References
Adamski Z, Bufo SA, Chowański S, et al. (2019) Beetles as model organisms in physiological, biomedical and environmental studies–a review. Frontiers in physiology 10 , 319.
Addo‐Bediako A, Chown S, Gaston K (2002) Metabolic cold adaptation in insects: a large‐scale perspective. Functional Ecology16 , 332-338.
Alfsnes K, Leinaas HP, Hessen DO (2017) Genome size in arthropods; different roles of phylogeny, habitat and life history in insects and crustaceans. Ecology and evolution 7 , 5939-5947.
Alqahtani F, Măndoiu I (2019) SMART2: Multi-library Statistical Mitogenome Assembly with Repeats, 184-198.
Altenhoff AM, Levy J, Zarowiecki M, et al. (2019) OMA standalone: orthology inference among public and custom genomes and transcriptomes.Genome Research 29 , 1152-1163.
Ammar E-D, Hogenhout SA (2006) Mollicutes associated with arthropods and plants. In: Insect Symbiosis, Volume 2 (eds. Bourtzis K, Miller TA), pp. 119-140. CRC press, Boca Raton.
Attygalle AB, Meinwald J, Eisner T (1992) Defensive secretion of a carabid beetle,Helluomorphoides clairvillei . Journal of Chemical Ecology 18 , 489-498.
Bale J (1987) Insect cold hardiness: freezing and supercooling—an ecophysiological perspective. Journal of Insect Physiology33 , 899-908.
Bale J (2002) Insects and low temperatures: from molecular biology to distributions and abundance. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 357 , 849-862.
Ballinger MJ, Perlman SJ (2019) The defensive Spiroplasma .Current Opinion in Insect Science 32 , 36-41.
Baust JG (1972) Insect Freezing Protection in Pterostichus brevicornis (Carabidae). Nature New Biology 236 , 219-221.
Behrensmeyer A, Turner A (2013) Taxonomic occurrences of Suidae recorded in the Paleobiology Database. Fossilworks.
Bernt M, Donath A, Jühling F, et al. (2013) MITOS: improved de novo metazoan mitochondrial genome annotation. Molecular Phylogenetics and Evolution 69 , 313-319.
Beutel RG, Haas F (2000) Phylogenetic relationships of the suborders of Coleoptera (Insecta). Cladistics 16 , 103-141.
Bishop TR, Robertson MP, Van Rensburg BJ, Parr CL (2017) Coping with the cold: minimum temperatures and thermal tolerances dominate the ecology of mountain ants. Ecological Entomology 42 , 105-114.
Blin K, Shaw S, Steinke K, et al. (2019) antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Research 47 , W81-W87.
Blommaert J (2020) Genome size evolution: towards new model systems for old questions. Proceedings of the Royal Society B 287 , 20201441.
Bouchard P, Smith AB, Douglas H, et al. (2017) Biodiversity of Coleoptera. Insect Biodiversity: Science and Society. John Wiley & Sons Ltd , 337-417.
Bray NL, Pimentel H, Melsted P, Pachter L (2016) Near-optimal probabilistic RNA-seq quantification. Nature Biotechnology34 , 525-527.
Brooks DR, Bater JE, Clark SJ, et al. (2012) Large carabid beetle declines in a United Kingdom monitoring network increases evidence for a widespread loss in insect biodiversity. Journal of Applied Ecology 49 , 1009-1019.
Buchfink B, Xie C, Huson DH (2015) Fast and sensitive protein alignment using DIAMOND. Nature Methods 12 , 59-60.
Bushnell B (2014) BBMap: a fast, accurate, splice-aware aligner. Lawrence Berkeley National Lab.(LBNL), Berkeley, CA (United States).
Butler D, Bahr BA (2006) Oxidative stress and lysosomes: CNS-related consequences and implications for lysosomal enhancement strategies and induction of autophagy. Antioxid Redox Signal 8 , 185-196.
Camacho C, Coulouris G, Avagyan V, et al. (2009) BLAST+: architecture and applications. BMC Bioinformatics 10 , 421.
Canapa A, Barucca M, Biscotti MA, Forconi M, Olmo E (2015) Transposons, genome size, and evolutionary insights in animals. Cytogenetic and Genome Research 147 , 217-239.
