Genetic Differentiation between Sympatric Populations of Bacillus cereus and Bacillus thuringiensis

Little is known about genetic exchanges in natural populations of bacteria of the spore-forming Bacillus cereus group, because no population genetics studies have been performed with local sympatric populations. We isolated strains of Bacillus thuringiensis and B. cereus from small samples of soil collected at the same time from two separate geographical sites, one within the forest and the other at the edge of the forest. A total of 100 B. cereus and 98 B. thuringiensis strains were isolated and characterized by electrophoresis to determine allelic composition at nine enzymatic loci. We observed genetic differentiation between populations of B. cereus and B. thuringiensis. Populations of a given Bacillus species—B. thuringiensis or B. cereus—were genetically more similar to each other than to populations of the other Bacillus species. Hemolytic activity provided further evidence of this genetic divergence, which remained evident even if putative clones were removed from the data set. Our results suggest that the rate of gene flow was higher between strains of the same species, but that exchanges between B. cereus and B. thuringiensis were nonetheless possible. Linkage disequilibrium analysis revealed sufficient recombination for B. cereus populations to be considered panmictic units. In B. thuringiensis, the balance between clonal proliferation and recombination seemed to depend on location. Overall, our data indicate that it is not important for risk assessment purposes to determine whether B. cereus and B. thuringiensis belong to a single or two species. Assessment of the biosafety of pest control based on B. thuringiensis requires evaluation of the extent of genetic exchange between strains in realistic natural conditions.     

Genetic Variation and Differentiation among Populations of Chum Salmon Oncorhynchus ketaWalbaum from Southern Russian Far East

Allozyme variation of populations of chum salmon Oncorhynchus ketafrom southern Russian Far East was examined. Of 55 loci screened, 31 were polymorphic. Within-population variation accounted for most of the allele diversity; F _STaveraged over loci was 0.052. Linkage disequilibrium was found in less than 5% of locus pairs in the chum population examined. Analysis of within- and among-population variance components of linkage disequilibrium using D-statistics (Ohta, 1982) showed that most genetic variation was distributed among populations.     

Development and Application of Microsatellites in Carcinus maenas: Genetic Differentiation between Northern and Central Portuguese Populations

Carcinus maenas, the common shore crab of European coastal waters, has recently gained notoriety due to its globally invasive nature associated with drastic ecological and economic effects. The native ubiquity and worldwide importance of C. maenas has resulted in it becoming one of the best-studied estuarine crustacean species globally. Accordingly, there is significant interest in investigating the population genetic structure of this broadly distributed crab along European and invaded coastlines. Here, we developed polymerase chain reaction (PCR) primers for one dinucleotide and two trinucleotide microsatellite loci, resulting from an enrichment process based on Portuguese populations. Combining these three new markers with six existing markers, we examined levels of genetic diversity and population structure of C. maenas in two coastal regions from Northern and Central Portugal. Genotypes showed that locus polymorphism ranged from 10 to 42 alleles (N = 135) and observed heterozygosity per locus ranged from 0.745 to 0.987 with expected heterozygosity ranging from 0.711 to 0.960; values typical of marine decapods. The markers revealed weak, but significant structuring among populations (global F_ST = 0.004) across a 450 km (over-water distance) spatial scale. Combinations of these and existing markers will be useful for studying population genetic parameters at a range of spatial scales of C. maenas throughout its expanding species range.     

Differentiation of the Mitochondrial Subhaplogroup U4 in the Populations of Eastern Europe,Ural, and Western Siberia: Implication to the Genetic History of the Uralic Populations

