scholarly journals Evolutionary Insights from DNA Sequences from Chaetanthera Ruiz & Pav. and Oriastrum Poepp. & Endl. (Asteraceae; Mutisieae). I. Of Molecules and Systematics

2021 ◽  
Author(s):  
Mark Hershkovitz
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Reconstruction ◽  
Intergenic Spacer ◽  
Nominal Species ◽  
Gene Trees ◽  
Species Trees ◽  
Phylogenetic Resolution ◽  
Extraterrestrial Origin ◽  
Epistemological Framework ◽  
Combined Data

Phylogenetic analysis of combined ribosomal DNA internal transcribed spacer (ITS) and chloroplast DNA rpl32-trnL intergenic spacer sequences greatly improves phylogenetic resolution of Chaetanthera Ruiz & Pav. and Oriastrum Poepp. & Endl. (Asteraceae; Mutisieae) over a previously published phylogeny based on ITS alone. The results support segregation of Chaetanthera subg. Liniphyllum Less. from C. subg. Chaetanthera. One sample with peculiar ITS and rpl32-trnL sequences may be of extraterrestrial origin. Fifteen of 16 nominal species sampled more than once for both loci were polymorphic for at least one of them, and only half of the polymorphic samples were demonstrably monophyletic in the combined data analysis. An additional five species sampled only for ITS all were polymorphic. These results underscore the ontological difference between gene trees and species trees and further discredit the notion of “species barcodes.” The gene trees for both loci manifest departures from all evolutionary models implemented for phylogenetic reconstruction. This result is explained as a consequence of evolutionary idiosyncraticity, in turn a function of the determinacy of biological organisms and processes consequent to autopoiesis. This determinacy implicates a chaotic evolutionary function that theoretically cannot be reconstructed or predicted by stochastic models. However, because phylogenetic history and clades are materially tangible entities, their reconstruction is within the realm of scientific inquiry. I discuss the phylogeny of Chaetanthera/Oriastrum in this epistemological framework.

More Miocene Dispersal Between Africa and Asia—the Case of Bridelia (Phyllanthaceae)

2009 ◽  
Vol 34 (3) ◽  
pp. 521-529 ◽  
Author(s):  
Yongquan Li ◽  
Stefan Dressler ◽  
Dianxiang Zhang ◽  
Susanne S. Renner
Keyword(s):  
Dna Sequences ◽  
Gene Trees ◽  
Long Distance ◽  
Directional Bias ◽  
Tropical Asia ◽  
Asian Clade ◽  
Chloroplast Dna Sequences ◽  
Commercially Important ◽  
Morphological Species ◽  
Combined Data

Several hundred angiosperm genera range from Africa to Asia and Australia, among them Bridelia (Phyllanthaceae), with ca. 40 species, including commercially important timber trees. We here use nuclear and chloroplast DNA sequences from herbarium material, plus new collections from China, to test the monophyly of Bridelia and to infer the geologic times when it acquired its disjunct range. For the Southeast Asian mainland, within-species sampling, including material collected close to the type localities, allowed testing current species concepts. Based on a sample of 114 chloroplast matK sequences of Phyllanthaceae, Bridelia is monophyletic and sister to an Asian clade which requires resurrecting an older generic name to make the African Cleistanthus monophyletic. Within Bridelia, gene trees from the combined data (3,177 aligned nucleotides from 25 species of Bridelia plus outgroups) agree with most morphological species boundaries. Exceptions are that B. tomentosa must include B. harmandii and B. curtisii to become monophyletic and that B. fordii is distinct from B. retusa. The topology, together with relaxed clock divergence times, implies that Bridelia dispersed from tropical Asia to Africa once or twice between 10 and 1.85 million years ago (Ma). Australia was reached, probably from New Guinea, at least twice, both times ca. 2 Ma. Together with earlier studies, there are now at least eight cases of Neogene long distance dispersal between Africa and Asia (followed by speciation), with no directional bias apparent so far.

