Abstract
While inbreeding is known to affect individual fitness and thus population extinction risk, studies often under-represent non-model species of conservation concern and rarely examine the conditionality of inbreeding depression. Here, using genomic markers (SNPs), we determined inbreeding depression in a threatened bird, the aquatic warbler Acrocephalus paludicola – a habitat specialist with depleted genetic diversity that went through a steep recent decline. We also explored whether the magnitude of inbreeding depression depends on phenotypic (tarsus and wing length) and environmental (timing of breeding and brood size) factors. In adult males, the relationship between genomic inbreeding and breeding success depended on tarsus length, a proxy for body size, being strongly negative in small-tarsus males. We also detected a weak interaction effect between genomic inbreeding and wing length on male survival, with short-winged males being negatively affected by inbreeding. By contrast, models that did not include these interactions provided little evidence for inbreeding effects on male fitness, and estimates of inbreeding load were highly uncertain for both survival and breeding success. In adult females, we found little support for associations between genomic inbreeding and clutch size, hatching success, nestling survival, or fledged brood size, and no evidence that these relationships were conditional on the phenotypic and environmental variables examined. Accordingly, estimates of inbreeding load in females were close to zero. We conclude that inbreeding depression on fitness components is phenotype-dependent, being stronger in small-bodied males, and that considering interactions with phenotypic variables enables more accurate estimation of inbreeding depression.
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Data availability
Raw sequencing data and metadata are available in the Sequence Read Archive (Bioproject PRJNA1155693). The Python scripts used in the R2SCOs pipeline are available at https://git.imp.fu-berlin.de/begendiv/stacks2r2scos, and those used to process the population libraries can be found at https://git.imp.fu-berlin.de/begendiv/radseq-preprocessing-pipeline/-/tree/main/scripts. Individual genotype data, datasets, and R code used for the analysis can be downloaded from https://data.mendeley.com/datasets/z3fhnkjsd3.
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Acknowledgements
Grzegorz Kiljan, Pedro Costa, Piotr Guzik, Marta Celej, Julien Foucher, Beata Głębocka, Aneta Gołębiewska, Maciej Kamiński, Agnieszka Kuczyńska, Romuald Mikusek, Łukasz Mucha, Felix Närmann, Edyta Podmokła, Aneta Rybińska, Paulina Siejka, Michał Walesiak, and Laura Zani assisted in the field. Alina Gerlée kindly prepared the map. Gugny Field Station of the University of Białystok provided accommodation and workspace during fieldwork. Susan Mbedi, Ismael Reyes, and Katarzyna Dudek supported the preparation and sequencing of RAD libraries, and Wiesław Babik provided lab space and equipment. The lab work and bioinformatic analysis were partially funded by the German Federal Ministry of Education and Research (BMBF, Förderkennzeichen 033W034A). The sequencing was performed in cooperation with the Competence Center for Genome Analysis at the Christian-Albrechts-University in Kiel and at the Berlin Center for Genomics in Biodiversity Research. We thank Przemysław Chylarecki, who provided advice on the statistical analysis. The study was funded by the Polish National Science Centre’s grant no. 2016/20/S/NZ8/00434. We thank the editor and three anonymous referees for comments on previous versions of the manuscript.
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JK designed and performed research; SS, JK & MHR carried out lab work; LSA, MHR, CJM & JK performed bioinformatic analysis; JK conducted statistical and parentage analysis; JK, TO & CJM provided funding and resources; JK wrote the paper; all the authors edited drafts.
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The study was aligned with the Polish animal welfare and conservation law. Bird capture was conducted under permits from the Polish Ministry of Environment (DOP-WPN.286.38.2016.AN, DOP-WPN.286.40.2016.AN) and the Regional Directorate of Environmental Protection in Białystok (WPN.6401.244.2016.MN). Ringing was performed by licensed ringers. Blood samples were collected under a permit from the I Local Ethical Committee in Warsaw (185/2016).
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Kubacka, J., Arantes, L.S., Herdegen-Radwan, M. et al. It is hard to be small: Inbreeding depression on male breeding success depends on body size in a threatened songbird.
Heredity (2026). https://doi.org/10.1038/s41437-026-00859-0
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DOI: https://doi.org/10.1038/s41437-026-00859-0
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