天山一号冰川前沿生态系统真菌群落结构演替及分布格局

【目的】分析真菌群落结构和多样性随着一号冰川退缩前沿年代序列的变化,揭示真菌群落的演替轨迹及环境因子对群落组成的影响。【方法】采用宏基因组学研究方法,结合生物信息学和统计学分析技术,对取自一号冰川末端表面冰尘,底部和前沿14个样品进行总DNA的提取,ITS基因的扩增并使用Illumina Miseq平台测序,通过相关生物地理化学特性综合分析在不同年代序列下真菌群落结构及其演替规律。【结果】经测序,筛选和质控分析获得185103条rawreads,占78.3%的非单序列在97%的相似度聚类分析共得到300个操作分类单元(OTU),共划分为6个门:子囊菌门(Ascomycota,52.7%)、担子菌门(Basidiomycota,16.9%)、壶菌门(Chytridiomycota,15.1%)、接合菌门(Zygomycota,2.4%)和球囊菌门(Glomeromycota,1.2%)。从演替初期到后期阶段虽然子囊菌的序列数逐渐下降而担子菌出现缓慢上升趋势,但子囊菌随着土壤年代序列的增加始终为优势类群,壶菌在冰川底部和前沿基层普遍存在且丰度仅次于子囊菌和担子菌。我们在缺乏植被的最新退缩基层发现依靠自养型宿主存活的活体营养菌,如Taphrinomycetes、Urediniomycetes和Ustilaginomycetes。从冰川底部和前沿基层检测到丰度较高的酵母菌,而粪生真菌(coprophilous fungi)仅仅出现在冰川前沿基层,共23个操作分类单元。球囊菌仅在前沿部分样品中存在,有着十分狭小的生态位分布。【结论】一号冰川前沿随着年代序列的增加真菌群落存在明显的演替轨迹和多样性的显著变化,不同生态位真菌类群组成的相似性较低且都存在明显的指示性真菌类群。     

Analysis of spatial genetic structure in an expanding Pinus halepensis population reveals development of fine-scale genetic clustering over time

We analysed the change of spatial genetic structure (SGS) of reproductive individuals over time in an expanding Pinus halepensis population. To our knowledge, this is the first empirical study to analyse the temporal component of SGS by following the dynamics of successive cohorts of the same population over time, rather than analysing different age cohorts at a single time. SGS is influenced by various factors including restricted gene dispersal, microenvironmental selection, mating patterns and the spatial pattern of reproductive individuals. Several factors that affect SGS are expected to vary over time and as adult density increases. Using air photo analysis, tree-ring dating and molecular marker analysis we reconstructed the spread of reproductive individuals over 30 years beginning from five initial individuals. In the early stages, genotypes were distributed randomly in space. Over time and with increasing density, fine-scale (< 20 m) SGS developed and the magnitude of genetic clustering increased. The SGS was strongly affected by the initial spatial distribution and genetic variation of the founding individuals. The development of SGS may be explained by fine-scale environmental heterogeneity and possibly microenvironmental selection. Inbreeding and variation in reproductive success may have enhanced SGS magnitude over time.     

Initial genetic diversity enhances population establishment and alters genetic structuring of a newly established Daphnia metapopulation

When newly created habitats are initially colonized by genotypes with rapid population growth rates, later arriving colonists may be prevented from establishing. Although these priority effects have been documented in multiple systems, their duration may be influenced by the diversity of the founding population. We conducted a large‐scale field manipulation to investigate how initial clonal diversity influences temporal and landscape patterns of genetic structure in a developing metapopulation. Six genotypes of obligately asexual Daphnia pulex were stocked alone (no clonal diversity) or in combination (‘high’ clonal diversity) into newly created experimental woodland ponds. We also measured the population growth rate of all clones in the laboratory when raised on higher‐quality and lower‐quality resources. Our predictions were that in the 3 years following stocking, clonally diverse populations would be more likely to persist than nonclonally diverse populations and exhibit evidence for persistent founder effects. We expected that faster growing clones would be found in more pools and comprise a greater proportion of individuals genotyped from the landscape. Genetic composition, both locally and regionally, changed significantly following stocking. Six of 27 populations exhibited evidence for persistent founder effects, and populations stocked with ‘high’ clonal diversity were more likely to exhibit these effects than nonclonally diverse populations. Performance in the laboratory was not predictive of clonal persistence or overall dominance in the field. Hence, we conclude that although laboratory estimates of fitness did not fully explain metapopulation genetic structure, initial clonal diversity did enhance D. pulex population establishment and persistence in this system.     

