Porter ML, Blasic JR, Bok MJ, Cameron EG, Pringle T, Cronin TW, Robinson PR. Shedding new light on opsin evolution. Proc R Soc B Biol Sci. 2012;279(1726):3–14.
Article
Google Scholar
Cronin TW, Johnsen S, Marshall NJ, Warrant EJ. Visual ecology. Princeton: Princeton University Press; 2014.
Smith SO. Structure and activation of the visual pigment rhodopsin. Annu Rev Biophys. 2010;39:309–28.
Article
CAS
PubMed
Google Scholar
Ramirez MD, Pairett AN, Pankey MS, Serb JM, Speiser DI, Swafford AJ, Oakley TH. The last common ancestor of most bilaterian animals possessed at least nine opsins. Genome Biol Evol. 2016;8(12):3640–52.
CAS
PubMed
PubMed Central
Google Scholar
Land MF, Nilsson D-E. Animal eyes. Oxford: Oxford University Press; 2012.
Briscoe AD, Chittka L. The evolution of color vision in insects. Annu Rev Entomol. 2001;46(1):471–510.
Article
CAS
PubMed
Google Scholar
Futahashi R, Kawahara-Miki R, Kinoshita M, Yoshitake K, Yajima S, Arikawa K, Fukatsu T. Extraordinary diversity of visual opsin genes in dragonflies. Proc Natl Acad Sci. 2015;112(11):1247–56.
Article
CAS
Google Scholar
Lord NP, Plimpton RL, Sharkey CR, Suvorov A, Lelito JP, Willardson BM, Bybee SM. A cure for the blues: opsin duplication and subfunctionalization for short-wavelength sensitivity in jewel beetles (Coleoptera: Buprestidae). BMC Evol Biol. 2016;16(1):107.
Article
PubMed
PubMed Central
CAS
Google Scholar
Giraldo-Calderón GI, Zanis MJ, Hill CA. Retention of duplicated long-wavelength opsins in mosquito lineages by positive selection and differential expression. BMC Evol Biol. 2017;17(1):84.
Article
PubMed
PubMed Central
CAS
Google Scholar
Porter ML, Speiser DI, Zaharoff AK, Caldwell RL, Cronin TW, Oakley TH. The evolution of complexity in the visual systems of stomatopods: insights from transcriptomics. Oxford: Oxford University Press; 2013.
Google Scholar
Bracken-Grissom HD, DeLeo DM, Porter ML, Iwanicki T, Sickles J, Frank TM. Light organ photosensitivity in deep-sea shrimp may suggest a novel role in counterillumination. Sci Rep. 2020;10(1):4485.
Article
CAS
PubMed
PubMed Central
Google Scholar
DeLeo DM, Bracken-Grissom HD. Illuminating the impact of diel vertical migration on visual gene expression in deep-sea shrimp. Mol Ecol. 2020;29(18):3494–510.
Article
CAS
PubMed
Google Scholar
Wong JM, Pérez-Moreno JL, Chan T-Y, Frank TM, Bracken-Grissom HD. Phylogenetic and transcriptomic analyses reveal the evolution of bioluminescence and light detection in marine deep-sea shrimps of the family oplophoridae (crustacea: Decapoda). Mol Phylogenet Evol. 2015;83:278–92.
Article
CAS
PubMed
Google Scholar
Pérez-Moreno JL, Balázs G, Bracken-Grissom HD. Transcriptomic insights into the loss of vision in Molnár János Cave’s crustaceans. Integr Comp Biol. 2018;58(3):452–64.
Article
PubMed
CAS
Google Scholar
Pérez-Moreno JL, DeLeo DM, Palero F, Bracken-Grissom HD. Phylogenetic annotation and genomic architecture of opsin genes in Crustacea. Hydrobiologia. 2018;825(1):159–75.
Article
CAS
Google Scholar
Ramos AP, Gustafsson O, Labert N, Salecker I, Nilsson D-E, Averof M. Analysis of the genetically tractable crustacean Parhyale hawaiensis reveals the organisation of a sensory system for low-resolution vision. BMC Biol. 2019;17(1):67.
