Mitochondrial DNA sequence diversity in extant Irish horse populations and in ancient horses

Equine mitochondrial DNA sequence variation was investigated in three indigenous Irish horse populations (Irish Draught Horse, Kerry Bog Pony and Connemara Pony) and, for context, in 69 other horse populations. There was no evidence of Irish Draught Horse or Connemara Pony sequence clustering, although the majority of Irish Draught Horse sequences (47%) were assigned to haplogroup D. Conversely, 31% of the Kerry Bog Pony sequences were assigned to the rare haplogroup E. In addition to the extant population analyses, ancient DNA sequences were generated from three out of four Irish archaeological specimens, all of which were assigned to haplogroup A.     

Mitochondrial sequence variation in the Guahibo Amerindian population from Venezuela

New data were obtained on mitochondrial DNA (mtDNA) from Guahibo from Venezuela, a group so far not studied using molecular data. A population sample (n = 59) was analyzed for mtDNA variation in two control-region hypervariable segments (HV1 and HV2) by sequencing. The presence or absence of a 9-bp polymorphism in the COII/tRNA(Lys) region was studied by direct amplification and electrophoretic identification. Thirty-eight variable sites were detected in regions HV1 and HV2, defining 26 mtDNA lineages; 23.7% of these were present in a single individual. The 9-bp deletion was found in 3.39% of individuals. Nucleotide and haplotype diversities were relatively high compared with other New World populations. The identified sequence haplotypes were classified into four major haplogroups (A-D) according to previous studies, with high frequencies for A (47.46%) and C (49.15%), low frequency for B (3.39%), and an absence of D.     

Mitochondrial DNA D‐loop sequence variation in maternal lineages of Iranian native horses

To understand the origin and genetic diversity of Iranian native horses, mitochondrial DNA (mtDNA) D‐loop sequences were generated for 95 horses from five breeds sampled in eight geographical locations in Iran. Sequence analysis of a 247‐bp segment revealed a total of 27 haplotypes with 38 polymorphic sites. Twelve of 19 mtDNA haplogroups were identified in the samples. The most common haplotypes were found within haplogroup X2. Within‐population haplotype and nucleotide diversities of the five breeds ranged from 0.838 ± 0.056 to 0.974 ± 0.022 and 0.011 ± 0.002 to 0.021 ± 0.001 respectively, indicating a relatively high genetic diversity in Iranian horses. The identification of several ancient sequences common between the breeds suggests that the lineage of the majority of Iranian horse breeds is old and obviously originated from a vast number of mares. We found in all native Iranian horse breeds lineages of the haplogroups D and K, which is concordant with the previous findings of Asian origins of these haplogroups. The presence of haplotypes E and K in our study also is consistent with a geographical west–east direction of increasing frequency of these haplotypes and a genetic fusion in Iranian horse breeds.     

Mitochondrial DNA variation in Pleistocene and modern Atlantic salmon from the Iberian glacial refugium

Current understanding of the postglacial colonization of Nearctic and Palearctic species relies heavily on inferences drawn from the phylogeographic analysis of contemporary generic variants. Modern postglacial populations are supposed to be representative of their Pleistocene ancestors, and their current distribution is assumed to reflect the different colonization success and dispersal patterns of refugial lineages. Yet, testing of phylogeographic models against ancestral genomes from glacial refugia has rarely been possible. Here we compare ND1 mitochondrial DNA variation in late Pleistocene (16,000-40,000 years before present), historical and contemporary Atlantic salmon (Salmo salar) populations from northern Spain and other regions of western Europe. Our study demonstrates the presence of Atlantic salmon in the Iberian glacial refugium during the last 40,000 years and points to the Iberian Peninsula as the likely source of the most common haplotype within the Atlantic lineage in Europe. However, our findings also suggest that there may have been significant changes in the genetic structure of the Iberian refugial stock since the last ice age, and question whether modern populations in refugial areas are representative of ice age populations. A common haplotype that persisted in the Iberian Peninsula during the Pleistocene last glacial maximum is now extremely rare or absent from European rivers, highlighting the need for caution when making phylogeographic inferences about the origin and distribution of modern genetic types.     

Mitochondrial genomes from modern and ancient Turano-Mongolian cattle reveal an ancient diversity of taurine maternal lineages in East Asia

Turano-Mongolian cattle are a group of taurine cattle from Northern and Eastern Asia with distinct morphological traits, which are known for their ability to tolerate harsh environments, such as the Asian steppe and the Tibetan plateau. Through the analysis of 170 mitogenomes from ten modern breeds, two sub-lineages within T3 (T3₁₁₉ and T3₀₅₅) were identified as specific of Turano-Mongolian cattle. These two T3 sub-lineages, together with the previously identified T4, were also present in six Neolithic samples, dated to ~3900 years BP, which might represent the earliest domestic taurine stocks from Southwest Asia. The rare haplogroup Q, found in three Tibetan cattle, testifies for the legacy of ancient migrations from Southwest Asia and suggests that the isolated Tibetan Plateau preserved unique prehistoric genetic resources. These findings confirm the geographic substructure of Turano-Mongolian cattle breeds, which have been shaped by ancient migrations and geographic barriers.Subject terms: Animal migration, Haplotypes, Phylogenetics     

Mitochondrial DNA sequence variation in Greeks.

