Allozyme and morphological variation in two subspecies of Dryas octopetala (Rosaceae)in Alaska

The Alaskan endemic shrub Dryas octopetala ssp. alaskensis and its circumpolar conspecific ssp. octopetala are adapted to closely adjacent habitats in alpine areas of Alaska. These alpine areas form geographically disjunct "islands" among which there are limited opportunities for gene flow. Allozyme electrophoresis and a common garden experiment were used to examine genetic variation between subspecies and among disjunct populations of each subspecies. Overall, allozyme variation in D. octopetala is low with little differentiation among populations or between subspecies. Morphological differences, however, are greater between subspecies than among populations within subspecies. Divergence for a few morphological and life-history characters has apparently occurred in response to strong selection, but without divergence at allozyme loci. The ancestors of both subspecies of D. octopetala in Alaska were isolated during the Pleistocene in the glacial refugia of Alaska and Yukon, which may explain low overall variation. Dryas. o. alaskensis is thought to be a Pleistocene derivative of ssp. octopetala, which may account for the low allozyme divergence between subspecies. Recent restriction to alpine areas may explain the low differentiation among disjunct populations.     

High functional diversity in deep‐sea fish communities and increasing intraspecific trait variation with increasing latitude

Variation in both inter‐ and intraspecific traits affects community dynamics, yet we know little regarding the relative importance of external environmental filters versus internal biotic interactions that shape the functional space of communities along broad‐scale environmental gradients, such as latitude, elevation, or depth. We examined changes in several key aspects of functional alpha diversity for marine fishes along depth and latitude gradients by quantifying intra‐ and interspecific richness, dispersion, and regularity in functional trait space. We derived eight functional traits related to food acquisition and locomotion and calculated seven complementary indices of functional diversity for 144 species of marine ray‐finned fishes along large‐scale depth (50–1200 m) and latitudinal gradients (29°–51° S) in New Zealand waters. Traits were derived from morphological measurements taken directly from footage obtained using Baited Remote Underwater Stereo‐Video systems and museum specimens. We partitioned functional variation into intra‐ and interspecific components for the first time using a PERMANOVA approach. We also implemented two tree‐based diversity metrics in a functional distance‐based context for the first time: namely, the variance in pairwise functional distance and the variance in nearest neighbor distance. Functional alpha diversity increased with increasing depth and decreased with increasing latitude. More specifically, the dispersion and mean nearest neighbor distances among species in trait space and intraspecific trait variability all increased with depth, whereas functional hypervolume (richness) was stable across depth. In contrast, functional hypervolume, dispersion, and regularity indices all decreased with increasing latitude; however, intraspecific trait variation increased with latitude, suggesting that intraspecific trait variability becomes increasingly important at higher latitudes. These results suggest that competition within and among species are key processes shaping functional multidimensional space for fishes in the deep sea. Increasing morphological dissimilarity with increasing depth may facilitate niche partitioning to promote coexistence, whereas abiotic filtering may be the dominant process structuring communities with increasing latitude.     

湖北海棠的等位酶变异和遗传多样性研究

采用超薄平板微型聚丙烯酰胺等电聚焦电泳方法对湖北海棠（Malus hupehensis)的9个野生居群和2个人工栽培居群的等位酶变异和遗传多样性进行了初步研究。通过对12个酶系统29个酶位点的检测,结果表明湖北海棠有25个酶位点的等位基因频率分布差异,,有10个居群发现稀有等位基因,并有11个（37．9％）重复位点;湖北海棠的遗传多样性水平很高,等位基因平均数A＝2．127,多态位点百分率P＝74．927,平均预期杂合度He=0.376;居群间的基因分化系数GST＝0．224。与其他苹果属植物相比,湖北海棠具有中等丰富的遗传变异水平。居群间的基因流仅为Nm=0.866,表明遗传漂变是影响居群遗传变异和遗传结构的一个重要因素。     

Microsatellite markers in coast redwood (Sequoia sempervirens)

Five polymorphic microsatellite markers are described for coast redwood, a hexaploid conifer. Dinucleotide (three), trinucleotide (one) and tetranucleotide (one) repeat loci were isolated from a genomic plasmid library and amplified in a test population of 25 second‐growth redwoods. There were three to 11 alleles per locus and observed heterozygosities ranged from 0.00 to 0.80. The nonheterozygous locus (a CTTA repeat) is probably of chloroplast origin and may have potential as a marker for paternal inheritance.     

