(re)Producing mtEve

The discovery that the rate of evolution of vertebrate mitochondrial DNA is rapid, compared to the rate for vertebrate nuclear DNA, has resulted in its widespread use in evolutionary studies. Comparison of mitochondrial and nuclear DNA divergences among echinoid and vertebrate taxa of similar ages indicates that the rapid rate of vertebrate mitochondrial DNA evolution is, in part, an artifact of a widely divergent rate of nuclear DNA evolution. This disparity in relative rates of mitochondrial and nuclear DNA divergence suggests that the controls and constraints under which the mitochondrial and nuclear genomes operate are evolving independently, and provides evidence that is independent of fossil dating for a robust rejection of a generalized molecular clock hypothesis of DNA evolution.

Mitochondrial DNA (mtDNA) lineages are recognized as important components of intra- and interspecific biodiversity, and allow to reveal colonization routes and phylogeographic structure of many taxa. Among these is the genus Cervus that is widely distributed across the Holarctic. We obtained sequences of complete mitochondrial genomes from 13 Cervus taxa and included them in global phylogenetic analyses of 71 Cervinae mitogenomes. The well-resolved phylogenetic trees confirmed Cervus to be monophyletic. Molecular dating based on several fossil calibration points revealed that ca. 2.6 Mya two main mitochondrial lineages of Cervus separated in Central Asia, the Western (including C. hanglu and C. elaphus) and the Eastern (comprising C. albirostris, C. canadensis and C. nippon). We also observed convergent changes in the composition of some mitochondrial genes in C. hanglu of the Western lineage and representatives of the Eastern lineage. Several subspecies of C. nippon and C. hanglu have accumulated a large portion of deleterious substitutions in their mitochondrial protein-coding genes, probably due to drift in the wake of decreasing population size. In contrast to previous studies, we found that the relic haplogroup B of C. elaphus was sister to all other red deer lineages and that the Middle-Eastern haplogroup E shared a common ancestor with the Balkan haplogroup C. Comparison of the mtDNA phylogenetic tree with a published nuclear genome tree may imply ancient introgressions of mtDNA between different Cervus species as well as from the common ancestor of South Asian deer, Rusa timorensis and R. unicolor, to the Cervus clade.

The topology of the network of western Eurasian mitochondrial DNA (mtDNA) lineage clusters in the context of their expansion and spread in this geographic area is analysed. Special attention is devoted to the inner nods of the reconstructed median network tree, ancestral to mtDNA lineage clusters H and V, to the Caucasus and Trans-Caucasus area populations and to the problem of timing of the expansion of the Caucasoid-specific mtDNA lineage clusters in western Europeversusin the Trans-Caucasus. It appears on several examples that typical for Western Europe mtDNA lineage clusters exhibit significantly earlier expansion in the Trans-Caucasus area. Furthermore, the lineage cluster, radiating from the pre-HV node, is significantly more frequent and divergent in the Trans-Caucasus populations than it is in Europe. Meanwhile, a comparison of the Central Asian and the Trans-Caucasus area populations shows that the former have a significant share of eastern Asian-specific mtDNA lineages, which are almost absent in the latter. Finally, a picture starts to emerge, revealing an ancient Indian—Trans-Caucasian—European continuum of a significant proportion of human maternal lineage clusters, dating back to the period between the Upper and Lower Pleniglacials.KeywordsBefore PresentRFLP TypingLineage ClusterEuropean HaplogroupDemic DiffusionThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Ganoderma lucidum is one of the well-known medicinal basidiomycetes worldwide. The mitochondrion, referred to as the second genome, is an organelle found in most eukaryotic cells and participates in critical cellular functions. Elucidating the structure and function of this genome is important to understand completely the genetic contents of G. lucidum. In this study, we assembled the mitochondrial genome of G. lucidum and analyzed the differential expressions of its encoded genes across three developmental stages. The mitochondrial genome is a typical circular DNA molecule of 60,630 bp with a GC content of 26.67%. Genome annotation identified genes that encode 15 conserved proteins, 27 tRNAs, small and large rRNAs, four homing endonucleases, and two hypothetical proteins. Except for genes encoding trnW and two hypothetical proteins, all genes were located on the positive strand. For the repeat structure analysis, eight forward, two inverted, and three tandem repeats were detected. A pair of fragments with a total length around 5.5 kb was found in both the nuclear and mitochondrial genomes, which suggests the possible transfer of DNA sequences between two genomes. RNA-Seq data for samples derived from three stages, namely, mycelia, primordia, and fruiting bodies, were mapped to the mitochondrial genome and qualified. The protein-coding genes were expressed higher in mycelia or primordial stages compared with those in the fruiting bodies. The rRNA abundances were significantly higher in all three stages. Two regions were transcribed but did not contain any identified protein or tRNA genes. Furthermore, three RNA-editing sites were detected. Genome synteny analysis showed that significant genome rearrangements occurred in the mitochondrial genomes. This study provides valuable information on the gene contents of the mitochondrial genome and their differential expressions at various developmental stages of G. lucidum. The results contribute to the understanding of the functions and evolution of fungal mitochondrial DNA.

