胡杨、灰叶胡杨开花生物学特性研究

从居群水平研究了胡杨、灰叶胡杨不同居群的开花物候特征.结果表明:胡杨、灰叶胡杨各居群均表现为雄株开花物候早于雌株,一般可授期开始较散粉期晚1～4 d,结束较散粉期晚2～5 d,并且居群散粉期和可授期的重叠期较长.在同一居群内,胡杨、灰叶胡杨同性单株间开花期的不一致性较高.两个种相比较,胡杨居群的开花进程比灰叶胡杨居群早2～5 d,并且从每日开花株数累积分布来看,胡杨散粉期、可授期为双峰型,灰叶胡杨为单峰型.     

塔里木河上游胡杨与灰杨光合水分生理特性

在自然条件下对塔里木河上游优势树种-胡杨、灰杨的光合水分生理特性进行比较研究.结果表明,整个生长季胡杨、灰杨的光合速率(Pn)、蒸腾速率(Tr,除8月份)日进程均为单峰曲线,水分利用效率(WUE)变化无明显规律性.胡杨与灰杨12:00后Pn的下降主要取决于非气孔因素限制.胡杨Pn、WUE高于灰杨,而Tr低于灰杨,表明胡杨属高光合、低蒸腾、高WUE型树种,灰杨属低光合、高蒸腾、低WUE型树种.胡杨、灰杨枝水势(Ψw)、清晨与正午水势日进程均呈"V"字型曲线,胡杨水势日变幅、正午水势月变幅均小于灰杨,但两树种水势间无显著差异.胡杨与灰杨具有较强的水分吸收和减少水分丧失的能力,但胡杨调节气孔导度(Gs)控制蒸腾失水的能力较强,对干旱环境表现出更强的生态适应性,从而导致两树种产生了种群地理分化.     

胡杨根际细菌提高木本植物对重金属胁迫的耐受性

胡杨是我国西北荒漠地区特有的、对多种非生物逆境具有高抗逆性的树种,但其相关微生物的生态和生理功能研究还比较缺乏.本文从新疆沙雅地区原始胡杨林根际土壤中分离出重金属抗性细菌共72株.其中具有单一重金属(Cu²⁺、Ni²⁺、Pb²⁺或Zn²⁺)抗性的细菌菌株50株,有三重以上重金属抗性的菌株9株.将其中5株多重重金属抗性细菌接种至生根的竹柳插条,进行重金属胁迫下的盆栽培养.结果表明: 在铜或锌胁迫下,5株多重重金属抗性细菌对竹柳的生长抑制有不同程度的缓解,其中假单胞菌Z30和贪铜菌N8菌对铜和锌两种胁迫下竹柳生物量的增长与不接菌对照相比均达到显著差异水平.说明在非重金属污染区生长的胡杨根际存在多样性的重金属抗性细菌,其中一些多重重金属抗性菌对改善重金属胁迫下植物的生长有显著作用,具有应用于木本植物-微生物联合修复环境重金属污染的价值.     

塔河源荒漠河岸林群落物种组成、结构与植物区系特征

为了更好地了解荒漠河岸林植被动态与生物多样性维持机制,于塔里木河干流源头荒漠河岸林内建立6个1 hm²样地,对群落物种组成、数量特征和空间格局等进行综合分析。结果表明,塔河源荒漠河岸林群落结构简单、物种多样性低,共有物种12科15属16种,杨柳科重要值最大（28.97%）,是群落优势建群科。取样面积在0.04 hm²时,包括了87.5%的物种;样地内稀有种和偶见种均占所有物种的12.5%。植物区系贫乏,单种科、属多,温带成分占绝对优势,古地中海成分也占有重要地位,具典型温带区系性质。样地内DBH ≥ 1 cm的活木本个体有2497株,灰胡杨多度占92.95%,胸高断面积和重要值最大,在群落中占绝对优势地位。群落内科、属、种的数量随植株高度级的增加而减少,垂直结构层次分明,由乔木层、灌木层和草本层构成。样地内所有树种平均胸径15.57 cm,径级与高度级结构均呈偏正态分布,缺乏高度≤ 2 m的个体,群落更新不良。优势种灰胡杨、胡杨径级结构均呈单峰型,其中胡杨幼树出现断层,灰胡杨幼苗向幼树发展过程中死亡率极高（92.56%）,均为衰退型种群。两个优势种空间格局呈聚集分布,不同生境下随径级增大空间分布格局变化不同;且两个优势种在空间上相互排斥而占据不同生境,暗示着种间竞争与生境异质性是影响荒漠河岸林物种空间分布格局和物种共存的重要因素。     

