都市農村交流に対応した果樹園芸経営の多角化方策とその展開方向

研究種目:科学研究費補助金基盤研究(C)報告年度:2003年度研究課題番号:13660213研究概要:本年度の研究実績の概要は、以下のとおりである。1)農業経営活動の多角化のための、これまでの農家像に関する検討を行い、従来の農家=農業生産という図式から、経営活動領域(ドメイン)の拡大の必要性を明らかにした。次いで、農家経営の多角化を明示的に扱う概念的フレームワークを提示して、農業経済学の領域の拡大を図った。具体的には、農家経営の多角化を明確に位置付けるため、農家経営活動の生産物が1種類のみの伝統的な農産物の場合に加えて、サービス財的特徴を有する農村ツーリズム関連財の存在を明示的に考慮した2種類の生産物を前提とすべきであることを提示した。2)農村ツーリズムが誕生した社会的背景を総括し、農村ツーリズムを新旧二つのタイプに区分してその特徴を整理した結果、わが国の農村ツーリズムが新旧の移行期にあることを明らかにした。そして、農村ツーリズムの具体的形態として、わが国の農林漁業体験民宿を対象にし、その稼働率の推計を行い、長期休暇制度の成立していないわが国における今後の展開への課題を明らかにした。3)都市農村交流の展開を踏まえて、中山間地域における農村ツーリズムによる活性化の可能性を、リカード比較優位論を用いて考察し、農村ツーリズムの需要者の特性分析を行った。その結果、農村ツーリズムの需要層の特性が、欧州の先行研究で指摘される高学歴世帯が中心となるという点と同様の結果を得ており、農村ツーリズムの需要者層に関して共通した特徴があることを明らかにした。

Reconstruction of MRCA dates and changes in population size.

<p>Analyses were based on analyses of 846 non-recombinant, non-repetitive, non-mobile concatenated core SNPs by the relaxed GMRF model in Beast v1.7.1 <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003471#pgen.1003471-Drummond1" target="_blank">[36]</a>. (A) A maximum clade credibility tree. Branch colors indicate substitution rates transformed to a logarithmic scale (Rate Key), except that posterior probabilities of <0.5 for nodes and branches are indicated in black. (B) Bayesian skyride plot showing changes in effective population size of serovar Agona over time (black line) with the extent of the 95% confidence intervals shaded in blue.</p

Histograms of the frequencies of numbers of differences between pairs of genomes in SNPs, genomic islands, accessory genes, or PFGE bands.

<p>Histograms of the frequencies of numbers of differences between pairs of genomes in SNPs (A), genomic islands (B), accessory genes (C), or PFGE bands (D). The X axes of histograms A and C indicate the maximal number of differences within the indicated ranges in order to ensure that the first column only includes identical pairs (maximum = 0). These frequency distributions correspond to the same data which were used for comparisons in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003471#pgen-1003471-g008" target="_blank">Figure 8</a>, except that those referred to genetic similarity and the data here refer to the converse, which are differences.</p

Insertions (solid lines) and deletions (dashed lines) of IS elements (Tables S7, S8, S9) in mobile elements (red boxes) or the core genome (black ellipses) mapped on a SNP genealogy of 73 Agona genomes.

<p>The SNP genealogy is based on a maximum parsimony tree based on 846 non-recombinant, non-mobile core SNPs (as in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003471#pgen-1003471-g001" target="_blank">Figure 1</a>), but drawn in radial fashion (Mega) for convenience. The tips of the branches include strain ID numbers, as in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003471#pgen-1003471-g001" target="_blank">Figure 1</a> and Dataset S2. Node, clade and branch designations are also according to <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003471#pgen-1003471-g001" target="_blank">Figure 1</a> and Dataset S2.</p

Lack of association of CDSs in the accessory genome with outbreak clades and statistical test of neutrality of non-synonymous mutations in the core genome.

