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A genomic history of Aboriginal Australia
Abstract
The population history of Aboriginal Australians remains largely uncharacterized. Here we generate high-coverage genomes for 83 Aboriginal Australians (speakers of Pama-Nyungan languages) and 25 Papuans from the New Guinea Highlands. We find that Papuan and Aboriginal Australian ancestors diversified 25-40 thousand years ago (kya), suggesting pre-Holocene population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania). However, all of the studied Aboriginal Australians descend from a single founding population that differentiated ∼10-32 kya. We infer a population expansion in northeast Australia during the Holocene epoch (past 10,000 years) associated with limited gene flow from this region to the rest of Australia, consistent with the spread of the Pama-Nyungan languages. We estimate that Aboriginal Australians and Papuans diverged from Eurasians 51-72 kya, following a single out-of-Africa dispersal, and subsequently admixed with archaic populations. Finally, we report evidence of selection in Aboriginal Australians potentially associated with living in the desert. © 2016 Macmillan Publishers Limited, part of Springer Nature. All rights reserved
Supplementary resource (1)
... Our study is among the first major genomic surveys of Indigenous Australians. Previous publications that include genomic data from Aboriginal and/or Torres Strait Islander peoples have largely focused on historical demographic processes [26][27][28][29][30] . These relied on mitochondrial 29,31 or short-read whole genome sequencing [26][27][28]30 . ...
... Previous publications that include genomic data from Aboriginal and/or Torres Strait Islander peoples have largely focused on historical demographic processes [26][27][28][29][30] . These relied on mitochondrial 29,31 or short-read whole genome sequencing [26][27][28]30 . Hence, we have generated the first suitable dataset to begin exploring the landscape of Indigenous genomic structural variation. ...
Indigenous Australians harbour rich and unique genomic diversity. However, Aboriginal and Torres Strait Islander ancestries are historically under-represented in genomics research and almost completely missing from reference databases. Addressing this representation gap is critical, both to advance our understanding of global human genomic diversity and as a prerequisite for ensuring equitable outcomes in genomic medicine. Here, we apply population-scale whole genome long-read sequencing to profile genomic structural variation across four remote Indigenous communities. We uncover an abundance of large indels (20-49bp; n=136,797) and structural variants (SVs; ≥50bp; n=159,912), the majority of which are composed of tandem repeat or interspersed mobile element sequences (90%) and have not been previously annotated (73%). A large fraction of SVs appear to be exclusive to Indigenous Australians (>30%) and the majority of these are found in only a single community, underscoring the need for broad and deep sampling to achieve a comprehensive catalogue of genomic structural variation across the Australian continent. Finally, we explore short-tandem repeats (STRs) throughout the genome to characterise allelic diversity at 50 known disease loci, uncover hundreds of novel repeat expansion sites within protein-coding genes, and identify unique patterns of diversity and constraint among STR sequences. Our study sheds new light on the dimensions, diversity and evolutionary trajectories of genomic structural variation within and beyond Australia.
... To provide an independent estimate of the primary split time between the S. avenae-like lineage and the S. miscanthi-like lineage based on whole genome sequences (rather than GBS samples), we estimated the past demographic history of the JIC1 and LF1 clonal lineages using MSMC2 [70] which implements the multiple sequentially Markovian coalescent (MSMC) model. This analysis indicates that JIC1 and LF1 demographic histories begin to diverge around 500 Kya ago and are fully separated by approximately 250 Kya (Fig. 5d), providing a slightly earlier estimate of divergence between the S. avenae-like and S. miscanthi-like lineages than the SNPAPP analysis (Fig. 5c). ...
... We reconstructed historical changes in effective population size for S. miscanthi and S. avaenae using MSMC2 v2.0 [70], which implements the multiple sequentially Markovian coalescent (MSMC) model. We used read mappings (against the S. avenae JIC1 v2.1 reference genome) from the population genomic analysis described above for the Langfang-1 and JIC1 whole genome samples and called variants in each sample with SAMtools mpileup v1.3 (parameters: "-q 20 -Q 20 -C 50 -u ") and BCFtools call v1.3.1 (parameters: "-c -V indels "). ...
Background
Aphids are common crop pests. These insects reproduce by facultative parthenogenesis involving several rounds of clonal reproduction interspersed with an occasional sexual cycle. Furthermore, clonal aphids give birth to live young that are already pregnant. These qualities enable rapid population growth and have facilitated the colonisation of crops globally. In several cases, so-called “super clones” have come to dominate agricultural systems. However, the extent to which the sexual stage of the aphid life cycle has shaped global pest populations has remained unclear, as have the origins of successful lineages. Here, we used chromosome-scale genome assemblies to disentangle the evolution of two global pests of cereals—the English (Sitobion avenae) and Indian (Sitobion miscanthi) grain aphids.
Results
Genome-wide divergence between S. avenae and S. miscanthi is low. Moreover, comparison of haplotype-resolved assemblies revealed that the S. miscanthi isolate used for genome sequencing is likely a hybrid, with one of its diploid genome copies closely related to S. avenae (~ 0.5% divergence) and the other substantially more divergent (> 1%). Population genomics analyses of UK and China grain aphids showed that S. avenae and S. miscanthi are part of a cryptic species complex with many highly differentiated lineages that predate the origins of agriculture. The complex consists of hybrid lineages that display a tangled history of hybridisation and genetic introgression.
Conclusions
Our analyses reveal that hybridisation has substantially contributed to grain aphid diversity, and hence, to the evolutionary potential of this important pest species. Furthermore, we propose that aphids are particularly well placed to exploit hybridisation events via the rapid propagation of live-born “frozen hybrids” via asexual reproduction, increasing the likelihood of hybrid lineage formation.
