Balancing selection shapes population differentiation of major histocompatibility complex genes in wild golden snub-nosed monkeys

Small and isolated populations face several intrinsic risks,such as genetic drift,inbreeding depression,and reduced gene fow.Thus,patterns of genetic diversity and differentiation have become an important focus of conservation genetics research.The golden snub-nosed monkey Rhinopithecus roxellana,an endangered species endemic to China,has experienced rapid reduction in population size and severe population fragmentation over the past few decades.We measured the patterns of genetic diversity and population differentiation using both neutral microsatellites and adaptive major histocompatibility complex(MHC)genes in 2 R.roxellana populations(DPY and GNG)distributed on the northern and southern slopes of the Qinling Mountains,respectively.Eight MHC-linked haplotypes formed by 5 DQA1 alleles,5 DQB1 alleles,5 DRB1 alleles,and 4 DRB2 alleles were detected in the 2 populations.The larger GNG population showed higher genetic variation for both MHC and microsatellites than the smaller DPY population,suggesting an effect of genetic drift on genetic variation.Genetic differentiation index(FST)outlier analyses,principal coordinate analysis(PCoA),and inferred population genetic structure showed lower genetic differentiation in the MHC variations than microsatellites,suggesting that pathogen-mediated balancing selection,rather than local adaptation,homogenized the MHC genes of both populations.This study indicates that both balancing selection and genetic drift may shape genetic variation and differentiation in small and fragmented populations.

Population differentiation in the dominant species(Ulva prolifera)of green tide in coastal waters of China

Since 2015,green tides with Ulva prolifera as the dominant species in the Qinhuangdao coastal waters have continued to occur.In this study,the relationship between green tides in Qinhuangdao and the Yellow Sea(setting sites in Rudong and Qingdao)was evaluated by genetic analyses of U.prolifera.Single nucleotide polymorphism(SNP)markers were used to analyze genetic diversity and genetic relationships among groups.Genetic differentiation was lower among floating U.prolifera populations in Rudong and Qingdao than in Qinhuangdao.The floating U.prolifera population had higher genetic diversity and polymorphism levels in Qingdao and Rudong than in Qinhuangdao.Physiological experiments showed that the growth rate and net buoyancy of floating U.prolifera were highest in Qinhuangdao and Qingdao,respectively,under the same environmental conditions(temperature and light).Overall,these findings showed that U.prolifera populations in the Qinhuangdao and Yellow Sea green tides(Rudong and Qingdao)differ significantly at the molecular and physiological levels.Therefore,the Qinhuangdao green tide is not correlated with the Yellow Sea green tide and has a different origin and development mode.This study provides insight into the mechanism underlying green tide blooms in coastal waters of China.

Genetic Differentiation of Japanese Sardinella(Sardinella zunasi) Populations in the Northwest Pacific Revealed by ISSR Analysis

Knowledge of population genetic structure plays an important role in fisheries management.In this research,In-ter-Simple-Sequence-Repeat(ISSR)markers were employed to evaluate the genetic structure of Japanese sardinella(Sardinella zun-asi)populations in the Northwest Pacific.Eighty seven individuals from 5 locations were screened using 4 highly polymorphic prim-ers.A total of 173 polymorphic loci were detected out of 191 loci amplified.Small but significant genetic differentiation was de-tected between the Chinese and Japanese populations by both AMOVA and pairwise FST analyses,which was further supported by cluster analysis.We consider that climate change during glaciations should be responsible for the genetic differentiation.Isolation by geographic distance among populations was observed,indicating that the distance might also lead to the genetic differentiation.However,no genetic structure was found within the populations off both the Chinese and Japanese coasts,indicating a high-level along-coast gene flow,which might result from ocean current transport and common ground for over-wintering.

