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Savolainen O, Lascoux M, Merilä J. Ecological genomics of native adaptation. Nat Rev Genet. 2013;14(11):807–20.
An X, Mao L, Wang Y, Xu Q, Liu X, Zhang S, et al. Genomic structural variation is related to hypoxia adaptation in high-altitude zokors. Nat Ecol Evol. 2024;8(2):339–51.
Wang Ok, Shen Y, Yang Y, Gan X, Liu G, Hu Ok, et al. Morphology and genome of a snailfish from the Mariana Trench present insights into deep-sea adaptation. Nat Ecol Evol. 2019;3(5):823–33.
Liu S, Lorenzen ED, Fumagalli M, Li B, Harris Ok, Xiong Z, et al. Population genomics reveal current speciation and fast evolutionary adaptation in polar bears. Cell. 2014;157(4):785–94.
Bentley P. Adaptations of amphibia to arid environments: novel physiological mechanisms not seen in fish assist frogs and toads to preserve water and stay in deserts. Sci Cult. 1966;152(3722):619–23.
Davies KTJ, Bennett NC, Faulkes CG, Rossiter SJ. Limited proof for parallel molecular variations related to the subterranean area of interest in mammals: a comparative examine of three superorders. Mol Biol Evol. 2018;35(10):2544–59.
Liu X, Zhang S, Cai Z, Kuang Z, Wan N, Wang Y, et al. Genomic insights into zokors’ phylogeny and speciation in China. Proc Natl Acad Sci U S A. 2022;119(19):e2121819119.
He Ok, Shinohara A, Helgen KM, Springer MS, Jiang XL, Campbell KL. Talpid mole phylogeny unites shrew moles and illuminates missed cryptic species range. Mol Biol Evol. 2017;34(1):78–87.
Montoya-Sanhueza G, Šaffa G, Šumbera R, Chinsamy A, Jarvis JUM, Bennett NC. Fossorial variations in African mole-rats (Bathyergidae) and the distinctive appendicular phenotype of bare mole-rats. Commun Biol. 2022;5(1):526.
Policarpo M, Fumey J, Lafargeas P, Naquin D, Thermes C, Naville M, et al. Contrasting gene decay in subterranean vertebrates: insights from cavefishes and fossorial mammals. Mol Biol Evol. 2021;38(2):589–605.
Park TJ, Reznick J, Peterson BL, Blass G, Omerbašić D, Bennett NC, et al. Fructose-driven glycolysis helps anoxia resistance within the bare mole-rat. Science. 2017;356(6335):307–11.
Jiao H, Wang Q, Wang B-J, Li Ok, Lövy M, Nevo E, et al. Local adaptation of bitter style and ecological speciation in a wild mammal. Mol Biol Evol. 2021;38(10):4562–72.
Hadid Y, Tzur S, Pavlícek T, Šumbera R, Šklíba J, Lövy M, et al. Possible incipient sympatric ecological speciation in blind mole rats (Spalax). Proc Natl Acad Sci U S A. 2013;110(7):2587–92.
Cloudsley-Thompson JL. Adaptations of arthropoda to arid environments. Annu Rev Entomol. 1975;20:261–83.
Newell FL, Ausprey IJ, Robinson SK. Wet and dry extremes scale back arthropod biomass independently of leaf phenology within the moist tropics. Glob Change Biol. 2023;29(2):308–23.
Lo Cascio Sætre C, Coleiro C, Austad M, Gauci M, Sætre GP, Voje KL, et al. Rapid adaptive phenotypic change following colonization of a newly restored habitat. Nat Commun. 2017;8:14159.
Szűcs M, Vahsen ML, Melbourne BA, Hoover C, Weiss-Lehman C, Hufbauer RA. Rapid adaptive evolution in novel environments acts as an architect of inhabitants vary growth. Proc Natl Acad Sci U S A. 2017;114(51):13501–6.
Han Z, Wang Z, Rittschof D, Huang Z, Chen L, Hao H, et al. New genes helped acorn barnacles adapt to a sessile life-style. Nat Genet. 2024;56(5):970–81.
Romero PA, Arnold FH. Exploring protein health landscapes by directed evolution. Nat Rev Mol Cell Biol. 2009;10(12):866–76.
Alkan C, Coe BP, Eichler EE. Genome structural variation discovery and genotyping. Nat Rev Genet. 2011;12(5):363–76.
Galbraith JD, Hayward A. The affect of transposable parts on animal colouration. Trends Genet. 2023;39(8):624–38.
