Genetic influences on serum bilirubin in American Indians: The Strong Heart Family Study

Abstract

Objective: To identify genetic variation influencing serum bilirubin levels in American Indians, we performed genome-wide screening and association analyses in the Strong Heart Family Study. Bilirubin is an endogenous antioxidant that has demonstrated an inverse relationship with cardiovascular disease. Genetic variation within the promoter region of uridine diphosphate glucuronosyltransferase (UGT1A1) on chromosome 2q has been associated with elevated serum bilirubin levels in European populations. However, no study has investigated the UGT1A1 promoter in American Indians.

Methods: Statistical analyses were carried out with 3,484 participants aged 14 to 93 years recruited from three geographic areas in the United States; Arizona, Oklahoma, and North and South Dakota.

Results:Variance components linkage analysis detected a quantitative trait locus (QTL) for bilirubin on chromosome 2q in the combined centers (LOD = 6.61, P = 4.24 × 10⁻⁶) and in Oklahoma (LOD = 5.65, P = 4.57 24 × 10⁻⁵). Genetic association of the UGT1A1 promoter polymorphism was significant for all geographic locations. After adjustment using conditional linkage for UGT1A1 promoter variance, the linkage signal dropped to 1.10 in the combined sample and to 3.32 (P = 0.02) in Oklahoma, indicating this polymorphism is not completely responsible for the linkage signal in American Indians. We also detected suggestive linkage signals in the Dakotas on chromosome 10p12 (LOD = 2.18) and in the combined centers (LOD = 2.24) on chromosome 10q21.

Conclusions: Replication of a serum bilirubin QTL on chromosome 2q in American Indians implicates UGT1A1 but further genotyping is warranted to identify additional causative polymorphisms. Evidence also supports a potential novel locus for bilirubin on chromosome 10.

Talking Thursday - NeanderRAD Genome News

Neanderthal DNA shown to be in 1-4 % of non-Africans. Thank God! Now all the paleoanthropologists that I've met that look like Neanderthals don't have to feel like they belong to a different species.

Here are links to people are more erudite at discussing these things and to the paper

A Draft Sequence of the Neandertal Genome - Paper #1

Targeted Investigation of the Neandertal Genome by Array-Based Sequence Capture - Paper #2

The Neandertal Genome Project - Press Info from the Max Planck Institute

Skull Caps and Genomes - The Loom

NEANDERTALS LIVE! - John Hawks

Breaking: there’s a little bit of Neandertal in all of us - Gene Expression

You're a Neanderthal: Genes say yes — a little bit - Associated Press

Mitochondial DNA diversity in Mennonite communities from the Midwestern United States

Human Biology Volume 82,issue 3

Phillip E. Melton, MJ Mosher, R. Rubicz, M. Zlojutro, MH Crawford

This study examined mitochondrial DNA (mtDNA) variation in six Mennonite communities from Kansas (Goessel, Lone Tree, Garden View, Meridian, and Garden City) and Nebraska (Henderson) in order to determine their genetic structure and its relationship to population history. Mitochondrial DNA haplogroup and haplotype information were obtained for 118 individuals from blood samples. Molecular genetic variation was analyzed using diversity measures, neutrality test statistics, spatial analysis of molecular variance (SAMOVA), and multidimensional scaling plots. The Mennonite samples exhibited eight western European mtDNA haplogroups – H, HV0, I, J, K, T, U, and X. Comparable to other populations of European descent, haplogroup H was the most frequent in all six communities and ranged from 35% in Lone Tree to 75% in Old Order Mennonites from Garden City, Kansas. A total of 58 different mtDNA haplotypes were found in these groups with only one shared among all six populations. Haplotype diversities varied from 0.81 in Goessel to 0.96 in Henderson and Garden View. Multivariate statistical analysis of these populations indicates that these Anabaptist communities formed new congregations by fissioning along familial lines. Population subdivision of these communities into congregations support previously documented patterns of fission-fusion. In conclusion these haploid molecular data provide a more accurate reflection of biological relationships between Midwestern Mennonite communities than evidence based on classical genetic markers.

Talking Points Thursday - Havasupai Indians and the Ethical Use of Genetic Data

So the idea for today's theme is to discuss a current topic in anthropological or medical genetics. I was originally going to discuss Gene Set Enrichment Analysis (GSEA) and the modern use of transcriptomic data to infer biological pathways but instead came across a very important article on the use of genetic data and the Havasupai Indians in the New York Times by Amy Harmon. The basic gist of the article is that in the early 1990s, researchers from Arizona State University collected blood from the Havasupai for a study on diabetes, which is in high frequencies in the community. This research didn't lead to anything but it was used for a number of other studies regarding population history. The problem arises is that population history (added 4/24/2010) is not what the individuals who provided the samples consented too and they were never informed regarding these changes. This led to ASU settling for 700,000 dollars and agreeing to furnish the Havasupai with a number of items.

