High mitochondrial sequence diversity in linguistic isolates of the Alps.

Segment I of the control region of mtDNA (360 bases) was sequenced in seven samples, each of 10 individuals inhabiting villages in the eastern Italian Alps (South Tyrol and Trentino). Three linguistic groups, German, Italian, and Ladin, were represented by two samples each; the seventh sample comes from an isolated group of German origin, the Mocheni, who are linguistically distinct and geographically separated from the bulk of the German speakers. Seventy-four polymorphic sites were identified, defining 63 different haplotypes. Mocheni and Ladin speakers tend to form two clusters in the evolutionary trees inferred from sequences. Analysis of molecular variance shows significant differentiation within samples, among them, and among linguistic groups. Genetic differences between the Ladins and the other groups are not much smaller than between Europeans and some Africans; variation is large within groups, as well, with the exception of only the Mocheni. In the evolutionary trees where the four alpine groups are compared with other European populations, Mocheni and especially Ladins appear as clear outliers. Romansch-speaking Swiss, who are linguistically related to Ladins, are not genetically similar to them, for this segment of DNA. Because the time elapsed since colonization of the Alps (< or = 12,000 years) is short in mutational terms, the only model accounting for the observed relationships between mtDNA variation and linguistic identity seems one in which a population ancestral to Ladin speakers was already differentiated long before the Alps were settled and the current linguistic affiliations were established. For the Mocheni, the results are consistent with a simpler episode of allele loss, from an original genetic pool common to the ancestors of the current German speakers.     

Mitochondrial DNA as a marker of molecular diversity: a reappraisal

Over the last three decades, mitochondrial DNA has been the most popular marker of molecular diversity, for a combination of technical ease-of-use considerations, and supposed biological and evolutionary properties of clonality, near-neutrality and clock-like nature of its substitution rate. Reviewing recent literature on the subject, we argue that mitochondrial DNA is not always clonal, far from neutrally evolving and certainly not clock-like, questioning its relevance as a witness of recent species and population history. We critically evaluate the usage of mitochondrial DNA for species delineation and identification. Finally, we note the great potential of accumulating mtDNA data for evolutionary and functional analysis of the mitochondrial genome.     

Mitochondrial genome sequence diversity of Indian Plasmodium falciparum isolates

We have analysed the whole mitochondrial (mt) genome sequences (each ~6 kilo nucleotide base pairs in length) of four field isolates of the malaria parasite Plasmodium falciparum collected from different locations in India. Comparative genomic analyses of mt genome sequences revealed three novel India-specific single nucleotide polymorphisms. In general, high mt genome diversity was found in Indian P. falciparum, at a level comparable to African isolates. A population phylogenetic tree placed the presently sequenced Indian P. falciparum with the global isolates, while a previously sequenced Indian isolate was an outlier. Although this preliminary study is limited to a few numbers of isolates, the data have provided fundamental evidence of the mt genome diversity and evolutionary relationships of Indian P. falciparum with that of global isolates.     

Origins of linguistic diversity in the Aleutian Islands

The Aleut language, currently spoken along the Aleutian chain and the Pribilof and Commander islands, is the only language in its branch of the Eskimo-Aleut language family, and traditional methods of linguistic reconstruction have neither satisfactorily explained its relationship with languages on the Asian continent nor its development from Proto-Eskimo-Aleut. Linguistic reconstruction has always been important in understanding the prehistory and history of the Aleuts, and new approaches in comparative linguistics, more comprehensive information on typological features of neighboring languages, and continuing language documentation allow us to propose a rich and continuous history of contact with various groups of people. I evaluate evidence that the Aleut language may have been shaped by contact with neighbors in Asia and Alaska, eventually giving rise to its differentiation from the Eskimo languages. I look at dialect differentiation along the Aleutian chain and what this differentiation reveals about the migration trends of the Aleut along the chain. I look at the colonial expansion of the Aleut-speaking area and resulting additional varieties of Aleut in the historical period. Finally, I review the effects of the Russian and American colonial periods on the Aleut language and the severe endangerment that the language faces today as a result. I conclude that there is evidence of possible Aleut contact with both neighboring peoples; however, much of this evidence has not yet been subjected to systematic comparative reconstructions. Linguistic evidence supports theories of at least two westward expansions of Aleuts along the island chain, but it is not yet clear what motivated the dialect differentiations. Finally, I offer some thoughts on directions for future dialect studies and the continuing documentation of Aleut.     

Mitochondrial lineages in Ladin-speaking communities of the eastern Alps.