Genetic Analysis of Cultured and Wild Populations of Mytilus coruscus Based on Mitochondrial DNA

DNA sequences from the mitochondrial gene cytochrome oxidase subunit I （mtDNA CO I） were used to estimate the genetic variability in two wild populations and two cultured populations of the hard shelled mussel, Mytilus coruscus. Thirty haplotypes were identified in the four populations. The cultured populations exhibited a lower number of haplotypes and genetic diversity than those of the wild populations, suggesting that a small number of effective founding breeders contributed to the genetic variation of the cultured populations. No significant differentiation was observed between the cultured population and local wild population, implying that persistent gene flow occurred in these populations. This genetic survey is intended as a baseline for future genetic monitoring of M. coruseus aquaculture stocks.

Population Genetic Analysis of the Rice Stem Borer, Chilo suppressalis, in the South China

Genetic variation and patterns of genetic differentiation of the rice stem borer, Chilo suppressalis （Lepidoptera： Pyralidae）, from the South China were analyzed using 6 microsatellite markers and two partial mtDNA （cox1 and cox2） regions. All of the 6 microsatellite loci were polymorphic in the studied seven populations. The allelic richness per population ranged between 5.67 and 14.00, and average H E and H O values were 0.6246-0.8329 and 0.2634-0.6061, respectively. As the mitochondrial genome is a single genetic locus, we only present results for the concatenated data set （cox1 plus cox2 gene sequences, 513 bp）. The concatenated data showed high level of genetic diversity and there are 23 variable polymorphic sites among the 513 sites in concatenated data. Nearly all of （20 of 21） pairwise F ST comparisons among populations showed genetic differentiation with moderate to high pairwise F ST values based on microsatellite markers. However, for the mtDNA data, most of the seven populations did not show significant differentiation with other populations. The differences of population differentiation obtained with the two different genetic markers could be mainly attributed to the different mutation rates of microsatellite and mtDNA. There was not genetic structure existed in these studied populations based on microsatellite loci and mtDNA data. The analysis based on network, mismatch distribution, Tajima＇s D and F S indicated that the studied populations were from the recent same ancestor or the same refuge and followed by a sudden demographic expansion condition.

Genetic Variation of Grey-rumped Pheasant (Torquatus group) Populations in China

The polymerase chain reaction combined with direct sequencing was employed to deduce the variety of the grey-rumped pheasant populations in China. Totally 1079 basepair sequences of mitochondrial DNA （mtDNA） control-region gene were analyzed from 121 grey-rumpod pheasants obtained from 13 Chinese lo- calities, 76 variable sites resulted in 91 haplotypes. These populations possessed a high level of genetic diversity, indicating that during their evolution effective population size and polymorphism were not reduced by climatic fluctuations in the Pleistocene ice ages. Phylogenetie analysis indicates that all populations were clustered into two groups, western and eastern. The degree of population differentiation presumably results from a low gene flow （ N, = 0. 33, F,, = 0. 60, P 〈 0. 001 ） between the two groups, and the divergence occurred in the years （2.1 ×10^5 - 2.2 × 105 ）. The genetic structure of grey-rumped pheasants in China ap- pears to be the result of the uplift of Qinghai-Tibet Plateau, the existence of Qinling Mountains and Liupan Mountains and cyclical climatic oscillations during the late Pleistocene.

Molecular phylogeography and population genetic structure of the planktonic copepod Calanus sinicus Brodsky in the coastal waters of China

Planktonic copepod Calanus sinicus is the dominant meso-zooplankton in the Northwest Pacific Ocean. To better understand its population dynamics and phylogeographic patterns, 243 C. sinicus individuals were collected from seven locations across the shelf waters of China and its population genetics was studied by mitochondrial DNA cytochrome oxidase I（mtCOI） sequences analyses. Thirty-nine different sequences, or haplotypes, were detected with moderate haplotype diversity（h=0.749） and low nucleotide diversity（π=0.003） for all populations. The evolutionary divergence between geographic populations varied from 0.24% to 0.37%, indicative of very limited genetic differentiation. Visualized minimum spanning network（MSN） and phylogenetic analysis of all the detected haplotypes did not reveal any clear phylogeographic pattern. Furthermore, AMOVA data showed no significant spatial population differentiation existed among the individuals collected across China shelf waters. Pairwise FST values showed that population collected from northwest of the East China Sea（ECS） displayed a low difference to other populations. Mismatch distribution analyses and neutrality tests indicated that C. sinicus might undergo a demographic/population expansion. No significant population genetic structuring was detected, indicating an extensive gene flow among the C. sinicus populations. Our results provide molecular evidence for the hypothesis that C. sinicus in the northwestern South China Sea in winter is transported from the East China Sea and the Yellow Sea by the China Coastal Current during the northeast monsoon period.

