Forest characteristics,population structure and growth trends of threatened relict Pseudotsuga forrestii in China

Pseudotsuga forrestii is a relict evergreen coniferous tree species in Pinaceae endemic to China.P.forrestii tree numbers have greatly decreased due to deforestation,over-utilization and habitat degradation.Here we clarify P.forrestii community types,structure,species diversity,seedling recruitments and growth trends.We identified four P.forrestii community types:(1)Pseudotsuga forrestii-Quercus guyavifolia-Acer davidii evergreen coniferous and broad-leaved mixed forest;(2)Pseudotsuga forrestii-Pinus yunnanensis-Quercus guyavifolia evergreen coniferous and broad-leaved mixed forest;(3)Pseudotsuga forrestii evergreen coniferous forest;(4)Pseudotsuga forrestii-Abies georgei var.smithii evergreen coniferous forest.P.forrestii forests are characterized by both warm temperate and temperate affinities.Simpson diversity,Pielou evenness,Shannon-Wiener diversity indices ranged from 0.75 to 0.76,0.74-0.81,and 1.62-1.93,respectively,with no significant differences among the four forest types.The forest stratification was multilayered.The canopy layer was generally 10-25 m tall,with the emergent layer reached 25-42 m.DBH and age structures of P.forrestii showed multimodal distributions.Its maximum age P.forrestii was 570 years with a DBH of 143 cm.The growth of annual ring width of P.forrestii was slow,and generally decreased with age,whereas the basal area at the breast height increased with age.Established seedlings/saplings were mainly found in unstable micro-habitats.Regeneration of P.forrestii depends on moderate natural disturbances.Finally,we provide recommendations for P.forrestii conservation.

Analysis of genetic diversity and population structure in sweetpotato using SSR markers

Sweetpotato, Ipomoea batatas(L.) Lam., is an important food crop worldwide. Large scale evaluation of sweetpotato germplasm for genetic diversity is necessary to determine the genetic relationships between them and effectively use them in the genetic improvement. In this study, the genetic diversity of 617 sweetpotato accessions, including 376landraces and 162 bred varieties from China and 79 introduced varieties from 11 other countries, was assessed using 30 simple sequence repeat(SSR) primer pairs with high polymorphism. Based on the population structure analysis,these sweetpotato accessions were divided into three groups, Group 1, Group 2 and Group 3, which included 228, 136and 253 accessions, respectively. Consistent results were obtained by phylogenic analysis and principal coordinate analysis(PCoA). Of the three groups, Group 2 showed the highest level of genetic diversity and its accessions were mainly distributed in low-latitude regions. The accessions from South China exhibited the highest level of genetic diversity, which supports the hypothesis that Fujian and Guangdong were the first regions where sweetpotato was introduced to China. Analysis of molecular variance(AMOVA) indicated significant genetic differentiations between the different groups, but low levels of genetic differentiation existed between the different origins and accession types.These results provide valuable information for the better utilization of these accessions in sweetpotato breeding.

Genetic diversity and population structure of the sea star Asterias amurensis in the northern coast of China

The sea star Asterias amurensis is widely viewed as a severe“marine pest”because of its broad feeding habits.Over the past few decades,A.amurensis undergoes massive and sporadic population outbreaks worldwide,causing extensive economic and ecological losses to the local aquaculture industry and marine ecosystem.Understanding the genetic diversity and population structure of A.amurensis can provide vital information for resource management.By analyzing the polymorphism of the mitochondrial cytochrome C oxidase subunit I(COI)gene and ten simple sequence repeat(SSR)microsatellites markers,the genetic diversity and population structure of A.amurensis of four populations along the northern coast of China was uncovered.A total of 36 haplotypes were identified,and a main haplotype was found in four populations.The Qingdao(QD)population displayed the highest genetic diversity among all the populations.The AMOVA and pairwise F_(st)showed that there was small but statistically significant population differentiation among the four populations,especially between QD and Weihai(WH).Moreover,the principal component analysis(PCA)and admixture analysis showed that several individuals in Yantai(YT)and Dalian(DL)had little genetic association with other individuals.Overall,this study provided useful information of the genetic diversity and population structure of A.amurensis and will contribute to the resource management of A.amurensis in China.