European mitochondrial alleles cluster into five haplogroups. Haplogroup 2 is rare in general, but represents more than half of the few known sequences among Ladin speakers of the Alps. Here we describe DNA diversity in control region I of the hypervariable D-loop in 43 Ladins, and in 25 Italian speakers. Analysis of these data, and of previously published sequences, confirms a high degree of differentiation among Ladins and their geographical neighbours. This cannot be regarded as a simple effect of isolating factors, geographic or linguistic, as diversity is high within Ladin communities too. Rather, allele genealogies, population trees, and principal component analysis suggest a relationship between Ladin and Near Eastern samples. Two evolutionary hypotheses seem compatible with these findings. The view whereby Ladins could be descended from Palaeolithic inhabitants of the Alps is supported by the identification, in this study, of the probable ancestral haplotype of group 2, never previously observed in central Europe. Alternatively, a comparatively recent, Neolithic immigration of the ancestors of current Ladin speakers seems consistent with recent linguistic theories. In both cases, the number of lineages present, and their extensive diversity, are not compatible with a serious bottleneck in the Ladin population''s history.     

Mitochondrial genome diversity in parasites

Mitochondrial genomes have been sequenced from a wide variety of organisms, including an increasing number of parasites. They maintain some characteristics in common across the spectrum of life-a common core of genes related to mitochondrial respiration being most prominent-but have also developed a great diversity of gene content, organisation, and expression machineries. The characteristics of mitochondrial genomes vary widely among the different groups of protozoan parasites, from the minute genomes of the apicomplexans to amoebae with 20 times as many genes. Kinetoplastid protozoa have a similar number of genes to metazoans, but the details of gene organisation and expression in kinetoplastids require extraordinary mechanisms. Mitochondrial genes in nematodes and trematodes appear quite sedate in comparison, but a closer look shows a strong tendency to unusual tRNA structure and alternative initiation codons among these groups. Mitochondrial genes are increasingly coming into play as aids to phylogenetic and epidemiologic analyses, and mitochondrial functions are being recognised as potential drug targets. In addition, examination of mitochondrial genomes is producing further insights into the diversity of the wide-ranging group of organisms comprising the general category of parasites.     

Mitochondrial genome diversity in soybean: repeats and rearrangements

Mitochondrial (mt) genome organization in soybean was examined at the molecular level. This study builds upon previous reports that four soybean cytoplasmic groups, Bedford, Arksoy, Lincoln, and soja-forage, are differentiated by polymorphisms detected with a 2.3 kb Hind III mtDNA probe [12]. The variation detected results from DNA alterations in a region within and around a 4.8 kb repeat. The Bedford-type cytoplasm is the only cytoplasm that contains copies of a 4.8 kb repeat in four different genomic environments, evidence that it is recombinationally active. The Lincoln- and Arksoy-type cytoplasms each contain two copies of the repeat, as well as unique fragments that appear to result from rare recombination events outside, but near, the repeat. The soja-forage-type cytoplasm contains no complete copies of the repeat, but does contain a unique truncated version of the repeat. Sequence analysis indicates that the truncation is a result of recombination across a 9 bp repeated sequence, CCCCTCCCC. The structural rearrangements that have occurred in the region surrounding the 4.8 kb repeat may provide a means to dissect species relationships and evolution within the subgenus soja.     

Mitochondrial DNA diversity in Kazym Khanty

New data on mitochondrial DNA polymorphism in the representatives of Kazym territorial group of Northern Khanty are presented. MtDNA diversity observed in Kazym Khanty was compared with that in Khanty from Shuryshkarskii raion of Yamalo-Nenets Autonomous Okrug.     

Mitochondrial DNA sequence diversity in Russians

The article presents the results of the first regular study of Russian populations by sequencing the control region of mitochondrial DNA (mtDNA). The sequenced region is the most variable on mtDNA molecule and is commonly used for population and evolutionary studies. Russians form one of the largest ethnic groups (more than 129 million). However, their genetic diversity had only been characterized with RFLP and biochemical markers, although there are already established mtDNA sequence databases for many ethnic groups of the world. We have obtained sequence data from 103 individuals living in three Russian regions: Kostroma, Kursk, and Rjazan. The sequenced fragment analyzed is 360 bp in length (positions from 16024 to 16383). Fifty nine nucleotide positions have been found polymorphic in Russians, among those were 57 transitions and two transversions. One individual is found having two insertions of two cytosines between positions 16184 and 16193. Among 64 different mitotypes identified in the study 52 were unique in these samples. The index of genetic diversity (Nei, 1987) for Russians is 0.96. This value is within the established range for European populations (0.93 to 0.98). Genetic distances calculated from our data show that Russians form a cluster with Germans, Bulgarians, Swedes, Estonians, and Volgo-Finns are more distant from Karelians and Finns, and much more differ from Turks and especially Mongolians.     

