Double‐digest RAD sequencing outperforms microsatellite loci at assigning paternity and estimating relatedness: A proof of concept in a highly promiscuous bird

Abstract

Information on genetic relationships among individuals is essential to many studies of the behaviour and ecology of wild organisms. Parentage and relatedness assays based on large numbers of single nucleotide polymorphism (SNP) loci hold substantial advantages over the microsatellite markers traditionally used for these purposes. We present a double-digest restriction site-associated DNA sequencing (ddRAD-seq) analysis pipeline that, as such, simultaneously achieves the SNP discovery and genotyping steps and which is optimized to return a statistically powerful set of SNP markers (typically 150-600 after stringent filtering) from large numbers of individuals (up to 240 per run). We explore the trade-offs inherent in this approach through a set of experiments in a species with a complex social system, the variegated fairy-wren (Malurus lamberti) and further validate it in a phylogenetically broad set of other bird species. Through direct comparisons with a parallel data set from a robust panel of highly variable microsatellite markers, we show that this ddRAD-seq approach results in substantially improved power to discriminate among potential relatives and considerably more precise estimates of relatedness coefficients. The pipeline is designed to be universally applicable to all bird species (and with minor modifications to many other taxa), to be cost- and time-efficient, and to be replicable across independent runs such that genotype data from different study periods can be combined and analysed as field samples are accumulated.

Comparing RADseq and microsatellites for estimating genetic diversity and relatedness — Implications for brown trout conservation

“…While the fast mutation rate and high polymorphism of microsatellites allow for resolving fine-scale population structuring (Putman & Carbone, 2014), they may be less suitable for inferring genome-wide or individual-level patterns in genetic diversity (Väli, Einarsson, Waits, & Ellegren, 2008), as the number of sampled loci may not be sufficient to represent the total genome of an individual. It has also been demonstrated that SNPs obtained by RADseq produce more precise estimates of relatedness than microsatellites in a range of bird species (Thrasher, Butcher, Campagna, Webster, & Lovette, 2018). Microsatellites may be less efficient for identifying relatives particularly in populations with prior population bottlenecks and lack of gene flow, which limit allelic diversity.…”

In the surf zone: Reproductive strategy of the calico surfperch (Amphistichus koelzi) in a comparative context

“…Paternity was assigned for every offspring from seven calico surfperch broods in COLONY with an error rate of 0.01 following Thrasher et al . (). All broods examined were sired by multiple males.…”

“…Utilizing RADseq for paternity assignment is relatively new (Andrews et al ., ; Thrasher et al ., ). The accuracy of paternity assignment utilizing SNPs has been well documented, especially for the use in livestock and fisheries management (Anderson & Garza, ; Fernandez et al ., ; Hauser et al ., ; Jones et al ., ).…”

“…In DENOVO_MAP there are three main parameters: m, the minimum number of reads required to form a stack within an individual; M, the maximum number of mismatches allowed between stacks to merge them into one locus; and n, the maximum number of mismatches allowed between stacks from different individuals to merge into one locus (Catchen et al, 2013). We utilized the parameters m -3, M -3, n -1 in DENOVO_MAP following the parameter optimization studies of Mastretta-Yanes et al (2015), Andrews et al (2018) and Thrasher et al (2018). We retained 34,103 loci with 6764 variant sites remained.…”

A cost‐and‐time effective procedure to develop SNP markers for multiple species: A support for community genetics

“…Alternatively, HTS approaches could help to develop a few tens to hundreds of SNPs markers, possibly more efficiently than Sanger sequencing did in the past (Garvin, Saitoh, & Gharrett, 2010). Thrasher, Butcher, Campagna, Webster, and Lovette (2018) used ddRAD to perform relatedness analyses based on 150-600 optimized SNP markers. Other authors characterized small sets of SNP markers to be genotyped through a classical, affordable technology compared to GBS for large numbers of samples (e.g., Ackerman & Campbell, 2012;Westgaard et al, 2017).…”