... Archaeologists High coverage and mtDNA analyses of Aboriginal genomes suggest that Australian populations diverged from Papuans ~37 ka and became internally geographically structured by around 10-32 ka (Malaspinas et al. 2016;Tobler et al. 2017), with population expansions noticeable after the Last Glacial Maximum (Pedro et al. 2020) and in the Holocene ~10 ka (Malaspinas et al. 2016). ...
... Archaeologists High coverage and mtDNA analyses of Aboriginal genomes suggest that Australian populations diverged from Papuans ~37 ka and became internally geographically structured by around 10-32 ka (Malaspinas et al. 2016;Tobler et al. 2017), with population expansions noticeable after the Last Glacial Maximum (Pedro et al. 2020) and in the Holocene ~10 ka (Malaspinas et al. 2016). ...
Mainland Australia was connected to New Guinea and Tasmania at various times throughout the Pleistocene and formed the supercontinent of Sahul. Sahul contains some of the earliest known archaeological evidence for Homo sapiens outside of Africa, with a growing record of early complex social, technological, and artistic life. Here we present an overview of the oldest known sites in Australia along with key evidence pertaining to the dynamic cultures of early Aboriginal peoples. We review debates surrounding the age of rst settlement and present evidence for the earliest technology, economy, and symbolism in Australia, emphasizing maritime skills, a large founding population size, novel technology, and adaptation to a wide range of environments.
... MSMC2 (Malaspinas et al., 2016) was used to estimate the recent and historical N e . As the method can (with a reasonable runtime) analyse at most eight haplotypes, we selected and utilised the four individuals with the highest sequencing coverage from each population. ...
... The average long-term N e (N e LT ) were estimated using the formula (Kimura, 1983) N e = π/(4µ), where µ is the mutation rate, assumed to be 4.37⨉10 -9 per site per generation. π was obtained from folded site frequency spectra (SFS), estimated for each population directly from the bam data with ANGSD v.0.921 (Malaspinas et al., 2016), using the R script from Walsh et al., (2022) modified to fit folded SFSs. Sites with more than 70% heterozygote counts were removed and the mappability masks (Kivikoski et al., 2021) were applied in data filtering. ...
Effective population size (Ne) is a quantity of central importance in evolutionary biology and population genetics, but often notoriously challenging to estimate. Analyses of Ne are further complicated by the many interpretations of the concept and the alternative approaches to quantify Ne utilising widely different properties of the data. On the other hand, alternative methods are informative for different time scales such that a set of complementary methods should allow piecing together the entire continuum of Ne from a few generations before the present to the distant past. To test this in practice, we inferred the continuum of Ne for 45 nine-spined stickleback populations (Pungitius pungitius) using whole-genome data. We found that the marine populations had the largest historical and recent Ne, followed by coastal and other freshwater populations. We identified the impact of both recent and historical gene flow on the Ne estimates obtained from different methods and found that simple summary statistics are informative in comprehending the events in the very recent past. Overall, our analyses showed that the coalescence-based trajectories of Ne in the recent past and the LD-based estimates of near-contemporary Ne are incongruent, though in some cases the incongruence might be explained by specific demographic events. Despite still lacking accuracy and resolution for the very recent past, the sequentially Markovian coalescent-based methods seem to provide the most meaningful interpretation of the real-life Ne varying across time.
... We used the Multiple Sequentially Markovian Coalescent 2 v2.1.1 (MSMC2) (Malaspinas et al., 2016) to reconstruct the demographic histories of the selected populations. As SMC-based methods have been benchmarked on Primates datasets (Schiffels & Wang, 2020), ...
... ployed two approaches based on the sequentially Markov coalescent framework to infer the demographic histories of the selected populations. We first used the multiple sequentially Markov coalescent version 2, MSMC2(Malaspinas et al., 2016) to get insights into populations sizes at the polymorphism scale (i.e. from present time to the time of the most recent common ancestor of the sample). We then employed the IMCoalHMM approach to fit a model of isolation with migration between S. cerevisiae and S. paradoxus(Mailund et al., 2012), allowing us to estimate the population size at the time of the divergence between the two species. ...
Through its fermentative capacities, Saccharomyces cerevisiae was central in the development of civilisation during the Neolithic period, and the yeast remains of importance in industry and biotechnology, giving rise to bona fide domesticated populations. Here, we conduct a population genomic study of domesticated and wild populations of S. cerevisiae. Using coalescent analyses, we report that the effective population size of yeast populations decreased since the divergence with S. paradoxus. We fitted models of distributions of fitness effects to infer the rate of adaptive ( ω a $$ {\omega}_a $$ ) and non-adaptive ( ω na $$ {\omega}_{na} $$ ) non-synonymous substitutions in protein-coding genes. We report an overall limited contribution of positive selection to S. cerevisiae protein evolution, albeit with higher rates of adaptive evolution in wild compared to domesticated populations. Our analyses revealed the signature of background selection and possibly Hill-Robertson interference, as recombination was found to be negatively correlated with ω na $$ {\omega}_{na} $$ and positively correlated with ω a $$ {\omega}_a $$ . However, the effect of recombination on ω a $$ {\omega}_a $$ was found to be labile, as it is only apparent after removing the impact of codon usage bias on the synonymous site frequency spectrum and disappears if we control for the correlation with ω na $$ {\omega}_{na} $$ , suggesting that it could be an artefact of the decreasing population size. Furthermore, the rate of adaptive non-synonymous substitutions is significantly correlated with the residue solvent exposure, a relation that cannot be explained by the population's demography. Together, our results provide a detailed characterisation of adaptive mutations in protein-coding genes across S. cerevisiae populations.
