DNA-DNA Hybridization, Phylogenetic Reconstruction and the Fossil Record

Short Courses in Paleontology ◽

10.1017/s2475263000000684 ◽

1988 ◽

Vol 1 ◽

pp. 75-88 ◽

Cited By ~ 1

Author(s):

Charles R. Marshall

Keyword(s):

Dna Hybridization ◽

Nuclear Dna ◽

Phylogenetic Reconstruction ◽

Cost Effective ◽

Single Copy ◽

Molecular Techniques ◽

Phylogenetic Information ◽

Molecular Approaches ◽

Molecular Characters ◽

Rates Of Molecular Evolution

In 1962 Zuckerkandl & Pauling suggested that the amino acid sequence of proteins might evolve in a clock-like fashion and thus may be useful for phylogenetic reconstruction. Since then, many different molecular approaches to phylogenetic reconstruction have been proposed (Wilson et al., 1977). Enthusiasm for the clock hypothesis was dampened by the discovery that rates of molecular evolution for many macromolecules have been highly variable through time (Romero-Herrera et al., 1979). However, the contribution of molecular characters to the study of phylogeny is not necessarily dependent on the notion of a molecular clock and molecular approaches continue to be an important source of phylogenetic information. One of the more powerful and cost-effective molecular techniques for phylogenetic purposes is DNA-DNA hybridization, which measures the single-copy nuclear DNA sequence divergences between species.

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Mark-recapture cloning: a straightforward and cost-effective cloning method for population genetics of single-copy nuclear DNA sequences in diploids

Molecular Ecology Notes ◽

10.1111/j.1471-8286.2007.01685.x ◽

2007 ◽

Vol 7 (4) ◽

pp. 562-566 ◽

Cited By ~ 12

Author(s):

N. BIERNE ◽

A. TANGUY ◽

M. FAURE ◽

B. FAURE ◽

E. DAVID ◽

...

Keyword(s):

Population Genetics ◽

Dna Sequences ◽

Nuclear Dna ◽

Cost Effective ◽

Single Copy ◽

Mark Recapture ◽

Cloning Method

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

Genetics ◽

10.1093/genetics/118.4.671 ◽

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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A new species of Contomastix (Squamata, Teiidae) supported by total evidence, with remarks on diagnostic characters defining the genus

Herpetological Journal ◽

10.33256/hj29.1.2336 ◽

2019 ◽

pp. 23-36

Author(s):

Mario. R. Cabrera

Keyword(s):

New Species ◽

Geographic Distribution ◽

Phylogenetic Reconstruction ◽

Total Evidence ◽

Molecular Evidence ◽

Proximal Margin ◽

Diagnostic Characters ◽

Morphological Differences ◽

A New Species ◽

Molecular Characters

Formerly Cnemidophorus was thought to be the most speciose genus of Teiidae. This genus comprised four morphological groups that were later defined as four different genera, Ameivula, Aurivela, Cnemidophorus and Contomastix. The last appears as paraphyletic in a recent phylogenetic reconstruction based on morphology, but monophyletic in a reconstruction using molecular characters. Six species are allocated to Contomastix. One of them, C. lacertoides, having an extensive and disjunct geographic distribution in Argentina, Uruguay and Brazil. Preliminary analyses revealed morphological differences among its populations, suggesting that it is actually a complex of species. Here, we describe a new species corresponding to the Argentinian populations hitherto regarded as C. lacertoides, by integrating morphological and molecular evidence. Furthermore, we demonstrate that the presence of notched proximal margin of the tongue is a character that defines the genus Contomastix.

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Current and Future Pathotyping Platforms for Plasmodiophora brassicae in Canada

Plants ◽

10.3390/plants10071446 ◽

2021 ◽

Vol 10 (7) ◽

pp. 1446

Author(s):

Heather H. Tso ◽

Leonardo Galindo-González ◽

Stephen E. Strelkov

Keyword(s):

Crop Production ◽

Plasmodiophora Brassicae ◽

Cost Effective ◽

Turnaround Time ◽

Molecular Techniques ◽

Differential Set ◽

Management Plans ◽

Increased Sensitivity ◽

Phenotypic Methods ◽

Important Disease

Clubroot, caused by Plasmodiophora brassicae, is one of the most detrimental threats to crucifers worldwide and has emerged as an important disease of canola (Brassica napus) in Canada. At present, pathotypes are distinguished phenotypically by their virulence patterns on host differential sets, including the systems of Williams, Somé et al., the European Clubroot Differential set, and most recently the Canadian Clubroot Differential set and the Sinitic Clubroot Differential set. Although these are frequently used because of their simplicity of application, they are time-consuming, labor-intensive, and can lack sensitivity. Early, preventative pathotype detection is imperative to maximize productivity and promote sustainable crop production. The decreased turnaround time and increased sensitivity and specificity of genotypic pathotyping will be valuable for the development of integrated clubroot management plans, and interest in molecular techniques to complement phenotypic methods is increasing. This review provides a synopsis of current and future molecular pathotyping platforms for P. brassicae and aims to provide information on techniques that may be most suitable for the development of rapid, reliable, and cost-effective pathotyping assays.

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Physical map of the Saccharomyces cerevisiae genome at 110-kilobase resolution.

