A standardized approach to empirically define reliable assignment thresholds and appropriate management categories in deeply introgressed populations

Abstract

Anthropogenic hybridization is recognized as a major threat to the long-term survival of natural populations. While identifying F1 hybrids might be simple, the detection of older admixed individuals is far from trivial and it is still debated whether they should be targets of management. Examples of anthropogenic hybridization have been described between wolves and domestic dogs, with numerous cases detected in the Italian wolf population. After selecting appropriate wild and domestic reference populations, we used empirical and simulated 39-autosomal microsatellite genotypes, Bayesian assignment and performance analyses to develop a workflow to detect different levels of wolf x dog admixture. Membership proportions to the wild cluster (q iw ) and performance indexes identified two qthresholds which allowed to efficiently classify the analysed genotypes into three assignment classes: pure (with no or negligible domestic ancestry), older admixed (with a marginal domestic ancestry) and recent admixed (with a clearly detectable domestic ancestry) animals. Based on their potential to spread domestic variants, such classes were used to define three corresponding management categories: operational pure, introgressed and operational hybrid individuals. Our multiple-criteria approach can help wildlife managers and decision makers in more efficiently targeting the available resources for the long-term conservation of species threatened by anthropogenic hybridization.Over the last decades, thanks to the growing availability of genetic and genomic data, hybridization has been increasingly studied for its evolutionary and conservational implications on the long-term survival of the involved taxa 1-5 . However, while natural hybridization between closely related taxa is frequently acknowledged as an evolutionary process providing novel adaptive gene assemblages 6,7 , anthropogenic hybridization (AH), mainly caused by intentional admixture, translocations, habitat modifications and climate changes 8-10 , is globally considered a serious conservation threat to the genetic integrity of local populations, which might be compromised by gene introgression from alien or domesticated species [11][12][13][14][15][16] . Thus, the consequences of such human-mediated process should be continuously monitored to evaluate their real effects on the viability of natural populations 5,17 .However, to date, even in the era of genomics 4,18 , the concept of hybrid itself is rather fleeting and, consequently, legal status and management of hybrids are often poorly regulated by national and international laws, hampering the conservation of endangered species 12,14,[19][20][21][22]

Estimating Admixture at the Population Scale: Taking Imperfect Detectability and Uncertainty in Hybrid Classification Seriously

“…We performed Bayesian clustering procedures on the 12‐loci multilocus reliable genotypes obtained from the 4−8 replicated amplifications per locus per sample using the R package parallel structure (Besnier and Glover 2013). Such software can produce more stable assignment coefficients that are not affected by sample sizes or samples with variable levels of admixture (Caniglia et al 2020) because the software automatically subdivides a dataset of genotypes to be assigned to predefined reference populations into multiple single projects (each project is composed of the reference populations and 1 of the genotypes to be assigned), which are independently run. For each individual genotype, we estimated the individual proportions of membership ( q i ) and the 90% Bayesian credible intervals (BCI) to the 2 inferred clusters (K); details about the Bayesian assignment test models are reported in Caniglia et al (2020).…”

“…In Europe, several wolf populations are currently re‐expanding their range across human‐dominated landscapes (Chapron et al 2014) where dogs have become the most abundant carnivore (Ritchie et al 2014). Accordingly, recent introgressive hybridization (i.e., up to 3 generations in the past; Caniglia et al 2020) has been recently detected in several wolf populations in Eurasia (Galaverni et al 2017, Pacheco et al 2017, Pilot et al 2018, Salvatori et al 2020). Detection and monitoring of wolf‐dog hybridization within wolf populations is therefore considered a conservation priority at the European scale (Hindrikson et al 2017, Donfrancesco et al 2019, Salvatori et al 2020).…”

“…We applied a multievent capture‐recapture (CR) model developed by Santostasi et al (2019) to estimate prevalence of admixture in a wolf population in the northern Apennines, Italy, accounting for imperfect detectability and uncertainty in the probabilistic assignment of admixed individuals. Building on previous work aimed at optimizing the genetic procedures to detect wolf‐dog hybrids (Caniglia et al 2020), our first objective was to estimate the proportion of admixture accounting for the sampling and estimation problems that affect naïve estimates of prevalence; in doing so, we explored 2 alternative rationales to classify admixed individuals: the current practice to minimize Type 1 error versus a more precautionary approach to balance between Type 1 and 2 error rates. Our second objective was to investigate the reproductive status of admixed individuals within the studied population.…”

Hybridization and range expansion in tamarisk beetles (Diorhabda spp.) introduced to North America for classical biological control

“…Using those diagnostic samples to assign clusters to species identity, we examined the confidence intervals across independent runs to conservatively identify the threshold at which ancestry could be confidently inferred, q = 0.067 (i.e. the lower-bound of the 90% credible interval), below which admixture identification could be unreliable and due to technical biases (Caniglia et al, 2020).…”

Reliable Wolf-Dog Hybrid Detection in Europe Using a Reduced SNP Panel Developed for Non-Invasively Collected Samples

“…Further, microsatellites markers, either solely or in combination with other markers, have been used to assess the admixture between wolves and domestic dogs (C. l. familiaris); reported rates of admixed animals in local wolf populations range between 0 and 10 % (e.g., Godinho et al 2011, Moura et al 2014, Dufresnes et al 2019, but see for instance Salvatori et al 2019 for locally higher admixture rates). However, identi cation of wolf-dog hybrids based on microsatellite data is far from trivial, due to the low number of alleles with distinctive frequencies between wolves and dogs, the rather limited number of loci used in many studies, and the fact that results strongly depend on reference samples and the extent of population substructure in the dataset (Primmer & Vähä 2006, Steyer et al 2018, Caniglia et al 2020. Moreover, the fact that most laboratories have relied on different panels of microsatellite markers, has hampered the comparability of data on wolf-dog admixture across populations, limiting our knowledge on the extent of hybridization (de Groot et al 2016).…”