Population Genetic Structure of Two Columnar Cacti with a Patchy Distribution in Eastern Brazil

The genetic variability and population genetic structure of six populations of Praecereus euchlorus and Pilosocereus machrisii were investigated. The genetic variability in single populations of Pilosocereus vilaboensis, Pilosocereus aureispinus, and Facheiroa squamosa was also examined. All of these cacti species have a patchy geographic distribution in which they are restricted to small areas of xeric habitats in eastern Brazil. An analysis of genetic structure was used to gain insights into the historical mechanisms responsible for the patchy distribution of P. euchlorus and P. machrisii. High genetic variability was found at the populational level in all species (P=58.9–92.8%, A_p=2.34–3.33, H_e=0.266–0.401), and did not support our expectations of low variability based on the small population size. Substantial inbreeding was detected within populations (F_IS=0.370–0.623). In agreement with their insular distribution patterns, P. euchlorus and P. machrisii had a high genetic differentiation (F_ST=0.484 and F_ST=0.281, respectively), with no evidence of isolation by distance. Accordingly, estimates of gene flow (N_m) calculated from F_ST and private alleles were below the level of N_m=1 in P. machrisii and P. euchlorus. These results favored historical fragmentation as the mechanism responsible for the patchy distribution of these two species. The genetic distance between P. machrisii and P. vilaboensis was not compatible with their taxonomic distinction, indicating a possible local speciation event in this genus, or the occurrence of introgression events.     

Genetic Structure of a Population Occupying a Circular Habitat

The geographical structure of a finite population distributed continuously and homogeneously along a circular habit is explored. Selection is supposed to be absent, and the analysis is restricted to a single locus with discrete, non-overlapping generations. Assuming every mutant is new to the population, the rate of decay of genetic variability is obtained, and the probability that two homologous genes separated by a given distance are different alleles is calculated. If moments of the migration function higher than second are neglected, the eigenvalue equation is shown to be a simple trigonometric one, and the Fourier series giving the transient and stationary probabilities of allelism are summed in terms of elementary functions. The proportion of homozygotes, the effective number of alleles maintained in the population, and the amount of local differentiation of gene frequencies are discussed.     

Bat Pollination Breakdown in the Caribbean Columnar Cactus Pilosocereus royenii1

Generalized pollination systems may be advantageous on island systems or regions of substantial disturbance. We examined whether or not specialization breakdown has occurred in a presumably bat‐pollinated columnar cactus, Pilosocereus royenii, on Puerto Rico, an island subjected to periodic hurricanes. The flowers show characteristics related to bat pollination including nocturnal anthesis, morphology, and amount and quality of nectar reward. The cactus produces flowers whose styles are temporally and mechanically separated from its anthers and do not self‐pollinate. Hand manipulations indicated that it is partially self‐incompatible or suffers some inbreeding depression. In 217 h of observations conducted biweekly over the course of 1 yr, P. royenii received visits from bats, moths, bees, and birds, but the only effective pollinator was the carpenter bee, Xylocopa mordax. Only four bat visits were recorded, all prior to stigma receptiveness. Floral morphology of P. royenii was significantly more variable than that of other bat‐pollinated species of the genus. We propose that infrequent bat visits are a consequence of a population crash and that floral variability is due to either relaxed selection for bat pollination or a transitional stage from bat pollination to bee pollination.     

Population Genetic Structure of a Microalgal Species under Expansion

Biological invasions often cause major perturbations in the environment and are well studied among macroorganisms. Less is known about invasion by free-living microbes. Gonyostomum semen (Raphidophyceae) is a freshwater phytoplankton species that has increased in abundance in Northern Europe since the 1980''s and has expanded its habitat range. In this study, we aimed to determine the genetic population structure of G. semen in Northern Europe and to what extent it reflects the species'' recent expansion. We sampled lakes from 12 locations (11 lakes) in Norway, Sweden and Finland. Multiple strains from each location were genotyped using Amplified Fragment Length Polymorphism (AFLP). We found low differentiation between locations, and low gene diversity within each location. Moreover, there was an absence of genetic isolation with distance (Mantel test, p = 0.50). According to a Bayesian clustering method all the isolates belonged to the same genetic population. Together our data suggest the presence of one metapopulation and an overall low diversity, which is coherent with a recent expansion of G. semen.     