塔里木荒漠优势树种气体交换特性与环境因子的关系研究

在自然条件下对塔里木荒漠区优势树种--胡杨、灰叶胡杨的气体交换特性及其与环境因子的关系进行研究.结果表明:(1)在6～9月生长季,胡杨和灰叶胡杨的净光合速率(Pn)、蒸腾速率(Tr,除8月)日进程均为单峰曲线,胞间CO2浓度(GI)呈"V"字型曲线,Pn的峰值出现在12:00,Tr峰值明显滞后于Pn.生长季内胡杨各月份的Pn、水分利用率(WUE)、光能利用率(LUE)均高于灰叶胡杨,而Tr低于灰叶胡杨,气孔导度(Gs)相近.(2)气体交换与环境因子的统计分析表明,光量子通量密度(PPFD)是决定胡杨和灰叶胡杨Pn和Tr的主要环境因子,其次为气温(Tair).(3)灰叶胡杨对PPFD、Tair,、空气相对湿度(RH)的敏感性强于胡杨,通过高蒸腾耗水、低WUE来减轻高温干旱的伤害;胡杨通过主动调节Gs来控制蒸腾失水、提高光合效率,以较高的WUE和LUE适应日益干旱的荒漠环境,表现出较强的生态适应性.     

Divergence population genetic analysis of hybridization between rhesus and cynomolgus macaques

The geographic ranges of rhesus ( Macaca mulatta ) and cynomolgus ( M. fascicularis ) macaques adjoin in Indochina where they appear to hybridize. We used published and newly generated DNA sequences from 19 loci spanning ~20 kb to test whether introgression has occurred between these macaque species. We studied introgression at the level of nuclear DNA and distinguished between incomplete lineage sorting of ancestral polymorphisms or interspecific gene flow. We implemented a divergence population genetics approach by fitting our data to an isolation model implemented in the software IMa. The model that posits no gene flow from the rhesus into the cynomolgus macaque was rejected ( P  = 1.99 × 10⁻⁸). Gene flow in this direction was estimated as 2 Nm ~1.2, while gene flow in the reverse direction was nonsignificantly different from zero ( P  = 0.16). The divergence time between species was estimated as ~1.3 million years. Balancing selection, a special case of incomplete sorting, was taken into consideration, as well as potential crossbreeding in captivity. Parameter estimates varied between analyses of subsets of data, although we still rejected isolation models. Geographic sampling of the data, where samples of cynomolgus macaques derived from Indochina were excluded, revealed a lost signature of gene flow, indicating that interspecific gene flow is restricted to mainland Indochina. Our results, in conjunction with those by others, justify future detailed analyses into the genetics of reproductive barriers and reticulate evolution in these two genome-enabled primates. Future studies of the natural hybridization between rhesus and cynomolgus macaques would expand the repertoire of systems available for speciation studies in primates.     

塔里木荒漠河岸林灰胡杨群落最小面积确定与研究方法比较

荒漠河岸林是塔里木极端干旱区唯一的森林群落类型,群落结构组成简单。我们采用种-面积曲线、群落系数-面积曲线与重要值-面积曲线3种方法对塔里木河上游荒漠河岸林灰胡杨（Populus pruinosa Schrenk）群落最小面积进行研究。结果显示,4种饱和种-面积曲线的拟合效果差异明显,S=aA/（1+bA）和S=a（1-e^-bA）模型拟合的相关系数较高（P < 0.01）,拟合效果优于其它2种模型。当取样面积为100 m²时,可包括群落60%~80%的物种数,取样面积为200 m²时,则可包括群落90%的物种数。群落系数-面积曲线与重要值-面积曲线2种方法确定的群落最小面积均为400 m²,二者克服了种-面积曲线仅关注物种出现与否和饱和种的估算问题,拟合结果更符合实际情况,更适用于塔里木荒漠河岸林最小取样面积的确定。本研究结果表明荒漠河岸林包括60%、80%、90%群落物种的临界抽样面积分别为100 m²、200 m²和400 m ²,可以满足不同研究精度的要求;塔里木河上游荒漠河岸林灰胡杨群落学调查的最适取样面积是400 m²。     

Climatic adaptation and ecological divergence between two closely related pine species in Southeast China