... The paleoanthropological data from the Nile Valley and the Horn of Africa have potential implications concerning the debate about plausible population dynamics that could have led to the out-of-Africa expansion. The genomes of non-Africans harbor the signature of a bottleneck, or a reduction in overall diversity, which can be dated to around 70 ka (Malaspinas et al., 2016). Putting together genetic evidence for a Northern exit OoA (Pagani et al., 2015), archaeological and palaeoclimatic evidence for a drastic reduction in human presence along the lower Nile Valley from MSI 4 (70-60 ka) until ~ 25 ka (Vermeersch et al., 1990;Van Peer, 2004;Vermeersch and Van Neer, 2015), as well as the paleoanthropological data presented here suggesting isolation and fragmentation of Late Pleistcocene human populations in the Nile Valley, we may postulate that the progressive drying out of the North-East African region from 70 ka triggered a population bottleneck (Pagani and Crevecoeur, 2019). ...
Although subjected to growing interest, the debates related to Homo sapiens' evolution in Africa during the Late Pleistocene and the beginning of the Holocene are currently mainly tied to the success of palaeogenetic studies of Holocene skeletons from sub-Sa-haran Africa. These genetic results have opened new perspectives pertaining the origin of present-day African diversity and the nature of such diversity in the past, confirming previous assumptions based on the study of African fossils suggesting deep sub-structuration of human populations. In Northeast Africa, the end of the Late Pleistocene and the beginning of the Holocene were marked by major climatic changes whose effects on human settlements are still poorly understood. Geological evidence support generally dry conditions during the Last Glacial Maximum followed by the so-called African Humid Period which ends abruptly with the second half of the Holocene and the onset of more arid conditions. In parallel with these climatic fluctuations, this transitional period witnessed the emergence of new subsistence strategies with the introduction of pastoralism. However, the scarcity of human remains in northeast Africa has limited our understanding of modern human diversity and population processes during this transitional period. Through a review of the key human fossils and assemblages associated to the Late Pleistocene and the Early Holocene period in Egypt, Sudan, Ethiopia, Somalia and the Republic of Djibouti, this contribution aims at discussing phenotypic and cultural diversity, addressing hypotheses of population isolation, replacement and/or continuity.
... The 44 ka date on rock art for Leang Bulu' Sipong 4 supports the suggestion of a broader dispersal of our species at this time, while the rockshelter sequences of Leang Burung 2 and Goa Topogaro beginning at 35 and 30 ka, respectively (Figure 1), suggest an increase inpopulation that may also be related to initial occupations of Salebabu and Gebe. It may be signi cant that a genetic coalescence estimate of the split between Australians and Papuans is 37 ka(Malaspinas et al. 2016), ...
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... To date, this relationship between mankind and whale has been more-or-less acknowledged and recorded as colonist driven. Indigenous Australians are descendants of the first people found in Australia (Rasmussen et al. 2011;Malaspinas et al. 2016), and one of the oldest living civilizations globally. They have a connection with their land which has been deeply rooted in their culture, including the Dreamtime. ...
Cooperative hunting between humans and killer whales (Orcinus orca) targeting baleen whales was reported in Eden, New South Wales, Australia, for almost a century. By 1928, whaling operations had ceased, and local killer whale sightings became scarce. A killer whale from the group, known as "Old Tom, " washed up dead in 1930 and his skeleton was preserved. How these killer whales from Eden relate to other populations globally and whether their genetic descendants persist today remains unknown. We extracted and sequenced DNA from Old Tom using ancient DNA techniques. Genomic sequences were then compared with a global dataset of mitochondrial and nuclear genomes. Old Tom shared a most recent common ancestor with killer whales from Australasia, the North Atlantic, and the North Pacific, having the highest genetic similarity with contemporary New Zealand killer whales. However, much of the variation found in Old Tom's genome was not shared with these widespread populations, suggesting ancestral rather than ongoing gene flow. Our genetic comparisons also failed to find any clear descendants of Tom, raising the possibility of local extinction of this group. We integrated Traditional Custodian knowledge to recapture the events in Eden and recognize that Indigenous Australians initiated the relationship with the killer whales before European colonization and the advent of commercial whaling locally. This study rectifies discrepancies in local records and provides new insight into the origins of the killer whales in Eden and the history of Australasian killer whales.
... The merger of West Rote Island with East Rote Island was caused by high vertical deformation in this area . Rote Ndao itself was formed from the Indo-Australian plate which was separated from the Australian continent due to the subduction of the Eurasian plate (Hall, 2011;Malaspinas et al., 2016;Suhadha & Julzarika, 2020). ...
... The earliest dated human remains for inland southern Australia were identified at Lake Mungo, dated to 40,000 ± 2,000 thousand years ago (ka) (Fig. 1, Bowler et al., 2003). Ancient DNA (aDNA) studies place Australian arrival at no earlier than 50 ka (Mallick et al., 2016;Malaspinas et al., 2016), while other dated evidence from archaeological sites ranges from 50 to 65 ka (Roberts et al., 1990;Bird et al., 2002;Clarkson et al., 2015). Consensus has agreed with earlier entry into Australia, likely from 50 to 65 ka. ...
