留言板

尊敬的读者、作者、审稿人, 关于本刊的投稿、审稿、编辑和出版的任何问题, 您可以本页添加留言。我们将尽快给您答复。谢谢您的支持!

姓名
邮箱
手机号码
标题
留言内容
验证码

Mitochondrial phylogenomics provides insights into the phylogeny and evolution of spiders (Arthropoda: Araneae)

Min Li Wen-Ting Chen Qi-Lin Zhang Min Liu Cheng-Wei Xing Ya Cao Fang-Zhen Luo Ming-Long Yuan

Min Li, Wen-Ting Chen, Qi-Lin Zhang, Min Liu, Cheng-Wei Xing, Ya Cao, Fang-Zhen Luo, Ming-Long Yuan. Mitochondrial phylogenomics provides insights into the phylogeny and evolution of spiders (Arthropoda: Araneae). Zoological Research, 2022, 43(4): 566-584. doi: 10.24272/j.issn.2095-8137.2021.418
Citation: Min Li, Wen-Ting Chen, Qi-Lin Zhang, Min Liu, Cheng-Wei Xing, Ya Cao, Fang-Zhen Luo, Ming-Long Yuan. Mitochondrial phylogenomics provides insights into the phylogeny and evolution of spiders (Arthropoda: Araneae). Zoological Research, 2022, 43(4): 566-584. doi: 10.24272/j.issn.2095-8137.2021.418

线粒体谱系基因组学为蜘蛛的系统发育与进化提供见解

doi: 10.24272/j.issn.2095-8137.2021.418

Mitochondrial phylogenomics provides insights into the phylogeny and evolution of spiders (Arthropoda: Araneae)

Funds: This study was supported by the Second Tibetan Plateau Scientific Expedition and Research (STEP) Program (2019QZKK0302), Natural Science Foundation of Gansu Province (20JR5RA252), and Innovation and Entrepreneurship Project of Lanzhou University (20210010020, 20210010002)
More Information
    Corresponding author: E-mail: yuanml@lzu.edu.cn
  • #Authors contributed equally to this work
  • 摘要: 蜘蛛是陆地生态系统中物种数量最丰富的捕食类群之一,其形态、生态和行为极具多样性。利用形态学和分子生物学数据,对蜘蛛系统发育及进化历史的已有研究取得了较大进展。该研究新测了8科23种蜘蛛的线粒体基因组,并基于29科78种蜘蛛的线粒体基因组数据对蜘蛛进行了线粒体谱系基因组学分析。中纺亚目保留了节肢动物祖先美洲鲎的基因排序,而后纺亚目(Opisthothelae)表现出频繁的线粒体基因重排,共发现12种基因重排模式。蜘蛛线粒体基因重排,仅涉及线粒体tRNA基因和控制区。蜘蛛线粒体tRNA基因长度极度缩短,导致缺失DHU臂或TΨC臂,使得tRNA基因表现出高度的结构多样性。特别是,trnS1的反密码子在蜘蛛的不同进化谱系中存在多样性。蜘蛛线粒体基因的进化速率可能与基因重排及tRNA长度的缩短有关。蜘蛛线粒体基因组序列及基因重排均包含有效的系统发育信号,且支持与先前研究相同的蜘蛛主要类群间的系统发育关系。系统发育分析结果表明,蜘蛛的每个亚目、每个下目、RTA类群及除盗蛛科外的12个科均为单系群。蜘蛛高阶元的系统发育关系为:(中纺亚目, (原蛛下目, (复杂生殖器类, (Synspermiata, 古筛蛛科))))。此外,该研究还确定了隆头蛛科、拟壁钱科和隐石蛛科等的系统进化位置。采用两种方法对蜘蛛结网性状进行祖先状态重建,获得了几乎一致的结果;蜘蛛的共同祖先可能是依靠洞口有丝的洞穴取食。该研究是迄今为止最大规模的蜘蛛线粒体谱系基因组学分析,强调了线粒体基因组数据在蜘蛛进化研究中的重要价值,不仅可为蜘蛛系统发育提供有效的系统发育信号,还可用于探讨蜘蛛进化的性状多样化过程。
    #Authors contributed equally to this work
  • Figure  1.  Phylogenetic relationships among 29 families within Araneae based on mitogenomic data

    A: Best phylogeny of Araneae inferred from amino acid sequences of 13 protein-coding genes using Bayesian inference (MrBayes) and maximum-likelihood (RAxML), summarized from Supplementary Figures S1A, F. The 13 arrangement modes (M1–M13) of mitochondrial genomes are mapped to the phylogenetic tree. B: Phylogenetic relationships within Clades A–C summarized from (1) Supplementary Figures S1D–E, Supplementary Figures S1G–H; (2) Supplementary Figure S1C; (3) Supplementary Figure S1B; (4) Supplementary Figures S1E, H; (5) Supplementary Figure S1D; (6) Supplementary Figure S1B; (7) Supplementary Figures S1B, C, D, G; and (8) Supplementary Figure S1H. See Supplementary Figure S1 for detailed information. Clade A includes six families: Salticidae, Selenopidae, Clubionidae, Miturgidae, Gnaphosidae, and Philodromidae. Clade B includes three families: Agelenidae, Sparassidae, and Cybaeidae. Clade C includes three families: Theraphosidae, Dipluridae, and Nemesiidae.

    Figure  5.  Ancestral state reconstruction of web type in spiders using Phytools

    Tree topology was the best phylogenetic tree obtained from Bayesian inference analysis using the 13P123AA dataset (see Supplementary Figure S1A). All reconstructed webs and divergence times of the main clades were mapped to the phylogenetic tree. Original divergence times are shown in Supplementary Figure S5. Original different web trait evolution results are shown in Supplementary Figure S6.

