ORCID Profile
0000-0001-6417-4702
Current Organisation
Australian National University School of Culture History and Language
Does something not look right? The information on this page has been harvested from data sources that may not be up to date. We continue to work with information providers to improve coverage and quality. To report an issue, use the Feedback Form.
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Population, Ecological and Evolutionary Genetics | Genetics | Biological Adaptation
Expanding Knowledge in the Biological Sciences | Expanding Knowledge in History and Archaeology |
Publisher: Elsevier BV
Date: 06-2021
Publisher: Cold Spring Harbor Laboratory
Date: 22-03-2017
DOI: 10.1101/119529
Abstract: Balancing selection maintains advantageous ersity in populations through various mechanisms. While extensively explored from a theoretical perspective, an empirical understanding of its prevalence and targets lags behind our knowledge of positive selection. Here we describe the Non-Central Deviation ( NCD ), a simple yet powerful statistic to detect long-term balancing selection (LTBS) that quantifies how close frequencies are to expectations under LTBS, and provides the basis for a neutrality test. NCD can be applied to a single locus or genomic data, and can be implemented considering only polymorphisms ( NCD1 ) or also considering fixed differences with respect to an outgroup ( NCD2 ) species. Incorporating fixed differences improves power, and NCD2 has higher power to detect LTBS in humans under different frequencies of the balanced allele(s) than other available methods. Applied to genome-wide data from African and European human populations, in both cases using chimpanzee as an outgroup, NCD2 shows that, albeit not prevalent, LTBS affects a sizable portion of the genome: about 0.6% of analyzed genomic windows and 0.8% of analyzed positions. Significant windows ( p 0.0001) contain 1.6% of SNPs in the genome, which disproportionally fall within exons and change protein sequence, but are not enriched in putatively regulatory sites. These windows overlap about 8% of the protein-coding genes, and these have larger number of transcripts than expected by chance even after controlling for gene length. Our catalog includes known targets of LTBS but a majority of them (90%) are novel. As expected, immune-related genes are among those with the strongest signatures, although most candidates are involved in other biological functions, suggesting that LTBS potentially influences erse human phenotypes.
Publisher: Elsevier BV
Date: 12-2014
DOI: 10.1016/J.GDE.2014.08.001
Abstract: Most human polymorphisms are neutral or slightly deleterious, but some genetic variation is advantageous and maintained in populations by balancing selection. Considered a rarity and overlooked for years, balanced polymorphisms have recently received renewed attention with several lines of evidence showing their relevance in human evolution. From theoretical work on its role in adaptation to empirical studies that identify its targets, recent developments have showed that balancing selection is more prevalent than previously thought. Here we review these developments and discuss their implications in our understanding of the influence of balancing selection in human evolution. We also review existing evidence on the biological functions that benefit most from advantageous ersity, and the functional consequences of these variants. Overall, we argue that balancing selection must be considered an important selective force in human evolution.
Publisher: Proceedings of the National Academy of Sciences
Date: 19-02-2021
Abstract: The current rate of species extinction is rapidly approaching unprecedented highs, and life on Earth presently faces a sixth mass extinction event driven by anthropogenic activity, climate change, and ecological collapse. The field of conservation genetics aims at preserving species by using their levels of genetic ersity, usually measured as neutral genome-wide ersity, as a barometer for evaluating population health and extinction risk. A fundamental assumption is that higher levels of genetic ersity lead to an increase in fitness and long-term survival of a species. Here, we argue against the perceived importance of neutral genetic ersity for the conservation of wild populations and species. We demonstrate that no simple general relationship exists between neutral genetic ersity and the risk of species extinction. Instead, a better understanding of the properties of functional genetic ersity, demographic history, and ecological relationships is necessary for developing and implementing effective conservation genetic strategies.
Publisher: Cold Spring Harbor Laboratory
Date: 03-04-2020
DOI: 10.1101/2020.04.01.021006
Abstract: The role of natural selection in shaping biological ersity is an area of intense interest in modern biology. To date, studies of positive selection have primarily relied upon genomic datasets from contemporary populations, which are susceptible to confounding factors associated with complex and often unknown aspects of population history. In particular, admixture between erged populations can distort or hide prior selection events in modern genomes, though this process is not explicitly accounted for in most selection studies despite its apparent ubiquity in humans and other species. Through analyses of ancient and modern human genomes, we show that previously reported Holocene-era admixture has masked more than 50 historic hard sweeps in modern European genomes. Our results imply that this canonical mode of selection has likely been underappreciated in the evolutionary history of humans and suggests that our current understanding of the tempo and mode of selection in natural populations may be quite inaccurate.
