Evidence from genetic diversity analyses suggest that wheat germplasm from other countries should be introduced into Chinese winter wheat and distant hybridization should be adopted to create new wheat germplasm with increased genetic diversity. The results of this study should provide valuable information for future association mapping using this Chinese winter wheat collection.To ascertain genetic diversity, population structure and linkage disequilibrium (LD) among a representative collection of Chinese winter wheat cultivars and lines, 90 winter wheat accessions were analyzed with 269 SSR markers distributed throughout the wheat genome. A total of 1,358 alleles were detected, with 2 to 10 alleles per locus and a mean genetic richness of 5.05. The average genetic diversity index was 0.60, with values ranging from 0.05 to 0.86. Of the three genomes of wheat, ANOVA revealed that the B genome had the highest genetic diversity (0.63) and the D genome the lowest (0.56); significant differences were observed between these two genomes (P<0.01). The 90 Chinese winter wheat accessions could be divided into three subgroups based on STRUCTURE, UPGMA cluster and principal coordinate analyses. The population structure derived from STRUCTURE clustering was positively correlated to some extent with geographic eco-type. LD analysis revealed that there was a shorter LD decay distance in Chinese winter wheat compared with other wheat germplasm collections. The maximum LD decay distance, estimated by curvilinear regression, was 17.4 cM (r Triticum aestivum L.) is one of the most important cereal crops worldwide. In China, wheat is grown on about 24 million hectares with a total annual production of 115 million tons and an average yield of 4.75 tons ha-1. Winter wheat occupies about 93% of the area planted in wheat and comprises approximately 94% of total wheat production in 2010 (http://faostat.fao.org/site/567/DesktopDefault.aspx?PageID=567#ancor). Genetic diversity is one of the most important factors for crop improvement. Over the past 60 years, wheat breeders have made remarkable progress in improving grain yield, disease resistance, quality and agronomic performance by using excellent germplasm resources. The recurrent use of a few elite germplasm lines as parental stock, however, has led to a decrease in genetic diversity and has narrowed the genetic base for wheat improvement Wheat , or nonrandom association of alleles between linked or unlinked loci, is becoming increasingly important for identifying genetic regions associated with agronomic traits Estimates of LD decay in wheat at the whole genome level and with large genetic representations of wheat genotypes are of great value. From an analysis of 242 genomic SSRs among 43 elite US wheat cultivars, it was reported that genome-wide LD estimates were generally less than 1 cM for genetically linked locus pairs, and that most of the LD was between loci less than 10 cM apart In this study, a representative collection of 90 elite winter wheat accessions from the major wheat production regions of northern China were analyzed using 269 SSR loci distributed over all 21 chromosomes. Our objectives were to estimate the levels of genetic diversity and LD decay distance, and to characterize the population structure of this Chinese winter wheat germplasm collection. The results are intended to provide a molecular basis for understanding Chinese winter wheat genetic diversity, put forward suggestions for further improvement of wheat, and serve as a resource for association mapping using this collection.Using 269 SSR markers, genetic diversity of the Chinese winter wheat collection was characterized and evaluated at the genome level . Among tThe 269 SSR loci were evenly distributed between the A, B and D genomes of wheat  . AverageComparison of genetic diversity among the seven homoeologous groups of wheat  revealedThe number of loci, number of alleles, average genetic richness and genetic diversity index for the 21 wheat chromosomes are shown in 2 = 0.552.The genetic diversity index was usually positively correlated with number of alleles and there was a positive linear relationship between the two indices within a given range. Simple correlation analysis  indicatePopulation structure of the 90 accessions was estimated using STRUCTURE V2.3.3 software based on 269 whole-genome unlinked SSR markers. The number of subpopulations (K) was identified based on maximum likelihood and delta K (ΔK) values, with accessions falling into three subgroups . Using aUPGMA cluster analysis also clearly divided the 90 accessions into three groups when the genetic distance was about 0.294. Subpopulations 1–3 comprised 36, 36 and 18 accessions, respectively . The denPrincipal coordinate analysis separated the 90 accessions into three major groups, which was consistent with assignments generated by STRUCTURE and UPGMA clustering . The acc2>0.1 and P<0.001. Among all locus pairs, 1,692 linked locus pairs were detected. Among linked locus pairs, 162 (9.57%) were in LD at the P<0.001 level  showed an r2 value greater than 0.1.The SSR data  were used to evaluate the extent of LD on a whole genome level . Across 01 level . Of all 2 vs. genetic distance (cM) and estimated LD decay distances using curvilinear regression  decay distance extended maximally to 17.4 cM. An LD decay distance of about 2.2 cM was estimated for the whole genome, and LD decay distances for A, B, and D genomes were approximately 2.2, 0.6, and 8.6 cM, respectively  and average number of alleles per locus (5.05). Other researchers have reported averages of 4.81 to 18.1 alleles per locus and mean genetic diversity values ranging from 0.46 to 0.77 in various wheat collections Population structure is one of several important factors that strongly influence LD. The presence of population stratification and an unequal distribution of alleles within groups can result in nonfunctional spurious associations With a membership probability threshold of 0.60, 24 accessions were assigned by STRUCTURE to SG 1, 27 to SG 2, 13 to SG 3, and 26 to the admixed group (AD) . AccordiAlthough there were only 11 landraces and 6 introduced germplasm representatives in this study, principal coordinate analysis indicated that they differed to some extent from cultivars , 4 and 5Population structure is an important component in association mapping analyses between molecular markers and traits because it may reduce both type I and II errors. All three population structure approaches, i.e., STRUCTURE, UPGMA, and principal coordinate analysis, showed a more-or-less positive correlation between population structure and geographic eco-types. Because the population structure revealed by STRUCTURE analysis based on many SSR markers distributed throughout the wheat genome was more accurate than using geographic eco-type information, this program was concluded to be the most suitable for investigating population genetic structure.It is important to estimate LD decay distances when carrying out association mapping. The LD decay distance determines the marker density needed to effectively associate genotypes with traits and influences the precision of association mapping. A higher level of LD might be expected in hexaploid wheat than in maize and sorghum because of the rapid rate of inbreeding in wheat with a high degree of self-pollination 2>0.1) in 205 U.S. elite wheat breeding lines 2>0.05 (P<0.001); mean LD decay distance for 157 landraces at the whole genome level was 5 cM compared with 5–10 cM for the 93 modern varieties investigated. For 189 bread wheat and 93 durum wheat accessions, the LD between adjacent locus pairs extended (r2>0.2) approximately 2–3 cM on average, and it was suggested that LD mapping of wheat could be performed with SSRs to a resolution of <5 cM 2>0.2 (P<0.01), and that most LD was less than 10 cM apart between loci 2>0.1) was 17.4 cM, with an average LD decay distance of about 2.2 cM for the whole Chinese winter wheat genome  used for the estimations. Most LD decay distances were estimated with r2 = 0.1.Numerous studies in wheat have reported LD decay distances. Mean genome-wide LD decay was estimated to be 10 cM (rt genome . This ovTriticum aestivum) cultivars from 17 populations across the United States and Mexico revealed that the highest extent of significant LD was observed in the wheat D genome, followed by lower LD in the A and B genomes Our results also demonstrate that LD decay distances differ among the three wheat genomes – the LD decay distance in A, B and D genomes of wheat was about 2.2, 0.6 and 8.6 cM, respectively . The higIn summary, this study demonstrates that genetic diversity in Chinese winter wheat, especially on D and A genomes, is lower than that of many other wheat germplasm collections. Continuous introduction of wheat germplasm from other countries and the adoption of distant hybridization technology to create new wheat germplasm are necessary to increase genetic diversity. The population structure revealed using STRUCTURE analysis of many SSR markers distributed throughout the wheat genome was more accurate than using geographic eco-type information and was available for investigating population genetic structure. LD analysis revealed that LD decay distance is shorter in Chinese winter wheat compared with other wheat collections. The development of high-density markers in these varieties will thus be required for association mapping.To ensure a broadly representative sampling of Chinese winter wheat, 328 Chinese winter wheat accessions were grown during the 2009–2010 growing season on the experimental farm of the Institute of Water Saving Agriculture in Arid Areas of China, Northwest A & F University, Yangling, Shaanxi, China. A representative collection of 90 cultivars and lines was chosen by discarding accessions with similar pedigrees as well as those that failed to mature normally. The name, pedigree (if available), origin and geographic eco-type of these 90 accessions are listed in http://wheat.pw.usda.gov/GG2) (Genomic DNA was extracted from approximately 200 mg fresh leaf tissue using the cetyltrimethylammonium bromide (CTAB) method gov/GG2) .−1 Taq DNA polymerase, 0.4 µL 10 mM dNTPs, and 2 µL each of 2.5 µM primer. PCR protocols consisted of 35 cycles of 94°C for 45 s, an annealing temperature appropriate for the particular primer pair for 45 s, and 72°C for 60 s, and a final extension step of 72°C for 10 min. PCR products were analyzed by 8% polyacrylamide gel electrophoresis (PAGE) and visualized by silver staining.PCR amplifications were carried out in 20 µL reaction volumes containing 2 µL template DNA, 2 µL 10X buffer, 0.1 µL of 5 units µLij is the frequency of the j-th allele for the i-th locus summed across all alleles for that locus. The program PowerMarker v3.25 was used to calculate allele number, allele frequency, and gene diversity of each locus For each SSR locus, polymorphic bands were scored as 1 or 0 for presence or absence of the bands at the same mobility, respectively. Gene diversity, or PIC http://pritch.bsd.uchic-ago.edu/structure.html) The population structure of the 90 winter wheat accessions was assessed using the model-based (Bayesian clustering) method implemented in STRUCTURE v2.3.3  with 1000 permutations. The LD parameter r2 among loci, which is the squared correlation coefficient between two loci and which summarizes both mutational and recombination history, was calculated separately for unlinked loci on different chromosomes and for linked loci on the same chromosome . Loci were considered to be in significant LD if P<0.001. LD decay scatter plots of syntenic r2 vs. genetic distance (cM) between markers were generated using SPSS18.0. LD decay was calculated according to the method described in Linkage disequilibrium estimates and significance for each pair of SSR loci were evaluated using TASSEL v2.1 (Table S1Detailed information for the 90 accessions used in this study.(XLSX)Click here for additional data file.Table S2List of 269 SSR loci used in this study.(XLSX)Click here for additional data file.Table S3Summary statistics of the 269 SSR loci in this study.(XLSX)Click here for additional data file.Table S4Linkage disequilibrium (LD) of 162 linked locus pairs at the P<0.001 level.(XLSX)Click here for additional data file.


