• Scheffers, B. R. et al. The broad footprint of climate change from genes to biomes to people. Science 354, aaf7671 (2016).

    Article 

    Google Scholar
     

  • Aitken, S. N. & Whitlock, M. C. Assisted gene flow to facilitate local adaptation to climate change. Annu. Rev. Ecol. Evol. Syst. 44, 367–388 (2013).

    Article 

    Google Scholar
     

  • Browne, L. et al. Adaptational lag to temperature in valley oak (Quercus lobata) can be mitigated by genome-informed assisted gene flow. Proc. Natl Acad. Sci. USA 116, 25179–25185 (2019).

    Article 
    CAS 

    Google Scholar
     

  • De-Kayne, R. et al. Genomic architecture of adaptive radiation and hybridization in Alpine whitefish. Nat. Commun. 13, 4479 (2022).

    Article 
    CAS 

    Google Scholar
     

  • Kagawa, K. & Takimoto, G. Hybridization can promote adaptive radiation by means of transgressive segregation. Ecol. Lett. 21, 264–274 (2018).

    Article 

    Google Scholar
     

  • Brauer, C. J. et al. Natural hybridization reduces vulnerability to climate change. Nat. Clim. Chang 13, 282–289 (2023).


    Google Scholar
     

  • Chen, Y. et al. The combination of genomic offset and niche modelling provides insights into climate change-driven vulnerability. Nat. Commun. 13, 4821 (2022).

    Article 
    CAS 

    Google Scholar
     

  • Rahbek, C. et al. Building mountain biodiversity: geological and evolutionary processes. Science 365, 1114–1119 (2019).

    Article 
    CAS 

    Google Scholar
     

  • Fjeldså, J., Bowie, R. C. K. & Rahbek, C. The role of mountain ranges in the diversification of birds. Annu. Rev. Ecol. Evol. Syst. 43, 249–265 (2012).

    Article 

    Google Scholar
     

  • Wu, Y. J. et al. Explaining the species richness of birds along a subtropical elevational gradient in the Hengduan Mountains. J. Biogeogr. 40, 2310–2323 (2013).

    Article 

    Google Scholar
     

  • Qu, Y. et al. Long-term isolation and stability explain high genetic diversity in the Eastern Himalaya. Mol. Ecol. 23, 705–720 (2014).

    Article 

    Google Scholar
     

  • Qu, Y. et al. Lineage diversification and historical demography of a montane bird Garrulax elliotii—implications for the Pleistocene evolutionary history of the eastern Himalayas. BMC Evol. Biol. 11, 174 (2011).

    Article 

    Google Scholar
     

  • Chen, Y. et al. 2023. Alpine burrow-sharing mammals and birds show similar population-level climate change risks. Nat. Clim. Change 13, 990–996 (2023).

    Article 

    Google Scholar
     

  • Ruegg, K. et al. Ecological genomics predicts climate vulnerability in an endangered southwestern songbird. Ecol. Lett. 21, 1085–1096 (2018).

    Article 

    Google Scholar
     

  • Bay, R. A. et al. Genomic signals of selection predict climate driven population declines in a migratory bird. Science 359, 83–86 (2018).

    Article 
    CAS 

    Google Scholar
     

  • Li, C. et al. Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment. Gigascience 3, 27 (2014).

    Article 

    Google Scholar
     

  • Pirri, F. et al. Selection-driven adaptation to the extreme Antarctic environment in Emperor penguin. Heredity 129, 317–326 (2022).

    Article 

    Google Scholar
     

  • Wang, L. C. et al. Involvement of the Arabidopsis HIT1/AtVPS53 tethering protein homologue the acclimation of the plasma membrane to heat stress. J. Exp. Bot. 62, 3609–3620 (2011).

    Article 
    CAS 

    Google Scholar
     

  • Piñol, R. A. et al. Preoptic BRS3 neurons increase body temperature and heart rate via multiple pathways. Cell Metab. 33, 1389–1403 (2021).

    Article 

    Google Scholar
     

  • Guilherme, A. et al. Neuronal modulation of brown adipose activity through perturbation of white adipocyte lipogenesis. Mol. Metab. 16, 116–125 (2018).

    Article 
    CAS 

    Google Scholar
     

  • Graham, A. M. et al. Adaptive introgression of the beta-globin cluster in two Andean waterfowl. Heredity 127, 107–123 (2021).

    Article 
    CAS 

    Google Scholar
     

  • Pizzagalli, M. D., Bensimon, A. & Superti-Furga, G. A guide to plasma membrane solute carrier proteins. FEBS J. 288, 2784–2835 (2020).

