Intercontinental genetic divergence of Castanea species in eastern Asia and eastern North America

Castanea is one of the many plant genera with a disjunct distribution pattern between eastern Asia and eastern North America. Five species from three sections of the genus were investigated to examine genetic divergence between eastern Asian and eastern North American species. A total of 62 native populations were sampled for allelic variation at isozyme loci. The Chinese chestnut C. mollissima had the highest genetic variability, while the American C. dentata had the lowest genetic variability. The highest intracontinental genetic identities were observed between the Allegheny and Ozark chinkapins (0.931) and between C. mollissima and C. seguinii (0.870), while lower identities were detected between the American C. pumila and C. dentata (0.720-0.729). In intercontinental comparisons, genetic identities of 0.505, 0.495 and 0.507 were observed between the American chestnut and the Chinese C. mollissima, C. seguinii and C. henryi, respectively, whereas the Ozark chinkapin C. pumila var. ozarkensis had lower identities of 0.469, and 0.435 with C. mollissima and C. seguinii, respectively, but a slightly higher identity of 0.520 with C. henryi, the Chinese chinkapin. Divergence times were estimated at 10-13 million years before present between C. dentata and C. mollissima, and C. pumila var. ozarkensis and C. henryi.     

Heterozygote excess in small populations and the heterozygote-excess effective population size

It has been proposed that effective size could be estimated in small dioecious population by considering the heterozygote excess observed at neutral markers. When the number of breeders is small, allelic frequencies in males and females will slightly differ due to binomial sampling error. However, this excess of heterozygotes is not generated by dioecy but by the absence of individuals produced through selfing. Consequently, the approach can also be applied to self-incompatible monoecious species. Some inaccuracies in earlier equations expressing effective size as function of the heterozygote excess are also corrected in this paper. The approach is then extended to subdivided populations, where time of sampling becomes crucial. When adults are sampled, the effective size of the entire population can be estimated, whereas when juveniles are sampled, the average effective number of breeders per subpopulations can be estimated. The main limitation of the heterozygote excess method is that it will only perform satisfactorily for populations with a small number of reproducing individuals. While this situation is unlikely to happen frequently at the scale of the entire population, structured populations with small subpopulations are likely to be common. The estimation of the average number of breeders per subpopulations is thus expected to be applicable to many natural populations. The approach is straightforward to compute and independent of equilibrium assumptions. Applications to simulated data suggest the estimation of the number of breeders to be robust to mutation and migration rates, and to specificities of the mating system.     

栗的 PGI遗传和多样性

采用超薄聚丙烯酰４胺平板凝胶等电聚焦电泳和单株后代法,分析了栗属种的ＰＧＩ同工酶的遗传,研究发现Ｐｇｉ位点（Ｐｇｉ－ｉ）主要有３个等位基因并呈共显性遗传。在栗属的自然居群中还检测了出现频率较少的另外２个等位基因。     

Allozyme and RAPD analysis of the genetic diversity and geographic variation in wild populations of the American chestnut (Fagaceae)

Genetic variation among 12 populations of the American chestnut (Castanea dentata) was investigated. Population genetic parameters estimated from allozyme variation suggest that C. dentata at both the population and species level has narrow genetic diversity as compared to other species in the genus. Average expected heterozygosity was relatively low for the population collected in the Black Rock Mountain State Park, Georgia (He = 0.096 +/- 0.035), and high for the population in east central Alabama (He = 0.196 +/- 0.048). Partitioning of the genetic diversity based on 18 isozyme loci showed that ~10% of the allozyme diversity resided among populations. Cluster analysis using unweighted pair-group method using arithmetric averages of Rogers' genetic distance and principal components analysis based on allele frequencies of both isozyme and RAPD loci revealed four groups: the southernmost population, south-central Appalachian populations, north-central Appalachian populations, and northern Appalachian populations. Based on results presented in this study, a conservation strategy and several recommendations related to the backcross breeding aimed at restoring C. dentata are discussed.     

