Context of maternal lineages in the Greater Southwest

We present mitochondrial haplogroup characterizations of the prehistoric Anasazi of the United States (US) Southwest. These data are part of a long-term project to characterize ancient Great Basin and US Southwest samples for mitochondrial DNA (mtDNA) diversity. Three restriction site polymorphisms (RSPs) and one length polymorphism identify four common Native American matrilines (A, B, C, and D). The Anasazi (n = 27) are shown to have a moderate frequency of haplogroup A (22%), a high frequency of haplogroup B (56%), and a low frequency of C (15%). Haplogroup D has not yet been detected among the Anasazi. In comparison to modern Native American groups from the US Southwest, the Anasazi are shown to have a distribution of haplogroups similar to the frequency pattern exhibited by modern Pueblo groups. A principal component analysis also clusters the Anasazi with some modern (Pueblo) Southwestern populations, and away from other modern (Athapaskan speaking) Southwestern populations. The Anasazi are also shown to have a significantly different distribution of the four haplogroups as compared to the eastern Great Basin Great Salt Lake Fremont (n = 32), although both groups cluster together in a principal component analysis. The context of our data suggests substantial stability within the US Southwest, even in the face of the serious cultural and biological disruption caused by colonization of the region by European settlers. We conclude that although sample numbers are fairly low, ancient DNA (aDNA) data are useful for assessing long-term populational affinities and for discerning regional population structure.     

Mitochondrial DNA polymorphisms in Chilean aboriginal populations: implications for the peopling of the southern cone of the continent

The mitochondrial DNAs (mtDNAs) from individuals belonging to three Chilean tribes, the Mapuche, the Pehuenche, and the Yaghan, were studied both by RFLP analysis and D-loop (control region) sequencing. RFLP analysis showed that 3 individuals (1.3%) belonged to haplogroup A, 19 (8%) to haplogroup B, 102 (43%) to haplogroup C, and 113 (47.7%) to haplogroup D. Among the 73 individuals analyzed by D-loop sequencing, we observed 37 different haplotypes defined by 52 polymorphic sites. Joint analysis of data obtained by RFLP and sequencing methods demonstrated that, regardless of the method of analysis, the mtDNA haplotypes of these three contemporary South American aborigine groups clustered into four main haplogroups, in a way similar to those previously described for other Amerindians. These results further revealed the absence of haplogroup A in both the Mapuche and Yaghan as well as the absence of haplogroup B in the Yaghan. These results suggest that the people of Tierra del Fuego are related to tribes from south-central South America.     

Distribution of mtDNA haplogroup X among Native North Americans.

Mitochondrial DNA (mtDNA) samples of 70 Native Americans, most of whom had been found not to belong to any of the four common Native American haplogroups (A, B, C, and D), were analyzed for the presence of Dde I site losses at np 1715 and np 10394. These two mutations are characteristic of haplogroup X which might be of European origin. The first hypervariable segment (HVSI) of the non-coding control region (CR) of mtDNA of a representative selection of samples exhibiting these mutations was sequenced to confirm their assignment to haplogroup X. Thirty-two of the samples exhibited the restriction site losses characteristic of haplogroup X and, when sequenced, a representative selection (n = 11) of these exhibited the CR mutations commonly associated with haplogroup X, C --> T transitions at np 16278 and 16223, in addition to as many as three other HVSI mutations. The wide distribution of this haplogroup throughout North America, and its prehistoric presence there, are consistent with its being a fifth founding haplogroup exhibited by about 3% of modern Native Americans. Its markedly nonrandom distribution with high frequency in certain regions, as for the other four major mtDNA haplogroups, should facilitate establishing ancestor/descendant relationships between modern and prehistoric groups of Native Americans. The low frequency of haplogroups other than A, B, C, D, and X among the samples studied suggests a paucity of both recent non-Native American maternal admixture in alleged fullblood Native Americans and mutations at the restriction sites that characterize the five haplogroups as well as the absence of additional (undiscovered) founding haplogroups.     

mtDNA diversity in Chukchi and Siberian Eskimos: implications for the genetic history of Ancient Beringia and the peopling of the New World.

