Highly diverse and highly successful: invasive Australian acacias have not experienced genetic bottlenecks globally

Background and AimsInvasive species may undergo rapid evolution despite very limited standing genetic diversity. This so-called genetic paradox of biological invasions assumes that an invasive species has experienced (and survived) a genetic bottleneck and then underwent local adaptation in the new range. In this study, we test how often Australian acacias (genus Acacia), one of the world’s most problematic invasive tree groups, have experienced genetic bottlenecks and inbreeding.MethodsWe collated genetic data from 51 different genetic studies on Acacia species to compare genetic diversity between native and invasive populations. These studies analysed 37 different Acacia species, with genetic data from the invasive ranges of 11 species, and data from the native range for 36 species (14 of these 36 species are known to be invasive somewhere in the world, and the other 22 are not known to be invasive).Key ResultsLevels of genetic diversity are similar in native and invasive populations, and there is little evidence of invasive populations being extensively inbred. Levels of genetic diversity in native range populations also did not differ significantly between species that have and that do not have invasive populations.ConclusionWe attribute our findings to the impressive movement, introduction effort and human usage of Australian acacias around the world.     

微卫星DNA标记技术及其在遗传多样性研究中的应用

微卫星DNA的高突变率、中性、共湿性及其在真核基因组中的普遍性,使其成为居群遗传学研究、种质资源鉴定、亲缘关系分析和图谱构建的优越的分子标记。本研究系统介绍了微卫星DNA在结构和功能上的特点,并对微卫星DNA标记技术应用的遗传学机理和一般方法进行了扼要的阐述。另外,本研究还探讨了微卫星DNA标记技术在遗传多样性研究中的应用现状,并进一步提出其发展前景。     

Understanding invasion history: genetic structure and diversity of two globally invasive plants and implications for their management

Aim Resolving the origin of invasive plant species is important for understanding the introduction histories of successful invaders and aiding strategies aimed at their management. This study aimed to infer the number and origin(s) of introduction for the globally invasive species, Macfadyena unguis‐cati and Jatropha gossypiifolia using molecular data. Location Native range: Neotropics; Invaded range: North America, Africa, Europe, Asia, Pacific Islands and Australia. Methods We used chloroplast microsatellites (cpSSRs) to elucidate the origin(s) of introduced populations and calculated the genetic diversity in native and introduced regions. Results Strong genetic structure was found within the native range of M. unguis‐cati, but no genetic structuring was evident in the native range of J. gossypiifolia. Overall, 27 haplotypes were found in the native range of M. unguis‐cati. Only four haplotypes were found in the introduced range, with more than 96% of introduced specimens matching a haplotype from Paraguay. In contrast, 15 haplotypes were found in the introduced range of J. gossypiifolia, with all invasive populations, except New Caledonia, comprising multiple haplotypes. Main conclusions These data show that two invasive plant species from the same native range have had vastly different introduction histories in their non‐native ranges. Invasive populations of M. unguis‐cati probably came from a single or few independent introductions, whereas most invasive J. gossypiifolia populations arose from multiple introductions or alternatively from a representative sample of genetic diversity from a panmictic native range. As introduced M. unguis‐cati populations are dominated by a single haplotype, locally adapted natural enemies should make the best control agents. However, invasive populations of J. gossypiifolia are genetically diverse and the selection of bio‐control agents will be considerably more complex.     

Genetic diversity does not affect the invasiveness of fountain grass (Pennisetum setaceum) in Arizona, California and Hawaii

Pennisetum setaceum (Poaceae) is a perennial bunch grass that invaded the United States during the 20th century and is highly invasive in Hawaii, moderately invasive in Arizona, and not yet invasive in southern California. Pennisetum setaceum is apomictic, a condition that is normally associated with low genetic variation within populations, but even moderate levels of genetic variation among populations could account for differences in invasiveness. To determine whether genetic factors are causing the variable invasion success, we used Inter‐Simple Sequence Repeat markers (ISSRs) to examine genetic variation in populations from the three areas. Screening of 16 primers revealed no genetic variation within any population or between any geographical areas, a pattern consistent with complete apomixis. Variation in invasion success appears unrelated to genetic differences among populations. Differences in the seasonal timing of rainfall among the regions may be the cause of variable invasiveness of fountain grass. Alternatively, differences in timing of introduction or duration of lag phase may have limited invasiveness in Arizona and southern California.     

