Genetic diversity analysis of spawner and recaptured populations of Chinese shrimp(Fenneropenaeus chinensis)during stock enhancement in the Bohai Bay based on an SSR marker

Eight microsatellite markers were used to analyze genetic diversity, level of inbreeding, and effective population size of spawner and recaptured populations of Chinese shrimp（Fenneropenaeus chinensis） during stock enhancement in the Bohai Bay in 2013. A total of 254 and 238 alleles were identified in the spawner and recaptured populations, respectively, and the numbers of alleles（N_a） were 8–63 and 6–60, respectively. The numbers of effective alleles（N_e） were 2.52–21.60 and 2.67–20.72, respectively. The polymorphism information content ranged from 0.529 to 0.952. The observed heterozygosity（H_o） values（0.638–0.910 and 0.712–0.927） were lower than the expected heterozygosity（H_e） values（0.603–0.954 and 0.625–0.952）, which indicated that the two populations possessed a rich genetic diversity. In 16 tests（2 populations×8 loci）, 13 tests deviated from the HardyWeinberg equilibrium. F_（is） values were positive at seven loci and the inbreeding coefficients（F） of the two populations estimated by trio ML were 13.234% and 11.603%, suggesting that there was a relatively high degree of inbreeding. A certain level of inbreeding depression had occurred in the Chinese shrimp population. F_（st） values ranged from 0 to 0.059, with a mean of 0.028, displaying a low level of genetic differentiation in the two populations. Effective population sizes（3 060.2 and 3 842.8） were higher than the minimum number suggested for retaining the evolutionary potential to adapt to new environmental conditions. For enhancement activity in 2014,the ideal number of captured shrimp spawners should have ranged from 7 686 to 19 214 to maintain genetic diversity and effective population size. Further strategies to adjust the balance of economic cost, fishing effort and ideal number of shrimp spawners to maintain a satisfactory effective population size for ensuring the sustainability of Chinese shrimp are proposed.

Analysis of the diversity of population and convergence of genetic algorithms based on Negentropy

With its wide use in different fields, the problem of the convergence of simple genetic algorithms (GAs) has been concerned. In the past, the research on the convergence of GAs was based on Holland's model theorem. The diversity of the evolutionary population and the convergence of GAs are studied by using the concept of negentropy based on the discussion of the characteristic of GA. Some test functions are used to test the convergence of GAs, and good results have been obtained. It is shown that the global optimization may be obtained by selecting appropriate parameters of simple GAs if the evolution time is enough.

Genetic Diversity and Population Structure in Landraces and Improved Rice Varieties from India

A set of 50 rice genotypes comprising landraces, local selections, and improved varieties were characterized using simple sequence repeat（SSR） and inter simple sequence repeat（ISSR） markers to study genetic diversity and population structure. Following unweighted pair group method with arithmetic mean based clustering using binary data of polymorphic markers, the genotypes were grouped into 5 clusters and 11 sub-clusters, whereas population structure analysis separated 50 rice genotypes into 5 sub-populations. Grouping of rice genotypes showed better resemblance with the pedigree information of the genotypes. Both genetic diversity and population structure analysis separated majority of the improved varieties from landraces and local selections. Some of the SSR markers amplified unique alleles which were specific to a particular genotype and could distinguish them from the rest. The results indicate that these rice genotypes exhibit a higher genetic diversity and can be very useful in rice improvement program.

Improved Harris Hawks Algorithm and Its Application in Feature Selection

This research focuses on improving the Harris’Hawks Optimization algorithm(HHO)by tackling several of its shortcomings,including insufficient population diversity,an imbalance in exploration vs.exploitation,and a lack of thorough exploitation depth.To tackle these shortcomings,it proposes enhancements from three distinct perspectives:an initialization technique for populations grounded in opposition-based learning,a strategy for updating escape energy factors to improve the equilibrium between exploitation and exploration,and a comprehensive exploitation approach that utilizes variable neighborhood search along with mutation operators.The effectiveness of the Improved Harris Hawks Optimization algorithm(IHHO)is assessed by comparing it to five leading algorithms across 23 benchmark test functions.Experimental findings indicate that the IHHO surpasses several contemporary algorithms its problem-solving capabilities.Additionally,this paper introduces a feature selection method leveraging the IHHO algorithm(IHHO-FS)to address challenges such as low efficiency in feature selection and high computational costs(time to find the optimal feature combination and model response time)associated with high-dimensional datasets.Comparative analyses between IHHO-FS and six other advanced feature selection methods are conducted across eight datasets.The results demonstrate that IHHO-FS significantly reduces the computational costs associated with classification models by lowering data dimensionality,while also enhancing the efficiency of feature selection.Furthermore,IHHO-FS shows strong competitiveness relative to numerous algorithms.