    Figure  2.  Evolution of gene rearrangement modes in spider mitogenomes

    Underlined genes are encoded in minor strand (N-strand). Different types of genes are marked with different colored backgrounds: tRNAs, bright yellow and blue; protein-coding genes (PCGs), pink and green; ribosomal genes (rRNAs) bright green; and control regions, red. PCGs and rRNAs are shown with standard abbreviations. The tRNA genes are abbreviated by one-letter amino acid codes, L1=CUN, L2=UUR, S1=AGN, and S2=UCN.

    Figure  3.  Pairwise correlation between the three gene arrangement distances (breakpoints (BP), rearrangement score (RS), and reversal distance (RD)) and evolutionary rates of mitochondrial genes

    Pairwise p-genetic distances were used for tRNAs, while ratio of nonsynonymous to synonymous substitutions of protein-coding genes was used for spider mitogenomes. Red horizontal line (P=0.05) indicates level of significance. Abbreviations of each mitochondrial gene are in Figure 2.

    Figure  4.  Secondary structures of tRNAs in spider mitogenomes

    A: Three types of tRNA structures inferred for spider mitogenomes. Left, tRNA representative that can form a typical cloverleaf secondary structure; Middle, tRNA representative that lacks TΨC arms in all spiders; Right, tRNA representative that lacks DHU arms in all spiders. Four bases A, T, G, and C are represented by green, red, black, and blue dots, respectively. Dashes (-) indicate Watson-Crick base pairing and yellow dots (•) indicate G-U base pairing. B: Three anticodons (typical TCT, uncommon CCT, and GCT) present in trnS1 of spider mitogenomes. Three bases marked in red are codons corresponding to anticodons of the species.

    Table  1.   Fossils used as calibrations and relevant settings for fossil calibrations in molecular dating analysis

