ORCID Profile
0000-0002-4603-1473
Current Organisation
Australian National University
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Research Topics
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.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Aboriginal and Torres Strait Islander History | Evolutionary Biology | Biogeography and Phylogeography | Biological Adaptation | Evolutionary Impacts of Climate Change | Aboriginal and Torres Strait Islander history | Quaternary environments | Aboriginal and Torres Strait Islander archaeology | Aboriginal and Torres Strait Islander culture language and history | Genetics | Archaeological science | Population, Ecological and Evolutionary Genetics |
ANZSRC Socio-Economic Objective (SEO)
Expanding Knowledge in the Biological Sciences | Understanding Australia's Past | Conserving Aboriginal and Torres Strait Islander Heritage | Indigenous Health not elsewhere classified |
Related Links
Publications
High rate of translocation-based gene birth on the Drosophila Y chromosome
Publisher: Proceedings of the National Academy of Sciences
Date: 19-10-2017
Abstract: Using a powerful method that uses inexpensive short reads to detect Y-linked transfers, we show that gene traffic onto the Drosophila Y chromosome is 10 times more frequent than previously thought and includes the first Y-linked retrocopies discovered in these taxa. All 25 identified Y-linked gene transfers were relatively young ( million years old), although most appear to be pseudogenes because only three of these transfers show signs of purifying selection. Our method provides compelling evidence that the Drosophila Y chromosome is a highly challenging and dynamic genetic environment that is capable of rapidly erging between species and promises to reveal fundamental insights into Y chromosome evolution across many taxa.
Systematic benchmark of ancient DNA read mapping
Publisher: Oxford University Press (OUP)
Date: 08-04-2021
DOI: 10.1093/BIB/BBAB076
Abstract: The current standard practice for assembling in idual genomes involves mapping millions of short DNA sequences (also known as DNA ‘reads’) against a pre-constructed reference genome. Mapping vast amounts of short reads in a timely manner is a computationally challenging task that inevitably produces artefacts, including biases against alleles not found in the reference genome. This reference bias and other mapping artefacts are expected to be exacerbated in ancient DNA (aDNA) studies, which rely on the analysis of low quantities of damaged and very short DNA fragments (~30–80 bp). Nevertheless, the current gold-standard mapping strategies for aDNA studies have effectively remained unchanged for nearly a decade, during which time new software has emerged. In this study, we used simulated aDNA reads from three different human populations to benchmark the performance of 30 distinct mapping strategies implemented across four different read mapping software—BWA-aln, BWA-mem, NovoAlign and Bowtie2—and quantified the impact of reference bias in downstream population genetic analyses. We show that specific NovoAlign, BWA-aln and BWA-mem parameterizations achieve high mapping precision with low levels of reference bias, particularly after filtering out reads with low mapping qualities. However, unbiased NovoAlign results required the use of an IUPAC reference genome. While relevant only to aDNA projects where reference population data are available, the benefit of using an IUPAC reference demonstrates the value of incorporating population genetic information into the aDNA mapping process, echoing recent results based on graph genome representations.
A simple genetic basis of adaptation to a novel thermal environment results in complex metabolic rewiring in Drosophila
Publisher: Springer Science and Business Media LLC
Date: 20-08-2018
Additional evaluations show that specific BWA‐aln settings still outperform BWA‐mem for ancient DNA data alignment
Publisher: Wiley
Date: 12-2021
DOI: 10.1002/ECE3.8297
Sequencing pools of individuals — mining genome-wide polymorphism data without big funding
Publisher: Springer Science and Business Media LLC
Date: 23-09-2014
DOI: 10.1038/NRG3803
Abstract: The analysis of polymorphism data is becoming increasingly important as a complementary tool to classical genetic analyses. Nevertheless, despite plunging sequencing costs, genomic sequencing of in iduals at the population scale is still restricted to a few model species. Whole-genome sequencing of pools of in iduals (Pool-seq) provides a cost-effective alternative to sequencing in iduals separately. With the availability of custom-tailored software tools, Pool-seq is being increasingly used for population genomic research on both model and non-model organisms. In this Review, we not only demonstrate the breadth of questions that are being addressed by Pool-seq but also discuss its limitations and provide guidelines for users.