Large scale genetic landscape and population structure of Ethiopian sesame (Sesamum indicum L.) germplasm revealed through molecular marker analysis

Sesame(Sesamum indicum L.) plays a crucial role in Ethiopian agriculture,serving both subsistence and commercial purposes.However,our understanding of the extensive genetic diversity and population structure of Ethiopian sesame remains limited.To address this knowledge gap,we genotyped 368 Ethiopian sesame germplasms,categorizing into four distinct breeding groups:Accessions,landraces,improved varieties,and wild types,using a comprehensive set of 28 polymorphic markers,including 23 simple sequence repeat(SSR) and five Insertion-Deletion(InDel) markers.These markers ensured robust genomic representation,with at least two markers per linkage group.Our results unveiled substantial genetic diversity,identifying a total of 535 alleles across all accessions.On average,each locus displayed 8.83 alleles,with observed and expected heterozygosity values of 0.30 and 0.36,respectively.Gene Diversity and Polymorphic Information Content(PIC) were recorded at 0.37 and 0.35.The percentage of polymorphic loci varied significantly among breeding groups,ranging from8.00% to 82.40%,indicating high diversity in accessions(82.4%),moderate diversity in improved varieties(31.20%) and landraces(29.60%),and limited diversity in wild types(8.00).Analysis of Molecular Variance(AMOVA) results emphasized significant genetic differentiation among populations,with substantial diversity(P<0.001) within each population.Approximately 8% of the entire genetic diversity could be attributed to distinctions among populations,while the larger proportion of genetic diversity(92%) resided within each individual sesame population,showcasing heightened diversity within each group.Our study’s findings received support from both Bayesian clustering and Neighbor-joining(NJ) analysis,reaffirming the credibility of our genetic structure insights.Notably,Population structure analysis at its highest Δk value(k=2) revealed the existence of two primary genetic clusters,further subdivided into four sub-populations at k=4.Similarly,NJ analysis identified two prominent clusters,each displaying additional sub-clustering.In conclusion,our research provides a comprehensive understanding of genetic groups,subpopulations,and overall diversity within Ethiopian sesame populations.These findings underscore the significant genetic diversity and population structure within Ethiopian sesame germplasm collections.This genetic richness holds promise for breeding and conservation efforts,highlighting the importance of preserving genetic diversity to ensure adaptation to changing environments and meet the needs of farmers and consumers.

Genetic Diversity and Population Structure Analysis of Barley Landraces from Shanghai Region Using Genotyping-by-Sequencing

Barley(Hordeum vulgare L.)is an important economic crop for food,feed and industrial raw materials.In the present research,112 barley landraces from the Shanghai region were genotyped using genotyping-by-sequencing(GBS),and the genetic diversity and population structure were analyzed.The results showed that 210,268 Single Nucleotide Polymorphisms(SNPs)were present in total,and the average poly-morphism information content(PIC)was 0.1642.Genetic diversity and population structure analyses suggested that these barley landraces were differentiated and could be divided into three sub-groups,with morphological traits of row-type and adherence of the hulls the main distinguishing factors between groups.Genotypes with similar or duplicated names were also investigated according to their genetic backgrounds and seed appearances.This study provided valuable information on barley landraces from the Shanghai region,and showed that all these barley landraces should be protected and used for future breeding programs.

