Clonal diversity along a water depth gradient in a declining reed stand as detected by three different genetic methods

Isozyme, RAPD (random amplified polymorphic DNA) and microsatellite techniques were applied to determine the genetic diversity of a reed stand declining at the open water fringe for several decades and the accuracy of these methods was evaluated. Sampling was carried out along three transects parallel with and one transect at right angle to the lakeshore. In isoenzyme investigation, esterase and further 11 polymorphic loci of seven isozymes (with a total of 26 alleles) were analysed and 39 clones were distinguished. RAPD analysis involved 11 random decamer primers and, based on 141 repeatably amplifying and polymorphic RAPD fragments, 52 multilocus genotypes were differentiated. In microsatellite investigation, four primer pairs provided 47 polymorphic allelic variants that determined 37 multilocus phenotypes.Besides the differences, all the three methods revealed high number and intermingling (mixed) arrangement of clones at lower water depths, and low clone number and successive structure at the open water fringe of the stands. Only microsatellite analysis revealed different stages of colonization: old successful clone (colonizing the deeper water but almost completely disappearing at the lakeshore edge) and successful but young clone (with large extension at the lakeshore and just reaching the open water edge of the stand) were also distinguished. Finally, the present paper demonstrated that an appropriate data evaluation could make the result of RAPD comparable to that of microsatellite studies.     

Genetic diversity of Lotus corniculatus in relation to habitat type,species composition and species diversity

The genetic variability of Lotus corniculatus, a common and important fodder legume, was studied in relation to habitat type and to species diversity at a local level. The study was conducted in Cholomontas mountain, northern Greece, at altitudes of 760–870 m. Genetic material was selected from four forested, at the edge of forest, and four open grassland sites, and was studied with the aid of ISSR molecular markers. The plant cover at each study site was measured and the floristic composition was estimated. The percentage of graminoides increased in grassland sites with high grazing intensity, while the abundance of legumes, including L. corniculatus, forbs and woody species, increased in forested sites with low grazing intensity. Gene diversity H_E within the studied populations of L. corniculatus ranged from 0.167 to 0.213 and Shannon index (I) from 0.269 to 0.340. Genetic differentiation was detected between habitats as well as among the populations in each habitat, although it was low, 3% and 7% respectively. However, genetic differentiation was significant within the populations (90%). Genetic diversity of L. corniculatus was not correlated with species diversity (richness and evenness) either within or between populations, while was negatively correlated with L. corniculatus abundance.     

Diversity, host, and habitat specificity of oomycete communities in declining reed stands (Phragmites australis) of a large freshwater lake

We studied the diversity of oomycetes in a declining reed belt (Phragmites australis) of Lake Constance, Germany, using conventional baiting with specific reed and standard oak baits, accompanied by molecular techniques. Apart from an Aphanomyces sp. and a Phytophthora sp., baiting from reed rhizosphere samples from flooded, as well as drier, littoral sites revealed only Pythium spp. A total of 67 oomycete isolates was classified according to PCR-RFLP banding patterns and ITS sequencing, and 18 different sequence types could be separated. The majority of these seemed previously unknown species, as indicated by the degree of similarity to those deposited in nucleotide databases. Species communities in both flooded and drier habitats or both reed and oak baits clearly differed from one another, and only few species occurred in both dry and flooded sites, or in both oak and reed baits. A frequently occurring group of related Pythium species appeared to be specifically associated with reed, and these were the only species that proved pathogenic towards this host in vitro. Our study proved that unexplored natural ecosystems harbour diverse communities of oomycete species with specific habitat and host preferences within close-by, but ecologically contrasting, sites. Among the species isolated, those associated with the predominating plant might accumulate and thus may be reed pathogens of considerable importance.     