We aimed to explore the distribution and variation of porcine mitochondrial DNA (mtDNA) lineages in northern India, expanding on previous local-scale research by incorporating a broader, global context. A total of 82 domestic pigs samples from Uttarakhand and Jharkhand were sequenced for the mtDNA control region (417bp) and compared to 1517 published sequences of Sus scrofa from various regions worldwide. The Uttarakhand sequences, previously analyzed in a local context by our research group, were incorporated into this study for a broader global comparative analysis. The analysis revealed complex clustering patterns of 18 haplotypes with distinct phylogeographic signals, reflecting diverse maternal lineages within the domestic pig populations in these two states of India. Two distinct subspecies of wild boar (W1 and W2) were identified, providing strong phylogeographic evidence for their distribution in India. A novel cluster (MC-I), localized to the Chotanagpur plateau, was detected, offering insights into its connection with the D5 cluster. Significantly, the study found evidence for a separate domestication center in the Himalayan foothills, supported by the presence of most Uttarakhand samples in Cluster D3, linking it to ancient human migration and subsequent pig dispersal across the region. The diverse maternal lineages in Uttarakhand may be linked to ancient human migration, suggesting human-mediated dispersal of pigs in the region. These findings contribute to the understanding of Sus scrofa's evolutionary history and global migration patterns, emphasizing the genetic uniqueness of pigs in the Indian subcontinent and its significance in the broader context of porcine genetic resources.

Recently, two divergent mitochondrial lineages were described in a survey of 12 scattered populations of the threespine stickleback (Gasterosteus aculeatus) on the Queen Charlotte Islands (QCI), western Canada, one of which, possibly a relict lineage, was subsequently shown to characterize stickleback from the western Pacific near Japan. In the present study, we assayed 985 fish from 85 QCI populations for mitochondrial lineage using a restriction enzyme test. Our data indicate that the relict lineage was largely limited (18 of 20 populations) to adjacent watersheds in the northeast corner of the QCI close to a suspected glacial refugium, but we also found the lineage in two remote lakes on the west coast of the QCI, distant from any known refugia. We obtained a sample of 33 stickleback from the mid-Pacific and found both mitochondrial DNA (mtDNA) lineages, strongly suggesting ongoing dispersal of these fish across the Pacific, and inconsistent with previous suggestions of relict status for one of the lineages. Morphologically derived traits, such as loss of armour and loss of spines, occurred in both lineages, but these were more prevalent in the Japanese lineage. Surprisingly, 19 localities had both lineages, and within each of these there were no significant univariate or multivariate associations between lineages and morphology, suggesting few if any reproductive barriers between the divergent mtDNA lineages.

Positive and negative selection on the mitochondrial genome

The Bearing of Fossils and Mitochondrial DNA on the Evolution of Modern Humans, with a Critique of the 'Mitochondrial Eve' Hypothesis

Evolutionary rates of and selective constraints on the mitochondrial genomes of Orthoptera insects with different wing types

