Sunday 22 November 2009

Ina's clan

http://inaclan.blogspot.com/

Wake up Colombia mestiza!!!
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Ina's clan

Esta es Marta Lucia con su bebe Isabel de Silvia, Colombia
Ina's Clan - Haplogroup B

Welcome

Introduction

Mitochondrial DNA (or mtDNA for short) is present in every cell in the body, and it remains virtually unchanged (aside from random mutations which may occur every 10,000 years or so) as it passes from mother to daughter.

By quantifying and analyzing the mutations of this relatively stable circle of DNA, Bryan Sykes, professor of human genetics at the University of Oxford and founder of Oxford Ancestors, was able to determine that nearly all modern Europeans descend from one of seven "clan mothers" who lived at different times during the Ice Age. He named these women Xenia, Ursula, Helena, Velda, Tara, Katrina, and Jasmine; and his findings were made popular in his book, "The Seven Daughters of Eve".

In addition to those seven women, Sykes also discovered 29 others from whom the rest of the world's population descend. Of those 29, just four are the ancestresses of the earliest colonizers of North and South America. Their names are Aiyana/Ai, Ina, Chochmingwu/Chie, and Djigonasee/Sachi. The haplogroups used to identify each "clan mother" are based upon the grouping of genetic sequences (known as "polymorphisms") into distinct families. Ina's clan are identified by Haplogroup B (the B clade of the human family tree).

Unlike the other three, Ina's clan is known to have populated not only North and South America, but the Pacific Islands and possibly Madagascar as well. Her name comes form the Polynesian mythological figure "Ina", who appears on the banknotes of Rarotonga in the Cook Islands riding on the back of a shark to the island Mangaia. She is representative of the "first woman" and is also often personified in the moon

All of these women are daughters of the 'Mitochondrial Eve', a single East African woman who lived approximately 150,000 years ago and from whom all of humanity descend. Obviously, she was not the only woman alive during her time, but only her maternal lineage has survived unbroken to the present day.

Origins

After coming out of Africa, modern humans first spread to Asia following two main routes - a Southern one and a Northern one. The Southern one is represented by macro-haplogroup M which radiated some 30,000–57,600 yrs BP (before present) and is overwhelmingly present in India [1] and Eastern Asia where it possibly originated and expanded as haplogroups C, D, G, and others [2].

The other major branch that left Africa, the Northern one, is represented by macro-haplogroup N. It has a lower bound of 43,000–53,000 yrs BP, and spread into at least three main clusters. The first cluster comprises haplogroups X and A, with only a shared mutation between them and different geographic distributions (A is widespread in Asia, X is mainly restricted to Europe).

The second cluster groups minor haplogroups W, I, and N1b (each of which is present in low frequencies in Europe, the Near East, and the Caucasus). The last cluster radiated around 39,000–52,000 yrs BP and gave rise to four major ancestral clusters: Two of them, B and F, derive from N through a common ancestor with most Europeans - phylogenetic node R [3]. The others originated haplogroups J, T, H, V, K, and U, which expanded from the Near East-Caucasus area. [4]

Haplogroup B expanded from Central Asia to Eastern Asia, reaching Japan and the Southeastern Pacific Archipelagos. And, unlike previously believed, it is also found in some Siberian populations. [3, 5, 6]. From there, a substantial number of Ina's descendants then reached North America, either with the other colonists around 13,000 yrs BP via the Bering land bridge, or in a sea-borne colonization along the coast (or both).

These are the results of my Mtdna test

These are the results of my Mtdna HVR-1 region

16183 Substitution A > c
16189 Substitution T > c
16217 Substitution T > c
16519 Substitution T > c

My mtDNA HVR-2 region differs from the Cambridge Reference Sequence (CRS) at the following sequence locations in HVR-2

LocationMutation TypeNucleotide Change
73 Substitution A > g
263 Substitution A > g
309 Insertion C > CCC
315 Insertion C > CC

mtDNA Backbone SNP Results
20 Certified

Based on mtDNA Backbone SNP Test, my mtDNA haplogroup has been confirmed as B.

SNP Location Mutations SNP Identity Result
2352 T > C
 T Negative
3594 C > T
 C Negative
3693 G > A
 G Negative
4312 C > T
 C Negative
4580 G > A
 G Negative
4833 A > G
 A Negative
5178 C > A
 C Negative
7028 C > T
 T Positive
7055 A > G
 A Negative
7598 G > A
 G Negative
8618 T > C
 T Negative
10086 A > G
 A Negative
10310 G > A
 G Negative
10400 C > T
 C Negative
10873 T > C
 T Negative
11251 A > G
 A Negative
11719 G > A
 A Positive
12308 A > G
 A Negative
12705 C > T
 C Negative
14766 C > T
 T Positive

Mtdna haplogroup B story

DNA study: Most Native Americans traced to 6 women
Updated 3/13/2008 11:18 AM | Comments 30 | Recommend 10 Subscribe to stories like this


By Malcolm Ritter, Associated Press
NEW YORK — Nearly all of today's Native Americans in North, Central and South America can trace part of their ancestry to six women whose descendants immigrated around 20,000 years ago, a DNA study suggests.

Those women left a particular DNA legacy that persists to today in about about 95% of Native Americans, researchers said.

PLOS ONE ARTICLE: The Phylogeny of the Four Pan-American MtDNA Haplogroups: Implications for Evolutionary and Disease Studies

The finding does not mean that only these six women gave rise to the migrants who crossed into North America from Asia in the initial populating of the continent, said study co-author Ugo Perego.

The women lived between 18,000 and 21,000 years ago, though not necessarily at exactly the same time, he said.

The work was published this week by the journal PLoS One. Perego is from the Sorenson Molecular Genealogy Foundation in Salt Lake City and the University of Pavia in Italy.

The work confirms previous indications of the six maternal lineages, he said. But an expert unconnected with the study said the findings left some questions unanswered.

Perego and his colleagues traced the history of a particular kind of DNA that represents just a tiny fraction of the human genetic material, and reflects only a piece of a person's ancestry.