To the importance of genetic diversity of Phragmites australisin the development of reed stands

Reed stands in Germany and Europe were investigatedwith respect to their genetic diversity by means ofRandom Amplified Polymorphic DNA (RAPD) via thePolymerase Chain Reaction (PCR-fingerprinting).Different types of clonal distribution could bedistinguished: monoclonal reed stands and polyclonalreed stands, and among the latter, stands with low orhigh numbers of different clones as well as standswith mosaic-like coexisting or intermingling clones.Furthermore, clonal distribution and the expansion ofdifferent clones was observed within a newlydeveloping reed population. The findings appear tosupport a model of colonization postulating thatpopulations initiated by seeds are initiallygenetically diverse, but over time become dominated byone or a few clones adapted to the prevailing siteconditions. Thus, low genetic diversity seems to bethe result of a natural selection process. Clonaldiversity within a reed population and the type ofclonal distribution are discussed with regard to theirimportance for the reed stand's ability to adapt tochanging site conditions and eventually for itssurvival or die-back.     

Clonal diversity of Phragmites australis propagating along water depth gradient

Clonal composition of a large, expanding reed stand was studied with two genetic profiling methods. Sampling was carried out along two parallel, and two perpendicular transects at the shore of Lake Balaton, Hungary, in a 900 m long reed stand, with distances between sampling points ranging from 15 to 30 m. The four primer pairs involved in microsatellite comparisons provided a total of 45 polymorphic allelic variants that determined 61 multilocus phenotypes. Along the transects, clone number decreased towards the deep water. RAPD analysis involved eleven random decamer primers and 115 repeatably amplifying and polymorphic RAPD fragments. Applying our new data evaluation method, highly similar information was gained from RAPD investigation and the microsatellite method on the number and extension of the clones. The results demonstrated that clone competition along a water depth gradient where generative reproduction is allowed only at the lakeshore edge brings about decreasing genetic diversity irrespectively of the health status of reed stand.     

Partitioning the diversity of riverine fish: the roles of habitat types and non-native species

1. Quantifying how biological diversity is distributed in the landscape is one of the central themes of conservation ecology. For this purpose, landscape classifications are being intensively used in conservation planning and biodiversity management, although there is still little information about their efficacy. 2. I used data from 158 running water sites in Hungary to examine the contribution of six a priori established habitat types to regional level diversity of fish assemblages. Three community measures [species richness, diversity (Shannon, Simpson indices), assemblage composition] were examined at two assemblage levels (entire assemblage, the native assemblage). The relative role of non‐native species was quantified to examine their contribution to patterns in diversity in this strongly human influenced landscape. 3. Additive diversity partitioning revealed the primary importance of beta diversity (i.e. among‐site factors) to patterns in species richness. Landscape‐scale patterns in species richness were best explained by between‐habitat type (beta₂: 41.2%), followed by within‐habitat type (beta₁: 37.7%) and finally within‐site (alpha: 21.1%) diversity. Diversity indices showed patterns different from species richness, indicating the importance of relative abundance distributions on the results. Exclusion of non‐natives from the analysis gave similar results to the entire‐assemblage level analysis. 4. Canonical analysis of principal coordinates, complemented with indicator species analysis justified the separation of fish assemblages among the habitat types, although classification error was high. Multivariate dispersion, a measure of compositional beta diversity, showed significant differences among the habitat types. Contrary to species diversity (i.e. richness, diversity indices), patterns in compositional diversity were strongly influenced by the exclusion of non‐natives from the analyses. 5. This study is the first to quantify how running water habitat types contribute to fish diversity at the landscape scale and how non‐native species influence this pattern. These results on riverine fish assemblages support the hypothesis that environmental variability (i.e. the diversity of habitat types) is an indication of biodiversity and can be used in large‐scale conservation designs. The study emphasises the joint application of additive diversity partitioning and multivariate statistics when exploring the contribution of landscape components to the overall biodiversity of the landscape mosaic.     