    FamilyFossilMean age (Ma)Assignable toFossil source
    Attercopus fimbriungui380 (SD=0.05)Araneae stemSelden, 1996
    LiphistiidaePalaeothele montceauensis300 (SD=0.1)Mesothelae stemSelden & Gall, 1992
    HexathelidaeRosamygale grauvogeli260 (SD=0.1)Mygalomorphae stemSelden & Gall, 1992
    NemesiidaeCretamygale chasei168 (SD=0.4)Nemesiidae stemSelden, 2002
    OxyopidaeLinyphiinae’ indet135 (SD=0.2)Araneoidea stemPenney & Selden, 2002
    TheridiidaeCretotheridion inopinatum110 (SD=0.3)Theridiidae stemShi et al., 2012
    Ma: Million years ago. –: Not available.
    下载: 导出CSV
  • [1] Abascal F, Posada D, Zardoya R. 2012. The evolution of the mitochondrial genetic code in arthropods revisited. Mitochondrial DNA, 23(2): 84−91. doi: 10.3109/19401736.2011.653801
    [2] Arita M, Suematsu T, Osanai A, Inaba T, Kamiya H, Kita K, et al. 2006. An evolutionary 'intermediate state' of mitochondrial translation systems found in Trichinella species of parasitic nematodes: co-evolution of tRNA and EF-Tu. Nucleic Acids Research, 34(18): 5291−5299. doi: 10.1093/nar/gkl526
    [3] Arribas P, Andújar C, Lourdes Moraza M, Linard B, Emerson BC, Vogler AP. 2020. Mitochondrial metagenomics reveals the ancient origin and phylodiversity of soil mites and provides a phylogeny of the Acari. Molecular Biology and Evolution, 37(3): 683−694. doi: 10.1093/molbev/msz255
    [4] Babbucci M, Basso A, Scupola A, Patarnello T, Negrisolo E. 2014. Is it an ant or a butterfly? Convergent evolution in the mitochondrial gene order of Hymenoptera and Lepidoptera. Genome Biology and Evolution, 6(12): 3326−3343. doi: 10.1093/gbe/evu265
    [5] Ballesteros JA, Santibáñez-López CE, Baker CM, Benavides LR, Cunha TJ, Gainett G, et al. 2022. Comprehensive species sampling and sophisticated algorithmic approaches refute the monophyly of Arachnida. Molecular Biology and Evolution, 39(2): msac021. doi: 10.1093/molbev/msac021
    [6] Ballesteros JA, Sharma PP. 2019. A critical appraisal of the placement of Xiphosura (Chelicerata) with account of known sources of phylogenetic error. Systematic Biology, 68(6): 896−917. doi: 10.1093/sysbio/syz011
    [7] Bayer S, Schönhofer AL. 2013. Phylogenetic relationships of the spider family psechridae inferred from molecular data, with comments on the lycosoidea (Arachnida: Araneae). Invertebrate Systematics, 27(1): 53−80. doi: 10.1071/IS12017
    [8] Bernt M, Braband A, Schierwater B, Stadler PF. 2013a. Genetic aspects of mitochondrial genome evolution. Molecular Phylogenetics and Evolution, 69(2): 328−338. doi: 10.1016/j.ympev.2012.10.020
    [9] Bernt M, Donath A, Jühling F, Externbrink F, Florentz C, Fritzsch G, et al. 2013b. MITOS: improved de novo metazoan mitochondrial genome annotation. Molecular Phylogenetics and Evolution, 69(2): 313−319. doi: 10.1016/j.ympev.2012.08.023
    [10] Bernt M, Merkle D, Ramsch K, Fritzsch G, Perseke M, Bernhard D, et al. 2007. CREx: inferring genomic rearrangements based on common intervals. Bioinformatics, 23(21): 2957−2958. doi: 10.1093/bioinformatics/btm468
    [11] Blackledge TA, Kuntner M, Agnarsson I. 2011. The form and function of spider orb webs: evolution from silk to ecosystems. Advances in Insect Physiology, 41: 175−262.
    [12] Blackledge TA, Scharff N, Coddington JA, Szüts T, Wenzel JW, Hayashi CY, et al. 2009. Reconstructing web evolution and spider diversification in the molecular era. Proceedings of the National Academy of Sciences of the United States of America, 106(13): 5229−5234. doi: 10.1073/pnas.0901377106
    [13] Bond JE, Garrison NL, Hamilton CA, Godwin RL, Hedin M, Agnarsson I. 2014. Phylogenomics resolves a spider backbone phylogeny and rejects a prevailing paradigm for orb web evolution. Current Biology, 24(15): 1765−1771. doi: 10.1016/j.cub.2014.06.034
    [14] Boore JL. 1999. Animal mitochondrial genomes. Nucleic Acids Research, 27(8): 1767−1780. doi: 10.1093/nar/27.8.1767
    [15] Boore JL, Lavrov DV, Brown WM. 1998. Gene translocation links insects and crustaceans. Nature, 392(6677): 667−668. doi: 10.1038/33577
    [16] Bouckaert R, Vaughan TG, Barido-Sottani J, Duchêne S, Fourment M, Gavryushkina A, et al. 2019. BEAST 2.5: an advanced software platform for Bayesian evolutionary analysis. PLoS Computational Biology, 15(4): e1006650. doi: 10.1371/journal.pcbi.1006650
    [17] Cameron SL. 2014. Insect mitochondrial genomics: implications for evolution and phylogeny. Annual Review of Entomology, 59: 95−117. doi: 10.1146/annurev-ento-011613-162007
    [18] Chan PP, Lowe TM. 2019. tRNAscan-SE: searching for tRNA genes in genomic sequences. Methods in Molecular Biology, 1962: 1−14. doi: 10.1007/978-1-4939-9173-0_1
    [19] Chen YX, Chen YS, Shi CM, Huang ZB, Zhang Y, Li SK, et al. 2018. SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. GigaScience, 7(1): gix120.
    [20] Coddington JA. 2005. Phylogeny and classification of spiders. In: Ubick D, Paquin P, Cushing PE, Roth V. Spiders of North America: An Identification Manual. Washington: American Arachnological Society, 18–24.
    [21] Coddington JA, Agnarsson I, Hamilton CA, Bond JE. 2019. Spiders did not repeatedly gain, but repeatedly lost, foraging webs. PeerJ, 7: e6703. doi: 10.7717/peerj.6703
