Resolution Roundup #6 - June

It is hard to believe the year is half over and I'm still a horrible blogger. Oddly, I can find the time to read pretty much the entire fantasy series for the Song of Ice and Fire in a fortnight. I'm currently on Feast of Crows and will start Dance of Dragons after that then wait 8 million plus years for George RR Martin to finish the last two books unless he decides to break this into a thirty part series and break HBO in the process or he dies and has someone else finish it. I also spent part of the month of June back in the old haunts of Lawrence, KS. I was there doing some research on male genetic variation in American midwestern Mennonites. I stayed at a wonderful B&B called the Halycon house (highly recommend), hung out in the newly constructed lab and got to see a lot of friends that I now only generally see at conferences. Here are some pics of the visit (P.S. the girls didn't come along but they are cute).

Personal Fitness
1) Do P90X at least once this year: Due to the intense heat I have kind of put this on hold and will probably take it up when it cools down or rains for longer than 10 minutes at a time.


2) Learn to Jog: Once again off the table due the habitation of the surface of the sun. I swear squirrels spontaneously combust outside AC homes and humans are melting left and right. Probably why traffic isn't so bad this time of year, look at that upside.

Finance
3) Go to a cash-based only system for at least 3 months out of the year: We will revisit this a little later in the year.


4) Don't eat out for at least 3 months of the year: This may become mandatory as we are finding that potentially other kids are gluten-sensitive besides Cordy. Granted a few restaurants have gluten-free items but sometimes things are hidden in it that make it difficult. 

Professional
5) Publish an article from my Ph.D. dissertation: I actually have completed one of these but now need to revamp it to go once again. I'm sure by the time it is finished it will look nothing like what I had in mind but that can be a good thing as well. However, at this point is in on the back burner. I currently have two articles and a book chapter in press, then another book chapter, article, and a grant that need to be written by the end of July so after that I can relax for the rest of the year. No wait I have to do two presentations so no rest until Novemember at the earliest.
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6) Organize a symposium for a meeting: This is now off the radar.

Family:
7) Sunday Dinners: Seeing as it stays hot, we continue to try and eat breakfast together or we have a light dinner and play a board game after.

8) Spend one on one time with each child, each month: For Spencer's b-day we went out and got him a bike, and went out to lunch and to see Rango, which was quirky kid movie western about a lizard.

Other
9) Begin writing a novel: I plan to still work on it but I may shorten it and write a short story instead. The dream of novel writing is still there but I have no time unless to read recreationly or write non-fiction.

10) Blog at least once a week: I'm like the worst blogger in the world but you guys probably already knew that.

11) Read 13 Non-fiction books this year: Aside from spending my time with George RR Martin, I have also read the Long Walk, by a Polish guy who claims to have walked from Siberia to India during WWII after escaping a Russian work camp about 100 miles north of Lake Baikal. There is some controversy about walking that far or if he even did it but I'm inclined to believe him as who want to make something like walking across the Gobi desert without water.

So until next month enjoy.

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 #15 - Migrating to Kansas.

I've been busy this week preparing for a presentation I'm giving at a conference in Kansas, next week. The theme of the conference is on Why do Human Migrate? and how can we better understand the wanderlust that has driven our ancestors to and fro. The conference program looks pretty interesting and I'm on two of the abstracts, which are listed here.

1) Mennonite migrations: Demographic and genetic consequences: This is a summary of some work I did some time ago and will be published in a forthcoming article in the journal Human Biology.

Throughout history, religious persecution has often led to human migration. Prime examples of these demographic events are those that impacted populations belonging to the Anabaptist movement (Amish, Hutterites, and Men-nonites) after the Reformation in 16th century Europe. Each of these groups went through persecutions and demographic events that led to population movement in Europe and eventual emigration to the Americas. This study focuses on maternal molecular genetic diversity in six Mennonite communities from Kansas (Goessel, Lone Tree, Garden View, Meridian, and Garden City) and Ne-braska (Henderson) in order to determine their genetic structure and its relationship to understanding the biologi-cal impact of these demographic events. 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. Molecular genetic variation was ex-amined and compared to classical genetic markers. The Goessel and Henderson communities demonstrate a shared biological relationship with a comparative population from the Netherlands. Additional analyses of molecular data indicate these Anabaptist communities formed new con-gregations by fissioning along familial lines. This popula-tion subdivision of into congregations support previously documented patterns of fission-fusion from classical genetic data but demonstrates a more accurate reflection of these communities into their modern day congregations.

2) Understanding the Genetic Structure and Migration of the Rama Indians from the Caribbean Coast of Nicaragua: Some of the results for this article were drawn from my dissertation and further fieldwork that my co-author conducted a couple of years later on the coast of Nicaragua. The picture on the cover of the program is from the Rama.

This study investigated genetic and cultural data in order to understand the population history and migration of the Rama Indians in relation to neighboring Central American indigenous groups. The Rama belong to the Chibchan linguistic family (Votic sub-family) and inhabit the coast and rivers of southern Nicaragua. Due to limited ethno-historical and ethnographical information, the origins and population dynamics of the Rama remain unclear, both prior to and after the colonization of the Caribbean coast of Nicaragua. We analyzed maternal (mtDNA) and paternal (Y-chromosome) molecular genetics from 75 Rama partici-pants in order to assess the provenience of the Rama to neighboring Native American populations. These data were analyzed using median-joining networks, multi-dimensional scaling plots, and analysis of molecular vari-ance (AMOVA). Ethnographic and genealogical data were used to better understand both cultural ecology and inter-nal migration of the Rama within their ancestral territory. The results of this study indicate that the Rama are diver-gent from comparative Chibchan populations and are char-acterized by a high frequency of mtDNA haplogroup B (92%) and low frequency of haplogroup A (8%). This re-duced haplogroup diversity characterize the Rama and in-dicate maternal genetic drift. In addition, Y chromosome data indicate paternal gene flow between the Rama and neighboring Mesoamerican groups. Together, these data challenge previous assumptions regarding the relation-ships of the Rama with neighboring Central American groups, and suggest an early divergence from other Votic populations as well as a pattern of seasonal movements within their territory.

3) New type of genetic variation discovered

4)Potential for Revealing Individual-Level Information in Genome-wide Association Studies. An interesting article from JAMA regarding the high level sequencing data and privacy protection.

5) Identification of functional modules that correlate with phenotypic difference: the influence of network topology: a interesting article that looks at comparing pathways between phenotypes.

One of the important challenges to post-genomic biology is relating phenotypic alterations to the collective alterations in genes underlying observed state changes. Current inferential methods, however, invariably omit large bodies of information on the relationships between genes. We present a method that takes account of such information - expressed in terms of the topology of a correlation network - and we apply the method in the context of current procedures for gene set enrichment analysis.

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.