Genetic diversity of pepper(Capsicum spp.) germplasm resources in China reflects selection for cultivar types and spatial distribution

Pepper（Capsicum spp.） is an important vegetable crop in the world. Now the pepper in China contributes one-third of the world＇s peppers production. Genetic diversity of the pepper germplasm of China is expected interesting to know. To explore the structure of genetic diversity in Chinese pepper germplasm resources and possible relationship with cultivar types or geographic origin, we sampled and compared 372 Gen Bank pepper accessions（local cultivars and landraces） from 31 provinces, autonomous regions and municipalities of China and 31 additional accessions from other countries. These accessions were genotyped using 28 simple sequence repeat（SSR） markers spanning the entire pepper genome. We then investigated the genetic structure of the sampled collection using model-based analysis in STRUCTURE v2.3.4 and examined genetic relationships by the unweighted pair-group method of mathematical averages（UPGMA） in MEGA. In addition to geographic origin, we evaluated eight plant and fruit traits. In total, 363 alleles were amplified using the 28 SSR primers. Gene diversity, polymorphism information content and heterozygosity of the 28 SSR loci were estimated as 0.09–0.92, 0.08–0.92 and 0.01–0.34, respectively. The UPGMA cluster analysis clearly distinguished Capsicum annuum L. from other cultivated pepper species. Population structure analysis of the 368 C. annuum accessions uncovered three genetic groups which also corresponded to distinct cultivar types with respect to the plant and fruit descriptors. The genetic structure was also related to the geographic origin of the landraces. Overall results indicate that genetic diversity of Chinese pepper landraces were structured by migration of genotypes followed by human selection for cultivar types in agreement with consumption modes and adaptation to the highly diversified agro-climatic conditions.

Bayesian Reliability——Growth Analysis for Statistical of Diverse Population Based on Non-homogeneous Poisson Process

New armament systems are subjected to the method for dealing with multi-stage system reliability-growth statistical problems of diverse population in order to improve reliability before starting mass production. Aiming at the test process which is high expense and small sample-size in the development of complex system, the specific methods are studied on how to process the statistical information of Bayesian reliability growth regarding diverse populations. Firstly, according to the characteristics of reliability growth during product development, the Bayesian method is used to integrate the testing information of multi-stage and the order relations of distribution parameters. And then a Gamma-Beta prior distribution is proposed based on non-homogeneous Poisson process（NHPP） corresponding to the reliability growth process. The posterior distribution of reliability parameters is obtained regarding different stages of product, and the reliability parameters are evaluated based on the posterior distribution. Finally, Bayesian approach proposed in this paper for multi-stage reliability growth test is applied to the test process which is small sample-size in the astronautics filed. The results of a numerical example show that the presented model can make use of the diverse information synthetically, and pave the way for the application of the Bayesian model for multi-stage reliability growth test evaluation with small sample-size. The method is useful for evaluating multi-stage system reliability and making reliability growth plan rationally.

Abundance and Fluctuation in Spider Diversity in Citrus Fruits from Located in Vicinity of Faisalabad Pakistan

Spiders for the present study were collected from different fruit gardens（i.e. citrus） located at various localities（i.e., Tehsil Samundri, Jaranwala, Tandlianwala and Faisalabad） of District Faisalabad, Pakistan. Spiders belonging to six families and 33 species were captured from the two fruit gardens during the one year of this study. The citrus fruits garden was found to be best populated habitat as compared to other fruit garden. These sites were sampled by using pitfall traps; each month for five consecutive days from September 2010 to March 2011. As a result, 1 054 specimens were captured representing six families viz： lycosidae, thomosidae, gnaphosidae, saltisidae, araneidae and clubionidae. Lycosidae was more abundant, while clubionidae was less diverse during the study. Maximum population fluctuation among the spider specimens showed during the months from September and October, while the least abundance of spider specimens was reordered during June, November and December. Maximum taxonomic diversity was recorded from September to November, with the peak in September. It was concluded during these three months, when the citrus and guava gardens were attacked by the most of the pest insects. During the months of July and November diversity was moderate and mutually comparable, while in June and December, it was the least. This study contributed to the identification of spider diversity in the agro-ecosystem which could be used in the biological pest control.

Y‑STR Kits and Y‑STR Diversity in the South African Population: A Review

The South African population consists of four ethnic groups,i.e.,Blacks,Coloreds,Indians,and Whites,and is considered the most diverse conglomeration of humans.In addition to autosomal short tandem repeat(STR)variation,an important tool to study population diversity is Y-chromosome(Y)-STR analysis.Y-STRs aid in forensic investigations and provide essential data about paternal lineage origins.Y-STR kits consisting of an array of stable and rapidly mutating markers offer crucial information on a given population’s genetic and haplotype diversity.This review discusses the development of Y-STR kits over the years and highlights some prominent Y-STR studies conducted on the South African population.The earliest Y-STR kit developed was the Y-PLEX™6,with the most recent being the UniQTyper™Y-10 Multiplex.The South African population studies show varying data,with the“minimal haplotype”having low discrimination capacity among the ethnic groups and the UniQTyper™Y-10 showing high genetic diversity among the ethnic groups of the country.There is a dearth of Y-STR studies on the South African population.With the advent of new Y-STR kits with increased discriminatory markers,additional studies are required to represent the South African population in the Y-STR databases.Considering the diversity of the South African population,establishment of a local/regional population database would be beneficial.In addition,data on the origins and prevalence of mutations and silent alleles should be obtained from STR datasets generated during kinship investigations(specifically,parentage tests)so that detailed information about the frequencies of mutations,silent alleles,and uniparental disomy in the South African population at Y STR loci can be estimated.

