PREDICTING NUCLEAR GENE COALESCENCE FROM MITOCHONDRIAL DATA: THE THREE-TIMES RULE

Abstract.— Coalescence theory predicts when genetic drift at nuclear loci will result in fixation of sequence differences to produce monophyletic gene trees. However, the theory is difficult to apply to particular taxa because it hinges on genetically effective population size, which is generally unknown. Neutral theory also predicts that evolution of monophyly will be four times slower in nuclear than in mitochondrial genes primarily because genetic drift is slower at nuclear loci. Variation in mitochondrial DNA (mtDNA) within and between species has been studied extensively, but can these mtDNA data be used to predict coalescence in nuclear loci? Comparison of neutral theories of coalescence of mitochondrial and nuclear loci suggests a simple rule of thumb. The “three‐times rule” states that, on average, most nuclear loci will be monophyletic when the branch length leading to the mtDNA sequences of a species is three times longer than the average mtDNA sequence diversity observed within that species. A test using mitochondrial and nuclear intron data from seven species of whales and dolphins suggests general agreement with predictions of the three‐times rule. We define the coalescence ratio as the mitochondrial branch length for a species divided by intraspecific mtDNA diversity. We show that species with high coalescence ratios show nuclear monophyly, whereas species with low ratios have polyphyletic nuclear gene trees. As expected, species with intermediate coalescence ratios show a variety of patterns. Especially at very high or low coalescence ratios, the three‐times rule predicts nuclear gene patterns that can help detect the action of selection. The three‐times rule may be useful as an empirical benchmark for evaluating evolutionary processes occurring at multiple loci.     

Parallel changes in genetic diversity and species diversity following a natural disturbance

We examined the spatial and temporal variation of species diversity and genetic diversity in a metacommunity comprising 16 species of freshwater gastropods. We monitored species abundance at five localities of the Ain river floodplain in southeastern France, over a period of four years. Using 190 AFLP loci, we monitored the genetic diversity of Radix balthica , one of the most abundant gastropod species of the metacommunity, twice during that period. An exceptionally intense drought occurred during the last two years and differentially affected the study sites. This allowed us to test the effect of natural disturbances on changes in both genetic and species diversity. Overall, local (alpha) diversity declined as reflected by lower values of gene diversity H _S and evenness. In parallel, the among-sites (beta) diversity increased at both the genetic ( F _ST) and species ( F _STC) levels. These results suggest that disturbances can lead to similar changes in genetic and community structure through the combined effects of selective and neutral processes.     

The evolution of MHC diversity: evidence of intralocus gene conversion and recombination in a single-locus system

Gene conversion, the unidirectional exchange of genetic material between homologous sequences, is thought to strongly influence patterns of genetic diversity. The high diversity of major histocompatibility complex (MHC) genes in many species is thought to reflect a long history of gene conversion events both within and among loci. Theoretical work suggests that intra- and interlocus gene conversion leave characteristic signatures of nucleotide diversity, but empirical studies of MHC variation have rarely been able to analyze the effects of conversion events in isolation, due to the presence of multiple gene copies in most species. The potbellied seahorse (Hippocampus abdominalis), a species with a single copy of the MH class II beta-chain gene (MHIIb), provides an ideal system in which to explore predictions on the effects of intralocus gene conversion on patterns of genetic diversity. The genetic diversity of the MHIIb peptide binding region (PBR) is high in the seahorse, similar to other vertebrate species. In contrast, the remainder of the gene shows a total absence of synonymous variation and low levels of intronic sequence diversity, concentrated in 3 short repetitive regions and 1-12 SNPs per intron. The distribution of substitutions across the gene results in a patchwork pattern of shared polymorphism between otherwise divergent sequences. The pattern of nucleotide diversity observed in the seahorse MHIIb gene is congruent with theoretical expectations for intralocus gene conversion, indicating that this evolutionary mechanism has played an important role in MHC gene evolution, contributing to both the high diversity in the PBR and the low diversity outside this region. Neutral variation at this locus may be further reduced due to biases in nucleotide composition and functional constraints.     

