scholarly journals Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data.

Genetics ◽  
1992 ◽  
Vol 131 (2) ◽  
pp. 479-491 ◽  
Author(s):  
L Excoffier ◽  
P E Smouse ◽  
J M Quattro
Keyword(s):  
Mitochondrial Dna ◽  
Analysis Of Variance ◽  
Variance Components ◽  
Molecular Data ◽  
Human Mitochondrial Dna ◽  
Analysis Of Molecular Variance ◽  
Molecular Variance ◽  
Monte Carlo Studies ◽  
Different Types ◽  
Metric Distances

Abstract We present here a framework for the study of molecular variation within a single species. Information on DNA haplotype divergence is incorporated into an analysis of variance format, derived from a matrix of squared-distances among all pairs of haplotypes. This analysis of molecular variance (AMOVA) produces estimates of variance components and F-statistic analogs, designated here as phi-statistics, reflecting the correlation of haplotypic diversity at different levels of hierarchical subdivision. The method is flexible enough to accommodate several alternative input matrices, corresponding to different types of molecular data, as well as different types of evolutionary assumptions, without modifying the basic structure of the analysis. The significance of the variance components and phi-statistics is tested using a permutational approach, eliminating the normality assumption that is conventional for analysis of variance but inappropriate for molecular data. Application of AMOVA to human mitochondrial DNA haplotype data shows that population subdivisions are better resolved when some measure of molecular differences among haplotypes is introduced into the analysis. At the intraspecific level, however, the additional information provided by knowing the exact phylogenetic relations among haplotypes or by a nonlinear translation of restriction-site change into nucleotide diversity does not significantly modify the inferred population genetic structure. Monte Carlo studies show that site sampling does not fundamentally affect the significance of the molecular variance components. The AMOVA treatment is easily extended in several different directions and it constitutes a coherent and flexible framework for the statistical analysis of molecular data.

Is the subspecies classification of the freshwater eels Anguilla australis australis Richardson and A. a. schmidtii Phillipps still valid?

1999 ◽  
Vol 50 (3) ◽  
pp. 261 ◽  
Author(s):  
L. H. Dijkstra ◽  
D. J. Jellyman
Keyword(s):  
Mitochondrial Dna ◽  
New Zealand ◽  
Fisheries Management ◽  
Gene Pool ◽  
Molecular Evidence ◽  
Analysis Of Molecular Variance ◽  
Molecular Variance ◽  
Anguilla Australis ◽  
Freshwater Eels

The validity of the subspecies classification of Anguilla australis was reviewed by sequencing the control region of mitochondrial DNA. Samples of A. a. australis (Australia) and A. a. schmidtii (New Zealand), collected from two sites within each country were compared by analysis of molecular variance (AMOVA) and neighbour joining. There was no molecular evidence to support the present subspecies designation and they would be more appropriately merged into the single classification of A. australis, the Australasian shortfinned eel. As Australian and New Zealand populations of this species share a common gene pool, fisheries management needs to be carried out cooperatively between the two countries.

Geographic Origin of Human Mitochondrial DNA Revisited

1992 ◽  
Vol 41 (3) ◽  
pp. 384-391 ◽  
Author(s):  
M. Stoneking ◽  
S. T. Sherry ◽  
L. Vigilant
Keyword(s):  
Mitochondrial Dna ◽  
Geographic Origin ◽  
Human Mitochondrial Dna

Human Mitochondrial DNA Polymerase Holoenzyme: Reconstitution and Characterization†

Biochemistry ◽  
2000 ◽  
Vol 39 (7) ◽  
pp. 1702-1708 ◽  
Author(s):  
Allison A. Johnson ◽  
Yu-chih Tsai ◽  
Steven W. Graves ◽  
Kenneth A. Johnson
Keyword(s):  
Mitochondrial Dna ◽  
Dna Polymerase ◽  
Human Mitochondrial Dna ◽  
Mitochondrial Dna Polymerase

scholarly journals Modular Architecture of the Hexameric Human Mitochondrial DNA Helicase