First evidence of cryptic species diversity and significant population structure in a widespread freshwater nematode morphospecies (Tobrilus gracilis)

Free‐living nematodes are ubiquitous and highly abundant in terrestrial and aquatic environments, where they sustain ecosystem functioning by mineralization processes and nutrient cycling. Nevertheless, very little is known about their true diversity and intraspecific population structure. Recent molecular studies on marine nematodes indicated cryptic diversity and strong genetic differentiation of distinct populations, but for freshwater nematode species, analogous studies are lacking. Here, we present the first extensive molecular study exploring cryptic species diversity and genetic population structure of a widespread freshwater nematode morphospecies, Tobrilus gracilis, from nine postglacially formed European lakes. Taxonomic species status of individuals, analysed for fragments of the mitochondrial COI gene and for the large (LSU) and small (SSU) ribosomal subunits, were determined by morphological characteristics. Mitochondrial and nuclear markers strongly supported the existence of three distinct genetic lineages (Tg I–III) within Tobrilus gracilis, suggesting that this morphospecies indeed represents a complex of highly differentiated biological species. High genetic diversity was also observed at the population level. Across the nine lakes, 19 mitochondrial, and seven (LSU) and four (SSU) nuclear haplotypes were determined. A phylogeographical analysis revealed remarkable genetic differentiation even among neighbouring lake populations for one cryptic lineage. Priority and persistent founder effects are possible explanations for the observed population structure in the postglacially colonized lakes, but ask for future studies providing direct estimates of freshwater nematode dispersal rates. Our study suggests therefore that overall diversity of limnetic nematodes has been so far drastically underestimated and challenges the assumed ubiquitous distribution of other, single freshwater nematode morphospecies.     

Spatial and demographic population genetic structure in Catasetum viridiflavum across a human-disturbed habitat

Spatial and temporal genetic structures were examined across sites on islands and mainland (continuous forest) populations of an epiphytic orchid, Catasetum viridiflavum, using 17 polymorphic allozyme loci. I tested whether patches on islands or at mainland sites comprised small local populations or a large population. Low among population differentiation was observed across the landscape suggesting that the species-specific pollinator and tiny wind-dispersed seeds maintain interconnections among distant patches. Temporal genetic structure among stage classes, and among breeding individuals are important components of the maintenance of genetic variation in this orchid. The natural history of this species including small breeding populations, probable high frequency of mating among relatives, and the high rates of seed movement among sites contribute to the high FIS. These data show that physically isolated patches in this epiphytic orchid comprise a single larger genetic population, which is independent of the physical distances among sites. Although quite different in ecological and life history characteristics, the genetic structure of this orchid demonstrates a pattern similar to temperate and tropical trees in fragmented landscapes.     

Population genetic structure and the effect of founder events on the genetic variability of moose, Alces alces, in Canada