The making of a rapid plant invader: genetic diversity and differentiation in the native and invaded range of Senecio inaequidens

To become invasive, exotic species have to succeed in the consecutive phases of introduction, naturalization, and invasion. Each of these phases leaves traces in genetic structure, which may affect the species’ success in subsequent phases. We examined this interplay of genetic structure and invasion dynamics in the South African Ragwort (Senecio inaequidens), one of Europe’s fastest plant invaders. We used AFLP and microsatellite markers to analyze 19 native African and 32 invasive European populations. In combination with historic data, we distinguished invasion routes and traced them back to the native source areas. This revealed that different introduction sites had markedly different success in the three invasion phases. Notably, an observed lag‐phase in Northern Germany was evidently not terminated by factors increasing the invasiveness of the resident population but by invasive spread from another introduction centre. The lineage invading Central Europe was introduced to sites in which winters are more benign than in the native source region. Subsequently, this lineage spread into areas in which winter temperatures match the native climate more closely. Genetic diversity clearly increases with population age in Europe and less clearly decreases with spread rate up to population establishment. This indicates that gene flow along well‐connected invasion routes counteracted losses of genetic diversity during rapid spread. In summary, this study suggests that multiple introductions, environmental preadaptation and high gene flow along invasion routes contributed to the success of this rapid invader. More generally, it demonstrates the benefit of combining genetic, historical, and climatic data for understanding biological invasions.     

Comparison of genetic diversity of the invasive weed Rubus alceifolius poir. (Rosaceae) in its native range and in areas of introduction, using amplified fragment length polymorphism (AFLP) markers

Theory predicts that colonization of new areas will be associated with population bottlenecks that reduce within-population genetic diversity and increase genetic differentiation among populations. This should be especially true for weedy plant species, which are often characterized by self-compatible breeding systems and vegetative propagation. To test this prediction, and to evaluate alternative scenarios for the history of introduction, the genetic diversity of Rubus alceifolius was studied with amplified fragment length polymorphism (AFLP) markers in its native range in southeast Asia and in several areas where this plant has been introduced and is now a serious weed (Indian Ocean islands, Australia). In its native range, R. alceifolius showed great genetic variability within populations and among geographically close populations (populations sampled ranging from northern Vietnam to Java). In Madagascar, genetic variability was somewhat lower than in its native range, but still considerable. Each population sampled in the other Indian Ocean islands (Mayotte, La Réunion, Mauritius) was characterized by a single different genotype of R. alceifolius for the markers studied, and closely related to individuals from Madagascar. Queensland populations also included only a single genotype, identical to that found in Mauritius. These results suggest that R. alceifolius was first introduced into Madagascar, perhaps on multiple occasions, and that Madagascan individuals were the immediate source of plants that colonized other areas of introduction. Successive nested founder events appear to have resulted in cumulative reduction in genetic diversity. Possible explanations for the monoclonality of R. alceifolius in many areas of introduction are discussed.     

Low genetic diversity of the successful invasive African clawed frog Xenopus laevis (Pipidae) in Chile

In Africa, the genus Xenopus presents cryptic species and diverse hybrids between species. It has been assumed that the invasive populations of this genus correspond to X. laevis and that they are derived from the subspecies that inhabits the Mediterranean Cape region of South Africa. In part, this is supported by the successful establishment of this species in several Mediterranean regions of the world. In Mediterranean Chile, Xenopus has invaded an area of about 21,000 km², with scarce attention to genetic aspects underlying its invasion. Using mitochondrial DNA sequences we determined that Xenopus laevis laevis from the Cape region of South Africa is the subspecies that invaded Chile. The analysis indicated that the invaders have low genetic diversity (only two haplotypes, compared to 10 in two localities of their native range), and that probably the invasion in Chile occurred only once. Landscape genetics revealed that factors such as aridity and elevation have determined the spread of the species, both from the ecological and genetic points of view. Our results show that the invasion of the African clawed frog in Chile has been successful for at least 30 years, in spite of low genetic variability, few events of introduction, low propagule pressure, and bottlenecks in the founding population.     