Canapa A, Biscotti M, Barucca M, et al. (2020) Shedding light upon the complex net of genome size, genome composition and environment in chordates. The European Zoological Journal 87 , 192-202.
Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T (2009) trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.Bioinformatics 25 , 1972-1973.
Chernov YI, Makarov K, Eremin P (2000) Family of ground beetles (Coleoptera, Carabidae) in the Arctic fauna: Communication 1.Entomological Review 80 , 1009-1021.
Cicconardi F, Krapf P, D’Annessa I, et al. (2020) Genomic signature of shifts in selection in a subalpine ant and its physiological adaptations. Molecular Biology and Evolution37 , 2211-2227.
Clark MS, Worland MR (2008) How insects survive the cold: molecular mechanisms—a review. Journal of Comparative Physiology B178 , 917-933.
Danks HV (1981) Arctic arthropods. A review of systematics and ecology with particular reference to the north American fauna.608 .
Danks HV (2005) Key themes in the study of seasonal adaptations in insects I. Patterns of cold hardiness. Applied Entomology and Zoology 40 , 199-211.
Danks HV, Smith AB, Foottit R, Adler P (2017) Insect biodiversity in the Nearctic region. Insect biodiversity science and society1 , 47-63.
Davidson NM, Oshlack A (2018) Necklace: combining reference and assembled transcriptomes for more comprehensive RNA-Seq analysis.Gigascience 7 , giy045.
Dennis AB, Dunning LT, Sinclair BJ, Buckley TR (2015) Parallel molecular routes to cold adaptation in eight genera of New Zealand stick insects.Scientific reports 5 , 13965-13965.
Duman JG (2001) Antifreeze and ice nucleator proteins in terrestrial arthropods. Annual Review of Physiology 63 , 327-357.
Ebbert MA, Nault LR (1994) Improved overwintering ability in Dalbulus maidis (Homoptera: Cicadellidae) vectors infected with Spiroplasma kunkelii (Mycoplasmatales: Spiroplasmataceae). Environmental Entomology 23 , 634-644.
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32 , 1792-1797.
Ehrlich PR, Raven PH (1964) Butterflies and plants: A study in coevolution. Evolution 18 , 586-608.
Enriquez T, Colinet H (2019) Cold acclimation triggers lipidomic and metabolic adjustments in the spotted wing drosophila. American Journal of Physiology - Regulatory, Integrative and Comparative Physiology 316 , R751-R763.
Erwin TL (1997) Biodiversity at its utmost: tropical forest beetles.Biodiversity II: understanding and protecting our biological resources , 27-40.
Farah CS, Miyamoto CA, Ramos C, et al. (1994) Structural and regulatory functions of the NH2-and COOH-terminal regions of skeletal muscle troponin I. Journal of Biological Chemistry 269 , 5230-5240.
Fishilevich E, Bowling AJ, Frey ML, et al. (2019) RNAi targeting of rootworm Troponin I transcripts confers root protection in maize.Insect Biochemistry and Molecular Biology 104 , 20-29.
Forbes AA, Bagley RK, Beer MA, Hippee AC, Widmayer HA (2018) Quantifying the unquantifiable: why Hymenoptera, not Coleoptera, is the most speciose animal order. BMC Ecology 18 , 21.
Francke W, Dettner K (2005) Chemical signalling in beetles. In:The chemistry of pheromones and other semiochemicals II , pp. 85-166. Springer.
Ganote C, Mendes F, Henschel R, Hahn M, Fulton B (2018) Introducing CAFE: Computational Analysis of (gene) Family Evolution.Bioinformatics 22 , 1269–1271.
Georgescu E, Rîșnoveanu L, Toader M, et al. (2017) Actual problems concerning protection of the wheat crops against cereal ground beetle (Zabrus tenebrioides Goeze) attack in south-east of the Romania. Scientific Papers-Series A, Agronomy 60 , 256-263.
Gerth M, Montoya HM, Ramirez P, et al. (2020) Rapid molecular evolution of Spiroplasma symbionts of Drosophila. BioRxiv .
Gharib WH, Robinson-Rechavi M (2013) The branch-site test of positive selection is surprisingly robust but lacks power under synonymous substitution saturation and variation in GC. Molecular Biology and Evolution 30 , 1675-1686.