The population genetics of a biological control introduction: mitochondrial DNA and microsatellie variation in native and introduced populations of Aphidus ervi, a parisitoid wasp

Introductions of biological control agents may cause bottlenecks in population size despite efforts to avoid them. We examined the population genetics of Aphidius ervi (Hymenoptera: Braconidae), a parasitoid that was introduced to North America from Western Europe in 1959 to control pea aphids. To explore the phylogeographical relationships of A. ervi we sequenced 1249 bp of mitochondrial DNA (mtDNA) from 27 individuals from the native range and 51 individuals from the introduced range. Most individuals from Western Europe, the Middle East and North America shared one of two common haplotypes, consistent with the known history of the introduction. However, some A. ervi from the Pacific Northwest have a haplotype that is most similar to haplotypes found in Japan, raising the possibility of a second accidental introduction. To examine population structure and assess whether a bottleneck occurred upon introduction to North America, we assayed variation at 5 microsatellite loci in 62 individuals from 2 native populations and 230 individuals from 6 introduced populations. Introduced samples had fewer rare alleles than native samples (F1,34 = 13.5, P = 0.0008), but heterozygosity did not differ significantly. These results suggest that a mild bottleneck occurred in spite of the introduction of over 1000 individuals. Using a hierarchical Bayesian approach, the founding population size was estimated to be 245 individuals. amova showed significant genetic differentiation between the European and North American samples, and a Bayesian assignment approach clustered individuals into four groups, with most European individuals in one group and most North American individuals in the other three. These results highlight that genetic changes are associated with founder events in rapidly growing natural populations, even when the founding population size is relatively large.     

Mating system parameters in species of genus Prosopis (Leguminosae)

The section Algarobia of genus Prosopis involves important natural resources in arid and semiarid regions of the world. Their rationale use requires a better knowledge of their biology, genetics and mating system. There are contradictory information about their mating system. Some authors claim they are protogynous and obligate outcrosser. However, some evidence have been shown indicating that they might not be protogynous and that they might be somewhat self-fertile. The current paper analyses genetic structure and mating system parameters in populations of seven species of this section from South and North America based on isozyme data. In all species a significant homozygote excess was found in the offspring population but not in mother plant genotypes. Multilocus and mean single locus outcrossing rates (tm, ts) indicated that about 15% selfing can occur in the studied populations. The heterogeneity between pollen and ovule allele frequencies was low suggesting population structuration, in agreement with the estimates of correlation of tm within progeny (rt) and correlation of outcrossed paternity (rp). The difference of FIS estimates between offspring and mother plants suggest some selection favouring heterozygotes between seedling and adult stages.     

Land, language, and loci: mtDNA in Native Americans and the genetic history of Peru

Despite a long history of complex societies and despite extensive present-day linguistic and ethnic diversity, relatively few populations in Peru have been sampled for population genetic investigations. In order to address questions about the relationships between South American populations and about the extent of correlation between genetic distance, language, and geography in the region, mitochondrial DNA (mtDNA) hypervariable region I sequences and mtDNA haplogroup markers were examined in 33 individuals from the state of Ancash, Peru. These sequences were compared to those from 19 American Indian populations using diversity estimates, AMOVA tests, mismatch distributions, a multidimensional scaling plot, and regressions. The results show correlations between genetics, linguistics, and geographical affinities, with stronger correlations between genetics and language. Additionally, the results suggest a pattern of differential gene flow and drift in western vs. eastern South America, supporting previous mtDNA and Y chromosome investigations.     

Molecular evidence for an Asian origin and a unique westward migration of species in the genus Castanea via Europe to North America

The genus Castanea (Fagaceae) is widely distributed in the deciduous forests of the Northern Hemisphere. The striking similarity between the floras of eastern Asia and those of eastern North America and the difference in chestnut blight resistance among species has been of interest to botanists for a century. To infer the biogeographical history of the genus, the phylogeny of Castanea was estimated using DNA sequence data from different regions of the chloroplast genome. Sequencing results support the genus Castanea as a monophyletic group with Castanea crenata as basal. The three Chinese species form a strongly supported sister clade to the North American and European clade. A unique westward expansion of extant Castanea species is hypothesized with Castanea originating in eastern Asia, an initial diversification within Asia during the Eocene followed by intercontinental dispersion and divergence between the Chinese and the European/North American species during the middle Eocene and a split between the European and the North American species in the late Eocene. The differentiation within North America and China might have occurred in early or late Miocene. The North America species are supported as a clade with C. pumila var. ozarkensis, the Ozark chinkapin, as the basal lineage, sister to the group comprising C. pumila var. pumila, the Allegheny chinkapin, and Castanea dentata, the American chestnut. Morphological evolution of one nut per bur in the genus may have occurred independently on two continents.     