This DNA is found in the mitochondria, the power plants of cells. Unlike the DNA found in the nucleus, mitochondrial DNA is passed along only by the mother. So it follows a lineage that connects a person to his or her mother, then the mother's mother, and so on.

The researchers created a "family tree" that traces the different mitochondrial DNA lineages found in today's Native Americans. By noting mutations in each branch and applying a formula for how often such mutations arise, they calculated how old each branch was. That indicated when each branch arose in a single woman.

The six "founding mothers" apparently did not live in Asia because the DNA signatures they left behind aren't found there, Perego said. They probably lived in Beringia, the now-submerged land bridge that stretched to North America, he said.

Connie Mulligan of the University of Florida, an anthropolgist who studies the colonization of the Americas but didn't participate in the new work, said it's not surprising to trace the mitochondrial DNA to six women. "It's an OK number to start with right now," but further work may change it slightly, she said.

That finding doesn't answer the bigger questions of where those women lived, or of how many people left Beringia to colonize the Americas, she said Thursday.

The estimate for when the women lived is open to question because it's not clear whether the researchers properly accounted for differing mutation rates in mitochondrial DNA, she said. Further work could change the estimate, "possibly dramatically," she said.

Copyright 2008 The Associated Press. All rights reserved. This material may not be published, broadcast, rewritten or redistributed.

Amerindian Mtdna founding women in America

The Phylogeny of the Four Pan-American MtDNA Haplogroups: Implications for Evolutionary and Disease Studies

Only a limited number of complete mitochondrial genome sequences belonging to Native American haplogroups were available until recently, which left America as the continent with the least amount of information about sequence variation of entire mitochondrial DNAs.

In this study, a comprehensive overview of all available complete mitochondrial DNA (mtDNA) genomes of the four pan-American haplogroups A2, B2, C1, and D1 is provided by revising the information scattered throughout GenBank and the literature, and adding 14 novel mtDNA sequences.

The phylogenies of haplogroups A2, B2, C1, and D1 reveal a large number of sub-haplogroups but suggest that the ancestral Beringian population(s) contributed only six (successful) founder haplotypes to these haplogroups. The derived clades are overall starlike with coalescence times ranging from 18,000 to 21,000 years (with one exception) using the conventional calibration.

The average of about 19,000 years somewhat contrasts with the corresponding lower age of about 13,500 years that was recently proposed by employing a different calibration and estimation approach.

Our estimate indicates a human entry and spread of the pan-American haplogroups into the Americas right after the peak of the Last Glacial Maximum and comfortably agrees with the undisputed ages of the earliest Paleoindians in South America.

In addition, the phylogenetic approach also indicates that the pathogenic status proposed for various mtDNA mutations, which actually define branches of Native American haplogroups, was based on insufficient grounds.

Amerindians

Mitochondrial DNA Diversity in Indigenous Populations of the Southern Extent of Siberia, and the Origins of Native American Haplogroups





Aymara and mtdna haplogroup B

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

Bert F, Corella A, Gené M, Pérez-Pérez A, Turbón D.

Departament de Biologia Animal, Facultat de Biologia, Universitat de Barcelona, Spain.

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.

Mtdna haplogroup B

Genetic Markers M and B in Aboriginals and Native Americans

A Haplogroup is a specific related group of haplotypes, which are related genes (with some possible minor variation), all located at the same spot on a specific chromosome in descendants from a common ancestor. Peoples that share a Haplogroup are related genetically.

Both M and B Haplogroups represent the first peoples to migrate out of Africa, according to the Human Migration Program. Both groups are traced through the female line (mitrochondrial DNA or mDNA)

Haplogroup M (mitochondrial DNA) is found in substantial numbers of Aboriginals [especially Australia, Papua New Guinea, Irian Java, the Philippines, New Zealand,a nd french Polynesia] and Native American Nations/Canadian First Nations. M is also found in Central Asia, where it is possessed by 10-15% of people, this population being related to Aboriginals and Native American Nations/Canadian First Nations. This creates a relationship between Central Asia and Aboriginals.

Haplogroup B (mitochondrial DNA) is also found in Aboriginals as well as in Indigenous Peoples from Canada all the way down to the tip of South America. Haplogroup B is found in all "American Indians" throughout the Western Hemisphere, but most strongly among those in North America. Haplogroup B is found in 17% of Southeast Asians and 20% of Chinese, and to a somewhat lesser extent, in the Japanese and even among Siberians (also related to Native Americans and First Nations).

Memorial pole in Papua New Guinea. (c)AP
Memorial pole in Papua New Guinea. (c)AP


Mtdna haplogroup B

Wolfram or DIDMOAD (Diabetes Insipidus, Diabetes Mellitus, Optic Atrophy and Deafness) syndrome, which has long been known as an autosomal-recessive disorder, has recently been proposed to be a mitochondrial-mediated disease with either a nuclear or a mitochondrial genetic background.

The phenotypic characteristics of the syndrome resemble those found in other mitochondrial (mt)DNA mediated disorders such as Leber's hereditary optic neuropathy (LHON) or maternally inherited diabetes and deafness (MIDD).

Therefore, we looked for respective mtDNA alterations in blood samples from 7 patients with DIDMOAD syndrome using SSCP-analysis of PCR-amplified fragments, encompassing all mitochondrial ND and tRNA genes, followed by direct sequencing.

Subsequently, we compared mtDNA variants identified in this disease group with those detected in a group of LHON patients (n = 17) and in a group of 69 healthy controls. We found that 4/7 (57%) DIDMOAD patients harbored a specific set of point mutations in tRNA and ND genes including the so-called class II or secondary LHON mutations at nucleotide positions (nps) 4216 and 4917 (haplogroup B).

In contrast, LHON-patients were frequently (10/17, 59%) found in association with another cluster of mtDNA variants including the secondary LHON mutations at nps 4216 and 13708 and further mtDNA polymorphisms in ND genes (haplogroup A), overlapping with haplogroup B only by variants at nps 4216 and 11251.