The analysis of genetic diversity and differentiation of six Chinese cattle populations using microsatellite markers

A total of 321 individuals from six cattle populations of four species in a bovine subfamily in China were studied using 12 pairs of microsatellite markers. The genetic diversities within and between populations were calculated. The phylogenetic trees were constructed by （δμ）^2 and DA distances, and the divergence times between populations were estimated by （δμ）^2. Altogether, 144 microsatellite alleles were detected including 24 private alleles and nine shared alleles. Chinese Holstein had the largest number of private alleles （10）, whereas Bohai black and Buffalo had the smallest number of private alleles （2）. Chinese Holstein showed the highest genetic variability. Its observed number of alleles （Na）, mean effective number of alleles （MNA）, and mean heterozygosity （He） were 7.7500, 4.9722, and 0.7719, respectively, whereas, the Buffalo and Yak showed low genetic variability. In the phylogenetic trees, Luxi and Holstein grouped first, followed by Bohai and Minnan. Yak branched next and buffalo emerged as the most divergent population from other cattle populations. Luxi and Bohai were estimated to have diverged 0.039-0.105 million years ago （MYA）, however, buffalo and Holstein diverged 0.501-1.337 MYA. The divergence time of Yak versus Minnan, Holstein and buffalo was 0.136-0.363, 0.273-0.729, and 0.326-0.600 MYA, respectively.     

海南岛海菖蒲种群克隆多样性和遗传结构

海草是生长在潮间带和潮下带的单子叶植物,由海草植物组成的海草床是生态系统服务价值最高的生态系统之一.然而,近几十年人类活动干扰、全球气候变化等因素导致海草床衰退严重.海菖蒲是分布于热带、体型最大的雌雄异株海草,我国位于该物种的分布北缘,本文对其克隆多样性和遗传结构进行研究,以期为该海草的保护提供参考.采用4对多态微卫星标记对采自海南岛4个地点的现存海菖蒲种群的样品进行基因型分型.结果表明:海菖蒲种群克隆多样性和遗传多样性较低,这与所研究种群处于分布区北缘有关;种群间遗传分化值范围较大(0.073~0.309),这可能是由于分布于不同港湾的种群间距离范围较大以及局域绝灭/再拓殖的遗传漂变效应所致;各种群未发现近期经历种群瓶颈的信号,很可能是由于种群内遗传多样性已经很低,种群减小未能导致遗传多样性明显降低.根据种群遗传特征,提出了重点保护种群的建议,鉴于目前我国海菖蒲等海草快速衰退的局面,应强化海草保护并实施海草床生态恢复.     

A set of 37 microsatellite DNA markers for genetic diversity and structure analysis of Atlantic salmon Salmo salar populations

Atlantic salmon Salmo salar microsatellite markers from a large database were analysed and selected with technical, economic and genetic criteria to provide an optimized set of polymorphic DNA markers for the analysis of the genetic diversity and the structure of anadromous Atlantic salmon populations. A set of 37 microsatellite markers was identified that are easy to use and provide a high level of differentiation power.     

Using molecular markers and multivariate methods to study the genetic diversity of local European and Asian chicken breeds

French and Asian subsets of chicken breeds were first analysed using 22 microsatellites and then compared to the AVIANDIV European set using 14 loci. Positive correlations were observed between F _IT or F _ST and typological values or variance of markers using the multivariate analysis mcoa . The first axis of the multivariate representation separated Asian from European breeds, revealing breeds with Asian ancestor. Using all or 14 loci, correct assignation rate was always higher than 93%. The Weitzman index and the aggregate diversity D were calculated using 22 loci within French and Asian breeds. The French breed Coucou de Rennes and the Hua-Tung breed seemed to contribute the most to the global diversity of each subset. This approach on French-only breeds and then on French with AVIANDIV domestic breeds (14 loci) showed that the Marans breed contributed the most. The AVIANDIV framework could be useful to evaluate the genetic diversity of local breeds and to help in connecting national and regional conservation policies.     