Genetic evidence for multiple introduction events of raccoons (Procyon lotor) in Spain

The common raccoon (Procyon lotor) is endemic to Central and North America, although non-native populations have become established around the world. In Spain, growing evidence of the introduction of raccoons has been reported across the country in the last decade, especially in Central Spain where the largest population is thought to occur. We used mitochondrial and microsatellite DNA data to investigate the genetics of invasive raccoons in Central Spain and to infer: the number of introduction events, the number of founders and the genetic variability of the introduced populations compared to a native population. We found that at least two introduction events have occurred along the Jarama and Henares Rivers in Central Spain, which currently constitute two genetically differentiated subpopulations. In both localities the number of effective founders from a native population was estimated as 2–4 individuals. These newly founded populations have expanded and show evidence of incipient contact and reproduction between them. This may allow for an increase in the genetic variability and adaptive potential of the population(s), possibly increasing the difficulty of controlling this invasive species. Our results reveal the ability to longitudinally monitor the genetics of the raccoon range expansion and emphasize the urgent need to control the pet trade of potentially invasive species.     

Comparative genetic diversity in a sample of pony breeds from the U.K. and North America: a case study in the conservation of global genetic resources

Most species exist as subdivided ex situ daughter population(s) derived from a single original group of individuals. Such subdivision occurs for many reasons both natural and manmade. Traditional British and Irish pony breeds were introduced to North America (U.S.A. and Canada) within the last 150 years, and subsequently equivalent breed societies were established. We have analyzed selected U.K. and North American equivalent pony populations as a case study for understanding the relationship between putative source and derived subpopulations. Diversity was measured using mitochondrial DNA and a panel of microsatellite markers. Genetic signatures differed between the North American subpopulations according to historical management processes. Founder effect and stochastic drift was apparent, particularly pronounced in some breeds, with evidence of admixture of imported mares of different North American breeds. This demonstrates the importance of analysis of subpopulations to facilitate understanding the genetic effects of past management practices and to lead to informed future conservation strategies.     

Development of a panel of genome-wide ancestry informative markers to study admixture throughout the Americas

Most individuals throughout the Americas are admixed descendants of Native American, European, and African ancestors. Complex historical factors have resulted in varying proportions of ancestral contributions between individuals within and among ethnic groups. We developed a panel of 446 ancestry informative markers (AIMs) optimized to estimate ancestral proportions in individuals and populations throughout Latin America. We used genome-wide data from 953 individuals from diverse African, European, and Native American populations to select AIMs optimized for each of the three main continental populations that form the basis of modern Latin American populations. We selected markers on the basis of locus-specific branch length to be informative, well distributed throughout the genome, capable of being genotyped on widely available commercial platforms, and applicable throughout the Americas by minimizing within-continent heterogeneity. We then validated the panel in samples from four admixed populations by comparing ancestry estimates based on the AIMs panel to estimates based on genome-wide association study (GWAS) data. The panel provided balanced discriminatory power among the three ancestral populations and accurate estimates of individual ancestry proportions (R2 > 0.9 for ancestral components with significant between-subject variance). Finally, we genotyped samples from 18 populations from Latin America using the AIMs panel and estimated variability in ancestry within and between these populations. This panel and its reference genotype information will be useful resources to explore population history of admixture in Latin America and to correct for the potential effects of population stratification in admixed samples in the region.     

Genetic variation and population structure in native Americans

We examined genetic diversity and population structure in the American landmass using 678 autosomal microsatellite markers genotyped in 422 individuals representing 24 Native American populations sampled from North, Central, and South America. These data were analyzed jointly with similar data available in 54 other indigenous populations worldwide, including an additional five Native American groups. The Native American populations have lower genetic diversity and greater differentiation than populations from other continental regions. We observe gradients both of decreasing genetic diversity as a function of geographic distance from the Bering Strait and of decreasing genetic similarity to Siberians--signals of the southward dispersal of human populations from the northwestern tip of the Americas. We also observe evidence of: (1) a higher level of diversity and lower level of population structure in western South America compared to eastern South America, (2) a relative lack of differentiation between Mesoamerican and Andean populations, (3) a scenario in which coastal routes were easier for migrating peoples to traverse in comparison with inland routes, and (4) a partial agreement on a local scale between genetic similarity and the linguistic classification of populations. These findings offer new insights into the process of population dispersal and differentiation during the peopling of the Americas.     

