Unsupervised AI reveals insect species-specific genome signatures

Insects are a highly diverse phylogeny and possess a wide variety of traits, including the presence or absence of wings and metamorphosis. These diverse traits are of great interest for studying genome evolution, and numerous comparative genomic studies have examined a wide phylogenetic range of insects. Here, we analyzed 22 insects belonging to a wide phylogenetic range (Endopterygota, Paraneoptera, Polyneoptera, Palaeoptera, and other insects) by using a batch-learning self-organizing map (BLSOM) for oligonucleotide compositions in their genomic fragments (100-kb or 1-Mb sequences), which is an unsupervised machine learning algorithm that can extract species-specific characteristics of the oligonucleotide compositions (genome signatures). The genome signature is of particular interest in terms of the mechanisms and biological significance that have caused the species-specific difference, and can be used as a powerful search needle to explore the various roles of genome sequences other than protein coding, and can be used to unveil mysteries hidden in the genome sequence. Since BLSOM is an unsupervised clustering method, the clustering of sequences was performed based on the oligonucleotide composition alone, without providing information about the species from which each fragment sequence was derived. Therefore, not only the interspecies separation, but also the intraspecies separation can be achieved. Here, we have revealed the specific genomic regions with oligonucleotide compositions distinct from the usual sequences of each insect genome, e.g., Mb-level structures found for a grasshopper Schistocerca americana. One aim of this study was to compare the genome characteristics of insects with those of vertebrates, especially humans, which are phylogenetically distant from insects. Recently, humans seem to be the “model organism” for which a large amount of information has been accumulated using a variety of cutting-edge and high-throughput technologies. Therefore, it is reasonable to use the abundant information from humans to study insect lineages. The specific regions of Mb length with distinct oligonucleotide compositions have also been previously observed in the human genome. These regions were enriched by transcription factor binding motifs (TFBSs) and hypothesized to be involved in the three-dimensional arrangement of chromosomal DNA in interphase nuclei. The present study characterized the species-specific oligonucleotide compositions (i.e., genome signatures) in insect genomes and identified specific genomic regions with distinct oligonucleotide compositions

A Stand Structure Dominated by Betula maximowicziana in the Chichibu Mountains, Central Japan

1．秩父山地の標高1,300m地点にあるウダイカンバ優占林分内に0.96haの調査区（以下，秩父区）を設置し，毎木調査から林分構造を，樹齢測定から林齢を明らかにした。2．秩父区内に出現した樹種数は39種，立木本数は1,177本/ha，BA合計は42.0m2/ha，材積は330.0m3/haであった。そのうちウダイカンバは本数が83本/ha（7.1％），BA合計が15.8m2/ha（37.5％），材積が154.7m3/ha（46.9％）であった。3．秩父区では22m以上の階層でウダイカンバが圧倒的に優占する第一層，14～22mの階層はミズメ，ミズナラ，イヌシデなどの多い第二層，および4～14mの階層はカエデ類，シデ類，アラゲアオダモ，リョウブの多い第三層の3つの階層が確認された。4．秩父区内とその周辺にある枯死木20本の樹齢測定の結果から，調査木の年輪数は83～120年の範囲にあり，そのうち近年枯死した5個体の年輪数から秩父区は約120年前に更新したものと推定された。5．秩父区と，山火事後に更新したウダイカンバ優占二次林である東京大学北海道演習林固定標準地の北演5133（3回間伐，林齢91年），北演5236（無間伐，林齢86年）を比較したところ，秩父区は本数密度と年直径成長量で北演5133に近い値を示し，平均胸高直径と材積で北演5133と北演5236より大きかった。しかし，秩父区のウダイカンバは用材として評価した場合，北演5133のそれより劣っており，秩父演習林に多い林齢100年未満のウダイカンバ二次林で用材生産をする場合には，優良木を選木してその直径成長を促すための間伐を実施する必要があると考えられた。6．秩父区ではミズナラがウダイカンバに比べて寿命が長く，耐陰性も高いことから，今後の長い遷移過程において徐々にウダイカンバが枯死し，それに代わって現在第一層，第二層にあるミズナラが優占していくものと推察された。In order to investigate the floristic composition and structure of a stand dominated by Betula maximowizciana, a research plot with an area of 0.96 ha was established at an altitude of 1,300m a.s.l. in the Chichibu Mountains, central Japan. Diameter at breast height (dbh) and the height of all the trees with dbh larger than 5.0cm were measured in the plot. Thirty-nine tree species were recorded in the plot. The number of trees, basal area and stand volume were 1,177/ha, 42.0m2/ha and 330.0m3/ha, respectively. For B. maximowicziana, these values were 83/ha (7.1%), 15.8m2/ha (37.5%) and 154.7m3/ha (46.9%), respectively. The stand was stratified into three layers, the first-layer (height of layer: hl>22m) in which the predominant species was B. maximowicziana, the second-layer (14<hl≦22m) in which B. grossa, Quercus crispula and Carpinus tschonoskii were abundant and the third-layer (4<hl≦14m) in which Acer spp. Carpinus spp., Fraxinus languinosa and Clethra barvinervis were abundant. From the age analysis of twenty dead trees sampled within the plot and its surroundings, tree ages were in the range of 83 to 120 years. From the age analysis of five sample trees, which seemed to die recently, it was estimated that this stand was regenerated about 120 years ago. Numerical values of the stand in Chichibu plot were compared to those of the stands dominated by B. maximowicziana in two plots (plot no. 5133 and 5236) in the Tokyo Univ. Forest in Hokkaido, northern Japan. They were regenerated after forest fire and the stand age of plot no. 5133 and 5236 were 91 and 86 years, respectively. Qualitative thinning has been conducted three times in the former plot but this was not the case in the latter. Tree density and mean annual diameter growth rate of the Chichibu plot were similar to those of plot no. 5133. On the other hand, mean dbh and stand volume at the Chichibu plot was larger than those of the two plots in Hokkaido. However, from the viewpoint of the commercial value of wood utilization, the morphological characteristics of the B. maximowizciana trees in the Chichibu plot are inferior to those of the trees in plot no. 5133 where qualitative thinning has been conducted. Hence, for the production of high-quality large diameter trees, qualitative thinning should also be conducted especially to B. maximowicziana stands with an age less than 100 years. These are abundant in the Tokyo Univ. Forest in Chichibu. It is thought that the B. maximowicziana trees composing the canopy layer in the Chichibu plot at present are gradually being replaced by Quercus crispula in the long course of succession, since the latter, characterized by its longer life span and higher shade tolerance, has an advantage over the former