Maternal lineage diversity based on mitochondrial DNA in a population sample from Mexico City.

mtDNA Haplogroup X: An Ancient Link between Europe/Western Asia and North America?

A five-generation Hispanic family expressing maternally transmitted Leber hereditary optic neuropathy and/or early-onset dystonia associated with bilateral basal ganglia lesions was studied. Buffy coat mitochondrial DNA (mtDNA) from a severely affected child was amplified by the polymerase chain reaction and greater than 90% sequenced. The mtDNA proved to be a Native American haplogroup D genotype and differed from the standard "Cambridge" sequence at 40 nucleotide positions. One of these variants, a G-to-A transition at nucleotide pair (np) 14459, changed a moderately conserved alanine to a valine at NADH dehydrogenase subunit 6 (ND6) residue 72. The np 14459 variant was not found in any of 38 Native American haplogroup D mtDNAs, nor was it detected in 108 Asian, 103 Caucasian, or 99 African mtDNAs. Six maternal relatives in three generations were tested and were found to harbor the mutation, with one female affected with Leber hereditary optic neuropathy being heteroplasmic. Thus, the np 14459 G-to-A missense mutation is specific to this family, alters a moderately conserved amino acid in a complex I gene, is a unique mtDNA variant in Native American haplogroup D, and is heteroplasmic, suggesting that it is the disease-causing mutation.

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.

We analyzed Mestizo (admixed) population samples from different geographic regions of Mexico (n= 1283) with 20 autosomal STRs (PowerPlex® 21, Promega Corp.). Allele frequencies and forensic parameters from the Northwest, Northeast, West, Center, and Southeast regions are reported, as well as from the pooled Mexican population sample. The combined PD and PE for this 20 STR system were > 0.9999999999 and > 0.99999996593% in all five population samples, respectively. Analysis of molecular variance (AMOVA) of these Mexican population samples, plus Monterrey (Northeast) and Mexico (Center) Cities, showed low but significant differences among Mexican-Mestizos from the seven populations (Fst = 0.20%; p = 0.0000). Structure analysis showed the highest proportion of Native American ancestry in Mexico City, Center, and Southeast regions, respectively, which was in agreement with the estimated genetic distances represented in a MDS plot and a NJ tree. The best fit of population clusters (K = 4) obtained with the Structure software indicates that Mexican-Mestizos are mainly composed by European, African, and two Native American ancestries. The European and Native American ancestries displayed a contrary gradient, increasing toward the North-West and South-Southeast, respectively. These 20 autosomal STR loci improved the admixture estimation regarding previous studies with the 13 CODIS-STRs, as supported by the higher similarity with previous estimates based on genome-wide SNP. In brief, this study validates the confident use of the PowerPlex® 21 system for human identification purposes in Mestizo populations throughout the Mexican territory.

After the European colonization of the Americas, there was a dramatic population collapse of the Indigenous inhabitants caused in part by the introduction of new pathogens. Although there is much speculation on the etiology of the Colonial epidemics, direct evidence for the presence of specific viruses during the Colonial era is lacking. To uncover the diversity of viral pathogens during this period, we designed an enrichment assay targeting ancient DNA (aDNA) from viruses of clinical importance and applied it to DNA extracts from individuals found in a Colonial hospital and a Colonial chapel (16th-18th century) where records suggest that victims of epidemics were buried during important outbreaks in Mexico City. This allowed us to reconstruct three ancient human parvovirus B19 genomes and one ancient human hepatitis B virus genome from distinct individuals. The viral genomes are similar to African strains, consistent with the inferred morphological and genetic African ancestry of the hosts as well as with the isotopic analysis of the human remains, suggesting an origin on the African continent. This study provides direct molecular evidence of ancient viruses being transported to the Americas during the transatlantic slave trade and their subsequent introduction to New Spain. Altogether, our observations enrich the discussion about the etiology of infectious diseases during the Colonial period in Mexico.

In epidemiological studies, it is easier to glean information from isolated populations with simple genetic backgrounds than from populations with relatively complex genetic backgrounds. Regarded as an isolated population, the Minz (Hei-Yi Zhuang) in Napo County (in the China-Vietnam borderland) has been the subject of numerous recent studies. To assess the genetic isolation of this population, we studied Y chromosome and mitochondrial DNA from Minz and Han in Napo. Both populations exhibited southern Chinese genetic characteristics in both paternal and maternal lineages. Using NETWORK analyses, we found pronounced gene flow between these two populations only in maternal lineages. We also observed gene flow from other populations into the Minz gene pool. We thus concluded that the Minz is not a genetically isolated population and it is increasingly difficult to find isolated populations in mainland East Asia.