Phylogenetic relationships between the sequences of the mitochondrial DNA (mtDNA) hypervariable segment 1, belonging to subhaplogroup U4, were examined in the populations of Eastern Europe, Ural, and Northwest Siberia. It was shown that the frequency of subhaplogroup U4, as well as its proportion in the U-component of the gene pools, increased eastwards, reaching maximum values in the populations of Northwest Siberia. Phylogenetic analysis it was showed that the appearance of specific U4-lineage (16113C–16356–16362) in the ancestors of Mansi was most likely caused by its divergence from the East European cluster 16356–16362 in the Late Upper Paleolithic (18566 ± 12915 years before present). Other U4 mtDNA lineages (16189–16356 and 16311–16356), typical mostly of the indigenous populations of Northwest Siberia (Mansi, Nganasans, and Kets) may have formed during the Neolithic–early Bronze Age (6055 ± 3599 years before present, on average). It seems likely that the isolation of ancient populations inhabiting the region between the Ob' and Yenisei rivers was the key factor, providing the appearance of the unique Caucasoid mtDNA lineages in their gene pools. These results were consistent with the traditional point of view on the mixed origin of the Finno-Ugric populations of the Volga–Ural region and West Siberia, resulted from the genetic relationships between the populations of Europe and Asia.     

Genetic Affinities between Trans-Oceanic Populations of Non-Buoyant Macroalgae in the High Latitudes of the Southern Hemisphere

Marine biologists and biogeographers have long been puzzled by apparently non-dispersive coastal taxa that nonetheless have extensive transoceanic distributions. We here carried out a broad-scale phylogeographic study to test whether two widespread Southern Hemisphere species of non-buoyant littoral macroalgae are capable of long-distance dispersal. Samples were collected from along the coasts of southern Chile, New Zealand and several subAntarctic islands, with the focus on high latitude populations in the path of the Antarctic Circumpolar Current or West Wind Drift. We targeted two widespread littoral macroalgal species: the brown alga Adenocystisutricularis (Ectocarpales, Heterokontophyta) and the red alga Bostrychiaintricata (Ceramiales, Rhodophyta). Phylogenetic analyses were performed using partial mitochondrial (COI), chloroplast (rbcL) and ribosomal nuclear (LSU / 28S) DNA sequence data. Numerous deeply-divergent clades were resolved across all markers in each of the target species, but close phylogenetic relationships – even shared haplotypes – were observed among some populations separated by large oceanic distances. Despite not being particularly buoyant, both Adenocystisutricularis and Bostrychiaintricata thus show genetic signatures of recent dispersal across vast oceanic distances, presumably by attachment to floating substrata such as wood or buoyant macroalgae.     

Behavioral and Genetic Differentiation Between Native and Introduced Populations of the Argentine Ant

In this paper, we examine the hypothesis that reduced intraspecific aggression underlies the competitive prowess of Argentine ants in their introduced range. Specifically, we test three predictions of this hypothesis by comparing the genetic diversity, behavior, and ecology of Argentine ants in their native range to introduced populations. Differences between native and introduced populations of Argentine ants were consistent with our predictions. Introduced populations of the Argentine ant appear to have experienced a population bottleneck at the time of introduction, as evidenced by much reduced variation in polymorphic microsatellite DNA markers. Intraspecific aggression was rare in introduced populations but was common in native populations. Finally, in contrast to the Argentine ant's ecological dominance throughout its introduced range, it did not appear dominant in the native ant assemblages studied in Argentina. Together these results identify a possible mechanism for the widespread success of the Argentine ant in its introduced range.     

Genetic Differentiation among Populations of the Cave Fish Schistura Oedipus (Cypriniformes: Balitoridae)

DNA sequences were determined for portions of the mitochondrial control region and 16S rRNA genes in five populations of Schistura oedipus, a troglobitic fish from northwestern Thailand. Based on variation at seven sites out of 593 sequenced, the five populations fall into three groups, apparently isolated by altitude and distance. Nucleotide diversity within groups is on the order of 1.0×10^–3 while the extra increment of diversity among groups is on the order of 5.0×10^–3. While the groups are distinct, the level of differentiation among them is low enough to accept provisionally that the five populations represent a single species. On the basis of 16S sequence, Schistura oedipus appears to be more closely related to S. poculi than to S. reidi, a proposed sister taxon.     