Evaluation of the multispecies coalescent method to explore intra-Trypanosoma cruzi I relationships and genetic diversity

Parasitology ◽  
2019 ◽  
Vol 146 (8) ◽  
pp. 1063-1074 ◽  
Author(s):  
César Gómez-Hernández ◽  
Sergio D. Pérez ◽  
Karine Rezende-Oliveira ◽  
Cecilia G. Barbosa ◽  
Eliane Lages-Silva ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Trypanosoma Cruzi ◽  
Dna Sequences ◽  
Complex Dynamics ◽  
Housekeeping Genes ◽  
Gene Trees ◽  
Species Trees ◽  
Random Set ◽  
Phylogenetic Incongruence ◽  
Multispecies Coalescent

AbstractChagas Disease is a zoonosis caused by the parasite Trypanosoma cruzi. Several high-resolution markers have subdivided T. cruzi taxon into at least seven lineages or Discrete Typing Units (DTUs) (TcI-TcVI and TcBat). Trypanosoma cruzi I is the most diverse and geographically widespread DTU. Recently a TcI genotype related to domestic cycles was proposed and named as TcIDOM. Herein, we combined traditional markers and housekeeping genes and applied a Multispecies Coalescent method to explore intra-TcI relationships, lineage boundaries and genetic diversity in a random set of isolates and DNA sequences retrieved from Genbank from different countries in the Americas. We found further evidence supporting TcIDOM as an independent and emerging genotype of TcI at least in Colombia and Venezuela. We also found evidence of high phylogenetic incongruence between parasite's gene trees (including introgression) and embedded species trees, and a lack of genetic structure among geography and hosts, illustrating the complex dynamics and epidemiology of TcI across the Americas. These findings provide novel insights into T. cruzi systematics and epidemiology and support the need to assess parasite diversity and lineage boundaries through hypothesis testing using different approaches to those traditionally employed, including the Bayesian Multispecies coalescent method.

scholarly journals Phylogenetics of the plant genera Dracaena and Pleomele (Asparagaceae)

1970 ◽  
Vol 7 ◽  
pp. 64-72 ◽  
Author(s):  
Pei-Luen Lu ◽  
Clifford Morden
Keyword(s):  
Chloroplast Dna ◽  
Dna Sequences ◽  
World Wide ◽  
Significant Contribution ◽  
Molecular Taxonomy ◽  
Phylogenetic Reconstruction ◽  
Intergenic Spacer ◽  
Natural Resource Conservation ◽  
History Of ◽  
The Relationship

This research focuses on the biodiversity and the evolutionary history of the world-wide medicinal plant genus, Dracaena, and the plant genus Pleomele. The debate concerning the relationship between Dracaena and Pleomele has continued till date - some botanists continue to include Pleomele within Dracaena but others claimed to separate the two genera. Dracaena is a genus comprising of about 40-100 species world wide, mainly in tropics and subtropics, with the exception of America. Pleomele is a genus that has been circumscribed consisting of 10-50 species in Asia. Till date, its center of biodiversity is unknown. Pleomele is only classified well in Hawaii, but confused with Dracaena in the other parts of Asia. Phylogenetic relationship among the 33 taxa within the Dracaena and Pleomele were reconstructed. DNA sequences from the chloroplast DNA intergenic spacer, trnL-trnF and trnH-psbA were analyzed. A phylogeny was reconstructed using neighbor-joining, maximum parsimony in PAUP*, and likelihood criteria in RAxML, and Bayesian inference in MrBayes. The phylogeny with Agave missionum and Agave attenuata as outgroup taxa indicates that Pleomele is mixed with Dracaena. This study provides the first phylogenetic reconstruction with taxonomic sampling of the Dracaena and Pleomele to resolve their questionable placement. The relationships of the climate change adaptation, biogeography, and conservation with the two plant genera will be further discussed in this study. Some suggestions for the benefits of the biodiversity and natural resource conservation in Himalaya regions will be addressed. One significant contribution of this research will be in promoting molecular taxonomy to solve problems in systematics especially in cases when the classification is in debate. Key-words: Phylogeny; chloroplast DNA; Asparagaceae; Dracaena; Pleomele. DOI: 10.3126/botor.v7i0.4385Botanica Orientalis – Journal of Plant Science (2010) 7: 64-72

scholarly journals Bayes Estimation of Species Divergence Times and Ancestral Population Sizes Using DNA Sequences From Multiple Loci

