ORCID Profile
0000-0002-5550-9176
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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)
Genetics | Evolutionary Biology | Population, Ecological and Evolutionary Genetics | Evolutionary Impacts of Climate Change | Quaternary Environments | Archaeology | Aboriginal and Torres Strait Islander History | Archaeological Science | Aboriginal and Torres Strait Islander Archaeology | Epigenetics (incl. Genome Methylation and Epigenomics) | Genomics | Ecological Impacts of Climate Change | Immunogenetics | Population And Ecological Genetics | Animal Growth and Development | Archaeology not elsewhere classified | Molecular Evolution | Anthropological Genetics | Biogeography and Phylogeography
ANZSRC Socio-Economic Objective (SEO)
Expanding Knowledge in the Biological Sciences | Understanding Australia's Past | Ecosystem Adaptation to Climate Change | Climate Change Adaptation Measures | Beef Cattle | Immune system and allergy | Conserving Aboriginal and Torres Strait Islander Heritage | Health related to specific ethnic groups | Biological sciences | Aboriginal and Torres Strait Islander Health - Determinants of Health | Expanding Knowledge in the Earth Sciences | Flora, Fauna and Biodiversity at Regional or Larger Scales | Expanding Knowledge in History and Archaeology |
Related Links
Publications
AmericaPlex26: A SNaPshot Multiplex System for Genotyping the Main Human Mitochondrial Founder Lineages of the Americas
Publisher: Public Library of Science (PLoS)
Date: 26-03-2014
Data-sharing for indigenous peoples
Publisher: Springer Science and Business Media LLC
Date: 22-06-2017
DOI: 10.1038/546474A
Deep FASTQ and BAM co-compression in Genozip 15
Publisher: Cold Spring Harbor Laboratory
Date: 07-07-2023
DOI: 10.1101/2023.07.07.548069
Abstract: We introduce Genozip Deep, a method for losslessly co-compressing FASTQ and BAM files. Benchmarking demonstrates improvements of 75% to 96% versus the already-compressed source files, translating to 2.3X to 6.8X better compression than current state-of-the-art algorithms that compress FASTQ and BAM separately. The Deep method is independent of the underlying FASTQ and BAM compressors, and here we present its implementation in Genozip, an established genomic data compression software.
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.
Paleogenomic study of the Mexican past
Publisher: American Association for the Advancement of Science (AAAS)
Date: 12-05-2023
A 1000-year-old case of Klinefelter's syndrome diagnosed by integrating morphology, osteology, and genetics
Publisher: Elsevier BV
Date: 08-2022
Parallel palaeogenomic transects reveal complex genetic history of early European farmers
Publisher: Springer Science and Business Media LLC
Date: 11-2017
DOI: 10.1038/NATURE24476
Genetic Determinants of Systolic and Pulse Pressure in an Intercross Between Normotensive Inbred Rats
Publisher: Ovid Technologies (Wolters Kluwer Health)
Date: 11-2006
DOI: 10.1161/01.HYP.0000244758.50351.29
Abstract: By continuous monitoring of abdominal aortic blood pressure via telemetry in conscious rats, we have observed that systolic, diastolic, and pulse pressures of male Brown–Norway rats were all significantly lower than that of male Wistar–Kyoto rats, despite the fact that all of the values in both strains were within normotensive ranges. Further analyses performed in 166 animals from the progeny of an F2 intercross between Brown–Norway and Wistar–Kyoto rats revealed that, despite a high correlation between systolic blood pressure and diastolic blood pressure, there was no correlation between pulse pressure and diastolic blood pressure, and the value of the correlation between systolic blood pressure and pulse pressure was lower than that of systolic blood pressure with diastolic blood pressure. Two major and highly significant ( P .001) quantitative trait loci linked to pulse pressure were found on chromosome 4 ( Pp1 ) and 16 ( Pp2). Only suggestive quantitative trait loci were found for systolic blood pressure, but the strongest one ( Sbp1 ) had the same peak and linkage probability profile as Pp1. Altogether, these data show that genetic determinants affecting pulse pressure in normotensive animals are either stronger or independent from the ones affecting systolic blood pressure and are of interest in light of evidence showing that pulse pressure is highly heritable in humans and that elevated pulse pressure is a predictor of cardiovascular risk.
Hypertensive Cardiac Remodeling in Males and Females
Publisher: Ovid Technologies (Wolters Kluwer Health)
Date: 03-2007
Using Ancient DNA Analysis and Radiocarbon Dating to Determine the Provenance of an Unusual Whaling Artifact
Publisher: Frontiers Media SA
Date: 11-09-2020
Ancient DNA reveals elephant birds and kiwi are sister taxa and clarifies ratite bird evolution
Publisher: American Association for the Advancement of Science (AAAS)
Date: 23-05-2014
Abstract: The evolution of the ratite birds has been widely attributed to vicariant speciation, driven by the Cretaceous breakup of the supercontinent Gondwana. The early isolation of Africa and Madagascar implies that the ostrich and extinct Madagascan elephant birds (Aepyornithidae) should be the oldest ratite lineages. We sequenced the mitochondrial genomes of two elephant birds and performed phylogenetic analyses, which revealed that these birds are the closest relatives of the New Zealand kiwi and are distant from the basal ratite lineage of ostriches. This unexpected result strongly contradicts continental vicariance and instead supports flighted dispersal in all major ratite lineages. We suggest that convergence toward gigantism and flightlessness was facilitated by early Tertiary expansion into the diurnal herbivory niche after the extinction of the dinosaurs.
Ancient DNA Analysis Suggests Negligible Impact of the Wari Empire Expansion in Peru’s Central Coast during the Middle Horizon
Publisher: Public Library of Science (PLoS)
Date: 06-2016
Differential gene expression profiling of orbital adipose tissue in thyroid orbitopathy
Publisher: Association for Research in Vision and Ophthalmology (ARVO)
Date: 07-10-2015
Abstract: We aimed to determine differentially expressed genes relevant to orbital inflammation and orbital fat expansion in thyroid orbitopathy (TO) using microarray gene profiling in a case-control study. Human orbital adipose s les were obtained from in iduals with active TO (n = 12), inactive TO (n = 21), and normal controls (n = 21). Gene expression profiles were examined using microarray analysis and were compared between active and inactive TO, and between active TO and normal controls. Top ranked differentially expressed genes were validated by real-time RT-PCR in an additional eight active TO, 13 inactive TO, and 11 normal controls and correlated with gene set enrichment analysis (GSEA) and molecular pathways analysis. Seven hundred twenty-one probes (683 genes) and 806 probes (735 genes) were significantly differentially expressed in comparing active to inactive TO and in comparing active TO to healthy controls, respectively. All selected genes were confirmed to be differentially expressed by real-time RT-PCR. Multiple top ranked genes in active versus inactive TO comparison are overrepresented by immune and inflammatory response genes. They include defensins (DEFA1, DEFA1B, DEFA3), which were overexpressed by 3.05- to 4.14-fold and TIMD4 by 4.20-fold. Markers for adipogenesis were overexpressed including SCD, FADS1, and SCDP1. Gene set enrichment analysis revealed dysregulation of epigenetic signatures, T-cell activation, Th1 differentiation, defensin pathway, cell adhesion, cytoskeleton organization, apoptosis, cell cycling, and lipid metabolism in active TO. Active TO is characterized by upregulation of genes involved in cell-mediated immune, innate immune, and inflammatory response and enhanced orbital adipogenesis. TIMD4, DEFA1, DEFA1B, and DEFA3 genes may be involved in the innate immune-mediated orbital inflammation in TO. Epigenetic mechanisms may play a role in the pathogenesis of TO.