2007 ◽  
Vol 367 (5) ◽  
pp. 1382-1391 ◽  
Author(s):  
Tawn D. Ziebarth ◽  
Carol L. Farr ◽  
Laurie S. Kaguni
Keyword(s):  
Mitochondrial Dna ◽  
Dna Helicase ◽  
Modular Architecture ◽  
Human Mitochondrial Dna

Assignment of two mitochondrially synthesized polypeptides to human mitochondrial DNA and their use in the study of intracellular mitochondrial interaction

1982 ◽  
Vol 2 (1) ◽  
pp. 30-41
Author(s):  
N A Oliver ◽  
D C Wallace
Keyword(s):  
Mitochondrial Dna ◽  
Restriction Site ◽  
Mitochondrial Protein ◽  
Mitochondrial Protein Synthesis ◽  
Human Mitochondrial Dna ◽  
Ht1080 Cells ◽  
Mitochondrial Dnas ◽  
A Cell ◽  
Dna Restriction ◽  
Restriction Site Polymorphisms

Two mitochondrially synthesized marker polypeptides, MV-1 and MV-2, were found in human HeLa and HT1080 cells. These were assigned to the mitochondrial DNA in HeLa-HT1080 cybrids and hybrids by demonstrating their linkage to cytoplasmic genetic markers. These markers include mitochondrial DNA restriction site polymorphisms and resistance to chloramphenicol, an inhibitor of mitochondrial protein synthesis. In the absence of chloramphenicol, the expression of MV-1 and MV-2 in cybrids and hybrids was found to be directly proportional to the ratio of the parental mitochondrial DNAs. In the presence of chloramphenicol, the marker polypeptide linked to the chloramphenicol-sensitive mitochondrial DNA continued to be expressed. This demonstrated that resistant and sensitive mitochondrial DNAs can cooperate within a cell for gene expression and that the CAP-resistant allele was dominant or codominant to sensitive. Such cooperation suggests that mitochondrial DNAs can be exchanged between mitochondria.

Species delimitation of colour polymorphic Cladophorus (Coleoptera: Lycidae) from New Guinea

Zootaxa ◽  
2017 ◽  
Vol 4320 (3) ◽  
pp. 505 ◽  
Author(s):  
ROMANA KALOUSOVA ◽  
LADISLAV BOCAK
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Dna ◽  
Related Species ◽  
Species Delimitation ◽  
Morphological Differentiation ◽  
Morphological Characters ◽  
Molecular Data ◽  
Closely Related Species ◽  
Dna Fragment ◽  
Colour Patterns

Cladophorus Guérin-Méneville, 1830 are endemic Papuan net-winged beetles which take part in highly diverse Müllerian mimicry rings. Available specimens were sequenced for cox1–tRNA-Leu–cox2 mitochondrial DNA fragment and the species delimitations were based on the genetic distance, phylogenetic analysis, and morphology. Three earlier described species were identified in the recently collected material and further 10 species are described: C. pallescens sp. nov., C. bicolor sp. nov., C. craterensis sp. nov., C. motykai sp. nov., C. mindikensis sp. nov., C. kailakiensis sp. nov., C. manokwarensis sp. nov., C. haiaensis sp. nov., C. humeralis sp. nov., and C. boceki sp. nov. DNA-based identifications provided some ambiguous results and closely related species could not be robustly delimited using solely molecular data. Additionally, the species limits were based on clearly defined morphological characters and the morphological differentiation was found unlinked from the genetic divergence. Colour patterns cannot be used for identification because all species available in more specimens were polymorphic and followed various local co-mimics. The Papuan fauna of Cladophorus is very diverse and the closely related species regularly occur in limited regions. Differentiation within restricted ranges is therefore considered as the main speciation mode. 

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