The Parramatta Sand Body (PSB) in Parramatta, New South Wales, Australia is an ancient sedimentary sand deposit bordering parts of the Parramatta River which today flows into Sydney Harbour. Whilst the lower portions of the sand deposit pre-date human occupation, some locations with near surface sand deposits contain dense Aboriginal archaeological sites with a profusion of stone tools and remains of hearths. We explored the timing of human occupation in Parramatta by applying optically stimulated luminescence (OSL) ages to archaeological evidence from site AT14. Interpretation of the OSL data was guided by particle size analysis and the resulting age estimates agreed with the radiocarbon dating of charcoal sampled from archaeological deposits at AT14, to provide a secure age for human occupation evidence in the Sydney region at 31 ± 2 ka. Results link the single grain overdispersion found in quartz OSL samples to trampling actions resultant of Aboriginal occupation and forms a future consideration for the effective dating of archaeological sites.
... A single major migration of modern humans into the continents of Asia and Sahul was strongly supported by earlier studies using mitochondrial DNA, the non-recombining portion of Y chromosomes, and autosomal SNP data [42][43][44][45]. Ancestral Ancient South Indians with no West Eurasian relatedness, East Asians, Onge (Andamanese huntergatherers) and Papuans all derive in a short evolutionary time from the eastward dispersal of an out-of-Africa population [46,47], although Europeans and East Asians are suggested to share more recent common ancestors than with Papuans [48]; but see [49]. ...
An unsolved archaeological puzzle of the East Asian Upper Palaeolithic is why the southward expansion of an innovative lithic technology represented by microblades stalled at the Qinling–Huaihe Line. It has been suggested that the southward migration of foragers with microblades stopped there, which is consistent with ancient DNA studies showing that populations to the north and south of this line had differentiated genetically by 19 000 years ago. Many infectious pathogens are believed to have been associated with hominins since the Palaeolithic, and zoonotic pathogens in particular are prevalent at lower latitudes, which may have produced a disease barrier. We propose a mathematical model to argue that mortality due to infectious diseases may have arrested the wave-of-advance of the technologically advantaged foragers from the north.
... Genotypes for all ibex were phased together using Beagle V.4.1 [41]. We used time as the relative cross coalescent rate (RCCR) which dropped to 50% and was used as a rough estimate of the splitting time [40,42]. For each model, we performed 100 independent runs with varying starting points. ...
Pleistocene glaciations had profound impact on the spatial distribution and genetic makeup of species in temperate ecosystems. While the glacial period trapped several species into glacial refugia and caused abrupt decline in large populations, the interglacial period facilitated population growth and range expansion leading to allopatric speciation. Here, we analyzed 40 genomes of four species of ibex and found that Himalayan ibex in the Pamir Mountains evolved independently after splitting from its main range about 0.1 mya following the Pleistocene species pump concept. Demographic trajectories showed Himalayan ibex experienced two historic bottlenecks, one each c. 0.8–0.5 mya and c. 50–30 kya, with an intermediate large population expansion c. 0.2–0.16 mya coinciding with Mid-Pleistocene Transitions. We substantiate with multi-dimensional evidence that Himalayan ibex is an evolutionary distinct phylogenetic species of Siberian ibex which need to be prioritized for special management and conservation planning at a regional and global scale.
... When the British arrived in Australia, the different indigenous populations in Australia were roughly in a transitional period from the Paleolithic era to the Neolithic era, meaning their level of civilization lagged behind modern civilization by tens of thousands of years. Additionally, research indicates that the genes of Australian indigenous peoples became isolated from other human populations on Earth approximately thirty thousand years ago, creating a genetic island [10]. However, David Unaipon, an Australian indigenous man who received an education in a church school during his childhood, demonstrated exceptional abilities in engineering, literature, and several other fields that surpassed the 9 of 16 average person. ...
The article delves into the intricate relationship between emotions and swarm intelligence, highlighting the pivotal role of knowledge accumulation (akin to memory in the brain or a computer) in the progression of human civilization, it is considered to play a more important role than Genes/DNA and neurons during human evolution. Additionally, after dissecting the elements of consciousness and creativity, the article presents the proposition that machines can also possess consciousness and creativity. This article also presents some ideas regarding developing strong AI, aiming to highlight that the current progress of AI should not only draw inspiration from individual intelligence but also learn from the development path of swarm intelligence.
... Australia's first peoples, the Aboriginal and Torres Strait Islander Peoples, represent the oldest continuous culture on earth (Malaspinas et al 2016). For over 50,000 years they have established deep spiritual and cultural connections to Country of the Australian continent and adjacent seas. ...
First Nations Australians have a cultural obligation to look after land and sea Country, and Indigenous-partnered science is beginning to drive socially inclusive initiatives in conservation. The Australian Institute of Marine Science has partnered with Indigenous communities in systematically collecting monitoring data to understand the natural variability of ecological communities and better inform sea Country management. Monitoring partnerships are centred around the 2-way sharing of Traditional Ecological Knowledge, training in science and technology, and developing communication products that can be accessed across the broader community. We present a case study with the Bardi Jawi Rangers in northwest Australia focusing on a 3-year co-developed and co-delivered monitoring dataset for culturally important fish in coral reef ecosystems. We show how uncertainty estimated by Bayesian statistics can be incorporated into monitoring indicators and facilitate fuller communication between scientists and First Nations partners about the limitations of monitoring to identify change.
... To account for such variation, we considered that the number of reads at a given site follows a negative binomial distribution (nBin), previously shown to fit empirical distributions (e.g. Malaspinas et al., 2016). More precisely, we assumed that, for each SNP, the number of reads C j for the j th populations follows: ...