Moose, Alces alces, occur naturally throughout most of Canada but successful introductions of known numbers of animals have been made to the islands of Newfoundland and Cape Breton. Five microsatellite loci were used to investigate the population genetic structure and any change in genetic variability due to founder events of moose in Canada. Comparisons of allele frequencies for moose from 11 regions of the country suggested that there are at least seven genetically distinct populations (P < 0.05) in North America, namely Alberta, eastern Ontario, New Brunswick, Cape Breton, Labrador, western Newfoundland, and the Avalon Peninsula of Newfoundland. The average population heterozygosity was approximately 33% (range from 22 to 41%). UPGMA analysis of Nei's genetic distances produced phenograms similar to what would be expected when geographical location and population history are considered. The loss of heterozygosity due to a single founder event (n = 3; two introductions and a natural colonization) ranged from 14 to 30%, and the cumulative loss of heterozygosity due to two successive founder events (an introduction followed by a natural colonization) was 46%. In these examples loss of genetic variability has not been associated with any known phenotypic deviances, suggesting that populations may be established from a small number of founders. However, the viability of these founded populations over evolutionary timescales cannot be determined and is highly dependent upon chance.     

Species diversity and population density affect genetic structure and gene dispersal in a subtropical understory shrub

Aims The dispersal of pollen and seeds is spatially restricted and may vary among plant populations because of varying biotic interactions, population histories or abiotic conditions. Because gene dispersal is spatially restricted, it will eventually result in the development of spatial genetic structure (SGS), which in turn can allow insights into gene dispersal processes. Here, we assessed the effect of habitat characteristics like population density and community structure on small-scale SGS and estimate historical gene dispersal at different spatial scales.Methods In a set of 12 populations of the subtropical understory shrub Ardisia crenata, we assessed genetic variation at 7 microsatellite loci within and among populations. We investigated small-scale genetic structure with spatial genetic autocorrelation statistics and heterogeneity tests and estimated gene dispersal distances based on population differentiation and on within-population SGS. SGS was related to habitat characteristics by multiple regression.Important findings The populations showed high genetic diversity (H e = 0.64) within populations and rather strong genetic differentiation (F ′ ST = 0.208) among populations, following an isolation-by-distance pattern, which suggests that populations are in gene flow–drift equilibrium. Significant SGS was present within populations (mean Sp = 0.027). Population density and species diversity had a joint effect on SGS with low population density and high species diversity leading to stronger small-scale SGS. Estimates of historical gene dispersal from between-population differentiation and from within-population SGS resulted in similar values between 4.8 and 22.9 m. The results indicate that local-ranged pollen dispersal and inefficient long-distance seed dispersal, both affected by population density and species diversity, contributed to the genetic population structure of the species. We suggest that SGS in shrubs is more similar to that of herbs than to trees and that in communities with high species diversity gene flow is more restricted than at low species diversity. This may represent a process that retards the development of a positive species diversity–genetic diversity relationship.     

Agrobacterium rhizogenes-mediated genetic transformation and regeneration of a conifer:Larix decidua

Summary Gene transfer and plant regeneration systems have been developed for European larch (Larix decidua Mill.) in our laboratory. Aseptically germinated young seedlings were hypocotyl wound-inoculated withAgrobacterium rhizogenes strains 11325 containing a wild-type Ri (root-inducing) plasmid. Swollen stems appeared at infected wounds followed by either abundant hairy roots or adventitious shoot buds that developed within 3 to 4 wk after inoculation. No symptoms were seen on wounded but uninoculated seedlings. We demonstrated agrobacteria attached to larch cells by examination of scanning electron micrographs. Subsequently, calli derived from symptomatic tissues exhibited phytohormone autotrophic growth. Adventitious buds were elongated and rooted in vitro before being transferred to the greenhouse where the transformed whole plants grew normally. Transformants tested positive for opine production and transformation was further confirmed by Southern blot analysis with larch genomic DNAs isolated from both proliferated calli and needle tissue of transgenic plants.     

A hierarchical analysis of population genetic structure in Rhizobium leguminosarum bv. trifolii

Little is known about the population processes that shape the genetic diversity in natural populations of rhizobia. A sample of 912 Rhizobium leguminosarum biovar trifolii isolates were collected from naturalized red clover populations ( Trifolium pratense ) and analyzed for 15 allozyme loci to determine the levels and distribution of genetic diversity. Hierarchical analyses compared different sampling levels, geographical separation, and temporal separation. Total genetic diversity across all isolates was H = 0.426, with 57.6% of the total diversity found among isolates obtained from individual red clover plants. Relatively low genetic differentiation among populations and high differentiation among plants within populations was observed; this suggests that gene flow and founder effect act differently at geographical and local scales. Significant differences were observed in (i) allele frequencies among populations and among plants within populations, and (ii) the frequency distribution of the most widespread and the most abundant strains. When multilocus linkage disequilibrium was calculated, significant levels of disequilibrium were observed in the total sample and in three of the eight populations.     

