Lineage-specific Alu subfamily analysis

The RepeatMasker utility program COSEG was applied to the lineage-specific owl monkey and capuchin monkey Alu insertions to determine the subfamily composition based on co-segregating mutations. Alu insertions determined to be lineage-specific were aligned via Crossmatch (www.phrap.org/phredphrapconsed.html, accessed on 1 January 2023 with the default settings, then analyzed via COSEG (www.repeatmasker.org/COSEGDownload.html; accessed on 19 December 2022) to determine the subfamily structure. The dataset was aligned against the AluS consensus sequence [30 (link)]. COSEG was then used to group the Alu subfamilies. The middle A-rich region of the AluS consensus sequence was excluded from the analysis when determining the subfamilies, whereas tri and di segregating mutations were considered. A group of ten or more identical sequences was considered a separate Alu subfamily. The consensus sequences were subjected to a RepeatMasker analysis using 24 subfamilies previously defined by RepBase [15 (link),24 (link)], as well as the 86 from marmoset and 46 from squirrel monkey (see Section 1) to remove exact matches. Eliminating subfamilies duplicated in owl monkey or capuchin resulted in non-overlapping datasets. These 189 Alu subfamilies were then aligned in BioEdit [31 ] and a network analysis was completed based on the accumulation of diagnostic mutations.