Land, language, and loci: mtDNA in Native Americans and the genetic history of Peru

Despite a long history of complex societies and despite extensive present-day linguistic and ethnic diversity, relatively few populations in Peru have been sampled for population genetic investigations. In order to address questions about the relationships between South American populations and about the extent of correlation between genetic distance, language, and geography in the region, mitochondrial DNA (mtDNA) hypervariable region I sequences and mtDNA haplogroup markers were examined in 33 individuals from the state of Ancash, Peru. These sequences were compared to those from 19 American Indian populations using diversity estimates, AMOVA tests, mismatch distributions, a multidimensional scaling plot, and regressions. The results show correlations between genetics, linguistics, and geographical affinities, with stronger correlations between genetics and language. Additionally, the results suggest a pattern of differential gene flow and drift in western vs. eastern South America, supporting previous mtDNA and Y chromosome investigations.     

Genetic variation and population structure of the mosquito Anopheles jeyporiensis in southern China

Genetic differentiation among populations of Anopheles jeyporiensis was examined using 76 mtDNA COII sequences from 16 sites throughout southern China and northern Vietnam. The COII sequences are AT-rich (74.58%) and reveal high levels of diversity with 39 of 685 sites polymorphic and 50 different haplotypes present. Genetic variation is high within populations and significant geographical structure was detected at both population and regional levels. In the larger samples, the distributions of haplotypes suggest recent population expansion.     

African DNA Lineages in the Mitochondrial Gene Pool of Europeans

Mitochondrial DNA (mtDNA) nucleotide sequences of African origin are found in various European populations at a low frequency (on average, less than 1%). Data on mtDNA variation in Eurasian and African populations have been analyzed, and African mtDNA lineages have been found in Europeans. It has been demonstrated that, despite the high diversity of mtDNA haplotypes of African origin in Europeans, few monophyletic clusters of African lineages are characterized by long-term diversity formed in Europe. Only two such mtDNA clusters (from haplogroups L1b and L3b) have been found, their evolutionary age not exceeding 6500 years. European and African populations have been compared with respect to the frequency distributions of the alleles of autosomal microsatellite loci found in Russian carriers of African mtDNA haplotypes. It has been demonstrated that alleles typical of Europeans are characteristic of the autosomal genotypes of these Russian individuals.     

Biological relationship between Central and South American Chibchan speaking populations: evidence from mtDNA

We examined mitochondrial DNA (mtDNA) haplogroup and haplotype diversity in 188 individuals from three Chibchan (Kogi, Arsario, and Ijka) populations and one Arawak (Wayuú) group from northeast Colombia to determine the biological relationship between lower Central American and northern South American Chibchan speakers. mtDNA haplogroups were obtained for all individuals and mtDNA HVS-I sequence data were obtained for 110 samples. Resulting sequence data were compared to 16 other Caribbean, South, and Central American populations using diversity measures, neutrality test statistics, sudden and spatial mismatch models, intermatch distributions, phylogenetic networks, and a multidimensional scaling plot. Our results demonstrate the existence of a shared maternal genetic structure between Central American Chibchan, Mayan populations and northern South American Chibchan-speakers. Additionally, these results suggest an expansion of Chibchan-speakers into South America associated with a shift in subsistence strategies because of changing ecological conditions that occurred in the region between 10,000-14,000 years before present.     

The 9-bp deletion between the mitochondrial lysine tRNA and COII genes in tribal populations of India

A 9-base-pair (bp) deletion located between the lysine tRNA (MTTK) and COII (MTCOX*2) genes in the human mitochondrial genome is a valuable marker for tracing population relationships. Previous research has shown that the 9-bp deletion is associated with two major clusters of control region sequences; one occurs in sub-Saharan Africa, while the other is associated with Asian populations and populations of Asian origin. We surveyed 898 individuals from 16 tribal populations in India and found 6 individuals with the 9-bp deletion. Sequences of the first hypervariable segment (HV1) of the mtDNA control region from these 9-bp deletion-bearing mtDNAs were compared to those previously reported from Asian and African populations. Phylogenetic analysis indicates three distinct clusters of tribal Indian 9-bp deletion mtDNA types. One cluster, found in northeast India, includes southeast Asian and Indonesian mtDNA types. The remaining two clusters appear to have unique origins in southern India. These data provide further evidence of past migrations from Asia into the northeast corner of the Indian subcontinent.     

Population variation of human mtDNA control region sequences detected by enzymatic amplification and sequence-specific oligonucleotide probes.

A method for detecting sequence variation of hypervariable segments of the mtDNA control region was developed. The technique uses hybridization of sequence-specific oligonucleotide (SSO) probes to DNA sequences that have been amplified by PCR. The nucleotide sequences of the two hypervariable segments of the mtDNA control region from 52 individuals were determined; these sequences were then used to define nine regions suitable for SSO typing. A total of 23 SSO probes were used to detect sequence variants at these nine regions in 525 individuals from five ethnic groups (African, Asian, Caucasian, Japanese, and Mexican). The SSO typing revealed an enormous amount of variability, with 274 mtDNA types observed among these 525 individuals and with diversity values, for each population, exceeding .95. For each of the nine mtDNA regions significant differences in the frequencies of sequence variants were observed between these five populations. The mtDNA SSO-typing system was successfully applied to a case involving individual identification of skeletal remains; the probability of a random match was approximately 0.7%. The potential useful applications of this mtDNA SSO-typing system thus include the analysis of individual identity as well as population genetic studies.     

