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Hybridization mitigates climate change risk in mountainous birds

Nature Climate Change volume 15, pages 1378–1387 (2025)Cite this article

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Abstract

Climate change is rapidly driving environmental shifts, posing an increasing threat to global biodiversity. Interspecific introgression—in which genetic material is transferred from one species to another following hybridization—may facilitate climate adaptation by introducing new genetic variation, which could mitigate species’ vulnerability to changing conditions. Here, using population and ecological genomic approaches and genetic offset modelling for future climates, we show that hybrid mountainous birds showed reduced vulnerability to climate change compared with non-hybrid counterparts. While geographic isolation and ecological heterogeneity promoted species divergence and distinct climatic niche requirements, gene flow persists at contact zones between these species. Maintaining current gene flow rates is projected to buffer against climate change risks over the next 40 generations. These findings demonstrate the role of interspecific introgression in enhancing climate resilience and future survival, and emphasize the conservation importance of preserving gene flow among species with narrow environmental tolerances.

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Fig. 1: Genomic divergence and interspecific introgression of the fulvettas.
Fig. 2: Ecological niche changes and introgressed climate-associated genetic variants of the fulvettas.
Fig. 3: Interspecific introgression mitigates the climate change risk.
Fig. 4: Landscape genetic analysis indicates that landscape connectivity would be maintained under future climate change.

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Data availability

Resequencing data generated in this study have been deposited in the National Genomics Data Centre (https://db.cngb.org/) under the accession number CNP0006945. Datasets used in this study have been deposited to GitHub at https://github.com/willright28/Project-for-three-Fulvetta-species and Zenodo at https://doi.org/10.5281/zenodo.17271739 (ref. 104). Source data are provided with this paper.

Code availability

Analysis scripts can be found at GitHub at https://github.com/willright28/Project-for-three-Fulvetta-species and Zenodo at https://doi.org/10.5281/zenodo.17271739 (ref. 104).

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Acknowledgements

This research was funded by the National Natural Science Foundation of China (NSFCU23A20162 and NSFC32401393). This research was funded by Young Elite Scientists Sponsorship Program by CAST (2023QNRC001), the Postdoctoral Fellowship Program of CPSF (GZC20232646), the China Postdoctoral Science Foundation (2023M743478) and Bingzhi Postdoctoral Fellowship Program of IOZ, CAS and Chinese Academy of Sciences President’s International Fellowship Initiative (2025PVA0187).

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Author notes

  1. These authors contributed equally: Shuai Zhang, Yilin Chen.

Authors and Affiliations

  1. Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing, China

    Shuai Zhang, Yilin Chen, Wenqing Zang, Xinlai Wu, Fumin Lei & Yanhua Qu

  2. College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China

    Shuai Zhang, Wenqing Zang, Xinlai Wu, Fumin Lei & Yanhua Qu

  3. Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden

    Per G. P. Ericson & Yanhua Qu

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  1. Shuai Zhang
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  2. Yilin Chen
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  3. Wenqing Zang
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  4. Xinlai Wu
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  5. Per G. P. Ericson
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Contributions

Conceptualization: Y.Q. and P.G.P.E. Methodology: S.Z. and Y.C. Investigation: Y.Q. and Y.C. Visualization: S.Z., Y.C., W.Z. and X.W. Funding acquisition: Y.Q. and Y.C. Project administration: Y.Q. and F.L. Supervision: P.G.P.E., Y.Q. and W.Z. Writing – original draft: Y.Q. and S.Z. Writing – review and editing: Y.Q., P.G.P.E., S.Z. and Y.C.

Corresponding author

Correspondence to Yanhua Qu.

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Nature Climate Change thanks Luciano Beheregaray, Junhu Su and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Extended data

Extended Data Fig. 1 The historical demography of the three species inferred by pairwise sequentially Markovian coalescent (PSMC).

Following their divergence (Tdiv) approximately 216-221 thousand years ago, fratercula exhibited an initial population decline, hueti maintained a relatively stable population sizes, and davidi underwent continuous population growth. Notably, all species experienced synchronous population expansions beginning approximately 47 kya, a period that coincides with the estimated onset of interspecific gene flow (Tmig). However, all species decreased their effective population sizes (Ne) following the last glacial maximum (LGM).

Extended Data Fig. 2 Hybrid index estimations among davidi and hueti.

Pure reference populations are coded as S0 (blue, davidi) and S1 (red, hueti). The point estimates are based on the mode from the posterior distribution, and error bars indicate 95% credibility intervals based on an initial burn-in of 1,000 MCMC iterations followed by 5,000 iterations. Dashed blue and red lines define the 95% credible intervals for classifying a sample as parental or hybrid.

Extended Data Fig. 3 Triangle plots for hybrid index and interspecific heterozygosity.