The role of habitat patches on mammalian diversity in cork oak agroforestry systems

Habitat patches, depending on the degree of differentiation from the matrix, can add few or many elements to the species pool of a particular landscape. Their importance to biodiversity is particularly relevant in areas with complex landscapes, where natural, naturalized, or managed habitats are interspersed by small patches of habitat types with very different biophysical characteristics; e.g., fruit orchards and riparian areas. This is the case of the montado landscape, a cork oak agroforestry system that largely covers south-western Portugal. We evaluated whether the high mammalian biodiversity found in this system is, in part, the cumulative result of the species found in the non-matrix habitats. Our results indicate that in areas where there are inclusions of orchards/olive yards and riparian vegetation in the cork oak woodland, a significantly higher number of mammalian species are present. We further detected a positive effect of low human disturbance on mammal diversity. Ultimately, our results can be used by managers to augment their management options, since we show that the inclusion and maintenance of non-matrix habitat patches in cork oak agro-silvo-forestry systems can help to maximize mammal biodiversity without compromising services associated with agriculture and forestry.     

利用微卫星研究普洱亚洲象种群的遗传多样性

本文采用非损伤性取样法获得普洱地区亚洲象粪便样品113份,试剂盒法提取粪便基因组总DNA,利用9对微卫星引物对DNA进行特异性扩增,CERVUS 3.0软件基因分型得到49个独特的基因型。利用GenAlEx v6.5与Arlequin v3.5进行位点遗传信息检测和种群遗传多样性分析,结果表明：研究采用的所有微卫星位点均未偏离哈迪温伯格平衡,位点的平均等位基因数为3.111,平均香农信息指数为0.804,平均期望杂合度为0.468,平均观测杂合度为0.476。比较相同位点上不同地区亚洲象的遗传杂合度,表明普洱地区亚洲象的种群遗传多样性较低。     

Benthic macrocrustacean and insect assemblages in relation to spring habitat characteristics: patterns in abundance and diversity

We studied variation in benthic macrocrustacean and insect assemblages in relation to spring habitat characteristics in six springs located in a single groundwater area in south-west Finland. We defined five habitat types in the studied springs according to water flow and benthic substrate characteristicsminerogenic brooks, organogenic brooks, helocrenes, floating moss carpets and limnocrene pools. Most studied invertebrate orders, as well as individual taxa, showed differences in relative abundances between the habitat types, but the most common taxa occurred in all springs and habitat types. The studied macroinvertebrates were most abundant in the moss carpet sites and least abundant in the pool sites, but the difference was not statistically significant. We did not observe significant differences in mean taxonomic richness per sample between habitat classes. The observed taxonomic richness in pooled samples of habitat classes was highest in moss carpet habitat and lowest in pool habitat, and the rarefied richness estimate was lowest in pool habitat. Benthic macrocrustacean and insect assemblages varied more between habitat types than between individual springs. In an Nonmetric Multidimensional Scaling ordination analysis, spring brook sites were separated from the moss carpet and pool sites, whereas helocrene sites were widely scattered among sites in other habitat classes. The strongest ecological gradients were related to water flow and the presence of minerogenic substrate, separating lentic and lotic habitats. Abundances of moss and coarse detritus accounted for most of the within-class variation. We identified several indicator species for minerogenic and organogenic brooks and for moss carpet and pool habitats, but none for the helocrenes. We found several occurrences of two crenobiont insect species considered threatened in Finland. We suggest that combined studies on macroinvertebrate and bryophyte assemblages would be a powerful approach in assessing the biodiversity of springs.     

Genetic diversity and population structure of the ark shell Scapharca broughtonii along the coast of China based on microsatellites

As a commercially important species in East Asia, the natural resources of Scapharca broughtonii have been suffering from severe population decline across its main habitats. In China, recovery efforts for S. broughtonii are in progress. To provide scientific bases for fisheries management and conservation program, genetic diversity and population structure of seven wild populations of S. broughtonii from the northern China coast was assessed using seven microsatellite loci in this study. High genetic diversity was present in all the seven populations, as observed in mean allelic richness per locus (11.3–12.5), and average expected heterozygosity (0.835–0.867). No significant difference in allelic richness or expected heterozygosity was observed among the seven populations. Pairwise F_ST estimates and NJ tree topologies based on D_C distances indicated that the seven populations fell into two groups, showing a clear division between the populations from the south and north of the Shandong Peninsula. Genetic differentiation was further analyzed using AMOVA and assignation tests. Genetic barrier analysis using Monmonier algorithm also confirmed that the Shandong Peninsula was the putative barrier separating the northern and southern populations. In addition, marine currents probably play an important role in high gene flow among three populations from the same marine gyre.     