Genetic Diversity,Population Structure,and Genome-Wide Association Study of Seven Agronomic Traits in 273 Diverse Upload Cotton Accessions

Upland cotton(Gossypium hirsutum)is the most important plant producing natural fibers for the textile industry.In this study,we first investigated the phenotypic variation of seven agronomic traits of 273 diverse cotton accessions in the years 2017 and 2018,which were from 18 geographical regions.We found large variations among the traits in different geographical regions and only half of the traits in either years 2017 or 2018 followed a normal distribution.We then genotyped the collection with 81,612 high quality SNPs.Phylogenetic tree and population structure revealed a diverse genetic structure of the core collection,and geographical diversification was an important factor,but account for part of the variances of genetic diversification.We then performed genome-wide association study for the seven traits in the years 2017 and 2018,and the average values of each trait in the two years,respectively.We identified a total of 19 significant marker-trait associations and found that Pollen Ole e 1 allergen/extension could be the candidate gene associated with the fall-off cotton bolls from the last three branches.In addition,large variations were observed for the heritability of traits in the years 2017 and 2018.These results provide new potential candidate genes for further functional validation,which could be useful for genetic improvement and breeding of new cotton cultivars with better agronomic performances.

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.

Population Structures and Diets of Two Species of <i>Pisodonophis</i>(Ophichthidae) from the Southwest Coast of Taiwan

This study was used to lift nets and trap net fishing at intertidal zone of lagoon and estuarine regions of southern Taiwan. From July 2013 to July 2018, a total 420 specimens of Pisodonophis were analyzed, the average total body length (TL) and average body weight (W) of P. boro eels are 68.4 ± 11.9 cm and 140.4 ± 86.1 g (N = 194), respectively. Typically, P. cancrivorus eels are smaller (TL = 52.8 ± 9.2 cm) and lighter (W = 107.9 ± 73.7 g [N = 119]) than P. boro eels. The natural logarithmic linear relationships between the TL and W of P. boro and P. cancrivorus are respectively expressed as ln(W)b = 2.4405 ln(TL) − 5.4448 (R2 = 0.796, N = 194) and ln(W)c = 3.2168 ln(TL) − 8.2027, (R2 = 0.934, N= 119). P. cancrivorus typically preys on shrimp, crab, and fish;lab assessment revealed that the frequencies of occurrence of these foods in their guts were 49%, 21%, and 15%, respectively (N = 100). The main catch months of P. boro were during the rainy season, and that of P. cancrivorus were the winter season in Taiwan. The average W values of P. boro from Jhuoshuei and Puzih estuaries were 343.2 ± 218.8 g (N = 91) and 140.4 ± 86.1 g (N = 194), respectively. Furthermore, the results of the study revealed that the Puzih estuary is overfished. We suggest that fishery management units should develop some protection measures for the conservation of aquatic ecosystems in estuarine regions. For example, the P. boro weighing less than 113 g will be released back to the estuary.

Genetic diversity and population structure of Robinia pseudoacacia from six improved variety bases in China as revealed by simple sequence repeat markers

Robinia pseudoacacia is an important afforesta-tion tree introduced to China in 1878.In the present study,we examined the genetic diversity among 687 strains rep-resenting four improved varieties and two secondary prov-enances,comprising 641 clones and 46 seedlings.Ninety-one simple sequence repeats(SSRs)were selected through segregation analysis and polymorphism characterization,and all sampled individuals were genotyped using well-characterized SSR markers.After excluding loci with non-neutral equilibrium,missing locus data and null alleles,we used 36 primer pairs to assess the genetic diversity of these germplasm resources,revealing vast genetic differentiation among the samples,with an average of 8.352 alleles per locus and a mean Shannon′s index of 1.302.At the popula-tion level,the partitioning of variability was assessed using analysis of molecular variance,which revealed 93%and 7%variation within and among collection sites,respectively.Four clusters were detected using structure analysis,indi-cating a degree of genetic differentiation among the six populations.Insights into the genetic diversity and structure of R.pseudoacacia provide a theoretical basis for the con-servation,breeding and sustainable development in China.

