Reduced genetic diversity, increased isolation and multiple introductions of invasive giant hogweed in the western Swiss Alps

The giant hogweed ( Heracleum mantegazzianum ) has successfully invaded 19 European countries as well as parts of North America. It has become a problematic species due to its ability to displace native flora and to cause public health hazards. Applying population genetics to species invasion can help reconstruct invasion history and may promote more efficient management practice. We thus analysed levels of genetic variation and population genetic structure of H. mantegazzianum in an invaded area of the western Swiss Alps as well as in its native range (the Caucasus), using eight nuclear microsatellite loci together with plastid DNA markers and sequences. On both nuclear and plastid genomes, native populations exhibited significantly higher levels of genetic diversity compared to invasive populations, confirming an important founder event during the invasion process. Invasive populations were also significantly more differentiated than native populations. Bayesian clustering analysis identified five clusters in the native range that corresponded to geographically and ecologically separated groups. In the invaded range, 10 clusters occurred. Unlike native populations, invasive clusters were characterized by a mosaic pattern in the landscape, possibly caused by anthropogenic dispersal of the species via roads and direct collection for ornamental purposes. Lastly, our analyses revealed four main divergent groups in the western Swiss Alps, likely as a consequence of multiple independent establishments of H. mantegazzianum .     

Invasive species of Heracleum in Europe: an insight into genetic relationships and invasion history

Several species of the genus Heracleum (Umbelliferae) were introduced into Europe from south-west Asia in the 19th century and are now widespread in many countries. At least three invasive taxa with unresolved relationships to one another are thought to occur in Europe: Heracleum mantegazzianum Sommier & Levier, H. sosnowskyi Manden, and H. persicum Desf. ex Fischer. They are tall plants forming extensive stands with a high cover. To elucidate genetic relationships between the species, and gain insight into their invasion history, samples were collected from native ranges in Asia and invaded ranges of the three species in Europe and analysed using amplified fragment length polymorphism. Five other Heracleum species were also studied and in total, 189 samples from 72 populations were analysed. The results confirmed that there are three distinct tall Heracleum species invading in Europe. Within each of the three species, plants collected in the invaded range are genetically close to those from their native ranges. A close genetic relationship between the three invasive Heracleum species in Europe was also found. A high overall genetic variability detected in the invaded range suggests that the majority of invading populations were not affected by a genetic bottleneck and that rapid evolution, drift, or hybridization played a role in genetic structuring of invading populations. For H. mantegazzianum , genetic distance of populations in the native range significantly decreased with geographical distance, but not in the invaded range. It is likely that the current pattern of genetic diversity in Europe resulted from multiple introductions of all three species.     

Microsatellite marker development and analysis in the eastern oyster (Crassostrea virginica): confirmation of null alleles and non-Mendelian segregation ratios

Eighteen microsatellite markers were developed for the Crassostrea virginica nuclear genome, including di-, tri-, and tetranucleotide microsatellite repeat regions that included perfect, imperfect, and compound repeat sequences. A reference panel with DNA from the parents and four progeny of 10 full-sib families was used for a preliminary confirmation of polymorphism at these loci and indications of null alleles. Null alleles were discovered at three loci; in two instances, primer redesign enabled their amplification. Two to five representative alleles from each locus were sequenced to ensure that the targeted loci were amplifying. The sequence analysis revealed not only variation in the number of simple sequence repeat units, but also polymorphisms in the microsatellite flanking regions. A total of 3626 bp of combined microsatellite flanking region from the 18 loci was examined, revealing indels as well as nucleotide site substitutions. Overall, 16 indels and 146 substitutions were found with an average of 4.5% polymorphism across all loci. Eight markers were tested on the parents and 39-61 progeny from each of four families for examination of allelic inheritance patterns and genotypic ratios. Twenty-six tests of segregation ratios revealed eight significant departures from expected Mendelian ratios, three of which remained significant after correction for multiple tests. Deviations were observed in both the directions of heterozygote excess and deficiency.     