Amblyomma hebraeum and Hyalomma rufipes was performed to test the influence of host specificity and host movement on dispersion. Pairwise AMOVA analyses of 277 mtDNA COI sequences supported significant population differentiation among the majority of sampling sites. The geographic mitochondrial structure was not supported by nuclear ITS-2 sequencing, probably attributed to a recent divergence. The three-host generalist, A. hebraeum, showed less mtDNA geographic structure, and a lower level of genetic diversity, while the more host-specific H. rufipes displayed higher levels of population differentiation and two distinct mtDNA assemblages (one predominantly confined to South Africa/Namibia and the other to Mozambique and East Africa). A zone of overlap is present in southern Mozambique. A mechanistic climate model suggests that climate alone cannot be responsible for the disruption in female gene flow. Our findings furthermore suggest that female gene dispersal of ticks is more dependent on the presence of juvenile hosts in the environment than on the ability of adult hosts to disperse across the landscape. Documented interspecific competition between the juvenile stages of H. rufipes and H. truncatum is implicated as a contributing factor towards disrupting gene flow between the two southern African H. rufipes genetic assemblages.A comparative phylogeographic study on two economically important African tick species,  Successful dispersal and the subsequent ability to reproduce with conspecifics are central to maintaining the integrity of sexually reproducing species . The facIdentifying the factors influencing the dispersal and genetic connectivity among tick populations of different geographic origin is thus not a trivial exercise and several hypotheses have been proposed. Key to the discussions are host specificity and the mobility of the hosts of adult ticks ,6,7, theAmblyomma hebraeum and Hyalomma rufipes. Amblyomma hebraeum is responsible for the transmission of Ehrlichia ruminantium (the cause of heartwater in bovine species) [Theileria mutans (causing benign theileriosis in cattle) [Rickettsia africae (causing African tick bite fever in humans) [H. rufipes is probably the most important vector of Crimean-Congo hemorrhagic fever (CCHF) virus to humans [Anaplasma marginale, the causative organism of bovine anaplasmosis [Babesia occultans, the cause of benign babesiosis in cattle [Ricketsia conorii, the cause of tick typhus in humans [A better understanding of the dispersal ability of ticks is essential since they constitute an economically important group of arthropods that act as vectors of diseases to domestic livestock and wild animals ,17,18. Ispecies) ,20, Thei cattle) ,22, and  humans) ,24. In to humans ,26. It alasmosis , Babesian cattle  and Rickn humans .Hyalomma rufipes and A. hebraeum exhibit differences in life history traits, and when examined in a comparative fashion across a broadly speaking similar abiotic landscape, the data may help to explain some of the mechanisms involved in tick dispersion. The two species have partially overlapping distributions in southern Africa . Proteinase K (20mg/µl) digestion at 56°C was extended to 48 hours and the extracted DNA was eluted in 250µl of AE buffer and stored at -20°C.Genomic DNA was extracted from individual ticks following the manufacturer’s protocol for animal tissues using a DNeasy® Blood & Tissue kit  and the reverse primer RIB-11 (5’-GAGTACGACGCCCTACC-3’) [A ~800 base pair stretch of the mitochondrial COI region was amplified by polymerase chain reaction (PCR), using a tick specific forward AR-U-COIa (5’-AAACTRTKTRCCTTCAAAG-3’) and reverse primer AR-L-COIa (5’-GTRTTAAARTTTCGATCSGTTA-3’), respectively . For the nuclear DNA, a portion of the ITS-2 was amplified by PCR from selected individuals of TACC-3’) . PCR reahttp://www.ebi.ac.uk/Tools/emboss/transeq/index.htm) in order to ensure that there were no stop codons. Species authenticity was further confirmed with BlastN searches (http://blast.ncbi.nlm.nih.gov/Blast.cgi). The nuclear DNA haplotype reconstruction was conducted using DnaSP v 5.10 [Sequences were manually inspected and edited with the software BioEdit v 7.0.5 . The mitP v 5.10  and the P v 5.10  with 1 0h), and nucleotide diversities (π) were estimated in Arlequin v 3.5 [Haplotype diversities (in v 3.5 . Uncorrein v 3.5 . Sequencin v 3.5  and evolin v 3.5 . Geneticin v 3.5 ) to deteST; Fst), a model-based Bayesian clustering method was used to investigate the genetic structure across the geographic range . AnalysPS v 5.3 , as implPS v 5.3  was usedIn order to obtain information about processes that could have caused observed genetic variation, historical demography of populations were analyzed using two approaches. Firstly, to test for selective neutrality, Fu’s Fs , was estH. rufipes from collection records obtained between 1985 and 2010. The ‘Maximum Entropy Approach’ within the Maxent computer program for modelling species geographic distributions (v.3.3.3k [We assessed the suitability of climate for permanent populations of v.3.3.3k ) was empv.3.3.3k . All modv.3.3.3k . The docv.3.3.3k  and recov.3.3.3k . We downv.3.3.3k ). Modelsv.3.3.3k .A. hebraeum individuals revealed 22 haplotypes for the mitochondrial COI gene fragment  of 0.009 was higher than that found for A. hebraeum and ranged between 0.001 at Stutterheim and 0.017 at Changara . The analysis clusters one of the Mozambique sampling sites (Changara) within the Southern assemblage.A star-shaped statistical parsimony network for lineages . The mosA. hebraeum haplotypes, and the complete absence of mtDNA geographic structure for this species, only H. rufipes was targeted for nuclear ITS-2 sequencing. The 64 H. rufipes haplotypes retrieved by the mitochondrial COI analyses were amplified. Three individuals failed to amplify resulting in a total of 122 nuclear alleles available for the analyses. Nineteen nuclear haplotypes were retrieved in DnaSP v 5  with an overall haplotype diversity (h) of 0.618 (±0.039) and an overall nucleotide diversity of 0.005 (±0.003). Contrary to the mitochondrial DNA analysis, the statistical parsimony network resulted in one haplogroup for all the alleles with no evidence of geographic structure . Contrary to the expectations based on the star-shaped haplotype network, pairwise Φst comparisons between geographic localities were significant in most instances supporting some degree of population differentiation across the range  and a similar scenario existed when each clade of H. rufipes was analyzed separately . For both A. hebraeum and H. rufipes Fu’s Fs was negative and significant . To compare the potential effect of the demographic history on diversity estimates of the two tick species, the entire mtDNA data sets for the two species were used respectively to calculate the time since expansion for each. Given τ = 1.056 for A. hebraeum and τ = 0.486 for H. rufipes the time since expansion is 70 400 years ago for A. hebraeum (approximately 1 year of generation time [H. rufipes (6 months of generation time [The Mantel test Mantel 1967) for the mtDNA data showed no relationship between genetic and geographic distances for nificant  and subsion time ) and 64  for the H. rufipes shows large areas of high climate suitability in Africa . We argue that the more pronounced genetic diversity and geographic structure obtained for H. rufipes is rather a result of the restrictions in their abilities to disperse  while the less structured pattern obtained in A. hebraeum supports a higher level of dispersal among geographic sampling sites .The comparative phylogeographic patterns obtained in this study are useful towards gaining greater insights into the factors influencing the dispersal of ticks. A striking difference between the two species involves haplotypic and nucleotide diversity estimates  is morfe cycle ).H. rufipes  suggest that the two genetic clades cannot be explained by unsuitable climate. Local host associations for different hare species, however, has been documented as an important factor for the successful completion of the life cycle of certain tick species [A. hebraeum seems to be more robust in withstanding harsh environmental conditions [H. rufipes.If the physical environment, and particularly the availability of suitable hosts for the immature stages, play an important role in the phylogeographic structure of these two tick species, it is interesting to speculate on the reason/s for the two distinct mtDNA genetic clades found in  rufipes . The obs species  and even species . Since Anditions , and juvH. rufipes does not seem to provide a plausible for obtaining two genetic assemblages in southern Africa. Hares acting as hosts for juvenile H. rufipes are abundant within the region where the genetic break has been observed (Kruger Park Region in South Africa and southern part of Mozambique). We thus propose that the structure could have been facilitated by a secondary enigmatic complexity related to competition between different tick species [A. hebraeum its geographic distribution seems to be limited because of interspecific competition with A. variegatum [H. rufipes, the immature stages have to compete with H. truncatum for the predilection attachment site around the neck of hares [H. rufipes is virtually exclusively present on hares as hosts for their immature stages [H. rufipes larvae on scrub hares and in this this region, they are replaced by H. truncatum [H. rufipes assemblages, it is thus plausible to speculate that competitive habitat exclusion on hosts for immature stages may severely limit gene exchange across this region, and thereby play a further role in the genetic differentiation between the two H. rufipes assemblages.At first site, the availability of a suitable host to the juvenile stages of  species ,87,88. Iriegatum ,82,89. Fof hares . This coof hares ,90,91. Oruncatum ,90,92. G


