Mitochondrial genetic variation in European, African and Indian cattle populations

Mitochondrial DNA from representative animals of 13 different cattle breeds was assayed for restriction fragment length polymorphisms (RFLP) to determine phylogenetic relationships and levels of variation among breeds; 16 different mitotypes were found, described by 20 polymorphisms. Within these 16 mitotypes two major lineages were apparent: an Afro-European and an Asian type. These were found to differ at over 2.3% of sites surveyed. None of the mitotypes found in the Asian lineage was detectable in the Afro-European lineage and vice versa. Within each of the major mitotypes there were no further significant differences within or among breeds. Using rates of mitochondrial evolution estimated from other species, the two lineages were estimated to have diverged between 575000 and 1150000 years ago; well outside the 10000 years bp timeframe postulated by a single domestication hypothesis. The results presented are concordant with those generated in other studies and provide strong evidence for an independent domestication of Asian Bos indicus. Furthermore, the grouping of all African indicine populations within the clade containing all Bos taurus lineages points to the hybrid origins of the humped cattle of that continent.     

Patterns of molecular genetic variation among African elephant populations

The highly threatened African elephants have recently been subdivided into two species, Loxodonta africana (savannah or bush elephant) and L. cyclotis (forest elephant) based on morphological and molecular studies. A molecular genetic assessment of 16 microsatellite loci across 20 populations (189 individuals) affirms species level genetic differentiation and provides robust genotypic assessment of species affiliation. Savannah elephant populations show modest levels of phylogeographic subdivision based on composite microsatellite genotype, an indication of recent population isolation and restricted gene flow between locales. The savannah elephants show significantly lower genetic diversity than forest elephants, probably reflecting a founder effect in the recent history of the savannah species.     

MtDNA of Fulani nomads and their genetic relationships to neighboring sedentary populations

Despite the large size of the contemporary nomadic Fulani population (roughly 13 million people), the genetic diversity and degree of differentiation of Fulanis compared to other sub-Saharan populations remain unknown. We sampled four Fulani nomad populations (n = 186) in three countries of sub-Saharan Africa (Chad, Cameroon, and Burkina Faso) and analyzed sequences of the first hypervariable segment of the mitochondrial DNA. Most of the haplotypes belong to haplogroups of West African origin, such as L1b, L3b, L3d, L2b, L2c, and L2d (79.6% in total), which are all well represented in each of the four geographically separated samples. The haplogroups of Western Eurasian origin, such as J1b, U5, H, and V, were also detected but in rather low frequencies (8.1% in total). As in African hunter-gatherers (Pygmies and Khoisan) and some populations from central Tunisia (Kesra and Zriba), three of the Fulani nomad samples do not reveal significant negative values of Fu's selective neutrality test. The multidimensional scaling of FST genetic distances of related sub-Saharan populations and the analysis of molecular variance (AMOVA) show clear and close relationships between all pairs of the four Fulani nomad samples, irrespective of their geographic origin. The only group of nomadic Fulani that manifests some similarities with geographically related agricultural populations (from Guinea-Bissau and Nigeria) comes from Tcheboua in northern Cameroon.     

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.     

Analysis of mtDNA variation in African populations reveals the most ancient of all human continent-specific haplogroups.

mtDNA sequence variation was examined in 140 Africans, including Pygmies from Zaire and Central African Republic (C.A.R.) and Mandenkalu, Wolof, and Pular from Senegal. More than 76% of the African mtDNAs (100% of the Pygmies and 67.3% of the Senegalese) formed one major mtDNA cluster (haplogroup L) defined by an African-specific HpaI site gain at nucleotide pair (np) 3592. Additional mutations subdivided haplogroup L into two subhaplogroups, each encompassing both Pygmy and Senegalese mtDNAs. A novel 12-bp homoplasmic insertion in the intergenic region between tRNA(Tyr) and cytochrome oxidase I (COI) genes was also observed in 17.6% of the Pygmies from C.A.R. This insertion is one of the largest observed in human mtDNAs. Another 25% of the Pygmy mtDNAs harbored a 9-bp deletion between the cytochrome oxidase II (COII) and tRNA(Lys) genes, a length polymorphism previously reported in non-African populations. In addition to haplogroup L, other haplogroups were observed in the Senegalese. These haplogroups were more similar to those observed in Europeans and Asians than to haplogroup L mtDNAs, suggesting that the African mtDNAs without the HpaI np 3592 site could be the ancestral types from which European and Asian mtDNAs were derived. Comparison of the intrapopulation sequence divergence in African and non-African populations confirms that African populations exhibit the largest extent of mtDNA variation, a result that further supports the hypothesis that Africans represent the most ancient human group and that all modern humans have a common and recent African origin. The age of the total African variation was estimated to be 101,000-133,000 years before present (YBP), while the age of haplogroup L was estimated at 98,000-130,000 YBP. These values substantially exceed the ages of all Asian- and European-specific mtDNA haplogroups.     

