Supplementary Material

Supplementary Table S1. Results (P-values) of population differentiation tests based on Alu allele frequencies between the Waorani community (Ecuadorian Amazon) and other Native American groups. Statiscally signicant differences are highlighted in bold.

Population key:

North American populations: Mvskoke (MVSK), Alaskan Inuits (ALSK) and Greenland Inuits (GREL)

Central American populations: Maya from Yucatan (MAYA)

South American populations: Yanomamo from Venezuela (YNMM), Quechua from Arequipa (QARE) and from Tayacaja (QTAY) provinces in Peru, Aché from Paraguay (ACHE), and Cinta Larga (CNTL), Gavião (GAVI), Surui (SURU), Wai-Wai (WWAI), Zoró (ZORO), Guarani (GUAR), Kaingang (KAIG) and Xavante (XAVT) from Brazil.

ALSK / GREL / MVSK / MAYA / YNMM / QARE / QTAY / ACHE / CNTL / GAVI / SURU / WWAI / ZORO / GUAR / KAIG / XAVT
A25 / 0.1195 / 0.0466 / 0.0066 / 0.0070 / 0.0138 / 0.1652 / 0.5437 / 0.3283 / 0.0143 / 0.0142 / 1.0000 / 0.5361 / 0.1666 / 0.6131 / 0.5393 / 0.0023
ACE / 0.0000 / 0.0000 / 0.0000 / 0.0000 / 0.0000 / 0.0000 / 0.0000 / 1.0000 / 0.0000 / 0.0137 / 0.0002 / 0.4985 / 0.1235 / 0.0000 / 0.0000 / 0.0000
APO / 0.0073 / 0.0290 / 0.1220 / 0.0284 / 1.0000 / 1.0000 / 0.4941 / 1.0000 / 0.1207 / 1.0000 / 1.0000 / 1.0000 / 0.4956 / 0.0145 / 0.2447 / 1.0000
B65 / 0.6700 / 0.0014 / 0.3896 / 0.0532 / 0.3169 / - / - / - / - / - / - / - / - / - / - / -
D1 / 0.0000 / 0.0000 / 0.0000 / 0.0000 / 0.0000 / 0.0000 / 0.0002 / - / 0.0000 / 0.0000 / 0.0000 / 0.0000 / 0.0000 / - / - / -
FXIIIB / 0.0069 / 0.0000 / 0.0000 / 0.0020 / 1.0000 / 1.0000 / 0.0006 / 0.0000 / 0.0298 / 1.0000 / 1.0000 / 0.0002 / 1.0000 / 0.0065 / 0.0003 / 1.0000
HS3.23 / 0.0006 / 0.0000 / 0.0000 / 0.4715 / 0.2440 / 0.5717 / 0.2574 / 0.0000 / 0.7735 / 0.0028 / 0.1966 / 0.3232 / 0.2039 / 0.0000 / 0.0668 / 0.0449
HS4.32 / 0.1184 / 0.0000 / 0.0014 / 0.0072 / 0.0236 / 0.0001 / 0.0020 / 0.1664 / 0.8327 / 0.5349 / 0.0855 / 1.0000 / 0.0583 / 0.4043 / 0.0140 / 0.0241
HS4.59 / 0.1160 / 0.0005 / 0.6568 / 0.8819 / 0.0001 / 0.0862 / 0.3565 / 0.0000 / 0.0000 / 0.0055 / 0.3106 / 0.2210 / 0.0875 / 0.5598 / 0.0023 / 0.2808
HS4.65 / 0.0149 / 0.2466 / 0.4948 / 0.4975 / 1.0000 / 1.0000 / 0.0035 / 1.0000 / 0.1215 / 0.0000 / 0.0032 / 0.2481 / 0.1215 / 0.2494 / 0.0000 / 0.0000
PV92 / 0.0000 / 0.0000 / 0.0000 / 0.0001 / 1.0000 / 0.0000 / 0.0000 / 0.0020 / 0.0000 / 0.0835 / 0.4934 / 0.0162 / 0.0014 / 0.0000 / 0.0001 / 0.0005
TPA25 / 0.0053 / 0.0208 / 1.0000 / 0.0447 / 0.0089 / 0.0630 / 0.0038 / 0.0000 / 0.4916 / 0.0001 / 0.2586 / 0.0000 / 0.0106 / 0.0031 / 0.0237 / 0.3986