A comparison of 16 DNA regions for use as phylogenetic markers in the pleurocarpous moss genus Plagiothecium (Hypnales).

Abstract:

PREMISE OF THE STUDY:Within the Hypnales-the most derived and species-rich order of pleurocarpous mosses - phylogenies at or below the family level often show poor resolution. In preparation for a phylogeny of the genus Plagiothecium, we wished to identify the DNA markers best suited for evolutionary reconstruction in this group of hypnalean pleurocarps. METHODS:For each of 25 collections of Plagiothecium and associated taxa, 16 DNA regions were sequenced: nuclear ITS and 26S, and plastid rps4, rps4-trnL, trnL-F, trnK (matK)-psbA, psbA-trnH, trnM-V, trnD-T, rbcL, atpB-rbcL, psbT-H, rpoC1 exon 2 (partial), the trnG intron, the rpl16 intron and the plastid ribosomal spacer DNA (cpITS). Each region was evaluated on the basis of its ability to resolve clades, the amount of homoplasy present in the data set, and the relative ease of obtaining the data. Descriptive statistics for each region are given. KEY RESULTS:Under-utilized plastid markers for bryophytes such as trnK-psbA, rps4-trnL, and trnD-T outperformed more traditional markers such as trnL-F and rps4. Individual plastid topologies were similar, suggesting that only a limited amount of plastid data are needed to recover a backbone phylogeny. Adding a small amount of nuclear ribosomal data to a large plastid matrix restructured the recovered topology, emphasizing the importance of sampling multiple genomes and the need for new low-copy nuclear markers in bryophyte systematics. CONCLUSIONS:Future genus-level phylogenies of pleurocarpous mosses should target under-utilized plastid markers such as trnK-psbA and rps4-trnL in conjunction with low-copy nuclear markers.

journal_name

Am J Bot

authors

Wynns JT,Lange CB

doi

10.3732/ajb.1300269

subject

Has Abstract

pub_date

2014-04-01 00:00:00

pages

652-69

issue

4

eissn

0002-9122

issn

1537-2197

pii

ajb.1300269

journal_volume

101

pub_type

杂志文章
  • Dynamics of chromosome number and genome size variation in a cytogenetically variable sedge (Carex scoparia var. scoparia, Cyperaceae).

    abstract:PREMISE OF THE STUDY:High intraspecific cytogenetic variation in the sedge genus Carex (Cyperaceae) is hypothesized to be due to the "diffuse" or non-localized centromeres, which facilitate chromosome fission and fusion. If chromosome number changes are dominated by fission and fusion, then chromosome evolution will re...

    journal_title:American journal of botany

    pub_type: 杂志文章

    doi:10.3732/ajb.1000046

    authors: Chung KS,Weber JA,Hipp AL

    更新日期:2011-01-01 00:00:00

  • Ever since Klekowski: testing a set of radical hypotheses revives the genetics of ferns and lycophytes.

    abstract::There have been three periods of significant discovery in the exploration of fern and lycophyte genetics. First, during the 1930s, Andersson-Kottö conducted crossing studies on ferns. The publication of Manton's magnum opus on fern chromosomes in 1950 stimulated the second. The third emerged from Klekowski's 1973 Amer...

    journal_title:American journal of botany

    pub_type: 杂志文章,评审

    doi:10.3732/ajb.1400317

    authors: Haufler CH

    更新日期:2014-12-01 00:00:00

  • Seasonal changes in physiological performance in wild Clarkia xantiana populations: Implications for the evolution of a compressed life cycle and self-fertilization.

    abstract:PREMISE OF THE STUDY:One explanation for the evolution of selfing, the drought escape hypothesis, proposes that self-fertilization may evolve under conditions of intensifying seasonal drought as part of a suite of traits that enable plants to accelerate the completion of their life cycle, thereby escaping late-season d...

    journal_title:American journal of botany

    pub_type: 杂志文章

    doi:10.3732/ajb.1400557

    authors: Dudley LS,Hove AA,Emms SK,Verhoeven AS,Mazer SJ

    更新日期:2015-06-01 00:00:00

  • Spatial genetic structure in four understory Psychotria species (Rubiaceae) and implications for tropical forest diversity.

