Consistency of population genetics parameters estimated from isozyme and RAPDs dataset in species of genus <Emphasis Type="Italic">Prosopis</Emphasis> (Leguminosae,Mimosoideae)

Genetic variability, population structure and differentiation among 17 populations of 5 species and 2 natural interspecific hybrids of section Algarobia of genus Prosopis were analyzed from data of 23 isozyme and 28 RAPD loci. Both markers indicated that the studied populations are highly variable. P. alba populations in average showed lower values of genetic variability estimates from isozyme data, but this trend was not observed for RAPD markers. The hierarchical analyses of the distribution of genetic variability showed that the highest proportion of variation occurred within populations, the differentiation among species was intermediate and the lowest component was observed among populations within species. The consistency between results from both dataset implies that they are not biased and reflect the actual genetic structure of the populations analyzed. The matrices of Euclidean distances obtained from the two sets of markers were highly correlated according to Mantel test. In both cases the corresponding phenogram and MDS plot tended to cluster conspecific populations while hybrid populations were not intermediate between putative parents. Some disagreements between isozyme and RAPD phenograms were observed mainly in the affinities of hybrid populations. Such inconsistencies might result from reticular rather than dichotomic evolutionary relationships. The phenetic associations retrieved gave no support to the division of the section Algarobia into series.     

Genetic diversity and structure of the endemic Caesalpinia hintonii complex (Leguminosae: Caesalpinioideae) in Mexico

The Caesalpinia hintonii complex is formed by five endemic species (C. hintonii, C. laxa, C. macvaughii, C. melanadenia and C. epifanioi) occurring in central Mexico. This species complex is under incipient genetic divergence as by-product of local adaptations in reproductive and morphological traits to different habitats. We estimate the genetic variation and structure of populations of this species complex to assess the extent of genetic differentiation among populations and related species along its geographic distribution. Estimations of genetic diversity and structure were done based on ten enzymes and 18 loci. Mean number of alleles per locus ranged from 1.5 to 1.9. Polymorphic loci ranged from 42.1 to 68.4. Observed (H_o: range 0.191–0.275) and expected (H_e: range 0.205–0.317) heterozygosities in this complex were higher compared with other endemic and legume species. Neis genetic diversity estimates showed that most genetic variation was found within (H_S = 0.325) rather than among populations (D_ST = 0.085). Populations of the species C. hintonii showed a considerable genetic differentiation (F_ST = 0.207). The results of genetic diversity and structure within and among populations are in accord with the great morphological differentiation described for this species complex.     

基于SSR标记探讨三种金花茶植物的遗传多样性和遗传结构

薄叶金花茶、小花金花茶和小瓣金花茶是三种濒危金花茶植物,为了解珍稀濒危植物遗传多样性和遗传结构,该研究利用微卫星标记对他们的7个种群共184个个体进行了遗传多样性和遗传结构分析。结果表明:11个位点共检测到等位基因92个。在物种水平上,小瓣金花茶平均等位基因数(N_A)为3.9、有效等位基因数(N_E)为2.328、观测杂合度(H_o)为0.520、期望杂合度(H_e)为0.501,高于薄叶金花茶和小花金花茶。在种群水平上,有效等位基因数(N_E)在1.788～2.466之间,期望杂合度(H_e)在0.379～0.543之间;种群间遗传分化系数(FST)在0.143 7～0.453 3之间,种群间基因流(N_m)在0.301 5～1.488 9之间。AMOVA分子变异分析显示65.72%的变异存在于种群内。三种金花茶具有较低水平的遗传多样性和高水平的种群间遗传分化。STRUCTURE和PCoA种群遗传结构分析结果将取样种群分为2组,即薄叶金花茶和小花金花茶大部分个体分为一组,小瓣金花茶大部分个体分为一组。现存所有种群应根据实际情况尽快采取就地保护或迁地保护措施。     

Allozyme diversity in Chinese,Seguin and American chestnut (Castanea spp.)

