Development and characterization of polymorphic microsatellite markers in Cyclobalanopsis glauca (Fagaceae)

? Premise of the study: We isolated and characterized polymorphic microsatellite loci in Cyclobalanopsis glauca (Fagaceae), an evergreen broadleaved monoecious tree, to provide tools for analyzing parentage and mating system. ? Methods and Results: Thirteen polymorphic microsatellite markers were developed and tested in three C. glauca populations. The number of alleles per locus varied from two to 22. The observed and expected heterozygosities within populations were 0.000-0.967 and 0.033-0.949, respectively. ? Conclusions: These polymorphic primers showed high levels of polymorphism within tested populations, and can be used in parentage analysis and mating system estimation of C. glauca.     

桂林岩溶石山青冈群落主要乔木树种的种间关联

分析桂林岩溶石山青冈群落主要种群的种间关联性,揭示其种群间的共生关系,可为桂林岩溶石山植被的修复与重建、经营管理和生物多样性保护提供理论依据.基于样方调查,采用χ²检验、联结系数(AC)、共同出现百分率(PC)、Ochiai指数(OI)、Dice指数(DI)和主成分分析(PCA)等方法,对桂林岩溶石山青冈群落中重要值前22位的乔木物种进行种间关联测定和生态种组划分.结果表明: 研究区22个主要乔木物种总体呈显著正联结,表明该地区青冈群落处于较稳定的顶极阶段;χ²检验结果显示,231个种对中有108个种对呈正联结,115个种对呈负联结,8个种对无联结,正负联结比为93.9%,绝大多数种对呈不显著联结,种对间的独立性较强,主要原因可能在于桂林岩溶石山较高的生境异质性导致物种间的生态位产生分化;AC、PC、OI和DI与χ²检验结果基本一致,种间关联性分析应以χ²检验为基础,辅以AC、PC、OI和DI等指数进行综合研究;根据PCA排序和种间关联关系,将22个主要乔木种群划分为3个生态种组,组内物种对生境具有趋同适应性,组间物种具有不同的生态要求.     

中国东部亚热带青冈种群叶片的生态解剖

运用生态解剖学的方法对我国亚热带东部分布的１０个青冈种群叶片的解剖特征进行了比较分析,结果如下：①青冈叶片结构在种群间存在着广泛的差异,这种差异是青冈适应不同环境条件的结构基础。青冈叶片各部分结构特征在种群间的变化不晃同步的,变异系数（ＣＶ）在６．０％～２０．５％之间;变异幅度最大的是栅栏组织和上角质膜厚度,最小的是下表皮厚度。②相关分析表明,温度和降雨是影响青冈叶片地理变异的主导因子,其中温度、     

Relationships Between Geographical Distribution of Cyclobalanopsis glauca and Climate in China

Cyclobalanopsis glauca (Thunb.) Oerst., which belongs to China-Japan subtype of East Asia district, is a evergreen broadleaved tree of Fagaceae. It is distributed widely in the subtropical region of China and also in Japan, Korea, India, Burma, etc. According to the data on geographical distribution of this species collected extensively, the indexes of vegetation-climate interaction which used widely in the world were calculated. These indexes include Kira' s water-temperature indexes, Penman's formula, Thornthwaite's indexes and climatic classification, Holdridge's life zone classification system, annual average temperature, mean temperature in January, mean temperature in July, maximum temperature, minimum temperature, ≥10 ℃ accumulated temperature and precipitation. The relationships between geographical distribution of Cyclobalanopsis glauca and climate in China has been analysed and the Kira's water-temperature indexes on the distributional upper limit, lower limit and north limit have been discussed. The relation of species versus climate in historial period and the relation of species versus climate in historial period have also been discussed according to palynological and written records. The potential change of the tree species distributional area under elevated CO2 concentration has been forecast based on Holdridge' s indexes of life zone classification system and GCM models' conclusions.     

