Phylogeny in the genus Hordeum based on nucleotide sequences closely linked to the vrs1 locus (row number of spikelets)

Genome ◽  
1999 ◽  
Vol 42 (5) ◽  
pp. 973-981 ◽  
Author(s):  
Takao Komatsuda ◽  
Ken-ichi Tanno ◽  
Björn Salomon ◽  
Tomas Bryngelsson ◽  
Roland von Bothmer
Keyword(s):  
Nuclear Dna ◽  
Sister Group ◽  
Single Copy ◽  
Nucleotide Sequences ◽  
Restriction Maps ◽  
Deletion Event ◽  
Single Base ◽  
Genome Group ◽  
The Difference ◽  
Hordeum Species

The phylogenetic relationship between four basic genomes designated H, I, Xa, and Xu in the genus Hordeum was studied using a nuclear DNA sequence. The sequence, cMWG699, is single copy in the H. vulgare genome, and tightly linked to the vrs1 locus which controls two- and six-rowed spikes. DNA fragments homologous to cMWG699 were amplified from diploid Hordeum species and the nucleotide sequences were determined. A phylogeny based on both base substitutions and an insertion-deletion event showed that the H- and Xa-genome groups are positioned in one monophyletic group indicating that the Xa-genome taxa should be included in the H-genome group. The large H-genome group is highly homogeneous. The I and Xu genomes are distinctly separated from H and Xa, and form sister groups. Another phylogeny pattern based on data excluding the insertion-deletion gave a result that the Xa genome forms a sister group to the H-genome group. The difference between the H and Xa genomes was affected only by a single base insertion-deletion event, thus the H and Xa genomes are likely to be closely related. The I and Xu genomes were again distinctly separated from the H and Xa genomes.Key words: genome DNA, molecular markers, restriction maps, barley, Psathyrostachys.

Nuclear DNA Evolution and Phylogeny of the New World Nine-Primaried Oscines

The Auk ◽  
1988 ◽  
Vol 105 (3) ◽  
pp. 504-515 ◽  
Author(s):  
Anthony H. Bledsoe
Keyword(s):  
Dna Sequences ◽  
Goodness Of Fit ◽  
New World ◽  
Nuclear Dna ◽  
Thermal Dissociation ◽  
Branch Length ◽  
Sister Group ◽  
Single Copy ◽  
The North ◽  
Dissociation Curves

Abstract Estimates of phylogeny were derived from measures of dissimilarity of single-copy nuclear-DNA sequences for 13 species that represent the currently recognized major groups of New World nine-primaried oscines and an outgroup (Passer). The dissimilarity coefficients (delta mode and delta T50H) calculated from thermal dissociation curves of reassociated DNA sequences exhibited the properties of a metric. No statistically significant increase in goodness-of-fit of the raw data to a phylogeny estimated from a least-squares analysis of the 13 × 13 matrix of distances was achieved when the lengths of sister branches were allowed to vary. "Jackknife" and negative branch-length analyses identified unstable stems that resulted from non-additivity caused in part by measurement error. Such stems were collapsed to produce a more robust topology, which served as the basis for estimating the positions of taxa not included in the 13 × 13 matrix. The clade that subsumed several "typical" tanagers (e.g. Tachyphonus rufus) also included Sicalis luteola and Diuca diuca (usually allied with the North American emberizine sparrows); Cyanerpes cyaneus, two species of Diglossa, and Coereba flaveola (often split among several major groups); and Tersina viridis, Catamblyrhynchus diadema, and Nephelornis oneilli (whose affinities are often considered uncertain). This "tanager" clade and its sister group, the cardinals (represented by Cardinalis cardinalis), together formed one fork of a trichotomy. Several emberizine sparrows (e.g. Pooecetes gramineus) formed the second fork, and wood-warblers (e.g. Dendroica striata) and New World orioles (e.g. Psarocolius angustifrons) formed the third. The chaffinches (represented by Fringilla coelebs) and several cardueline finches (e.g. Carduelis pinus) together formed the sister group of the other New World nine-primaried oscines included in the study. This phylogeny implies that convergence in feeding specializations among lineages is more extensive than traditional arrangements of the assemblage would suggest.

