scholarly journals Models of mitochondrial DNA transmission genetics and evolution in higher eucaryotes

1982 ◽  
Vol 40 (1) ◽  
pp. 41-57 ◽  
Author(s):  
Robert W. Chapman ◽  
J. Claiborne Stephens ◽  
Robert A. Lansman ◽  
John C. Avise
Keyword(s):  
Mitochondrial Dna ◽  
Population Biology ◽  
Sequence Information ◽  
Random Allocation ◽  
Cell Lineages ◽  
Daughter Cells ◽  
Mtdna Sequence ◽  
Population Sizes ◽  
Future Value ◽  
Mtdna Evolution

SUMMARYThe future value of mitochondrial DNA (mtDNA) sequence information to studies in population biology will depend in part on understanding of mtDNA transmission genetics both within cell lineages and between animal generations. A series of stochastic models has been constructed here based on various possibilities concerning this transmission. Several of the models generate predictions inconsistent with available data and, hence, their assumptions are provisionally rejected. Other models cannot yet be falsified. These latter models include assumptions that (1) mtDNA's are sorted through cellular lineages by random allocation to daughter cells in germ cell lineages; (2) the effective intracellular population sizes (nM's) of mtDNA's are small; and (3) sperm may (or may not) provide a low level ‘gene-flow’ bridge between otherwise isolated female lineages. It is hoped that the models have helped to identify and will stimulate further empirical study of various parameters likely to strongly influence mtDNA evolution. In particular, critical experiments or measurements are needed to determine the effective sizes of mtDNA populations in germ (and somatic) cells and to examine possible paternal contributions to zygote mtDNA composition.

New approaches to dating suggest a recent age for the human mtDNA ancestor

1992 ◽  
Vol 337 (1280) ◽  
pp. 167-175 ◽  
Keyword(s):  
Mitochondrial Dna ◽  
Confidence Intervals ◽  
Standard Errors ◽  
Sequence Evolution ◽  
African Origin ◽  
Human Mitochondrial Dna ◽  
Mtdna Sequence ◽  
Mtdna Evolution ◽  
Recent Origin ◽  
Origin Hypothesis

The most critical and controversial feature of the African origin hypothesis of human mitochondrial DNA (mtDNA) evolution is the relatively recent age of about 200 ka inferred for the human mtDNA ancestor. If this age is wrong, and the actual age instead approaches 1 million years ago, then the controversy abates. Reliable estimates of the age of the human mtDNA ancestor and the associated standard error are therefore crucial. However, more recent estimates of the age of the human ancestor rely on comparisons between human and chimpanzee mtDNAs that may not be reliable and for which standard errors are difficult to calculate. We present here two approaches for deriving an intraspecific calibration of the rate of human mtDNA sequence evolution that allow standard errors to be readily calculated. The estimates resulting from these two approaches for the age of the human mtDNA ancestor (and approximate 95% confidence intervals) are 133 (63-356) and 137 (63-416) ka ago. These results provide the strongest evidence yet for a relatively recent origin of the human mtDNA ancestor.

scholarly journals The role of matrilineality in shaping patterns of Y chromosome and mtDNA sequence variation in southwestern Angola

2018 ◽  
Author(s):  
Sandra Oliveira ◽  
Alexander Hübner ◽  
Anne-Maria Fehn ◽  
Teresa Aço ◽  
Fernanda Lages ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Sequence Data ◽  
Population History ◽  
Female Population ◽  
Bantu Languages ◽  
Mtdna Sequence ◽  
Population Sizes ◽  
Group Variation ◽  
History Of ◽  
Previous Demonstration

