Biologia futura: confessions in genes.

Alzheimer's disease (AD) is a major cause of dementia. While maternal inheritance has been recognized for late-onset AD (LOAD), risk factors have not been identified consistently on the X chromosome. We recently developed a new method to identify an apparent risk of 70% mediated by the X chromosome in newly-presenting cognitive disorders clinic patients with amnestic mild cognitive impairment (aMCI) or early LOAD with unilateral parental lineage for AD or dementia. We sought to confirm our preliminary findings in the Utah Population Database (UPDB). We obtained previously published aggregate data on the risk of AD in the UPDB based on family history, stratified the data by the sex of the proband, and analyzed them using the new method. The X chromosome-attributable relative risk was estimated by calculating the following: Odds ratio (OR) = (women with paternal lineage: Women with maternal lineage)/(men with paternal lineage: Men with maternal lineage). The proportion of genetic risk attributable to the X chromosome is equal to (OR-1)/OR. The analysis did not reveal any risk mediated by the X chromosome, and the null result could be attributed to methodological limitations. Factors that impact the initial or early presentation (incidence) of LOAD, which are appropriate for consideration as risk factors, may not be detectable in a (prevalent) population of deceased individuals. Thus, epidemiological evidence for the contribution of the X chromosome to the development of LOAD will need to be sought prospectively in incident patient populations with newly diagnosed, biologically-confirmed aMCI or LOAD.

Madagascar is located at the crossroads of the Asian and African worlds and is therefore of particular interest for studies on human population migration. Within the large human diversity of the Great Island, we focused our study on a particular ethnic group, the Antemoro. Their culture presents an important Arab-Islamic influence, but the question of an Arab biological inheritance remains unresolved. We analyzed paternal (n=129) and maternal (n=135) lineages of this ethnic group. Although the majority of Antemoro genetic ancestry comes from sub-Saharan African and Southeast Asian gene pools, we observed in their paternal lineages two specific haplogroups (J1 and T1) linked to Middle Eastern origins. This inheritance was restricted to some Antemoro sub-groups. Statistical analyses tended to confirm significant Middle Eastern genetic contribution. This study gives a new perspective to the large human genetic diversity in Madagascar.

Genealogical Analysis of Maternal and Paternal Lineages in the Quebec Population

Genealogical Analysis of Maternal and Paternal Lineages in the Quebec Population

Background: Highly polymorphic genetic markers like short tandem repeats (STRs) have been used successfully in disease analysis and studies of human evolution and population genetic diversity. However, DNA-based population genetic studies of Indian populations are limited. Subjects and Methods: To enlarge our understanding of genetic variation in Indian populations, a population genetic study was carried out on Jat Sikh (Punjab, North India) individuals ( n = 150) using a battery of the STR loci. The STR loci analysed by means of PCR amplification followed by electrophoresis and silver staining included HUMCSF1PO, HUMTPOX, HUMTHO1, HUMLPL, HUMF13A01, HUMF13B, HUMFESFPS and HUMVWA loci. Results: The overall pattern of allele frequencies was similar to many Caucasian and Indian populations and heterozygosity varied from 65% (HUMLPL) to 85% (HUMVWA). For all eight loci, no deviations from the Hardy-Weinberg equilibrium hypothesis were detected. Significant differences were observed between Jat Sikhs and African, Chinese and Indian tribes. The mean exclusion probability ranged from 35% to 70%, and the power of discrimination from 81% to 93%, indicating the potential of these loci for forensic and paternity investigations. Conclusion: The allele frequency spectrum, heterozygosity, probability of exclusion, match probability and discrimination probability estimates show interesting variation and suggest the usefulness of these loci for anthropogenetic, paternity and forensic investigations in Indian populations.

In males, defective reproductive traits induced by an exposure to an endocrine disruptor are transmitted to future generations via epigenetic modification of the germ cells. Interestingly, the impacted future generations display a wide range of heterogeneity in their reproductive traits. In this study, the role that the Y chromosome plays in creating such heterogeneity is explored by testing the hypothesis that the Y chromosome serves as a carrier of the exposure impact to future generations. This hypothesis implies that a male who has a Y chromosome that is from a male that was exposed to an endocrine disruptor will display a more severe reproductive phenotype than a male whose Y chromosome is from an unexposed male. To test this hypothesis, we used a mouse model in which F1 generation animals were exposed prenatally to an endocrine disruptor, di-2-ethylhexyl phthalate (DEHP), and the severity of impacted reproductive traits was compared between the F3 generation males that were descendants of F1 males (paternal lineage) and those from F1 females (maternal lineage). Pregnant dams (F0 generation) were exposed to the vehicle or 20 or 200 μg/kg/day of DEHP from gestation day 11 until birth. Paternal lineage F3 DEHP males exhibited decreased fertility, testicular steroidogenic capacity, and spermatogenesis that were more severely impaired than those of maternal lineage males. Indeed, testicular transcriptome analysis found that a number of Y chromosomal genes had altered expression patterns in the paternal lineage males. This transgenerational difference in the DEHP impact can be attributed specifically to the Y chromosome.