Dissecting linkage disequilibrium in African-American genomes: roles of markers and individuals

Substantial increases of linkage disequilibrium (LD) both in magnitude and in range have been observed in recently admixed populations such as African-American (AfA). On the other hand, it has also been shown that LD in AfAs was very similar to that of African. In this study, we attempted to resolve these contradicting observations by conducting a systematic examination of the LD structure in AfAs by genotyping a sample of AfA individuals at 24,341 single nucleotide polymorphisms (SNPs) spanning almost the entire chromosome 21, with an average density of 1.5 kb/SNP. The overall LD in AfAs is similar to that in African populations and much less than that in European populations. Even when the ancestry-informative markers (AIMs) were used, extended LD in AfA was found to be limited to certain magnitude range (0.2 < or = r(2) < or = 0.8) and certain distance range, that is, between-marker distance more than 200 kb. Furthermore, the inclusion of AfA individuals with predominant African ancestry was found to reduce the overall magnitude of LD. Elevation of LD in the AfA population, compared with its parental populations, can only be observed at the markers with large allele frequency differences between 2 parental populations at limited scenario. AfA individuals of wholly African ancestry contribute little to the extended LD in the AfA population, and further genotyping or association analysis conducted using only admixed individuals may lead to higher statistical power and possibly reduced cost.     

The linkage disequilibrium between chloroplast DNA and mitochondrial DNA haplotypes in Beta vulgaris ssp. maritima (L.): the usefulness of both genomes for population genetic studies

The structure and evolution of the plant mitochondrial genome may allow recurrent appearance of the same mitochondrial variants in different populations. Whether the same mitochondrial variant is distributed by migration or appears recurrently by mutation (creating homoplasy) in different populations is an important question with regard to the use of these markers for population genetic analyses. The genetic association observed between chloroplasts and mitochondria (i.e. two maternally inherited cytoplasmic genomes) may indicate whether or not homoplasy occurs in the mitochondrial genome. Four-hundred and fourteen individuals sampled in wild populations of beets from France and Spain were screened for their mitochondrial and chloroplast polymorphisms. Mitochondrial DNA (mtDNA) polymorphism was investigated with restriction fragment length polymorphism (RFLP) and chloroplast DNA (cpDNA) polymorphism was investigated with polymerase chain reaction PCR-RFLP, using universal primers for the amplification. Twenty and 13 variants for mtDNA and cpDNA were observed, respectively. Most exhibited a widespread geographical distribution. As a very strong linkage disequilibrium was estimated between mtDNA and cpDNA haplotypes, a high rate of recurrent mutation was excluded for the mitochondrial genome of beets. Identical mitochondrial variants found in populations of different regions probably occurred as a result of migration. We concluded from this study that mtDNA is a tool as valuable as cpDNA when a maternal marker is needed for population genetics analyses in beet on a large regional scale.     

Recombination and linkage disequilibrium among mitochondrial genes in structured populations of the gynodioecious plant Silene vulgaris

The impact of intergenic recombination on the population genetics of plant mitochondrial genomes is unknown. In an effort to study this in the gynodioecious plant Silene vulgaris three-locus PCR/RFLP genotypes (based on the mitochondrial genes atpA, cox1, and cob) were determined for 239 individuals collected from 20 North American populations. Seventeen three-locus PCR/RFLP genotypes were found. Recombination was indicated by observation of each of the four two-locus genotypes possible when the two most common alleles are considered for each of two loci. Based on these common alleles the absolute values of standardized linkage disequilibrium |D'| between pairs of loci range from 0.17 to 0.78. This indicates modest disequilibrium, rather than the maximum value expected in the absence of recombination |D'=1|, or the linkage equilibrium expected if recombination is pervasive (D'=0). Values of D' did not depend on which pair of loci contributed alleles to the analysis. The direction of D' obtained for the common atpA and cox1 alleles was comparable in sign and magnitude to that obtained by examining similar information obtained in a prior study of European samples. All three loci indicated a high degree of population structure (average FST=0.63), which would limit the within-population genetic diversity required for intergenic recombination to create novel genotypes, if most mating is local. Thus, population structure acts as a constraint on the approach to linkage equilibrium.     

