Supplementary Materials

This PDF file includes:

  • fig. S1. Maximum likelihood phylogeny of Euarchontoglires based on an alignment of 631 orthologous protein-coding sequences.
  • fig. S2. Insertion-deletion evidence for colugo phylogenetic relationships based on transposons.
  • fig. S3. Description of the transposon screening strategy.
  • fig. S4. Phylogenetically informative protein-coding gene indels supporting Primatomorpha (P1 to P15), Sundatheria (S1 to S5), and Primates + Scandentia (PS1 to PS5).
  • fig. S5. Maximum likelihood timetree showing seven nodes with external fossil calibrations.
  • fig. S6. Maximum likelihood timetree showing seven nodes with external fossil calibrations, with euarchontan monophyly enforced.
  • fig. S7. Maximum likelihood mtDNA tree based on a matrix of 53 colugos with ≥90% mitogenome coverage.
  • fig. S8. Maximum likelihood mtDNA tree based on a matrix of 65 colugos with ≥30% mitogenome coverage.
  • fig. S9. Maximum likelihood tree based on a combined nuclear (biparental + Y) matrix of 17 taxa.
  • fig. S10. Maximum likelihood tree based on biparental data set (18 taxa).
  • fig. S11. Maximum likelihood Y chromosome tree (depth 2) (15 taxa).
  • fig. S12. Maximum likelihood Y chromosome tree (depth 3) (14 taxa).
  • fig. S13. Biplot of PC1 and PC2 from PCA of colugo X chromosome variants.
  • fig. S14. Biplot of PC2 and PC3 from PCA of colugo X chromosome variants.
  • fig. S15. Biplot of PC3 and PC4 from PCA of colugo X chromosome variants.
  • fig. S16. Biplot of PC4 and PC5 from PCA of colugo X chromosome variants.
  • fig. S17. Biplot of PC5 and PC6 from PCA of colugo X chromosome variants.
  • fig. S18. Biplot of morphometric PCA with males and females, and no dwarf specimens removed.
  • fig. S19. Biplot of colugo morphometric PCA, with male, female, and dwarf specimens, where all measurements are normalized by body size.
  • table S1. Mammals used in phylogenetic analyses.
  • table S2. Presence/absence of phylogenetically informative retroposon markers and species distribution.
  • table S3. Location of diagnostic retroposon markers in the human genome.
  • table S4. χ2 calculation for phylogenetically informative indels.
  • table S5. Colugo and select mammal V1R and OR gene annotation summaries.
  • table S6. Nuclear capture efficiency.
  • table S7. Adapter blocking oligos.
  • table S8. Off-target mtDNA assembly statistics.
  • table S9. External fossil calibrations used to calculate divergence time between the two colugo genera.
  • table S10. Principal component loadings for morphometric PCA using males and females with no dwarf individuals.
  • table S11. Principal component loadings for morphometric PCA using males, females, and dwarf individuals, and all measurements were normalized for body size.
  • table S12. mtDNA maximum composite likelihood + Γ distance matrix calculated between seven Sunda colugo groups and five Philippine groups.
  • table S13. X chromosome maximum composite likelihood + Γ distance matrix calculated between seven Sunda colugo groups and three Philippine groups.
  • table S14. Between-group mtDNA composite likelihood + Γ distance matrix for Sunda colugos from Thailand, Peninsular Malaysia, and Sumatra, and their satellite islands.
  • table S15. Within-group mtDNA maximum composite likelihood + Γ distance matrix.
  • table S16. Between-group mtDNA composite likelihood + Γ distance matrix for 10 Sunda colugo groups and 5 Philippine groups.
  • table S17. BPP species estimation results for Sunda colugos.
  • table S18. BPP species estimation results for Philippine colugos.
  • table S19. Principal component loadings for X chromosome genetic variants.
  • Legends for database S1 to S7
  • References (75–80)

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Other Supplementary Material for this manuscript includes the following:

  • database S1 (Microsoft Excel format). Dermopteran positively selected genes.
  • database S2 (Microsoft Excel format). Dermopteran WebGestalt results.
  • database S3 (Microsoft Excel format). Ancestral primate positively selected genes.
  • database S4 (Microsoft Excel format). Ancestral primate WebGestalt results.
  • database S5 (Microsoft Excel format). Museum specimen information.
  • database S6 (Microsoft Excel format). Primers used to amplify nuclear DNA capture probes.
  • database S7 (Microsoft Excel format). Craniodental morphometric measurements for 125 Sunda colugos.

Download databases S1 to S7

Files in this Data Supplement: