scholarly journals A method for calibrating molecular clocks and its application to animal mitochondrial DNA.

Genetics ◽  
1993 ◽  
Vol 135 (4) ◽  
pp. 1197-1208 ◽  
Author(s):  
M Lynch ◽  
P E Jarrell
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Substitution Rate ◽  
Nuclear Dna ◽  
Average Rate ◽  
Divergence Time ◽  
Poisson Model ◽  
Generalized Least Squares ◽  
Molecular Clocks ◽  
Empirical Estimates

Abstract A generalized least-squares procedure is introduced for the calibration of molecular clocks and applied to the complete mitochondrial DNA sequences of 13 animal species. The proposed technique accounts for both nonindependence and heteroscedasticity of molecular-distance data, problems that have not been taken into to account in such analyses in the past. When sequence-identity data are transformed to account for multiple substitutions/site, the molecular divergence scales linearly with time, but with substantially more variation in the substitution rate than expected under a Poisson model. Significant levels of divergence are predicted at zero divergence time for most loci, suggesting high levels of site-specific heterozygosity among mtDNA molecules establishing in sister taxa. For nearly all loci, the baseline heterozygosity is lower and the substitution rate is higher in mammals relative to other animals. There is considerable variation in the evolutionary rate among loci but no compelling evidence that the average rate of mtDNA evolution is elevated with respect to that of nuclear DNA. Using the observed patterns of interspecific divergence, empirical estimates are derived for the mean coalescence times of organelles colonizing sister taxa.

scholarly journals Some maternal lineages of domestic horses may have origins in East Asia revealed with further evidence of mitochondrial genomes and HVR-1 sequences

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4896 ◽  
Author(s):  
Hongying Ma ◽  
Yajiang Wu ◽  
Hai Xiang ◽  
Yunzhou Yang ◽  
Min Wang ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
East Asia ◽  
Dna Sequences ◽  
De Novo ◽  
Divergence Time ◽  
Upper Paleolithic ◽  
Phylogenetic Study ◽  
Mitochondrial Genomes ◽  
Domestic Horses ◽  
Matrilineal Inheritance

Objectives There are large populations of indigenous horse (Equus caballus) in China and some other parts of East Asia. However, their matrilineal genetic diversity and origin remained poorly understood. Using a combination of mitochondrial DNA (mtDNA) and hypervariable region (HVR-1) sequences, we aim to investigate the origin of matrilineal inheritance in these domestic horses. Methods To investigate patterns of matrilineal inheritance in domestic horses, we conducted a phylogenetic study using 31 de novo mtDNA genomes together with 317 others from the GenBank. In terms of the updated phylogeny, a total of 5,180 horse mitochondrial HVR-1 sequences were analyzed. Results Eightteen haplogroups (Aw-Rw) were uncovered from the analysis of the whole mitochondrial genomes. Most of which have a divergence time before the earliest domestication of wild horses (about 5,800 years ago) and during the Upper Paleolithic (35–10 KYA). The distribution of some haplogroups shows geographic patterns. The Lw haplogroup contained a significantly higher proportion of European horses than the horses from other regions, while haplogroups Jw, Rw, and some maternal lineages of Cw, have a higher frequency in the horses from East Asia. The 5,180 sequences of horse mitochondrial HVR-1 form nine major haplogroups (A-I). We revealed a corresponding relationship between the haplotypes of HVR-1 and those of whole mitochondrial DNA sequences. The data of the HVR-1 sequences also suggests that Jw, Rw, and some haplotypes of Cw may have originated in East Asia while Lw probably formed in Europe. Conclusions Our study supports the hypothesis of the multiple origins of the maternal lineage of domestic horses and some maternal lineages of domestic horses may have originated from East Asia.

scholarly journals Microhomology-mediated end joining is the principal mediator of double-strand break repair during mitochondrial DNA lesions

2016 ◽  
Vol 27 (2) ◽  
pp. 223-235 ◽  
Author(s):  
Satish Kumar Tadi ◽  
Robin Sebastian ◽  
Sumedha Dahal ◽  
Ravi K. Babu ◽  
Bibha Choudhary ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Nuclear Dna ◽  
Ex Vivo ◽  
Strand Break ◽  
Mitochondrial Disorders ◽  
Dna Lesions ◽  
End Joining ◽  
Dsb Repair

