长江口及其南部邻近地区大弹涂鱼种群遗传结构及种群历史分析

应用随机扩增多态性DNA（RAPD）技术及细胞色素b（Cytｂ）基因序列,分析了长江口及其南部邻近地区大弹涂鱼（Boleophthalmus pecinirostris）群体遗传结构及种群历史,结果显示这一区域大弹涂鱼群体的遗传多样性水平很高。（1）RAPD分析结果：从100个10碱基随机引物中筛选出30个多态性引物,对长江口九段沙湿地、浙江舟山定海、福建霞浦群体各20个体进行RAPD分析,3个群体分别获得236、270、274条带,共301个有效位点。3群体多态位点比例（P）、Nei基因多样性指数（H）、Shannon多样性指数（I）分别在93.02%—96.35%、0.3890—0.4219、0.5618—0.6044。分子方差分析（AMOVA）表明,大弹涂鱼群体间存在显著的遗传分化（Fst= 0.03004-0.03254,P<0.05）,但仅3.2%的遗传变异来自群体间。（2）Cytｂ基因序列分析结果：从采自九段沙、定海、霞浦及浙江慈溪的42尾大弹涂鱼样本中,共获得33个Cytｂ基因单倍型（序列长1 141 bp）。4群体的平均单倍型多样性（h）、核甘酸多样性（π）分别为0.9814、0.0048。4群体间的遗传分化指数Fst为0.00043—0.07814,仅1.93%的变异来自群体间（AMOVA分析）,而基因交流值却达14.50—30.79,群体间K2-P遗传距离为0.0040—0.0056,从而显示大弹涂鱼群体间没有发生明显的地理分化。以Cyt b基因序列构建的NJ树揭示4个群体的个体组成2个谱系,但这2个谱系与地理分布并不相关。中性检验、错配分析和网络亲缘关系分析皆表明大弹涂鱼群体有过种群扩张,扩张时间约在更新世末期的0.057—0.023百万年前。     

Population Genetic History of Aristeus antennatus (Crustacea: Decapoda) in the Western and Central Mediterranean Sea

Aristeus antennatus is an ecologically and economically important deep-water species in the Mediterranean Sea. In this study we investigated the genetic variability of A. antennatus sampled from 10 sampling stations in the Western and Central Mediterranean. By comparing our new samples with available data from the Western area, we aim to identify potential genetic stocks of A. antennatus and to reconstruct its historical demography in the Mediterranean. We analyzed two regions of mitochondrial DNA in 319 individuals, namely COI and 16S. We found two main results: i) the genetic diversity values consistent with previous data within the Mediterranean and the absence of barriers to gene flow within the Mediterranean Sea; ii) a constant long-term effective population size in almost all demes but a strong signature of population expansion in the pooled sample about 50,000 years B.P./ago. We propose two explanation for our results. The first is based on the ecology of A. antennatus. We suggest the existence of a complex meta-population structured into two layers: a deeper-dwelling stock, not affected by fishing, which preserves the pattern of historical demography; and genetically homogeneous demes inhabiting the fishing grounds. The larval dispersal, adult migration and continuous movements of individuals from “virgin” deeper grounds not affected by fishing to upper fishing areas support an effective ‘rescue effect’ contributing to the recovery of the exploited stocks and explain their genetic homogeneity throughout the Mediterranean Sea. The second is based on the reproduction model of this shrimp: the high variance in offspring production calls for a careful interpretation of the data observed under classical population genetics and Kingman’s coalescent. In both cases, management policies for A. antennatus will therefore require careful evaluation of the meta-population dynamics of all stocks in the Mediterranean. In the future, it will be particularly relevant to sample the deepest ones directly.     