Variation and correlation in functional traits of main woody plants in the Cyclobalanopsis glauca community in the karst hills of Guilin,southwest China

研究植物功能性状变异以及不同性状之间的关系, 有助于了解植物对环境的适应策略, 对揭示群落构建和生物多样性维持机制具有重要意义。本研究以桂林岩溶石山青冈群落18种主要木本植物为研究对象, 采用单因素方差分析、混合线性模型以及Pearson相关分析和主成分分析等方法探讨了不同生长型和生活型物种的9个枝、叶功能性状(叶绿素含量、叶片厚度、叶面积、叶干质量、比叶面积、叶干物质含量、叶组织密度、小枝干物质含量和小枝组织密度)的变异与关联。结果表明: (1) 9个功能性状的变异程度不同, 叶面积和叶干质量的种内和种间变异系数最大, 小枝干物质含量和小枝组织密度的种内和种间变异系数最小。(2)在生长型水平上, 乔木、灌木和木质藤本的绝大部分功能性状差异显著。(3)对于不同生活型植物, 除叶面积和比叶面积为落叶植物显著大于常绿植物外, 其余7个功能性状皆为常绿植物显著大于落叶植物。(4)不同生长型和生活型植物功能性状的种内和种间变异大小存在差异, 除部分植物功能性状在一些功能型上表现为种内变异高于种间变异, 其余功能性状的种间变异皆高于种内变异。(5)各功能性状之间关系在个体水平和物种水平大致相同, 但是个体水平上的显著相关比例高于物种水平。研究发现, 植物功能性状的种间变异基本高于种内变异, 但种内变异不容忽略。此外, 不同生长型和生活型物种采取不同的生态策略来适应喀斯特生境。今后的研究应基于个体水平采样并结合环境因子从生长型和生活型等不同功能型角度上深入探究植物功能性状在种内和种间等不同尺度上的变异与关联。     

Measuring the extent of linkage disequilibrium in commercial pig populations

To evaluate the extent of linkage disequilibrium in domestic pigs, we genotyped 33 and 44 unrelated individuals from two commercial populations for 29 and five microsatellite markers located on chromosomes 15 and 2 respectively. A high proportion of marker pairs up to 40 cM apart exhibited significant linkage disequilibrium in both populations. Pair-wise r(2) values averaged between 0.15 and 0.50 (depending on chromosome and population) for markers <1 cM apart and declined to values of 0.05 for more distant syntenic markers. Our results suggest that both populations underwent a bottleneck approximately 20 generations ago, which reduced the effective population size from thousands to <200 animals.     

高大乔木原位与离体叶片气体交换特征的比较——以三种环境下的青冈栎(Cyclobalanopsis glauca)为例

乔木由于个体高大,采用便携式仪器(如Li-6400)进行气体交换测定时的采样存在很多困难.研究了岩溶区、非岩溶区和盆栽等3种生境条件下的青冈栎植物叶片离体后的气体交换参数衰变特性并与活体状态进行比较,以确定叶片离体后仍能代表原位状态的最佳测定时间.叶片离开母体后,气孔短时内略微变大,然后逐渐关闭.不同条件下气孔的这种变化差异较大;蒸腾作用与气孔导度极显著线性相关,蒸腾作用受到气孔关闭的影响明显.离体叶片的蒸腾作用的大小与叶片的温度高低相一致.光合效率与气孔导度也呈显著相关,但相关程度较前者弱.不同温度条件下离体叶片的气体交换特征是不一样的,岩溶区高温加速了叶片的蒸腾速率,减少叶片组织自由含水量,导致水分胁迫的提前到来.温度越低离体叶片光合作用的衰减过程越慢.离体叶片的气体交换参数的在一定时间范围内的可靠性取决于叶片温度.在温度较低的时候(如20℃),离体叶片的可靠性20min以上,温度比较高(非岩溶区,温度约为32℃))的情况下,只有10min左右,而温度很高(岩溶区,叶温≥32℃)的情况下,这种可靠时间只有3～6min.     