Allozyme genetic variability in three chestnut (Castanea) species was investigated using 19 loci from ten enzyme systems. G-tests of heterogeneity of isozymic allele distribution showed significant differences between the three species at 15 of the 19 loci, and between the 13 C. mollissima populations at 13 of the 19 loci examined. C. mollissima was found to possess a significantly-higher value of mean gene heterozygosity (H=0.3050±0.0419), the percentage of polymorphic loci (P=84.21%) and the average number of alleles per locus (A=2.05), than any other species in the Castanea section Eucastanon. When the genetic variability of populations of C. mollissima from four regions in China was investigated, the population from the Changjiang river region showed a markedly higher mean gene heterozygosity (H=0.3480±0.0436) than populations from the other regions. Genetic relationships among the four regions were assessed by Nei's genetic identity I and standard genetic distance D. An approximately-identical distance between the population from the Changjiang river region and populations from the three other regions was observed, while populations from the latter regions showed almost the same genetic distance from each other. These data, when considered with information existing prior to this study, contribute to an understanding of the possible origin and progenitor of the chestnut species.     

Genetic variation and phylogeographic history of <Emphasis Type="Italic">Picea likiangensis</Emphasis> revealed by RAPD markers

Repeated cycles of retreat and recolonization during the Quaternary ice ages are thought to have greatly influenced current species distributions and their genetic diversity. It remains unclear how this climatic oscillation has affected the distribution of genetic diversity between populations of wind-pollinated conifers in the Qinghai-Tibetan region. In this study, we investigated the within-species genetic diversity and phylogenetic relationships of Picea likiangensis, a dominant forest species in this region using polymorphic DNA (RAPD) markers. Our results suggest that this species has high overall genetic diversity, with 85.42% of loci being polymorphic and an average expected heterozygosity (H _E) of 0.239. However, there were relatively low levels of polymorphism at population levels and the differences between populations were not significant, with percentages of polymorphic bands (PPB) ranging from 46.88 to 69.76%, Nei’s gene diversity (H _E) from 0.179 to 0.289 and Shannon’s indices (Hpop) from 0.267 to 0.421. In accordance with our proposed hypothesis, a high level of genetic differentiation among populations was detected based on Nei’s genetic diversity (G _ST = 0.256) and AMOVA analysis (Phi _st = 0.236). Gene flow between populations was found to be limited (Nm = 1.4532) and far lower than reported for other conifer species with wide distribution ranges from other regions. No clusters corresponding to three morphological varieties found in the south, north and west, respectively, were detected in either UPGMA or PCO analyses. Our results suggest that this species may have had different refugia during the glacial stages in the southern region and that the northern variety may have multiple origins from these different refugia.     

Molecular diversity of species of the Elymus trachycaulus species complex and their relationships to non-North American taxa

Species of the E. trachycaulus complex species are known for their morphological variability, but little is known about their genetic basis. The delimitation of taxa within the complex has been controversial and difficult. E. trachycaulus is predominantly self-pollinating, and lacks clear morphological boundaries between it and E. alaskanus. Another controversial taxonomic issue of E. trachycaulus is the relationships of this complex species to non-North American E. caninus. The objectives of this study were to examine genetic diversity and the systematic relationships among the species of the E. trachycaulus complex and their relationships with E. caninus, E. alaskanus and E. mutabilis. Random amplified polymorphic DNA method was used to study 35 accessions of E. trachycaulus complex and other Elymus species. Higher genetic variation was detected within species of E. trachycaulus complex. Eurasian accessions are as variable as the North American ones. Both UPGMA and NJ analyses did not show clearly separation among species of the E. trachycaulus complex. No clear association between geographic origin and genetic grouping among these species was found. Eurasian E. trachycaulus probably originated from multiple North American populations.     

