Rare human mitochondrial HV lineages spread from the Near East and Caucasus during post-LGM and Neolithic expansions.

Of particular significance to human population history in Eurasia are the migratory events that connected the Near East to Europe after the Last Glacial Maximum (LGM). Utilizing 315 HV*(xH,V) mitogenomes, including 27 contemporary lineages first reported here, we found the genetic signatures for distinctive movements out of the Near East and South Caucasus both westward into Europe and eastward into South Asia. The parallel phylogeographies of rare, yet widely distributed HV*(xH,V) subclades reveal a connection between the Italian Peninsula and South Caucasus, resulting from at least two (post-LGM, Neolithic) waves of migration.

The Gateway from Near into Remote Oceania: New Insights from Genome-Wide Data.

A widely accepted two-wave scenario of human settlement of Oceania involves the first out-of-Africa migration circa 50,000 years ago (ya), and the more recent Austronesian expansion, which reached the Bismarck Archipelago by 3,450 ya. Whereas earlier genetic studies provided evidence for extensive sex-biased admixture between the incoming and the indigenous populations, some archaeological, linguistic, and genetic evidence indicates a more complicated picture of settlement. To study regional variation in Oceania in more detail, we have compiled a genome-wide data set of 823 individuals from 72 populations (including 50 populations from Oceania) and over 620,000 autosomal single nucleotide polymorphisms (SNPs).

Genomic insights into the peopling of the Southwest Pacific.

The appearance of people associated with the Lapita culture in the South Pacific around 3,000 years ago marked the beginning of the last major human dispersal to unpopulated lands. However, the relationship of these pioneers to the long-established Papuan people of the New Guinea region is unclear. Here we present genome-wide ancient DNA data from three individuals from Vanuatu (about 3,100-2,700 years before present) and one from Tonga (about 2,700-2,300 years before present), and analyse them with data from 778 present-day East Asians and Oceanians.

Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals.

Although Neandertal sequences that persist in the genomes of modern humans have been identified in Eurasians, comparable studies in people whose ancestors hybridized with both Neandertals and Denisovans are lacking. We developed an approach to identify DNA inherited from multiple archaic hominin ancestors and applied it to whole-genome sequences from 1523 geographically diverse individuals, including 35 previously unknown Island Melanesian genomes. In aggregate, we recovered 1.

Identification of Whole Mitochondrial Genomes from Venezuela and Implications on Regional Phylogenies in South America.

Recent studies have expanded and refined the founding haplogroups of the Americas using whole mitochondrial (mtDNA) genome analysis. In addition to pan-American lineages, specific variants have been identified in a number of studies that show higher frequencies in restricted geographical areas. To further characterize Native American maternal lineages and specifically examine local patterns within South America, we analyzed 12 maternally unrelated Yekuana whole mtDNA genomes from one village (Sharamaña) that include the four major Native American haplogroups A2, B2, C1, and D1.

Ancient DNA analysis of the oldest canid species from the Siberian Arctic and genetic contribution to the domestic dog.

Modern Arctic Siberia provides a wealth of resources for archaeological, geological, and paleontological research to investigate the population dynamics of faunal communities from the Pleistocene, particularly as the faunal material coming from permafrost has proven suitable for genetic studies. In order to examine the history of the Canid species in the Siberian Arctic, we carried out genetic analysis of fourteen canid remains from various sites, including the well-documented Upper Paleolithic Yana RHS and Early Holocene Zhokhov Island sites. Estimated age of samples range from as recent as 1,700 years before present (YBP) to at least 360,000 YBP for the remains of the extinct wolf, Canis cf.

A comprehensive whole-genome integrated cytogenetic map for the alpaca (Lama pacos).

Genome analysis of the alpaca (Lama pacos, LPA) has progressed slowly compared to other domestic species. Here, we report the development of the first comprehensive whole-genome integrated cytogenetic map for the alpaca using fluorescence in situ hybridization (FISH) and CHORI-246 BAC library clones. The map is comprised of 230 linearly ordered markers distributed among all 36 alpaca autosomes and the sex chromosomes.