Next-generation sequencing of pooled samples (Pool-seq) is a popular method to assess genome-wide diversity patterns in natural and experimental populations. However, Pool-seq is associated with specific sources of noise, such as unequal individual contributions. Consequently, using Pool-seq for the reconstruction of evolutionary history has remained underexplored. Here we describe a novel Approximate Bayesian Computation (ABC) method to infer demographic history, explicitly modelling Pool-seq sources of error. By jointly modelling Pool-seq data, demographic history and the effects of selection due to barrier loci, we obtain estimates of demographic history parameters accounting for technical errors associated with Pool-seq. Our ABC approach is computationally efficient as it relies on simulating subsets of loci (rather than the whole-genome) and on using relative summary statistics and relative model parameters. Our simulation study results indicate Pool-seq data allows distinction between general scenarios of ecotype formation (single versus parallel origin) and to infer relevant demographic parameters (e.g. effective sizes and split times). We exemplify the application of our method to Pool-seq data from the rocky-shore gastropod Littorina saxatilis, sampled on a narrow geographical scale at two Swedish locations where two ecotypes (Wave and Crab) are found. Our model choice and parameter estimates show that ecotypes formed before colonization of the two locations (i.e. single origin) and are maintained despite gene flow. These results indicate that demographic modelling and inference can be successful based on pool-sequencing using ABC, contributing to the development of suitable null models that allow for a better understanding of the genetic basis of divergent adaptation.
... To understand the nature of the evolutionary processes that shaped patterns of variation in C. hirsuta, we conducted a series of demographic inference analyses aiming at estimating changes in population sizes, the ages of population divergences, and the level of gene flow between populations. We estimated piece-wise constant distributions of population sizes and cross-coalescence rates through time for IBE, BAL, and NCE using the software relate [47] and MSMC2 [48][49][50] (Figs 1E, 1F, S1G and S1H). In both cases, results indicated that the oldest event in the history of our sample is the divergence between the ancestral lineages of IBE and the one ancestral to both BAL and NCE. ...
We study natural DNA polymorphisms and associated phenotypes in the Arabidopsis relative Cardamine hirsuta. We observed strong genetic differentiation among several ancestry groups and broader distribution of Iberian relict strains in European C. hirsuta compared to Arabidopsis. We found synchronization between vegetative and reproductive development and a pervasive role for heterochronic pathways in shaping C. hirsuta natural variation. A single, fast-cycling ChFRIGIDA allele evolved adaptively allowing range expansion from glacial refugia, unlike Arabidopsis where multiple FRIGIDA haplotypes were involved. The Azores islands, where Arabidopsis is scarce, are a hotspot for C. hirsuta diversity. We identified a quantitative trait locus (QTL) in the heterochronic SPL9 transcription factor as a determinant of an Azorean morphotype. This QTL shows evidence for positive selection, and its distribution mirrors a climate gradient that broadly shaped the Azorean flora. Overall, we establish a framework to explore how the interplay of adaptation, demography, and development shaped diversity patterns of 2 related plant species.
... PBS and α are powerful methods to find signatures of selection in red fox because global estimates of F ST between North Africa and Eurasian red foxes were sufficiently low (global F ST ≈ 0.13) and we had data from their immediate outgroup, Rueppell's fox. While PBS has proved effective for identifying population-specific selection in humans and canid populations adapted to extreme environmental conditions 13,125,127 , F ST -based methods are not useful when genetic differentiation between the focal group and the closely related ingroup is high (F ST > 0. 2; ref. 128). In sharp contrast to past F ST estimates using microsatellites (global F ST ≈ 0.14 between Rueppell's fox and North African red fox and global F ST ≈ 0.13 between Rueppell's fox and Eurasian red fox; ref. 12), we found Rueppell's fox and red fox to be highly differentiated using whole-genome data (global F ST ≈ 0.52 between Rueppell's fox and North African red fox and global F ST ≈ 0.51 between Rueppell's fox and Eurasian red fox). ...
Elucidating the evolutionary process of animal adaptation to deserts is key to understanding adaptive responses to climate change. Here we generated 82 individual whole genomes of four fox species (genus Vulpes) inhabiting the Sahara Desert at different evolutionary times. We show that adaptation of new colonizing species to a hot arid environment has probably been facilitated by introgression and trans-species polymorphisms shared with older desert resident species, including a putatively adaptive 25 Mb genomic region. Scans for signatures of selection implicated genes affecting temperature perception, non-renal water loss and heat production in the recent adaptation of North African red foxes (Vulpes vulpes), after divergence from Eurasian populations approximately 78 thousand years ago. In the extreme desert specialists, Rueppell’s fox (V. rueppellii) and fennec (V. zerda), we identified repeated signatures of selection in genes affecting renal water homeostasis supported by gene expression and physiological differences. Our study provides insights into the mechanisms and genetic underpinnings of a natural experiment of repeated adaptation to extreme conditions.
... Genetic data might in the future give reasonable estimates of past population, but ancient genetics are currently poorly resolved for Australia and their interpretation has often been complicated by discussions that seek to articulate genomic patterns with predictions from archaeological models of Late Holocene Intensification and demographic change. Nevertheless, estimates of effective population size from modern genomic data of Indigenous groups suggests i) regional variation in demographic trajectories during the Holocene, and ii) in some regions population increased during the early Holocene (Malaspinas et al. 2016).While those interpretations are conformable with our proposition that demographic growth likely occurred in the earlier rather than Later Holocene and under local control, detailed models of population growth and contraction are not yet robust. ...
... Consequently, as a larger range of traditional foods are developed for commercial markets, further work is needed to not only promote the safe use of Australian native foods within the wider community, but to also work alongside Traditional Owners to gain a greater understanding of how these foods have been successfully used in the past. In achieving this, there is an opportunity for the TK developed by the longest living continuous culture (52) to complement the food-safety science that is needed to identify potential risks which may be associated with the consumption of various native food items. However, before this is possible, the regulatory procedures that aim to assess the safety of traditional foods and critique the history of how these foods have been used in the past, also need to have the capacity to accommodate the fact that First Peoples have been using native Australian plants as a source of food for at least 65 000 years (29) . ...