This of course raises a number of issues from both an ethical and research standpoint but a couple of the more pertinent ones are what does this mean for people who have biological samples still in their freezer and how does that impact the modern day geneticists ability to do research with indigenous populations. Last week at the AAPA meetings, I was actually pondering how many geneticists actually do fieldwork with the populations they study. The most salient feature of anthropology is that is about people, and when you establish trust with individuals through interpersonal contact you are better able to meet both yours and their needs. However, when we talk about populations, this a fairly abstract expression of a group's identity. While it sounds like the researcher in this case did do fieldwork - she didn't establish a long-term relationship with these people and this led to the current situation. This is a big difference between cultural and biological anthropologists, where cultural anthros will stay years in the same community but biological anthropologists may only stay days and it may be the only time they visit the community. I suppose the lesson to learn from this case is to establish a dialogue with the community and always remember the table should be round so you can address their concerns if they arise.

The second issue that needs to be addressed is how does this affect individuals who keep biological samples in their freezer and have used them for other purposes than they were originally collected for. Will this cause a backlash against these researchers and their institutions? This decision may have far-reaching implications regarding access to samples. There has already been some backlash against genetic ancestry research in places such as Colombia, where analysis of genetic material is not allowed to occur outside the country, without express permission of the community. This harks back to a case in the late 1990s, where an individual sent some samples to be developed as immortal cell lines, without the permission of the populations they were collected from.

The problem becomes when you have a fairly stable item (like DNA) that can be used for several different purposes. A number of labs have genetic material that are often used for purposes beyond what they were originally collected for. This finding however indicates that researchers are going to need to be very specific in what they put in their Informed consent form. Also, it is quite likely IRB proposals are going to need to be more stringent and protective of individuals in the future and that all research will need approval.

Physical Anthropology Abstracts of interest

Here are a few Physical Anthropology abstracts that are from myself or colleagues from Kansas.

Microevolutionary analysis of Y chromosome variation in five Native American populations

PHILLIP E. MELTON, NORBERTO BALDI-SALAS, RAMIRO BARRANTES and MICHAEL H. CRAWFORD

This study investigated Y chromosomal genetic variation in 88 male participants from five lower Central American populations inhabiting Nicaragua (Rama) and Costa Rica (Chorotega, Maleku,Zapatón Huetar, and Guaymí-Abrojo) in order to determine male population dynamics that have occurred since European contact. We investigated eight short tandem repeats (STRs) (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, and DYS439) and Y haplogroup characteristic single nucleotide polymorphisms (SNPs). All five populations contained the Native American specific haplogroup, Q3, ranging in frequencies from 0.85 (Zapatón Huetar) to 0.35 (Chorotega). These populations were also characterized by the presence of Y haplogroup R1b representing European admixture. A total of 70 haplotypes were identified, of which 69 (97%) were population specific and 55 (80%) were found in only a single individual. Phylogenetic analysis using a multiple dimensional scaling plot demonstrated genetic similarities between Oto-Manguaen, Nahua Mesoamericans and Votic speaking Chibchan groups that arenot demonstrated by data frommitochondrial DNA. These populations demonstrate a high degree of paternal genetic differentiation indicating the importance of genetic structure in the region even in geographic proximate and linguistically related indigenous groups. We propose that this high amount of paternal genetic differentiation is due to two demographic events. The first of these events is the rise of the Toltec empire in central Mexico around 1200 years before present and the second is the arrival of Europeans in the region at the beginning of the sixteenth century.

Genetic structure of Mennonite General Conference, Haldermanand Old Colony populations: Molecular perspective.

MICHAEL H. CRAWFORD1,PHILLIP E. MELTON2, MJ MOSHER1, ROHINA RUBICZ2
and MARK ZLOJUTRO2.