Genetic diversity and dispersal of Phragmites australis in a small river system

Even though the reed, Phragmites australis, is an extensively studied wetland species, little is known about reproduction and dispersal modes within and among reed populations at the scale of small river systems. Using microsatellite analysis of 189 individuals from three adjacent river catchments in the Czech Republic, we elucidated the role of the river corridors in the dispersal of P. australis. Using Bayesian clustering of individuals, we found that 19% of clusters were distributed only along one river, which implied dispersal by water (or by wind) along river corridors, whereas 38% of clusters were widely distributed and were likely the product of wind long-distance dispersal among rivers. Intensive exchange of propagules among river systems is further demonstrated by only 6% of total variance being attributed to the variance among rivers in the AMOVA-analysis. Spatial autocorrelation analysis revealed a decreasing pattern up to 5–10 km and no clear pattern over longer distances. This gives an evidence for pollen and seed dispersal at short distances (up to 1 km), whereas most likely only seed dispersal at longer distances up to 10 km. We found five multilocus genotypes distributed in two different populations. The distances between populations with the same genotype ranged from 0.5 to 10.8 km. This can be interpreted as long-distance vegetative dispersal.     

Polygyny and the breeding success of the great reed warblerAcrocephalus arundinaceus

Settlement date, mating status, and breeding success of individually marked great reed warblers, Acrocephalus arundinaceus, were studied during the 1980–84 breeding seasons in Kahokugata, Ishikawa Prefecture, Japan. Twenty-five per cent of the territorial males were polygynous, of which the majority were bigamous. The settling periods of both sexes were long, extending for 65 days in males and 49 days in females. About 80% of males and females settled in the first half of the settling period, and the settlement date of 28–54% males overlapped with that of females. Many of the late settlers were bachelors and the males which mated earlier tended to be polygynous. The timing of a male's settlement is important in acquiring mates. Fifty-five per cent of eggs laid were lost before fledging, mainly due to predation. The mean number of fledglings was 3.19 per primary female, 2.41 per secondary female, and 2.80 per monogamous female. Comparison of the number of fledglings of females which mated during the same period showed that the presence of another female in the same territory did not adversely affect the breeding success of either of the polygynous females. Polygynous males have the advantage of decreasing the risk of breeding failure under high predation pressure.     

Genetic diversity and population differentiation of the Chinese soft-shelled turtle (Pelodiscus sinensis) in three geographical populations

The Chinese soft-shelled turtle (Pelodiscus sinensis) is one of the most important economical chelonians in the world. To understand the genetic variations of the Chinese soft-shelled turtle in China, 62 individuals were sampled from three localities and 18 polymorphic microsatellite loci tested were used to detect genetic diversity and population structure. Results showed that the genetic diversity of the wild P. sinensis was high. Except for the Wuhu populations, the majority of microsatellite loci are not deviation from Hardy–Weinberg equilibrium in the other two populations. AMOVA analysis indicated that genetic variations occurred mainly within populations (97.4%) rather than among populations (2.6%). The gene flow estimates (Nm) among three geographic populations demonstrated that strong gene flow existed (Nm > 1, mean 6). The present study supported that different habitats, breed turtles escaped, multiple paternity and long evolutionary history may be responsible for the current genetic diversity and differentiation in the wild Chinese soft-shelled turtle.     