As interest in Australian native products continues to grow worldwide, Aboriginal and Torres Strait Islander peoples (First Peoples) are striving to be industry leaders in the production of their traditional foods that are being developed for commercial markets. To successfully gain market approval both within Australia and globally, food regulatory authorities require at least a documented history of safe use to indicate dietary safety. Moreover, many countries also require compositional analysis and safety data to further support their safe human consumption. However, safety data are lacking for many of these traditional food items and the history that surrounds their safe use has rarely been recorded in written form, but rather passed on through cultural practices and language. This review evaluates the suitability of current frameworks for assessing the dietary safety of traditional foods and highlights the food-safety regulatory hurdles currently felt by First Peoples and their businesses attempting to enter the Australian native foods industry. These issues also extend to the requirements of food regulatory authorities around the world, when assessing the market eligibility of traditional food items. Potential solutions to these problems are discussed, including new proposed processes that can be incorporated into the current food regulatory frameworks. Importantly, these proposed processes would allow the dietary risk assessment of traditional foods to be completed in a manner that better accommodates the stories, traditional knowledge and interests of First Peoples, while also meeting the safety data requirements set out by regulatory bodies both within Australia and around the world.
... A second Pleistocene example of reduced technological complexity occurred during the peopling of Sahul. Homo sapiens populations dispersing out of Africa reached Sahul via Wallacea sometime between 65 and 50 thousand years ago, as evidenced by early occupations at the Northern Australian site of Madjedbebe Hiscock, 2017;Wood, 2017) and genetic analyses (Malaspinas et al., 2016;Tobler et al., 2017). Evidence for almost all of the behaviors used to define modern humans (sensu McBrearty and Brooks, 2000) are present in Sahul and Wallacea during the Pleistocene (Franklin and Habgood, 2007;Habgood and Franklin, 2008). ...
We propose a transmission time investment model for integrating the tenets of human behavioral ecology and cultural evolutionary theory to investigate agency and optimality in the social transmission of lithic technologies. While the cultural transmission process is often overlooked in discussions of optimality, we view it as a critical area for the application of adaptive reasoning to further understand the mechanisms responsible for change in lithic technologies. The proposed model modifies a technological intensification model based on the marginal value theorem (Bettinger et al. Journal of Archaeological Science, 33(4), 538–545, 2006; Mohlenhoff and Codding Evolutionary Anthropology, 26(5), 218–227, 2017) to explore how transmissibility may have affected the complexity of socially transmitted lithic production systems during the Pleistocene. This transmission investment model is contrasted with a passive demographic model derived from traditional explanations for changes in lithic technologies. To highlight how optimal considerations of transmissibility may have affected the long-term evolution of lithic technologies, we apply this model to three Pleistocene archaeological case studies investigating increases and decreases in lithic technological complexity. We propose that technological changes in each of these case studies is consistent with the predictions of the model, suggesting that time management strategies may have played a role in the long-term evolution of Pleistocene technologies. It is unlikely that transmission constraints alone were wholly responsible for the observed patterns, and future research should refine the measures of time availability and cost used here, as well as explore the interplay between transmission investment and other optimizing and social constraints.
... During the last few decades, great progress has been made in several domains, particularly palaeogenetics, which have revealed the complex ancestry of early Eurasians. This progressincluding the identification of a "ghost lineage" of Eurasians in the Middle East-is providing important new biogeographical hypotheses [1]. Recent molecular and morphological research a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 on the Neanderthal remains documents that this species appeared in Europe at least 400 ka [2][3][4] and ca. ...
The study of the cultural materials associated with the Neanderthal physical remains from the sites in the Caucasus, Central Asia and Siberian Altai and adjacent areas documents two distinct techno-complexes of Micoquian and Mousterian. These findings potentially outline two dispersal routes for the Neanderthals out of Europe. Using data on topography and Palaeoclimate, we generated computer-based least-cost-path modelling for the Neanderthal dispersal routes from Caucasus towards the east. In this regard, two dispersal routes have been identified: A northern route from Greater Caucasus associated with Micoquian techno-complex towards Siberian Altai and a southern route from Lesser Caucasus associated with Mousterian towards Siberian Altai via the Southern Caspian Corridor. Based on archaeological, bio- and physio-geographical data, our model hypothesises that during climatic deterioration phases (e.g. MIS 4) the connection between Greater and Lesser Caucasus was limited. This issue perhaps resulted in the separate development and spread of two cultural groups of Micoquian and Mousterian with an input from two different population sources of Neanderthal influxes: eastern and southern Europe refugia for these two northern and southern dispersal routes respectively. Of these two, we focus on the southern dispersal route, for it comprises a 'rapid dispersal route' towards east. The significant location of the Southern Caspian corridor between high mountains of Alborz and the Caspian Sea, provided a special biogeographical zone and a refugium. This exceptional physio-geographic condition brings forward the Southern Caspian corridor as a potential place of admixture of different hominin species including Neanderthals and homo sapiens.
Bringing together an international team of scholars, this pioneering book presents the first truly systematic, cross-linguistic study of variation in literacy development. It draws on a wide range of cross-cultural research to shed light on the key factors that predict global variation in children's acquisition of reading and writing skills, covering regions as diverse as North and South America, Asia, Australia, Europe and Africa. The first part of the volume deals with comprehensive reviews related to the variation of literacy in different regions of the globe as a function of socio-political, sociocultural, and language and writing system factors. The second part of the volume deals with comprehensive reviews related to the variation of literacy in different world regions. Offering a pioneering new framework for global literacy development, this groundbreaking volume will remain a landmark in the fields of literacy development and literacy teaching and learning for years to come.