Analyses of molecular genetic data have added a new dimension to human evolutionary research. Pioneering studies of variation in human populations were based on analyses of blood groups1 and electromorphs,2 both of which represent qualitative multistate phenotypes. With the development of recombinant DNA methods in the 1970s and 1980s, the focus shifted from gene products to a new and plentiful source of human variability, restriction fragment length polymorphisms (RFLPs).3,4 Finally, the addition of DNA sequencining survey data to the rapidly growing RFLP data base made it feasible for the first time to determine the exact number of nucleotide substitutions between different alleles, as well as to construct gene trees and reconstruct the phylogenetic history of populations.5–7

Identification and characterization of novel polymorphic LINE-1 insertions through comparison of two human genome sequence assemblies

Contributors from a range of disciplines consider the disconnect between human evolutionary studies and the rest of evolutionary biology. The study of human evolution often seems to rely on scenarios and received wisdom rather than theory and methodology, with each new fossil or molecular analysis interpreted as supporting evidence for the presumed lineage of human ancestry. We might wonder why we should pursue new inquiries if we already know the story. Is paleoanthropology an evolutionary science? Are analyses of human evolution biological? In this volume, contributors from disciplines that range from paleoanthropology to philosophy of science consider the disconnect between human evolutionary studies and the rest of evolutionary biology. All of the contributors reflect on their own research and its disciplinary context, considering how their fields of inquiry can move forward in new ways. The goal is to encourage a more multifaceted intellectual environment for the understanding of human evolution. Topics discussed include paleoanthropology's history of procedural idiosyncrasies; the role of mind and society in our evolutionary past; humans as large mammals rather than a special case; genomic analyses; computational approaches to phylogenetic reconstruction; descriptive morphology versus morphometrics; and integrating insights from archaeology into the interpretation of human fossils. Contributors Markus Bastir, Fred L. Bookstein, Claudine Cohen, Richard G. Delisle, Robin Dennell, Rob DeSalle, John de Vos, Emma M. Finestone, Huw S. Groucutt, Gabriele A. Macho, Fabrizzio Mc Manus, Apurva Narechania, Michael D. Petraglia, Thomas W. Plummer, J.W. F. Reumer, Jeff Rosenfeld, Jeffrey H. Schwartz, Dietrich Stout, Ian Tattersall, Alan R. Templeton, Michael Tessler, Peter J. Waddell, Martine Zilversmit

The identification of common genetic variants such as single nucleotide polymorphisms (SNPs) in the human genome has become central in human population genetics and evolution studies, as well as in the study of the genetic basis of complex traits and diseases. Crucial for the accurate identification of genetic variants is the availability of high quality genomic DNA (gDNA). Since popular sources of gDNA (buccal cells, lymphocytes, hair bulb) often do not yield sufficient quantities of DNA for molecular genetic applications, whole genome amplification methods have recently been introduced to generate a renewable source of double-stranded linear DNA. Here, we assess the fidelity of one method, multiple displacement amplification (MDA), which utilizes bacteriophage Phi29 DNA polymerase to generate amplified DNA from an original source of gDNA, in a representative SNP discovery and genetic association study at the melanocortin 1 receptor (MC1R) locus, a highly polymorphic gene in humans involved in skin and hair pigmentation. We observed that MDA has high fidelity for novel SNP discovery and can be a valuable tool in generating a potentially indefinite source of DNA. However, we observed an allele amplification bias that causes genotype miscalls at heterozygous sites. At loci with multiple polymorphic sites in linkage disequilibrium, such as at MC1R, this bias can create a significant number of heterozygote genotype errors that subsequently misrepresents haplotypes.

The emergence of next-generation sequencing technologies allowed access to the vast amounts of information that are contained in the human genome. This information has contributed to the understanding of individual and population-based variability and improved the understanding of the evolutionary history of different human groups. However, the genome of a representative of the Amerindian populations had not been previously sequenced. Thus, the genome of an individual from a South American tribe was completely sequenced to further the understanding of the genetic variability of Amerindians. A total of 36.8 giga base pairs (Gbp) were sequenced and aligned with the human genome. These Gbp corresponded to 95.92% of the human genome with an estimated miscall rate of 0.0035 per sequenced bp. The data obtained from the alignment were used for SNP (single-nucleotide) and INDEL (insertion-deletion) calling, which resulted in the identification of 502,017 polymorphisms, of which 32,275 were potentially new high-confidence SNPs and 33,795 new INDELs, specific of South Native American populations. The authenticity of the sample as a member of the South Native American populations was confirmed through the analysis of the uniparental (maternal and paternal) lineages. The autosomal comparison distinguished the investigated sample from others continental populations and revealed a close relation to the Eastern Asian populations and Aboriginal Australian. Although, the findings did not discard the classical model of America settlement; it brought new insides to the understanding of the human population history. The present study indicates a remarkable genetic variability in human populations that must still be identified and contributes to the understanding of the genetic variability of South Native American populations and of the human populations history.