The mtDNAs of 145 individuals representing the aboriginal populations of Chukotka-the Chukchi and Siberian Eskimos-were subjected to RFLP analysis and control-region sequencing. This analysis showed that the core of the genetic makeup of the Chukchi and Siberian Eskimos consisted of three (A, C, and D) of the four primary mtDNA haplotype groups (haplogroups) (A-D) observed in Native Americans, with haplogroup A being the most prevalent in both Chukotkan populations. Two unique haplotypes belonging to haplogroup G (formerly called "other" mtDNAs) were also observed in a few Chukchi, and these have apparently been acquired through gene flow from adjacent Kamchatka, where haplogroup G is prevalent in the Koryak and Itel'men. In addition, a 16111C-->T transition appears to delineate an "American" enclave of haplogroup A mtDNAs in northeastern Siberia, whereas the 16192C-->T transition demarcates a "northern Pacific Rim" cluster within this haplogroup. Furthermore, the sequence-divergence estimates for haplogroups A, C, and D of Siberian and Native American populations indicate that the earliest inhabitants of Beringia possessed a limited number of founding mtDNA haplotypes and that the first humans expanded into the New World approximately 34,000 years before present (YBP). Subsequent migration 16,000-13,000 YBP apparently brought a restricted number of haplogroup B haplotypes to the Americas. For millennia, Beringia may have been the repository of the respective founding sequences that selectively penetrated into northern North America from western Alaska.     

Origin of Amerindian Y-chromosomes as inferred by the analysis of six polymorphic markers

We analysed the frequency of six Y-specific polymorphisms in 105 Amerindian males from seven different populations, 42 Caucasian males, and a small number of males of African, Chinese, and Melanesian origin. The combination of three of the six polymorphisms studied produced four different Y-haplogroups. The haplogroup A (non-variant) was the most frequent one. Eighty-five percent of Amerindians showing haplogroup A have the alphoid II (αhII) and the DYS19A Y-specific markers, an association that is found only in 10% of Caucasians and that has not been detected in Asiatics and Africans. Haplogroups C (YAP+) and D (YAP+ plus an A → G transition in the locus DYS271) are of African origin. Four percent of Amerindians and ∼12% of Caucasians showed haplogroup C; ∼1% of Amerindians and ∼2% of Caucasians had haplogroup D. Haplogroup B is characterized by a C → T transition in nucleotide position 373 of the SRY gene domain; this haplogroup is found in Caucasians (∼12%) and Amerindians (∼4%). None of the Amerindians exhibiting the haplogroups B, C, or D show the haplotype αhII/DYS19A. By haplotyping the Alu insert and the DNA region surrounding the insert in YAP+ individuals, we could demonstrate that Amerindian Y chromosomes bearing African markers (haplogroups C and D) are due to recent genetic admixture. Most non-αhII/DYSl9A Amerindian Y-chromosomes in haplogroup A and most cases in haplogroup B are also due to gene flow. We show that haplotype αhII/DYS19A is in linkage disequilibrium with a C → T transition in the locus DYS199. Our results suggest that most Amerindian Y-chromosomes derive from a single paternal lineage characterized by the αhII/DYS19A/DYS199T Amerindian-specific haplotype. The analysis of a larger sample of native American Y-chromosomes will be required in order to confirm or correct this hypothesis. Am J Phys Anthropol 102:79–89, 1997. © 1997 Wiley-Liss, Inc.     

Analysis of distribution of "mongoloid" haplogroups of mitochondrial DNA among indigenous population of the Tuva Republic

Variation of Mongoloid-specific restriction sites of mitochondrial genome was analyzed in three territorial groups of Tuvinians. Distribution of mitochondrial DNA haplogroups A, B, C, and D on the territory of the Tuva Republic was estimated. The populations studied did not display distinct differentiation in respect to the mtDNA polymorphism. The specific feature of Tuvinian mitochondrial gene pool was the prevalence of only one haplogroup C (over 40%), mainly represented by two mitotypes. The high frequency of this haplogroup makes Tuvinians similar to more northern Siberian populations. On the other hand, the presence of haplogroup B indicates that Tuvinians have affinity to ethnic groups of Central Asia.     

