Transfer of mitochondrial DNA from the northern red-backed vole (Clethrionomys rutilus) to the bank vole (C. glareolus)

Summary Using a silver staining method to detect DNA fragments produced by restriction enzymes, it was possible to compare mitochondrial DNAs (mtDNAs) from 85 individuals of the bank vole (Clethrionomys glareolus) trapped at 25 localities in Fennoscandia. There are two distinctly different mtDNA lineages, one occurring in southern and central Fennoscandia and the other in the northern parts. A fragment comparison method shows about 12.7% nucleotide sequence divergence between these two lineages. This major difference between animals of the same species could theoretically be explained by intraspecific lineage survivorship independent of species hybridization, or by introduction of an atypical mtDNA via hybridization with a closely related species. Analysis of mtDNAs from the two otherClethrionomys species present in Fennoscandia (C. rutilus andC. rufocanus) shows that the mtDNA of northernC. glareolus is very similar to that ofC. rutilus and that the mtDNA lineages of these two species cluster together in a phenogram, with small genetic distances among them. By contrast, electrophoresis of proteins encoded by 17 nuclear loci reveals fixed allelic differences between these two species at 8 loci. Hence the presence of two distinctly different mtDNA lineages withinC. glareolus may be a consequence of a limited episode of hybridization betweenC. glareolus andC. rutilus, probably during the postglacial recolonization of Fennoscandia 8000–13,000 years ago.     

Ancient DNA Reveals That the Genetic Structure of the Northern Han Chinese Was Shaped Prior to 3,000 Years Ago

The Han Chinese are the largest ethnic group in the world, and their origins, development, and expansion are complex. Many genetic studies have shown that Han Chinese can be divided into two distinct groups: northern Han Chinese and southern Han Chinese. The genetic history of the southern Han Chinese has been well studied. However, the genetic history of the northern Han Chinese is still obscure. In order to gain insight into the genetic history of the northern Han Chinese, 89 human remains were sampled from the Hengbei site which is located in the Central Plain and dates back to a key transitional period during the rise of the Han Chinese (approximately 3,000 years ago). We used 64 authentic mtDNA data obtained in this study, 27 Y chromosome SNP data profiles from previously studied Hengbei samples, and genetic datasets of the current Chinese populations and two ancient northern Chinese populations to analyze the relationship between the ancient people of Hengbei and present-day northern Han Chinese. We used a wide range of population genetic analyses, including principal component analyses, shared mtDNA haplotype analyses, and geographic mapping of maternal genetic distances. The results show that the ancient people of Hengbei bore a strong genetic resemblance to present-day northern Han Chinese and were genetically distinct from other present-day Chinese populations and two ancient populations. These findings suggest that the genetic structure of northern Han Chinese was already shaped 3,000 years ago in the Central Plain area.     

Evidence for mitochondrial DNA recombination in a human population of island Melanesia

Mitochondrial DNA (mtDNA) analysis has proved useful in studies of recent human evolution and the genetic affinities of human groups of different geographical regions. As part of an extensive survey of mtDNA diversity in present-day Pacific populations, we obtained sequence information of the hypervariable mtDNA control region of 452 individuals from various localities in the western Pacific. The mtDNA types fell into three major groups which reflect the settlement history of the area. Interestingly, we detected an extremely rare point mutation at high frequency in the small island of Nguna in the Melanesian archipelago of Vanuatu. Phylogenetic analysis of the mtDNA data indicated that the mutation was present in individuals of separate mtDNA lineages. We propose that the multiple occurrence of a rare mutation event in one isolated locality is highly improbable, and that recombination between different mtDNA types is a more likely explanation for our observation. If correct, this conclusion has important implications for the use of mtDNA in phylogenetic and evolutionary studies.     