AbstractSouthwestern Angola is a region characterized by contact between indigenous foragers and incoming food-producers, involving genetic and cultural exchanges between peoples speaking Kx’a, Khoe-Kwadi and Bantu languages. Although present-day Bantu-speakers share a patrilocal residence pattern and matrilineal principle of clan and group membership, a highly stratified social setting divides dominant pastoralists from marginalized groups that subsist on alternative strategies and have previously been though to have pre-Bantu origins. Here, we compare new high-resolution sequence data from 2.3 Mb of the non-recombining Y chromosome (NRY) from 170 individuals with previously reported mitochondrial genomes (mtDNA), to investigate the population history of seven representative southwestern Angolan groups (Himba, Kuvale, Kwisi, Kwepe, Twa, Tjimba, !Xun) and to study the causes and consequences of sex-biased processes in their genetic variation. We found no clear link between the formerly Kwadi-speaking Kwepe and pre-Bantu eastern African migrants, and no pre-Bantu NRY lineages among Bantu-speaking groups, except for small amounts of “Khoisan” introgression. We therefore propose that irrespective of their subsistence strategies, all Bantu-speaking groups of the area share a male Bantu origin. Additionally, we show that in Bantu-speaking groups, the levels of among-group and between-group variation are higher for mtDNA than for NRY. These results, together with our previous demonstration that the matriclanic systems of southwestern Angolan Bantu groups are genealogically consistent, suggest that matrilineality strongly enhances both female population sizes and interpopulation mtDNA variation.

scholarly journals The WT1-like transcription factor Klumpfuss maintains lineage commitment of enterocyte progenitors in the Drosophila intestine

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Jerome Korzelius ◽  
Sina Azami ◽  
Tal Ronnen-Oron ◽  
Philipp Koch ◽  
Maik Baldauf ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Cell Differentiation ◽  
Cell Fate ◽  
Progenitor Cell ◽  
Lineage Commitment ◽  
Proneural Gene ◽  
Cell Lineages ◽  
Daughter Cells ◽  
Mechanistic Insight ◽  
Insight Into

Abstract In adult epithelial stem cell lineages, the precise differentiation of daughter cells is critical to maintain tissue homeostasis. Notch signaling controls the choice between absorptive and entero-endocrine cell differentiation in both the mammalian small intestine and the Drosophila midgut, yet how Notch promotes lineage restriction remains unclear. Here, we describe a role for the transcription factor Klumpfuss (Klu) in restricting the fate of enteroblasts (EBs) in the Drosophila intestine. Klu is induced in Notch-positive EBs and its activity restricts cell fate towards the enterocyte (EC) lineage. Transcriptomics and DamID profiling show that Klu suppresses enteroendocrine (EE) fate by repressing the action of the proneural gene Scute, which is essential for EE differentiation. Loss of Klu results in differentiation of EBs into EE cells. Our findings provide mechanistic insight into how lineage commitment in progenitor cell differentiation can be ensured downstream of initial specification cues.

scholarly journals The coevolution of toxin and antitoxin genes drives the dynamics of bacterial addiction complexes and intragenomic conflict

2012 ◽  
Vol 279 (1743) ◽  
pp. 3706-3715 ◽  
Author(s):  
Daniel J. Rankin ◽  
Leighton A. Turner ◽  
Jack A. Heinemann ◽  
Sam P. Brown
Keyword(s):  
Theoretical Model ◽  
Kin Selection ◽  
Population Biology ◽  
Bacterial Genomes ◽  
Daughter Cells ◽  
Intragenomic Conflict ◽  
Bacterial Chromosomes ◽  
Gene Complexes ◽  
Deleterious Genes

Bacterial genomes commonly contain ‘addiction’ gene complexes that code for both a toxin and a corresponding antitoxin. As long as both genes are expressed, cells carrying the complex can remain healthy. However, loss of the complex (including segregational loss in daughter cells) can entail death of the cell. We develop a theoretical model to explore a number of evolutionary puzzles posed by toxin–antitoxin (TA) population biology. We first extend earlier results demonstrating that TA complexes can spread on plasmids, as an adaptation to plasmid competition in spatially structured environments, and highlight the role of kin selection. We then considered the emergence of TA complexes on plasmids from previously unlinked toxin and antitoxin genes. We find that one of these traits must offer at least initially a direct advantage in some but not all environments encountered by the evolving plasmid population. Finally, our study predicts non-transitive ‘rock-paper-scissors’ dynamics to be a feature of intragenomic conflict mediated by TA complexes. Intragenomic conflict could be sufficient to select deleterious genes on chromosomes and helps to explain the previously perplexing observation that many TA genes are found on bacterial chromosomes.