Publisher: Oxford University Press (OUP)
Date: 03-2018
DOI: 10.1093/GBE/EVY054
Publisher: Elsevier BV
Date: 08-2022
Publisher: Springer Science and Business Media LLC
Date: 31-10-2022
DOI: 10.1038/S41559-022-01914-9
Abstract: The role of natural selection in shaping biological ersity is an area of intense interest in modern biology. To date, studies of positive selection have primarily relied on genomic datasets from contemporary populations, which are susceptible to confounding factors associated with complex and often unknown aspects of population history. In particular, admixture between erged populations can distort or hide prior selection events in modern genomes, though this process is not explicitly accounted for in most selection studies despite its apparent ubiquity in humans and other species. Through analyses of ancient and modern human genomes, we show that previously reported Holocene-era admixture has masked more than 50 historic hard sweeps in modern European genomes. Our results imply that this canonical mode of selection has probably been underappreciated in the evolutionary history of humans and suggest that our current understanding of the tempo and mode of selection in natural populations may be inaccurate.
Publisher: Wiley
Date: 11-06-2020
DOI: 10.1111/TAN.13956
Publisher: Portland Press Ltd.
Date: 31-01-2020
DOI: 10.1042/BIO04201006
Abstract: Who are we? Where did we come from? Why are we here? These fundamental questions have been widespread throughout human history, shared across different cultures from distant epochs and geographical locations. The search has been as much a philosophical as an empirical one, capturing the imagination of the philosopher, the theologian, the artist and the scientist alike. Hence, the quest for unveiling our origins is probably as old as humanity itself. From a scientific point of view, which we address in the present article, the question of human origins became deeply intertwined with Charles Darwin's theory of evolution in the late 19th century. This led to the development of scientific fields such as palaeoanthropology, which analyses fossil remains, stone tools and cultural artefacts to piece together our past. Recently, however, the possibility to assess genetic information from thousands of in iduals across the world and, more importantly, to obtain DNA from specimens that lived thousands of years in the past (so-called ancient DNA [aDNA] analyses) is rapidly transforming long-held beliefs about our origins. As such, we have never been in a better position to ask what do our genomes have to tell us about where we came from. Ultimately, however, can they tell us who we are?
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: Oxford University Press (OUP)
Date: 19-02-2015
Abstract: Balancing selection maintains advantageous genetic and phenotypic ersity in populations. When selection acts for long evolutionary periods selected polymorphisms may survive species splits and segregate in present-day populations of different species. Here, we investigate the role of long-term balancing selection in the evolution of protein-coding sequences in the Homo-Pan clade. We sequenced the exome of 20 humans, 20 chimpanzees, and 20 bonobos and detected eight coding trans-species polymorphisms (trSNPs) that are shared among the three species and have segregated for approximately 14 My of independent evolution. Although the majority of these trSNPs were found in three genes of the major histocompatibility locus cluster, we also uncovered one coding trSNP (rs12088790) in the gene LAD1. All these trSNPs show clustering of sequences by allele rather than by species and also exhibit other signatures of long-term balancing selection, such as segregating at intermediate frequency and lying in a locus with high genetic ersity. Here, we focus on the trSNP in LAD1, a gene that encodes for Ladinin-1, a collagenous anchoring filament protein of basement membrane that is responsible for maintaining cohesion at the dermal-epidermal junction the gene is also an autoantigen responsible for linear IgA disease. This trSNP results in a missense change (Leucine257Proline) and, besides altering the protein sequence, is associated with changes in gene expression of LAD1.
Publisher: Oxford University Press (OUP)
Date: 16-12-2019
DOI: 10.1093/HMG/DDZ304
Abstract: Selective pressures imposed by pathogens have varied among human populations throughout their evolution, leading to marked inter-population differences at some genes mediating susceptibility to infectious and immune-related diseases. Here, we investigated the evolutionary history of a common polymorphism resulting in a Y529 versus C529 change in the cadherin related family member 3 (CDHR3) receptor which underlies variable susceptibility to rhinovirus-C infection and is associated with severe childhood asthma. The protective variant is the derived allele and is found at high frequency worldwide (69–95%). We detected genome-wide significant signatures of natural selection consistent with a rapid increase of the haplotypes carrying the allele, suggesting that non-neutral processes have acted on this locus across all human populations. However, the allele has not fixed in any population despite multiple lines of evidence suggesting that the mutation predates human migrations out of Africa. Using an approximate Bayesian computation method, we estimate the age of the mutation while explicitly accounting for past demography and positive or frequency-dependent balancing selection. Our analyses indicate a single emergence of the mutation in anatomically modern humans ~150 000 years ago and indicate that balancing selection has maintained the beneficial allele at high equilibrium frequencies worldwide. Apart from the well-known cases of the MHC and ABO genes, this study provides the first evidence that negative frequency-dependent selection plausibly acted on a human disease susceptibility locus, a form of balancing selection compatible with typical transmission dynamics of communicable respiratory viruses that might exploit CDHR3.
