Genetic population structure and demography of an apex predator,the tiger shark Galeocerdo cuvier

Population genetics has been increasingly applied to study large sharks over the last decade. Whilst large shark species are often difficult to study with direct methods, improved knowledge is needed for both population management and conservation, especially for species vulnerable to anthropogenic and climatic impacts. The tiger shark, Galeocerdo cuvier, is an apex predator known to play important direct and indirect roles in tropical and subtropical marine ecosystems. While the global and Indo‐West Pacific population genetic structure of this species has recently been investigated, questions remain over population structure and demographic history within the western Indian (WIO) and within the western Pacific Oceans (WPO). To address the knowledge gap in tiger shark regional population structures, the genetic diversity of 286 individuals sampled in seven localities was investigated using 27 microsatellite loci and three mitochondrial genes (CR, COI, and cytb). A weak genetic differentiation was observed between the WIO and the WPO, suggesting high genetic connectivity. This result agrees with previous studies and highlights the importance of the pelagic behavior of this species to ensure gene flow. Using approximate Bayesian computation to couple information from both nuclear and mitochondrial markers, evidence of a recent bottleneck in the Holocene (2,000–3,000 years ago) was found, which is the most probable cause for the low genetic diversity observed. A contemporary effective population size as low as 111 [43,369] was estimated during the bottleneck. Together, these results indicate low genetic diversity that may reflect a vulnerable population sensitive to regional pressures. Conservation measures are thus needed to protect a species that is classified as Near Threatened.     

Impact of prey occupancy and other ecological and anthropogenic factors on tiger distribution in Thailand's western forest complex

相似文献   

Diversity and characterization of oxytetracycline-resistant bacteria associated with non-native species, white-leg shrimp (Litopenaeus vannamei), and native species, black tiger shrimp (Penaeus monodon), intensively cultured in Thailand

Aims: This study aimed at surveying prevalence of oxytetracycline (OTC)‐resistant bacteria in the white‐leg shrimp Litopenaeus vannamei, and the black tiger shrimp Penaeus monodon, intensively cultured in Thailand. We investigated the phylogenetic diversity of the bacterial isolates, as well as the minimum inhibitory concentration (MIC) of OTC, the occurrence of major OTC‐resistant genes and multiple‐antibiotic resistance in the isolates. Methods and Results: Shrimps were collected from culture ponds, and the homogenates of whole bodies were plated on tryptic soy agar supplemented with or without OTC. Percentages of OTC‐resistant bacteria were 0·3–52·1% in white‐leg samples and 0·008–22·3% in black tiger samples. Analyses of 16S rDNA sequences indicated that most OTC‐resistant isolates were closely related to Aeromonas spp. and Lactococcus garvieae. MICs of OTC were 4–128 μg ml^?1 in the OTC‐resistant aeromonads and 128–256 μg ml^?1 in OTC‐resistant L. garvieae. OTC resistance was found to be conferred by the genes tet(A), tet(C), tet(D), tet(E), tet(M) and tet(S), detected either singly or in pairs. No resistance to ceftazidime, imipenem or chloramphenicol was observed in any isolate. Conclusions: Both species of shrimp are associated with OTC‐resistant bacteria, occasionally at high densities exceeding 10⁶ cfu g^?1. The associated bacteria, predominantly Lactococcus and Aeromonas genera, are potential pathogens and are reservoirs of a variety of OTC‐resistant genes. Significance and Impact of the Study: Cultured shrimps can be vehicle to carry OTC‐resistant bacteria to domestic and foreign consumers via the food chain. Very low populations of OTC‐resistant bacteria observed in the several ponds suggest that levels of the resistant bacteria are artificially high and should be reduced in farmed shrimps.     

Enterocytozoon hepatopenaei sp. nov. (Microsporida: Enterocytozoonidae), a parasite of the black tiger shrimp Penaeus monodon (Decapoda: Penaeidae): Fine structure and phylogenetic relationships

A new microsporidian species, Enterocytozoon hepatopenaei sp. nov., is described from the hepatopancreas of the black tiger shrimp Penaeus monodon (Crustacea: Decapoda). Different stages of the parasite are described, from early sporogonal plasmodia to mature spores in the cytoplasm of host-cells. The multinucleate sporogonal plasmodia existed in direct contact with the host-cell cytoplasm and contained numerous small blebs at the surface. Binary fission of the plasmodial nuclei occurred during early plasmodial development and numerous pre-sporoblasts were formed within the plasmodium. Electron-dense disks and precursors of the polar tubule developed in the cytoplasm of the plasmodium prior to budding of early sporoblasts from the plasmodial surface. Mature spores were oval, measuring 0.7 × 1.1 μm and contained a single nucleus, 5-6 coils of the polar filament, a posterior vacuole, an anchoring disk attached to the polar filament, and a thick electron-dense wall. The wall was composed of a plasmalemma, an electron-lucent endospore (10 nm) and an electron-dense exospore (2 nm). DNA primers designed from microsporidian SSU rRNA were used to amplify an 848 bp product from the parasite genome (GenBank FJ496356). The sequenced product had 84% identity to the matching region of SSU rRNA from Enterocytozoon bieneusi. Based upon ultrastructural features unique to the family Enterocytozoonidae, cytoplasmic location of the plasmodia and SSU rRNA sequence identity 16% different from E. bieneusi, the parasite was considered to be a new species, E. hepatopenaei, within the genus Enterocytozoon.     

