Phenotypic disparity and adaptive radiation in the genus Cladia (Lecanorales, Ascomycota)

2010 ◽  
Vol 23 (4) ◽  
pp. 239 ◽  
Author(s):  
H. Thorsten Lumbsch ◽  
Sittiporn Parnmen ◽  
Achariya Rangsiruji ◽  
John A. Elix
Keyword(s):  
Dna Sequences ◽  
Adaptive Radiation ◽  
Alternative Hypothesis ◽  
Long Distance ◽  
Broad Distribution ◽  
Bayesian Analyses ◽  
Protein Coding ◽  
Morphological Disparity ◽  
Extant Species ◽  
Nuclear Its

Phylogenetic relationships of the genera Cladia, Heterodea and Ramalinora were reconstructed using a combined dataset of ribosomal nuclear ITS and LSU and mitochondrial SSU, and protein-coding Mcm7 DNA sequences. Maximum likelihood and Bayesian analyses strongly supported a monophyletic group in which the species of the foliose genus Heterodea and the crustose genus Ramalinora were nested within the fruticose genus Cladia. Alternative hypothesis testing rejected an independent status of Ramalinora. We tested the hypothesis that an adaptive radiation led to the morphological disparity found in the Cladia clade. Gamma-statistics indicated a significantly disproportional clustering of origins of extant lineages at the base of the Cladia clade and lineage-through-time plots were also consistent with the hypothesis of an adaptive radiation at the base of the Cladia clade. Ancestral-range reconstructions supported an origin of Cladia and the three major lineages within Cladia in Australia. On the basis of these results, we propose an evolutionary hypothesis for the genus. The results suggest that processes of adaptive radiation of the ancestor of Cladia in Australia led to the morphological disparity in the extant taxa, and that the broad distribution of some extant species is due to subsequent long-distance dispersal.

scholarly journals DNA sequences from three genomes reveal multiple long-distance dispersals and non-monophyly of sections in Australasian Plantago (Plantaginaceae)

2010 ◽  
Vol 23 (1) ◽  
pp. 47 ◽  
Author(s):  
Mei Lin Tay ◽  
Heidi M. Meudt ◽  
Philip J. Garnock-Jones ◽  
Peter A. Ritchie
Keyword(s):  
New Zealand ◽  
Dna Sequences ◽  
Molecular Dating ◽  
Long Distance ◽  
Mountain Ranges ◽  
Biogeographic Pattern ◽  
Geographic Origins ◽  
Molecular Phylogenetic ◽  
Nuclear Its ◽  
Dna Substitution

We examined the geographic origins and taxonomic placements of New Zealand and Australian Plantago (Plantaginaceae) by using molecular phylogenetic data. Plantago comprises over 200 species distributed worldwide. Analyses of three markers from the nuclear (ITS), chloroplast (ndhF–rpl32) and mitochondrial (coxI) genomes showed that the New Zealand species form three distinct, well supported clades that are not each others’ closest relatives, and were each derived relative to the sampled Australian species. Therefore, at least three long-distance directional dispersal events into New Zealand can be inferred for Plantago, likely from Australian ancestors. This result differs from the biogeographic pattern often reported for New Zealand plant genera of a single dispersal event followed by rapid radiation, and may be attributed to ready biotic dispersal of mucilaginous seeds and habitat similarities of the Australasian species. Molecular dating placed the arrival time and diversification of the New Zealand species between 2.291 and 0.5 million years ago, which coincides with the geological dates for the uplift of mountain ranges in New Zealand. The mitochondrial DNA substitution rate of the Australasian clade relative to the rest of the genus is discussed, as well as implications of the non-monophyly of sections Oliganthos, Mesembrynia and Plantago within subgenus Plantago.

scholarly journals Erratum to: DNA sequences from three genomes reveal multiple long-distance dispersals and non-monophyly of sections in Australasian Plantago (Plantaginaceae)

2010 ◽  
Vol 23 (4) ◽  
pp. 306
Author(s):  
Mei Lin Tay ◽  
Heidi M. Meudt ◽  
Philip J. Garnock-Jones ◽  
Peter A. Ritchie
Keyword(s):  
New Zealand ◽  
Dna Sequences ◽  
Molecular Dating ◽  
Long Distance ◽  
Mountain Ranges ◽  
Biogeographic Pattern ◽  
Geographic Origins ◽  
Molecular Phylogenetic ◽  
Nuclear Its ◽  
Dna Substitution