Article
PubMed
PubMed Central
CAS
Google Scholar
Sakamoto K, Hisatomi O, Tokunaga F, Eguchi E. Two opsins from the compound eye of the crab Hemigrapsus sanguineus. J Exp Biol. 1996;199(2):441–50.
Article
CAS
PubMed
Google Scholar
Regier JC, Shultz JW, Zwick A, Hussey A, Ball B, Wetzer R, Martin JW, Cunningham CW. Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. Nature. 2010;463(7284):1079–83.
Article
CAS
PubMed
Google Scholar
Schwentner M, Richter S, Rogers DC, Giribet G. Tetraconatan phylogeny with special focus on Malacostraca and Branchiopoda: highlighting the strength of taxon-specific matrices in phylogenomics. Proc R Soc B Biol Sci. 2018;285(1885):20181524.
Article
CAS
Google Scholar
Brandon CS, Greenwold MJ, Dudycha JL. Ancient and recent duplications support functional diversity of Daphnia opsins. J Mol Evol. 2017;84(1):12–28.
Article
CAS
PubMed
Google Scholar
Kashiyama K, Seki T, Numata H, Goto SG. Molecular characterization of visual pigments in Branchiopoda and the evolution of opsins in Arthropoda. Mol Biol Evol. 2009;26(2):299–311.
Article
CAS
PubMed
Google Scholar
Porter ML, Steck M, Roncalli V, Lenz PH. Molecular characterization of copepod photoreception. Biol Bull. 2017;233(1):96–110.
Article
CAS
PubMed
Google Scholar
Biscontin A, Frigato E, Sales G, Mazzotta GM, Teschke M, De Pittà C, Jarman S, Meyer B, Costa R, Bertolucci C. The opsin repertoire of the Antarctic krill Euphausia superba. Mar Genomics. 2016;29:61–8.
Article
PubMed
Google Scholar
Stern DB, Crandall KA. Phototransduction gene expression and evolution in cave and surface crayfishes. Integr Comp Biol. 2018;58(3):398–410.
Article
CAS
PubMed
Google Scholar
Poynton HC, Hasenbein S, Benoit JB, Sepulveda MS, Poelchau MF, Hughes DS, Murali SC, Chen S, Glastad KM, Goodisman MA, et al. The toxicogenome of Hyalella azteca: a model for sediment ecotoxicology and evolutionary toxicology. Environ Sci Technol. 2018;52(10):6009–22.
Article
CAS
PubMed
PubMed Central
Google Scholar
Carlini DB, Satish S, Fong DW. Parallel reduction in expression, but no loss of functional constraint, in two opsin paralogs within cave populations of Gammarus minus (Crustacea: Amphipoda). BMC Evol Biol. 2013;13(1):89.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bazikalova AY. Amphipods of Lake Baikal. Proc Baikal Limnol Stn. 1945;11:1–440.
Google Scholar
Panov VE, Berezina NA. Invasion history, biology and impacts of the Baikalian amphipod Gmelinoides fasciatus. In: Invasive aquatic species of Europe. Distribution, impacts and management. Berlin: Springer; 2002. pp. 96–103.
Porter ML, Awata H, Bok MJ, Cronin TW. Exceptional diversity of opsin expression patterns in Neogonodactylus oerstedii (stomatopoda) retinas. Proc Natl Acad Sci. 2020;117(16):8948–57.
Article
CAS
PubMed
PubMed Central
Google Scholar
Porter ML, Bok MJ, Robinson PR, Cronin TW. Molecular diversity of visual pigments in Stomatopoda (Crustacea). Vis Neurosci. 2009;26(3):255.
Article
PubMed
Google Scholar
Porter ML, Cronin TW, McClellan DA, Crandall KA. Molecular characterization of crustacean visual pigments and the evolution of pancrustacean opsins. Mol Biol Evol. 2007;24(1):253–68.
Article
CAS
PubMed
Google Scholar
Audzijonyte A, Pahlberg J, Viljanen M, Donner K, Väinölä R. Opsin gene sequence variation across phylogenetic and population histories in Mysis (Crustacea: Mysida) does not match current light environments or visual-pigment absorbance spectra. Mol Ecol. 2012;21(9):2176–96.
