リケラボ論文検索は、全国の大学リポジトリにある学位論文・教授論文を一括検索できる論文検索サービスです。

リケラボ 全国の大学リポジトリにある学位論文・教授論文を一括検索するならリケラボ論文検索大学・研究所にある論文を検索できる

リケラボ 全国の大学リポジトリにある学位論文・教授論文を一括検索するならリケラボ論文検索大学・研究所にある論文を検索できる

大学・研究所にある論文を検索できる 「Evolutionary study on the origins of rheophytic goldenrod (Solidago yokusaiana: Asteraceae) with genome and transcriptome analyses」の論文概要。リケラボ論文検索は、全国の大学リポジトリにある学位論文・教授論文を一括検索できる論文検索サービスです。
リケラボ

コピーが完了しました

URLをコピーしました

論文の公開元へ論文の公開元へ
書き出し

Evolutionary study on the origins of rheophytic goldenrod (Solidago yokusaiana: Asteraceae) with genome and transcriptome analyses

Kyan Ryuta 東北大学

2022.03.25

概要

Understanding adaptation mechanisms is one of most important issues in evolutionary biology. Convergent adaptation provides good opportunities to investigate adaptive evolution. Ecotype pairs, which are sets of populations of same species or closely related ones showing contrasting ecological characters, can be possible natural replicates of convergent adaptation.

　Rheophytes are riparian plants that are adapted and confined to frequently flooded riversides. The rheophytic phenotype has parallelly evolved in different phylogenetic groups and has convergent phenotypic traits, such as narrow leaves, thicker roots, and tough and flexible stems. These traits seem adaptive to flood; therefore, ecotype pair of a rheophyte and its ancestral species is one of representative natural replicates in contrasting environments and will provide a suitable model system for studying convergent adaption.

　The goldenrod species Solidago virgaurea (Asteraceae) is a perennial herb that is widely distributed in Eurasia. In the Japanese Archipelago, the S. virgaurea complex is extremely divergent ecologically and morphologically. Solidago yokusaiana, a rheophytic congener of S. virgaurea, is endemic to Japan, is distributed from Tohoku to Okinawa Districts.

　In chapter I, I examined the parallel origins of S. yokusaiana by distinguishing between multiple and single origins with subsequent gene flow between S. yokusaiana and its progenitor S. virgaurea to confirm convergent adaptation. Some chloroplast haplotypes were shared between S. yokusaiana and S. virgaurea. Also, the population genetic structures revealed by nSSR and SNPs did not correspond to the taxonomic species. The demographic modelling supported the multiple origins of S. yokusaiana in at least four districts and rejected a single origin with ongoing gene flow between the two species, suggesting that S. yokusaiana independently and repeatedly adapted to frequently flooding riversides (Kyan et al., 2021).

　The Japanese S. virgaurea complex may have expanded its range to the Japanese Archipelago during the last glacial period, and S. yokusaiana may have diverged from its progenitor after the last glacial maximum. Considering that the demographic analyses indicated multiple origins in at least four districts, and that the populations of S. yokusaiana have common rheophytic traits, it seems unlikely that the S. yokusaiana in each district evolved via independent de novo mutations after the last glacial maximum, because it is implausible that adaptive mutations arouse at loci related to rheophytic traits in multiple districts in a relatively short period. Therefore, independent selection from the standing genetic variation may have mainly caused the multiple origins of S. yokusaiana. Since mechanisms of the multiple origins are not mutually exclusive, some rheophytic traits or adaptive alleles possibly stemmed from other mechanisms. In addition, because mechanisms causing the multiple origins may also differ in scales of time or space, further studies on loci under divergent selection between the species are needed to elucidate the origins of the rheophytic traits of S. yokusaiana.

　In chapter II, I examined what levels of the genetic hierarchy in which rheophytic convergence have occurred to elucidate the adaptation mechanisms of rheophytism of S. yokusaiana. I compared the gene expression patterns of rheophytic S. yokusaiana and terrestrial S. virgaurea in two districts where both species were sampled. Differentially expressed genes (DEGs) in S. yokusaiana did not show convergence as a whole, and enriched biological functions of the DEGs were more similar between the two districts than the DEGs, suggesting that convergent adaptation of S. yokusaiana in the two districts mainly occurred at a level of the biological functions or their downstream.