Island endemic birds account for the majority of extinct vertebrates in the past few centuries. To date, the evolutionary characteristics of island endemic bird's is poorly known. In this research, we de novo assembled a high‐quality chromosome‐level reference genome for the Swinhoe's pheasant, which is a typical endemic island bird. Results of collinearity tests suggest rapid ancient chromosome rearrangement that may have contributed to the initial species radiation within Phasianidae, and a role for the insertions of CR1 transposable elements in rearranging chromosomes in Phasianidae. During the evolution of the Swinhoe's pheasant, natural selection positively selected genes involved in fecundity and body size functions, at both the species and population levels, which reflect genetic variation associated with island adaptation. We further tested for variation in population genomic traits between the Swinhoe's pheasant and its phylogenetically closely related mainland relative the silver pheasant, and found higher levels of genetic drift and inbreeding in the Swinhoe's pheasant genome. Divergent demographic histories of insular and mainland bird species during the last glacial period may reflect the differing impact of insular and continental climates on the evolution of species. Our research interprets the natural history and population genetic characteristics of the insular endemic bird the Swinhoe's pheasant, at a genome‐wide scale, provides a broader perspective on insular speciation, and adaptive evolution and contributes to the genetic conservation of island endemic birds.
Denisovans, a group of now extinct humans who lived in Eastern Eurasia in the Middle and Late Pleistocene, were first identified from DNA sequences just over a decade ago. Only ten fragmentary remains from two sites have been attributed to Denisovans based entirely on molecular information. Nevertheless, there has been great interest in using genetic data to understand Denisovans and their place in human history. From the reconstruction of a single high-quality genome, it has been possible to infer their population history, including events of admixture with other human groups. Additionally, the identification of Denisovan DNA in the genomes of present-day individuals has provided insights into the timing and routes of dispersal of ancient modern humans into Asia and Oceania, as well as the contributions of archaic DNA to the physiology of present-day people. In this Review, we synthesize more than a decade of research on Denisovans, reconcile controversies and summarize insights into their population history and phenotype. We also highlight how our growing knowledge about Denisovans has provided insights into our own evolutionary history.
Modern and ancient genomes are not necessarily drawn from homogeneous populations, as they may have been collected from different places and at different times. This heterogeneous sampling can be an issue for demographic inferences and results in biased demographic parameters and incorrect model choice if not properly considered. When explicitly accounted for, it can result in very complex models and high data dimensionality that are difficult to analyse. In this paper, we formally study the impact of such spatial and temporal sampling heterogeneity on demographic inference, and we introduce a way to circumvent this problem. To deal with structured samples without increasing the dimensionality of the site frequency spectrum (SFS), we introduce a new structured approach to the existing program fastsimcoal2. We assess the efficiency and relevance of this methodological update with simulated and modern human genomic data. We particularly focus on spatial and temporal heterogeneities to evidence the interest of this new SFS-based approach, which can be especially useful when handling scattered and ancient DNA samples, as in conservation genetics or archaeogenetics.
All humans carry a small fraction of archaic ancestry across the genome, the legacy of gene flow from Neanderthals, Denisovans, and other hominids into the ancestors of modern humans. While the effects of Neanderthal ancestry on human fitness and health have been explored more thoroughly, there are fewer examples of adaptive introgression of Denisovan variants. Here, we study the gene MUC19, for which some modern humans carry a Denisovan-like haplotype. MUC19 is a mucin, a glycoprotein that forms gels with various biological functions, from lubrication to immunity. We find the diagnostic variants for the Denisovan-like MUC19 haplotype at high frequencies in admixed Latin American individuals among global population, and at highest frequency in 23 ancient Indigenous American individuals, all predating population admixture with Europeans and Africans. We find that some Neanderthals - Vindija and Chagyrskaya - carry the Denisovan-like MUC19 haplotype, and that it was likely introgressed into human populations through Neanderthal introgression rather than Denisovan introgression. Finally, we find that the Denisovan-like MUC19 haplotype carries a higher copy number of a 30 base-pair variable number tandem repeat relative to the Human-like haplotype, and that copy numbers of this repeat are exceedingly high in American populations. Our results suggest that the Denisovan-like MUC19 haplotype served as the raw genetic material for positive selection as American populations adapted to novel environments during their movement from Beringia into North and then South America.
Changes in gene expression are thought to play a major role in adaptive evolution. While it is known that gene expression is highly sensitive to the environment, very few studies have determined the influence of genetic and environmental effects on adaptive gene expression differences in natural populations. Here, we utilize allele-specific expression to characterize cis and trans gene regulatory divergence in temperate and tropical house mice in two metabolic tissues under two thermal conditions. First, we show that gene expression divergence is pervasive between populations and across thermal conditions, with roughly 5 to 10% of genes exhibiting genotype-by-environment interactions. Second, we found that most expression divergence was due to cis -regulatory changes that were stable across temperatures. In contrast, patterns of expression plasticity were largely attributable to trans -effects, which showed greater sensitivity to temperature. Nonetheless, we found a small subset of temperature-dependent cis -regulatory changes, thereby identifying loci underlying expression plasticity. Finally, we performed scans for selection in wild house mice to identify genomic signatures of rapid adaptation. Genomic outliers were enriched in genes with evidence for cis -regulatory divergence. Notably, these genes were associated with phenotypes that affected body weight and metabolism, suggesting that cis- regulatory changes are a possible mechanism for adaptive body size evolution between populations. Our results show that gene expression plasticity, largely controlled in trans , may facilitate the colonization of new environments, but that evolved changes in gene expression are largely controlled in cis , illustrating the genetic and nongenetic mechanisms underlying the establishment of populations in new environments.