scholarly journals Geographic Structure of Mitochondrial and Nuclear Gene Polymorphisms in Australian Green Turtle Populations and Male-Biased Gene Flow

Genetics ◽  
1997 ◽  
Vol 147 (4) ◽  
pp. 1843-1854 ◽  
Author(s):  
Nancy N FitzSimmons ◽  
Craig Moritz ◽  
Colin J Limpus ◽  
Lisa Pope ◽  
Robert Prince
Keyword(s):  
Gene Flow ◽  
Genetic Structure ◽  
Green Turtle ◽  
Nuclear Dna ◽  
Nuclear Gene ◽  
Chelonia Mydas ◽  
Single Copy ◽  
Microsatellite Data ◽  
Ecological Data ◽  
Infinite Allele Model

Abstract The genetic structure of green turtle (Chelonia mydas) rookeries located around the Australian coast was assessed by (1) comparing the structure found within and among geographic regions, (2) comparing microsatellite loci vs. restriction fragment length polymorphism analyses of anonymous single copy nuclear DNA (ascnDNA) loci, and (3) comparing the structure found at nuclear DNA markers to that of previously analyzed mitochondrial (mtDNA) control region sequences. Significant genetic structure was observed over all regions at both sets of nuclear markers, though the microsatellite data provided greater resolution in identifying significant genetic differences in pairwise tests between regions. Inferences about population structure and migration rates from the microsatellite data varied depending on whether statistics were based on the stepwise mutation or infinite allele model, with the latter being more congruent with geography. Estimated rates of gene flow were generally higher than expected for nuclear DNA (nDNA) in comparison to mtDNA, and this difference was most pronounced in comparisons between the northern and southern Great Barrier Reef (GBR). The genetic data combined with results from physical tagging studies indicate that the lack of nuclear gene divergence through the GBR is likely due to the migration of sGBR turtles through the courtship area of the nGBR population, rather than male-biased dispersal. This example highlights the value of combining comparative studies of molecular variation with ecological data to infer population processes.

GENETIC VARIATION IN RARE AND WIDESPREAD LOMATIUM SPECIES (APIACEAE): A COMPARISON OF AFLP AND SSCP DATA

2001 ◽  
Vol 58 (2) ◽  
pp. 347-356 ◽  
Author(s):  
M. A. GITZENDANNER ◽  
P. S. SOLTIS
Keyword(s):  
Rare Species ◽  
Nucleotide Diversity ◽  
Nuclear Dna ◽  
Allelic Variation ◽  
Plant Conservation ◽  
Single Copy ◽  
Small Populations ◽  
Nucleotide Polymorphisms ◽  
Widespread Species ◽  
Low Levels

Plant conservation genetics has been hampered by a lack of markers for studies of levels and patterns of variation in rare species. We investigated the levels of variation in several rare and widespread species of the western North American genus Lomatium Raf. (Apiaceae) using two relatively new molecular markers: AFLPs and single-strand conformation polymorphisms (SSCPs). For each species, approximately 150 AFLP loci have been scored, yielding estimates of species-level percent polymorphic loci in rare species ranging from near zero to over 80%. Levels of AFLP diversity were similar in two of the rare species, L. bradshawii (Rose ex Mathias) Mathas & Constance and L. ochocense Helliwell & Constance, and the widespread species. The third rare species, L. cookii Kagan, which has small populations, has low levels of diversity based on AFLPs. We also examined nucleotide diversity at the single-copy nuclear-DNA locus glyceraldehyde 3-phosphate dehydrogenase (Gap-C). PCR-amplified segments were analysed for allelic variation using SSCPs, and intrapopulational nucleotide polymorphisms were identified in both L. bradshawii and L. cookii. In the 211bp segment of Gap-C analysed, five nucleotide sites were segregating within populations of L. bradshawii and two in L. cookii.

scholarly journals Phylogeny Reconstruction and Hybrid Analysis of Populus (Salicaceae) Based on Nucleotide Sequences of Multiple Single-Copy Nuclear Genes and Plastid Fragments

