No abstract

The main goal of non‐invasive genetic capture‐mark‐recapture (CMR) analysis is to gain an unbiased and reliable population size estimate of species that cannot be sampled directly. The method has become an important and widely used tool to research and manage wildlife populations. However, researchers have to struggle with low amplification success rates and genotyping errors, which substantially bias subsequent analysis. To receive reliable results and to minimize the time and costs required for non‐invasive microsatellite genotyping, one must carefully choose a species‐specific sampling design, methods that maximize the amount of template DNA, and methods that could overcome genotyping errors, especially when using low‐quality samples. This article reviews the literature and the pros and cons of the main methods used along the process described above. The review is strengthened by a case study on Eurasian otters (Lutra lutra) using feces; we tested several methods for their appropriateness to accommodate for genotyping errors. Based on this method testing, we demonstrated that high genotyping error rates are the key problem in this process leading to a severely flawed dataset if no consensus genotype is formed. However, even if generating consensus genotypes minimizes errors dramatically, we show that it may not achieve a definite eradication of all errors, which results in overestimated population sizes if conventional estimators are used. In conjunction with these findings, we offer a step‐by‐step protocol for non‐invasive genetic CMR studies to achieve a reliable estimate of population sizes in the presence of high genotyping error rates. © 2013 The Wildlife Society.

Although habitat loss and fragmentation threaten species throughout the world and are a major threat to biodiversity, it is apparent that some species are at greater risk of extinction in fragmented landscapes than others. Identification of these species and the characteristics that make them sensitive to habitat fragmentation has important implications for conservation management. Here, we present a comparative study of the population genetic structure of two arboreal gecko species (Oedura reticulata and Gehyra variegata) in fragmented and continuous woodlands. The species differ in their level of persistence in remnant vegetation patches (the former exhibiting a higher extinction rate than the latter). Previous demographic and modelling studies of these two species have suggested that their difference in persistence levels may be due, in part, to differences in dispersal abilities with G. variegata expected to have higher dispersal rates than O. reticulata. We tested this hypothesis and genotyped a total of 345 O. reticulata from 12 sites and 353 G. variegata from 13 sites at nine microsatellite loci. We showed that O. reticulata exhibits elevated levels of structure (FST=0.102 vs. 0.044), lower levels of genetic diversity (HE=0.79 vs. 0.88), and fewer misassignments (20% vs. 30%) than similarly fragmented populations of G. variegata, while all these parameters were fairly similar for the two species in the continuous forest populations (FST=0.003 vs. 0.004, HE=0.89 vs. 0.89, misassignments: 58% vs. 53%, respectively). For both species, genetic structure was higher and genetic diversity was lower among fragmented populations than among those in the nature reserves. In addition, assignment tests and spatial autocorrelation revealed that small distances of about 500 m through fragmented landscapes are a barrier to O. reticulata but not for G. variegata. These data support our hypothesis that G. variegata disperse more readily and more frequently than O. reticulata and that dispersal and habitat specialization are critical factors in the persistence of species in habitat remnants.

The effective population size (Ne) is proportional to the loss of genetic diversity and the rate of inbreeding, and its accurate estimation is crucial for the monitoring of small populations. Here, we integrate temporal studies of the gecko Oedura reticulata, to compare genetic and demographic estimators of Ne. Because geckos have overlapping generations, our goal was to demographically estimate NbI, the inbreeding effective number of breeders and to calculate the NbI/Na ratio (Na = number of adults) for four populations. Demographically estimated NbI ranged from 1 to 65 individuals. The mean reduction in the effective number of breeders relative to census size (NbI/Na) was 0.1 to 1.1. We identified the variance in reproductive success as the most important variable contributing to reduction of this ratio. We used four methods to estimate the genetic based inbreeding effective number of breeders NbI(gen) and the variance effective populations size NeV(gen) estimates from the genotype data. Two of these methods - a temporal moment-based (MBT) and a likelihood-based approach (TM3) require at least two samples in time, while the other two were single-sample estimators - the linkage disequilibrium method with bias correction LDNe and the program ONeSAMP. The genetic based estimates were fairly similar across methods and also similar to the demographic estimates excluding those estimates, in which upper confidence interval boundaries were uninformative. For example, LDNe and ONeSAMP estimates ranged from 14–55 and 24–48 individuals, respectively. However, temporal methods suffered from a large variation in confidence intervals and concerns about the prior information. We conclude that the single-sample estimators are an acceptable short-cut to estimate NbI for species such as geckos and will be of great importance for the monitoring of species in fragmented landscapes.