内蒙古高原小叶锦鸡儿(Caragana microphylla)、中间锦鸡儿(C. davazamcii)和柠条锦鸡儿(C. korshinskii)的遗传多样性及遗传关系

采用RAPD技术对10个具较大地理跨度的小叶锦鸡儿、中间锦鸡儿和柠条锦鸡儿种群的遗传多样性和遗传关系进行了研究.共检测到678个位点,多态条带比率(PPB)为100%;特有位点41个,占6.05%.总体上3种锦鸡儿的遗传多样性表现出自东向西递减的趋势,分析表明其与生长地点年均气温呈显著负相关.AMOVA表明:3种锦鸡儿种间变异只占总体变异的6.08%,且显著性检验表明这种变异不显著;种内种群间的变异占总变异的11.90%;总变异的主要部分来自种群内部(82.02%). 3种锦鸡儿各种群总体分析结果表明:种群内变异比率Hpop/Hsp为0.8013,基因分化系数Gst为0.1603,种群每代迁移数Nm为2.6192,显示种群间存在一定强度的基因流,3种锦鸡儿间表现为异交性.3种锦鸡儿多样性高低及种群聚类分布格局都表现出一定的地理连续性.     

Genetic diversity and genetic relationship of Caragana microphylla, Caragana davazamcii and Caragana korshinskii on the Inner Mongolia Plateau, China

C. microphylla, C. davazamcii and C. korshinskii exhibit a geographical replacement series from east to west on the Inner Mongolia Plateau. Currently, there is still a debate about the taxonomic and genetic relationship among these 3 species. We studied the genetic diversity and genetic relationship among these 3 species by analyzing DNA samples of individual plants from within 10 populations with random amplified polymorphic DNA (RAPD) markers. We identified 678 RAPD loci in total, of which all were polymorphic (PPB = 100%). There were 41 unique loci (6.05%). In general, a trend presented that the genetic diversity of these species decreased from east to west. Further, the genetic diversity was significantly negatively correlated with the local annual mean temperature. Analysis of molecular variation (AMOVA) showed that the genetic variation among these 3 species was only 6.08% of the total genetic variation. Between the species, the genetic variation was insignificant (P = 0.9961). The proportion of genetic variation among populations within each species was 11.90% (P < 0.001) of the total genetic variation, and the total genetic variation mainly existed within the populations (82.02%). Estimated with Shannon's index, genetic differentiation within the populations (Hpop/Hsp) was 0.8013, the coefficient of gene differentiation (Gst) was 0.1603, and the gene flow index (Nm) was 2.6192. This, thus, indicates that there is relatively high gene flow among these populations, and that these 3 species are crossbreeding. The genetic diversity level and the population distribution pattern showed geographic continuity to some extent.     

Genetic differences among brown trout, Salmo trutta, stocks and their importance for the conservation and management of the species

SUMMARY. 1. Review of published studies on genetic variation, as shown by electrophoretic studies of protein variation, in natural brown trout ( Salmo trutta L.) populations from Britain and Ireland, Finland, France, Greece, Iceland, Norway, Sweden, U.S.A. and U.S.S.R., revealed abundant geographical variation in gene frequency with individual populations containing only a limited part of the gene diversity of the species.
2. Thirty-eight (54%) of the seventy gene loci examined have been found to be polymorphic in the species with an average population showing polymorphism at 16% of its loci (range 0-34.8%).
3. The brown trout is naturally subdivided into a large number of reproductively isolated and genetically distinct populations within, as well as among, drainages.
4. Two independent post-glacial colonizations, by genetically distinct races, followed by independent evolution in separate drainages over the past 13,000 years is seen as responsible for the genetic diversity of brown trout in north-western Europe.
5. Many genetically unique populations have been lost in the past 100 years and there is an urgent need to identify and conserve the remaining genetic diversity. Genetically unique populations are an irreplaceable resource for rational management in relation to angling and future aquaculture potential.     

A comparative analysis of allozyme variability in vertebrate animals]

Comparative analysis of levels of the allozymic variation in the vertebrates is conducted using evaluation of a) within population heterozygosity of ferment coding homologous loci, b) average (per each species) allele frequencies of homologous loci, and c) overall sample of the loci being analyzed. It is established that amphibians and reptiles are characterized by the highest, birds and mammals--by the lowest, and fishes--by the middle level of genetic diversity. The diversity of genetic systems, if the constant heterozygosity of duplicated loci is taken into consideration, decreases from fishes to mammals and from cold-blooded to warm-blooded vertebrates. This tendency could be considered as an extrapolation of the "progressive specialization" rule on molecular level. Three basic factors determining certain level of genetic diversity of a species are acknowledged position in the phylogenetic system, population structure, and level of introgressive hybridization. From methodological viewpoint, evaluation of the genetic diversity by homologous loci seems to be most valid in comparative studies.     