Disparate differentiation in hemopoietic colonies derived from human paired progenitors

Blood ◽  
1985 ◽  
Vol 66 (2) ◽  
pp. 327-332 ◽  
Author(s):  
AG Leary ◽  
LC Strauss ◽  
CI Civin ◽  
M Ogawa
Keyword(s):  
Stem Cell ◽  
Blood Cells ◽  
Individual Cell ◽  
Stem Cell Differentiation ◽  
Cellular Composition ◽  
Human Stem Cell ◽  
Cell Lineages ◽  
Daughter Cells ◽  
Cord Blood Cells ◽  
The Individual

Abstract We analyzed the differentiation of hemopoietic colonies derived from human paired daughter cells. Candidate progenitor cells were isolated by use of a micromanipulation technique from cultures of My-10 antigen- positive cord blood cells. Then nine to 36 hours later, the paired daughter cells were separated with a micromanipulator and allowed to form colonies in methylcellulose medium containing erythropoietin, phytohemagglutinin leukocyte-conditioned medium, and platelet-poor plasma. The cellular composition of the colonies was determined by differentiating all of the cells of the May-Grunwald-Giemsa-stained preparation. Of a total of 75 evaluable pairs of colonies, 35 consisted of 28 types of disparate pairs revealing nonhomologous lineage combinations. Forty pairs were homologous in lineage expression. However, the proportions of the individual cell lineages were significantly different in the members of some of the homologous pairs. Some pairs revealed significant differences in colony size. These observations are similar to those reported for murine paired progenitors and are consistent with the stochastic model of human stem cell differentiation.

scholarly journals Mitochondrial DNA Sequence Diversity in Mammals: A Correlation between the Effective and Census Population Sizes

2020 ◽  
Vol 12 (12) ◽  
pp. 2441-2449
Author(s):  
Jennifer James ◽  
Adam Eyre-Walker
Keyword(s):  
Mitochondrial Dna ◽  
Metabolic Rate ◽  
Population Size ◽  
Effective Population Size ◽  
Dna Sequence ◽  
Range Size ◽  
Effective Population ◽  
Population Sizes ◽  
Census Population Size ◽  
The Relationship

Abstract What determines the level of genetic diversity of a species remains one of the enduring problems of population genetics. Because neutral diversity depends upon the product of the effective population size and mutation rate, there is an expectation that diversity should be correlated to measures of census population size. This correlation is often observed for nuclear but not for mitochondrial DNA. Here, we revisit the question of whether mitochondrial DNA sequence diversity is correlated to census population size by compiling the largest data set to date, using 639 mammalian species. In a multiple regression, we find that nucleotide diversity is significantly correlated to both range size and mass-specific metabolic rate, but not a variety of other factors. We also find that a measure of the effective population size, the ratio of nonsynonymous to synonymous diversity, is also significantly negatively correlated to both range size and mass-specific metabolic rate. These results together suggest that species with larger ranges have larger effective population sizes. The slope of the relationship between diversity and range is such that doubling the range increases diversity by 12–20%, providing one of the first quantifications of the relationship between diversity and the census population size.

Mitochondrial DNA (mtDNA) Sequence Heterogeneity among and within Single Human CD34 Cells, T Cells, B Cells and Granulocytes.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 3217-3217
Author(s):  
Yoji Ogasawara ◽  
Kazutaka Nakayama ◽  
Magdalena Tarnowka ◽  
J. Philip McCoy ◽  
Jeffrey J. Molldrem ◽  
...  
Keyword(s):  
Stem Cells ◽  
T Cells ◽  
Mitochondrial Dna ◽  
B Cells ◽  
Single Cells ◽  
Base Substitution ◽  
Sequence Heterogeneity ◽  
Cd34 Cells ◽  
Mtdna Sequence ◽  
High Degree

