Molecular variation of the shuttle craft and Lim3 genes, controlling the development of the nervous system, in a natural Drosophila melanogaster population

Comparative polymorphism of the first exon and first intron of the shuttle craft (stc) and Lim3 genes and their putative regulatory 5′-flanking sequences was analyzed using 20 sequenced natural alleles. A comparison of the stc and Lim3 genes showed that the extent of polymorphism was similar in their introns and corresponded to the variation level characteristic of Drosophila melanogaster, while the putative regulatory region and first intron of the stc gene proved to be more variable than the corresponding regions of the Lim3 gene. Since the genes under study occurred on the same chromosomes isolated from one population and were close together in a region having a high recombination rate, the difference in the extent of polymorphism between the regulatory and coding regions was explained by individual characteristics of each gene. The results made it possible to assume that the extent of polymorphism of the coding gene regions is maintained by balancing selection.     

Genetic effects of living in a highly polluted environment: the case of the silverside Basilichthys microlepidotus (Jenyns) (Teleostei: atherinopsidae) in the Maipo River basin,central Chile

Freshwater systems are one of the environments most impacted by human activity, with pollution being a highly important factor. In Chile, several rivers exhibit varied levels of pollution, one of which is the Maipo River basin where the city of Santiago is located. The silverside Basilichthys microlepidotus (Jenyns) is an endemic fish species that inhabits this basin, thus we hypothesized that pollution has affected gene diversity and migration in populations of B. microlepidotus from the Maipo River basin. The aim of this study was to identify the population structure of B. microlepidotus in this basin and to determine if the populations of the silverside inhabiting polluted sites present differences in gene diversity and gene flow compared to populations inhabiting non-polluted areas. Using the variability of eight microsatellites, five populations of silverside were detected; three inhabiting non-polluted sites and two inhabiting polluted sites. From this, it was inferred that B. microlepidotus has been able to tolerate pollution in the Maipo River basin. No differences in gene diversity or migration were detected between polluted and non-polluted sites but comparison with historical estimation revealed an increase in the current migration rate when all the data from the basin were compared. A reduction in current effective population size was also observed when compared to historical values, and this is probably due to river degradation. Despite the disappearance of other fish species recorded at this basin, our results suggest that B. microepidotus is tolerant to pollution, thus indicating that native species respond differently to this environmental factor.     

Genetic diversity and population connectivity of the Asian green mussel Perna viridis in South China Sea,inferred from mitochondria DNA markers

The Asian green mussel Perna viridis is ecologically and economically important in the coastal regions of China. In order to characterize the genetic diversity and population connectivity of P. viridis in South China Sea, a 664 bp region of mitochondrial COI gene and a 293 bp region of 16S rRNA gene were sequenced and analyzed for 78 and 92 individuals from four populations in South China Sea, respectively. A total of 15 haplotypes were defined by 14 variable nucleotide sites in COI gene, and 7 haplotypes by 6 variable nucleotide sites in 16S rRNA gene. High haplotype diversity and low nucleotide diversity were observed in COI gene, while moderate haplotype diversity and low nucleotide diversity were observed in 16S rRNA gene. Pairwise F_ST values of COI gene were all negative and those of 16S rRNA gene ranged from −0.01409 to 0.10289. The results showed that no significant genetic divergence (or shallow genetic structure) and high levels of population connectivity among the four populations of P. viridis in South China Sea.     

Genetic structure in urban and rural populations of Apodemus agrarius in Poland

The aims of this study were (i) to determine the genetic variability of the striped field mouse (Apodemus agrarius Pallas, 1771) population in the area of the Warsaw conurbation and the genetic differentiation among local populations of this species within the city, and (ii) to examine the influence of the degree of isolation on the appearance of such genetic structure. Comparison of the genetic structure of the urban population with that of populations inhabiting rural areas was intended to shed light on the depth of genetic changes in this species caused by life in an urban environment. Eight microsatellite loci were used for genotyping and these molecular analyses were successfully performed for 269 individuals. Genetic differentiation (F_ST) was much higher in the case of the urban population. STRUCTURE analysis indicated that this population was subdivided into several local populations, whereas for the rural locations, the highest likelihood was for a single genetic group (one genetically unstructured population). Moreover, in contrast to the rural population, we found no isolation by distance in the urban population. Despite clear subdivision of the urban population, the level of genetic variability was very similar in both analyzed groups. Our findings indicate the occurrence of an advanced process of differentiation of the urban population by microevolution, whereas populations from rural locations displayed very small and mainly insignificant genetic differentiation. Urban local populations, situated near the city borders or close to the natural ecological corridor (banks of the Vistula River), showed higher genetic variability and were less differentiated from populations inhabiting rural sites than from local populations in the city centre. These results provide support for the importance of ecological corridors in preserving the genetic variability of the urban striped field mouse population.     