Cuba: Exploring the History of Admixture and the Genetic Basis of Pigmentation Using Autosomal and Uniparental Markers

We carried out an admixture analysis of a sample comprising 1,019 individuals from all the provinces of Cuba. We used a panel of 128 autosomal Ancestry Informative Markers (AIMs) to estimate the admixture proportions. We also characterized a number of haplogroup diagnostic markers in the mtDNA and Y-chromosome in order to evaluate admixture using uniparental markers. Finally, we analyzed the association of 16 single nucleotide polymorphisms (SNPs) with quantitative estimates of skin pigmentation. In the total sample, the average European, African and Native American contributions as estimated from autosomal AIMs were 72%, 20% and 8%, respectively. The Eastern provinces of Cuba showed relatively higher African and Native American contributions than the Western provinces. In particular, the highest proportion of African ancestry was observed in the provinces of Guantánamo (40%) and Santiago de Cuba (39%), and the highest proportion of Native American ancestry in Granma (15%), Holguín (12%) and Las Tunas (12%). We found evidence of substantial population stratification in the current Cuban population, emphasizing the need to control for the effects of population stratification in association studies including individuals from Cuba. The results of the analyses of uniparental markers were concordant with those observed in the autosomes. These geographic patterns in admixture proportions are fully consistent with historical and archaeological information. Additionally, we identified a sex-biased pattern in the process of gene flow, with a substantially higher European contribution from the paternal side, and higher Native American and African contributions from the maternal side. This sex-biased contribution was particularly evident for Native American ancestry. Finally, we observed that SNPs located in the genes SLC24A5 and SLC45A2 are strongly associated with melanin levels in the sample.     

Octopus vulgaris (Cuvier, 1797) in the Mediterranean Sea: Genetic Diversity and Population Structure

The common octopus, Octopus vulgaris Cuvier 1797, is a largely exploited cephalopod species in the Mediterranean Sea and the Atlantic Ocean, as well as along the coasts of Africa, Brazil and Japan, where its taxonomic identity is still debated. The assessment of its genetic structure is a pressing need to correctly manage the resource and to avoid overfishing and collapsing of local stocks. Here we analysed genetic variation and population structure of O. vulgaris using thirteen microsatellite loci in seven sampling localities from the Mediterranean Sea and one from the Atlantic Ocean. We also used a DNA barcoding approach by COI gene fragment to understand the phylogenetic relationships among the specimens here investigated and the ones whose sequences are available in literature. Our results reveal high levels of allelic richness and moderate heterozygosity in all samples investigated, and a pronounced differentiation of the Atlantic and Sicilian specimens. This latter aspect seems to support the isolation of the biota within the Strait of Messina. A certain degree of differentiation was detected among the other geographic samples within the Mediterranean Sea, which is more compatible with an island model than isolation by distance. The occurrence of null alleles affected more genetic diversity indices than population structure estimations. This study provides new insights about the genetic diversity and structure of O. vulgaris in the area of interest, which can be used as guidelines for a fisheries management perspective.     

Use of SSR and Retrotransposon-Based Markers to Interpret the Population Structure of Native Grapevines from Southern Italy

Native grapevines are the quintessential elements of Southern Italy winemaking, and genomic characterization plays a role of primary importance for preservation and sustainable use of these unexploited genetic resources. Among the various molecular techniques available, SSR and retrotransposons-based markers result to be the most valuable for cultivars and biotypes distinctiveness. A total of 62 accessions including 38 local grape cultivars were analyzed with 30 SSR, four REMAP and one IRAP markers to assess their genetic diversity and obtain a complete genomic profiling. The use of VrZAG79, VrZAG112, VVS2, VVMD25 and VVMD5 combined with retrotransposon-based markers proved to be the most discriminating and polymorphic markers for the rapid and unambiguous identification of minority grapevines from Campania region, which is considered one of the most appreciated Italian districts for wine production. Results revealed 58 SSR marker-specific alleles, 22 genotype-specific SSR alleles, and four REMAP and IRAP private bands. Cases of synonymy and homonymy were discovered. In conclusion, we provided evidences that the integrating SSR and retrotransposon-based markers is an effective strategy to assess the genetic diversity of autochthonous grapes, allowing their easy identification.     