大连地区岛屿与大陆玉竹种群遗传多样性的ISSR分析

选取大连地区大陆与海岛共有植物玉竹为研究对象,采用ISSR分子标记技术对来自5个海岛和4个大陆种群的262个玉竹个体进行遗传多样性的比较和分析。从10个筛选出的ISSR引物扩增得到120个位点信息,其中多态性条带百分率为91.67%,Nei's基因多样性指数（h）为0.346 0,Shannon信息指数（I）为0.510 8。其遗传分化系数（G_st）为0.117 4,基因流（N_m）为3.758 5。研究结果表明玉竹天然种群的遗传多样性较为丰富,种群间基因交流较为频繁,遗传距离与地理距离具有一定的相关性。通过海岛与大陆种群遗传多样性的比对发现,海岛种群的遗传多样性略高于大陆种群,表明在孤立的生境和更为复杂的选择压力下,海岛玉竹种群可能会积累更多的遗传变异从而形成较高的遗传多样性水平。本文研究结果将为进一步探讨隔离生境中天然植物种群遗传进化规律提供证据。     

Marine Coastal Resources as an Engine of Development for the Lafkenche and Williche Populations of Southern Chile

Abstract

Lafkenche and Williche, the Mapuche coastal population in Chile, used coastal marine areas and resources for centuries. The Spanish colonization and the subsequent establishment of the Republic of Chile curtailed these access rights and traditional uses. In 2008, the government of Chile introduced the “Lafkenche Law” establishing exclusive access rights for traditional indigenous use of coastal marine areas and resources, but the law has not led to effective self-determination or the development of the ethnic Mapuche populations. Interviews with indigenous community leaders in October 2014 confirmed their dissatisfaction with this law. This article discusses whether the experience of other nations, such as the innovative Community Development Quota Program in Alaska in the United States, which allocates a portion of certain species in the Bering Sea to coastal communities, can help overcome marine resources access barriers affecting the Mapuche people.     

Clonal Evolution of Enterocytozoon bieneusi Populations in Swine and Genetic Differentiation in Subpopulations between Isolates from Swine and Humans

Enterocytozoon bieneusi is a widespread parasite with high genetic diversity among hosts. Its natural reservoir remains elusive and data on population structure are available only in isolates from primates. Here we describe a population genetic study of 101 E. bieneusi isolates from pigs using sequence analysis of the ribosomal internal transcribed spacer (ITS) and four mini- and microsatellite markers. The presence of strong linkage disequilibrium (LD) and limited genetic recombination indicated a clonal structure for the population. Bayesian inference of phylogeny, structural analysis, and principal coordinates analysis separated the overall population into three subpopulations (SP3 to SP5) with genetic segregation of the isolates at some geographic level. Comparative analysis showed the differentiation of SP3 to SP5 from the two known E. bieneusi subpopulations (SP1 and SP2) from primates. The placement of a human E. bieneusi isolate in pig subpopulation SP4 supported the zoonotic potential of some E. bieneusi isolates. Network analysis showed directed evolution of SP5 to SP3/SP4 and SP1 to SP2. The high LD and low number of inferred recombination events are consistent with the possibility of host adaptation in SP2, SP3, and SP4. In contrast, the reduced LD and high genetic diversity in SP1 and SP5 might be results of broad host range and adaptation to new host environment. The data provide evidence of the potential occurrence of host adaptation in some of E. bieneusi isolates that belong to the zoonotic ITS Group 1.     

Distribution and population genetic structure of the Mediterranean pine shoot beetle Tomicus destruens in the Iberian Peninsula and Southern France

1 The Mediterranean pine shoot beetle Tomicus destruens has long been indistinguishable from its congeneric Tomicus piniperda. Both species attack pines, and can be found in sympatry. The geographical distribution of T. destruens is still unclear in most of the Mediterranean Basin. 2 We aimed to describe the geographical distribution and zones of sympatry of both species in the Iberian Peninsula and France, and to study the molecular phylogeographical pattern of T. destruens. 3 Tomicus spp. adults were sampled in Portugal, Spain and France, and a portion of the mitochondrial genes COI and COII was sequenced for 84 individuals. Sequences were aligned to a data set previously obtained from French localities. 4 Tomicus destruens was found in all populations, except for one locality in Portugal and in the Landes (France). It was in sympatry with T. piniperda in two locations on Pinus pinaster and one location on Pinus radiata. 5 Within‐population genetic diversity was high, but we found a significant pattern of spatial distribution of genetic variation, as well as a significant effect of the host tree. 6 The data suggest the existence of two glacial refugia, from which T. destruens recolonized its current range. One refugium was located in Portugal where the beetle probably evolved on P. pinaster. The corresponding haplotypes show a West–East frequency gradient. The other refugium was probably in the eastern range, where the beetles evolved on Pinus halepensis and P. pinea. The corresponding haplotypes show an East–West frequency gradient.     