PATERNAL LEAKAGE OF MITOCHONDRIAL DNA IN A FUCUS (PHAEOPHYCEAE) HYBRID ZONE1

Eukaryotic mitochondria are mostly uniparentally (maternally) inherited, although mtDNA heteroplasmy has been reported in all major lineages. Heteroplasmy, the presence of more than one mitochondrial genome in an individual, can arise from recombination, point mutations, or by occasional transmission of the paternal mtDNA (=paternal leakage). Here, we report the first evidence of mtDNA paternal leakage in brown algae. In Denmark, where Fucus serratus L. and Fucus evanescens C. Agardh have hybridized for years, we found eight introgressed individuals that possessed the very distinct haplotypes of each parental species. The finding of heteroplasmy in individuals resulting from several generations of backcrosses suggests that paternal leakage occurred in earlier generations and has persisted through several meiotic bottlenecks.     

The use of PNAs and their derivatives in mitochondrial gene therapy

Human mitochondria contain their own genome, mtDNA. This small molecule encodes 24 RNA species and 13 polypeptides, which are essential components of the mitochondrial respiratory chain. The mitochondrial genome is present in hundreds or thousands of copies in each cell and is believed to turnover throughout the life of the cell. Defects of the mitochondrial genome (mtDNA) cause a variety of multisystemic disorders routinely affecting the muscle and nervous system. There is currently no effective treatment for patients with defects of the mitochondrial genome. In many patients, defective cells harbour two sub-populations of mtDNA (a situation termed heteroplasmy), one being normal, the other containing the pathogenic mutation. The mutated copy is often recessive, with biochemical and clinical defects only becoming apparent when the levels of mutated mtDNA outweigh the normal copies. It has therefore been postulated that by selectively preventing replication of the mutated mtDNA, the normal copy will propagate, restoring biochemical function. The search has therefore been on during recent years to identify an antigenomic molecule that will fulfil this criterion. Following evidence that peptide nucleic acids could selectively inhibit replication of templates carrying a known pathogenic mtDNA mutation in vitro,we report on the progress of this approach and the various modificationsthat are now being used to improve the efficacy of PNA-based antigenomic inhibition.     

The use of PNAs and their derivatives in mitochondrial gene therapy

Summary Human mitochondria contain their own genome, mtDNA. This small molecule encodes 24 RNA species and 13 polypeptides, which are essential components of the mitochondrial respiratory chain. The mitochondrial genome is present in hundreds or thousands of copies in each cell and is believed to turnover throughout the life of the cell. Defects of the mitochondrial genome (mtDNA) cause a variety of multisystemic disorders routinely affecting the muscle and nervous system. There is currently no effective treatment for patients with defects of the mitochondrial genome. In many patients, defective cells harbour two sub-populations of mtDNA (a situation termed heteroplasmy), one being normal, the other containing the pathogenic mutation. The mutated copy is often recessive, with biochemical and clinical defects only becoming apparent when the levels of mutated mtDNA outweigh the normal copies. It has therefore been postulated that by selectively preventing replication of the mutated mtDNA, the normal copy will propagate, restoring biochemical function. The search has therefore been on during recent years to identify an antigenomic molecule that will fulfil this criterion. Following evidence that peptide nucleic acids could selectively inhibit replication of templates carrying a known pathogenic mtDNA mutation in vitro, we report on the progress of this approach and the various modifications that are now being used to improve the efficacy of PNA-based antigenomic inhibition.     

Genetic analysis and uncertain taxonomic status of threatened Foskett Spring speckled dace

Foskett Spring is a small isolated desert spring in the Warner Basin of Oregon containing an undescribed subspecies of speckled dace protected under the US Endangered Species Act. Uncertainty regarding the taxonomic status of Foskett dace has raised questions about their evolutionary relationship to other more abundant populations in the Warner Basin. To address these questions, we sequenced 1,982 base pairs (bp) of the ND2 and cyt-b genes of mitochondrial DNA (mtDNA) for 85 fish from Foskett Spring, the surrounding Warner Basin, and the adjacent Goose Lake Basin. We observed 58 unique mtDNA haplotypes defined by 96 bp substitutions in both genes. MtDNA sequences were highly divergent and reciprocally monophyletic between dace from the Warner and Goose Lake Basins, with sequence divergences (5 and 3% at ND2 and cyt-b, respectively) in the range usually observed between fish species. In contrast, mean sequence divergence between Foskett dace and other Warner Basin populations was less than 1%, with no evidence of reciprocal monophyly among mtDNA lineages. These results indicate that Foskett dace and other populations in the Warner Basin are approximately equally diverged from one another evolutionarily, suggesting similar times of divergence since the late Pleistocene. We believe further studies are needed to determine if rapid evolution of novel traits have occurred in dace inhabiting the unique ecological setting of Foskett Spring during the past 10,000 years.     

