Phylogenomic inference of the interrelationships of Lake Baikal sponges

References

• Addis, J. S., & Peterson, K. J. (2005). Phylogenetic relationships of freshwater sponges (Porifera, Spongillina) inferred from analyses of 18S rDNA, COI mtDNA, and ITS2 rDNA sequences. Zoologica Scripta, 34(6), 549–557. https://doi.org/10.1111/j.1463-6409.2005.00211.x
   Web of Science ®Google Scholar
• Andrews, S. (2010). FastQC: A quality control tool for high throughput sequence data [Internet]. Retrieved May 12, 2020, from http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
   Google Scholar
• Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics, 30(15), 2114–2120. https://doi.org/10.1093/bioinformatics/btu170
   PubMed Web of Science ®Google Scholar
• Buchfink, B., Xie, C., & Huson, D. H. (2015). Fast and sensitive protein alignment using DIAMOND. Nature Methods, 12(1), 59–60. https://doi.org/10.1038/nmeth.3176
   PubMed Web of Science ®Google Scholar
• Bukshuk, N. A., & Maikova, O. O. (2020). A new species of Baikal endemic sponges (Porifera, Demospongiae, Spongillida, Lubomirskiidae). ZooKeys, 906, 113–130. https://doi.org/10.3897/zookeys.906.39534
   PubMedGoogle Scholar
• Capella-Gutiérrez, S., Silla-Martínez, J. M., & Gabaldón, T. (2009). trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics, 25(15), 1972–1973. https://doi.org/10.1093/bioinformatics/btp348
   PubMed Web of Science ®Google Scholar
• Carballo, J. L., Cruz-Barraza, J. A., Yáñez, B., & Gómez, P. (2018). Taxonomy and molecular systematic position of freshwater genus Racekiela (Porifera: Spongillida) with the description of a new species from North-west Mexico. Systematics and Biodiversity, 16(2), 160–170. https://doi.org/10.1080/14772000.2017.1359216
   Web of Science ®Google Scholar
• Efremova, S. M. (2004). New genus and new species of sponges from family Lubomirskiidae Rezvoj, 1936. In O. A. Timoshkin (Ed.), Index of animal species inhabiting Lake Baikal and its catchment area, Vol. 1, Lake Baikal, Book 2 (pp. 1261–1278). Nauka.
   Google Scholar
• Efremova, S. M., Itskovich, V. B., Parfenova, V., Drucker, V. V., Müller, W. E., & Schröder, H. C. (2002). Lake Baikal: A unique place to study evolution of sponges and their stress response in an environment nearly unimpaired by anthropogenic perturbation. Cellular and Molecular Biology, 48(4), 359–371.
   PubMed Web of Science ®Google Scholar
• Emms, D. M., & Kelly, S. (2019). OrthoFinder: Phylogenetic orthology inference for comparative genomics. Genome Biology, 20(1), 1–14. https://doi.org/10.1186/s13059-019-1832-y
   PubMed Web of Science ®Google Scholar
• Erpenbeck, D., Breeuwer, J. A. J., Parra-Velandia, F. J., & Van Soest, R. W. M. (2006). Speculation with spiculation? – Three independent gene fragments and biochemical characters versus morphology in demosponge higher classification. Molecular Phylogenetics and Evolution, 38(2), 293–305. https://doi.org/10.1016/j.ympev.2005.11.001
   PubMed Web of Science ®Google Scholar
• Erpenbeck, D., Galitz, A., Wörheide, G., Albrecht, C., Pronzato, R., & Manconi, R. (2020). Having the balls to colonize – The Ephydatia fluviatilis group and the origin of (ancient) lake “endemic” sponge lineages. Journal of Great Lakes Research. https://doi.org/10.1016/j.jglr.2019.09.028
   Google Scholar
• Erpenbeck, D., Steiner, M., Schuster, A., Genner, M. J., Manconi, R., Pronzato, R., Ruthensteiner, B., van den Spiegel, D., van Soest, R. W., & Wörheide, G. (2019). Minimalist barcodes for sponges: A case study classifying African freshwater Spongillida. Genome, 62(1), 1–10. https://doi.org/10.1139/gen-2018-0098
   PubMed Web of Science ®Google Scholar
• Erpenbeck, D., Weier, T., De Voogd, N.J., Wörheide, G., Sutcliffe, P., Todd, J.A. and Michel, E. (2011). Insights into the evolution of freshwater sponges (Porifera: Demospongiae: Spongillina): Barcoding and phylogenetic data from Lake Tanganyika endemics indicate multiple invasions and unsettle existing taxonomy. Molecular Phylogenetics and Evolution, 61(1), 231–236.