Demography and Genetic Structure of a Recovering Grizzly Bear Population

ABSTRACT Grizzly bears (brown bears; Ursus arctos) are imperiled in the southern extent of their range worldwide. The threatened population in northwestern Montana, USA, has been managed for recovery since 1975; yet, no rigorous data were available to monitor program success. We used data from a large noninvasive genetic sampling effort conducted in 2004 and 33 years of physical captures to assess abundance, distribution, and genetic health of this population. We combined data from our 3 sampling methods (hair trap, bear rub, and physical capture) to construct individual bear encounter histories for use in Huggins—Pledger closed mark—recapture models. Our population estimate, Ň = 765 (95% CI = 715–831) was more than double the existing estimate derived from sightings of females with young. Based on our results, the estimated known, human-caused mortality rate in 2004 was 4.6% (95% CI = 4.2–4.9%), slightly above the 4% considered sustainable; however, the high proportion of female mortalities raises concern. We used location data from telemetry, confirmed sightings, and genetic sampling to estimate occupied habitat. We found that grizzly bears occupied 33,480 km² in the Northern Continental Divide Ecosystem (NCDE) during 1994–2007, including 10,340 km² beyond the Recovery Zone. We used factorial correspondence analysis to identify potential barriers to gene flow within this population. Our results suggested that genetic interchange recently increased in areas with low gene flow in the past; however, we also detected evidence of incipient fragmentation across the major transportation corridor in this ecosystem. Our results suggest that the NCDE population is faring better than previously thought, and they highlight the need for a more rigorous monitoring program.     

Population Genetic Structure of Wild Boars in Poland

The analysis involved wild boars from the Lublin region, Warmia and Mazury, and Wielkopolska. The study material comprised muscle tissue samples collected from 100 wild boars. We analysed loci S0008, SW1129, SW986, SW1465, SW1492, SW1514, SW2532, SW461, SW841, SW2021, and SW2496 [1, 2]. The largest number of specific alleles, i.e. in six loci, was observed in wild boars from Warmia and Mazury; in turn, there were only two alleles in the group of wild boars from Lublin, and no alleles in individuals from Wielkopolska. The average value of the observed heterozygosity was H_o = 0.51, and the average value of expected heterozygosity was H_e = 0.63. PIC was another analysed indicator, with its lowest value determined for wild boars from the Wielkopolska region (0.53), and the highest value (0.62) was found for the animals from Warmia and Mazury. In the study population of wild boars, we also determined the F_ST index, which was 0.073, and N_m had a value greater than 3 (3.15); therefore, it can be concluded that the number of migrants per generation was 3. Both coefficients confirm the possibility of gene transfer and reproduction within and between the analysed populations of the wild boars. In our study, we observed a greater genetic distance between the wild boar populations from Wielkopolska and the Lublin and Warmia and Mazury regions in spite of the smaller geographical distance of these lands. This may be caused the less extensive network of ecological corridors as well as the occurrence of anthropogenic barriers e.g. large urban centres, an extensive network of roads, and the high volume of traffic in the direction of the capital.     

我国盾叶薯蓣居群遗传结构分析

利用随机扩增多态DNA(RAPD)标记,分析研究了中国11个盾叶薯蓣居群82个个体的遗传多样性与遗传结构,15个寡聚核苷酸引物扩增共得到108条带,其中96条为多态带,占88．89％。Shannon多样性指数(I)为0．3093,居群水平的变异从0．1564到0．3098,物种水平的Nei基因多样度(h)为0．2499,居群水平的变化范围为0．1607到0．2137。遗传变异分析表明,物种水平的基因分化系数Gst为0．3415,居群间的基因流Nm为0．9641,居群间遗传交换小。分子方差分析(AMOVA)表明,居群内变异为68．96％,地区间变异为19．45％,居群问变异为11．58％。聚类结果以长江为界,将盾叶薯蓣分为南北两个大类群。研究结果对盾叶薯蓣种质的迁地保护有重要意义。     