Genetic Differentiation Among Peripheral Populations of Bombina bombina from Thrace and Anatolia: An Allozyme Analysis

Genetic structures of Bombina bombina populations, located as peripheral isolates in Turkish Thrace and northwestern Anatolia, were analyzed by polyacrylamide gel electrophoresis using 20 allozyme loci, to investigate the populations’ current genetic variation and possible colonization history. Significant genetic variability was detected in most of the loci and all populations. Allozyme pairwise F _ST matrices and distribution of allele frequencies indicate their very close genetic relationships and relatively recent formation. Mean genetic distance values between Thracian and Anatolian populations indicate a Middle or Upper Pleistocene lineage separation before the formation of the Bosporus as an isolating geographic barrier. All the samples show substantial heterozygosity excess, and there was statistically significant evidence of recent bottlenecks. The extent and patterns of genetic divergence indicate that the Anatolian and Thracian populations have probably experienced bottlenecks, and incipient speciation may have occurred in Anatolian populations of B. bombina.     

Investigation of Genetic Structure between Deep and Shallow Populations of the Southern Rock Lobster,Jasus edwardsii in Tasmania,Australia

The southern rock lobster, Jasus edwardsii, shows clear phenotypic differences between shallow water (red coloured) and deeper water (pale coloured) individuals. Translocations of individuals from deeper water to shallower waters are currently being trialled as a management strategy to facilitate a phenotypic change from lower value pale colouration, common in deeper waters, to the higher value red colouration found in shallow waters. Although panmixia across the J. edwardsii range has been long assumed, it is critical to assess the genetic variability of the species to ensure that the level of population connectivity is appropriately understood and translocations do not have unintended consequences. Eight microsatellite loci were used to investigate genetic differentiation between six sites (three shallow, three deep) across southern Tasmania, Australia, and one from New Zealand. Based on analyses the assumption of panmixia was rejected, revealing small levels of genetic differentiation across southern Tasmania, significant levels of differentiation between Tasmania and New Zealand, and high levels of asymmetric gene flow in an easterly direction from Tasmania into New Zealand. These results suggest that translocation among Tasmanian populations are not likely to be problematic, however, a re-consideration of panmictic stock structure for this species is necessary.     

Genetic Demographic Analysis of Western Ukrainian Populations: The Marriage Structure of Populations from the Khmel'nitskii Oblast with Respect to Ethnicity and Birthplace

Ukrainians account for 85 and 91% of the populations of the city of Khmel'nitskii and the town of Starokonstantinov (Khmel'nitskii oblast, western Ukraine), respectively, and for 97% of the rural population of the Khmel'nitskii oblast. The proportions of Russians in the urban and rural populations of the Khmel'nitskii oblast are 7–10 and 1%, respectively. Between 1960 and 1995–1998, the proportions of Ukrainians in all populations studied increased and the proportion of interethnic marriages steadily decreased. The marriage association coefficient (K) with respect to ethnicity varied from 0.35 to 0.76 in different years. The highest assortative marriage indices (A) with respect to ethnicity were 75–98 and 71–84% in Ukrainians and Jews, respectively. The migration coefficient was 0.58–0.77. Western Ukrainian populations differ from eastern Ukrainian ones in a steadily decreasing outbreeding component.     