Lepidium subulatum to unravel the effects of habitat fragmentation in levels of genetic diversity, genetic structure and gene flow among its populations. Using 454 pyrosequencing 12 microsatellite loci including di- and tri-nucleotide repeats were characterized in L. subulatum. They amplified a total of 80 alleles  in a sample of 35 individuals of L. subulatum, showing relatively high levels of genetic diversity, HO = 0.645, HE = 0.627. Cross-species transferability of all 12 loci was successful for the Iberian endemics Lepidium cardamines, Lepidium stylatum, and the widespread, Lepidium graminifolium and one species each of two related genera, Cardaria draba and Coronopus didymus. These microsatellite primers will be useful to investigate genetic diversity, population structure and to address conservation genetics in species of Lepidium.Polymorphic microsatellite markers were developed for the Ibero-North African, strict gypsophyte  Lepidium L. (Brassicaceae) is a cosmopolitan genus that includes about 175 species of annual to short-lived perennial herbs that inhabit predominantly ruderal habitats, shrublands and rock crevices on cliffs, primarily in temperate and subtropical regions [Lepidium subulatum L. (Sect. Dileptium (Raf.) DC.). This perennial gypsophyte  with L. subulatum. For this purpose we have conducted a microsatellite characterisation in L. subulatum in order to investigate the effects of habitat fragmentation on genetic diversity, population structure and levels of gene flow among populations. We will perform genotypic analysis of individuals based on this set of nuclear microsatellite loci to (i) interpret historical and ecological processes affecting the gypsum habitats, and (ii) to propose relevant genetic and ecological units for conservation detected among the fragmented landscape. This study will further provide a valuable molecular tool for addressing strategies for the conservation of the biodiversity of gypsum habitats and for promoting population restoration of altered areas with suitable genotypes.Our primary goal is to investigate the effects of habitat fragmentation on the population genetics of selected species from Iberian gypsum outcrops. Given their fragmented distribution and the diverse degree of geographical connectivity and geographical extension, such areas can be considered as true ecological islands . This ishabitats . In addiL. subulatum  to HO = 0.914 (locus Lsub03) and expected heterozygosities ranged from HE = 0.083 (locus Lsub09) to HE = 0.881 (locus Lsub04). None of the 12 loci showed significant heterozygote deficiency, with an overall non-significant inbreeding coefficient value of FIS = −0.030 . 8 and 10 of the 12 loci were polymorphic in the high mountain, Iberian, narrow endemic Lepidium stylatum (Sect. Lepia (Desv.) DC.), and in the widespread ruderal, L. graminifolium (Sect. Lepidium), respectively. However, in the latter species individual genotypes could not be reliably scored from the amplification patterns with individuals showing up to five amplified bands per individual .All 12 microsatellite loci were transferable to all assayed species . All locdividual . Ten andoth taxa . Thus, tC. didymus, and up to six bands were amplified in the octoploid C. draba  following the manufacturer’s instructions, and eluted in 130 μL TE. This DNA was used to construct 454 genomic libraries by the sequencing service from the University of Valencia  and to conduct shotgun sequencing on a GS Junior 454 sequencer . We obtained 119,732 reads with an average read length of 465.61 bp and a total amount of 55,748,981 bases that were trimmed of adaptor and low-quality regions and assembled into contigs using GS De Novo Assembler implemented in Newbler 2.5p1 , using default parameters . Generated contigs and unique reads not assigned to contigs were subjected to BLAST analysis and those matching organellar (chloroplast or mitochondria) sequences were discarded.Taq Buffer , 2 mM MgCl2, 0.4 mM of each dNTP, 5 pmol each of the labelled (forward) and unlabelled (reverse) primers, 1 U of Taq polymerase (Biotools) and 20 ng of template DNA. The PCR program consisted of one step of 4 min at 94 °C followed by 39 cycles each of 1 min at 94 °C, 1 min at 55 °C for annealing, and 1 min at 72 °C, and a final extension step of 7 min at 72 °C. The products were run on an ABI 3730XL automated sequencer (Applied Biosystems) using LIZ500 as the internal lane size standard, and the amplified fragment lengths were assigned to allelic sizes with GENEMARKER v. 1.85 software . After an initial screening of individuals, all 12 loci showed consistent amplification patterns and polymorphisms and were subsequently used for genotyping the entire set of samples.We screened all 8305 unique reads and non organellar contigs with iQDD v. 1.3.0.0 software . We set L. subulatum , observed (HO) and unbiased expected (HE) heterozygosities [FIS) and deviations from Hardy-Weinberg equilibrium and linkage disequilibrium between pairs of microsatellite loci, using 1000 permutations, were calculated using GENEPOP v.4.1.4 software [p < 0.05).Number of alleles , and Coronopus Zinn (C. didymus L., Cross-species transferability was assayed in one population each of three other species of L. subulatum with 12 novel nuclear polymorphic microsatellite loci support their use for conducting population genetics and to investigate the effects of habitat fragmentation on gene flow among populations and population genetic structure of this endemic gypsophyte. The successful cross-transferability of all these markers to L. cardamines and L. stylatum further expands their usefulness to address similar questions in these two restricted Iberian endemics. The genetic information rendered by these microsatellites will enable more efficient conservation programs for these species. The cross-transferability to other Lepidieae potentially broadens their applicability to a large number of taxa in Lepidieae, including polyploids.The results obtained in this exploratory analysis of the genetic diversity in


Andropogon gerardii populations across the U.S. Great Plains precipitation gradient, ranging from approximately 48 cm/year to 105 cm/year.Environmental variables such as moisture availability are often important in determining species prevalence and intraspecific diversity. The population genetic structure of dominant plant species in response to a cline of these variables has rarely been addressed. We evaluated the spatial genetic structure and diversity of Genomic diversity was evaluated with AFLP markers and diversity of a disease resistance gene homolog was evaluated by PCR-amplification and digestion with restriction enzymes. We determined the degree of spatial genetic structure using Mantel tests. Genomic and resistance gene homolog diversity were evaluated across prairies using Shannon's index and by averaging haplotype dissimilarity. Trends in diversity across prairies were determined using linear regression of diversity on average precipitation for each prairie. We identified significant spatial genetic structure, with genomic similarity decreasing as a function of distance between samples. However, our data indicated that genome-wide diversity did not vary consistently across the precipitation gradient. In contrast, we found that disease resistance gene homolog diversity was positively correlated with precipitation.Prairie remnants differ in the genetic resources they maintain. Selection and evolution in this disease resistance homolog is environmentally dependent. Overall, we found that, though this environmental gradient may not predict genomic diversity, individual traits such as disease resistance genes may vary significantly. Rana pretiosa was greatest at the center of the species range, corresponding to the peak model. In the gradient model, intraspecific variation changes from one end of a species range to the other, often corresponding to environmental variation. The gradient model has been demonstrated to apply to variation of both molecular markers and heat and cold tolerance phenotypes in Drosophila melanogasteret al.Intraspecific variation has been proposed to vary across space according to peak or gradient models Andropogon gerardii (Vitman) is the dominant plant species in the North American tallgrass prairie ecoregion. Because of its importance in conservation and restoration ecology, and more recently in potential biofuel systems, the spatial genetic structure of A. gerardii has been an ongoing subject of interest et al.et al.A. gerardiiArabidopsis, approximately 400 in Populus, and more than 500 in OryzaPlant disease resistance may vary across environmental gradients A. gerardii. This species presents a unique opportunity to address questions about the distribution of resistance gene variation. It has a relatively continuous spatial distribution across a wide range of environments in the Great Plains and has common pathogens with its more-studied relative Zea mays. Understanding the ecology and evolution of disease resistance genes in such widespread and abundant native plant species could have direct applications to agriculture, where many crop species are grown in monocultures over large areas. The spatial structure of resistance genes influences epidemic intensity in many systems A. gerardii populations A. gerardii may also be important in the development of biofuel systems based on prairie plant species, including ‘low-input high-diversity’ systems This study examines the diversity of a resistance gene homolog in A. gerardii, however we report the presence of a homolog of the maize gene Rxo1 in A. gerardii. Zhao et al.Rxo1 confers resistance to Burkholderia andropogonis and a resistance reaction to the rice bacterial streak pathogen Xanthomonas oryzae pv. oryzicola after transfer to rice, suggesting conserved functionality across different genera of grasses. It is known that Rxo1 recognizes avirulent B. andropogonis in maize, and that the same maize isolates of B. andropogonis infect A. gerardii . In addition, Rxo1 recognizes not only avirulent B. andropogonis, but also avrRxo1 in Xanthomonas oryzae pv. oryzicolaRxo1 recognizes conserved components of a bacterial effector or group of effectors A. gerardii Rxo1 homolog may recognize avirulent B. andropogonis strains.No disease resistance genes have been cloned from Burkholderia andropogonis is pathogenic to at least 51 plant species in 15 families of monocots and dicots A. gerardii at Konza Prairie Biological Station in Kansas under wet conditions in spring B. andropogonis infects sorghum and maize in warm and humid areas and is disseminated by splashing water B. andropogonis tends to be more severe during periods of wet and warm weather B. andropogonis is associated with rainstorms in Florida A. gerardii across the North American Great Plains allows for the examination of resistance gene homolog diversity across an east to west gradient in precipitation. Net primary productivity increases by a factor of 5.5 from the Shortgrass Steppe Long Term Ecological Research Site in northeastern Colorado to the Konza Prairie Biological Station in Kansas et al.Carex blanda field and herbarium specimens from western