In their correspondence, Slate and Pemberton [1xDoes reduced heterozygosity depress sperm quality in wild rabbits (Oryctolagus cuniculus)?. Slate, J. and Pemberton, J. Curr. Biol. 2006; 16: 790–791Abstract | Full Text | Full Text PDF | Scopus (27)See all References[1] argue that the key interpretation of our study, namely the finding of a negative correlation between heterozygosity and sperm abnormality across wild UK rabbits [2xReduced heterozygosity depresses sperm quality in wild rabbits, Oryctolagus cuniculus. Gage, M.J.G., Surridge, A.K., Tomkins, J.L., Green, E., Wiskin, L., Bell, D.J., and Hewitt, G.M. Curr. Biol. 2006; 16: 612–617Abstract | Full Text | Full Text PDF | PubMed | Scopus (72)See all References[2], is flawed. According to their view, the reason for this is that our analysis did not adequately deal with population stratification. Slate and Pemberton [1xDoes reduced heterozygosity depress sperm quality in wild rabbits (Oryctolagus cuniculus)?. Slate, J. and Pemberton, J. Curr. Biol. 2006; 16: 790–791Abstract | Full Text | Full Text PDF | Scopus (27)See all References[1] claim that demonstrations of heterozygosity–fitness correlations are only convincing when heterozygosity–fitness relationships are found across individuals within populations.Slate and Pemberton [1xDoes reduced heterozygosity depress sperm quality in wild rabbits (Oryctolagus cuniculus)?. Slate, J. and Pemberton, J. Curr. Biol. 2006; 16: 790–791Abstract | Full Text | Full Text PDF | Scopus (27)See all References[1] rightly point out that sampling individuals from different geographic origins could confound associations because of environmental heterogeneity at the sites. Such problems are inherent to all correlative studies in the natural environment. There is a subjective problem of defining which level of a ‘population’ will actually control for environmental heterogeneity. In our system, for instance, mobile male rabbits [3xNatal dispersal and genetic structure in a population of the European wild rabbit (Oryctolagus cuniculus). Webb, N.J., Ibrahim, K.M., Bell, D.J., and Hewitt, G.M. Mol. Ecol. 1999; 4: 239–247CrossrefSee all References[3] will be exposed to uncontrolled environmental variation even within a ‘site’.In our study [2xReduced heterozygosity depresses sperm quality in wild rabbits, Oryctolagus cuniculus. Gage, M.J.G., Surridge, A.K., Tomkins, J.L., Green, E., Wiskin, L., Bell, D.J., and Hewitt, G.M. Curr. Biol. 2006; 16: 612–617Abstract | Full Text | Full Text PDF | PubMed | Scopus (72)See all References[2], we explore some potential environmental heterogeneity: the correlation of population heterozygosity means shows that the relationship holds; moreover, there is no covariance with body mass or condition, which are possible indicators of environmental influence. The relationship we found also holds across separate ‘mainland’ or ‘island’ samples.Moreover, we applied the model suggested by Slate and Pemberton [1xDoes reduced heterozygosity depress sperm quality in wild rabbits (Oryctolagus cuniculus)?. Slate, J. and Pemberton, J. Curr. Biol. 2006; 16: 790–791Abstract | Full Text | Full Text PDF | Scopus (27)See all References[1] and controlled for ‘population’ by fitting it as a categorical term. Across individuals, the relationship remains significant (F = 23.3, P < 0.0001) (similar if we also include body mass, F = 15.8, P < 0.0001). However, as one of the referees observed, there are concerns about the validity of this analysis because non-random covariation exists between the independent variable (heterozygosity) and ‘population’, hence, the relationship across population means.A particular problem presented by UK rabbits is that their populations are genetically structured at extremely fine scales: sites in East Anglia separated by a few hundred metres are as different as those separated by 125 kilometres [4xFrom population structure to individual behaviour: genetic analysis of social structure in the European wild rabbit (Oryctolagus cuniculus). Surridge, A.K., Bell, D.J., and Hewitt, G.M. Biol. J. Linn. Soc. 1999; 68: 57–71CrossrefSee all References, 5xFine-scale genetic structuring in a natural population of European wild rabbits (Oryctolagus cuniculus). Surridge, A.K., Ibrahim, K.M., Bell, D.J., Webb, N.J., Rico, C., and Hewitt, G.M. Mol. Ecol. 1999; 8: 299–307Crossref | PubMed | Scopus (47)See all References, 6xPopulation structure and genetic variation of European wild rabbits (Oryctolagus cuniculus) in East Anglia. Surridge, A.K., Bell, D.J., Ibrahim, K.M., and Hewitt, G.M. Heredity. 1999; 82: 479–487Crossref | PubMedSee all References]. Such extreme differentiation means that insufficient genetic variation exists within discrete ‘populations’ to explore fitness relationships, with potential non-independence due to close relatedness.Our results clearly indicate the established importance [7xDoes heterozygosity estimate inbreeding in real populations?. Balloux, F., Amos, W., and Coulson, T. Mol. Ecol. 2004; 13: 3021–3031Crossref | PubMed | Scopus (290)See all References[7] of sampling very low heterozygosities for revealing possible fitness correlations: the relationship is heavily influenced by a small number (∼12) of strongly homozygous males (one homozygous at all 29 loci). These individuals will be rare in the wild in general, and even rarer within one discrete population that holds individuals with a high degree of heterozygosity. Without an isolation-by-distance relationship, such fine-scale structuring also means that our sampling sites contain numerous ‘populations’. As sampling was spread throughout most areas by several kilometres, we can be confident that most individuals represent single samples from different ‘populations’ by those criteria.A key consideration is what constitutes a discrete population? There are arguments for designating the UK to be a population at one level of interpretation: rabbits colonised the wild recently, in the 18th century [4xFrom population structure to individual behaviour: genetic analysis of social structure in the European wild rabbit (Oryctolagus cuniculus). Surridge, A.K., Bell, D.J., and Hewitt, G.M. Biol. J. Linn. Soc. 1999; 68: 57–71CrossrefSee all References, 8xThe European Rabbit: History and Biology of a Successful Colonizer. Thompson, H.V. and King, C.M. See all References], providing us with a natural experiment. However, we agree that we cannot eliminate all potential confounds. Although our study was founded upon evidence that heavily inbred big cats have unusually elevated sperm abnormalities [9xReproductive characteristics of male Florida panthers: comparative studies from Florida, Texas, Colorado, Latin America, and North American zoos. Barone, M.A., Roelke, M.E., Howard, J., Brown, J.L., Anderson, A.E., and Wildt, D.E. J. Mammal. 1994; 75: 150–162CrossrefSee all References[9], we cannot exclude additional interpretations, such as that proposed by Slate and Pemberton [1xDoes reduced heterozygosity depress sperm quality in wild rabbits (Oryctolagus cuniculus)?. Slate, J. and Pemberton, J. Curr. Biol. 2006; 16: 790–791Abstract | Full Text | Full Text PDF | Scopus (27)See all References[1]: abnormal sperm constrain reproductive output which leads to inbreeding. Ideally, we would match our natural environment correlations with experiments that applied tight ‘environmental’ control. However, complementary approaches are important because inbreeding depression could be influenced by both genetic and environmental variation [10xInbreeding effects in wild populations. Keller, L.F. and Waller, D.M. Trends Ecol. Evol. 2002; 17: 230–241Abstract | Full Text | Full Text PDF | Scopus (1423)See all References[10].