Spatial and temporal stability of mtDNA haplogroup frequencies in native North America

Mitochondrial DNA lineage frequencies in prehistoric Aleut, eastern Utah Fremont, Southwestern Anasazi, Pyramid Lake, and Stillwater Marsh skeletal samples from northwest Nevada and the Oneota of western Illinois are compared with those in 41 contemporary aboriginal populations of North America. The ancient samples range in age from 300 years to over 6,000 years. The results indicate that the prehistoric inhabitants of North America exhibit the same level of mtDNA variability as contemporary populations of the continent. Variation in modern mtDNA haplogroup frequencies is highly geographically structured, and the prehistoric samples exhibit the same geographic pattern of variation. This indicates that differentiation of regional patterns of mtDNA lineage variation occurred early in North American prehistory (much more than 2,000 years B.P.), has remained relatively stable since its origin, and was little influenced by the disruptions hypothesized for other genetic systems as a result of population declines and relocations at contact.     

Distribution of “Mongoloid” Haplogroups of Mitochondrial DNA Among Indigenous Population of the Tuva Republic

Variation of Mongoloid-specific restriction sites of mitochondrial genome was analyzed in three territorial groups of Tuvinians. Distribution of mitochondrial DNA haplogroups A, B, C, and D on the territory of the Tuva Republic was estimated. The populations studied did not display distinct differentiation in respect to the mtDNA polymorphism. The specific feature of Tuvinian mitochondrial gene pool was the prevalence of only one haplogroup C (over 40%), mainly represented by two mitotypes. The high frequency of this haplogroup makes Tuvinians similar to more northern Siberian populations. On the other hand, the presence of haplogroup B indicates that Tuvinians have affinity to ethnic groups of Central Asia.     

mtDNA variation of aboriginal Siberians reveals distinct genetic affinities with Native Americans.

The mtDNA variation of 411 individuals from 10 aboriginal Siberian populations was analyzed in an effort to delineate the relationships between Siberian and Native American populations. All mtDNAs were characterized by PCR amplification and restriction analysis, and a subset of them was characterized by control region sequencing. The resulting data were then compiled with previous mtDNA data from Native Americans and Asians and were used for phylogenetic analyses and sequence divergence estimations. Aboriginal Siberian populations exhibited mtDNAs from three (A, C, and D) of the four haplogroups observed in Native Americans. However, none of the Siberian populations showed mtDNAs from the fourth haplogroup, group B. The presence of group B deletion haplotypes in East Asian and Native American populations but their absence in Siberians raises the possibility that haplogroup B could represent a migratory event distinct from the one(s) which brought group A, C, and D mtDNAs to the Americas. Our findings support the hypothesis that the first humans to move from Siberia to the Americas carried with them a limited number of founding mtDNAs and that the initial migration occurred between 17,000-34,000 years before present.     

Major mitochondrial DNA haplotype heterogeneity in highland and lowland Amerindian populations from Bolivia

This study provides the frequencies of four mitochondrial DNA (mtDNA) haplogroups of 233 native South Amerindians in eight populations living in the Beni Department of Bolivia, including six populations not previously studied. Linguistically, these populations belong to the three principal South Amerindian language stocks, Andean, Equatorial-Tucanoan, and Ge-Pano-Carib. Frequency analyses under geographic, historic, linguistic, and genetic configurations using the theta statistic of Weir (Weir 1990) and analysis of molecular variance (AMOVA) show similar results. Results are also similar when phenetic cluster is used. Aymara belongs almost exclusively to haplogroup B, Quechua- and Moseten-speaking tribes belong to haplogroups A and B, but the first tribe presents high frequencies of haplogroup B. Yuracare, Trinitario, and Ignaciano exhibit high frequencies of A, B, and C haplogroups, and the Movima present a large proportion of haplogroup C. There is some correspondence between mtDNA haplogroup frequencies and language affiliation and historical connections, but less so with geographic aspects. The present study provides a context for understanding the relationship between different Amerindian populations living in a multiethnic area of Bolivia.     