The frequencies of both haplogroups were significantly lower in the control group versus the respective disease groups. We propose that haplogroup B represents a susceptibility factor for DIDMOAD which, by interaction with further exogeneous or genetic factors, might increase the risk for disease. (Mol Cell Biochem 174: 209–213, 1997)

Mtdna haplogroup B and diabetes

A mitochondrial DNA variant associated with left ventricular hypertrophy in diabetes

Yukihiko Momiyamaa, c, Michiko Furutanic, Yoshihiko Suzukib, Reiko Ohmoria, Shin-ichiro Imamurac, Atsuko Mokubob, Takayuki Asahinab, Chisato Muratab, Kiyoe Katob, Sonoko Anazawab, Kazuhiro Hosokawab, Yoshihito Atsumib, Kempei Matsuokab, Mitsuru Kimurab, Hiroshi Kasanukic, Fumitaka Ohsuzua and Rumiko MatsuokaCorresponding Author Contact Information, E-mail The Corresponding Author, c

a First Department of Internal Medicine, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan

b Division of Internal Medicine, Saiseikai Central Hospital, 1-4-17 Mita, Minato-ku, Tokyo 108-0073, Japan

c The Heart Institute of Japan, Tokyo Women’s Medical University, 8-1 Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan

Received 20 October 2003.
Available online 18 November 2003.

Abstract

Diabetes was reported to be associated with a mitochondrial (mt) DNA mutation at 3243 and variants at 1310, 1438, 3290, 3316, 3394, 12,026, 15,927, and 16,189. Among these mtDNA abnormalities, those at 3243, 3316, 15,927, and 16,189 were also suggested to cause cardiomyopathies.

We investigated the prevalence of such mtDNA abnormalities in 68 diabetic patients with LV hypertrophy (LVH), 100 without LVH, and 100 controls. Among the 9 mtDNA abnormalities, those at 3243, 3316, and 15,927 tended to be more prevalent in diabetic patients with LVH than in those without LVH (1%, 1%, and 4% vs. 0%, 0%, and 0%). Notably, the variant at 16,189 was more prevalent in diabetic patients with LVH than without LVH (46% vs. 24%, p

Mtdna haplogroup B

Mitochondrial Population Genomics Supports a Single Pre-Clovis Origin with a Coastal Route for the Peopling of the Americas

Abstract
It is well accepted that the Americas were the last continents reached by modern humans, most likely through Beringia. However, the precise time and mode of the colonization of the New World remain hotly disputed issues.

Native American populations exhibit almost exclusively five mitochondrial DNA (mtDNA) haplogroups (A–D and X). Haplogroups A–D are also frequent in Asia, suggesting a northeastern Asian origin of these lineages.

However, the differential pattern of distribution and frequency of haplogroup X led some to suggest that it may represent an independent migration to the Americas. Here we show, by using 86 complete mitochondrial genomes, that all Native American haplogroups, including haplogroup X, were part of a single founding population, thereby refuting multiple-migration models.

A detailed demographic history of the mtDNA sequences estimated with a Bayesian coalescent method indicates a complex model for the peopling of the Americas, in which the initial differentiation from Asian populations ended with a moderate bottleneck in Beringia during the last glacial maximum (LGM), around ∼23,000 to ∼19,000 years ago. Toward the end of the LGM, a strong population expansion started ∼18,000 and finished ∼15,000 years ago. These results support a pre-Clovis occupation of the New World, suggesting a rapid settlement of the continent along a Pacific coastal route.

Introduction
In the complex history of human migrations, it is widely accepted that the New World continents were the ones colonized most recently by Homo sapiens, most likely from Asia through Beringia.1 A popular model for the peopling of the Americas suggests that the archaeological remains known as the Clovis complex (thought to be the oldest unequivocal evidence of humans in the Americas) represent the people that first colonized the continent after a late-glacial migration through the ice-free corridor that separated the Laurentide and Cordilleran ice sheets.1

However, the recently re-evaluated age of the Clovis sites to only between about 12.7 and 13.2 thousand years ago (kya)2 and the confirmed human presence at the Monte Verde site located in southern South America around 14.5 kya3 challenge this Clovis-first model and call for alternative hypotheses. Because the earlier date for Monte Verde implies that peopling of the Americas south of Beringia occurred before the ice-free corridor was formed, a first migration along the Pacific coast may have been a viable route.4

Unfortunately, archaeological verification of this scenario is very difficult because most of the late Pleistocene coast is currently underwater; the sea level has risen more than 120 m since the end of the last glacial maximum (LGM).5
The maternally inherited mitochondrial DNA (mtDNA) has been widely used to understand the peopling of the Americas. Since the first studies, it has been found that extant Native American populations exhibit almost exclusively five mtDNA haplogroups (A–D and X)6 classified in the autochthonous haplogroups A2, B2, C1, D1, and X2a.7

Haplogroups A–D are found all over the New World and are frequent in Asia, supporting a northeastern Asian origin of these lineages.6,8 This distribution, together with the similar coalescence time for these haplogroups, was used to suggest a single-migration model.9–12 However, a different pattern of diversification and distribution of haplogroup B found in some studies led some authors to hypothesize that it could represent a later and separate migration from the joint arrival of haplogroups A, C, and D.13

The history of haplogroup X is more elusive; it is presently found in the New World at a relatively low frequency14 and only in North America,15 it is rare in West Eurasians, and it is almost absent in Siberia.16 In addition, some have claimed that Native American haplogroup X is less diverse and has a younger coalescence time than haplogroups A–D17.