Chromosome-wide linkage disequilibrium caused by an inversion polymorphism in the white-throated sparrow (Zonotrichia albicollis)

Chromosomal inversions have been of long-standing interest to geneticists because they are capable of suppressing recombination and facilitating the formation of adaptive gene complexes. An exceptional inversion polymorphism (ZAL2^m) in the white-throated sparrow (Zonotrichia albicollis) is linked to variation in plumage, social behavior and mate choice, and is maintained in the population by negative assortative mating. The ZAL2^m polymorphism is a complex inversion spanning >100 Mb and has been proposed to be a strong suppressor of recombination, as well as a potential model for studying neo-sex chromosome evolution. To quantify and evaluate these features of the ZAL2^m polymorphism, we generated sequence from 8 ZAL2^m and 16 ZAL2 chromosomes at 58 loci inside and 4 loci outside the inversion. Inside the inversion we found that recombination was completely suppressed between ZAL2 and ZAL2^m, resulting in uniformly high levels of genetic differentiation (F_ST=0.94), the formation of two distinct haplotype groups representing the alternate chromosome arrangements and extensive linkage disequilibrium spanning ∼104 Mb within the inversion, whereas gene flow was not suppressed outside the inversion. Finally, although ZAL2^m homozygotes are exceedingly rare in the population, occurring at a frequency of <1%, we detected evidence of historical recombination between ZAL2^m chromosomes inside the inversion, refuting its potential status as a non-recombining autosome.     

弄拉典型峰丛岩溶区青冈栎叶片形态特征及对环境的适应

选取广西弄拉典型峰丛洼地生态系统中不同地貌类型的青冈栎 (Cyclobalanopsisglauca)叶片进行形态解剖特征比较分析 ,结果表明 :( 1 )峰丛洼地生态系统中不同地貌青冈栎叶片形态解剖特征差异显著。山顶青冈栎叶片部分表皮结构 (角质膜、表皮毛、表皮细胞、气孔 )趋向旱化。山顶青冈栎下表皮毛比山腰青冈栎的浓密且长。两者叶片的厚度和宽度、上表皮细胞个数、气孔指数、下表皮厚度、栅栏组织厚度、海绵组织厚度存在着显著性差异 ;位于山顶的青冈栎受到水分的胁迫 ,在形态解剖上呈现出中生偏旱的结构。 ( 2 )青冈栎的各种形态解剖指标说明在岩溶区青冈栎的抗旱性主要是通过抵御干旱来适应水分的胁迫 ,并主要取决于减少蒸腾失水和维持水分吸收能力两个方面     

SHEsis, a powerful software platform for analyses of linkage disequilibrium, haplotype construction, and genetic association at polymorphism loci

In multiloci-based genetic association studies of complex diseases, a powerful and high efficient tool for analyses of linkage disequilibrium (LD) between markers, haplotype distributions and many chi-square/p values with a large number of samples has been sought for long. In order to achieve the goal of obtaining meaningful results directly from raw data,we developed a robust and user-friendly software platform with a series of tools for analysis in association study with high efficiency. The platform has been well evaluated by several sets of real data.     

Associative overdominance: Evaluating the effects of inbreeding and linkage disequilibrium

Expressions are obtained for the expected phenotypic values of homozygous and heterozygous genotypes for a neutral marker locus linked to a locus segregating for a recessive deleterious gene. The phenotypic values are functions of the allele frequencies at the marker locus, the inbreeding coefficient and the degree of association of the deleterious gene with the marker alleles. The analysis is extended to more than two alleles at the marker locus. Either linkage disequilibrium or inbreeding alone can produce an apparent superiority of heterozygotes for the marker locus (unless specified otherwise, the terms ‘homozygote’ and ‘heterozygote’ will refer to the marker locus). The effect of linkage disequilibrium on the difference between the heterozygote and homozygote values can be positive (associative overdominance) or negative (associative underdominance), depending on the frequencies of the marker alleles and the degree of their association with the deleterious gene. Inbreeding has always a positive effect. In general, the expected value of a homozygote is a positive function of its allele frequency. When the various homozygous genotypes are combined into one class and the various heterozygous genotypes into another, the phenotypic difference of the two classes is a function of the evenness of the allelic frequency distribution. Inbreeding is a more likely explanation of associative overdominance if the frequency of the deleterious gene is low, but its effect on the character high. Conversely, linkage disequilibrium is more likely if the frequency is high and the effect low. The degrees of association between marker alleles and the deleterious gene can, in principle, be estimated from the observed phenotypic scores and used to calculate expected multi-locus genotype scores. This could provide the basis for statistical tests of the associative overdominance hypothesis as an explanation of observed correlations between multi-locus heterozygosity and phenotypic traits.     