Divergent enhancer haplotype of ebony on inversion In(3R)Payne associated with pigmentation variation in a tropical population of Drosophila melanogaster

The pattern and intensity of pigmentation have direct impact on individual fitness through various ecological factors. In a Drosophila melanogaster population from southern Japan, thoracic trident pigmentation intensity of most of the strains could be classified into Dark or Light‐type. The expression level variation of the ebony gene correlated well with this phenotype and the allelic differences in expression indicated that the variation is partly due to cis‐regulatory changes. In the ～13 kb gene region, we identified 17 nucleotide sites and 2 indels that were in complete association with the thoracic trident pigmentation intensity. Interestingly, 11 out of 19 sites located within ～0.5 kb of the core epidermis enhancer. These sites had no obvious association with the abdominal pigmentation intensity in the previously analysed African populations from Uganda and Kenya, which suggested that multiple potential mutational pathways in the cis‐regulatory control region of a single gene could lead to similar phenotypic variation within this species. We also found that the Light‐type enhancer haplotype is strongly linked to a cosmopolitan inversion, In(3R)Payne, which is predominant in warmer climatic regions in both hemispheres. The sequence pattern suggested that the strong linkage may be due to selective forces related to thermal adaptation. The inferred selection for lighter pigmentation in the Japanese population is in the opposite direction of the previously reported case of selection for darker individuals in African populations. Nevertheless, both adaptive changes involved cis‐regulatory changes of ebony, which shows that this gene is likely to be a common target of natural selection.     

Molecular insights into the genetic and haplotype diversity among four populations of Catla catla from Madhya Pradesh revealed through mtDNA cyto b gene sequences

In the present investigation, the genetic structure of four populations of Catla catla, sequences of mitochondrial gene, cytochrome b (cyto b) from four populations were sequenced and analyzed. The sequences of mitochondrial regions revealed high haplotype diversity and low nucleotide diversity. The lowest 249 polymorphic sites and 0.00 parsimony informative sites were detected in populations of Fish Federation Pond (CCFFB) whereas highest 330 polymorphic sites and 56 parsimony informative sites were detected in populations of Narmada River (CCNRH) in the cyto b gene sequences in Catla catla populations. The twelve different haplotypes were detected among the four populations studied, lowest population specific haplotype as 2.00 was observed in Fish Federation Pond (CCFFB) and highest was in Population of Narmada River and Tighra reservoir. Sequencing of cyto b gene revealed 12 number of haplotypes (h) with haplotype (gene) diversity (Hd) 0.8736 and nucleotide diversity (π) 0.6474. These data clearly indicated that, feral/wild population showing highest values of polymorphisms, parsimony, haplotype diversity showing good, healthy habitat is lotic water (Narmada River) and lentic water body (Tighra reservoir). The results also concluded that the partial cyto b is polymorphic and can be a potential marker to determine ecological habitat based genetic differentiation among the populations.     

An observation of the loss of genetic variability in prenant’s schizothoracin,Schizothorax prenanti,inhabiting a plateau lake

Prenant’s schizothoracin (Schizothorax prenanti) was found naturally distributed in a plateau lake (Lake Wuxu) in upper reaches of the River Jiulong. The genetic diversities of the populations from L. Wuxu and R. Jiulong were investigated according to analysis of mtDNA control region and compared against three other reported river populations. The L. Wuxu population showed lower haplotype (h = 0.74) and nucleotide (π = 0.001) diversities compared to the R. Jiulong population (h = 0.87; π = 0.012); the lake population had suffered from a bottleneck, which might contribute to its low genetic diversity; the lake population significantly differentiated from the river populations, and significant gene flow was hardly found between river populations and L. Wuxu population, suggesting that there is a strong population structure between the lake and river populations. The L. Wuxu population was ecologically isolated from the R. Jiulong population, while the relatively low genetic variability had not affected its viability.     

Genetic differentiation of European grayling (Thymallus thymallus) populations in Serbia,based on mitochondrial and nuclear DNA analyses

Background

The structure and diversity of grayling (Thymallus thymallus) populations have been well studied in most of its native habitat; however the southernmost populations of the Balkan Peninsula remain largely unexplored. The purpose of this study was to assess the genetic diversity of Serbian grayling populations, detect the impact of stocking and provide guidelines for conservation and management.