Climate is one of the most important drivers for adaptive evolution in forest trees. Climatic selection contributes greatly to local adaptation and intraspecific differentiation, but this kind of selection could also have promoted interspecific divergence through ecological speciation. To test this hypothesis, we examined intra‐ and interspecific genetic variation at 25 climate‐related candidate genes and 12 reference loci in two closely related pine species, Pinus massoniana Lamb. and Pinus hwangshanensis Hisa, using population genetic and landscape genetic approaches. These two species occur in Southeast China but have contrasting ecological preferences in terms of several environmental variables, notably altitude, although hybrids form where their distributions overlap. One or more robust tests detected signals of recent and/or ancient selection at two‐thirds (17) of the 25 candidate genes, at varying evolutionary timescales, but only three of the 12 reference loci. The signals of recent selection were species specific, but signals of ancient selection were mostly shared by the two species likely because of the shared evolutionary history. F_ST outlier analysis identified six SNPs in five climate‐related candidate genes under divergent selection between the two species. In addition, a total of 24 candidate SNPs representing nine candidate genes showed significant correlation with altitudinal divergence in the two species based on the covariance matrix of population history derived from reference SNPs. Genetic differentiation between these two species was higher at the candidate genes than at the reference loci. Moreover, analysis using the isolation‐with‐migration model indicated that gene flow between the species has been more restricted for climate‐related candidate genes than the reference loci, in both directions. Taken together, our results suggest that species‐specific and divergent climatic selection at the candidate genes might have counteracted interspecific gene flow and played a key role in the ecological divergence of these two closely related pine species.     

濒危物种胡杨和灰叶胡杨总DNA提取及RAPD体系优化

以濒危物种胡杨和灰叶胡杨硅胶干燥的叶片为材料,研究其总DNA提取方法及RAPD-PCR体系优化条件。结果表明,用改良CTAB法提取的DNA适用于胡杨和灰叶胡杨的RAPD分析。优化的胡杨和灰叶胡杨RAPD-PCR体系为:20μL的反应体系中含Mg2+2.5 mmol·L-1、dNTP 0.15 mmol·L-1、引物0.2μmol·L-1、模板DNA100 ng和1.5 U Taq DNA聚合酶。用6条多态性引物对优化体系的稳定性进行检测,结果显示扩增结果稳定,多态性丰富。该优化体系为在分子水平开展胡杨和灰叶胡杨的保护生物学研究提供了技术支持和参考。     

胡杨、灰叶胡杨P-V曲线水分参数的初步研究

运用P-V技术初步研究了人工林胡杨、灰叶胡杨两个树种的水分参数差异,探讨了树种的抗旱性。结果表明灰叶胡杨的主要水分参数(ψ100、ψ0、ROWC、AWC、RWD、ε）明显低于胡杨,渗透调节能力和束缚水含量高于胡杨,表现对干旱环境具有较强的耐旱能力。综合评判表明灰叶胡杨对干旱的适应性较强。     

塔里木河上游天然胡杨林种群空间分布格局与动态研究

以新疆塔里木河上游阿瓦提县天然胡杨林为研究对象,采用相邻格子法进行实地调查,应用方差/均值比率法和5种聚集度指标研究了塔里木河上游天然胡杨林主要种群的空间分布格局与动态特征.结果显示:胡杨群落中除草本西北天冬种群空间分布格局呈随机分布外,其它主要种群均呈聚集分布;拟合检验表明,胡杨、灰叶胡杨种群为聚集分布.种群空间分布动态分析表明,灰叶胡杨在小树、中树与大树阶段均为聚集分布;胡杨种群在小树与中树阶段为聚集分布,但聚集强度减弱,到大树阶段为随机分布.研究表明,物种分布格局主要与物种本身的生物生态学特性和生境有关.     

塔里木河流域胡杨和灰叶胡杨克隆分株空间分布格局

以叶尔羌河下游阿瓦提县天然胡杨和灰叶胡杨混交林、塔里木河上游农一师16团天然灰叶胡杨林和塔里木河中游轮台县天然胡杨林为对象,研究胡杨和灰叶胡杨克隆分株种群的空间分布格局.结果表明: 8种不同取样尺度(5 m×5 m、5 m×10 m、5 m×15 m、10 m×10 m、10 m×15 m、15 m×15 m、15 m×20 m、20 m×20 m)下,3个研究区2物种克隆分株种群的空间分布格局均表现为集群分布,表明集群分布是研究区胡杨和灰叶胡杨克隆分株种群空间分布格局的基本属性;在5 m×5 m尺度上,3个研究区2物种克隆分株种群均表现出负二项参数最小、Cassie指标和聚块性指标最大、聚集强度最大的分布特征.     