    abstract::• Premise of the study: Tropical forests are the most species-rich terrestrial communities on Earth, and understory trees and shrubs comprise a large fraction of their plant species diversity, especially at high rainfalls. The mechanisms responsible for generating such high levels of diversity remain unknown. One hypo...

    journal_title:American journal of botany

    pub_type: 杂志文章

    doi:10.3732/ajb.1300460

    authors: Theim TJ,Shirk RY,Givnish TJ

    更新日期:2014-07-01 00:00:00

  • Molecular systematics of the Brassicaceae: evidence from coding plastidic matK and nuclear Chs sequences.

    abstract::Phylogenetic relationships were inferred using nucleotide sequence variation of the nuclear-encoded chalcone synthase gene (Chs) and the chloroplast gene matK for members of five tribes from the family Brassicaceae to analyze tribal and subtribal structures. Phylogenetic trees from individual data sets are mostly in c...

    journal_title:American journal of botany

    pub_type: 杂志文章

    doi:

    authors: Koch M,Haubold B,Mitchell-Olds T

    更新日期:2001-03-01 00:00:00

  • A comparative study of oak (Quercus, Fagaceae) seedling physiology during summer drought in southern California.

    abstract::Natural recruitment of oaks appears to be declining throughout the northern hemisphere. Summer drought poses a potentially important barrier to oak recruitment in southern California. To evaluate this barrier, we grew evergreen Quercus agrifolia and deciduous Q. lobata from seeds near parental trees. We measured water...

    journal_title:American journal of botany

    pub_type: 杂志文章

    doi:10.3732/ajb.0800247

    authors: Mahall BE,Tyler CM,Cole ES,Mata C

    更新日期:2009-04-01 00:00:00

  • Phylogenetic relationships in the cactus family (Cactaceae) based on evidence from trnK/ matK and trnL-trnF sequences.

    abstract::Cacti are a large and diverse group of stem succulents predominantly occurring in warm and arid North and South America. Chloroplast DNA sequences of the trnK intron, including the matK gene, were sequenced for 70 ingroup taxa and two outgroups from the Portulacaceae. In order to improve resolution in three major grou...

    journal_title:American journal of botany

    pub_type: 杂志文章

    doi:10.3732/ajb.89.2.312

    authors: Nyffeler R

    更新日期:2002-02-01 00:00:00

  • Estimation of temperature and precipitation from morphological characters of dicotyledonous leaves.

    abstract::The utility of regression and correspondence models for deducing climate from leaf physiognomy was evaluated by the comparative application of different predictive models to the same three leaf assemblages. Mean annual temperature (MAT), mean annual precipitation (MAP), and growing season precipitation (GSP) were esti...

    journal_title:American journal of botany

    pub_type: 杂志文章

    doi:

    authors: Wiemann MC,Manchester SR,Dilcher DL,Hinojosa LF,Wheeler EA

    更新日期:1998-12-01 00:00:00

  • The age and diversification of terrestrial New World ecosystems through Cretaceous and Cenozoic time.

    abstract::Eight ecosystems that were present in the Cretaceous about 100 Ma (million years ago) in the New World eventually developed into the 12 recognized for the modern Earth. Among the forcing mechanisms that drove biotic change during this interval was a decline in global temperatures toward the end of the Cretaceous, augm...

    journal_title:American journal of botany

    pub_type: 杂志文章,评审

    doi:10.3732/ajb.1000353

    authors: Graham A

    更新日期:2011-03-01 00:00:00

  • Ancient paralogy in the cpDNA trnL-F region in Annonaceae: implications for plant molecular systematics.

    abstract::The plastid trnL-F region has proved useful in molecular phylogenetic studies addressing diverse evolutionary questions from biogeographic history to character evolution in a broad range of plant groups. An important assumption for phylogenetic reconstruction is that data used in combined analyses contain the same phy...

    journal_title:American journal of botany

    pub_type: 杂志文章

    doi:10.3732/ajb.94.6.1003

    authors: Pirie MD,Vargas MP,Botermans M,Bakker FT,Chatrou LW

    更新日期:2007-06-01 00:00:00

  • Bryophyte diaspore bank: a genetic memory? Genetic structure and genetic diversity of surface populations and diaspore bank in the liverwort Mannia fragrans (Aytoniaceae).