A study was initiated in 1979 on the genetic structure and biological aging of Mennonite communities of Kansas and Nebraska. Initial analyses based on blood group and protein markers of General Conference Mennonites of Kansas and Nebraska yielded disagreement between the reconstructed history of the congregations and their genetic affinities. Congregations that underwent fission during the early 1900s differed significantly from each other and were suggestive of the action of the founder effect. Additional samples were collected from six communities including Old Order Mennonites, who had emigrated from Cuatemoc, Mexico, and two additional Halderman congregations (Lone Tree and Garden View) that had split off the original community, Meridian. Mitochondrial DNA was extracted from 117 individuals representing six of the congregations and characterized for ten major European RFLP haplogroups. HVSI sequences were generated using an ABI 370 capillary system sequencer. Eight (H,I,J,K,T,U, pre-V and X) of the ten most common western European haplogroups were observed. SAMOVA analyses, with k number of groups equaling from 2 to 6, provided the most parsimonious k =4 (FCT =0.07, pvalue= 0.02). The four groups were:1) Goessel/Henderson; 2)Meridian/Garden View; 3) LoneTree; 4) Old Order. Goessel and Henderson constituted a single congregation in the Ukraine until 1860 and split into two communities on relocation to Kansas and Nebraska. Garden View and Lone Tree split from Meridian during the 1970s. MDS plots (stress value = 0.02) reflect the ethnohistory of these populations more accurately than either phylogenetic trees or R-matrix analyses based on classical genetic markers.

Chuvash origins: Evidence from mtDNA Markers.

ORION M. GRAF1, JOHN MITCHELL2, STEPHEN WILCOX3, GREGORY LIVSHITS4, MICHAEL H. CRAWFORD1.

A sample of 96 unrelated individuals from Chuvashia, Russia was sequenced for hypervariable region-I (HVR-I) of the mtDNA molecule. The Chuvash speak a Turkic language that is not mutually intelligible to other extant Turkish groups, and their genetics are distinct from Turkic-speaking Altaic groups. Some scholars have suggested that they are remnants of the Golden Horde, while others have advocated that they are the products of admixture between Turkic and Finno-Ugric speakers who came into contact during the 13th century. Earlier genetic research using autosomal DNA markers suggested a Finno-Ugricorigin for the Chuvash. This study examines non-recombining DNA markers to better elucidate their origins. The majority of individuals in this sample exhibit haplogroups H (31%), U (22%), and K (11%), all representative of western and northern Europeans, but absent in Altaic or Mongolian populations. Multidimensional scaling (MDS) was used to examine distances between the Chuvash and 8 reference populations compiled from the literature. Mismatchanalysis showed a unimodal distribution. Along with neutrality tests (Tajima’s D (-1.43365) p<0.05, style="font-weight: bold;">

Mestizo identity in the Lower Huallaga region of Peruvian Amazonia: Molecular
perspectives.

ANNE E. JUSTICE, BARTHOLOMEW C. DEAN and MICHAEL H. CRAWFORD

The Lower Huallaga River Basin is part of the Huallaga, a prominent tributary of Amazon that runs through the tropical lowlands of northeastern Peru. The Cocama, Lamista Kichwa, Chayahuita, and Munichi are among the primary indigenous peoples residing in this poorly studied region. Most individuals along the Lower Huallaga River tend to self-identify as mestizos, a term used to describe Spanish-speaking individuals of mixed European and Native American ancestry. This study aims to characterize the genetic structure of the Lower Huallaga region by analyzing the area’s mtDNA haplogroup and sequence diversity and comparing its variability to surrounding Central and South Americans. Samples were collected in 2005 from several populations located along the Lower Huallaga River Basin, near the city of Yurimaguas, Loreto, Peru (n= 46). A 400 bp fragment of HVS1 was sequenced and haplogroup assignment confirmed using standard RFLP methods. Despite the predominant self-identification of mestizo, 100% of the sample exhibited a Native American mtDNA lineage (A2: 22%, B: 30%, C1: 37%, D: 11%). High estimates for gene diversity compared to other indigenous populations (h = 0.9952) also indicate that the sample contains descendants of several different indigenous groups rather than a single ethnic group. MJ network analysis, mismatch analysis, MDS plots, and neutrality tests were performed in order to characterize the genetic structure of this area compared to surrounding regions. Sequences highlight a closer relationship to South American populations rather than to European, African and Asian colonists, with similar diversity measures to other regions in Amazonia.

Are sex-specific effects of dietar phytosterol intake on adiponectin levels an underlying factorexplaining variation in TG/HDL ratio associated with APOE polymorphisms: The Kansas Nutrition Study.

MJ MOSHER1 3, DARIO DEMARCHI2, ROHINA RUBICZ4, MARK ZLOJUTRO4, PHILLIP E
MELTON4 and MICHAEL H CRAWFORD3.