These differential features have been cited to argue that haplogroup X represents an independent migration to the Americas from Asia or even Europe.17 More specifically, it has been used to support a putative connection between the European Solutrean and the American Clovis lithic technologies.18 This so called “Solutrean hypothesis” proposed the colonization of North America by Europeans through the North Atlantic, even though this interpretation is heavily debated (e.g.,19). All the five founding haplogroups have been shown to be present in Native Americas in pre-Columbian times.12,20

In general, the studies on mtDNA control-region variation have been taken to support a pre-Clovis migration, between ∼20 and 30 kya, before the LGM, for the single (or the most ancient) migration.6,21 However, the uncertainties about and range around these dates are very large. One cause for this variation is the limited information content of the mtDNA control region, which is also too divergent to allow reliable substitution-rate estimation by comparison with the chimpanzee.22

Alternatively, the complete coding region of the mtDNA is being increasingly used to circumvent these limitations in studies of human migrations (e.g.,22,23) but has not been used so far for studying the origin of Native Americans.
Another frequent controversy is about the size of the founding population during the peopling of the Americas. The initial results showing the existence of few founder haplogroups for the mtDNA and Y chromosome suggested a strong population bottleneck,6 although this interpretation was not supported by further mtDNA studies.21

However, a recent analysis of several genomic loci, including mtDNA, suggested that the Americas could have been founded by as few as 80 effective individuals, and even the largest values in the credible interval only comprise a few hundred effective individuals.24 On the other hand, the study of other single genetic systems does not seem to support much loss of genetic diversity during the initial settlement of the continent;25–28 instead, it concludes that a moderate-intensity bottleneck is the best scenario.

Another recent genomic study using exclusively autosomal intergenic markers also suggested moderate values, with the Native American founding population consisting of around 500 effective individuals (95% confidence interval 74–1332).
In this study, we analyze 86 mtDNA genomes (58 of them new) belonging to all five major Native American haplogroups (A2, B2, C1, D1, and X2a) to provide a better understanding of the timing and mode of the peopling of the New World.

Our analysis suggests a complex scenario for this migration, in which the founding population underwent a moderate bottleneck during the LGM to expand along the continent toward the end of the LGM, around 18 kya, probably via a Pacific coastal route. Furthermore, we support a model in which all mtDNA haplogroups were present in this expansion, thus refuting multiple-migration scenarios such as the Solutrean

T-to-C transition at the nucleotide 16189 in mitochondrial DNA

Association between a common mitochondrial DNA D-loop polycytosine variant and alteration of mitochondrial copy number in human peripheral blood cells

  1. C-W Liou1,
  2. T-K Lin1,
  3. J-B Chen2,
  4. M-M Tiao3,
  5. S-W Weng4,
  6. S-D Chen1,
  7. Y-C Chuang1,
  8. J-H Chuang5,
  9. P-W Wang4
  10. n; cwliou@ms22.hinet.net
  • Received 26 January 2010
  • Revised 7 April 2010
  • Accepted 21 April 2010
  • Published Online First 12 September 2010

Abstract

Background A T-to-C transition at mitochondrial DNA (mtDNA) nucleotide position 16189 can generate a variable length polycytosine tract (poly-C). This tract variance has been associated with disease. A suggested pathogenesis is that it interferes with the replication process of mtDNA, which in turn decreases the mtDNA copy number and generates disease.

Methods In this study, 837 healthy adults' blood samples were collected and determined for their mtDNA D-loop sequence. The mtDNA copy number in the leucocytes and serum levels of oxidative thiobarbituric acid reactive substance (TBARS) and antioxidative thiols were measured.

All subjects were then categorised into three groups: wild type or variant mtDNA with presence of an interrupted/uninterrupted poly-C at 16180–16195 segment.

Results A step-wise multiple linear regression analysis identified factors affecting expression of mtDNA copy number including TBARS, thiols, age, body mass index and the mtDNA poly-C variant. Subjects harbouring a variant uninterrupted poly-C showed lowest mean (SD) mtDNA copy number (330 (178)), whereas an increased copy number was noted in subjects harbouring variant, interrupted poly-C (420 (273)) in comparison with wild type (358 (215)).

The difference between the three groups and between the uninterrupted poly-C and the composite data from the interrupted poly-C and wild type remained consistent after adjustment for TBARS, thiols, age and body mass index (p=0.001 and p=0.011, respectively). A trend for decreased mtDNA copy number in association with increased number of continuous cytosine within the 16180–16195 segment was noted (ptrend

Conclusions Our results substantiate a previous suggestion that the mtDNA 16189 variant can cause alteration of mtDNA copy number in human blood cells.

T-to-C transition at the nucleotide 16189 in mitochondrial DNA

Association between a common mitochondrial DNA D-loop polycytosine variant and alteration of mitochondrial copy number in human peripheral blood cells. PDF Print E-mail

Journal: J Med Genet
Authors: Liou CW, Lin TK, Chen JB, Tiao MM, Weng SW, Chen SD, Chuang YC, Chuang JH, Wang PW
Published: 2010 Sep 12;
Pubmed ID: 20837494

Our origins in Mongolia

A commonly held theory is that the first wave of migrants into the New World was derivative from the ethnic groups then inhibiting eastern Siberia.

However, these ethnic groups lack a mtDNA haplogroup (B) that is well represented in Amerindian tribes. Also, the time depth of the other three mtDNA haplogroups found in Amerindians (A, C, and D) appears to be greater in the Amerindians than in the eastern Siberian ethnic groups.

In this communication we demonstrate that the human T-cell lymphotrophic virus type II, present in 11 of the 38 Amerindian tribes thus far examined, is not present in any of the 10 ethnic groups of eastern Siberia that we have studied. However, the virus has just been reported in the indigenous population of Mongolia, and mtDNA haplogroup B is also represented in this region.

On the basis of these facts, we propose that the ancestors of the first migrants to the New World were not derived from north and central Siberia but from populations to the south, inhabiting the regions of Mongolia, Manchuria, and/or the extreme southeastern tip of Siberia.

More about Mtdna haplogroup B

Haplogroup B. As shown by various studies, deletion mtDNAs from haplogroup B are broadly distributed in Asian populations.

Recent population expansions associated with the spread of Austronesian languages appear to have brought these haplotypes from Southeast Asia into Polynesia around 5000-1000 YBP.

Many Polynesian haplogroup B mtDNAs also possess a set of polymorphisms that distinguishes them from similar types in other Asian populations (Hagelberg and Clegg 1993; Hagelberg et al. 1994; Lum et al. 1994; Melton et al. 1995, 1998; Redd et al. 1995; Sykes et al. 1995; Lum and Cann 1998; Richards et al. 1998).