An ancient viral epidemic involving host coronavirus interacting genes more than 20,000 years ago in East Asia
Publisher: Elsevier BV
Date: 08-2021
smartsnp, an R package for fast multivariate analyses of big genomic data
Publisher: Wiley
Date: 08-08-2021
Abstract: Principal component analysis (PCA) is a powerful tool for the analysis of population structure, a genetic property that is essential to understand the evolutionary processes driving biological ersification and (pre)historical colonizations, migrations and extinctions. In the current era of high‐throughput sequencing technologies, population structure can be quantified from scores of genetic markers across hundreds to thousands of genomes. However, these big genomic datasets pose substantial computing and analytical challenges. We present the r package smartsnp for fast and user‐friendly computation of PCA on single‐nucleotide polymorphism (SNP) data. Inspired by the current field‐standard software EIGENSOFT, smartsnp includes appropriate SNP scaling for genetic drift and allows projection of ancient s les onto a modern genetic space while also providing permutation‐based multivariate tests for population differences in genetic ersity (both location and dispersion). Our extensive benchmarks show that smartsnp 's PCA is 2–4 times faster than EIGENSOFT's SMARTPCA algorithm across a wide range of s le and SNP sizes. All four smartsnp functions ( smart_pca , smart_permanova , smart_permdisp and smart_mva ) process datasets with up to 100 s les and 1 million simulated SNPs in less than 30 s and accurately recreate previously published SMARTPCA of ancient‐human and wolf genotypes. The package smartsnp provides fast and robust multivariate ordination and hypothesis testing for big genomic data that is also suitable for ancient and low‐coverage modern DNA. The simple implementation should appeal to biological conservation, evolutionary, ecological and (palaeo)genomic researchers, and be useful for phenotype, ancestry and lineage studies.
Response to Comment on “A global environmental crisis 42,000 years ago”
Publisher: American Association for the Advancement of Science (AAAS)
Date: 19-11-2021
Abstract: Our study on the exact timing and the potential climatic, environmental, and evolutionary consequences of the Lasch s Geomagnetic Excursion has generated the hypothesis that geomagnetism represents an unrecognized driver in environmental and evolutionary change. It is important for this hypothesis to be tested with new data, and encouragingly, none of the studies presented by Picin et al . undermine our model.
Unsupervized Quantification of Demographic Structure for Single-copy Alignments
Publisher: Cold Spring Harbor Laboratory
Date: 04-06-2018
DOI: 10.1101/338442
Abstract: Single-copy sequence alignments have been a valuable source of information for genetic studies their lack of recombination makes phylogenetic analyses tractable [1]. Specifically, mitochondrial DNA will continue to play an important role in genetic studies due to its high mutation rate and high copy per cell count of the molecule [2]. In this paper we develop a new method for the analysis of single-copy sequence data that simultaneously considers the relationships between sequenced in iduals and positions of interest in the genome. We then show that tests for relationships between genetic information and qualitative and quantitative characteristics can be calculated. We motivate the use of our method with ex les from empirical data.
Mitogenomes Reveal Two Major Influxes of Papuan Ancestry across Wallacea Following the Last Glacial Maximum and Austronesian Contact
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.