We examined the geographic origins and taxonomic placements of New Zealand and Australian Plantago (Plantaginaceae) by using molecular phylogenetic data. Plantago comprises over 200 species distributed worldwide. Analyses of three markers from the nuclear (ITS), chloroplast (ndhF?rpl32) and mitochondrial (coxI) genomes showed that the New Zealand species form three distinct, well supported clades that are not each others' closest relatives, and were each derived relative to the sampled Australian species. Therefore, at least three long-distance directional dispersal events into New Zealand can be inferred for Plantago, likely from Australian ancestors. This result differs from the biogeographic pattern often reported for New Zealand plant genera of a single dispersal event followed by rapid radiation, and may be attributed to ready biotic dispersal of mucilaginous seeds and habitat similarities of the Australasian species. Molecular dating placed the arrival time and diversification of the New Zealand species between 2.291 and 0.5�million years ago, which coincides with the geological dates for the uplift of mountain ranges in New Zealand. The mitochondrial DNA substitution rate of the Australasian clade relative to the rest of the genus is discussed, as well as implications of the non-monophyly of sections Oliganthos, Mesembrynia and Plantago within subgenus Plantago.

scholarly journals Eocene origin, Miocene diversification and intercontinental dispersal of the genus Drosera (Droseraceae)

2020 ◽  
Author(s):  
Sandeep Sen ◽  
Neha Tiwari ◽  
R Ganesan
Keyword(s):  
Dna Sequences ◽  
Evolutionary Biology ◽  
Charles Darwin ◽  
Long Distance ◽  
Data Set ◽  
Origin And Evolution ◽  
Fossil Calibration ◽  
History Of ◽  
Nuclear Its

AbstractResolving the evolutionary history of plant carnivory is of great interest to biologists throughout the world. Among the carnivorous plants, Genus Drosera (Droseraceae) is highly diverse with a wide pantropical distribution. Despite being a group of interest for evolutionary biology studies since the time of Charles Darwin, the historical biogeography of this group remains poorly understood. In this study, with an improved species sampling from Genbank, we present a reanalyzed phylogenetic hypothesis of the genus Drosera. We developed a dated molecular phylogeny of Drosera from DNA sequences of nuclear ITS and chloroplast rbcL genes. Divergence times were estimated on the combined dataset using an uncorrelated lognormal relaxed clock model and a known fossil calibration implemented in BEAST. The maximum clade credibility tree was then used for ancestral range estimations using DEC+J model implemented in BioGeoBEARS. Our analysis suggests that Drosera evolved during the Mid Eocene 36 Ma [95% HPD: 49.5-26] and have diversified and dispersed from the late Miocene onwards. Ancestral areas estimated using the DEC+J models suggest an African origin followed major radiation within Australia. Diversification in Drosera is temporally congruent with the prevailing drier conditions during the Miocene. From Miocene, grasslands and open habitats dominated across continents and might have provided ecological opportunities for their dispersal and diversification. Several long-distance dispersals and range extensions and in situ radiations coinciding with the evolution of drier conditions can explain their extant distribution across continents. Overall our data set provides fresh insights into the biogeographic factors that shaped the origin and evolution of the genus Drosera.

Systematics, Biogeography, and Morphological Character Evolution of the Hemiepiphytic Subfamily Monsteroideae (Araceae)

2019 ◽  
Vol 104 (1) ◽  
pp. 33-48 ◽  
Author(s):  
Alejandro Zuluaga ◽  
Martin Llano ◽  
Ken Cameron
Keyword(s):  
Dna Sequences ◽  
Pacific Islands ◽  
R Package ◽  
Morphological Characters ◽  
Ancestral State ◽  
Seed Shape ◽  
Long Distance ◽  
The Pacific ◽  
And Migration ◽  
The Tropics