Mitochondrial DNA (mtDNA) control region sequences were determined in 54 unrelated Greeks, coming from different regions in Greece, for both segments HVR-I and HVR-II. Fifty-two different mtDNA haplotypes were revealed, one of which was shared by three individuals. A very low heterogeneity was found among Greek regions. No one cluster of lineages was specific to individuals coming from a certain region. The average pairwise difference distribution showed a value of 7.599. The data were compared with that for other European or neighbor populations (British, French, Germans, Tuscans, Bulgarians, and Turks). The genetic trees that were constructed revealed homogeneity between Europeans. Median networks revealed that most of the Greek mtDNA haplotypes are clustered to the five known haplogroups and that a number of haplotypes are shared among Greeks and other European and Near Eastern populations.     

Mitochondrial cytochrome b sequence variation in Korean salmonids

The complete 1141 bp mitochondrial cytochrome b sequences were determined for lenok Brachymystax lenok , cherry salmon Oncorhynchus masou masou , Ishikawa's cherry salmon O. m. ishikawai , chum salmon O. keta , rainbow trout O. mykiss , and an albino mutant of rainbow trout. Common substitutions detected in these species were transitional mutations. There were no significant differences in the intraspecific variation of the cytochrome b genes. Interspecific divergences were greater than intraspecific variation. The level of variation ranged from 8·026–15·686%. The cherry salmon was closer to chum salmon than to rainbow trout, and the lenok was the most distantly related species.     

Mitochondrial control-region sequence variation in aboriginal Australians.

The mitochondrial D-loop hypervariable segment 1 (mt HVS1) between nucleotides 15997 and 16377 has been examined in aboriginal Australian people from the Darling River region of New South Wales (riverine) and from Yuendumu in central Australia (desert). Forty-seven unique HVS1 types were identified, varying at 49 nucleotide positions. Pairwise analysis by calculation of BEPPI (between population proportion index) reveals statistically significant structure in the populations, although some identical HVS1 types are seen in the two contrasting regions. mt HVS1 types may reflect more-ancient distributions than do linguistic diversity and other culturally distinguishing attributes. Comparison with sequences from five published global studies reveals that these Australians demonstrate greatest divergence from some Africans, least from Papua New Guinea highlanders, and only slightly more from some Pacific groups (Indonesian, Asian, Samoan, and coastal Papua New Guinea), although the HVS1 types vary at different nucleotide sites. Construction of a median network, displaying three main groups, suggests that several hypervariable nucleotide sites within the HVS1 are likely to have undergone mutation independently, making phylogenetic comparison with global samples by conventional methods difficult. Specific nucleotide-site variants are major separators in median networks constructed from Australian HVS1 types alone and for one global selection. The distribution of these, requiring extended study, suggests that they may be signatures of different groups of prehistoric colonizers into Australia, for which the time of colonization remains elusive.     

Mitochondrial cytochrome b DNA sequence variation of Atlantic cod from Iceland and Greenland

Sequence variation of a 250–bp (base pair) fragment of the mitochondrial cytochrome b gene has been studied using polymerase chain reaction and direct sequencing of 519 Atlantic cod Gadus morhua from Iceland and 78 cod from Greenland. Twenty-four variable nucleotide sites, mostly silent, define 34 haplotypes. The amount of variation is high ( ĥC =0·73, π=0·52 per 100 bp) with five haplotypes at polymorphic frequencies in Iceland and a number of widely dispersed rather rare haplotypes. A tree of genetic relationships among haplotypes has considerable homoplasy yet it is relatively shallow implying a high turnover of variants of the polymorphism. Net nucleotide genetic divergences among localities are nil. Geographic locality overall area, and inshore/offshore comparison explain none of the variation in an AMOVA, all the variation is among individuals and a null hypothesis of non-differentiation of haplotype frequencies among localities or overall areas cannot be rejected. A temporal year-class effect is found. The evolutionary difference between Greenland and Iceland cod is not significant and the percentage of variation accounted for by the Greenland/Iceland difference is half of what a temporal effect within Iceland explains. There is no evidence for considering the cod at Greenland and Iceland to consist of separate evolutionary units and the question of separate management units must address the lack of diagnostic genotypes and evidence for gene flow from clinal variation.     