Gosalvez J, López-Fernandez C, Esponda P (1980) Variability of the DNA content in five Orthopteran species. Caryologia 33 , 275-281.
Grimaldi D, Engel MS (2005) Evolution of the Insects Cambridge University Press.
Grissa I, Vergnaud G, Pourcel C (2007) CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats.Nucleic Acids Research 35 , W52-W57.
Gurevich A, Saveliev V, Vyahhi N, Tesler G (2013) QUAST: quality assessment tool for genome assemblies. Bioinformatics29 , 1072-1075.
Gustafson GT, Baca SM, Alexander AM, Short AE (2019) Phylogenomic analysis of the beetle suborder Adephaga with comparison of tailored and generalized ultraconserved element probe performance. Systematic Entomology .
Haas BJ, Papanicolaou A, Yassour M, et al. (2013) De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nature protocols8 , 1494.
Haas BJ, Salzberg SL, Zhu W, et al. (2008) Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biology 9 , R7.
Haghshenas E, Asghari H, Stoye J, Chauve C, Hach F (2020) HASLR: Fast Hybrid Assembly of Long Reads. iScience 23 , 101389.
Harumoto T, Lemaitre B (2018) Male-killing toxin in a bacterial symbiont of Drosophila . Nature 557 , 252-255.
Haselkorn TS, Jaenike J (2015) Macroevolutionary persistence of heritable endosymbionts: acquisition, retention and expression of adaptive phenotypes in Spiroplasma . Molecular Ecology24 , 3752-3765.
Hoff KJ, Lomsadze A, Borodovsky M, Stanke M (2019) Whole-genome annotation with BRAKER. Methods in Molecular Biology1962 , 65-95.
Holmstrup M, Hedlund K, Boriss H (2002) Drought acclimation and lipid composition in Folsomia candida : implications for cold shock, heat shock and acute desiccation stress. journal of insect physiology 48 , 961-970.
Hozza M, Vinař T, Brejová B (2015) How big is that genome? Estimating genome size and coverage from k-mer abundance spectra, 199-209.
Hu L, Zhao T, Pan Y (2020) Spinicaudatans from the Yixian Formation (Lower Cretaceous) and the Daohugou Beds (Jurassic) of Western Liaoning, China. Cretaceous Research 105 , 104073.
Humann JL, Lee T, Ficklin S, Main D (2019) Structural and functional annotation of eukaryotic genomes with GenSAS. In: Gene Prediction , pp. 29-51. Springer.
Jiang Z, Hu Z, Zeng L, et al. (2011) The role of the Golgi apparatus in oxidative stress: is this organelle less significant than mitochondria? Free Radical Biology and Medicine 50 , 907-917.
Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30 , 772-780.
Kavanaugh DH (1985) On wing atrophy in carabid beetles (Coleoptera: Carabidae), with special reference to Nearctic Nebria . In:Series Entomologica (Dordrecht) (ed. Ball GE), pp. 408-431. Dr W. Junk Publishers, Dordrecht.
Kelley JL, Peyton JT, Fiston-Lavier A-S, et al. (2014) Compact genome of the Antarctic midge is likely an adaptation to an extreme environment. Nature Communications 5 , 1-8.
Khani A, Moharramipour S, Barzegar M (2007) Cold tolerance and trehalose accumulation in overwintering larvae of the codling moth, Cydia pomonella (Lepidoptera: Tortricidae). European Journal of Entomology 104 , 385.
Kim D, Langmead B, Salzberg SL (2015) HISAT: a fast spliced aligner with low memory requirements. Nature methods 12 , 357.
Kim S, Oh M, Jung W, et al. (2017) Genome sequencing of the winged midge, Parochlus steinenii , from the Antarctic Peninsula.Gigascience 6 , 1-8.
Kimura MT (2004) Cold and heat tolerance of drosophilid flies with reference to their latitudinal distributions. Oecologia140 , 442-449.
Kirejtshuk A, Moseyko A, Ren D (2015) Mesozoic leaf beetles of the tribe Mesolpinini trib. nov.(Coleoptera, Chrysomelidae) from the Lower Cretaceous. Paleontological Journal 49 , 1424-1435.
