2. Use of the functions on biological datasets
We applied the designed functions (available at github.com/drobledoruiz/conservation genomics) on the de novo -scored DArT SNP datasets of two species: eastern yellow robin (EYR, Eopsaltria australis ) and yellow-tufted honeyeater (YTH, Lichenostomus melanops ). In order to assess the impact of removing sex-linked loci, we compared the biological inferences drawn from analyses of population genetic diversity, individual heterozygosity, population structure and parentage analyses before and after using the function filter.sex.linked(hereafter referred to as ‘before’ and ‘after’). For that, we applied two SNP filtering regimes to the EYR and YTH datasets: a) ‘Standard’, which included only standard filtering steps, and b) ‘Removing sex-linked loci’, which included standard filtering plus the use offilter.sex.linked function (Table 1). Functions infer.sex ,filter.excess.het and gl2colony were used in regime ‘Removing sex-linked loci’ where appropriate (Table 1). We also test what is the minimum number of known-sex individuals required by the combination of filter.sex.linked and infer.sex functions to be able to identify all sex-linked loci.