福建梅花山圈养华南虎遗传状况分析

华南虎是世界上密切关注的旗舰物种,在过去的10 年间没有发现野生华南虎存在的证据,因此它是极度濒危的虎亚种。福建梅花山圈养华南虎群体是整个圈养华南虎群体的重要组成部分,拥有 12 只华南虎。基于组合长度为 3934 bp 的线粒体序列分析发现梅花山圈养华南虎拥有 3 种线粒体单倍型; 而基于 20 个微卫星位点基因型分析显示梅花山圈养华南虎一共有71 个等位基因,平均等位基因数是3. 55,等位基因丰度的平均值是3. 32,平均期望杂合度和多态信息含量( PIC) 分别为0. 513 和0. 445。这些提示梅花山华南虎圈养群体维持着较高的遗传多样性。     

Assessment of microbial quality of commercial and home-made tiger-nut beverages

Aims: We aimed to assess the microbiological quality of Spanish commercial tiger‐nut beverages as well as home‐made samples collected from supermarkets, street vendors, juice bars and ice‐cream parlours located in Valencia. Methods and Results: Microbiological analysis of 44 tiger‐nut beverages samples were carried out according to International Standard Organization (ISO) norms and published works which included the total viable count, Enterobacteriaceae, Escherichia coli, Staphylococcus aureus, Salmonella, Bacillus cereus, yeasts, moulds, Yersinia enterocolitca, Clostridium perfringens, Vibrio spp. and Listeria monocytogenes. The obtained results indicated that all the commercial samples were below the detection limit for the viable microorganisms. Results of analysis of those home‐made tiger‐nut samples revealed that 67% (16 samples) harboured total plate counts while the rest of samples were free from these microorganisms. Enterobacteriaceae were detected in 62% (15 samples). E. coli were found in only one sample (4%), yeasts and moulds were detected in 62% (15 samples) each, Shigella was found in 21% (five samples); however, all samples were free from S. aureus, Salmonella, Y. enterocolotica, C. perfringens, Vibrio spp. and L. monocytogenes. Conclusions: These results reflected that there exists a rather high contamination level in home‐made tiger‐nut beverages indicating the need to apply correct and strict HACCP system(s) during manufacturing and storage of these food products. Significance and Impact of Study: This study demonstrates the great need to carry out microbiological tests frequently in these products and even more the need to apply correct HACCP system (s). Tiger‐nut beverages are especially well‐known products in Spain, hence it is extremely important to ensure an adequate microbiological quality to guarantee consumers health.     

Microsatellite DNA markers: evaluating their potential for estimating the proportion of hatchery-reared offspring in a stock enhancement programme

We describe a statistical method for estimating the effectiveness of a stock enhancement programme using nuclear DNA loci. It is based on knowing the population allele frequencies and the genotypes of the hatchery parents (mother only, or mother and father), and on determining the probability that a wild-born animal will by chance have a genotype consistent with hatchery origin. We show how to estimate the proportion of released animals in the wild population, and its standard error. The method is applied to a data set of eight microsatellite loci in brown tiger prawns (Penaeus esculentus), prior to the start of a possible enhancement programme. We conclude that, for this particular data set, the effectiveness of such an enhancement programme could be quantified accurately if both maternal and paternal genotypes are known, but not if maternal genotypes only are known. Full paternal genotyping would require offspring genotyping and thus would be expensive, but a partly typed paternal genotype from a mass homogenate of offspring would be almost as effective and much cheaper. The experiment would become feasible based on maternal genotypes alone, if a further three typical microsatellite loci could be found to add to the existing panel of eight. The methods detailed should be of interest to any enhancement project that relies on nuclear DNA markers to provide tags.     

Chromosome-scale genomes reveal genomic consequences of inbreeding in the South China tiger: A comparative study with the Amur tiger

The South China tiger (Panthera tigris amoyensis, SCT) is the most critically endangered subspecies of tiger due to functional extinction in the wild. Inbreeding depression is observed among the captive population descended from six wild ancestors, resulting in high juvenile mortality and low reproduction. We assembled and characterized the first SCT genome and an improved Amur tiger (P. t. altaica, AT) genome named AmyTig1.0 and PanTig2.0. The two genomes are the most continuous and comprehensive among any tiger genomes yet reported at the chromosomal level. By using the two genomes and resequencing data of 15 SCT and 13 AT individuals, we investigated the genomic signature of inbreeding depression of the SCT. The results indicated that the effective population size of SCT experienced three phases of decline, ~5.0–1.0 thousand years ago, 100 years ago, and since captive breeding in 1963. We found 43 long runs of homozygosity fragments that were shared by all individuals in the SCT population and covered a total length of 20.63% in the SCT genome. We also detected a large proportion of identical-by-descent segments across the genome in the SCT population, especially on ChrB4. Deleterious nonsynonymous single nucleotide polymorphic sites and loss-of-function mutations were found across genomes with extensive potential influences, despite a proportion of these loads having been purged by inbreeding depression. Our research provides an invaluable resource for the formulation of genetic management policies for the South China tiger such as developing genome-based breeding and genetic rescue strategy.