Ecological distribution and population structure of Litsea glaucescens(Lauraceae)in the ravines of Sierra Fría and Sierra Laurel,Central Mexico

Litsea glaucescens Kunth(Mexican bay leaf,laurel)has a wide distribution in Mexico,growing at both riparian and rupicolous environments in the mountainous region of the Central Highlands of the country.Sierra Fría-Sierra Laurel is a protected natural area covered by a dry forest.The Mexican bay leaf is associated with the oak forest,especially on ravines.The species has been considered at risk in recent years.This research is focused on analyzing the elements of the environment of the ravines,which are influencing the distribution and establishment of laurel populations in the region.Two mountainous regions of Aguascalientes were selected,Sierra Fría and Sierra Laurel.Three ravines of the basin were selected to obtain environmental data.Variables registered were topographic,edaphic,and biotic.Principal component analysis was used to identify ecological factors associated with the presence of L.glaucescens.Mexican bay leaf populations were registered in 10 ravines.At the structural level in the community,29 woody species were registered,Mexican bay leaf had an Importance Value Index of 15.8,ranking 10th among all species.Individuals of laurel were classified by size classes(S,individuals with heights ranging from 0 to 20 cm;S,heights ranging from 0.2 to 1.0 m;S,heights between 1 and 2 m with light trace of flowering;S,heights greater than 2 m with flowering greater than 30% of the canopy;and S,individuals with heights greater than 5 m,curved trunk and basal regrowth)to obtain the population structure.The importance index value for all the species in the riparian community was calculated to the community level.Edaphic factors that characterized the presence of Mexican bay leaf were a high percentage of rock coverage(90%),less mulch depth,and sandy loam shallow soils.Sites that showed higher cation exchange capacity had a higher presence of individuals of the S,S,and Ssize classes.Class Sindividuals were found in shady places with 97% of intercepted light.Individuals of classes Sand Sendure less shady places(75%–85% of intercepted light),and individuals class Sand Sare more frequent in open canopies and crag conditions.Regarding the ecological site factors,such as riverside stream,and rocks on mountain slopes,L.glaucescens life form is riparian and rupicolous.Cation exchange capacity,sodium and calcium levels play an important role in the presence of Mexican bay leaf.Distribution on the ravine and recruitment of the Mexican bay leaf populations are associated with shaded sites,mainly for individuals of size classes Sand S,versus sunny places for individuals of size classes Sand S.The overall population structure had a positive kurtosis with all plant size categories well represented;statistically,the population structure of L.glaucescens is very close to the normal distribution.The information obtained allows us to affirm that the laurel populations in the mountainous areas of Sierra Fría and Sierra Laurel from central Mexico are in good demographic condition.

Genetic diversity and population structure analysis of 161 broccoli cultivars based on SNP markers

To better understand the genetic diversity and population structure of broccoli cultivars planted in China,a total of 161 representative broccoli cultivars in the past 25 years were collected and analysed based on single nucleotide polymorphism(SNP)markers.Ten pairs of primers with good polymorphism and high resolution were screened from 315 pairs of SNP primers by 3 broccoli accessions(inbred lines)with different phenotypes and maturity.The 10 pairs of SNP primers were selected,producing 78 alleles.The diversity analysis indicated that the polymorphism information content(PIC)of SNP primer ranged from 0.64 to 0.90.The observed number of alleles(Na)was 2.00,the effective number of alleles(Ne)was 1.11–2.00,the Nei’s gene diversity(H)was 0.10–0.50,and Shannon information index(I)was 0.20–0.70 using PopGene32 software.The clustering results showed that the 161 broccoli cultivars could be divided into 4 major subgroups(A,B,C and D),foreign cultivars were all assigned to subgroup A,and domestic cultivars were assigned to 3 subgroups of B,C,and D.This study indicated that some domestic cultivars and foreign cultivars were similar in genetic background,but most domestic cultivars were still different from the Japanese cultivars.When K=2,the population structure result presented that 161 broccoli cultivars could be divided into 1 simple group(2 groups)and 1 mixed group.When Q≥0.6,143(88.82%)broccoli cultivars belonged to the simple groups.In simple groups 68(42.24%)broccoli cultivars of group 1 were derived from Japan,the United States,Switzerland,the Netherlands,China-Taiwan,and China-Mainland;75(46.58%)broccoli cultivars belonged to group 2;when Q<0.6,18(11.18%)broccoli cultivars belonged to the mixed groups.This study is helpful to understand the diversity and resolution of broccoli cultivars from worldwide,which is beneficial to plant breeding and materials innovation.And meanwhile,this result is also used for construction of broccoli fingerprint serving for cultivar identification.

