Genetic Structure and Gene Flows within Horses: A Genealogical Study at the French Population Scale

Since horse breeds constitute populations submitted to variable and multiple outcrossing events, we analyzed the genetic structure and gene flows considering horses raised in France. We used genealogical data, with a reference population of 547,620 horses born in France between 2002 and 2011, grouped according to 55 breed origins. On average, individuals had 6.3 equivalent generations known. Considering different population levels, fixation index decreased from an overall species F_IT of 1.37%, to an average of −0.07% when considering the 55 origins, showing that most horse breeds constitute populations without genetic structure. We illustrate the complexity of gene flows existing among horse breeds, a few populations being closed to foreign influence, most, however, being submitted to various levels of introgression. In particular, Thoroughbred and Arab breeds are largely used as introgression sources, since those two populations explain together 26% of founder origins within the overall horse population. When compared with molecular data, breeds with a small level of coancestry also showed low genetic distance; the gene pool of the breeds was probably impacted by their reproducer exchanges.     

昆虫种群调查抽样方法的几点探讨

本文对昆虫种群调查常用抽样方法的局限性和改进方法进行了探讨,提出了作者的新见解。     

Effects of Soil Trace Elements on Longevity Population in China

Based on background concentrations of elements in soils and the sixth population census data of China, this study discussed the distribution characteristics of soil elements and longevity population at province level in China. Percentages of the aging population are high in Southwest China and the eastern coastal region but low in western and northwestern regions. Provinces in South and Southwest China gain a high level of longevity, while the northern part of China has a low level of longevity. The background concentration of Se in soil has a significant positive correlation with longevity index, while Ba and Ni have a significant negative correlation with longevity indexes. By regression analysis, longevity index C/100,000 can be expressed as C/100,000?=?1.679?0.205 Ni?+?0.413 Co?+?0.006 Se (with R ²?=?0.402 and p?<?0.01), C/65+ can be expressed as C/65+=3.425?0.262 Ni?+?0.435 Co?+?0.006 Se (with R ²?=?0.369 and p?<?0.01).     

Genetic epidemiology of hereditary tyrosinemia in Quebec and in Saguenay-Lac-St-Jean.

Hereditary tyrosinemia type I is an autosomal recessive disorder that was recognized in Saguenay-Lac-St-Jean (SLSJ) (Quebec) in 1967. Ninety-eight tyrosinemic children, including some of the 113 children born in the SLSJ region, have been screened by the Quebec Network of Genetic Medicine in the whole province since 1970. The geographical distribution of the 98 children screened showed the majority of them to have been born in the northeastern part of Quebec. The prevalence at birth was estimated at 1/1,846 live borns, and the carrier rate was estimated at 1/20 inhabitants in the SLSJ region. Three control groups matched to the tyrosinemic obligate-carrier couples were generated using the population register of the SLSJ region kept at SOREP. The mean coefficient of inbreeding was only slightly elevated in the tyrosinemic group compared with the control groups and was due to remote consanguinity. The mean kinship coefficient was 2.3 times higher in the tyrosinemic group than in the control groups. In the SLSJ region the places of origin of the tyrosinemic children and their parents did not show a clustered nonuniform distribution. Endogamy was not found to be higher in the tyrosinemic group than in the control groups. All these results support both the hypothesis of a founder effect for tyrosinemia and a high gene frequency in northeastern Quebec.     

A Genealogical Study of Clonal Development of Escherichia coli

S ummary : The generation times of individual Escherichia coli cells inoculated on to a cellophane membrane surrounded by liquid synthetic medium in a continuous flow system were determined by direct observation for up to seven generations. The presence and production of nonviable cells was also recorded. A wide variety of developmental patterns was found among the developing clones; increased viability and a decrease in generation times with increasing age of the population were observed. The phenomenon of alternation of generations is described and discussed. Five factors contributory to the lag phase were distinguished, and their relative effect may be deduced from the results.     

Association of Mitochondrial DNA Haplogroups with Exceptional Longevity in a Chinese Population

Background

Longevity is a multifactorial trait with a genetic contribution, and mitochondrial DNA (mtDNA) polymorphisms were found to be involved in the phenomenon of longevity.