Genetic variation and population structure of the mushroom Pleurotus ferulae in China inferred from nuclear DNA analysis

To investigate the genetic diversity of an edible fungus Pleurotus ferulae, a total of 89 wild samples collected from six geographical locations in the Xinjiang Uygur Autonomous Region of China and two geographical locations in Italy, were analyzed using three DNA fragments including the translation elongation factor（EF1α）, the second largest subunit of t he RNA polymerase II（RPB2） and the largest subunit of the RNA polymerase II（RPB1）. The results indicated relatively abundant genetic variability in the wild resources of P. ferulae. The analysis of molecular variance（AMOVA） showed that the vast majority of the genetic variation was found within geographical populations. Both the Chinese populations and the Italian populations of P. ferulae displayed a limited genetic differentiation. The degree of differentiation between the Chinese populations and the Italian populations was obviously higher than that between the populations from the same region, and moreover the genetic differentiation among all the tested populations was correlated to the geographical distance. T he phylogeny analyses confirmed that samples from China and Italy belonged to another genetic group separated from Pleurotus eryngii. They were closely related to each other but were clustered according to their geographical origins, which implied the Chinese populations were highly differentiated from the Italian populations because of distance isolation, and the two populations from different regions might be still in the process of allopatric divergence.

Influence of Host Shift on Genetic Differentiation of the Oriental Fruit Fly,Bactrocera dorsalis

Invasion of the oriental fruit lfy, Bactrocera dorsalis, into new niches containing different food sources （a process referred to as host shift）, may cause population genetic differentiation and sympatric speciation. To attempt to infer that experimentally, test populations were established by transferring a subset of the original populations, which had been grown on banana for many generations, onto navel orange, and then subculturing the navel orange population and banana population for at least 20 generations. Four pairs of SSR primers with high polymorphism on laboratory strains were used to detect population genetic differentiation. All six tested populations （the 5th, 10th and 15th generations of B. dorsalis fed on banana and navel orange, respectively） were found to have low genetic diversity. Furthermore, the genetic diversity of the navel orange populations was found to decline after being crossed for several generations. Populations initially were deviated from Hardy-Weinberg equilibrium, however, equilibrium was achieved with increasing numbers of generations in both of the host populations. Limited gene lfows were found among the six populations. The Nei’s standard genetic distances between the two host populations of the same generation were initially low, but increased with generation number. Genetic distances between banana and navel orange populations of the same generation were lower than genetic distances between different generations grown on the same host plant. Analysis of molecular distance （AMOVA） results based on generation groups and host groups demonstrated that genetic variation among generations was greater than that between the two host populations. The results indicated that population genetic differentiation occurred after the host shift, albeit at low level. Biogeography and taxonomy of the B. dorsalis complex revealed that speciation of B. dorsalis might be tightly associated with host shift or host specialization of B. dorsalis following dispersal.

