东太平洋浅海长尾鲨母体和胚胎间痕量元素的迁移规律

大洋中上层鲨鱼多为金枪鱼渔业的兼捕渔获,因其生长缓慢、繁殖力低等生活史特征,极易被过度捕捞,90%种类资源已近危。而作为长生命周期的顶级捕食者,鲨鱼体内某些过高的痕量元素含量不利于资源恢复。本研究选取10尾东太平洋雌性浅海长尾鲨(Alopias pelagicus)及对应的18尾胚胎,测定其肌肉和肝脏中锌(Zn)、铜(Cu)、铬(Cr)、镍(Ni)、锰(Mn)、硒(Se)、钴(Co)、汞(Hg)、镉(Cd)、铅(Pb)和砷(As) 11种痕量元素,探寻浅海长尾鲨繁殖过程中母体与胚胎间痕量元素的迁移规律。结果表明: 对于必需元素,胚胎两种组织的Cr、Cu、Se和Mn含量均高于母体对应组织,而Ni和Zn含量在胚胎肌肉中较高、肝脏中较低;对于非必需元素,胚胎两种组织的As、Cd和Hg含量均低于母体对应组织。虽然Hg在母体和胚胎组织中含量均较高,但胚胎组织的Se/Hg均大于1,且其在胚胎中的值均大于母体,表明Se在胚胎中具有显著抑制Hg毒性的作用。肝脏作为鲨鱼胚胎发育的主要能量来源,其元素含量在胚胎与母体之间无显著相关性。由此推测,浅海长尾鲨可能存在特定的元素调控机制,以维持胚胎组织中元素含量的稳定。     

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。     

Population Genetic Structure of Pacific Herring Clupea pallasii in the Northwestern Pacific Ocean Based on Microsatellite Analysis

Journal of Ichthyology - The population genetic structure of Pacific herring Clupea pallasii in the northwestern Pacific Ocean is studied based on the polymorphism analysis of 11 microsatellite...     

独龙牛遗传多样性及其种群遗传结构的等位酶分析

采用水平片淀粉凝胶电泳技术,进行３０头独牛牛４１种蛋白质共计４４个遗传座位的等位酶分析,只在Ｔｒ,Ｈｐ,Ａｍｙ,Ｅｓｔ等４个座位发现多态性。每个座位等基因的平均数、多态座位百分比和平均杂合度值分别为Ａ＝１．０９０９、Ｐ＝０．０６８２和Ｈ＝０．０２６２。贡山县和福贡县独龙牛群体从酶基因的角度上看遗传多样性贫乏,可能是分别由小种群引种而来,受到瓶颈效应的作用,并伴随着创立者事件的发生。我们结合独龙牛在     

Genetic Diversity and Population Structure of Teucrium polium (Lamiaceae) in Tunisia

Random amplified polymorphic DNA markers were used to assess the genetic diversity within and among seven Tunisian diploid and polyploid populations of Teucrium polium L. from five bioclimatic areas. Out of the 141 bands generated from eight selected primers, 124 were polymorphic. The genetic diversity within a population (Shannon’s index) was high and varied according both the ploidal levels and bioclimatic zones. The genetic differentiation among populations assessed by G _ST and Φ_ST statistics was high, suggesting a low level of gene flow among them. The major proportion of the variation was attributable to individual differences within populations. The UPGMA analysis based on Nei and Li’s coefficient showed that individuals from each population clustered together. In a dendrogram using the Φ_ST distance matrix, population grouping is concordant with bioclimates and cytotypes. Conservation strategies should take into account the level of the genetic diversity of the populations according to their bioclimate and ploidal levels.     

Genetic Diversity and Population Structure of Alnus hirsuta (Betulaceae) in Korea

Alnus hirsuta in Korea was measured to estimate the amount and pattern of genetic diversity and population structure. The mean genetic diversity within populations was 0.166. Korean alder populations have slightly high levels of genetic diversity compared to those of two Canadian alder species. The genetic differentiation among populations accounted for 9% of the total variation. The rate of gene flow was estimated high (Nm=2.63). Analysis of inbreeding coefficient, calculated for all polymorphic loci in each population, showed a substantial heterozygote deficiency relative to Hardy-Weinberg expectations. The mean G _ST value of A. hirsuta in Korea was 0.087. The low value of G _ST in this species, reflecting little spatial genetic differentiation, may indicate extensive gene flow. A relationship between the mean heterozygosity and annual rainfall showed a positive relationship (r ²=0.54, F=4.67). Received 8 August 1998/ Accepted in revised form 7 July 1999     