Microsatellite analysis revealed genetic diversity and population structure among Chinese cashmere goats

Most cashmere goats are found in northern China and Mongolia. They are regarded as precious resources for their production of high quality natural fibre for the textile industry. It was the first time that the genetic diversity and population structure of nine Chinese cashmere populations has been assessed using 14 ISAG/FAO microsatellite markers. In addition, two Iranian populations and one West African goat population were genotyped for comparison. Results indicated that the genetic diversity of Chinese cashmere goats was rich, but less than those of the Iranian goat populations. All pairwise F_ST values between the Chinese cashmere goat populations reached a highly significant level (P < 0.001), suggesting that they should all be considered as separate breeds. Finally, clustering analysis divided Chinese cashmere goats into at least two clusters, with the Tibetan Hegu goats alone in one cluster. An extensive admixture was detected among the Chinese goat breeds (except the Hegu), which have important implications for breeding management.     

Development of simple sequence repeat (SSR) markers for the assessment of gene flow and genetic diversity in pigeonpea (Cajanus cajan)

Pigeonpea (Cajanus cajan) is an important subsistence crop in India where traditional landraces and improved hybrids are grown alongside each other. Gene flow may result in genetic erosion of these landraces and their wild relatives, whilst transgene escape from future genetically engineered varieties is another potential hazard. To assess the impact of these factors gene flow needs to be measured. A set of 10 simple sequence repeat markers have been developed, which exhibit polymorphism across a range of pigeonpea varieties. Use of these markers also offers an efficient system for the assessment of genetic diversity within populations of pigeonpea.     

Ecological consequences of genetic diversity

Understanding the ecological consequences of biodiversity is a fundamental challenge. Research on a key component of biodiversity, genetic diversity, has traditionally focused on its importance in evolutionary processes, but classical studies in evolutionary biology, agronomy and conservation biology indicate that genetic diversity might also have important ecological effects. Our review of the literature reveals significant effects of genetic diversity on ecological processes such as primary productivity, population recovery from disturbance, interspecific competition, community structure, and fluxes of energy and nutrients. Thus, genetic diversity can have important ecological consequences at the population, community and ecosystem levels, and in some cases the effects are comparable in magnitude to the effects of species diversity. However, it is not clear how widely these results apply in nature, as studies to date have been biased towards manipulations of plant clonal diversity, and little is known about the relative importance of genetic diversity vs. other factors that influence ecological processes of interest. Future studies should focus not only on documenting the presence of genetic diversity effects but also on identifying underlying mechanisms and predicting when such effects are likely to occur in nature.     

利用17个微卫星标记分析鳙鱼的遗传多样性

选用本实验室克隆的17个鳙鱼微卫星分子标记分析四川泸州和江西鄱阳湖的两个种群鳙鱼的遗传多样性及种质特性,计算和统计了杂合度、多态信息含量（PIC）、有效等位基因数、等位基因频率、遗传距离、遗传相似系数、Hardy-Weinberg平衡偏离指数等方面内容。结果表明：选择使用17个微卫星标记,其中有4个为单态标记,13个为多态标记。江西和四川鳙鱼群体每个微卫星位点的平均等位基因数分别为3.325及3.882,平均有效等位基因数分别为3.531及2.676,多态位点百分率分别为82.4及70.5, 17个微卫星标记共有等位基因71个,多态微卫星位点的PIC在0.114~0.960之间变动,平均为0.417 ,两群体位点平均观测杂合度为0.385和0.452,平均期望杂合度为0.360和0.422,两个群体间的遗传相似系数为0.897,群体间的遗传距离为0.109。     

戊型肝炎病毒遗传多样性和进化机制的研究进展

戊型肝炎病毒(hepatitis E virus, HEV)是一种引发全球急性病毒性肝炎的人兽共患病病原。HEV具有丰富的遗传多样性,不同基因型或基因亚型的流行与地理位置、宿主物种以及防控策略等密切相关。欧洲和美洲HEV流行株为HEV-3,包括3a-i亚型,而亚洲流行株含HEV-3和HEV-4;我国的流行毒株已从HEV-1进化到HEV-4。近年来,研究发现HEV进化的影响机制,包括同义密码子使用模式、氨基酸突变和基因重组等,其中氨基酸突变是病毒持续流行的主要驱动力。因此,本文就HEV的分类、全球流行特征、进化机制等进行综述,以期为戊型肝炎的有效防控以及疫苗开发提供参考。     