    [22] Coddington JA, Levi HW. 1991. Systematics and evolution of spiders (Araneae). Annual Review of Ecology and Systematics, 22: 565−592. doi: 10.1146/annurev.es.22.110191.003025
    [23] Coyle FA, Ketner ND. 1990. Observations on the prey and prey capture behaviour of the funnelweb mygalomorph spider genus Ischnothele (Araneae, Dipluridae). Bulletin of the British Arachnological Society, 8(4): 97−104.
    [24] Dai YT, Li H, Jiang P, Song F, Ye Z, Yuan XQ, et al. 2012. Sequence and organization of the mitochondrial genome of an urostylidid bug, Urochela quadrinotata Reuter (Hemiptera: Urostylididae). Entomotaxonomia, 34(4): 613−623. (in Chinese)
    [25] Dávila S, Piñero D, Bustos P, Cevallos MA, Dávila G. 2005. The mitochondrial genome sequence of the scorpion Centruroides limpidus (Karsch 1879) (Chelicerata; Arachnida). Gene, 360(2): 92−102. doi: 10.1016/j.gene.2005.06.008
    [26] Dierckxsens N, Mardulyn P, Smits G. 2017. NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Research, 45(4): e18.
    [27] Dimitrov D, Benavides LR, Arnedo MA, Giribet G, Griswold CE, Scharff N, et al. 2017. Rounding up the usual suspects: a standard target-gene approach for resolving the interfamilial phylogenetic relationships of ecribellate orb-weaving spiders with a new family-rank classification (Araneae, Araneoidea). Cladistics, 33(3): 221−250. doi: 10.1111/cla.12165
    [28] Dimitrov D, Hormiga G. 2021. Spider diversification through space and time. Annual Review of Entomology, 66: 225−241. doi: 10.1146/annurev-ento-061520-083414
    [29] Dimitrov D, Lopardo L, Giribet G, Arnedo MA, Álvarez-Padilla F, Hormiga G. 2012. Tangled in a sparse spider web: single origin of orb weavers and their spinning work unravelled by denser taxonomic sampling. Proceedings of the Royal Society B:Biological Sciences, 279(1732): 1341−1350. doi: 10.1098/rspb.2011.2011
    [30] Dowton M, Campbell NJH. 2001. Intramitochondrial recombination—is it why some mitochondrial genes sleep around?. Trends in Ecology and Evolution, 16(6): 269−271. doi: 10.1016/S0169-5347(01)02182-6
    [31] Drummond AJ, Suchard MA, Xie D, Rambaut A. 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution, 29(8): 1969−1973. doi: 10.1093/molbev/mss075
    [32] Duchêne AM, Pujol C, Maréchal-Drouard L. 2009. Import of tRNAs and aminoacyl-tRNA synthetases into mitochondria. Current Genetics, 55(1): 1−18. doi: 10.1007/s00294-008-0223-9
    [33] Eberhard W. 2020. Spider Webs: Behavior, Function, and Evolution. Chicago: University of Chicago Press.
    [34] Fernández R, Kallal RJ, Dimitrov D, Ballesteros JA, Arnedo MA, Giribet G, et al. 2018. Phylogenomics, diversification dynamics, and comparative transcriptomics across the spider tree of life. Current Biology, 28(9): 1489−1497.e5. doi: 10.1016/j.cub.2018.03.064
    [35] Foelix RF. 2011. Biology of Spiders. 3rd ed. New York: Oxford University Press.
    [36] Garb JE. 2013. Spider silk: an ancient biomaterial for the 21st century. In: Penney D. Spider Research in the 21st Century: Trends and Perspectives. Manchester: Siri Scientific Press, 252–281.
    [37] Garrison NL, Rodriguez J, Agnarsson I, Coddington JA, Griswold CE, Hamilton CA, et al. 2016. Spider phylogenomics: untangling the spider tree of life. PeerJ, 4: e1719. doi: 10.7717/peerj.1719
    [38] Giegé R, Jühling F, Pütz J, Stadler P, Sauter C, Florentz C. 2012. Structure of transfer RNAs: similarity and variability. WIREs RNA, 3(1): 37−61. doi: 10.1002/wrna.103
    [39] Gissi C, Iannelli F, Pesole G. 2008. Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species. Heredity, 101(4): 301−320. doi: 10.1038/hdy.2008.62
    [40] Greco G, Pugno NM. 2021. How spiders hunt heavy prey: the tangle web as a pulley and spider's lifting mechanics observed and quantified in the laboratory. Journal of the Royal Society Interface, 18(175): 20200907. doi: 10.1098/rsif.2020.0907
    [41] Griswold CE, Coddington JA, Platnick NI, Forster RR. 1999. Towards a phylogeny of entelegyne spiders (Araneae, Araneomorphae, Entelegynae). The Journal of Arachnology, 27(1): 53−63.
    [42] Griswold CE, Ramirez MJ, Coddington JA, Platnick NI. 2005. Atlas of phylogenetic data for entelegyne spiders (Araneae: Araneomorphae: Entelegynae) with comments on their phylogeny. Proceedings of the California Academy of Sciences, 56(S2): 1−324.
    [43] Haran J, Timmermans MJTN, Vogler AP. 2013. Mitogenome sequences stabilize the phylogenetics of weevils (Curculionoidea) and establish the monophyly of larval ectophagy. Molecular Phylogenetics and Evolution, 67(1): 156−166. doi: 10.1016/j.ympev.2012.12.022
    [44] Haupt J. 2005. Taxonomy of spiders. Toxin Reviews, 24(3-4): 249−256. doi: 10.1080/07313830500236101
    [45] Hawlena D, Schmitz OJ. 2010. Herbivore physiological response to predation risk and implications for ecosystem nutrient dynamics. Proceedings of the National Academy of Sciences of the United States of America, 107(35): 15503−15507. doi: 10.1073/pnas.1009300107
    [46] Hedin M, Derkarabetian S, Alfaro A, Ramírez MJ, Bond JE. 2019. Phylogenomic analysis and revised classification of atypoid mygalomorph spiders (Araneae, Mygalomorphae), with notes on arachnid ultraconserved element loci. PeerJ, 7: e6864. doi: 10.7717/peerj.6864