Dietary manipulation of plasma lipids remains an integral part of treatment for dyslipidemias and their sequelae of coronary artery disease (CAD). However, substantial conflicting evidence reported in the literature suggests that undetermined gene- by- sex variation affects dietary response. We examined blood samples for APOE polymorphisms and determined nutrient profiles from dietary diaries of 75 male and 83 female Central Kansas Mennonites. Previously we reported sex-specific associations of plasma lipids to plasma adiponectin, and APOE. diponectin, a hormone affecting lipid metabolism, is sexually dimorphic, lowered by both testosterone and higher percentages of visceral adipose tissue (VAT). Here we examine effects of phytosterol intake and APOE on adiponectin and the triglyceride/high-density lipoprotein (TG/HDL) ratio, an indicator of atherogenic dyslipidemias and a marker for (CAD). An inverse relationship between plasma adiponectin levels and TG/HDL ratio was significant in males only (P = 0.005 for males, P=0.106 for females). No significant change was noted after adjustments for age, location, or measures of central fat patterning. No sex-specific variation was found in dietary percent of fatty acids from animal sources. However, phytosterol intake was decidedly higher in females (P= 0.007), yet had no statistical affects on adiponectin levels in females. Sex specific tertiles denoting the percent of dietary phytosterol were compared. Males whose phytosterol intake was highest were the only ones to have adiponectin matching their female counterparts (P=0.041). Furthermore, 25% of the variation in male TG/HDL ratios can be explained by APOE by adiponectin interaction (P =0.015). Further sex-specific nutrigenetics comparisons are recommended.

Coalescent modeling of Yakut origins points to small founding population based on mtDNA variation.

MARK ZLOJUTRO1, LARISSA A. TARSKAIA2, MARK SORENSEN3, J. JOSH SNODGRASS4, WILLIAM R. LEONARD5 and MICHAEL H. CRAWFORD6.

Based on archaeological and ethnohistorical evidence, the Yakut people of northeastern Siberia are considered to be descendants of ancient Turkic-speaking populations once living in the distant Altai-Sayan region on the Russian- Mongolian border. The results of phylogeographic studies on Siberian mtDNA variation have been generally concordant with a southern Yakut origin, although the timing of the northern migration, the size of the founder group and the degree of genetic admixture with non-Turkic Siberian populations are less apparent. In an effort to better understand Yakut origins, we modeled 25 demographic scenarios, including parameters such as effective population size, growth rate andgene flow, and tested by coalescent simulation whether any are consistent with the patterns of mtDNA diversity observed in present-day Yakuts. The models consist of either two simulated demes that represent Yakuts and a South Siberian ancestral population, or three demes that also include a regional Northeast Siberian population that served as a source of localized gene flow into the Yakut deme. The model that produced the best fit to the observed data defined a founder group with an effective female population size of only 150 individuals, migrating northwards approximately 1,000 years BP and undergoing significant admixture with neighboring populations in Northeastern Siberia. These simulation results indicate a pronounced founder effect that was primarily kin-structured and reconcile reported discrepancies between Yakut mtDNA and Y chromosome diversity levels.

Genetic structure of native circumpolar populations based on autosomal, mitochondrial, and Y chromosome DNA markers

So here is a paper that I'm co-author on if you want to see the type of work I did during my graduate career. Granted, I'm still interested in anthro genetics but right now my time is subsumed my cardiovascular and statistical genetics.

Genetic structure of native circumpolar populations based on autosomal, mitochondrial, and Y chromosome DNA markers

Rohina Rubicz 1 *, Phillip E. Melton 1, Victor Spitsyn 2, Guangyun Sun 3, Ranjan Deka 3, Michael H. Crawford 4

1Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio, TX 78245 2Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, 117415 Russia 3Department of Environmental Health, University of Cincinnati Medical Center, Cincinnati, OH 45267 4Department of Anthropology, University of Kansas, Lawrence, KS 66045

This study investigates the genetic structure of the present-day inhabitants of Beringia in order to answer questions concerning their origins and evolution. According to recent studies, the ancestors of Native Americans paused for a time in Beringia, during which they differentiated genetically from other Asians before peopling the New World. Furthermore, the Koryaks of Kamchatka share a ubiquitous allele (D9S1120) with Native Americans, indicating they may have descended from the same ancestral Beringian population that gave rise to the New World founders. Our results show that a genetic barrier exists between Kamchatkans (Koryaks and Even) and Bering Island inhabitants (Aleuts, mixed Aleuts, and Russians), based on Analysis of Molecular Variance (AMOVA) and structure analysis of nine autosomal short tandem repeats (STRs). This is supported by mitochondrial DNA evidence, but not by analysis of Y chromosome markers, as recent non-native male admixture into the region appears to have partially obscured ancient population relationships. Our study indicates that while Aleuts are descended from the original New World founders, the Koryaks are unlikely to represent a Beringian remnant of the ancestral population that gave rise to Native Americans. They are instead, like the Even, more recent arrivals to Kamchatka from interior Siberia, and the ubiquitous allele in Koryaks may result from recent gene flow from Chukotka.

