Computational protocol: Estimating Population Size for Capercaillie (Tetrao urogallus L.) with Spatial Capture-Recapture Models Based on Genotypes from One Field Sample

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Protocol publication

[…] Extraction of DNA and genotyping of samples were done by Ecogenics GmbH in Zürich-Schlieren, Switzerland, following exactly the method described by Jacob et al. [].Ten nuclear microsatellite loci developed for the capercaillie [,] and two additional nuclear microsatellite loci, BG15 and BG18, developed for the black grouse (Tetrao tetrix L.; []) have been amplified. Details on forward and reverse primer sequences and repeat motifs are given in Jacob et al. []. The twelve microsatellite loci were amplified in four multiplex-PCRs, each containing three primer pairs differing in their fluorescent labeling dyes (FAM, HEX, NED; Applied Biosystems). A fragment of the chromo-helicase-DNA-binding (CHD) gene using the primer pair P2 and P8 of Griffiths et al. [] was amplified to sex the individual.Loci that could not be scored after eight PCR replicates were coded as missing values. Samples with a low prospect of producing a multi-locus genotype (no amplification products at any of the three loci) and those assigned to other grouse species were discarded. Capercaillie samples were typed with the nine remaining microsatellite markers, organized in three multiplex-PCRs, and the sex-specific locus following the same genotyping procedure. Based on the analyses by Ecogenics GmbH, only samples with at least 8 loci unambiguously genotyped were retained for further analyses. PIsib (see below) of the 8 least informative loci was below 0.01 (cf. [].Two multi-locus genotypes were considered to be identical if they shared all the alleles at all the loci, excluding loci with missing values. To reduce the chance of erroneously considering two genotypes as identical as a consequence of errors in the process of genotyping or recording of the data, those genotypes differing only because of missing values and those differing by a single allele were re-analyzed. An allelic combination representing one or several identical genotypes was considered to be unique if it differed from all the other allelic combinations by at least two alleles (excluding missing values).Probability of identity (PI) of the genotypes obtained as just described was calculated with Cervus 3.0.3 []. Estimation of PI assumes that individuals to be compared are unrelated. Because the samples potentially included relatives, we also calculated PIsib, which gives an alternative and more conservative estimate of the probability of identity than PI [].Loci were checked for departure of Hardy-Weinberg (HW) expectations using an exact test [] with 10,000 dememorization steps, 5,000 batches, and 10,000 iterations per batch in GENEPOP on the web (http://genepop.curtin.edu.au; [,]). Null allele frequencies (FNull) and measures of genetic diversity, i.e. alleles per locus (A), observed heterozygosity (Ho), and expected heterozygosity (He), were calculated using Cervus 3.0.3. We also computed a rarefied estimate of allelic richness (R) in FSTAT 2.9.3.2 [], which accounted for sample size differences among loci. […]

Pipeline specifications

Software tools Cervus, Genepop
Application Population genetic analysis