Population Structure and Diversity of Plankton in the Wetland of Qilihai in Tianjin

The population structure and diversity of plankton in the wetland of Qilihai in Tianjin was investigated in May, July and September, 2012 by fi eld investigation and sampling examination. The results showed that there were 44 species of phytoplankton belonged to 6 phyla, including 11 species of Cyanophyta, 18 species of Chlorophyta, 8 species of Bacillariophyta, 4 species of Euglenophyta, 1 species of Pyrrophyta and 2 species of Cryptophyta. There were 13 genus and 22 species of zooplankton, among which 4 genus and 4 species belonged to Cladocera; 2 genus and 2 species belonged to Copepoda; 7 genus and 16 species belonged to Rotifera. The investigation results of density and biomass of plankton in May, July and September showed that the density and biomass of phytoplankton was shown as September>July>May, and that of zooplanktonic was shown as May>September>July. In addition, the diversity of phytoplankton and zooplanktonic were evaluated using Shannon-Wiener index, and the results demonstrated that the phytoplankton species were rich in May, July and September, while the zooplanktonic species were poor in May and general in July and September. There were explicit relationships between the diversity characteristics of plankton and nutrient pollution which caused water eutrophication, and the extent of water eutrophication in the different months was also shown as May>July>September.

Genetic Diversity and Population Structure of Three Strains of Indigenous Tswana Chickens and Commercial Broiler Using Single Nucleotide Polymormophic (SNP) Markers

The Tswana chicken is native to Botswana and comprises strains such as the naked neck, normal, dwarf, frizzled, and rumples. The origins of the different strains of Tswana chicken remain unknown and it is not yet clear if the different strains represent distinct breeds within the large Tswana chicken population. Genetic characterization of different strains of Tswana chickens using SNP arrays can elucidate their genetic relationships and ascertain if the strains represent distinct breeds of Tswana chicken population. The aim of this study was therefore to investigate population structure and diversity and to estimate genetic distances/identity between the naked neck, normal and dwarf strains of Tswana chickens. A total of 96 chickens (normal strain (n = 39), naked neck strain (n = 32), dwarf strain (n = 13) and commercial broiler (n = 12)) were used in the study. SNP genotyping was carried out using the Illumina chicken iSelect SNP 60 Bead chip using the Infinium assay compatible with the Illumina HiScan SQ genotyping platform. The observed heterozygosity (Ho) values were 0.610 ± 0.012, 0.611 ± 0.014, 0.613 ± 0.0006 for normal, naked neck and dwarf strains of Tswana chickens respectively and averaged 0.611 ± 0.016 across the three strains of Tswana chickens compared to Ho of 0.347 ± 0.023 in commercial broiler chicken. The expected heterozygosity (He) values were 0.613 ± 0.00012, 0.614 ± 0.00013, 0.608 ± 0.00021 for normal, naked neck and dwarf strains of Tswana chickens respectively and averaged 0.612 ± 0.00015 across the three strains of Tswana chickens compared to He of 0.577 ± 0.00022 in commercial broiler chicken. Principal component analysis (PCA) was used to get an insight into the population structure of indigenous Tswana chickens. The first two principal components revealed a set of three clusters. The normal strain of Tswana chicken and commercial broiler clustered together in one group. The dwarf strain clustered separately in one group and the naked neck and normal strains clustered together in the last group. The separate clustering of the dwarf strain from the rest of Tswana chicken strains suggests significant genetic uniqueness of the dwarf strain and very close genetic similarities between the normal and naked neck strains. The clustering pattern was confirmed by less genetic differentiation and less genetic distances between the naked neck and normal strains of Tswana chicken than between the two strains and the dwarf strain of Tswana chicken.