    [47] Hormiga G, Griswold CE. 2014. Systematics, phylogeny, and evolution of orb-weaving spiders. Annual Review of Entomology, 59: 487−512. doi: 10.1146/annurev-ento-011613-162046
    [48] Huang DY, Hormiga G, Cai CY, Su YT, Yin ZJ, Xia FY, et al. 2018. Origin of spiders and their spinning organs illuminated by mid-Cretaceous amber fossils. Nature Ecology & Evolution, 2(4): 623−627.
    [49] Ishikawa SA, Zhukova A, Iwasaki W, Gascuel O. 2019. A fast likelihood method to reconstruct and visualize ancestral scenarios. Molecular Biology and Evolution, 36(9): 2069−2085. doi: 10.1093/molbev/msz131
    [50] Jeyaprakash A, Hoy MA. 2007. The mitochondrial genome of the predatory mite Metaseiulus occidentalis (Arthropoda: Chelicerata: Acari: Phytoseiidae) is unexpectedly large and contains several novel features. Gene, 391(1-2): 264−274. doi: 10.1016/j.gene.2007.01.012
    [51] Jühling F, Pütz J, Bernt M, Donath A, Middendorf M, Florentz C, et al. 2012a. Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements. Nucleic Acids Research, 40(7): 2833−2845. doi: 10.1093/nar/gkr1131
    [52] Jühling F, Pütz J, Florentz C, Stadler PF. 2012b. Armless mitochondrial tRNAs in Enoplea (Nematoda). RNA Biology, 9(9): 1161−1166. doi: 10.4161/rna.21630
    [53] Jühling T, Duchardt-Ferner E, Bonin S, Wöhnert J, Pütz J, Florentz C, et al. 2018. Small but large enough: structural properties of armless mitochondrial tRNAs from the nematode Romanomermis culicivorax. Nucleic Acids Research, 46(17): 9170–9180.
    [54] Kallal RJ, Kulkarni SS, Dimitrov D, Benavides LR, Arnedo MA, Giribet G, et al. 2021. Converging on the orb: denser taxon sampling elucidates spider phylogeny and new analytical methods support repeated evolution of the orb web. Cladistics, 37(3): 298−316. doi: 10.1111/cla.12439
    [55] King GF, Hardy MC. 2013. Spider-venom peptides: structure, pharmacology, and potential for control of insect pests. Annual Review of Entomology, 58: 475−496. doi: 10.1146/annurev-ento-120811-153650
    [56] Kishino H, Hasegawa M. 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea. Journal of Molecular Evolution, 29(2): 170−179. doi: 10.1007/BF02100115
    [57] Kovoor J. 1987. Comparative structure and histochemistry of silk-producing organs in arachnids. In: Nentwig W. Ecophysiology of Spiders. Berlin, Heidelberg: Springer, 160–186.
    [58] Kulkarni S, Kallal RJ, Wood H, Dimitrov D, Giribet G, Hormiga G. 2021. Interrogating genomic-scale data to resolve recalcitrant nodes in the spider Tree of Life. Molecular Biology and Evolution, 38(3): 891−903. doi: 10.1093/molbev/msaa251
    [59] Kumar S, Stecher G, Li M, Knyaz C, Tamura K. 2018. MEGA X: molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution, 35(6): 1547−1549. doi: 10.1093/molbev/msy096
    [60] Kumar V, Tyagi K, Chakraborty R, Prasad P, Kundu S, Tyagi I, et al. 2020. The complete mitochondrial genome of endemic giant tarantula, Lyrognathus crotalus (Araneae: Theraphosidae) and comparative analysis. Scientific Reports, 10(1): 74−84. doi: 10.1038/s41598-019-57065-8
    [61] Kumazawa Y, Miura S, Yamada C, Hashiguchi Y. 2014. Gene rearrangements in gekkonid mitochondrial genomes with shuffling, loss, and reassignment of tRNA genes. BMC Genomics, 15(1): 930. doi: 10.1186/1471-2164-15-930
    [62] Kumazawa Y, Ota H, Nishida M, Ozawa T. 1998. The complete nucleotide sequence of a snake (Dinodon semicarinatus) mitochondrial genome with two identical control regions. Genetics, 150(1): 313−329. doi: 10.1093/genetics/150.1.313
    [63] Lanfear R, Frandsen PB, Wright AM, Senfeld T, Calcott B. 2017. Partitionfinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Molecular Biology and Evolution, 34(3): 772−773.
    [64] Lavrov DV, Brown WM, Boore JL. 2000. A novel type of RNA editing occurs in the mitochondrial tRNAs of the centipede Lithobius forficatus. Proceedings of the National Academy of Sciences of the United States of America, 97(25): 13738–13742.
    [65] Lavrov DV, Pett W, Voigt O, Wörheide G, Forget L, Lang BF, et al. 2013. Mitochondrial DNA of Clathrina clathrus (Calcarea, Calcinea): six linear chromosomes, fragmented rRNAs, tRNA editing, and a novel genetic code. Molecular Biology and Evolution, 30(4): 865−880. doi: 10.1093/molbev/mss274
    [66] Li F, Lv YY, Wen ZY, Bian C, Zhang XH, Guo ST, et al. 2021. The complete mitochondrial genome of the intertidal spider (Desis jiaxiangi) provides novel insights into the adaptive evolution of the mitogenome and the evolution of spiders. BMC Ecology and Evolution, 21(1): 72. doi: 10.1186/s12862-021-01803-y
    [67] Li H, Leavengood JM, Chapman EG, Burkhardt D, Song F, Jiang P, et al. 2017. Mitochondrial phylogenomics of Hemiptera reveals adaptive innovations driving the diversification of true bugs. Proceedings of the Royal Society B:Biological Sciences, 284(1862): 20171223. doi: 10.1098/rspb.2017.1223
    [68] Lonergan KM, Gray MW. 1993. Predicted editing of additional transfer RNAs in Acathamoeba castellanii mitochondria. Nucleic Acids Research, 21(18): 4402. doi: 10.1093/nar/21.18.4402
    [69] Lorenz C, Lünse CE, Mörl M. 2017. tRNA modifications: impact on structure and thermal adaptation. Biomolecules, 7(2): 35.