The subfamily Monsteroideae (Araceae) is the third richest clade in the family, with ca. 369 described species and ca. 700 estimated. It comprises mostly hemiepiphytic or epiphytic plants restricted to the tropics, with three intercontinental disjunctions. Using a dataset representing all 12 genera in Monsteroideae (126 taxa), and five plastid and two nuclear markers, we studied the systematics and historical biogeography of the group. We found high support for the monophyly of the three major clades (Spathiphylleae sister to Heteropsis Kunth and Rhaphidophora Hassk. clades), and for six of the genera within Monsteroideae. However, we found low rates of variation in the DNA sequences used and a lack of molecular markers suitable for species-level phylogenies in the group. We also performed ancestral state reconstruction of some morphological characters traditionally used for genera delimitation. Only seed shape and size, number of seeds, number of locules, and presence of endosperm showed utility in the classification of genera in Monsteroideae. We estimated ancestral ranges using a dispersal-extinction-cladogenesis model as implemented in the R package BioGeoBEARS and found evidence for a Gondwanan origin of the clade. One tropical disjunction (Monstera Adans. sister to Amydrium Schott–Epipremnum Schott) was found to be the product of a previous Boreotropical distribution. Two other disjunctions are more recent and likely due to long-distance dispersal: Spathiphyllum Schott (with Holochlamys Engl. nested within) represents a dispersal from South America to the Pacific Islands in Southeast Asia, and Rhaphidophora represents a dispersal from Asia to Africa. Future studies based on stronger phylogenetic reconstructions and complete morphological datasets are needed to explore the details of speciation and migration within and among areas in Asia.

Human DNA sequences homologous to a protein coding region conserved between homeotic genes of Drosophila

Cell ◽  
1984 ◽  
Vol 38 (3) ◽  
pp. 667-673 ◽  
Author(s):  
Michael Levine ◽  
Gerald M. Rubin ◽  
Robert Tjian
Keyword(s):  
Dna Sequences ◽  
Homeotic Genes ◽  
Coding Region ◽  
Protein Coding ◽  
Human Dna

scholarly journals Evolutionary Relations of Hexanchiformes Deep-Sea Sharks Elucidated by Whole Mitochondrial Genome Sequences

2013 ◽  
Vol 2013 ◽  
pp. 1-11 ◽  
Author(s):  
Keiko Tanaka ◽  
Takashi Shiina ◽  
Taketeru Tomita ◽  
Shingo Suzuki ◽  
Kazuyoshi Hosomichi ◽  
...  
Keyword(s):  
Genetic Relationships ◽  
Close Relation ◽  
Rrna Genes ◽  
Gill Slit ◽  
Mtdna Sequences ◽  
Protein Coding ◽  
Bayesian Phylogenetic Analysis ◽  
Extant Species ◽  
Complete Mitogenome ◽  
Cartilaginous Fishes

Hexanchiformes is regarded as a monophyletic taxon, but the morphological and genetic relationships between the five extant species within the order are still uncertain. In this study, we determined the whole mitochondrial DNA (mtDNA) sequences of seven sharks including representatives of the five Hexanchiformes, one squaliform, and one carcharhiniform and inferred the phylogenetic relationships among those species and 12 other Chondrichthyes (cartilaginous fishes) species for which the complete mitogenome is available. The monophyly of Hexanchiformes and its close relation with all other Squaliformes sharks were strongly supported by likelihood and Bayesian phylogenetic analysis of 13,749 aligned nucleotides of 13 protein coding genes and two rRNA genes that were derived from the whole mDNA sequences of the 19 species. The phylogeny suggested that Hexanchiformes is in the superorder Squalomorphi,Chlamydoselachus anguineus(frilled shark) is the sister species to all other Hexanchiformes, and the relations within Hexanchiformes are well resolved asChlamydoselachus, (Notorynchus, (Heptranchias, (Hexanchus griseus,H. nakamurai))). Based on our phylogeny, we discussed evolutionary scenarios of the jaw suspension mechanism and gill slit numbers that are significant features in the sharks.