Low-cost cross-taxon enrichment of mitochondrial DNA using in-house synthesised RNA probes
Publisher: Public Library of Science (PLoS)
Date: 04-02-2019
Reply to Santiago-Rodriguez et al.: Was luxS really isolated from 25- to 40-million-year-old bacteria?
Publisher: Oxford University Press (OUP)
Date: 04-2014
Binding affinities of 438 HLA proteins to complete proteomes of seven pandemic viruses and distributions of strongest and weakest HLA peptide binders in populations worldwide.
Publisher: Wiley
Date: 11-06-2020
DOI: 10.1111/TAN.13956
QTL mapping for traits associated with stress neuroendocrine reactivity in rats
Publisher: Springer Science and Business Media LLC
Date: 07-2005
DOI: 10.1007/S00335-005-0022-2
Abstract: In the present study we searched for quantitative trait loci (QTLs) that affect neuroendocrine stress responses in a 20-min restraint stress paradigm using Brown-Norway (BN) and Wistar-Kyoto-Hyperactive (WKHA) rats. These strains differed in their hypothalamic-pituitary-adrenal axis (plasma ACTH and corticosterone levels, thymus, and adrenal weights) and in their renin-angiotensin-aldosterone system reactivity (plasma renin activity, aldosterone concentration). We performed a whole-genome scan on a F2 progeny derived from a WKHA x BN intercross, which led to the identification of several QTLs linked to plasma renin activity (Sr6, Sr8, Sr11, and Sr12 on chromosomes RNO2, 3, 19, and 8, respectively), plasma aldosterone concentration (Sr7 and Sr9 on RNO2 and 5, respectively), and thymus weight (Sr10, Sr13, and Srl4 on RNO5, 10, and 16, respectively). The type 1b angiotensin II receptor gene (Agtrlb) maps within the confidence intervals of QTLs on RNO2 linked to plasma renin activity (Sr6, highly significant LOD = 5.0) and to plasma aldosterone level (Sr7, suggestive LOD = 2.0). In vitro studies of angiotensin II-induced release of aldosterone by adrenal glomerulosa cells revealed a lower receptor potency (log EC50 = -8.16 +/- 0.11 M) and efficiency (Emax = 453.3 +/- 25.9 pg/3 x 10(4) cells/24 h) in BN than in WKHA (log EC50 = -10.66 +/- 0.18 M Emax = 573.1 +/- 15.3 pg/3 x 10(4) cells/24 h). Moreover, differences in Agtr1b mRNA abundance and sequence reinforce the putative role of the Agtr1b gene in the differential plasma renin stress reactivity between the two rat strains.
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.
Distinct QTLs are linked to cardiac left ventricular mass in a sex-specific manner in a normotensive inbred rat intercross
Publisher: Springer Science and Business Media LLC
Date: 09-2005
DOI: 10.1007/S00335-005-0041-Z
Abstract: Genetic mapping of the progeny of an F(2) inter-cross between WKY and WKHA rats had previously allowed us to detect male-specific linkage between locus Cm 24 and left ventricular mass index (LVMI). By further expanding that analysis, we detected additional loci that were all linked to LVMI in a sex-specific manner despite their autosomal location. In males, we detected one additional locus (Lvm 8) on Chromosome 5 (LOD=3.4), the two loci Lvm 13 (LOD=4.5) and Lvm 9 (LOD=2.8) on Chromosome 17, and locus Lvm 10 (LOD=4.2) on Chromosome 12. The locus Lvm 13 had the same boundaries as locus Cm 26 previously reported by others using a different cross. None of these loci showed linkage to LVM in females. In contrast, we identified in females the novel locus Lvm 11 on Chromosome 15 (LOD=2.8) and locus Lvm 12 (LOD=2.7) that had the same boundaries on Chromosome 3 as locus Cm 25 detected previously by others using a cross of other normotensive strains. In prepubertal males, there were no differences in the width of cardiomyocytes from WKY and WKHA rats, but cardiomyocytes from WKHA became progressively wider than that of WKY as sexual maturation progressed. Altogether, these results provide evidence that distinct genes may influence LVMI of rats in a sex-dependent manner, maybe by involving sex-specific interactions of sex steroids with particular genes involved in the determination of LVMI and/or cardiomyocyte width.
Mitochondrial Genome Sequencing in Mesolithic North East Europe Unearths a New Sub-Clade within the Broadly Distributed Human Haplogroup C1
Publisher: Public Library of Science (PLoS)
Date: 04-02-2014
The landscape of genomic structural variation in Indigenous Australians
Publisher: Cold Spring Harbor Laboratory
Date: 19-10-2023
Identification and Validation of Loci and Candidate Genes Linked to Cardiac Hypertrophy
Publisher: Humana Press
Date: 2005
DOI: 10.1385/1-59259-879-X:321
Abstract: Left ventricular hypertrophy (LVH) is a complex quantitative trait that has a strong prognostic value for cardiovascular mortality and morbidity. Cardiac mass is determined in part by the influence of genetic loci that are known as quantitative trait loci (QTLs), the localization of which can be performed experimentally in genetic animal crosses. The present chapter outlines standard procedures for the selection of appropriate animal strains, for assessment of mode of inheritance, for characterizing the cardiac phenotype, for performing whole-genome scans, and for conducting linkage analyses. Identification of QTLs may lead to the identification of candidate genes whose roles can be further investigated in either transgenic, knockout, or pharmacologically manipulated animal models.
Ancient DNA of northern China Hystricidae sub-fossils reveals the evolutionary history of old world porcupines in the Late Pleistocene
Publisher: Springer Science and Business Media LLC
Date: 18-07-2020
DOI: 10.1186/S12862-020-01656-X
Abstract: Old World porcupines (Family: Hystricidae) are the third-largest rodents and inhabit southern Europe, Asia, and most regions of Africa. They are a typical indicator of warm climate and their distribution is restricted to tropical and subtropical zones. In China, porcupines are widely distributed in southern areas of the Yangtze River. However, fossil remains have been identified in a few sites in northern China, among which Tianyuan Cave—near Zhoukoudian site—represents the latest known porcupine fossil record. So far, studies have focused mainly on porcupines’ husbandry and domestication but little is known about their intrafamilial phylogenetic relationships and evolutionary history. In this study, we sequence partial mitochondrial 12S rRNA and cyt b genes for seven Late Pleistocene porcupine in iduals from Northern, Southern and Central China. Phylogenetic analyses show that the Tianyuan Cave porcupines, which had been morphologically identified as Hystrix subcristata , have a closer relationship to Hystrix brachyura . Together with morphological adaptation characteristics, associated fauna, and climate change evidence, the molecular results reveal that a Late Quaternary extirpation has occurred during the evolutionary history of porcupines.