Mitochondrial DNA (mtDNA) deletions are associated with various mitochondrial disorders. The deletions identified in humans are flanked by short, directly repeated mitochondrial DNA sequences; however, the mechanism of such DNA rearrangements has yet to be elucidated. In contrast to nuclear DNA (nDNA), mtDNA is more exposed to oxidative damage, which may result in double-strand breaks (DSBs). Although DSB repair in nDNA is well studied, repair mechanisms in mitochondria are not characterized. In the present study, we investigate the mechanisms of DSB repair in mitochondria using in vitro and ex vivo assays. Whereas classical NHEJ (C-NHEJ) is undetectable, microhomology-mediated alternative NHEJ efficiently repairs DSBs in mitochondria. Of interest, robust microhomology-mediated end joining (MMEJ) was observed with DNA substrates bearing 5-, 8-, 10-, 13-, 16-, 19-, and 22-nt microhomology. Furthermore, MMEJ efficiency was enhanced with an increase in the length of homology. Western blotting, immunoprecipitation, and protein inhibition assays suggest the involvement of CtIP, FEN1, MRE11, and PARP1 in mitochondrial MMEJ. Knockdown studies, in conjunction with other experiments, demonstrated that DNA ligase III, but not ligase IV or ligase I, is primarily responsible for the final sealing of DSBs during mitochondrial MMEJ. These observations highlight the central role of MMEJ in maintenance of mammalian mitochondrial genome integrity and is likely relevant for deletions observed in many human mitochondrial disorders.

scholarly journals Integrative taxonomy of a new and highly-diverse genus of onchidiid slugs from the Coral Triangle (Gastropoda, Pulmonata, Onchidiidae)

ZooKeys ◽  
2018 ◽  
Vol 763 ◽  
pp. 1-111 ◽  
Author(s):  
Tricia C. Goulding ◽  
Munawar Khalil ◽  
Shau Hwai Tan ◽  
Benoît Dayrat
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Dna Analysis ◽  
Nuclear Dna ◽  
Comparative Anatomy ◽  
Morphological Characters ◽  
Integrative Taxonomy ◽  
The Philippines ◽  
Coral Triangle ◽  
Yellow Orange

A new genus of onchidiid slugs,WallaconchisGoulding & Dayrat,gen. n., is described, including ten species. Five species were previously described but known only from the type material:Wallaconchisater(Lesson, 1830),W.graniferum(Semper, 1880),W.nangkauriense(Plate, 1893),W.buetschlii(Stantschinsky, 1907), andW.gracile(Stantschinsky, 1907), all of which were originally classified inOnchidiumBuchannan, 1800. Many new records are provided for these five species, which greatly expand their known geographic distributions. Five species are new:WallaconchisachleitneriGoulding,sp. n.,W.comendadoriGoulding & Dayrat,sp. n.,W.melanesiensisGoulding & Dayrat,sp. n.,W.sinanuiGoulding & Dayrat,sp. n., andW.uncinusGoulding & Dayrat,sp. n.Nine of the tenWallaconchisspecies are found in the Coral Triangle (eastern Indonesia and the Philippines). Sympatry is high, with up to six species found on the island of Bohol (Philippines) and eight species overlapping in northern Sulawesi (Indonesia).Wallaconchisis distinguished from other onchidiids by its bright dorsal colors (red, yellow, orange) but those are extremely variable and not useful for specific identification. Internally, the reproductive system can be used to identify allWallaconchisspecies. The copulatory organs ofWallaconchisspecies are especially diverse compared to other onchidiid genera, and the possible role of reproductive incompatibility in species diversification is discussed. All specimens examined were freshly collected for the purpose of a worldwide revision of the Onchidiidae Rafinesque, 1815. The species are well delineated using DNA sequences and comparative anatomy. Mitochondrial DNA analysis yields thirteen molecular units separated by a large barcode gap, while nuclear DNA yields nine units. By integrating nuclear DNA and mitochondrial DNA with morphology, ten species are recognized. The natural history of each species (e.g., the microhabitat where they are found) is also documented. Nomenclature is addressed thoroughly (the types of all onchidiid species were examined, lectotypes were designated when needed,nomina dubiaare discussed). Morphological characters, transitions to new microhabitats, and diversification processes are discussed in the context of a robust molecular phylogeny.

A molecular perspective on the evolution of scleractinian corals

1996 ◽  
Vol 1 ◽  
pp. 39-57 ◽  
Author(s):  
Sandra L. Romano
Keyword(s):  
Dna Sequences ◽  
Fossil Record ◽  
Nuclear Dna ◽  
Genome Structure ◽  
Divergence Time ◽  
Morphological Diversity ◽  
Morphological Characters ◽  
Molecular Data ◽  
Scleractinian Corals ◽  
Molecular Techniques

The evolutionary history of scleractinian corals, based on morphological taxonomy and inferences from the fossil record, has been poorly understood. Molecular techniques developed over the past ten years are now being used to gain a new perspective on scleractinian phylogeny. DNA sequences, mitochondrial genome structure, and morphological characters support a basal position for the Anthozoa in the phylum Cnidaria. Mitochondrial and nuclear DNA sequences suggest a relatively derived position of the order Scleractinia within the class Anthozoa. Mitochondrial and nuclear DNA sequences have provided a new hypothesis for evolution within the Scleractinia that is different from hypotheses based on morphological characters of extant and fossil taxa. Groupings within the two major lineages defined by molecular data do not correspond to morphological suborder groupings although groupings of genera within families do correspond to traditional taxonomy. This new molecular hypothesis suggests that the Scleractinia are represented by two major lineages that diverged from each other before the appearance of the scleractinian skeleton in the fossil record. This divergence time supports the hypotheses that the Scleractinia are not related to the Rugosa of the Paleozoic and that the scleractinian skeleton has evolved more than once. These two major lineages may represent two architectural strategies within the Scleractinia that have led to their great morphological diversity.