    abstract::Propagule banks are assumed to be able to store considerable genetic variability. Bryophyte populations are expected to rely more heavily on stored propagules than those of seed plants due to the vulnerability of the haploid gametophyte. This reliance has important implications for the genetic structure and evolutiona...

    journal_title:American journal of botany

    pub_type: 杂志文章

    doi:10.3732/ajb.2007283

    authors: Hock Z,Szövényi P,Schneller JJ,Tóth Z,Urmi E

    更新日期:2008-05-01 00:00:00

  • Phylogenetic relationships in Disa based on non-coding trnL-trnF chloroplast sequences: evidence of numerous repeat regions.

    abstract::Sequence data from the intron and spacer of the trnL-F chloroplast region elucidate the phylogenetic relationships of the tribe Diseae (Orchidoideae: Orchidaceae). Within Diseae, 41 species of Disa, two of Brownleea, three of Satyrium, and two of Corycium were included, with five species of Habenaria sensu lato (Orchi...

    journal_title:American journal of botany

    pub_type: 杂志文章

    doi:

    authors: Bellstedt DU,Linder HP,Harley EH

    更新日期:2001-11-01 00:00:00

  • Maintenance of sexually dimorphic preadult traits in Marchantia inflexa (Marchantiacae).

    abstract::Marchantia inflexa, a dioecious thallose liverwort, is sexually dimorphic in clonal expansion traits. We used selection analyses to measure the magnitude and direction of selection on clonal fitness to uncover possible mechanisms for the maintenance of preadult sexually dimorphic characters. We planted replicates of g...

    journal_title:American journal of botany

    pub_type: 杂志文章

    doi:10.3732/ajb.89.4.592

    authors: Fuselier L,McLetchie N

    更新日期:2002-04-01 00:00:00

  • Origin of the disjunct tetraploid Cardamine amporitana (Brassicaceae) assessed with nuclear and chloroplast DNA sequence data.

    abstract::Seventy-four nucleotide sequences from the ITS regions of nuclear ribosomal DNA and 76 from the trnL-trnF spacer of chloroplast DNA were used to address the origin of tetraploid Cardamine amporitana, the conspecifity of central Italian and northeastern Spanish populations, and the possible cause for such geographic di...

    journal_title:American journal of botany

    pub_type: 杂志文章

    doi:10.3732/ajb.91.8.1231

    authors: Lihová J,Fuertes Aguilar J,Marhold K,Nieto Feliner G

    更新日期:2004-08-01 00:00:00

  • The influence of herbivory on pre- and postzygotic stages of reproduction following open, self, and outcross pollination.

    abstract:PREMISE OF THE STUDY:Herbivory affects pollination success and reproductive output in plants. However, the different stages in the process from pollination to seed maturation have hardly been investigated within the context of herbivory. Herbivory might affect these stages via its effect on geitonogamous pollination an...

    journal_title:American journal of botany

    pub_type: 杂志文章

    doi:10.3732/ajb.1500291

    authors: Ghyselen C,Bonte D,Brys R

    更新日期:2015-12-01 00:00:00

  • Climatic niche comparison among ploidal levels in the classic autopolyploid system, Galax urceolata.

    abstract:PREMISE OF THE STUDY:Autopolyploidy, or whole-genome duplication within a species, leads to closely related cytotypes in one geographic location. One hypothesized mechanism by which autopolyploids become established is climatic niche divergence from their diploid progenitor. Here we tested this hypothesis in diploid, t...

    journal_title:American journal of botany

    pub_type: 杂志文章

    doi:10.1002/ajb2.1161

    authors: Gaynor ML,Marchant DB,Soltis DE,Soltis PS

    更新日期:2018-10-01 00:00:00

  • Phylogenetic and geographic distribution of nickel hyperaccumulation in neotropical Psychotria.

    abstract:PREMISE:Hyperaccumulation of heavy metals in plants has never been documented from Central America or Mexico. Psychotria grandis, P. costivenia, and P. glomerata (Rubiaceae) have been reported to hyperaccumulate nickel in the Greater Antilles, but they also occur widely across the neotropics. The goals of this research...

