Effects of effective population size on the F_2 growth and survival of bay scallop Argopecten irradians irradians (Lamarck)

In 2002, six cohorts ofbroodstock bay scallop Argopecten irradians irradians （Ne=1, 2, 10, 30, 50 and control） were randomly chosen from a population of bay scallop to produce offspring. After one year rearing, with the progeny matured, the similar experiment was done to produce the F2 generation. To determine the magnitude of Ne effects, the growth and survival rates in larvae and adult of six F2 groups were compared. Results showed that inbreeding depression existed not only in the Ne=1 group but also in the Ne=2 group. The growth and survival rates of the two groups were significantly lower than those of the other groups （Ne=10, 30, 50, control）, and there were no significant differences among the latter （P〉0.05）. At the same time, the amount of depression in the Ne=1 group was significantly higher than that of the Ne=2 group （P〈0.05）. These results indicated that the low effective population size （Ne）, which increases the possibility of inbreeding, could lead to some harmful effects on the offspring. So it is essential to maintain a high level of Ne in commercial seed production. Fta＇thermore, as the high fecundity of bay scallop might lead to increased inbreeding, selecting broodstock from different growout sites is recommended.

Coherent population trapping magnetometer by differential detecting magneto–optic rotation effect

A pocket coherent population trapping（CPT） atomic magnetometer scheme that uses a vertical cavity surface emitting laser as a light source is proposed and experimentally investigated.Using the differential detecting magneto–optic rotation effect,a CPT spectrum with the background canceled and a high signal-to-noise ratio is obtained.The experimental results reveal that the sensitivity of the proposed scheme can be improved by half an order,and the ability to detect weak magnetic fields is extended one-fold.Therefore,the proposed scheme is suited to realize a pocket-size CPT magnetometer.

Assessment of parental contribution and effective population size from a 3×3 diallel cross of clam Meretrix meretrix

Unbalanced parental contribution and small effective population size （Ne） are common issues during the artificial breeding of marine bivalves. The impact of hatchery-spawning practices on parental contribution, effective population size, the Ne/Nratio, and genetic diversity are largely unknown. To address this, we conducted a parentage analysis on a complete 3×3 diallel cross of clam Meretrix meretrix using eight microsatellite markers. The genetic diversity of the parents was higher than that of their respective offspring in most crosses （8/9）. Sires or dams from the same family contributed unequally to the pool of offspring from a particular cross, and the same parent clam exhibited large variation in parental contribution among different crosses. The variance in male contribution was higher than that of the female contribution in most crosses, suggesting that male contribution was more skewed than for females. The No/N ratio for nine crosses ranged from 0.58 to 0.86. There was no linear relationship between the sex ratio and the Ne/Nratio （P〉0.05）. Moreover, a sex ratio closer to one-to-one does not necessarily mean a larger effective population size. A solution to small effective population size in commercial breeding programs is increasing broodstoek numbers and attempting to maintain a balanced sex ratio.

The Study of Health Effects of Vinyl Chloride AirPollution on Population

A series of indicators, including serum lysozyme activity, G-banding chromosome aberration (G-banding CA) analysis, sister chromatid exchanges (SCEs), chromosome aberration (CA), T-lymphocyte transformation rate (TcTR),-GT, GPT and AKP, were employed in the present survey among occupationally vinyl chloride (VC) exposed workers and inhabitants living in VC polluted area in a polyvinyl chloride (PVC) factory. The results showed that the serum lysozyme (S-LZM) activities in Group 3 (adult inhabitants exposed to 0.20 mg/m3 VC for at least 8 years), Group 2 (workers exposed to 4.1 mg/m3for at least 7 years occupationally), Group 1 (workers exposed to 25.7 mg/m3 for at least 2 years) were significantly higher than control. G-banding CA analysis showed that the total chromosome breakage rates in both Groups 1 and 2 were higher, but no difference existed between Group 3 and control. Only Group 1 was observed having higher SCEs, CA level and lower TcTR than control. AKP levels in Groups 1 and 2 were higher than control,but noγ-GT and GPT differences were found among groups. The study also suggests that G-banding CA analysis is more sensitive than CA and SCEs

Effect of Monocrotophos and Quinalphos on Soil Population and Nitrogen-Fixing Activity of Azospirillum sp.