Significant decrease in epiphytic lichen diversity in a remote area in the European Alps,Austria

We present long-term (1993–2010) monitoring results of lichens from a remote site in Austria. Whereas gaseous pollution is negligible in this area, levels of long-range air pollution of S and N via rain and fog are high. Lichen cover on tree trunks have decreased significantly. Accordingly, we found that the population of all species had declined. The analyses demonstrated significant changes in lichen community composition. The lichen flora suffered a significant decrease in diversity. Our hypothesis is that the breakdown of epiphytic lichens is mainly due to eutrophication through long-term N deposition, and more particularly to ammonia in precipitation and in fog. Since many areas in the European Alps receive high wet deposition loads, a decrease in the abundance and diversity of epiphytic lichens is most probably a widespread phenomenon.     

Across language families: Genome diversity mirrors linguistic variation within Europe

Objectives: The notion that patterns of linguistic and biological variation may cast light on each other and on population histories dates back to Darwin's times; yet, turning this intuition into a proper research program has met with serious methodological difficulties, especially affecting language comparisons. This article takes advantage of two new tools of comparative linguistics: a refined list of Indo‐European cognate words, and a novel method of language comparison estimating linguistic diversity from a universal inventory of grammatical polymorphisms, and hence enabling comparison even across different families. We corroborated the method and used it to compare patterns of linguistic and genomic variation in Europe. Materials and Methods: Two sets of linguistic distances, lexical and syntactic, were inferred from these data and compared with measures of geographic and genomic distance through a series of matrix correlation tests. Linguistic and genomic trees were also estimated and compared. A method (Treemix) was used to infer migration episodes after the main population splits. Results: We observed significant correlations between genomic and linguistic diversity, the latter inferred from data on both Indo‐European and non‐Indo‐European languages. Contrary to previous observations, on the European scale, language proved a better predictor of genomic differences than geography. Inferred episodes of genetic admixture following the main population splits found convincing correlates also in the linguistic realm. Discussion: These results pave the ground for previously unfeasible cross‐disciplinary analyses at the worldwide scale, encompassing populations of distant language families. Am J Phys Anthropol 157:630–640, 2015. © 2015 Wiley Periodicals, Inc.     

The microbial diversity in picoplankton enrichment cultures: a molecular screening of marine isolates

Picoplankton bacteria from a North Sea water sample were cultured under a variety of different conditions (nutrients, temperature, light, agitation, adhesion). Fluorescent in situ hybridization (FISH) analysis of the enrichments showed complex communities which were dominated by gamma-Proteobacteria or beta-Proteobacteria, followed by alpha-Proteobacteria and bacteria from the Cytophaga/Flavobacterium/Bacteroides (CFB) cluster. Among 410 isolates, a high degree of diversity was found, both with respect to colony color and morphology and with respect to genetic diversity. Isolated bacteria were classified into the main taxa by a special PCR approach, termed signature PCR (SIG-PCR). It was based on an oligo primer mixture targeting 16S rDNA which yielded PCR products of taxon-specific lengths. Again, gamma-Proteobacteria dominated (48%), followed by alpha-Proteobacteria (20%). beta-Proteobacteria were rarely isolated (eight strains of 410). The CFB cluster comprised the second largest phylum (14%), and 7.5% of all isolates belonged to the high-GC Gram-positives. Thus, isolated bacteria were representative of enrichment communities with the exception of the beta-Proteobacteria, which were detected in high abundance in certain enrichments by FISH but not isolated, and the high-GC Gram-positives, which were cultivated but not detected by FISH. A genomic fingerprinting technique, randomly amplified polymorphic DNA, showed that among 58 CFB isolates only 18 identical genotypes were found, and among the 84 alpha-Proteobacteria only eight identical genotypes were present. The data show the enormous diversity of cultivated bacteria from picoplankton enrichment cultures of one North Sea water sample, which is only a small fraction of the total picoplankton community.     

