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.

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.

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.

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.

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.

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.

Landscape genetics reveals inbreeding and genetic bottlenecks in the extremely rare short-globose cacti Mammillaria pectinifera (Cactaceae) as a result of habitat fragmentation

Mammillaria pectinifera is an endemic, short-globose cactus species, included in the IUCN list as a threatened species with only 18 remaining populations in the Tehuacán-Cuicatlán Valley in central Mexico. We evaluated the population genetic diversity and structure, connectivity, recent bottlenecks and population size, using nuclear microsatellites. M. pectinifera showed high genetic diversity but some evidence of heterozygote deficiency(F_(IS)), recent bottlenecks in some populations and reductions in population size. Also, we found low population genetic differentiation and high values of connectivity for M. pectinifera, as the result of historical events of gene flow through pollen and seed dispersal.M. pectinifera occurs in sites with some degree of disturbance leading to the isolation of its populations and decreasing the levels of gene flow among them. Excessive deforestation also changes the original vegetation damaging the natural habitats. This species will become extinct if it is not properly preserved.Furthermore, this species has some ecological features that make them more vulnerable to disturbance such as a very low growth rates and long life cycles. We suggest in situ conservation to prevent the decrease of population sizes and loss of genetic diversity in the natural protected areas such as the Tehuacán-Cuicatlán Biosphere Reserve. In addition, a long-term ex situ conservation program is need to construct seed banks, and optimize seed germination and plant establishment protocols that restore disturbed habitats. Furthermore, creating a supply of living plants for trade is critical to avoid further extraction of plants from nature.

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.

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.

Random Penetrance of Mutations Among Individuals:A New Type of Genetic Drift in Molecular Evolution

The determinative view of mutation penetrance is a fundamental assumption for the building of molecular evolutionary theory:individuals in the population with the same genotype have the same fitness effect.Since this view has been constantly challenged by experimental evidence,it is desirable to examine to what extent violation of this view could affect our under-standing of molecular evolution.To this end,the author formulated a new theory of molecular evolution under a random model of penetrance:for any individual with the same mutational genotype,the coefficient of selection is a random variable.It follows that,in addition to the conventional Ne-genetic drift(Ne is the effective population size),the variance of penetrance among individuals(ε^(2))represents a new type of genetic drift,coined by theε^(2)-genetic drift.It has been demonstrated that these two genetic drifts together provided new insights on the nearly neutral evolution:the evolutionary rate is inversely related to the log-of-Ne when theε^(2)-genetic drift is nontrivial.This log-of-Ne feature ofε^(2)-genetic drift did explain well why the dN/dS ratio(the nonsynonymous rate to the synonymous rate)in humans is only as twofold as that in mice,while the effective population size(Ne)of mice is about two-magnitude larger than that of humans.It was estimated that,for the first time,the variance of random penetrance in mammalian genes was approximatelyε^(2)≈5.89×10^(-3).