A path from mitochondria to the yeast nucleus

1988 ◽  
Vol 319 (1193) ◽  
pp. 127-133 ◽  
Keyword(s):  
Mitochondrial Dna ◽  
Control System ◽  
Mitochondrial Genome ◽  
Dna Sequences ◽  
Nuclear Dna ◽  
Nuclear Ribosomal Dna ◽  
Regulatory Function ◽  
Dna Repeat ◽  
Elevated Expression ◽  
Respiratory Deficient

We have identified a path in yeast, from mitochondria to the nucleus, which may have a regulatory function in mitochondrial biogenesis. This path is evident as an elevated expression of a number of nuclear DNA sequences in response to specific defects in the mitochondrial genome, including the absence of mitochondrial DNA in p 0 petites. Among those nuclear sequences preferentially expressed in certain respiratory-deficient cells are stable poly (A) + transcripts derived from the so-called non-transcribed spacer region of the nuclear ribosomal DNA repeat, where they are most abundant in the p 0 petite. Although the function of these unusual RNAs is unclear, the observations may reflect the presence of a mitochondrial homeostatic control system in yeast, which we suggest could function to adjust the mass of mitochondria and mitochondrial DNA in the cell in response to inequities in organelle apportionment during cell budding.

scholarly journals Evidence of hybridization, mitochondrial introgression and biparental inheritance of the kDNA minicircles in Trypanosoma cruzi I

2019 ◽  
Author(s):  
Fanny Rusman ◽  
Noelia Floridia-Yapur ◽  
Paula G. Ragone ◽  
Patricio Diosque ◽  
Nicolás Tomasini
Keyword(s):  
Mitochondrial Dna ◽  
Trypanosoma Cruzi ◽  
Dna Sequences ◽  
Dna Content ◽  
Nuclear Dna ◽  
Genetic Exchange ◽  
Natural Hybridization ◽  
Biparental Inheritance ◽  
Hybrid Strain ◽  
Mitochondrial Introgression

AbstractBackgroundGenetic Exchange in Trypanosoma cruzi is controversial not only in relation to its frequency but also in relation to its mechanism. A mechanism of parasexuality has been proposed based on laboratory hybrids, but population genomics strongly suggests meiosis. In addition, mitochondrial introgression has been reported several times in natural isolates although its mechanism is not clear. Moreover, hybrid DTUs (TcV and TcVI) have inherited at least part of the kinetoplastic DNA (kDNA = mitochondrial DNA) from both parents.Methodology/Principal findingsIn order to address such topics, we sequenced and analyzed fourteen nuclear DNA fragments and three kDNA maxicircle genes in three TcI stocks which are natural clones potentially involved in events of genetic exchange. We also deep-sequenced (a total of 6,146,686 paired-end reads) the hypervariable region of kDNA minicircles (mHVR) in such three strains. In addition, we analyzed the DNA content by flow cytometry to address cell ploidy. We observed that most polymorphic sites in nuclear loci showed a hybrid pattern in one cloned strain and the other two cloned strains were compatible as parental strains (or nearly related to the true parents). The three clones have almost the same ploidy and the DNA content was similar to the reference strain Sylvio (an almost diploid strain). Despite maxicircle genes evolve faster than nuclear housekeeping ones, we did not detect polymorphism in the sequence of three maxicircle genes showing mito-nuclear discordance. In addition, the hybrid stock shared 66% of its mHVR clusters with one putative parental and 47% with the another one. In contrast, the putative parental stocks shared less than 30% of the mHVR clusters among them.Conclusions/significanceThe results suggest a reductive division, a natural hybridization, biparental inheritance of the minicircles in the hybrid and maxicircle introgression. The models including such phenomena and that would explain the relationships between these three clones are discussed.Author summaryChagas disease, an important public health problem in Latin America, is caused by the parasite Trypanosoma cruzi. Despite it is a widely studied parasite, several questions about the biology of genetic exchange remain. Meiosis has not been yet observed in laboratory, although inferred from population genomic studies. In addition, previous results suggest that the mitochondrial DNA (called kDNA) may be inherited from both parents in hybrids. Here, we analyzed a hybrid strain and the potential parents to address about the mechanisms of genetic exchange at nuclear and mitochondrial level. We observed that the hybrid strain has heterozygous patterns and DNA content compatible with an event of meiosis. In addition, we observed that the evolutionary histories of nuclear DNA and maxicircles (a part of the kDNA) were discordant and the three strains share identical DNA sequences. Mitochondrial introgression of maxicircle DNA from one genotype to another may explain this observation. In addition, we detected that the hybrid strain shared minicircles (another part of the kDNA) with both parental strains. Our results suggest that hybridization implied meiosis and biparental inheritance of the kDNA. Further research is required to address such phenomena in detail.

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