Ancient mitochondrial genomes from the Argentinian Pampas inform the early peopling of the Southern Cone of South America
Publisher: Elsevier BV
Date: 06-2021
High-Resolution Analysis of Cytosine Methylation in Ancient DNA
Publisher: Public Library of Science (PLoS)
Date: 19-01-2012
A Genetic Locus Accentuates the Effect of Volume Overload on Adverse Left Ventricular Remodeling in Male and Female Rats
Publisher: Ovid Technologies (Wolters Kluwer Health)
Date: 2006
DOI: 10.1161/01.HYP.0000196732.22719.47
Abstract: Although increased left ventricular (LV) mass is highly predictive of cardiovascular morbidity and mortality in humans, it has never been verified in an experimental model that naturally occurring alleles linked to increased LV mass under basal conditions also associate with worsened cardiovascular prognosis. Because we have shown previously that locus Cm24 on chromosome 5 was responsible for differences in LV mass between WKY and WKHA rats, we used WKY.WKHA-( D5Rat45-D5Rat245 ) congenic rats (where locus Cm24 has been transferred from WKHA into WKY rats) to test how naturally occurring gene variants present in Cm24 would, in addition to their effects under basal conditions, affect LV mass remodeling and/or function in the context of overload. Volume overload was induced in WKY, WKHA, and WKY.WKHA congenic rats by surgical creation of an aorto-caval fistula. In females, the fistula had no effect on the hearts of WKY rats, yet it induced dilated eccentric hypertrophy and isolated diastolic dysfunction in WKHA and WKY.WKHA congenic rats, along with signs of congestive heart failure. In males, the surgical maneuver induced only mild or inconsistent responses in WKY rats but had much more pronounced effects in WKHA and WKY.WKHA congenic rats. Altogether, our data show that a genetic locus that induces, under basal conditions, either mild or no concentric LV remodeling in either male or female rats, respectively, associates with LV dilatation and dysfunction in both sexes when the hearts are additionally challenged.
Novel Effects of Chromosome Y on Cardiac Regulation, Chromatin Remodeling, and Neonatal Programming in Male Mice
Publisher: The Endocrine Society
Date: 12-2013
DOI: 10.1210/EN.2013-1699
Abstract: Little is known about the functions of chromosome Y (chrY) genes beyond their effects on sex and reproduction. In hearts, postpubertal testosterone affects the size of cells and the expression of genes differently in male C57BL/6J than in their C57.Y(A) counterparts, where the original chrY has been substituted with that from A/J mice. We further compared the 2 strains to better understand how chrY polymorphisms may affect cardiac properties, the latter being sexually dimorphic but unrelated to sex and reproduction. Genomic regions showing occupancy with androgen receptors (ARs) were identified in adult male hearts from both strains by chromatin immunoprecipitation. AR chromatin immunoprecipitation peaks (showing significant enrichment for consensus AR binding sites) were mostly strain specific. Measurements of anogenital distances in male pups showed that the biologic effects of perinatal androgens were greater in C57BL/6J than in C57.Y(A). Although perinatal endocrine manipulations showed that these differences contributed to the strain-specific differences in the response of adult cardiac cells to testosterone, the amounts of androgens produced by fetal testes were not different in each strain. Nonetheless, chrY polymorphisms associated in newborn pups' hearts with strain-specific differences in genomic regions showing either AR occupancy, accessible chromatin sites, or trimethylation of histone H3 Lysine 4 marks, as well as with differential expression of 2 chrY-encoded histone demethylases. In conclusion, the effects of chrY on adult cardiac phenotypes appeared to result from an interaction of this chromosome with the organizational programming effects exerted by the neonatal testosterone surge and show several characteristics of being mediated by an epigenetic remodeling of chromatin.
Dual Linkage of a Locus to Left Ventricular Mass and a Cardiac Gene Co-Expression Network Driven by a Chromosome Domain
Publisher: Frontiers Media SA
Date: 10-12-2014
Massive migration from the steppe was a source for Indo-European languages in Europe
Publisher: Springer Science and Business Media LLC
Date: 02-03-2015
DOI: 10.1038/NATURE14317
Iron Age and Anglo-Saxon genomes from East England reveal British migration history
Publisher: Springer Science and Business Media LLC
Date: 19-01-2016
DOI: 10.1038/NCOMMS10408
Abstract: British population history has been shaped by a series of immigrations, including the early Anglo-Saxon migrations after 400 CE. It remains an open question how these events affected the genetic composition of the current British population. Here, we present whole-genome sequences from 10 in iduals excavated close to Cambridge in the East of England, ranging from the late Iron Age to the middle Anglo-Saxon period. By analysing shared rare variants with hundreds of modern s les from Britain and Europe, we estimate that on average the contemporary East English population derives 38% of its ancestry from Anglo-Saxon migrations. We gain further insight with a new method, rarecoal, which infers population history and identifies fine-scale genetic ancestry from rare variants. Using rarecoal we find that the Anglo-Saxon s les are closely related to modern Dutch and Danish populations, while the Iron Age s les share ancestors with multiple Northern European populations including Britain.
Progress and prospects in rat genetics: a community view
Publisher: Springer Science and Business Media LLC
Date: 28-04-2008
DOI: 10.1038/NG.147
Abstract: The rat is an important system for modeling human disease. Four years ago, the rich 150-year history of rat research was transformed by the sequencing of the rat genome, ushering in an era of exceptional opportunity for identifying genes and pathways underlying disease phenotypes. Genome-wide association studies in human populations have recently provided a direct approach for finding robust genetic associations in common diseases, but identifying the precise genes and their mechanisms of action remains problematic. In the context of significant progress in rat genomic resources over the past decade, we outline achievements in rat gene discovery to date, show how these findings have been translated to human disease, and document an increasing pace of discovery of new disease genes, pathways and mechanisms. Finally, we present a set of principles that justify continuing and strengthening genetic studies in the rat model, and further development of genomic infrastructure for rat research.
Ethics of DNA research on human remains: five globally applicable guidelines
Publisher: Springer Science and Business Media LLC
Date: 20-10-2021
Human evolution: a tale from ancient genomes
Publisher: The Royal Society
Date: 05-02-2017
Abstract: The field of human ancient DNA (aDNA) has moved from mitochondrial sequencing that suffered from contamination and provided limited biological insights, to become a fully genomic discipline that is changing our conception of human history. Recent successes include the sequencing of extinct hominins, and true population genomic studies of Bronze Age populations. Among the emerging areas of aDNA research, the analysis of past epigenomes is set to provide more new insights into human adaptation and disease susceptibility through time. Starting as a mere curiosity, ancient human genetics has become a major player in the understanding of our evolutionary history. This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological ersity’.
Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore.