Survey of Heritable Endosymbionts in Southern Mexico Populations of the Fruit Fly Species Anastrepha striata and A. ludens

Heritable endosymbiotic bacteria associated with insects are ubiquitous and taxonomically diverse. Many of these endosymbionts influence the fitness of their hosts and/or manipulate their host reproduction. Exploiting the effects of endosymbionts on hosts for pest control is a growing research area, but requires knowledge of endosymbionts associated with the target pest population. In this study, we used molecular methods to screen southern Mexico populations of two species of tephritid fruit fly pests, Anastrepha ludens and A. striata, for heritable bacteria. The only heritable endosymbiont found was Wolbachia in A. striata. Based on multilocus sequence typing and phylogenetic analyses, this Wolbachia strain is new and belongs to the Wolbachia supergroup B. Wolbachia strains previously reported in members of the genus Anastrepha in South America belong to supergroup A. We discuss the potential implications for pest control of the presence of a different Wolbachia strain in southern Mexico.     

Molecular and Quantitative Genetic Differentiation in Sitobion avenae Populations from Both Sides of the Qinling Mountains

Quantitative trait differences are often assumed to be correlated with molecular variation, but the relationship is not certain, and empirical evidence is still scarce. To address this issue, we sampled six populations of the cereal aphid Sitobion avenae from areas north and south of the Qinling Mountains, and characterized their molecular variation at seven microsatellite loci and quantitative variation at nine life-history traits. Our results demonstrated that southern populations had slightly longer developmental times of nymphs but much higher lifetime fecundity, compared to northern populations. Of the nine tested quantitative characters, eight differed significantly among populations within regions, as well as between northern and southern regions. Genetic differentiation in neutral markers was likely to have been caused by founder events and drift. Increased subdivision for quantitative characters was found in northern populations, but reduced in southern populations. This phenomenon was not found for molecular characters, suggesting the decoupling between molecular and quantitative variation. The pattern of relationships between F_ST and Q_ST indicated divergent selection and suggested that local adaptation play a role in the differentiation of life-history traits in tested S. avenae populations, particularly in those traits closely related to reproduction. The main role of natural selection over genetic drift was also supported by strong structural differences in G-matrices among S. avenae populations. However, cluster analyses did not result in two groups corresponding to northern and southern regions. Genetic differentiation between northern and southern populations in neutral markers was low, indicating considerable gene flow between them. The relationship between molecular and quantitative variation, as well as its implications for differentiation and evolution of S. avenae populations, was discussed.     

Genetic Diversity and Evolution of Bradyrhizobium Populations Nodulating Erythrophleum fordii,an Evergreen Tree Indigenous to the Southern Subtropical Region of China

The nodulation of Erythrophleum fordii has been recorded recently, but its microsymbionts have never been studied. To investigate the diversity and biogeography of rhizobia associated with this leguminous evergreen tree, root nodules were collected from the southern subtropical region of China. A total of 166 bacterial isolates were obtained from the nodules and characterized. In a PCR-based restriction fragment length polymorphism (RFLP) analysis of ribosomal intergenic sequences, the isolates were classified into 22 types within the genus Bradyrhizobium. Sequence analysis of 16S rRNA, ribosomal intergenic spacer (IGS), and the housekeeping genes recA and glnII classified the isolates into four groups: the Bradyrhizobium elkanii and Bradyrhizobium pachyrhizi groups, comprising the dominant symbionts, Bradyrhizobium yuanmingense, and an unclassified group comprising the minor symbionts. The nodC and nifH phylogenetic trees defined five or six lineages among the isolates, which was largely consistent with the definition of genomic species. The phylogenetic results and evolutionary analysis demonstrated that mutation and vertical transmission of genes were the principal processes for the divergent evolution of Bradyrhizobium species associated with E. fordii, while lateral transfer and recombination of housekeeping and symbiotic genes were rare. The distribution of the dominant rhizobial populations was affected by soil pH and effective phosphorus. This is the first report to characterize E. fordii rhizobia.     