Article
CAS
PubMed
Google Scholar
Yuan J, Sun Y, Li S, Gao Y, Yu Y, Liu C, Wang Q, Lv X, Zhang X, Zhang X, et al. Penaeid shrimp genome provides insights into benthic adaptation and frequent molting. Nat Commun. 2019;10(1):1–14.
Article
CAS
Google Scholar
Lefébure T, Morvan C, Malard F, François C, Konecny-Dupré L, Weiss-Gayet M, Seguin-Orlando A, Ermini L, Der Sarkissian C, et al. Less effective selection leads to larger genomes. Genome Res. 2017;27(6):1016–28.
Article
PubMed
PubMed Central
CAS
Google Scholar
Arfianti T, Wilson S, Costello MJ. Progress in the discovery of amphipod crustaceans. PeerJ. 2018;6:5187.
Article
Google Scholar
Carlini DB, Fong DW. The transcriptomes of cave and surface populations of Gammarus minus (Crustacea: Amphipoda) provide evidence for positive selection on cave downregulated transcripts. PLoS One. 2017;12(10):0186173.
Article
CAS
Google Scholar
Sket B, Morino H, Tahkteev V, Rogers DC. Malacostraca: Amphipoda. In: Rogers, D.C. Thorp, J.H. editors. Thorp and Covich’s freshwater invertebrates, 4th edn. 2019; Amsterdam: Elsevier, pp. 808–835.
Martin P, Martens K, Goddeeris B. Oligochaeta from the abyssal zone of Lake Baikal (Siberia, Russia). Hydrobiologia. 1999;406:165–74.
Article
Google Scholar
Bowen BW, Forsman ZH, Whitney JL, Faucci A, Hoban M, Canfield SJ, Johnston EC, Coleman RR, Copus JM, Vicente J, et al. Species radiations in the sea: What the flock? J Heredity. 2020;111(1):70–83.
Article
Google Scholar
Sherbakov DY. Molecular phylogenetic studies on the origin of biodiversity in Lake Baikal. Trends Ecol Evol. 1999;14(3):92–5.
Article
Google Scholar
Cristescu ME, Adamowicz SJ, Vaillant JJ, Haffner DG. Ancient lakes revisited: from the ecology to the genetics of speciation. Mol Ecol. 2010;19(22):4837–51.
Article
PubMed
Google Scholar
Bowmaker J, Govardovskii V, Shukolyukov S, Zueva JL, Hunt D, Sideleva V, Smirnova O. Visual pigments and the photic environment: the cottoid fish of Lake Baikal. Vis Res. 1994;34(5):591–605.
Article
CAS
PubMed
Google Scholar
Hunt DM, Fitzgibbon J, Slobodyanyuk SJ, Bowmakers JK. Spectral tuning and molecular evolution of rod visual pigments in the species flock of cottoid fish in Lake Baikal. Vis Res. 1996;36(9):1217–24.
Article
CAS
PubMed
Google Scholar
Cowing JA, Poopalasundaram S, Wilkie SE, Bowmaker JK, Hunt DM. Spectral tuning and evolution of short wave-sensitive cone pigments in cottoid fish from Lake Baikal. Biochemistry. 2002;41(19):6019–25.
Article
CAS
PubMed
Google Scholar
Takhteev V, Levashkevich A, Govorukhina E. Effect of artificial illumination on the intensity of nocturnal vertical migrations of amphipods in Lake Baikal. Russ J Ecol. 2004;35(6):421–3.
Article
Google Scholar
Takhteev V, Karnaukhov DY, Govorukhina E, Misharin A. Diel vertical migrations of hydrobionts in the coastal area of Lake Baikal. Inland Water Biol. 2019;12(2):178–89.
Article
Google Scholar
Naumenko SA, Logacheva MD, Popova NV, Klepikova AV, Penin AA, Bazykin GA, Etingova AE, Mugue NS, Kondrashov AS, Yampolsky LY. Transcriptome-based phylogeny of endemic Lake Baikal amphipod species flock: fast speciation accompanied by frequent episodes of positive selection. Mol Ecol. 2017;26(2):536–53.
Article
CAS
PubMed
Google Scholar
Drozdova P, Rivarola-Duarte L, Bedulina D, Axenov-Gribanov D, Schreiber S, Gurkov A, Shatilina Z, Vereshchagina K, Lubyaga Y, Madyarova E, et al. Comparison between transcriptomic responses to short-term stress exposures of a common Holarctic and endemic Lake Baikal amphipods. BMC Genomics. 2019;20(1):712.