Genetics ◽  
2003 ◽  
Vol 164 (4) ◽  
pp. 1645-1656 ◽  
Author(s):  
Bruce Rannala ◽  
Ziheng Yang
Keyword(s):  
Dna Sequences ◽  
Gene Tree ◽  
Species Tree ◽  
Bayes Estimation ◽  
Ancestral Population ◽  
Divergence Times ◽  
Gene Trees ◽  
Species Divergence ◽  
Multiple Loci ◽  
Population Sizes

Abstract The effective population sizes of ancestral as well as modern species are important parameters in models of population genetics and human evolution. The commonly used method for estimating ancestral population sizes, based on counting mismatches between the species tree and the inferred gene trees, is highly biased as it ignores uncertainties in gene tree reconstruction. In this article, we develop a Bayes method for simultaneous estimation of the species divergence times and current and ancestral population sizes. The method uses DNA sequence data from multiple loci and extracts information about conflicts among gene tree topologies and coalescent times to estimate ancestral population sizes. The topology of the species tree is assumed known. A Markov chain Monte Carlo algorithm is implemented to integrate over uncertain gene trees and branch lengths (or coalescence times) at each locus as well as species divergence times. The method can handle any species tree and allows different numbers of sequences at different loci. We apply the method to published noncoding DNA sequences from the human and the great apes. There are strong correlations between posterior estimates of speciation times and ancestral population sizes. With the use of an informative prior for the human-chimpanzee divergence date, the population size of the common ancestor of the two species is estimated to be ∼20,000, with a 95% credibility interval (8000, 40,000). Our estimates, however, are affected by model assumptions as well as data quality. We suggest that reliable estimates have yet to await more data and more realistic models.

scholarly journals Gene Trees versus Species Trees: Reassessing Life-History Evolution in a Freshwater Fish Radiation

2010 ◽  
Vol 59 (5) ◽  
pp. 504-517 ◽  
Author(s):  
Jonathan M. Waters ◽  
Diane L. Rowe ◽  
Christopher P. Burridge ◽  
Graham P. Wallis
Keyword(s):  
Life History ◽  
Freshwater Fish ◽  
Life History Evolution ◽  
Gene Trees ◽  
Species Trees ◽  
History Evolution

An integrative redescription of Hypsibius dujardini (Doyère, 1840), the nominal taxon for Hypsibioidea (Tardigrada: Eutardigrada)

Zootaxa ◽  
2018 ◽  
Vol 4415 (1) ◽  
pp. 45 ◽  
Author(s):  
PIOTR GĄSIOREK ◽  
DANIEL STEC ◽  
WITOLD MOREK ◽  
ŁUKASZ MICHALCZYK
Keyword(s):  
Dna Sequences ◽  
Evolutionary Biology ◽  
Model Organism ◽  
Laboratory Strain ◽  
Sensu Stricto ◽  
Nominal Species ◽  
28S Rrna ◽  
The Family ◽  
The 19Th Century ◽  
Hypsibius Dujardini

A laboratory strain identified as “Hypsibius dujardini” is one of the best studied tardigrade strains: it is widely used as a model organism in a variety of research projects, ranging from developmental and evolutionary biology through physiology and anatomy to astrobiology. Hypsibius dujardini, originally described from the Île-de-France by Doyère in the first half of the 19th century, is now the nominal species for the superfamily Hypsibioidea. The species was traditionally considered cosmopolitan despite the fact that insufficient, old and sometimes contradictory descriptions and records prevented adequate delineations of similar Hypsibius species. As a consequence, H. dujardini appeared to occur globally, from Norway to Samoa. In this paper, we provide the first integrated taxonomic redescription of H. dujardini. In addition to classic imaging by light microscopy and a comprehensive morphometric dataset, we present scanning electron photomicrographs, and DNA sequences for three nuclear markers (18S rRNA, 28S rRNA, ITS-2) and one mitochondrial marker (COI) that are characterised by various mutation rates. The results of our study reveal that a commercially available strain that is maintained in many laboratories throughout the world, and assumed to represent H. dujardini sensu stricto, represents, in fact, a new species: H. exemplaris sp. nov. Redescribing the nominal taxon for Hypsibiidae, we also redefine the family and amend the definitions of the subfamily Hypsibiinae and the genus Hypsibius. Moreover, we transfer H. arcticus (Murray, 1907) and Hypsibius conifer Mihelčič, 1938 to the genus Ramazzottius since the species exhibit claws and eggs of the Ramazzottius type. Finally, we designate H. fuhrmanni as subjectively invalid because the extremely poor description precludes identifying neotype material. 