Publisher: Springer Science and Business Media LLC
Date: 11-12-2018
DOI: 10.1038/S41559-017-0417-Y
Abstract: The Tasmanian tiger or thylacine ( Thylacinus cynocephalus ) was the largest carnivorous Australian marsupial to survive into the modern era. Despite last sharing a common ancestor with the eutherian canids ~160 million years ago, their phenotypic resemblance is considered the most striking ex le of convergent evolution in mammals. The last known thylacine died in captivity in 1936 and many aspects of the evolutionary history of this unique marsupial apex predator remain unknown. Here we have sequenced the genome of a preserved thylacine pouch young specimen to clarify the phylogenetic position of the thylacine within the carnivorous marsupials, reconstruct its historical demography and examine the genetic basis of its convergence with canids. Retroposon insertion patterns placed the thylacine as the basal lineage in Dasyuromorphia and suggest incomplete lineage sorting in early dasyuromorphs. Demographic analysis indicated a long-term decline in genetic ersity starting well before the arrival of humans in Australia. In spite of their extraordinary phenotypic convergence, comparative genomic analyses demonstrated that amino acid homoplasies between the thylacine and canids are largely consistent with neutral evolution. Furthermore, the genes and pathways targeted by positive selection differ markedly between these species. Together, these findings support models of adaptive convergence driven primarily by cis -regulatory evolution.
The Collaborative Cross, a community resource for the genetic analysis of complex traits
Publisher: Springer Science and Business Media LLC
Date: 11-2004
DOI: 10.1038/NG1104-1133
Abstract: The goal of the Complex Trait Consortium is to promote the development of resources that can be used to understand, treat and ultimately prevent pervasive human diseases. Existing and proposed mouse resources that are optimized to study the actions of isolated genetic loci on a fixed background are less effective for studying intact polygenic networks and interactions among genes, environments, pathogens and other factors. The Collaborative Cross will provide a common reference panel specifically designed for the integrative analysis of complex systems and will change the way we approach human health and disease.
Current evidence allows multiple models for the peopling of the Americas
Publisher: American Association for the Advancement of Science (AAAS)
Date: 03-08-2018
Abstract: Current genetic and archeological evidence allows for inland, coastal, or multiple pathways to peopling of the Americas.
Ancient DNA helps trace the peopling of the world
Publisher: Portland Press Ltd.
Date: 31-01-2020
DOI: 10.1042/BIO04201018
Abstract: Many of us are fascinated by narratives regarding the origin and evolution of our species. Who are we? How did we people the world? Answers to these simple questions remain elusive even though researchers have been quite successful in describing past human morphology and culture using evidence from anthropology, archaeology, history, sociology and linguistics. However, when they address human migrations, archaeologists are somewhat restricted to surviving artifactual evidence and limited to descriptions of culture expansions, which may have occurred by the movement of either ideas or people. The advent of genomics, by which one can sequence whole or part of an in idual's DNA, provided a powerful means to dig into past human demographic history. Notably, the coalescent theory posits that in iduals in a population share genetic variants that originated from a common ancestor. This powerful theory is the basis for a number of bioanalytical innovations that utilize genetic data to reconstruct human movements around the world.
Genozip 14 - advances in compression of BAM and CRAM files
Publisher: Cold Spring Harbor Laboratory
Date: 14-09-2022
DOI: 10.1101/2022.09.12.507582
Abstract: Genozip performs compression of a wide range of genomic data, including widely used FASTQ, BAM and VCF file formats. Here, we introduce the latest advancement in Genozip technology, focused on compression of BAM and CRAM files. We demonstrate Genozip’s ability to compress data generated by a variety of study types (e.g., whole genome sequencing, DNA methylation, RNASeq), sequencing technologies and aligners, up to 2.7 times better than the current state of the art compressor, CRAM version 3.1. Genozip is freely available for academic research use and has been tested for Linux, Mac and Windows. Installation instructions are available at nstalling.html . A user manual is available at anual.html . Supplementary data are available.
Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus
Publisher: Springer Science and Business Media LLC
Date: 08-03-2017
DOI: 10.1038/NATURE21674
Abstract: Recent genomic data have revealed multiple interactions between Neanderthals and modern humans, but there is currently little genetic evidence regarding Neanderthal behaviour, diet, or disease. Here we describe the shotgun-sequencing of ancient DNA from five specimens of Neanderthal calcified dental plaque (calculus) and the characterization of regional differences in Neanderthal ecology. At Spy cave, Belgium, Neanderthal diet was heavily meat based and included woolly rhinoceros and wild sheep (mouflon), characteristic of a steppe environment. In contrast, no meat was detected in the diet of Neanderthals from El Sidrón cave, Spain, and dietary components of mushrooms, pine nuts, and moss reflected forest gathering. Differences in diet were also linked to an overall shift in the oral bacterial community (microbiota) and suggested that meat consumption contributed to substantial variation within Neanderthal microbiota. Evidence for self-medication was detected in an El Sidrón Neanderthal with a dental abscess and a chronic gastrointestinal pathogen (Enterocytozoon bieneusi). Metagenomic data from this in idual also contained a nearly complete genome of the archaeal commensal Methanobrevibacter oralis (10.2× depth of coverage)-the oldest draft microbial genome generated to date, at around 48,000 years old. DNA preserved within dental calculus represents a notable source of information about the behaviour and health of ancient hominin specimens, as well as a unique system that is useful for the study of long-term microbial evolution.
Molecular resolution to a morphological controversy: The case of North American fossil muskoxen Bootherium and Symbos.
Publisher: Elsevier BV
Date: 12-2018
DOI: 10.1016/J.YMPEV.2018.08.008
Abstract: The musk ox (Ovibos moschatus) is the only surviving member of a group of Pleistocene North American musk ox genera (Praeovibos, Ovibos, Bootherium, Euceratherium, and Soergelia) whose taxonomy is uncertain. The helmeted musk ox (Bootherium bombifrons) and the woodland musk ox (Symbos cavifrons) have been synonymised as male and female forms of a single Nearctic species found from Alaska, in the north, to Texas, in the south. However, this reclassification has not been tested using molecular data, despite the potential to use ancient DNA to examine these late Pleistocene taxa. In the present study, we sequenced mitochondrial genomes from seven subfossil musk ox specimens (originally identified as Bootherium and/or Symbos), allowing us to evaluate the identity of these muskoxen, explore their phylogeography, and estimate the timeline for their evolution. We also used nuclear genomic data to determine the sex of six of our seven s les. Ultimately, our molecular data support the synonymisation of the North American muskoxen Bootherium and Symbos.
Molecular phylogenetics supports the origin of an endemic Balearic shrew lineage (Nesiotites) coincident with the Messinian Salinity Crisis
Publisher: Elsevier BV
Date: 08-2018
DOI: 10.1016/J.YMPEV.2018.03.028
Abstract: The red-toothed shrews (Soricinae) are the most widespread subfamily of shrews, distributed from northern South America to North America and Eurasia. Within this subfamily, the tribe Nectogalini includes the fossil species Nesiotites hidalgo recorded from the Late Pleistocene to Holocene of the Balearic Islands (Western Mediterranean). Although there is a consensus about the close relationship between the extinct red-toothed shrew genera Nesiotites and Asoriculus based on morphology, molecular data are necessary to further evaluate the phylogenetic relationships of the Balearic fossils. We obtained a near complete mitochondrial genome of N. hidalgo, allowing the first molecular phylogenetic analysis of this species. Analyses based on 15,167 bp of the mitochondrial genome placed N. hidalgo as close relative to the extant Himalayan shrew (Soriculus nigrescens), and a combined analysis using molecular and morphological data confirm that N. hidalgo and Asoriculus gibberodon are sister-taxa with S. nigrescens as the immediate outgroup. Molecular clock and ergence estimates suggest that the split between N. hidalgo and its closest living relative occurred around 6.44 Ma, which is in agreement with the previously proposed colonisation of the Balearic Islands from mainland Europe by nectogaline shrews during the Messinian Salinity Crisis (5.97-5.33 My ago). Our results highlight that it is possible to retrieve genetic data from extinct small mammals from marginal environments for DNA preservation. Additional finds from the fossil record of Soricinae from the Eurasian Late Miocene/Early Pliocene are needed to shed further light on the still confusing taxonomy and paleobiogeography of this clade.