PLoS ONE ◽  
2014 ◽  
Vol 9 (8) ◽  
pp. e103645 ◽  
Author(s):  
Zhaoshan Wang ◽  
Shuhui Du ◽  
Selvadurai Dayanandan ◽  
Dongsheng Wang ◽  
Yanfei Zeng ◽  
...  
Keyword(s):  
Single Copy ◽  
Nucleotide Sequences ◽  
Nuclear Genes ◽  
Phylogeny Reconstruction ◽  
Hybrid Analysis

scholarly journals More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs

2012 ◽  
Vol 8 (5) ◽  
pp. 783-786 ◽  
Author(s):  
Nicholas G. Crawford ◽  
Brant C. Faircloth ◽  
John E. McCormack ◽  
Robb T. Brumfield ◽  
Kevin Winker ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Common Ancestor ◽  
Sister Group ◽  
Single Copy ◽  
Recent Analysis ◽  
Phylogenetic Position ◽  
Ultraconserved Elements ◽  
Sequence Capture ◽  
Genomic Scale ◽  
Nuclear Loci

We present the first genomic-scale analysis addressing the phylogenetic position of turtles, using over 1000 loci from representatives of all major reptile lineages including tuatara. Previously, studies of morphological traits positioned turtles either at the base of the reptile tree or with lizards, snakes and tuatara (lepidosaurs), whereas molecular analyses typically allied turtles with crocodiles and birds (archosaurs). A recent analysis of shared microRNA families found that turtles are more closely related to lepidosaurs. To test this hypothesis with data from many single-copy nuclear loci dispersed throughout the genome, we used sequence capture, high-throughput sequencing and published genomes to obtain sequences from 1145 ultraconserved elements (UCEs) and their variable flanking DNA. The resulting phylogeny provides overwhelming support for the hypothesis that turtles evolved from a common ancestor of birds and crocodilians, rejecting the hypothesized relationship between turtles and lepidosaurs.

scholarly journals Discovery of a new family of amphibians from northeast India with ancient links to Africa

2012 ◽  
Vol 279 (1737) ◽  
pp. 2396-2401 ◽  
Author(s):  
Rachunliu G. Kamei ◽  
Diego San Mauro ◽  
David J. Gower ◽  
Ines Van Bocxlaer ◽  
Emma Sherratt ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Nuclear Dna ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Northeast India ◽  
Sister Group Relationship ◽  
New Family ◽  
Ancient Lineage ◽  
Molecular Phylogenetic ◽  
Threatened Habitats

The limbless, primarily soil-dwelling and tropical caecilian amphibians (Gymnophiona) comprise the least known order of tetrapods. On the basis of unprecedented extensive fieldwork, we report the discovery of a previously overlooked, ancient lineage and radiation of caecilians from threatened habitats in the underexplored states of northeast India. Molecular phylogenetic analyses of mitogenomic and nuclear DNA sequences, and comparative cranial anatomy indicate an unexpected sister-group relationship with the exclusively African family Herpelidae. Relaxed molecular clock analyses indicate that these lineages diverged in the Early Cretaceous, about 140 Ma. The discovery adds a major branch to the amphibian tree of life and sheds light on both the evolution and biogeography of caecilians and the biotic history of northeast India—an area generally interpreted as a gateway between biodiversity hotspots rather than a distinct biogeographic unit with its own ancient endemics. Because of its distinctive morphology, inferred age and phylogenetic relationships, we recognize the newly discovered caecilian radiation as a new family of modern amphibians.

Genome structure of Halobacterium halobium: plasmid dynamics in gas vacuole deficient mutants

1989 ◽  
Vol 35 (1) ◽  
pp. 96-100 ◽  
Author(s):  
Felicitas Pfeifer ◽  
Ulrike Blaseio ◽  
Mary Horne
Keyword(s):  
Genome Structure ◽  
Gene Mutations ◽  
Halobacterium Halobium ◽  
Chromosomal Dna ◽  
Insertion Element ◽  
Deletion Event ◽  
High Frequencies ◽  
Insertion Elements ◽  
The Difference ◽  
Gas Vacuole

Halobacterium halobium contains two gas vacuole protein genes that are located in plasmid pHH1 (p-vac) and in the chromosomal DNA (c-vac). The mutation frequency for these genes is different: the constitutively expressed p-vac gene is mutated with a frequency of 10−2, while the chromosomal gene expressed in the stationary phase of growth is mutated with a frequency of 10−5. The difference in the mutation susceptibility is due to the dynamics of plasmid pHH1. p-vac gene mutations are caused (i) by the integration of an insertion element or (ii) by a deletion event encompassing the p-vac gene region. In contrast, c-vac mutants analyzed to date incurred neither insertion elements nor deletions. Deletion events within pHH1 occur at high frequencies during the development of a H. halobium culture. The investigation of the fusion regions resulting from deletion events indicates that insertion elements are involved. The analysis of pHH1 deletion variants led to a 4 kilobase pair DNA region containing the origin of replication of the pHH1 plasmid.Key words: gas vacuole protein gene, plasmid dynamics, deletions, insertion elements.