    [70] Lozano-Fernandez J, Tanner AR, Giacomelli M, Carton R, Vinther J, Edgecombe GD, et al. 2019. Increasing species sampling in chelicerate genomic-scale datasets provides support for monophyly of Acari and Arachnida. Nature Communications, 10(1): 2295. doi: 10.1038/s41467-019-10244-7
    [71] Lü L, Cai CY, Zhang X, Newton AF, Thayer MK, Zhou HZ. 2020. Linking evolutionary mode to palaeoclimate change reveals rapid radiations of staphylinoid beetles in low-energy conditions. Current Zoology, 66(4): 435−444. doi: 10.1093/cz/zoz053
    [72] Ludwig L, Barbour MA, Guevara J, Avilés L, González AL. 2018. Caught in the web: spider web architecture affects prey specialization and spider-prey stoichiometric relationships. Ecology and Evolution, 8(13): 6449−6462. doi: 10.1002/ece3.4028
    [73] Lunt DH, Hyman BC. 1997. Animal mitochondrial DNA recombination. Nature, 387(6630): 247. doi: 10.1038/387247a0
    [74] Magalhaes ILF, Azevedo GHF, Michalik P, Ramírez MJ. 2020. The fossil record of spiders revisited: implications for calibrating trees and evidence for a major faunal turnover since the Mesozoic. Biological Reviews, 95(1): 184−217. doi: 10.1111/brv.12559
    [75] Masta SE, Boore JL. 2004. The complete mitochondrial genome sequence of the spider Habronattus oregonensis reveals rearranged and extremely truncated tRNAs. Molecular Biology and Evolution, 21(5): 893−902. doi: 10.1093/molbev/msh096
    [76] Masta SE, Boore JL. 2008. Parallel evolution of truncated transfer RNA genes in arachnid mitochondrial genomes. Molecular Biology and Evolution, 25(5): 949−959. doi: 10.1093/molbev/msn051
    [77] Masta SE, McCall A, Longhorn SJ. 2010. Rare genomic changes and mitochondrial sequences provide independent support for congruent relationships among the sea spiders (Arthropoda, Pycnogonida). Molecular Phylogenetics and Evolution, 57(1): 59−70. doi: 10.1016/j.ympev.2010.06.020
    [78] Miller JA, Carmichael A, Ramírez MJ, Spagna JC, Haddad CR, Řezáč M, et al. 2010a. Phylogeny of entelegyne spiders: affinities of the family Penestomidae (NEW RANK), generic phylogeny of Eresidae, and asymmetric rates of change in spinning organ evolution (Araneae, Araneoidea, Entelegynae). Molecular Phylogenetics and Evolution, 55(3): 786−804. doi: 10.1016/j.ympev.2010.02.021
    [79] Miller MA, Pfeiffer WT, Schwartz T. 2010b. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In: Gateway Computing Environments Workshop (GCE). New Orleans: IEEE, 1–8.
    [80] Morley RJ. 2011. Cretaceous and Tertiary climate change and the past distribution of megathermal rainforests. In: Bush M, Flenley J, Gosling W. Tropical Rainforest Responses to Climatic Change. 2nd ed. Berlin: Springer, 1–34.
    [81] Ohtsuki T, Watanabe YI, Takemoto C, Kawai G, Ueda T, Kita K, et al. 2001. An "elongated" translation elongation factor Tu for truncated tRNAs in nematode mitochondria. Journal of Biological Chemistry, 276(24): 21571−21577. doi: 10.1074/jbc.M011118200
    [82] Paradis E. 2012. Analysis of Phylogenetics and Evolution with R. 2nd ed. New York: Springer.
    [83] Penney D, Selden PA. 2002. The oldest linyphiid spider, in Lower Cretaceous Lebanese amber (Araneae, Linyphiidae, Linyphiinae). The Journal of Arachnology, 30(3): 487−493. doi: 10.1636/0161-8202(2002)030[0487:TOLSIL]2.0.CO;2
    [84] Piacentini LN, Ramírez MJ. 2019. Hunting the wolf: a molecular phylogeny of the wolf spiders (Araneae, Lycosidae). Molecular Phylogenetics and Evolution, 136: 227−240. doi: 10.1016/j.ympev.2019.04.004
    [85] Platnick NI, Gertsch WJ. 1976. The Suborders of Spiders: a Cladistic Analysis (Arachnida, Araneae). New York: American Museum of Natural History.
    [86] Polotow D, Carmichael A, Griswold CE. 2015. Total evidence analysis of the phylogenetic relationships of Lycosoidea spiders (Araneae, Entelegynae). Invertebrate Systematics, 29(2): 124−163. doi: 10.1071/IS14041
    [87] Pons J, Bover P, Bidegaray-Batista L, Arnedo MA. 2019. Arm-less mitochondrial tRNAs conserved for over 30 millions of years in spiders. BMC Genomics, 20(1): 665. doi: 10.1186/s12864-019-6026-1
    [88] Qiu Y, Song DX, Zhou KY, Sun HY. 2005. The mitochondrial sequences of Heptathela hangzhouensis and Ornithoctonus huwena reveal unique gene arrangements and atypical tRNAs. Journal of Molecular Evolution, 60(1): 57−71. doi: 10.1007/s00239-004-0010-2
    [89] Ramírez MJ. 2014. The morphology and phylogeny of Dionychan spiders (Araneae: Araneomorphae). Bulletin of the American Museum of Natural History, 2014(390): 1−374.
    [90] Regier JC, Shultz JW, Zwick A, Hussey A, Ball B, Wetzer R, et al. 2010. Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. Nature, 463(7284): 1079−1083. doi: 10.1038/nature08742
    [91] Ren Y, Yu MJ, Low WY, Ruhlman TA, Hajrah NH, El Omri A, et al. 2020. Nucleotide substitution rates of diatom plastid encoded protein genes are positively correlated with genome architecture. Scientific Reports, 10(1): 14358. doi: 10.1038/s41598-020-71473-1
    [92] Revell LJ. 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
    [93] Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Hohna S, et al. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology, 61(3): 539−542. doi: 10.1093/sysbio/sys029