Population history of Manihot esculenta (Euphorbiaceae) inferred from nuclear DNA sequences

The nature of gene flow in plants -- including the propensity for interspecific introgression -- makes them interesting candidates for phylogeographical analysis. Plant phylogeography studies have been limited, however, by the availability of suitable intraspecific variation. In this study, DNA sequence variation from a nuclear gene [Glyceraldehyde 3-phosphate dehydrogenase; (G3pdh)] was used to examine the population history of Manihot esculenta ssp. flabellifolia and a potentially hybridizing species, M. pruinosa. These species occur in the rainforest-savanna ecotone adjoining the Amazon basin, a region believed to have undergone major habitat shifts since the Pleistocene. Geographical distributions of the G3pdh haplotypes indicate genetic isolation-by-distance across the range of M. esculenta ssp. flabellifolia. However, there is greater genetic similarity between northeastern and western populations than would be expected given the present species distribution. A nested clade analysis suggests that northeastern and western populations were connected by gene flow until relatively recently, when they became fragmented. This inferred fragmentation event is consistent with post-Pleistocene habitat shifts proposed for the Amazon basin. At the interspecific level, haplotype sharing with M. pruinosa may reflect either recent interspecific introgression or incomplete lineage sorting between these closely related species.     

Speciation of two desert poplar species triggered by Pleistocene climatic oscillations

Despite the evidence that the Pleistocene climatic fluctuations have seriously affected the distribution of intraspecific diversity, less is known on its impact on interspecific divergence. In this study, we aimed to test the hypothesis that the divergence of two desert poplar species Populus euphratica Oliv. and P. pruinosa Schrenk. occurred during the Pleistocene. We sequenced 11 nuclear loci in 60 individuals from the two species to estimate the divergence time between them and to test whether gene flow occurred after species separation. Divergence time between the two species was estimated to be 0.66–1.37 million years ago (Ma), a time at which glaciation was at its maximum in China and deserts developed widely in central Asia. Isolation-with-Migration model also indicated that the two species had diverged in the presence of gene flow. We also detected evidence of selection at GO in P. euphratica and to a lesser extent at PhyB2. Together, these results underscore the importance of Pleistocene climate oscillations in triggering plant speciation as a result of habitats divergence.     

Late Pleistocene climate change promoted divergence between Picea asperata and P. crassifolia on the Qinghai–Tibet Plateau through recent bottlenecks

Divergence during the early stage of speciation can be driven by a population bottleneck via reduced gene flow and enhanced lineage sorting. In this study, we aimed to examine whether such bottlenecks occurred during the initial speciation of two closely related spruce species Picea asperata and P. crassifolia occurring on the Qinghai–Tibet Plateau (QTP). We analyzed sequences of three chloroplast, two mitochondrial DNA fragments and a further 13 nuclear loci from 216 individuals of the two species. Both species showed a low level of genetic diversity in contrast to other congeners occurring in the QTP and adjacent regions. The estimated population sizes of P. asperata and P. crassifolia are less than the ancestral population size before splitting. These results together with multiple statistical tests (Tajima's D, Fu and Li's D* and F*) suggest that these two species underwent recent bottlenecks. Based on approximate Bayesian computation (ABC), we also determined that the period of the population shrinkage was consistent with the interspecific divergence during the late Pleistocene. The reduced population sizes and the divergent selection may together have triggered the initial divergence under high gene flow between these two species. Our results therefore highlight the importance of climatic oscillations during the late Pleistocene in promoting speciation through changing demographic sizes of the ancestral species on the QTP and in adjacent regions.     

MOLECULAR DEMOGRAPHIC HISTORY OF THE ANNUAL SUNFLOWERS HELIANTHUS ANNUUS AND H. PETIOLARIS—LARGE EFFECTIVE POPULATION SIZES AND RATES OF LONG-TERM GENE FLOW

Hybridization between distinct species may lead to introgression of genes across species boundaries, and this pattern can potentially persist for extended periods as long as selection at some loci or genomic regions prevents thorough mixing of gene pools. However, very few reliable estimates of long-term levels of effective migration are available between hybridizing species throughout their history. Accurate estimates of divergence dates and levels of gene flow require data from multiple unlinked loci as well as an analytical framework that can distinguish between lineage sorting and gene flow and incorporate the effects of demographic changes within each species. Here we use sequence data from 18 anonymous nuclear loci in two broadly sympatric sunflower species, Helianthus annuus and H. petiolaris , analyzed within an "isolation with migration" framework to make genome-wide estimates of the ages of these two species, long-term rates of gene flow between them, and effective population sizes and historical patterns of population growth. Our results indicate that H. annuus and H. petiolaris are approximately one million years old and have exchanged genes at a surprisingly high rate (long-term N_efm estimates of approximately 0.5 in each direction), with somewhat higher rates of introgression from H. annuus into H. petiolaris than vice versa. In addition, each species has undergone dramatic population expansion since divergence, and both species have among the highest levels of genetic diversity reported for flowering plants. Our results provide the most comprehensive estimate to date of long-term patterns of gene flow and historical demography in a nonmodel plant system, and they indicate that species integrity can be maintained even in the face of extensive gene flow over a prolonged period.     