Fudenberg G, Pollard KS. Chromatin options constrain structural variation throughout evolutionary timescales. Proc Natl Acad Sci U S A. 2019;116(6):2175–80.
Inversions C. Local Adaptation and Speciation. Genetics. 2018;208(1):433.
Sturtevant AH. Genetic components affecting the energy of linkage in Drosophila. Proc Natl Acad Sci U S A. 1917;3(9):555–8.
Kidd JM, Graves T, Newman TL, Fulton R, Hayden HS, Malig M, et al. A human genome structural variation sequencing useful resource reveals insights into mutational mechanisms. Cell. 2010;143(5):837–47.
Porubsky D, Sanders AD, Höps W, Hsieh P, Sulovari A, Li R, et al. Recurrent inversion toggling and nice ape genome evolution. Nat Genet. 2020;52(8):849–58.
Lupiáñez DG, Kraft Ok, Heinrich V, Krawitz P, Brancati F, Klopocki E, et al. Disruptions of topological chromatin domains trigger pathogenic rewiring of gene-enhancer interactions. Cell. 2015;161(5):1012–25.
Zhang S, Plummer D, Lu L, Cui J, Xu W, Wang M, et al. Deeploop robustly maps chromatin interactions from sparse allele-resolved or single-cell Hi-C information at kilobase decision. Nat Genet. 2022;54(7):1013–25.
Scheinfeldt LB, Tishkoff SA. Recent human adaptation: genomic approaches, interpretation and insights. Nat Rev Genet. 2013;14(10):692–702.
Flynn LJ. The antiquity of Rhizomys and impartial acquisition of fossorial traits in subterranean muroids. B Am Mus Nat Hist. 2009;2009(331):128–56.
Wan N, Duan Q, Cai Z, Zhu Z, Wang J, Tian Y, et al. Aplf/Dna2 variants drive chromosomal fission and speed up speciation in zokors. Sci Adv. 2025;11(36):eadt2282.
Shang Z, Chen Ok, Han T, Bu F, Sun S, Zhu N, et al. Natural foraging choice and intestine microecology of two subterranean rodents from the Eurasian Steppe in China. Animals. 2024. https://doi.org/10.3390/ani14162334.
Cai H, Zhang S, Yang X. Forest dynamics and their phenological response to local weather warming within the Khingan Mountains, northeastern China. Int J Environ Res Public Health. 2012;9(11):3943–53.
Bu P, Chen KY, Xiang Ok, Johnson C, Crown SB, Rakhilin N, et al. Aldolase B-Mediated Fructose Metabolism Drives Metabolic Reprogramming of Colon Cancer Liver Metastasis. Cell Metab. 2018;27(6):1249-1262.e1244.
Frezza C. Fructose: the candy(er) facet of the Warburg impact. Cell Death Differ. 2024;31(11):1395–7.
Cortese A, Zhu Y, Rebelo AP, Negri S, Courel S, Abreu L, et al. Biallelic mutations in SORD trigger a standard and doubtlessly treatable hereditary neuropathy with implications for diabetes. Nat Genet. 2020;52(5):473–81.
Ramos Pittol JM, Milona A, Morris I, Willemsen ECL, van der Veen SW, Kalkhoven E, et al. FXR Isoforms Control Different Metabolic Functions in Liver Cells through Binding to Specific DNA Motifs. Gastroenterology. 2020;159(5):1853-1865.e1810.
Lobov IB, Rao S, Carroll TJ, Vallance JE, Ito M, Ondr JK, et al. WNT7b mediates macrophage-induced programmed cell loss of life in patterning of the vasculature. Nature. 2005;437(7057):417–21.
Tian X, Azpurua J, Hine C, Vaidya A, Myakishev-Rempel M, Ablaeva J, et al. High-molecular-mass hyaluronan mediates the most cancers resistance of the bare mole rat. Nature. 2013;499(7458):346–9.
Zhang ZM, Lu R, Wang P, Yu Y, Chen D, Gao L, et al. Structural foundation for DNMT3A-mediated de novo DNA methylation. Nature. 2018;554(7692):387–91.
Puzachenko AY, Pavlenko MV, Korablev VP, Tsvirka MVJ. Karyotype, genetic and morphological variability in North China zokor, Myospalax psilurus (Rodentia, Spalacidae, Myospalacinae). Russ J Theriol. 2014;13(1):27–46.
Saraiva LR, Korsching SI. A novel olfactory receptor gene household in teleost fish. Genome Res. 2007;17(10):1448–57.
Gozashti L, Feschotte C, Hoekstra HE. Transposable ingredient interactions form the ecology of the deer mouse genome. Mol Biol Evol. 2023. https://doi.org/10.1093/molbev/msad069.
