ORCID Profile
0000-0001-7616-5977
Current Organisation
University of Adelaide
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Publisher: Oxford University Press (OUP)
Date: 05-07-2016
Publisher: MDPI AG
Date: 24-06-2021
Abstract: The tropical archipelago of Wallacea contains thousands of in idual islands interspersed between mainland Asia and Near Oceania, and marks the location of a series of ancient oceanic voyages leading to the peopling of Sahul—i.e., the former continent that joined Australia and New Guinea at a time of lowered sea level—by 50,000 years ago. Despite the apparent deep antiquity of human presence in Wallacea, prior population history research in this region has been h ered by patchy archaeological and genetic records and is largely concentrated upon more recent history that follows the arrival of Austronesian seafarers ~3000–4000 years ago (3–4 ka). To shed light on the deeper history of Wallacea and its connections with New Guinea and Australia, we performed phylogeographic analyses on 656 whole mitogenomes from these three regions, including 186 new s les from eight Wallacean islands and three West Papuan populations. Our results point to a surprisingly dynamic population history in Wallacea, marked by two periods of extensive demographic change concentrated around the Last Glacial Maximum ~15 ka and post-Austronesian contact ~3 ka. These changes appear to have greatly diminished genetic signals informative about the original peopling of Sahul, and have important implications for our current understanding of the population history of the region.
Publisher: Springer Science and Business Media LLC
Date: 22-03-2021
Publisher: Cold Spring Harbor Laboratory
Date: 18-07-2022
DOI: 10.1101/2022.07.17.500374
Abstract: We introduce Dual Coordinate VCF (DVCF), a file format that records genomic variants against two different reference genomes simultaneously and is fully compliant with the current VCF specification. As implemented in the Genozip platform, DVCF enables bioinformatics pipelines to seamlessly operate across two coordinate systems by leveraging the system most advantageous to each pipeline step, simplifying bioinformatics workflows and reducing file generation and associated data storage burden. Moreover, our benchmarking of Genozip DVCF shows that it produces more complete, less erroneous, and less biased translations across coordinate systems than two widely used alternative tools (i.e., LiftoverVcf and CrossMap). An open source (GPL) version of Genozip containing DVCF functionality but not compression functionality, and which includes scripts for reproducing the benchmarks presented here, is available at ivonlan/dvcf . Documentation is available at vcf .
Publisher: MDPI AG
Date: 16-12-2022
Abstract: Genomic sequence data from worldwide human populations have provided a range of novel insights into our shared ancestry and the historical migrations that have shaped our global genetic ersity. However, a comprehensive understanding of these fundamental questions has been impeded by the lack of inclusion of many Indigenous populations in genomic surveys, including those from the Wallacean archipelago (which comprises islands of present-day Indonesia located east and west of Wallace’s and Lydekker’s Lines, respectively) and the former continent of Sahul (which once combined New Guinea and Australia during lower sea levels in the Pleistocene). Notably, these regions have been important areas of human evolution throughout the Late Pleistocene, as documented by erse fossil and archaeological records which attest to the regional presence of multiple hominin species prior to the arrival of anatomically modern human (AMH) migrants. In this review, we collate and discuss key findings from the past decade of population genetic and phylogeographic literature focussed on the hominin history in Wallacea and Sahul. Specifically, we examine the evidence for the timing and direction of the ancient AMH migratory movements and subsequent hominin mixing events, emphasising several novel but consistent results that have important implications for addressing these questions. Finally, we suggest potentially lucrative directions for future genetic research in this key region of human evolution.
Publisher: Cold Spring Harbor Laboratory
Date: 24-07-2020
DOI: 10.1101/2020.07.24.219048
Abstract: The hominin fossil record of Island Southeast Asia (ISEA) indicates that at least two endemic ‘super-archaic’ species – Homo luzonensis and H. floresiensis – were present around the time anatomically modern humans (AMH) arrived in the region ,000 years ago. Contemporary human populations carry signals consistent with interbreeding events with Denisovans in ISEA – a species that is thought to be more closely related to AMH than the super-archaic endemic ISEA hominins. To query this disparity between fossil and genetic evidence, we performed a comprehensive search for super-archaic introgression in modern human genomes. Our results corroborate widespread Denisovan ancestry in ISEA populations but fail to detect any super-archaic admixture signals. By highlighting local megafaunal survival east of the Wallace Line as a potential signature of deep, pre- H. sapiens hominin-faunal interaction, we propose that this understudied region may hold the key to unlocking significant chapters in Denisovan prehistory.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 03-08-2018
Abstract: Flores Island in Indonesia has a long history of hominin occupation, including by the extinct Homo floresiensis and a more recent settlement by modern humans. Furthermore, Flores has an extant population of pygmy humans, and H. floresiensis exhibited a diminutive adult size relative to other hominins. Tucci et al. examined genetic variation among 32 in iduals, including 10 sequenced genomes, from a population of pygmies living close to the cave where H. floresiensis remains were discovered. These in iduals exhibit signatures of polygenic selection explaining the short stature and have genomic content from both Neanderthals and Denisovans, but no additional archaic lineages. Thus, restricted height is under selection at this location and has evolved independently at least twice in hominins. Science , this issue p. 511
No related grants have been discovered for Gludhug Ariyo Purnomo.