Phenotypic Characterization of Oryza nivara(Sharma et Shastry)Collected from Different Ecological Niches of Sri Lanka

Information on the genetic diversity of wild rice species in Sri Lanka is relatively meagre,though it plays a key role in crop improvement programs of cultivated rice(Oryza sativa L.).The present study was carried out to identify the morphological variation pattern of the wild populations of O.nivara in Sri Lanka.Seven populations(P1 to P7)collected from different agro-ecological regions were characterized in a common garden based on nine morphological traits.The findings revealed a high level of phenotypic variation between populations when compared to within a population.The most variable traits were the flag leaf panicle neck length(FLPNL)and flag leaf angle(FLA),whereas the least variable trait was the flag leaf length(FLL).Box plots clearly illustrated the large differentiation of phenotypic traits in the entire distribution of wild rice populations.The cumulative values of the two principal components,i.e.,FLPNL and FLA,explained 58.7%of the total variance.Populations from similar natural habitats clustered together.The P7 was adapted to intercept more sunlight by increasing flag leaf width(FLW)and FLA to compete with weeds and other shrubs.P2 and P5 were the most closely related populations representing approximately similar ecological conditions of the dry zone.The P3 population from the intermediate zone showed a vigorous plant growth with the highest plant height,culm girth and awn length(P<0.05).Knowledge of such morphological diversity would facilitate designing conservation strategies and basic information for the proper utilization of wild resources in rice genetic improvement.

Genomic differentiation with isolation by distance along a latitudinal gradient in the spotted-leg treefrog Polypedates megacephalus

The patterns of isolation by distance(IBD)entailing increased genetic differentiation among populations have aroused extensive concerns for evolutionary biologists.Although the IBD may act on spatial processes contribut-ing to the genetic differentiation among populations in anuran species,the factors shaping the IBD of frogs among populations in natural systems are largely unknown.Here,we studied the genetic differentiation among six popula-tions with 24 individuals of the spotted-leg treefrog along a latitudinal gradient(1860.31 km)based on 1020 single nucleotide polymorphisms from restriction site-associated DNA sequencing.The results showed that the genetic diversity differed significantly among populations and that the insular populations had higher genetic diversity than the mainland populations.Furthermore,we also found a significant genetic differentiation among populations(FST=0.277)and no sign of inbreeding(FUNI=-0.145).The IBD was detected for all populations,and a higher degree of the IBD was indicated when controlling for the effects of the isolation between Hainan and mainland populations caused by the Qiongzhou Strait.Ourfindings suggest that the form of the Qiongzhou Strait plays a key role in shaping the genetic diversity and population differentiation in treefrogs.

Elevated nitrogen and co-evolution history with competitors shape the invasion process of Galinsoga quadriradiata

Invasive plants usually experience population differentiation as they expand from their initial invasive range to the edge.Moreover,invasive plants usually encounter competitors which shared different co-evolutionary histories with them.These factors may lead to varying responses of invasive plant populations to elevated nitrogen deposition during expansion.However,this issue has received limited attention in prior research.To address these challenges,we conducted a greenhouse experiment to investigate how population differentiation of Galinsoga quadriradiata interacts with the presence of various competitors in response to increased nitrogen deposition.Competitor types(new or old that shared short or long co-evolutionary history with the invader,respectively)were set to compete with the invasive central and edge populations under different nitrogen addition treatments.Individuals from the central population of G.quadriradiata,originating from the initial invasion range,showed greater total mass,reproduction and interspecific competitiveness compared with the edge population.Nitrogen addition improved growth and reproductive performance in both populations,and the central population had a stronger response compared with the edge population.The performance of G.quadriradiata was inhibited more effectively by old competitors than new competitors.Our results indicate that population differentiation occurs in terms of growth and competitiveness during the range expansion of G.quadriradiata,with the central population exhibiting superior performance.Co-evolutionary history with competitors is considered unfavorable for invasive plants in this study.Our results highlight the combined effects of population differentiation in invasive species and their co-evolution history with competitors in the context of global change factors.