Genetic Diversity and Population Structure of Indian Golden Silkmoth (Antheraea assama)

Background

The Indian golden saturniid silkmoth (Antheraea assama), popularly known as muga silkmoth, is a semi-domesticated silk producing insect confined to a narrow habitat range of the northeastern region of India. Owing to the prevailing socio-political problems, the muga silkworm habitats in the northeastern region have not been accessible hampering the phylogeography studies of this rare silkmoth. Recently, we have been successful in our attempt to collect muga cocoon samples, although to a limited extent, from their natural habitats. Out of 87 microsatellite markers developed previously for A. assama, 13 informative markers were employed to genotype 97 individuals from six populations and analyzed their population structure and genetic variation.

Methodology/Principal Findings

We observed highly significant genetic diversity in one of the populations (WWS-1, a population derived from West Garo Hills region of Meghalaya state). Further analysis with and without WWS-1 population revealed that dramatic genetic differentiation (global F_ST = 0.301) was due to high genetic diversity contributed by WWS-1 population. Analysis of the remaining five populations (excluding WWS-1) showed a marked reduction in the number of alleles at all the employed loci. Structure analysis showed the presence of only two clusters: one formed by WWS-1 population and the other included the remaining five populations, inferring that there is no significant genetic diversity within and between these five populations, and suggesting that these five populations are probably derived from a single population. Patterns of recent population bottlenecks were not evident in any of the six populations studied.

Conclusions/Significance

A. assama inhabiting the WWS-1 region revealed very high genetic diversity, and was genetically divergent from the five populations studied. The efforts should be continued to identify and study such populations from this region as well as other muga silkworm habitats. The information generated will be very useful in conservation of dwindling muga culture in Northeast India.     

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.     

Genetic Diversity and Population Structure of Juniperus rigida (Cupressaceae) and Juniperus coreana

Enzyme electrophoresis was used to estimate genetic diversity and population structure of Juniperus rigida (Cupressaceae) and Juniperus coreana in Korea. In J. rigida, 16 of the 22 loci (72.7%) showed detectable polymorphism. Genetic diversity (0.224) was higher than average values for species with similar life history traits. The endemic species (J. coreana) was found to have fewer alleles per locus (1.39 vs. 1.61), fewer alleles per polymorphic locus (2.42 vs. 2.63), lower percent polymorphic locus (54.6 vs. 72.7%), and lower diversity (0.199 vs. 0.224) than J. rigida. These genetic diversity parameters indicated that J. coreana was genetically depauperate relative to its presumptive progenitor, J. rigida. Analysis of fixation indices showed a substantial deficiency of heterozygotes relative to Hardy–Weinberg expectations suggesting inbreeding in J. coreana. The G _ST values of J. rigida and J. coreana were 0.173 and 0.118 respectively. The indirect estimate of gene flow based on mean G _ST was moderate (Nm = 1.19 for J. rigida and 1.86 for J. coreana). This revised version was published online in July 2006 with corrections to the Cover Date.     

Genetic Diversity and Population Structure of Acacia senegal (L) Willd. in Kenya

The level of genetic diversity and population structure of Acacia senegal variety kerensis in Kenya was examined using seven polymorphic nuclear microsatellite loci and two chloroplast microsatellite loci. In both chloroplast and nuclear datasets, high levels of genetic diversity were found within all populations and genetic differentiation among populations was low, indicating extensive gene flow. Analysis of population structure provided support for the presence of two groups of populations, although all individuals had mixed ancestry. Groups reflected the influence of geography on gene flow, with one representing Rift Valley populations whilst the other represented populations from Eastern Kenya. The similarities between estimates derived from nuclear and chloroplast data suggest highly effective gene dispersal by both pollen and seed in this species, although population structure appears to have been influenced by distributional changes in the past. The few contrasts between the spatial patterns for nuclear and chloroplast data provided additional support for the idea that, having fragmented in the past, groups are now thoroughly mixed as a result of extensive gene flow. For the purposes of conservation and in situ management of genetic resources, sampling could target a few, large populations ideally distributed among the spatial groups identified. This should ensure the majority of extant variation is preserved, and facilitate the investigation of variation in important phenotypic traits and development of breeding populations.     

Genetic Diversity and Population Structure in Western Hoolock (Hoolock hoolock) Gibbons in India

International Journal of Primatology - Geographic and anthropogenic barriers can result in creating population structure in primates. We hypothesized that such features in the Northeast India could...     