Kirejtshuk AG (2020) Taxonomic review of fossil Coleopterous families (Insecta, Coleoptera). Suborder Archostemata: Superfamilies Coleopseoidea and Cupedoidea. Geosciences 10 , 73.
Kolde R, Kolde MR (2015) Package ‘pheatmap’. R Package1 , 790.
Koren S, Walenz BP, Berlin K, et al. (2017) Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Research 27 , 722-736.
Kotze DJ, Brandmayr P, Casale A, et al. (2011) Forty years of carabid beetle research in Europe–from taxonomy, biology, ecology and population studies to bioindication, habitat assessment and conservation. ZooKeys , 55.
Krzyżowski M, Francikowski J, Baran B, Babczyńska A (2020) The short-chain fatty acids as potential protective agents against Callosobruchus maculatus infestation. Journal of Stored Products Research 86 , 101570.
Kuznetsova I, Lugmayr A, Siira SJ, Rackham O, Filipovska A (2019) CirGO: an alternative circular way of visualising gene ontology terms.BMC Bioinformatics 20 , 1-7.
Laetsch DR, Blaxter ML (2017) BlobTools: Interrogation of genome assemblies. F1000Research 6 , 1287.
Lalouette L, Williams CM, Hervant F, Sinclair BJ, Renault D (2011) Metabolic rate and oxidative stress in insects exposed to low temperature thermal fluctuations. Comparative Biochemistry and Physiology - Part A Molecular & Integrative Physiology 158 , 229-234.
Li H (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint arXiv:1303.3997 .
Li H (2018) Minimap2: pairwise alignment for nucleotide sequences.Bioinformatics 34 , 3094-3100.
Li H, Handsaker B, Wysoker A, et al. (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25 , 2078-2079.
Linard B, Arribas P, Andújar C, Crampton‐Platt A, Vogler AP (2016) Lessons from genome skimming of arthropod‐preserving ethanol.Molecular Ecology Resources 16 , 1365-1377.
Lomsadze A, Ter-Hovhannisyan V, Chernoff YO, Borodovsky M (2005) Gene identification in novel eukaryotic genomes by self-training algorithm.Nucleic Acids Research 33 , 6494-6506.
López-López A, Vogler AP (2017) The mitogenome phylogeny of Adephaga (Coleoptera). Molecular Phylogenetics and Evolution 114 , 166-174.
Lorenz W (2020) CarabCat: Global database of ground beetles. In:Species 2000 & ITIS Catalogue of Life, 2020-12-01 eds. Roskov Y, Ower G, Orrell T, et al. ). Species 2000: Naturalis, Leiden, the Netherlands.
Lower SS, Johnston JS, Stanger-Hall KF, et al. (2017) Genome size in North American fireflies: substantial variation likely driven by neutral processes. Genome Biology and Evolution 9 , 1499-1512.
Lubawy J, Urbański A, Colinet H, Pflüger HJ, Marciniak P (2020) Role of the Insect Neuroendocrine System in the Response to Cold Stress.Frontiers in Physiology 11 , 376.
Lundgren JG, Lehman RM, Chee-Sanford J (2007) Bacterial communities within digestive tracts of ground beetles (Coleoptera: Carabidae).Annals of the Entomological Society of America 100 , 275-282.
Lyzenga WJ, Stone SL (2012) Abiotic stress tolerance mediated by protein ubiquitination. Journal of Experimental Botany 63 , 599-616.
MacMillan HA, Findsen A, Pedersen TH, Overgaard J (2014) Cold-induced depolarization of insect muscle: differing roles of extracellular K+ during acute and chronic chilling. Journal of Experimental Biology 217 , 2930-2938.
Malhotra JD, Kaufman RJ (2007) Endoplasmic reticulum stress and oxidative stress: a vicious cycle or a double-edged sword?Antioxidants & redox signaling 9 , 2277-2294.
Mani MS (1968) Ecology and Biogeography of High Altitude InsectsDr. W. Junk N.V. Publishers, The Hague.
Marcais G, Kingsford C (2011) A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics27 , 764-770.
McDaniel EA, Anantharaman K, McMahon K (2019) metabolisHMM: Phylogenomic analysis for exploration of microbial phylogenies and metabolic pathways. bioRxiv .
McKenna A, Hanna M, Banks E, et al. (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research 20 , 1297-1303.