Article
PubMed
PubMed Central
CAS
Google Scholar
Bushmanova E, Antipov D, Lapidus A, Prjibelski AD. rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data. GigaScience. 2019;8(9):100.
Article
CAS
Google Scholar
Cogne Y, Degli-Esposti D, Pible O, Gouveia D, François A, Bouchez O, Eché C, Ford A, Geffard O, Armengaud J, et al. De novo transcriptomes of 14 gammarid individuals for proteogenomic analysis of seven taxonomic groups. Sci Data. 2019;6(1):184.
Article
PubMed
PubMed Central
CAS
Google Scholar
Consortium GRD, Baratti M, Cattonaro F, Di Lorenzo T, Galassi DMP, Iannilli V, Iannucci A, Jensen J, Larsen PF, Nielsen RO, et al. Genomic resources notes accepted 1 October 2014–30 November 2014. Mol Ecol Resour. 2015;15(2):458–9.
Article
Google Scholar
Truebano M, Tills O, Spicer JI. Embryonic transcriptome of the brackishwater amphipod Gammarus chevreuxi. Mar Genomics. 2016;28:5–6.
Article
PubMed
Google Scholar
Collins M, Tills O, Spicer JI, Truebano M. De novo transcriptome assembly of the amphipod Gammarus chevreuxi exposed to chronic hypoxia. Mar Genomics. 2017;33:17–9.
Article
Google Scholar
Kobayashi H, Nagahama T, Arai W, Sasagawa Y, Umeda M, Hayashi T, Nikaido I, Watanabe H, Oguri K, Kitazato H, et al. Polysaccharide hydrolase of the hadal zone amphipods Hirondellea gigas. Biosci Biotechnol Biochem. 2018;82(7):1123–33.
Article
CAS
PubMed
Google Scholar
Hiki K, Nakajima N, Watanabe H, Nakajima F, Tobino T. De novo transcriptome sequencing of an estuarine amphipod Grandidierella japonica exposed to zinc. Mar Genomics. 2018;39:11–4.
Article
Google Scholar
Hook SE, Twine NA, Simpson SL, Spadaro DA, Moncuquet P, Wilkins MR. 454 pyrosequencing-based analysis of gene expression profiles in the amphipod Melita plumulosa: transcriptome assembly and toxicant induced changes. Aquat Toxicol. 2014;153:73–88.
Article
CAS
PubMed
Google Scholar
O’Grady JF, Hoelters LS, Swain MT, Wilcockson DC. Identification and temporal expression of putative circadian clock transcripts in the amphipod crustacean Talitrus saltator. PeerJ. 2016;4:2555.
Article
CAS
Google Scholar
Weston DP, Poynton HC, Wellborn GA, Lydy MJ, Blalock BJ, Sepulveda MS, Colbourne JK. Multiple origins of pyrethroid insecticide resistance across the species complex of a nontarget aquatic crustacean, Hyalella azteca. Proc Natl Acad Sci. 2013;110(41):16532–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Christie AE, Cieslak MC, Roncalli V, Lenz PH, Major KM, Poynton HC. Prediction of a peptidome for the ecotoxicological model Hyalella azteca (Crustacea; Amphipoda) using a de novo assembled transcriptome. Mar Genomics. 2018;38:67–88.
Article
PubMed
Google Scholar
Hunt BJ, Mallon E, Rosato E. In silico identification of a molecular circadian system with novel features in the crustacean model organism Parhyale hawaiensis. Front Physiol. 2019;10:1325.
Article
PubMed
PubMed Central
Google Scholar
Jin S, Bian C, Jiang S, Sun S, Xu L, Xiong Y, Qiao H, Zhang W, You X, Li J, et al. Identification of candidate genes for the plateau adaptation of a Tibetan amphipod, Gammarus lacustris, through integration of genome and transcriptome sequencing. Front Genet. 2019;10:53.
Article
CAS
PubMed
PubMed Central
Google Scholar
Patra AK, Chung O, Yoo JY, Kim MS, Yoon MG, Choi J-H, Yang Y. First draft genome for the sand-hopper Trinorchestia longiramus. Sci Data. 2020;7(1):85.
