U5a1 Mitochondrial DNA Haplotype Identified in Eneolithic Skeleton from Shatar Chuluu, Mongolia.

The mitochondrial haplotype U5a1 was identified from an Eneolithic grave associated with the Afanasievo archaeological culture in Bayankhongor Province, Erdenetsogt Township, at the site of Shatar Chuluu. This is the earliest appearance of an mtDNA haplotype associated with modern European populations on the Mongol Steppe. This evidence demonstrations that people with "western" mtDNA lived on the Mongol Steppe east of the Altai Mountains before the Bronze Age and refutes the notion that the Altai Mountains were a substantial barrier to gene flow, and definitively expands the acknowledged range of the Afanasievo archaeological culture.

Chimpanzee (Pan troglodytes schweinfurthii) Population Spans Multiple Protected Areas in the Albertine Rift.

We used mitochondrial DNA to examine gene flow in a region of western Uganda that has received little attention regarding chimpanzee population dynamics. The area is critical to gene flow between isolated Democratic Republic of Congo populations and the rest of East Africa. None of the chimpanzees in each of the 4 protected areas under consideration (Toro-Semliki Wildlife Reserve, Semuliki National Park, Rwenzori Mountains National Park and Itwara Central Forest Reserve) are fully habituated. Therefore, it is not clear whether one or more populations have historically used this fragmented landscape for (1) regular ranging and/or (2) infrequent dispersal. We incorporated the published sequences of the first hypervariable region of the D-loop of the mitochondrial genome from 3 previously sampled sites (n = 39) while also contributing the first extensive genetic sampling of chimpanzees in Toro-Semliki (n = 80). Our goal was to generate a historical baseline model of metapopulation dynamics in this region and determine which, if any, of these protected areas forms a fragmented landscape for a single chimpanzee population. According to a discriminant analysis of principal components, the haplotypes at Toro-Semliki form a central cluster, and Itwara is its nearest genetic neighbor. Rwenzori Mountains National Park is the most distant neighbor of all protected areas. We performed an analysis of molecular variance for 14 different population models that divided the samples from the 4 protected areas into 2, 3 or 4 populations. The best fit model included 3 populations: Toro-Semliki Wildlife Reserve and Itwara Forest Reserve comprised a single population; Semuliki National Park and Rwenzori Mountains National Park formed 2 additional separate populations (variance among = 9%, p = 0.014). The results indicated that some protected areas comprised distinctive populations, while others formed a fragmented landscape for a population's ranging for foraging purposes. Therefore, the edges of a protected area do not always define a chimpanzee population. We propose a closer examination of those dynamics through renewed sampling. Advances in DNA extraction and next-generation sequencing will allow us to compare thousands of single nucleotide polymorphisms in the genomes of unhabituated chimpanzees living in each of these protected areas.

Is genetic drift to blame for testicular dysgenesis syndrome in Semliki chimpanzees (Pan troglodytes schweinfurthii)?

BACKGROUND: We present 3 likely cases of testicular dysgenesis syndrome (TDS) within a community of chimpanzees (Pan troglodytes schweinfurthii). We tested whether genetic drift may be the culprit, as a genetic cause has been suspected to account for TDS among other wildlife. METHODS: We successfully sequenced a 367-bp segment spanning the first hypervariable region within the D-loop of the mitochondrial genome for 78 DNA samples. RESULTS: We found 24 polymorphic sequence sites consisting of 7 singletons and 17 parsimony informative sites. This sample contained 9 haplotypes with a diversity index of 0.78 (SD = 0.03). All tests against the null hypothesis of neutral polymorphisms were non-significant (P > .10). The mismatch distribution of pairwise differences does not fit a Poisson's curve (raggedness index = 0.166; SSD = 0.12; P = 1). CONCLUSIONS: Thus, we found no significant signs of genetic isolation, population expansion, or genetic bottleneck. Alternative causes of TDS and how they might pertain to this population are discussed.