Mitochondrial DNA sequence diversity in three ethnic populations from the South-west Iran: a preliminary study

To investigate the genetic structure of human populations in the South-west region of Iran, mitochondrial first hypervariable DNA sequences were obtained from 50 individuals representing three different ethnic groups from Khuzestan Province. Studied groups were Shushtari Persians and Chahar Lang Bakhtiyaries from Indo-European-speaking populations and Bani Torof Arabs from Semitic-speaking linguistic families. Genetic analysis of mtDNA data showed high similarity of Chahar Lang Bakhtiyaries with other Iranian Indo-European-speaking populations while Shushtaries and Bani Torofs had a closer affinity with Semitic-speaking groups rather than to other Iranian populations. The relationship of Chahar Lang Bakhtiyaries and Bani Torof Arabs with their neighbor populations can be explained by linguistic and geographic proximity. Whereas, the greater similarity of Shushtari Persians with West Asian Arabs is probably according to high gene flow between them. This article represents a preliminary study of three major ethnic groups of South-west Iran which investigates the potential genetic substructure of the region.     

Mitochondrial diversity and the origin of Iberian sheep

Mitochondrial DNA diversity was analysed in 19 Iberian and six foreign sheep breeds. Three mtDNA lineages (B, A and C) were found in the Iberian sheep, with type B clearly predominating over the others. The results were analysed for each of the morphologically determined breed groups in Iberian sheep: Merino, Entrefino, Churro and Iberian trunks. MtDNA lineage C was found only in the Iberian trunk composed of Montesina and Ojalada. These two populations had high mtDNA variability, and in the Iberian sheep only Merino Branco had more variation. The other three Merino types studied showed moderate variability, including the most authentic Merino, the Spanish Merino. These three Merinos clustered closely in a multidimensional scaling representation of distances, while the fourth breed (Merino Branco) showed a clear separation. As for the other two trunks, breeds from the Churro group showed greater maternal uniformity while results for populations included in the so-called Entrefino trunk seemed to have a more heterogeneous maternal origin. The results obtained are discussed with available data from nuclear markers and with morphological classifications, and all this information is analysed in relation to the origin of the different Iberian sheep breeds.     

Mitochondrial DNA diversity of Pakistani goats

Pakistan contains numerous domestic goat breeds, but until now there has been no comprehensive study on genetic diversity or a phylogenetic analysis of Pakistani goats. In this study, we analysed the complete mitochondrial DNA D-loop and the cytochrome b gene of 13 Pakistani domestic goat breeds (Capra hircus) and one wild goat, the Sindh Ibex (Capra aegagrus blythi). The phylogenetic analyses and sequence divergence (SD) established four distinct mt-lineages termed as A, B and C (previously reported) and a new lineage D. The Sindh Ibex appeared as an outgroup of domestic goats. The estimated divergence times between the most recently evolved mt-lineages A and D were from 260,483 to 371,052 YA. This suggested that at least four different strains of wild Capra might have been the source of the modern domestic goats. The new mt-lineage D revealed high SD from mt-lineage A and may be the oldest branch under domestication, while mt-lineages B and C showed lower SD and might have been domesticated during an advanced stage of the domestication process.     

Mitochondrial DNA diversity patterns in Pakistani buffalo

The Indian subcontinent is considered to be the likely centre of river buffalo domestication, based on population dynamics, archaeological evidence and genetic diversity. Recent studies on mitochondrial DNA diversity have drawn useful conclusions about the domestication history of Bubalus bubalis. The conclusions of these studies are, however, incomplete, unless samples can also be analysed from Pakistan, which contains the second largest buffalo population of the world. Here, we report the results of the first study on mitochondrial D-loop sequence diversity in five breeds of Pakistani buffalo. Analysis of sequence variations in 503-bp of the D-loop region of 123 animals revealed 52 haplotypes, including 40 singletons. Multidimensional display of breed pairwise F(ST) values revealed no strong clustering of breeds. Bayesian, maximum parsimony, neighbour joining and UPGMA trees revealed a topology consistent with domestication as well as subsequent introgression of multiple maternal lineages from the wild stocks. Reduced median network analysis provided evidence of population expansion from more than one set of haplotypes. The study also confirmed that Pakistani buffalo are of the river type. The observed mitochondrial D-loop sequence diversity suggests that Pakistani areas bordering India might have contributed to the initiation of domestication of the present-day river buffalo.     