　The biological functions specific to S. yokusaiana, which were shared among the two districts were mainly related to DNA replication, suggesting that rheophytism of S. yokusaiana are caused by accelerated cell proliferation through the enriched functions. To regulate species specific leaves size, some mechanisms must coordinate the number and size of leaf cells, and SPL gene family is known to compensate the increased number of cells with decreased size of cells. Also, narrow leaves found commonly in rheophytes were caused by a decreased number of cells in angiosperms and altered cell-elongation process in fern. Therefore, the enriched functions related to DNA replication might be a consequence of the compensation. Considering that functions directly related to cell proliferation were not enriched, endoreduplication, a modified cell cycle lacking mitosis, might contribute to the narrow leaf development, because it contributes to the relationship between the number and size of cells. Furthermore, endoreduplication, which could shorten time and cost of cytokinesis, seems adaptive to environments requiring rapid development, due to frequently disturbed riparian environment.

論文の公開元へ

この論文で使われている画像

関連論文

関連論文をもっと見る

参考文献

Akaike, H. (1974). A new look at the statistical model identification. IEEE Transactions on Automatic Control, 19(6), 716–723. doi: 10.1109/TAC.1974.1100705

Anderson, C. J. R. (2012). The role of standing genetic variation in adaptation of digital organisms to a new environment. The 2019 Conference on Artificial Life, 24, 3–10. doi: 10.1162/978-0- 262-31050-5-ch001

Arendt, J., & Reznick, D. (2008). Convergence and parallelism reconsidered: What have we learned about the genetics of adaptation? Trends in Ecology & Evolution, 23(1), 26–32. doi: 10.1016/j.tree.2007.09.011

Arroyo-García, R., Ruiz-Garcia, L., Bolling, L., Ocete, R., Lopez, M. A., Arnold, C., … Cabello, F. (2006). Multiple origins of cultivated grapevine (Vitis vinifera L. ssp. Sativa) based on chloroplast DNA polymorphisms. Molecular Ecology, 15(12), 3707–3714.

Barow, M., & Meister, A. (2003). Endopolyploidy in seed plants is differently correlated to systematics, organ, life strategy and genome size. Plant, Cell & Environment, 26(4), 571–584. doi: 10.1046/j.1365-3040.2003.00988.x

Barrett, R. D. H., & Schluter, D. (2008). Adaptation from standing genetic variation. Trends in Ecology & Evolution, 23(1), 38–44. doi: 10.1016/j.tree.2007.09.008

Beerli, P. (2004). Effect of unsampled populations on the estimation of population sizes and migration rates between sampled populations. Molecular Ecology, 13(4), 827–836. doi: 10.1111/j.1365-294X.2004.02101.x

Benjamini, Y., & Hochberg, Y. (1995). Controlling the false discovery rate: A practical and powerful approach to multiple testing. Journal of the Royal Statistical Society. Series B (Methodological), 57(1), 289–300.

Berens, A. J., Hunt, J. H., & Toth, A. L. (2015). Comparative transcriptomics of convergent evolution: Different genes but conserved pathways underlie caste phenotypes across lineages of eusocial insects. Molecular Biology and Evolution, 32(3), 690–703. doi: 10.1093/molbev/msu330

Bierne, N., Gagnaire, P.-A., & David, P. (2013). The geography of introgression in a patchy environment and the thorn in the side of ecological speciation. Current Zoology, 59(1), 72–86. doi: 10.1093/czoolo/59.1.72

Bryant, D. M., Johnson, K., DiTommaso, T., Tickle, T., Couger, M. B., Payzin-Dogru, D., … Whited, J. L. (2017). A tissue-mapped axolotl de novo transcriptome enables identification of limb regeneration factors. Cell Reports, 18(3), 762–776. doi: 10.1016/j.celrep.2016.12.063

Butlin, R. K., Saura, M., Charrier, G., Jackson, B., André, C., Caballero, A., … Rolán‐Alvarez, E. (2014). Parallel evolution of local adaptation and reproductive isolation in the face of gene flow. Evolution, 68(4), 935–949. doi: 10.1111/evo.12329