Population genetics of an invasive species,Heracleum mantegazzianum: implications for the role of life history,demographics and independent introductions

The population genetic structure of an invasive, nonindigenous riparian weed (Heracleum mantegazzianum) in the northeast of England was investigated using microsatellite DNA markers. Data were used to assess the size and frequency of introductions into three catchments and the subsequent spread. We sampled 13 populations, including a remote population (Perivale, London) for comparison. Five loci were screened and considerable variation was found. Results revealed greater overall variation between populations from different catchments than those in the same catchment, and suggested the generation of population structure in the relatively short time since the initial introduction. Between-catchment variation may reflect population structure generated by local founders as the species spread and may indicate a large initial founder population at the time of the introduction into Britain, or multiple introductions. Within-catchment variation was consistent with expectations based on the water-borne dispersal of seeds in this species, and the relatively small dispersal range of likely pollinators. Independent introductions stand out in some cases as exceptions to the general pattern. Taken together the results are consistent with a relatively large initial founder population, and the subsequent spread of the species in local founder populations, followed by some level of inbreeding within local populations and novel introductions in some localities.     

Predicting the distribution of the invasive alien Heracleum mantegazzianum at two different spatial scales

Modelling the distribution of invasive alien species is widely used for predicting future dispersal, response to climate change, and effects of management, but little information is available on the scale dependence of spatial models. This study is focused on Heracleum mantegazzianum , a problematic invasive plant in central and north-western Europe. The main objective was to model the current distribution of this species at national (43,000 km²) and regional scale (4900 km²) using autologistic regression with a Danish data set. Presence–absence data were used in a grid system with 5 × 5 km² or 2 × 2 km² as basic units. To avoid misleading presence–absence models and unreliable probability values due to unbalanced data, the prevalence was used as cut-off value, and a favourability function was applied to the model predictions. The national model showed a widespread distribution of H. mantegazzianum with highest habitat suitability in the eastern and northern parts of the country where human population density is high, winters more severe and/or loamy soils more common. At a regional scale the distribution of H. mantegazzianum is associated with alluvial sand cover, high human population density, spring precipitation, and presence of the species in neighbour grid units. The observed widespread national distribution is likely the result of anthropogenic spread of this ornamental plant, while the locally clumped distribution suggests that H. mantegazzianum naturally spreads mainly over short distances. The current distribution in Denmark resembles an intermediate invasion stage where long-distance dispersal is less important, while spread from suitable neighbour habitats is significant. The study demonstrates that the favourability function leads to improved mapping standards for invasive species.     

Analysis of particle motion in sieve tubes of Heracleum

Abstract. We have cine-filmed the random motion of microscopic particles, mostly starch grains from ruptured plastids, in sieve tubes of Heracleum mantegazzianum L. and H. sphohdylium Somm. and Lev. Our frame-by-frame analysis of the positions of the particles shows that they move much less than calculated when generally accepted estimates for the viscosity of sieve-lube sap are inserted in the Stokes-Einstein and other equations for Brownian motion. Our analysis of a film, of similar particles, made by previous workers leads us to disagree with their conclusion that particle movement in sieve tubes was greater than should be expected for ordinary Brownian motion. Particles in their film and in ours moved less than expected even when we allow for the possibility that the particles are restricted by cell walls and by each other. We suggest that the particles move less than expected because the viscosity of sieve-lube sap may be higher than has been assumed by physiologists.     

Epidermal features of Heracleum mantegazzianum Somm. & Lev., H. sphondyliutn L. and their hybrid

Leaf surfaces of the native Heracleum sphondyliutn , the alien Heracleum mantegazzianum and the interspecific hybrid were examined using SEM and light microscopy. The surfaces differed in hairiness, especially in the length of the hairs, although the hairs did not differ in general form, or distribution on the leaf surface. Stomata differed little in length, width or frequency, but there were differences in the sort of stomata in relation to the surrounding epidermal cells. The hybrid material was intermediate between the parental species, and sometimes displayed aberrant trichomes that were contorted in contiguous pairs.
The results are discussed in relation to other work on the epidermal features of the Umbelliferae: as a means of discriminating the three taxa, and in relation to the ecological distributions of the species.     

Reconciling patterns of inter-ocean molecular variance from four classes of molecular markers in blue marlin (Makaira nigricans)