Kansas compared to eastern Kansas. This trend was attributed to the drier conditions in western Kansas providing an environment less suitable for the disease, the fact that western Kansas was at the edge of the range for C. blanda, and that western populations were smaller and more isolated, decreasing the potential for successful dispersal. Disease in A. gerardii caused by B. andropogonis likely also changes across this environmental gradient. The scale of selection for resistance can be relatively small. For example, differences in selection for herbivore resistance were found within a 4 ha stand of oak seedlings Rxo1 homolog may result in different levels of diversity among populations of A. gerardii.The widespread distribution of A. gerardii across the U.S. Great Plains precipitation gradient using AFLP markers. We found novel evidence for spatial genetic structuring in A. gerardii, but not evidence for a change in genomic diversity across the gradient. Second, we assessed diversity in Rxo1 homologs in the same natural populations of A. gerardii. We found that diversity in the resistance gene homologs decreased with decreasing precipitation across the gradient, in a pattern distinct from that of genomic diversity. The patterns of AFLP and Rxo1 homolog diversity within and between prairies also provide perspectives on the spatial scale at which intraspecific variation occurs for both the entire genome and for a presumably adaptive gene family, as context for planning tallgrass prairie conservation and restoration.In this study, our first objective was to determine genome-wide diversity of Tallgrass prairie remnants can be found in much of the eastern US, but are most common in the Great Plains where a sharp east-west precipitation gradient occurs ; Fig. 1.et al.EcoRI-AAA/MseI-CTG primer-pair and 32 polymorphic fragments were scored for the HEX-labeled EcoRI-ACC/MseI-CTG primer-pair. Capillary electrophoresis was used to identify fragments and GeneMarker version 1.6 software  was used to score AFLP markers. Statistical analyses described below were conducted using R software AFLP fingerprinting was performed according to Vos Rxo1 gene and its four other tightly linked family members from the maize inbred B73 (GenBank accessions AY935244-AY935248) were compared to identify conserved sequences near the predicted start codon and nucleotide binding site (NBS) regions. Two conserved primers were designed from these sequences: ATG forward (5′-GAAGGGATGGCAGAGATTGCTGT-3′) and MHD reverse (5′-CAAGTTCACGCACAAGATCATGCAT-3′). These primers amplified fragments of approximately 1500 nt from genomic DNA of a single A. gerardii plant  obtained from Konza Prairie Biological Station. Cloning and partial sequence analysis of these fragments identified three different sequences highly similar to the maize Rxo1 gene which were then used to design RACE 5′ and 3′ PCR primers for 5′-TCTTTTTCAGGACAAGAACA-3′ and 5′-CGACGGAGCATGCTTCATGTTGCAGAGAG-3′ for 3′, respectively. Transcripts corresponding to the full coding region were then amplified with primers that were conserved among the RACE PCR amplicons; the primers 5′BRxo forward (5′-GGTATTGGGGCTAAAGAGTGAGCTTTGAC-3′) corresponded to sequences in the 5′UTR and 3′BRxo including the predicted stop codon (5′-GAGTTCTGCTATTTCATCTTAACCGGGCC-3′). RACE PCRs and cDNA amplifications were performed using the BD smart RACE cDNA amplification Clontech kit . One cDNA corresponding to the full coding region had a 2793 nt open reading frame that was approximately 91% identical to the maize Rxo1 coding region (Genbank sequence # pending).The sequences of the maize A. gerardii clones originating from diverse locations (5′-AGATTCTCGACGAGTTGCTGTGCT-3′ and 5′-AGCCTAAGAAGCCCATTTCCGTGA-3′). The primers did not require pre-screening for polymorphism, and amplified fragments from plant samples collected throughout the gradient and beyond in Colorado, Illinois, and Indiana. Four restriction enzymes were used to perform RFLP assays: BsaMI, RsaI, TaqI (Promega), and MseI (New England Biolabs). The PCR amplicons were digested individually. Digestion products were electrophoresed on 2% agarose gels and scored for the presence or absence of fragments. Five fragments were scored for BsaMI, nine for MseI, nine for RsaI, and 14 for TaqI. We found the RFLP markers to be greater than 99% repeatable.We amplified sequences from the leucine-rich repeat (LRR) encoding region from ocations . A primeA. gerardii exists in populations with multiple ploidy levels A. gerardii populations consist predominantly of hexaploids and enneaploids with some individuals of intermediate ploidy levels A. gerardii, it is necessary to account for the potential effects of spatial trends in ploidy. Population analyses of A. gerardii may be influenced by two factors. First, enneaploid and hexaploid individuals may be acting as separate populations. This could influence our results if enneaploids and hexaploids do not contribute equally to our diversity measures and if the proportion of enneaploids varies among prairies. Second, enneaploids may exhibit more AFLP amplicons compared to hexaploids because enneaploids contain 50% more chromosomes. In order to determine if enneaploids and hexaploids were acting as distinct populations, we measured AFLP dissimilarity among and within individuals of the two ploidy groups from the Boulder population. In order to test if enneaploid individuals were more diverse than hexaploid individuals we calculated the average number of AFLP fragments amplified in enneaploids and compared this to the hexaploid average. Assuming the polymorphic fragments analyzed in this study are distributed equally across chromosomes, we expected to find more fragments in enneaploids than in hexaploids. These ploidy analyses were conducted with data from the mapped Boulder population to determine if there is an inherent relationship between ploidy and diversity in A. gerardii.Like many perennial plant species, Rxo1-RFLP datasets, a similarity matrix with an entry for each pairwise comparison of ramets from all prairies outside Colorado was calculated for each of the two datasets. To estimate pairwise genetic similarity for this study, we used the simple match coefficient (s), which Kosman & Leonard s). The mean dissimilarities of all ramet pairs at a particular distance from each other were used to calculate the overall mean dissimilarity for that distance. For example, since there were five plants in the first transect subgroup of a transect and five in the second transect subgroup, the mean of all of the comparisons among these two transect subgroups was used as one datum in calculating the overall 10 meter mean dissimilarity. Mean dissimilarity was calculated for approximately 1.8 m (average within-subgroup distance), 10 m, 20 m, 30 m, 40 m, 2139 m (average distance between transects), and 473,025 m (average distance between prairies). In order to test for spatial genetic structure, a regression was performed for mean dissimilarity versus distance between sampled locations. This test is similar to a Mantel test Scale of sampling is important in determining spatial autocorrelation in clonal species H′ = −Σ ip log ip, where ip is the frequency of the amplified fragment. H′ was calculated for each population and used to determine the average population diversity: aH. The total diversity for all individuals used in this study was calculated and denoted as sH.Shannon's information measure was used to determine the proportion of diversity among populations: Rxo1 and AFLP dissimilarity for each prairie. This measure of diversity includes haplotype diversity in addition to diversity of individual alleles since individual haplotypes were used in calculating dissimilarity. Shannon's information measure was also calculated for each population for both AFLP and Rxo1 data. This measure of diversity considers allelic diversity alone. We used R to perform linear regression analyses of both Rxo1 and AFLP diversity measures, with annual average precipitation  for enneaploids.Samples collected in Boulder, Colorado, were from mapped clones of known ploidy. AFLP dissimilarity was calculated among hexaploid clones (n = 38), among eaneaploid clones (n = 21), and between hexaploid and enneaploid clones. The mean dissimilarity for each of these comparisons was found to be 0.10 indicating equal dissimilarity both within and among ploidy groups. There was no difference in average fragment number among ploidy levels. Average number of fragments for hexaploids was 59.37  and 59.33  for enneaploids. Similarly, the average number of A. gerardii populations (which may ultimately be described best by an asymptotic function). The trend of increasing dissimilarity with increasing distance was also significant using the Rxo1-RFLP data (data not shown). We found 6.35% of the AFLP variation to be present among populations based on Shannon's information measure. For Rxo1-RFLP data, 13.00% of the variation was distributed among populations.Mean pairwise dissimilarity based on AFLP markers increased with increasing distance between individuals . These dRxo1 homolog dissimilarity must be examined in the context of mean AFLP dissimilarity to determine whether the pattern in dissimilarity across longitude for Rxo1 is different from the pattern for the genome as a whole. We found a positive relationship between average annual precipitation and Rxo1 homolog dissimilarity  in a coevolutionary manner, measurements of disease pressure in a common garden experiment of clones with known resistance levels across the precipitation gradient could be used to test the hypothesis that the diversity cline is associated with a gradient of disease pressure.A compelling explanation for the Rxo1 homolog diversity was significantly higher in the eastern prairies. This may be due to selection for multiple alleles or gene family members in the disease-conducive environments, which would be consistent with the Red Queen hypothesis Rpm1 locus in ArabidopsisRxo1 homolog diversity.Rxo1 homologs was disproportionately low relative to the neutral markers. Pathogens may be shared between tallgrass prairie and agricultural systems , drier conditions and more isolated plant populations would tend to result in lower disease pressure ms e.g., , increasRxo1 homologous genes within and among natural populations of A. gerardii will allow assessment of what types of selection are controlling diversity at the Rxo1 homolog locus. It has been demonstrated in models that coevolutionary clines may result from multiple