Analysis of allozyme variability in three Plantago species and a comparison to morphological variability

Summary The level of electrophoretic variability in three Plantago species, P. major, P. coronopus, and P. lanceolata, was analyzed in relation to their breeding systems and compared with their morphological variability. From each species several populations were analyzed. The outcrossing P. lanceolata had the highest level of electrophoretic variability and the lowest population differentiation. The inbreeding P. major showed the opposite: a low level of electrophoretic variability and a high population differentiation. P. coronopus, with an intermediate breeding system, had an intermediate level of variability and differentiation. In comparing the species, it appeared that P. coronopus and P. major showed good concordance in the distribution of both kinds of variability, each having only a slightly higher morphological than electrophoretic differentiation between populations. P. lanceolata showed a higher morphological than electrophoretic differentiation between populations. A comparison of populations, within species, revealed good concordance of electrophoretic and morphological variability only within P. coronopus, while some populations of the other two species had relatively lower morphological variability compared with electrophoretic variability.Grassland Species Research Group Publication No. 182     

Phylogeography of island canary (Serinus canaria) populations

Island canaries (Serinus canaria) are characterised as a species living exclusively on North Atlantic islands, mainly on the Azores, Madeira and Canary Islands. Although they are very common in their habitats, their behaviour and breeding system has only recently been studied systematically. To advance the understanding of their ecology and to see if the rather isolated archipelagos are already promoting a genetic differentiation, we investigated their phylogeographic relationship as revealed by mtDNA sequences of the cytochrome b gene and investigated whether this measure corresponds to morphological characteristics within the islands. Genetic distances were very low throughout the distribution range of the species. Although the variation of genetic distances within the population of Pico (Azores) was larger than that on Madeira and Canary Islands, the genetic distances between island populations were very low throughout which prevented a clear phylogeographic differentiation. Moreover, morphological measurements did not reveal a consistent pattern to reliably separate the populations, although the measures of beak length and body weight revealed a clear island-specific differentiation. These data lead to the assumption that the colonisation of the Atlantic islands by the canaries occurred very recently, while there is no persisting gene flow between the populations.     

Molecular and phenotypic diversity in Chionactis occipitalis (Western Shovel-nosed Snake), with emphasis on the status of C. o. klauberi (Tucson Shovel-nosed Snake).

Chionactis occipitalis (Western Shovel-nosed Snake) is a small colubrid snake inhabiting the arid regions of the Mojave, Sonoran, and Colorado deserts. Morphological assessments of taxonomy currently recognize four subspecies. However, these taxonomic proposals were largely based on weak morphological differentiation and inadequate geographic sampling. Our goal was to explore evolutionary relationships and boundaries among subspecies of C. occipitalis, with particular focus on individuals within the known range of C. o. klauberi (Tucson Shovel-nosed snake). Population sizes and range for C. o. klauberi have declined over the last 25 years due to habitat alteration and loss prompting a petition to list this subspecies as endangered. We examined the phylogeography, population structure, and subspecific taxonomy of C. occipitalis across its geographic range with genetic analysis of 1100 bases of mitochondrial DNA sequence and reanalysis of 14 morphological characters from 1543 museum specimens. We estimated the species gene phylogeny from 81 snakes using Bayesian inference and explored possible factors influencing genetic variation using landscape genetic analyses. Phylogenetic and population genetic analyses reveal genetic isolation and independent evolutionary trajectories for two primary clades. Our data indicate that diversification between these clades has developed as a result of both historical vicariance and environmental isolating mechanisms. Thus these two clades likely comprise ‘evolutionary significant units’ (ESUs). Neither molecular nor morphological data are concordant with the traditional C. occipitalis subspecies taxonomy. Mitochondrial sequences suggest specimens recognized as C. o. klauberi are embedded in a larger geographic clade whose range has expanded from western Arizona populations, and these data are concordant with clinal longitudinal variation in morphology.     

Genetic differentiation among populations ofArabis serrata (Brassicaceae) along its geographic distribution