北沙柳群体遗传多样性和遗传结构分析

以内蒙古北沙柳(Salix psammophila)国家种质资源库内9个群体(P1~P9)288个无性系为实验材料,利用TP-M13-SSR技术,选取22对具有多态性EST-SSR北沙柳引物,采用毛细管电泳对PCR产物进行检测,分析北沙柳遗传多样性、分化程度和群体遗传结构,为北沙柳种质资源库遗传管理、无性系鉴定、品种选育、遗传改良和构建指纹图谱提供理论依据。结果显示:(1)22对EST-SSR引物共检测到222个等位基因,各位点平均等位基因数(A)为10,四倍体基因型丰富度(G)和特异基因型(G1)总和分别为1 460和802个,平均特异基因型比率(P1)和种质鉴别率(P2)分别为45.86%和13.21%。(2)9个群体平均等位基因数(A)为7.475,基因型丰富度(G)为15.586,观察杂合度(Ho)和期望杂合度(He)分别为0.577和0.638。以期望杂合度He为标准,北沙柳群体遗传多样性水平最低的是P1和P9。(3)北沙柳群体遗传分化系数仅为0.02,AMOVA分子变异分析显示,北沙柳群体大部分遗传变异来自群体内(97%),群体间变异仅为3%。(4)三维主成分、聚类和Structure群体遗传结构分析显示,9个群体被划分为2个组,Mantel检验表明北沙柳遗传距离与地理距离极显著相关(r=0.684 P0.001)。研究表明,北沙柳种质资源具有丰富的遗传多样性,这是其具有耐旱、耐寒、耐高温、耐沙埋和抗风蚀等适应性较强的分子基础;北沙柳的遗传变异集中在群体内;分布区群体呈现由中心向边缘群体扩张分化的趋势。     

云杉矮槲寄生遗传多样性及其群体遗传结构分析

该研究采用CTAB法提取云杉矮槲寄生(Arceuthobium sichuanense)的基因组DNA,利用ITS1片段的序列信息对中国9个不同地理群体的62份云杉矮槲寄生样本的遗传多样性及群体遗传结构进行分析。结果表明:(1)62条ITS1序列共定义16个单倍型(H1~H16),表现出较低的遗传多样性水平(h=0.678 5,π=0.005 9),而群体间的遗传多样性水平则表现出较大差异(h=0~1.000 0,π=0~0.009 4);AMOVA分析显示云杉矮槲寄生群体内的遗传变异占到51.37%,群体间为48.63%。(2)Network单倍型网络分析表明,单倍型H1和H12较为古老,且所有群体对2种单倍型无共享现象;单倍型H1是广布单倍型,存在于青海和甘肃的6个群体中,单倍型H12仅在四川的2个群体中有分布。(3)基于最大似然法(ML)构建的群体聚类和中介邻接法构建的单倍型网络图均显示,四川的3个群体为独立类群,区别于青海、甘肃群体,且甘肃和青海的群体之间没有明显分化。该研究首次报道了云杉矮槲寄生遗传多样性和遗传结构,为进一步研究其进化及后续的病害防控提供了一定的参考。     

Spatial Genetic Structure of the Abundant and Widespread Peatmoss Sphagnum magellanicum Brid.

Spore-producing organisms have small dispersal units enabling them to become widespread across continents. However, barriers to gene flow and cryptic speciation may exist. The common, haploid peatmoss Sphagnum magellanicum occurs in both the Northern and Southern hemisphere, and is commonly used as a model in studies of peatland ecology and peatmoss physiology. Even though it will likely act as a rich source in functional genomics studies in years to come, surprisingly little is known about levels of genetic variability and structuring in this species. Here, we assess for the first time how genetic variation in S. magellanicum is spatially structured across its full distribution range (Northern Hemisphere and South America). The morphologically similar species S. alaskense was included for comparison. In total, 195 plants were genotyped at 15 microsatellite loci. Sequences from two plastid loci (trnG and trnL) were obtained from 30 samples. Our results show that S. alaskense and almost all plants of S. magellanicum in the northern Pacific area are diploids and share the same gene pool. Haploid plants occur in South America, Europe, eastern North America, western North America, and southern Asia, and five genetically differentiated groups with different distribution ranges were found. Our results indicate that S. magellanicum consists of several distinct genetic groups, seemingly with little or no gene flow among them. Noteworthy, the geographical separation of diploids and haploids is strikingly similar to patterns found within other haploid Sphagnum species spanning the Northern Hemisphere. Our results confirm a genetic division between the Beringian and the Atlantic that seems to be a general pattern in Sphagnum taxa. The pattern of strong genetic population structuring throughout the distribution range of morphologically similar plants need to be considered in future functional genomic studies of S. magellanicum.     