Molecular Genetic Differentiation of the Ethnic Populations of South and East Siberia Based on Mitochondrial DNA Polymorphism

Using the data on mitochondrial DNA (mtDNA) polymorphism, genetic structures of the ethnic groups inhabiting South and East Siberia, including Altaians, Buryats, Tuvinians, Todjins, Tofalars, Yakuts, and Evenks were described. Mitochondrial gene pools of the populations examined were characterized by different ratios between Mongoloid (M*, C, D, E/G, G, A, B, and F) and Caucasoid (H, HV, I, J, K, T, U, and X) mtDNA lineages. All the populations studied carried a marked Mongoloid component, maximum frequency of which was observed in Evenks (92.4%) and Buryats (90.1%). Maximum frequencies of Caucasoid mtDNA lineages were detected in Tofalars (20.7%) and Yakuts (14.5%). Statistically significant interpopulation differences regarding the frequencies of mtDNA haplogroups were observed between all populations examined, excluding the pairs of Evenks–Yakuts, Evenks–Tuvinians, and Tuvinians-Todjins. Differentiation of the ethnic groups inhabiting South and East Siberia, as well as Central and Middle Asia, is discussed based on genetic, linguistic, and anthropological data.     

Genetic Differentiation of Colombian Populations of <Emphasis Type="Italic">Anopheles darlingi</Emphasis> Root (Diptera: Culicidae)

Anopheles darlingi Root is a primary vector of malaria in the neotropic region, a species not just highly anthropophilic but very efficient in transmitting Plasmodium species and considered the most important vector in the Amazon region. The main goal of this study was to determine the genetic structure of the A. darlingi populations using microsatellites (STR) in western and eastern regions of Colombia. DNA extraction was done with the cited protocol of band using the Genomic Prep? cell and tissue isolation commercial kits. We used the STR reported by Conn et al (Mol Ecol Notes 1: 223-225, 2001). The analysis with STR proved there was a high genetic diversity and significant alterations of the Hardy-Weinberg equilibrium. The greatest genetic diversity was recorded in Mitu (Vaupes) (Na = 14, Ho = 0.520). The lowest was in Pueblo Nuevo (Cordoba) (Na = 12, Ho = 0.457). The eastern region and the Mitu (Vaupes) populations presented the highest number of primer alleles (Ap = 30; Ap = 13; Ap = 9), with variations between 0.010 and 0.097. The AMOVA revealed that the whole population underwent moderate genetic differentiation (F _ST = 0.063, p < 0.05). The same differentiation was noticed (0.06 < F _ST > 0.06, p < 0.05) with five of the six populations included in this job, and there was a low differentiation in the Las Margaritas (Santander) area (F _ST = 0.02s3, p < 0.05). Our results suggest a slight positive correlation, which does not show a statistical significance between the geographic and genetic distances, probably suggesting that the moderate genetic differentiation found between pairs of populations does not need to be explained for the hypothesis of separation by distance.     

Genetic,Epigenetic, and HPLC Fingerprint Differentiation between Natural and Ex Situ Populations of Rhodiola sachalinensis from Changbai Mountain,China

Rhodiola sachalinensis is an endangered species with important medicinal value. We used inter-simple sequence repeat (ISSR) and methylation-sensitive amplified polymorphism (MSAP) markers to analyze genetic and epigenetic differentiation in different populations of R. sachalinensis, including three natural populations and an ex situ population. Chromatographic fingerprint was used to reveal HPLC fingerprint differentiation. According to our results, the ex situ population of R. sachalinensis has higher level genetic diversity and greater HPLC fingerprint variation than natural populations, but shows lower epigenetic diversity. Most genetic variation (54.88%) was found to be distributed within populations, and epigenetic variation was primarily distributed among populations (63.87%). UPGMA cluster analysis of ISSR and MSAP data showed identical results, with individuals from each given population grouping together. The results of UPGMA cluster analysis of HPLC fingerprint patterns was significantly different from results obtained from ISSR and MSAP data. Correlation analysis revealed close relationships among altitude, genetic structure, epigenetic structure, and HPLC fingerprint patterns (R² = 0.98 for genetic and epigenetic distance; R² = 0.90 for DNA methylation level and altitude; R² = –0.95 for HPLC fingerprint and altitude). Taken together, our results indicate that ex situ population of R. sachalinensis show significantly different genetic and epigenetic population structures and HPLC fingerprint patterns. Along with other potential explanations, these findings suggest that the ex situ environmental factors caused by different altitude play an important role in keeping hereditary characteristic of R. sachalinensis.