Complete mitochondrial genomes reveal neolithic expansion into Europe

The Neolithic transition from hunting and gathering to farming and cattle breeding marks one of the most drastic cultural changes in European prehistory. Short stretches of ancient mitochondrial DNA (mtDNA) from skeletons of pre-Neolithic hunter-gatherers as well as early Neolithic farmers support the demic diffusion model where a migration of early farmers from the Near East and a replacement of pre-Neolithic hunter-gatherers are largely responsible for cultural innovation and changes in subsistence strategies during the Neolithic revolution in Europe. In order to test if a signal of population expansion is still present in modern European mitochondrial DNA, we analyzed a comprehensive dataset of 1,151 complete mtDNAs from present-day Europeans. Relying upon ancient DNA data from previous investigations, we identified mtDNA haplogroups that are typical for early farmers and hunter-gatherers, namely H and U respectively. Bayesian skyline coalescence estimates were then used on subsets of complete mtDNAs from modern populations to look for signals of past population expansions. Our analyses revealed a population expansion between 15,000 and 10,000 years before present (YBP) in mtDNAs typical for hunters and gatherers, with a decline between 10,000 and 5,000 YBP. These corresponded to an analogous population increase approximately 9,000 YBP for mtDNAs typical of early farmers. The observed changes over time suggest that the spread of agriculture in Europe involved the expansion of farming populations into Europe followed by the eventual assimilation of resident hunter-gatherers. Our data show that contemporary mtDNA datasets can be used to study ancient population history if only limited ancient genetic data is available.     

Accelerated molecular evolution in Microtus (Rodentia) as assessed via complete mitochondrial genome sequences

Microtus is one of the most taxonomically diverse mammalian genera, including over 60 extant species. These rodents have evolved rapidly, as the genus originated less than 2 million years ago. If these numbers are taken at face value, then an average of 30 microtine speciation events have occurred every million years. One explanation for the rapid rate of cladogenesis in Microtus could be the karyotypic differentiation exhibited across the genus: diploid numbers range from 17 to 64. Despite the striking chromosomal variability within Microtus, phenotypic variation is unremarkable. To determine whether nucleotide substitution rates are also elevated in voles, we sequenced the entire mitochondrial DNA (mtDNA) genome of the Eurasian sibling vole (Microtus rossiaemeridionalis). We compared this genome to another previously sequenced vole mtDNA genome (Microtus kikuchii) and performed pairwise sequence comparisons with the mtDNA genomes of ten additional mammalian genera. We found that microtine mtDNA genomes are evolving more rapidly than any other mammalian lineage we sampled, as gauged by the rate of nucleotide substitution across the entire mtDNA genome as well as at each individual protein-coding gene. Additionally, we compared substitution rates within the cytochrome b gene to seven other rodent genera and found that Microtus mtDNA is evolving fastest. The root cause of accelerated evolution in Microtus remains uncertain, but merits further investigation. The mitochondrial genome sequence from this article has been deposited with the GenBank database under accession number DQ015676.     

