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the median ratio of orthologs found in 2:1 and 1:2 ratios across arthropods is about 1.4 and 1.2, respectively, while across the 1x genome group the medians are 0.92 and 0.44, respectively (figure 5). while the median for the comparison between arthropods and the 1x genome group is 0.92, a distinction can still be made between the groups. closer examination of the 2:1 ortholog ratio shows a higher proportion of 1:2 orthologs among the genome comparisons within arthropods. this suggests that within the arthropod group, the 1x genome group may not have one to two copies of each gene, but rather only a single copy. when taking this into account, the median orthology ratio for arthropod comparisons to the 1x genome group is 0.88. both values show a decrease from arthropod to 1x genome, confirming the hypothesis that 1x genome arthropods possess fewer orthologs overall. from a biological perspective, this can be interpreted as a lack of orthologs shared by taxa in which duplications have occurred and no common paralogs have been lost.to look for evidence of this with regard to duplications across arthropods, we used a more stringent set of taxa for which duplicate files were available for all four arthropod genomes. we removed arthropod taxa for which no duplicate files were available, including platyhelminthes, nematoda, and heterolobosea. we also removed taxa in which orthologous matrix analysis showed significantly fewer 1:1 orthologs than expected (figure 5a). this removed trematodes, platyhelminth cestodes, cestodes, and cnidarian flatworms, as well as several nematode lineages within the panarthropoda (see the electronic supplementary material, figure s2). b magnification of the 1:2 ortholog ratio category in (a) shows a significantly higher number of duplicated genes in comparisons of arthropods to the arthropoda 1x genome (p=6.67104). c distribution of orthology ratios for a subset of genes benchmarked as putatively single copy across arthropoda (busco-ar). as before, a significantly higher number of 1:1 orthologs is recovered within the 1x genome group (p=3.43108). d magnification of the 1:2 ortholog ratio category in (c) shows a significantly higher number of duplicated genes in spiders and scorpions (p=7.28109)
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