Climate Change Influenced Female Population Sizes Through Time Across the Indonesian Archipelago

Abstract

Lying at the crossroads of Asia and the Pacific world, the Indonesian archipelago hosts one of the world's richest accumulations of cultural, linguistic, and genetic variation. While the role of human migration into and around the archipelago is now known in some detail, other aspects of Indonesia's complex history are less understood. Here, we focus on population size changes from the first settlement of Indonesia nearly 50 kya up to the historic era. We reconstructed the past effective population sizes of Indonesian women using mitochondrial DNA sequences from 2,104 individuals in 55 village communities on four islands spanning the Indonesian archipelago (Bali, Flores, Sumba, and Timor). We found little evidence for large fluctuations in effective population size. Most communities grew slowly during the late Pleistocene, peaked 15-20 kya, and subsequently declined slowly into the Holocene. This unexpected pattern may reflect population declines caused by the flooding of lowland hunter/gatherer habitat during sea-level rises following the last glacial maximum. Keywords Indonesia, Mitochondrial Dna, Bayesian Skyline PlotThis open access article is available in Human Biology: http://digitalcommons.wayne.edu/humbiol/vol85/iss1/6 Abstract Lying at the crossroads of Asia and the Pacific world, the Indonesian archipelago hosts one of the world's richest accumulations of cultural, linguistic, and genetic variation. While the role of human migration into and around the archipelago is now known in some detail, other aspects of Indonesia's complex history are less understood. Here, we focus on population size changes from the first settlement of Indonesia nearly 50 kya up to the historic era. We reconstructed the past effective population sizes of Indonesian women using mitochondrial DNA sequences from 2,104 individuals in 55 village communities on four islands spanning the Indonesian archipelago (Bali, Flores, Sumba, and Timor). We found little evidence for large fluctuations in effective population size. Most communities grew slowly during the late Pleistocene, peaked 15-20 kya, and subsequently declined slowly into the Holocene. This unexpected pattern may reflect population declines caused by the flooding of lowland hunter/gatherer habitat during sea-level rises following the last glacial maximum.The prehistory of Island Southeast Asia is made especially complex by its position as a waypoint between mainland Asia, Australia, and the Pacific world. The region's prehistory is dominated by population movements, beginning with its first settlement by modern humans approximately 50 kya and continuing to the Islamization of Indonesia during the historic period. Reflecting the rich cultural and linguistic diversity of Indonesia's inhabitants, these eras have also left their mark on the genetic diversity of the individuals who inhabit Indonesia today (Cox et al.

Human settlement history between Sunda and Sahul: a focus on East Timor (Timor-Leste) and the Pleistocenic mtDNA diversity

“…The diverse haplogroup spectrum of East Timor revealed in this first representative mtDNA study illustrates its position at the crossroads of several migrations between ISEA, Melanesia and Australia – and likely also the area’s rapid change from a large continental landmass to an archipelago [4]. We detected 164 different CR haplotypes in the 324 mtDNAs (disregarding cytosine indels around nps 16193, 309 and 573); 116 of these (35.8%) were unique in the dataset.…”

“…We do not find that “ the mitochondrial genomes of Timorese women predominantly derive from Papuan progenitors ” [4], but rather that additional migration after initial colonization is necessary to explain the predominant proportion of (S)EA lineages, mirrored by high haplotype sharing rates and relatively small genetic, despite large geographic, distance (Figure 2, Additional files 7, 8, 9 and 10). We investigated East Timor’s mtDNA composition (as a pooled sample from this study and [3]) in the light of four particular “later” migratory events postulated to have occurred between (S)EA and Melanesia during late Pleistocene and mid-Holocene in previous studies, often overlapping in terms of time and geography.…”

“…The peak of Sahul’s surface area ~30-18 kya coincides with the highly dynamic migratory period we report and might have triggered it. Population dispersals (geographic expansions) do not necessarily also mean population expansion [4], but BSPs from thousands of samples in the HVS-I range (Indonesia) and tens of complete mitogenomes (Philippines and Malaysia) from mixed haplogroups have (remarkably similarly to our BSP from haplogroup P1; Figure 6) indicated a slowly growing population in the Pleistocene that peaked at 20–15 kya and declined thereafter [4,30,87]. This seems to pinpoint “ substantial impact of common environmental forces ” in ISEA [4].…”

“…The blurring of older “footprints” by subsequent migrations, and the paucity of available (founder lineage) mitogenomic data may have confounded our assumptions on dispersal and time estimates. In any event, the migration history (to be) reconstructed from mtDNA is only the “female side” of the medal, but “ necessarily coupled ” to the history of the entire population [4]. Other genetic markers ( cf .…”

“…Australia, New Guinea, Tasmania and nearby islands) became partly submersed again by the rising sea. Dramatic coastline shifts occurred ~14.5, 11.5, and 7.5 kya, creating the extant archipelago topography [4,5,14-16]. Timor was an island even during the LGM.…”