    Article 

    Google Scholar
     

  • Zhang, Y., Guo, W., Zhang, Y., Zhang, H. & Wu, C. Insights into hypoxic adaptation in Tibetan chicken embryos from comparative proteomics. Comp. Biochem. Physiol. Part D. 31, 100602 (2019).

    CAS 

    Google Scholar
     

  • Qu, Y. et al. Rapid phenotypic evolution with shallow genomic differentiation during early stages of high elevation adaptation in Eurasian tree sparrows. Natl Sci. Rev. 7, 113–127 (2020).

    Article 

    Google Scholar
     

  • Huerta-Sánchez, E. et al. Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA. Nature 512, 194–197 (2014).

    Article 

    Google Scholar
     

  • Marchese, C. Biodiversity hotspots: a shortcut for a more complicated concept. Glob. Ecol. Conserv. 3, 297–309 (2015).


    Google Scholar
     

  • He, J. K., Lin, S. L., Li, J. T., Yu, J. H. & Jiang, H. S. Evolutionary history of zoogeographical regions surrounding the Tibetan Plateau. Commun. Biol. 3, 415 (2020).

    Article 

    Google Scholar
     

  • Freeman, B. G., Scholer, M. N., Ruiz-Gutierrez, V. & Fitzpatrick, J. W. Climate change causes upslope shifts and mountaintop extirpations in a tropical bird community. Proc. Natl Acad. Sci. USA 115, 11982–11987 (2018).

    Article 
    CAS 

    Google Scholar
     

  • Qu et al. The influence of geological events on the endemism of East Asian birds studied through comparative phylogeography. J. Biogeogr. 42, 179–192 (2015).

    Article 

    Google Scholar
     

  • Song, G. et al. Phylogeography of the Alcippe morrisonia (Aves: Timaliidae): long population history beyond late Pleistocene glaciations. BMC Evol. Biol. 9, 143 (2009).

    Article 

    Google Scholar
     

  • Excoffier, L., Dupanloup, I., Huerta-Sanchez, E., Sousa, V. C. & Foll, M. Robust demographic inference from genomic and SNP data. PLoS Genet. 9, e1003905 (2013).

    Article 

    Google Scholar
     

  • Li, H. & Durbin, R. Inference of human population history from individual whole-genome sequences. Nature 475, 493–496 (2011).

    Article 
    CAS 

    Google Scholar
     

  • Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009).

    Article 
    CAS 

    Google Scholar
     

  • Bailey, R. I. Bayesian hybrid index and genomic cline estimation with the R package gghybrid. Mol. Ecol. Resour. 24, e13910 (2024).

    Article 

    Google Scholar
     

  • Blischak, P. D. et al. HyDe: a python package for genome-scale hybridization detection. Syst. Biol. 67, 821–829 (2018).

    Article 

    Google Scholar
     

  • Schrider, D. R., Ayroles, J., Matute, D. R. & Kern, A. D. Supervised machine learning reveals introgressed loci in the genomes of Drosophila simulans and D. sechellia. PLoS Genet. 14, e1007341 (2018).

    Article 

    Google Scholar
     

  • Atwater, D. Z., Ervine, C. J. & Barney, N. Climatic niche shifts are common in introduced plants. Nat. Ecol. Evol. 2, 34–43 (2018).

    Article 

    Google Scholar
     

  • Petitpierre, P. et al. Climatic niche shifts are rare among terrestrial plant invaders. Science 335, 1344–1348 (2012).

    Article 
    CAS 

    Google Scholar
     

  • Liu, C., Wolter, C., Xian, W. & Jeschke, J. M. Most invasive species largely conserve their climatic niche. Proc. Natl Acad. Sci. USA 38, 23643–23651 (2020).

    Article 

    Google Scholar
     

  • Brown, J. L. & Carnaval, A. C. A tale of two niches: methods, concepts, and evolution. Front. Biogeogr. 11, e44158 (2019).

    Article 

    Google Scholar
     

  • Thuiller, W., Lafourcade, B., Engler, R. & Araújo, M. B. BIOMOD—a platform for ensemble forecasting of species distributions. Ecography 32, 369–373 (2009).

    Article 

    Google Scholar
     

  • Guo, Y., Li, X., Zhao, Z. & Nawaz, Z. Predicting the impacts of climate change, soils and vegetation types on the geographic distribution of Polyporus umbellatus in China. Sci. Total Environ. 648, 1–11 (2019).