effects Rxo1 diversity is adaptive. Sequence data for Rxo1 homologs across the different populations could help to elucidate whether or not the diversity cline is conferred by adaptive evolution. However, a substantial effort would be required to sequence the potentially multiple Rxo1 homologs in each individual. Functional analysis of the genes would also be valuable to more fully understand the molecular evolution of the Rxo1 homologs.Comparative sequence analysis of the Andropogon gerardii is often found in populations of mixed ploidy Rxo1-RFLP dissimilarities, there was no differentiation between individuals of different ploidy. This is consistent with allozyme data suggesting that individuals of dissimilar ploidy level from the same plot were more similar than individuals of the same ploidy level from different plots Rxo1-RFLP band number was also the same across ploidy levels. While it is possible that the relationship between ploidy and band number could differ among populations of A. gerardii, this finding in the Boulder population suggests that relative proportions of hexaploid and enneaploid ramets in the other populations was not important for determining dissimilarity and diversity in our analyses.Our finding of no difference in band number between the two ploidy levels has implications for the origin and establishment of enneaploids in mixed ploidy populations. Since enneaploids were not found to have an increase in heterozygosity, our data suggest that enneaploids may be produced through second division restitution (SDR) of hexaploid gametes. This process may be mediated by temperature, as chromosome doubling has been observed at high temperatures for maize and other species of the tribe Triticeae A. gerardii varies with precipitation, one of the most important environmental drivers of plant disease. Diversity of resistance phenotypes has been shown to vary with ecoregion previously in the Linum marginale – Melampsora lini pathosystem, where higher host phenotypic diversity (significantly associated with population mean resistance) was present in hill populations compared to bog populations Linum marginale also showed higher diversity at neutral allozyme loci and were significantly distinct from bog populations as measured by these neutral markers. Also, the proportion of Aegilops tauschii resistance to stem and leaf rust was found to vary greatly by region, with the highest resistance exhibited by populations adjacent to the Caspian Sea We have demonstrated that resistance gene diversity in Chamaecrista fasciculata populations in the Great Plains Diversity of important genes in native populations may prove to be particularly valuable if selection pressures shift rapidly due to changing climate Appendix S1This appendix provides additional details about the methods.(DOCX)Click here for additional data file.


Lobaria pulmonaria, studied the importance of primeval forest reserves for the conservation of genetically diverse populations and analyzed differences in spatial genetic structure between primeval and managed forests with fungus-specific microsatellite markers. Populations belonged to either of two genepools or were admixed. Gene diversity was higher in primeval than in managed forests. At small distances up to 170 m, genotype diversity was lower in managed compared with primeval forests. We found significant associations between groups of tree species and two L. pulmonaria genepools, which may indicate “hitchhiking” of L. pulmonaria on forest communities during postglacial migration. Genepool B of L. pulmonaria was associated with European Beech (Fagus sylvatica) and we can hypothesize that genepool B survived the last glaciation associated within the refuge of European Beech on the Coastal and Central Dinarides. The allelic richness of genepool A was highest in the Alps, which is the evidence for a northern refuge of L. pulmonaria. Vicariant altitudinal distributions of the two genepools suggest intraspecific ecological differentiation.Availability of suitable trees is a primary determinant of range contractions and expansions of epiphytic species. However, switches between carrier tree species may blur co-phylogeographic patterns. We identified glacial refugia in southeastern Europe for the tree-colonizing lichen  Ecological processes at various spatial and temporal scales leave their genetic footprints in populations. Congruent genetic pattern between coexisting or interacting species has been attributed to either, or a combination of three processes, that is, (1) congruent response to shared environmental change, (2) joint dispersal, or (3) nested habitat requirement such as the presence of a carrier tree for an obligate epiphytic species. First, congruent response to environmental change has been studied by a phylogeographic approach for a broad diversity of organisms (Bermingham and Moritz Lobaria pulmonaria (L.) Hoffm. via clonal, symbiotic propagules accounts for more than 70% of reproduction within populations  the importance of primeval forest reserves for the conservation of large and genetically diverse populations compared with populations surviving in managed forests, and (3) to study differences in the spatial genetic structure between primeval and managed forests.Our study aimed at elucidating (1) the phylogeography of L. pulmonaria from the Austrian Alps (4), Dinarides from Slovenia (2), Bosnia and Herzegovina (3) and Montenegro (9), Strandzha Mountains (3) and the Central Balkan Mountains (1) of Bulgaria and the Pindos Mountains in Greece (2) (L. pulmonaria (Bilovitz L. pulmonaria was scarce but the species was rather frequent in the vicinity of the reserve (SL8) in managed stands. Perućica in Bosnia and Herzegovina and Biogradska gora in Montenegro are among the largest and best preserved primeval forests in Europe (Parviainen We sampled 24 populations of eece (2) . Whereveeece (2)  and the Bilovitz . In the Bilovitz  L. pulmoL. pulmonaria were sampled from 20 trees from forest stands of approximately 3 ha. From the geographic center of a population we sampled 10 nearest neighbor trees colonized by L. pulmonaria. Additionally, 10 trees on a circle with radius of about 150 m from the plot center were sampled. From each tree three thallus fragments were collected from different parts of the trunk. Fragments had no necrotic parts and were without visible parasites or fruit bodies and measured up to 7 × 5 cm. Samples were air dried and kept frozen at −20°C until further treatment.Small fragments of L. pulmonaria using the DNeasy 96 plant kit  according to the manufacturer's protocol. Eight unlinked, fungal microsatellite loci, LPu03, LPu09, LPu15, LPu23, LPu24, LPu25, LPu28,  assumed to be in gametic equilibrium . We ran three replicate simulations for each K = {1,…, 15}, and, after a burn-in period of 1 × 105 iterations, 1 × 106 iterations were run in order to sample the posterior distribution. An admixture model was used in which the fraction of ancestry from each genepool was estimated for each sampled individual. The prior of individual admixture was set to be uniform for all genepools. Panmictic genepool allele frequencies were assumed independent of each other , effective mean number of alleles (Ne) and percentage of different genotypes (M) were calculated with Genalex  based on the number of different alleles were calculated with Arlequin 3.5.1.2  mediterranean Europe. Submediterranean tree species such as Carpinus orientalis, Castanea sativa, Quercus sp., and Quercus frainetto have their distribution center in Mediterranean mountain regions and warmer areas in Central Europe. Fagus sylvatica was the most frequent tree species and was treated as a separate group.Analyses of variance and one-way ANOVA examining Nei's gene diversity H with categorical, environmental variables were performed with JMP 8.0.2  strongly increased between K = 1 and K = 2 and it reached a plateau between K = 2 and K = 5 before it decreased up to K = 15. The highest value of ΔK as a function of K was reached at K = 2 . The analyses of the data sets with and without clones gave the same results. Visual inspections of the bar plots provided by STRUCTURE confirmed two genepools because at K > 2 one of the genepools split in fully admixed populations. Further analyses were therefore carried out assuming the presence of two distinct genepools. The analysis of the inferred ancestry of individuals resulted in 1088 individuals belonging either to genepool A or to genepool B. Only six specimens from six populations  revealed a mixed ancestry (proportion of membership of each predefined population in each of the genepools >0.25<0.75) and only one specimen from the population AU6 contributed equally to the two genepools . At the population level 9 and 10 populations belonged to genepools A and B , respectively, and five populations revealed admixture to varying degrees  252 pairs (84%) and in the clone-corrected dataset (441 samples) 138 pairs (46%) revealed significant levels of genetic differentiation .FST of the complete data set that included clones was 0.143 compared to 0.198 of the clone-corrected dataset (data not shown). Lobaria pulmonaria populations growing on F. sylvatica were not differentiated from populations growing on other tree species  and populations from managed forests were not differentiated from those of primeval forests .The AMOVA analyses revealed that only 8.91% of the genetic variation of the clone-corrected dataset was explained by the five biogeographic regions Alps, Dinarides, Strandzha, Balkan- and Pindus Mountains and the fixation index Because some populations were small and only scarce material of the rare and locally threatened lichen species was found, it was not possible to collect the planned 60 specimens in each population. To avoid damage on small populations, less than the planned number of specimens was collected in 14 of the 24 populations . The numP < 0.07) and B (P < 0.04) was positively correlated with latitude . Because primeval forest reserves were not equally distributed over the entire study area we also tested this difference for the 13 populations analyzed in Montenegro and Austria where primeval and managed forests were found closely together, and were able to confirm statistically higher H values for the primeval forest reserves .L. pulmonaria in South Eastern Europe was F. sylvatica, but F. excelsior, A. pseudoplatanus, Quercus sp. played a role in floodplain forests and A. cephalonica was a frequent habitat in Greece. Although we did not find significant