Catchen, J. M., Amores, A., Hohenlohe, P., Cresko, W., & Postlethwait, J. H. (2011). Stacks: Building and genotyping loci de novo from short-read sequences. G3: Genes, Genomes, Genetics, 1(3), 171–182. doi: 10.1534/g3.111.000240

Catchen, J. M., Hohenlohe, P. A., Bassham, S., Amores, A., & Cresko, W. A. (2013). Stacks: An analysis tool set for population genomics. Molecular Ecology, 22(11), 3124–3140. doi: 10.1111/mec.12354

Chaparro, C., Gayraud, T., de Souza, R. F., Domingues, D. S., Akaffou, S., Laforga Vanzela, A. L., … Guyot, R. (2015). Terminal-repeat retrotransposons with GAG domain in plant genomes: A new testimony on the complex world of transposable elements. Genome Biology and Evolution, 7(2), 493–504. doi: 10.1093/gbe/evv001

Clark, P. U., Dyke, A. S., Shakun, J. D., Carlson, A. E., Clark, J., Wohlfarth, B., … McCabe, A. M. (2009). The last glacial maximum. Science, 325(5941), 710–714. doi: 10.1126/science.1172873

Clement, M., Posada, D., & Crandall, K. A. (2000). TCS: A computer program to estimate gene genealogies. Molecular Ecology, 9(10), 1657–1659. doi: 10.1046/j.1365-294x.2000.01020.x

Cooper, T. F., Rozen, D. E., & Lenski, R. E. (2003). Parallel changes in gene expression after 20,000 generations of evolution in Escherichia coli. Proceedings of the National Academy of Sciences, 100(3), 1072–1077. doi: 10.1073/pnas.0334340100

Costa, L. M. S., Goetze, M., Rodrigues, A. V., Seger, G. D. dos S., & Bered, F. (2020). Global rheophytes data set: Angiosperms and gymnosperms. Ecology, 101(8), e03056. doi: 10.1002/ecy.3056

Crandal, K. A., Harris, D. J., & Fetzner, J. W. (2000). The monophyletic origin of freshwater crayfish estimated from nuclear and mitochondrial DNA sequences. Proceedings of the Royal Society of London. Series B: Biological Sciences, 267(1453), 1679–1686. doi: 10.1098/rspb.2000.1195

Doyle, J. J., & Doyle, J. L. (1990). Isolation of plant DNA from fresh tissue. Focus, 12, 13–15.

Dray, S., & Dufour, A.-B. (2007). The ade4 package: Implementing the duality diagram for ecologists. Journal of Statistical Software, 22(1), 1–20. doi: 10.18637/jss.v022.i04

Earl, D. A., & vonHoldt, B. M. (2012). STRUCTURE HARVESTER: A website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources, 4(2), 359–361. doi: 10.1007/s12686-011-9548-7

Evanno, G., Regnaut, S., & Goudet, J. (2005). Detecting the number of clusters of individuals using the software structure: A simulation study. Molecular Ecology, 14(8), 2611–2620. doi: 10.1111/j.1365-294X.2005.02553.x

Excoffier, L., Dupanloup, I., Huerta-Sánchez, E., Sousa, V. C., & Foll, M. (2013). Robust demographic inference from genomic and SNP data. PLOS Genetics, 9(10), e1003905. doi: 10.1371/journal.pgen.1003905

Excoffier, L., & Lischer, H. E. L. (2010). Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources, 10(3), 564–567. doi: 10.1111/j.1755-0998.2010.02847.x

Excoffier, L., Smouse, P. E., & Quattro, J. M. (1992). Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction data. Genetics, 131(2), 479–491.