Purple dots indicate pure davidi individuals. Green dots indicate pure hueti individuals. Hybrid individuals (red open circles) show reduced levels of interspecific heterozygosity, consistent with advanced-generation hybridization.

Extended Data Fig. 4 Principal component analysis of the 19 climatic variables selected the four climatic variable representing climate requirement of fulvettas.

Bio4, the temperature seasonality; bio10, the mean temperature of the warmest quarter; bio11, the mean temperature of the coldest quarter; bio17, the precipitation of the driest quarter.

Extended Data Fig. 5 Candidate genes showing signals of introgression.

Individual SNPs fixed for different alleles between parental A. davidi (purple) and hueti (blue) with heterozygous genotypes in hybrid individuals. (a) IRAK4, (b) KBTBD2, (c) IL6, (d) RAPGEF5. (a)-(d) Note the number of introgressed SNPs varies among hybrid individuals. (e) Introgressed climate-associated SNPs displayed clinal variation across the hybrid zone, with most cline centers coinciding with the primary contact zone.

Extended Data Fig. 6 The allele frequencies of the candidate genes showed cline variation with climatic variables.

Relationships between the allele frequency of SNPs in either of the KBTBD2, IRAK4, IL6 and RAPGEF5 and the mean temperature of the warmest quarter (bio10, left) or the precipitation of the driest quarter (bio17, right) were shown. Species distribution ranges produced by BirdLife International and Handbook of the Birds of the World from the IUCN Red List of Threatened Species (https://www.iucnredlist.org/species/22716644/94504173). Contemporary climate layers were sourced from the Climatologies at High Resolution for the Earth’s Land Surface Areas (CHELSA) database (https://chelsa-climate.org/).

Extended Data Fig. 7 Allele frequencies of the introgressed climate-associated SNPs in the hybrids and pure parental species.

(a) The introgressed climate-associated loci showed greater heterozygosity in hybrids than in pure parental species. Boxes show the median (centre line), interquartile range (box bounds: 25th and 75th percentiles), and minimum/maximum values (whiskers). Outliers are shown as individual points. P values were calculated using two-sided Wilcoxon rank-sum tests and adjusted for multiple comparisons using the Benjamini–Hochberg procedure. (b) Percentage of allele absence of the introgressed climate-associated SNPs from the hybrids and the parental species (relative to 2100 SSP5-8.5 climate scenario).

Source data

Extended Data Fig. 8 fd-detected introgressed climate-associated variants mitigates the climate change risk.

(a) Hybrid populations (that is, site-scale GO modeling, n = 7 sampling localities) exhibit lower genetic offset than non-hybrid populations (n = 13 sampling localities) under the 2070 and 2100 SSP5-8.5 climate scenarios. (b) Hybrid individuals (that is, range-based GO modeling, n = 3,925 grids) show the least genetic offset compared to each of the three species (fratercula, n = 12,521 grids, davidi, n = 9,477 grids, hueti, n = 11,427 grids). Box plots in (a) and (b) show the median (center line), interquartile range (box bounds: 25th and 75th percentiles), and minimum/maximum values (whiskers). Outliers are shown as individual points. P values were calculated using two-sided Wilcoxon rank-sum tests and adjusted for multiple comparisons using the Benjamini–Hochberg procedure. Species distribution ranges produced by BirdLife International and Handbook of the Birds of the World from the IUCN Red List of Threatened Species (https://www.iucnredlist.org/species/22716644/94504173).

Source data

Extended Data Fig. 9 The parapatric distributions and contact zones of the fulvettas.

The ranges of fratercula, davidi, and hueti are delineated by black outlines. Putative contact zones, inferred from genetic admixture analyses, are highlighted in blue shade, with a putative hybrid zone marked in red outline. It is important to note that these inferred zones are dependent on the current sampling design and may represent underestimations of the true areas of sympatry. Species distribution ranges produced by BirdLife International and Handbook of the Birds of the World from the IUCN Red List of Threatened Species (https://www.iucnredlist.org/species/22716644/94504173). Map generated with ArcGIS v.10.6 (Esri) with elevation data from the Global Multi-resolution Terrain Elevation Data 2010 (GMTED2010), US Geological Survey105.

Extended Data Fig. 10 Slim simulations with varying σe, Esd, and σt yielded consistent results.

Each parameter combination was run 20 times to assess robustness. Results were consistent across simulations.

Supplementary information

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Supplementary Figs. 1–9 and Tables 1–8.

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Sampling and sequencing information for the individuals used in this study.

Supplementary Data 2 (download XLSX )

Statistical source data for Supplementary Fig. 7.

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Zhang, S., Chen, Y., Zang, W. et al. Hybridization mitigates climate change risk in mountainous birds. Nat. Clim. Chang. 15, 1378–1387 (2025). https://doi.org/10.1038/s41558-025-02485-w

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