Genetic Structure in a Heterocyanic Population of Trillium sessile (Liliaceae)

Abstract Species of Trillium in the subgenus Phyllantherum are either polymorphic for flower color, or monomorphic for flower color and related to a polymorphic species. This leads to the suggestion that polymorphic species may be the progenitors for monomorphic ones. For this to be true, it must be demonstrated that genetic divergence among flower morphs can occur within polymorphic populations. Genetic structure was assessed in a population of T. sessile that contains a polymorphism for flower color. A survey of 11 enzyme systems using starch gel electrophoresis revealed three polymorphic loci: 6PGD-1, AAT-1 and AAT-2. Analysis of large and small scale spatial structure, stage classes, and flower color classes revealed significant genetic divergence in all instances. Spatial structure in the population is likely a result of genetic neighborhoods which can maintain populational variation via random genetic drift. Genetic divergence of the yellow flower color morph was probably initiated through genetic drift since the morph occurs in low frequencies. The results imply that the initial genetic divergence of species in the subgenus can arise within polymorphic populations.     

羚牛的遗传多样性及其种群遗传结构分析

羚牛是亚洲大陆一种特有的大型珍稀动物,目前正面临着栖息地丧失、片段化和人类活动的严重威胁。为了有效地保护这种濒危动物,全面了解羚牛的种群结构、进化历史和整个分布区内遗传多样性的分布是至关重要的。本研究以mtDNA D-loop330bp基因片段为分子标记,比较分析了来自陕西秦岭、甘肃南部、四川岷山、邛崃山和云南贡山的40个样品的序列差异,根据分布特点将所采集到的羚牛分为3个地理单元,即秦岭、四川和云南。结果表明,在3个地理单元中存在4种单倍型,且地理单元间不存在共享单倍型,相互单倍型之间的平均序列差异为1.66％。进一步分析表明,3个地理单元间的基因流较低,存在着显的遗传分化 ,说明羚牛具有明显的系统地理分布格局。同时提出应将分布于秦岭山区、唐家河青川地区、天全以及云南贡山地区作为独立的管理单元分别加以保护。     

Genetic Structure of the Ancestral Population of Modern Humans

Neutral DNA polymorphisms from an 8-kb segment of the dystrophin gene, previously ascertained in a worldwide sample (n= 250 chromosomes), were used to characterize the population ancestral to the present-day human groups. The ancestral state of each polymorphic site was determined by comparing human variants with their orthologous sites in the great apes. The ``age before fixation' of the underlying mutations was estimated from the frequencies of the new alleles and analyzed in the context of these polymorphisms' distribution among 13 populations from Africa, Europe, Asia, New Guinea, and the Americas (n= 860 chromosomes in total). Seventeen polymorphisms older tan 100,000–200,000 years, which contributed ∼90% to the overall nucleotide diversity, were common to all human groups. Polymorphisms endemic to human groups or continentally restricted were younger than 100,000–200,000 years. Africans (six populations) with 13 such sites stood out from the rest of the world (seven populations), where only 2 population-specific variants were observed. The similarity of the frequencies of the old polymorphisms in Africans and non-Africans suggested a similar profile of genetic variability in the population before the modern human's divergence. This ancestral population was characterized by an effective size of about 10,000 as estimated from the nucleotide diversity; this size may describe the number of breeding individuals over a long time during the Middle Pleistocene or reflect a speciation bottleneck from an initially larger population at the end of this period. Received: 3 February 1998 / Accepted: 9 February 1998     