Long distance dispersal and the fate of a gene from the colonization front

There is an increasing recognition that long distance dispersal (LDD) plays a key role in establishing spatial genetic structure during colonization. Recent works, focused on short distance dispersal, demonstrated that a neutral mutation arising at the colonization front can either ‘surf’ with the wave front and reach high frequencies or stay near its place of origin at low frequencies. Here, we examine how LDD, and more generally the shape of the dispersal kernel, modifies this phenomenon and how the width of the colonization corridor affects the fate of the mutation. We demonstrate that when LDD events are more frequent, the ‘surfing phenomenon’ is less frequent, probably because any alleles can get far ahead from the colonization front and preclude the invasion by others alleles, thus leading to an attenuation of the diversity loss. We also demonstrate that the width of the colonization corridor influences the fate of the mutation, wide spaces decreasing the probability of invasion. Overall, the genetic structure of diversity resulted not only from LDD but also particularly from the shape of the dispersal kernel.     

Spatial population genetic structure in Trillium grandiflorum: the roles of dispersal, mating, history, and selection

The roles of the various potential ecological and evolutionary causes of spatial population genetic structure (SPGS) cannot in general be inferred from the extant structure alone. However, a stage-specific analysis can provide clues as to the causes of SPGS. We conducted a stage-specific SPGS analysis of a mapped population of about 2000 Trillium grandiflorum (Liliaceae), a long-lived perennial herb. We compared SPGS for juvenile (J), nonreproductive (NR), and reproductive (R) stages. Fisher's exact test showed that genotypes had Hardy-Weinberg frequencies at all loci and stage classes. Allele frequencies did not differ between stages. Bootstrapped 99% confidence intervals (99%CI) indicate that F-statistic values are indistinguishable from zero, (except for a slightly negative FIT for the R stage). Spatial autocorrelation was used to calculate f the average kinship coefficient between individuals within distance intervals. Null hypothesis 99%CIs for f were constructed by repeatedly randomizing genotypic locations. Significant positive fine-scale genetic structure was detected in the R and NR stages, but not in the J stage. This structure was most pronounced in the R stage, and declined by about half in each remaining stage: near-neighbor f = 0.122, 0.065, 0.027, for R, NR, and J, respectively. For R and NR, the near-neighbor f lies outside the null hypothesis 99%CI, indicating kinship at approximately the level of half-sibs and first cousins, respectively. We also simulated the expected SPGS of juveniles post dispersal, based on measured R-stage SPGS, the mating system, and measured pollen and seed dispersal properties. This provides a null hypothesis expectation (as a 99%CI) for the J-stage correlogram, against which to test the likelihood that post-dispersal events have influenced J-stage SPGS. The actual J correlogram lies within the null hypothesis 99%CI for the shortest distance interval and nearly all other distance intervals indicating that the observed low recruitment, random mating and seed dispersal patterns are sufficient to account for the disappearance of SPSG between the R and the J stages. The observed increase in SPGS between J and R stages has two potential explanations: history and local selection. The observed low total allelic diversity is consistent with a past bottleneck: a possible historical explanation. Only a longitudinal stage-specific study of SPGS structure can distinguish between historical events and local selection as causes of increased structure with increasing life history stage.     