Methods

Eighty grayling individuals were collected from four rivers (Ibar, Lim, Drina and Rzav). The mitochondrial DNA control region (CR; 595 bp of the 3''end and 74 bp of flanking tRNA) and the ATP6 gene (630 bp fragment) were sequenced for 20 individuals (five from each locality). In addition, all individuals were genotyped with 12 microsatellite loci. The diversity and structure of the populations as well as the recent and ancient population declines were studied using specialized software.

Results

We detected three new haplotypes in the mtDNA CR and four haplotypes in the ATP6 gene of which three had not been described before. Previously, one CR haplotype and two ATP6 gene haplotypes had been identified as allochthonous, originating from Slovenia. Reconstruction of phylogenetic relations placed the remaining two CR haplotypes from the River Danube drainage of Serbia into a new clade, which is related to the previously described sister Slovenian clade. These two clades form a new Balkan clade. Microsatellite marker analysis showed that all four populations are genetically distinct from each other without any sign of intra-population structure, although stocking of the most diverse population (Drina River) was confirmed by mtDNA analysis. Recent and historical population declines of Serbian grayling do not differ from those of other European populations.

Conclusions

Our study shows that (1) the Ibar, Lim and Drina Rivers grayling populations are genetically distinct from populations outside of Serbia and thus should be managed as native populations in spite of some introgression in the Drina River population and (2) the Rzav River population is not appropriate for further stocking activities since it originates from stocked Slovenian grayling. However, the Rzav River population does not represent an immediate danger to other populations because it is physically isolated from these.     

Population Substructuring in a Migratory Freshwater Fish Prochilodus argenteus (Characiformes, Prochilodontidae) from the São Francisco River

The construction of hydroelectric dams, pollution of rivers and other environmental changes are responsible for the disappearance of many natural fish stocks. The purpose of this work was to analyze the fish Prochilodus argenteus inhabiting the region of the Três Marias dam in the São Francisco River (Brazil) collected in two sites having distinct environmental characteristics. Three novel homologous and one known cross-specific microsatellites were used to assess genetic variation within and between the two collection sites (namely A and B) in order to confirm the occurrence of population substructuring previously suggested using RAPD markers. A higher number of exclusive alleles and a greater genetic variability in region B strongly reinforce the co-existence of different reproductive units in this area. F _ST estimates showed a significant population differentiation between the two sites, indicating the possible existence of distinct gene pools. Considering the economic importance of this fishery resource in the São Francisco River, these findings could provide very important information for fisheries management, aquaculture and conservation of the stocks of this species.     

The Underlying Structure of Adaptation under Strong Selection in 12 Experimental Yeast Populations

The aims of this study were to determine (i) whether adaptation under strong selection occurred through mutations in a narrow target of one or a few nucleotide sites or a broad target of numerous sites and (ii) whether the programs of adaptation previously observed from three experimental populations were unique or shared among populations that underwent parallel evolution. We used archived population samples from a previous study, representing 500 generations of experimental evolution in 12 populations under strong selection, 6 populations in a high-salt environment and 6 populations in a low-glucose environment. Each set of six populations included four with sexual reproduction and two with exclusively asexual reproduction. Populations were sampled as resequenced genomes of 115 individuals and as bulk samples from which frequencies of mutant alleles were estimated. In a high-salt environment, a broad target of 11 mutations within the proton exporter, PMA1, was observed among the six populations, in addition to expansions of the ENA gene cluster. This pattern was shared among populations that underwent parallel evolution. In a low-glucose environment, two programs of adaptation were observed. The originally observed pattern of mutation in MDS3/MKT1 in population M8 was a narrow target of a single nucleotide, unique to this population. Among the other five populations, the three mutations were shared in a broad target, sensing/signaling genes RAS1 and RAS2. RAS1/RAS2 mutations were not observed in the high-salt populations; PMA1 mutations were observed only in a high-salt environment.     