Microevolution in prehistoric Andean populations: chronologic mtDNA variation in the desert valleys of northern Chile

Archeological evidence suggests that the iconographic and technological developments that took place in the highlands around Lake Titicaca in the Central Andean region had an influence on the cultural elaborations of the human groups in the valleys and the Pacific coast of northern Chile. In a previous communication, we were able to show, by means of a distance analysis, that a craniofacial differentiation accompanied the process of cultural evolution in the valleys (Rothhammer and Santoro [2001] Lat. Am. Antiq. 12:59-66). Recently, numerous South Amerindian mtDNA studies were published, and more accurate molecular techniques to study ancient mtDNA are available. In view of these recent developments, we decided 1) to study chronological changes of ancient mtDNA haplogroup frequencies in the nearby Lluta, Azapa, and Camarones Valleys, 2) to identify microevolutionary forces responsible for such changes, and 3) to compare ancient mtDNA haplogroup frequencies with previous data in order to validate craniometrical results and to reconstruct the biological history of the prehistoric valley groups in the context of their interaction with culturally more developed highland populations. From a total of 97 samples from 83 individuals, 68 samples (61 individuals) yielded amplifications for the fragments that harbor classical mtDNA markers. The haplogroup distribution among the total sample was as follows: 26.2%, haplogroup A; 34.4%, haplogroup B; 14.8%, haplogroup C; 3.3%, haplogroup D; and 21.3%, other haplogroups. Haplogroup B tended to increase, and haplogroup A to decrease during a 3,900-year time interval. The sequence data are congruent with the haplogroup analysis. In fact, the sequencing of hypervariable region I of 30 prehistoric individuals revealed 43 polymorphic sites. Sequence alignment and subsequent phylogenetic tree construction showed two major clusters associated with the most common restriction haplogroups. Individuals belonging to haplogroups C and D tended to cluster together with nonclassical lineages.     

Five ovine mitochondrial lineages identified from sheep breeds of the near East

Archaeozoological evidence indicates that sheep were first domesticated in the Fertile Crescent. To search for DNA sequence diversity arising from previously undetected domestication events, this survey examined nine breeds of sheep from modern-day Turkey and Israel. A total of 2027 bp of mitochondrial DNA (mtDNA) sequence from 197 sheep revealed a total of 85 haplotypes and a high level of genetic diversity. Six individuals carried three haplotypes, which clustered separately from the known ovine mtDNA lineages A, B, and C. Analysis of genetic distance, mismatch distribution, and comparisons with wild sheep confirmed that these represent two additional mtDNA lineages denoted D and E. The two haplogroup E sequences were found to link the previously identified groups A and C. The single haplogroup D sequence branched with the eastern mouflon (Ovis orientalis), urial (O. vignei), and argali (O. ammon) sheep. High sequence diversity (K = 1.86%, haplogroup D and O. orientalis) indicates that the wild progenitor of this domestic lineage remains unresolved. The identification in this study of evidence for additional domestication events adds to the emerging view that sheep were recruited from wild populations multiple times in the same way as for other livestock species such as goat, cattle, and pig.     