Foster, S. A., McKinnon, G. E., Steane, D. A., Potts, B. M., & Vaillancourt, R. E. (2007). Parallel evolution of dwarf ecotypes in the forest tree Eucalyptus globulus. New Phytologist, 175(2), 370–380. doi: 10.1111/j.1469-8137.2007.02077.x

Grabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D. A., Amit, I., … Regev, A. (2011). Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology, 29(7), 644–652. doi: 10.1038/nbt.1883

Haenel, Q., Roesti, M., Moser, D., MacColl, A. D. C., & Berner, D. (2019). Predictable genome- wide sorting of standing genetic variation during parallel adaptation to basic versus acidic environments in stickleback fish. Evolution Letters, 3(1), 28–42. doi: 10.1002/evl3.99

Hall, T. A. (1999). BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95–98. [London]: Information Retrieval Ltd., c1979-c2000.

Hamilton, M. B. (1999). Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation. Molecular Ecology, 8(3), 521–523.

Hermisson, J., & Pennings, P. S. (2005). Soft sweeps: Molecular population genetics of adaptation from standing genetic variation. Genetics, 169(4), 2335–2352. doi: 10.1534/genetics.104.036947

Huang, M., Sanchez-Moreiras, A. M., Abel, C., Sohrabi, R., Lee, S., Gershenzon, J., & Tholl, D. (2012). The major volatile organic compound emitted from Arabidopsis thaliana flowers, the sesquiterpene (E)-β-caryophyllene, is a defense against a bacterial pathogen. New Phytologist, 193(4), 997–1008. doi: 10.1111/j.1469-8137.2011.04001.x

Ichihashi, Y., Aguilar-Martínez, J. A., Farhi, M., Chitwood, D. H., Kumar, R., Millon, L. V., … Sinha, N. R. (2014). Evolutionary developmental transcriptomics reveals a gene network module regulating interspecific diversity in plant leaf shape. Proceedings of the National Academy of Sciences, 111(25), E2616–E2621. doi: 10.1073/pnas.1402835111

Ignatiadis, N., Klaus, B., Zaugg, J. B., & Huber, W. (2016). Data-driven hypothesis weighting increases detection power in genome-scale multiple testing. Nature Methods, 13(7), 577–580. doi: 10.1038/nmeth.3885

Jakobsson, M., & Rosenberg, N. A. (2007). CLUMPP: A cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics, 23(14), 1801–1806. doi: 10.1093/bioinformatics/btm233

Jeukens, J., Renaut, S., St-Cyr, J., Nolte, A. W., & Bernatchez, L. (2010). The transcriptomics of sympatric dwarf and normal lake whitefish (Coregonus clupeaformis spp., Salmonidae) divergence as revealed by next-generation sequencing. Molecular Ecology, 19(24), 5389– 5403. doi: 10.1111/j.1365-294X.2010.04934.x

Johannesson, K., Panova, M., Kemppainen, P., André, C., Rolán-Alvarez, E., & Butlin, R. K. (2010). Repeated evolution of reproductive isolation in a marine snail: Unveiling mechanisms of speciation. Philosophical Transactions of the Royal Society B: Biological Sciences, 365(1547), 1735–1747. doi: 10.1098/rstb.2009.0256

Jones, F. C., Grabherr, M. G., Chan, Y. F., Russell, P., Mauceli, E., Johnson, J., … Kingsley, D. M. (2012). The genomic basis of adaptive evolution in threespine sticklebacks. Nature, 484(7392), 55–61. doi: 10.1038/nature10944

Kamvar, Z. N., Tabima, J. F., & Grünwald, N. J. (2014). Poppr: An R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. PeerJ, 2, e281. doi: 10.7717/peerj.281

Kato, M. (2003). Evolution and adaptation in the rheophytes. Bunrui, 3(2), 107–122. doi: 10.18942/bunrui.KJ00004649576

Kawano, S. (1988). Life history of Solidago virgaurea. Shokubutsu No Sekai, 3, 52–79.