Friday Five #8 - Welcome 2010

So I was back at work this week, trying to finish a few things prior to the impending end of the decade if it is actually the end of the decade. This a matter of whether you believe if there is a year 0, which is unlikely. So here we go with this Friday's top five.

1) Explaining the Imperfection of the Molecular Clock of Hominid Mitochondria - It should be now surprise at this point that the mtDNA clock isn't all that great of time device, you definitely would not want to set you clock by it.

The molecular clock of mitochondrial DNA has been extensively used to date various genetic events. However, its substitution rate among humans appears to be higher than rates inferred from human-chimpanzee comparisons, limiting the potential of interspecies clock calibrations for intraspecific dating. It is not well understood how and why the substitution rate accelerates. We have analyzed a phylogenetic tree of 3057 publicly available human mitochondrial DNA coding region sequences for changes in the ratios of mutations belonging to different functional classes. The proportion of non-synonymous and RNA genes substitutions has reduced over hundreds of thousands of years. The highest mutation ratios corresponding to fast acceleration in the apparent substitution rate of the coding sequence have occurred after the end of the Last Ice Age. We recalibrate the molecular clock of human mtDNA as 7990 years per synonymous mutation over the mitochondrial genome. However, the distribution of substitutions at synonymous sites in human data significantly departs from a model assuming a single rate parameter and implies at least 3 different subclasses of sites. Neutral model with 3 synonymous substitution rates can explain most, if not all, of the apparent molecular clock difference between the intra- and interspecies levels. Our findings imply the sluggishness of purifying selection in removing the slightly deleterious mutations from the human as well as the Neandertal and chimpanzee populations. However, for humans, the weakness of purifying selection has been further exacerbated by the population expansions associated with the out-of Africa migration and the end of the Last Ice Age.

2) Why Diseased Heart Muscle Cells Don't Communicate Properly An interesting article from Science Daily on a gene associated (EB1) with heart rate gap junctions.

3) Even If Obama Passed Single Payer, Primary Care Doctors Still Wouldn't Get It: A good look at one of the major problems with health care in this country today as physicians treat the disease and not the patient. One of the major reasons that an anthropological perspective would help medical schools and their students.

4) Richard Dawkins on ‘Elders’ (via Neuroanthropology): A good look at Richard Dawkins and why he probably isn't the best spokesman for a defender of evolutionary theory. He tends to look at those who having any sort of faith as the great unwashed masses of ignorance, which is probably not the best strategy for explaining evolution. The point being here that if your goal is to educate it is best not to berate those seeking to learn. I think most of those that seek out Dawkins, already agree with him and this leads to an "O'Reily Show type effect", where those who listen are you perpuating what they already believe. This of course leads them to be less understanding when explaining evolutionary concepts to someone seeking knowledge.

5) Non-Darwinian estimation: My ancestors, my genes' ancestors This article from Genome Research is from a while ago but is an excellent review and rebuke of a number of studies that rely on the idea of identifying ancestry through genetics, particularly the program Structure, but then ignore all of assumptions associated with this technique.

There is widespread interest in characterizing the organization of human genetic variation around the world from a population perspective. Related to this are attempts to describe the pattern of genetic variation in the human species generally, including “recreational” genomics, the genome-based estimation of the ancestry of individuals. These approaches rest on subtle concepts of variation, time, and ancestry that are perhaps not widely appreciated. They share the idea that there are, or were, discrete panmictic human populations such that every person is either a member of such a population or is an admixed descendant of them. Ancestry fraction estimation is biased by assumptions about past and present human population structure, as when we trace ancestry to hypothetical unmixed ancestral populations, or assign an individual's ancestry to continental populations that are indistinguishable from classical “races.” Attempts to identify even individuals' local subpopulations are less precise than most (geneticists included) expect, because that is usually based on a small portion of a person's ancestry, relative to the much larger pool of comparably related ancestors. It is easier to show that two people have some relationship than to show who or where the actual ancestor was. There is an important distinction between individuals' demographic ancestry and the ancestry of their genes. Despite superficial appearances, these interpretations of genetic data are often based on typological rather than Darwinian thinking, raising important issues about the questions that are actually being asked.

Day 68: Genetic Landscape (5/27/2008)

I've been playing around with this program that creates "genetic landscapes". This picture shows a 3D plot of 16 populations (unnamed for certain reasons) plotted on the XY axis and the residuals of a regression of pairwise differences on the Z axis. populations that appear above the plane display higher differentiation than expected while those below the plane display a closer than expected genetic similarity.