Integrating morphology and mitochondrial DNA for species delimitation within the spruce budworm (Choristoneura fumiferana) cryptic species complex (Lepidoptera: Tortricidae)

Species in cryptic complexes tend to be very difficult, if not impossible, to identify using morphological characters. One such complex is the spruce budworm (Choristoneura fumiferana Clemens, 1865) species group, an economically important group of Nearctic forest pests. Morphological, ecological, behavioural and genetic characters have been studied to try to understand the taxonomy of this group better, but diagnostic character states differ in frequency rather than being complete replacements between each species. We used mitochondrial DNA (mtDNA), together with a new morphology‐based character system that focuses on forewing colour components, to determine if one or a combination of character sources can be used for species diagnoses within the spruce budworm complex. We characterized 47 forewing morphometric measurements and sequenced a 470 bp region of cytochrome c oxidase I mtDNA for 111 ingroup individuals comprising five taxa within the complex. Larval host association and coloration or adult pheromone attraction were used as the prior method for grouping individuals. Our results showed that linear discriminant analysis of morphometric wing characters gave unique clusters for all species on the first and second canonical axes, except for a partial overlap between C. fumiferana and C. biennis, which are not sympatric in nature. In contrast, mtDNA distinguished C. fumiferana, C. pinus pinus Freeman, 1953 and a group of western species, but the three western species (C. occidentalis Freeman, 1967 , C. biennis Freeman, 1967 and C. lambertiana Busck, 1915) shared mtDNA haplotypes. On the basis of the linear discriminant analysis of the combined character set, this study supports the application of both morphology and mtDNA within a framework of integrative taxonomy as the most accurate method for species identification. Furthermore, it demonstrates the utility of quantitative colour analysis, which may be particularly helpful for groups in which colour characters are difficult to divide into discrete units due to intergrading hues.     

Current versus historical population sizes in vertebrate species with high gene flow: a comparison based on mitochondrial DNA lineages and inbreeding theory for neutral mutations

Using inbreeding theory as applied to neutral alleles inherited maternally, we generate expected probability distributions of times to identity by descent for random pairs of mitochondrial genotypes within a population or within an entire species characterized by high gene flow. For comparisons with these expectations, empirical distributions of times to most recent common ancestry were calculated (by conventional mtDNA clock calibrations) from mtDNA haplotype distances observed within each of three vertebrate species--American eels, hardhead catfish, and redwinged blackbirds. These species were chosen for analysis because census population size in each is currently large and because both genetic and life-history data are consistent with the postulate that historical gene flow within these species has been high. The observed molecular distances among mtDNA lineages were two to three orders of magnitude lower than predicted from census sizes of breeding females, suggesting that rate of mtDNA evolution is decelerated in these species and/or that long-term effective population size is vastly smaller than present-day population size. Several considerations point to the latter possibility as most likely. The genetic structure of any species is greatly influenced by historical demography; even for species that are currently abundant, mtDNA gene lineages appear to have been channeled through fairly small numbers of ancestors.      

Polymerase chain reaction analysis of mitochondrial DNA polymorphism in N'Dama and Zebu cattle

A study of polymorphisms of mitochondrial DNA (mtDNA) of West African N'Dama (Bos taurus) and East African Zebu (B. indicus) cattle was carried out to obtain information on maternal phylogenetic relationships between these breeds. A relatively large sample size was made possible by using polymerase chain reaction (PCR) amplification of DNA prepared from small blood samples to generate fragments of two known polymorphic mtDNA regions, one within the gene encoding subunit 5 of NADH dehydrogenase and one encompassing the entire D-loop. This approach allowed us to achieve a higher resolution restriction analysis on mtDNA from more animals than would have been possible by conventional methods. PCR-amplified mtDNA of 58 animals from five populations was examined at 26 restriction sites by 16 enzymes. In this way 154 nucleotides of mtDNA were scanned for polymorphism. Six polymorphic sites were located by this means, five of which were within the D-loop and one of which was within the NADH dehydrogenase 5 gene. None of the polymorphisms observed could be con sidered typical of breed or type.     

Recombination in human mitochondrial DNA?

The possibility of recombination in human mitochondrial DNA (mtDNA) has been hotly debated over the last few years. In this study, a general model of recombination in circular molecules is developed and applied to a recently published African sample (n = 21) of complete mtDNA sequences. It is shown that the power of correlation measures to detect recombination in circular molecules can be vanishingly small and that the data are consistent with the given model and no recombination only if the overall heterogeneity in mutation rate is <0.09.     