Transcriptional and posttranscriptional regulation of maize mitochondrial gene expression

1991 ◽  
Vol 11 (1) ◽  
pp. 533-543
Author(s):  
R M Mulligan ◽  
P Leon ◽  
V Walbot
Keyword(s):  
Dna Sequences ◽  
Transcription Initiation ◽  
Posttranscriptional Regulation ◽  
Rank Order ◽  
Mitochondrial Gene ◽  
Initiation Site ◽  
Gene Copy ◽  
Promoter Strength ◽  
Protein Coding

Lysed maize mitochondria synthesize RNA in the presence of radioactive nucleoside triphosphates, and this assay was utilized to compare the rates of transcription of seven genes. The rates of incorporation varied over a 14-fold range, with the following rank order: 18S rRNA greater than 26S rRNA greater than atp1 greater than atp6 greater than atp9 greater than cob greater than cox3. The products of run-on transcription hybridized specifically to known transcribed regions and selectively to the antisense DNA strand; thus, the isolated run-on transcription system appears to be an accurate representation of endogenous transcription. Although there were small differences in gene copy abundance, these differences cannot account for the differences in apparent transcription rates; we conclude that promoter strength is the main determinant. Among the protein coding genes, incorporation was greatest for atp1. The most active transcription initiation site of this gene was characterized by hybridization with in vitro-capped RNA and by primer extension analyses. The DNA sequences at this and other transcription initiation sites that we have previously mapped were analyzed with respect to the apparent promoter strengths. We propose that two short sequence elements just upstream of initiation sites form at least a portion of the sequence requirements for a maize mitochondrial promoter. In addition to modulation at the level of transcription, steady-state abundance of protein-coding mRNAs varied over a 20-fold range and did not correlate with transcriptional activity. These observations suggest that posttranscriptional processes are important in the modulation of mRNA abundance.

Identification of the principal promoter sequence of the c-H-ras transforming oncogene: deletion analysis of the 5'-flanking region by focus formation assay

1987 ◽  
Vol 7 (8) ◽  
pp. 2933-2940
Author(s):  
H Honkawa ◽  
W Masahashi ◽  
S Hashimoto ◽  
T Hashimoto-Gotoh
Keyword(s):  
Dna Sequences ◽  
Promoter Sequence ◽  
Ras Oncogene ◽  
Coding Region ◽  
Focus Formation ◽  
S1 Nuclease ◽  
Protein Coding ◽  
Consensus Sequences ◽  
Flanking Region ◽  
Virus C

A number of deletion mutants were isolated, including 5', 3', and internal deletions in the 5'-flanking region of the human cellular oncogene related to the Harvey sarcoma virus (c-H-ras), and their transforming activities were examined in NIH 3T3 cells. DNA sequences which could not be detected without losing transforming activity were localized to a relatively short stretch upstream of the region which showed homology to the 5'-flanking region of v-H-ras oncogene. S1 nuclease analysis indicated that there were two clusters of mRNA start sites at positions that were about 1,371 and 1,298 base pairs upstream of the first coding ATG. The minimum region required for promoter function was estimated to be a 51-base-pair-long (or less) DNA segment. The promoter was GC rich (78%) and did not contain the consensus sequences that are usually observed in PolII-directed promoters but contained a GC box within which one of the mRNA start sites was included. In addition, two sets of positive and negative elements seemed to be located between the promoter and the protein-coding region, which appeared to influence positively and negatively, respectively, the efficiency of transformation with the c-H-ras oncogene.

scholarly journals A DNA investigation into the mysterious disappearance of the Rocky Mountain grasshopper, mega-pest of the 1800s

2017 ◽  
Author(s):  
W. Chapco ◽  
G. Litzenberger
Keyword(s):  
Dna Sequences ◽  
Nucleotide Diversity ◽  
Rocky Mountain ◽  
Species Group ◽  
Pest Species ◽  
History Of Agriculture ◽  
Extant Species ◽  
Remarkable Event ◽  
History Of ◽  
Major Pest

The mysterious extinction of the Rocky Mountain Grasshopper, Melanoplus spretus, a major pest species on the prairies and plains of the 1800s, is truly a remarkable event in the history of agriculture. Recently, we obtained specimens of M. spretus from museums and from 400-year-old glacial deposits in Wyoming. We report success in obtaining mitochondrial DNA sequences from both sources. This permitted us to examine two issues surrounding the species’ disappearance. First, a long-standing view that M. spretus and the extant species Melanoplus sanguinipes are (if not phase transforms of one another) sister taxa, is disputed, but cannot be rejected with certainty. Interestingly, there is some evidence that suggests there may be a closer affinity with another member of the Mexicanus species-group, Melanoplus bruneri. Second, because M. spretus still possesses considerable nucleotide diversity (1.15 ± 0.19%), a depletion of variation cannot be considered a factor contributing to its demise.

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