The contribution of mitochondrial genetics to heart failure is thought to be reciprocal. Its complex traits are influenced by genetic and environmental factors. Genetically diverse mouse strains form a vital repository to uncover the interaction between the mitochondrial and nuclear genomes underlying heart failure due to their traceable genetic origins, maternal lineages and controlled genetic variation. Using systems genetics, we studied this cross-talk in the Collaborative Cross (CC) mice challenged with heart failure (HF).We used 63 strains of CC-mice that grouped into 8 mitochondrial haplotypes and subjected them to HF using isoproterenol (Iso), a beta-adrenergic stimulant that mimics progressive stress induced HF in humans. The Alzet osmotic pumps delivered a consistent dose of the drug for 21 days following which the mice were euthanized for organ collection. A group of mice with saline loaded pumps acted as control (Ctrl). Baseline and end of study echocardiography were recorded for these mice. Bulk RNA sequencing was carried out on the left ventricles and data analyzed on R-studio.The CC-strains showed differences across the haplotypes for organ weights and heart function. Noticeable treatment specific gene expression differences were observed for 34 nuclear encoded genes from MitoCarta3.0 unlike mt-DNA encoded genes that were insignificant after correcting for sex and haplotypes. These genes were associated with multiple metabolic pathways in the cell. Trait-GWAS associations with markers from the mitochondrial genome were observed only for mice from Iso group with cell surface area (p = 6.19e-06) and change in ejection fraction (p = 9.22e-05) as top hits under FWER threshold of 0.01. Cyfip2 was the top candidate gene (p = 2.66e-07) among the 831 hits (47-MitoCarta & 784 other nuclear) based on our trans-eQTL analysis. The eQTL genes influenced critical pathways of OXPHOS, myogenesis, apoptosis etc. Our approach uncovered 24 gene candidates associated with mt-DNA and HF that overlapped with our previous mi-eQTL reports. CC-mice revealed ancestry dependent effects underlying HF for studying mito-nuclear interactions. Despite establishing differences, modeling these interaction needs development of complex cybrid systems to evaluate the bidirectional impact on HF.

An attempt was made to examine the influence of Malaysian continental drift on the genetic and haplotype diversity of Malaysian horseshoe crab (Tachypleus gigas [Muller, 1785]) distributed along the east coast of Peninsular Malaysia and distant Borneo Island. Mitochondrial DNA (AT rich region = 369bp) analysis showed that T. gigas has higher haplotype diversity in peninsular Malaysia compared to east Malaysian (Sarawak) samples. Highest haplotype diversity (h±SD) was observed among the Terengganu samples (0.813 ± 0.071) followed by Pahang samples (0.813 ± 0.065). There were no difference in nucleotide diversity (Pi) noted in east cost of Peninsular Malaysian (PM) samples. Overall haplotype (h±SD) and nucleotide (Pi±SD) diversity of T. gigas in PM samples including Sarawak was 0.827 ± 0.051 and 0.0078 ± 0.0014 respectively. A total of 6 unique haplotypes were recorded of which 2, 2 and 1 were unique to Terengganu, Sarawak and Pahang samples respectively. Pair wise haplotype frequency (FST) value was not statistically significant (P > 0.05) for all the groups indicating the limited gene flow among the population. In addition phylogenetic scrutiny visibly clustered T. gigas samples from T. tridentatus samples representing sound phylogenetic signals in mtDNA AT rich region. The findings from this study have important implications for proper management and conservation of horseshoe crab in Malaysia.

Variable Genotype of Leber's Hereditary Optic Neuropathy Patients

(re)Producing mtEve

Mitochondrial DNA (mtDNA) control region sequences from hair samples of 213 individuals from Thailand were analyzed using Sanger sequencing. A total of 170 different haplotypes were identified, of which 146 occurred only once (unique haplotypes). The dataset showed a random match probability of 0.87% and a haplotype diversity of 0.9960. The samples were assigned to 85 different haplogroups with B5a, F1a1a, and M being the most frequent ones. Pairwise FST-values between this and other Southeast and East Asian populations revealed significant but relatively low differences, indicating a close relation. Heteroplasmic positions were observed in 12.2% of hair samples confirming the frequent appearance of heteroplasmic positions in hairs. This dataset will complement existing data as an mtDNA reference for forensic investigations.

In this study mitochondrial DNA (mtDNA) analysis was carried out on 9 Bronze Age horses recovered from Dashan-qian and Jinggouzi archaeological sites in Chifeng region, Inner Mongolia, China to explore the origin of Chinese domestic horses. Both mtDNA 16S rRNA gene and control region (D-loop) fragments of ancient horses were amplified and sequenced. The analysis of the highly conservative 16S rRNA gene sequences indicated that the burial environment of Chifeng region is suitable for the preservation of ancient DNA (aDNA). Combing 465 mtDNA D-loop sequences representing different breeds from East Asia, Central Asia, Near East and Europe, we constructed a phylogenetic network to investigate the relationship between ancient and modern horses. The phylogenetic network showed that the 9 horses were distributed into different modern horse clusters which were closely related to them representing a certain geographical distribution. Our results showed that the maternal genetic line of the ancient horses in Chifeng region was highly diversified, which contributed to the gene pool of modern domestic horses and suggested a complex origin of domestic horses in China.