Different classes of molecular markers occasionally yield discordant views of population structure within a species. Here, we examine the distribution of molecular variance from 14 polymorphic loci comprising four classes of molecular markers within approximately 400 blue marlin individuals (Makaira nigricans). Samples were collected from the Atlantic and Pacific Oceans over 5 years. Data from five hypervariable tetranucleotide microsatellite loci and restriction fragment length polymorphism (RFLP) analysis of whole molecule mitochondrial DNA (mtDNA) were reported and compared with previous analyses of allozyme and single-copy nuclear DNA (scnDNA) loci. Temporal variance in allele frequencies was nonsignificant in nearly all cases. Mitochondrial and microsatellite loci revealed striking phylogeographic partitioning among Atlantic and Pacific Ocean samples. A large cluster of alleles was present almost exclusively in Atlantic individuals at one microsatellite locus and for mtDNA, suggesting that, if gene flow occurs, it is likely to be unidirectional from Pacific to Atlantic oceans. Mitochondrial DNA inter-ocean divergence (FST) was almost four times greater than microsatellite or combined nuclear divergences including allozyme and scnDNA markers. Estimates of Neu varied by five orders of magnitude among marker classes. Using mathematical and computer simulation approaches, we show that substantially different distributions of FST are expected from marker classes that differ in mode of inheritance and rate of mutation, without influence of natural selection or sex-biased dispersal. Furthermore, divergent FST values can be reconciled by quantifying the balance between genetic drift, mutation and migration. These results illustrate the usefulness of a mitochondrial analysis of population history, and relative precision of nuclear estimates of gene flow based on a mean of several loci.     

中国独活属的分支分类学研究

研究运用分支分析方法研究了16种独活属植物的系统发育关系。采用最简约性分析的分支与界限法Branch—and—Bound(bandh)的严格一致树(thestrict consensus cladogram)和非加权配对算术平均法up weighted pair group method using arithmetic average method(UPGMA)对其进行分支分析。研究结果表明：两种方法均支持将独活属分为4个组,即多裂叶组Sect．Millefolia、多毛组Sect．Villosa、多管组Sect．Plurivittata、独活组Sect．Heracleum。《中国植物志》中少管组Sect．Wendia的法落海Heracleum apaense没有独立成组,它的系统位置还需要进一步研究。根据PAUP软件分析中的不同处理方法,探讨了中国独活属植物的系统进化及其起源问题。     

Development and characterization of polymorphic markers for the sap-stain fungus Ophiostoma quercus

Eight polymorphic markers were developed from South African isolates of Ophiostoma quercus. The genome was screened for repeat regions using the fast isolation by amplified fragment length polymorphism of sequences containing repeats protocol and 20 de novo primer pairs flanking putative microsatellite regions were designed. Eight loci were optimized and their polymorphisms evaluated by sequencing. The repeat and flanking regions were highly polymorphic containing both indels and base-pair substitutions revealing a total of 46 alleles in 14 isolates and an average heterozygosity of 0.68. Substantial sequence variability makes these markers useful for genotyping populations in order to calculate diversity and monitor global movement of O. quercus.     

A novel set of microsatellite marker loci linkage-mapped in the house musk shrew, Suncus murinus.

Ten microsatellite DNA loci developed for the white-toothed shrew (Crocidura russula) were tested for PCR amplification and for utility in linkage studies in the house musk shrew, Suncus murinus. Four primer pairs successfully yielded PCR amplicons and showed polymorphism between two mutant strains, BAN-kc,oeb and WZ. Cloning and sequencing of the PCR amplicons of all the four loci confirmed the presence of microsatellite sequences. Alleles segregating in an F2 resource population constructed from the two strains ranged between two and five. Linkage analysis of the four loci together with 18 other polymorphic markers and three mutant loci resulted in five linkage groups containing three newly mapped microsatellite loci. This study reports the first microsatellite markers being registered in this species.     

林麝微卫星座位的分离和鉴定

利用改进的磁珠富集法从林麝(Moschus berezovskii)的基因组中分离到10个新的(AC)n重复微卫星座位,并分析其在24个林麝个体(取样于中国四川金凤山群体)中的多态性。其中,5个位点在24个林麝个体中具有4—13个等位基因,观察杂合度和期望杂合度分别是0.429—0.957和0.587—0.902,平均多态信息含量是0.730。表明这5个微卫星位点具有高度的多态性,可以用于林麝遗传多样性研究,对林麝的保护具有很重要的意义。     

Isolation and characterization of polymorphic microsatellite loci in the field vole,Microtus agrestis,and their cross‐utility in the common vole,Microtus arvalis

We developed nine polymorphic microsatellite loci for the field vole, Microtus agrestis. The number of alleles ranged from five to 15 and observed heterozygosities ranged from 0.40 to 1.00. We also tested the microsatellite loci for amplification and polymorphism in the congeneric species Microtus arvalis. Five of the nine loci were successfully analysed in this species. The microsatellite markers will be employed in studies of reproductive success and fine‐scale spatial genetic structure.     