Systematic status of Campydora Cobb, 1920 (Nematoda: Campydorina)

Nematology ◽  
2003 ◽  
Vol 5 (5) ◽  
pp. 699-711 ◽  
Author(s):  
Peter Mullin ◽  
Timothy Harris ◽  
Thomas Powers
Keyword(s):  
Maximum Likelihood ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Maximum Parsimony ◽  
Phylogenetic Analyses ◽  
Small Subunit ◽  
Systematic Position ◽  
Nominal Species ◽  
Competing Hypotheses ◽  
Small Subunit Ribosomal Dna

AbstractThe systematic position of Campydora Cobb, 1920, which possesses many unique morphological features, especially in pharyngeal structure and stomatal armature, has long been a matter of uncertainty with the 'position of the Campydorinae' (containing only Campydora) being questionable. A review of the morphology of C. demonstrans, the only nominal species of Campydora concluded that the species warranted placement as the sole member of a monotypic suborder, Campydorina, in the order Dorylaimida. Others placed Campydorina in the order Enoplida. We conducted phylogenetic analyses, using 18s small subunit ribosomal DNA sequences generated from a number of taxa in the subclasses Enoplia and Dorylaimia, to evaluate these competing hypotheses. Although precise taxonomic placement of the genus Campydora and the identity of its closest living relatives is in need of further investigation, our analyses, under maximum parsimony, distance, and maximum likelihood criteria, unambiguously indicate that Campydora shares a common, more recent, ancestry with genera such as Alaimus, Pontonema, Tripyla and Ironus (Enoplida), rather than with any members of Dorylaimida, Mononchida or Triplonchida.

Highly Condensed Potato Pericentromeric Heterochromatin Contains rDNA-Related Tandem Repeats

Genetics ◽  
2002 ◽  
Vol 162 (3) ◽  
pp. 1435-1444 ◽  
Author(s):  
Robert M Stupar ◽  
Junqi Song ◽  
Ahmet L Tek ◽  
Zhukuan Cheng ◽  
Fenggao Dong ◽  
...  
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Tandem Repeats ◽  
Intergenic Spacer ◽  
Pericentromeric Heterochromatin ◽  
Dna Repeats ◽  
Solanum Bulbocastanum ◽  
Origin And Evolution ◽  
Potato Genome ◽  
Dna Elements

Abstract The heterochromatin in eukaryotic genomes represents gene-poor regions and contains highly repetitive DNA sequences. The origin and evolution of DNA sequences in the heterochromatic regions are poorly understood. Here we report a unique class of pericentromeric heterochromatin consisting of DNA sequences highly homologous to the intergenic spacer (IGS) of the 18S•25S ribosomal RNA genes in potato. A 5.9-kb tandem repeat, named 2D8, was isolated from a diploid potato species Solanum bulbocastanum. Sequence analysis indicates that the 2D8 repeat is related to the IGS of potato rDNA. This repeat is associated with highly condensed pericentromeric heterochromatin at several hemizygous loci. The 2D8 repeat is highly variable in structure and copy number throughout the Solanum genus, suggesting that it is evolutionarily dynamic. Additional IGS-related repetitive DNA elements were also identified in the potato genome. The possible mechanism of the origin and evolution of the IGS-related repeats is discussed. We demonstrate that potato serves as an interesting model for studying repetitive DNA families because it is propagated vegetatively, thus minimizing the meiotic mechanisms that can remove novel DNA repeats.

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