Normal and Adverse Genetic Processes in Subdivided Populations of the Island Type: Computer Simulation

A computer model simulating genetic dynamics of a subdivided population at the level of a one-locus diallele system is proposed. In contrast to the earlier publications, this model is based on Wright's island model. The computer experiments were focused on genetic changes occurring during relatively short time intervals comparable to the duration of economic activities of humans (tens of generations). The process of attaining stationary state and reorganization of the genetic structure of the system under anthropogenic influence were simulated. The results are interpreted graphically as a spatial–temporal distribution of subpopulations by classes of gene frequencies as well as in quantitative terms of Nei's G-statistics.     

新疆阜康荒漠红砂种群遗传结构及其与生态因子的耦合关系

应用RAPD标记技术对分布于新疆阜康荒漠的重要植物红砂(Reaumuria soongorica(Pall.)Maxim)种群遗传结构和遗传多样性进行了分析。15条随机引物对红砂7个亚种群的136个个体进行扩增,共检测71个位点,其中多态位点69个。研究结果表明:红砂种群的多态位点比率(PPB)为97.18％,显示出分布于过渡带的红砂种群内存在较高的遗传多样性。Shannon多样性指数(0.307 5)、Nei基因多样性指数(0.312 7)和基因分化系数(G_(ST)=0.312 0)揭示了红砂种群遗传变异多存在于亚种群内,而亚种群间的遗传分化则较小。红砂业种群间的基因流Nm=1.102 8,Nm>1但低于一般风媒传粉植物(Nm=5.24)的基因流水平,处于分化的临界状态。AMOVA分析说明红砂种群变异的61.58％存在于亚种群内,而亚种群间的变异占总变异的38.02％。另外,通过RAPD资料的聚类分析及相关性分析研究,发现红砂自然种群的遗传结构与绿洲荒漠过渡带的微生境生态因子(主要是土壤因子)相关,其中红砂亚种群遗传多样性水平与土壤中全磷和CI含量呈显著负相关,与CO_3~2含量呈显著正相关。而其它土壤生态因子则与红砂的遗传多样性指数的相关性均不显著(P>0.05)。表明红砂个体的分布可能与过渡带土壤的某些易溶性盐分相关。研究还发现,随着土壤中有机质、水分、全氮和全磷含量的减     

新疆阜康荒漠红砂种群遗传结构及其与生态因子的耦合关系

Genetic structure and differentiation of Reaumuria soongorica (Pall.) Maxim population from the desert of Fukang, Xinjiang, were assessed by means of random amplified polymorphic DNA (RAPD) markers. High genetic diversity and differentiation were revealed in the population of R. soongorica by 15 random primers. One hundred and thirty-six individuals from seven subpopulations were sampled in the study. Seventy-one loci have been detected, and among them 69 were polymorphic. The mean proportion of polymorphic loci (PPB) was 97.18%. The analyses of Shannon information index (0.307 5), Nei抯 gene diversity (0.312 7) and GST (0.312 0) indicated that there were more genetic variations within the subpopu-lations than those among the subpopulations. The results of AMOVA analysis showed that 61.58% of the genetic variations existed within subpopulations, and 38.02% among the subpopulations. The gene flow among the subpopulations of R. soongorica (Nm = 1.102 8) was much less than that of the common anemophytes (Nm = 5.24), so genetic differentiation among the subpopulations occurred to some extent. Additionally, through the use of clustering and the correlation analyses, we found that the genetic struc-ture of natural population of R. soongorica was related to some ecological factors (soil factors mainly) of the oasis-desert transition zone. The genetic diversity level of R. soongorica had negative correlation with the content of total soil P and Cl- significantly (P＜0.05). On the contrary, it had significant positive correlation with CO32- (P＜0.05), showing that the distribution of the individuals of R. soongorica in the sampled areas correlates with certain soluble salt. Furthermore, the genetic diversity of the natural population of R. soongorica increased with the decreasing of the content of soil organic matters, water, total N and total P in soil. The paper concluded that the microenvironment ecological factors played an important role in the adaptive evolution of R. soongorica population.     