This set of mutations, which includes the 16217 T->C, 16247 A->G, and 16261 C->T transitions (or "CGT"), has been called the "Polynesian Motif" because of its uniqueness to Polynesian and related populations (Hagelberg and Clegg 1993; Hagelberg et al. 1994; Lum et al. 1994).

The Polynesian Motif evolved from mtDNAs bearing the ancestral 16189C and 16217C sequence motif through a series of mutational steps (CAC->CAT->CGT) that probably began in Taiwan and continued as populations spread south into the Philippines, Indonesia, and Melanesia (Melton et al. 1995, 1998; Redd et al. 1995), although some favor an Indonesian source for this lineage (Richards et al. 1998).

More Articles of Interest

Haplogroup B mtDNAs are also found in Vietnamese, Malaysian, and Bornean populations (Ballinger et al. 1992). However, none of the HVS-I sequences identified in these deletion haplotypes show the Polynesian Motif (CGT), and only one (Sabah Aborigine, SA26; Ballinger et al. 1992) has the hypothesized intermediate state, CAT.

These findings are generally concordant with those of Melton et al. (1995, 1998), who observed the Polynesian Motif at the highest frequency in Polynesians and coastal Papua New Guineans, and at modest frequencies in East Indonesians and Malays, with the intermediate form (CAT) occurring at the highest frequencies in Taiwanese aborigines and moderate frequencies in Filipinos and east Indonesians.

Ballinger et al. (1992) also suggested that two deletion haplogroups were present in Asian populations, with these being called C* and D*. Haplogroup D* has since been renamed haplogroup B (Torroni et al. 1992), but C* has received little attention since its first description. So as not to confuse it with haplogroup C, which is not closely related to either deletion lineage, haplogroup C* will henceforth be called haplogroup B*, since this letter designation will associate it with the other major deletion haplogroup.

With respect to their mutational composition, haplogroup B is characterized by the Region V 9-bp deletion and the HaeIII 16517 mutation, while, in addition to these polymorphisms, haplogroup B* also has the -DdeI 3534, -AluI 3537, DdeI 10394, -HinfI 15234; and MboI 15235 mutations (Ballinger et al. 1992; Passarino et al. 1993) (Table 4).

When subjected to phylogenetic analysis, the haplotypes from both of these haplogroups clustered together but formed separate branches (Figure 2 in Ballinger et al. 1992). However, this association occurred in part because of the inclusion of the 9-bp deletion as an RFLP character in the haplotype data matrix.

If this marker is eliminated from the data set, then the two branches are positioned in separate portions of the Asian mtDNA tree because of the presence of the DdeI 10394 site in B* mtDNAs (data not shown). Regardless of their positions, however, haplogroup B* had long branches connecting mutationally diverse haplotypes, whereas haplogroup B had shorter and shallower branches of haplotypes.

These data suggested that B* could be an older deletion lineage, or else a highly divergent subbranch of haplogroup B. By contrast, the shallower branches of shorter lengths for haplogroup B suggested that it could be a younger deletion lineage that had rapidly diversified and been spread in East Asia in relatively recent prehistory.

However, both of these putative deletion lineages are approximately the same age. Based on the maximum likelihood estimates of haplogroup diversity presented in Ballinger et al. (1992), haplogroup B arose between 33,500-16,750 YBP, while haplogroup B* emerged between 44,500-22,250 YBP (Table 5).

These age estimates are supported by a recent median network analysis of RFLP and HVS-I sequence data from haplogroup B in which its expansion in Asia was calculated to be 29,100 /- 7100 YBP (Forster et al. 2001).

Such findings suggested that haplogroup B could possibly have evolved from haplogroup B*, or, alternatively, that both haplogroups represented independent occurrences of the Region V 9-bp deletion in different mtDNA lineages that were subsequently distributed in Asia at similar times.

To discriminate between these possibilities, it will be necessary to determine whether the DdeI 10394 site present in B* haplotypes is the same phylogenetically ancient site that is present in African mtDNAs, or, instead, a secondary occurrence of this polymorphism in mtDNAs that originally lacked the DdeI/ AluI sites.

Mtdna haplogroup B

Analysis of the mitochondrial DNA from patients with Wolfram (DIDMOAD) syndrome.

Hofmann S, Bezold R, Jaksch M, Kaufhold P, Obermaier-Kusser B, Gerbitz KD.

Institute of Clinical Chemistry, Academic Hospital Schwabing, Munich, Germany.

Wolfram or DIDMOAD (Diabetes Insipidus, Diabetes Mellitus, Optic Atrophy and Deafness) syndrome, which has long been known as an autosomal-recessive disorder, has recently been proposed to be a mitochondrial-mediated disease with either a nuclear or a mitochondrial genetic background.

The phenotypic characteristics of the syndrome resemble those found in other mitochondrial (mt)DNA mediated disorders such as Leber's hereditary optic neuropathy (LHON) or maternally inherited diabetes and deafness (MIDD). Therefore, we looked for respective mtDNA alterations in blood samples from 7 patients with DIDMOAD syndrome using SSCP-analysis of PCR-amplified fragments, encompassing all mitochondrial ND and tRNA genes, followed by direct sequencing.

Subsequently, we compared mtDNA variants identified in this disease group with those detected in a group of LHON patients (n = 17) and in a group of 69 healthy controls. We found that 4/7 (57%) DIDMOAD patients harbored a specific set of point mutations in tRNA and ND genes including the so-called class II or secondary LHON mutations at nucleotide positions (nps) 4216 and 4917 (haplogroup B).

In contrast, LHON-patients were frequently (10/17, 59%) found in association with another cluster of mtDNA variants including the secondary LHON mutations at nps 4216 and 13708 and further mtDNA polymorphisms in ND genes (haplogroup A), overlapping with haplogroup B only by variants at nps 4216 and 11251.

The frequencies of both haplogroups were significantly lower in the control group versus the respective disease groups. We propose that haplogroup B represents a susceptibility factor for DIDMOAD which, by interaction with further exogeneous or genetic factors, might increase the risk for disease.