The Origins of Domesticated Cattle

The origin of domestic cattle has perplexed archaeologists for more than a century. Researchers have proposed various theories, which offer alternative spatial and chronological models for the origin and spread of domesticated cattle. One point of discussion is whether domestic cattle had a single or multiple origins; however, most authorities considered that the first steps towards cattle domestication were taken in southwest Asia and that domesticated cattle entered Europe with pastoralists migrating from this region. Domesticated taurine cattle were thought to have entered Africa in successive waves from southwest Asia, while zebu cattle migrated into Africa at a later date from Arabia and the Indian subcontinent. Analysis of mitochondrial DNA (mtDNA) shows that taurine and zebu cattle divergence before the Holocene and were probably domesticated independently. Recent mtDNA sequence data shows that African and European taurine cattle were probably domesticated independently, but that there was a process of genetic introgression between taurine and zebu cattle in Africa. Ancient DNA studies over the last 10 years suggest that Northern European aurochsens apparently contributed little or nothing to domestic cattle while Southern European aurochsens apparently made a significant input. However, Middle Eastern aurochsen, unfortunately not typed yet, are expected to be to be very similar to European breeds as well, both because archeological data suggest that the major center of domestication for European Bos taurus breeds was the Fertile Crescent (9), and also because a mtDNA sequence from a Syrian specimen dated at 8,000–9,000 years ago shows a typical European haplotype found both in modern breeds and the Italian aurochsen. Evidence seems to suggest that small to moderate levels of local gene flow from wild Bos primigenius females in selected breeds were either accepted or may be reinforced by Neolithic breeders.     

Genetic structure of a 2,500-year-old human population in China and its spatiotemporal changes

To examine temporal changes in population genetic structure, we compared the mitochondrial DNA (mtDNA) sequences of three populations that lived in the same location, Linzi, China, in different periods: 2,500 years ago (the Spring-Autumn era), 2,000 years ago (the Han era), and the present day. Two indices were used to compare the genetic differences: the frequency distributions of the radiating haplotype groups and the genetic distances among the populations. The results indicate that the genetic backgrounds of the three populations are distinct from each other. Inconsistent with the geographical distribution, the 2,500-year-old Linzi population showed greater genetic similarity to present-day European populations than to present-day east Asian populations. The 2, 000-year-old Linzi population had features that were intermediate between the present-day European/2,500-year-old Linzi populations and the present-day east Asian populations. These relationships suggest the occurrence of drastic spatiotemporal changes in the genetic structure of Chinese people during the past 2,500 years.     

BIOGEOGRAPHY OF A WIDESPREAD FRESHWATER CRUSTACEAN: PSEUDOCONGRUENCE AND CRYPTIC ENDEMISM IN THE NORTH AMERICAN DAPHNIA LAEVIS COMPLEX

The lack of morphological variation in many freshwater invertebrates over vast distances has been cited as evidence for their frequent, long-distance dispersal. This scenario implies that vicariance will be an insignificant determinant of species distributions or diversity. We carried out a phylogeographic and population genetics study of one widespread crustacean group, the North American Daphnia laevis complex. Allozyme and sequence variation of two mtDNA genes (12S and 16S rRNA) clearly indicates the existence of five morphologically cryptic, largely allopatric groups (Daphnia dubia, D. laevis laevis, D. laevis gessneri, D. magniceps magniceps, and D. magniceps pacifica ssp. n.). Within each of these groups, there is weak or no genetic differentiation over large geographic areas suggesting their recent long-distance dispersal. The present-day distributions and phylogeography of the regional groups suggests the occurrence of both deep and shallow vicariance events. Although divergence times from mtDNA sequences do indicate both deep and shallow divergences, these estimates are incongruent with their proposed vicariance times. The results show that even within closely related freshwater invertebrates, a complex biogeography exists, whose analysis is made difficult by long-distance dispersal, cryptic endemism, and pseudocongruence.     