Admixed Colombians

The American Journal of Human Biology has an interesting article by Salas et. al. (2008) on admixture in Colombian populations at least from the maternal perspective. They investigate mtDNA sequence variation in 185 Colombians that define themselves as "mestizo", "mulatto", and "afro-Colombian" what they find is based on mtDNA, "mestizo" are primarily Native American (97%), and "mulatto" (~81% haplogroup L) and "afro-Colombian" (72% L and 23% Native American) are primarily from Africa. They conclude that self-reported ancestry is not a reliable source of information. Their concern is that if a forensic scientists believes a population is genetically homogeneous than they will increase the likelihood of type I statistical error.

One thing I wasn't sure about was this quote

"Haplotype C16111T C16223T C16290T G16319A T16362C is observed at high frequency in the Haida from Queen Charlotte Islands (North America), but it is also present in the Xavante Brazilians (Ward et al., 1996) or in the Kuna from Panama (Batista et al., 1995)" Salas et al. 1997

isn't this haplogroup A2 and common throughout the Americas as it also found in the Embera (Kolman and Bermingham 1997), the Ache (Schmidt et al. 2004) among others. The Xavante are characterized by a high frequency of haplogroup B as are the Ache.

I however found this quote incredibly insightful

"Undetected population stratification has an important bearing in forensic casework if an expert consulting a database wrongly assumes that the populations (lacking correctly defined genetic ancestry) are genetically homogenous." (Salas et al. 1997)

References Cited

Batista O,Kolman CJ,Bermingham E. 1995. Mitochondrial DNA diversity in the Kuna Amerinds of Panama. Hum Mol Genet 4: 921-929.

Kolman CJ, Bermingham E. 1997. Mitochondrial and nuclear DNA diversity in the Chocó and Chibcha Amerinds of Panamá. Genetics. 1997 Nov;147(3):1289-302.

Salas A. , A. Acosta , V. Álvarez-Iglesias , M. Cerezo , C. Phillips , M. V. Lareu, Á. Carracedo. (2008) "The mtDNA ancestry of admixed Colombian populations" Am. J. Hum. Bio. Early View.

Schmitt R, Bonatto SL, Freitas LB, Muschner VC, Hill K, Hurtado AM, Salzano FM. 2004. Extremely limited mitochondrial DNA variability among the Aché Natives of Paraguay. Ann Hum Biol. 2004 Jan-Feb;31(1):87-94.

Ward RH,Salzano FM,Bonatto SL,Hutz MH,Coimbra CEA,Santos RV. 1996. Mitochondrial DNA polymorphism in 3 Brazilian Indian tribes. Am J Hum Biol 8: 317-323.

Mobile Elements in the Humane Genome

This article does pretty good job of reviewing mobile elements for the uninitiated. The only drawback is that they didn't include endogenous retroviruses as an important component that constitute about 8% of the human genome.

Mobile DNA elements in primate and human evolution

Jinchuan Xing , David J. Witherspoon , David A. Ray , Mark A. Batzer , Lynn B. Jorde

Yrbk Phys Anthropol 50:2-19, 2007.

Abstract: Roughly 50% of the primate genome consists of mobile, repetitive DNA sequences such as Alu and LINE1 elements. The causes and evolutionary consequences of mobile element insertion, which have received considerable attention during the past decade, are reviewed in this article. Because of their unique mutational mechanisms, these elements are highly useful for answering phylogenetic questions. We demonstrate how they have been used to help resolve a number of questions in primate phylogeny, including the human-chimpanzee-gorilla trichotomy and New World primate phylogeny. Alu and LINE1 element insertion polymorphisms have also been analyzed in human populations to test hypotheses about human evolution and population affinities and to address forensic issues. Finally, these elements have had impacts on the genome itself. We review how they have influenced fundamental ongoing processes like nonhomologous recombination, genomic deletion, and X chromosome inactivation.

Autosomal STR Variation in Native America

This is a huge dataset from an article in PLOS Genetics. While the amount of samples and the work that went into this is impressive (it is nice that they included all of their data as supplementary figures and tables), there are a few problems. One is the small amount of Native North American samples used in this project. There are only three populations north of Mexico (Chippewa, Cree, and Ojibwa) and the data set is heavily weighted to the south I don't know if it is fully representative of Native North America. A problem with the HGDP originally was the reluctance of the Native Americans from the US to participate and this continues to this day (see this NY Time article). For a good background on the furor over the HGDP check out this issue of Cultural Survival Quarterly.