Devonian and modern relatives of the Precambrian Eosphaera: possible significance for the early eukaryotes

The Middle Precambrian problematical microorganism Eosphaera Barghoorn and Eosphaera- like structures known from Early and Middle Precambrian banded iron formations have been compared with the recently discovered Devonian volvocacean alga Eovolvox Kaźmierczak and some modern colonial Volvocales. The volvocacean interpretation of Eosphaera implies that algal eukaryotes (green phytoflagellates) werc already prewmt in the earth biosphere before at least 1.9 b. y. ago (Gunflint Iron Formaticn), and probably before 2.7 b. y. ago (Soudan Iron Formation). The type of metabolism and thc oxygen requirements of modern colonial Volvocales indicate that Eosphaera was most probably a photoorgano-trophic (mixotrophic) organism able to live in the extremely oxygen-deficicnt or anoxy-genous Early Precambrian environment. As an oxygen-releasing photosynthesizer, Eosphaera could have played a considerable role in the production of free oxygen during the Precambrian. The abundance of Eospkaera- like ferriferous structures in the iron microbands of many banded iron formations implies active participation of these organisns in the formation of Precambrian sedimentary iron ores. The exclusively fresh-water habitat of extant volvocacean algae suggests that the Procambrian environments inhabited by Eosphaera were non-marine.     

Mitochondrial sequence variation suggests an African influence in Portuguese cattle

A total of 49 samples from indigenous Portuguese cattle breeds were analysed for sequence variation in the hypervariable region of the mitochondrial DNA D-loop. Sequence comparison and phylogenetic analyses revealed that haplotypes fell into two distinct groups. These corresponded with two separate haplotype clusters into which, respectively, all African, or alternatively all sequences of European origin, have previously been shown to fall. Here, the majority of sequences of African type were encountered in three southern, as compared to three northern breeds. This pattern of African influence may reflect an intercontinental admixture in the initial origins of Iberian breeds, or it is perhaps an introgression dating from the long and influential Moorish occupation of the south of the Iberian peninsula.     

Mitochondrial DNA variation and crossability of leek (Allium porrum) and its wild relatives from the Allium ampeloprasum complex

 Mitochondrial (mt) DNA variation in the cultigens leek, kurrat and prei-anak is limited compared to that of their wild relatives in the Allium ampeloprasum complex. The phylogenetic relationships among these cultigens and their wild relatives is quite close, with the majority of the species clustering within one mitochondrial clade. The presence in leek of an extra-mitochondrial genetic element was noted. Analysis of crossability showed that all species were interfertile with leek. It is suggested that the genetic variation present within the A. ampeloprasum complex could be exploited in order to broaden the genetic basis of leek. Received: 14 August 1996 / Accepted: 23 August 1996     

Mitochondrial DNA sequence variation and phylogeographic patterns in harbour porpoises (Phocoena phocoena) from the North Atlantic

The harbour porpoise (Phocoena phocoena)experiences high rates of incidental mortalityin commercial fisheries, and in some areasthese rates are sufficiently high to justifyconcern over population sustainability. Giventhe high incidental mortality, the resolutionof population structure will be important toconservation and management, but in the NorthAtlantic the relationships among many of theputative populations remain unclear. Aprevious genetic study demonstrated substantialgenetic differences between eastern and westernNorth Atlantic populations, however thelocation of this break remained unresolved. Inthe present study, we addressed this issue byincluding new samples from Iceland. Toinvestigate population structure, variation inthe mitochondrial DNA of 370 porpoises wascompared among six locations corresponding toseveral of the putative populations (Gulf ofMaine, Gulf of St. Lawrence, Newfoundland, WestGreenland, Iceland, Norway). The first 342base pairs of the control region were sequencedand genetic variation investigated by analysisof molecular variance (F _ST and _ST ) and ² withpermutation. Although some fine scalepopulation structure was detected, porpoisesfrom Iceland were found to be more similar tothe western populations (W. Greenland, Gulf ofSt. Lawrence, Newfoundland, Gulf of Maine) thanto Norway. Furthermore, porpoises from Norwaywere different from all other regions. Thesepatterns suggest the existence of adiscontinuity between Iceland and Norway,possibly the result of isolating events causedby repeated range contractions and expansionsthroughout Quaternary glaciation events withinthe North Atlantic. These results suggest thatharbour porpoise populations within the NorthAtlantic are distinguishable, but patterns mustbe interpreted in light of their historicalbiogeography.     