Pollination ecology of the high latitude, dioecious cloudberry (Rubus chamaemorus; Rosaceae)

In a 3-yr study, we examined the pollinator guild and intersexual floral characteristics of the dioecious, perennial cloudberry (Rubus chamaemorus), which flowers in early spring. The findings contribute to our general understanding of pollination ecology at high latitudes and provide important information for the commercialization of cloudberry. Female flowers were smaller than males but provided more nectar, although this resource was low in both sexes. Insects from 43 families visited cloudberry flowers, yet four families (Apidae, Halictidae, Muscidae, Syrphidae) represented ca. 87% of all visitors observed. Introduction experiments revealed that apids and muscids are significantly poorer pollinators (based on fruit production) than halictids and syrphids, but when fruit mass or seed set was considered, there were no significant differences between families. Pollinator importance, a product of flower visitation frequency and seed set effectiveness, revealed that the dipterans were of paramount importance to the pollination of cloudberry. Furthermore, they are limited to cloudberry because their lapping mouthparts exclude them from accessing the nutritional rewards of competing Ericaceae flowers. While the total number of pollinator families observed suggest a generalist pollination system, if one considers the dominant pollinators (flies) as a functional group, then this insect-flower relationship could be considered a specialized one.     

Microsatellite markers for assessing genetic diversity of the medicinal plant Paris polyphylla var. chinensis (Trilliaceae)

Paris polyphylla var. chinensis is a perennial herb with medicinal properties that is widely used in traditional Chinese medicine. However, this plant has been on the edge of extinction during the last few decades because of excessive deforestation based on the intense ethnopharmaceutical interest. We isolated 12 microsatellite loci from a (CT)(n)-enriched genomic library of P. polyphylla var. chinensis. The polymorphism at each locus was analyzed by screening 30 individuals from a natural population. The number of alleles ranged from 2 to 5. The observed and expected heterozygosities ranged from 0.000 to 0.467, with a mean of 0.247, and from 0.383 to 0.662 with a mean of 0.537, respectively. Six loci (Pp1, Pp3, Pp6, Pp7, Pp9, and Pp12) were found to significantly deviate from Hardy-Weinberg equilibrium. This may be due to the small population size, inbreeding or null alleles. Five of the pairwise comparisons (Pp1 and Pp4, Pp2 and Pp5, Pp2 and Pp9, Pp2 and Pp12, Pp11 and Pp12) exhibited significant linkage disequilibrium (P < 0.05). We conclude that these microsatellite markers will be useful for population genetic studies of P. polyphylla var. chinensis.     

Chloroplast DNA diversity in the genusRubus (Rosaceae) revealed by Southern hybridization

The variability in chloroplast DNA type of 20Rubus genotypes was examined by Southern hybridization. DNA extracted from theRubus accessions was digested with two restriction enzymes (EcoRI and EcoRV) and heterologous chloroplast DNA sequences from barley and pea were used as probes to detectRubus chloroplast DNA sequences on Southern blots ofRubus total DNA. Restriction fragment length polymorphism was detected and a total of 92 restriction fragments were generated by the probe/enzyme combinations examined. Cladistic principles based on the parsimony assumption were used to assemble a phylogenetic tree based on chloroplast restriction fragment length data. The phylogenetic tree grouped the taxonomically defined species and is in general agreement with information based on morphological criteria. However, the Japanese red raspberryR. illecebrosus was shown to have diverged considerably in terms of evolutionary time from other species in subg.Idaeobatus. Furthermore, the molecular approach provides a quantitative estimate of the relationship between species that is difficult to obtain from morphological data. In order to complement the chloroplast DNA information a ribosomal DNA probe was also included in the analysis and provided further information on the phylogenetic relationships withinRubus.     

S-allele diversity in Sorbus aucuparia and Crataegus monogyna (Rosaceae: Maloideae)

RT-PCR was used to obtain the first estimates from natural populations of allelic diversity at the RNase-based gametophytic self-incompatibility locus in the Rosaceae. A total of 20 alleles were retrieved from 20 Sorbus aucuparia individuals, whereas 17 alleles were found in 13 Crataegus monogyna samples. Estimates of population-level allele numbers fall within the range observed in the Solanaceae, the only other family with RNase-based incompatibility for which estimates are available. The nucleotide diversity of S-allele sequences was found to be much lower in the two Rosaceae species as compared with the Solanaceae. This was not due to a lower sequence divergence among most closely related alleles. Rather, it is the depth of the entire genealogy that differs markedly in the two families, with Rosaceae S-alleles exhibiting more recent apparent coalescence. We also investigated patterns of selection at the molecular level by comparing nucleotide diversity at synonymous and nonsynonymous sites. Stabilizing selection was inferred for the 5' region of the molecule, while evidence of diversifying selection was present elsewhere.     