The Influence of Environmental Factors on the Population Structure and Reproductive Biology of Idotea balthica basteri (Isopoda, Valvifera) of the Bizerte Lagoon (Northern Tunisia)

The reproductive biology of a natural population of Idotea balthica basteri (Pallas, 1772) collected from Menzel Jemil (Bizerte lagoon, Tunisia) was monthly studied from October 2009 to October 2010. Besides water temperature, salinity, turbidity, pH, and dissolved oxygen were measured. Based on the state of differentiation of individuals, the population was divided into 8 categories. Their numbers depend on the one hand to intrinsic factors imposed by the specimens and the structure of the population themselves, and to extrinsic factors due to the variability of environmental conditions on the other hand. Females were morphologically recognisable at smaller size than males. Reproductive activity, which was reflected through the presence of ovigerous females and juveniles, underwent fluctuations throughout the year, but it was continuous. Moreover, salinity, temperature, nitrates, and plant biomass have a noticeable effect on the fecundity and fertility. The Principal Component Analysis also confirmed that the richness of the water in nitrates would be favorable to fecundity and fertility of Idotea balthica basteri. However, higher phosphate concentrations, in April and May seem to have a positive effect on the sex ratio. Otherwise, the temperature would be responsible for increasing the percentage of ovigerous females.

Genetic diversity and population structure of Prochilodus costatus and Prochilodus argenteus preceding dam construction in the Paraopeba River,Sao Francisco River Basin,Minas Gerais,Brazil

Curimat?-pioa (Prochilodus costatus) and curimat?-pacu (Prochilodus argenteus) are migratory fish species endemic to the S?o Francisco River Basin in Brazil. Both species play important roles in local fisheries and ecology in the Paraopeba River. A dam was recently constructed on this river and to help in the development and conservation programs, we characterized the genetic variation of both species before dam construction. Complex hypervariable repeats micro-satellite was used to asses genetic variation for both species within and between the five collection sites in order to detect population substructuring. Nucleotide substitutions and insertion/deletion polymorphisms (indels) resulted in 35 P. costatus haplotypes (sample size = 89) and 22 P. argenteus haplotypes (sample size = 32). Significant genetic diversity and population differentiation was detected between five sampling sites for both species. Therefore, each of the five sites should be regarded as a group comprising significant genetic differences in species conservation and maintenance plans. Comparing these results to genetic diversity measures after dam construction will be critical for future management in this region.

An instantaneous coalescent method insensitive to population structure

Conventional coalescent inferences of population history make the critical assumption that the population under examination is panmictic.However,most populations are structured.This complicates the prevailing coalescent analyses and sometimes leads to inaccurate estimates.To develop a coalescent method unhampered by population structure,we perform two analyses.First,we demonstrate that the coalescent probability of two randomly sampled alleles from the immediate preceding generation(one generation back)is independent of population structure.Second,motivated by this finding,we propose a new coalescent method:i-coalescent analysis.The i-coalescent analysis computes the instantaneous coalescent rate by using a phylogenetic tree of sampled alleles.Using simulated data,we broadly demonstrate the capability of i-coalescent analysis to accurately reconstruct population size dynamics of highly structured populations,although we find this method often requires larger sample sizes for structured populations than for panmictic populations.Overall,our results indicate i-coalescent analysis to be a useful tool,especially for the inference of population histories with intractable structure such as the developmental history of cell populations in the organs of complex organisms.