The effects of monocrotophos and quinalphos on population and nitrogen-fixing activity of Azospirillum sp.in four agricultural soils were determined in a laboratory study.Concentrations of the two insecticides up to a 5 kg ha^(-1)level were either stimulatory or innocuous to the popula- tion of Azospirillum in the soils.Four successive applications of the insecticides to soils resulted in a significant increase in the population density.Cultures of Azospirillum sp.,isolated from insecticide-treated soils,exhibited greater nitrogen-fixing activity.Three consecutive subcultur- ings of the isolates from insecticide-treated soils had no effect on their nitrogen-fixing activity.1989 Academic Press,Inc.

Benchmark Dose Estimation for Cadmium-Induced Renal Effects Based on a Large Sample Population from Five Chinese Provinces

A survey involving 6103 participants from five Chinese provinces was conducted to evaluate the threshold value of urinary cadmium （UCd） for renal dysfunction as benchmark dose low （BMDL）. The urinary N-acetyl-13-D-glucosaminidase （UNAG） was chosen as an effect biomarker. The UCd BMDLs for UNAG ranged from 2.18μg/g creatinine （cr） to 4.26μg/g cr in the populations of different provinces. The selection of the sample population and area affect the evaluation of the BMDL. The reference level of UCd for renal effects was further evaluated based on the data of all 6103 subjects. With benchmark responses （BMR） of 10%/5%, the overall UCd BMDLs for males in the total population were 3.73/2.08 μg/g cr. The BMD was slightly lower in females, thereby indicating that females may be relatively more sensitive to Cd exposure than are males.

Yield Increasing and Quality Improving Effects of Smash-ridging Method("4453" Effects) and Its Potential in Benefiting the Nation and the People

Yuan Longping proposed that smash-ridging technology could be extend-ed widely nationwide. ln the research, smash-ridging technology reconstruct cultiva-tion layers with loose soils in agricultural fields, creating ＂4453＂ effects, as fol ows： ＂Four increases＂ include to increase loosen soil quantity in cultivation layers, soil nutri-ents use, ＂water pool＂ in soils, and ＂oxygen pool＂ in soils. Four reductions are to reduce soil erosion, carbon emission, salt content and heavy metal in soils. Five resistances refer to improve crop resistance capacity in terms of drought, high tem-perature, lower temperature, disease and lodging. Three improvements indicate to enhance photosynthetic efficiency over 10%, yield in 10%-30% and quality over 5%. lt is researched that without additional chemical fertilizer, yield could increase by 10% by labor force, animal, tractor or smash-ridging machine. What’s more, by smash-ridging cultivation, the depth can be 20 times or higher compared with tractor cultivation, with looser soils. lt is estimated that if smash-ridging cultivation is applied once in agricultural lands in China, present soil layers can be twice as deep as present. Specifical y, the thickness of loose soil-layers could be extended from 10-18 cm at present to 25-35 cm, and natural rainfal would increase by 40 bil ion cm3. After vitalization of soil nutrients, chemical fertilizer would decrease by 7 bil ion kg, and the increased c rops would feed more than 300 mil ion population as per yield at 7 50 kg/hm2.

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.

Population Size, Genetic Diversity and Molecular Evidence of a Recent Population Bottleneck in Hynobius chinensis, an Endangered Salamander Species

Severe population declines can reduce species to small populations, offering permissive conditions for deleterious processes. For example, following such events, species can become prone to inbreeding and genetic drift which can lead to a loss of genetic diversity and evolutionary potentials. Hynobius chinensis is a poorly studied very rare and declining endangered amphibian species endemic to China in Changyang County. We investigated adult census population size by monitoring breeding populations from 2015 to 2018, developed microsatellite markers from the transcriptome and used them to investigate genetic diversity, and a population bottleneck in this species. We found H. chinensis in 4 different localities in a total area of 2.18 km^2 and estimated the overall adult census population size at 386–404 individuals. The adult census size（mean ± SE） per breeding pond ranged from 44 ± 6 to 141 ± 8 individuals and appeared smaller than that reported in closely related species in undisturbed habitats. We developed and characterized 13 microsatellite markers in total. Analysis of data at 7 loci（N = 118） in Hardy-Weinberg equilibrium gathered from the largest population showed that genetic diversity level was low. The average number of alleles per locus was 2.14. The observed and expected heterozygosities averaged 0.38 and 0.40, respectively. The inbreeding coefficient was –0.06. All tests performed to investigate a population bottleneck, i.e. The Garza-Williamson test, Heterozygosity excess test, Mode shift test of allele frequency, and effective population size estimates detected a population bottleneck. The contemporary and the historical effective population sizes were estimated at 36 and 234 individuals, respectively. We argue that as bottleneck effects, the studied population may have become prone to genetic drift and inbreeding, losing microsatellite alleles and heterozygosity. Our results suggest that populations of H. chinensismay have been extirpated in the study area.