Article
PubMed
PubMed Central
Google Scholar
Kang S, Kim S, Park H. Transcriptome of the Antarctic amphipod Gondogeneia antarctica and its response to pollutant exposure. Mar Genomics. 2015;24:253–4.
Article
PubMed
Google Scholar
Macdonald Iii KS, Yampolsky L, Duffy JE. Molecular and morphological evolution of the amphipod radiation of Lake Baikal. Mol Phylogenet Evol. 2005;35(2):323–43.
Article
CAS
Google Scholar
Moskalenko VN, Neretina TV, YAMPOLSKY LY. To the origin of lake baikal endemic gammarid radiations, with description of two new Eulimnogammarus spp. Zootaxa. 2020;4766(3):457–71.
Article
Google Scholar
Horton T, Lowry J, De Broyer C, Bellan-Santini D, Coleman CO, Corbari L, Costello MJ, Daneliya M, Dauvin J-C, Fišer C, Gasca R, Grabowski M, Guerra-García JM, Hendrycks E, Hughes L, Jaume D, Jazdzewski K, Kim Y-H, King R, Krapp-Schickel T, LeCroy S, Lörz A-N, Mamos T, Senna AR, Serejo C, Sket B, Souza-Filho JF. Tandberg A.H. Thomas J.D. Thurston M. Vader W. Väinölä R. Vonk R. White K. Zeidler W. World Amphipoda Database. Accessed through: World Register of Marine Species (2020). http://www.marinespecies.org/aphia.php?p=taxdetails&id=101411. Accessed 23 Jul 2020.
Board WE. World Register of Marine Species (WoRMS). 2017. http://www.marinespecies.org. Accessed 23 Jul 2020.
Hou Z, Sket B, Fišer C, Li S. Eocene habitat shift from saline to freshwater promoted Tethyan amphipod diversification. Proc Natl Acad Sci. 2011;108(35):14533–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hou Z, Sket B, Li S. Phylogenetic analyses of Gammaridae crustacean reveal different diversification patterns among sister lineages in the Tethyan region. Cladistics. 2014;30(4):352–65.
Article
PubMed
Google Scholar
Copilaş-Ciocianu D, Borko Š, Fišer C. The late blooming amphipods: global change promoted post-Jurassic ecological radiation despite Palaeozoic origin. Mol Phylogenet Evol. 2020;143:106664.
Article
PubMed
Google Scholar
Chen J, Liu H, Cai S, Zhang H. Comparative transcriptome analysis of Eogammarus possjeticus at different hydrostatic pressure and temperature exposures. Sci Rep. 2019;9(1):3456.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lan Y, Sun J, Tian R, Bartlett DH, Li R, Wong YH, Zhang W, Qiu JW, Xu T, He LS, et al. Molecular adaptation in the world’s deepest-living animal: insights from transcriptome sequencing of the hadal amphipod Hirondellea gigas. Mol Ecol. 2017;26(14):3732–43.
Article
CAS
PubMed
Google Scholar
Karnaukhov D, Biritskaya S, Teplykh M, Silenko N, Dolinskaya E, Silow E. The abundance and structure of population of pelagic amphipod Macrohectopus branickii in the coastal zone of Lake Baikal. Acta Biologica Sibirica. 2019;5(3):154–8.
Article
Google Scholar
Holmes SJ. Phototaxis in the Amphipoda. Am J Physiol Legacy Content. 1901;5(4):211–34.
Article
Google Scholar
Wolsky A, Huxley J. The reactions of normal and mutant types of Gammarus chevreuxi to light. J Exp Biol. 1932;9(4):427–40.
Article
Google Scholar
Bethel WM, Holmes JC. Altered evasive behavior and responses to light in amphipods harboring acanthocephalan cystacanths. J Parasitol. 1973;945–956:
Stom D, Zhdanova G, Saksonov M, Balayan A, Tolstoy MY. Light avoidance in Baikalian amphipods as a test response to toxicants. Contemp Probl Ecol. 2017;10(1):77–83.
Article
Google Scholar
Omasits U, Ahrens CH, Müller S, Wollscheid B. Protter: interactive protein feature visualization and integration with experimental proteomic data. Bioinformatics. 2014;30(6):884–6.