While they cite an article I wrote (how exciteing) and their data shown in figure 8 appear to supports the assumption of a separate Chibchan migration from Central America into South America they should also acknowledge Keyeaux et al. (2002) who also suggested the same migratory pattern based on mtDNA haplogroup data in Colombia. The inclusion of Zenu in Chibchan-Paezan is somewhat spurious as it is an extinct language but some linguists do include it. I'm also curious as to which Mexican Maya (there are more than one or is it an amalgamation) group they are using and why are they so different than the Kaqchikel (a Mayan group from Guatemala). The authors also mention a connection between Mesoamerica and the Andes but don't mention the fact that the Spanish moved thousands of Native Americans from Nicaragua (primarily Nicarao) and elsewhere to work in Peru during the 1600s. This is fairly well documented by Spanish historians and mixture between Indian groups over the last 400 years may have created this relationship.

Genetic Variation and Population Structure in Native Americans

Sijia Wang, Cecil M. Lewis Jr., Mattias Jakobsson, Sohini Ramachandran, Nicolas Ray, Gabriel Bedoya, Winston Rojas, Maria V. Parra, Julio A. Molina, Carla Gallo, Guido Mazzotti, Giovanni Poletti, Kim Hill, Ana M. Hurtado, Damian Labuda, William Klitz, Ramiro Barrantes, Maria Cátira Bortolini, Francisco M. Salzano, Maria Luiza Petzl-Erler, Luiza T. Tsuneto, Elena Llop, Francisco Rothhammer, Laurent Excoffier, Marcus W. Feldman, Noah A. Rosenberg, Andrés Ruiz-Linares

Abstract

We examined genetic diversity and population structure in the American landmass using 678 autosomal microsatellite markers genotyped in 422 individuals representing 24 Native American populations sampled from North, Central, and South America. These data were analyzed jointly with similar data available in 54 other indigenous populations worldwide, including an additional five Native American groups. The Native American populations have lower genetic diversity and greater differentiation than populations from other continental regions. We observe gradients both of decreasing genetic diversity as a function of geographic distance from the Bering Strait and of decreasing genetic similarity to Siberians—signals of the southward dispersal of human populations from the northwestern tip of the Americas. We also observe evidence of: (1) a higher level of diversity and lower level of population structure in western South America compared to eastern South America, (2) a relative lack of differentiation between Mesoamerican and Andean populations, (3) a scenario in which coastal routes were easier for migrating peoples to traverse in comparison with inland routes, and (4) a partial agreement on a local scale between genetic similarity and the linguistic classification of populations. These findings offer new insights into the process of population dispersal and differentiation during the peopling of the Americas.

Mexican Native American mtDNA

Considering the sheer size of Mexican Native American population (6 million) it is good to get an idea of the mtDNA haplogroup frequencies of these populations. I do have problems with the ordination of Figure 2 (PCA population plot) and Figure 3 (haplogroup plot). This is not an uncommon problem in the literature. If you look the axes are different values which doesn't accurately discriminate the population because the Huichol (more than likely due to haplogroup X) are having such an effect as an outlier in the plot that the whole thing is skewed (they should have probably bootstrapped this and recalulated without haplogroup X). So when you plot this these two populations with small frequencies of haplogroup X (Huichol and Tarahumara) demonstrate a much larger effect than the other populations in the plot. This current calculation results in this weird bimodal looking plot, which should be more evenly distributed. Also, in figure 3, why use X2 and then only state haplogroups A, B, C, and D when in the text and Table 1 you list A1, A2, B1, B2, C1, C2, D1, D2, if you found them plot them. Also, if the PC plots are compatible then why is A pulling out the Huichol and not X? Overall, would have been better to use an R-matrix (standardized PCA) or MDS plot and measured stress. There is of course the whole how much information can you determine from just mtDNA haplogroup frequency data question but that can wait for another rant.

Characterization of mtDNA Haplogroups in 14 Mexican
Indigenous Populations

rosenda i. penaloza-espinosa, diego arenas-aranda, ricardo m. cerdaflores, leonor buentello-malo, gerardo gonzalez-valencia, javier torres, berenice alvarez, irma mendoza, mario flores, lucila sandoval, francisco loeza, irma ramos, leopoldo munoz, and fabio salamanca1

Human Biology, June 2007, v. 79, no. 3, pp. 313–320.