    journal_title:American journal of botany

    pub_type: 杂志文章

    doi:10.1002/ajb2.1362

    authors: McCartha GL,Taylor CM,van der Ent A,Echevarria G,Navarrete Gutiérrez DM,Pollard AJ

    更新日期:2019-10-01 00:00:00

  • Genomics: a potential panacea for the perennial problem.

    abstract::Perennial crops represent important fresh and processed food sources worldwide, but advancements in breeding perennials are often impeded due to their very nature. The perennial crops we rely on most for food take several years to reach production maturity and require large spaces to grow, which make breeding new cult...

    journal_title:American journal of botany

    pub_type: 杂志文章

    doi:10.3732/ajb.1400143

    authors: McClure KA,Sawler J,Gardner KM,Money D,Myles S

    更新日期:2014-10-01 00:00:00

  • Related allopolyploids display distinct floral pigment profiles and transgressive pigments.

    abstract:PREMISE OF THE STUDY:Both polyploidy and shifts in floral color have marked angiosperm evolution. Here, we investigate the biochemical basis of the novel and diverse floral phenotypes seen in allopolyploids in Nicotiana (Solanaceae) and examine the extent to which the merging of distinct genomes alters flavonoid pigmen...

    journal_title:American journal of botany

    pub_type: 杂志文章

    doi:10.3732/ajb.1600350

    authors: McCarthy EW,Berardi AE,Smith SD,Litt A

    更新日期:2017-01-01 00:00:00

  • Common garden test of range limits as predicted by a species distribution model in the annual plant Mimulus bicolor.

    abstract:PREMISE OF THE STUDY:Direct tests of a species distribution model (SDM) were used to evaluate the hypothesis that the northern and southern edges of Mimulus bicolor's geographical range are limited by temperature and precipitation. METHODS:Climatic suitability was predicted using an SDM informed only by temperature an...

    journal_title:American journal of botany

    pub_type: 杂志文章

    doi:10.3732/ajb.1600414

    authors: Dixon AL,Busch JW

    更新日期:2017-06-01 00:00:00

  • Analysis of substage associations in prophase I of meiosis in floral buds of wild-type Arabidopsis thaliana (Brassicaceae).

    abstract::We developed an improved cytological protocol for producing high quality, light microscope images of plant meiotic chromosomes. Because the technique works on species with small genomes and thick microsporocyte cell walls, it should be useful for studying the wild relatives of Arabidopsis and other eudicots with small...

    journal_title:American journal of botany

    pub_type: 杂志文章

    doi:10.3732/ajb.94.12.2063

    authors: Stronghill PE,Hasenkampf CA

    更新日期:2007-12-01 00:00:00

  • Molecular phylogeny of the Magnoliaceae: the biogeography of tropical and temperate disjunctions.

    abstract::The boreotropical flora concept suggests that relictual tropical disjunctions between Asia and the Americas are a result of the expansion of the circumboreal tropical flora from the middle to the close of the Eocene. Subsequently, temperate species diverged at high latitudes and migrated to other continents. To test t...

    journal_title:American journal of botany

    pub_type: 杂志文章

    doi:

    authors: Azuma H,García-Franco JG,Rico-Gray V,Thien LB

    更新日期:2001-12-01 00:00:00

  • Biomechanical properties of the trunk of the devil's walking stick (Aralia spinosa; Araliaceae) during the crown-building phase: implications for tree architecture.

    abstract::During the crown-building phase, the mechanical architecture of the trunk of Aralia spinosa exhibits considerable ontogenetic variation. All trunks were tapered along their length, and taper was dependent on both ramet size and age; older, larger trunks were more tapered than younger, smaller trunks. Trunk specific gr...

    journal_title:American journal of botany

    pub_type: 杂志文章

    doi:

    authors: Briand CH,Campion SM,Dzambo DA,Wilson KA

    更新日期:1999-12-01 00:00:00

  • Development and characterization of microsatellite loci for Khaya senegalensis (Meliaceae)1.

    abstract:UNLABELLED: PREMISE OF THE STUDY:Microsatellite loci were developed to characterize genetic variation and population subdivision in Khaya senegalensis (Desr.) A. Juss. (Meliaceae). • METHODS AND RESULTS:Microsatellite loci were identified from genomic DNA sequences generated using the 454 GS-FLX titanium platform. Pr...