Impact of the Qinghai-Tibet Railway on Population Genetic Structure of the Toad-Headed Lizard,Phrynocephalus vlangalii

Using data from nine microsatellite DNA loci and a population genetic approach,we evaluate the barrier effect of the Qinghai-Tibet Railway on toad-headed lizard,Phrynocephalus vlangalii. The study area is along a 20 km stretch of the railway on northern Qinghai-Tibet Plateau,and this section of the railway was constructed between 1958–1979. Both assignment tests and analysis of molecular variance(AMOVA) were used for data analysis. We found significant genetic differentiation between the populations from the study area and those from a further southeastern area,which are separated by a 20 km gap. This suggests the existence of population substructure at a fine-scale. However,we did not detect any difference between samples from the western and eastern sides of the railway within the study area,and concluded that the railway may not impose a significant barrier effect on these lizard populations at the present time. Available suitable habitat alongside the railway and bridge underpasses may have facilitated the gene exchange between the sides. The relatively short time since the completion of the railway may not allow the differentiation to accumulate to a detectable level. Since the Qinghai-Tibet Plateau maintains a unique and fragile ecosystem,long-term monitoring of such man-made landscape features is imperative for protecting this ecosystem.

Genetic diversity and population structure of indigenous chicken breeds in South China

A total of 587 individuals from 12 indigenous chicken breeds from South China and two commercial breeds were genotyped for 26 microsatellites to investigate the genetic diversity and population structure.All microsatellites were found to be polymorphic.The number of alleles per locus ranged from 5 to 36,with an average of12.10±7.00(SE).All breeds,except White Recessive Rock,had high allelic polymorphism(>0.5).Higher genetic diversity was revealed in the indigenous chicken breeds rather than in the commercial breeds.Potential introgression from the commercial breeds into the indigenous chickens was also detected.The population structure of these indigenous chicken breeds could be explained by their geographical distribution,which suggested the presence of independent history of breed formation.Data generated in this study will provide valuable information to the conservation for indigenous chicken breeds in future.

Genetic diversity and population structure of the Chinese lake gudgeon (Sarcocheilichthys sinensis) using microsatellite markers

The Chinese lake gudgeon is a small benthopelagic freshwater fish.It is presently threatened by human activities and environmental factors in China.Understanding the genetic diversity and population structure is fundamental for implementation of appropriate conservation measures and a sustainable management program.However,little is reported about the current genetic diversity and population structure.Here,we used ten microsatellite markers to genotype 175 individuals from six populations.Low levels of genetic diversity were found in all six tested populations.The Xiang river population showed the highest level of genetic diversity.Genetic differentiation was very low but significant among the Changyang,Changqidang and Mayang populations,but the Qiandao lake,Gan river,Xiang river populations all showed significant and strong differentiation from the other three populations.Contemporary gene flow was observed in among Changyang,Changqidang and Mayang populations and between Gan and Xiang river populations,respectively.This is the first genetic study to report the genetic diversity and population structure of S.sinensis and the results will be used to develop management and conservation strategies.

Pairwise Shared Genealogical Ancestry in Structured Populations

Simulation was used to investigate the effects of population structure and migration on metrics of pairwise shared ancestry. Random and hierarchical structures, or migration geometries, were examined. Compared to panmictic populations, progress to all qualitative metrics of pairwise ancestry is delayed in structured populations. However, unless migration is very low, the time required is generally less than triple and often less than twice that required in a panmictic population of the same total size. Population structure also increases, to a similar degree, the time required for a population-wide most recent common ancestor (MRCA). As a result, the relationships between various qualitative metrics of pairwise shared ancestry and MRCA time are relatively unaffected by population structure. For example, the mean time to most recent shared ancestor (MRSA) with global sampling of pairs is 40% - 50% of the MRCA time for almost all simulated structures and migration levels. Quantitative pairwise genealogical overlap is strongly affected by population structure. With global sampling, pairwise quantitative overlap never approaches 1.0, as it does in panmictic populations;and instead eventually becomes stationary at much lower values. Possible implications of the present results for human pairwise shared ancestry are discussed. For globally sampled pairs, the longest time to most recent shared ancestor (MRSA) for humans is suggested to be approximately 2100 years before the present. If generation time is 30 years, then all humans are 69th, or closer, cousins. For people with recent European ancestry, the MRSA time may be only half as long, about 1000 years.