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

Accurate monitoring of the North Atlantic air-sea CO2 flux from a network of voluntary observing ships

Ocean Sciences Meeting, March 2-7, 2008, Orlando, FloridaSince the start of 2005 under the EU’s Carbo-Ocean project, we have participated in co-ordinated observations of sea surface pCO2 and related variables from a network of commercial vessels in the North Atlantic. Typically five vessels are operating at any one time. The observations can be used to reconstruct the sea-surface pCO2 field, and thence estimate air-sea fluxes, with unprecedented resolution and accuracy. Using the observations for the calendar year 2005, we use a variety of geostatistical methods to derive the precision with which regional fluxes can be obtained. The observations are generalized to the entire N Atlantic from 10N to 65N by exploiting relations between surface pCO2, SST and mixed layer depth. Using semi-variograms or an empirical technique of selective data deletion applied to the residuals, we obtain a 1-sigma uncertainty of 6% on the annual flux into the region as a whole. This is very much more precise than has been possible for any comparable region of the world (land or ocean) up to nowN

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2–4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2,3,4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

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

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