Pastor WA, Stroud H, Nee Ok, Liu W, Pezic D, Manakov S, et al. Erratum: MORC1 represses transposable parts within the mouse male germline. Nat Commun. 2015;6:7604.
Bristow RG, Hill RP. Hypoxia and metabolism. Hypoxia, DNA restore and genetic instability. Nat Rev Cancer. 2008;8(3):180–92.
Álvarez-Quilón A, Serrano-Benítez A, Lieberman JA, Quintero C, Sánchez-Gutiérrez D, Escudero LM, et al. ATM particularly mediates restore of double-strand breaks with blocked DNA ends. Nat Commun. 2014;5:3347.
Cortez D, Guntuku S, Qin J, Elledge SJ. ATR and ATRIP: companions in checkpoint signaling. Science. 2001;294(5547):1713–6.
Lossaint G, Larroque M, Ribeyre C, Bec N, Larroque C, Décaillet C, et al. FANCD2 binds MCM proteins and controls replisome operate upon activation of s part checkpoint signaling. Mol Cell. 2013;51(5):678–90.
Machado RD, James V, Southwood M, Harrison RE, Atkinson C, Stewart S, et al. Investigation of second genetic hits on the BMPR2 locus as a modulator of illness development in familial pulmonary arterial hypertension. Circulation. 2005;111(5):607–13.
Arbiser JL, Petros J, Klafter R, Govindajaran B, McLaughlin ER, Brown LF, et al. Reactive oxygen generated by Nox1 triggers the angiogenic change. Proc Natl Acad Sci USA. 2002;99(2):715–20.
Hidalgo D, Bejder J, Pop R, Gellatly Ok, Hwang Y, Maxwell Scalf S, et al. EpoR stimulates fast biking and bigger crimson cells throughout mouse and human erythropoiesis. Nat Commun. 2021;12(1):7334.
Ravid O, Shams I, Ben Califa N, Nevo E, Avivi A, Neumann D. An extracellular area of the erythropoietin receptor of the subterranean blind mole rat Spalax enhances receptor maturation. Proc Natl Acad Sci U S A. 2007;104(36):14360–5.
Avivi A, Oster H, Joel A, Beiles A, Albrecht U, Nevo E. Circadian genes in a blind subterranean mammal half II: conservation and uniqueness of the three Period homologs within the blind subterranean mole rat, Spalax ehrenbergi superspecies. Proc Natl Acad Sci U S A. 2002;99(18):11718–23.
Li Ok, Liu Y, Zhang Y, Fan Z, Hu X, Lai X, et al. Host genomic convergence, moderately than intestine microbiome convergence, underlies the convergent evolution of subterranean adaptation in mammals. Cell Rep. 2025;44(8):116110.
Lin J, Fan L, Han Y, Guo J, Hao Z, Cao L, et al. The mTORC1/eIF4E/HIF-1α Pathway Mediates Glycolysis to Support Brain Hypoxia Resistance within the Gansu Zokor. Eospalax cansus Front Physiol. 2021;12:626240.
Izraelson M, Metsger M, Davydov AN, Shagina IA, Dronina MA, Obraztsova AS, et al. Distinct group of adaptive immunity within the long-lived rodent Spalax galili. Nat Aging. 2021;1(2):179–89.
An Ok, Yao B, Tan Y, Kang Y, Wang Z, Su J. Spermatocytes are the terminals of germ cell differentiation in plateau zokor (Eospalax baileyi) through the non-breeding season. Integr Zool. 2025;20(3):608–22.
Zhang T, Chen J, Zhang J, Guo YT, Zhou X, Li MW, et al. Phenotypic and genomic variations to the extraordinarily excessive elevation in plateau zokor (Myospalax baileyi). Mol Ecol. 2021;30(22):5765–79.
Fang X, Seim I, Huang Z, Gerashchenko MV, Xiong Z, Turanov AA, et al. Adaptations to a subterranean atmosphere and longevity revealed by the evaluation of mole rat genomes. Cell Rep. 2014;8(5):1354–64.
Jarad G, Cunningham J, Shaw AS, Miner JH. Proteinuria precedes podocyte abnormalities inLamb2-/- mice, implicating the glomerular basement membrane as an albumin barrier. J Clin Invest. 2006;116(8):2272–9.
Levéen P, Pekny M, Gebre-Medhin S, Swolin B, Larsson E, Betsholtz C. Mice poor for PDGF B present renal, cardiovascular, and hematological abnormalities. Genes Dev. 1994;8(16):1875–87.