Levels and distribution of genetic variation were investigated in ten populations of the perennialArabis serrata distributed along a latitudinal gradient throughout Japan. Populations of this endemic species occupy predominantly three types of habitats: limestone and derived soils, volcanic and disturbed sites. Previous studies showed that plants ofA. serrata are differentiated in morphological and ecological traits under both natural conditions and common garden experiments suggesting genetic differentiation among populations. To assess the degree of genetic differentiation under different habitats ofA. serrata populations, we analyzed the isozyme genetic structure. Ten populations, located in mountains of central and northern Honshu and Hokkaido, were analyzed by starch gel enzyme electrophoresis. Fourteen loci of eight enzymes were resolved and six loci were monomorphic for all the populations. Populations sampled maintain low levels of genetic variation (P=0.16;H=0.05;A=1.16) compared to that maintained by other outcrossing seed plants. In some cases, few or no heterozygous individuals were detected, and consequently, mean observed heterozygosity was zero or near zero. Six (29%) of the fixation indices,F, estimated deviated significantly from Hardy Weinberg genotypic expectations indicating a deficiency of heterozygotes in most of the cases. The mean genetic identity (Nei'sI) between population pairs was 0.852 and indicates a moderate level of genetic differentiation among populations.Arabis serrata has most of its genetic variation distributed among rather than within populations. The among-population component of the total genetic diversity (G _ST mean value) was 0.416, indicating genetic differentiation between populations. There groups of populations were recognized in an unrooted tree generated by the Neighbor-Joining method. These results suggest groups of populations differentiated regionally. Estimates of interpopulational gene flow (Nm) were very variable (range 0.049–3.718) with a meanNm=1.203 for all populations.     

Low genetic differentiation betweenAdiantum capillusveneris L. andA. ogasawarense Tagawa (Adiantaceae), an endemic pteriodophyte of the bonin (ogasawara) islands

Genetic differentiation was examined betweenAdiantum capillus-veneris L. andA. ogasawarense Tagawa. A total of 136 individuals from two populations ofA. ogasawarense and three populations ofA. capillus-veneris were sampled. Allozymes encoded by 19 putative loci for nine enzyme systems were observed. The populations ofA. ogasawarense are genetically differentiated from those ofA. capillus-veneris; conspecific populations cluster together. However, genetic identity between two species was estimated to be 0.815, and indicates that the degree of allozyme differentiation is lower than those between endemic flowering plants and their progenitors. It is possible that the low genetic differentiation observed betweenA. ogasawarense andA. capillus-veneris results from a recent origin of the endemic species,A. ogasawarense.     

四川西部濒危植物桃儿七遗传多样性的RAPD分析

桃儿七是一种具有重要药用价值的珍稀濒危植物。采用RAPD分子标记技术,对在四川西部地区的桃儿七7个自然种群的遗传多样性水平和遗传结构进行了分析。用12个RAPD引物对7个种群共140个样品进行了扩增,共得到111条清晰带,其中32条具有多态性,在物种水平上多态位点百分率(PPB)为28.83%,在种群内的多态位点百分率变动幅度为4.50%至16.22%。同其它一些濒危植物相比,桃儿七种群具有较低的遗传多样性(He=0.0622,Ho=0.0987)。7个自然种群间出现了很强的遗传分化,分化指数接近70%。种群间的基因流低(Nm=0.2240)。造成上述结果的可能原因是与桃儿七的繁育方式和有限的基因流等因素有关。应将遗传多样性相对较高的松潘县牟尼沟种群作为原位保护的核心种群进行保护,尽量保护所有现有种群。     

Single nucleotide polymorphisms of Gcyc1 (Cycloidea) in Conandron ramondioides (Gesneriaceae) from Southeast China

Conandron ramondioides with actinomorphic flower in Gesneriaceae is an endemic species distributed in Taiwan, Southeast of China and Japan. Populations are usually small and isolated in typically fragmented habitat. Based on SNPs of Gcyc1 (Cycloidea), a TCP gene known in patterning the floral dorsoventral asymmetry, we have explored the molecular evolution and genetic differentiation of Gcyc1 at population level, and the population history of C. ramondioides populations distributed in SE China. Eighteen SNPs are detected in 774-bp of the gene, of which eleven are non-synonymous. However, morphological observation of flowers shows that there is no visible differentiation in shape and size across the dorsoventral axis within each whorl. None of the eighteen SNPs is by all shared the eleven populations. Population differentiation is significant. These results reveal that evolution of Gcyc1 at population level is well in accord with the neutral theory. Our study indicates that the SNPs of developmental genes are also useful molecular markers for exploring the genetic differentiation and population history in non-model organisms.     