Article
CAS
PubMed
Google Scholar
Saito T, Koyanagi M, Sugihara T, Nagata T, Arikawa K, Terakita A. Spectral tuning mediated by helix iii in butterfly long wavelength-sensitive visual opsins revealed by heterologous action spectroscopy. Zool Lett. 2019;5(1):35.
Article
Google Scholar
Salcedo E, Zheng L, Phistry M, Bagg EE, Britt SG. Molecular basis for ultraviolet vision in invertebrates. J Neurosci. 2003;23(34):10873–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kingston AC, Cronin TW. Diverse distributions of extraocular opsins in crustaceans, cephalopods, and fish. Integr Comp Biol. 2016;56(5):820–33.
Article
CAS
PubMed
Google Scholar
Donohue MW, Carleton KL, Cronin TW. Opsin expression in the central nervous system of the mantis shrimp Neogonodactylus oerstedii. Biol Bull. 2017;233(1):58–69.
Article
CAS
PubMed
Google Scholar
Li F, Qiao H, Fu H, Sun S, Zhang W, Jin S, Jiang S, Gong Y, Xiong Y. Wu Y et al Identification and characterization of opsin gene and its role in ovarian maturation in the oriental river prawn Macrobrachium nipponense. Comp Biochem Physiol Part B Biochem Mol Biol. 2018;218:1–12.
Article
CAS
Google Scholar
Hampton SE, Galloway AW, Powers SM, Ozersky T, Woo KH, Batt RD, Labou SG, O’Reilly CM, Sharma S, Lottig NR, et al. Ecology under lake ice. Ecol Lett. 2017;20(1):98–111.
Article
PubMed
Google Scholar
Bradley RS, Zhisheng A. Environmental processes of East Eurasia: past, present, and future. Eos Trans Am Geophys Union. 2005;86(9):89–92.
Article
Google Scholar
Hunt DM, Fitzgibbon J, Slobodyanyuk SJ, Bowmaker JK, Dulai KS. Molecular evolution of the cottoid fish endemic to Lake Baikal deduced from nuclear DNA evidence. Mol Phylogenet Evol. 1997;8(3):415–22.
Article
CAS
PubMed
Google Scholar
Kontula T, Kirilchik SV, Väinölä R. Endemic diversification of the monophyletic cottoid fish species flock in Lake Baikal explored with mtDNA sequencing. Mol Phylogenet Evol. 2003;27(1):143–55.
Article
CAS
PubMed
Google Scholar
Mats V, Shcherbakov DY, Efimova I. Late cretaceous-cenozoic history of the Lake Baikal depression and formation of its unique biodiversity. Stratigr Geol Correl. 2011;19(4):404.
Article
Google Scholar
Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016;32(19):3047–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc. 2013;8(8):1494–512.
Article
CAS
PubMed
Google Scholar
Seppey M, Manni M, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness. In: Gene prediction. Berlin: Springer; 2019. pp. 227–245.
Speiser DI, Pankey MS, Zaharoff AK, Battelle BA, Bracken-Grissom HD, Breinholt JW, Bybee SM, Cronin TW, Garm A, Lindgren AR, et al. Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms. BMC Bioinform. 2014;15(1):350.
Article
Google Scholar
Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics. 2009;25(11):1422–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Huerta-Cepas J, Serra F, Bork P. ETE 3: reconstruction, analysis, and visualization of phylogenomic data. Mol Biol Evol. 2016;33(6):1635–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC Bioinform. 2009;10(1):421.
Article
CAS
Google Scholar
Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12(1):59–60.
Article
CAS
PubMed
Google Scholar
Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006;22(13):1658–9.
Article
CAS
PubMed
Google Scholar
Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012;28(23):3150–2.
Article
CAS
PubMed
PubMed Central
Google Scholar
Köster J, Rahmann S. Snakemake–a scalable bioinformatics workflow engine. Bioinformatics. 2012;28(19):2520–2.
Article
PubMed
CAS
Google Scholar
Mölder F, Jablonski KP, Letcher B, Hall MB, Tomkins-Tinch CH, Sochat V, Forster J, Lee S, Twardziok SO, Kanitz A, et al. Sustainable data analysis with snakemake. Research. 2021;10(33):33.