Stochastic models support rapid peopling of Late Pleistocene Sahul
Publisher: Springer Science and Business Media LLC
Date: 29-04-2021
DOI: 10.1038/S41467-021-21551-3
Abstract: The peopling of Sahul (the combined continent of Australia and New Guinea) represents the earliest continental migration and settlement event of solely anatomically modern humans, but its patterns and ecological drivers remain largely conceptual in the current literature. We present an advanced stochastic-ecological model to test the relative support for scenarios describing where and when the first humans entered Sahul, and their most probable routes of early settlement. The model supports a dominant entry via the northwest Sahul Shelf first, potentially followed by a second entry through New Guinea, with initial entry most consistent with 50,000 or 75,000 years ago based on comparison with bias-corrected archaeological map layers. The model’s emergent properties predict that peopling of the entire continent occurred rapidly across all ecological environments within 156–208 human generations (4368–5599 years) and at a plausible rate of 0.71–0.92 km year −1 . More broadly, our methods and approaches can readily inform other global migration debates, with results supporting an exit of anatomically modern humans from Africa 63,000–90,000 years ago, and the peopling of Eurasia in as little as 12,000–15,000 years via inland routes.
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.
Genetic studies of the peopling of the Americas: What insights do diachronic mitochondrial genome datasets provide?
Publisher: Elsevier BV
Date: 07-2017
Experimental conditions improving in‐solution target enrichment for ancient DNA
Publisher: Wiley
Date: 18-09-2016
Abstract: High-throughput sequencing has dramatically fostered ancient DNA research in recent years. Shotgun sequencing, however, does not necessarily appear as the best-suited approach due to the extensive contamination of s les with exogenous environmental microbial DNA. DNA capture-enrichment methods represent cost-effective alternatives that increase the sequencing focus on the endogenous fraction, whether it is from mitochondrial or nuclear genomes, or parts thereof. Here, we explored experimental parameters that could impact the efficacy of MYbaits in-solution capture assays of ~5000 nuclear loci or the whole genome. We found that varying quantities of the starting probes had only moderate effect on capture outcomes. Starting DNA, probe tiling, the hybridization temperature and the proportion of endogenous DNA all affected the assay, however. Additionally, probe features such as their GC content, number of CpG dinucleotides, sequence complexity and entropy and self-annealing properties need to be carefully addressed during the design stage of the capture assay. The experimental conditions and probe molecular features identified in this study will improve the recovery of genetic information extracted from degraded and ancient remains.
Ancient DNA Studies in Pre-Columbian Mesoamerica
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.
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.
Equity, diversity, and inclusion at the Global Alliance for Genomics and Health
Publisher: Elsevier BV
Date: 10-2023
From the field to the laboratory: Controlling DNA contamination in human ancient DNA research in the high-throughput sequencing era
Publisher: Informa UK Limited
Date: 30-11-2017
Cardiac mass and cardiomyocyte size are governed by different genetic loci on either autosomes or chromosome Y in recombinant inbred mice
Publisher: American Physiological Society
Date: 10-2007
DOI: 10.1152/PHYSIOLGENOMICS.00072.2007
Abstract: Left ventricular hypertrophy is one of the main risk factors for cardiovascular mortality and morbidity. It has been proposed that hypertrophic stimuli act in great part by increasing the size of cardiomyocytes, and that the latter characteristic is a necessary condition to differentiate left ventricular hypertrophy from other benign forms of cardiac enlargement. To test whether the same genetic loci control the size of cardiomyocytes and left ventricular mass, we performed whole genome linkage analyses in a panel of 24 recombinant inbred AXB/BXA mouse strains. Whereas one major locus was linked to left ventricular mass in both males and females, loci linked to the size of cardiomyocytes were clearly distinct and showed sex-specific linkage. Moreover, the parental origin of chromosome Y had strong effects on the size of cardiomyocytes in male mice but did not affect left ventricular mass. In addition to showing that genetic loci that increase the size of cardiomyocytes are not necessarily linked to increased left ventricular mass, our findings have important consequences in evaluating cardiac phenotypes when performing genetic manipulations in mice, and in determining the cause of sex-specific differences when using models derived from C57BL/6J mice.
Individuals with Inflammatory Bowel Disease Have an Altered Gut Microbiome Composition of Fungi and Protozoa
Publisher: MDPI AG
Date: 26-09-2022
DOI: 10.3390/MICROORGANISMS10101910
Abstract: It is known that the bacterial gut microbiome is altered in inflammatory bowel disease (IBD), but far less is known about the role of eukaryotic microorganisms in IBD. While eukaryotes are rarer than bacteria within the gastrointestinal environment, the current literature suggests that they may also be implicated in IBD. In our study, we characterized these often-neglected eukaryotic microbial communities by identifying fungi and protozoa in published shotgun stool metagenomes from 355 people with IBD (206 with Crohn’s disease, 126 with ulcerative colitis, and 23 with IBD-unclassified) and 471 unaffected healthy in iduals. The in iduals with IBD had a higher prevalence of fungi, particularly Saccharomyces cerevisiae, and a lower prevalence of protozoa, particularly Blastocystis species (subtypes 1, 2, 3, and 4). Regression analysis showed that disease state, age, and BMI were associated with the prevalence and abundance of these two genera. We also characterized the eukaryotic gut microbiome in a shotgun stool metagenomic dataset from people with IBD who received fecal transplants, with s les pre- and post-transplantation, and from their donors. We found that in some FMT recipients, a single eukaryotic species remained stable over time, while in other recipients, the eukaryotic composition varied. We conclude that the eukaryotic gut microbiome is altered and varies over time in IBD, and future studies should aim to include these microbes when characterizing the gut microbiome in IBD.
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
Further dissection of a genomic locus associated with behavioral activity in the Wistar–Kyoto hyperactive rat, an animal model of hyperkinesis
Publisher: Springer Science and Business Media LLC
Date: 03-2003
Ten millennia of hepatitis B virus evolution
Publisher: American Association for the Advancement of Science (AAAS)
Date: 08-10-2021
Abstract: Hepatitis B virus (HBV) infections represent a worldwide human health concern. To study the history of this pathogen, Kocher et al . identified 137 human remains with detectable levels of virus dating between 400 and 10,000 years ago. Sequencing and analyses of these ancient viruses suggested a common ancestor between 12,000 and 20,000 years ago. There is no evidence indicating that HBV was present in the earliest humans as they spread out of Africa however, HBV was likely present in human populations before farming. Furthermore, the virus was present in the Americas by about 9000 years ago, representing a lineage sister to the viral strains found in Eurasia that erged about 20,000 years ago. —LMZ
Population size history from short genomic scaffolds: how short is too short?