Genetic ecological monitoring in human populations: heterozygosity, mtDNA haplotype variation, and genetic load

Yu. P. Altukhov suggested that heterozygosity is an indicator of the state of the gene pool. The idea and a linked concept of genetic ecological monitoring were applied to a new dataset on mtDNA variation in East European ethnic groups. Haplotype diversity (an analog of the average heterozygosity) was shown to gradually decrease northwards. Since a similar trend is known for population density, interlinked changes were assumed for a set of parameters, which were ordered to form a causative chain: latitude increases, land productivity decreases, population density decreases, effective population size decreases, isolation of subpopulations increases, genetic drift increases, and mtDNA haplotype diversity decreases. An increase in genetic drift increases the random inbreeding rate and, consequently, the genetic load. This was confirmed by a significant correlation observed between the incidence of autosomal recessive hereditary diseases and mtDNA haplotype diversity. Based on the findings, mtDNA was assumed to provide an informative genetic system for genetic ecological monitoring; e.g., analyzing the ecology-driven changes in the gene pool.     

Mutant allele frequencies in domestic cat populations on the Spanish Mediterranean coast,and their genetic distances from other European and North African cat populations

New genetic profiles of domestic cat populations were studied in different parts of the Spanish Mediterranean coast. The t ^b frequency is the most outstanding differentiated factor between the populations analyzed. The low t ^b frequencies found in Barcelona and other Catalan localities are the most important characteristic of these populations and, probably, find an explanation in the extraordinarily high historical and commercial relationships between Barcelona and the Eastern Mediterranean (Greece, especially) during the 14th and 15th centuries. In other Spanish Mediterranean littoral cities the t ^b frequencies reach higher values and are more similar to those found in other Western European cat populations. Significant differences found in certain allelic frequencies (Orange and Blotched) caused by the urban-rural effect are discovered between Barcelona and two nearby rural cat populations.     

Genetic composition of Chilean aboriginal populations: HLA and other genetic marker variation

Phenotypes and gene frequencies for eight genetic systems are presented for five Chilean Indian tribes. Results agree with the pattern expected for Andean Indians. Genetic distances and dendrograms were obtained separately for HLA and traditional genetic markers. The similarity of both is noteworthy. Linguistic distances exhibit a correlation with genetic distances based on traditional markers. © 1996 Wiley-Liss, Inc.     

Genetic variation in the genus Leiopelma and relationships to other primitive frogs

Allozyme variation was studied the three living species of Leiopelma. L. hamiltoni and L. archeyi are shown to be closely related to each other although L. hamiltoni is slightly more divergent relative to L. hochstetteri. This parallels previous cytoenetic data. The rarity and insularity of L. hamiltoni enables the calculation of a mutation rate based on genetic variance and population size. A mutation rate per generation of 2.7times 10^--⁶ is sufficient to account for the observed levels of variation. Six populations of L. hochstetteri show a pattern of genetic divergence that also closely parallels previously detected cytogenetic variation. L. hochstetteri is genetically distant from its congeneric species while all species of Leiopelma are at an extreme genetic distance from Ascaphus truei, the only other living amphicoelous fro At the limits of resolution of the allozme technique, Ascaphus clusters with the more morphologically advanced frogs, Discogiossus and Bombina, rather than with Leiopelma. Taken with other evidence, this supports recognition of two families, Leiopelmatidae anl Ascaphidae, with Leiopelma the probable sister group of all other frogs.     

Some genetic erythrocyte polymorphisms in the Mbugu and other populations of the Central African Republic with an analysis of genetic distances

Phenotype and gene frequencies of four blood group polymorphisms (ABO, MNSs, Rhesus, and Duffy) as well as hemoglobin types of four populations of the Republic of Central Africa are reported. All these polymorphisms are in Hardy-Weinberg equilibrium. Regarding the four blood group polymorphisms mentioned above the genetic distances according to NEI have been computed for fifteen populations of the Central-Eastern and Central-Western areas of Africa, including the four own samples. The results of these analyses are discussed.     

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.     

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.     

Molecular relationships between populations of South African citrus thrips (Scirtothrips aurantii Faure) in South Africa and Queensland, Australia

Abstract   In response to the recent establishment of a population of South African citrus thrips ( Scirtothrips aurantii Faure) in Australia, we used DNA sequence data to examine whether this population is distinct from populations in South Africa. Mitochondrial and internal transcribed spacer (ITS2) DNA from populations from different host plants in Australia and South Africa showed no clear separation between populations that was entirely congruent with host plant or country of origin. Analysis of the ITS2 data was confounded by the presence of multiple different copies of the spacer in some populations. Neither the presence or absence, nor the sequence of these copies was clearly diagnostic for any one population. These preliminary data suggest that the Australian population is not a distinct species or subspecies from the populations of S. aurantii on either citrus or Bryophyllum in South Africa.     