   Google Scholar
• Fernandez-Valverde, S. L., Calcino, A. D., & Degnan, B. M. (2015). Deep developmental transcriptome sequencing uncovers numerous new genes and enhances gene annotation in the sponge Amphimedon queenslandica. BMC Genomics, 16(1), 387. https://doi.org/10.1186/s12864-015-1588-z
   PubMedGoogle Scholar
• Grabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D. A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R., Zeng, Q., Chen, Z., Mauceli, E., Hacohen, N., Gnirke, A., Rhind, N., di Palma, F., Birren, B. W., Nusbaum, C., Lindblad-Toh, K., Friedman, N., & Regev, A. (2011). Trinity: Reconstructing a full-length transcriptome without a genome from RNA-Seq data. Nature Biotechnology, 29(7), 644–652. https://doi.org/10.1038/nbt.1883
   PubMed Web of Science ®Google Scholar
• Guindon, S., Dufayard, J. F., Lefort, V., Anisimova, M., Hordijk, W., & Gascuel, O. (2010). New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0. Systematic Biology, 59(3), 307–321. https://doi.org/10.1093/sysbio/syq010
   PubMed Web of Science ®Google Scholar
• Itskovich, V. B. (2020). Intragenomic variation of rDNA internal transcribed spacers in the endemic Baikal sponge Lubomirskia baiсalensis: Implications for Porifera barcoding. Journal of Great Lakes Research, 46(1), 62–66. https://doi.org/10.1016/j.jglr.2019.10.009
   Web of Science ®Google Scholar
• Itskovich, V. B., Belikov, S. I., Efremova, S. M., & Masuda, Y. (1999). Phylogenetic relationships between Lubomirskiidae, Spongillidae and some marine sponges according partial sequences of 18S rRNA. Memoirs of the Queensland Museum, 44(1-2), 275–280.
   Google Scholar
• Itskovich, V., Glyzina, O., & Kaluzhnaya, O. (2017). Intraspecific and interspecific sequence variability in the ITS region of the rDNA of freshwater sponges of Lake Baikal and East Siberia. Inland Waters, 7(3), 259–266. https://doi.org/10.1080/20442041.2017.1320507
   Web of Science ®Google Scholar
• Itskovich, V., Gontcharov, A., Masuda, Y., Nohno, T., Belikov, S., Efremova, S., Meixner, M., & Janussen, D. (2008). Ribosomal ITS sequences allow resolution of freshwater sponge phylogeny with alignments guided by secondary structure prediction. Journal of Molecular Evolution, 67(6), 608–620. https://doi.org/10.1007/s00239-008-9158-5
   PubMed Web of Science ®Google Scholar
• Itskovich, V. B., Kaluzhnaya, O. V., & Belikov, S. I. (2013). Investigation of nuclear and mitochondrial DNA polymorphism in closely related species of endemic Baikal sponges. Russian Journal of Genetics, 49(8), 839–846. https://doi.org/10.1134/S1022795413080036
   Web of Science ®Google Scholar
• Itskovich, V. B., Kaluzhnaya, O. V., Veynberg, E., & Erpenbeck, D. (2015). Endemic Lake Baikal sponges from deep water. 1: Potential cryptic speciation and discovery of living species known only from fossils. Zootaxa, 3990(1), 123–137. https://doi.org/10.11646/zootaxa.3990.1.7
   PubMed Web of Science ®Google Scholar
• Katoh, K., Kuma, K. I., Toh, H., & Miyata, T. (2005). MAFFT version 5: Improvement in accuracy of multiple sequence alignment. Nucleic Acids Research, 33(2), 511–518. https://doi.org/10.1093/nar/gki198
   PubMed Web of Science ®Google Scholar
• Kenny, N. J., Francis, W. R., Rivera-Vicéns, R. E., Juravel, K., de Mendoza, A., Díez-Vives, C., Lister, R., Bezares-Calderon, L., Grombacher, L., Roller, M., Barlow, L. D., Camilli, S., Ryan, J. F., Wörheide, G., Hill, A. L., Riesgo, A., & Leys, S. P. (2020). Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri. Nature Communications, 11(1), 3676https://doi.org/10.1038/s41467-020-17397-w
   PubMed Web of Science ®Google Scholar