真菌学的二百五十年*

本文对真菌学的发展历史作了简要的回顾并将其分为4个发展阶段:(1)前真菌学阶段(B.C.5000—A.D.1700);(2)古真菌学阶段(1701—1850);(3)近代真菌学阶段(1851—1950);(4)现代真菌学的发展(1951—现在)。     

Distribution of four founding mtDNA haplogroups among Native North Americans

The mtDNA of most Native Americans has been shown to cluster into four lineages, or haplogroups. This study provides data on the haplogroup affiliation of nearly 500 Native North Americans including members of many tribal groups not previously studied. Phenetic cluster analysis shows a fundamental difference among 1) Eskimos and northern Na-Dene groups, which are almost exclusively mtDNA haplogroup A, 2) tribes of the Southwest and adjacent regions, predominantly Hokan and Uto-Aztecan speakers, which lack haplogroup A but exhibit high frequencies of haplogroup B, 3) tribes of the Southwest and Mexico lacking only haplogroup D, and 4) a geographically heterogeneous group of tribes which exhibit varying frequencies of all four haplogroups. There is some correspondence between language group affiliations and the frequencies of the mtDNA haplogroups in certain tribes, while geographic proximity appears responsible for the genetic similarity among other tribes. Other instances of similarity among tribes suggest hypotheses for testing with more detailed studies. This study also provides a context for understanding the relationships between ancient and modern populations of Native Americans. © 1996 Wiley-Liss, Inc.     

A new subclade of mtDNA haplogroup C1 found in icelanders: Evidence of pre‐columbian contact?

Although most mtDNA lineages observed in contemporary Icelanders can be traced to neighboring populations in the British Isles and Scandinavia, one may have a more distant origin. This lineage belongs to haplogroup C1, one of a handful that was involved in the settlement of the Americas around 14,000 years ago. Contrary to an initial assumption that this lineage was a recent arrival, preliminary genealogical analyses revealed that the C1 lineage was present in the Icelandic mtDNA pool at least 300 years ago. This raised the intriguing possibility that the Icelandic C1 lineage could be traced to Viking voyages to the Americas that commenced in the 10th century. In an attempt to shed further light on the entry date of the C1 lineage into the Icelandic mtDNA pool and its geographical origin, we used the deCODE Genetics genealogical database to identify additional matrilineal ancestors that carry the C1 lineage and then sequenced the complete mtDNA genome of 11 contemporary C1 carriers from four different matrilines. Our results indicate a latest possible arrival date in Iceland of just prior to 1700 and a likely arrival date centuries earlier. Most surprisingly, we demonstrate that the Icelandic C1 lineage does not belong to any of the four known Native American (C1b, C1c, and C1d) or Asian (C1a) subclades of haplogroup C1. Rather, it is presently the only known member of a new subclade, C1e. While a Native American origin seems most likely for C1e, an Asian or European origin cannot be ruled out.     

MtDNA variation in the Altai-Kizhi population of southern Siberia: a synthesis of genetic variation

The native peoples of Gorno Altai in southern Siberia represent a genetically diverse population and have been of great interest to anthropological genetics. In particular, the southern Altaian population is argued to be the best candidate for the New World ancestral population. In this study we sampled Altai-Kizhi from the southern Altaian village of Mendur-Sokkon, analyzed mtDNA RFLP markers and HVS-I sequences, and compared the results to other published mtDNA data from Derenko et al. (2003) and Shields et al. (1993) encompassing the same region. Because each independent study uses different sampling techniques in characterizing gene pools, in this paper we explore the accuracy and reliability of evolutionary studies on human populations. All the major Native American haplogroups (A, B, C, and D) were identified in the Mendur-Sokkon sample, including a single individual belonging to haplogroup X. The most common mtDNA lineages are C (35.7%) and D (13.3%), which is consistent with the haplogroup profiles of neighboring Siberian groups. The Mendur-Sokkon sample exhibits depressed HVS-I diversity values and neutrality test scores, which starkly differs from the Derenko et al. (2003) data set and more closely resembles the results for neighboring south Siberian groups. Furthermore, the multidimensional scaling plot of DA genetic distances does not cluster the Altai samples, showing different genetic affinities with various Asian groups. The findings underscore the importance of sampling strategy in the reconstruction of evolutionary history at the population level.     

