rate homogeneity was not rejected in many comparisons, in cases of significant rate heterogeneity annuals frequently exhibited faster substitution rates. Our results suggest that annual taxa may exhibit a less than 2-fold rate acceleration at ITS. Since the rate difference is small and ITS lacks statistical power to reject rate homogeneity, further studies with greater power will be required to adequately test the hypothesis that annual and perennial plants have heterogeneous substitution rates. Arabidopsis sequence data suggest that relative rate tests based on multiple loci may be able to distinguish a weak acceleration in annual plants. The failure to detect rate heterogeneity with ITS in past studies may be largely a product of low statistical power.This work was supported by a doctoral fellowship to D. F. Soria-Hernanz from the Spanish Ministerio de Educación y Ciencia, graduate support from Georgetown University and the Department of Biology, the Cosmos Foundation, and a National Science Foundation grant to M.B.H. (DEB9983014). Publication charges supported by the Department of Biology, Georgetown University.Peer reviewe

Sistemática y evolución de la familia geraniaceae. Relaciones filogenéticas del género Erodium

Tesis Doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Biología. Fecha de lectura: 14-09-200

A new concept for Dictyostelium sphaerocephalum based on morphology and phylogenetic analysis of nuclear ribosomal internal transcribed spacer region sequences

Three dictyostelid isolates were found in Spain and Argentina that are morphologically different from known species. These isolates have some features similar to Dictyostelium sphaerocephalum (Oudem.) Sacc., Marchal & E´ .J. Marchal, but differ in size and sorocarp branching pattern. We sequenced the nuclear ribosomal internal transcribed spacer region to explore phylogenetic relationships among this group of species, including the three new isolates and their closest relatives. In all phylogenetic analyses performed, sequences of all three isolates group together with sequences from ‘‘typical’’ D. sphaerocephalum samples. This result supports previous observations of the morphological plasticity in dictyostelids, especially D. sphaerocephalum, leading us to broaden the classical concept of this species.Les auteurs ont re´colte´ trois isolats de dictyoste´lides, en Espagne et en Argentine, lesquels diffe`rent morphologiquement des espe`ces connues. Ces isolats ressemblent pour certains caracte`res au Dictyostelium sphaerocephalum (Oudem.) Sacc., Marchal & E´ .J. Marchal, mais en diffe`rent par la dimension et le patron de ramification des sorocarpes. Afin d’explorer les relations phyloge´ne´tiques parmi ce groupe d’espe`ces, les auteurs ont se´quence´ la re´gion de l’ITS ribosomique nucle´ique, incluant les trois nouveaux isolats et leurs plus proches parents. Ce resultat toutes les analyses phyloge ´ne´tiques re´alise´es, les trois isolats montrent des se´quences ‘typiques’ d’e´chantillons du D. sphaerocephalum. Cette re´sulte supporte les observations ante´ce´dentes sur la plasticite´ des dictyoste´lides, surtout du D. sphaerocephalum, et conduit les auteurs a` e´largir le concept classique de cette espe`ce.Ministry of Education and Science of Spain,Peer reviewe

Dating the origin of the genus Flavivirus in the light of Beringian biogeography

The genus Flavivirus includes some of the most important human viral pathogens, and itsmembers are found in all parts of the populated world. The temporal origin of diversification of thegenus has long been debated due to the inherent problems with dating deep RNA virus evolution.A generally accepted hypothesis suggests that Flavivirus emerged within the last 10 000 years.However, it has been argued that the tick-borne Powassan flavivirus was introduced into NorthAmerica some time between the opening and closing of the Beringian land bridge that connectedAsia and North America 15 000–11 000 years ago, indicating an even older origin for Flavivirus.To determine the temporal origin of Flavivirus, we performed Bayesian relaxed molecular clockdating on a dataset with high coverage of the presently available Flavivirus diversity by combiningtip date calibrations and internal node calibration, based on the Powassan virus and Beringianland bridge biogeographical event. Our analysis suggested that Flavivirus originated ~85 000(64 000–110 000) or 120 000 (87 000–159 000) years ago, depending on the circumscriptionof the genus. This is significantly older than estimated previously. In light of our results, wepropose that it is likely that modern humans came in contact with several members of the genusFlavivirus much earlier than suggested previously, and that it is possible that the spread of severalflaviviruses coincided with, and was facilitated by, the migration and population expansion ofmodern humans out of Africa

Taxonomic Revision of Geranium sect. Dissecta (Geraniaceae)

