Maternal and paternal lineage analysis of Island Southeast Asian goats reveals continental propagation routes and introgression through the Indian ocean

Abstract

The Philippines and Indonesia, located at the crossroads of historical human migrations in the Asia-Pacific region, lie in the southeasternmost part of Mainland Southeast Asia. Both countries are recognized as mega-diverse nations, hosting a wide variety of species. However, the history of goat propagation in Island Southeast Asia remains unclear due to limited molecular studies and the absence of archaeological evidence in this region. This study conducted phylogeographic analyses of mtDNA hypervariable region 1 and SRY 3'UTR sequences of goats from the Philippines and Indonesia, comparing them with Old World domestic goats. Philippine goat mtDNA haplotypes were classified into haplogroups B (152/206, 73.8%) and A (54/206, 26.2%), whereas all Indonesian goat mtDNA haplotypes belonged to haplogroup B (72/72, 100%). The distribution of mtDNA haplogroup B and regional differences suggest two propagation routes: one from China/Taiwan to the Philippines and another from Mainland Southeast Asia to Indonesia. The distribution of five SRY haplotypes demonstrated that haplotype Y2A, absent in Mainland Southeast Asia, was present in Island Southeast Asia, indicating gene introgression through the Indian Ocean from the African continent and/or southern Europe. This introgression may have been driven by human activities, such as European migrations between the 16th and 19th centuries.

Keywords: Capra hircus; SRY gene; Indian ocean; Island Southeast Asia; MtDNA; Propagation route.

Fig. 1

Median joining network of 481 bp in the mtDNA HV1 sequence. Separator lines on the Network indicate mutation positions. Blue and yellow colors are shown haplogroup A and B, respectively. The size of nodes is proportional to the number of goats present in the node. Each short bar on the edges represents a nucleotide mutation. (a) Philippine goats; (b) Indonesian goats.

Fig. 2

Geographic distribution of caprine mtDNA haplogroups in the Old World and Island Southeast Asia. The size of nodes is proportional to the number of goats present in the node. The used data were shown in Table S5. The map was generated using Microsoft PowerPoint 2019 based on a free map website by 3kaku-K (https://www.freemap.jp/item/world/world1.html).

Fig. 3

Geographic distribution of caprine SRY haplotypes in the Old World and Island Southeast Asia. The size of nodes is proportional to the number of goats present in the node. The used data were shown in Table S6. The map was generated using Microsoft PowerPoint 2019 based on a free map website by 3kaku-K (https://www.freemap.jp/item/world/world1.html).

Fig. 4

Evolutionary scenarios for the propagation route of ISEA goats. Scenario 1: ISEA goats were introduced from MSEA. Scenario 2: Philippine and Indonesian goats were independently introduced from China/Taiwan and MSEA, respectively. Scenario 3: Philippine goats were introduced by two routes, from China/Taiwan and from MSEA via Indonesia, with admixture occurring in the Philippines. Upper figures show scenarios indicated by the trees; lower figures show geographic regions on maps. Colors of the tree correspond to the geographic regions on the map (Green: Philippines; Red: Indonesia; Light blue: China; Pink: MSEA; Yellow: Outgroup). The map was generated using Microsoft PowerPoint 2019 based on a free map website by 3kaku-K (https://www.freemap.jp/item/world/world1.html).