Google Scholar
Lechner M, Findeiß S, Steiner L, Marz M, Stadler PF, Prohaska SJ. Proteinortho: detection of (co-) orthologs in large-scale analysis. BMC Bioinform. 2011;12(1):124.
Article
Google Scholar
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772–80.
Article
CAS
PubMed
PubMed Central
Google Scholar
Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009;25(15):1972–3.
Article
PubMed
PubMed Central
CAS
Google Scholar
Nguyen L-T, Schmidt HA, Von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32(1):268–74.
Article
CAS
PubMed
Google Scholar
Kalyaanamoorthy S, Minh BQ, Wong TK, Von Haeseler A, Jermiin LS. Modelfinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 2017;14(6):587–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of phyml 3.0. Syst Biol. 2010;59(3):307–21.
Article
CAS
PubMed
Google Scholar
Anisimova M, Gil M, Dufayard J-F, Dessimoz C, Gascuel O. Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes. Syst Biol. 2011;60(5):685–99.
Article
PubMed
PubMed Central
Google Scholar
Revell LJ. phytools: An r package for phylogenetic comparative biology (and other things). Methods Ecol Evol. 2012;3:217–23.
Article
Google Scholar
Team R.C. et al. R: a language and environment for statistical computing. Vienna: Austria; 2019.
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357.
Article
CAS
PubMed
PubMed Central
Google Scholar
Löytynoja A. Phylogeny-aware alignment with PRANK. In: Multiple sequence alignment methods. Berlin: Springer; 2014. pp. 155–170.
Okonechnikov K, Golosova O, Fursov M, Team U. Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics. 2012;28(8):1166–7.
Golosova O, Henderson R, Vaskin Y, Gabrielian A, Grekhov G, Nagarajan V, Oler AJ, Quinones M, Hurt D, Fursov M, et al. Unipro UGENE NGS pipelines and components for variant calling. RNA-seq and ChIP-seq data analyses. PeerJ. 2014;2:644.
Article
Google Scholar
Shirley MD, Ma Z, Pedersen BS, Wheelan SJ. Efficient ”pythonic” access to FASTA files using pyfaidx. PeerJ PrePrints: Technical report; 2015.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078–9.
Article
PubMed
PubMed Central
CAS
Google Scholar
Shen W, Le S, Li Y, Hu F. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PloS One. 2016;11(10):0163962.
Google Scholar
Wickham H. Ggplot2: elegant graphics for data analysis. Berlin: Springer; 2016.
Makowski D. The psycho package: an efficient and publishing-oriented workflow for psychological science. J Open Source Softw. 2018;3(22):470.
Article
Google Scholar
Schliep K, Potts AA, Morrison DA, Grimm GW. Intertwining phylogenetic trees and networks. PeerJ Preprints: Technical report; 2016.
Yu G, Smith DK, Zhu H, Guan Y, Lam TT-Y. ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol Evol. 2017;8(1):28–36.
Article
Google Scholar
Yu G, Lam TT-Y, Zhu H, Guan Y. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Mol Biol Evol. 2018;35(12):3041–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Letunic I, Bork P. Interactive tree of life (itol) v4: recent updates and new developments. Nucleic Acids Res. 2019;47(W1):256–9.
Article
CAS
Google Scholar
Huson DH, Bryant D. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol. 2006;23(2):254–67.
Article
CAS
PubMed
Google Scholar
Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B, et al. Fiji: an open-source platform for biological-image analysis. Nat Methods. 2012;9(7):676–82.
Article
CAS
PubMed
Google Scholar
Schneider CA, Rasband WS, Eliceiri KW. NIH image to ImageJ: 25 years of image analysis. Nat Methods. 2012;9(7):671–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Drozdova P, Kizenko A, Saranchina A, Timofeyev M. The data from: the diversity of opsins in Lake Baikal Amphipods (Amphipoda: Gammaridae). Dryad Digital Repository. https://doi.org/10.5061/dryad.fj6q573r9.
Drozdova P, Kizenko A, Saranchina A. Timofeyev M. The data from: the diversity of opsins in Lake Baikal Amphipods (Amphipoda: Gammaridae). Harvard Dataverse. https://doi.org/10.7910/DVN/XG1BJC.