中日5个岛屿山茶种群遗传多样性研究

运用ISSR分子标记法对中、日两国5个岛屿天然山茶种群共150个个体进行遗传多样性分析。结果表明:筛选出的20条引物扩增得到205条清晰条带,其中183条为多态性条带,多态位点百分比(PPB)为89.27%。经POPGENE软件分析,山茶种群平均多态位点百分比(PPB)为72.00%,Nei’s基因多样性指数(HE)为0.2743,Shannon信息多态性指数(H)为0.4023,种群水平遗传多样性较高。基因分化系数Gst=0.2033,表明遗传变异主要存在于种群内个体间。Mantel检验(r=0.7989,P<0.05)和UPGMA聚类表明岛屿地理隔离对山茶种群遗传分化具有重要影响。基于岛屿山茶种群遗传结构的分析,建议加强我国岛屿自然种群的就地保护力度。     

中国地方黄牛的遗传多样性*

中国黄牛起源复杂,我国地方黄牛群体不同品种在毛色、形态外貌、细胞遗传学、血液蛋白座位分析均表现出多样性。计算我国黄牛群体6个毛色座位平均杂合度和6个血液蛋白座位平均杂合度分别为0.3144和0.4873,表明我国地方黄牛群体的遗传多样性非常丰富。计算我国黄牛群体的6个毛色座位和6个血液蛋白座位的基因分化系数分别为0.3404和0.095,表明我国黄牛群体毛色差异中有34.04％是由品种间的差异造成的。血液蛋白的多态性有9.5％是由品种间的差异造成的。我国黄牛群体的遗传多样性主要来自品种内的遗传多样性。保存我国黄牛品种资源多样性不仅要从整个中国黄牛群体上考虑,而且要针对每个品种（或类群）进行保种。     

RAPD variation and population genetic structure in Prunus mahaleb (Rosaceae), an animal-dispersed tree

We examined the patterns of random amplified polymorphic DNA (RAPD) variation among seven Prunus mahaleb (Rosaceae) populations extending over approximately 100 km2 to examine local differentiation in relation to spatial isolation due to both geographical distance and differences in elevation. No less than 51. 4% of the RAPD loci were polymorphic, but very few were fixed and among-population variation accounted for 16.46% of variation in RAPD patterns. Mean gene diversity was 0.1441, with mean Nei's genetic diversity for individual populations ranging between 0.089 and 0.149. Mean GST value across loci was 0.1935 (range, 0.0162-0.4685), giving an average estimate for Nm of 1.191. These results suggest extensive gene flow among populations, but higher GST and lower Nm values relative to other outcrossing, woody species with endozoochorous dispersal, also suggest a process of isolation by distance. The combined effect of both geographical and elevation distances and nonoverlapping flowering and fruiting phenophases on the GST matrix was partially significant, revealing only marginal isolation of the P. mahaleb populations. The matrix correlation between estimated Nm values among populations and the geographical + elevation distance matrices (r = -0.4623, P = 0.07), suggests a marginal trend for more isolated populations to exchange less immigrants. Long-distance seed dispersal by efficient medium-sized frugivorous birds and mammals is most likely associated to the high levels of within-population genetic diversity. However, vicariance factors and demographic bottlenecks (high postdispersal seed and seedling mortality) explain comparatively high levels of local differentiation.     