association between individual tree species and genepools, our dataset revealed significant association of genepools with three tree species groups with different ecological preferences  and genepools, which may indicate “hitchhiking” of L. pulmonaria on forest communities during postglacial migrations. However, we did not find an association with individual tree species, which indicates that frequent switches of carrier tree species within ecological groups have occurred.We found significant association between three ecologically defined groups of tree species (L. pulmonaria is associated with F. sylvatica and we can hypothesize genepool B survived the last glaciation associated within the refuge of F. sylvatica on the Coastal and Central Dinarides (Magri et al. Fagus (Magri et al. L. pulmonaria likely spread southwards from the northern part of the Dinarides. This is supported by decreasing allelic richness from the northern part of the Dinarides toward the South. However, the fact that Nei's gene diversity was not decreasing with latitude indicates that postglacial migration distances were small. It is therefore likely that in the southern part of the study area, genepool B was associated with additional tree species including A. cephalonica.Genepool B of L. pulmonaria was possibly limited by aridity and the lack of suitable carrier trees, rather than by temperature. Elevated levels of air humidity, which is more important than precipitation for this poikilohydric lichen (Scheidegger et al. L. pulmonaria including A. alba (Linares F. excelsior (Heuertz et al. F. sylvatica on the Coastal and Central Dinarides (Magri et al. Genepool A has a wider geographic distribution compared with genepool B. All over this area, Nei's gene diversity was not significantly changing along the long latitudinal and longitudinal gradients. We interpret this result as evidence for the existence of multiple refugia including the Black Sea Coast near the Strandzha Mountains, the Balkan Mountains, ravine forests in the Central Dinarides and possibly the South Eastern Alps. Because temperature anomalies in Southeastern Europe were small compared with Southwestern or Central and Northern Europe (Davis et al.  Linares , F. exceL. pulmonaria associated with mesophytic tree species such as F. excelsior (Heuertz et al. Taking into account the current distribution of genepool A in ravine forests along river valleys such as Tara and Mrtvica in Montenegro we hypothesize a Central Dinarides refuge of Unlike the two genepools A and B where allelic richness and latitude are positively correlated, admixed populations showed a significant decrease in Nei's gene diversity with increasing latitude. The highest values of Nei's gene diversity were found in western Montenegro and eastern Bosnia and Herzegovina where suture zones between genepools A and B were found in our study. Decreasing gene diversity with latitude indicates postglacial spread over larger distances from a refugial area of admixed populations. Because no pure populations belonging to genepool B could be found in the Alps, it is likely that admixture of the two genepools occurred prior to postglacial spread. The data available so far even point to the possibility that the admixed genepool survived the last glacial maximum in Slovenia and the Eastern Alps. Because our results indicate an independent glacial history of the admixed populations, we can conclude that the distinct genepools A and B reflect an evolutionary history longer than the last glacial–interglacial cycle. The Quaternary history of this epiphytic lichen species thus suggests that the modern genetic diversity is likely the result of multiple interglacial–glacial cycles, possibly since the middle Pleistocene (Magri et al. Lobaria pulmonaria populations can be maintained in managed forests only if management intensity is low and a large portion of retention trees carrying this lichen are maintained during forest management (Scheidegger et al. L. pulmonaria, long before the abundance of this species might be negatively affected. This confirms earlier studies on effects of disturbance gradients on genetic diversity of this lichen species. Werth et al. (L. pulmonaria in a regenerating stand after a forest fire, compared with stands, which were managed by single-stem harvest since early medieval times. In Estonia L. pulmonaria had a higher genetic diversity and more juvenile thalli were found in old-growth forests compared with managed forests and wooded meadows (Jüriado et al. L. pulmonaria population (Otalora et al. L. pulmonaria is likely the result of genetic drift after significant reduction of regional population size and fragmentation into small, spatially isolated populations. Because genetic drift accumulates over many generations (Frankham et al. h et al.  found reL. pulmonaria is a heterothallic species (Zoller et al. L. pulmonaria. In general an increased average distance between carrier trees will reduce gene flow and thus lower the genetic diversity of Lobaria at the tree level. Only primeval forests and forest reserves can maintain the required small-scale connectivity of habitats over centuries and thus facilitate genetically diverse L. pulmonaria populations.A comparison of the spatial genetic diversity between managed and protected primeval populations revealed that genotype diversity was substantially lower up to 170 m in managed forests compared with primeval forests. With a reduced genotype diversity at low distances in managed forests we conclude that while clonal spread is dominant at low distance classes (Dal Grande et al. L. pulmonaria and possibly other old-growth forest dependent species. Therefore, we are concerned that none of the primeval forests harbored genepool A of L. pulmonaria. All populations belonging to genepool A were found in currently or previously managed forest stands and deserve high conservation priority in future.Large-scale primeval forest reserves can thus be considered reference systems for characteristic levels of genetic diversity of populations of


In 1661, Kaspar Schott published his comprehensive textbook “Cursus mathematicus” in Würzburg for the first time, his “Encyclopedia of all mathematical sciences”. It was so successful that it was published again in 1674 and 1677. In its 28 books, Schott gave an introduction for beginners in 22 mathematical disciplines by means of 533 figures and numerous tables. He wanted to avoid the shortness and the unintelligibility of his predecessors Alsted and Hérigone. He cited or recommended far more than hundred authors, among them Protestants like Michael Stifel and Johannes Kepler, but also Catholics like Nicolaus Copernicus. The paper gives a survey of this work and explains especially interesting aspects: The dedication to the German emperor Leopold I., Athanasius Kircher’s letter of recommendation as well as Schott’s classification of sciences, explanations regarding geometry, astronomy, and algebra. The German Association of Mathematicians (Deutsche Mathematiker-Vereinigung) was founded in 1890. Since 1902, it has had its own seal: (Illustration The temple represents a religious context. Geometry is indispensable in the An opened book shows the Latin inscription: “Artem geometriae discere atque exercere publice interest” (“It is in public interest to learn and to practise the art of geometry”). Knobloch :34. Yet,In the first paragraph, it is stated that it is worse to extinguish a man by poison than to kill him with a sword. This seems to be a really astonishing context for geometry. The second paragraph reads: “Artem geometriae discere atque exerceri publice intersit. ars autem mathematica damnabilis interdicta est.” The first sentence is—in principle—the inscription of the German seal. The second sentence just means: “But the damnable mathematical art is forbidden.” At last the reader now recognizes that the mathematicians in this juridical text of the sixth century A.C. are the astrologers. The mathematical art is astrology.When in 1661 the German Jesuit Kaspar Schott published his mathematical textbook “Cursus mathematicus” he addressed both aspects of mathematics or—more specifically—of geometry: its great utility and the religious ideas. For him, arithmetic and geometry were the wings for the beginner (tyro) in order to penetrate the sanctuaries of mathematics (mathematicae adyta). A sanctuary (adytum) is the innermost part of a temple, strictly speaking what must not be entered, as in the case of the American Mathematical Society seal. In other words, from the very beginning, Schott put his work into a religious context.I would like to give a survey of this impressing work by dealing with four issues: (1) The work, its dedication and eulogies, (2) conception, (3) realization, (4) examples taken from the chapters on geometry, astronomy, and algebra.First of all, the title page is worth studying more diligently:  dates back to that coronation year. A crowned lady with a pair of compasses and a ruler in her left hand offers the “Cursus mathematicus” to the emperor. This emperor highly esteemed the arts and sciences and was himself a gifted musician in spite of the many wars he had still to carry on. Thanks to the insignia, the lady can be undoubtedly identified with geometry. Its crown underlines its importance. An angel holds a laurel wreath that was meant for the author of the work. We will come back to this issue in the epilogue.mathesis that is moved along below the emperor as is stated in the dedication (advolvitur). The course is originally a running, a race track.On the ground-floor, a strange vehicle is drawn by the true constellations Bear and Lion. They draw the terrestrial and the celestial globes that is the vehicle has two ‘wheels’ as in the case of Roman chariots. The armillary sphere that is a world model replaces the driver. The globes or spheres are symbolizing Schott’s The globes reveal 12 tilings of the ground-floor that is paved by squares. Nine of them can be easily identified : ballistics (warfare), military architecture (fortification), Tychonic world system, statics, gnomonics, practical geometry, algebra, geometry, and trigonometry. Obviously, the interests of an emperor being at war, shown in the armor of a knight, have influenced the selection of these nine represented mathematical disciplines out of the 22 dealt with in the volume.Utility is the leading aspect. It is not by chance that Schott will call practical geometry the noblest and most useful among all mathematical disciplines, trigonometry necessary and useful in the highest degree, gnomonics even divine.The dedication to Leopold I. contains some important hints at the work: “Regi encyclopaediam mathematicam o(ffert) d(at) c(onsecrat) Casparus Schott” .Encouraged by the emperor, Schott says, he has covered the immeasurable sea of mathematical disciplines (“immensum mathematicarum disciplinarum pelagus…percurrerem”) Schott :p.