A cytogenetic and comparative map of camelid chromosome 36 and the minute in alpacas.

Recent advances in camelid genomics have provided draft sequence assemblies and the first comparative and gene maps for the dromedary (CDR) and the alpaca (LPA). However, no map information is currently available for the smallest camelid autosome-chr36. The chromosome is also of clinical interest because of its involvement in the minute chromosome syndrome (MCS) in infertile alpacas.

Maternal history of Oceania from complete mtDNA genomes: contrasting ancient diversity with recent homogenization due to the Austronesian expansion.

Archaeology, linguistics, and existing genetic studies indicate that Oceania was settled by two major waves of migration. The first migration took place approximately 40 thousand years ago and these migrants, Papuans, colonized much of Near Oceania. Approximately 3.

Characterization of population structure from the mitochondrial DNA vis-à-vis language and geography in Papua New Guinea.

Situated along a corridor linking the Asian continent with the outer islands of the Pacific, Papua New Guinea has long played a key role in understanding the initial peopling of Oceania. The vast diversity in languages and unique geographical environments in the region have been central to the debates on human migration and the degree of interaction between the Pleistocene settlers and newer migrants. To better understand the role of Papua New Guinea in shaping the region's prehistory, we sequenced the mitochondrial DNA (mtDNA) control region of three populations, a total of 94 individuals, located in the East Sepik Province of Papua New Guinea.

Titanic's unknown child: the critical role of the mitochondrial DNA coding region in a re-identification effort.

This report describes a re-examination of the remains of a young male child recovered in the Northwest Atlantic following the loss of the Royal Mail Ship Titanic in 1912 and buried as an unknown in Halifax, Nova Scotia shortly thereafter. Following exhumation of the grave in 2001, mitochondrial DNA (mtDNA) hypervariable region 1 sequencing and odontological examination of the extremely limited skeletal remains resulted in the identification of the child as Eino Viljami Panula, a 13-month-old Finnish boy. This paper details recent and more extensive mitochondrial genome analyses that indicate the remains are instead most likely those of an English child, Sidney Leslie Goodwin.

The effects of different maceration techniques on nuclear DNA amplification using human bone.

Forensic anthropologists routinely macerate human bone for the purposes of identity and trauma analysis, but the heat and chemical treatments used can destroy genetic evidence. As a follow-up to a previous study on nuclear DNA recovery that used pig ribs, this study utilizes human skeletal remains treated with various bone maceration techniques for nuclear DNA amplification using the standard Combined DNA Index System (CODIS) markers. DNA was extracted from 18 samples of human lower leg bones subjected to nine chemical and heat maceration techniques.

The genetic structure of Pacific Islanders.

Human genetic diversity in the Pacific has not been adequately sampled, particularly in Melanesia. As a result, population relationships there have been open to debate. A genome scan of autosomal markers (687 microsatellites and 203 insertions/deletions) on 952 individuals from 41 Pacific populations now provides the basis for understanding the remarkable nature of Melanesian variation, and for a more accurate comparison of these Pacific populations with previously studied groups from other regions.

The impact of group fissions on genetic structure in Native South America and implications for human evolution.

In a series of publications beginning in the 1960s, Neel and colleagues suggested that genetically nonrandom, or "lineal", population fissions contributed to genetic structure in ancient human groups. The authors reached this conclusion by studying the genetic consequences of village fissions among the Yanomamo, a Native South American group thought to have been relatively unaffected by European contact and, therefore, representative of the human past. On the basis of ethnographic accounts and pedigree data, they further concluded that patrilineal relationships were particularly important in shaping the genetic structure of villages following fissions.

Melanesian mtDNA complexity.