Bouzakri Ok, Zachrisson A, Al-Khalili L, Zhang BB, Koistinen HA, Krook A, et al. siRNA-based gene silencing reveals specialised roles of IRS-1/Akt2 and IRS-2/Akt1 in glucose and lipid metabolism in human skeletal muscle. Cell Metab. 2006;4(1):89–96.
Grand-Perret T, Bouillot A, Perrot A, Commans S, Walker M, Issandou M. SCAP ligands are potent new lipid-lowering medication. Nat Med. 2001;7(12):1332–8.
Login FH, Nejsum LN. Aquaporin water channels: roles past renal water dealing with. Nat Rev Nephrol. 2023;19(9):604–18.
Chen P, Xiao WF, Pan MH, Xiao JS, Feng YJ, Dong ZQ, et al. Comparative genome-wide DNA methylation evaluation reveals epigenomic variations in response to heat-humidity stress in Bombyx mori. Int J Biol Macromol. 2020;164:3771–9.
Tigano A, Colella JP, MacManes MD. Comparative and inhabitants genomics approaches reveal the idea of adaptation to deserts in a small rodent. Mol Ecol. 2020;29(7):1300–14.
Hager ER, Harringmeyer OS, Wooldridge TB, Theingi S, Gable JT, McFadden S, et al. A chromosomal inversion contributes to divergence in a number of traits between deer mouse ecotypes. Science. 2022;377(6604):399–405.
Sanchez-Donoso I, Ravagni S, Rodríguez-Teijeiro JD, Christmas MJ, Huang Y, Maldonado-Linares A, et al. Massive genome inversion drives coexistence of divergent morphs in widespread quails. Curr Biol. 2022;32(2):462-469.e466.
Jay P, Whibley A, Frézal L, Rodríguez de Cara M, Nowell RW, Mallet J et al: Supergene Evolution Triggered by the Introgression of a Chromosomal Inversion. Curr Biol. 2018, 28(11):1839–1845.e1833.
Funk ER, Mason NA, Pálsson S, Albrecht T, Johnson JA, Taylor SA. A supergene underlies linked variation in colour and morphology in a Holarctic songbird. Nat Commun. 2021;12(1):6833.
Gompert Z, Feder JL, Parchman TL, Planidin NP, Whiting FJH, Nosil P. Adaptation repeatedly makes use of complicated structural genomic variation. Science. 2025;388(6744):eadp3745.
Harringmeyer OS, Hoekstra HE. Chromosomal inversion polymorphisms form the genomic panorama of deer mice. Nat Ecol Evol. 2022(12). https://doi.org/10.1038/s41559-022-01890-0.
Beagan JA, Phillips-Cremins JE. On the existence and performance of topologically associating domains. Nat Genet. 2020;52(1):8–16.
Samonte RV, Eichler EE. Segmental duplications and the evolution of the primate genome. Nat Rev Genet. 2002;3(1):65–72.
Huang Ok, Ostevik KL, Elphinstone C, Todesco M, Bercovich N, Owens GL, et al. Mutation load in sunflower inversions is negatively correlated with inversion heterozygosity. Mol Biol Evol. 2022. https://doi.org/10.1093/molbev/msac101.
Hecker N, Hiller M. A genome alignment of 120 mammals highlights ultraconserved ingredient variability and placenta-associated enhancers. Gigascience. 2020;9(1):giz159.
Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, et al. Aligning a number of genomic sequences with the threaded blockset aligner. Genome Res. 2004;14(4):708–15.
Stamatakis AJ. RAxML model 8: a software for phylogenetic evaluation and post-analysis of huge phylogenies. Bioinformatics. 2014;30(9):1312–3.
Yang Z. PAML4: phylogenetic evaluation by most probability. Mol Biol Evol. 2007;24(8):1586–91.
Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA. Posterior summarization in Bayesian phylogenetics utilizing Tracer 1.7. Syst Biol. 2018;67(5):901.
De Bruijn H, Marković Z, Wessels W. Late Oligocene rodents from Banovići (Bosnia and Herzegovina). Palaeodiversity. 2013;6:63–105.
Hedges SB, Marin J, Suleski M, Paymer M, Kumar S. Tree of life reveals clock-like speciation and diversification. Mol Biol Evol. 2015;32(4):835–45.
Astrin JJ, Höfer H, Spelda J, Holstein J, Bayer S, Hendrich L, et al. Towards a DNA barcode reference database for spiders and harvestmen of Germany. PLoS ONE. 2016;11(9):e0162624.