Informative ISSR Markers Help Identify Genetically Distinct Accessions of Oryza rufipogon in Yield Improvement

Inter simple sequence repeat（ISSR） polymorphism was used to determine genetic diversity and phylogenetic relationships in 90 genotypes of wild and cultivated species of Oryza from different geographical regions of the world. In all the 17 primers used in ISSR-PCR, a total of 11 464 bands were amplified at 253 band positions/loci. The primer UBC-809 amplified the maximum bands（1 059） at 21 band positions. UBC-810 and UBC-835 amplified the minimum of 391 bands each at 7 and 14 band positions, respectively. The mean polymorphism information content ranged from 0.44 to 0.84 and resolving power ranged from 8.69 to 23.53. Un-weighted pair group method with arithmetic mean dendrogram and population structure based on the 17 primers separated all genotypes into 4 major clusters with a genetic similarity of 53%–100%. The first two clusters consisted of 30 O. rufipogon accessions each. In the third cluster, O. nivara and O. longistaminata grouped as one sub-cluster and all other O. nivara accessions and cultivars grouped as another sub-cluster. The fourth cluster had only five O. rufipogon accessions which can be a source of new genes. Four sub-populations were identified within O. rufipogon and two sub-populations within O. nivara at K = 7. A subset of six primers with high resolving power values were the most informative and grouped all genotypes almost similarly as the 17 primers did. Use of these six highly informative primers in ISSR-PCR is a cost effective and robust method for assessing genetic diversity in large germplasm collections of wild rice species.

Population transcriptomics reveals a potentially positive role of expression diversity in adaptation

While it is widely accepted that genetic diversity determines the potential of adaptation,the role that gene expression variation plays in adaptation remains poorly known.Here we show that gene expression diversity could have played a positive role in the adaptation of Miscanthus lutarioriparius.RNA-seq was conducted for 80 individuals of the species,with half planted in the energy crop domestication site and the other half planted in the control site near native habitats.A leaf reference transcriptome consisting of 18,503 high-quality transcripts was obtained using a pipeline developed for de novo assembling with population RNA-seq data.The population structure and genetic diversity of M.lutarioriparius were estimated based on 30,609 genic single nucleotide polymorphisms.Population expression（Ep） and expression diversity（Ed）were defined to measure the average level and the magnitude of variation of a gene expression in the population,respectively.It was found that expression diversity increased while genetic Resediversity decreased after the species was transplanted from the native habitats to the harsh domestication site,especially for genes involved in abiotic stress resistance,histone methylation,and biomass synthesis under water limitation.The increased expression diversity could have enriched phenotypic variation directly subject to selections in the new environment.

Assessing the genetic diversity of the critically endangered Chinese sturgeon Acipenser sinensis using mitochondrial markers and genome-wide single-nucleotide polymorphisms from RAD-seq

As a living fossil, the endangered Chinese sturgeon(Acipenser sinensis) has been considered a national treasure in China. Here,the famous Gezhouba Dam and Three Gorges Dam on the Yangtze River were built in 1988 and 2006, for economic purposes.The natural population of Chinese sturgeon has declined since then, as these dams block its migratory route to the original spawning grounds in the middle reaches of the Yangtze River. In 2013 and 2014, there was an absence of spawning where it typically happened near the Gezhouba Dam. Nevertheless, from April to June in 2015, over 1,000 larvae with different body lengths(10–35 cm) were detected along the Shanghai Yangtze Estuary; but only little is currently known about the population genetic structure of the Chinese sturgeon. Herein, we inferred population genetic parameters from 462 available Chinese sturgeon specimens based on a 421-bp fragment of the mitochondrial DNA(mtDNA) D-loop region and 1,481,620 SNPs(singlenucleotide polymorphisms) generated by restriction site-associated DNA sequencing(RAD-seq). For the D-loop dataset, 15 haplotypes were determined. Randomly picked 23 individuals, representing the 15 D-loop haplotype groups, were subsequently used for further RAD-seq validation. The average nucleotide diversity calculated from the mtDNA and RAD datasets was 0.0086 and 0.000478, respectively. The overall effective female population size was calculated to be 1,255 to 2,607, and the long-term effective population size was estimated to range from 11,950 to 119,500. We observed that the genetic variability and the effective female population size of the current population in the Yangtze River are severely low, which are similar to the data reported over 10 years ago. The deduced relatively small effective population of female fish, limiting the genetic connectivity among Chinese sturgeon, should be considered a serious threat to this endangered species.