Melanesian populations are known for their diversity, but it has been hard to grasp the pattern of the variation or its underlying dynamic. Using 1,223 mitochondrial DNA (mtDNA) sequences from hypervariable regions 1 and 2 (HVR1 and HVR2) from 32 populations, we found the among-group variation is structured by island, island size, and also by language affiliation. The more isolated inland Papuan-speaking groups on the largest islands have the greatest distinctions, while shore dwelling populations are considerably less diverse (at the same time, within-group haplotype diversity is less in the most isolated groups).

A formal test of linguistic and genetic coevolution in native Central and South America.

This paper investigates a mechanism of linguistic and genetic coevolution in Native Central and South America. This mechanism proposes that a process of population fissions, expansions into new territories, and isolation of ancestral and descendant groups will produce congruent language and gene trees. To evaluate this population fissions mechanism, we collected published mtDNA sequences for 1,381 individuals from 17 Native Central and South American populations.

Population structure and admixture in Cerro Largo, Uruguay, based on blood markers and mitochondrial DNA polymorphisms.

Recent studies of the Uruguayan population revealed different amounts of Amerindian and African genetic contributions. Our previous analysis of Afro-Uruguayans from the capital city of the Department of Cerro Largo showed a high proportion of African genes, and the effects of directional mating involving Amerindian women. In this paper, we extended the analysis to a sample of more than 100 individuals representing a random sample of the population of the whole Department.

Is the genetic structure of Gran Chaco populations unique? Interregional perspectives on native South American mitochondrial DNA variation.

This study reevaluates the hypothesis in Demarchi et al. (2001 Am. J.

Skin and hair pigmentation variation in Island Melanesia.

Skin and hair pigmentation are two of the most easily visible examples of human phenotypic variation. Selection-based explanations for pigmentation variation in humans have focused on the relationship between melanin and ultraviolet radiation, which is largely dependent on latitude. In this study, skin and hair pigmentation were measured as the melanin (M) index, using narrow-band reflectance spectroscopy for 1,135 individuals from Island Melanesia.

Evidence of the domestication history of flax (Linum usitatissimum L.) from genetic diversity of the sad2 locus.

A phylogenetic analysis was conducted on 34 alleles of 2.5 kb sized stearoyl-ACP desaturase II (sad2), obtained from 30 accessions of cultivated and pale flax (Linum spp.), to elucidate the history of flax domestication.

Ancient mitochondrial M haplogroups identified in the Southwest Pacific.

Based on whole mtDNA sequencing of 14 samples from Northern Island Melanesia, we characterize three formerly unresolved branches of macrohaplogroup M that we call haplogroups M27, M28, and M29. Our 1,399 mtDNA control region sequences and a literature search indicate these haplogroups have extremely limited geographical distributions. Their coding region variation suggests diversification times older than the estimated date for the initial settlement of Northern Island Melanesia.

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).

A 9.1-kb insertion/deletion polymorphism suggests a common pattern of genetic diversity in Island Melanesia.

Earlier reports suggest a distinct pattern of genetic variation linked to both language and geographic distance in Island Melanesia. Inland Papuan-speaking populations from different islands tend to share one allelic profile, while shore-based or more cosmopolitan populations share another, related to Southeast Asian influence over the past 3000 years. In the present paper, we report the genotypes and allele frequencies of an informative 9.

A cautionary tale on ancient migration detection: mitochondrial DNA variation in Santa Cruz Islands, Solomon Islands.

Over the past decade, the origin of the first Malayo-Polynesian settlers of the island Pacific has become a contentious issue in molecular anthropology as well as in archaeology and historical linguistics. Whether the descendants of the ancestral Malayo-Polynesian speakers moved rapidly through Indonesia and Island Melanesia in a few hundred years, or whether they were the product of considerable intermingling within the more westerly part of the latter region, it is widely accepted that they were the first humans to colonize the distant Pacific islands beyond the central Solomon Islands approximately 3,000 years ago. The Santa Cruz Islands in the Eastern Solomons would have most likely been the first in Remote Oceania to be colonized by them.