Ancient DNA from the Schild site in Illinois: Implications for the Mississippian transition in the Lower Illinois River Valley.

Archaeologists have long debated whether rapid cultural change in the archaeological record is due to in situ developments, migration of a new group into the region, or the spread of new cultural practices into an area through existing social networks, with the local peoples adopting and adapting practices from elsewhere as they see fit (acculturation). Researchers have suggested each of these explanations for the major cultural transition that occurred at the beginning of the Mississippian period (AD 1050) across eastern North America. In this study, we used ancient DNA to test competing hypotheses of migration and acculturation for the culture change that occurred between the Late Woodland (AD 400-1050) and Mississippian (AD 1050-1500) periods in the Lower Illinois River Valley. We obtained sequences of the first hypervariable segment of the mitochondrial genome (mtDNA) from 39 individuals (17 Late Woodland, 22 Mississippian) interred in the Schild cemetery in western Illinois, and compared these lineages to ancient mtDNA lineages present at other sites in the region. Computer simulations were used to test a null hypothesis of population continuity from Late Woodland to Mississippian times at the Schild site and to investigate the possibility of gene flow from elsewhere in the region. Our results suggest that the Late Woodland to Mississippian cultural transition at Schild was not due to an influx of people from elsewhere. Instead, it is more likely that the transition to Mississippian cultural practices at this site was due to a process of acculturation.

Brief communication: Conjoined twins at angel mounds? an ancient DNA perspective.

Conjoined twins are born when a single fertilized egg partially splits into two fetuses. A hypothetical case of infant conjoined twins from Angel Mounds, a Middle Mississippian site (A.D. 1050-1400) on the Ohio River near Evansville, Indiana, was discovered in 1941. Morphological analysis does not rule out the field interpretation of this double burial as twins. Ancient mitochondrial DNA recovered from both infants demonstrates that they were not maternal relatives, and hence that they cannot have been conjoined twins.

Investigation of ancient DNA from Western Siberia and the Sargat culture.

Mitochondrial DNA from 14 archaeological samples at the Ural State University in Yekaterinburg, Russia, was extracted to test the feasibility of ancient DNA work on their collection. These samples come from a number of sites that fall into two groupings. Seven samples are from three sites, dating to the 8th-12th century AD, that belong to a northern group of what are thought to be Ugrians, who lived along the Ural Mountains in northwestern Siberia. The remaining seven samples are from two sites that belong to a southern group representing the Sargat culture, dating between roughly the 5th century BC and the 5th century AD, from southwestern Siberia near the Ural Mountains and the present-day Kazakhstan border. The samples are derived from several burial types, including kurgan burials. They also represent a number of different skeletal elements and a range of observed preservation. The northern sites repeatedly failed to amplify after multiple extraction and amplification attempts, but the samples from the southern sites were successfully extracted and amplified. The sequences obtained from the southern sites support the hypothesis that the Sargat culture was a potential zone of intermixture between native Ugrian and/or Siberian populations and steppe peoples from the south, possibly early Iranian or Indo-Iranian, which has been previously suggested by archaeological analysis.

LRP5 sequence and polymorphisms in the baboon.

BACKGROUND: LRP5 is known to have an important relationship with bone density and a variety of other biological processes. Mapping to human chromosome 11q13.2, LRP5 shows considerable evolutionary conservation. Orthologs of this gene exist in many species, although comparison of human LRP5 with other non-human primates has not been performed until now. METHODS: We reported the complementary DNA (cDNA) sequence and deduced amino acid sequence for baboon LRP5, and compared the baboon and human sequences. cDNA sequences for 21 baboons were examined to identify single-nucleotide polymorphisms (SNPs). RESULTS: Sequences of coding regions in human and baboon LRP5 showed 97- 99% homology. Twenty-five SNPs were identified in the coding region of baboon LRP5. CONCLUSION: The observed degree of coding sequence homology in LRP5 led us to expect that the baboon may serve as a useful model for future research into the role(s) of this gene in primate metabolic diseases.

