Establishment and characterization of Caspian horse fibroblast cell bank in Iran

Caspian horse, a rare horse breed found in 1965 by Louise Firouz in northern Iran, is a small horse which is reported to be in danger of extinction in its original homeland. There seems to be a great need to prevent extinction of this valuable horse. In this study, 51 fibroblast cell lines from Caspian horse ear marginal tissue were successfully established by sampling 60 horses using primary explant technique. Cells were authenticated and growth curve was plotted. According to results obtained, population doubling time (PDT) was calculated 23 ± 0.5 h for all cell lines. Multiplex polymerase chain reaction (multiplex PCR) revealed that cell lines had no cross-contamination with other species. Bacteria, fungi, and mycoplasma contamination were checked using standard methods such as PCR, direct culture, and Hoechst staining. In addition to providing a valuable source for genomic, postgenomic, and somatic cloning researches, the established cell lines would preserve Caspian horse genetic resources. It will also create an accessible database for researchers.     

mtDNA variation in the South African Kung and Khwe-and their genetic relationships to other African populations

The mtDNA variation of 74 Khoisan-speaking individuals (Kung and Khwe) from Schmidtsdrift, in the Northern Cape Province of South Africa, was examined by high-resolution RFLP analysis and control region (CR) sequencing. The resulting data were combined with published RFLP haplotype and CR sequence data from sub-Saharan African populations and then were subjected to phylogenetic analysis to deduce the evolutionary relationships among them. More than 77% of the Kung and Khwe mtDNA samples were found to belong to the major mtDNA lineage, macrohaplogroup L* (defined by a HpaI site at nucleotide position 3592), which is prevalent in sub-Saharan African populations. Additional sets of RFLPs subdivided macrohaplogroup L* into two extended haplogroups-L1 and L2-both of which appeared in the Kung and Khwe. Besides revealing the significant substructure of macrohaplogroup L* in African populations, these data showed that the Biaka Pygmies have one of the most ancient RFLP sublineages observed in African mtDNA and, thus, that they could represent one of the oldest human populations. In addition, the Kung exhibited a set of related haplotypes that were positioned closest to the root of the human mtDNA phylogeny, suggesting that they, too, represent one of the most ancient African populations. Comparison of Kung and Khwe CR sequences with those from other African populations confirmed the genetic association of the Kung with other Khoisan-speaking peoples, whereas the Khwe were more closely linked to non-Khoisan-speaking (Bantu) populations. Finally, the overall sequence divergence of 214 African RFLP haplotypes defined in both this and an earlier study was 0.364%, giving an estimated age, for all African mtDNAs, of 125,500-165,500 years before the present, a date that is concordant with all previous estimates derived from mtDNA and other genetic data, for the time of origin of modern humans in Africa.     

Mitochondrial DNA polymorphism in populations of the Caspian region and southeastern Europe

Mitochondrial DNA (mtDNA) restriction polymorphism was examined in Turkmens, Eastern Iranians, and Ukrainians. The gene pools of all populations studied were characterized by the presence of European mtDNA lineages. Mongoloid component observed in Turkmen and Iranian populations with the frequencies of about 20% was represented by groups C, D, and E/G in Turkmens, and by M*, D, A, and B in Iranians. The relative positions of the populations studied, of populations from the Caucasus, Western Iran, and Russian populations from the Krasnodar krai and Belgorod oblast in the space of principal components revealed a geographically specific pattern of the population clustering. The data on mtDNA polymorphism indicated pronounced differentiation of Eastern and Western Iranians. The latter were characterized by a mtDNA group composition similar to that in Eastern Slavs. The historical role of the Caspian populations in the formation of the population of Southeastern Europe is discussed.     

Haplotype diversity in mtDNA and Y-chromosome in populations of Altai-Sayan region

Polymorphism of mtDNA was examined in five ethnic populations that belong to the Turkic language group and inhabit the territory of the Altai-Sayan upland (N = 1007). Most of the haplogroups identified in the examined populations belonged to East Eurasian lineages. In all five populations, only three haplogroups, C, D, and F, were prevailing. The frequencies of the other six haplogroups (A, B, G, M, Y, and Z) varied in the range from 1.1 to 6.5%. Among West Eurasian haplogrous, the most common were haplogroups H, J, T, and U. An analysis of Y-chromosome haplogroups in 407 individuals showed that only two haplogroups, N* and R1a1, were present in all five populations examined. Moreover, in different ethnic groups, the highest frequencies were observed for C-M130, N-P43, and N-Tat haplogroups. The differences in the distribution patterns of ancient West Eurasian and East Eurasian haplotypes from Gorny Altai in the present-day populations from the northern part of Eurasia revealed can be explained in terms of the multistage expansion of humans across these territories. The ubiquity of haplotypes from haplogroup H and cluster U across the wide territory from the Yenisei River basin to the Atlantic Ocean can indicate directional human expansion, which most likely occurred out of Central Asia as early as in the Paleolithic era, and took place in several waves with the glacier retreat.     