Methodology/Principal Findings

To explore the effects of mtDNA haplogroups on the prevalence of extreme longevity (EL), a population based case-control study was conducted in Rugao – a prefecture city in Jiangsu, China. Case subjects include 463 individuals aged ≥95 yr (EL group). Control subjects include 926 individuals aged 60–69 years (elderly group) and 463 individuals aged 40–49 years (middle-aged group) randomly recruited from Rugao. We observed significant reduction of M9 haplogroups in longevity subjects (0.2%) when compared with both elderly subjects (2.2%) and middle-aged subjects (1.7%). Linear-by-linear association test revealed a significant decreasing trend of N9 frequency from middle-aged subjects (8.6%), elderly subjects (7.2%) and longevity subjects (4.8%) (p = 0.018). In subsequent analysis stratified by gender, linear-by-linear association test revealed a significant increasing trend of D4 frequency from middle-aged subjects (15.8%), elderly subjects (16.4%) and longevity subjects (21.7%) in females (p = 0.025). Conversely, a significant decreasing trend of B4a frequency was observed from middle-aged subjects (4.2%), elderly subjects (3.8%) and longevity subjects (1.7%) in females (p = 0.045).

Conclusions

Our observations support the association of mitochondrial DNA haplogroups with exceptional longevity in a Chinese population.     

Homocysteine and familial longevity: the Leiden Longevity Study

Homocysteine concentrations are a read-out of methionine metabolism and have been related to changes in lifespan in animal models. In humans, high homocysteine concentrations are an important predictor of age related disease. We aimed to explore the association of homocysteine with familial longevity by testing whether homocysteine is lower in individuals that are genetically enriched for longevity. We measured concentrations of total homocysteine in 1907 subjects from the Leiden Longevity Study consisting of 1309 offspring of nonagenarian siblings, who are enriched with familial factors promoting longevity, and 598 partners thereof as population controls. We found that homocysteine was related to age, creatinine, folate, vitamin B levels and medical history of hypertension and stroke in both groups (all p<0.001). However, levels of homocysteine did not differ between offspring enriched for longevity and their partners, and no differences in the age-related rise in homocysteine levels were found between groups (p for interaction 0.63). The results suggest that homocysteine metabolism is not likely to predict familial longevity.     

A Genealogical Study of Essential Hypertension with and without Obesity in French Canadians

Objectives: To investigate genetic homogeneity in a set of hypertensive families and in subsets chosen for high and low prevalence of obesity; and to compare fasting insulin and lipids, ion transport, and water homeostasis in the obese and lean families. Research Methods and Procedures: The study was carried out in a relative population isolate of the Saguenay/Lac St. Jean region in Canada. Genetic homogeneity was evaluated with the mean coeffigcients of kinship (φ) and inbreeding (F) computed with ascending genealogies. Serum insulin and lipids were measured after overnight fasting. Total body water was estimated with bioelectrical impedance. Sodium‐lithium countertransport and sodium‐potassium co‐transport were determined in freshly isolated erythrocytes. Results: F and φ were increased in hypertensive families compared with families selected at random. F and φ were further increased within the subsets of obese and lean families. In addition, fasting insulin, total body water, sodium‐lithium countertransport, and sodium‐potassium co‐transport were higher in the obese than in the lean families. The two subsets of families did not differ by fasting lipids. Discussion: In the Saguenay/Lac St. Jean population, the degree of genetic homogeneity was increased in families selected for hypertension, and it was further increased in subsets of hypertensive families with high and low prevalence of obesity. This suggests that hypertension in lean and obese individuals may represent, at least in part, separate genetic entities. Some of the extra genes shared in common within the subsets may contribute to their differences in body weight, insulin sensitivity, ion transport, and water homeostasis.     

