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.
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