Publisher: Cold Spring Harbor Laboratory
Date: 03-08-2018
DOI: 10.1101/382036
Abstract: The Pairwise Sequentially Markov Coalescent (PSMC), and its extension PSMC′, model past population sizes from a single diploid genome. Both models have been widely applied, even to organisms with scaffold-level genome reference assemblies of limited contiguity. However it is unclear how PSMC and PSMC′ perform on short scaffolds. We evaluated psmc and msmc , implementations of the PSMC and PSMC′ models respectively, on simulated genomes with low contiguity, and compared results to those from fully contiguous data. Simulations with scaffolds from 100 Mb to 10 kb revealed that psmc maintains high accuracy down to lengths of 100 kb, while msmc is accurate down to 1 Mb. The discrepancy is not due to differing models, but stems from an implementation detail of msmc —homozygous tracts at the ends of scaffolds are discarded, making msmc unreliable for low contiguity genomes. We recommend excluding data that are aligned to shorter scaffolds when undertaking demographic inference.
Unraveling the phylogenetic relationships of the extinct bovid Myotragus balearicus Bate 1909 from the Balearic Islands
Publisher: Elsevier BV
Date: 07-2019
Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas
Publisher: American Association for the Advancement of Science (AAAS)
Date: 04-2016
Abstract: Native American population history is reexamined using a large data set of pre-Columbian mitochondrial genomes.
Ancient mitochondrial genomes clarify the evolutionary history of New Zealand’s enigmatic acanthisittid wrens
Publisher: Elsevier BV
Date: 09-2016
DOI: 10.1016/J.YMPEV.2016.05.038
Abstract: The New Zealand acanthisittid wrens are the sister-taxon to all other "perching birds" (Passeriformes) and - including recently extinct species - represent the most erse endemic passerine family in New Zealand. Consequently, they are important for understanding both the early evolution of Passeriformes and the New Zealand biota. However, five of the seven species have become extinct since the arrival of humans in New Zealand, complicating evolutionary analyses. The results of morphological analyses have been largely equivocal, and no comprehensive genetic analysis of Acanthisittidae has been undertaken. We present novel mitochondrial genome sequences from four acanthisittid species (three extinct, one extant), allowing us to resolve the phylogeny and revise the taxonomy of acanthisittids. Reanalysis of morphological data in light of our genetic results confirms a close relationship between the extant rifleman (Acanthisitta chloris) and an extinct Miocene wren (Kuiornis indicator), making Kuiornis a useful calibration point for molecular dating of passerines. Our molecular dating analyses reveal that the stout-legged wrens (Pachyplichas) erged relatively recently from a more gracile (Xenicus-like) ancestor. Further, our results suggest a possible Early Oligocene origin of the basal Lyall's wren (Traversia) lineage, which would imply that Acanthisittidae survived the Oligocene marine inundation of New Zealand and therefore that the inundation was not complete.
A Paleogenomic Reconstruction of the Deep Population History of the Andes
Publisher: Elsevier BV
Date: 05-2020
Ancient DNA from an extinct Mediterranean micromammal-Hypnomys morpheus (Rodentia: Gliridae)-Provides insight into the biogeographic history of insular dormice
Publisher: Hindawi Limited
Date: 25-11-2020
DOI: 10.1111/JZS.12343
DNA capture and next-generation sequencing can recover whole mitochondrial genomes from highly degraded samples for human identification
Publisher: Springer Science and Business Media LLC
Date: 12-2013
Abstract: Mitochondrial DNA (mtDNA) typing can be a useful aid for identifying people from compromised s les when nuclear DNA is too damaged, degraded or below detection thresholds for routine short tandem repeat (STR)-based analysis. Standard mtDNA typing, focused on PCR licon sequencing of the control region (HVS I and HVS II), is limited by the resolving power of this short sequence, which misses up to 70% of the variation present in the mtDNA genome. We used in-solution hybridisation-based DNA capture (using DNA capture probes prepared from modern human mtDNA) to recover mtDNA from post-mortem human remains in which the majority of DNA is both highly fragmented ( base pairs in length) and chemically damaged. The method ‘immortalises’ the finite quantities of DNA in valuable extracts as DNA libraries, which is followed by the targeted enrichment of endogenous mtDNA sequences and characterisation by next-generation sequencing (NGS). We sequenced whole mitochondrial genomes for human identification from s les where standard nuclear STR typing produced only partial profiles or demonstrably failed and/or where standard mtDNA hypervariable region sequences lacked resolving power. Multiple rounds of enrichment can substantially improve coverage and sequencing depth of mtDNA genomes from highly degraded s les. The application of this method has led to the reliable mitochondrial sequencing of human skeletal remains from unidentified World War Two (WWII) casualties approximately 70 years old and from archaeological remains (up to 2,500 years old). This approach has potential applications in forensic science, historical human identification cases, archived medical s les, kinship analysis and population studies. In particular the methodology can be applied to any case, involving human or non-human species, where whole mitochondrial genome sequences are required to provide the highest level of maternal lineage discrimination. Multiple rounds of in-solution hybridisation-based DNA capture can retrieve whole mitochondrial genome sequences from even the most challenging s les.
Early cave art and ancient DNA record the origin of European bison
Publisher: Springer Science and Business Media LLC
Date: 18-10-2016
DOI: 10.1038/NCOMMS13158
Abstract: The two living species of bison (European and American) are among the few terrestrial megafauna to have survived the late Pleistocene extinctions. Despite the extensive bovid fossil record in Eurasia, the evolutionary history of the European bison (or wisent, Bison bonasus ) before the Holocene ( .7 thousand years ago (kya)) remains a mystery. We use complete ancient mitochondrial genomes and genome-wide nuclear DNA surveys to reveal that the wisent is the product of hybridization between the extinct steppe bison ( Bison priscus ) and ancestors of modern cattle (aurochs, Bos primigenius ) before 120 kya, and contains up to 10% aurochs genomic ancestry. Although undetected within the fossil record, ancestors of the wisent have alternated ecological dominance with steppe bison in association with major environmental shifts since at least 55 kya. Early cave artists recorded distinct morphological forms consistent with these replacement events, around the Last Glacial Maximum (LGM, ∼21–18 kya).
A Multidisciplinary Review of the Inka Imperial Resettlement Policy and Implications for Future Investigations
Publisher: MDPI AG
Date: 02-02-2021
Abstract: The rulers of the Inka empire conquered approximately 2 million km2 of the South American Andes in just under 100 years from 1438–1533 CE. Inside the empire, the elite conducted a systematic resettlement of the many Indigenous peoples in the Andes that had been rapidly colonised. The nature of this resettlement phenomenon is recorded within the Spanish colonial ethnohistorical record. Here we have broadly characterised the resettlement policy, despite the often incomplete and conflicting details in the descriptions. We then review research from multiple disciplines that investigate the empirical reality of the Inka resettlement policy, including stable isotope analysis, intentional cranial deformation morphology, ceramic artefact chemical analyses and genetics. Further, we discuss the benefits and limitations of each discipline for investigating the resettlement policy and emphasise their collective value in an interdisciplinary characterisation of the resettlement policy.