Kigoshi, T., Kumon, F., Kawai, S., & Kanauchi, A. (2017). Quantitative reconstruction of paleoclimate in central Japan for the past 158,000 years based on a modern analogue technique of pollen composition. Quaternary International, 455, 126–140. doi: 10.1016/j.quaint.2017.05.015

Kyan, R., Kimura, T., Yamashiro, T., Fujii, S., Sakaguchi, S., Ito, M., … Maki, M. (2021). Phylogeographic and demographic modeling analyses of the multiple origins of the rheophytic goldenrod Solidago yokusaiana Makino. Heredity, 126(5), 831–845. doi: 10.1038/s41437-021-00408-x

Langenheim, J. H. (1994). Higher plant terpenoids: A phytocentric overview of their ecological roles. Journal of Chemical Ecology, 20(6), 1223–1280. doi: 10.1007/BF02059809

Leaché, A. D., Harris, R. B., Rannala, B., & Yang, Z. (2014). The influence of gene flow on species tree estimation: A simulation study. Systematic Biology, 63(1), 17–30. doi: 10.1093/sysbio/syt049

Li, G., Wang, J., Rossiter, S. J., Jones, G., Cotton, J. A., & Zhang, S. (2008). The hearing gene Prestin reunites echolocating bats. Proceedings of the National Academy of Sciences, 105(37), 13959–13964. doi: 10.1073/pnas.0802097105

Li, J., Li, H., Jakobsson, M., Li, S., Sjödin, P., & Lascoux, M. (2012). Joint analysis of demography and selection in population genetics: Where do we stand and where could we go? Molecular Ecology, 21(1), 28–44. doi: 10.1111/j.1365-294X.2011.05308.x

Li, Y., Liu, Z., Shi, P., & Zhang, J. (2010). The hearing gene Prestin unites echolocating bats and whales. Current Biology, 20(2), R55–R56. doi: 10.1016/j.cub.2009.11.042

Liu, A., He, F., Zhou, J., Zou, Y., Su, Z., & Gu, X. (2019). Comparative transcriptome analyses reveal the role of conserved function in electric organ convergence across electric fishes. Frontiers in Genetics, 10, 664. doi: 10.3389/fgene.2019.00664

Liu, Y., Cotton, J. A., Shen, B., Han, X., Rossiter, S. J., & Zhang, S. (2010). Convergent sequence evolution between echolocating bats and dolphins. Current Biology, 20(2), R53–R54. doi: 10.1016/j.cub.2009.11.058

Losos, J. B. (2011). Convergence, adaptation, and constraint. Evolution, 65(7), 1827–1840. doi: 10.1111/j.1558-5646.2011.01289.x

Love, M. I., Huber, W., & Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15(12), 550. doi: 10.1186/s13059-014- 0550-8

Mantel, N. (1967). The detection of disease clustering and a generalized regression approach. Cancer Research, 27(2 Part 1), 209–220.

Matsui, H., Tada, R., & Oba, T. (1998). Low-salinity isolation event in the Japan Sea in resoponse to Eustatic sea-level drop during LGM: Reconstruction based on salinity-balance model. The Quaternary Research (Daiyonki-Kenkyu), 37(3), 221–233. doi: 10.4116/jaqua.37.221

Matsui, R., Takei, S., Ohga, K., Hayakawa, H., Yoshida, M., Yokoyama, J., … Fukuda, T. (2013).

Morphological and anatomical variations in rheophytic ecotype of violet, Viola mandshurica var. Ikedaeana (Violaceae). American Journal of Plant Sciences, 2013. doi: 10.4236/ajps.2013.44106

Meier, J. I., Sousa, V. C., Marques, D. A., Selz, O. M., Wagner, C. E., Excoffier, L., & Seehausen, O. (2017). Demographic modelling with whole-genome data reveals parallel origin of similar Pundamilia cichlid species after hybridization. Molecular Ecology, 26(1), 123–141. doi: 10.1111/mec.13838

Meredith, M., & Kruschke, J. (2018). HDInterval: Highest (posterior) density intervals (Version 0.2.0). Retrieved from https://CRAN.R-project.org/package=HDInterval

Mitsui, Y., Nomura, N., Isagi, Y., Tobe, H., & Setoguchi, H. (2011). Ecological barriers to gene flow between riparian and forest species of Ainsliaea (asteraceae). Evolution, 65(2), 335–349. doi: 10.1111/j.1558-5646.2010.01129.x

Mitsui, Y., & Setoguchi, H. (2012). Recent origin and adaptive diversification of Ainsliaea (Asteraceae) in the Ryukyu Islands: Molecular phylogenetic inference using nuclear microsatellite markers. Plant Systematics and Evolution, 298(5), 985–996. doi: 10.1007/s00606-012-0608-6