Hubisz MJ, Pollard KS, Siepel A. PHAST and RPHAST: phylogenetic evaluation with house/time fashions. Brief Bioinform. 2011;12(1):41–51.
Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom Ok, et al. Evolutionarily conserved parts in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005;15(8):1034–50.
Li H, Durbin R. Fast and correct quick learn alignment with Burrows-Wheeler remodel. Bioinformatics. 2009;25(14):1754–60.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078–9.
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis Ok, Kernytsky A, et al. The genome evaluation toolkit: a MapReduce framework for analyzing next-generation DNA sequencing information. Genome Res. 2010;20(9):1297–303.
Boeva V, Zinovyev A, Bleakley Ok, Vert JP, Janoueix-Lerosey I, Delattre O, et al. Control-free calling of copy quantity alterations in deep-sequencing information utilizing GC-content normalization. Bioinformatics. 2011;27(2):268–9.
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, et al. The variant name format and VCFtools. Bioinformatics. 2011;27(15):2156–8.
Zhang C, Dong SS, Xu JY, He WM, Yang TL. Poplddecay: a quick and efficient software for linkage disequilibrium decay evaluation based mostly on variant name format information. Bioinformatics. 2019;35(10):1786–8.
Price AL, Jones NC, Pevzner PA. De novo identification of repeat households in massive genomes. Bioinformatics. 2005;21(suppl_1):i351–8.
Baril T, Galbraith J, Hayward A. Earl gray: a completely automated user-friendly transposable ingredient annotation and evaluation pipeline. Mol Biol Evol. 2024. https://doi.org/10.1093/molbev/msae068.
Bolger AM, Lohse M, Usadel B. Trimmomatic: a versatile trimmer for Illumina sequence information. Bioinformatics. 2014;30(15):2114–20.
Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019;37(8):907–15.
Jin Y, Tam OH, Paniagua E, Hammell M. TEtranscripts: a package deal for together with transposable parts in differential expression evaluation of RNA-seq datasets. Bioinformatics. 2015;31(22):3593–9.
Goubert C, Craig RJ, Bilat AF, Peona V, Vogan AA, Protasio AV. A newbie’s information to guide curation of transposable parts. Mob DNA. 2022;13(1):7.
Shen W, Sipos B, Zhao L. SeqKit2: a swiss military knife for sequence and alignment processing. iMeta. 2024;3(3):e191.
Kirilenko BM, Munegowda C, Osipova E, Jebb D, Sharma V, Blumer M, et al. Integrating gene annotation with orthology inference at scale. Science. 2023;380(6643):eabn3107.
Gaspar JM, Hart RP. Dmrfinder: effectively figuring out differentially methylated areas from MethylC-seq information. BMC Bioinformatics. 2017;18(1):528.
Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, et al. The human genome browser at UCSC. Genome Res. 2002;12(6):996–1006.
Quinlan AR, Hall IM. BEDtools: a versatile suite of utilities for evaluating genomic options. Bioinformatics. 2010;26(6):841–2.
Goel M, Sun H, Jiao W-B, Schneeberger Ok. SyRI: discovering genomic rearrangements and native sequence variations from whole-genome assemblies. Genome Biol. 2019;20(1):1–13.
Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A. MUMmer4: a quick and versatile genome alignment system. PLoS Comput Biol. 2018;14(1):e1005944.
Li HJ. Minimap and miniasm: quick mapping and de novo meeting for noisy lengthy sequences. Bioinformatics. 2016;32(14):2103–10.
Li A, Wang J, Sun Ok, Wang S, Zhao X, Wang T, et al. Two reference-quality sea snake genomes reveal their divergent evolution of adaptive traits and venom programs. Mol Biol Evol. 2021;38(11):4867–83.
Numanagić I, Gökkaya AS, Zhang L, Berger B, Alkan C, Hach FJ. Fast characterization of segmental duplications in genome assemblies. Bioinformatics. 2018;34(17):i706–14.
Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, et al. A program for annotating and predicting the consequences of single nucleotide polymorphisms, SnpEff: SNPs within the genome of Drosophila melanogaster pressure w1118; iso-2; iso-3. Fly. 2012;6(2):80–92.
Servant N, Varoquaux N, Lajoie BR, Viara E, Chen C-J, Vert J-P, et al. HiC-Pro: an optimized and versatile pipeline for Hi-C information processing. Genome Biol. 2015;16(1):1–11.
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357–9.
Crane E, Bian Q, McCord RP, Lajoie BR, Wheeler BS, Ralston EJ, et al. Condensin-driven remodelling of X chromosome topology throughout dosage compensation. Nature. 2015;523(7559):240–4.
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