Genetic Diversity and Population Structure of the Brachiaria brizantha Germplasm

Brachiaria brizantha (Hochst. ex A. Rich.) Stapf. (syn. Urochloa brizantha (Hochst. ex A. Rich.) R.D. Webster) is a species used primarily as forage in tropical America and Southeast Asia. B. brizantha has been extensively researched since the 1980s with the initiation of the Tropical Forages Breeding Program conducted by the Brazilian Agricultural Research Corporation (Empresa Brasileira de Pesquisa Agropecuária; EMBRAPA), holding one of the largest germplasm collections in the world. This work has identified 15 new microsatellite markers for this species, which have been used in addition to five previously reported markers, to estimate the genetic similarities among 172 accessions and six cultivars of this species. Similarity index values ranged from 0.40 to 1.00. Two duplications were found in the germplasm. A Bayesian analysis performed using the STRUCTURE 2.3.3 program revealed the presence of three clusters with different allelic pools. This analysis is valuable for the performance of crosses to explore heterosis; however, the mode of reproduction of the accessions and ploidy barriers must be observed for effective exploration. A grouping analysis using the neighbor-joining method was consistent with the STRUCTURE analysis, and a combination approach suggested that this germplasm collection does not exhibit considerable genetic variability despite the presence of three distinct allelic pools. The lack of correlation between the genetic and geographic distances is also discussed.     

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。     

Insights into vertebral band pair deposition rate in the juvenile common thresher shark (Alopias vulpinus) in the northeastern Pacific Ocean

Validation of band pair deposition rates in elasmobranch vertebrae is essential for accurate age estimation using band pair counting techniques. We present a validation study of the vertebral band pair deposition rate for juvenile common thresher sharks Alopias vulpinus in the northeastern Pacific Ocean (NEPO) using tag and recapture with oxytetracycline (OTC) injection. A total of 14 juvenile A. vulpinus marked with OTC from 1998 through 2013 were recaptured with times at liberty ranging from 1.08 to 3.81 years with an average of 2.14 years (±0.97 years standard deviation, SD). Shark size ranged from 80 to 128 cm fork length (LF) at the time of OTC injection and from 112 to 168 cm LF for those measured at recapture. The slopes of the relationships between band pairs post OTC and years at liberty for each reader ranged from 0.84 to 0.95, slightly lower than the 1.0 slope expected from annual band pair formation. These findings preliminarily support previous age and growth assumptions based on a one band pair per year deposition rate. However, high variation in band pair deposition rates between samples, coupled with regression slopes falling just under one band pair per year, indicates that further investigation is needed to refine band pair deposition rate estimates.     

Genetic Diversity and Population Structure of Theileria annulata in Oman

Background

Theileriosis, caused by a number of species within the genus Theileria, is a common disease of livestock in Oman. It is a major constraint to the development of the livestock industry due to a high rate of morbidity and mortality in both cattle and sheep. Since little is currently known about the genetic diversity of the parasites causing theileriosis in Oman, the present study was designed to address this issue with specific regard to T. annulata in cattle.

Methods

Blood samples were collected from cattle from four geographically distinct regions in Oman for genetic analysis of the Theileria annulata population. Ten genetic markers (micro- and mini-satellites) representing all four chromosomes of T. annulata were applied to these samples using a combination of PCR amplification and fragment analysis. The resultant genetic data was analysed to provide a first insight into the structure of the T. annulata population in Oman.

Results

We applied ten micro- and mini-satellite markers to a total of 310 samples obtained from different regions (174 [56%] from Dhofar, 68 [22%] from Dhira, 44 [14.5%] from Batinah and 24 [8%] from Sharqia). A high degree of allelic diversity was observed among the four parasite populations. Expected heterozygosity for each site ranged from 0.816 to 0.854. A high multiplicity of infection was observed in individual hosts, with an average of 3.3 to 3.4 alleles per locus, in samples derived from Batinah, Dhofar and Sharqia regions. In samples from Dhira region, an average of 2.9 alleles per locus was observed. Mild but statistically significant linkage disequilibrium between pairs of markers was observed in populations from three of the four regions. In contrast, when the analysis was performed at farm level, no significant linkage disequilibrium was observed. Finally, no significant genetic differentiation was seen between the four populations, with most pair-wise F_ST values being less than 0.03. Slightly higher F_ST values (G_ST’ = 0.075, θ = 0.07) were detected when the data for T. annulata parasites in Oman was compared with that previously generated for Turkey and Tunisia.

Conclusion

Genetic analyses of T. annulata samples representing four geographical regions in Oman revealed a high level of genetic diversity in the parasite population. There was little evidence of genetic differentiation between parasites from different regions, and a high level of genetic diversity was maintained within each sub-population. These findings are consistent with a high parasite transmission rate and frequent movement of animals between different regions in Oman.     

