Genetic variation in Haworthia pumila and H. herbacea

Horizontal starch gel electrophoresis was used to examine genetic diversity within and differences between one population each of two morphologically different species of Haworthia, namely H. pumila and H. herbacea. Twenty-five leaf samples of each species were surveyed for 24 proteins of which 13 were useful for routine analysis, and gene products of 16 protein coding loci revealed genetic variation at 7 (43.8%) thereof in both species. Values of 1.63 (± 0.20) and 1.56 (± 0.18) were obtained for the mean number of alleles per locus and the average heterozygosity per locus was calculated at 0.168 (± 0.058) and 0.144 (± 0.048) for H. herbacea and H. pumila respectively. The malate dehydrogenase-2 locus is a potential genetic marker to identify the species studied electrophoretically. The mean genotypic distance index between the populations studied was 0.184, an indication of large degree of differentiation between the species. These values are much higher than values obtained for other members of the Aloaceae, showing that normal levels of genetic variation can be expected in at least some succulent monocotyledons.     

Genetic diversity and population structure in Tunisian Lavandula stoechas L. and Lavandula multifida L. (Lamiaceae)

The genetic diversity and population structure of 20 Tunisian Lavandula stoechas L. and Lavandula multifida L. populations, from different bioclimates, were analysed by starch gel electrophoresis using seven isozymes. The genetic diversity within populations varied according to species. Variation in L. multifida was higher than that observed for L. stoechas, and exclusive alleles were detected for taxa.

A high differentiation among populations, for each species, estimated by Wright's F-statistics was revealed. The genetic structure of populations from the same bioclimate was substantial. Nei's, R. [1978. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89, 583–590] genetic distance among pairs of populations was low. The UPGMA cluster analysis of genetic distance values revealed that populations for each species were not strictly clustered together according to bioclimate or geographic proximity.

For each species, the low genetic divergence among populations and their substantial structure indicate their recent fragmentation due to anthropic pressures. The dendrogram generated from pairwise genetic distance among all populations showed two distinct clusters each corresponding to one species. The high genetic divergence between the two species, based on isozymes, corroborates their taxonomic status, as previously reported using morphological traits. The strategy for the management and conservation of populations should be made for each taxa according to its level of diversity and bioclimate.     

Genetic differentiation between the freshwater subspecies of Gasterosteus aculeatus in Southern California

Samples of Gasterosteus aculeatus microcephalus and the endangered G. aculeatus williamsoni were obtained from downstream and headwaters regions, respectively, of the Santa Clara River system in southern California and electrophoretically examined for the products of 45 loci, six of which were polymorphic. Significant departures from Hardy-Weinberg expectations were evident in genotypic distributions at four of the polymorphic loci indicating a severe restriction of gene flow within the drainage. The genetic distance between these two subspecies was calculated as D = 0.034 ± 0.029, a value comparable to that reported between G. aculeatus microcephalus and G. aculeatus aculeatus from different drainages in northern California.     

Geographical variation in the monoterpenes of Valeriana officinalis Leaf

The variation in terpene composition of the leaf essential oil was studied in three populations of Valeriana officinalis L. subsp, collina. These populations grow in Italy in environmentally very different areas. Our examination of geographically and ecologically distant populations has provided evidence for substantial Iocal intrasubspecific differentiation. Statistical treatment of chemical data revealed two distinct chemical varieties of subspecies collina.     

Morphological, chemical and genetic differentiation of two subspecies of Cistus creticus L. (C. creticus subsp. eriocephalus and C. creticus subsp. corsicus)

Cistus creticus L., an aromatic species from the Mediterranean area, contains various diterpenes bearing the labdane skeleton. The production of essential oil from this species has potential economic value, but so far, it has not been optimized. In order to contribute to a better knowledge of this species and to its differentiation, the morphological characters, volatile chemical composition and genetic data of two subspecies (C. creticus subsp. eriocephalus and C. creticus subsp. corsicus) were investigated. The leaf trichomes were studied using scanning electron microscopy. The chemical composition of Corsican essential oil (C. creticus subsp. corsicus) has been reported using GC, GC/MS and ¹³C NMR; the main constituents were oxygenated labdane diterpenes (33.9%) such as 13-epi-manoyl oxide (18.5%). Using plant material (54 samples) collected from 18 geographically distinct areas of the islands of Corsica and Sardinia, the basis of variation in the headspace solid-phase microextraction volatile fraction and an inter-simple sequence repeat genetic analysis were also examined. It was shown that the two subspecies of C. creticus differed in morphology, essential oil production, volatile fraction composition and genetic data.     