McKenna DD (2018) Beetle genomes in the 21st century: prospects, progress and priorities. Curr Opin Insect Sci 25 , 76-82.
McKenna DD, Shin S, Ahrens D, et al. (2019) The evolution and genomic basis of beetle diversity. Proceedings of the National Academy of Sciences 116 , 24729-24737.
McManus R, Ravenscraft A, Moore W (2018) Bacterial associates of a gregarious riparian beetle with explosive defensive chemistry.Frontiers in microbiology 9 , 2361.
Medina P, Russell SL, Corbett-Detig R (2019) Deep data mining reveals variable abundance and distribution of microbial reproductive manipulators within and among diverse host species. bioRxiv , 679837.
Mehmood A, Laiho A, Venäläinen MS, et al. (2019) Systematic evaluation of differential splicing tools for RNA-seq studies.Brief Bioinform .
Menzel P, Ng KL, Krogh A (2016) Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nature communications7 , 1-9.
Miller IJ, Rees ER, Ross J, et al. (2019) Autometa: automated extraction of microbial genomes from individual shotgun metagenomes.Nucleic Acids Research 47 , e57-e57.
Misof B, Liu S, Meusemann K, et al. (2014) Phylogenomics resolves the timing and pattern of insect evolution. Science 346 , 763-767.
Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M (2007) KAAS: an automatic genome annotation and pathway reconstruction server.Nucleic Acids Res 35 , W182-185.
Nagy L, Grabherr G (2009) The biology of alpine habitats Oxford University Press.
Neven LG, Duman JG, Low MG, Sehl LC, Castellino FJ (1989) Purification and characterization of an insect hemolymph lipoprotein ice nucleator: evidence for the importance of phosphatidylinositol and apolipoprotein in the ice nucleator activity. Journal of Comparative Physiology B 159 , 71-82.
O’Donovan C, Martin MJ, Gattiker A, et al. (2002) High-quality protein knowledge resource: SWISS-PROT and TrEMBL. Briefings in bioinformatics 3 , 275-284.
O’Leary NA, Wright MW, Brister JR, et al. (2016) Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res 44 , D733-745.
Overgaard J, MacMillan HA (2017) The integrative physiology of insect chill tolerance. Annual Review of Physiology 79 , 187-208.
Palmer DH, Rogers TF, Dean R, Wright AE (2019) How to identify sex chromosomes and their turnover. Molecular Ecology 28 , 4709-4724.
Parker DJ, Wiberg RAW, Trivedi U, et al. (2018) Inter and intraspecific genomic divergence in Drosophila montana shows evidence for cold adaptation. Genome Biology and Evolution10 , 2086-2101.
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW (2015) CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Research25 , 1043-1055.
Pascua-Maestro R, Diez-Hermano S, Lillo C, Ganfornina MD, Sanchez D (2017) Protecting cells by protecting their vulnerable lysosomes: Identification of a new mechanism for preserving lysosomal functional integrity upon oxidative stress. PLoS Genet 13 , e1006603.
Pflug JM, Holmes VR, Burrus C, Johnston JS, Maddison DR (2020) Measuring genome sizes using read-depth, k-mers, and flow cytometry: methodological comparisons in beetles (Coleoptera). G3 (Bethesda)10 , 3047-3060.
Picard (2018) Picard toolkit. Broad Institute, GitHub repository, http://broadinstitute.github.io/picard/.
Pivovarov AS, Calahorro F, Walker RJ (2019) Na+/K+-pump and neurotransmitter membrane receptors. Invertebrate Neuroscience19 , 1.
Pizzolotto R, Mazzei A, Bonacci T, et al. (2018) Ground beetles in Mediterranean olive agroecosystems: Their significance and functional role as bioindicators (Coleoptera, Carabidae). PLoS ONE13 , e0194551.
Poplin R, Ruano-Rubio V, DePristo MA, et al. (2017) Scaling accurate genetic variant discovery to tens of thousands of samples.bioRxiv , 201178.
Quesneville H (2015) Impact of transposable elements on insect genomes and biology. Current Opinion in Insect Science 7 , 1-7.
Ranallo-Benavidez TR, Jaron KS, Schatz MC (2020) GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes.Nature Communications 11 , 1432.