Genetic Diversity and Population Structure of Cucumber (Cucumis sativus L.)

Knowing the extent and structure of genetic variation in germplasm collections is essential for the conservation and utilization of biodiversity in cultivated plants. Cucumber is the fourth most important vegetable crop worldwide and is a model system for other Cucurbitaceae, a family that also includes melon, watermelon, pumpkin and squash. Previous isozyme studies revealed a low genetic diversity in cucumber, but detailed insights into the crop''s genetic structure and diversity are largely missing. We have fingerprinted 3,342 accessions from the Chinese, Dutch and U.S. cucumber collections with 23 highly polymorphic Simple Sequence Repeat (SSR) markers evenly distributed in the genome. The data reveal three distinct populations, largely corresponding to three geographic regions. Population 1 corresponds to germplasm from China, except for the unique semi-wild landraces found in Xishuangbanna in Southwest China and East Asia; population 2 to Europe, America, and Central and West Asia; and population 3 to India and Xishuangbanna. Admixtures were also detected, reflecting hybridization and migration events between the populations. The genetic background of the Indian germplasm is heterogeneous, indicating that the Indian cucumbers maintain a large proportion of the genetic diversity and that only a small fraction was introduced to other parts of the world. Subsequently, we defined a core collection consisting of 115 accessions and capturing over 77% of the SSR alleles. Insight into the genetic structure of cucumber will help developing appropriate conservation strategies and provides a basis for population-level genome sequencing in cucumber.     

Genetic Population Structure of Pacific Hake, Merluccius productus, in the Pacific Northwest

This study presents the first protein electrophoretic study of population structure within the Georgia Basin Pacific hake Distinct Population Segment, as defined under the U.S. Endangered Species Act. Forty-one allozyme loci (29 polymorphic) were analyzed in samples from three Pacific hake spawning populations on the west coast of North America: (1) Port Susan, Puget Sound, Washington (three temporal samples); (2) south-central Strait of Georgia, British Columbia, Canada (two temporal samples); and (3) offshore of southern California (two temporal samples) (total n = 664). Mean heterozygosity over all loci was 12–13% for all populations. Within-population temporal samples were not significantly different from one another, but statistically significant differences were detected at 15 of the 29 polymorphic loci (p < 0.05) among the three populations. Differences at eight of these loci were highly significant (p < 0.001): ADA ^*, ALAT ^*, bGALA ^*, GPI-A ^*, sIDHP ^*, LDH-A ^*, MPI ^*, and PEP-B ^*. The two Georgia Basin populations were significantly different at six loci: bGALA ^*, sIDHP ^*, LDH-A ^*, MPI ^*, PGK ^*, and PGM-2 ^* (p < 0.05). Nei's genetic distance (D) was 0.0006 between Port Susan and Strait of Georgia pooled temporal samples, and 0.005 between these populations and offshore Pacific hake. F_ST was 0.02 and 0.0046 among all three populations and among the Georgia Basin populations, respectively. Both F_ST estimates were significantly greater than zero, and the results suggest a high degree of demographic isolation among all three populations.     

Genetic Variations in Two Seahorse Species (Hippocampus mohnikei and Hippocampus trimaculatus): Evidence for Middle Pleistocene Population Expansion

Population genetic of seahorses is confidently influenced by their species-specific ecological requirements and life-history traits. In the present study, partial sequences of mitochondrial cytochrome b (cytb) and control region (CR) were obtained from 50 Hippocampus mohnikei and 92 H. trimaculatus from four zoogeographical zones. A total of 780 base pairs of cytb gene were sequenced to characterize mitochondrial DNA (mtDNA) diversity. The mtDNA marker revealed high haplotype diversity, low nucleotide diversity, and a lack of population structure across both populations of H. mohnikei and H. trimaculatus. A neighbour-joining (NJ) tree of cytb gene sequences showed that H. mohnikei haplotypes formed one cluster. A maximum likelihood (ML) tree of cytb gene sequences showed that H. trimaculatus belonged to one lineage. The star-like pattern median-joining network of cytb and CR markers indicated a previous demographic expansion of H. mohnikei and H. trimaculatus. The cytb and CR data sets exhibited a unimodal mismatch distribution, which may have resulted from population expansion. Mismatch analysis suggested that the expansion was initiated about 276,000 years ago for H. mohnikei and about 230,000 years ago for H. trimaculatus during the middle Pleistocene period. This study indicates a possible signature of genetic variation and population expansion in two seahorses under complex marine environments.