Microarrays can be a cost-effective alternative to high-throughput sequencing for discovering novel single-nucleotide polymorphisms (SNPs). Illumina’s iScan platform dominates the market, but their commercial microarray products are designed for model organisms. Further, the platform outputs data in a proprietary format. This cannot be easily converted to human-readable genotypes or be merged with pre-existing data. To address this, we present and validate a novel pipeline to facilitate data analysis from cross-species application of Illumina microarrays. This facilitates the generation of a compatible VCF from iScan data and the merging of this with a second VCF comprising genotypes derived from other samples and sources. Our pipeline includes a custom script, iScanVCFMerge (presented as a Python package), which we validate using iScan data from three great ape genera. We conclude that cross-species application of microarrays can be a rapid, cost-effective approach for SNP discovery in non-model organisms. Our pipeline surmounts the common challenges of integrating iScan genotypes with pre-existing data.
The role of vocalisation for the Philippine hornbills' ecology and speciation and their implication in understanding speciation is not well understood. We described and compared recorded calls of seven hornbill taxa in captivity namely Mindanao Wrinkled hornbill (Rhabdotorrhinus leucocephalus), Rufous-headed hornbill (Rhabdotorrhinus waldeni), Luzon Rufous hornbill (Buceros hydrocorax hydrocorax), Samar Rufous hornbill (Buceros hydrocorax semigaleatus), Mindanao Rufous hornbill (Buceros hydrocorax mindanensis), Mindanao Tarictic hornbill (Penelopides affinis), Samar Tarictic hornbill (Penelopides samarensis), Visayan Tarictic hornbill (Penelopides panini) and Luzon Tarictic hornbill (Penelopides manillae), as well as comparison with the non-native Papuan hornbill (Rhyticeros plicatus). Vocalisation analysis included call duration, minimum frequency, maximum frequency, bandwidth and peak frequency. For each species in the sample, the mean and standard deviation were used to calculate the Cohen’s d statistic by using an effect size calculator. Results showed that the effect size for minimum frequency was small for P. panini vs. P. samarensis and B. hydrocorax vs. B. h. mindanensis. However, bandwidth, duration, minimum frequency, maximum frequency and peak frequency have large effect sizes for the rest of the allopatric species pairs. Hornbills' conspicuous resonating calls are sufficiently quantifiable for bioacoustic analysis and may provide new insights for their taxonomic review.
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