Conservation genomics analysis reveals recent population decline and possible causes in bumblebee Bombus opulentus

Bumblebees are a genus of pollinators(Bombus)that play important roles in natural ecosystem and agricultural production.Several bumblebee species have been recorded as under population decline,and the proportion of species experiencing popula-tion decline within subgenus Thoracobombus is higher than average.Bombus opulentus is 1 species in Thoracobombus,but little is known about its recent population dynamics.Here,we employed conservation genomics methods to investigate the population dynam-ics of B.opulentus during the recent past and identify the likely environmental factors that may cause population decline.Firstly,we placed the scaffold-level of B.opulentus ref-erence genome sequence onto chromosome-level using Hi-C technique.Then,based on this reference genome and whole-genome resequencing data for 51 B.opulentus samples,we reconstructed the population structure and effective population size(Ne)trajectories of B.opulentus and identified genes that were under positive selection.Our results revealed that the collected B.opulentus samples could be divided into 2 populations,and 1 of them experienced a recent population decline;the declining population also exhibited lower ge-netic diversity and higher inbreeding levels.Genes related to high-temperature tolerance,immune response,and detoxication showed signals of positive selection in the declining population,suggesting that climate warming and pathogen/pesticide exposures may con-tribute to the decline of this B.opulentus population.Taken together,our study provided insights into the demography of B.opulentus populations and highlighted that popula-tions of the same bumblebee species could have contrasting Ne trajectories and population decline could be caused by a combination of various stressors.

Estimation of Probability of Swarming Pedestrians' Violation at Signalized Intersections in Developing Cities

We made an on-site investigation about pedestrian violation of traffic signals at a signalized intersection in Xi＇an, Shaanxi province, China. Based on it, we studied the impact of pedestrian＇s waiting time on violation decision and the impact of the number of pedestrians in colony on the probability of swarming pedestrians＇ violation. The result revealed that the probability of pedestrian violation rose with the waiting time for the pedestrians＇ green signal. Then we developed a Monte Carlo model for simulating mixed vehicles and pedestrians and used the on-site investigation data to validate the model. When traffic volume is fight, the error between the simulated values and the measured ones is 2.67%. When traffic volume is heavy, the error is 3.38%.

Exploring the genetic features and signatures of selection in South China indigenous pigs

To explore the genetic features and signatures of selection in indigenous pigs from South China and Duroc pigs,259 pigs from six populations were genotyped using single-nucleotide polymorphism(SNP)BeadChips.Principal component analysis(PCA),effective population size(Ne),linkage disequilibrium(LD),and signatures of selection were explored and investigated among the six pig populations.The results showed the Ne of five South China indigenous pig populations has been decreasing rapidly since 100 generations ago.The LD between pairwise SNP distance at 100 kb ranged from 0.16 to 0.20 for the five indigenous pig populations,while it was 0.32 for the Duroc population.However,the LD of all six pig populations showed the opposite order at long distances(>5 Mb).Furthermore,15 potential signatures of selection associated with meat quality and age at puberty were exclusively detected in South China indigenous pigs,while eight potential signatures of selection associated with growth traits were detected in Duroc pigs.Our work provides valuable insights for the utilization and conservation of South China indigenous pigs.

Genetic Variation Assessed with Microsatellites in Mass Selection Lines of the Pacific Oyster (Crassostrea gigas) in China

Abstract Four successive mass selection lines of the Pacific oyster, Crassostrea gigas, selected for faster growth in breeding pro- grams in China were examined at ten polymorphic microsatellite loci to assess the level of allelic diversity and estimate the effective population size. These data were compared with those of their base population. The results showed that the genetic variation of the four generations were maintained at high levels with an average allelic richness of 18.8-20.6, and a mean expected heterozygosity of 0.902-0.921. They were not reduced compared with those of their base population. Estimated effective population sizes based on temporal variances in microsatellite frequencies were smaller to that of sex ratio-corrected broodstock count estimates. Using a rela- tively large number ofbroodstock and keeping an equal sex ratio in the broodstock each generation may have contributed to retaining the original genetic diversity and maintaining relatively large effective population size. The results obtained in this study showed that the genetic variation was not affected greatly by mass selection progress and high genetic variation still existed in the mass selection lines, suggesting that there is still potential for increasing the gains in future generations of C. gigas. The present study provided im- portant information for future genetic improvement by selective breeding, and for the design of suitable management guidelines for genetic breeding of C. gigas.