Genetic profile of cosmopolitan populations: effects of hidden subdivision

Natural populations of many organisms exhibit excess of rare alleles in comparison with the predictions of the neutral mutation hypothesis. It has been shown before that either a population bottleneck or the presence of slightly deleterious mutations can explain this phenomenon. A third explanation is presented in this work, showing that hidden subdivision within a population can also lead to an excess of rare alleles in the total population when the expectations of the neutral model are based on the allele frequency profile of the entire population data. With two examples (mitochondrial DNA-morph distribution and isozyme allele frequency distributions), it is shown that most cosmopolitan human populations exhibit excess of rare as well as total allele counts, when these are compared with the expectations of the neutral mutation hypothesis. The mitochondrial data demonstrate that such excesses can be detected from genetic variation at a single locus as well, and this is not due to stochastic error of allele frequency distributions. Contrast of the present observations with the allele frequency profiles in agglomerated tribal populations from South and Central America shows that even when the neutral expectations hold for individual subpopulations, if all subpopulations are grouped into a single population, the pooled data exhibit an excess of total number of alleles that is mainly due to the excess of rare alleles. Therefore, a primary cause of the excess number of rare alleles could be the hidden subdivision, and the magnitude of the excess indicates the extent of substructuring. The two components of hidden subdivision are: 1) Number of subpopulations, and 2) the average genetic distance among them. The implications of this observation in estimating mutation rate are discussed indicating the difficulties of comparing mutation rates from different population surveys.     

Roseate Terns Sterna dougallii on the southeast coast of South Africa: information on moult and migratory status

Determining the migratory status of seabird populations is crucial for addressing conservation concerns. The Roseate Tern Sterna dougallii is considered endangered in South Africa in view of its small breeding population and the threats to eggs and chicks. Earlier works based on capture-recapture data suggest that this population adopts a partial migratory strategy. Updated capture-recapture data were combined with new data on moult and stable isotopes of scapular feathers to determine whether subpopulations could be identified in the South African breeding population. Moult data on 404 individuals failed to identify subpopulations, but two groups were identifiable with the stable isotopes: one group of four individuals exhibiting low carbon and nitrogen stable isotope ratios and a second group (comprising the remaining 152 individuals) with significantly higher ratios. The isotope data suggest that birds from the two groups moulted in different areas. Comparisons with published studies showed that the 152 individuals had likely moulted their scapulars in South African waters, but the moulting area for the remaining four individuals could not be ascertained due to the absence of detailed isoscapes in the southern part of the Mozambique Channel. Further work investigating the genetic differentiation between South African and Madagascan Roseate Terns may bring new insight into the migratory behaviour of the South African population.     

普通野生稻小种群的交配系统与遗传多样性

小种群的遗传动态是保育遗传学关注的核心问题之一,而种群遗传动态又与交配系统密切相关.普通野生稻(Oryza rufipogon Griff.)是具有重要经济价值的濒危物种,目前其种群规模都较小,研究其小种群交配系统与遗传变异性对普通野生稻的保护具有重要意义.运用7对SSR引物,对采自江西东乡普通野生稻小种群的36份种茎和其中20个家系共计601份子代进行了分析.结果显示:该种群的表观异交率为0.318,多位点法估计(MLTR)的多位点异交率为0.481;50%以上的子代共享亲本,非随机交配明显;东乡普通野生稻种群交配系统属于混合交配类型.比较亲本和子代种群的遗传变异性显示:子代种群比亲本种群遗传变异性更丰富;子代种群的杂合子不足与种群变小自交比例上升有关;而亲本种群杂合子过剩可能与杂合基因型的选择优势有关.这些结果说明创造条件扩大种群规模对普通野生稻的原生境保护显得尤为重要.     

Relationships among cave swallow populations (Petrochelidon fulva) determined by comparisons of microsatellite and cytochrome b data

The cave swallow (Petrochelidon fulva) is a polytypic species with isolated populations in northwestern South America, southwestern North America, Yucatan, Greater Antilles, and Florida. We compared microsatellite genotypes of at least five individuals each from five populations and cytochrome b sequence data of two individuals each from seven populations plus two outgroups. Microsatellite allelic diversity was substantial, and the North American populations were about equally variable. In contrast, the Ecuadorian population had far less genetic variation. Gene flow was apparent among populations, especially between Texas and Florida. Genetic structure was greater than in widespread North American species but less than that of sedentary Neotropical birds. Microsatellite genetic distances indicated a close affinity between Ecuadorian and northern populations, especially Texas and Florida, but this finding was inconsistent with cytochrome b data, which indicated that the Ecuadorian population is the clear outgroup to the northern populations. Its outgroup status is consistent with recent classifications that designate South American populations as their own species (P. rufocollaris). The cytochrome b data further suggested that the northern populations are divided into two clades: Texas/Yucatan and Florida/Greater Antilles. The microsatellite data incorrectly measured the diversity and affinities of Ecuadorian birds apparently because of an ascertainment bias that results from the use of heterologous PCR primers. Despite these problems in measuring phylogenetic relationships, the microsatellite data appeared to work well as a population genetic marker in indicating population structure and gene flow.     