Diversity and divergence patterns in regulatory genes suggest differential gene flow in recently derived species of the Hawaiian silversword alliance adaptive radiation (Asteraceae)

The impact of gene flow and population size fluctuations in shaping genetic variation during adaptive radiation, at both the genome-wide and gene-specific levels, is very poorly understood. To examine how historical population size and gene flow patterns within and between loci have influenced lineage divergence in the Hawaiian silversword alliance, we have investigated the nucleotide sequence diversity and divergence patterns of four floral regulatory genes (ASAP1-A, ASAP1-B, ASAP3-A, ASAP3-B) and a structural gene (ASCAB9). Levels and patterns of molecular divergence across these five nuclear loci were estimated between two recently derived species (Dubautia ciliolata and Dubautia arborea) which are presumed to be sibling species. This multilocus analysis of genetic variation, haplotype divergence and historical demography indicates that population expansion and differential gene flow occurred subsequent to the divergence of these two lineages. Moreover, contrasting patterns of allele- sharing for regulatory loci vs. a structural locus between these two sibling species indicate alternative histories of genetic variation and partitioning among loci where alleles of the floral regulatory loci are shared primarily from D. arborea to D. ciliolata and alleles of the structural locus are shared in both directions. Taken together, these results suggest that adaptively radiating species can exhibit contrasting allele migration rates among loci such that allele movement at specific loci may supersede genetic divergence caused by drift and that lineage divergence during adaptive radiation can be associated with population expansion.     

iGLASS: an improvement to the GLASS method for estimating species trees from gene trees

Several methods have been designed to infer species trees from gene trees while taking into account gene tree/species tree discordance. Although some of these methods provide consistent species tree topology estimates under a standard model, most either do not estimate branch lengths or are computationally slow. An exception, the GLASS method of Mossel and Roch, is consistent for the species tree topology, estimates branch lengths, and is computationally fast. However, GLASS systematically overestimates divergence times, leading to biased estimates of species tree branch lengths. By assuming a multispecies coalescent model in which multiple lineages are sampled from each of two taxa at L independent loci, we derive the distribution of the waiting time until the first interspecific coalescence occurs between the two taxa, considering all loci and measuring from the divergence time. We then use the mean of this distribution to derive a correction to the GLASS estimator of pairwise divergence times. We show that our improved estimator, which we call iGLASS, consistently estimates the divergence time between a pair of taxa as the number of loci approaches infinity, and that it is an unbiased estimator of divergence times when one lineage is sampled per taxon. We also show that many commonly used clustering methods can be combined with the iGLASS estimator of pairwise divergence times to produce a consistent estimator of the species tree topology. Through simulations, we show that iGLASS can greatly reduce the bias and mean squared error in obtaining estimates of divergence times in a species tree.     

Molecular demographic history of the annual sunflowers Helianthus annuus and H. petiolaris--large effective population sizes and rates of long-term gene flow.

Hybridization between distinct species may lead to introgression of genes across species boundaries, and this pattern can potentially persist for extended periods as long as selection at some loci or genomic regions prevents thorough mixing of gene pools. However, very few reliable estimates of long-term levels of effective migration are available between hybridizing species throughout their history. Accurate estimates of divergence dates and levels of gene flow require data from multiple unlinked loci as well as an analytical framework that can distinguish between lineage sorting and gene flow and incorporate the effects of demographic changes within each species. Here we use sequence data from 18 anonymous nuclear loci in two broadly sympatric sunflower species, Helianthus annuus and H. petiolaris, analyzed within an "isolation with migration" framework to make genome-wide estimates of the ages of these two species, long-term rates of gene flow between them, and effective population sizes and historical patterns of population growth. Our results indicate that H. annuus and H. petiolaris are approximately one million years old and have exchanged genes at a surprisingly high rate (long-term N(ef)m estimates of approximately 0.5 in each direction), with somewhat higher rates of introgression from H. annuus into H. petiolaris than vice versa. In addition, each species has undergone dramatic population expansion since divergence, and both species have among the highest levels of genetic diversity reported for flowering plants. Our results provide the most comprehensive estimate to date of long-term patterns of gene flow and historical demography in a nonmodel plant system, and they indicate that species integrity can be maintained even in the face of extensive gene flow over a prolonged period.