    Article 
    CAS 

    Google Scholar
     

  • Fournier-Level, A. et al. A map of local adaptation in Arabidopsis thaliana. Science 34, 86–80 (2011).

    Article 

    Google Scholar
     

  • Frichot, E. & François, O. L. E. A. An R package for landscape and ecological association studies. Methods Ecol. Evol. 6, 925–929 (2015).

    Article 

    Google Scholar
     

  • Forester, B. R. et al. Detecting spatial genetic signatures of local adaptation in heterogeneous landscapes. Mol. Ecol. 25, 104–120 (2016).

    Article 
    CAS 

    Google Scholar
     

  • Dikmen, S. et al. Genome-wide association mapping for identification of quantitative trait loci for rectal temperature during heat stress in Holstein cattle. PLoS ONE 8, e69202 (2013).

    Article 
    CAS 

    Google Scholar
     

  • Kim, T. W. et al. A critical role for IRAK4 kinase activity in Toll-like receptor–mediated innate immunity. J. Exp. Med. 204, 1025–1036 (2007).

    Article 
    CAS 

    Google Scholar
     

  • Weldenegodguad, M. et al. Adipose gene expression profiles reveal insights into the adaptation of northern Eurasian semi-domestic reindeer (Rangifer tarandus). Commun. Biol. 4, 1170 (2021).

    Article 
    CAS 

    Google Scholar
     

  • Heinrich, E. C. et al. Increased levels of interleukin-6 (IL-6) in Andean males with chronic mountain sickness and sea-level participants after one day at high altitude may reflect differences in IL-6 regulation. FASEB J. 32, lb479 (2018).

    Article 

    Google Scholar
     

  • Ferrer-Admetlla, A., Liang, M., Korneliussen, T. & Nielsen, R. On detecting incomplete soft or hard selective sweeps using haplotype structure. Mol. Biol. Evol. 31, 1275–1291 (2014).

    Article 
    CAS 

    Google Scholar
     

  • Voight, B. F., Kudaravalli, S., Wen, X. & Pritchard, J. K. A map of recent positive selection in the human genome. PLoS Biol. 4, e72 (2006).

    Article 

    Google Scholar
     

  • Ellis, N., Smith, S. J. & Pitcher, C. R. Gradient forests: calculating importance gradients on physical predictors. Ecology 93, 156–168 (2012).

    Article 

    Google Scholar
     

  • Haller, B. C. & Messer, P. W. SLiM 4: multispecies eco-evolutionary modeling. Am. Nat. 201, E127 (2023).

    Article 

    Google Scholar
     

  • Matz, M. V., Treml, E. A., Aglyamova, G. V. & Bay, L. K. Potential and limits for rapid genetic adaptation to warming in a Great Barrier Reef coral. PLoS Genet. 14, e1007220 (2018).

    Article 

    Google Scholar
     

  • Matz, M. V., Treml, E. A. & Haller, B. C. Estimating the potential for coral adaptation to global warming across the Indo-West Pacific. Glob. Change Biol. 26, 3473–3481 (2020).

    Article 

    Google Scholar
     

  • Dong, F. et al. Potential millennial-scale avian declines by humans in southern China. Glob. Change Biol. 28, 5505–5513 (2022).

    Article 
    CAS 

    Google Scholar
     

  • Bird, J. P. et al. Generation lengths of the world’s birds and their implications for extinction risk. Conserv. Biol. 34, 1252–1261 (2020).

    Article 

    Google Scholar
     

  • Clarke, R. T. et al. Confidence limits for regression relationships between distance matrices: estimating gene flow with distance. J. Agric. Biol. Environ. Stat. 7, 361–372 (2002).

    Article 

    Google Scholar
     

  • Rieseberg, L. H., Archer, M. A. & Wayne, R. K. Transgressive segregation, adaptation and speciation. Heredity 83, 363–372 (1999).

    Article 

    Google Scholar
     

  • Seehausen, O. Hybridization and adaptive radiation. Trends Ecol. Evol. 19, 198–207 (2004).

    Article 

    Google Scholar
     

  • Rieseberg, L. H. Hybrid speciation in wild sunflowers. Ann. Mo. Bot. Gard. 93, 34–48 (2006).

    Article 

    Google Scholar
     

  • Rieseberg, L. H. et al. Major ecological transitions in wild sunflowers facilitated by hybridization. Science 301, 1211–1216 (2003).