Computational and Genetic Reduction of a Cell Cycle to Its Simplest,Primordial Components

What are the minimal requirements to sustain an asymmetric cell cycle? Here we use mathematical modelling and forward genetics to reduce an asymmetric cell cycle to its simplest, primordial components. In the Alphaproteobacterium Caulobacter crescentus, cell cycle progression is believed to be controlled by a cyclical genetic circuit comprising four essential master regulators. Unexpectedly, our in silico modelling predicted that one of these regulators, GcrA, is in fact dispensable. We confirmed this experimentally, finding that ΔgcrA cells are viable, but slow-growing and elongated, with the latter mostly due to an insufficiency of a key cell division protein. Furthermore, suppressor analysis showed that another cell cycle regulator, the methyltransferase CcrM, is similarly dispensable with simultaneous gcrA/ccrM disruption ameliorating the cytokinetic and growth defect of ΔgcrA cells. Within the Alphaproteobacteria, gcrA and ccrM are consistently present or absent together, rather than either gene being present alone, suggesting that gcrA/ccrM constitutes an independent, dispensable genetic module. Together our approaches unveil the essential elements of a primordial asymmetric cell cycle that should help illuminate more complex cell cycles.     

Genetic Analysis of Population Structure and Reproductive Mode of the Termite Reticulitermes chinensis Snyder

The subterranean termite Reticulitermes chinensis Snyder is an important pest of trees and buildings in China. Here, we characterized genetic structure and reproductive modes of R. chinensis from China for the first time. A total of 1,875 workers from 75 collection sites in Huanggang, Changsha and Chongqing cities were genotyped at eight microsatellite loci. Analysis of genetic clusters showed two subpopulations in Chongqing city. The Huanggang population showed a uniform genetic pattern and was separated from the other populations by the largest genetic distances (F _ST: 0.17–0.20). In contrast, smaller genetic distances (F _ST: 0.05–0.12) separated Changsha, Chongqing-1 and Chongqing-2 populations. Chongqing-1 was the only population showing a genetic bottleneck. Isolation by distance among colonies in the Huanggang population indicated limited alate dispersal or colony budding. Lack of isolation by distance among colonies within the populations of Changsha, Chongqing-1 and Chongqing-2, suggested long-range dispersal by alates and/or human-mediated transport. Overall, extended family colonies (73.91%) were predominant in all four populations, followed by simple (20.29%), and mixed family colonies (5.80%). Most simple families were headed by inbred related reproductive pairs in the Changsha population, while most simple families in the Chongqing-1 population were headed by outbred unrelated pairs. Simple families in the Huanggang population were a mixture of colonies headed by outbred or inbred reproductive pairs. The sample size of simple families in the Chongqing-2 population was too small to yield significant results. Extended families in all four populations were headed on the average by ≤10 neotenics. Mixed families likely originated from pleometrosis. Presence of heterozygote genotypes showed that all neotenic reproductives collected in addition from five field colonies in Wuhan city were sexually produced, suggesting that these colonies did not undergo parthenogenesis. This study contributes to better understanding of the variance of genetic structure and reproductive mode in the genus Reticulitermes.     

DNA Polymorphism in a Subdivided Population: The Expected Number of Segregating Sites in the Two-Subpopulation Model

Using the two subpopulation model, the expected numbers of segregating sites in a number of DNA sequences randomly sampled from a subdivided population were examined for several types of population subdivisions. It is shown that, in the case where the pattern of migration is symmetrical such as the finite island model, the expected number of segregating sites is independent of the migration rate when two or three DNA sequences are randomly sampled from the same subpopulation, but depends on the migration rate when more than three DNA sequences are sampled. It is also shown that the population subdivision can increase the amount of DNA polymorphism even in a subpopulation in some cases.     

Multilocus Electrophoretic Assessment of the Genetic Structure and Diversity of Yersinia ruckeri

Multilocus isoenzyme electrophoresis was used to screen 47 field isolates of Yersinia ruckeri for electrophoretic variation at 15 enzyme loci. Only four electrophoretic types were observed, thus indicating that the genetic structure of Y. ruckeri is clonal. Forty-two isolates were of one electrophoretic type, a reflection of the low amount of genetic diversity extant in this species. Although sorbitol fermentation has been considered to be indicative of a second biotype, no significant gene frequency differences were found between the group of 20 isolates that readily used sorbitol as the sole carbon source and the group of 27 that did not.     