Genealogical data and the biodemography of human longevity

Biodemography of human longevity is an emerging interdisciplinary field of sociobiological research with deep historical roots. Two research questions are examined in this article: (1) What evidence is there for the familial transmission of human longevity?, and (2) what are the effects of parental age at reproduction on offspring longevity, and in particular, are there long-term adverse health consequences associated with the trend toward delayed reproduction? The ability of scientists to conduct biodemographic studies depends not only on merging theoretical and methodological elements from the biological and demographic/actuarial sciences, but unique sources of data and statistical methods must also be developed. In this article we describe how gencalogical data have been used for over a century to explore basic questions about human longevity, and how similar kinds of data now being developed are driving the formation of new testable research hypotheses in the field of biodemography.     

The Genealogical Population Dynamics of HIV-1 in a Large Transmission Chain: Bridging within and among Host Evolutionary Rates

Transmission lies at the interface of human immunodeficiency virus type 1 (HIV-1) evolution within and among hosts and separates distinct selective pressures that impose differences in both the mode of diversification and the tempo of evolution. In the absence of comprehensive direct comparative analyses of the evolutionary processes at different biological scales, our understanding of how fast within-host HIV-1 evolutionary rates translate to lower rates at the between host level remains incomplete. Here, we address this by analyzing pol and env data from a large HIV-1 subtype C transmission chain for which both the timing and the direction is known for most transmission events. To this purpose, we develop a new transmission model in a Bayesian genealogical inference framework and demonstrate how to constrain the viral evolutionary history to be compatible with the transmission history while simultaneously inferring the within-host evolutionary and population dynamics. We show that accommodating a transmission bottleneck affords the best fit our data, but the sparse within-host HIV-1 sampling prevents accurate quantification of the concomitant loss in genetic diversity. We draw inference under the transmission model to estimate HIV-1 evolutionary rates among epidemiologically-related patients and demonstrate that they lie in between fast intra-host rates and lower rates among epidemiologically unrelated individuals infected with HIV subtype C. Using a new molecular clock approach, we quantify and find support for a lower evolutionary rate along branches that accommodate a transmission event or branches that represent the entire backbone of transmitted lineages in our transmission history. Finally, we recover the rate differences at the different biological scales for both synonymous and non-synonymous substitution rates, which is only compatible with the ‘store and retrieve’ hypothesis positing that viruses stored early in latently infected cells preferentially transmit or establish new infections upon reactivation.     

Regional Distribution of Longevity Population and Elements in Drinking Water in Jiangjin District,Chongqing City,China

This study was carried out to determine the protective effects of lithium borate (LTB) on blood parameters and histopathological findings in experimentally induced acute cadmium (Cd) toxicity in rats. Twenty-eight male Wistar albino rats were used, weighing 200–220 g, and they were randomly divided into four groups, including one control and the following three experimental groups: a Cd group (0.025 mmol/kg), a LTB group (15 mg/kg/day orally for 5 days), and a LTB + Cd group (15 mg/kg/day orally for 5 days and Cd 0.025 mmol/kg by intraperitoneal injection on the fifth day). All the rats in the study were anesthetized with ketamine at the end of the sixth day, blood was taken from their hearts, and then the rats were decapitated. The values in the control and LTB group were usually close to each other. White blood cell (WBC), neutrophil %, and C-reactive protein (CRP) levels increased in the Cd and LTB + Cd groups while lymphocyte and monocyte levels decreased in a statistically significant manner, in comparison to the other groups. It was determined that the levels of red blood cells (RBCs), hematocrit (Htc), and hemoglobin (Hb) did not change in the groups. The levels of aspartate aminotransferase (AST) and alanine aminotransferase (ALT) in the Cd and LTB + Cd groups significantly increased, in comparison to the other groups, while the glucose, alkaline phosphatase (ALP), albumin (ALB), and total protein (TP) levels decreased. According to histopathological findings in the control and LTB groups, the liver and kidney tissues were found to have normal histological structures. In the Cd group, severe necrotic hemorrhagic hepatitis, mild steatosis, and mononuclear cell infiltration were detected in the liver. In the LTB + Cd group, degeneration and mild mononuclear cell infiltration were found in the liver. Regarding the kidney tissue in the Cd group, severe intertubular hyperemia in both kidney cortex and medulla, as well as degeneration and necrosis in the tubulus epithelium, was observed. In the LTB + Cd group, mild interstitial hyperemia and mononuclear cell infiltration was detected. Resultantly, it can be said that LTB at this dose has non-toxic effects and some beneficial effects for liver and kidney damage caused by acute Cd toxicity.     