• Kenny, N. J., Plese, B., Riesgo, A., & Itskovich, V. B. (2019). Symbiosis, selection and novelty: Freshwater adaptation in the unique sponges of Lake Baikal. Molecular Biology and Evolution, 36(11), 2462–2480. https://doi.org/10.1093/molbev/msz151
   Web of Science ®Google Scholar
• Kocot, K. M., Citarella, M. R., Moroz, L. L., & Halanych, K. M. (2013). PhyloTreePruner: a phylogenetic tree-based approach for selection of orthologous sequences for phylogenomics. Evolutionary Bioinformatics, 9, EBO.S12813. https://doi.org/10.4137/EBO.S12813
   Web of Science ®Google Scholar
• Kück, P., & Longo, G. C. (2014). FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies. Frontiers in Zoology, 11(1), 81. https://doi.org/10.1186/s12983-014-0081-x
   PubMed Web of Science ®Google Scholar
• Lavrov, D. V., Maikova, O. O., Pett, W., & Belikov, S. I. (2012). Small inverted repeats drive mitochondrial genome evolution in Lake Baikal sponges. Gene, 505(1), 91–99. https://doi.org/10.1016/j.gene.2012.05.039
   PubMed Web of Science ®Google Scholar
• Le, S., & Gascuel, O. (2008). An improved general amino-acid replacement matrix. Molecular Biology and Evolution, 25(7), 1307–1320. https://doi.org/10.1093/molbev/msn067
   PubMed Web of Science ®Google Scholar
• Lefort, V., Longueville, J. E., & Gascuel, O. (2017). SMS: smart model selection in PhyML. Molecular Biology and Evolution, 34(9), 2422–2424. https://doi.org/10.1093/molbev/msx149
   PubMed Web of Science ®Google Scholar
• Maikova, O., Khanaev, I., Belikov, S., & Sherbakov, D. (2015). Two hypotheses of the evolution of endemic sponges in Lake Baikal (Lubomirskiidae). Journal of Zoological Systematics and Evolutionary Research, 53(2), 175–179. https://doi.org/10.1111/jzs.12086
   Web of Science ®Google Scholar
• Maikova, O., Sherbakov, D., & Belikov, S. (2016). The complete mitochondrial genome of Baikalospongia intermedia (Lubomirskiidae): Description and phylogenetic analysis. Mitochondrial DNA Part B, 1(1), 569–570. https://doi.org/10.1080/23802359.2016.1172273
   PubMed Web of Science ®Google Scholar
• Maikova, O. O., Bukshuk, N. A., Itskovich, V. B., Khanaev, I. V., Nebesnykh, I. A., Onishchuk, N. A., & Sherbakov, D. Y. (2017). Transformation of Baikal sponges (family Lubomirskiidae) after penetration into the Angara River. Russian Journal of Genetics, 53(12), 1343–1349. https://doi.org/10.1134/S1022795417120092
   Web of Science ®Google Scholar
• Meixner, M. J., Luter, C., Eckert, C., Itskovich, V., Janussen, D., von Rintelen, T., Bohne, A. V., Meixner, J. M., & Hess, W. R. (2007). Phylogenetic analysis of freshwater sponges provide evidence for endemism and radiation in ancient lakes. Molecular Phylogenetics and Evolution, 45(3), 875–886. https://doi.org/10.1016/j.ympev.2007.09.007
   PubMed Web of Science ®Google Scholar
• Morrow, C., & Cárdenas, P. (2015). Proposal for a revised classification of the Demospongiae (Porifera). Frontiers in Zoology, 12(1), 7. https://doi.org/10.1186/s12983-015-0099-8
   PubMedGoogle Scholar
• Naumenko, S. A., Logacheva, M. D., Popova, N. V., Klepikova, A. V., Penin, A. A., Bazykin, G. A., Etingova, A. E., Mugue, N. S., Kondrashov, A. S., & Yampolsky, L. Y. (2017). Transcriptome‐based phylogeny of endemic Lake Baikal amphipod species flock: Fast speciation accompanied by frequent episodes of positive selection. Molecular Ecology, 26(2), 536–553. https://doi.org/10.1111/mec.13927
   PubMed Web of Science ®Google Scholar
• Nguyen, L. T., Schmidt, H. A., von Haeseler, A., & Minh, B. Q. (2015). IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution, 32(1), 268–274. https://doi.org/10.1093/molbev/msu300
