Conservation genetics of otters: Review about the use of non-invasive samples

Abstract

Wild population management programs require determining some fundamental aspects for conservation, including population structure, flow between populations, evolutionary history and kinship, among others. Since sample collection from wild mammals for DNA extraction is a complex task, conservation genetics has developed non-invasive sampling techniques, which allow obtaining DNA without the need to capture individuals. For the genetic characterization of otter populations, stools are frequently used as source of DNA for amplification of molecular markers (microsatellites, mitochondrial segments and sequences for determining sex) in studies on genetic diversity, phylogeography, population structure and size, among others. This review summarizes the application of non-invasive sampling techniques in genetic studies of otter species. Genetic characterization studies that use stools as source of DNA support the usefulness of this material to get amplified markers in the genotyping of individuals. They also suggest the use of fresh samples and appropriate conservation methods to avoid DNA degradation, as well as quantify the potential errors in genotyping, such as false and null alleles. En los programas de manejo de poblaciones silvestres es necesario conocer algunos aspectos fundamentales para su conservación como la estructura poblacional, el flujo entre poblaciones, la historia evolutiva y el parentesco, entre otros. Dado que en mamíferos silvestres es difícil acceder a muestras para la extracción de ADN, la genética de la conservación ha desarrollado técnicas de muestreo no invasivas, que permiten obtener ADN sin necesidad de capturar los individuos. En la caracterización genética de poblaciones de nutrias se emplean frecuentemente las heces como fuente de ADN para la amplificación de marcadores moleculares (microsatélites, segmentos mitocondriales y secuencias para la determinación del sexo) en estudios de diversidad genética, filogeografía, estructura y tamaño de las poblaciones, entre otros. En ésta revisión se presenta una síntesis de la aplicación de técnicas de muestreo no invasivas en los estudios genéticos de las especies de nutria. Los estudios de caracterización genética, utilizando heces como fuente de ADN, coinciden en la utilidad de este material para obtener amplificados de calidad en la genotipificación de individuos. También sugieren el uso de muestras frescas y la aplicación de métodos de conservación apropiados para evitar la degradación del ADN y cuantificar los posibles errores de genotipificación como los alelos falsos y nulos. ADN mitocondrial, diversidad genética, microsatélites, marcadores moleculares, muestreos no invasivos, nutrias.

Two hundred and five newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates

“…Although the number of whole genomes available for nonmodel organisms has grown dramatically, mitochondrial DNA (mtDNA) remains a cornerstone for many areas of research, including species diversification dynamics, phylogenetics, and conservation genetics (Cardeñosa et al, 2021; Flores‐Manzanero et al, 2022; Reese et al, 2020; Schmidt et al, 2018; Serrao et al, 2018), especially for study species from which high‐quality tissue samples cannot be easily obtained. Difficulties with invasive sampling for high‐quality tissues or blood include practical issues with trapping large‐bodied, arboreal, or marine animals, as well as ethical considerations, such as risks to the animal and to researchers (Aristizabal Duque et al, 2018). These difficulties apply to collecting invasive samples from most primates, and many genetic and genomic studies in primatology continue to rely on materials that can be collected noninvasively (Arandjelovic & Vigilant, 2018; Aylward et al, 2018; Orkin et al, 2016), or on historic samples, such as from museum skins (Burrell et al, 2015).…”

Comparison of DNA quantity and quality from fecal samples of mammals transported in ethanol or lysis buffer

“…This method is noninvasive, especially when researchers can directly observe the animal excreting the stool, as seen in the case of Atelidae primates [ 8 ], or when the samples exhibit species-specific characteristics, as in Andean bears, tapirs, felines, and certain domestic animals [ 9 ]. Additionally, the relatively low cost associated with fecal sample collection sets it apart from more invasive methods, such as blood draws or tissue biopsies, which may require pre-medication or physical constraints [ 10 , 11 ].…”

A Noninvasive Genetic Insight into the Spatial and Social Organization of an Endangered Population of the Eurasian Otter (Lutra lutra, Mustelidae, Carnivora)

“…Technical advances in molecular ecology offer an alternative way to monitor these rare and elusive species in a noninvasive way. Specifically, the analysis of variable microsatellite loci allows obtaining a genetic fingerprint that can be used to estimate population abundance, genetic structure, and degree of relatedness in many species, including otters [4,[30][31][32][33][34][35][36][37], as well as to gather information on territorial and social behavior [38][39][40][41][42][43][44][45][46][47][48][49]. Most noninvasive genetic sampling on otters is based on DNA extraction from spraints (i.e., feces) and anal jelly produced by their anal glands and used for scent marking [49][50][51].…”

“…Most noninvasive genetic sampling on otters is based on DNA extraction from spraints (i.e., feces) and anal jelly produced by their anal glands and used for scent marking [49][50][51]. Although this technique has been applied to gather information on the population density and genetic structure of otters in various European countries [4,[34][35][36][37][38][39][40][41][42][43][44][45], its use in exploring spatial and social organization has yet to be examined except by a few studies [38][39][40]42,43,45]. Specifically, noninvasively collected sample material has been used to explore the marking behavior of male and female otters in Germany [49] and individual distribution and dispersal in Spain, Germany, Portugal, France, and the Netherlands [38,39,[43][44][45].…”