Abstract Abnormalities of mitochondrial DNA (mtDNA) are responsible for a variety of inherited syndromes and have been broadly implicated in aging, cancer, and autoimmunity diseases. Mutations in mtDNA have been reported in myelodysplasia and leukemia, although their pathogenic mechanism remains uncertain. We have described age-dependent accumulation of mtDNA mutations, leading to a high degree of mtDNA sequence heterogeneity among normal marrow and blood CD34 cells as well as in granulocytes (Shin M et al, Blood101:3118 [2003], 103:553 [2004], 103:4466 [2004]). In order to examine mtDNA heterogeneity in detail, we developed a method for analysis of the mtDNA control region from single cells that were sorted by flow cytometry. Highly purified populations of CD34 cells, T cells, B cells, and granulocytes were obtained from five healthy adult donors. The sequence of the individual cells’ mtDNA was compared to the aggregate mtDNA for the respective cell type and differences were expressed as a measure of mtDNA heterogeneity among cells. Overall, heterogeneity was high: for circulating CD34 cells, 38±3.4%; for T cells, 37±14%; B cells, 36±10.8%; and for granulocytes, 48±7.2% (the value for granulocytes statistically differed from CD34 cells; p = 0.03). Most intercellular heterogeneity was due to polyC tract length variability; however, mtDNA base substitution mutations were also prevalent: 15±5.5% in CD34 cells; 15±9.0% in T cells, 15±6.7% in B cells; and 33±2.4% for granulocytes (granulocytes were significantly higher than other cells; p < 0.01). The higher rate of base substitution in granulocytes may reflect their greater exposure to reactive oxygen species. Surprisingly, for both polyC tract length differences and point mutations, the specific mtDNA abnormalities and the proportion of circulating cells characterized by these changes were similar among different cell lineages and relatively constant over time (~2 years) in the same donors. One inference from these results is that mtDNA heterogeneity during development is fixed in the primitive lymphohematopoietic stem cell compartment. In contrast to normal adults, circulating CD34 cells from patients obtained even years after successful allogeneic stem cell transplantation showed a remarkable level of mtDNA homogeneity, similar to the uniformity we have previously observed in cord blood CD34 cells and consistent with limited numbers of stem cells active in these individuals. Leukemic blast cells (from patients with AML-M2, AML evolving from CMML, and T-PLL) also showed a high degree of homogeneity. We propose that mtDNA sequence of single cells may be utilized as a natural genetic marker of hematopoietic progenitors and stem cells; to detect minimal residual disease in leukemia; and as a measure of the accumulation of mutagenic events in mammalian cells in vivo and in vitro.

Biological Significance and Profile of Length Heteroplasmy in the Hypervariable Segments of the Human Mitochondrial DNA Control Regions from Blood Cells.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 3815-3815
Author(s):  
Myung-Geun Shin ◽  
Hyeoung-Joon Kim ◽  
Hye-Ran Kim ◽  
Hee-Nam Kim ◽  
Il-Kwon Lee ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Control Region ◽  
Blood Cells ◽  
Biological Significance ◽  
Length Heteroplasmy ◽  
Conserved Sequence ◽  
Healthy Donors ◽  
Mtdna Sequence ◽  
Mtdna Replication ◽  
Two Peaks