Patterns of Genetic Variability in Island Populations of the Cane Toad (Rhinella marina) from the Mouth of the Amazon

The Amazonian coast has several unique geological characteristics resulting from the interaction between drainage pattern of the Amazon River and the Atlantic Ocean. It is one of the most extensive and sedimentologically dynamic regions of the world, with a large number of continental islands mostly formed less than 10,000 years ago. The natural distribution of the cane toad (Rhinella marina), one of the world’s most successful invasive species, in this complex Amazonian system provides an intriguing model for the investigation of the effects of isolation or the combined effects of isolation and habitat dynamic changes on patterns of genetic variability and population differentiation. We used nine fast-evolving microsatellite loci to contrast patterns of genetic variability in six coastal (three mainlands and three islands) populations of the cane toad near the mouth of the Amazon River. Results from Bayesian multilocus clustering approach and Discriminant Analyses of Principal Component were congruent in showing that each island population was genetically differentiated from the mainland populations. All F_ST values obtained from all pairwise comparisons were significant, ranging from 0.048 to 0.186. Estimates of both recent and historical gene flow were not significantly different from zero across all population pairs, except the two mainland populations inhabiting continuous habitats. Patterns of population differentiation, with a high level of population substructure and absence/restricted gene flow, suggested that island populations of R. marina are likely isolated since the Holocene sea-level rise. However, considering the similar levels of genetic variability found in both island and mainland populations, it is reliable to assume that they were also isolated for longer periods. Given the genetic uniqueness of each cane toad population, together with the high natural vulnerability of the coastal regions and intense human pressures, we suggest that these populations should be treated as discrete units for conservation management purposes.     

陕西省林麝mtDNA D-loop区序列结构和种群遗传多样性

林麝(Moschus berezovskii)曾广泛分布于中国,由于盗猎和栖息地缩小,秦岭地区野生种群数量迅速下降,圈养繁殖种群已成立了几十年,但大多数圈养种群的遗传背景不清,种群规模增长非常缓慢。为了给这一物种的保护和管理提供有用的信息,调查了陕西省林麝1个圈养种群3个野生种群线粒体DNA(mt DNA)D-Loop 632 bp片段的遗传多样性和种群结构。在69个个体中其碱基组成为A+T的平均含量63.2%高于G+C含量36.8%,共检测到变异位点171个(约占总位点数的27.05%)。核苷酸多样性(Pi)为0.04424,平均核苷酸差异数(K)为19.908。69个个体分属32个单倍型,单倍型间的平均遗传距离(P)为0.070。32个单倍型构建的NJ系统树聚为3个分支,4个林麝群体中的单倍型是随机分布的。4个群体的平均遗传距离为0.043(标准误SE为0.005),凤县养殖场群体与留坝和陇县群体的亲缘关系较远。单倍型间的平均遗传距离为0.043,可见其遗传分化尚未达到种群分化的水平。结果表明,陕西省林麝群体mt DNA D-loop区序列存在着较丰富的变异和遗传多样性,凤县野生群体和凤县养殖场群体的核苷酸多样性和单倍型多样较高,养殖场种群没有出现近亲繁殖及遗传多样性下降的情况。凤县野生群体和凤县养殖场群体两者遗传分化较小,存在着较高的基因流水平。     

Genetic variation and Phylogeography of Sinibrama Macrops (Teleostei: Cyprinidae) in Qiantang River Basin,China

A 924 bp segment of the mitochondrial control region (d-loop) was sequenced and analyzed in 334 specimens of Sinibrama macrops from 13 sites in Qiantang River Basin, China. Haplotype diversity (h = 0.724 ± 0.063) and nucleotide diversity (π = 0.00263 ± 0.00027) were lowest in Shengzhou population which had been separated from mainstream of Qiantang River Basin by seawater. The results of pairwise Fst values and average genetic distance revealed significant divergence between Shengzhou and other populations. No geographic clustering was observed in haplotype network, suggesting that there were gene flow among populations except Shengzhou. Pairwise mismatch distributions and Tajima's d-test showed demographic history of Shengzhou population was different from others. Base on the analysis of mitochondrial control region, the differentiation of Shengzhou population was considered to be the result of the transgression and regression in the last interglacial period.     

Genetic variation and population structure of a threatened timber tree <Emphasis Type="Italic">Dalbergia cochinchinensis</Emphasis> in Cambodia

Dalbergia cochinchinensis Pierre ex Laness. (Fabaceae) is a commercially important tree in Southeast Asia. Although this species is under legal protections, illegal logging and disorderly developments have reduced its populations, and the conservation of this species is currently of much concern. In this study, we determined nucleotide sequences at six chloroplasts and ten nuclear loci in four populations of D. cochinchinensis in Cambodia, followed by population genetic analyses. The average silent nucleotide diversity over the nuclear loci, excluding one with an exceptionally high value, was 0.0057 in the entire population, and the mean F _ST across the nuclear loci between each population pair was between 0.135 and 0.467. Thus, the nucleotide diversity in the studied populations was not low compared with that in other tree species, and the level of population differentiation was high. Neutrality test statistics indicated a recent reduction of population size and a subdivision of the population within this species. The divergence times and migration rates were estimated with a likelihood-based method assuming the isolation with migration model. Based on the results, the three populations split 68,000–138,000 years ago, possibly corresponding to the start of the last glacial period, and the level of gene flow among the populations was very low thereafter. Moreover, after the split, population sizes were reduced considerably. Notably, the nucleotide diversity in an insertion sequence in a noncoding region of nuclear C4H was much higher than the mean nucleotide diversity in silent sites across other nuclear genes, indicating that the region was affected by selection.     