应用ISSR-PCR分析蒙古栎种群的遗传多样性

本研究应用ISSR标记技术对东北地区的优势树种蒙古栎(Quercus mongolica)的25个种群遗传多样性进行了分析, 目的是为蒙古栎早期选择提供依据。从60条ISSR引物中筛选出10个特异性强、稳定性好的引物进行ISSR分析。共获得位点数71个, 其中多态位点数56个, 多态位点百分率为78.87%。PopGene分析结果表明: 种群的平均多态位点百分率为45.2%, Shannon表型多样性指数(I)平均值为0.25, 具有较高的遗传多样性, 种群间存在一定程度的基因流(N_m为1.3818)和遗传分化(Nei’s信息多样性指数平均值为0.1068, G_st平均值为0.2657), 种群内的基因多样度占总种群的73.43%, 种群间占26.57%, 表明蒙古栎种群的变异主要来源于种群内。结合聚类分析和地理变异规律把种群划分为两个大的种群组: 小兴安岭种群组和长白山种群组。以上结果可为栎属种质资源的保护和利用以及物种分化研究提供基础资料。     

A comparison of the genetic diversity in Dipteronia sinensis Oliv. and Dipteronia dyeriana Henry

Dipteronia is an endemic genus to China and includes only two species, Dipteronia sinensis and D.dyeriana.Based on random amplified polymorphic DNA (RAPD) markers,a comparative study of the genetic diversity and genetic structure of Dipteronia was performed.In total,128 and 103 loci were detected in 17 D.sinensis populations and 4 D.dyeriana populations,respectively,using 18 random primers.These results showed that the proportions of polymorphic loci for the two species were 92.97% and 81.55%,respectively,indicating that the genetic diversity of D.sinensis was higher than that of D.dyeriana.Analysis,based on similarity coefficients,Shannon diversity index and Nei gene diversity index,also confirmed this result.AMOVA analysis demonstrated that the genetic variation of D.sinensis within and among populations accounted for 56.89% and 43.11% of the total variation,respectively,and that of D.dyeriana was 57.86% and 42.14%,respectively.The Shannon diversity index and Nei gene diversity index showed similar results.The abovementioned characteristics indicated that the genetic diversity levels of these two species were extremely similar and that the interpopulational genetic differentiation within both species was relatively high.Analysis of the genetic distance among populations also supported this conclusion.Low levels of interpopulational gene flow within both species were believed to be among the leading causes for the above-mentioned phenomenon.The correlation analysis between genetic and geographical distances showed the existence of a remarkably significant correlation between the genetic distance and the longitudinal difference among populations of D.sinensis (p＜0.01),while no significant correlation was found between genetic and geographical distances among populations of D.dyeriana.This indicated that genetic distance was correlated with geographical distances on a large scale rather than on a small scale.This result may be related to differences in the selection pressure on species by their habitats with different distribution ranges.We suggest that in situ conservation efforts should focus on establishing more sites to protect the natural populations and their habitats.Ex situ conservation efforts should focus on enhancing the exchange of seeds and seedlings among populations to facilitate gene exchange and recombination,and to help conserve genetic diversity.     

Karyotype and genetic evolution in speciation of subterranean mole rats of the genus Spalax in Turkey

Karyotype (2fl) and allozymc diversity at 37 gene loci were determined in 69 subterranean mole rats in Turkey belonging to the two superspecies: the ancestor Spalax leucodon ( n = 55; 20 populations) and the descendant S. ehrenbergi ( n = 14; lour populations). We identified remarkable variation of diploid chromosome numbers in the S. leucodon superspecies: 2 n = 38. 40. 50, 54, 60 and 62; and in the S. ehrenbergi superspecies: 2 n = 52, 56 and 58. Genetic diversity indices were low on average in both S. leucodon and S. ehrenbergi superspecies: Allele diversity, A = 1.081 and 1.074; polymorphism, P-5%= 0.077 and 0.068; heterozygosity, H = 0.038 and 0.027; and gene diversity, H, = 0.038 and 0.034, respectively. H ranged from 0 in mesic or semimesic regions to 0.088 in arid Anatolia. We consider the populations with different diploid chromosome numbers, 2 n , as good biological species. Karyotypic diversity may mark extensive ecological speciation. Nei's genetic distances, D (average 0.174, range 0.002 0.422) and ecogeographical criteria suggest that almost each population may represent a different biological species, but critical future testing is necessary to support this claim. Karyotypes and allozymes are nonrandomly distributed across Turkey, displaying remarkable correlations with climatic and biolir factors. Both In and H are significantly correlated with aridity stress (2 n /rainfall, r , =–0.74; P < 0.001), and in our region also with climatic unpredictability. These results support the niche-width genetic variation hypothesis in space and time. Climatic selection in Turkey appears to be a major architect of karyotype and genetic (allozymc) diversity and divergence in mole rat evolution, in both speciation and adaptation.     