Mitochondrial DNA sequence variation in whiting Merlangius merlangus in the North East Atlantic

Genetic variation in whiting Merlangius merlangus was examined using a 621 base pair fragment of the cytochrome c oxidase subunit I mitochondrial gene in 138 individuals sampled from Iceland, Norway and the North Sea. In total 10 segregating sites were observed defining 12 haplotypes. Three of the haplotypes were found at high frequencies (>5 %). All but one mutations were synonymous and the nonsynonymous mutation was found as a singleton. This suggests weak or no natural selection acting on the observed polymorphism making it useful for examination of population breeding structure. The genetic variation suggests that the whiting population has undergone sudden expansion in the past, estimated to have started 70 Kyr ago, during the last glacial period. Spatial genetic analysis reveals genetic uniformity across long geographic distances suggesting high level of gene flow. The long pelagic phase at early age, allowing for high dispersal rate, may partly explain the observed pattern.     

Mitochondrial DNA sequence and haplotype variation analysis in the chicken (Gallus gallus)

Although it is known to be useful for certain genotype:phenotype assignments, our knowledge of the nature and extent of variation in the entire chicken (Gallus gallus) mitochondrial genome (mtGenome) is limited. Here, we used experimental and in silico tools to identify nucleotide variants in the mtGenome, including the coding and non-coding (D-loop) regions. The distribution of the experimentally identified mitochondrial DNA variants in meat- (broilers) and egg-type (White Leghorn) chickens was also assessed. A total of 113 single-nucleotide polymorphisms (SNPs) were identified. The in silico analysis revealed a total of 91 SNPs, with 70 in the coding region and 21 in the non-coding region. Of the 41 experimentally identified SNPs, 27 were in the D-loop. Together, the experimentally identified SNPs in the non-coding region formed 11 haplotypes, whereas the 14 SNPs in the coding region formed 6. Though, 9 of the D-loop region haplotypes were observed only in broilers, 3 of the 6 haplotypes from the coding region occurred at a significantly higher frequency in broilers. To our knowledge, this investigation represents the first whole-mtGenome scan for variation and an evaluation, though limited in sample size, of the haplotype distribution in meat- and egg-type populations, using the SNPs and haplotypes identified.     

Mitochondrial cytochrome b DNA sequence variation of Atlantic cod Gadus morhua, from Norway

We studied sequence variation of a fragment of the mitochondrial cytochrome b gene using polymerase chain reaction (PCR) and direct sequencing among 85 Norwegian Atlantic cod Gadus morhua, from nine sampling localities representing three overall areas: arctic, coastal and middle. In the analysis we include an additional 15 cod studied by Carr & Marshall (1991a). Nine base changes were found among the 100 sequences defining 11 haplotypes which differ from each other by one to five mutations. Two sites have been hit twice. All but one mutation are at third position silent sites. The variation passes several neutral-theory tests and is thus suitable as marker for studying population differentiation. Coefficients of coancestry or intraclass correlation coefficient are negative both at the level of individuals within localities and localities within areas. This implies greater differences among individuals within populations than between populations. Intralocality nucleotide diversity is high and masks interlocality nucleotide divergence such that the net interlocality nucleotide divergence is nil. Similarly the net interarea nucleotide divergence is nil.     

Mitochondrial DNA variation of modern Tuscans supports the near eastern origin of Etruscans

The origin of the Etruscan people has been a source of major controversy for the past 2,500 years, and several hypotheses have been proposed to explain their language and sophisticated culture, including an Aegean/Anatolian origin. To address this issue, we analyzed the mitochondrial DNA (mtDNA) of 322 subjects from three well-defined areas of Tuscany and compared their sequence variation with that of 55 western Eurasian populations. Interpopulation comparisons reveal that the modern population of Murlo, a small town of Etruscan origin, is characterized by an unusually high frequency (17.5%) of Near Eastern mtDNA haplogroups. Each of these haplogroups is represented by different haplotypes, thus dismissing the possibility that the genetic allocation of the Murlo people is due to drift. Other Tuscan populations do not show the same striking feature; however, overall, ~5% of mtDNA haplotypes in Tuscany are shared exclusively between Tuscans and Near Easterners and occupy terminal positions in the phylogeny. These findings support a direct and rather recent genetic input from the Near East--a scenario in agreement with the Lydian origin of Etruscans. Such a genetic contribution has been extensively diluted by admixture, but it appears that there are still locations in Tuscany, such as Murlo, where traces of its arrival are easily detectable.     

Amplification of oak DNA from ancient and modern wood

A polymorphic noncoding region of chloroplast DNA (cpDNA) was successfully amplified by the polymerase chain reaction (PCR) from various oak wood samples, including recent and more ancient (about 600-years-old) samples from different oak species. Adaptation of DNA isolation and amplification protocols was necessary to obtain this result. Polymorphisms useful to distinguish species or geographical origin of these samples could be scored through sequencing. These polymorphisms include one substitution and two microsatellite-type polymorphisms, due to a variable number of A/T repeats. Identical results were obtained independently in two separate laboratories.