Structural diversity and regeneration of the endangered Prunus africana (Rosaceae) in Zimbabwe

Prunus africana is endemic to Africa and was included in Appendix II of the Convention on International Trade in Endangered Species (CITES) in 1995. In Zimbabwe, the species was reported to be rare and confined to the Eastern Highlands. The objective of this study was to assess size–class distribution and regeneration levels and to characterize structural diversity of P. africana. Given the clustered nature of the species, adaptive cluster sampling was used based on the assumption that there were more P. africana trees in the neighbourhood of reference trees. Each cluster was terminated when there were no more P. africana trees within a distance of 500 m. Data on diameter and height were collected in each cluster using standard forestry procedures. Regeneration was determined by counting seedlings and saplings within a radial distance of 14 m from the mother tree. Structural indices, that ie, diameter and height differentiation and mingling were determined for a structural group of four trees. Findings from this study indicated poor regeneration, fewer P. africana trees in small and large size classes, dominance of positive height and diameter differentiation and high mingling. These findings have implications on management and conservation of P. africana in Zimbabwe.     

Development of microsatellite markers in a riparian shrub, Spiraea thunbergii (Rosaceae)

? Premise of the study: Microsatellite primers in the deciduous shrub Spiraea thunbergii were developed to investigate genetic diversity and population genetic structure. Cross-species transferability was assayed in four congeneric species. ? Methods and Results: Using a compound simple sequence repeat (SSR) marker method, 10 primer sets were identified in Japanese populations of S. thunbergii. The primers amplified compound SSRs with two to five alleles per locus. More than half of the primers were also amplified in S. prunifolia, S. nipponica var. nipponica, and S. japonica. ? Conclusions: These markers might be useful for future studies of population genetics of S. thunbergii and congeneric species.     

Microsatellite loci for assessing genetic diversity, dispersal and clonality of coral symbionts in 'stress-tolerant' clade D Symbiodinium

Reef corals harbouring clade D Symbiodinium spp. (endosymbiotic dinoflagellates) appear more tolerant of environmental stress. As sea surface temperatures rise, symbioses involving Symbiodinium D may increase in prevalence. For this reason, eight polymorphic microsatellite loci were developed for clade D Symbiodinium. From the analysis of 132 samples originating from cnidarian hosts in the Atlantic, Pacific and Indian Oceans, 4 to 35 alleles were found at each haploid locus and diversity indices ranged from 0.35 to 0.97. Population genetic analyses of these symbionts should reveal how environmental perturbations affect genetic diversity, geographical distributions, and possible host-range expansions to new coral species.     

Microsatellite analysis of relationships among North American plums (Prunus sect. Prunocerasus, Rosaceae)

Fifteen microsatellite primer pairs developed in sweet cherry and peach were used to explore genetic relationships among North American plums (Prunus section Prunocerasus). In all, 186 putative alleles were detected with a mean value of 12.4 per locus. The Jaccard coefficient of similarity was calculated between all pairs of accessions and their genetic similarities represented by a UPGMA dendrogram. Despite the apparent closeness among native American plums as evidenced by their ability to hybridize freely and their very similar ITS and trnL-trnF nucleotide sequences, all pairs of accessions among the North American plums shared fewer than half of their alleles. Some of the relationships suggested by the UPGMA dendrogram are congruent with current taxonomic hypotheses, but others are difficult to interpret. Further resolution of relationships among American plums will require molecular markers more variable than ITS yet less variable than microsatellites.     

Microsatellite markers in the tree peony, Paeonia suffruticosa (Paeoniaceae)

? Premise of the study: Microsatellite primers were developed in the tree peony, Paeonia suffruticosa, to perform paternity tests as well as assignment to variety in special Austrian collections. ? Methods and Results: Using SSR-enriched libraries and EST-mining, 8 polymorphic primer sets were identified in Austrian collections of Paeonia sect. Moutan DC. The primers amplified di- and trinucleotide repeats with 2-6 alleles per locus. All primers also amplified in P. ostii, P. pontaninii var. trolloides, P. delavayi, and P. lutea, and in the herbaceous species P. peregrina and P. tenuifolia (Paeonia sect. Paeon). ? Conclusions: These results show the usefulness of primers in P. suffruticosa for population genetic studies and their ability to cross amplify in related taxa across the genus.     