Serum proteins and erythrocyte enzymes of populations in Iran

The genetic polymorphisms of nine biochemical genetic markers were investigated in four populations (Turks, Kurds, Tehranis and Kermanis) living in the north-east and south-east regions of Iran. Only one of the nine loci studied (acid phosphatase) showed significant gene frequency differences and for the C3 system the F allele frequencies in these populations were the lowest ever reported from Iran.     

Ecological effects of forest roads on plant species diversity in Caspian forests of Iran

Current research includes the effects of asphalt forest roads on changes of plant cover and tree regeneration from asphalt forest roads edges towards its inner parts in two compartments of Nave Asalem forests located in the north of Iran. For this reason, in each side of road, 6 sample plots (20 m × 20 m) were established for measuring plant species diversity. In each sample plot, ground vegetation and tree regeneration were assessed within nine 2 × 2 m micro plots. In total, 12 sample plots and 108 μ plots were established. Results indicated that the road positions were effective on plant species diversity. The highest diversity and evenness indices value were observed down of the road compared to the up of the road position for herbal and tree regeneration layers. The same results were found also for herbal richness indices. Up of road position had the greatest value of richness indices in comparison to the other road position for tree regeneration layer. Also, the results showed that diversity, richness, and evenness indices were decreased with the increasing of distance from the road side for herbs and tree regeneration layers. This study indicated that roads can increase plant biodiversity; that is, tree regeneration density.     

Hare populations in Europe: intra and interspecific analysis of mtDNA variation

We report results of a project aimed at analysing genetic diversification in Lepus corsicanus (italian hare), carried out at the INFS as part of an ongoing project on the biology of L. corsicanus. Samples of Italian hare were collected in different localities in central-southern Italy and Sicily. Moreover samples of L. europaeus (brown hare), as well as other species of the genus Lepus, were collected in Italy and Europe in order to define the phylogenetic relationships of the Italian hare. Results show a clear genetic distinction of the Italian hare. Consequently the status of true species is warranted at the molecular level. Phylogenetic relationships among species suggest the presence of two distinct groups, the Italian hare belonging to an evolutionary lineage including species which probably originated in a glacial refugia in southern Europe before colonization by the brown hare. On the other hand the brown hare belongs to a different lineage including species of African origins.     

Ancient local evolution of African mtDNA haplogroups in Tunisian Berber populations

Our objective is to highlight the age of sub-Saharan gene flows in North Africa and particularly in Tunisia. Therefore we analyzed in a broad phylogeographic context sub-Saharan mtDNA haplogroups of Tunisian Berber populations considered representative of ancient settlement. More than 2,000 sequences were collected from the literature, and networks were constructed. The results show that the most ancient haplogroup is L3*, which would have been introduced to North Africa from eastern sub-Saharan populations around 20,000 years ago. Our results also point to a less ancient western sub-Saharan gene flow to Tunisia, including haplogroups L2a and L3b. This conclusion points to an ancient African gene flow to Tunisia before 20,000 BP. These findings parallel the more recent findings of both archaeology and linguistics on the prehistory of Africa. The present work suggests that sub-Saharan contributions to North Africa have experienced several complex population processes after the occupation of the region by anatomically modern humans. Our results reveal that Berber speakers have a foundational biogeographic root in Africa and that deep African lineages have continued to evolve in supra-Saharan Africa.     

