Population and subpopulation dynamics of Soldanella hungarica Simonk. (Primulaceae) in spruce forests of the Carpathians

Regularities in the dynamics of natural populations of Soldanella hungarica Simonk. in spruce forests of the Ukrainian Carpathians are generalized from the results of long-term monitoring (1974–2009). It is proved that the size and vitality structure are the major factors determining of the asynchronous functioning principle and the large range of dynamics of elements in subpopulation loci. The rate and scale of the local dynamics are smoothed out at the population level. The populations are characterized by reversibility of population number and a low range of dynamics with long-term cycles of natural turnover of generations. It is suggested that the use of the term “small population” to referring to subpopulation loci is inappropriate.     

The genetic dynamics of the rapid and recent colonization of Denmark by <Emphasis Type="Italic">Arion lusitanicus</Emphasis> (Mollusca,Pulmonata, Arionidae)

We describe the genetic dynamics of the recent establishment of the ‘Iberian slug’, Arion lusitanicus J. Mabille 1868, in Denmark and compare its population structure to two other members of the ‘large Arion complex’, Arion ater ater, native to Denmark, and Arion ater rufus, introduced into Denmark in the early 1900s. Assaying allozyme polymorphism at seven enzyme loci, we found that: (1) None of the three taxa reproduce primarily by self-fertilization. Differences among loci and colonies in the pattern of deviation from Hardy–Weinberg equilibrium are most consistent with isolate mixing and perhaps with low amounts of selfing. (2) For both A. lusitanicus and A. a. rufus, gene diversity is lower in Danish colonies than in southern German colonies, implying population bottlenecks in the establishment of Danish colonies. (3) Significant linkage disequilibrium values usually involve the same three loci, viz. PGI, MDH-1 and MDH-2, suggesting physical linkage among these loci. (4) For both A. a. rufus and A. lusitanicus, the overall gene frequencies from Denmark and southern Germany are homogeneous, while variation among colonies within these regions ranges from around 15 to 28% for the three taxa. This indicates strong, local population genetic subdivision but with little restriction to gene flow from possible source areas. The heterogeneity in measures of diversity and differentiation indicates that population structure for all three taxa is dominated by ongoing founder effects, local extinction/colonisation dynamics, and genetic drift processes.     

Genetic variation,population structure and identification of yellow catfish, <Emphasis Type="Italic">Mystus nemurus</Emphasis> (C&;V) in Thailand using RAPD,ISSR and SCAR marker

Random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers were used to investigate the genetic structure of four subpopulations of Mystus nemurus in Thailand. The 7 RAPD and 7 ISSR primers were selected. Of 83 total RAPD fragments, 80 (96.39%) were polymorphic loci, and of 81 total ISSR fragments, 75 (92.59%) were polymorphic loci. Genetic variation and genetic differentiation obtained from RAPD fragments or ISSR fragments showed similar results. Percentage of polymorphic loci (%P), observed number of alleles, effective number of alleles, Nei’s gene diversity (H) and Shannon’s information index revealed moderate to high level of genetic variations within each M. nemurus subpopulation and overall population. High levels of genetic differentiations were received from pairwise unbiased genetic distance (D) and coefficient of differentiation. Mantel test between D or gene flow and geographical distance showed a low to moderate correlation. Analysis of molecular variance indicated that variations among subpopulations were higher than those within subpopulations. The UPGMA dendrograms, based on RAPD and ISSR, showing the genetic relationship among subpopulations are grouped into three clusters; Songkhla (SK) subpopulation was separated from the other subpopulations. The candidate species-specific and subpopulation-specific RAPD fragments were sequenced and used to design sequence-characterized amplified region primers which distinguished M. nemurus from other species and divided SK subpopulation from the other subpopulations. The markers used in this study should be useful for breeding programs and future aquacultural development of this species in Thailand.     

