Genetic fingerprinting proves cross‐correlated automatic photo‐identification of individuals as highly efficient in large capture–mark–recapture studies

Abstract

Capture–mark–recapture (CMR) approaches are the backbone of many studies in population ecology to gain insight on the life cycle, migration, habitat use, and demography of target species. The reliable and repeatable recognition of an individual throughout its lifetime is the basic requirement of a CMR study. Although invasive techniques are available to mark individuals permanently, noninvasive methods for individual recognition mainly rest on photographic identification of external body markings, which are unique at the individual level. The re-identification of an individual based on comparing shape patterns of photographs by eye is commonly used. Automated processes for photographic re-identification have been recently established, but their performance in large datasets (i.e., > 1000 individuals) has rarely been tested thoroughly. Here, we evaluated the performance of the program AMPHIDENT, an automatic algorithm to identify individuals on the basis of ventral spot patterns in the great crested newt (Triturus cristatus) versus the genotypic fingerprint of individuals based on highly polymorphic microsatellite loci using GENECAP. Between 2008 and 2010, we captured, sampled and photographed adult newts and calculated for 1648 samples/photographs recapture rates for both approaches. Recapture rates differed slightly with 8.34% for GENECAP and 9.83% for AMPHIDENT. With an estimated rate of 2% false rejections (FRR) and 0.00% false acceptances (FAR), AMPHIDENT proved to be a highly reliable algorithm for CMR studies of large datasets. We conclude that the application of automatic recognition software of individual photographs can be a rather powerful and reliable tool in noninvasive CMR studies for a large number of individuals. Because the cross-correlation of standardized shape patterns is generally applicable to any pattern that provides enough information, this algorithm is capable of becoming a single application with broad use in CMR studies for many species.

Genotyping validates photo‐identification by the head scale pattern in a large population of the European adder (Vipera berus)

“…Double-marking studies provide a reliable way to compare the performance of two independent individual recognition procedures, but have rarely been applied to studies of natural markings (but see (Stevick, Palsbøll, Smith, Bravington, & Hammond, 2001;Gosselin, Sainte-Marie, & Sévigny, 2007;Drechsler, Helling, & Steinfartz, 2015)). Our double-marking study convincingly demonstrates that The first image of each animal was taken within weeks after its birth, and the next images at their recapture as an adult several years later.…”

Photographic identification of individuals of a free‐ranging, small terrestrial vertebrate

“…2013; Drechsler et al. 2015). A simple and freely available software package, Interactive Individual Identification System, I 3 S Pattern v.4.0.2 (Hartog and Reijns 2014), is a pattern‐matching algorithm that has the potential to be applied to any species with variable markings (Speed et al.…”

“…2013; Drechsler et al. 2015). This reintroduces the potential stress that the noninvasive technique is supposed to avoid, and involves a large effort to capture the animal for photography.…”

“…One way to overcome the difficulty of cross-matching large datasets is by computer-assisted matching of photos of unknown individuals to a reference library. A number of algorithms have been developed for this purpose, but many are highly specialized for particular species or for specific morphological features (Speed et al 2007;Bolger et al 2012;Town et al 2013;Drechsler et al 2015). A simple and freely available software package, Interactive Individual Identification System, I 3 S Pattern v.4.0.2 (Hartog and Reijns 2014), is a pattern-matching algorithm that has the potential to be applied to any species with variable markings (Speed et al 2007;Hartog and Reijns 2014).…”

“…For smaller taxa (<500 g), parallax effects are likely to be exacerbated because of the comparatively small body areas being photographed. Most studies of smaller-sized fauna have controlled for the parallax problem by capturing the animal and manipulating it into a fixed position relative to the camera, photographing either in-hand or using a holding pen (Bradfield 2004;Frisch and Hobbs 2007;Sacchi et al 2007;Hachtel et al 2009;Kenyon et al 2009;Knox et al 2013;Rocha et al 2013;Drechsler et al 2015). This reintroduces the potential stress that the noninvasive technique is supposed to avoid, and involves a large effort to capture the animal for photography.…”