Secondary contact and local adaptation contribute to genome-wide patterns of clinal variation in Drosophila melanogaster
Publisher: Cold Spring Harbor Laboratory
Date: 13-09-2014
DOI: 10.1101/009084
Abstract: Populations arrayed along broad latitudinal gradients often show patterns of clinal variation in phenotype and genotype. Such population differentiation can be generated and maintained by historical demographic events and local adaptation. These evolutionary forces are not mutually exclusive and, moreover, can in some cases produce nearly identical patterns of genetic differentiation among populations. Here, we investigate the evolutionary forces that generated and maintain clinal variation genome-wide among populations of Drosophila melanogaster s led in North America and Australia. We contrast patterns of clinal variation in these continents with patterns of differentiation among ancestral European and African populations. Using established and novel methods we derive here, we show that recently derived North America and Australia populations were likely founded by both European and African lineages and that this admixture event contributed to genome-wide patterns of parallel clinal variation. The pervasive effects of admixture meant that only a handful of loci could be attributed to the operation of spatially varying selection using an FST outlier approach. Our results provide novel insight into the well-studied system of clinal differentiation in D. melanogaster and provide a context for future studies seeking to identify loci contributing to local adaptation in a wide variety of organisms, including other invasive species as well as some temperate endemics.
A simple genetic basis of adaptation to a novel thermal environment results in complex metabolic rewiring in Drosophila
Publisher: Cold Spring Harbor Laboratory
Date: 11-08-2017
DOI: 10.1101/174011
Abstract: Population genetic theory predicts that rapid adaptation is largely driven by complex traits encoded by many loci of small effect. Because large effect loci are quickly fixed in natural populations, they should not contribute much to rapid adaptation. To investigate the genetic architecture of thermal adaptation - a highly complex trait - we performed experimental evolution on a natural Drosophila simulans population. Transcriptome and respiration measurements revealed extensive metabolic rewiring after only ∼60 generations in a hot environment. Analysis of genome-wide polymorphisms identified two interacting selection targets, Sestrin and SNF4Aγ , pointing to AMPK, a central metabolic switch, as a key factor for thermal adaptation. Our results demonstrate that large-effect loci segregating at intermediate allele frequencies can allow natural populations to rapidly respond to selection. Because SNF4Aγ also exhibits clinal variation in various Drosophila species, we suggest that this large effect polymorphism is maintained by temporal and spatial temperature variation in natural environments.
Erratum: “An ancient viral epidemic involving host coronavirus interacting genes more than 20,000 years ago in East Asia” (Current Biology (2021) 31(16) (3504–3514.e9), (S0960982221007946), (10.1016/j.cub.2021.05.067))
Publisher: Elsevier BV
Date: 08-2021
Genetic redundancy fuels polygenic adaptation in Drosophila
Publisher: Public Library of Science (PLoS)
Date: 04-02-2019
Molecular dissection of a natural transposable element invasion
Publisher: Cold Spring Harbor Laboratory
Date: 30-04-2018
Abstract: The first tracking of the dynamics of a natural invasion by a transposable element (TE) provides unprecedented details on the establishment of host defense mechanisms against TEs. We captured a D. simulans population at an early stage of a P - element invasion and studied the spread of the TE in replicated experimentally evolving populations kept under hot and cold conditions. We analyzed the factors controlling the invasion by NGS, RNA-FISH, and gonadal dysgenesis assays. Under hot conditions, the P - element spread rapidly for 20 generations, but no further spread was noted later on. This plateauing of the invasion was mediated by the rapid emergence of P - element -specific piRNAs. Under cold conditions, we observed a lower expression of the P - element and a slower emergence of the piRNA defense, resulting in a three times slower invasion that continued beyond 40 generations. We conclude that the environment is a major factor determining the evolution of TEs in their host.