Heterogeneity and concordance in locus‐specific differentiation and introgression between species of towhees

The maintenance or breakdown of reproductive isolation is an observable outcome of secondary contact between species. In cases where hybrids beyond the F1 are formed, the representation of each species' ancestry can vary dramatically among genomic regions. This genomic heterogeneity in ancestry and introgression can offer insight into evolutionary processes, particularly if introgression is compared in multiple hybrid zones. Similarly, considerable heterogeneity exists across the genome in the extent to which populations and species have diverged, reflecting the combined effects of different evolutionary processes on genetic variation. We studied hybridization across two hybrid zones of two phenotypically well‐differentiated bird species in Mexico (Pipilo maculatus and P. ocai), to investigate genomic heterogeneity in differentiation and introgression. Using genotyping‐by‐sequencing (GBS) and hierarchical Bayesian models, we genotyped 460 birds at over 41 000 single nucleotide polymorphism (SNP) loci. We identified loci exhibiting extreme introgression relative to the genome‐wide expectation using a Bayesian genomic cline model. We also estimated locus‐specific F_ST and identified loci with exceptionally high genetic divergence between the parental species. We found some concordance of locus‐specific introgression in the two independent hybrid zones (6–20% of extreme loci shared across zones), reflecting areas of the genome that experience similar gene flow when the species interact. Additionally, heterogeneity in introgression and divergence across the genome revealed another subset of loci under the influence of locally specific factors. These results are consistent with a history in which reproductive isolation has been influenced by a common set of loci in both hybrid zones, but where local environmental and stochastic factors also lead to genomic differentiation.     

Eleven new microsatellite markers for the tropical sea urchin Tripneustes gratilla and cross‐amplification in Tripneustes ventricosa

We describe the isolation, characterization, and application of 11 polymorphic microsatellite loci from the tropical sea urchin Tripneustes gratilla. We genotyped a total of 73 individuals in three subpopulations (two in Hawaii, and one in the Philippines) and found between eight and 33 alleles per locus. We found significant heterozygote deficits within at least one subpopulation at seven out of 11 loci. We were successful at cross‐amplifying four loci in the congeneric Tripneustes ventricosus. When used appropriately, this set of loci will be useful for quantifying population structure in Tripneustes urchins across broad geographical ranges.     

Single‐cell sequencing unveils the lifestyle and CRISPR‐based population history of Hydrotalea sp. in acid mine drainage

Acid mine drainage (AMD) is characterized by an acid and metal‐rich run‐off that originates from mining systems. Despite having been studied for many decades, much remains unknown about the microbial community dynamics in AMD sites, especially during their early development, when the acidity is moderate. Here, we describe draft genome assemblies from single cells retrieved from an early‐stage AMD sample. These cells belong to the genus Hydrotalea and are closely related to Hydrotalea flava. The phylogeny and average nucleotide identity analysis suggest that all single amplified genomes (SAGs) form two clades that may represent different strains. These cells have the genomic potential for denitrification, copper and other metal resistance. Two coexisting CRISPR‐Cas loci were recovered across SAGs, and we observed heterogeneity in the population with regard to the spacer sequences, together with the loss of trailer‐end spacers. Our results suggest that the genomes of Hydrotalea sp. strains studied here are adjusting to a quickly changing selective pressure at the microhabitat scale, and an important form of this selective pressure is infection by foreign DNA.     

ALLOZYME VARIATION IN A SNAIL (LITTORINA SAXATILIS)—DECONFOUNDING THE EFFECTS OF MICROHABITAT AND GENE FLOW

It is commonly observed that a restricted gene flow among populations of a species generates genetic differentiation in, for example, allozyme markers. However, recent studies suggest that microhabitat-specific variation may contribute to the total differentiation. To appreciate the relative contributions of geographic variation and habitat-specific variation, we sampled 42 subpopulations of the intertidal snail Littorina saxatilis from three different microhabitats (boulders, low and high rocky intertidal) on five small islands within a distance of 15 km. We used a modified orthogonal version of Nei's gene diversity analysis with a modified analysis of variance (ANOVA) that estimated the significance of habitat and geographic separation and the interaction between them. Between subpopulation differentiation (G_ST) was usually in the range of 5% to 10% but was exceptionally high in one locus (Aat; 53%). Genetic differentiation attributable to different habitats accounted for 10% to 81% (mean 35%) of the between subpopulation variation and was significant (P < 0.05) in six loci. Differentiation due to geographic separation accounted for 11% to 61% (mean 36%) and was significant (P < 0.05) in seven loci. Furthermore, three loci showed interactions between habitat and island, suggesting varying effects of habitat in different islands. Microhabitat-specific variation, probably through spatially varying fitness, seems particularly likely in Aat and Pgm-2. Moderate levels of habitat associated variation added to the observed differentiation due to gene flow in Pgi, Pnp, and Pgm-1, whereas in the remaining three loci either the habitat effect was confused by strong habitat-island interaction (Ark) or was virtually absent (Pep and Mpi).     