Multilocus Patterns of Nucleotide Diversity, Population Structure and Linkage Disequilibrium in Boechera stricta, a Wild Relative of Arabidopsis

Information about polymorphism, population structure, and linkage disequilibrium (LD) is crucial for association studies of complex trait variation. However, most genomewide studies have focused on model systems, with very few analyses of undisturbed natural populations. Here, we sequenced 86 mapped nuclear loci for a sample of 46 genotypes of Boechera stricta and two individuals of B. holboellii, both wild relatives of Arabidopsis. Isolation by distance was significant across the species range of B. stricta, and three geographic groups were identified by structure analysis, principal coordinates analysis, and distance-based phylogeny analyses. The allele frequency spectrum indicated a genomewide deviation from an equilibrium neutral model, with silent nucleotide diversity averaging 0.004. LD decayed rapidly, declining to background levels in ~10 kb or less. For tightly linked SNPs separated by <1 kb, LD was dependent on the reference population. LD was lower in the specieswide sample than within populations, suggesting that low levels of LD found in inbreeding species such as B. stricta, Arabidopsis thaliana, and barley may result from broad geographic sampling that spans heterogeneous genetic groups. Finally, analyses also showed that inbreeding B. stricta and A. thaliana have ~45% higher recombination per kilobase than outcrossing A. lyrata.     

Genetic Demographic Structure of the Belgorod Population: Age,Ethnicity, Education,and Occupation

Data from marriage records of the city of Belgorod for 1960, 1985, and 1995 have been used to determine some parameters of population structure in this city. The coefficients of correlation with respect to age of marriage between spouses in the couples contracting marriages in these years were 0.74, 0.62, and 0.80, respectively. Women of reproductively unfavorable age (under 20 or over 30 years) accounted for 5.5, 0.83, and 19% of all women contracting marriages in these years, respectively. The proportions of interethnic marriages in these years were 16.9, 14.9, and 15.6%, respectively. The percentage of Slavs decreased from 99 to 97% during the 35 years studied, whereas the proportion of Russians insignificantly increased (from 90.4 to 91.4%). The proportion of Caucasian ethnic groups increased by six time (from 0.3 to 1.8%), and that of other non-Slavic ethnic groups increased by almost two times (from 0.7 to 1.2%). The marriage convergence (K) with respect to ethnicity (0.095, 0.106, and 0.090 in 1960, 1985, and 1995, respectively) was lower than that with respect to education (0.296 and 0.350 in 1985 and 1995, respectively) or occupation (0.212 and 0.231 in 1985 and 1995, respectively). The maximum coefficients of ethnically, educationally, and occupationally assortative marriage have been found, respectively, in ethnic minority groups (A′ = 20%); in persons with higher and primary education (A′ = 37.5 and 49.9%, respectively); and in the military officers/soldiers, engineers, healthcare professionals, and researchers (the respective A′ values are 65.6, 32.2, 31.5, and 39.8%).__________Translated from Genetika, Vol. 41, No. 6, 2005, pp. 823–829.Original Russian Text Copyright © 2005 by Atramentova, Filiptsova.     

Relationship between the Social Structure and Potential Reproductive Success in Muroid Rodents (Rodentia,Myomorpha)

Biology Bulletin - In many systematic groups of mammalian species, the evolution of sociality leads to the formation of large social groups (group-size evolution). In rodents, however, the most...     

Population Genetic Structure and Reproductive Strategy of the Introduced Grass Centotheca lappacea in Tropical Land-Use Systems in Sumatra

Intensive transformation of lowland rainforest into oil palm and rubber monocultures is the most common land-use practice in Sumatra (Indonesia), accompanied by invasion of weeds. In the Jambi province, Centotheca lappacea is one of the most abundant alien grass species in plantations and in jungle rubber (an extensively used agroforest), but largely missing in natural rainforests. Here, we investigated putative genetic differentiation and signatures for adaptation in the introduced area. We studied reproductive mode and ploidy level as putative factors for invasiveness of the species. We sampled 19 populations in oil palm and rubber monocultures and in jungle rubber in two regions (Bukit Duabelas and Harapan). Amplified fragment length polymorphisms (AFLP) revealed a high diversity of individual genotypes and only a weak differentiation among populations (F_ST = 0.173) and between the two regions (F_ST = 0.065). There was no significant genetic differentiation between the three land-use systems. The metapopulation of C. lappacea consists of five genetic partitions with high levels of admixture; all partitions appeared in both regions, but with different proportions. Within the Bukit Duabelas region we observed significant isolation-by-distance. Nine AFLP loci (5.3% of all loci) were under natural diversifying selection. All studied populations of C. lappacea were diploid, outcrossing and self-incompatible, without any hints of apomixis. The estimated residence time of c. 100 years coincides with the onset of rubber and oil palm planting in Sumatra. In the colonization process, the species is already in a phase of establishment, which may be enhanced by efficient selection acting on a highly diverse gene pool. In the land-use systems, seed dispersal might be enhanced by adhesive spikelets. At present, the abundance of established populations in intensively managed land-use systems might provide opportunities for rapid dispersal of C. lappacea across rural landscapes in Sumatra, while the invasion potential in rainforest ecosystems appears to be moderate as long as they remain undisturbed.     