Polygenic adaptation fuels genetic redundancy inDrosophila
Publisher: Cold Spring Harbor Laboratory
Date: 28-05-2018
DOI: 10.1101/332122
Abstract: The genetic architecture of adaptive traits is of key importance to predict evolutionary responses. Most adaptive traits are polygenic – i.e. result from selection on a large number of genetic loci – but most molecularly characterized traits have a simple genetic basis. This discrepancy is best explained by the difficulty in detecting small allele frequency changes across many contributing loci. To resolve this, we use laboratory natural selection, a framework that is powerful enough to detect signatures for selective sweeps and polygenic adaptation. We exposed 10 replicates of a Drosophila simulans population to a new temperature regime and uncovered a polygenic architecture of an adaptive trait with high genetic redundancy among adaptive alleles. We observed convergent phenotypic responses, e.g. fitness, metabolic rate and fat content, and a strong polygenic response (99 selected alleles mean s =0.061). However, each of these selected alleles increased in frequency only in a subset of the evolving replicates. Our results show that natural D. simulans populations harbor a vast reservoir of adaptive variation facilitating rapid evolutionary responses. The observed genetic redundancy potentiates this genotypic variation through multiple genetic pathways leading to phenotypic convergence. This key property of adaptive alleles requires the modification of testing strategies in natural populations beyond the search for convergence on the molecular level.
Massive Habitat-Specific Genomic Response in D. melanogaster Populations during Experimental Evolution in Hot and Cold Environments
Publisher: Oxford University Press (OUP)
Date: 22-10-2013
Human Genetic Research in Wallacea and Sahul: Recent Findings and Future Prospects
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.
What Do the First 597 Global Fungal Red List Assessments Tell Us about the Threat Status of Fungi?
Publisher: MDPI AG
Date: 07-09-2022
DOI: 10.3390/D14090736
Abstract: Fungal species are not immune to the threats facing animals and plants and are thus also prone to extinction. Yet, until 2015, fungi were nearly absent on the IUCN Red List. Recent efforts to identify fungal species under threat have significantly increased the number of published fungal assessments. The 597 species of fungi published in the 2022-1 IUCN Red List update (21 July 2022) are the basis for the first global review of the extinction risk of fungi and the threats they face. Nearly 50% of the assessed species are threatened, with 10% NT and 9% DD. For regions with a larger number of assessments (i.e., Europe, North America, and South America), subanalyses are provided. Data for lichenized and nonlichenized fungi are also summarized separately. Habitat loss/degradation followed by climate change, invasive species, and pollution are the primary identified threats. Bias in the data is discussed along with knowledge gaps. Suggested actions to address these gaps are provided along with a discussion of the use of assessments to facilitate on-the-ground conservation efforts. A research agenda for conservation mycology to assist in the assessment process and implementation of effective species/habitat management is presented.
Ancestral population reconstitution from isofemale lines as a tool for experimental evolution
Publisher: Wiley
Date: 30-08-2016
DOI: 10.1002/ECE3.2402
Introgression, hominin dispersal and megafaunal survival in Late Pleistocene Island Southeast Asia
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.
Erratum: Combining experimental evolution with next-generation sequencing: a powerful tool to study adaptation from standing genetic variation
Publisher: Springer Science and Business Media LLC
Date: 13-01-2016
DOI: 10.1038/HDY.2015.85
Fluctuating selection and the determinants of genetic variation
Publisher: Elsevier BV
Date: 06-2023
Drosophila simulans: A Species with Improved Resolution in Evolve and Resequence Studies
Publisher: Oxford University Press (OUP)
Date: 07-2017
Abstract: The combination of experimental evolution with high-throughput sequencing of pooled in iduals—i.e., evolve and resequence (E& R)—is a powerful approach to study adaptation from standing genetic variation under controlled, replicated conditions. Nevertheless, E& R studies in Drosophila melanogaster have frequently resulted in inordinate numbers of candidate SNPs, particularly for complex traits. Here, we contrast the genomic signature of adaptation following ∼60 generations in a novel hot environment for D. melanogaster and D. simulans. For D. simulans, the regions carrying putatively selected loci were far more distinct, and thus harbored fewer false positives, than those in D. melanogaster. We propose that species without segregating inversions and higher recombination rates, such as D. simulans, are better suited for E& R studies that aim to characterize the genetic variants underlying the adaptive response.
A Genome-Wide, Fine-Scale Map of Natural Pigmentation Variation in Drosophila melanogaster
Publisher: Public Library of Science (PLoS)
Date: 06-06-2013
Ancient human genomes reveal a hidden history of strong selection in Eurasia
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.