Genetic diversity in an Andean population from Peru and regional migration patterns of Amerindians in South America: data from Y chromosome and mitochondrial DNA

The genetic variability of a Quechua-speaking Andean population from Peru was examined on the basis of four Y chromosome markers and restriction sites that define the Amerindian mitochondrial DNA (mtDNA) haplogroups. Forty-nine out of 52 (90.4%) individuals had mtDNA which belonged to one of the four common Amerindian haplogroups, with 54% of the samples belonging to haplogroup B. Among 25 males, 12 had an Amerindian Y chromosome, which exists as four haplotypes defined on the basis of the DYS287, DYS199, DYS392 and DYS19 markers, three of which are shared by Amazonian Amerindians. Thus, there is a clear directionality of marriages, with an estimated genetic admixture with non-Amerindians that is 9 times lower for mtDNA than for Y chromosome DNA. The comparison of mtDNA of Andean Amerindians with that of people from other regions of South America in a total of 1,086 individuals demonstrates a geographical pattern, with a decreasing frequency of A and C haplotypes and increasing frequency of the D haplotype from the north of the Amazon River to the south of the Amazon River, reaching the lowest and the highest frequencies, respectively, in the more southern populations of Chile and Argentina. Conversely, the highest and lowest frequencies of the haplogroup B are found, respectively, in the Andean and the North Amazon regions, and it is absent from some southern populations, suggesting that haplotypes A, C and D, and haplotype B may have been dispersed by two different migratory routes within the continent.     

Geographic patterns of genetic and morphological divergence amongst populations of a river crab (Decapoda, Potamonautidae) with the description of a new species from mountain streams in the Western Cape, South Africa

Recent systematic research has revealed that Potamonautes brincki comprises two genetically and morphologically distinct population groups. The systematic affinities between these population groups have remained uncertain. In the present study, the relationship between the population groups was examined. Eleven populations were collected from high mountain streams in the Western Cape, South Africa and used in the genetic and morphological analyses. Allozyme electrophoresis of 13 protein coding loci separated two main population groups: group A (Cape Peninsular groups) and group B (Hottentot's Holland) at I  = 0.73. Two additional genetic groups were evident, with group B being conspecific to group A, and group D being conspecific to group C. Morphological examination of pleopod 1 and the terminal segment of the mandibular palp showed considerable differences between the two main population groups, with groups A and B being similar and groups C and D being similar. The morphometric data for the four main groups were examined using discriminant functions analysis and the two main groups were compared using analyses of covariance. Discriminant functions analysis showed a moderate degree of overlap between the groups. Additional morphometric data showed a clear discrimination between the two main population groups. The genetic and morphometric data sets exhibited congruent patterns of variation and the data showed the presence of a species boundary. A new freshwater crab species, P. parvicorpus sp. n., is described. The results of the present study are discussed in the light of historical and contemporary factors that are likely to have contributed to speciation.     

Molecular characterization of mitochondrial Amerindian haplogroups and the amelogenin gene in human ancient DNA from three archaeological sites in Lambayeque - Peru

Important pre-Inca civilizations, known by their great political and religious structures, inhabited the northern coast of Peru. Archeological and anthropological studies have shown that people from these villages have hierarchical strata, but the genetic structure has been poorly studied. Here, we aimed to perform a molecular characterization of the Amerindian maternal lineages and the amelogenin gene in skeletons collected from three archeological sites in Lambayeque. Ancient DNA (aDNA) samples were analyzed with conventional PCR to assess the nine-base pair (9 bp) deletion corresponding to mitochondrial haplogroup B and the identification of haplogroups A, C, and D were obtained with PCR-RFLP experiments. The sex was characterized via amplification of the AMEL(X/Y) locus. Haplogroup frequencies were compared with available data from other ancient and modern civilizations from the Peruvian coast and highlands using statistical methods. Our results showed that haplogroup C had the highest frequency, while haplogroup B showed variable diversity in the analyzed populations. The meta-analysis revealed a positive correlation among some coastal villages. We concluded that ancient populations analyzed in our study showed the presence of four Amerindian mitochondrial haplogroups, which is consistent with previous studies.