Comparing the rate of invasion by Heracleum mantegazzianum at continental, regional, and local scales

This paper compares the rate of invasion of Heracleum mantegazzianum (Apiaceae), a Caucasian species invading Europe, at three spatial scales (continental, regional, and local). The rate of invasion was evaluated using inclusion curves, by plotting the cumulative number of invaded countries against time on the continental scale of Europe, number of occupied grid cells at the regional scale of the Czech Republic, and invaded area inferred from a series of aerial photographs taken at the local scale over a period of 49 years in the Slavkovký les region, Czech Republic. Time of 50% inclusion (with 95% confidence intervals, CI) of invaded countries, occupied grid cells, and invaded area was assessed. The invasion was slowest at the continental scale (62 years, CI = 53–70) and did not differ significantly between regional (16 years, CI = 10–20) and local (22 years, CI = 19–24) scales. Our results indicate that there are two different mechanisms of spread acting together in this system, namely human influences and natural spread, and the relative influence of these mechanisms appears to change in an inverse proportion from the largest to the smallest scale. At the local scale, under suitable habitat conditions, the process is driven by biological traits of the species related to dispersal. At the continental and regional scales, humans played a crucial role in the invasion of H. mantegazzianum by planting it as a garden ornamental. At these scales, human-mediated dispersal seems to have been the major driver of spread, responsible for creating dispersal foci in the initial phases of invasion. Species traits played an important role in local spread, resulting in the colonization of new sites.     

The relationship between microsatellite polymorphism and recombination hot spots in the human genome

Although previous studies have failed to detect an association between microsatellite polymorphism and broadscale recombination rates in the human genome, there are several possible reasons why such a relationship could exist. For instance, there might be a direct link if recombination is mutagenic to microsatellite sequences or if polymorphic microsatellites act as recombination signals. Alternatively, recombination could exert an indirect effect by uncoupling of natural selection at linked loci, promoting polymorphism. As recombination is concentrated in narrow hotspot regions in the human genome, we investigated the relationship between microsatellite polymorphism and recombination hot spots. By using data from a common allele frequency database, we found several polymorphism estimates to be similar for hot spots and the genomic average. However, this is likely explained by an ascertainment bias because markers with high polymorphism information content are usually selected for genotyping in human populations and pedigrees. In contrast, by using an unbiased set of shotgun sequence data, we found an excess of microsatellite polymorphism in recombination hot spots of 14%. However, when other genomic variables are taken into account in a generalized model and using wavelet analysis, the effect is no longer detectable and the only firm predictor of microsatellite polymorphism is the incidence of SNPs and indels. One possible neutral explanation to these observations is that there is a common denominator affecting the local rate of mutation in unique as well as in repetitive DNA, for example, base composition.     

Characterization of 13 polymorphic microsatellite loci in the Japanese land leech

We developed 13 polymorphic microsatellite loci of the Japanese land leech (Haemadipsa japonica; Haemadipsidea) using an Illumina MiSeq sequencing approach. A total of 42,064 nuclear DNA contigs were filtered for microsatellite motifs, among which 30,873 simple sequence repeat loci were identified. From these sequences, we selected 30 primer sets, and 13 of these loci were successfully amplified. Polymorphism of the 13 loci was tested using 16 individuals sampled from sixteen populations across Japan. The number of alleles and polymorphism information content varied from 5 to 17 and 0.335 to 0.883, respectively, and observed and expected heterozygosity values ranged from 0.143 to 0.875 and 0.349 to 0.893, respectively, indicating that these loci are polymorphic. Furthermore, we established useful multiplex PCR using these loci. The 13 microsatellite loci described in this paper are the first nuclear microsatellite markers for a land leech species.     

Novel Polymorphic Microsatellite Markers for Panulirus ornatus and their Cross-species Primer Amplification in Panulirus homarus

Polymorphic microsatellite loci were isolated for Panulirus ornatus using 454 GS-FLX Titanium pyrosequencing. Fifteen markers containing perfect di-, tri-, tetra-, and penta-nucleotide motifs were consistently co-amplified in five multiplexes in a panel of 91 randomly selected samples. Observed number of alleles varied from 2 to 14 per locus. Observed and expected heterozygosity ranged from 0.090 to 0.79 and 0.08 to 0.87, respectively. Ten loci deviated from Hardy-Weinberg equilibrium after sequential Bonferroni correction. Genetic linkage disequilibrium analysis between all pairs of the loci showed significant departure from the null hypothesis between 11 loci. The microsatellite markers were also amplified successfully in related Panulirus homarus species with adequate level of polymorphism. The successful cross-species primer amplification of the 15 microsatellites indicates the potential of the developed markers to be transferred to other Panulirus species. The 15 novel microsatellite markers reported in this work add to the previously characterized markers by our group, exhibit adequate levels of polymorphism for wide range of future studies investigating population structure, genetic diversity, and evolutionary relationships among Panulirus species.     