基于线粒体控制区和微卫星标记探讨秦岭细鳞鲑物种有效性

文章基于线粒体控制区基因序列和微卫星标记比较秦岭细鳞鲑(Brachymystax tsinlingensis Li)、黑龙江流域的尖吻细鳞鲑(Brachymystax lenok Pallas)和钝吻细鳞鲑(Brachymystax tumensis Mori)的分子遗传差异,为澄清其分类地位争议提供分子证据。结果表明:(1)扩增217个样本的mtDNA D-loop区序列,共获得45个单倍型,类群间无共享单倍型;基于单倍型构建的系统进化树显示三个细鳞鲑类群呈独立的支系;(2)基于14个呈多态性位点的遗传分化结果表明,秦岭细鳞鲑与尖吻或钝吻细鳞鲑之间的遗传距离均大于尖吻细鳞鲑和钝吻细鳞鲑之间的遗传距离;(3)基于线粒体D-loop和多态性微卫星位点计算出的遗传分化系数(F_ST)都远高于0.25表明三个类群间的遗传分化程度极高。这些结果表明,秦岭细鳞鲑与黑龙江流域细鳞鲑之间遗传分化程度高,结合前期发现秦岭细鳞鲑与黑龙江细鳞鲑类群有明显形态分化的研究结果及它们之间地理隔离已久的现状,研究初步判定秦岭细鳞鲑为独立物种,并建议以Brachymystax tsinlinge...     

Population genetic structure among populations of three predaceous nabid species: Nabis alternatus Parshley, Nabis roseipennis Reuter and Nabis americoferous Carayon (Hemiptera: Nabidae)

An electrophoretic survey of 28 presumptive loci distributed among 15 enzyme systems was conducted to determine the genetic structure among local populations of three predaceous nabid species: Nabis alternatus, N. roseipennis and N.americoferous in human-disturbed habitat. For all three species, F_IS values indicated a deficiency of heterozygotes at most loci in most populations. The amount of genetic differentiation based on the standardized variance, F_ST when combined across all poulations was 0.100 for N. alternatus, 0.189 for N. roseipennis, and 0.335 for N. americoferous. When local populations were grouped according to a set of defined geographical limits, based on the naturally occurring spatial arrangement of the sampled localities, some unexpected patterns of genetic variation were revealed. The degree of genetic differentiation detected among local populations of nabids is discussed in light of the frequent disruptions and ecological changes in their ephemeral habitats.     

海南岛蚯蚓物种组成及其系统发育分析

海南岛独特的地理位置和复杂的古地理事件使其成为我国生物多样性的热点地区。已有的海南岛蚯蚓资料显示, 该岛的蚯蚓区系十分特殊, 且与大陆地区蚯蚓存在扩散与迁移。然而, 当海南岛与周围大陆断开形成独立岛屿后, 海南岛蚯蚓如何为适应海南岛的环境而逐渐形成现在岛内的分布与区系, 仍然是一个值得研究和探讨的问题。因此, 本研究在海南岛全面调查和采集蚯蚓标本, 整理海南岛地区的蚯蚓物种组成及其地理分布特征, 并联合5个线粒体基因COⅠ、COⅡ、ND1、12S rRNA和16S rRNA构建海南岛蚯蚓的分子系统发育树, 推测其分化时间和祖先分布区域, 探讨海南岛蚯蚓在岛内的分化与扩散过程。研究结果表明: (1)海南岛共有蚯蚓6科9属122种, 巨蚓科蚯蚓为优势科, 且全部为环毛类蚯蚓, 其中103种为海南岛特有种。蚯蚓物种数沿海拔呈先增加后减少的趋势, 在800‒1,000 m最大; (2)海南岛环毛类蚯蚓不同水平的遗传距离与我国巨蚓科蚯蚓的遗传距离区间基本一致。物种水平上, 美丽远盲蚓(Amynthas scitulus*)与纬向远盲蚓(A. zonarius)的基因遗传距离最小。在亚种水平, 保宁腔蚓指名亚种(Metaphire magna magna)和保宁腔蚓小型亚种(M. magna minuscula)的遗传距离均接近整体的物种水平。在种群水平, 等毛远盲蚓(A. homosetus)不同种群间遗传距离均接近整体的亚种水平; (3)海南岛环毛类蚯蚓可划分为7个类群, 其祖先于68.26 Ma开始分化, 可能起源于吊罗山。在新生代, 7个类群均得到较大发展。通过对海南岛蚯蚓组成及系统发育的梳理, 不仅为我国蚯蚓物种多样性研究提供基础资料, 也为岛屿蚯蚓物种系统发育关系分析提供科学参考。     

International study on Artemia. XXXII. Combined effects of temperature and salinity on the survival of Artemia of various geographical origin

The brine shrimp inhabits geographically isolated biotopes with specific biotic and abiotic conditions. This has resulted in various geographical strains between which marked genetical, biological and chemical differentiation exists. The response of 13 different Artemia strains to the combined effect of temperature and salinity has been studied. Experimental temperatures tested ranged from 18 to 34°C and salinities from 5 to 120%..