Reconstructing the Population Genetic History of the Caribbean

The Caribbean basin is home to some of the most complex interactions in recent history among previously diverged human populations. Here, we investigate the population genetic history of this region by characterizing patterns of genome-wide variation among 330 individuals from three of the Greater Antilles (Cuba, Puerto Rico, Hispaniola), two mainland (Honduras, Colombia), and three Native South American (Yukpa, Bari, and Warao) populations. We combine these data with a unique database of genomic variation in over 3,000 individuals from diverse European, African, and Native American populations. We use local ancestry inference and tract length distributions to test different demographic scenarios for the pre- and post-colonial history of the region. We develop a novel ancestry-specific PCA (ASPCA) method to reconstruct the sub-continental origin of Native American, European, and African haplotypes from admixed genomes. We find that the most likely source of the indigenous ancestry in Caribbean islanders is a Native South American component shared among inland Amazonian tribes, Central America, and the Yucatan peninsula, suggesting extensive gene flow across the Caribbean in pre-Columbian times. We find evidence of two pulses of African migration. The first pulse—which today is reflected by shorter, older ancestry tracts—consists of a genetic component more similar to coastal West African regions involved in early stages of the trans-Atlantic slave trade. The second pulse—reflected by longer, younger tracts—is more similar to present-day West-Central African populations, supporting historical records of later transatlantic deportation. Surprisingly, we also identify a Latino-specific European component that has significantly diverged from its parental Iberian source populations, presumably as a result of small European founder population size. We demonstrate that the ancestral components in admixed genomes can be traced back to distinct sub-continental source populations with far greater resolution than previously thought, even when limited pre-Columbian Caribbean haplotypes have survived.     

Population Structure of Osmunda regalis in Relation to Environment and Vegetation: An Example in the Mediterranean Area

The structure of 42 natural populations of the endangered fern Osmunda regalis was studied at the southern limit of its European distribution. The aims were to i) investigate the population structures and status of the species; ii) test which local habitat and population characteristics correlate with the different population structures in the Mediterranean area; iii) evaluate which habitat types are suitable to support viable populations. The structure of populations is determined by the attribution of different stages of development of the sporophyte. This study documented the life-stage structure of O. regalis using an original classification of life stages that may be applicable to other fern populations with similar morphology. Using statistical analyses we distinguished: i) dynamic populations, which are characterized by a large proportion of sporelings and vegetative adults and are associated with streams and nemoral species; ii) stable populations, with a higher proportion of generative adults, growing prevalently in habitats rich in hygrophilous grasses and shrubs, with lower tree cover; iii) senile populations, with a relatively higher proportion of senescent individuals and with marked rejuvenation dominated by vegetative adults, which are prevalently located in spring swamps. The proportion of senescent stage individuals is positively correlated with the mean geographic distance between populations. Spring swamps, with populations that provide a clear example of remnant dynamics, are the habitat with the most stable conditions for O. regalis in the Mediterranean area.     

Soil-Atmosphere Methane Exchange in Undisturbed and Burned Mediterranean Shrubland of Southern Italy

Soils represent the primary biotic sink for atmospheric methane (CH₄). Uncertainty is associated, however, with global soil CH₄ consumption because of the few data available from many areas and, in particular, from Mediterranean-type ecosystems. In this study, soil-atmosphere CH₄ exchange was measured for one year in a coastal Italian shrubland (maquis), from both undisturbed areas and areas treated with experimental fire. Although fire represents one of the most frequent disturbance factors in seasonally dry environments, very few studies in these ecosystems have focused on its effect on soil CH₄ fluxes. Significant differences in soil ammonium content, water content, and temperature were measured between burned and unburned plots, however, no statistical differences were observed for CH₄ fluxes. CH₄ fluxes varied between −0.39 and −16.1 mg CH₄ m⁻² day⁻¹ and temporal variations were mainly driven by variations in soil water content and temperature. The highest CH₄ oxidation rates were measured during the driest and warmest period. Low gravimetric soil water content in the top 10 cm, as well as high NH₄⁺ concentration, did not seem to reduce methanotrophic activity, suggesting that maximal CH₄ oxidation activity might take place deeper in the soil profile, at least during part of the year.     