The peopling of the Americas

New Ideas About Human Migration From Asia To Americas

ScienceDaily (Oct. 29, 2007) — Questions about human migration from Asia to the Americas have perplexed anthropologists for decades, but as scenarios about the peopling of the New World come and go, the big questions have remained. Do the ancestors of Native Americans derive from only a small number of “founders” who trekked to the Americas via the Bering land bridge? How did their migration to the New World proceed? What, if anything, did the climate have to do with their migration? And what took them so long?

A team of 21 researchers, led by Ripan Malhi, a geneticist in the department of anthropology at the University of Illinois, has a new set of ideas. One is a striking hypothesis that seems to map the peopling process during the pioneering phase and well beyond, and at the same time show that there was much more genetic diversity in the founder population than was previously thought.

“Our phylogeographic analysis of a new mitochondrial genome dataset allows us to draw several conclusions,” the authors wrote.

“First, before spreading across the Americas, the ancestral population paused in Beringia long enough for specific mutations to accumulate that separate the New World founder lineages from their Asian sister-clades.” (A clade is a group of mitochondrial DNAs (mtDNAs ) that share a recent common ancestor, Malhi said. Sister-clades would include two groups of mtDNAs that each share a recent common ancestor and the common ancestor for each clade is closely related.)

Or, to express this first conclusion another way, the ancestors of Native Americans who first left Siberia for greener pastures perhaps as much as 30,000 years ago, came to a standstill on Beringia – a landmass that existed during the last glacial maximum that extended from Northeastern Siberia to Western Alaska, including the Bering land bridge – and they were isolated there long enough – as much as 15,000 years – to maturate and differentiate themselves genetically from their Asian sisters.

“Second, founding haplotypes or lineages are uniformly distributed across North and South America instead of exhibiting a nested structure from north to south. Thus, after the Beringian standstill, the initial North to South migration was likely a swift pioneering process, not a gradual diffusion.”

The DNA data also suggest a lot more to-ing and fro-ing than has been suspected of populations during the past 30,000 years in Northeast Asia and North America. The analysis of the dataset shows that after the initial peopling of Beringia, there were a series of back migrations to Northeast Asia as well as forward migrations to the Americas from Beringia, thus “more recent bi-directional gene flow between Siberia and the North American Arctic.”

To investigate the pioneering phase in the Americas, Malhi and his team, a group of geneticists from around the world, pooled their genomic datasets and then analyzed 623 complete mitochondrial DNAs (mtDNAs) from the Americas and Asia, including 20 new complete mtDNAs from the Americas and seven from Asia. The sequence data was used to direct high-resolution genotyping from 20 American and 26 Asian populations. Mitochondrial DNA, that is, DNA found in organelles, rather than in the cell nucleus, is considered to be of separate evolutionary origin, and is inherited from only one parent – the female.

The team identified three new sub-clades that incorporate nearly all of Native American haplogroup C mtDNAs – all of them widely distributed in the New World, but absent in Asia; and they defined two additional founder groups, “which differ by several mutations from the Asian-derived ancestral clades.”

What puzzled them originally was the disconnect between recent archaeological datings. New evidence places Homo sapiens at the Yana Rhinoceros Horn Site in Siberia – as likely a departure point for the migrants as any in the region – as early as 30,000 years before the present, but the earliest archaeological site at the southern end of South America is dated to only 15,000 years ago.

“These archaeological dates suggested two likely scenarios,” the authors wrote: Either the ancestors of Native Americans peopled Beringia before the Last Glacial Maximum, but remained locally isolated – likely because of ecological barriers – until entering the Americas 15,000 years before the present (the Beringian incubation model, BIM); or the ancestors of Native Americans did not reach Beringia until just before 15,000 years before the present, and then moved continuously on into the Americas, being recently derived from a larger parent Asian population (direct colonization model, DCM).

Thus, for this study the team set out to test the two hypotheses: one, that Native Americans’ ancestors moved directly from Northeast Asia to the Americas; the other, that Native American ancestors were isolated from other Northeast Asian populations for a significant period of time before moving rapidly into the Americas all the way down to Tierra del Fuego.

“Our data supports the second hypothesis: The ancestors of Native Americans peopled Beringia before the Last Glacial Maximum, but remained locally isolated until entering the Americas at 15,000 years before the present.”

The team’s findings appear in a recent issue of the Public Library of Science in an article titled, “Beringian Standstill and Spread of Native American Founders.”

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American Indian Origins

Early Americans May Have Been 'Stuck' for 20,000 Years

Thursday, February 14, 2008
By Charles Q. Choi


The epic journey by which the Americas were first settled has been a great mystery for centuries.

Did it happen by land or by sea? Did it happen one dozen or so millennia ago, or three dozen?

The answer might be "yes."

• Click here to visit FOXNews.com's Archaeology Center.

New findings reveal the settling of the New World did not come in a single burst, as is suggested by most theories, but was, in a way, a play with three acts, each separated by thousands of generations.

The first stage of this voyage involved a gradual migration of people from Asia through Siberia starting about 40,000 years ago into Beringia, a once-habitable grassland populated with steppe bison, mammoths, horses, lions, musk oxen, sheep, wooly rhinoceros and caribou that nowadays lies submerged under the icy waters of the Bering Strait.

The second phase of the journey was basically a layover in Beringia.

"Two major glaciers blocked their progress into the New World. So they basically stayed put for about 20,000 years," said researcher Connie Mulligan, a molecular anthropologist at the University of Florida in Gainesville.

The population there apparently did not grow or shrink much during this era, which suggests Beringia "wasn't paradise, but they survived."

In the final act, "when the North American ice sheets started to melt and a passage into the New World opened, we think they left Beringia to go to a better place," Mulligan explained.

That resulted in a rapid expansion into the New World about 15,000 years ago.

Research done by Mulligan and her colleagues suggests the New World was settled by approximately 1,000 to 5,000 people — a substantially higher number than the 100 or fewer individuals of some prior estimates.

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The research was detailed online Feb. 13 in the journal PLoS ONE.