    Article 
    CAS 

    Google Scholar
     

  • Ungerer, M. C., Baird, S. J. E., Pan, J. & Rieseberg, L. H. Rapid hybrid speciation in wild sunflowers. Proc. Natl Acad. Sci. USA 95, 11757–11762 (1998).

    Article 
    CAS 

    Google Scholar
     

  • Stelkens, R. B., Brockhurst, M. A., Hurst, G. D. D. & Greig, D. Hybridization facilitates evolutionary rescue. Evol. Appl. 7, 1209–1217 (2014).

    Article 

    Google Scholar
     

  • Stelkens, R. B., Brockhurst, M. A., Hurst, G. D. D., Miller, E. L. & Greig, D. The effect of hybrid transgression on environmental tolerance in experimental yeast crosses. J. Evol. Biol. 27, 2507–2519 (2014).

    Article 
    CAS 

    Google Scholar
     

  • Zhang, D. C., Zhang, Y. H., Boufford, D. E. & Sun, H. Elevational patterns of species richness and endemism for some important taxa in the Hengduan Mountains, southwestern China. Biodivers. Conserv. 18, 699–716 (2009).

    Article 

    Google Scholar
     

  • Zhang, R. Z., Zheng, D., Yang, Q. Y. & Liu, Y. H. Physical Geography of Hengduan Mountains (Science Press, 1997).

  • Allendorf, F. W., Leary, R. F., Spruell, P. & Wenburg, J. K. The problems with hybrids: setting conservation guidelines. Trends Ecol. Evol. 16, 613–622 (2001).

    Article 

    Google Scholar
     

  • Todesco, M. et al. Hybridization and extinction. Evol. Appl. 9, 892–908 (2016).

    Article 
    CAS 

    Google Scholar
     

  • Hirashiki, C., Kareiva, P. & Marvier, M. Concern over hybridization risks should not preclude conservation interventions. Conserv. Sci. Pract. 3, e424 (2021).

    Article 

    Google Scholar
     

  • Chen, Y. et al. Large-scale genome-wide reveals climate adaptive variability in a cosmopolitan pest. Nat. Commun. 12, 7206 (2021).

    Article 
    CAS 

    Google Scholar
     

  • Urban, M. C. Escalator to extinction. Proc. Natl Acad. Sci. USA 115, 11871–11873 (2018).

    Article 
    CAS 

    Google Scholar
     

  • Chen, S. Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp. iMeta 2, e107 (2023).

    Article 
    CAS 

    Google Scholar
     

  • Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).

    Article 
    CAS 

    Google Scholar
     

  • Van Der Auwera, G. & O’Connor, B. D. Genomics in the Cloud: Using Docker, GATK, and WDL in Terra (O’Reilly Media, 2020).

  • Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

    Article 

    Google Scholar
     

  • Chang, C. C. et al. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience 4, 7 (2015).

    Article 

    Google Scholar
     

  • Lefort, V., Desper, R. & Gascuel, O. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol. Biol. Evol. 32, 2798–2800 (2015).

    Article 
    CAS 

    Google Scholar
     

  • Wiens, B. J., DeCicco, L. H. & Colella, J. P. triangulaR: an R package for identifying AIMs and 825 building triangle plots using SNP data from hybrid zones. Heredity 134, 251–262 (2025).

    Article 
    CAS 

    Google Scholar
     

  • Danecek, P. et al. Twelve years of SAMtools and BCFtools. GigaScience 10, giab008 (2021).

  • Martin, S. H., Davey, J. W. & Jiggins, C. D. Evaluating the use of ABBA–BABA statistics to locate introgressed loci. Mol. Biol. Evol. 32, 244–257 (2015).

    Article 
    CAS 

    Google Scholar
     

  • Cai et al. Near-complete phylogeny and taxonomic revision of the world’s babblers (Aves: Passeriformes). Mol. Phylogenet. Evol. 130, 346–356 (2019).

    Article 

    Google Scholar
     

  • Ericson, P. G. & Irestedt, M. Comparative population genomics reveals glacial cycles to drive diversifications in tropical montane birds (Aves, Timaliidae). Avian Res. 13, 100063 (2022).

    Article 

    Google Scholar
     

  • Browning, S. R. & Browning, B. L. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am. J. Hum. Genet. 81, 1084–1097 (2007).

    Article 
    CAS 

    Google Scholar
     

  • Xiao, H. et al. Adaptive and maladaptive introgression in grapevine domestication. Proc. Natl Acad. Sci. USA 120, e2222041120 (2023).