栗与美国板栗化感作用的比较

以种子发芽率和发芽势为种子萌发参数, 以胚根、胚芽长度和鲜重变化为幼苗生长参数, 研究了栗(Castanea mollissima)叶水提取物对双子叶植物莴苣(Lactuca sativa)、萝卜(Raphanus sativus)、黄瓜(Cucumis sativus), 和单子叶植物洋葱(Allium cepa)、水稻(Oryza sativa)、小麦(Triticum aestivum)的化感作用; 比较了美国板栗(Castanea dentata)与栗叶水提取物及经X-5大孔树脂分离获得的11个洗脱组分间的化感作用强弱; 利用液相色谱-质谱联用技术结合标准物质的反证实验, 解析了美国板栗与栗化感作用最强分离组分的物质结构。研究结果表明, 栗叶化感效应强于美国板栗; 美国板栗与栗化感作用最强分离组分中(5:5洗脱组分)存在绿原酸、对羟基苯甲酸、原儿茶酸和没食子酸等物质。在利用栗基因恢复美国板栗种群时, 有必要考虑美国板栗与栗植物化学生态特性的差异。     

The benefits of pre-release population genetics: A case study using Ceutorhynchus scrobicollis,a candidate agent of garlic mustard,Alliaria petiolata

Incorporating population genetics into research on candidate biological control agents can help improve the safety and success rates of biological control of weeds. As a case in point, the population structure of Ceutorhynchus scrobicollis, a candidate agent for garlic mustard (Alliaria petiolata) in North America, was evaluated using mitochondrial sequence data and amplified fragment length polymorphisms (AFLPs). The region surrounding Berlin, Germany, from which individuals have been collected for host-specificity tests, was examined to determine whether individuals from this area constitute one or more populations, to estimate numbers of individuals required to capture 90–99% of the diversity in AFLPs within the region, and to evaluate dispersal capabilities. Significant differentiation of C. scrobicollis between sites was observed, however most (94%) of the genetic diversity was found within sites. The area around Berlin appears to be a network of connected subpopulations. Estimates for the number of individuals needed from the focal area to capture 90% and 99% of the diversity present in AFLP loci were 10 and 27. Assignment tests indicated that while few individuals disperse, some move up to 65 km. Inclusion of more distant samples from Romania and Georgia revealed substantial genetic differentiation between them and German samples. These areas might therefore be useful to explore further should populations with different ecological characteristics be sought. These findings increase confidence in host-specificity tests, which incorporated more than 4000 individual weevils from the Berlin area, provide guidance for eventual release strategies, and illustrate how basic population genetic data can be incorporated into biological control programs to increase safety and efficacy.     

Population structure and introduction history of the pink bollworm, Pectinophora gossypiella, in China

The pink bollworm, Pectinophora gossypiella (Saunders) (Lepidoptera: Gelechiidae), a cotton pest probably native to Indo-Pakistan, invaded China at the beginning of the 20th century. Chinese P. gossypiella have been assumed to be the result of indiscriminate introductions from Pakistan and America by transport of cotton seed. We tested this long-held hypothesis and genotyped a total of 527 individuals from 14 sites at 13 microsatellite loci. We analyzed these data with traditional statistics as well as with Bayesian methods. The loci were, for the most part, highly polymorphic. The allelic richness of Chinese populations at six loci was greater than those of the Pakistani and American populations. Significant deficits of heterozygotes were recorded for all 14 populations, and null alleles were the most probable factor contributing to these deficits. Pairwise F_ST estimates showed that there was significant differentiation among the pooled Chinese, Pakistani, and American populations, and there was structure within most of the Chinese populations. The Bayesian analysis revealed that the combined Chinese, American, and Pakistani populations formed separate clusters, and the nine Chinese populations were divided into two clusters. Allelic frequency distributions showed that private and shared alleles within Chinese P. gossypiella were derived only partly from the Pakistani and American populations. The microsatellite-based genetic analyses suggested that the Chinese P. gossypiella populations originated from multiple sources.