Evaluation of genetic diversity in Chinese indigenous chicken breeds using microsatellite markers

China is rich in chicken genetic resources, and many indigenous breeds can be found throughout the country. Due to poor productive ability, some of them are threatened by the commercial varieties from domestic and foreign breeding companies. In a large-scale investigation into the current status of Chinese poultry genetic resources, 78 indigenous chicken breeds were surveyed and their blood samples collected. The genomes of these chickens were screened using microsatellite analysis. A total of 2740 individuals were genotyped for 27 microsatellite markers on 13 chromosomes. The number of alleles of the 27 markers ranged from 6 to 51 per locus with a mean of 18.74. Heterozygosity (H) values of the 78 chicken breeds were all more than 0.5. The average H value (0.622) and polymorphism information content (PIC, 0.573) of these breeds suggested that the Chinese indigenous chickens possessed more genetic diversity than that reported in many other countries. The fixation coefficients of subpopulations within the total population (F _ST) for the 27 loci varied from 0.065 (LEI0166) to 0.209 (MCW0078), with a mean of 0.106. For all detected microsatellite loci, only one (LEI0194) deviated from Hardy-Weinberg equilibrium (HWE) across all the populations. As genetic drift or non-random mating can occur in small populations, breeds kept on conservation farms such as Langshan chicken generally had lower H values, while those kept on large populations within conservation regions possessed higher polymorphisms. The high genetic diversity in Chinese indigenous breeds is in agreement with great phenotypic variation of these breeds. Using Nei’s genetic distance and the Neighbor-Joining method, the indigenous Chinese chickens were classified into six categories that were generally consistent with their geographic distributions. The molecular information of genetic diversity will play an important role in conservation, supervision, and utilization of the chicken resources.     

湘江野鲤养殖群体和自然群体遗传多样性的微卫星分析

采用微卫星技术,用17对微卫星引物对湘江野鲤养殖群体和自然群体的的遗传多样性进行分析.结果表明:有15对引物扩增出清晰的条带,其中13对引物在群体间呈现多态性;2个群体中,13对多态性引物分别扩增等位基因2～12个,共90个,其中35个等位基因为2群体共有,55个等位基因具有群体特异性,引物平均等位基因数为6.92个,等位基因频率为0.0667～0.8333;养殖群体和自然群体的平均遗传杂合度和平均多态信息含量分别为0.5688、0.5152,0.5860、0.5347;2个群体间遗传相似性指数为0.6762,遗传距离为0.3238,表明湘江野鲤养殖和自然群体遗传多样性均较为丰富,2个群体间遗传变异程度较高.     

9种石斑鱼遗传多样性和系统发生关系的微卫星分析

利用实验室克隆的13个青石斑鱼微卫星分子标记, 对中国南海海域9种石斑鱼(青石斑鱼、蜂巢石斑鱼、鲑点石斑鱼、黑边石斑鱼、鞍带石斑鱼、赤点石斑鱼、七带石斑鱼、斜带石斑鱼和棕点石斑鱼)进行了遗传多样性和系统发生关系的分析。研究结果显示, 13个微卫星标记共检测到了84个等位基因, 9种石斑鱼中的平均等位基因数、平均多态信息含量(PIC)、平均观测杂合度(Ho)、平均期望杂合度(He)和平均Hardy-Weinberg遗传偏离指数(D)分别在2.69~5.38、0.1976~0.4267、0.4615~0.6239、0.3510~0.4754和0.1097~0.2836之间变动, 说明9种石斑鱼的遗传多样性都处于中等水平。用NJ法进行聚类分析的结果将9种石斑鱼分为3个支系：斜带石斑鱼、棕点石斑鱼和鞍带石斑鱼为第1支; 青石斑鱼、赤点石斑鱼和七带石斑鱼为第2支系; 蜂巢石斑鱼、黑边石斑鱼和鲑点石斑鱼为第3支系, 该支系与第2支系的关系较近。本研究支持将宽额鲈(鞍带石斑鱼)归入石斑鱼属。