Genomic constitution and phylogenetic position of several New Zealand Triticeae species revealed by two single copy nuclear genes

2011 ◽  
Vol 59 (1) ◽  
pp. 1 ◽  
Author(s):  
Aimee G. Oliver ◽  
Kara Harnish ◽  
Genlou Sun
Keyword(s):  
New Zealand ◽  
North American ◽  
Diploid Species ◽  
Single Copy ◽  
Nuclear Genes ◽  
Phylogenetic Position ◽  
Genome Constitution ◽  
Elymus Species ◽  
New Zealand Flora ◽  
Hordeum Species

Three genera of Triticeae, Elymus, Stenostachys and Australopyrum, are described in the New Zealand flora. Cytological analyses suggested that five basic genomes (St, H, Y, P and W) donated by different diploid species in different combinations exist in the genera Elymus and Stenostachys, whereas Australopyrum species contain the W genome only. Morphological and cytogenetic data suggested that the genome constitution for both E. apricus and E. multiflorus is StYW. Chloroplast DNA and ITS data supported the genome constitution of these Elymus species, but the HW genome constitution was assigned to the Stenostachys species. In this study, sequences of two single copy nuclear genes, RPB2 and DMC1, were used to confirm or refute the genome constitutions of the two Stenostachys species and the two Elymus species from New Zealand, and to analyse their phylogenetic relationships with other Elymus species. Our RPB2 and DMC1 data confirmed that the genome constitution of hexaploid E. apricus is StWY, and tetraploid S. gracilis is HW. The presence of the StW genome in hexaploid E. multiflorus, and the W genome in tetraploid S. laevis is also confirmed. No obvious St genome differentiation between New Zealand and non-New Zealand species is observed. The H genomes in the S. gracilis and S. laevis are closely related to the H genome from North American species, indicating that the H genomes in these two New Zealand species might originate from North American Hordeum species.

Rates and patterns of scnDNA and mtDNA divergence within the Drosophila melanogaster subgroup.

Genetics ◽  
1988 ◽  
Vol 118 (4) ◽  
pp. 671-683
Author(s):  
A Caccone ◽  
G D Amato ◽  
J R Powell
Keyword(s):  
Drosophila Melanogaster ◽  
Dna Hybridization ◽  
Nuclear Dna ◽  
Single Copy ◽  
Rate Of Change ◽  
Drosophila Genome ◽  
Island Species ◽  
Drosophila Melanogaster Subgroup ◽  
Chromosomal Data ◽  
Group 2

Abstract Levels of DNA divergence among the eight species of the Drosophila melanogaster subgroup and D. takahashii have been determined using the technique of DNA-DNA hybridization. Two types of DNA were used: single-copy nuclear DNA (scnDNA) and mitochondrial DNA (mtDNA). The major findings are: (1) A phylogeny has been derived for the group based on scnDNA which is congruent with chromosomal data, morphology, and behavior. The three homosequential species, simulans, sechellia, and mauritiana, are very closely related; the scnDNA divergence indicate the two island species are a monophyletic group. (2) The rates of change of scnDNA and mtDNA are not greatly different; if anything scnDNA evolves faster than mtDNA. (3) The rates of scnDNA evolution are not closely correlated to chromosomal (inversion) evolution. (4) The Drosophila genome appears to consist of two distinct classes of scnDNA with respect to rate of evolutionary change, a very rapidly evolving fraction and a relatively conservative fraction. (5) The absolute rate of change was estimated to be at least 1.7% nucleotide substitution per one million years. (6) DNA distance estimates based on restriction site variation are correlated with distances based on DNA-DNA hybridization, although the correlation is not very strong.

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