Genetics ◽

10.1093/genetics/127.4.681 ◽

1991 ◽

Vol 127 (4) ◽

pp. 681-698 ◽

Cited By ~ 6

Author(s):

A J Link ◽

M V Olson

Keyword(s):

Saccharomyces Cerevisiae ◽

Dna Hybridization ◽

Physical Map ◽

Single Copy ◽

Restriction Endonucleases ◽

Yeast Genome ◽

Hybridization Probes ◽

Copy Dna ◽

Single Copy Dna

Abstract A physical map of the Saccharomyces cerevisiae genome is presented. It was derived by mapping the sites for two restriction endonucleases, SfiI and NotI, each of which recognizes an 8-bp sequence. DNA-DNA hybridization probes for genetically mapped genes and probes that span particular SfiI and NotI sites were used to construct a map that contains 131 physical landmarks--32 chromosome ends, 61 SfiI sites and 38 NotI sites. These landmarks are distributed throughout the non-rDNA component of the yeast genome, which comprises 12.5 Mbp of DNA. The physical map suggests that those genes that can be detected and mapped by standard genetic methods are distributed rather uniformly over the full physical extent of the yeast genome. The map has immediate applications to the mapping of genes for which single-copy DNA-DNA hybridization probes are available.

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

Genetics ◽

10.1093/genetics/147.4.1843 ◽

1997 ◽

Vol 147 (4) ◽

pp. 1843-1854 ◽

Cited By ~ 8

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.

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Molecular Epidemiology of Tuberculosis: Current Insights

Clinical Microbiology Reviews ◽

10.1128/cmr.00061-05 ◽

2006 ◽

Vol 19 (4) ◽

pp. 658-685 ◽

Cited By ~ 220

Author(s):

Barun Mathema ◽

Natalia E. Kurepina ◽

Pablo J. Bifani ◽

Barry N. Kreiswirth

Keyword(s):

Vaccine Development ◽

Epidemiologic Studies ◽

Molecular Techniques ◽

Tb Control ◽

Molecular Approaches ◽

Accuracy And Precision ◽

Outbreak Investigations ◽

Short And Long Term ◽

Exogenous Reinfection

SUMMARY Molecular epidemiologic studies of tuberculosis (TB) have focused largely on utilizing molecular techniques to address short- and long-term epidemiologic questions, such as in outbreak investigations and in assessing the global dissemination of strains, respectively. This is done primarily by examining the extent of genetic diversity of clinical strains of Mycobacterium tuberculosis. When molecular methods are used in conjunction with classical epidemiology, their utility for TB control has been realized. For instance, molecular epidemiologic studies have added much-needed accuracy and precision in describing transmission dynamics, and they have facilitated investigation of previously unresolved issues, such as estimates of recent-versus-reactive disease and the extent of exogenous reinfection. In addition, there is mounting evidence to suggest that specific strains of M. tuberculosis belonging to discrete phylogenetic clusters (lineages) may differ in virulence, pathogenesis, and epidemiologic characteristics, all of which may significantly impact TB control and vaccine development strategies. Here, we review the current methods, concepts, and applications of molecular approaches used to better understand the epidemiology of TB.

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Modernizing the Toolkit for Arthropod Bloodmeal Identification

Insects ◽

10.3390/insects12010037 ◽

2021 ◽

Vol 12 (1) ◽

pp. 37

Author(s):

Erin M. Borland ◽

Rebekah C. Kading

Keyword(s):

Nuclear Dna ◽

Point Of Care ◽

Isotope Analysis ◽

Digital Pcr ◽

Lessons Learned ◽

Molecular Techniques ◽

Melting Analysis ◽

Field Deployment ◽

Blood Meal Identification ◽

Bloodmeal Identification

Understanding vertebrate–vector interactions is vitally important for understanding the transmission dynamics of arthropod-vectored pathogens and depends on the ability to accurately identify the vertebrate source of blood-engorged arthropods in field collections using molecular methods. A decade ago, molecular techniques being applied to arthropod blood meal identification were thoroughly reviewed, but there have been significant advancements in the techniques and technologies available since that time. This review highlights the available diagnostic markers in mitochondrial and nuclear DNA and discusses their benefits and shortcomings for use in molecular identification assays. Advances in real-time PCR, high resolution melting analysis, digital PCR, next generation sequencing, microsphere assays, mass spectrometry, and stable isotope analysis each offer novel approaches and advantages to bloodmeal analysis that have gained traction in the field. New, field-forward technologies and platforms have also come into use that offer promising solutions for point-of-care and remote field deployment for rapid bloodmeal source identification. Some of the lessons learned over the last decade, particularly in the fields of DNA barcoding and sequence analysis, are discussed. Though many advancements have been made, technical challenges remain concerning the prevention of sample degradation both by the arthropod before the sample has been obtained and during storage. This review provides a roadmap and guide for those considering modern techniques for arthropod bloodmeal identification and reviews how advances in molecular technology over the past decade have been applied in this unique biomedical context.

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Clinical Translation of Anti-aging Associated Genetics: Current Progress and Challenges

Current Aging Science ◽

10.2174/1874609814666210419104547 ◽

2021 ◽

Vol 14 ◽

Author(s):

Yi Wang

Keyword(s):

Genetic Manipulation ◽

Large Body ◽

Cost Effective ◽

Clinical Applications ◽

Biological Aging ◽

Aging Research ◽

Gene Therapies ◽

Molecular Approaches ◽

Gerontological Research ◽

Tremendous Challenge

Background: Currently, the focus of anti-aging research has been changed from geriatrics to biogerontology. This has taken anti-aging strategies from cost-effective but palliative therapeutics to active, molecular approaches. Outline: Over the years, a large body of basic gerontological research has indicated that the process of biological aging is closely associated with genetic factors. This leads to the development of various gene therapies such as RNA interference technology and results in a subsequent need of translating laboratory achievements into clinical applications. The translation has been a tremendous challenge at this stage with respect to practicality, safety and effectiveness of the genetic manipulation techniques. Objective: This review summarizes the current development of anti-aging strategies and the progress in the translation of laboratory achievements into clinical applications, highlights challenges encountered, and provides a prospective outlook for future anti-aging research.

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