Climate change and hydrological regime in arid lands: Impacts of dams on the plant diversity,vegetation structure and soil in Saudi Arabia

As the direct effects of climate change on the hydrological regime, Saudi Arabia has constructed more than 522 dams of various capacities as part of economic and environmental development. The study aims to assess the impact of dams on plant diversity, vegetation structure and soil in Saudi Arabia. Thirty-five stands were selected from the dams of different sizes of Saudi Arabia. Vegetation samples were established before (upstream) and after (downstream) the dam, and at the undammed (unaffected by the dam) to compare species diversity in the dam sites and undammed sites and to document the potential effects of dams on vegetation structure. A total of 151 plant species belonging to 36 families have been recorded. The vegetation associations are essentially shrubby with widespread annuals. Six novel associations were identified with the application of TWINSPAN, DCA, and CCA programs. They were named after the characteristic species as follows: VG I: Acacia gerrardii-Caralluma retrospiciens; VGII: Acacia tortilis-Maerua oblongifolia; VGIII: Lycium shawii-Farsetia aegyptiaca; VG IV: Farsetia stylosa-Cornulaca monocantha; VG V: Suaeda aegyptiaca-Salsola imbricata-Prosopis farcta and VGVI: Xanthium strumarium-Ochradenus baccatus. These plant communities are evaluated and discussed according to their floristic structure, vegetation diversity and edaphic variables. The riparian or streamside zones upstream and downstream that are periodically flooded contain highly diverse plant communities that are structured by flooding, which creates disturbance and acts as a dispersal mechanism for plants than undammed sites.     

Genetic diversity analysis by microsatellite markers in four captive populations of the sika deer (Cervus nippon)

The Chinese sika deer (Cervus nippon) is a rare and vulnerable animal in China for medical use. In this study, the genetic diversity and population genetic structure of 113 Chinese sika deer from 4 populations (Linyi Farm, LF; Linyi Park, LP, Yangzhou Farm, YF; Yangzhou Zoo, YZ) were investigated with 14 microsatellite loci. Eighty-three alleles were detected at the 14 loci in all populations. The expected heterozygosity ranged from 0.257 to 0.863 and the observed heterozygosity from 0.226 to 0.821. The polymorphism information content at different loci ranged from 0.217 to 0.825. The results of the HWE (Hardy–Weinberg equilibrium) tests indicated that only four loci (CEH-5, BL42, Mber70, and CEH-2) were in HWE (P > 0.01). The mean number of alleles per population ranged from 3.21 to 5.64, observed and expected heterozygosities ranged from 0.568 to 0.685, respectively. Positive inbreeding coefficient (F_IS) values were found in every population. F_ST values ranged from 0.101 in the LF to 0.155 in the YZ. The genetic identity ranged from 0.1236 to 0.1645. The genetic distance ranged from 0.4746 to 0.6025. The results of this study indicate moderate genetic variation and polymorphism across the loci. Appropriate breeding strategies should be designed for deer in captivity.     

Genetic diversity and distribution patterns of Ecuadorian capuli (Prunus serotina)

Prunus serotina subsp. capuli (Cav.) is an arboreal species with promising economic prospects in the timber, health-food and neutraceutical markets. Despite its cultural and commercial significance, limited information exists with regards to the degree of genetic variation and ecological history of P. serotina in Ecuador. The main objective of this study was to evaluate the degree of genetic diversity and population structure of Ecuadorian P. serotina, as a preliminary step towards understanding the distribution history of this species in Ecuador and establishing germplasm conservation programs. P. serotina samples (217, representing 8 provinces from the Ecuadorian highlands) were characterized using 8 heterologous SSR markers derived from related Prunus species. Expected heterozygosity across samples (H_e = 0.71) reveals a moderate level of genetic diversity for Ecuadorian P. serotina. Nevertheless, simple allele-count analysis indicates that Ecuadorian capuli has a narrower degree of allelic richness relative to collections from the species’ center of origin in North America. Furthermore, pairwise F statistics (0.0069 ≤ Fst ≤ 0.0319) and Nei genetic distance estimates (0.02 ≤ Ds ≤ 0.09) indicate minimal population differentiation within Ecuadorian capuli. However, Bayesian population structure analysis suggests a subtle genetic contrast between germplasm from the Northern and Southern highlands. Certainly, it is of interest to analyze whether this underlying genetic differentiation between the Northern- and Southern-Highland groups is also manifested in morphological, agronomic or other phenotypic characters that could indicate adaptive differences to divergent agro-ecosystems.