Secondary contact and local adaptation contribute to genome‐wide patterns of clinal variation in Drosophila melanogaster
Publisher: Wiley
Date: 18-01-2016
DOI: 10.1111/MEC.13455
Ethics of DNA research on human remains: five globally applicable guidelines
Publisher: Springer Science and Business Media LLC
Date: 20-10-2021
Parallel trait adaptation across opposing thermal environments in experimentalDrosophila melanogasterpopulations
Publisher: Wiley
Date: 07-2015
DOI: 10.1111/EVO.12705
An ancient viral epidemic involving host coronavirus interacting genes more than 20,000 years ago in East Asia
Publisher: Cold Spring Harbor Laboratory
Date: 16-11-2021
DOI: 10.1101/2020.11.16.385401
Abstract: The current SARS-CoV-2 pandemic has emphasized the vulnerability of human populations to novel viral pressures, despite the vast array of epidemiological and biomedical tools now available. Notably, modern human genomes contain evolutionary information tracing back tens of thousands of years, which may help identify the viruses that have impacted our ancestors – pointing to which viruses have future pandemic potential. Here, we apply evolutionary analyses to human genomic datasets to recover selection events involving tens of human genes that interact with coronaviruses, including SARS-CoV-2, that likely started more than 20,000 years ago. These adaptive events were limited to the population ancestral to East Asian populations. Multiple lines of functional evidence support an ancient viral selective pressure, and East Asia is the geographical origin of several modern coronavirus epidemics. An arms race with an ancient coronavirus, or with a different virus that happened to use similar interactions as coronaviruses with human hosts, may thus have taken place in ancestral East Asian populations. By learning more about our ancient viral foes, our study highlights the promise of evolutionary information to better predict the pandemics of the future. Importantly, adaptation to ancient viral epidemics in specific human populations does not necessarily imply any difference in genetic susceptibility between different human populations, and the current evidence points toward an overwhelming impact of socioeconomic factors in the case of COVID-19.
Admixture has obscured signals of historical hard sweeps in humans
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.
The role of genetic selection and climatic factors in the dispersal of anatomically modern humans out of Africa
Publisher: Proceedings of the National Academy of Sciences
Date: 23-05-2023
Abstract: The evolutionarily recent dispersal of anatomically modern humans (AMH) out of Africa (OoA) and across Eurasia provides a unique opportunity to examine the impacts of genetic selection as humans adapted to multiple new environments. Analysis of ancient Eurasian genomic datasets (~1,000 to 45,000 y old) reveals signatures of strong selection, including at least 57 hard sweeps after the initial AMH movement OoA, which have been obscured in modern populations by extensive admixture during the Holocene. The spatiotemporal patterns of these hard sweeps provide a means to reconstruct early AMH population dispersals OoA. We identify a previously unsuspected extended period of genetic adaptation lasting ~30,000 y, potentially in the Arabian Peninsula area, prior to a major Neandertal genetic introgression and subsequent rapid dispersal across Eurasia as far as Australia. Consistent functional targets of selection initiated during this period, which we term the Arabian Standstill, include loci involved in the regulation of fat storage, neural development, skin physiology, and cilia function. Similar adaptive signatures are also evident in introgressed archaic hominin loci and modern Arctic human groups, and we suggest that this signal represents selection for cold adaptation. Surprisingly, many of the candidate selected loci across these groups appear to directly interact and coordinately regulate biological processes, with a number associated with major modern diseases including the ciliopathies, metabolic syndrome, and neurodegenerative disorders. This expands the potential for ancestral human adaptation to directly impact modern diseases, providing a platform for evolutionary medicine.
genozip: a fast and efficient compression tool for VCF files
Publisher: Oxford University Press (OUP)
Date: 14-05-2020
DOI: 10.1093/BIOINFORMATICS/BTAA290
Abstract: genozip is a new lossless compression tool for Variant Call Format (VCF) files. By applying field-specific algorithms and fully utilizing the available computational hardware, genozip achieves the highest compression ratios amongst existing lossless compression tools known to the authors, at speeds comparable with the fastest multi-threaded compressors. genozip is freely available to non-commercial users. It can be installed via conda-forge, Docker Hub, or downloaded from ivonlan/genozip. Supplementary data are available at Bioinformatics online.