    [94] San Mauro D, Gower DJ, Zardoya R, Wilkinson M. 2006. A hotspot of gene order rearrangement by tandem duplication and random loss in the vertebrate mitochondrial genome. Molecular Biology and Evolution, 23(1): 227−234. doi: 10.1093/molbev/msj025
    [95] Schäffer S, Koblmüller S, Klymiuk I, Thallinger GG. 2018. The mitochondrial genome of the oribatid mite Paraleius leontonychus: new insights into tRNA evolution and phylogenetic relationships in acariform mites. Scientific Reports, 8(1): 7558. doi: 10.1038/s41598-018-25981-w
    [96] Segovia R, Pett W, Trewick S, Lavrov DV. 2011. Extensive and evolutionarily persistent mitochondrial tRNA editing in velvet worms (phylum Onychophora). Molecular Biology and Evolution, 28(10): 2873−2881. doi: 10.1093/molbev/msr113
    [97] Selden PA. 1996. First fossil mesothele spider, from the Carboniferous of France. Revue suisse de Zoologie, 2: 585−596.
    [98] Selden PA. 2002. First British mesozoic spider, from cretaceous amber of the isle of wight, southern England. Palaeontology, 45(5): 973−983. doi: 10.1111/1475-4983.00271
    [99] Selden PA, Gall JC. 1992. A Triassic mygalomorph spider from the northern Vosges, France. Palaeontology, 35: 211−235.
    [100] Selden PA, Penney D. 2010. Fossil spiders. Biological Reviews, 85(1): 171−206. doi: 10.1111/j.1469-185X.2009.00099.x
    [101] Selden PA, Shear WA, Bonamo PM. 1991. A spider and other arachnids from the Devonian of New York, and reinterpretations of Devonian Araneae. Palaeontology, 34: 241−281.
    [102] Sensenig A, Agnarsson I, Blackledge TA. 2010. Behavioural and biomaterial coevolution in spider orb webs. Journal of Evolutionary Biology, 23(9): 1839−1856. doi: 10.1111/j.1420-9101.2010.02048.x
    [103] Shao LL, Li SQ. 2018. Early Cretaceous greenhouse pumped higher taxa diversification in spiders. Molecular Phylogenetics and Evolution, 127: 146−155. doi: 10.1016/j.ympev.2018.05.026
    [104] Shao RF, Campbell NJH, Barker SC. 2001. Numerous gene rearrangements in the mitochondrial genome of the Wallaby Louse, Heterodoxus macropus (Phthiraptera). Molecular Biology and Evolution, 18(5): 858−865. doi: 10.1093/oxfordjournals.molbev.a003867
    [105] Shao RF, Dowton M, Murrell A, Barker SC. 2003. Rates of gene rearrangement and nucleotide substitution are correlated in the mitochondrial genomes of insects. Molecular Biology and Evolution, 20(10): 1612−1619. doi: 10.1093/molbev/msg176
    [106] Shao RF, Mitani H, Barker SC, Takahashi M, Fukunaga M. 2005. Novel mitochondrial gene content and gene arrangement indicate illegitimate inter-mtDNA recombination in the chigger mite. Leptotrombidium pallidum. Journal of Molecular Evolution, 60(6): 764−773. doi: 10.1007/s00239-004-0226-1
    [107] Sharma PP, Ballesteros JA, Santibáñez-López CE. 2021. What is an "Arachnid"? Consensus, consilience, and confirmation bias in the phylogenetics of chelicerata. Diversity, 13(11): 568. doi: 10.3390/d13110568
    [108] Shi GH, Grimaldi DA, Harlow GE, Wang J, Wang J, Yang MC, et al. 2012. Age constraint on Burmese amber based on U–Pb dating of zircons. Cretaceous Research, 37: 155−163. doi: 10.1016/j.cretres.2012.03.014
    [109] Shi W, Miao XG, Kong XY. 2014. A novel model of double replications and random loss accounts for rearrangements in the mitogenome of Samariscus latus (Teleostei: Pleuronectiformes). BMC Genomics, 15: 352. doi: 10.1186/1471-2164-15-352
    [110] Shimodaira H. 2002. An approximately unbiased test of phylogenetic tree selection. Systematic Biology, 51(3): 492−508. doi: 10.1080/10635150290069913
    [111] Shimodaira H, Hasegawa M. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution, 16(8): 1114−1114. doi: 10.1093/oxfordjournals.molbev.a026201
    [112] Song H, Sheffield NC, Cameron SL, Miller KB, Whiting MF. 2010. When phylogenetic assumptions are violated: base compositional heterogeneity and among-site rate variation in beetle mitochondrial phylogenomics. Systematic Entomology, 35(3): 429−448. doi: 10.1111/j.1365-3113.2009.00517.x
    [113] Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30(9): 1312−1313. doi: 10.1093/bioinformatics/btu033
    [114] Strimmer K, Rambaut A. 2002. Inferring confidence sets of possibly misspecified gene trees. Proceedings of the Royal Society B:Biological Sciences, 269(1487): 137−142. doi: 10.1098/rspb.2001.1862
    [115] Thao ML, Baumann L, Baumann P. 2004. Organization of the mitochondrial genomes of whiteflies, aphids, and psyllids (Hemiptera, Sternorrhyncha). BMC Evolutionary Biology, 4: 25. doi: 10.1186/1471-2148-4-25
    [116] Toft S. 2013. Nutritional aspects of spider feeding. In: Nentwig W. Spider Ecophysiology. Berlin, Heidelberg: Springer, 373–384.
    [117] Trifinopoulos J, Nguyen LT, von Haeseler A, Minh BQ. 2016. W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Research, 44(W1): W232−W235. doi: 10.1093/nar/gkw256
    [118] Tyagi K, Kumar V, Poddar N, Prasad P, Tyagi I, Kundu S, et al. 2020. The gene arrangement and phylogeny using mitochondrial genomes in spiders (Arachnida: Araneae). International Journal of Biological Macromolecules, 146: 488−496. doi: 10.1016/j.ijbiomac.2020.01.014