(2v°) According to Schott, the emperor knows that the mathematical sciences, combined with the experience of philosophy, are jewels in the hands of princes, kings, and emperors. Kings and monarchs of the world always attached great interest to the mathematical sciences. One might think of Alphonse the Wise of Castile or Charles the Great. Without question, in the eyes of the princes of the seventeenth century mathematics was a discipline supporting the state, it was powerful.This is demonstrated for example by Daniel Bretschneider the Elder, citizen and painter in Dresden by his “Book about various inventions” :  to the English king James, his “Astronomia nova” (“New astronomy”) and his “Astronomiae pars optica”  to the emperor Rudolph II., his “Tabulae Rudolphinae” (“Rudolfinian tables”) to the emperor Ferdinand II., the father of Leopold I.: A similar behavior is true of Clavius, Kircher, and Grégoire de Saint Vincent. But up to then nobody has dedicated a whole encyclopedia of the mathematical sciences to a sovereign. Schott’s citation of Kepler’s works should be all the more emphasized because they do not play any role in the “Mathematical course”. " (“Nothing is more beautiful than to know everything.”).Schott had inherited his yearning for universality from his Lullistic teacher Athanasius Kircher. Already his “Magia universalis naturae et artis”  whose four volumes were published between paraeneses, exhortations. He printed three of them at the beginning of his volume. One of these writings was the letter of his admired teacher Athanasius Kircher to mathematical beginners. Kircher wrote a classical enkomium, a eulogy on mathematics as we meet it again and again in the Renaissance, especially in Johannes Regiomontanus’s famous inaugural address in Padua from 1464.While Schott was elaborating his encyclopedia, he was encouraged by many contemporaries. He received officina). For a long time, the mathematical community (res publica mathematica) has waited for an author like Schott who would write a “Mathematical course”, an encyclopedia of the whole mathematics, clearly structured and based on an easy method in order to foster the scientific community (res publica litteraria) and to encourage beginners.Kircher explains that in his dialog “Symposion” Plato had Alcibiades speak of Socrates as a pharmacist’s pot. He, Kircher, preferred to compare the studies of mathematics with a workshop (sacra mathesis) (Schott divinum matheseos studium) that alone imparts recognition and knowledge of all the celestial things:Kircher speaks about the comprehensive use of the divine mathematics  Schott , p..There cannot be any doubt: Kircher and Schott following him gained their explanations from the “Prolegomena”, the preface that Christoph Clavius, chief mathematician of the Jesuits, had placed in front of his edition of Euclid’s “Elements”. God himself was the first geometer who had created the world according to arithmetical and geometrical principles.Knowledge about the world presupposed the language of mathematics. Regularity and perfection of the unchangeable, geometrical structure of the world testified for its divine origin Romano :133–178.God was the inventor of all mathematical disciplines. Schott explicitly said it in his “Horographia” (“Gnomonics”) Schott :389: “Pe ." (“The gods grant everything on the strength of pains.”). Kircher cites Epicharmus, the best known poet of the Doric comedy.This importance compensates by far for the trouble of acquiring it because: "Schott planned his textbook most carefully. He placed a preface in front of the whole work and in front of every of the 28 chapters as well. Therein he commented upon his aims and methods and defined the single mathematical, partial disciplines: a model of clarity and order!He addressed beginners and first candidates of mathematics. That he emphasized again and again. Hence, he inserted short introductions into areas or surveys of areas. He referred to further literature for additional studies. More than hundred authors are mentioned, among them Protestants like Michael Stifel or Johannes Kepler, but also Catholics like Copernicus whose theory was still rejected by the Catholic church in Schott’s time.Schott did not want to be an innovator, any more than Kepler, nor did he want to treat everything exhaustively. Here, if anywhere the wisdom proved to be true: Only when restricted does somebody prove to be a master. On the contrary, thanks to a wise self-restriction, he intended to explain the essentials in an easily comprehensible form for beginners. In his opinion, his two predecessors Johann Heinrich Alsted and Pierre Hérigone had violated this criterion. They were the only authors who had accomplished a similar work before him.Alsted’s encyclopedia comprehended the whole system of sciences in seven volumes: (Illustration varia). Mathematics is subsumed in this last group as it is indicated by the right lower picture and went short for that reason. Arithmetic, music, geometry, and astronomy are represented. Five chapters offered a medley of disciplines (farragines disciplinarum).The title page enumerates and illustrates theology, jurisprudence, medicine, philosophy, mechanics, and various subjects   Schott :261, in He likes to refer to his own books, too, for example to his “Pantometrum Kircherianum” (“Kircher’s instrument for measuring everything” 1660) or to his “Magia universalis naturae et artis”. Its third volume deals with mathematics and its fourth with physics: .Yet, Schott remained a self-critical realist and remarked  Schott gives the traditional definition of mathematics from ancient times Schott :2: “Ex hThis definition is still valid in the eighteenth century and occurs in Christian Wolff’s “Mathematisches Lexicon”  dating from 1716 Wolff :605.In view of numerous classifications of the mathematical disciplines, Schott decides on a classification that is similar to that of Clavius Schott :3: The dichotomic classification principle discrete/continuous, abstract/concrete, speculative/practical is only neglected in the case of concrete, continuous mathematics: music occurs twice. Every subdivision is divided into further subunits. It might suffice to enumerate all 22 disciplines dealt with by Schott: Arithmetic, geometry, trigonometry, astronomy, astrology, chronology, geography, navigation, gnomonics, mechanics, statics, hydrostatics, hydraulic engineering, optics, catoptrics, dioptrics, fortification, warfare, tactics, musical theory, algebra, and theory of logarithms.Apart from some few differences, this is Hérigone’s list  are geometry, geography, trigonometry, algebra, and astronomy. The shortest chapters (four to six pages) are dioptrics, statics, and tactics. Schott does not deal with theoretical arithmetic that is number theory in the sense of the Euclidean books 7–9, only with practical arithmetic. Hence this chapter comprehends only forty pages. But this first chapter was already published 1 year later, in 1662, as a book on its own and was reprinted many times in a more or less abridged version Vollrath :XII: . Thus, gnomonics is a divine science Schott :389. Thipura/mixta (pure/mixed), not on discreta/continua. The following schemes represent parts of this comprehensive classification: At the end of his work, Schott puts the synopsis of all mathematical sciences due to an author whom he is not permitted to mention Schott :611–620.Mixed mathematics is subdivided in the following way: The disciplines are again subdivided. Astronomy might serve as an example: Elements like those of Johann Vögelin, Joachim Camerarius, Jan Pietersz, Henric Coets restricted themselves to the first six books . Schott did the same in his “Geometria elementaris sive Elementorum geometricorum Euclidis sex libri primi” .Many editions of Euclid’s He believed that he had solved the famous parallel problem in the sense that he had shown that the parallel postulate is a demonstrable theorem Schott :73 “tame“If the sum of the two angles α and β is smaller than two right angles, the straight lines g, h have a point of intersection on the side of these two angles.” The inversion reads: “If the straight lines g, h have a point of intersection, the sum of the two angles α and β is smaller than two right angles.” The inversion can be indeed demonstrated and is equivalent with theorem I, 28 of Euclid’s “Elements”: , Saturn has two.The semi-Tychonic system: There is no depth of the heavens. Moon, sun, Jupiter, and Saturn turn around the earth. Mercury, Venus, and Mars turn around the sun.In theoretical astronomy, Schott explains six world systems: (Illustration Astronomia elementaris sive de sphaera mundi (Elementary astronomy or on the sphere of the world), Schott defends geocentrism concluding   Kepler .In principle, Schott explains the Ptolemaic planetary theory  that was based on excentric deferents, epicycles, equants (puncta aequantia) saying Schott :273: .subtilitas) and excellence (excellentia)  Schott .There were a second and a third edition of Schott’s textbook that appeared in 1674 and in 1677, respectively: The volume was a great success. In the seventeenth and eighteenth centuries, many similar mathematical encyclopedias followed, also by Jesuits like that of François Milliet Dechales. The mathematical method achieved great triumphs, especially in Christian Wolff’s “Elementa matheseos universae” (“Elements of the whole mathematics”) .Schott himself remained modest saying Schott :660: “NuHanc linque Sphyngem barbytos Oedipo;Vatumque sacro percitus entheoFutura praedic. HIC PERENNESCURSUS AGET TIBI SCHOTTE LAUDES.Leave this sphinx, lyre, to Oedipus;Foretell the future excited by theinspired holy action of the prophets. Thistextbook will bring you eternal glory.The Polish Jesuit and Professor of Mathematics Adam Adamandus Kochanski had sent 47 Alcaic Strophes to Schott. This meter had been introduced into Roman poetry by Horace. Such a strophe comprehends two verses, each of eleven syllables, a third consisting of nine, and a fourth verse consisting of ten syllables. Hence Kochanski spoke of Horace’s lyre. The last strophe reads Schott , p.(6vNothing has to be added to this statement.