Molecular variation of the shuttle craft and Lim3 genes, controlling the development of the nervous system, in a natural Drosophila melanogaster population

Comparative polymorphism of the first exon and first intron of the shuttle craft (stc) and Lim3 genes and their putative regulatory 5'-flanking sequences was analyzed using 20 sequenced natural alleles. A comparison of the stc and Lim3 genes showed that the extent of polymorphism was similar in their introns and corresponded to the variation level characteristic of Drosophila melanogaster, while the putative regulatory region and first intron of the stc gene proved to be more variable than the corresponding regions of the Lim3 gene. Since the genes under study occurred on the same chromosomes isolated from one population and were close together in a region having a high recombination rate, the difference in the extent of polymorphism between the regulatory and coding regions was explained by individual characteristics of each gene. The results made it possible to assume that the extent of polymorphism of the coding gene regions is maintained by balancing selection.     

Genetic variations of mitochondrial antiviral signaling gene (MAVS) in domestic chickens

Mitochondrial antiviral signaling (MAVS) gene plays a key role in antiviral regulation in mammals potentially by activating IRF3/7 and NF-κB and leading to the induction of type I interferon (IFN)-mediated antiviral and inflammatory responses. In this study, we screened genetic polymorphisms of the MAVS gene in various Chinese domestic chicken breeds/populations and evaluated its potential effect on gene expression. Among the sequenced fragment (4678 bp), a total of 75 single nucleotide polymorphisms (SNPs) were identified in 46 chickens from 10 breeds/populations, including 30 coding SNPs and 45 non-coding SNPs. Extremely high haplotype diversity (37 nucleotide haplotypes, 18 amino acid haplotypes) was observed in the coding region (CDS), and a similar pattern of high polymorphisms was also observed for the 3′-untranslated region (3′-UTR). Luciferase assays of two representative 3′-UTR haplotypes were performed in both HEK293 cells and DF-1 chicken fibroblast cells, and we found that they were differentially associated with different abilities on regulating mRNA expression level (P < 0.05). Collectively, we observed a considerably high genetic variability of the MAVS gene, and the 3′-UTR variants had an ability to regulate mRNA expression. These results would cast some clues on understanding the potential role of MAVS on viral resistance in chicken.     

Inferring Multiple Refugia and Phylogeographical Patterns in Pinus massoniana Based on Nucleotide Sequence Variation and DNA Fingerprinting

Background

Pinus massoniana, an ecologically and economically important conifer, is widespread across central and southern mainland China and Taiwan. In this study, we tested the central–marginal paradigm that predicts that the marginal populations tend to be less polymorphic than the central ones in their genetic composition, and examined a founders'' effect in the island population.

Methodology/Principal Findings

We examined the phylogeography and population structuring of the P. massoniana based on nucleotide sequences of cpDNA atpB-rbcL intergenic spacer, intron regions of the AdhC2 locus, and microsatellite fingerprints. SAMOVA analysis of nucleotide sequences indicated that most genetic variants resided among geographical regions. High levels of genetic diversity in the marginal populations in the south region, a pattern seemingly contradicting the central–marginal paradigm, and the fixation of private haplotypes in most populations indicate that multiple refugia may have existed over the glacial maxima. STRUCTURE analyses on microsatellites revealed that genetic structure of mainland populations was mediated with recent genetic exchanges mostly via pollen flow, and that the genetic composition in east region was intermixed between south and west regions, a pattern likely shaped by gene introgression and maintenance of ancestral polymorphisms. As expected, the small island population in Taiwan was genetically differentiated from mainland populations.

Conclusions/Significance

The marginal populations in south region possessed divergent gene pools, suggesting that the past glaciations might have low impacts on these populations at low latitudes. Estimates of ancestral population sizes interestingly reflect a recent expansion in mainland from a rather smaller population, a pattern that seemingly agrees with the pollen record.