Mitochondrial DNA variation in the grasshopper Sinipta dalmani: application of long-PCR to the development of a homologous probe

Genome ◽  
2005 ◽  
Vol 48 (6) ◽  
pp. 971-976 ◽  
Author(s):  
S M Pensel ◽  
J C Vilardi ◽  
M I Remis
Keyword(s):  
Mitochondrial Dna ◽  
Nucleotide Diversity ◽  
Natural Populations ◽  
Rflp Analysis ◽  
Universal Primers ◽  
Chromosome Polymorphism ◽  
Genetic Studies ◽  
Dna Variation ◽  
Long Pcr ◽  
Complete Mtdna

RFLP analysis of mtDNA in natural populations is a valuable tool for phylogeographic and population genetic studies. The amplification of long DNA fragments using universal primers may contribute to the development of novel homologous probes in species for which no previous genomic information is available. Here we report how we obtained the complete mtDNA genome of Sinipta dalmani (Orthoptera) in 2 fragments (7 and 9 kb) using primers of conserved regions. The specificity of the PCR reactions was ultimately confirmed by several lines of evidence. These fragments were used as a probe for a mtDNA RFLP study in S. dalmani that analyzed the pattern of haplotype distribution and nucleotide diversity within and among chromosomally differentiated natural populations. Our results suggest that the restriction in gene flow detected at the molecular level may explain the chromosome differentiation detected previously and the maintenance of chromosome polymorphism in some areas of S. dalmani geographic distribution.Key words: long-PCR, mitochondrial DNA, universal primers, RFLP, grasshopper.

Mitochondrial DNA variation in natural populations of the mushroomAgaricus bisporus

1998 ◽  
Vol 7 (1) ◽  
pp. 19-33 ◽  
Author(s):  
JIANPING XU ◽  
RICHARD W. KERRIGAN ◽  
ANTON S. SONNENBERG ◽  
PHILIPPE CALLAC ◽  
PAUL A. HORGEN ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Natural Populations ◽  
Dna Variation

scholarly journals Application of a random walk model to geographic distributions of animal mitochondrial DNA variation.

Genetics ◽  
1993 ◽  
Vol 135 (4) ◽  
pp. 1209-1220 ◽  
Author(s):  
J E Neigel ◽  
J C Avise
Keyword(s):  
Mitochondrial Dna ◽  
Isolation By Distance ◽  
Natural Populations ◽  
Data Sets ◽  
Long Distance ◽  
Dna Variation ◽  
Distance Model ◽  
Limited Dispersal ◽  
Geographic Distributions ◽  
Lineage Structure

Abstract In rapidly evolving molecules, such as animal mitochondrial DNA, mutations that delineate specific lineages may not be dispersed at sufficient rates to attain an equilibrium between genetic drift and gene flow. Here we predict conditions that lead to nonequilibrium geographic distributions of mtDNA lineages, test the robustness of these predictions and examine mtDNA data sets for consistency with our model. Under a simple isolation by distance model, the variance of an mtDNA lineage's geographic distribution is expected be proportional to its age. Simulation results indicated that this relationship is fairly robust. Analysis of mtDNA data from natural populations revealed three qualitative distributional patterns: (1) significant departure of lineage structure from equilibrium geographic distributions, a pattern exhibited in three rodent species with limited dispersal; (2) nonsignificant departure from equilibrium expectations, exhibited by two avian and two marine fish species with potentials for relatively long-distance dispersal; and (3) a progression from nonequilibrium distributions for younger lineages to equilibrium distributions for older lineages, a condition displayed by one surveyed avian species. These results demonstrate the advantages of considering mutation and genealogy in the interpretation of mtDNA geographic variation.

Ribosomal DNA variation in the grasshopper, Dichroplus elongatus

Genome ◽  
2002 ◽  
Vol 45 (6) ◽  
pp. 1125-1133 ◽  
Author(s):  
M Clemente ◽  
M I Remis ◽  
J C Vilardi
Keyword(s):  
Ribosomal Dna ◽  
Fragment Size ◽  
Natural Populations ◽  
Size Variation ◽  
Rflp Analysis ◽  
Restriction Enzymes ◽  
Genetic Distances ◽  
Climatic Variables ◽  
Dna Variation ◽  
And Migration