• Click here to read the full journal article.

How did the researchers come up with their findings? Well, DNA allows scientists to deduce the history of populations.

For instance, mutations that all New World populations have in common with each other and no one else means they share a common ancestry, suggesting there was just one wave of migration into the Americas, as opposed to several unrelated waves.

However, the molecular evidence was confusing as to when this wave of migration took place.

DNA accumulates mutations over time, serving like a clock, but some DNA suggested people came to the New World about 13,000 years ago, while other sequences hinted at 30,000 or more years ago.

Mulligan and her colleagues' new analysis of DNA from Native American and Asian populations seem to help resolve conflicts in past research by suggesting a long waiting period on the doorstep to the New World.

As for Beringia, sea levels rose about 10,000 to 11,000 years ago as the peak of the ice age waned, submerging the land and creating the Bering Strait, which now separates the New World from Siberia with at least 60 miles of open, frigid water.

The expansion into the New World may have occurred by land after the ice sheets covering what is now Canada began to retreat 14,000 to 17,000 years ago, the scientists noted.

However, they added that glaciers on the northwest Pacific coast of North American also might have receded by about 17,000 years ago, thus presenting a viable coastal route by sea to the continent.

"It doesn't have to be an either-or thing. They could have used both routes," Mulligan said.

Innovative work

Anthropologist and population geneticist Henry Harpending at the University of Utah, who did not participate in the research, said he found the work innovative.

"The idea that people were stuck in Beringia for a long time is obvious in retrospect, but it has never been promulgated," said Harpending, who found it very plausible that people were stuck in Beringia "for thousands of years."

Although this new theory could resolve some of the conflicting results scientists have come up with over the years, "I don't pretend this inclusive approach will make us any friends, just more critics," Mulligan told LiveScience.

For instance, one criticism Mulligan anticipates is the fact that "20,000 years in Beringia is a long time. Some people will say, 'Get real — where's the evidence?' We would say that there's no one that does Arctic underwater archaeology."

Researcher Andrew Kitchen added, "Our theory predicts much of the archaeological evidence is underwater. That may explain why scientists hadn’t really considered a long-term occupation of Beringia."

Mulligan noted one might also contend that any evidence of such a 20,000-year stay in Beringia might have left evidence in Siberia or Alaska.

"But we envision a small population there that probably left a relatively light footprint on the landscape," she explained. "And the areas we're talking about — Siberia, Alaska — there's no way to argue that researchers have covered those areas thoroughly, with their incredibly harsh climates."

American Indians Origins

First Americans Arrived As Two Separate Migrations, According To New Genetic Evidence

ScienceDaily (Jan. 21, 2009) — The first people to arrive in America traveled as at least two separate groups to arrive in their new home at about the same time, according to new genetic evidence published online in Current Biology.

After the Last Glacial Maximum some 15,000 to 17,000 years ago, one group entered North America from Beringia following the ice-free Pacific coastline, while another traversed an open land corridor between two ice sheets to arrive directly into the region east of the Rocky Mountains. (Beringia is the landmass that connected northeast Siberia to Alaska during the last ice age.) Those first Americans later gave rise to almost all modern Native American groups of North, Central, and South America, with the important exceptions of the Na-Dene and the Eskimos-Aleuts of northern North America, the researchers said.

" Recent data based on archeological evidence and environmental records suggest that humans entered the Americas from Beringia as early as 15,000 years ago, and the dispersal occurred along the deglaciated Pacific coastline," said Antonio Torroni of Università di Pavia, Italy. "Our study now reveals a novel alternative scenario: Two almost concomitant paths of migration, both from Beringia about 15,000 to 17,000 years ago, led to the dispersal of Paleo-Indians—the first Americans."

Such a dual origin for Paleo-Indians has major implications for all disciplines involved in Native American studies, he said. For instance, it implies that there is no compelling reason to presume that a single language family was carried along with the first migrants.

When Columbus reached the Americas in 1492, Native American occupation stretched from the Bering Strait to Tierra del Fuego, Torroni explained. Those native populations encompassed extraordinary linguistic and cultural diversity, which has fueled extensive debate among experts over their interrelationships and origins.

Recently, molecular genetics, together with archaeology and linguistics, has begun to provide some insights. In the new study, Ugo Perego and Alessandro Achilli of Torroni's team analyzed mitochondrial DNA from two rare haplogroups, meaning mitochondrial types that share a common maternal ancestor. Mitochondria are cellular components with their own DNA that allow scientists to trace ancestry and migration because they are passed on directly from mother to child over generations.

Their results show that the haplogroup called D4h3 spread from Beringia into the Americas along the Pacific coastal route, rapidly reaching Tierra del Fuego. The other haplogroup, X2a, spread at about the same time through the ice-free corridor between the Laurentide and Cordilleran Ice Sheets and remained restricted to North America.

" A dual origin for the first Americans is a striking novelty from the genetic point of view and makes plausible a scenario positing that within a rather short period of time, there may have been several entries into the Americas from a dynamically changing Beringian source," the researchers concluded.

The evidence that separate groups of people with distinctive genetic roots entered the Americas independently at the same time strongly implies linguistic and cultural differences between them. "The origin of the first Americans is very controversial to archaeologists and even more so to linguists," said study corresponding author Professor Antonio Torroni, heading the University of Pavia group. "Our genetic study reveals a scenario in which more than one language family could have arrived in the Americas with the earliest Paleo-Indians."