Gonadal histology and plasma sex steroid concentrations in maturing and mature spring migrants of Caspian lamprey Caspiomyzon wagneri in the Shirud River,southern Caspian Sea,Iran

Maturing degree-days, gonadal histology, and changes in serum sex steroids (progesterone, P; testosterone, T; and 17β-estradiol, E2) were examined in maturing and mature spring migrant Caspian lamprey Caspiomyzon wagneri (Kessler, 1870) in the Shirud River (southern Caspian Sea). Blood and gonad samples were collected from ten fish when they first entered the river (maturing stage) and from ten fish that showed spawning readiness after being held in cages in the river (mature stage). The maturing degree-days of Caspian lamprey from the start of upstream migration to maturation was 208–470°C.day. Serum P and E2 concentrations in maturing females were significantly higher than in maturing males, but in the mature stage, serum P and E2 concentrations of females were lower than males. In both stages, there were no differences in serum concentration of T between females and males. In both males and females, P increased significantly with maturation; T levels likewise appeared to increase, but the difference was not significant. E2 increased significantly with maturation in males, but females showed a significant decrease. Maturing females had similar stage gonads with the germinal vesicle in the polar position. Maturing males had testes that primarily contained secondary spermatocytes with an occasional occurrence of spermatozoa. These results suggest that males mature earlier than females, which is a pattern similar to that found in the sea lamprey.     

Isozyme variation in some populations of wild diploid wheats in Iran

Isozyme electrophoresis data of seed extracts from 11 populations of diploid wheat species (Triticum boeoticum Bioss. and Triticum urartu Thumanian ex Gandilyan), distributed mainly in the western and west-northern Iran, were investigated. The five enzyme systems used were peroxidase, polyphenol oxidase, superoxide dismutase, malate dehydrogenase and catalase. The first three were found to be useful as molecular marker for characterization of diploid wheat populations. A total of 13 bands from three enzyme systems were recorded. The value of a ‘Jaccard's’ similarity coefficient ranges from 0.333 to 1.000. Data analysis was done using clustering method UPGMA. On the basis of Jaccard's coefficient, the obtained dendrogram supports previous relationship between T. boeoticum and T. urartu as separate species as well as reflecting their distinct gene pools and substantiating their specific recognition despite the overall morphological similarity.     

Succession and replacement in the development of Silurian brachiopod populations

Fluctuating water depths in platform seas covering central North America during late Llandovery time introduced shifts in the spectrum of coral-algal, pentameran, and stricklandian communities. Opportunistic orthotetacean brachiopods were common during these times of community replacement. A pavement constructed by their flat shells was sometimes used as the initial substrate for attachment by the spat of pentameran brachiopods. Both orthotetacean and pentameran shells served as the initial substrate for stricklandian brachiopods. With the decline of a pentameran or stricklandian population, disarticulated shells provided a substrate for repopulation. An assemblage of immature Pentamerus in life position indicates that the typical umbo-down posture was an early result of maximum packing. Development of more advantageously placed individuals severely restricted the growth of others trapped between the substrate and the beak regions of surrounding neighbors. After pentameran assemblages were buried in life position, scouring of the sea bottom frequently produced erosion surfaces which truncated their thin shells. These surfaces were sometimes penetrated by boring organisms, and were firm enough for brachiopod repopulation.     

假眼小绿叶蝉地理种群的线粒体DNA 16S rRNA基因序列分析及遗传分化研究

测定了12个不同地理种群的茶树害虫假眼小绿叶蝉Empoasca vitis(Gothe)和1个外群共103个个体的线粒体DNA 16S rRNA基因部分序列,比较其同源性,计算核苷酸组成,并构建单倍型进化关系图。结果表明:在获得的假眼小绿叶蝉536 bp的序列中A+T含量占76.8%,其中56个核苷酸位点存在变异;100个个体共检测出56种单倍型,单倍型多样性指数(H)为0.971,核苷酸多样性指数(Pi)0.006;12个种群间的平均基因流(Nm)为1.64。总群体的固定系数Fst为0.026;AMOVA分子方差分析结果表明假眼小绿叶蝉的遗传分化主要来自于种群内部(97.4%)。各地理种群的遗传距离与地理分布不具有直接对应的关系。根据构建的单倍型进化关系网,各地理种群的单倍型呈现一种混杂的分布格局,未显示出与地理分布的一致性。     

Deep Rooting In-Situ Expansion of mtDNA Haplogroup R8 in South Asia

Background

The phylogeny of the indigenous Indian-specific mitochondrial DNA (mtDNA) haplogroups have been determined and refined in previous reports. Similar to mtDNA superhaplogroups M and N, a profusion of reports are also available for superhaplogroup R. However, there is a dearth of information on South Asian subhaplogroups in particular, including R8. Therefore, we ought to access the genealogy and pre-historic expansion of haplogroup R8 which is considered one of the autochthonous lineages of South Asia.