浙江北部保护区青冈常绿阔叶林物种多样性

在野外调查的基础上 ,对浙江北部地区保护区 (风景区、森林公园 )的青冈常绿阔叶林物种多样性进行了研究 ,并对不同地点的多样性进行比较分析。结果表明 :群落中不同层次的植物物种多样性大小不一样 ,排列顺序为 :下木层 >林木层 >草本层 ,且不同地点样地的多样性在不同层次上也是不同。样地的坡度与林木层的均匀度指数 J、坡向与林木层多样性指数 H有明显相关 ,建议对北坡及坡度较大的区域给予更大的关注。     

Population differences in levels of linkage disequilibrium in the wild

Information about the levels of linkage disequilibrium (LD) in wild animal populations is still limited, and this is true particularly with respect to possible interpopulation variation in the levels of LD. We compared the levels and extent of LD at the genome‐wide scale in three Siberian jay (Perisoreus infaustus) populations, two of which (Kuusamo and Ylläs) represented outbred populations within the main distribution area of the species, whereas the third (Suupohja) was a semi‐isolated, partially inbred population at the margin of the species’ distribution area. Although extensive long‐range LD (>20 cM) was observed in all three populations, LD generally decayed to background levels at a distance of 1–5 cM or c. 200–600 kb. The degree and extent of LD differed markedly between populations but aligned closely with both observed levels of within‐population genetic variation and expectations based on population history. The levels of LD were highest in the most inbred population with strong population substructure (Suupohja), compared with the two outbred populations. Furthermore, the decay of LD with increasing distance was slower in Suupohja, compared with the other two populations. By demonstrating that levels of LD can vary greatly over relatively short geographical distances within a species, these results suggest that prospects for association mapping differ from population to population. In this example, the prospects are best in the Suupohja population, given that minimized marker genotyping and a minimum marker spacing of 1–5 cM (c. 200–600 kb) would be sufficient for a whole genome scan for detecting QTL.     

桂林岩溶石山青冈群落主要木本植物功能性状变异与关联

研究植物功能性状变异以及不同性状之间的关系, 有助于了解植物对环境的适应策略, 对揭示群落构建和生物多样性维持机制具有重要意义。本研究以桂林岩溶石山青冈群落18种主要木本植物为研究对象, 采用单因素方差分析、混合线性模型以及Pearson相关分析和主成分分析等方法探讨了不同生长型和生活型物种的9个枝、叶功能性状(叶绿素含量、叶片厚度、叶面积、叶干质量、比叶面积、叶干物质含量、叶组织密度、小枝干物质含量和小枝组织密度)的变异与关联。结果表明: (1) 9个功能性状的变异程度不同, 叶面积和叶干质量的种内和种间变异系数最大, 小枝干物质含量和小枝组织密度的种内和种间变异系数最小。(2)在生长型水平上, 乔木、灌木和木质藤本的绝大部分功能性状差异显著。(3)对于不同生活型植物, 除叶面积和比叶面积为落叶植物显著大于常绿植物外, 其余7个功能性状皆为常绿植物显著大于落叶植物。(4)不同生长型和生活型植物功能性状的种内和种间变异大小存在差异, 除部分植物功能性状在一些功能型上表现为种内变异高于种间变异, 其余功能性状的种间变异皆高于种内变异。(5)各功能性状之间关系在个体水平和物种水平大致相同, 但是个体水平上的显著相关比例高于物种水平。研究发现, 植物功能性状的种间变异基本高于种内变异, 但种内变异不容忽略。此外, 不同生长型和生活型物种采取不同的生态策略来适应喀斯特生境。今后的研究应基于个体水平采样并结合环境因子从生长型和生活型等不同功能型角度上深入探究植物功能性状在种内和种间等不同尺度上的变异与关联。     