Population continuity or replacement? A novel computer simulation approach and its application to the Numic expansion (Western Great Basin, USA).

In a previous study, Kaestle and Smith [Am J Phys Anthropol 115 (2001) 1-12] supported a recent (A.D. 1000) Numic expansion into the Great Basin region based on a molecular and statistical analysis of mitochondrial DNA (mtDNA) of ancient and modern native inhabitants of the region. Their statistical methodology could not rule out the possibility that observed differences in haplogroup frequencies are instead the result of long-term microevolutionary change within a single population. To distinguish more effectively between a Numic expansion versus population continuity, we employed a novel computer simulation approach that incorporates microevolutionary factors likely to affect human population genetic variation. We test whether the observed differences in haplogroup frequencies between ancient and modern Great Basin groups could have been produced solely via in situ microevolutionary change. Our results indicate that for reasonable demographic conditions, the observed genetic differences between the observed samples are consistent with population continuity if gene flow among prehistoric Great Basin local groups was less than 1% of local group size per generation. Our analysis also supports a recent population expansion if gene flow between neighboring groups exceeded 8% of local group size per generation. The simulations demonstrate that relatively low gene flow levels and random genetic drift can produce the observed degree of genetic differences between population samples. Although this study focuses on the Numic expansion, this simulation approach can be applied to any geographic region for which genetic data have been collected to address similar questions of population relationships over time.

Tuberculosis in the New World: a study of ribs from the Schild Mississippian population, West-Central Illinois

Vertebral lesions have been the main evidence for infection by the Mycobacterium tuberculosis complex (MTC) in paleopathology. Skeletal involvement is expected in a small percentage of infected individuals. Recently, several authors report a correlation between rib lesions and tuberculosis (TB) complex infection. This study tests the hypothesis that rib lesions can serve as a useful marker for MTC infection within the Mississippian Schild skeletal collection from West-Central Illinois. Ribs from 221 adults and juveniles were examined, and affected individuals were tested for TB complex infection. DNA from rib samples of affected individuals was amplified with primers targeting the IS6110 insertion element, which is common to all members of the TB complex. Although it cannot allow discrimination between different species of TB, IS6110 is present in many copies within their genomes, and its presence is thus an indication of MTC infection. The results support the use of rib lesions as a marker for TB infection. Additionally, we demonstrate that MTC DNA can be recovered from ribs that lack lesions in individuals who have lesions of other bones. We recommend that an examination of ribs be incorporated into investigations for TB.

Reanalysis of Eurasian population history: ancient DNA evidence of population affinities.

Mitochondrial hypervariable region I genetic data from ancient populations at two sites in Asia-Linzi in Shandong (northern China) and Egyin Gol in Mongolia-were reanalyzed to detect population affinities. Data from 51 modern populations were used to generate distance measures (Fst's) to the two ancient populations. The tests first analyzed relationships at the regional level and then compiled the top regional matches for an overall comparison to the two probe populations. The reanalysis showed that the Egyin Gol and Linzi populations have clear distinctions in genetic affinity. The Egyin Gol population as a whole appears to bear close affinities with modern populations of northern East Asia. The Linzi population seems to have some genetic affinities with the West, as suggested by the original analysis, although the original attribution of "European-like" seems to be misleading. We suggest that the Linzi individuals are potentially related to early Iranians, who are thought to have been widespread in parts of Central Eurasia and the steppe regions in the first millennium B.C., although some significant admixture between a number of populations of varying origin cannot be ruled out. We also examine the effect of sequence length on this type of genetic data analysis and discuss the results of previous studies on the Linzi sample.

Tuberculosis in the New World: a study of ribs from the Schild Mississippian population, West-Central Illinois.