Reviewed by: The Atlantic Economy during the Seventeenth and Eighteenth Centuries: Organization, Operation, Practice, and Personnel Elizabeth Mancke The Atlantic Economy during the Seventeenth and Eighteenth Centuries: Organization, Operation, Practice, and Personnel. Edited by Peter A. Coclanis. Columbia: University of South Carolina Press, 2005. 377 pp. $49.95 (cloth). In "The Dutch Atlantic Economies," the opening essay of this fine collection, Jan de Vries shows that by the 1770s the Dutch imported [End Page 237] more from the West Indies than from Asia, a "point [that] will surprise even specialists in the economic history of the early modern period" (p. xiii), notes Peter Coclanis, the editor. European trade with Asia had been expanding at about 1 percent per annum, and at 2 percent in the Atlantic basin, which the Dutch shift reflects. In Asia, the Dutch entered a centuries-old economic world, while in the Atlantic they participated in creating one. Yet the "organization, operation, practice, and personnel" of that economy, as distinct from the internal economies of societies around the Atlantic, is understudied. This collection of essays helps fill that gap, and in its entirety makes two striking and complementary contributions. First, commercial networks crisscrossed the Atlantic like a "spider's web" (p. 31), rather than in a linear fashion as envisaged by mercantilist conceits or scholarly models of triangular trades. Second, these complex and "self-organizing" (p. 31) networks were integral to the rapid and often chaotic growth of the Atlantic economy. Attention to networks allows scholars to study the permeability of empires, which were not self-contained units. Daviken Studnicki-Gizbert's analysis of Iberian commercial controversies shows the tension between conservative Spaniards connected to the royal court and Portuguese merchants and bankers who operated in Spain's empire after the union of the crowns in 1580 and espoused more liberal trade policies. In essays on seventeenth-century Anglo-Dutch relations, Claudia Schnurmann and April Lee Hatfield document the extensive integration of the Dutch into English America. Hatfield shows that inVirginia they muted their national identities by anglicizing their names, speaking English, and associating with coreligionists. Schnurmann reconstructs Anglo-Dutch networks to question the nature of religious, regional, and national identities in the Atlantic world. "Supranational trade" (p. 196) networks, she suggests, often reflected regional identities, for example ties between Massachusetts and Dutch Surinam, which conflicted with national objectives. Breaching the commercial boundaries established by imperial policies became commonplace in the French Antilles as Kenneth Banks shows in his work on the smuggling of slaves into eighteenth-century Martinique. French mercantilist policies, as elaborated by Jean-Baptiste Colbert in the 1660s, were designed to curb trade with foreigners, but economic and diplomatic objectives could work in opposition. After France acquired St. Domingue in 1697, the demand for slaves rose beyond what French merchants could supply. A scarcity of slaves encouraged foreign smugglers, whom some colonial officials ignored, some courted, and few challenged. Licit trade was also complex. David [End Page 238] Hancock's analysis of the transformation of Madeira wine "from common plonk into the highest status, most expensive wine in America" (p. 60), tracks the personal networks between Madeira producers and British colonial consumers that allowed them to craft highly localized varieties. His work shows how colonial demand shaped innovations in the production of an Atlantic commodity. Robert S. DuPlessis compares changing patterns of local demand of cloth consumption in Montreal, Philadelphia, Charleston, and New Orleans, ca. 1680–1770. His data show a general decline in woolen consumption and an increase in cotton consumption, consistent with the work of others on the "standardization of colonial consumer goods" (p. 81), but with quite particular ethnic and regional patterns. Amerindians continued to prefer woolens, but gradually increased their purchases of cottons. Wearing cotton tended to be gendered; women wore it more than men. Slaves also wore more cottons and of lower grades than did others. Colonial consumers of cloth, as with consumers of Madeira wine, influenced local markets, notwithstanding transatlantic trends toward more standardized demand. Regional commodity production, the Atlantic economy, and colonial image are explored in essays by S. Max Edelson and Laura Náter. Colonial commodities gained "reputations" in the Atlantic world that affected their valuation...

The Y-STR DYS19 is firmly established in the repertoire of Y-chromosomal markers used in forensic analysis yet is poorly understood at the molecular level, lying in a complex genomic environment and exhibiting null alleles, as well as duplications and occasional triplications in population samples. Here, we analyse three null alleles and 51 duplications and show that DYS19 can also be involved in inversion events, so that even its location within the short arm of the Y chromosome is uncertain. Deletion mapping in the three chromosomes carrying null alleles shows that their deletions are less than approximately 300 kb in size. Haplotypic analysis with binary markers shows that they belong to three different haplogroups and so represent independent events. In contrast, a collection of 51 DYS19 duplication chromosomes belong to only four haplogroups: two are singletons and may represent somatic mutation in lymphoblastoid cell lines, but two, in haplogroups G and C3c, represent founder lineages that have spread widely in Central Europe/West Asia and East Asia, respectively. Consideration of candidate mechanisms underlying both deletions and duplications provides no evidence for the involvement of non-allelic homologous recombination, and they are likely to represent sporadic events with low mutation rates. Understanding the basis and population distribution of these DYS19 alleles will aid in the utilisation and interpretation of profiles that contain them.

Reduced genetic diversity in a meiobenthic copepod exposed to a xenobiotic