Physical linkage and mate preference generate linkage disequilibrium for behavioral isolation in two parapatric crickets

Behavioral isolation is a potent barrier to gene flow and a source of striking diversity in the animal kingdom. However, it remains unclear if the linkage disequilibrium (LD) between sex‐specific traits required for behavioral isolation results mostly from physical linkage between signal and preference loci or from directional mate preferences. Here, we test this in the field crickets Gryllus rubens and G. texensis. These closely related species diverged with gene flow and have strongly differentiated songs and preference functions for the mate calling song rhythm. We map quantitative trait loci for signal and preference traits (pQTL) as well as for gene expression associated with these traits (eQTL). We find strong, positive genetic covariance between song traits and between song and preference. Our results show that this is in part explained by incomplete physical linkage: although both linked pQTL and eQTL couple male and female traits, major effect loci for different traits were never on the same chromosome. We suggest that the finely tuned, highly divergent preference functions are likely an additional source of LD between male and female traits in this system. Furthermore, pleiotropy of gene expression presents an underappreciated mechanism to link sexually dimorphic phenotypes.     

桂西南石漠化山区灌草丛对青冈和蒜头果直播造林的影响

为探讨石漠化山区立地类型对青冈(Cyclobalanopsis glauca)和蒜头果(Malania oleifera)直播造林的影响及其机理,本研究采取小区播种试验方法,并监测这2个树种在石漠化山区3种立地类型(灌丛、草丛和裸地)中种子萌发、幼苗存活与生长量情况,以及各立地类型中枯落物储量和小气候环境因子特征。结果显示,灌丛和草丛中枯落物储量分别为(182.55±47.94)g/m2和(99.88±35.76)g/m2;灌丛和草丛距离地面150cm处的光照强度和气温显著低于裸地、空气湿度显著高于裸地,且距离地面越近效果越明显;灌丛和草丛地下5cm处的土壤温度显著低于裸地;青冈种子萌发率、幼苗保存率和幼苗生长量在3种立地类型间差异不显著(P0.05);蒜头果种子萌发率在裸地和灌丛间差异显著(P=0.014),一年生幼苗株高生长量在裸地和灌丛之间、草丛和灌丛之间差异显著(P=0.011和P=0.041),幼苗基径生长量在裸地和灌丛之间差异显著(P=0.043),在草丛和灌丛之间差异极显著(P=0.003)。本实验结果表明,在桂西南石漠化山区灌、草丛的保育作用下,蒜头果种子发芽率较高,幼苗生长较快,可选择种子直播方式造林;而青冈因一年生幼苗越冬后死亡率很高,需要改进幼苗抚育措施或改变造林方式,才能取得较理想的效果。     

Evidence for a large-scale population structure among accessions of Arabidopsis thaliana: possible causes and consequences for the distribution of linkage disequilibrium

The existence of a large-scale population structure was investigated in Arabidopsis thaliana by studying patterns of polymorphism in a set of 71 European accessions. We used sequence polymorphism surveyed in 10 fragments of approximately 600 nucleotides and a set of nine microsatellite markers. Population structure was investigated using a model-based inference framework. Among the accessions studied, the presence of four groups was inferred using genetic data, without using prior information on the geographical origin of the accessions. Significant genetic isolation by geographical distance was detected at the group level, together with a geographical gradient in allelic richness across groups. These results are discussed with respect to the previously proposed scenario of postglacial colonization of Europe from putative glacial refugia. Finally, the contribution of the inferred structure to linkage disequilibrium among 171 pairs of essentially unlinked markers was also investigated. Linkage disequilibrium analysis revealed that significant associations detected in the whole sample were mainly due to genetic differentiation among the inferred groups. We discuss the implication of this finding for future association studies in A. thaliana.