Experimental evolution reveals habitat‐specific fitness dynamics amongW olbachiaclades inD rosophila melanogaster
Publisher: Wiley
Date: 29-01-2014
DOI: 10.1111/MEC.12643
Aboriginal mitogenomes reveal 50,000 years of regionalism in Australia
Publisher: Springer Science and Business Media LLC
Date: 08-03-2017
DOI: 10.1038/NATURE21416
Abstract: Aboriginal Australians represent one of the longest continuous cultural complexes known. Archaeological evidence indicates that Australia and New Guinea were initially settled approximately 50 thousand years ago (ka) however, little is known about the processes underlying the enormous linguistic and phenotypic ersity within Australia. Here we report 111 mitochondrial genomes (mitogenomes) from historical Aboriginal Australian hair s les, whose origins enable us to reconstruct Australian phylogeographic history before European settlement. Marked geographic patterns and deep splits across the major mitochondrial haplogroups imply that the settlement of Australia comprised a single, rapid migration along the east and west coasts that reached southern Australia by 49-45 ka. After continent-wide colonization, strong regional patterns developed and these have survived despite substantial climatic and cultural change during the late Pleistocene and Holocene epochs. Remarkably, we find evidence for the continuous presence of populations in discrete geographic areas dating back to around 50 ka, in agreement with the notable Aboriginal Australian cultural attachment to their country.
Patterns of Linkage Disequilibrium and Long Range Hitchhiking in Evolving ExperimentalDrosophila melanogasterPopulations
Publisher: Oxford University Press (OUP)
Date: 17-11-2014
A global environmental crisis 42,000 years ago
Publisher: American Association for the Advancement of Science (AAAS)
Date: 19-02-2021
Abstract: Do terrestrial geomagnetic field reversals have an effect on Earth's climate? Cooper et al. created a precisely dated radiocarbon record around the time of the Lasch s geomagnetic reversal about 41,000 years ago from the rings of New Zealand sw kauri trees. This record reveals a substantial increase in the carbon-14 content of the atmosphere culminating during the period of weakening magnetic field strength preceding the polarity switch. The authors modeled the consequences of this event and concluded that the geomagnetic field minimum caused substantial changes in atmospheric ozone concentration that drove synchronous global climate and environmental shifts. Science , this issue p. 811
Widespread Denisovan ancestry in Island Southeast Asia but no evidence of substantial super-archaic hominin admixture
Publisher: Springer Science and Business Media LLC
Date: 22-03-2021
Genozip - A Universal Extensible Genomic Data Compressor
Publisher: Oxford University Press (OUP)
Date: 15-02-2021
DOI: 10.1093/BIOINFORMATICS/BTAB102
Abstract: We present Genozip, a universal and fully featured compression software for genomic data. Genozip is designed to be a general-purpose software and a development framework for genomic compression by providing five core capabilities—universality (support for all common genomic file formats), high compression ratios, speed, feature-richness and extensibility. Genozip delivers high-performance compression for widelyused genomic data formats in genomics research, namely FASTQ, SAM/BAM/CRAM, VCF, GVF, FASTA, PHYLIP and 23andMe formats. Our test results show that Genozip is fast and achieves greatly improved compression ratios, even when the files are already compressed. Further, Genozip is architected with a separation of the Genozip Framework from file-format-specific Segmenters and data-type-specific Codecs. With this, we intend for Genozip to be a general-purpose compression platform where researchers can implement compression for additional file formats, as well as new codecs for data types or fields within files, in the future. We anticipate that this will ultimately increase the visibility and adoption of these algorithms by the user community, thereby accelerating further innovation in this space. Genozip is written in C. The code is open-source and available on www.genozip.com. The package is free for non-commercial use. It is distributed through the Conda package manager, github, and as a Docker container on DockerHub. Genozip is tested on Linux, Mac and Windows. Supplementary data are available at Bioinformatics online.