Modeling Black-Tailed Deer Population Dynamics Using Structured and Unstructured Approaches

Abstract: We used cohort analysis to reconstruct the female segment of a Columbian black-tailed deer (Odocoileus hemionus columbianus) population from 1979 to 2000 in the western Cascades of Washington, USA. We used reconstructed population estimates and age class representations to analyze relationships between population change and female density, forage availability, and weather influences. We applied stage structured and unstructured modeling approaches and used information-theoretic methods to select the best models. We used habitat covariates to develop predictive functions for fertility and survival parameters in structured models. The best structured and unstructured models were composed of combinations of factors including population density, forage availability, and winter weather. Structured and unstructured models could assist with management of black-tailed deer by providing the ability to predict deer population change given covariate values.     

Genealogical concordance and the specific status of Peromyscus sejugis

Peromyscus sejugis, a peripheral isolate of Peromyscus maniculatus, is a threatened taxon endemic to 2 small islands in the Sea of Cortés. Although its insularity makes the specific recognition of P. sejugis inherently problematic, resolution of this problem has important conservation implications. To evaluate the specific validity and evolutionary history of P. sejugis, we compared sequence variation (ND3/ND4L/ND4) in mtDNA for both island populations of P. sejugis with that for 8 populations of P. maniculatus from mainland Baja California. Each island population of P. sejugis had a single haplotype (0.7% sequence divergence), whereas 11 different haplotypes (mean sequence divergence = 0.68%) were obtained for the populations of P. maniculatus. The mean sequence divergence between the populations of the 2 species was 2.0%. Nested clade analysis supports the conclusion that P. sejugis is an insular isolate of P. maniculatus from mainland Baja California. Although our analysis confirms a low level of mtDNA divergence between P. sejugis and P. maniculatus from Baja California, the genealogical concordance of morphological, chromosomal, microsatellite, and mtDNA haplotype distinctiveness supports the conclusion that the 2 island populations of P. sejugis constitute independent evolutionarily significant units and together represent a phylogenetic species distinct from the P. maniculatus from Baja California.     

The Effect of Marriage Migration on the Genetic Structure of the Taimyr Nganasan Population: Genealogical Analysis Inferred from MtDNA Markers

The marriage structure of Nganasans during the time period from 1796 to 1991 and genealogy of carriers of mitochondrial DNA haplotypes was studied in a sample of 280 individuals. It was shown that, from the beginning of its formation to the late 1970s, the population exhibited high endogamy (1976, 83.8%; 1926, 88.4%; 1976, 74.3%). The main source of traditional marriage migration (preferentially female) was populations of Entsy and, indirectly, Nentsy. Intense assimilation of Nganasans by the immigrant population, and to a lesser extent, by Dolgans, in the second half of the 20th century resulted in a reduction of endogamy index in Avam Nganasans to 42.5% by 1991. Assimilation by the immigrants was predominantly paternal, promoting preservation of the historically formed genetic diversity of the Nganasan mitochondrial gene pool. Genealogical analysis of mtDNA haplotypes showed that a relatively high total frequency of Western Eurasian mtDNA haplogroups (20.4%) in the Mongoloid (according to anthropological type) Nganasan population is explained not only by the common ethnic origin with Entsy and Nentsy, but also by direct marriage migration from the Entsy population and indirect marriage migration, from the Nentsy population. This migration led to accumulation of Entsy-Nentsy maternal lineages in the genealogy of Avam Nganasans (38.9 in 2000 of the total number). Of all mtDNA haplotypes, seven (of 21) were introduced to Avam Nganasans by female Entsy and Nentsy, whereas the total frequency of these haplotypes was 0.204. Genetic diversity of mitochondrial DNA haplotypes was 0.935.__________Translated from Genetika, Vol. 41, No. 7, 2005, pp. 954–965.Original Russian Text Copyright © 2005 by Goltsova, Osipova, Zhadanov, Villems.