Vertebral lesions have been the main evidence for infection by the Mycobacterium tuberculosis complex (MTC) in paleopathology. Skeletal involvement is expected in a small percentage of infected individuals. Recently, several authors report a correlation between rib lesions and tuberculosis (TB) complex infection. This study tests the hypothesis that rib lesions can serve as a useful marker for MTC infection within the Mississippian Schild skeletal collection from West-Central Illinois. Ribs from 221 adults and juveniles were examined, and affected individuals were tested for TB complex infection. DNA from rib samples of affected individuals was amplified with primers targeting the IS6110 insertion element, which is common to all members of the TB complex. Although it cannot allow discrimination between different species of TB, IS6110 is present in many copies within their genomes, and its presence is thus an indication of MTC infection. The results support the use of rib lesions as a marker for TB infection. Additionally, we demonstrate that MTC DNA can be recovered from ribs that lack lesions in individuals who have lesions of other bones. We recommend that an examination of ribs be incorporated into investigations for TB.

Expanding Southwest Pacific mitochondrial haplogroups P and Q.

Modern humans have occupied New Guinea and the nearby Bismarck and Solomon archipelagos of Island Melanesia for at least 40,000 years. Previous mitochondrial DNA (mtDNA) studies indicated that two common lineages in this region, haplogroups P and Q, were particularly diverse, with the coalescence for P considered significantly older than that for Q. In this study, we expand the definition of haplogroup Q so that it includes three major branches, each separated by multiple mutational distinctions (Q1, equivalent to the earlier definition of Q, plus Q2 and Q3). We report three whole-mtDNA genomes that establish Q2 as a major Q branch. In addition, we describe 314 control region sequences that belong to the expanded haplogroups P and Q from our Southwest Pacific collection. The coalescence dates for the largest P and Q branches (P1 and Q1) are similar to each other (approximately 50,000 years old) and considerably older than prior estimates. Newly identified Q2, which was found in Island Melanesian samples just to the east, is somewhat younger by more than 10,000 years. Our coalescence estimates should be more reliable than prior ones because they were based on significantly larger samples as well as complete mtDNA-coding region sequencing. Our estimates are roughly in accord with the current suggested dates for the first settlement of New Guinea-Sahul. The phylogeography of P and Q indicates almost total (female) isolation of ancient New Guinea-Island Melanesia from Australia that may have existed from the time of the first settlement. While Q subsequently diversified extensively in New Guinea-Island Melanesia, it has not been found in Australia. The only shared mtDNA haplogroup between Australia and New Guinea identified to date remains one minor branch of P.

Patterns of mtDNA diversity in northwestern North America.

The mitochondrial DNA (mtDNA) haplogroups of 54 full-blooded modern and 64 ancient Native Americans from northwestern North America were determined. The control regions of 10 modern and 30 ancient individuals were sequenced and compared. Within the Northwest, the frequency distribution for haplogroup A is geographically structured, with haplogroup A decreasing with distance from the Pacific Coast. The haplogroup A distribution suggests that a prehistoric population intrusion from the subarctic and coastal region occurred on the Columbia Plateau in prehistoric times. Overall, the mtDNA pattern in the Northwest suggests significant amounts of gene flow among Northwest Coast, Columbia Plateau, and Great Basin populations.

Mitochondrial DNA and prehistoric settlements: native migrations on the western edge of North America.

We analyzed previously reported mtDNA haplogroup frequencies of 577 individuals and hypervariable segment 1 (HVS1) sequences of 265 individuals from Native American tribes in western North America to test hypotheses regarding the settlement of this region. These data were analyzed to determine whether Hokan and Penutian, two hypothesized ancient linguistic stocks, represent biological units as a result of shared ancestry within these respective groups. Although the pattern of mtDNA variation suggests regional continuity and although gene flow between populations has contributed much to the genetic landscape of western North America, some evidence supports the existence of both the Hokan and Penutian phyla. In addition, a comparison between coastal and inland populations along the west coast of North America suggests an ancient coastal migration to the New World. Similarly high levels of haplogroup A among coastal populations in the Northwest and along the California coast as well as shared HVS1 sequences indicate that early migrants to the New World settled along the coast with little gene flow into the interior valleys.