The researchers include Ugo A. Perego, Universita` di Pavia, Pavia, Italy, Sorenson Molecular Genealogy Foundation, Salt Lake City, UT; Alessandro Achilli, Universita` di Pavia, Pavia, Italy, Universita` di Perugia, Perugia, Italy; Norman Angerhofer, Sorenson Molecular Genealogy Foundation, Salt Lake City, UT; Matteo Accetturo, Universita` di Pavia, Pavia, Italy; Maria Pala, Universita` di Pavia, Pavia, Italy; Anna Olivieri, Universita` di Pavia, Pavia, Italy; Baharak Hooshiar Kashani, Universita` di Pavia, Pavia, Italy; Kathleen H. Ritchie, Sorenson Molecular Genealogy Foundation, Salt Lake City, UT; Rosaria Scozzari, Universita` La Sapienza, Rome, Italy; Qing-Peng Kong, Chinese Academy of Sciences, Kunming, Yunnan, China, Yunnan University, Kunming, Yunnan, China; Natalie M. Myres, Sorenson Molecular Genealogy Foundation, Salt Lake City, UT; Antonio Salas, Unidade de Xenetica, Instituto de Medicina Legal, Universidad de Santiago de Compostela, Galicia, Spain; Ornella Semino, Universita` di Pavia, Pavia, Italy; Hans-Jurgen Bandelt, University of Hamburg, Hamburg, Germany; Scott R. Woodward, Sorenson Molecular Genealogy Foundation, Salt Lake City, UT; and Antonio Torroni, Universita` di Pavia, Pavia, Italy.

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The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by Cell Press, via EurekAlert!, a service of AAAS.

Journal Reference:

  1. . Distinctive Paleo-Indian Migration Routes from Beringia Marked by Two Rare MtDNA Haplogroups. Current Biology, Online January 8; In Print January 13, 2009
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Latin Americans are mestizos

Genetic Study Of Latin Americans Sheds Light On A Troubled History

ScienceDaily (Mar. 24, 2008) — A recent molecular analysis of ancestry across Latin America has revealed a marked differentiation between regions and demonstrated a "genetic continuity" between pre-and post Columbian populations. This study provides the first broad description of how the genome diversity of populations from Latin America has been shaped by the colonial history of the region. The research involved the collaboration of teams at universities across Latin America, the US and Europe, led by Dr. Andres Ruiz-Linares from University College London.

The European colonization of the American continent, initiated in the late fifteenth century, brought with it not only social and political change, but also a dramatic shift from a Native American population to a largely mixed population. The genetic traces of this turbulent period in history are only now beginning to be explored with the molecular tools provided by the human genome project.

The researchers examined genetic markers across the human genome, in hundreds of individuals drawn from 13 mestizo populations found in seven Latin American countries. The picture obtained is that of a great variation in ancestry within and across regions, linked to and led by the colonization that occurred. It also appears that mostly Native and African women and European men contributed genes to the subsequent generations.

Interestingly, despite the fact that the European colonization occurred centuries ago, Latin Americans still preserve the genetic heritage of the local (in many cases now extinct) Native populations that mixed with the immigrants. This connection with the past has not been erased despite the current high mobility of individuals. Furthermore, it brings to life the "brotherhood" of each Latin American population to the Native populations that currently inhabit different countries.

In addition to providing a window into the past, the authors hope that these analyses will contribute to the design of studies aimed at identifying genes for diseases with different frequency in Native Americans and Europeans. Researchers have so far focused on populations from areas settled mainly by Native Americans and Europeans. The genomic diversity of populations across regions in the Americas with large African immigration is still mostly unexplored.

Journal reference: Wang S, Ray N, Rojas W, Parra MV, Bedoya G, et al. (2008) Geographic Patterns of Genome Admixture in Latin American Mestizos. PLoS Genet 4(3): e1000037. doi:10.1371/journal.pgen.1000037

The peopling of the Americas

Mitochondrial genome analysis revises view of the initial peopling of North America

June 28, 2010

The initial peopling of North America from Asia occurred approximately 15,000-18,000 years ago, however estimations of the genetic diversity of the first settlers have remained inaccurate. In a report published online today in Genome Research, researchers have found that the diversity of the first Americans has been significantly underestimated, underscoring the importance of comprehensive sampling for accurate analysis of human migrations.

Substantial evidence suggests that humans first crossed into North America from Asia over a called Beringia, connecting eastern Siberia and Alaska. Genetic studies have shed light on the initial lineages that entered North America, distinguishing the earliest Native American groups from those that arrived later. However, a clear picture of the number of initial migratory events and routes has been elusive due to incomplete analysis.

In this work, an international group of researchers coordinated by Antonio Torroni of the University of Pavia in Italy performed a detailed mitochondrial analysis of a poorly characterized lineage known as C1d. (mtDNA) is passed down through the maternal lineage, and mtDNA sequence markers are extremely useful tools for mapping ancestry.

Similar to other haplogroups that were among the first to arrive in North America, C1d is distributed throughout the continent, suggesting that it may have been also present in the initial founding populations. However, C1d has not been well represented in previous , and the estimated age of approximately 7,000 years, much younger than the other founding haplogroups, was likely inaccurate.

To resolve these inconsistent lines of evidence, the group sequenced and analyzed 63 C1d mtDNA genomes from throughout the Americas. This high-resolution study not only confirmed that C1d was one of the founding lineages in North America 15,000 to 18,000 years ago, but revealed another critical insight.

"These first female American founders carried not one but two different C1d genomes," said Ugo Perego of the Sorenson Molecular Genealogy Foundation and primary author of the study, "thus further increasing the number of recognized maternal lineages from Beringia."

These findings raise the number of founding maternal lineages in North America to fifteen. Furthermore, this work emphasizes the critical need for comprehensive analysis of relevant populations to gather a complete picture of migratory events.

Alessandro Achilli of the University of Perugia, a coauthor of the report, suggests that the number of distinct mitochondrial genomes that passed from Asian into North America is probably much higher.

"These yet undiscovered maternal lineages will be identified within the next three to four years," Achilli noted, "when the methodological approach that we used in our study will be systematically applied."

More information: Perego UA, Angerhofer N, Pala M, Olivieri A, Lancioni H, Hooshiar Kashani B, Carossa V, Ekins JE, Gómez-Carballa A, Huber G, Zimmermann B, Corach D, Babudri N, Panara F, Myres NM, Parson W, Semino O, Salas A, Woodward SR, Achilli A, Torroni A. The initial peopling of the Americas: A growing number of founding mitochondrial genomes from Beringia. Genome Res. doi:10.1101/gr.109231.110

Mestizage

Mis gentes