[EN] Geranium section Dissecta (Geraniaceae) consists of four species centered in Eurasia, between the Mediterranean region and the Himalaya Mountains. In contrast to the current literature, we consider G. chelikii, and G. davisianum to be synonyms of G. sintenisii, and G. pallens to be a synonym of G. asphodeloides. We also accept G. dissectum and G. crenophilum, the latter sometimes considered as subspecies of G. asphodeloides. A multivariate morphometric study showed that some quantitative characters such as deeply divided leaves, shorter and narrower petals, and shorter filaments clearly distinguished the annual G. dissectum. The characters contributing most to separation of the three remaining perennial species were petal width and the length of glandular hairs of stem and pedicels. In G. asphodeloides and G. dissectum the rootstock and stem base has a very starch-rich parenchyma in the cortex, while in G. sintenisii and G. crenophilum the starch-rich parenchyma is mainly developed in the pith. A new key is provided, as well as new and detailed descriptions. Geranium crenophilum and G. sintenisii are here illustrated for the first time. Nine lectotypes and a neotype are designated, and distribution maps are presented. Analyses of the plastid trnL-trnF spacer, nuclear ITS sequences, and morphological data reveal that sect. Dissecta is strongly supported as monophyletic. In these analyses G. dissectum appeared as sister group to the rest of the species.[ES] Geranium sección Dissecta (Geraniaceae) está formada por cuatro especies cuya área principal es eurasiática, entre la región Mediterránea y las montañas del Himalaya. En este estudio consideramos G. chelikii y G. davisianum como sinónimos de G. sintenisii y G. pallens como sinónimo de G. asphodeloides. Además, aceptamos G. dissectum y G. crenophilum, este último considerado a veces como subespecie de G. asphodeloides. Un análisis morfométrico mostró que los caracteres cuantitativos más importantes para diferenciar G. dissectum son sus hojas profundamente divididas, sus cortos y estrechos pétalos y sus cortos filamentos estaminales. Los principales caracteres cuantitativos que separan las especies perennes son la anchura de los pétalos y la longitud de los pelos glandulíferos de tallo y pedicelos. El rizoma y la base del tallo de G.asphodeloides y G. dissectum se caracterizan por un parénquima con células ricas en almidón situado en el cortex, mientras que, en G. sintenisii y G. crenophilum, dicho pare´nquima se localiza principalmente en médula. Se presenta una nueva clave, así como nuevas y detalladas descripciones y mapas de distribucio´n para cada una de las especies y se eligen nueve lectotipos y un neo´tipo. Geranium crenophilum y G. sintenisii, son aquı´ dibujados por primera vez. Tanto el ana´lisis cladı´stico de los caracteres morfolo´gicos, como el de las secuencias de ADN de un marcador cloroplástico (trnL-trnF) y uno nuclear (ITS) indican que la monofilia de la sect. Dissecta está fuertemente apoyada. En estos ana´lisis G. dissectum aparece como grupo hermano de las restantes especies.Peer reviewe

Phylogeny and Historical Biogeography of Geraniaceae in Relation to Climate Changes and Pollination Ecology

Chloroplast (trnL–F and rbcL) sequences were used to reconstruct the phylogeny of Geraniaceae and Hypseocharitaceae. According to these data Hypseocharitaceae and Geraniaceae are monophyletic. Pelargonium and Monsonia are sisters to the largest clade of Geraniaceae, formed by Geranium, Erodium and California. According to molecular dating and dispersal-vicariance analysis, the split of the stem branches of Geraniaceae probably occurred during the Oligocene, in southern Africa or in southern Africa plus the Mediterranean area. However, their diversification occurred during the Miocene, coinciding with the beginning of major aridification events in their distribution areas. An ancestor of the largest clade of Geraniaceae (Geranium, Erodium, and California) colonised a number of habitats in the northern hemisphere and in South American mountain ranges. In summary, the evolution of the Geraniaceae is marked by the dispersal of ancestors from Southern Africa to cold, temperate and often disturbed habitats in the rest of world, where only generalist pollination and facultative autogamy could ensure sufficient seed production and survival.This work was partly financed by the Spanish Dirección General de Investigación Científica y Técnica (DGICYT) through the research project REN2000-0818/GLO and REN2003-04397/GLO.Peer reviewe

Old Lineages in a New Ecosystem : Diversification of Arcellinid Amoebae (Amoebozoa) and Peatland Mosses

Arcellinid testate amoebae (Amoebozoa) form a group of free-living microbial eukaryotes with one of the oldest fossil records known, yet several aspects of their evolutionary history remain poorly understood. Arcellinids occur in a range of terrestrial, freshwater and even brackish habitats; however, many arcellinid morphospecies such as Hyalosphenia papilio are particularly abundant in Sphagnum-dominated peatlands, a relatively new ecosystem that appeared during the diversification of Sphagnum species in the Miocene (5-20 Myr ago). Here, we reconstruct divergence times in arcellinid testate amoebae after selecting several fossils for clock calibrations and then infer whether or not arcellinids followed a pattern of diversification that parallels the pattern described for Sphagnum. We found that the diversification of core arcellinids occurred during the Phanerozoic, which is congruent with most arcellinid fossils but not with the oldest known amoebozoan fossil (i.e. at ca. 662 or ca. 750 Myr). Overall, Sphagnum and the Hyalospheniidae exhibit different patterns of diversification. However, an extensive molecular phylogenetic analysis of distinct clades within H. papilio species complex demonstrated a correlation between the recent diversification of H. papilio, the recent diversification of Sphagnum mosses, and the establishment of peatlands