Many species have mitochondrial DNA lineages that are phylogenetically intermixed with other species, but studies have rarely tested the cause of such paraphyly. In this study, we tested two hypotheses that could explain mitochondrial paraphyly of Holarctic gadwalls (Anas strepera) with respect to Asian falcated ducks (A. falcata). First, hybridization could have resulted in falcated duck mitochondrial DNA (mtDNA) introgressing into the gadwall gene pool. Second, gadwalls and falcated ducks could have diverged so recently that mtDNA lineages have not sorted to reciprocal monophyly. We used coalescent analyses of three independent loci to distinguish between these two hypotheses. Two lines of evidence support introgression. First, analyses of the three loci combined show that some introgression is necessary to explain current genetic diversity in gadwalls. Second, we generated alternative predictions regarding time since divergence estimated from mtDNA: falcated ducks and gadwalls would have diverged between 65,000 and 700,000 years before present (ybp) under the introgression hypothesis and between 11,000 and 76,000 ybp under the incomplete lineage sorting hypothesis. The two independent nuclear introns indicated that these species diverged between 210,000 and 5,200,000 ybp, which did not overlap the predicted time for incomplete lineage sorting. These analyses also suggested that ancient introgression ( approximately 14,000 ybp) has resulted in the widespread distribution and high frequency of falcated-like mtDNA (5.5% of haplotypes) in North America. This is the first study to use a rigorous quantitative framework to reject incomplete lineage sorting as the cause of mitochondrial paraphyly.

Summary1. We determined whether two sympatric mitochondrial DNA (mtDNA) lineages of freshwater shrimp (Decapoda: Atyidae: Paratya australiensis) represent biological species and if they had concerted or independent population responses to hydrographic factors in small streams (the Granite Creeks) in southeastern Australia.2. Allozyme data indicated the presence of two gene pools at sites where the P. australiensis lineages were co‐occurring and the gene pools were statistically assigned with high probability to each respective lineage. This indicated that these mtDNA lineages in P. australiensis were reproductively isolated and thus biological species.3. Populations of both lineages were genetically homogeneous among lowland sites within streams, but were isolated by steep stream gradients among upland sites and for lowland–upland site comparisons. However, the magnitude of differentiation was markedly different between the two lineages. Allozyme diversity also differed between the two lineages, suggesting that they have different effective population sizes. Thus, differences in the magnitude of genetic divergence among populations were probably because of different life‐history characteristics, including dispersal ability and population size.4. Genetic population structure was mostly temporally stable, despite the extreme effects of drought during the first year and substantial stream‐flow during the second. However, stable isotope analyses revealed greater local movement in both lineages during the second year, as greater hydrological connectivity provided more opportunities for dispersal. Thus, although lowland populations within streams were genetically homogeneous, stable isotope data indicated that connections may be sporadic and result from accumulated small‐scale movements among refugial pools.5. Both lineages were therefore found to have similar small‐scale population responses to the unstable habitats of the Granite Creeks. Results highlight the importance of refugia for the capacity of biota to recover from drought and the need for multiple restored patches to reinstate natural population processes (e.g. resilience, recolonization) in degraded systems.

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.

Complete primary structures for the major non-coding region of 13 human and two chimpanzee mitochondrial DNAs (mtDNAs) were determined by direct sequencing via the polymerase chain reaction and compared to published sequences for one other human and two other chimpanzees. The human mtDNAs were chosen to represent the deepest branches found in a genealogical tree relating the restriction maps of 182 types of mtDNA. With the four chimpanzee sequences as outgroups, it was possible to place a root on the tree relating the human sequences. This root is consistent with the idea of an African origin for human mtDNA but does not rule out alternative hypotheses. Our sequences confirm a previous finding that the probability of substitution varies greatly among sites in the control region, some sites being so variable that they have probably changed many times since chimpanzees and humans had a common ancestor. In addition, our results show that the pattern of substitution in the control region has diverged since chimpanzees and humans had a common ancestor. These two observations may help to explain why it is hard to root the human tree with chimpanzee sequences as well as to determine the time of common ancestry for humans using the control region. Therefore, sequences were also obtained for a more slowly-evolving part of mtDNA, viz an 896-bp segment which includes parts of the genes for NADH dehydrogenase subunits 4 and 5. They show that the extent of divergence among humans in this segment of mtDNA is less than 3/79 of that between humans and chimpanzees. This result reinforces estimates based on restriction mapping that the last common ancestor of the humans sampled existed less than 200,000 years ago.

Thermal habit, metabolic rate and the evolution of mitochondrial DNA

Bioenergetics: Molecular biology, biochemistry, and pathology: 484 pp. 1990. Price: $110.00 U.S.; $132.00 outside U.S.