Genetic diversity of wild grapevine populations in Spain and their genetic relationships with cultivated grapevines

The wild grapevine, Vitis vinifera L. ssp. sylvestris (Gmelin) Hegi, considered as the ancestor of the cultivated grapevine, is native from Eurasia. In Spain, natural populations of V. vinifera ssp. sylvestris can still be found along river banks. In this work, we have performed a wide search of wild grapevine populations in Spain and characterized the amount and distribution of their genetic diversity using 25 nuclear SSR loci. We have also analysed the possible coexistence in the natural habitat of wild grapevines with naturalized grapevine cultivars and rootstocks. In this way, phenotypic and genetic analyses identified 19% of the collected samples as derived from cultivated genotypes, being either naturalized cultivars or hybrid genotypes derived from spontaneous crosses between wild and cultivated grapevines. The genetic diversity of wild grapevine populations was similar than that observed in the cultivated group. The molecular analysis showed that cultivated germplasm and wild germplasm are genetically divergent with low level of introgression. Using a model‐based approach implemented in the software structure , we identified four genetic groups, with two of them fundamentally represented among cultivated genotypes and two among wild accessions. The analyses of genetic relationships between wild and cultivated grapevines could suggest a genetic contribution of wild accessions from Spain to current Western cultivars.     

Concomitant replacement of language and mtDNA in South Caspian populations of Iran

The Gilaki and Mazandarani occupy the South Caspian region of Iran and speak languages belonging to the North-Western branch of Iranian languages . It has been suggested that their ancestors came from the Caucasus region, perhaps displacing an earlier group in the South Caspian . Linguistic evidence supports this scenario, in that the Gilaki and Mazandarani languages (but not other Iranian languages) share certain typological features with Caucasian languages . We analyzed patterns of mtDNA and Y chromosome variation in the Gilaki and Mazandarani. Based on mtDNA HV1 sequences, the Gilaki and Mazandarani most closely resemble their geographic and linguistic neighbors, namely other Iranian groups. However, their Y chromosome types most closely resemble those found in groups from the South Caucasus. A scenario that explains these differences is a south Caucasian origin for the ancestors of the Gilaki and Mazandarani, followed by introgression of women (but not men) from local Iranian groups, possibly because of patrilocality. Given that both mtDNA and language are maternally transmitted, the incorporation of local Iranian women would have resulted in the concomitant replacement of the ancestral Caucasian language and mtDNA types of the Gilaki and Mazandarani with their current Iranian language and mtDNA types. Concomitant replacement of language and mtDNA may be a more general phenomenon than previously recognized.     

Seasonal variation in the diet of South African Galagos

The feeding behavior and diet of two species of bushbaby, Galago senegalensisand Galago crassicaudatus,in South Africa were examined in relation to seasonal changes in climate. The populations studied were allopatric, but both fed predominantly on Acaciagum and invertebrates. Data on their diet were collected by direct observation of a radiocollared female of each species and by analysis of fecal samples. Differences in diet were found between the species within seasons and within species between the seasons. Both spent more time gum-feeding in winter than in summer. Prey size and type differed between the species in summer but converged in winter. The quantity of insects taken was fairly similar between seasons for G. senegalensisbut dropped considerably for G. crassicaudatusin winter. These observations are interpreted in terms of interspecific differences in feeding strategies, which are considered to be a function of the difference in body size of the two galago species.     

Mitochondrial DNA sequence variation and phylogenetic relationships among Iberian pigs and other domestic and wild pig populations

Nucleotide sequences of mitochondrial DNA (mtDNA) cytochrome B gene (1140 bp) and control region (707 bp) were used to determine the phylogenetic relationships among 51 pig samples representing ancient and current varieties of Iberian pigs (26), Spanish wild boars (seven) and other domestic pigs (18) of cosmopolitan (Duroc, Large White, Landrace, Pietrain and Meishan) and local (Spotted Black Jabugo, Basque and Mangalitza) breeds. A neighbour-joining tree constructed from pairwise distances provide evidence of the European origin of both Iberian pigs and Spanish wild boars. The introgression of Asian mtDNA haplotypes in the genetic pool of the Iberian breed seems unlikely. Four estimates of sequence divergence between European and Asian clades were calculated from the two main domains of the D-loop region and the synonymous and nonsynonymous nucleotide substitutions in the cytochrome B gene. The time since the divergence of pig ancestors was estimated at about 600,000 years before present.