We report an RFLP analysis of ribosomal DNA variation in natural populations of the grasshopper, Dichroplus elongatus, previously analyzed for mitochondrial DNA variation. DNA samples were digested with five restriction enzymes, BamHI, EcoRI, HindIII, PstI, andXbaI.BamHI was the only enzyme that showed no variation. The remaining enzymes showed fragment size variation at both intra- and interpopulation levels. Stepwise regression analysis revealed that the average number of length variants per individual is significantly associated with altitude. Moreover, the same analysis indicated that the frequency of some restriction variants exhibits a significant regression on both geographic and climatic variables. The intra- and interpopulation variability of rDNA was analysed by Lynch's and Hedrick's similarity indices using presence or absence of a fragment and band intensities, respectively. The corresponding neighbour-joining (N-J) trees based on Lynch's and Hedrick's genetic distances resulted in similar topologies. However, these trees were not in agreement with the N-J dendrogram obtained from mtDNA data previously reported by Clemente et al. (2000). The disagreement between mtDNA and rDNA phenograms along with the observed correlation between rDNA variability and geographical and climatic variables suggest some form of selection, besides genetic drift and migration, is involved in the pattern of rDNA variation.Key words: Dichroplus elongatus, ribosomal DNA, RFLP, environmental variables.

scholarly journals Thermal adaptation and clinal mitochondrial DNA variation of European anchovy

2014 ◽  
Vol 281 (1792) ◽  
pp. 20141093 ◽  
Author(s):  
Gonçalo Silva ◽  
Fernando P. Lima ◽  
Paulo Martel ◽  
Rita Castilho
Keyword(s):  
Mitochondrial Dna ◽  
Natural Populations ◽  
Thermal Adaptation ◽  
Secondary Contact ◽  
Nutrient Concentrations ◽  
Clinal Variation ◽  
Oxygen Utilization ◽  
Low Frequencies ◽  
Dna Variation ◽  
European Anchovy

Natural populations of widely distributed organisms often exhibit genetic clinal variation over their geographical ranges. The European anchovy, Engraulis encrasicolus , illustrates this by displaying a two-clade mitochondrial structure clinally arranged along the eastern Atlantic. One clade has low frequencies at higher latitudes, whereas the other has an anti-tropical distribution, with frequencies decreasing towards the tropics. The distribution pattern of these clades has been explained as a consequence of secondary contact after an ancient geographical isolation. However, it is not unlikely that selection acts on mitochondria whose genes are involved in relevant oxidative phosphorylation processes. In this study, we performed selection tests on a fragment of 1044 bp of the mitochondrial cytochrome b gene using 455 individuals from 18 locations. We also tested correlations of six environmental features: temperature, salinity, apparent oxygen utilization and nutrient concentrations of phosphate, nitrate and silicate, on a compilation of mitochondrial clade frequencies from 66 sampling sites comprising 2776 specimens from previously published studies. Positive selection in a single codon was detected predominantly (99%) in the anti-tropical clade and temperature was the most relevant environmental predictor, contributing with 59% of the variance in the geographical distribution of clade frequencies. These findings strongly suggest that temperature is shaping the contemporary distribution of mitochondrial DNA clade frequencies in the European anchovy.

scholarly journals Nonneutral Mitochondrial DNA Variation in Humans and Chimpanzees

Genetics ◽  
1996 ◽  
Vol 142 (3) ◽  
pp. 953-963 ◽  
Author(s):  
Michael W Nachman ◽  
Wesley M Brown ◽  
Mark Stoneking ◽  
Charles F Aquadro
Keyword(s):  
Mitochondrial Dna ◽  
Sequence Data ◽  
Mitochondrial Protein ◽  
Mitochondrial Diseases ◽  
Neutral Model ◽  
Nucleotide Substitutions ◽  
Dna Variation ◽  
Mtdna Sequence ◽  
Restriction Sites ◽  
Complete Mtdna

Abstract We sequenced the NADH dehydrogenase subunit 3 (ND3) gene from a sample of 61 humans, five common chimpanzees, and one gorilla to test whether patterns of mitochondrial DNA (mtDNA) variation are consistent with a neutral model of molecular evolution. Within humans and within chimpanzees, the ratio of replacement to silent nucleotide substitutions was higher than observed in comparisons between species, contrary to neutral expectations. To test the generality of this result, we reanalyzed published human RFLP data from the entire mitochondrial genome. Gains of restriction sites relative to a known human mtDNA sequence were used to infer unambiguous nucleotide substitutions. We also compared the complete mtDNA sequences of three humans. Both the RFLP data and the sequence data reveal a higher ratio of replacement to silent nucleotide substitutions within humans than is seen between species. This pattern is observed at most or all human mitochondrial genes and is inconsistent with a strictly neutral model. These data suggest that many mitochondrial protein polymorphisms are slightly deleterious, consistent with studies of human mitochondrial diseases.