Genetic diversity and morphological differentiation in Liatris helleri (Asteraceae), a threatened plant species

Liatris helleri (Asteraceae) is an insect-pollinated herbaceous perennial endemic to several high-elevation sites in the Blue Ridge Mountains of North Carolina. Allozymes were used to describe the genetic diversity and population structure in nine populations of this rare, federally listed species. Differences in leaf morphology were also examined for greenhouse-grown plants representing several populations. The proportion of the total genetic diversity found among populations, as indicated by the allozyme data, was 16%. Higher levels of population differentiation were found for differences in leaf shape; population of origin accounted for 37% of the variation in maximum leaf width, while families within populations accounted for 7%. In contrast to many endemic species, L. helleri maintains fairly high levels of genetic diversity. For the species, the percent polymorphic loci was 87.5, the average number of alleles at variable loci was 3.00 and the gene diversity was 0.276. Mean population values were percent polymorphic loci =58.4, mean number of alleles per polymorphic locus =2.59 and gene diversity =0.219. The estimated gene flow was low (Nm=0.85–1.32) and a relatively high correlation (r=0.55; p<0.005) was found between linear geographic and genetic distance. This suggests that the populations are partially isolated by distance, despite the limited range (<60 km) of the species. We recommend that population distinetiveness be maintained in restoration efforts.     

大别山山核桃天然群体遗传结构的初步分析

利用RAPD分子标记技术检测了大别山山核桃3个天然居群的遗传多样性和遗传结构。20条10 bp随机引物共检测到238个扩增位点,其中多态性位点162个,多态位点百分率(PPB)为68.1%。居群水平Shannon’s多态性信息指数(I)介于0.2651~0.2801之间;居群水平Ne i’s基因多样性指数(H)介于0.1789~0.1890之间。遗传变异计算显示大别山山核桃居群间基因分化系数(Gst)为0.4063,分子方差分析(AMOVA)表明居群间基因分化水平为0.4177,居群间基因流(Nm)为0.7306,说明大别山山核桃大部分变异存在于居群内,居群间基因交流相对较少。这一结果符合大别山山核桃风媒、异交的繁育系统特点,但其居群间基因分化程度明显高于异交植物的平均水平(Gst=0.1930)。地理隔离、居群内近交及居群间基因流受阻可能是形成目前大别山山核桃天然群体遗传结构的主要因素。     

濒危植物三棱栎遗传多样性的RAPD分析

用随机扩增多态DNA (RAPD)标记对 5个三棱栎 (Trigonobalanusdoichangensis)居群共 99个个体进行遗传多样性和居群遗传结构分析。 16个引物共检测到 15 7个位点 ,其中多态位点 83个 ,占 5 2 87%。物种水平Shannon多样性指数I =0 2 4 31,Nei基因多样度h =0 15 95 ,种内总遗传变异量Ht=0 16 0 0 ,居群内遗传变异量Hs =0 0 74 9,居群间变异量大于居群内变异量 ,表明三棱栎的遗传变异主要存在于居群之间。与同科植物相比 ,三棱栎遗传多样性较低 ,遗传分化系数Gst =0 5 32 0 ,说明居群间的遗传变异占 5 3 2 0 % ,居群间已出现强烈的遗传分化。当地人的强烈活动造成的生境破碎化和居群隔离 ,以及三棱栎演化过程中的地史变化对其种群发展的影响等 ,可能是造成其居群间强烈的遗传分化和较低遗传多样性的原因。基于本研究结果 ,提出了三棱栎遗传多样性的保护策略。     

刚毛柽柳天然居群遗传多样性初探

柽柳是荒漠地区主要的灌木资源树种。以刚毛柽柳为代表,运用RAPD技术分析了广布于新疆境内9个刚毛柽柳(Tamarix hispida L．)天然居群的遗传多样性及居群间的遗传分化。10条随机引物检测到157个可重复的位点,其中多态位点155个,占总位点数的98．7％。由Shannon表型多样性指数和Nei基因多样性指数估计居群间遗传分化百分比分别为62．5％和55．30％,表明刚毛柽柳种内的遗传变异主要存在于居群间。根据以上结果,我们认为新疆境内刚毛柽柳天然居群的遗传多样性很丰富,居群间分化程度较高;繁育系统属于一种自交和不完全异交混合的交配类型;形成并维持其分布格局的主要因素是基因流的隔离。     