Molina, J., Sikora, M., Garud, N., Flowers, J. M., Rubinstein, S., Reynolds, A., … Purugganan, M. D. (2011). Molecular evidence for a single evolutionary origin of domesticated rice. Proceedings of the National Academy of Sciences, 108(20), 8351–8356. doi: 10.1073/pnas.1104686108

Morjan, C. L., & Rieseberg, L. H. (2004). How species evolve collectively: Implications of gene flow and selection for the spread of advantageous alleles. Molecular Ecology, 13(6), 1341– 1356. doi: 10.1111/j.1365-294X.2004.02164.x

Nei, M. (1972). Genetic distance between populations. The American Naturalist, 106(949), 283–292. doi: 10.1086/282771

Nomura, N., Takaso, T., Peng, C.-I., Kono, Y., Oginuma, K., Mitsui, Y., & Setoguchi, H. (2010). Molecular phylogeny and habitat diversification of the genus Farfugium (Asteraceae) based on nuclear rDNA and plastid DNA. Annals of Botany, 106(3), 467–482. doi: 10.1093/aob/mcq139

Nosil, P., & Feder, J. L. (2013). Genome evolution and speciation: Toward quantitative descriptions of pattern and process. Evolution, 67(9), 2461–2467. doi: 10.1111/evo.12191

Oliver, K. R., McComb, J. A., & Greene, W. K. (2013). Transposable elements: Powerful contributors to angiosperm evolution and diversity. Genome Biology and Evolution, 5(10), 1886–1901. doi: 10.1093/gbe/evt141

Ong-Abdullah, M., Ordway, J. M., Jiang, N., Ooi, S., Kok, S.-Y., Sarpan, N., … Martienssen, R. A. (2015). Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm. Nature, 525(7570), 533–537. doi: 10.1038/nature15365

Paradis, E. (2010). pegas: An R package for population genetics with an integrated–modular approach. Bioinformatics, 26(3), 419–420. doi: 10.1093/bioinformatics/btp696

Paradis, E., & Schliep, K. (2019). ape 5.0: An environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics, 35(3), 526–528. doi: 10.1093/bioinformatics/bty633

Patro, R., Duggal, G., Love, M. I., Irizarry, R. A., & Kingsford, C. (2017). Salmon provides fast and bias-aware quantification of transcript expression. Nature Methods, 14(4), 417–419. doi: 10.1038/nmeth.4197

Peterson, B. K., Weber, J. N., Kay, E. H., Fisher, H. S., & Hoekstra, H. E. (2012). Double digest RADseq: An inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLOS ONE, 7(5), e37135. doi: 10.1371/journal.pone.0037135

Pritchard, J. K., Stephens, M., & Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics, 155(2), 945–959.

Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., … Sham, P. C. (2007). PLINK: A tool set for whole-genome association and population-based linkage analyses. The American Journal of Human Genetics, 81(3), 559–575. doi: 10.1086/519795

R Core Team. (2021). R: a language and environment for statistical computing. Vienna, Austria. Retrieved from https://www.r-project.org/

Ralph, P. L., & Coop, G. (2015). The role of standing variation in geographic convergent adaptation. The American Naturalist, 186(S1), S5–S23. doi: 10.1086/682948

Revell, L. J. (2012). phytools: An R package for phylogenetic comparative biology (and other things). Methods in Ecology and Evolution, 3(2), 217–223. doi: 10.1111/j.2041- 210X.2011.00169.x

Rieseberg, L. H., & Burke, J. M. (2001). The biological reality of species: Gene flow, selection, and collective evolution. TAXON, 50(1), 47–67. doi: 10.2307/1224511

Roda, F., Liu, H., Wilkinson, M. J., Walter, G. M., James, M. E., Bernal, D. M., … Ortiz‐Barrientos, D. (2013). Convergence and divergence during the adaptation to similar environments by an Australian groundsel. Evolution, 67(9), 2515–2529. doi: 10.1111/evo.12136