催乳素受体基因与羊驼繁殖性能关系的初探

通过氯仿/异戊醇法制备羊驼血液基因组DNA,采用PCR方法首次扩增出羊驼催乳素受体基因(prolactin receptor gene,PRLR)exon8-exon9序列(GenBank登录号为DQ198164),该片段长度为622bp。通过NCBI blast(http://www.ncbi.nlm.nih.gov/BLAST/)比较,结果表明:该序列包括exon8的82bp、intron8全序列472bp和exon9的68bp。同源性比较发现,羊驼PRLR基因exon8和exon9核苷酸序列与其它哺乳动物的相应区域的同源性特高,均≥92%;同时还发现羊驼exon8引物后第19个碱基为G,而其它哺乳动物(猪除外)均为A,猪则是在羊驼exon8引物后的第34个碱基处由G变为A,通过推导氨基酸序列分析发现,这种单碱基的突变使得羊驼与其它哺乳动物相比,该处的氨基酸由亮氨酸取代了异亮氨酸;在羊驼exon9引物前第22个碱基处也发生了A-G碱基替换现象,但这个碱基的突变发生在密码子的第3个碱基上,编码的氨基酸均为脯氨酸。在这些动物中只有羊驼为单胎动物,羊驼exon8核苷酸序列中A-G的碱基替换并引起编码氨基酸序列发生改变是否与羊驼繁殖性能有关还有待进一步研究。     

生长素结构与其活性关系的揭示

生长素结构与活性之间关系是长期以来悬而未决的一个难题。最近的研究证明,生长素分子像“胶水”一样将受体TIR1与效应蛋白Aux／IAA“粘合”后,形成SCF^TIR1-生长素-Aux／IAA复合物,进而激活泛素连接酶3（SCF^TIR1）,起着促使Aux／IAA泛素化后的降解,转录因子ARFs得到活化后,启动一系列生长素响应基因的转录,于是植物表现出相应的生长发育状态。     

Genetic and Demographic Structure of the Yakut Population: Reproduction Indices

Genetic and demographic information for the Yakut population living in the Republic of Sakha (Yakutia) is presented. The mean number of children per woman constituted 4.605. Crow's index (I _tot) and its components (I _m and I _f) were 0.483, 0.104, and 0.343, respectively.     

Genetic Diversity and Population Structure of Dioscorea tokoro Makino, a Dioecious Climber

Abstract Dioscorea tokoro Makino is a herbaceous climber species widespread in East Asia. Genetic structure of a natural population of D. tokoro was examined employing starch gel electrophoresis of allozymes. Genotypes of seven loci were studied for 1,128 individuals. Twenty-six populations located mainly in the Kinki district of Japan were subgrouped into four large clusters by the geographical distribution of alleles. The D. tokoro population was revealed to contain greater total genetic diversity ( H_T =0.282) and higher intrapopulational genetic diversity ( H_S =0.258) than other outcrossing species for which data are available. On the other hand, interpopulational differentiation ( G_ST =0.096) was smaller than in other outcrossers. For the heterozygosity deficiency observed ( F_IT =0.125), population subdivision ( F_ST =0.096) and inbreeding within the population ( F_IS =0.067) were revealed to contribute to the same extent. From these F -statistics, the migration rate among subpopulations and the rate of between-relative matings were estimated. Overall results on the genetic structure of the D. tokoro population indicated a high gene flow among its subpopulations, and this may be the consequence of its life form as a climber and its habitat in a disturbed environment. During the study, the geographical cline of Pgi allele frequencies was observed. This finding was supposed to be the result of the selection imposed on Pgi by the temperature differences between localities.     