Rapaport F, Khanin R, Liang Y, et al. (2013) Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data. Genome Biology 14 , 1-13.
Rastogi A, Gupta D (2014) GFF-Ex: a genome feature extraction package.BMC Research Notes 7 , 315.
Receveur JP, Fenoglio S, Benbow ME (2020) Insect-associated bacterial communities in an alpine stream. Hydrobiologia 847 , 331-344.
Ritchie H, Jamieson AJ, Piertney SB (2017) Genome size variation in deep-sea amphipods. Royal Society Open Science 4 , 170862.
Ritchie ME, Phipson B, Wu D, et al. (2015) limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Research 43 , e47.
Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.Bioinformatics 26 , 139-140.
Rocha DF, Wouters FC, Zampieri DS, et al. (2013) Harvestman phenols and benzoquinones: characterisation and biosynthetic pathway.Molecules 18 , 11429-11451.
Schmidt J (2009) Taxonomic and biogeographical review of the genusTrechus Clairville, 1806, from the Tibetan Himalaya and the southern central Tibetan Plateau (Coleoptera: Carabidae: Trechini).Zootaxa 2178 , 1-72.
Schmidt J, Böhner J, Brandl R, Opgenoorth L (2017) Mass elevation and lee effects markedly lift the elevational distribution of ground beetles in the Himalaya-Tibet orogen. PLoS ONE 12 , e0172939.
Schmitz JF, Zimmer F, Bornberg-Bauer E (2016) Mechanisms of transcription factor evolution in Metazoa. Nucleic Acids Research44 , 6287-6297.
Schoville SD, Simon S, Bai M, et al. (2020) Comparative transcriptomics of ice-crawlers demonstrates cold specialization constrains niche evolution in a relict lineage. Evolutionary Applications .
Schowalter TD (2013) Insects and sustainability of ecosystem services CRC Press.
Seemann T (2014) Prokka: rapid prokaryotic genome annotation.Bioinformatics 30 , 2068-2069.
Seppey M, Ioannidis P, Emerson BC, et al. (2019a) Genomic signatures accompanying the dietary shift to phytophagy in polyphagan beetles. Genome biology 20 , 98.
Seppey M, Manni M, Zdobnov EM (2019b) BUSCO: Assessing Genome Assembly and Annotation Completeness. Methods in Molecular Biology1962 , 227-245.
Serrano J, Galián J (1998) A review of karyotypic evolution and phylogeny of carabid beetles (Coleoptera). Phylogeny and classification of Caraboidea (Coleoptera: Adephaga). Museo Regionale di Scienze Naturali, Torino , 191-228.
Serrano J, Yadav J (1984) Chromosome numbers and sex-determining mechanisms in Adephagan Coleoptera. The Coleopterists’ Bulletin , 335-357.
Shaffer JF, Gillis TE (2010) Evolution of the regulatory control of vertebrate striated muscle: the roles of troponin I and myosin binding protein-C. Physiological Genomics 42 , 406-419.
Sinclair BJ, Vernon P, Klok CJ, Chown SL (2003) Insects at low temperatures: an ecological perspective. Trends in Ecology & Evolution 18 , 257-262.
Slade EM, Bagchi R, Keller N, Philipson CD (2019) When do more species maximize more ecosystem services? Trends in Plant Science24 , 790-793.
Slatyer RA, Nash MA, Hoffmann AA (2016) Scale‐dependent thermal tolerance variation in Australian mountain grasshoppers.Ecography 39 , 572-582.
Slatyer RA, Schoville SD (2016) Physiological limits along an elevational gradient in a radiation of montane ground beetles.PLoS ONE 11 , e0151959.
Smit A, Hubley R, Green P (2015) RepeatMasker Open-4.0 [http://www. repeatmasker. org] Accessed September, 2020. Accessed.
Smit AF, Hubley R (2008) RepeatModeler Open-1.0. Available fom http://www. repeatmasker. org .
Smith SA, O’Meara BC (2012) treePL: divergence time estimation using penalized likelihood for large phylogenies. Bioinformatics28 , 2689-2690.
Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics30 , 1312-1313.
Stanke M, Diekhans M, Baertsch R, Haussler D (2008) Using native and syntenically mapped cDNA alignments to improve de novo gene finding.Bioinformatics 24 , 637-644.