Except for Chaplin Lake (itCanada) Artemia, all strains showed high survival over a wide range of salinities (35–110%.). For all strains the common temperature optimum was between 20 and 25°C. Interaction 7between temperature and salinity was negligible or very limited. Substantial differences in tolerance were recorded in particular at the lower end of the range of experimental salinities and at the upper end of the range of temperatures. Resistance to high temperature seems to be related to the genetic classification of the Artemia strains in different sibling species. Differences, however, also exist among strains from the same sibling species. Genetic adaptation to high temperature seems to take place in Artemia.

The data obtained provide a first guideline for strain selection for specific aquacultural purposes.     

Genomic landscape of parallel domestication of upland rice and its implications

Parallel domestication has been widely acknowledged but itsgenetic basis remains largely unclear. As an important rice ecotype, upland rice was assumedly domesticated multiple times in two rice subspecies (Indica and Japonica) and provides a feasible system to explore the genetic basis of parallel domestication. To uncover the genome‐wide pattern of genetic differentiation between upland and lowland rice and explore the parallelism of genetic changes during upland rice domestication, we obtained whole‐genome sequences of 95 rice landraces and yielded genome‐wide expression data for five tissues of representative accessions of upland and lowland rice. Our phylogenetic analyses confirmed multiple domestications of the upland ecotype in two rice subspecies. Genomic scans based on resequencing data identified substantial differentiation between the upland and lowland ecotypes with 11.4% and 14.8% of the genome diverged between the two ecotypes in Indica and Japonica, respectively. Further genome‐wide gene expression analyses found that 30% of effectively expressed genes were significantly differentiated between two ecotypes, indicating the importance of regulation changes in the domestication of upland rice. Importantly, we found that only 1.8% of differentiated genomes and 1.6% of differentially expressed genes were shared by upland Indica and upland Japonica, suggestive of largely unparallel genetic alterations during upland rice domestication. These findings not only provide new insights into the genetic basis of parallel domestication at the genome scale but could also facilitate geneticimprovement and breeding of rice and crops in general.     

基于COI和ND5序列的中国南部唇鱼骨和间鱼骨群体遗传结构

唇鱼骨和间鱼骨均为分布较广的初级淡水鱼类,是理想的亲缘地理研究材料;且两者形态特征较为相似,不易鉴别,故两者的分布记述和物种有效性存在争议.为了解我国南部唇鱼骨和间鱼骨的群体遗传结构并探讨两者的物种有效性,本研究对8条水系的唇鱼骨和9条水系的间鱼骨共130尾个体的COI和ND5基因序列片段进行了测定,并对这两个基因的组合序列(2151 bp)进行了分析.结果表明: 在130尾个体的COI和ND5基因组合序列中,共有196个核苷酸变异位点,共检测出50个单倍型,单倍型多样性为0.964,核苷酸多样性为0.019,遗传多样性较高.基于COI和ND5基因组合序列构建的 NJ 树显示,所有种群可分为两支,支系Ⅰ包含了韩江和九龙江的全部单倍型以及瓯江的部分单倍型,余下的单倍型组成了支系Ⅱ.两支系间的遗传距离为0.036,而唇鱼骨与间鱼骨之间的遗传距离为0.027.单倍型网络图表明,韩江、九龙江种群和其他水系种群分化较大;漠阳江种群由海南岛种群扩散而来;海南岛各种群及漠阳江种群的单倍型分支与珠江水系单倍型的分支之间的亲缘关系较近,与长江水系单倍型分支之间的亲缘关系则较远;湘江、桂江和柳江之间的亲缘关系较近.AMOVA分析结果显示,地理区之间的变异约占71.2%,地理区内种群间变异约占16.6%,种群内的变异占12.2%,表明其遗传分化主要来自地理区之间.错配分析及中性检验结果显示,全部种群、唇鱼骨种群、间鱼骨种群、支系Ⅰ和支系Ⅱ在历史上均没有发生过明显的扩张.     