Molecular Phylogeny, Biogeography, and Habitat Preference Evolution of Marsupials
Publisher: Oxford University Press (OUP)
Date: 30-05-2014
Abstract: Marsupials exhibit great ersity in ecology and morphology. However, compared with their sister group, the placental mammals, our understanding of many aspects of marsupial evolution remains limited. We use 101 mitochondrial genomes and data from 26 nuclear loci to reconstruct a dated phylogeny including 97% of extant genera and 58% of modern marsupial species. This tree allows us to analyze the evolution of habitat preference and geographic distributions of marsupial species through time. We found a pattern of mesic-adapted lineages evolving to use more arid and open habitats, which is broadly consistent with regional climate and environmental change. However, contrary to the general trend, several lineages subsequently appear to have reverted from drier to more mesic habitats. Biogeographic reconstructions suggest that current views on the connectivity between Australia and New Guinea/Wallacea during the Miocene and Pliocene need to be revised. The antiquity of several endemic New Guinean clades strongly suggests a substantially older period of connection stretching back to the Middle Miocene and implies that New Guinea was colonized by multiple clades almost immediately after its principal formation.
Widespread male sex bias in mammal fossil and museum collections
Publisher: Proceedings of the National Academy of Sciences
Date: 03-09-2019
Abstract: The extent to which the fossil record provides an accurate picture of past life is an important issue that is often difficult to assess. We genetically sexed 277 mammalian subfossils using high-throughput sequencing of ancient DNA, and found a strong male bias (∼75%) in Pleistocene bison ( n = 186) and brown bears ( n = 91), matching signals previously reported for mammoth. Similarly, a male bias was also found in species of nearly all mammal orders in 4 large museum collections. For mammals, we suggest both male behavior and appearance can lead to increased chances of representation in fossil and museum collections, and this previously unrecognized sex bias could have substantial implications for views of past population and ecological processes.
Pleistocene Chinese cave hyenas and the recent Eurasian history of the spotted hyena, Crocuta crocuta
Publisher: Wiley
Date: 09-12-2014
DOI: 10.1111/MEC.12576
Abstract: The living hyena species (spotted, brown, striped and aardwolf) are remnants of a formerly erse group of more than 80 fossil species, which peaked in ersity in the Late Miocene (about 7-8 Ma). The fossil history indicates an African origin, and morphological and ancient DNA data have confirmed that living spotted hyenas (Crocuta crocuta) of Africa were closely related to extinct Late Pleistocene cave hyenas from Europe and Asia. The current model used to explain the origins of Eurasian cave hyena populations invokes multiple migrations out of Africa between 3.5-0.35 Ma. We used mitochondrial DNA sequences from radiocarbon-dated Chinese Pleistocene hyena specimens to examine the origin of Asian populations, and temporally calibrate the evolutionary history of spotted hyenas. Our results support a far more recent evolutionary timescale (430-163 kya) and suggest that extinct and living spotted hyena populations originated from a widespread Eurasian population in the Late Pleistocene, which was only subsequently restricted to Africa. We developed statistical tests of the contrasting population models and their fit to the fossil record. Coalescent simulations and Bayes Factor analysis support the new radiocarbon-calibrated timescale and Eurasian origins model. The new Eurasian biogeographic scenario proposed for the hyena emphasizes the role of the vast steppe grasslands of Eurasia in contrast to models only involving Africa. The new methodology for combining genetic and geological data to test contrasting models of population history will be useful for a wide range of taxa where ancient and historic genetic data are available.
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.
More than dirt: Sedimentary ancient DNA and Indigenous Australia
Publisher: Wiley
Date: 12-07-2023
Abstract: The rise of sedimentary ancient DNA (sedaDNA) studies has opened new possibilities for studying past environments. This groundbreaking area of genomics uses sediments to identify organisms, even in cases where macroscopic remains no longer exist. Managing this substrate in Indigenous Australian contexts, however, requires special considerations. Sediments and soils are often considered as waste by‐products during archaeological and paleontological excavations and are not typically regulated by the same ethics guidelines utilised in mainstream ‘western’ research paradigms. Nevertheless, the product of sedaDNA work—genetic information from past fauna, flora, microbial communities and human ancestors—is likely to be of cultural significance and value for Indigenous peoples. This article offers an opinion on the responsibilities of researchers in Australia who engage in research related to this emerging field, particularly when it involves Indigenous communities. One aspect that deserves consideration in such research is the concept of benefit sharing. Benefit sharing refers to the practice of ensuring that the benefits that arise from research are shared equitably with the communities from which the research data were derived. This practice is particularly relevant in research that involves Indigenous communities, who may have unique cultural and spiritual connections to the research material. We argue that the integration of Traditional Knowledges into sedaDNA research would add enormous value to research and its outcomes by providing genomic outputs alongside and within the rich context of multimillennia oral histories.
Arrival routes of first Americans uncertain
Publisher: American Association for the Advancement of Science (AAAS)
Date: 16-03-2018
Ancient mitochondrial genome reveals unsuspected taxonomic affinity of the extinct Chatham duck (Pachyanas chathamica) and resolves divergence times for New Zealand and sub-Antarctic brown teals
Publisher: Elsevier BV
Date: 2014
DOI: 10.1016/J.YMPEV.2013.08.017
Abstract: The Chatham duck (Pachyanas chathamica) represented one of just three modern bird genera endemic to the Chatham archipelago (situated ~850 km east of New Zealand) but became extinct soon after humans first settled the islands (c. 13th-15th centuries AD). The taxonomic affinity of the Chatham duck remains largely unresolved previous studies have tentatively suggested placements within both Tadornini (shelducks) and Anatini (dabbling ducks). Herein, we sequence a partial mitochondrial genome (excluding the D-loop) from the Chatham duck and discover that it was a phenotypically- ergent species within the genus Anas (Anatini). This conclusion is further supported by a re-examination of osteological characters. Our molecular analyses convincingly demonstrate that the Chatham duck is the most basal member of a sub-clade comprising the New Zealand and sub-Antarctic brown teals (the brown teal [A. chlorotis], Auckland Island teal [A. aucklandica] and C bell Island teal [A. nesiotis]). Molecular clock calculations based on an ingroup fossil calibration support a ergence between the Chatham duck and its sister-taxa that is consistent with the estimated time of emergence of the Chatham Islands. Additionally, we find that mtDNA ergence between the two sub-Antarctic teal species (A. aucklandica and A. nesiotis) significantly pre-dates the last few glacial cycles, raising interesting questions about the timing of their dispersal to these islands, and the recent phylogeographic history of brown teal lineages in the region.
Corticosteroid Binding Globulin: A New Target for Cortisol-Driven Obesity
Publisher: The Endocrine Society
Date: 07-2004
DOI: 10.1210/ME.2004-0005
Equitable Expanded Carrier Screening Needs Indigenous Clinical and Population Genomic Data
Publisher: Elsevier BV
Date: 08-2020
A strategy for building and using a human reference pangenome
Publisher: F1000 Research Ltd
Date: 14-10-2019
DOI: 10.12688/F1000RESEARCH.19630.1
Abstract: In March 2019, 45 scientists and software engineers from around the world converged at the University of California, Santa Cruz for the first pangenomics codeathon. The purpose of the meeting was to propose technical specifications and standards for a usable human pangenome as well as to build relevant tools for genome graph infrastructures. During the meeting, the group held several intense and productive discussions covering a erse set of topics, including advantages of graph genomes over a linear reference representation, design of new methods that can leverage graph-based data structures, and novel visualization and annotation approaches for pangenomes. Additionally, the participants self-organized themselves into teams that worked intensely over a three-day period to build a set of pipelines and tools for specific pangenomic applications. A summary of the questions raised and the tools developed are reported in this manuscript.