Roesti, M., Gavrilets, S., Hendry, A. P., Salzburger, W., & Berner, D. (2014). The genomic signature of parallel adaptation from shared genetic variation. Molecular Ecology, 23(16), 3944–3956. doi: 10.1111/mec.12720

Rosenblum, E. B., Römpler, H., Schöneberg, T., & Hoekstra, H. E. (2010). Molecular and functional basis of phenotypic convergence in white lizards at White Sands. Proceedings of the National Academy of Sciences, 107(5), 2113–2117. doi: 10.1073/pnas.0911042107

Rougemont, Q., Gagnaire, P.-A., Perrier, C., Genthon, C., Besnard, A.-L., Launey, S., & Evanno, G. (2017). Inferring the demographic history underlying parallel genomic divergence among pairs of parasitic and nonparasitic lamprey ecotypes. Molecular Ecology, 26(1), 142–162. doi: 10.1111/mec.13664

Saitou, N., & Nei, M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4(4), 406–425. doi: 10.1093/oxfordjournals.molbev.a040454

Sakaguchi, S., Horie, K., Kimura, T., Nagano, A. J., Isagi, Y., & Ito, M. (2018). Phylogeographic testing of alternative histories of single-origin versus parallel evolution of early flowering serpentine populations of Picris hieracioides L. (Asteraceae) in Japan. Ecological Research, 33(3), 537–547. doi: 10.1007/s11284-017-1536-2

Sakaguchi, S., & Ito, M. (2014). Development and characterization of EST-SSR markers for the Solidago virgaurea complex (Asteraceae) in the Japanese archipelago. Applications in Plant Sciences, 2(7), 1400035. doi: 10.3732/apps.1400035

Sakaguchi, S., Kimura, T., Kyan, R., Maki, M., Nishino, T., Ishikawa, N., … Ito, M. (2018). Phylogeographic analysis of the East Asian goldenrod (Solidago virgaurea complex, Asteraceae) reveals hidden ecological diversification with recurrent formation of ecotypes. Annals of Botany, 121(3), 489–500. doi: 10.1093/aob/mcx182

Sakata, Y., Kaneko, S., Hayano, A., Inoue-Murayama, M., Ohgushi, T., & Isagi, Y. (2013). Isolation and characterization of microsatellite loci in the invasive herb Solidago altissima (Asteraceae). Applications in Plant Sciences, 1(4), 1200313. doi: 10.3732/apps.1200313

Schluter, D. (1996). Adaptive radiation along genetic lines of least resistance. Evolution, 50(5), 1766–1774. doi: 10.1111/j.1558-5646.1996.tb03563.x

Schluter, D., & Conte, G. L. (2009). Genetics and ecological speciation. Proceedings of the National Academy of Sciences, 106(Supplement 1), 9955–9962. doi: 10.1073/pnas.0901264106

Semple, J. C. (2016). An intuitive phylogeny and summary of chromosome number variation in the goldenrod genus Solidago (Asteraceae: Astereae). Phytoneuron, 32, 1–9.

Semple, J. C., & Ohi-Toma, T. (2017). Typification of Solidago yokusaiana (Asteraceae: Astereae), a distinctive Japanese species. Phytoneuron, 16, 1–6.

Shaw, J., Lickey, E. B., Schilling, E. E., & Small, R. L. (2007). Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: The tortoise and the hare III. American Journal of Botany, 94(3), 275–288. doi: 10.3732/ajb.94.3.275

Sheldon, J. C., & Burrows, F. M. (1973). The dispersal effectiveness of the achene–pappus units of selected Compositae in steady winds with convection. New Phytologist, 72(3), 665–675. doi: 10.1111/j.1469-8137.1973.tb04415.x

Smouse, P. E., Long, J. C., & Sokal, R. R. (1986). Multiple regression and correlation extensions of the Mantel test of matrix correspondence. Systematic Zoology, 35(4), 627–632. JSTOR. doi: 10.2307/2413122

Sokal, R. R., & Michener, C. D. (1958). A statistical method for evaluating systematic relationships. Univ. Kansas, Sci. Bull., 38, 1409–1438.

