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.