Population genomics provides insights into the evolution and adaptation of tree shrews(Tupaia belangeri)in China

Physiological adaptation of tree shrews(Tupaia belangeri)to changing environmental temperature has been re-ported in detail.However,the T.belangeri origin(mainland or island),population history,and adaptation to histor-ical climate change remain largely unknown or controversial.Here,for thefirst time,we sequenced the simplified genome of 134 T.belangeri individuals from 12 populations in China and further resequenced one individual from each population.Using population genomic approaches,wefirst observed considerable genetic variation in T.be-langeri.Moreover,T.belangeri populations formed obvious genetic structure and reflected different demographic histories;they generally exhibited high genetic diversity,although the isolated populations had relatively low ge-netic diversity.The results presented in this study indicate that T.b.modesta and T.b.tonquinia were separated recently and with a similar population dynamics.Second,physical barriers rather than distance were the driving factors of divergence,and environmental heterogeneity may play an important role in genetic differentiation in T.belangeri.Moreover,our analyses highlight the role of historical global climates in the T.belangeri population dynamics and indicate that the decrease of the T.belangeri population size may be due to the low temperature.Finally,we identified the olfaction-associated adaptive genes between different altitude populations and found that olfactory-related genes of high-altitude populations were selectively eliminated.Our study provides demographic history knowledge of T.belangeri;their adaption history offers new insights into their evolution and adaptation,and provides valuable baseline information for conservation measures.

Integrative demographic study of the Iberian painted frog(Discoglossus galganoi):inter-annual variation in the effective to census population size ratio,with insights on mating system and breeding success

In the face of worldwide amphibian declines,integrative studies combining individual-based information and genetic data represent a powerful approach to produce robust,reliable,and comparable assessments of demographic dynamics.The Iberian painted frog(Discoglossus galganoi)is endemic to Spain and Portugal and shows decreasing population trends across its range,but few studies have attempted to estimate census sizes or assess genetic diversity in wild populations,and little is known about their reproductive biology.We applied an integrative approach based on the combination of capture-mark-recapture data and multilocus genotypes to monitor a breeding population of D.galganoi in central Spain during two consecutive breeding seasons,focusing on the estimation of demographic parameters and their temporal variation.Specifically,we estimated the number of adults(Na),the effective population size(Ne),and the effective number of breeders(Nb),as well as survival and migration rates.We documented a>50%decrease in the estimated number of adults of both sexes between the breeding seasons of 2018 and 2019,probably associated with reduced rainfall in the latter.Estimates of Nb and the Nb/Na ratio were low in both seasons,with a 20–30%decrease in Nb and a 47%increase in the Nb/Na ratio in 2019.Based on the reconstruction of pedigrees from larval and adult genotypes,we provide the first genetic evidence of polygamy in males and females of D.galganoi and the first estimates of breeding success in the species.

Genotype-environment interaction in Cordia trichotoma(Vell.)Arráb.Ex Steud.progenies in two different soil conditions

Investment in silvicultural techniques is noticeably lacking,especially in breeding programs for non-conventional wood species.Studying genotype×environment interaction(G×E)is essential to the development of breeding programs.Thus,this study aimed to estimate genetic diversity of and the effects of G×E interaction on two progeny tests of Cordia trichotoma,including the estimation of genetic gain and genetic diversity after selection.For the experiment,30 progenies of C.trichotoma were tested at two sites with differing soil textures.Diameter at breast height(1.30 m above soil surface,dbh-cm),total height,diameter at 30 cm from the soil,first branch height,and survival were all monitored for four years.Statistical deviance,best linear unbiased estimator,and harmonic mean of relative performance of genetic values(MHPRVG)were all calculated to predict breeding values,estimate genetic parameters,and analyze deviance.All quantified traits varied significantly among progenies by soil type,with greatest variation recorded for genetic variability.Heritability of the progenies led to predictions of genetic gain,ranging from 7.73 to 15.45%,for dbh at four years of age.The calculated decrease in genetic diversity after selection showed that this parameter should be monitored in subsequent breeding cycles.G×E was low for all tests.The best-performing progenies proved most stable and best adapted to the different environmental conditions tested.