Abstract
In this descriptive study we investigated the genetic structure of 513 Mexican indigenous subjects grouped in 14 populations (Mixteca- Alta, Mixteca-Baja, Otomi, Purépecha, Tzeltal, Tarahumara, Huichol, Nahua- Atocpan, Nahua-Xochimilco, Nahua-Zitlala, Nahua-Chilacachapa, Nahua- Ixhuatlancillo, Nahua-Necoxtla, and Nahua-Coyolillo) based on mtDNA haplogroups. These communities are geographically and culturally isolated; parents and grandparents were born in the community. Our data show that 98.6% of the mtDNA was distributed in haplogroups A1, A2, B1, B2, C1, C2, D1, and D2. Haplotype X6 was present in the Tarahumara (1/53) and Huichol (3/15), and haplotype L was present in the Nahua-Coyolillo (3/38). The first two principal components accounted for 95.9% of the total variation in the sample. The mtDNA haplogroup frequencies in the Purépecha and Zitlala were intermediate to cluster 1 (Otomi, Nahua-Ixhuatlancillo, Nahua- Xochimilco, Mixteca-Baja, and Tzeltal) and cluster 2 (Nahua-Necoxtla, Nahua-Atocpan, and Nahua-Chilacachapa). The Huichol, Tarahumara, Mixteca-Alta, and Nahua-Coyolillo were separated from the rest of the populations. According to these findings, the distribution of mtDNA haplogroups
found in Mexican indigenous groups is similar to other Amerindian haplogroups, except for the African haplogroup found in one population.

Maya STRs

This article abstract is for early view article from AJPA. This is actually a fairly important article as few studies have investigated the genetic structure of Mayan populations even though as the abstract says there are 7.5 million living inhabitants speaking 28 languages throughout Central America. The typical view of individuals is to assume that the Maya are an extinct culture and not a modern vibrant culture that is suffering from a number of hardships suffered by indigenous groups throughout the region.

Delineating genetic relationships among the Maya
Lisa Ibarra-Rivera, Sheyla Mirabal, Manuela M. Regueiro, Rene J. Herrera

Abstract
By 250 AD, the Classic Maya had become the most advanced civilization within the New World, possessing the only well-developed hieroglyphic writing system of the time and an advanced knowledge of mathematics, astronomy and architecture. Though only ruins of the empire remain, 7.5 million Mayan descendants still occupy areas of Mexico, Guatemala, Belize, El Salvador, and Honduras. Although they inhabit distant and distinct territories, speak more than 28 languages, and have been historically divided by warfare and a city-state-like political system, and they share characteristics such as rituals, artistic, architectural motifs that distinguish them as unequivocally Maya. This study was undertaken to determine whether these similarities among Mayan communities mirror genetic affinities or are merely a reflection of their common culture. Four Mayan populations were investigated (i.e., the K'iche and Kakchikel from Guatemala and the Campeche and Yucatan from Mexico) and compared with previously published populations across 15 autosomal STR loci. As a whole, the Maya emerge as a distinct group within Mesoamerica, indicating that they are more similar to each other than to other Mesoamerican groups. The data suggest that although geographic and political boundaries existed among Mayan communities, genetic exchanges between the different Mayan groups have occurred, supporting theories of extensive trading throughout the empire. Am J Phys Anthropol, 2007. © 2007 Wiley-Liss, Inc.

Genetic Polymorphisms in French Guiana

Uniparental (mtDNA, Y-chromosome) Polymorphisms in French Guiana and Two Related Populations - Implications for the Region's Colonization.

Mazières S, Guitard E, Crubézy E, Dugoujon JM, Bortolini MC, Bonatto SL, Hutz MH, Bois E, Tiouka F, Larrouy G, Salzano FM.

Laboratoire d'Anthropobiologie, FRE 2960 CNRS, Toulouse, France.

Blood samples collected in four Amerindian French Guiana populations (Palikur, Emerillon, Wayampi and Kali'na) in the early 1980s were screened for selected mtDNA and Y-chromosome length polymorphisms, and sequenced for the mtDNA hypervariable segment I (HVS-I). In addition, two other Amerindian populations (Apalaí and Matsiguenga) were examined for the same markers to establish the genetic relationships in the area. Strong dissimilarities were observed in the distribution of the founding Amerindian haplogroups, and significant p-values were obtained from F(ST) genetic distances. Interpopulation similarities occurred mainly due to geography. The Palikur did not show obvious genetic similarity to the Matsiguenga, who speak the same language and live in a region from where they could have migrated to French Guiana. The African-origin admixture observed in the Kali'na probably derives from historical contacts they had with the Bushinengue (Noir Marron), a group of escaped slaves who now lead independent lives in a nearby region. This analysis has identified significant clues about the Amerindian peopling of the North-East Amazonian region.