Population structure of Sicily: beta-thalassemia and HbS

Summary The population structure of two alleles with similar characteristics, HbS and beta-thalassemia, was studied in the same area in Sicily. It was observed that beta-thalassemia has uniform frequencies over the island, and that HbS shows a South-North cline. A singularity exists for HbS in the town of Butera, where the frequency of the S gene is six times higher than the island average. It was suggested that HbS entered Sicily from Greece (or directly from North Africa) when the beta-thalassemia allele was already established in the Island.     

Comparative Population Genetic Structure of the Endangered Southern Brown Bandicoot,Isoodon obesulus,in Fragmented Landscapes of Southern Australia

Genetic connectivity is a key factor for maintaining the persistence of populations in fragmented landscapes. In highly modified landscapes such us peri-urban areas, organisms’ dispersal among fragmented habitat patches can be reduced due to the surrounding matrix, leading to subsequent decreased gene flow and increased potential extinction risk in isolated sub-populations. However, few studies have compared within species how dispersal/gene flow varies between regions and among different forms of matrix that might be encountered. In the current study, we investigated gene flow and dispersal in an endangered marsupial, the southern brown bandicoot (Isoodon obesulus) in a heavily modified peri-urban landscape in South Australia, Australia. We used 14 microsatellite markers to genotype 254 individuals which were sampled from 15 sites. Analyses revealed significant genetic structure. Our analyses also indicated that dispersal was mostly limited to neighbouring sites. Comparisons of these results with analyses of a different population of the same species revealed that gene flow/dispersal was more limited in this peri-urban landscape than in a pine plantation landscape approximately 400 km to the south-east. These findings increase our understanding of how the nature of fragmentation can lead to profound differences in levels of genetic connectivity among populations of the same species.     

Uncovering the Genetic History of the Present-Day Greenlandic Population

Because of past limitations in samples and genotyping technologies, important questions about the history of the present-day Greenlandic population remain unanswered. In an effort to answer these questions and in general investigate the genetic history of the Greenlandic population, we analyzed ∼200,000 SNPs from more than 10% of the adult Greenlandic population (n = 4,674). We found that recent gene flow from Europe has had a substantial impact on the population: more than 80% of the Greenlanders have some European ancestry (on average ∼25% of their genome). However, we also found that the amount of recent European gene flow varies across Greenland and is far smaller in the more historically isolated areas in the north and east and in the small villages in the south. Furthermore, we found that there is substantial population structure in the Inuit genetic component of the Greenlanders and that individuals from the east, west, and north can be distinguished from each other. Moreover, the genetic differences in the Inuit ancestry are consistent with a single colonization wave of the island from north to west to south to east. Although it has been speculated that there has been historical admixture between the Norse Vikings who lived in Greenland for a limited period ∼600–1,000 years ago and the Inuit, we found no evidence supporting this hypothesis. Similarly, we found no evidence supporting a previously hypothesized admixture event between the Inuit in East Greenland and the Dorset people, who lived in Greenland before the Inuit.     