    [119] Vollrath F, Selden P. 2007. The role of behavior in the evolution of spiders, silks, and webs. Annual Review of Ecology, Evolution, and Systematics, 38: 819−846. doi: 10.1146/annurev.ecolsys.37.091305.110221
    [120] Wang B, Dunlop JA, Selden PA, Garwood RJ, Shear WA, Müller P, et al. 2018. Cretaceous arachnid Chimerarachne yingi gen. et sp. nov. illuminates spider origins. Nature Ecology & Evolution, 2(4): 614−622.
    [121] Wang Y, Li H, Wang P, Song F, Cai WZ. 2014. Comparative mitogenomics of plant bugs (Hemiptera: Miridae): identifying the AGG codon reassignments between serine and lysine. PLoS One, 9(7): e101375. doi: 10.1371/journal.pone.0101375
    [122] Warren JM, Sloan DB. 2021. Hopeful monsters: unintended sequencing of famously malformed mite mitochondrial tRNAs reveals widespread expression and processing of sense–antisense pairs. NAR Genomics and Bioinformatics, 3(1): lqaa111. doi: 10.1093/nargab/lqaa111
    [123] Watanabe YI, Suematsu T, Ohtsuki T. 2014. Losing the stem-loop structure from metazoan mitochondrial tRNAs and co-evolution of interacting factors. Frontiers in Genetics, 5: 109.
    [124] Wende S, Platzer EG, Jühling F, Pütz J, Florentz C, Stadler PF, et al. 2014. Biological evidence for the world's smallest tRNAs. Biochimie, 100: 151−158. doi: 10.1016/j.biochi.2013.07.034
    [125] Weng ML, Blazier JC, Govindu M, Jansen RK. 2014. Reconstruction of the ancestral plastid genome in Geraniaceae reveals a correlation between genome rearrangements, repeats, and nucleotide substitution rates. Molecular Biology and Evolution, 31(3): 645−659. doi: 10.1093/molbev/mst257
    [126] Wheeler WC, Coddington JA, Crowley LM, Dimitrov D, Goloboff PA, Griswold CE, et al. 2017. The spider tree of life: phylogeny of Araneae based on target-gene analyses from an extensive taxon sampling. Cladistics, 33(6): 574−616. doi: 10.1111/cla.12182
    [127] Wolfson AD, Khvorova AM, Sauter C, Florentz C, Giegé R. 1999. Mimics of yeast tRNAAsp and their recognition by aspartyl-tRNA synthetase. Biochemistry, 38(37): 11926−11932. doi: 10.1021/bi9908383
    [128] World Spider Catalog. 2022. World spider catalog. Version 23.0. Natural History Museum Bern,http://wsc.nmbe.ch.
    [129] Xia XH. 2013. DAMBE5: a comprehensive software package for data analysis in molecular biology and evolution. Molecular Biology and Evolution, 30(7): 1720−1728. doi: 10.1093/molbev/mst064
    [130] Xin X, Liu FX, Chen J, Ono H, Li DQ, Kuntner M. 2015. A genus-level taxonomic review of primitively segmented spiders (Mesothelae, Liphistiidae). ZooKeys, 488: 121−151. doi: 10.3897/zookeys.488.8726
    [131] Xu W, Jameson D, Tang B, Higgs PG. 2006. The relationship between the rate of molecular evolution and the rate of genome rearrangement in animal mitochondrial genomes. Journal of Molecular Evolution, 63(3): 375−392. doi: 10.1007/s00239-005-0246-5
    [132] Xue XF, Deng W, Qu SX, Hong XY, Shao RF. 2018. The mitochondrial genomes of sarcoptiform mites: are any transfer RNA genes really lost?. BMC Genomics, 19(1): 466. doi: 10.1186/s12864-018-4868-6
    [133] Xue XF, Guo JF, Dong Y, Hong XY, Shao RF. 2016. Mitochondrial genome evolution and tRNA truncation in Acariformes mites: new evidence from eriophyoid mites. Scientific Reports, 6: 18920. doi: 10.1038/srep18920
    [134] Yang ZH. 2007. PAML 4: phylogenetic analysis by Maximum Likelihood. Molecular Biology and Evolution, 24(8): 1586−1591. doi: 10.1093/molbev/msm088
    [135] Yokobori SI, Ueda T, Feldmaier-Fuchs G, Pääbo S, Ueshima R, Kondow A, et al. 1999. Complete DNA sequence of the mitochondrial genome of the Ascidian Halocynthia roretzi (Chordata, Urochordata). Genetics, 153(4): 1851−1862. doi: 10.1093/genetics/153.4.1851
    [136] Yuan ML, Wei DD, Wang BJ, Dou W, Wang JJ. 2010. The complete mitochondrial genome of the citrus red mite Panonychus citri (Acari: Tetranychidae): high genome rearrangement and extremely truncated tRNAs. BMC Genomics, 11: 597. doi: 10.1186/1471-2164-11-597
    [137] Yuan ML, Zhang LJ, Zhang QL, Zhang L, Li M, Wang XT, et al. 2020. Mitogenome evolution in ladybirds: potential association with dietary adaptation. Ecology and Evolution, 10(2): 1042−1053. doi: 10.1002/ece3.5971
    [138] Yuan ML, Zhang QL, Zhang L, Guo ZL, Liu YJ, Shen YY, et al. 2016. High-level phylogeny of the Coleoptera inferred with mitochondrial genome sequences. Molecular Phylogenetics and Evolution, 104: 99−111. doi: 10.1016/j.ympev.2016.08.002
    [139] Zhang B, Havird JC, Wang ED, Lv JL, Xu XN. 2021. Massive gene rearrangement in mitogenomes of phytoseiid mites. International Journal of Biological Macromolecules, 186: 33−39. doi: 10.1016/j.ijbiomac.2021.07.011
    [140] Zhang JF, Kan XZ, Miao GP, Hu SJ, Sun Q, Tian WD. 2020. qMGR: a new approach for quantifying mitochondrial genome rearrangement. Mitochondrion, 52: 20−23. doi: 10.1016/j.mito.2020.02.004
    [141] Zwick A, Regier JC, Zwickl DJ. 2012. Resolving discrepancy between nucleotides and amino acids in deep-level arthropod phylogenomics: differentiating serine codons in 21-amino-acid aodels. PLoS One, 7(11): e47450. doi: 10.1371/journal.pone.0047450
  • 加载中
图(5) / 表(1)
计量
  • 文章访问数:  544
  • HTML全文浏览量:  266
  • PDF下载量:  120
  • 被引次数: 0
出版历程
  • 收稿日期:  2022-02-27
  • 录用日期:  2022-05-25
  • 网络出版日期:  2022-05-27

目录

    /

    返回文章
    返回