scholarly journals Mitochondrial DNA variation in natural populations of Japanese larch (Larix kaempferi)

2009 ◽  
Vol 58 (1-6) ◽  
pp. 234-241 ◽  
Author(s):  
Lerma San Jose-Maldia ◽  
Kohji Uchida ◽  
Nobuhiro Tomaru
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Variation ◽  
Southern Hybridization ◽  
Mitochondrial Gene ◽  
Natural Populations ◽  
Rflp Analysis ◽  
Japanese Larch ◽  
Larix Kaempferi ◽  
Marginal Population ◽  
Sequence Tagged Sites

AbstractLevels of genetic variation within and among natural populations of Japanese larch [Larix kaempferi (Lamb.) Carrière] were evaluated by Restriction Fragment Length Polymorphism (RFLP) analysis of mitochondrial DNA (mtDNA) obtained from 209 individuals representing 14 natural populations distributed across most of the species’ natural range in central Japan. Polymorphisms were screened by two RFLP techniques: Southern hybridization of mitochondrial gene probes and Polymerase Chain Reaction (PCR)-RFLP analysis of sequence-tagged sites. However, obvious polymorphism was only detected around the coxIII gene, following digestion with the EcoRI restriction enzyme, in the Southern hybridization analysis. Five haplotypes were identified across the 14 populations, with 11 populations exhibiting little or no genetic variation. Within-population genetic variation was low (HS = 0.158), while population differentiation was substantial (a standardized genetic differentiation measure, G’ST = 0.581). The northernmost, marginal population on Mt. Manokamidake made a significant contribution to the total detected genetic variation. The mtDNA variation displayed geographic structure despite the restricted natural distribution of Japanese larch. Results of this study should be useful for establishing criteria for the genetic conservation and management of natural populations of the species.

Mitochondrial DNA variation in natural populations of endangered Indian Feather-Back Fish, Chitala chitala

2011 ◽  
Vol 39 (2) ◽  
pp. 1765-1775 ◽  
Author(s):  
Anup Mandal ◽  
Vindhya Mohindra ◽  
Rajeev Kumar Singh ◽  
Peyush Punia ◽  
Ajay Kumar Singh ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Natural Populations ◽  
Dna Variation ◽  
Chitala Chitala

Mitochondrial DNA Diversity in Jackass Morwong (Nemadactylus macropterus: Teleostei) from Australian and New Zealand Waters

1994 ◽  
Vol 51 (5) ◽  
pp. 1101-1109 ◽  
Author(s):  
Peter M. Grewe ◽  
Adam J. Smolenski ◽  
Robert D. Ward
Keyword(s):  
Mitochondrial Dna ◽  
New Zealand ◽  
Nucleotide Diversity ◽  
Restriction Enzymes ◽  
Spatial Patterning ◽  
Stock Structure ◽  
Dna Variation ◽  
Tasman Sea ◽  
Significant Divergence ◽  
Nucleotide Divergence

The jackass morwong (Nemadactylus macropterus), a commercially valuable marine fish in the Australian–New Zealand region, was surveyed for genetic variation as part of a larger project aimed at clarifying its stock structure. Mitochondrial DNA variation in 166 jackass morwong from seven southern Australian localities was examined using nine restriction enzymes. The 28 haplotypes identified gave an overall nucleon diversity of 0.671. Mean nucleotide diversity per sample was 0.458%, with a (corrected) nucleotide divergence among samples of 0.001%. There was no significant spatial patterning. Five hundred individuals from eight southern Australian localities and one New Zealand locality were examined using three restriction enzymes detecting polymorphic cut sites. The 33 haplotypes identified gave an overall nucleon diversity of 0.635. Mean nucleotide diversity per sample was 1.247%, with a (corrected) nucleotide divergence among samples of 0.002%. No differentiation was detected among the Australian localities. The New Zealand sample showed weak but significant divergence from the Australian samples. These results were similar to those from a concurrent allozyme analysis, and we conclude that there is appreciable nuclear and mitochondrial DNA gene flow among Australian localities, while the Tasman Sea separating Australia from New Zealand acts as a partial barrier.

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