   PubMed Web of Science ®Google Scholar
• Philippe, H., Delsuc, F., Brinkmann, H., & Lartillot, N. (2005). Phylogenomics. Annual Review of Ecology, Evolution, and Systematics, 36(1), 541–562. https://doi.org/10.1146/annurev.ecolsys.35.112202.130205
   Google Scholar
• Pile, A. J., Patterson, M. R., Savarese, M., Chernykh, V. I., & Fialkov, V. A. (1997). Trophic effects of sponge feeding within Lake Baikal’s littoral zone: 2. Sponge abundance, diet, feeding efficiency, and carbon flux. Limnology and Oceanography, 42(1), 178–184. https://doi.org/10.4319/lo.1997.42.1.0178
   Web of Science ®Google Scholar
• Plese, B., Rossi, M. E., Kenny, N. J., Taboada, S., Koutsouveli, V., & Riesgo, A. (2019). Trimitomics: An efficient pipeline for mitochondrial assembly from transcriptomic reads in nonmodel species. Molecular Ecology Resources, 19(5), 1230–1239. https://doi.org/10.1111/1755-0998.13033
   PubMed Web of Science ®Google Scholar
• Qiu, F., Ding, S., Ou, H., Wang, D., Chen, J., & Miyamoto, M. M. (2015). Transcriptome changes during the life cycle of the red sponge, Mycale phyllophila (Porifera, Demospongiae, Poecilosclerida). Genes, 6(4), 1023–1052. https://doi.org/10.3390/genes6041023
   PubMed Web of Science ®Google Scholar
• Rambaut, A., Drummond, A. J., Xie, D., Baele, G., & Suchard, M. A. (2018). Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Systematic Biology, 67(5), 901–904. https://doi.org/10.1093/sysbio/syy032
   PubMed Web of Science ®Google Scholar
• Reid, P. J. W., Matveev, E., McClymont, A., Posfai, D., Hill, A. L., & Leys, S. P. (2018). Wnt signaling and polarity in freshwater sponges. BMC Evolutionary Biology, 18(1), 12.
   PubMedGoogle Scholar
• Riesgo, A., Farrar, N., Windsor, P. J., Giribet, G. and Leys, S. P. (2014). The analysis of eight transcriptomes from all poriferan classes reveals surprising genetic complexity in sponges. Molecular biology and evolution, 31(5), 1102–1120.
   Google Scholar
• Ronquist, F., & Huelsenbeck, J. P. (2003). MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19(12), 1572–1574. https://doi.org/10.1093/bioinformatics/btg180
   PubMed Web of Science ®Google Scholar
• Schröder, H. C., Efremova, S. M., Itskovich, V. B., Belikov, S., Masuda, Y., Krasko, A., Müller, I. M., & Müller, W. E. G. (2003). Molecular phylogeny of the freshwater sponges in Lake Baikal. Journal of Zoological Systematics and Evolutionary Research, 41(2), 80–86. https://doi.org/10.1046/j.1439-0469.2003.00199.x
   Web of Science ®Google Scholar
• Simao, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V., & Zdobnov, E. M. (2015). BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics, 31(19), 3210–3212. https://doi.org/10.1093/bioinformatics/btv351
   PubMed Web of Science ®Google Scholar
• Sokolova, A. M., Palatov, D. M., & Itskovich, V. B. (2020). Genetic analysis confirms the freshwater origin of the endemic Caspian sponges (Demospongiae, Spongillida, Metschnikowiidae). ZooKeys, 915, 1–16. https://doi.org/10.3897/zookeys.915.47460
   PubMedGoogle Scholar
• Timoshkin, O. A. (2001). Lake Baikal: Fauna diversity, problems of its immiscibility and origin, ecology and exotic communities. In O. A. Timoshkin (Eds.), Index of animal species inhabiting Lake Baikal and its catchment area. Nauka Publishers.
   Google Scholar
• Yakhnenko, A. S., & Itskovich, V. B. (2020). Analysis of the variability of mtDNA in closely related species of Baikalian sponges for the development of new barcoding markers. Limnology, 21(1), 49–57. https://doi.org/10.1007/s10201-019-00599-7
   Web of Science ®Google Scholar