Soneson, C., Love, M. I., & Robinson, M. D. (2016). Differential analyses for RNA-seq: Transcript- level estimates improve gene-level inferences. F1000Research, 4, 1521. doi: 10.12688/f1000research.7563.2

Specht, C. D., & Howarth, D. G. (2015). Adaptation in flower form: A comparative evodevo approach. New Phytologist, 206(1), 74–90. doi: 10.1111/nph.13198

Strimmer, K., & Pybus, O. G. (2001). Exploring the demographic history of DNA sequences using the generalized skyline plot. Molecular Biology and Evolution, 18(12), 2298–2305. doi: 10.1093/oxfordjournals.molbev.a003776

Trucchi, E., Frajman, B., Haverkamp, T. H. A., Schönswetter, P., & Paun, O. (2017). Genomic analyses suggest parallel ecological divergence in Heliosperma pusillum (Caryophyllaceae). New Phytologist, 216(1), 267–278. doi: 10.1111/nph.14722

Tsukaya, H. (2014). Comparative leaf development in angiosperms. Current Opinion in Plant Biology, 17, 103–109. doi: 10.1016/j.pbi.2013.11.012

van Steenis, C. (1981). Rheophytes of the world. Alpen aan den Rijn: Sijthoff and Noordhoff.

Welch, J. J., & Jiggins, C. D. (2014). Standing and flowing: The complex origins of adaptive variation. Molecular Ecology, 23(16), 3935–3937. doi: 10.1111/mec.12859

Wessinger, C. A., & Rausher, M. D. (2012). Lessons from flower colour evolution on targets of selection. Journal of Experimental Botany, 63(16), 5741–5749. doi: 10.1093/jxb/ers267

Yamagiwa, Y., Inagaki, Y., Ichinose, Y., Toyoda, K., Hyakumachi, M., & Shiraishi, T. (2011). Talaromyces wortmannii FS2 emits β-caryphyllene, which promotes plant growth and induces resistance. Journal of General Plant Pathology, 77(6), 336–341. doi: 10.1007/s10327-011-0340-z

Yashima, K., & Miyauchi, T. (1990). The Tsugaru land bridge problem related to Quaternary coastal tectonics, northeast Japan. The Quaternary Research (Daiyonki-Kenkyu), 29(3), 267–275. doi: 10.4116/jaqua.29.267

Yatabe, Y., Tsutsumi, C., Hirayama, Y., Mori, K., Murakami, N., & Kato, M. (2009). Genetic population structure of Osmunda japonica, rheophilous Osmunda lancea and their hybrids. Journal of Plant Research, 122(6), 585. doi: 10.1007/s10265-009-0254-4

Yin, Z., Zhang, H., Liu, M., Zhang, W., Song, H., Lan, H., … Liu, W. (2021). RabbitQC: High- speed scalable quality control for sequencing data. Bioinformatics, 37(4), 573–574. doi: 10.1093/bioinformatics/btaa719

Yoichi, W., Kawamata, I., Matsuki, Y., Suyama, Y., Uehara, K., & Ito, M. (2018). Phylogeographic analysis suggests two origins for the riparian azalea Rhododendron indicum (L.) Sweet. Heredity, 121(6), 594–604. doi: 10.1038/s41437-018-0064-3

Yoshimura, H., Arakaki, S., Hamagawa, M., Kitamura, Y., Yokota, M., & Denda, T. (2019). Differentiation of germination characteristics in Scutellaria rubropunctata (Lamiaceae) associated with adaptation to rheophytic habitats in the subtropical Ryukyu Islands of Japan. Journal of Plant Research, 132(3), 359–368. doi: 10.1007/s10265-019-01103-z

Yu, G., Wang, L.-G., Han, Y., & He, Q.-Y. (2012). clusterProfiler: An R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology, 16(5), 284–287. doi: 10.1089/omi.2011.0118

Yuan, J.-H., Cornille, A., Giraud, T., Cheng, F.-Y., & Hu, Y.-H. (2014). Independent domestications of cultivated tree peonies from different wild peony species. Molecular Ecology, 23(1), 82–95. doi: 10.1111/mec.12567

参考文献をもっと見る

全国の大学の
卒論・修論・学位論文
を
一発検索！

この論文の関連論文を見る