Native American mtDNA prehistory in the American Southwest.

This study examines the mtDNA diversity of the proposed descendants of the multiethnic Hohokam and Anasazi cultural traditions, as well as Uto-Aztecan and Southern-Athapaskan groups, to investigate hypothesized migrations associated with the Southwest region. The mtDNA haplogroups of 117 Native Americans from southwestern North America were determined. The hypervariable segment I (HVSI) portion of the control region of 53 of these individuals was sequenced, and the within-haplogroup diversity of 18 Native American populations from North, Central, and South America was analyzed. Within North America, populations in the West contain higher amounts of diversity than in other regions, probably due to a population expansion and high levels of gene flow among subpopulations in this region throughout prehistory. The distribution of haplogroups in the Southwest is structured more by archaeological tradition than by language. Yumans and Pimans exhibit substantially greater genetic diversity than the Jemez and Zuni, probably due to admixture and genetic isolation, respectively. We find no evidence of a movement of mtDNA lineages northward into the Southwest from Central Mexico, which, in combination with evidence from nuclear markers, suggests that the spread of Uto-Aztecan was facilitated by predominantly male migration. Southern Athapaskans probably experienced a bottleneck followed by extensive admixture during the migration to their current homeland in the Southwest.

The structure of diversity within New World mitochondrial DNA haplogroups: implications for the prehistory of North America.

The mitochondrial DNA haplogroups and hypervariable segment I (HVSI) sequences of 1,612 and 395 Native North Americans, respectively, were analyzed to identify major prehistoric population events in North America. Gene maps and spatial autocorrelation analyses suggest that populations with high frequencies of haplogroups A, B, and X experienced prehistoric population expansions in the North, Southwest, and Great Lakes region, respectively. Haplotype networks showing high levels of reticulation and high frequencies of nodal haplotypes support these results. The haplotype networks suggest the existence of additional founding lineages within haplogroups B and C; however, because of the hypervariability exhibited by the HVSI data set, similar haplotypes exhibited in Asia and America could be due to convergence rather than common ancestry. The hypervariability and reticulation preclude the use of estimates of genetic diversity within haplogroups to argue for the number of migrations to the Americas.

Ancient DNA in anthropology: methods, applications, and ethics.

Anthropologists were quick to recognize the potential of new techniques in molecular biology to provide additional lines of evidence on questions long investigated in anthropology, as well as those questions that, while always of interest, could not have been addressed by more traditional techniques. The earliest ancient DNA studies, both within anthropology and in other fields, lacked rigorous hypothesis testing. However, more recently the true value of ancient DNA studies is being realized, and methods are being applied to a wide variety of anthropological questions. We review the most common methods and applications to date, and describe promising avenues of future research. We find that ancient DNA analyses have a valuable place in the array of anthropological techniques, but argue that such studies must not be undertaken merely to demonstrate that surviving DNA is present in organic remains, and that no such work should be performed before a careful consideration of the possible ethical ramifications of the research is undertaken.

A DNA Analysis of Pre-Contact TB.

Apresentação que estudou e analisou o DNA dos americanos nativos e dos americanos modernos e a relação entre eles, como forma de identificar as migrações de povos que formaram a atual população americana. Alerta para a dificuldade de se avaliar grandes períodos de tempo devido a mudanças culturais, anatômicas e de idioma e que nos últimos 20 anos muitos geneticistas discutiram a evidência de migrações múltiplas, o que a autora discorda. Os americanos nativos modernos pertencem a um dos cinco “halougroups” descobertos e os outros quatro são difundidos na Ásia. A autora acredita que os habitantes mais antigos das Américas não são os antepassados diretos dos americanos nativos modernos, devido a não terem descendentes vivos e pela substituição por migrações posteriores.