Methodology/Principal Findings

Upon screening the mtDNA of 5,836 individuals belonging to 104 distinct ethnic populations of the Indian subcontinent, we found 54 individuals with the HVS-I motif that defines the R8 haplogroup. Complete mtDNA sequencing of these 54 individuals revealed two deep-rooted subclades: R8a and R8b. Furthermore, these subclades split into several fine subclades. An isofrequency contour map detected the highest frequency of R8 in the state of Orissa. Spearman''s rank correlation analysis suggests significant correlation of R8 occurrence with geography.

Conclusions/Significance

The coalescent age of newly-characterized subclades of R8, R8a (15.4±7.2 Kya) and R8b (25.7±10.2 Kya) indicates that the initial maternal colonization of this haplogroup occurred during the middle and upper Paleolithic period, roughly around 40 to 45 Kya. These results signify that the southern part of Orissa currently inhabited by Munda speakers is likely the origin of these autochthonous maternal deep-rooted haplogroups. Our high-resolution study on the genesis of R8 haplogroup provides ample evidence of its deep-rooted ancestry among the Orissa (Austro-Asiatic) tribes.     

Peopling of Sahul: mtDNA variation in aboriginal Australian and Papua New Guinean populations.

We examined genetic affinities of Aboriginal Australian and New Guinean populations by using nucleotide variation in the two hypervariable segments of the mtDNA control region (CR). A total of 318 individuals from highland Papua New Guinea (PNG), coastal PNG, and Aboriginal Australian populations were typed with a panel of 29 sequence-specific oligonucleotide (SSO) probes. The SSO-probe panel included five new probes that were used to type an additional 1,037 individuals from several Asian populations. The SSO-type data guided the selection of 78 individuals from Australia and east Indonesia for CR sequencing. A gene tree of these CR sequences, combined with published sequences from worldwide populations, contains two previously identified highland PNG clusters that do not include any Aboriginal Australians; the highland PNG clusters have coalescent time estimates of approximately 80,000 and 122,000 years ago, suggesting ancient isolation and genetic drift. SSO-type data indicate that 84% of the sample of PNG highlander mtDNA belong to these two clusters. In contrast, the Aboriginal Australian sequences are intermingled throughout the tree and cluster with sequences from multiple populations. Phylogenetic and multidimensional-scaling analyses of CR sequences and SSO types split PNG highland and Aboriginal Australian populations and link Aboriginal Australian populations with populations from the subcontinent of India. These mtDNA results do not support a close relationship between Aboriginal Australian and PNG populations but instead suggest multiple migrations in the peopling of Sahul.     

South African populations of Littorina rudis

Littorina rudis was collected from stands of Spartina capensis in saltmarsh habitats within Langebaan and knysna lagoon, Cape Province. It was absent from rocky sores and from saltmarshes east of Knysna. The shell, radular and penial morphology are described. L. rudis from both localities bore tessellated colour patterns similar to those of British saltmarsh ecotypes. The Knysna population contained individuals with a unique amber background colour. The shells from Knysna and Langebaan were very thin in accordance with the sheltered habitats. The number of embryos carried in the brood puch was similar in both countries. Sexual maturity was attained at about 4 mm shell length; the male and female modal sizes were 4.9 mm and 5.1 mm respectively at Langebaan. No. published records were found for L. rudis in South West Africa. Some possible origins of the South African L. rudis populations are discussed.     

History of click-speaking populations of Africa inferred from mtDNA and Y chromosome genetic variation

Little is known about the history of click-speaking populations in Africa. Prior genetic studies revealed that the click-speaking Hadza of eastern Africa are as distantly related to click speakers of southern Africa as are most other African populations. The Sandawe, who currently live within 150 km of the Hadza, are the only other population in eastern Africa whose language has been classified as part of the Khoisan language family. Linguists disagree on whether there is any detectable relationship between the Hadza and Sandawe click languages. We characterized both mtDNA and Y chromosome variation of the Sandawe, Hadza, and neighboring Tanzanian populations. New genetic data show that the Sandawe and southern African click speakers share rare mtDNA and Y chromosome haplogroups; however, common ancestry of the 2 populations dates back >35,000 years. These data also indicate that common ancestry of the Hadza and Sandawe populations dates back >15,000 years. These findings suggest that at the time of the spread of agriculture and pastoralism, the click-speaking populations were already isolated from one another and are consistent with relatively deep linguistic divergence among the respective click languages.