    Article 
    CAS 

    Google Scholar
     

  • Lukicheva, S. & Mardulyn, P. Whole-genome sequencing reveals asymmetric introgression between two sister species of cold-resistant leaf beetles. Mol. Ecol. 30, 4077–4089 (2021).

    Article 
    CAS 

    Google Scholar
     

  • Geneva, A. J., Muirhead, C. A., Kingan, S. B. & Garrigan, D. A new method to scan genomes for introgression in a secondary contact model. PLoS ONE 10, e0118621 (2015).

    Article 

    Google Scholar
     

  • Hudson, R. R. A new statistic for detecting genetic differentiation. Genetics 155, 2011–2014 (2000).

    Article 
    CAS 

    Google Scholar
     

  • Tian, J. et al. Projections of precipitation over China based on CMIP6 models. Stoch. Environ. Res. Risk Assess. 35, 831–848 (2021).

    Article 

    Google Scholar
     

  • Lu, K. et al. Evaluating observed and future spatiotemporal changes in precipitation and temperature across China based on CMIP6-GCMs. Int. J. Climatol. 42, 7703–7729 (2022).

    Article 

    Google Scholar
     

  • Boria, R. A., Olson, L. E., Goodman, S. M. & Anderson, R. P. Spatial filtering to reduce sampling bias can improve the performance of ecological niche models. Ecol. Model. 275, 73–77 (2014).

    Article 

    Google Scholar
     

  • Liu, C. R., White, M. & Newell, G. Selecting thresholds for the prediction of species occurrence with presence-only data. J. Biogeogr. 40, 778–789 (2013).

    Article 

    Google Scholar
     

  • Ge, S. X., Jung, D. & Yao, R. ShinyGO: a graphical gene-set enrichment tool for animals and plants. Bioinformatics 36, 2628–2629 (2020).

    Article 
    CAS 

    Google Scholar
     

  • Szpiech, Z. A. & Hernandez, R. D. Selscan: an efficient multithreaded program to perform EHH-based scans for positive selection. Mol. Biol. Evol. 31, 2824–2827 (2014).

    Article 
    CAS 

    Google Scholar
     

  • Meier, J. I., Marques, D. A., Wager, C. E., Excoffier, L. & Seehausen, O. Genomics of parallel ecological speciation in lake Victoria cichilids. Mol. Biol. Evol. 35, 1489–1506 (2018).

    Article 
    CAS 

    Google Scholar
     

  • Kim-Hellmuth, S. et al. Genetic regulatory effects modified by immune activation contribute to autoimmune disease association. Nat. Commun. 8, 266 (2017).

    Article 

    Google Scholar
     

  • Blumstein, M. et al. Protocol for projecting allele frequency change under future climate change at adaptive-associated loci. STAR Protoc. 1, 100061 (2020).

    Article 

    Google Scholar
     

  • Gain, C. et al. A quantitative theory for genomic offset statistics. Mol. Biol. Evol. 40, msad140 (2023).

    Article 
    CAS 

    Google Scholar
     

  • Yair, S. & Coop, G. Population differentiation of polygenic score predictions under stabilizing selection. Philos. Trans. R. Soc. B 377, 20200416 (2022).

    Article 

    Google Scholar
     

  • Peterman, W. E. ResistanceGA: an R package for the optimization of resistance surfaces using genetic algorithms. Methods Ecol. Evol. 9, 1638–1647 (2018).

    Article 

    Google Scholar
     

  • Keenan, K., Mcginnity, P., Cross, T. F., Crozier, W. W. & Prodöhl, P. A. diveRsity: an R package for the estimation and exploration of population genetics parameters and their associated errors. Methods Ecol. Evol. 4, 782–788 (2013).

    Article 

    Google Scholar
     

  • Bates, D., Mächler, M., Bolker, B. & Walker, S. Fitting linear mixed effects models using lme4. J. Stat. Softw. 67, 1–48 (2015).

    Article 

    Google Scholar
     

  • Anderson, D. R. & Burnham, K. P. Avoiding pitfalls when using information-theoretic methods. J. Wildl. Manag. 66, 912–918 (2002).

    Article 

    Google Scholar
     

  • Zhang, S. et al. Code and data for ‘Hybridisation mitigates climate change risk in mountainous birds’. Zenodo https://doi.org/10.5281/zenodo.17271739 (2025).

  • Danielson, J. J. & Gesch, D. B. Global Multi-resolution Terrain Elevation Data 2010 (GMTED2010) US Geological Survey Open-File Report 2011-1073, 26 p (2011).