On a Reproductive Stage-Structured Model for the Population Dynamics of the Malaria Vector

A reproductive stage-structured deterministic differential equation model for the population dynamics of the human malaria vector is derived and analysed. The model captures the gonotrophic and behavioural life characteristics of the female Anopheles sp. mosquito and takes into consideration the fact that for the purposes of reproduction, the female Anopheles sp. mosquito must visit and bite humans (or animals) to harvest necessary proteins from blood that it needs for the development of its eggs. Focusing on mosquitoes that feed exclusively on humans, our results indicate the existence of a threshold parameter, the vectorial reproduction number, whose size increases with increasing number of gonotrophic cycles, and is also affected by the female mosquito’s birth rate, its attraction and visitation rate to human residences, and its contact rate with humans. A stability analysis of the model indicates that the mosquito can establish itself in the environment if and only if the value of the vectorial reproduction number exceeds unity and that mosquito eradication is possible if the vectorial reproduction number is less than unity, since, then, the trivial steady state which always exist is unique and is globally and asymptotically stable. When a persistent vector population steady state exists, it is locally and asymptotically stable for a range of reproduction numbers, but can also be driven to instability via a Hopf bifurcation as the reproduction number increases further away from unity. The model derivation identifies and characterizes control parameters relating to activities such as human-mosquito contact and the mosquito’s survival chances between blood meals and egg laying. Our results show that the total mosquito population size increases with increasing number of gonotrophic cycles. Therefore understanding the fundamental aspects of the mosquito’s behaviour provides a pathway for the study of human-mosquito contact and mosquito population control. Control of the mosquito population densities would ultimately lead to malaria control.     

A Computer Simulation Study of Vntr Population Genetics: Constrained Recombination Rules Out the Infinite Alleles Model

Extensive allelic diversity in variable numbers of tandem repeats (VNTRs) has been discovered in the human genome. For population genetic studies of VNTRs, such as forensic applications, it is important to know whether a neutral mutation-drift balance of VNTR polymorphism can be represented by the infinite alleles model. The assumption of the infinite alleles model that each new mutant is unique is very likely to be violated by unequal sister chromatid exchange (USCE), the primary process believed to generate VNTR mutants. We show that increasing both mutation rates and misalignment constraint for intrachromosomal recombination in a computer simulation model reduces simulated VNTR diversity below the expectations of the infinite alleles model. Maximal constraint, represented as slippage of single repeats, reduces simulated VNTR diversity to levels expected from the stepwise mutation model. Although misalignment rule is the more important variable, mutation rate also has an effect. At moderate rates of USCE, simulated VNTR diversity fluctuates around infinite alleles expectation. However, if rates of USCE are high, as for hypervariable VNTRs, simulated VNTR diversity is consistently lower than predicted by the infinite alleles model. This has been observed for many VNTRs and accounted for by technical problems in distinguishing alleles of neighboring size classes. We use sampling theory to confirm the intrinsically poor fit to the infinite alleles model of both simulated VNTR diversity and observed VNTR polymorphisms sampled from two Papua New Guinean populations.     

Demography and Genetic Structure of a Recovering Grizzly Bear Population

ABSTRACT Grizzly bears (brown bears; Ursus arctos) are imperiled in the southern extent of their range worldwide. The threatened population in northwestern Montana, USA, has been managed for recovery since 1975; yet, no rigorous data were available to monitor program success. We used data from a large noninvasive genetic sampling effort conducted in 2004 and 33 years of physical captures to assess abundance, distribution, and genetic health of this population. We combined data from our 3 sampling methods (hair trap, bear rub, and physical capture) to construct individual bear encounter histories for use in Huggins—Pledger closed mark—recapture models. Our population estimate, Ň = 765 (95% CI = 715–831) was more than double the existing estimate derived from sightings of females with young. Based on our results, the estimated known, human-caused mortality rate in 2004 was 4.6% (95% CI = 4.2–4.9%), slightly above the 4% considered sustainable; however, the high proportion of female mortalities raises concern. We used location data from telemetry, confirmed sightings, and genetic sampling to estimate occupied habitat. We found that grizzly bears occupied 33,480 km² in the Northern Continental Divide Ecosystem (NCDE) during 1994–2007, including 10,340 km² beyond the Recovery Zone. We used factorial correspondence analysis to identify potential barriers to gene flow within this population. Our results suggested that genetic interchange recently increased in areas with low gene flow in the past; however, we also detected evidence of incipient fragmentation across the major transportation corridor in this ecosystem. Our results suggest that the NCDE population is faring better than previously thought, and they highlight the need for a more rigorous monitoring program.