Genetic diversity and structure of Cordyceps sinensis populations from extensive geographical regions in China as revealed by inter-simple sequence repeat markers

Cordyceps sinensis is one of the most valuable medicinal caterpillar fungi native to China. However, its productivity is extremely limited and the species is becoming endangered. The genetic diversity of eighteen C. sinensis populations across its major distributing regions in China was evaluated by inter-simple sequence repeat (ISSR) markers. A total of 141 markers were produced in 180 individuals from the 18 populations, of which 99.3% were polymorphic. The low average of Shannon (0.104) and Nei index (0.07) of the 18 populations indicates that there are little genetic variations within populations. For all 18 populations, estimates of total gene diversity (H_T), gene diversity within populations (H_S), coefficient of genetic differentiation (G_ST), and gene flow (Nm) were 0.170, 0.071, 0.583, and 0.357, respectively. This pattern suggests that the genetic diversity of C. sinensis is low and most of the ISSR variations are found among populations with little gene exchange. The 18 populations are divided into five groups based on the genetic distance and the grouping pattern matches with the geographic distribution along the latitudinal gradient. The five groups show obvious difference in the G_ST and Nm values. Therefore, the genetic diversification of C. sinensis populations may be determined by geographic isolation and the combined effects of life history characters and the interaction with host insect species. The information illustrated by this study is useful for selecting in situ conservation sites of C. sinensis.     

Isolation and characterization of polymorphic microsatellite markers in <Emphasis Type="Italic">Cupressus </Emphasis><Emphasis Type="Italic">chenggiana</Emphasis> S. Y. Hu (Cupressaceae)

Cupressus chenggiana S. Y. Hu (Cupressaceae) is an endemic and endangered conifer species in southwest China. In order to study the population genetics and design the effective conservation methods, we aimed to develop microsatellite primers for this species in the present study. We developed eight new microsatellite loci for this species through biotin capture method. Polymorphism of each locus was further assessed in 18 individuals from three geographically distant populations. The number of alleles per locus ranged from 6 to 11 with an average of 8.13. The observed and expected heterozygosities ranged from 0.219 to 0.296 and from 0.374 to 0.470, with averages of 0.254 and 0.417, respectively. We further found that three of nine microsatellite loci developed previously for another congeneric species showed polymorphic banding patters. We performed primer-crossing tests of these loci in the other two congeneric species which are closely related to C. chenggiana (C. gigantea and C. duclouxiana). These microsatellite markers would be effective for analyzing genetic diversity and population genetic structure of this species and its morphological differentiation with the close relatives.     

Genetic Variation in Hippophae rhamnoides ssp. sinensis (Elaeagnaceae) Revealed by RAPD Markers

Hippophae rhamnoides ssp. sinensis is endemic to China, and it is a dioecious, outcrossing plant. Although many studies have been undertaken mainly on its agricultural, nutritional, medical, and ornamental value, little is known about its population genetics. This study uses random amplified polymorphic DNA to investigate the genetic diversity and population genetic structure of 13 natural populations of the subspecies sinensis. Fifteen primers amplified 107 reproducible bands, with 95 (88.79%) being polymorphic. The gene diversity within population was 0.168, considerably lower than that of tree species and most perennial, outcrossing species, but higher than that of annual or short-lived, selfing species. The Gst value showed that 18.3% of the total genetic variation resided among populations, a little lower than that of outcrossing species. The present results are quite similar to those previously reported in another subspecies, H ssp. . rhamnoides rhamnoides. The low genetic differentiation among populations in ssp. sinensis may be attributed to the long-distance dispersal of seeds facilitated by birds, in addition to its characteristics of outcrossing, wind pollination, and widespread distribution. No association between genetic distance and geographical distribution was found. The population relationships revealed by the UPGMA dendrogram parallel this result, in that genetic distance did not increase with geographic separation. This pattern of population differentiation may imply the adaptation of ssp. s populations to the local environment, given that its habitats vary greatly across its distribution.     