Chromosome Y variants from different inbred mouse strains are linked to differences in the morphologic and molecular responses of cardiac cells to postpubertal testosterone
Publisher: Springer Science and Business Media LLC
Date: 07-04-2009
Abstract: We have reported previously that when chromosome Y (chrY) from the mouse strain C57BL/6J (ChrY C57 ) was substituted for that of A/J mice (ChrY A ), cardiomyocytes from the resulting "chromosome substitution" C57BL/6J-chrY A strain were smaller than that of their C57BL/6J counterparts. In reverse, when chrY A from A/J mice was substituted for that of chrY C57 , cardiomyocytes from the resulting A/J-chrY C57 strain were larger than in their A/J counterparts. We further used these strains to test whether: 1) the origin of chrY could also be linked to differences in the profile of gene expression in the hearts of adult male mice, and 2) post-pubertal testosterone could play a role in the differential morphologic and/or molecular effects of chrY C57 and chrY A . The increased size of cardiomyocytes from adult male C57BL/6J mice compared to C57BL/6J-chrY A resulted from the absence of hypertrophic effects of post-pubertal testosterone on cells from the latter strain. However, gene profiling revealed that the latter effect could not be explained on the basis of an insensitivity of cells from C57BL/6J-chrY A to androgens, since even more cardiac genes were affected by post-pubertal testosterone in C57BL/6J-chrY A hearts than in C57BL/6J. By testing for interaction between the effects of surgery and strain, we identified 249 "interaction genes" whose expression was affected by post-pubertal testosterone differentially according to the genetic origin of chrY. These interaction genes were found to be enriched within a limited number of signaling pathways, including: 1) p53 signaling , which comprises the interacting genes Ccnd1 , Pten and Cdkn1a that are also potential co-regulators of the androgen receptors, and 2) circadian rhythm , which comprises Arntl/Bmal1 , which may in turn regulate cell growth via the control of Cdkn1a . Although post-pubertal testosterone increased the size of cardiomyocytes from male C56BL/6J mice but not that from their C57BL/6J-chrY A counterparts, it affected gene expression in the hearts from both strains. However, several cardiac genes responded to post-pubertal testosterone in a strict strain-selective manner, which provides possible mechanisms explaining how chrY may, in part via interference with androgen regulatory events, be linked to morphologic differences of cardiac cells of adult male mice.
An extinct nestorid parrot (Aves, Psittaciformes, Nestoridae) from the Chatham Islands, New Zealand
Publisher: Oxford University Press (OUP)
Date: 28-08-2014
DOI: 10.1111/ZOJ.12164
Ethnic and Mouse Strain Differences in Central Corneal Thickness and Association with Pigmentation Phenotype
Publisher: Public Library of Science (PLoS)
Date: 10-08-2011
The origin and phylogenetic relationships of the New Zealand ravens
Publisher: Elsevier BV
Date: 2017
DOI: 10.1016/J.YMPEV.2016.09.022
Abstract: The relationships of the extinct New Zealand ravens (Corvus spp.) are poorly understood. We sequenced the mitogenomes of the two currently recognised species and found they were sister-taxa to a clade comprising the Australian raven, little raven, and forest raven (C.coronoides, C. mellori and C. tasmanicus respectively). The ergence between the New Zealand ravens and Australian raven clade occurred in the latest Pliocene, which coincides with the onset of glacial deforestation. We also found that the ergence between the two putative New Zealand species C. antipodum and C. moriorum probably occurred in the late Pleistocene making their separation as species untenable. Consequently, we consider Corax antipodum (Forbes, 1893) to be a subspecies of Corvus moriorum Forbes, 1892. We re-examine the osteological evidence that led 19th century researchers to assign the New Zealand taxa to a separate genus, and re-assess these features in light of our new phylogenetic hypotheses. Like previous researchers, we conclude that the morphology of the palate of C. moriorum is unique among the genus Corvus, and suggest this may be an adaptation for a specialist diet.
A paleogenetic perspective on the early population history of the high altitude Andes
Publisher: Elsevier BV
Date: 12-2017
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.
Spatiotemporal landscape genetics: Investigating ecology and evolution through space and time
Publisher: Wiley
Date: 17-12-2020
DOI: 10.1111/MEC.15315
Abstract: Genetic time-series data from historical s les greatly facilitate inference of past population dynamics and species evolution. Yet, although climate and landscape change are often touted as post-hoc explanations of biological change, our understanding of past climate and landscape change influences on evolutionary processes is severely hindered by the limited application of methods that directly relate environmental change to species dynamics through time. Increased integration of spatiotemporal environmental and genetic data will revolutionize the interpretation of environmental influences on past population processes and the quantification of recent anthropogenic impacts on species, and vastly improve prediction of species responses under future climate change scenarios, yielding widespread revelations across evolutionary biology, landscape ecology and conservation genetics. This review encourages greater use of spatiotemporal landscape genetic analyses that explicitly link landscape, climate and genetic data through time by providing an overview of analytical approaches for integrating historical genetic and environmental data in five key research areas: population genetic structure, demography, phylogeography, metapopulation connectivity and adaptation. We also include a tabular summary of key methodological information, suggest approaches for mitigating the particular difficulties in applying these techniques to ancient DNA and palaeoclimate data, and highlight areas for future methodological development.
The immunogenetic impact of European colonization in the Americas
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.
Did the historical range of the European bison (Bison bonasus L.) extend further south?—a new finding from the Yenikapı Metro and Marmaray excavation, Turkey
Publisher: Springer Science and Business Media LLC
Date: 23-11-2016
Climate change underlies global demographic, genetic, and cultural transitions in pre-Columbian southern Peru
Publisher: Proceedings of the National Academy of Sciences
Date: 16-06-2014
Abstract: It has long been assumed that climate played a major role in the population history of the Central Andes. Although adaptations of the Andean populations to climatic changes such as the intensification of agriculture have been inferred from the archaeological record, evidence for demographic adaptations such as migration is missing so far. In this paper, ancient DNA data from populations that lived in southern Peru between 840 BC and 1450 AD provide evidence for two large-scale migrations in the Central Andes coincident with episodes of drought and increased climatic variability. These migrations led to a successive genetic homogenization of southern Peruvian populations generally attributed to intrusions by the late pre-Columbian highland empires such as the Wari, Tiwanaku, or Inca.
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.
Runes from Lány (Czech Republic) - The oldest inscription among Slavs. A new standard for multidisciplinary analysis of runic bones
Publisher: Elsevier BV
Date: 03-2021
Allelic bias when performing in‐solution enrichment of ancient human DNA
Publisher: Wiley
Date: 15-09-2023
Genome-wide patterns of selection in 230 ancient Eurasians
Publisher: Springer Science and Business Media LLC
Date: 23-11-2015
DOI: 10.1038/NATURE16152
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