Response to Comment on “A global environmental crisis 42,000 years ago”
Publisher: American Association for the Advancement of Science (AAAS)
Date: 19-11-2021
Abstract: Our paper about the impacts of the Lasch s Geomagnetic Excursion 42,000 years ago has provoked considerable scientific and public interest, particularly in the so-called Adams Event associated with the initial transition of the magnetic poles. Although we welcome the opportunity to discuss our new ideas, Hawks’ assertions of misrepresentation are especially disappointing given his limited examination of the material.
Genozip Dual-Coordinate VCF format enables efficient genomic analyses and alleviates liftover limitations
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 .
BWA-mem is not the best aligner for ancient DNA short reads
Publisher: Cold Spring Harbor Laboratory
Date: 03-08-2021
DOI: 10.1101/2021.08.02.454401
Abstract: Xu and colleagues (Xu et al., 2021) recently suggested a new parameterisation of BWA-mem (Li, 2013) as an alternative to the current standard BWA-aln (Li and Durbin, 2009) to process ancient DNA sequencing data. The authors tested several combinations of the -k and -r parameters to optimise BWA-mem ’s performance with degraded and contaminated ancient DNA s les. They report that using BWA-mem with − k 19 − r 2.5 parameters results in a mapping efficiency comparable to BWA-aln with − I 1024 − n 0.03 (i.e. a derivation of the standard parameters used in ancient DNA studies (Schubert et al., 2012)), while achieving significantly faster run times. We recently performed a systematic benchmark of four mapping software (i.e. BWA-aln , BWA-mem , NovoAlign ( roducts/novoalign ), and Bowtie2 (Langmead and Salzberg, 2012) for ancient DNA sequencing data and quantified their precision, accuracy, specificity, and impact on reference bias (Oliva et al., 2021). Notably, while multiple parameterisations were tested for BWA-aln , NovoAlign , and Bowtie2 , we only tested BWA-mem with default parameters. Here, we use the alignment performance metrics from Oliva et al. to directly compare the recommended BWA-mem parameterisation reported in Xu et al. with the best performing alignment methods determined in the Oliva et al. benchmarks, and we make recommendations based on the results.
Combining experimental evolution with next-generation sequencing: a powerful tool to study adaptation from standing genetic variation
Publisher: Springer Science and Business Media LLC
Date: 10-2015
DOI: 10.1038/HDY.2014.86
No evidence for ovarian synchrony or asynchrony in hamadryas baboons
Publisher: Elsevier BV
Date: 11-2010
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Using Genetics To Reconstruct The Peopling And Diversification Of Sahul
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View Funded ActivityAdaptation And Diversification Of The First Peoples Of Sahul
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End Date: 2021
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View Funded ActivityARC Centre Of Excellence For Indigenous And Environmental Histories And Futures
Start Date: 2024
End Date: 2031
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View Funded ActivityThe Genomic History Of Indigenous Australia
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View Funded ActivityDiscovery Early Career Researcher Award - Grant ID: DE190101069
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Amount: $390,000.00
Funder: Australian Research Council
View Funded ActivityDiscovery Indigenous - Grant ID: IN160100007
Start Date: 2016
End Date: 06-2019
Amount: $635,000.00
Funder: Australian Research Council
View Funded ActivityDiscovery Indigenous - Grant ID: IN180100017
Start Date: 02-2018
End Date: 06-2021
Amount: $512,688.00
Funder: Australian Research Council
View Funded ActivityARC Centres Of Excellence - Grant ID: CE230100009
Start Date: 07-2024
End Date: 06-2031
Amount: $35,000,000.00
Funder: Australian Research Council
View Funded Activity