The genetic signature of rapid range expansion by flying squirrels in response to contemporary climate warming

Climate is an important factor limiting species distributions. Historic climate‐change related range movements have modified the genetic diversity of species by the merging and splitting of gene pools and by the effects associated with recurrent founder events. These effects are often inferred, either from retrospective analyses of current genetic patterns or from simulations. Rarely has it been possible for the population genetic effects of range expansion to be examined with contemporaneous demographic data. We characterized the genetic signature of rapid range expansion by southern flying squirrels (Glaucomys volans) and compared these results to a stationary population of the closely related northern flying squirrel (Glaucomys sabrinus) in Ontario, Canada. Samples were taken during an approximately 200 km range expansion by G. volans (1994–2003) and genotyped at 6 (G. sabrinus) and 8 (G. volans) microsatellite loci. For G. volans, but not G. sabrinus, we found evidence of a latitudinal gradient in allele frequencies and a decrease in allelic richness along the axis of expansion. We found no evidence of isolation‐by‐distance in either species or of genetic bottlenecks in the area of G. volans expansion. These results suggest that serial founder events can cause an immediate reduction in genetic diversity following rapid range expansion with high levels of gene flow giving rise to heterogeneity within what would classically be termed panmixia. Given the pace of anthropogenic climate change, and the increasing incidence of range movements in response, this may be an important, immediate consequence of climate change.     

Subpopulation genetic structure of a plant panmictic population of Castanea sequinii as revealed by microsatellite markers

Castanea squinii Dode,an endemic tree widely distributed in China,plays an important role both in chestnut breeding and forest ecosystem function.The spatial genetic structure within and among populations is an important part of the evolutionary and ecological genetic dynamics of natural populations,and can provide insights into effective conservation of genetic resources.In the present study,the spatial genetic structure of a panmictic natural population of C.sequinii in the Dabie Mountain region was investigated using microsatellite markers.Nine prescreened microsatellite loci generated 29-33 alleles each,and were used for spatial autocorrelation analysis.Based on Moran's I coefficient,a panmictic population of C.sequinii in the Dabie Mountain region was found to be lacking a spatial genetic structure.These results suggest that a high pollen-mediated gene flow among subpopulations counteract genetic drift and/or genetic differentiation and plays an important role in maintaining a random and panmictic population structure in C.sequinii populations.Further,a spatial genetic structure was detected in each subpopulation's scale (0.228 km),with all three subpopulations showing significant fine-scale structure.The genetic variation was found to be nonrandomly distributed within 61 m in each subpopulation (Moran's I positive values).Although Moran's I values varied among the different subpopulations,Moran's I in all the three subpopulations reached the expected values with an increase in distances,suggesting a generally patchy distribution in the subpopulations.The fine-scale structure seems to reflect restricted seed dispersal and microenvironment selection in C.sequinii.These results have important implications for understanding the evolutionary history and ecological process of the natural population of C.sequinii and provide baseline data for formulating a conservation strategy of Castanea species.     

The last 50 years of climate‐induced melting of the Maliy Aktru glacier (Altai Mountains,Russia) revealed in a primary ecological succession

In this article, we report and discuss the results obtained from a survey of plants, microorganisms (bacteria and fungi), and soil elements along a chronosequence in the first 600 m of the Maliy Aktru glacier's forefront (Altai Mountains, Russia). Many glaciers of the world show effects of climate change. Nonetheless, except for some local reports, the ecological effects of deglaciation have been poorly studied and have not been quantitatively assessed in the Altai Mountains. Here, we studied the ecological changes of plants, fungi, bacteria, and soil elements that take the form of a primary ecological succession and that took place over the deglaciated soil of the Maliy Aktru glacier during the last 50 year. According to our measurements, the glacier lost about 12 m per year during the last 50 years. Plant succession shows clear signs of changes along the incremental distance from the glacier forefront. The analysis of the plant α‐ and β‐diversity confirmed an expected increase of them with increasing distance from the glacier forefront. Moreover, the analysis of β‐diversity confirmed the hypothesis of the presence of three main stages of the plant succession: (a) initial (pioneer species) from 30 to 100 m; (b) intermediate (r‐selected species) from 110 to 120–150 m; and (c) final (K‐selected species) from 150 to 550. Our study also shows that saprotrophic communities of fungi are widely distributed in the glacier retreating area with higher relative abundances of saprotroph ascomycetes at early successional stages. The evolution of a primary succession is also evident for bacteria, soil elements, and CO₂ emission and respiration. The development of biological communities and the variation in geochemical parameters represent an irrefutable proof that climate change is altering soils that have been long covered by ice.     