In this study, geographic and linguistic distributions of contemporary and ancient matches with the paternal and maternal lineages of two individuals exhumed from the exemplary Pazyryk culture burial site of Ak-Alakha-1 mound 1 were investigated. Using the shared paternal and maternal haplotypes observed in both ancient individuals, extensive database and literature searches were conducted revealing numerous full matches among contemporary Eurasians, majority of whom speak Altaic Languages. Despite the current focus on the two Pazyryk individuals, a rare glimpse into the ancient migrations was gained through the discovery of paternal and maternal haplotype matches across an immense geography that spans from Yakutia to Turkey. In addition to a vast array of archaeological findings in such Scythian “frozen graves” across Central Asia, accumulating archaeogenetic data are expected to shed light on the anthropology of these otherwise mysterious people.

Simple SummaryA systematic investigation of the genetic diversity and structure of different sika deer populations is conducive to their population management, protection, and reproduction. Using mitochondria and genes on the Y chromosome, we found that the sika deer population consists of nine maternal lineages and three paternal lineages. The overall maternal genetic diversity of sika deer is relatively high, while that of the paternal line is low. In addition, the tandem repeat units in the control region in Japanese populations exhibit significantly higher diversity in both type and copy number. Notably, we identified a 26 bp tandem repeat motif unique to southern Japanese populations. Sika deer (Cervus nippon), a species mainly distributed in the northeast of Asia, hold significant economic value in China due to their contributions to traditional Chinese medicine. A systematic investigation of their genetic structure is needed for population management. In this study, mitochondrial genome and AMELY, DBY, USP9Y, and SRY gene fragments on Y chromosome were used to elucidate the genetic structure of 303 individuals across 8 distinct populations. The mitosome analysis identified 72 haplotypes, with a haplotype diversity (Hd) of 0.917 and nucleotide diversity (π) of 0.0143, respectively. Meanwhile, 13 haplotypes were defined by Y chromosome genes with a Hd of 0.791. Analysis of the mitochondrial control region (CR) revealed subspecies-specific patterns of tandem repeat unit organization between continental and Japanese groups. Y chromosome analyses demonstrated a homogeneous paternal lineage across Japanese populations.

The ambiguity and conciseness of the law on the citizenship of the children of Iranian mothers, on the one hand, and some dense social problems for the children of Iranian women married to Iraqi nationals and increasingly Afghan migrants, on the other hand, led the legislator to pass a single article in 2006. However, the conceptual ambiguities and implementation problems of this single article caused the legislator to repeal the previous single article by approving a new article in 1398.This article is an attempt to illustrate the article’s strengths and weaknesses by reconsidering the “critical-corrective” nature of the new single article, and especially to explain its incompatibility with the forty-first principle of the constitution; it is finally suggested that due to the truth and nature of citizenship and more compatibility with Article 41 of the Constitution, maternal lineage, like paternal lineage, secure the Iranian citizenship to the child.

Introduction: The Koraga tribe are an isolated endogamous tribal group found in the southwest coastal region of India. The Koraga language shares inherited grammatical features with North Dravidian languages. To seek a possible genetic basis for this exceptionality and understand the maternal lineage pattern, we have aimed to reconstruct the inter-population and intra-population relationships of the Koraga tribal population by using mtDNA markers for the hypervariable regions along with a partial coding region sequence analysis.Methods and Results: Amongst the 96 individuals studied, we observe 11 haplogroups, of which a few are shared and others are unique to the clans Soppu, Oṇṭi and Kuṇṭu. In addition to several deep rooted Indian-specific lineages of macrohaplogroups M and U, we observe a high frequency of the U1 lineage (∼38%), unique to the Koraga. A Bayesian analysis of the U1 clade shows that the Koraga tribe share their maternal lineage with ancestral populations of the Caucasus at the cusp of the Last Glacial Maximum.Discussion: Our study suggests that the U1 lineage found in the Indian subcontinent represents a remnant of a post-glacial dispersal. The presence of West Asian U1 when viewed along with historical linguistics leads us to hypothesise that Koraga represents a mother tongue retained by a vanquished population group that fled southward at the demise of the Indus civilisation as opposed to a father tongue, associated with a particular paternal lineage.