<p>A) Likelihood of association of individual CDSs within the accessory genome with outbreak clades. Each of the 79 genomic islands and plasmids is indicated by alternating light and dark blue segments consisting of one vertical line per CDS. Individual genomes were assigned to one of four outbreak clades or one of 28 non-outbreak clades. Only eight CDSs within GI21 were significantly associated with all outbreak clades (Fisher exact test, p = 0.032). After a Bonferroni correction for multiple tests, no CDS was significantly associated with outbreak clades. B) Numbers of non-synonymous mutations per CDS in the non-recombinant, non-repetitive core genome as a function of gene length whose mean expectations are indicated by an internal white line. Each gene is represented by a circle, whose size is proportional to the deviation according to a χ² statistic from theoretical expectations of a non-parametric test (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003471#pgen.1003471.s015" target="_blank">Figure S5</a>). Shades of blue indicate different α-thresholds (0.05, 0.01, 0.001) of the confidence intervals of the theoretical expectations, where 0.05 indicate CI 95%. The sole outlier identified in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003471#pgen.1003471.s017" target="_blank">Figure S7B</a> is indicated in red.</p

Comparisons of genetic similarities between core, non-repetitive, non-mobile SNPs, genomic islands, accessory genes, and PFGE bands.

<p>A–F) Plots of the frequencies of pairs of similarity scores for two matrices as indicated above each subplot. Matrices of the pair-wise genetic similarities were generated for UPGMA trees of the 72 new genomes in Bionumerics 6.5, and correspond to the interpretations provided in Dataset S1 (genomic islands), Dataset S3 (PFGE bands), Dataset S4 (SNPs), and Dataset S7 (accessory genes). The frequency of each pair of similarity values within a pair of matrices is indicated by circle size. A linear regression (solid line) with 95% confidence intervals (dotted lines) is shown for each pair of matrices as well as the coefficient of determination (<i>R</i>²). All comparisons were statistically significant in Mantel tests of the paired matrices, with <i>p</i>≤10⁻⁴ except for part A, where <i>p</i> = 5×10⁻⁴.</p

Multiple introductions and deletions of mobile elements.

<p>Each introduction or deletion in a node of the genealogy is counted only once, even if that introduced mobile element is present in multiple descendent genomes. The number of distinct sequence variants within each category is indicated by (Number) after Type. Where mobile elements integrated into multiple locations within the genome, each such integration was associated with a distinct sequence variant (Dataset S1), and they represent independent insertions. Additional, unrelated non-IS mobile elements were each introduced on a single occasion (Dataset S1), consisting of 2 ICE/IMEs, 3 bacteriophages, 3 plasmids and 4 other genomic islands, for a total of 95 introductions of non-IS mobile elements. Five other genomic islands were each deleted once, for a total of 22 deletions of non-IS mobile elements. Similarly, five IS elements were introduced on one occasion each (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003471#pgen.1003471.s027" target="_blank">Table S8</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003471#pgen.1003471.s028" target="_blank">S9</a>), for a total of 54 introductions.</p

Number of CDSs <i>versus</i> number of genomes in which they were present.

<p>All CDSs in the pan-genome were used for these calculations, except that repetitive CDSs such as IS elements were each counted as one CDS.</p

SNP densities in recombinant and non-recombinant regions of the Agona core genome.

<p>(A) Average frequency of SNPs per Kb from pair-wise, 1 Kb sliding window comparisons between the genome of Agona SL483 <i>versus</i> 12 genomes from serovars Choleraesuis, Dublin, Enteritidis, Gallinarium, Heidelberg, Newport, Paratyphi A, Paratyphi B, Paratyphi C, Schwarzengrund, Typhi, and Typhimurium (hatched boxes). A comparable distribution of mean pair-wise diversity between all 73 Agona genomes is indicated by black boxes. (B). SNP density in recombination segments. (C) Frequency distributions of the length of recombinant segments (x-axis) and number of SNPs per recombinant region (y-axis). Each recombination region is indicated by an open circle with an internal dot. The linear regression of these data indicates that 9.2 SNPs are found per recombinant Kb (<i>R</i>² = 0.97).</p

Features of the <i>S. enterica</i> Agona non-repetitive non-mobile core genome.

<p>Features of the <i>S. enterica</i> Agona non-repetitive non-mobile core genome.</p