Stanke M, Schöffmann O, Morgenstern B, Waack S (2006) Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics 7 , 62.
Storey KB, Storey JM (2010) Oxygen: Stress and adaptation in cold-hardy insects.
Storey KB, Storey JM (2012) Insect cold hardiness: metabolic, gene, and protein adaptation. Canadian Journal of Zoology 90 , 456-475.
Supek F, Bošnjak M, Škunca N, Šmuc T (2011) REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS ONE6 , e21800.
Teets NM, Denlinger DL (2013) Physiological mechanisms of seasonal and rapid cold‐hardening in insects. Physiological Entomology38 , 105-116.
Teets NM, Kawarasaki Y, Lee RE, Denlinger DL (2011) Survival and energetic costs of repeated cold exposure in the Antarctic midge,Belgica antarctica : a comparison between frozen and supercooled larvae. Journal of Experimental Biology 214 , 806-814.
Teets NM, Kawarasaki Y, Potts LJ, et al. (2019) Rapid cold hardening protects against sublethal freezing injury in an Antarctic insect. Journal of Experimental Biology 222 .
Ter-Hovhannisyan V, Lomsadze A, Chernoff YO, Borodovsky M (2008) Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. Genome Research 18 , 1979-1990.
Timmermans MJ, Vogler AP (2012) Phylogenetically informative rearrangements in mitochondrial genomes of Coleoptera, and monophyly of aquatic elateriform beetles (Dryopoidea). Molecular Phylogenetics and Evolution 63 , 299-304.
UniProt Consortium (2019) UniProt: a worldwide hub of protein knowledge.Nucleic Acids Research 47 , D506-D515.
Vaser R, Sović I, Nagarajan N, Šikić M (2017) Fast and accurate de novo genome assembly from long uncorrected reads. Genome Research27 , 737-746.
Venkat A, Hahn MW, Thornton JW (2018) Multinucleotide mutations cause false inferences of lineage-specific positive selection. Nature ecology & evolution 2 , 1280-1288.
Vinogradov AE (1999) Genome in toto. Genome 42 , 361-362.
Wagner A (2005) Energy constraints on the evolution of gene expression.Molecular Biology and Evolution 22 , 1365-1374.
Wang Y, Tang H, DeBarry JD, et al. (2012) MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity.Nucleic Acids Research 40 , e49-e49.
Weng YM, Kavanaugh DH, Schoville SD (2020) Drainage basins serve as multiple glacial refugia for alpine habitats in the Sierra Nevada Mountains, California. Molecular Ecology .
Weng YM, Francoeur CB, Currie C, Kavanaugh DH, Schoville SD (2020) A high-quality carabid genome provides insights into beetle genome evolution and cold adaptation, Dryad, Dataset, https://doi.org/10.5061/dryad.8cz8w9gp5
Weyenberg G, Huggins PM, Schardl CL, Howe DK, Yoshida R (2014) kdetrees: Non-parametric estimation of phylogenetic tree distributions.Bioinformatics 30 , 2280-2287.
Williams CM, Szejner-Sigal A, Morgan TJ, et al. (2016) Adaptation to Low Temperature Exposure Increases Metabolic Rates Independently of Growth Rates. Integrative and Comparative Biology 56 , 62-72.
Wolfe JM, Daley AC, Legg DA, Edgecombe GD (2016) Fossil calibrations for the arthropod Tree of Life. Earth-Science Reviews 160 , 43-110.
Wright NA, Gregory TR, Witt CC (2014) Metabolic ‘engines’ of flight drive genome size reduction in birds. Proceedings of the Royal Society B: Biological Sciences 281 , 20132780.
Xie J, Vilchez I, Mateos M (2010) Spiroplasma cacteria enhance survival of Drosophila hydei attacked by the parasitic waspLeptopilina heterotoma . PLoS ONE 5 , e12149.
Young MD, Wakefield MJ, Smyth GK, Oshlack A (2010) Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biology 11 , R14.
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 , 284-287.
Zhang SQ, Che LH, Li Y, et al. (2018) Evolutionary history of Coleoptera revealed by extensive sampling of genes and species.Nature Communications 9 , 205.
Zhu BH, Xiao J, Xue W, et al. (2018) P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads.BMC Genomics 19 , 175.