Assessing the Genetic Influence of Ancient Sociopolitical Structure: Micro-differentiation Patterns in the Population of Asturias (Northern Spain)

The human populations of the Iberian Peninsula are the varied result of a complex mixture of cultures throughout history, and are separated by clear social, cultural, linguistic or geographic barriers. The stronger genetic differences between closely related populations occur in the northern third of Spain, a phenomenon commonly known as “micro-differentiation”. It has been argued and discussed how this form of genetic structuring can be related to both the rugged landscape and the ancient societies of Northern Iberia, but this is difficult to test in most regions due to the intense human mobility of previous centuries. Nevertheless, the Spanish autonomous community of Asturias shows a complex history which hints of a certain isolation of its population. This, joined together with a difficult terrain full of deep valleys and steep mountains, makes it suitable for performing a study of genetic structure, based on mitochondrial DNA and Y-Chromosome markers. Our analyses do not only show that there are micro-differentiation patterns inside the Asturian territory, but that these patterns are strikingly similar between both uniparental markers. The inference of barriers to gene flow also indicates that Asturian populations from the coastal north and the mountainous south seem to be relatively isolated from the rest of the territory. These findings are discussed in light of historic and geographic data and, coupled with previous evidence, show that the origin of the current genetic patterning might indeed lie in Roman and Pre-Roman sociopolitical divisions.     

An Overview of the Genetic Structure within the Italian Population from Genome-Wide Data

In spite of the common belief of Europe as reasonably homogeneous at genetic level, advances in high-throughput genotyping technology have resolved several gradients which define different geographical areas with good precision. When Northern and Southern European groups were considered separately, there were clear genetic distinctions. Intra-country genetic differences were also evident, especially in Finland and, to a lesser extent, within other European populations. Here, we present the first analysis using the 125,799 genome-wide Single Nucleotide Polymorphisms (SNPs) data of 1,014 Italians with wide geographical coverage. We showed by using Principal Component analysis and model-based individual ancestry analysis, that the current population of Sardinia can be clearly differentiated genetically from mainland Italy and Sicily, and that a certain degree of genetic differentiation is detectable within the current Italian peninsula population. Pair-wise F_ST statistics Northern and Southern Italy amounts approximately to 0.001 between, and around 0.002 between Northern Italy and Utah residents with Northern and Western European ancestry (CEU). The Italian population also revealed a fine genetic substructure underscoring by the genomic inflation (Sardinia vs. Northern Italy = 3.040 and Northern Italy vs. CEU = 1.427), warning against confounding effects of hidden relatedness and population substructure in association studies.     

Genetic and Demographic Structure of the Yakut Population: Reproduction Indices

Genetic and demographic information for the Yakut population living in the Republic of Sakha (Yakutia) is presented. The mean number of children per woman constituted 4.605. Crow's index (I _tot) and its components (I _m and I _f) were 0.483, 0.104, and 0.343, respectively.     

Population Genetic Structure and Demographic History of Atrina pectinata Based on Mitochondrial DNA and Microsatellite Markers

The pen shell, Atrina pectinata, is one of the commercial bivalves in East Asia and thought to be recently affected by anthropogenic pressure (habitat destruction and/or fishing pressure). Information on its population genetic structure is crucial for the conservation of A. pectinata. Considering its long pelagic larval duration and iteroparity with high fecundity, the genetic structure for A. pectinata could be expected to be weak at a fine scale. However, the unusual oceanography in the coasts of China and Korea suggests potential for restricted dispersal of pelagic larvae and geographical differentiation. In addition, environmental changes associated with Pleistocene sea level fluctuations on the East China Sea continental shelf may also have strongly influenced historical population demography and genetic diversity of marine organisms. Here, partial sequences of the mitochondrial Cytochrome c oxidase subunit I (COI) gene and seven microsatellite loci were used to estimate population genetic structure and demographic history of seven samples from Northern China coast and one sample from North Korea coast. Despite high levels of genetic diversity within samples, there was no genetic differentiation among samples from Northern China coast and low but significant genetic differentiation between some of the Chinese samples and the North Korean sample. A late Pleistocene population expansion, probably after the Last Glacial Maximum, was also demonstrated for A. pectinata samples. No recent genetic bottleneck was detected in any of the eight samples. We concluded that both historical recolonization (through population range expansion and demographic expansion in the late Pleistocene) and current gene flow (through larval dispersal) were responsible for the weak level of genetic structure detected in A. pectinata.