Mitochondrial and nuclear DNA analyses reveal pronounced genetic structuring in Tunisian wild boar <Emphasis Type="Italic">Sus scrofa</Emphasis>

We analysed 74 wild boars from Tunisia with respect to patterns of genetic differentiation and diversity based on sequences of the mitochondrial control region and genotypes at eight nuclear microsatellite loci. Analysis of molecular variance for both marker systems and Bayesian structure analysis of our microsatellite data revealed a clear break between northern and southern populations. Southern wild boar were monomorphic for one of three mtDNA haplotypes; the other two (one of which only occurred in three individuals) were confined to the north. A comparison with published sequences showed all three haplotypes to belong to the major European clade E1. Microsatellite diversity was similar to that found in earlier studies of wild boar (expected heterozygosity of 0.695 and 0.597 for the north and south, respectively). Contrary to the mtDNA results, we did not find unequivocal evidence of a bottleneck in Tunisian wild boar based on our microsatellite data. The clear distinction between northern and southern populations may be due to an Algerian origin of the southern animals.     

Molecular evolution and population genetics of Greater Caribbean green turtles (Chelonia mydas) as inferred from mitochondrial DNA control region sequences

The molecular evolution and population genetics of migratory green turtles (Chelonia mydas) in the Greater Caribbean were examined with mitochondrial DNA (mtDNA) control region I sequences. A total of 488 base positions (bp) per individual were aligned for 44 individuals from four nesting populations in Florida, Costa Rica, Aves Island (Venezuela), and Surinam. Twelve sequence polymorphisms were detected, representing ten transitions, one transversion, and one 10-bp repeat. Sequence analyses of within- and between-population diversity revealed a deep divergence between western and eastern Caribbean nesting colonies and an inverse relationship between reproductive female population size and mtDNA diversity. In small populations, genetic admixture was important to maintaining high diversity, whereas larger populations appear to have experienced historical bottlenecks or resulted from founder effects. Mitochondrial DNA sequences of the control region offer an order of magnitude greater resolution than restriction site data for addressing questions about mtDNA variation, both within and between populations of green turtles.     

Mitochondrial DNA variation in Indo-Pacific populations of the giant tiger prawn,Penaeus monodon

Surveys of mitochondrial DNA (mtDNA) variation in the giant tiger prawn, Penaeus monodon, using restriction fragment length polymorphisms have provided the first clear evidence that the Indo-West Pacific region is a site of accumulation of genetic diversity rather than a site of origin of genetic diversity. No haplotyes were found in common between a group of five southeast African populations and a group of five Australian (including Western Australia) and three southeast Asian populations. The dominant haplotype was different in the Australian and southeast Asian population groups. Genetic diversity (pi) was greatest in Indonesia (pi averaged 0.05), less in the Philippines and Australia (pi averaged 0.01), and markedly less in the southeast African and the West Australian populations (pi averaged 0.003). The high diversity of the southeast Asian populations resulted from the occurrence in those populations of a set of haplotypes found only in southeast Asia but derived from the southeast African haplotypes. These genetic variants therefore evolved in the Indian Ocean and later migrated into the Indo-West Pacific region. Low genetic variation in the geographically marginal populations in southeast Africa and Western Australia is considered to be the result of bottlenecks, but mismatch distributions suggest that large population sizes have been maintained in Indonesian populations for long periods.     

Population structure and phylogeography of Aphyocypris kikuchii (Oshima) based on mitochondrial DNA variation

Aphyocypris kikuchii is a cyprinid species endemic to northern and eastern Taiwan and is the only primary freshwater fish native east of the Coastal Mountain Range. In total, 92 individuals of A. kikuchii from seven populations in three regions of the island were surveyed for mitochondrial DNA (mtDNA) variation. High haplotype diversity ( h = 0·989) and low nucleotide diversity ( π = 0·009) of mtDNA were detected. Negative values of Tajima's D and unimodal mismatch distributions probably reflect a history of recent demographic expansions from small populations. Three major haplotype clusters displayed geographically non-overlapping distributions, indicating a long-term isolation between regions. Hierarchical analysis of molecular variance showed significant genetic structuring among populations ( Φ _ST= 0·66). Significant haplotype heterogeneity was also detected among populations within regions ( Φ _SC= 0·41, P < 0·001) and among regions ( Φ _CT= 0·43, P < 0·05). Molecular clock estimates of coalescence in the three major mtDNA lineages indicated coalescence in the most recent common ancestor c. 0·11–0·39 million years ago. Haplotypes of cluster B nested as interior nodes in the haplotype network, indicating that migrations from Shueilian (SL) populations to the northern region (cluster A) and to the eastern region (cluster C) may have occurred independently. Lineages A and B + C should be managed as two distinct evolutionarily significant units, while the northern, SL and southern groups should be managed as separate management units.