One panel to rule them all: DArTcap genotyping for population structure, historical demography, and kinship analyses, and its application to a threatened shark

Abstract

With recent advances in sequencing technology, genomic data are changing how important conservation management decisions are made. Applications such as Close-Kin Mark-Recapture demand large amounts of data to estimate population size and structure, and their full potential can only be realised through ongoing improvements in genotyping strategies. Here we introduce DArTcap, a cost-efficient method that combines DArTseq and sequence capture, and illustrate its use in a high resolution population analysis of Glyphis garricki, a rare, poorly known and threatened euryhaline shark. Clustering analyses and spatial distribution of kin pairs from four different regions across northern Australia and one in Papua New Guinea, representing its entire known range, revealed that each region hosts at least one distinct population. Further structuring is likely within Van Diemen Gulf, the region that included the most rivers sampled, suggesting additional population structuring would be found if other rivers were sampled. Coalescent analyses and spatially explicit modelling suggest that G. garricki experienced a recent range expansion during the opening of the Gulf of Carpentaria following the conclusion of the Last Glacial Maximum. The low migration rates between neighbouring populations of a species that is found only in restricted coastal and riverine habitats show the importance of managing each population separately, including careful monitoring of local and remote anthropogenic activities that may affect their environments. Overall we demonstrated how a carefully chosen SNP panel combined with DArTcap can provide highly accurate kinship inference and also support population structure and historical demography analyses, therefore maximising cost-effectiveness.

Genomics versus mtDNA for resolving stock structure in the silky shark (Carcharhinus falciformis)

“…Though pool-seq has been shown to be an affordable and reliable tool for population genomics ( Futschik & Schlötterer, 2010 ; Gautier et al, 2013 ; Rellstab et al, 2013 ; Konczal et al, 2014 ; Schlötterer et al, 2014 ; Kurland et al, 2019 ), projects with larger budgets could allocate funds for any of a variety of other genomic sequencing techniques such as individual RADseq libraries ( Hohenlohe et al, 2010 ), GBS ( Narum et al, 2013 ), SNP arrays ( Qi et al, 2017 ), bait capture ( Feutry et al, 2020 ), or low coverage genomewide sequencing ( Therkildsen & Palumbi, 2017 ). These approaches allow for individual genotyping to examine questions that require individual-level information and could provide a deeper assessment of populations.…”

hiphop: Improved paternity assignment among close relatives using a simple exclusion method for biallelic markers

“…During the process of genome assembly we used assignment to, and position on, chromosome fragments to identify a candidate set of SNPs for which oligonucleotide baits were synthesised. The DNA captured by these baits (the DaRTcap procedure-https://www.diver sitya rrays.com/techn ology -and-resou rces/targe ted-genot yping/; see also Feutry et al (2020), was then subject to high intensity sequencing (approximately *100-fold) which was carried out on 1405 individuals, and each SNP was scored as homozygous for the most frequent allele, homozygous for the least frequent allele, heterozygous, or null.…”

Close-kin methods to estimate census size and effective population size

“…Costs are in USD$ and apply to SNP discovery and genotyping, but not DNA extraction, using DArT/DArTseq technology (Jaccoud et al 2001) as implemented in Feutry et al (2020);…”

“…Data shown in Figure 3 provide an opportunity to illustrate the relationship between experimental design and genotyping costs. The following parameters apply to prices discussed below: Costs are in USD$ and apply to SNP discovery and genotyping, but not DNA extraction, using DArT/DArTseq technology (Jaccoud et al 2001) as implemented in Feutry et al (2020); Costs include discovering and genotyping 1,500+ high quality SNPs (low error rate, high call rate, and MAF>0.1); Costs assume 94 samples per plate, with 1 positive and 1 negative control; Costs include a fixed component for SNP discovery (1 plate of DArTseq @ $3800) + a fixed component for SNP panel synthesis + $11.4/individual); Costs assume a species with at least moderate levels of genetic diversity; species with low diversity might require more sequencing at extra cost for SNP discovery. …”