Distinguishing the victim from the threat: SNP-based methods reveal the extent of introgressive hybridization between wildcats and domestic cats in Scotland and inform future in situ and ex situ management options for species restoration

Abstract

The degree of introgressive hybridization between the Scottish wildcat and domestic cat has long been suspected to be advanced. Here, we use a 35-SNP-marker test, designed to assess hybridization between wildcat and domestic cat populations in Scotland, to assess a database of 295 wild-living and captive cat samples, and test the assumptions of the test using 3,097 SNP markers generated independently in a subset of the data using ddRAD. We discovered that despite increased genetic resolution provided by these methods, wild-living cats in Scotland show a complete genetic continuum or hybrid swarm structure when judged against reference data. The historical population of wildcats, although hybridized, clearly groups at one end of this continuum, as does the captive population of wildcats. The interpretation of pelage scores against nuclear genetic data continues to be problematic. This is probably because of a breakdown in linkage equilibrium between wildcat pelage genes as the two populations have become increasingly mixed, meaning that pelage score or SNP score alone is poor diagnostic predictors of hybrid status. Until better tools become available, both should be used jointly, where possible, when making management decisions about individual cats. We recommend that the conservation community in Scotland must now define clearly what measures are to be used to diagnose a wildcat in the wild in Scotland, if future conservation action is to be effective.

Keywords: captive populations; carnivores; conservation management; invasive species.

Figure 1

Verification of the 35SNP test. (a) Structure algorithm run only on the complete set of data of wild‐living cats (35SNP_non‐ref_dataset), in the absence of any other reference data captive or domestic, reveals that results still correlate highly with scores generated for the full dataset; thus, any potential effect introduced by inbreeding within the captive population or biases in the reference data can be ruled out. (b) Independent assessment of 76 cats using 3,097 SNPs gleaned from the ddRAD pipeline reveals that the majority of estimates fall within the 90% CI obtained from the original test. (c) And the management decision taken on the basis of the 35SNP test would not appear to differ greatly where the estimate from the larger 3097SNP dataset taken to be the true hybrid score (see in text for details).(d) A graphical presentation of the absolute difference in values obtained by the 3097SNP and 35SNP test against the values obtained by the 35SNP test illustrates in more detail the expected variance in the results

Figure 2

Hybrid scores obtained from the different datasets. Each score represents an individual cat. Each cat is given an estimated hybrid score Q by the software STRUCTURE with the limits of the lower and upper boundary of the 90% credibility interval marked with the vertical error bars. The scores have been ranked according to their position in the global dataset of all 35 SNP‐typed cats (all rankings are given as the grey shadow) and are presented in separate windows for each dataset. Cat that meet the 75% cut‐off for wildcat (LBQ ≥ 0.75) are presented in blue, those classed as hybrid are orange, and those with UBQ ≤ 0.25 are classed as domestic and are presented in red. Details of each dataset can be found in text

Figure 3

A map of Scotland with the locations of cats samples within the datasets 35SNP_historical_cats (circles), 35SNP_wildliving_dead_cats (triangles) and 35SNP_wildliving_survey_cats (squares). Where only a verbal location was given, the approximate location was chosen with the aid of Google Maps (e.g., the blue cluster in the map centre). Overlapping points were separated manually for ease of viewing, whilst respecting the boundaries of the Wildcat Priority Areas which are given in red. Points are coloured using the same genetic categories used for Figure 2

Figure 4

(a) The relationship between Q_35 and the 7PS pelage score. (b) Prediction from the model in Table 2 for logit‐transformed Q_35. Dashed lines represent the cut‐off values of Q = Logit(0.75) and 7Ps = 17 for genetic and pelage systems, respectively. (c) The number of individuals in the genetic and pelage categories for management purposes