EVIDENCE FOR GENETIC DIFFERENTIATION BETWEEN CHOKE-INDUCING AND ASYMPTOMATIC STRAINS OF THE EPICHLOË GRASS ENDOPHYTE FROM BRACHYPODIUM SYLVATICUM

Life cycle and breeding system variation in Epichloë grass endophytes (choke disease) is tightly linked to the degree of stroma formation. It is not known whether this variation results from differences in host resistance, fungal virulence, or environmental conditions. We found genetic differentiation between 173 asymptomatic (NS) and 93 stromata-forming (S) Epichloë strains isolated from one grass species, Brachypodium sylvaticum, based on 13 presumed allozyme loci, of which six were variable. The fungal strains originated from 10 sites in Switzerland, three sites of which were represented by both NS and S subpopulations. In total, 19 allozyme genotypes, that were nonrandomly distributed among S and NS were detected. Genetic variation measured as G_ST between S and NS strains isolated from the same site ranged from 0.73 to 0.98. Clonality, measured as linkage disequilibrium at one site, was significant in the NS subpopulation (P ? 0.001), but not in the S subpopulation (P = 0.21), implying asexual reproduction by NS strains as well as successful horizontal transmission of S strains. Since all seeds are usually infected vegetatively, horizontal transmission implies the occurrence of multiple host infections. Altogether, these results provide indirect evidence that NS and S strains do not belong to one panmictic population and that differentiation patterns of stroma formation found in nature are due to genetic differences among fungi in associations with their host plants. We discuss the direction of evolution of disease expression in this system. The distribution of genetic variability suggests that the asymptomatic strains were derived from stromata-forming populations.     

Analysis of F ST outliers at allozyme loci in Pacific salmon: implications for natural selection

Natural selection has been invoked to explain the observed geographic distribution of allozyme allele frequencies for a number of teleost species. The effects of selection on allozyme loci in three species of Pacific salmon were tested. A simulation-based approach to estimate the null distribution of population differentiation (F _ST) and test for F _ST outliers was used. This approach showed that a majority of allozyme loci conform to neutral expectations predicted by the simulation model, with relatively few F _ST outliers found. No consistent F _ST outlier loci were found across species. Analysis of population sub-groups based on geography and genetic identity reduced the number of outlier loci for some species, indicating that large geographic groups may include genetically divergent populations and/or that there is geographic heterogeneity in selection pressure upon allozyme loci. Two outlier allozyme loci found in this analysis, lactate dehydrogenase-B and malic enzyme, have been shown to be influenced by selection in other teleost species. This approach is also useful in identifying allozyme loci (or other genetic markers) that meet assumptions for population genetic study.     

HOW SEDENTARY ARE GREYWING FRANCOLINS (FRANCOLINUS AFRICANUS)?

Phasianids are considered to be sedentary birds with limited dispersal so that populations may be expected to show genetic isolation by distance. To test this, we examined genetic variability in 618 greywing francolins (Francolinus africanus) at 24 localities over a 1,500 km² area. We subdivided the samples to measure genetic population structure among localities separated by 6–60 km, and among coveys separated by 0.1–6 km. Thirteen of 30 (43%) allozyme loci were polymorphic, and heterozygosity ranged from 5.3 to 8.5% over 24 localities and averaged 7.0%, a value much larger than that found for other phasianids. Significant allele-frequency heterogeneity was detected among localities and among coveys at several localities for several loci. Mantel's test, however, showed that there was no correlation between geographical distance and the allele-frequency difference between localities for all but one allele. Although spatial autocorrelation was detected with Moran's I and Geary's c for two alleles, the geographical patterns of I in correlograms of 18 independent alleles showed a “crazy-quilt” pattern of allele-frequency patches. This shows that the isolation-by-distance model of subpopulation structure is inappropriate for these birds. Individuals, therefore, appear to disperse far beyond neighboring populations. “Private-allele” and F_ST estimates of migration under the island model were 8–9 individuals between localities of each generation. Allele-frequency heterogeneity, large amounts of gene flow, and the general lack of spatial autocorrelation imply that the small, socially-structured populations of greywing are subject to high rates of turnover, founder effects, and random drift.     