    journal_title:American journal of botany

    pub_type: 杂志文章

    doi:10.3732/ajb.1000300

    authors: Sexton GJ,Frere CH,Dieters MJ,Godwin ID,Prentis PJ

    更新日期:2010-11-01 00:00:00

  • AN ANALYSIS OF VARIABILITY IN SEED SETTLING VELOCITIES OF SEVERAL WIND-DISPERSED ASTERACEAE.

    abstract::Dispersal is an important life history component. Seed settling velocity may be a useful surrogate for the measurement of dispersal ability in wind-dispersed plants, particularly those whose seeds have plumose dispersal structures. I measured settling velocities on seeds of eight species of Asteraceae, including annua...

    journal_title:American journal of botany

    pub_type: 杂志文章

    doi:10.1002/j.1537-2197.1992.tb13702.x

    authors: Andersen MC

    更新日期:1992-10-01 00:00:00

  • ISOZYMATIC VARIATION IN GUATEMALAN RACES OF MAIZE.

    abstract::Isozymatic data taken from 67 Guatemalan collections of maize were subjected to numerical taxonomic analyses to elucidate systematic relationships among the 19 maize races and subraces described for Guatemala by Wellhausen et al. As with Bolivian and Mexican races, isozymatic variation in Guatemalan maize was strongly...

    journal_title:American journal of botany

    pub_type: 杂志文章

    doi:10.1002/j.1537-2197.1990.tb13547.x

    authors: Bretting PK,Goodman MM,Stuber CW

    更新日期:1990-02-01 00:00:00

  • Geographic patterns in the reproductive ecology of Agave lechuguilla (Agavaceae) in the Chihuahuan desert. I. Floral characteristics, visitors, and fecundity.

    abstract::Floral characteristics such as morphology and flower color have been interpreted as adaptive traits that evolved through selective pressures generated by pollinators. Differences among populations in the expression of floral characters could result from natural selection for their adaptive value to local conditions. W...

    journal_title:American journal of botany

    pub_type: 杂志文章

    doi:10.3732/ajb.90.3.377

    authors: Silva-Montellano A,Eguiarte LE

    更新日期:2003-03-01 00:00:00

  • Population history of the two carnivorous plants Drosera peltata var. nipponica and Drosera rotundifolia (Droseraceae) in Korea.

    abstract:PREMISE OF THE STUDY:Drosera peltata var. nipponica, an element of the East Asia warm-temperate vegetation, and D. rotundifolia, a widely distributed boreal species, reach one of their northernmost and southernmost limits, respectively, on the Korean Peninsula. Because the Last Glacial Maximum (LGM)-Holocene dynamics o...

    journal_title:American journal of botany

    pub_type: 杂志文章

    doi:10.3732/ajb.1200486

    authors: Chung MY,López-Pujol J,Chung MG

    更新日期:2013-11-01 00:00:00

  • Origins and nature of vessels in monocotyledons: 8. Orchidaceae.

    abstract::Xylem of the orchids studied provided unusually favorable material to demonstrate how conductive tissue evolves in monocotyledons. In the end walls of tracheary elements of many Orchidaceae, remnants of pit membranes were observed with scanning electron microscopy and minimally destructive methods. The full range from...

    journal_title:American journal of botany

    pub_type: 杂志文章

    doi:10.3732/ajb.93.7.963

    authors: Carlquist S,Schneider EL

    更新日期:2006-07-01 00:00:00

  • A set of novel microsatellite markers developed for the traditional Tibetan medicinal plant Halenia elliptica (Gentianaceae).

    abstract:PREMISE OF THE STUDY:Microsatellite primers were developed in the traditional Tibetan medicinal plant Halenia elliptica D. Don to investigate its genetic diversity and population genetic structure. METHODS AND RESULTS:Using the Fast Isolation by AFLP of Sequences Containing (FIASCO) repeats protocol, 24 primer sets we...

    journal_title:American journal of botany

    pub_type: 杂志文章

    doi:10.3732/ajb.1000534

    authors: Zhang ZR,Yang J,Sun Y,Gao TG,Li DZ,Xue CY

    更新日期:2011-07-01 00:00:00