Rapid range expansion increases genetic differentiation while causing limited reduction in genetic diversity in a damselfly

Many ectothermic species are currently expanding their geographic range due to global warming. This can modify the population genetic diversity and structure of these species because of genetic drift during the colonization of new areas. Although the genetic signatures of historical range expansions have been investigated in an array of species, the genetic consequences of natural, contemporary range expansions have received little attention, with the only studies available focusing on range expansions along a narrow front. We investigate the genetic consequences of a natural range expansion in the Mediterranean damselfly Coenagrion scitulum, which is currently rapidly expanding along a broad front in different directions. We assessed genetic diversity and genetic structure using 12 microsatellite markers in five centrally located populations and five recently established populations at the edge of the geographic distribution. Our results suggest that, although a marginal significant decrease in the allelic richness was found in the edge populations, genetic diversity has been preserved during the range expansion of this species. Nevertheless, edge populations were genetically more differentiated compared with core populations, suggesting genetic drift during the range expansion. The smaller effective population sizes of the edge populations compared with central populations also suggest a contribution of genetic drift after colonization. We argue and document that range expansion along multiple axes of a broad expansion front generates little reduction in genetic diversity, yet stronger differentiation of the edge populations.     

Microspatial population genetic structure of the Mediterranean shrub Fumana thymifolia

Fumana thymifolia (Cistaceae) is an insect-pollinated, gravity-dispersed evergreen shrub, which is a common component of fire-prone Mediterranean shrubland ecosystems. Despite the availability of basic knowledge on its ecology, little is known of its breeding system and no information is available on its population genetic structure. We explored the within-population genetic structure of this species using amplified fragment length polymorphism (AFLP) molecular markers and related this to predictions based on its breeding system, pollen and seed dispersal. Existing information on the reproductive ecology of F. thymifolia was supplemented by artificial pollination experiments. We determined that self-fertilisation can occur in F. thymifolia but results in reduced fruit set. Significant genetic structuring was detected within the population, a likely consequence of localised seed dispersal in combination with a mixed mating system. In a study site covering approximately 0.5 ha, amova revealed that approximately 9% of genetic variability was distributed among population subsamples. Significant spatial genetic structure was detected, with kinship coefficients being significantly elevated above the null expectation in the first six distance classes (maximum 5 m), and a value of Sp of up to 0.0342, comparable with species having similar ecological characteristics. Weak isolation by distance at the plot scale was detected, suggesting that insect-mediated pollen flow is non-random, despite being more extensive than seed dispersal. Fumana thymifolia provides a promising model for the investigation of both short- and long-term population dynamics in relation to fire frequency within this plant community.     

The effect of geographic range and dichogamy on genetic variability and population genetic structure in Tricyrtis section Flavae

Populations of each of the four species of Tricyrtis sect. Flavae were sampled using enzyme electrophoresis to examine the effect of geographic range and dichogamy on the genetic diversity of the species. The most widespread species, T. nana, had the lowest level of genetic diversity at both the population and the species level. The depauperate genetic diversity at the population level of T. nana appears to result from the high self-fertilization of the species. The low genetic diversity at the species level of T. nana probably resulted from the bottleneck effect during the speciation process in which this species diverged from the progenitor species, T. flava. Genetic differentiation among populations was high in both adichogamous T. nana and protandrous T. flava. High self-fertilization in T. nana and the colonizing nature of T. flava are likely the main factors causing the differentiated population genetic structure. In contrast to a previous study on chloroplast DNA (cpDNA) variation in Tricyrtis sect. Flavae, T. nana was most closely related to T. flava, which corresponds to the morphological resemblance of both species.