New insights into the genetic basis of natural chilling and cold shock tolerance in rice by genome‐wide association analysis

In order to understand cold adaptability and explore additional genetic resources for the cold tolerance improvement of rice, we investigated the genetic variation of 529 rice accessions under natural chilling and cold shock stress conditions at the seedling stage using genome‐wide association studies; a total of 132 loci were identified. Among them, 12 loci were common for both chilling and cold shock tolerance, suggesting that rice has a distinct and overlapping genetic response and adaptation to the two stresses. Haplotype analysis of a known gene OsMYB2, which is involved in cold tolerance, revealed indica–japonica differentiation and latitude tendency for the haplotypes of this gene. By checking the subpopulation and geographical distribution of accessions with tolerance or sensitivity under these two stress conditions, we found that the chilling tolerance group, which mainly consisted of japonica accessions, has a wider latitudinal distribution than the chilling sensitivity group. We conclude that the genetic basis of natural chilling stress tolerance in rice is distinct from that of cold shock stress frequently used for low‐temperature treatment in the laboratory and the cold adaptability of rice is associated with the subpopulation and latitudinal distribution.     

Immediate unidirectional epigenetic reprogramming of NORs occurs independently of rDNA rearrangements in synthetic and natural forms of a polyploid species <Emphasis Type="Italic">Brassica napus</Emphasis>

The dynamics of genome modification that occurred from the initial hybridization event to the stabilization of allopolyploid species remains largely unexplored. Here, we studied inheritance and expression of rDNA loci in the initial generations of Brassica napus allotetraploids (2n = 38, AACC) resynthesized from Brassica oleracea (2n = 18, CC) and B. rapa (2n = 20, AA) and compared the patterns to natural forms. Starting already from F1 generation, there was a strong uniparental silencing of B. oleracea genes. The epigenetic reprogramming was accompanied with immediate condensation of C-genome nucleolar organizer region (NOR) and progressive transgeneration hypermethylation of polymerase I promoters, mainly at CG sites. No such changes were observed in the A-genome NORs. Locus loss and gains affecting mainly non-NOR loci after the first allotetraploid meiosis did not influence established functional status of NORs. Collectively, epigenetic and genetic modifications in synthetic lines resemble events that accompanied formation of natural allopolyploid species.     

Spatial dynamics of regeneration in a conifer/broad‐leaved forest in northern Japan

Abstract. This study deals with stand dynamics over a 6‐yr period in a conifer/broad‐leaved mixed forest in Hokkaido, northern Japan. The annual rates of gap formation and recovery were 81.3 m²/ha and 66.7 m²/ha, respectively and turnover time of the canopy was 125 yr. The recruitment processes of the component species in this cool‐temperate forest were governed by different canopy types: gap, canopy edge and closed canopy. Magnolia obovata regenerated in canopy edges, and Acer mono and Prunus ssiori regenerated in canopy edges and gaps. The results suggested that the mosaic structure made up of closed canopy, canopy edge and gap was related to various regeneration niches. Abies sachalinensis had high mortality rates, initiating gap expansion. The transition probabilities from closed canopy or canopy edge to gap for deciduous broad‐leaved trees were lower than for A. sachalinensis, which implies that the difference in degeneration patterns of conifer and broad‐leaved canopies contributes to the heterogeneity of spatial structure in the mixed forests. Spatial dynamics were determined by a combination of gap expansion by A. sachalinensis (neighbour‐dependent disturbance) and gap formation by deciduous broad‐leaved trees (random disturbance).     

Landscape heterogeneity shapes host‐parasite interactions and results in apparent plant–virus codivergence

Knowledge on how landscape heterogeneity shapes host–parasite interactions is central to understand the emergence, dynamics and evolution of infectious diseases. However, this is an underexplored subject, particularly for plant–virus systems. Here, we analyse how landscape heterogeneity influences the prevalence, spatial genetic structure, and temporal dynamics of Pepper golden mosaic and Pepper huasteco yellow vein begomoviruses infecting populations of the wild pepper Capsicum annuum glabriusculum (chiltepin) in Mexico. Environmental heterogeneity occurred at different nested spatial scales (host populations within biogeographical provinces), with levels of human management varying among host population within a province. Results indicate that landscape heterogeneity affects the epidemiology and genetic structure of chiltepin‐infecting begomoviruses in a scale‐specific manner, probably related to conditions favouring the viruses' whitefly vector and its dispersion. Increased levels of human management of the host populations were associated with higher virus prevalence and erased the spatial genetic structure of the virus populations. Also, environmental heterogeneity similarly shaped the spatial genetic structures of host and viruses. This resulted in the congruence between host and virus phylogenies, which does not seem to be due to host‐virus co‐evolution. Thus, results provide evidence of the key role of landscape heterogeneity in determining plant–virus interactions.     