Abstract A high incidence of mitochondrial DNA (mtDNA) variations was observed in both hypervariable region (HV) 1 and HV2; most mtDNA sequence variations were localized at poly C tract at nucleotides (nt) 303-315 (CCCCCCCTCCCCC, 7CT5C) in the HV2. Another poly C tract variant in HV1 at nt 16184-6193 have been suggested to be related with diabetes, dilated cardiomyopathy and some cancers. Poly C tract in HV2 is part of the conserved sequence block II located in 92-bp from the heavy strand replication origin. It is not yet clear whether poly C variants at nt 303–315 would lead to alterations in mtDNA replication. We hypothesized that some severe alterations in poly C tracts may lead to impairment of mtDNA replication. Here we present the profile of length heteroplasmy in HV from blood cells and its biological significance. A total of 57 maternally unrelated healthy donors were included and heparinized bloods were obtained from five age groups including 12 cord bloods. We amplified and sequenced the 1,121-bp control region including HV1 and HV2. In an attempt to investigate mtDNA length heteroplasmy, we carried out a qualitative and quantitative profiling length heteroplasmy using size-based PCR product separation by capillary electrophoresis (ABI 3100 Genetic Analyzer and ABI Prism Genotyper version 3.1). Length heteroplasmy was further confirmed by cloning and sequencing. Quantitative analysis of mtDNA molecules was performed using the QuantiTect SYBR Green PCR kit (Qiagen) and Rotor-Gene 3000 (Corbett Research) and standard plot was obtained from cloned cytochrome b gene. The mtDNA control region sequences showed 57 different haplotypes resulting from 77 polymorphic positions. Common polymorphisms were 73A>G (98%), 263A>G (91%), 16223C>T (47%), 16189T>C (35%), 150C>T (25%) and 152T>C (18%). The patterns of length heteroplasmy in the HV2 region were classified into 6 types. In the HV1 region, length heteroplasmy showed 8 variant peak patterns. The distribution of length heteroplasmy in poly C tracts at nt 303 – 315 was mtDNA mixture of 7CT6C+8CT6C (53%), 8CT6C+9CT6C (26%), 8CT6C+9CT6C+10CT6C (11%), 9CT6C+10CT6C +11CT6C (5%), 9CT6C+10CT6C (3%) and 7CT6C+6CT6C (2%). The distribution of length heteroplasmy pattern in poly C tract at nt 16184 – 16193 was 5CT4C+5CT3C (60%), 9C+10C+11C+12C (21%), 9C+10C+11C (5%), 3CT6C+3CT5C (3%), 9C+10C+11C+12C+13C (3%), 3CT4C+3CT3C (3%), 10C+11C+12C (2%), and 8C+9C+10C+11C+12C (2%). Interestingly, this study revealed that all healthy subjects showed length heteroplasmy in the HV1 and HV2 regions in contrast to previous studies. Length heteroplasmy in poly C 303–315 showed two groups of two peaks (n = 48) and more than three peaks (n = 9). MtDNA content from group with three peaks in poly C 303–315 (61,983,373 molecules/ul ± 33,219,871, mean±SD) was markedly lower than those with two peaks (133,777,955 molecules/ul ± 87,209,377). In conclusion, significantly higher rate of length heteroplasmy was observed in HV1 and HV2 from healthy donors and the presence of more than three mtDNA types in poly C at nt 303 – 315 might be associated with impairment of mtDNA replication.

Mitochondrial DNA Polymorphism, Population Structure, and Life History Variation in American Shad (Alosa sapidissima)

1989 ◽  
Vol 46 (8) ◽  
pp. 1446-1454 ◽  
Author(s):  
Paul Bentzen ◽  
Gregory C. Brown ◽  
William C. Leggett
Keyword(s):  
Mitochondrial Dna ◽  
Population Structure ◽  
Reproductive Traits ◽  
Restriction Endonuclease Analysis ◽  
American Shad ◽  
Life History Variation ◽  
Alosa Sapidissima ◽  
Mitochondrial Dna Polymorphism ◽  
Mtdna Variation ◽  
Mtdna Sequence

Restriction endonuclease analysis of mitochondrial DNA (mtDNA) variation was used to assess genetic differentiation and population structure in American shad (Alosa sapidissima) sampled from 14 rivers spanning the native range of the species (Florida to Quebec). Estimated mtDNA sequence divergences among 52 shad surveyed with 16 endonucleases were relatively low (mean 0.2%). The low level of mtDNA variation in shad may be a consequence of population bottlenecks that occurred during Pleistocene glacial maxima. A survey of 243 shad with four enzymes revealed several genotypes that were distributed across the range of the species. Three genotypes, a length variant and two single-enzyme genotypes, exhibited nonrandom, geographically clumped distributions. The distributions of shad mtDNA genotypes may have been influenced primarily by founder effects in the northern (glaciated) part of the range, and gene flow in the southern part of the range. The mtDNA data suggest that differences in the reproductive traits of northern and southern populations of shad, if genetically mediated, are likely to have evolved since the Pleistocene. The results of this study support theoretical predictions that mtDNA analysis is a highly sensitive means of examining population structures.

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