Population structure within and between subspecies of the Mediterranean triplefin fish Tripterygion delaisi revealed by highly polymorphic microsatellite loci

Although F(ST) values are widely used to elucidate population relationships, in some cases, when employing highly polymorphic loci, they should be regarded with caution, particularly when subspecies are under consideration. Tripterygion delaisi presents two subspecies that were investigated here, using 10 microsatellite loci. A Bayesian approach allowed us to clearly identify both subspecies as two different evolutionary significant units. However, low F(ST) values were found between subspecies as a consequence of the large number of alleles per locus, while homoplasy could be disregarded as indicated by the standardized genetic distance G'(ST). Heterozygosity saturation was observed in highly polymorphic loci containing more than 15 alleles, and this threshold was used to define two loci pools. The less variable loci pool revealed higher genetic variance between subspecies, while the more variable pool showed higher genetic variance between populations. Furthermore, higher differentiation was also observed between populations using G'(ST) with the more variable loci. Nonetheless, a more reliable population structure within subspecies was obtained when all loci were included in the analyses. In T. d. xanthosoma, isolation by distance was detected between the eight analysed populations, and six genetically homogeneous clusters were inferred by Bayesian analyses that are in accordance with F(ST) values. The neighbourhood-size method also indicated rather small dispersal capabilities. In conclusion, in fish with limited adult and larval dispersal capabilities, continuous rocky habitat seems to allow contact between populations and prevent genetic differentiation, while large discontinuities of sand or deep-water channels seems to reduce gene flow.     

Genetic variation and bill size dimorphism in a passerine bird, the reed bunting Emberiza schoeniclus

In passerine birds morphological differentiation in bill size within species is not commonly observed. Bill size is usually associated with a trophic niche, and strong differences in it may reflect the process of genetic differentiation and, possibly, speciation. We used both mitochondrial DNA (mtDNA) and nuclear microsatellites to study genetic variation between two subspecies of reed bunting, Emberiza schoeniclus schoeniclus and E.s. intermedia , along their distributional boundary in western Europe. These two subspecies are characterized by a high dimorphism in bill size and, although breeding populations of the two subspecies are found very close to each other in northern Italy, apparently no interbreeding occurs. The observed morphological pattern between the two subspecies may be maintained by geographically varying selective forces or, alternatively, may be the result of a long geographical separation followed by a secondary contact. MtDNA sequences of cytochrome b and ND5 (515 bp) showed little variation and did not discriminate between the two subspecies, indicating a divergence time of less than 500 000 years. The analysis of four microsatellite loci suggested a clear, although weak, degree of genetic differentiation in the large- and small-billed populations, as indicated by F _ST and R _ST values and genetic distances. The correlation between bill size and genetic distance between populations remained significant after accounting for the geographical distances between sampling localities. Altogether, these results indicate a very recent genetic differentiation between the two bill morphs and suggest that a strong selection for large bills in the southern part of the breeding range is probably involved in maintaining the geographical differentiation of this species.     

Genetic diversity and population structure of endangered Isoetes coreana in South Korea based on RAPD analysis

Isoetes coreana Chung and Choi is on the list of critically endangered species in South Korea. Using randomly amplified polymorphic DNA (RAPD) markers, we investigated the genetic diversity within and between seven local populations of I. coreana. Ten RAPD primers produced a total of 94 bands, of which 59 (62.8%) were polymorphic. A low level of genetic diversity was recognized within the populations of I. coreana: polymorphic loci (P), with values ranging from 3.4% to 33.9%, and a mean value of 15.5% being observed. Analysis of molecular variance (AMOVA) showed that genetic diversity was greater among populations (81.6%) than within populations (19.7%) or among the three regions included in this study (Han River, Youngsan River, and Nakdong River). In addition, a high degree of genetic differentiation (θ^B = 0.742) was detected among the populations. These results indicate that genetic differentiation has occurred very rapidly. However, the rate of gene flow between populations was found to be as low as 0.059, irrespective of the genetic and geographical distances between the populations, which indicates that genetic drift must have played an important role in forming the present populations of I. coreana. Because a reduction of genetic diversity as a result of genetic drift is undesirable, increasing the gene flow between populations of Korean quillwort I. coreana should be considered as a conservation strategy.     

Genetic differentiation of two distinct chemotypes of Ferula communis (Apiaceae) in Sardinia (Italy)

The giant fennel, Ferula communis L. (Apiaceae) is a circum-Mediterranean species responsible of severe haemorrhagic intoxication of livestock. Electrophoretic analysis of 14 putative enzyme loci was carried out to assess genetic differentiation among poisonous and non-poisonous chemotypes of F. communis in Sardinia. Genetic structuring characterises all the five populations examined. However, differentiation was higher between poisonous and non-poisonous populations (P<0.00001), and was independent from geographic distances, suggesting a reduced gene flow between the two chemotypes.     