Genetic diversity and structure of Drimys brasiliensis in southern Brazil:insights for conservation

Population genetics studies are widely recognized for generating useful knowledge for biodiversity conservation.To date,however,little is known about the levels and distribution of genetic diversity of Drymis brasiliensis(Miers LC),a tree species from the Atlantic Rainforest.Therefore,in this study,we investigated how genetic diversity is distributed within and among populations of D.brasiliensis from southern Brazil using allozyme markers to genotype reproductive trees(8 populations)and seedlings(3 populations).Furthermore,in two populations,we established two permanent plots(5.1 and 1 ha)to analyze fine-scale genetic structure(FSGS).Studied populations presented low levels of genetic diversity(reproductive=0.085;seedlings=0.054)and high fixation indexes(reproductive=0.396;seedlings=0.231).Genetic divergence among populations was equal to 0.05,which is significant,signaling that few populations can conserve large portions of the species total genetic diversity.FSGS was only detected for one population,when reproductive individuals were separated by less than40 m.Low genetic diversity combined with high fixation indexes clearly signal a risk of losing diversity.Therefore,conservation efforts should be aimed at enhancing gene flow within the studied populations.

The Association Between Epoxide Hydrolase Genetic Variant and Effectiveness of Nicotine Replacement Therapy in a Han Chinese Population

Dear Editor, Nicotine is a psychoactive alkaloid that is thought to play a key role in addiction to commercial tobacco products [1] and cotinine is its primary metabolite [2]. Pharmacological treatment, such as nicotine replacement therapy （NRT）, is a valid solution to this problem. Tobacco smoke contains many carcinogens such as nitrosamines .

Genetic Diversity and Ancestral History of the German Angler and the Red-and-White Dual-Purpose Cattle Breeds Assessed through Pedigree Analysis

Local cattle breeds continue to decline in numbers partly due to the use of high performing breeds in advanced production systems where genetic material of elite animals is widely spread. The objective of this study was to assess the within and across breed genetic diversity of the Angler and Red-and-White dual-purpose (DP) cattle breeds applying different inbreeding concepts. Classical and ancestral inbreeding coefficients were computed from pedigree data using the gene dropping method. Effective population size was calculated based on the increase of classical inbreeding, and based on ancestral inbreeding to obtain what was termed as ancestral effective population size. Furthermore, the effective number of founders and ancestors were computed to assess the disequilibrium of founder contribution in the reference populations. The analyses were performed separately for each breed and for a combined dataset. The Angler pedigree was more complete (88%) in the first parental generation but completeness declined with increasing pedigree depth. Average classical inbreeding coefficients of inbred individuals were 2.19%, 1.94% and 2.07%, while average Ballou’s ancestral inbreeding coefficients were 3.69%, 1.39% and 2.21% for the Angler, Red-and-White DP and the combined breed pedigree analyses, respectively. Ancestral history coefficient is a novel coefficient and its estimates were similar and strongly correlated to Ballou’s coefficients (r = 0.99, p < 0.001). The effective population size estimates ranged from 156 to 170 for the classical inbreeding based method, and as low as from 50 to 54 for the ancestral history coefficient based method. The effective number of founders and ancestors ranged from 310 to 532, and 90 to 189, respectively. Our results show that the Red Holstein breed is a key progenitor of the breed populations under study. This highlights cross breeding schemes introduced to improve the milk trait performance of the Angler and Red-and-White DP breeds some decades ago.

A chromosome-level genome of electric catfish(Malapterurus electricus)provided new insights into order Siluriformes evolution

The electric catfish(Malapterurus electricus),belonging to the family Malapteruridae,order Siluriformes(Actinopterygii:Ostariophysi),is one of the six branches that has independently evolved electrical organs.We assembled a 796.75 Mb M.electricus genome and anchored 88.72%sequences into 28 chromosomes.Gene family analysis revealed 295 expanded gene families that were enriched on functions related to glutamate receptors.Convergent evolutionary analyses of electric organs among different lineage of electric fishes further revealed that the coding gene of rho guanine nucleotide exchange factor 4-like(arhgef4),which is associated with G-protein coupled receptor(GPCR)signaling pathway,underwent adaptive parallel evolution.Gene identification suggests visual degradation in catfishes,and an important role for taste in environmental adaptation.Our findings fill in the genomic data for a branch of electric fish and provide a relevant genetic basis for the adaptive evolution of Siluriformes.