Allozyme variation in the diploid (A genome) populations ofScilla scilloides (Hyacinthaceae)

Allozyme variation at eleven loci encoding seven enzyme systems were examined in 20 populations of diploid (genome AA, 2n = 16)Scilla scilloides in China. In comparison with the average species of seed plants studied, populations of this species display a high amount of genetic variation (A = 2.0, P = 58.6%, H_o = 0.172, and H_e = 0.185). Allozyme variation pattern revealed predominant outcrossing within populations and considerable differentiation (F_ST = 0.314) among populations as well as between the subtropic and temperate regions. The wide distribution, long existence and outcrossing are presumably the main factors responsible for the high genetic diversity within populations. But the gravity dispersal of seeds and pollination by small insects set limits to the increase of genetic variation within populations and promote differentiation between populations and regions. In addition, allozyme variation does not distinguishS. scilloides var.albo-viridis and suggests that subtropic populations may be considered as a genetic entity.     

Differences in allozyme patterns between Diaphanosoma brachyurum and Diaphanosoma mongolianum,as revealed in Central European populations

Recent taxonomic revisions in the genus Diaphanosoma have made the uncertainty in species discrimination with morphological characters obvious. Therefore species characterization on a genetic basis seems to be required.Here we examined the genetic structure of two Diaphanosoma mongolianum populations and three Diaphanosoma brachyurum populations in Central Europe by allozyme electrophoresis. A genetic differentiation between both species was evident. 5 out of 9 tested loci carried diagnostic alleles. Both species differed in their habitat choice: D. mongolianum was adapted to higher trophic levels than D. brachyurum. Co-occurrence was observed in a eutrophic lake. Populations sampled from their preferred habitats showed high genotype diversities.Most genotype frequency distributions were in agreement with Hardy-Weinberg expectations and temporal (between years) changes in genotypic compositions were not common. This indicated annually occurring bouts of sexual reproduction, similar to intermittent Daphnia populations. Genetic differentiation among lakes suggested restricted gene flow.     

Genetic relationships between European and Siberian larch,Larix spp. (Pinaceae), studied by allozymes. Is the Polish larch a hybrid between these two species?

Thirteen populations ofLarix decidua subsp.decidua and subsp.polonica, and three populations ofL. sibirica were investigated by starch-gel electrophoresis. In the populations assayed 61 alleles at 17 loci were revealed. The allozyme data support the earlier observations about close relationships between these two larch species. Nei's genetic distances betweenL. decidua andL. sibirica were relatively small (D = 0.057), however, almost five times larger, on average, than those between populations of the same species. Results obtained in this study disagree withBobrov's hypothesis about the hybrid origin of the Polish larch and suggest a direct origin from the European larch.     

西南地区6种魔芋属植物基于cpDNA序列的遗传多样性研究

研究野生作物资源的遗传变异及分化机制对种质资源的收集与改良具有重要意义。魔芋是我国西南地区的特色经济作物,但由于受到人为活动干扰,野生种群不断衰退。为评估西南地区魔芋属(Amorphophallus)野生群体的遗传多样性,探究代表性物种的系统发育地位,该研究利用3个叶绿体DNA(cpDNA)片段,分析了魔芋6个物种的遗传多样性,重建了种间系统发育关系。结果表明:(1)西南地区野生魔芋群体的遗传多样性普遍较低,虽然单倍型多样性(H_d)均值为0.428,但近一半群体只有1个单倍型,6个物种整体水平上的单倍型多样性在0.704到0.983之间。(2)在6个物种间检测到高水平的遗传分化,遗传分化系数(F_ST)值在0.481到0.967之间。(3)系统发育分析表明,选取的27个魔芋种主要聚成3个分支:非洲分支、东南亚分支和东亚大陆分支。疣柄魔芋(A. paeoniifolius)隶属于东南亚分支,而东亚大陆分支A包含花魔芋(A. konjac)和西盟魔芋(A. krausei),东亚大陆分支B由东亚魔芋(A. kiusianus)、滇魔芋(A. yunnanensis)和东京魔芋(A. tonkinensis)构成。生境隔离与人为干扰造成了西南地区野生魔芋群体较低的遗传多样性,魔芋属东亚大陆分支的分化可能与早期的快速扩张和生态适应有关。该研究为西南地区魔芋资源的合理保护、可持续利用和杂交育种提供了参考资料。