内蒙古西伯利亚杏群体遗传多样性和遗传结构分析

利用27对SSR分子标记对内蒙古地区13个西伯利亚杏群体的遗传多样性和遗传结构进行分析,评价其遗传多样性水平和分化程度,为内蒙古西伯利亚杏资源的合理保护与利用提供理论依据。结果显示:(1)27对SSR引物共检测到512个等位基因(Na),各位点平均等位基因数(Na)和多态性信息含量(PIC)分别为19和0.84;物种水平上Shannons信息指数(I)和期望杂合度(He)分别为2.25和0.73。(2)群体水平上的等位基因(Na)、有效等位基因(Ne)、Shannons信息指数(I)、期望杂合度(He)和观察杂合度(Ho)分别为6.95、4.48、1.60、0.76和0.56;其中科左后旗群体遗传多样性最丰富,克什克腾旗群体遗传多样性最低。(3)基于F统计量分析的遗传分化系数(Fst)为0.12,基因流(Nm)为1.86;分子方差分析显示内蒙古西伯利亚杏群体大部分遗传变异来自群体内(92%),群体间的遗传变异仅占8%。(4)内蒙古西伯利亚杏群体遗传距离为0.04~0.67,遗传相似度为0.33~0.83;遗传相似度的聚类分析、遗传距离的主坐标分析和遗传结构分析(Structure)均将供试13个群体划分为4组。Mantel检测显示,内蒙古西伯利亚杏群体遗传距离与地理距离呈显著相关关系(r=0.453,P0.01)。研究表明,内蒙古西伯利亚杏资源具有丰富的遗传多样性,这一特性与其群体的大小、悠久的演化历史以及自身生物学特性相关;内蒙古西伯利亚杏群体间存在中等程度的遗传分化,这可能源于自然地理隔离以及近期人类活动引起的生境片段化。     

柴达木山羊群体遗传结构及系统地位的研究

采用简单随机抽样法对柴达木山羊群体进行了遗传检测,从毛色、外型特征、体尺、血液蛋白与DNA多态性等5个方面进行了群体遗传结构分析,并探索了其系统地位。结果表明：(1)毛色和形态特征的平均表型异质度分别为0.3419、0.5207;(2)血液蛋白在6个基因座上具有多态性,平均基因座杂合度为0.2584;(3)DNA-RAPD标记表现丰富的多样性,基因多样度为0.4085～0.5318。通过对柴达木山羊与其他国内山羊的系统聚类,初步探索了该山羊群体的形成及所属,这些都表明柴达木山羊是一个比较古老的未经较高强度选育的地方山羊品种,其基因资源是我国山羊遗传资源中宝贵的一部分。Abstract: Genetic structure and character of Chaidamu Goats were studied through simple random sampling. Genetic structure was analysed from five aspects, and phylogeny status was also investigated. The results indicated that: (1) the average phenotypic heterogeneity degree of coat color and morphological character were 0.3419 and 0.5207,respectively; (2) polymorphous blood albumen existed in 6 loci and the average loci heterozygosity was 0.2584; and (3) polymorphism existed in marked genes by DND-RAPD with diversity of 0.4085～0.5318. Phylogeny status was investigated through clustering by Ward’s method on Chaidamu Goats and other domestic goats. All these indicated that Chaidamu Goats was a domestic goat with less intensively selected breed.     

Genetic Structure and Symbiotic Characteristics of a Bradyrhizobium Population Recovered from a Pasture Soil

We examined the genetic structure and symbiotic characteristics of Bradyrhizobium isolates recovered from four legume species (Lupinus albus [white lupine], Lupinus angustifolius [blue lupine], Ornithopus compressus [yellow serradella], and Macroptilium atropurpureum [sirato]) grown in an Oregon soil. We established that multilocus enzyme electrophoresis (MLEE) can provide insights into the genetic relatedness among Bradyrhizobium strains by showing a positive correlation (r² = ≥0.90) between the relatedness of Bradyrhizobium japonicum strains determined by MLEE at 13 enzyme loci and that determined by other workers using either DNA-DNA hybridization or DNA sequence divergence estimates. MLEE identified 17 electrophoretic types (ETs) among 95 Bradyrhizobium isolates recovered from the four hosts. Although the overall genetic diversity among the ETs (H = 0.69) is one of the largest measured to date in a local population of any soilborne bacterial species, there was no evidence of multilocus structure (linkage disequilibrium) within the population. The majority of the isolates (73%) were represented by two closely related ETs (2 and 3) which dominated the root nodules of white lupine, serradella, and siratro. In contrast, ET1 dominated nodules of blue lupine. Although representative isolates from all of the 17 ETs nodulated siratro, white lupine, blue lupine, and big trefoil (Lotus pedunculatus), they were either completely ineffective or poorly effective at fixing nitrogen on these hosts. Despite the widespread use of serradella as a surrogate host for lupine-nodulating bradyrhizobia, 7 of the 17 ETs did not nodulate this host, and the remaining 10 ETs were ineffective at fixing nitrogen.