Morphological and molecular evolution and their consequences for conservation and taxonomy in the Le Conte's thrasher Toxostoma lecontei

We evaluated geographic variation and subspecific taxonomy in the Le Conte's thrasher Toxostoma lecontei by analyzing DNA sequences from 16 nuclear loci, one mitochondrial DNA locus, and four study skin characters, and compared these data sets with previously published data on plumage coloration and different mtDNA genes. Morphological support for the southernmost taxon, T. l. arenicola, is relatively weak: multivariate analyses of morphometrics or back coloration do not provide diagnostic support, although one color character differs statistically. However, combined DNA analyses indicate that T. l. arenicola is diagnosable and reciprocally monophyletic, diverging from T. l. lecontei at least 140 000 yr ago. Little to no past introgression across a very short geographic distance despite the long period of isolation is strong evidence of independently evolving taxa. We suggest that the lack of morphological divergence in traits related to niche use has prevented the two taxa from invading each other's range. Despite relatively weak morphological differences we suggest that these two deeply divergent lineages merit species status, and we suggest Vizcaíno thrasher for the common name corresponding to T. l. arenicola. The population size of T. l. arenicola is small and the taxon is in need of preservation attention.     

Lost populations and preserving genetic diversity in the lion Panthera leo: Implications for its ex situ conservation

Two of the eight recognized lion subspecies, North African Barbary lion (Panthera leo leo) and South African Cape lion (Panthera leo melanochaita), have become extinct in the wild in the last 150 years. Based on sequences of mitochondrial DNA (mtDNA) control region (HVR1) extracted from museum specimens of four Barbary and one Cape lion, the former was probably a distinct population characterized by an invariable, unique mtDNA haplotype, whilst the latter was likely a part of the extant southern African lion population. Extinction of the Barbary line, which may still be found in “generic” zoo lions, would further erode lion genetic diversity. Therefore, appropriate management of such animals is important for maintaining the overall genetic diversity of the species. The mtDNA haplotype unique to the Barbary lion, in combination with the small size of the HVR1 analyzed (c. 130 bp), makes it possible and cost-effective to identify unlabelled Barbary specimens kept in museums and “generic” captive lions that may carry the Barbary line. An initial study of five samples from the lion collection of the King of Morocco, tested using this method, shows that they are not maternally Barbary.     

Involvement of autophagy and mitochondrial dynamics in determining the fate and effects of irreparable mitochondrial DNA damage

Mitochondrial DNA (mtDNA) is different in many ways from nuclear DNA. A key difference is that certain types of DNA damage are not repaired in the mitochondrial genome. What, then, is the fate of such damage? What are the effects? Both questions are important from a health perspective because irreparable mtDNA damage is caused by many common environmental stressors including ultraviolet C radiation (UVC). We found that UVC-induced mtDNA damage is removed slowly in the nematode Caenorhabditis elegans via a mechanism dependent on mitochondrial fusion, fission, and autophagy. However, knockdown or knockout of genes involved in these processes—many of which have homologs involved in human mitochondrial diseases—had very different effects on the organismal response to UVC. Reduced mitochondrial fission and autophagy caused no or small effects, while reduced mitochondrial fusion had dramatic effects.     

The structure of the small mitochondrial DNA of Kluyveromyces thermotolerans is likely to reflect the ancestral gene order in fungi

Mapping the 23-kb circular mitochondrial DNA from the yeast Kluyveromyces thermotolerans has shown that only one change occurs in the gene order in comparison to the 19-kb mtDNA of Candida (Torulopsis) glabrata. Sequence analysis of the mitochondrially encoded cytochrome oxidase subunit 2 gene reveals that despite their conserved gene order, the two small genomes are more distantly related than larger mtDNA molecules with multiple rearrangements. This result supports a previous observation that larger mitochondrial genomes are more prone to rearrange than smaller forms and suggests that the architecture of the two small molecules is likely to represent the structure of an ancestor.Correspondence to: G.D. Clark-Walker 0592