Publisher: Frontiers Media SA
Date: 05-08-2022
DOI: 10.3389/FGENE.2022.918227
Abstract: The introduction of pathogens originating from Eurasia into the Americas during early European contact has been associated with high mortality rates among Indigenous peoples, likely contributing to their historical and precipitous population decline. However, the biological impacts of imported infectious diseases and resulting epidemics, especially in terms of pathogenic effects on the Indigenous immunity, remain poorly understood and highly contentious to this day. Here, we examine multidisciplinary evidence underpinning colonization-related immune genetic change, providing contextualization from anthropological studies, paleomicrobiological evidence of contrasting host-pathogen coevolutionary histories, and the timings of disease emergence. We further summarize current studies examining genetic signals reflecting post-contact Indigenous population bottlenecks, admixture with European and other populations, and the putative effects of natural selection, with a focus on ancient DNA studies and immunity-related findings. Considering current genetic evidence, together with a population genetics theoretical approach, we show that post-contact Indigenous immune adaptation, possibly influenced by selection exerted by introduced pathogens, is highly complex and likely to be affected by multifactorial causes. Disentangling putative adaptive signals from those of genetic drift thus remains a significant challenge, highlighting the need for the implementation of population genetic approaches that model the short time spans and complex demographic histories under consideration. This review adds to current understandings of post-contact immunity evolution in Indigenous peoples of America, with important implications for bettering our understanding of human adaptation in the face of emerging infectious diseases.
Publisher: MDPI AG
Date: 13-11-2020
Abstract: Mesoamerica is a historically and culturally defined geographic area comprising current central and south Mexico, Belize, Guatemala, El Salvador, and border regions of Honduras, western Nicaragua, and northwestern Costa Rica. The permanent settling of Mesoamerica was accompanied by the development of agriculture and pottery manufacturing (2500 BCE–150 CE), which led to the rise of several cultures connected by commerce and farming. Hence, Mesoamericans probably carried an invaluable genetic ersity partly lost during the Spanish conquest and the subsequent colonial period. Mesoamerican ancient DNA (aDNA) research has mainly focused on the study of mitochondrial DNA in the Basin of Mexico and the Yucatán Peninsula and its nearby territories, particularly during the Postclassic period (900–1519 CE). Despite limitations associated with the poor preservation of s les in tropical areas, recent methodological improvements pave the way for a deeper analysis of Mesoamerica. Here, we review how aDNA research has helped discern population dynamics patterns in the pre-Columbian Mesoamerican context, how it supports archaeological, linguistic, and anthropological conclusions, and finally, how it offers new working hypotheses.
Publisher: Springer Science and Business Media LLC
Date: 22-03-2021
Publisher: Proceedings of the National Academy of Sciences
Date: 12-07-2019
Abstract: The dispersal of anatomically modern human populations out of Africa and across much of the rest of the world around 55 to 50 thousand years before present (ka) is recorded genetically by the multiple hominin groups they met and interbred with along the way, including the Neandertals and Denisovans. The signatures of these introgression events remain preserved in the genomes of modern-day populations, and provide a powerful record of the sequence and timing of these early migrations, with Asia proving a particularly complex area. At least 3 different hominin groups appear to have been involved in Asia, of which only the Denisovans are currently known. Several interbreeding events are inferred to have taken place east of Wallace’s Line, consistent with archaeological evidence of widespread and early hominin presence in the area. However, archaeological and fossil evidence indicates archaic hominins had not spread as far as the Sahul continent (New Guinea, Australia, and Tasmania), where recent genetic evidence remains enigmatic.
Publisher: Springer Science and Business Media LLC
Date: 29-06-2021
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.
Location: Australia
Location: Germany
Start Date: 2012
End Date: 2015
Funder: Fundação para a Ciência e a Tecnologia
View Funded ActivityStart Date: 2016
End Date: 2017
Funder: Institut Pasteur
View Funded ActivityStart Date: 2021
End Date: End date not available
Funder: Australian Research Council
View Funded ActivityStart Date: 07-2022
End Date: 12-2025
Amount: $424,500.00
Funder: Australian Research Council
View Funded Activity