Inter- and intra-species heterogeneity in germination of Aspergillus conidia

Aspergilli are among the most abundant fungi worldwide. They degrade organic material and can be pathogens of plants and animals. Aspergilli spread by forming high numbers of conidia. Germination of these stress resistant asexual spores is characterized by a swelling and a germ tube stage. Here, we show that conidia of Aspergillus niger, Aspergillus oryzae, Aspergillus clavatus, Aspergillus nidulans and Aspergillus terreus show different swelling and germ tube formation dynamics in pure water or in water supplemented with (in)organic nutrients. Apart from inter-species heterogeneity, intra-species heterogeneity was observed within spore populations of the aspergilli except for A. terreus. Sub-populations of conidia differing in size and/or contrast showed different swelling and germ tube formation dynamics. Together, data imply that aspergilli differ in their competitive potential depending on the substrate. Moreover, results suggest that intra-species heterogeneity provides a bet hedging mechanism to optimize survival of aspergilli.

     

Phenotypic heterogeneity in mycobacterial stringent response

Background  

A common survival strategy of microorganisms subjected to stress involves the generation of phenotypic heterogeneity in the isogenic microbial population enabling a subset of the population to survive under stress. In a recent study, a mycobacterial population of M. smegmatis was shown to develop phenotypic heterogeneity under nutrient depletion. The observed heterogeneity is in the form of a bimodal distribution of the expression levels of the Green Fluorescent Protein (GFP) as reporter with the gfp fused to the promoter of the rel gene. The stringent response pathway is initiated in the subpopulation with high rel activity.     

Genetic and QTL analysis of resistance to <Emphasis Type="Italic">Xiphinema index</Emphasis> in a grapevine cross

Resistance to the dagger nematode Xiphinema index has been an important objective in grape rootstock breeding programs. This nematode not only causes severe feeding damage to the root system, but it also vectors grapevine fanleaf virus (GFLV), the causal agent of fanleaf degeneration and one of the most severe viral diseases of grape. The established screening procedures for dagger nematode resistance are time consuming and can produce inconsistent results. A fast and reliable greenhouse-based system for screening resistance to X. index that is suitable for genetic studies and capable of evaluating breeding populations is needed. In this report, the dynamics of nematode numbers, gall formation, and root weight loss were investigated using a variety of soil mixes and pot sizes over a 52-week period. Results indicated that the number of galls formed was correlated with the size of the nematode population and with the degree of root weight loss. After inoculation with 100 nematodes, gall formation could be reliably evaluated in 4–8 weeks in most plant growth conditions and results were obtained 6 months more rapidly than past evaluation methods. This modified X. index resistance screening method was successfully applied to 185 of the 188 F₁ progeny from a cross of D8909-15 × F8909-17 (the 9621 population), which segregates for a form of X. index resistance originally derived from Vitis arizonica. Quantitative trait loci (QTL) analysis was carried out on both parental genetic maps of 255 markers using MapQTL 4.0. Results revealed that X. index resistance is controlled by a major QTL, designated Xiphinema index Resistance 1 (XiR1), near marker VMC5a10 on chromosome 19. The XiR1 QTL was supported by a LOD score of 36.9 and explained 59.9% of the resistance variance in the mapping population. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Regeneration in <Emphasis Type="Italic">Macrostomum lignano</Emphasis> (Platyhelminthes): cellular dynamics in the neoblast stem cell system

Neoblasts are potentially totipotent stem cells and the only proliferating cells in adult Platyhelminthes. We have examined the cellular dynamics of neoblasts during the posterior regeneration of Macrostomum lignano. Double-labeling of neoblasts with bromodeoxyuridine and the anti-phospho histone H3 mitosis marker has revealed a complex cellular response in the first 48 h after amputation; this response is different from that known to occur during regeneration in triclad platyhelminths and in starvation/feeding experiments in M. lignano. Mitotic activity is reduced during the first 8 h of regeneration but, at 48 h after amputation, reaches almost twice the value of control animals. The total number of S-phase cells significantly increases after 1 day of regeneration. A subpopulation of fast-cycling neoblasts surprisingly shows the same dynamics during regeneration as those in control animals. Wound healing and regeneration are accompanied by the formation of a distinct blastema. These results present new insights, at the cellular level, into the early regeneration of rhabditophoran Platyhelminthes. This work was supported by FWF Grant (P16618; P.I. Rieger, Innsbruck).