Genetic and genomic monitoring with minimally invasive sampling methods

Abstract

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 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 datasets 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.PeerJ Preprints | https://doi.org/10.7287/peerj.preprints.3209v1 | CC BY 4.0 Open Access |

Genetic tagging in the Anthropocene: scaling ecology from alleles to ecosystems

“…Indeed, these approaches have recently been used to assess shark diversity (Bakker et al 2017) and niche partitioning (Kartzinel et al 2015), but challenges remain in using eDNA to infer abundance (Rice et al 2018). Integrating these rapidly advancing community-level approaches with the population-level advances detailed here and the growing field of genomics (Carroll et al 2018), presents further opportunity for ecological insight that scales from the allele to the ecosystem. With the rise of evidence-based policy under a rapidly changing environmental context, genetic tags are poised to advance the frontiers of ecology, conservation, and our understanding of the natural world in the Anthropocene.…”

“…MIS of genetic material, often scat or hair, is more likely to degrade or become contaminated by sampling procedures , Carroll et al 2018. For example, hair follicles exposed to ultraviolet light and moisture may result in DNA broken into 100-500 base pair fragments; limiting the number and length of molecular markers that can be generated (Andrews et al 2018).…”

“…The majority of studies reviewed here have relied on microsatellite loci to identify individuals and reconstruct family dyads and pedigrees. Due to the cost and time required to develop species and population-specific parameters from microsatellite loci, this approach provides a limited number of genetic markers to create accurate pedigrees, reconstruct population-level parameter estimates, and infer connectivity and gene flow (reviewed here; Andrews et al 2018, Carroll et al 2018. However, Russello et al (2015) and others (Andrews et al 2018, Carroll et al 2018, Ekblom et al 2018 provide new approaches to assess genome-wide data in wild populations using MIS approaches.…”

“…Genetic tags derived from spoors (e.g., scat, hair, feathers, saliva), which are used to genotype individuals, produce a unique and immutable identification tag for each organism. Information from genetic tags can also include sex (Waits and Paetkau 2005), and for some material, such as hair, additional molecular and hormone analyses can provide age class (Carroll et al 2018, Cattet et al 2018, reproductive status (Cattet et al 2017), diet , and stress level (Lafferty et al 2015). These spoors can be collected using minimally invasive methods (e.g., Piggott and Taylor [2003] or Henry and Russello [2011], also termed "noninvasive"), over vast areas, and by non-specialist participants like citizen scientists.…”

Quantitative analysis of connectivity in populations of a semi‐aquatic mammal using kinship categories and network assortativity

“…Noninvasive and minimally invasive samples such as hair samples are prone to genotyping errors due to low DNA quality and quantity (Carroll et al, 2018;Pompanon, Bonin, Bellemain, & Taberlet, 2005).…”