雌雄异株稀有植物伞花木(Eurycorymbus caraleriei)自然居群的等位酶遗传多样性研究

伞花木（Eurycorymbus caraleriei）为中国特有的第三纪孑遗单种属植物,雌雄异株。采用超薄平板微型聚丙烯酰胺等电聚焦电泳方法对其5个自然居群和1个人工迁地保护居群的等位酶变异进行了初步研究。对7个酶系统中14个位点的等位酶居群遗传多样性及遗传结构分析结果表明：伞花木具有较高水平的遗传多样性,其每位点平均等位基因数A=1．6,平均多态位点比率P=42．9％,平均预期遗传杂合度Hr=0．216;各居群的遗传多样性无显著性差异,但都表现为严重偏离Hardy-Weinberg平衡的杂合子过量;其遗传变异主要发生在居群内（93．1％）,居群间分化较小（Gst=0．069）,居群问遗传一致度较高（I=0．965～1．000）。推断这可能是由于其古老孑遗性、雌雄异株、混和传粉方式的生物学特性以及其长寿命的生活史等原因所导致;同时,居群间的较高基因流（Nm=3．128）也可能起到很大的作用。还使用UPGMA聚类方法推断了武汉植物园迁地保护的野外居群来源,在对迁地保护居群的评价中发现迁地保护居群仅保存了该物种基因型多样性的16％,在此基础上提出了今后进一步的保育策略。     

Footprints of divergent selection in natural populations of Castanopsis fargesii (Fagaceae)

Given predicted rapid climate change, an understanding of how environmental factors affect genetic diversity in natural populations is important. Future selection pressures are inherently unpredictable, so forest management policies should maintain both overall diversity and identify genetic markers associated with the environmental factors expected to change most rapidly, like temperature and rainfall. In this study, we genotyped 648 individuals in 28 populations of Castanopsis fargesii (Fagaceae) using 32 expressed sequence tag (EST)-derived microsatellite markers. After removing six loci that departed from Hardy–Weinberg equilibrium, we measured genetic variation, population structure and identified candidate loci putatively under selection by temperature and precipitation. We found that C. fargesii populations possessed high genetic diversity and moderate differentiation among them, indicating predominant outcrossing and few restrictions to gene flow. These patterns reduce the possible impact of stochastic effects or the influence of genetic isolation. Clear footprints of divergent selection at four loci were discovered. Frequencies of five alleles at these loci were strongly correlated with environmental factors, particularly extremes in precipitation. These alleles varied from being near fixation at one end of the gradient to being completely absent at the other. Our study species is an important forest tree in the subtropical regions of China and could have a major role in future management and reforestation plans. Our results demonstrate that the gene flow is widespread and abundant in natural populations, maintaining high diversity, while diversifying selection is acting on specific genomic regions.     

GENETIC STRUCTURE OF NORWAY SPRUCE (PICEA ABIES): CONCORDANCE OF MORPHOLOGICAL AND ALLOZYMIC VARIATION

This study describes the population structure of Norway spruce (Picea abies) as revealed by protein polymorphisms and morphological variation. Electrophoretically detectable genetic variability was examined at 22 protein loci in 70 populations from the natural range of the species in Europe. Like other conifers, Norway spruce exhibits a relatively large amount of genetic variability and little differentiation among populations. Sixteen polymorphic loci (73%) segregate for a total of 51 alleles, and average heterozygosity per population is 0.115. Approximately 5% of the total genetic diversity is explained by differences between populations (G_ST = 0.052), and Nei's standard genetic distance is less than 0.04 in all cases. We suggest that the population structure largely reflects relatively recent historical events related to the last glaciation and that Norway spruce is still in a process of adaptation and differentiation. There is a clear geographic pattern in the variation of allele frequencies. A major part of the allelefrequency variation can be accounted for by a few synthetic variables (principal components), and 80% of the variation of the first principal component is “explained” by latitude and longitude. The central European populations are consistently depauperate of genetic variability, most likely as an effect of severe restrictions of population size during the last glaciation. The pattern of differentiation at protein loci is very similar to that observed for seven morphological traits examined. This similarity suggests that the same evolutionary forces have acted upon both sets of characters.