Heterologous nuclear and chloroplast microsatellite amplification and variation in tea, Camellia sinensis.

The advantage of the cross transferability of heterologous chloroplast and nuclear microsatellite primers was taken to detect polymorphism among 24 tea (Camellia sinensis (L.) O. Kuntze) genotypes, including both the assamica and the sinensis varieties. Primer information was obtained from the closely related Camellia japonica species for four nuclear microsatellites, and from Nicotiana tabaccum for seven universal chloroplast microsatellites. All of the nuclear microsatellite loci tested generated an expected DNA fragment in tea, revealing between three and five alleles per locus. Four out of the seven chloroplast microsatellites primers amplified positively, and of these only one was polymorphic with three alleles, which is in agreement with the conserved nature of chloroplast microsatellites at the intraspecific level. A factorial correspondence analysis carried out on all genotypes and nuclear microsatellite alleles separated the assamica and sinensis genotypes into two groups, thus demonstrating the value of these markers in establishing the genetic relationship between tea varieties. Genetic diversity measured with nuclear microsatellites was higher than that measured with other types of molecular markers, offering prospects for their use in fingerprinting, mapping, and population genetic studies, whereas polymorphisms detected at a cpSSR locus will allow the determination of plastid inheritance in the species.     

食蟹猴微卫星DNA标记遗传监测及多态性分析

目的研究国内食蟹猴种群的遗传背景特性,建立食蟹猴种群遗传质量监测方法。方法采用微卫星DNA遗传标记技术对50只食蟹猴种群个体进行遗传质量监测及DNA多态性分析。结果从100个微卫星DNA位点中筛选出20个多态性高的位点,其食蟹猴种群个体的等位基因数目为5-10条,个体间均呈现高度的多态性;其观察等位基因数（Na）为5.0～10.0,有效等位基因数（Ne）为4.6118～8.3404,基因多样性（H）为0.7832～0.8801和香隆信息指数（I）为1.5651～2.1592。结论本实验有效地分析了食蟹猴种群的遗传多态性,为今后筛选特异性微卫星位点来建立食蟹猴种群遗传质量监测方法提供了理论依据。     

Karyotype and cytogeography of the genus Heracleum （Apiaceae） in the Hengduan Mountains

In the present study, the karyotypes of 34 populations belonging to 11 species and one variety of Heracleum from the Hengduan Mountains in China were examined. Chromosome numbers and the karyotypes of three species （H. souliei, H. la＇ngdoni, and H. wenchuanense） are reported for the first time, as are the karyotypes of H. moellendorffii and H. henryi （tetraploid）. Populations of H. candicans, H. franchetii, and H. kingdoni in the Hengduan Mountains were found to consist of a mixture of diploid and tetraploid plants. Except for four species of Heracleum, namely H. candicans, H. franchetii, H. henryi, and H.kingdoni, which have both diploid and tetraploid karyotypes, all other species of Heracleum are were found to be diploid. All karyotypes were found to belong to the 2A type of Stebbins, with the exception ofH. candicans var. obtusifolium, which belongs to 2B, and H. hemsleyanum and H. franchetii （Mt. Dujuan, Daocheng, Sichuan, China）, which belong to 1A. There was only a slight difference in the karyotype asymmetry index, which suggests a close kinship for species of Heracleum and that the entire phylogenetic development of Heracleum is relatively primitive. Species that exhibited advanced morphological features were also more advanced in karyotype structure, with the order ofkaryotype evolution being 1A→2A→2B. This phenomenon indicates that the species distributed in the Hengduan Mountains have not diverged completely and that the Hengduan Mountains are a relatively young and active area for the evolution of Heracleum. Polyploidization in Heracleum may be an important evolutionary mechanisms for some species, generating diversity. The biological attributes, distribution range, and the geological history of the genus have all played a part in accelerating the evolution through polyploidization or aneuploidization. It is known that as the distribution latitude of Heracleum decreases from north to south, the chromosome number, ploidy level, and asymmetry structure appear to increase. In the Hengd