Anopheles gambiae sensu stricto has a complex population structure. In west Africa, this species is split into two molecular forms and displays local and regional variation in chromosomal arrangements and behaviors. To investigate patterns of macrogeographic population substructure, 25 An. gambiae samples from 12 African countries were genotyped at 13 microsatellite loci. This analysis detected the presence of additional population structuring, with the M-form being subdivided into distinct west, central, and southern African genetic clusters. These clusters are coincident with the central African rainforest belt and northern and southern savannah biomes, which suggests restrictions to gene flow associated with the transition between these biomes. By contrast, geographically patterned population substructure appears much weaker within the S-form.The primary Afrotropical malaria mosquito vector  Many studies have attempted to identify genetic discontinuities between conspecific populations and to determine the factors that promote differentiation. This is a critical step for predicting the evolution of populations under different scenarios, including those that involve human-made environmental changes , Anopheles gambiae sensu stricto (hereafter termed ‘An. gambiae’) is a primary vector of human malaria in Africa. It is widely distributed throughout sub-Saharan Africa in close association with humans. There is evidence that this species is undergoing a process of incipient speciation. The speciation process appears to be restricted to west Africa and involves sympatric populations. Initially, heterogeneities have been found in the distribution of paracentric inversions at chromosome 2, which displayed strong heterokaryotype deficits. This led to the description of five chromosomal forms (cytoforms) each in Hardy–Weinberg equilibrium and characterized by distinct arrangements of inversions  mutations found between molecular forms. In spite of widespread sympatry between M- and S-forms, for a decade following their discovery in An. gambiae  or linkage with genomic regions of M/S divergence on chromosome X  and one negative control (no template) were also included to assess PCR quality. Allele sizes were scored from electropherograms using the software genemarker® .Thirteen microsatellite loci were genotyped. All loci were located on chromosome 3 to avoid potential bias resulting from reduced recombination or selective pressures acting at chromosomal inversions (frequent in chromosome 2) or linkage with genomic regions of M/S divergence on chromosome X  among populations  in the whole data set and within each molecular form separately. Analyses were carried out without prior information of sampling locations. A model with correlated allele frequencies within populations was assumed (λ = 1). The software was run with the option of admixture, allowing for some mixed ancestry within individuals, and the degree of admixture (α) was allowed to vary. For each value of K (K = 1–10), 10 independent runs were carried out with a burn-in period of 10 000 and 100 000 iterations. The ΔK statistic of Evanno et al. (structure harvester (Earl and vonHoldt K was compiled by the greedy method implemented in clumpp (Jakobsson and Rosenberg Tq) determined by the analysis of simulated parental and admixed individuals generated by hybridlab v1.0 . Simulated genotypes were analyzed by STRUCTURE under the same conditions as above. Following the example of Vähä and Primmer .The nonspatial Bayesian clustering analysis method implemented in o et al.  was calc Primmer , power atess v.2.3. . The Deviance Information Criterion (DIC) was used to select the admixture model that performed better and to infer the number of clusters. The maximum number of clusters was selected from DIC versus Kmax plots as the lowest value at which the DIC curve reached a plateau. The estimated individual membership probabilities of the ten runs of the optimal Kmax were averaged using the greedy algorithm in clumpp to correct for discrepancies between runs.Spatial genetic clustering analysis was conducted with the whole data set and with M- and S-form data sets using the software genalex 6.41  was used to visualize patterns of genetic differentiation among samples in a two-dimensional plot. Calculations were performed in FST) values .Isolation by distance was tested by the linear regression between logarithmic geographic distances and linearized 1/(1- Rousset . Pair-wiα = 0.05) was adjusted by the sequential Bonferroni procedure  of the microsatellite loci varied from 5.4 (AG3H242) to 12.7 (AG3H128) and expected heterozygosity (He) from 0.575 (AG3H577) to 0.894 (AG3H128). There were 48 significant departures from Hardy–Weinberg proportions of 325 tests performed. These were associated with positive FIS values indicating heterozygote deficits. Loci AG3H88, AG3H127, and AG3H750 comprised 39 (81.3%) of the 48 significant tests, suggesting that departures from Hardy–Weinberg expectations were locus-specific. Presence of null alleles was detected by microchecker in 44 of the 48 (92.7%) significant heterozygote deficits  and S (cluster 2) molecular form composition of the samples and it was independent of geographic location. However, samples from west African sites  displayed more inconsistencies between the form determined by the IGS marker and the respective genetic background when compared to samples from central and southern Africa. In west African samples, the average probability of assignment to cluster 1 for M-form specimens was 0.515 and 0.636 for S-form assignment to cluster 2. When individuals were assigned to each cluster based on a Tq ≥ 0.8, as determined by the analysis of simulated data (see Tq < 0.80) was 83.7% and 65.2% for M- and S-form, respectively. In contrast, the average probabilities of assignment for M- and S-form individuals from central and southern African sites were 0.831 and 0.847, respectively. The proportion of consistent assignments was also much higher: 73.3% (225 of 307) in the M-form and 75.8% (229 of 302) in the S-form. The second highest ΔK value corresponded to K = 3. Here, M-form populations were subdivided into two genetic clusters : cluster 1 contained mainly individuals from the samples collected in west Africa (samples 1–9) and also from Bayanga, CAR (sample 12); cluster 2 included the remaining samples from central Africa  and Angola (samples 21–23). These results did not differ qualitatively when analyses were repeated excluding the three loci that revealed most heterozygote deficits indicating that locus-specific Hardy–Weinberg deficits had little impact in the analysis  were assigned to the central African cluster 2.ent Fig. , M-form.structure analysis was performed with these samples only  decreased from 97.8% in Libreville (sample 15) to 28.9% , 17.8% , 13.3% , 8.5% , and 6.7% in the southernmost Kikudo (sample 20). Finally, a third cluster comprised specimens from the southeast African sample of Furvela (sample 24), in Mozambique.Subdivision among S-form populations was also observed when nly Fig. , S-form.structure.The geographic structuring of M-form populations was also evident in the principal coordinates analysis Fig. . The distess were very similar for the two admixture models used. The car model gave, however, less-dispersed DIC values between runs, so that only the results for this model are presented , but did not disclose any subdivision between central and west African samples  with logarithmic distance (r2) was generally low, particularly when both M- and S-form were analyzed together . When the most distant S-form sample of Furvela, Mozambique (sample 24), was removed, the regression remained significant but with a lower r2 (0.28). Plots of the regression of linearized FST and logarithmic distance for M- and S-forms are shown in Fig. structure) had in general lower FST than comparisons involving sites from distinct genetic clusters . The S-form displayed Rs and He values similar to those of the M-central cluster. The average number of shared alleles among clusters was higher between the S-form and M-west clusters than between any other comparison (Table FST estimate (0.023) with the highest (0.075) being observed between S-form and M-south  displaying a higher proportion of an M-west genetic background in spite of its rainforest location. Bayesian clustering methods may overestimate genetic structure by generating spurious clusters when applied to populations displaying isolation by distance  in central Africa also suggested a role of the evergreen forest as a barrier to gene flow in this vector species  was much lower in these samples. However, sequence analysis of an X-linked locus revealed that the majority of M-form individuals in Angola had a 16-bp insertion that was fixed in the S-form but absent in M-form individuals from west and central Africa . Rainforest samples of Gabon also appeared more closely related in the PCoA. However, S-form samples from savannah biomes in west Africa (Ghana) and Angola were grouped together in the PCoA and into a single cluster in structure. The intergradation between S-form clusters observed southwards of Libreville in the STRUCTURE analysis also suggests gradual differentiation, in line with an expectation of isolation by distance. Moreover, the results of the spatial genetic analysis conducted by tess for the S-form did not show a clustering of central African samples within the rainforest belt. Instead, the two major clusters corresponded to the separation of the East African sample of Mozambique from central and west African samples. However, it should be noted that in spite of the continent-wide distribution of the S-form, the number of samples available for this study was quite limited, particularly in west Africa. Moreover, central African samples were also concentrated within a relatively small area separated by a maximum distance of <500 km. This restricted sampling could have influenced the results, especially for the spatial cluster analysis as the accuracy of these methods tends to increase with the inclusion of more spatial points (Guillot et al. Kmax (Durand et al. tess, the optimal K obtained reflected both the M/S subdivision and the geographic partitioning within each form.The results obtained for the S-form did not conclusively show a genetic discontinuity at the transition between rainforest and savannah. A central African S-form cluster was detected by kdr haplotypes, forest/savannah restrictions to gene flow may also contribute to the observed heterogeneities.The apparent shallow differentiation between west and southern African S-form samples is consistent with previous studies pointing to an overall shallow population differentiation within this form (Lehmann et al. An. gambiae, at least within the M-form. This trend appears to be associated with the transition between forest and savannah biomes and appears to be evident both northwards and southwards from the central African rainforest belt. This complexity is of importance to the management of malaria vector control programs. A genetic discontinuity between savannah and forest biomes is likely to influence dispersal and distribution of genes of practical importance to malaria epidemiology and control, such as genes associated with insecticide resistance or with vector competence.The results obtained in this study show that in addition to the M- and S-forms partitioning and to the existence of local or regional genetic variants (Coluzzi et al.