Nuclear integrations: challenges for mitochondrial DNA markers

Zhang, Dexing; Hewitt, Godfrey M.

doi:10.1016/0169-5347(96)10031-8

Cited by 801 publications

(605 citation statements)

References 24 publications

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“…The mean base frequency for C. carbonaria was 31% A, 27% T, 28% C and 14% G, and for C. denticulata was 32% A, 27% T, 27% C and 14% G, confirming an under-representation of guanine as is normally observed in all mitochondrial genome (Zhang and Hewitt, 1996). The nucleotide sequence data determined for the present work are deposited in GenBank (accession numbers: EF 490386-EF 490401).…”

Section: Haplotypessupporting

confidence: 55%

Population genetics of the Amazonian tortoises, Chelonoidis denticulata and C. carbonaria, (Cryptodira: Testudinidae) in an area of sympatry

et al. 2007

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We conducted a population genetic analysis of the two Amazonian tortoises, Chelonoidis denticulata (n = 40) and Chelonoidis carbonaria (n = 39) in a region of sympatry within the Xingú River basin. High levels of gene flow among sampled localities indicated lack of population structure for both species. Genetic parameters indicated a moderate level of genetic diversity in C. denticulata and neutrality tests suggested that populations of this species were in demographic equilibrium with respect to mitochondrial DNA. On the other hand, C. carbonaria presented low levels of genetic diversity and a signal of population expansion. Most records of C. denticulata are from areas of humid forest while those for C. carbonaria are from areas of semi-deciduous forests and transitional areas between humid and semi-deciduous forests. Therefore, the demographic expansion observed in C. carbonaria population could reflect an increase in the availability of suitable habitats for this species due to anthropogenic or natural processes. Additionally, we observed haplotype sharing between these two tortoise species indicating hybridization or incomplete lineage sorting.

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Section: Haplotypessupporting

confidence: 55%

Population genetics of the Amazonian tortoises, Chelonoidis denticulata and C. carbonaria, (Cryptodira: Testudinidae) in an area of sympatry

et al. 2007

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“…The existence of nuclear copies of mitochondrial genes or gene fragments has been recognized for many years now (Zhang and Hewitt 1996). These copies, if not properly identified, may lead to confusion in phylogeographic and systematic studies due to the comparison of non-homologous loci (mitochondrial markers in some individuals and nuclear copies others).…”

Section: Discussionmentioning

confidence: 99%

“…Kim et al 2006) and may be numerous (Richly and Leister 2004;Triant and DeWoody 2007b). Amplification of numts can be a problem in phylogenetic and systematic studies which are based on mitochondrial genes when numts are amplified in some taxa and mitochondrial copies in others, because the sequences being compared are not homologous and therefore are unlikely to reveal the evolutionary relationships of the taxa in question (Arctander 1995;Zhang and Hewitt 1996;Triant and DeWoody 2007a).…”

Section: Introductionmentioning

confidence: 99%

Nuclear copies of mitochondrial genes: another problem for ancient DNA

et al. 2010

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The application of ancient DNA techniques is subject to many problems caused primarily by low quality and by low quantity of DNA. For these reasons most studies employing ancient DNA rely on the characterization of mitochondrial DNA, which is present in many more copies per cell than nuclear DNA and hence more copies are likely to survive. We used universal and taxon specific mitochondrial primers to amplify DNA from museum specimens, and found many instances where the amplification of nuclear copies of the mitochondrial gene (numts) instead of the targeted mitochondrial fragment had occurred. Furthermore, the likelihood of amplifying numts increased dramatically when universal primers were utilized. Here we suggest that ancient DNA practitioners must consider the possibility that numts can be amplified at higher rates than previously thought. This is another complication for ancient DNA studies, but it also suggests that more extensive inclusion of nuclear markers in ancient DNA studies should be feasible.R.-J. den Tex · J. A. Leonard (&)

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“…This included the 5 0 end of the mtDNA cytochrome b gene (800 bp) which was sequenced: (1) to increase the nucleotide sample of mtDNA protein coding genes, and (2) because cyt b is physically separated by roughly 8000 bp from the ATPase gene region within the mtDNA genome. Thus, comparison of the two gene regions can provide modest evidence against inadvertent amplification of a nuclear pseudogene (Bermingham et al, 1996;Zhang and Hewitt, 1996; but see also Lopez et al, 1994). We also sequenced 1005 bp of the mtDNA ribosomal genes representing portions of the 12S (429 bp) and 16S (576 bp) ribosomal subunits.…”

Section: Dna Sequencingmentioning

confidence: 99%