Mitochondrial DNA diversity in Southeast Asian populations

In a previous study of Southeast Asian genetic variation, we characterized mitochondrial DNAs (mtDNAs) from six populations through high-resolution restriction fragment length polymorphism (RFLP) analysis. Our analysis revealed that these Southeast Asian populations were genetically similar to each other, suggesting they had a common origin. However, other patterns of population associations also emerged. Haplotypes from a major founding haplogroup in Papua New Guinea were present in Malaysia; the Vietnamese and Malaysian aborigines (Orang Asli) had high frequencies of haplogroup F, which was also seen in most other Southeast Asian populations; and haplogroup B, defined by the Region V 9-base-pair deletion, was present throughout the region. In addition, the Malaysian and Sabah (Borneo) aborigine populations exhibited a number of unique mtDNA clusters that were not observed in other populations. Unfortunately, it has been difficult to compare these patterns of genetic diversity with those shown in subsequent studies of mtDNA variation in Southeast Asian populations because the latter have typically sequenced the first hypervariable segment (HVS-I) of the control region (CR) sequencing rather than used RFLP haplotyping to characterize the mtDNAs present in them. For this reason, we sequenced the HVS-I of Southeast Asian mtDNAs that had previously been subjected to RFLP analysis, and compared the resulting data with published information from other Southeast Asian and Oceanic groups. Our findings reveal broad patterns of mtDNA haplogroup distribution in Southeast Asia that may reflect different population expansion events in this region over the past 50,000-5,000 years.     

The impact of overgrazing on dung beetle diversity in the Italian Maritime Alps

Dung beetles (Coleoptera: Scarabaeidae) are undoubtedly the most typical and ecologically relevant insects of grazed alpine habitats because they provide valuable ecological services such as biological pest control and soil fertilization. Despite the great ecological contribution of these insects to pasture ecosystem functioning, little is known about their direct or indirect relationships with pastoral activities. The main aim of the study was to assess whether dung beetle diversity was influenced by different intensities of cattle grazing. Dung beetle communities of two adjacent alpine valleys within the Maritime Alps Natural Park (north-western Italian Alps), representing overgrazed and ungrazed pastures, were studied by pitfall trapping. A hierarchical design (three levels: valleys, transects, and replicates) was established for additive partitioning of γ-diversity and Indicator Species Analysis. Evenness and Shannon diversity were significantly higher at the ungrazed than at the overgrazed site because abundances were much more evenly distributed at the former than at the latter site (where one species was dominant over all the others). Dung beetle abundance and species richness of the overgrazed graminaceous pasture vegetation types were in most cases significantly lower than those of the ungrazed nongraminaceous vegetation type. In the additive partitioning of γ -diversity analysis relative to the whole study area, the randomization procedure indicated that the contribution of β to γ-diversity was significantly different from that expected by chance, suggesting that one or more environmental factors has intervened to change the partition of total diversity in the system considered. The analysis of the preferences and fidelity of species (Indicator Species Analysis) showed that only one species chose overgrazed pastures; all the others positively selected the ungrazed site, or the only ungrazed pasture vegetation type (Rumicetum alpini Beger) occurring at the overgrazed site. Results conformed to evidences that overgrazing represents a serious threat to the conservation of alpine dung beetles. To conserve local dung beetle assemblages, especially in protected areas, cattle overgrazing should be avoided. This does not mean, however, that pastoral activities are incompatible with biodiversity conservation. The contemporaneous presence of wild ungulates and low intensity extensive pastoral activities may be useful to preserve both local dung beetle assemblages and alpine pasture ecosystems.     

Mitochondrial DNA diversity in Siberian Tatars of the Tobol-Irtysh basin

Data on the variation of the nucleotide sequence of hypervariable segment I (HVSI) and restriction fragment length polymorphism (RFLP) of the coding region of mitochondrial DNA (mtDNA) have been used to characterize the mitochondrial gene pool of Siberian Tatars of the Tobol-Irtysh basin (N = 218), one of three geographic/linguistic groups of Siberian Tatars. The gene pool of Siberian Tatars has been shown to contain both Asian and European mtDNA lineages at a ratio of 1 : 1.5. The mtDNA diversity of Siberian Tatars is substantially higher than that of other Turkic-speaking populations of North and Central Asia. The position of the mitochondrial gene pool of Tatars of the Tobol-Irtysh basin in the genetic space of northern Eurasia populations has been determined.     

Mitochondrial DNA diversity in Siberian Tatars of the Tobol-Irtysh basin

Data on the variation of the nucleotide sequence of hypervariable segment I (HVSI) and restriction fragment length polymorphism (RFLP) of the coding region of mitochondrial DNA (mtDNA) have been used to characterize the mitochondrial gene pool of Siberian Tatars of the Tobol-Irtysh basin (N = 218), one of three geographic/linguistic groups of Siberian Tatars. The gene pool of Siberian Tatars has been shown to contain both Asian and European mtDNA lineages at a ratio of 1.0 : 1.5. The mtDNA diversity of Siberian Tatars is substantially higher than that of other Turkic-speaking populations of North and Central Asia. The position of the mitochondrial gene pool of Tatars of the Tobol-Irtysh basin in the genetic space of northern Eurasia populations has been determined.