Microsatellite markers reveal genetic diversity of wild soybean in different habitats and implications for conservation strategies (Glycine soja) in China

Wild soybean individuals were sampled from ten habitat sites in Beijing region, China and were assessed using 36 SSR markers for the genetic variation among the habitat subpopulations. AMOVA analysis showed 57.46 % inter-population and 42.54 % intrapopulation genetic variation. The genetic variation had geographical regionality. The drought-stressed and founder subpopulations intensively reduced genetic diversity, and along-river system habitats appeared to have closer genetic similarity. The bottleneck impact of drought stress appeared to be inferior to the founding effect on subpopulation genetic diversity but superior on genetically geographical grouping. Here, all the subpopulations were found to contain unique alleles. The phenotypic and genetic diversities had similarly fluctuated patterns across the subpopulations. These results here suggest that a conservation strategy should be taken: theoretically as many as possible populations are sampled to maximize the genetic diversity in ex situ conservation of wild soybean within an area in China. Spatial distance should be considered for isolating wild soybean populations when genetically modified soybeans are cultivated in China.     

Comparisons of within-population genetic variation in sexual and agamospermousAmelanchier (Rosaceae) using RAPD markers

We compared genetic variation of sexualAmelanchier bartramiana and facultatively agamospermous (asexually seed-producing)A. laevis at one site where the two species are sympatric. We analyzed 77 random amplified polymorphic DNA (RAPD) markers in 29A. bartramiana individuals and 76 RAPD markers in 31A. laevis individuals. The two species do not differ significantly in mean genetic variation. However, 22.4% of genetic similarity values betweenA. laevis individuals exceed the highest value ofA. bartramiana and may represent the effect of agamospermy. Variation withinA. laevis may be the result of sexuality, hybridization, polyploidy, and other factors.     

Microsatellite markers for genetic studies in the weasel (Mustela nivalis)

This study reports the first set of microsatellite markers for the weasel (Mustela nivalis). We chose to isolate loci with tetranucleotide repeat motifs because they can be scored less ambiguously than the more commonly used dinucleotide loci. All 11 loci showed considerable variation within a population sample of 28 individuals from Portugal, with number of alleles ranging from four to nine per locus and observed and expected heterozygosities ranging from 0.21 to 0.86 and from 0.40 to 0.84, respectively. No linkage disequilibrium was detected between pairs of loci, and only one locus (Mn 1.30) deviated from Hardy–Weinberg equilibrium expectations in the analyzed population sample. Among the 11 loci, Mn 1.30 was the only one for which all known males were homozygous. Analysis of an additional population sample of 23 individuals (14 males and 9 females) from Denmark revealed that all males, but only four females, were homozygous for Mn 1.30, supporting the idea that the locus is X-linked. These novel polymorphic microsatellite markers should be useful in studies of population genetics and molecular ecology of the weasel.     

Chloroplast DNA-based genetic diversity and phylogeography of Pyrus betulaefolia (Rosaceae) in Northern China

Pyrus betulaefolia Bunge, considered as an intermediate between oriental and occidental pear groups, is one of the most important wild pear species. The number of its populations is decreasing because of habitat destruction, fragmentation, and continuous exploitation, so protection and conservation measures are urgently needed. Assessment of its genetic diversity and phylogeography are imperative for its efficient conservation. Two chloroplast DNA intergenic fragments were used to detect genetic diversity and phylogeography of 320 individuals from 18 wild P. betulaefolia populations. Haplotype variation, genetic differentiation, and historical events of the populations were estimated. The results showed that P. betulaefolia populations sampled in northern China contained a high level of genetic diversity (H _T?=?0.826). A significant isolation-by-distance value (r?=?0.587, P?<?0.001, 1,000 permutations) among all 18 populations indicated a correlation between genetic divergence and geographic distance. Four population groups were identified in a neighbor-joining tree based on the genetic distance. Analyses of molecular variation showed that the genetic variation mainly existed among population groups, representing 64.61 % of the total variation. Phylogeographic analyses indicated that the populations of P. betulaefolia experienced a scenario of rapid range expansion, which probably occurred between 608,000 and 204,580 years ago. Meanwhile, both the restricted gene flow with isolation by distance and allopatric fragmentation were crucial processes responsible for shaping the genetic patterns of P. betulaefolia. The occurrence of specific haplotypes might be ascribed to an ancestral introgression or joint retention of an ancestral polymorphism with other Pyrus species at the northern edge of the distribution of P. betulaefolia. Three populations displaying a high level of haplotype diversity and unique haplotypes were assumed to be relict populations of Quaternary glaciation and should have conservation priority. Three additional large populations should also be preferentially protected by building natural preservation zones.