Genetic structure of populations of Calomys laucha (muridae, sigmodontinae) from central Argentina

The genetic structure of populations of the Sigmodontinae rodent Calomys laucha was studied by means of allozyme electrophoresis. This highly opportunistic species is found preferably in periodically perturbed habitats of crop fields in central Argentina, where it can attain very high densities. A total of 17 enzymatic proteins assayed gave information on 25 loci; only four were monomorphic in the seven populations studied. Levels of genetic variability (H_o from 0.144 to 0.171; P_95% from 44% to 56%) were higher than mean values reported for mammals and rodents. These high levels of heterozygosity could be maintained by large populations that do not experience great fluctuations in size, or by a social structure consistent in many small breeding groups that are formed and dissappear every breeding season. Genetic differentiation at a macrogeographical scale (θ=0.018) was low but statistically significant, and showed no correlation with geographic distance between pairs of populations. The pattern of population differentiation found is compatible with a relatively recent range expansion.     

Africa goes Europe: The complete phylogeography of the marbled white butterfly species complex Melanargia galathea/M. lachesis (Lepidoptera: Satyridae)

Climatic oscillations influence the distribution of species in time. Thermophilic species survived the ice ages in refugia around the Mediterranean. Northern Africa is one of the possibly important refugia. In this study we test the genetic differentiation between northern African and European populations, using the marbled white butterfly species complex, Melanargia galathea/M. lachesis, as a model. We studied 18 allozyme loci in 876 individuals from 23 populations representing a major part of Europe (northern Spain to Romania) and the western part of northern Africa (Atlas Mountains). The African populations resemble the European ones in allelic richness; their genetic diversity is higher than in Europe. Cluster analysis discriminated five European genetic groups: M. lachesis, a western European lineage, and three eastern European lineages. However, the African samples did not form a separate cluster within this phenogram, but clustered randomly within the Balkan/southeastern European groups. The genetic differentiation among the African populations (F_ST 8.8%) was higher than that within any of the European lineages (F_ST 2.6–5.5%). The high genetic diversity and the relatively strong differentiation of the four African populations sampled in a comparatively limited area of the Atlas Mountains indicate that the most probable origin of M. galathea is northern Africa, with its sibling species, M. lachesis, evolving in parallel in Iberia. Most probably, M. galathea colonised Europe first during the Eem interglacial, some 130 ky ago. Since M. lachesis must have existed on the Iberian peninsula during that period already, M. galathea should have reached Europe via Italy. The genetic differentiation to distinct groups in Europe most probably evolved during the following Würm glacial period.     

Genetic differentiation between the yellow-shafted and red-shafted subspecies of the northern flicker

Red-shafted and yellow-shafted subspecies of the northern flicker do not show statistically significant genetic differentiation. Genetic distance between hybridizing flicker subspecies is lower than average interspecific avian values (as expected), and is small relative to genetic distance values between 'pure' samples from other bird hybrid zones.     

Structure of Pinus sylvestris L. populations in Bulgaria revealed by chloroplast microsatellites and terpenes analysis: Provenance tests

In the present study we investigated the genetic structure and genetic diversity of Pinus sylvestris populations in Bulgaria using chloroplast microsatellite markers and terpene analysis. We were interested in addressing the following questions: (1) can population structure in Scots pine be detected via chloroplast microsatellites markers and terpenes; (2) are there differences in population differentiation between the two analyses; and (3) how are the patterns related to geographic distances. Twelve provenances were chosen throughout the species' range in Bulgaria. Following DNA extraction, chloroplast microsatellite (cpSSR) loci were surveyed using six primer pairs. Between 4 to 8 size variants were identified at each locus. A total of 35 size variants at the six loci were identified, 11 occurring at low frequencies (<1%). They were combined in 134 different haplotypes, of which seven represent 1/3 of the genetic structure. AMOVA analysis revealed that 10.99% of the variation was found among populations, while 89.01% was expressed within populations. The cpSSR analysis divided Scots pine populations into two groups, the first represented by populations located in the south-western part of the Rhodopes and Pirin mountains, while the second group is located in the northeast of Rhodopes and Rila mountains. Terpene analysis revealed that on average, 53% of the monoterpene pool in P. sylvestris was accounted for by -pinene (range 47–59%) followed by β-pinene (range 6–12%). The presence of two distinct groups is weekly consistent with physical distances between populations, similar significant correlation between genetic distance determined by chloroplast microsatellites analysis and chemotype distance (determined by terpenes) was observed. Our results suggest that the structural pattern of genetic diversity of cpDNA in Scots pine populations is the consequence of historical biogeographic processes.