Genetic diversity and differentiation follow secondary succession in a multi-species study on woody plants from subtropical China

Aims Species diversity and genetic diversity may be affected in parallel by similar environmental drivers.However,genetic diversity may also be affected independently by habitat characteristics.We aim at disentangling relationships between genetic diversity,species diversity and habitat characteristics of woody species in subtropical forest.Methods We studied 11 dominant tree and shrub species in 27 plots in Gutianshan,China,and assessed their genetic diversity(A_(r))and population differentiation(F′_(ST))with microsatellite markers.We tested if Ar and population specific F′_(ST) were correlated to local species diversity and plot characteristics.Multi-model inference and model averaging were used to determine the relative importance of each predictor.Additionally,we tested for isolation-by-distance(IBD)and isolation-by-elevation by regressing pairwise F′_(ST) against pairwise spatial and elevational distances.Important Findings Genetic diversity was not related to species diversity for any of the study species.Thus,our results do not support joint effects of habitat characteristics on these two levels of biodiversity.Instead,genetic diversity in two understory shrubs,Rhododendron simsii and Vaccinium carlesii,was affected by plot age with decreasing genetic diversity in successionally older plots.Population differentiation increased with plot age in R.simsii and Lithocarpus glaber.This shows that succession can reduce genetic diversity within,and increase genetic diversity between populations.Furthermore,we found four cases of IBD and two cases of isolation-by-elevation.The former indicates inefficient pollen and seed dispersal by animals whereas the latter might be due to phenological asynchronies.These patterns indicate that succession can affect genetic diversity without parallel effects on species diversity and that gene flow in a continuous subtropical forest can be restricted even at a local scale.

Genomic and transcriptomic analysis unveils population evolution and development of pesticide resistance in fall armyworm Spodoptera frugiperda

The fall armyworm(FAW),Spodoptera frugiperda,is a destructive pest native to America and has recently become an invasive insect pest in China.Because of its rapid spread and great risks in China,understanding of FAW genetic background and pesticide resistance is urgent and essential to develop effective management strategies.Here,we assembled a chromosome-level genome of a male FAW(SFynMstLFR)and compared re-sequencing results of the populations from America,Africa,and China.Strain identification of 163 individuals collected from America,Africa and China showed that both C and R strains were found in the American pop-ulations,while only C strain was found in the Chinese and African populations.Moreover,population geno-mics analysis showed that populations from Africa and China have close relationship with significantly genetic differentiation from American populations.Taken toge-ther,FAWs invaded into China were most likely origi-nated from Africa.Comparative genomics analysis displayed that the cytochrome p450 gene family is extremely expanded to 425 members in FAW,of which 283 genes are specific to FAW.Treatments of Chinese populations with twenty-three pesticides showed the variant patterns of transcriptome profiles,and several detoxification genes such as AOX,UGT and GST spe-cially responded to the pesticides.These findings will be useful in developing effective strategies for manage-ment of FAW in China and other invaded areas.

The road to opportunities： landscape change promotes body-size divergence in a highly mobile species

Landscape change provides a suitable framework for investigating population-level responses to novel ecological pressures. However, relatively little attention has been paid to examine the poten- tial influence of landscape change on the geographic scale of population differentiation. Here, we tested for morphological differentiation of red-necked nightjars Caprimulgus ruficollis breeding in a managed property and a natural reserve situated less than 10 km apart. At both sites, we also esti- mated site fidelity over 5 years and quantified the potential foraging opportunities for nightjars. Breeding birds in the managed habitat were significantly larger in size--as indexed by keel length--than those in the natural one. However, there were no significant differences in wing or tail length. Immigration from neighboring areas was almost negligible and, furthermore, no individual （out of 1130 captures overall） exchanged habitats between years, indicating strong site fidelity. Food supply for nightjars was equally abundant in both habitats, but the availability of foraging sites was remarkably higher in the managed property. As a result, nightjars--particularly fledg- lings-in the latter habitat benefited from increased foraging opportunities in relation to those in the natural site. It seems likely that the fine-scale variation in nightjar morphology reflects a pheno- typic response to unequal local conditions, since non-random dispersal or differential mortality had been determined not to be influential. High site fidelity appears to contribute to the mainten- ance of body-size differences between the two habitats. Results from this nightjar population high- light the potential of human-induced landscape change to promote population-level responses at exceedingly small geographic scales.