Genetic and genomic monitoring with minimally invasive sampling methods

Abstract

The decreasing cost and increasing scope and power of emerging genomic technologies are reshaping the field of molecular ecology. However, many modern genomic approaches (e.g., RAD‐seq) require large amounts of high‐quality template DNA. This poses a problem for an active branch of conservation biology: genetic monitoring using minimally invasive sampling (MIS) methods. Without handling or even observing an animal, MIS methods (e.g., collection of hair, skin, faeces) can provide genetic information on individuals or populations. Such samples typically yield low‐quality and/or quantities of DNA, restricting the type of molecular methods that can be used. Despite this limitation, genetic monitoring using MIS is an effective tool for estimating population demographic parameters and monitoring genetic diversity in natural populations. Genetic monitoring is likely to become more important in the future as many natural populations are undergoing anthropogenically driven declines, which are unlikely to abate without intensive adaptive management efforts that often include MIS approaches. Here, we profile the expanding suite of genomic methods and platforms compatible with producing genotypes from MIS, considering factors such as development costs and error rates. We evaluate how powerful new approaches will enhance our ability to investigate questions typically answered using genetic monitoring, such as estimating abundance, genetic structure and relatedness. As the field is in a period of unusually rapid transition, we also highlight the importance of legacy data sets and recommend how to address the challenges of moving between traditional and next‐generation genetic monitoring platforms. Finally, we consider how genetic monitoring could move beyond genotypes in the future. For example, assessing microbiomes or epigenetic markers could provide a greater understanding of the relationship between individuals and their environment.

Monitoring vultures in the 21st century: The need for standardized protocols

“…The use of non-invasive genetic-based techniques, in particular, has enabled the estimation of demographic parameters for many long-lived species that are elusive, wide-ranging or rare. The identification of individuals by their multi-locus genotypes enables a 'capture-recapture' framework to estimate vital rates (such as survival and recruitment), and derive population size, growth and viability (Carroll et al, 2018). Rapid development of genetic techniques are making non-invasive monitoring more efficient and financially viable (Carroll et al, 2018).…”

“…The identification of individuals by their multi-locus genotypes enables a 'capture-recapture' framework to estimate vital rates (such as survival and recruitment), and derive population size, growth and viability (Carroll et al, 2018). Rapid development of genetic techniques are making non-invasive monitoring more efficient and financially viable (Carroll et al, 2018). However, a 'conservation genetic gap' has emerged between genetic research and its practical application, partially due to lack of access to expertise and funding by conservation managers, particularly in developing countries (Taylor, Dussex, & van Heezik, 2017).…”

“…Yet, molecular techniques continue to be improved for their implementation by personnel with limited training, and a large number of laboratories offer these services (see Data S1). Even with laboratory services, this approach is more cost effective when compared with live-capturing and marking individuals (Carroll et al, 2018).…”

Targeted resequencing of codingDNAsequences forSNPdiscovery in nonmodel species

“…SNP genotyping techniques such as GT-seq (Campbell, Harmon, & Narum, 2015) were not considered; although these perform well when invasive sampling is possible, they have lower success rates when working with low DNA concentrations (e.g., Carroll et al, 2018).…”

Next‐generation conservation genetics and biodiversity monitoring

“…Carroll et al (2018) target the interface between MIS methods and NGS approaches. Minimally invasive samples are often opportunistically collected from the environment and consequently contain limited amounts of DNA, which can restrict the subsequent molecular analyses of these samples, especially when applying NGS methods.The authors provide guidance on how to transition legacy datasets of microsatellites or mitochondrial DNA to genomic platforms and integrate novel methods such as microbiome and epigenetic studies Swift et al (2018).…”