Archaeology, palaeoanthropology and linguistics have provided valuable insights into human history. However, over the last two decades, fuelled by the advent of improved sequencing technologies, the study of the diversity of the human genome has greatly increased our understanding of the peopling history of the world. The information provided by these genomic data is highly complementary to these other disciplines as it offers another dimensionality for the study of population history. Here, we review how evolutionary and population genetic approaches have allowed the detailed reconstruction of the migratory history of our species, admixture episodes between modern human populations or between humans and now-extinct hominins, and events of human adaptation to new environments.
Polyploidy is recurrent across the tree of life and known as an evolutionary driving force in plant diversification and crop domestication. How polyploid plants adapt to various habitats has been a fundamental question that remained largely unanswered. Brassica napus is a major crop cultivated worldwide, resulting from allopolyploidy between unknown accessions of diploid Brassica rapa and Brassica oleracea. Here, we used whole-genome resequencing data of accessions representing the majority of morphotypes and ecotypes from the species B. rapa, B. oleracea and B. napus to investigate the role of polyploidy during domestication. To do so we first reconstructed the phylogenetic history of B. napus which supported the hypothesis that the emergence of B. napus derived from the hybridization of European turnip of B. rapa and wild B. oleracea. These analyses also showed that morphotypes of swede and Siberian kale (used as vegetable and fodder) were domesticated before rapeseed (oil crop). We next observed that frequent interploidy introgressions from sympatric diploids were prominent throughout the domestication history of B. napus. Introgressed genomic regions were shown to increase the overall genetic diversity and tend to be localized in regions of high recombination. We detected numerous candidate adaptive introgressed regions and found evidence that some of the genes in these regions contributed to phenotypic diversification and adaptation of different morphotypes. Overall, our results shed light on the origin and domestication of B. napus and demonstrate interploidy introgression as an important mechanism that fuels rapid diversification in polyploid species.
Background:
Chronic hepatitis B virus (HBV) infection is a major health problem for all Indigenous Australians. Post-2000, HBsAg prevalence has decreased, although remaining four times higher in Indigenous compared with non-Indigenous people.
Aims:
This study aimed to characterise the HBV from Indigenous populations in Queensland and the Torres Strait Islands.
Methods:
Serum samples were collected, with consent, from people within Queensland Indigenous communities prior to 1990 as part of the Queensland Health vaccination program. Ethics approval was subsequently obtained to further characterise the HBV from 93 of these stored samples. HBV DNA was extracted and genotype obtained from 82 samples. HBV full genome sequencing was carried out for a subset of 14 samples.
Results:
78 samples were identified as genotype C (2xC12, 3xC13, and 73xC14), one sample as genotype A (A2) and three samples as genotype D (1xD2, 1xD3, 1xD4). The HBV/C sequences identified were most closely related to sequences isolated from Papua New Guinea and Indonesia (Papua Province).
Conclusions:
The HBV isolated from the Torres Strait Islanders was notably different to the HBV/C4 strain isolated from Indigenous people of mainland northern Australia, with no evidence of recombination. This reflects the differences in culture and origin between Torres Strait Islanders, and mainland Indigenous people. This article is protected by copyright. All rights reserved.
The timing of the first arrival of Homo sapiens in East Asia from Africa and the degree to which they interbred with or replaced local archaic populations is controversial. Previous discoveries from Tam Pà Ling cave (Laos) identified H. sapiens in Southeast Asia by at least 46 kyr. We report on a recently discovered frontal bone (TPL 6) and tibial fragment (TPL 7) found in the deepest layers of TPL. Bayesian modeling of luminescence dating of sediments and U-series and combined U-series-ESR dating of mammalian teeth reveals a depositional sequence spanning ~86 kyr. TPL 6 confirms the presence of H. sapiens by 70 ± 3 kyr, and TPL 7 extends this range to 77 ± 9 kyr, supporting an early dispersal of H. sapiens into Southeast Asia. Geometric morphometric analyses of TPL 6 suggest descent from a gracile immigrant population rather than evolution from or admixture with local archaic populations.
Aboriginal and Torres Strait Islander People (respectfully referred to as Indigenous Australians herein) are disparately burdened by many infectious and chronic diseases relative to Australians with European genetic ancestry. Some of these diseases are described in other populations to be influenced by the inherited profile of complement genes. These include complement factor B, H, I and complement factor H-related (CFHR) genes that can contribute to a polygenic complotype. Here the focus is on the combined deletion of CFHR1 and 3 to form a common haplotype (CFHR3-1Δ). The prevalence of CFHR3-1Δ is high in people with Nigerian and African American genetic ancestry and correlates to a higher frequency and severity of systemic lupus erythematosus (SLE) but a lower prevalence of age-related macular degeneration (AMD) and IgA-nephropathy (IgAN). This pattern of disease is similarly observed among Indigenous Australian communities. Additionally, the CFHR3-1Δ complotype is also associated with increased susceptibility to infection with pathogens, such as Neisseria meningitidis and Streptococcus pyogenes, which also have high incidences in Indigenous Australian communities. The prevalence of these diseases, while likely influenced by social, political, environmental and biological factors, including variants in other components of the complement system, may also be suggestive of the CFHR3-1Δ haplotype in Indigenous Australians. These data highlight a need to define the Indigenous Australian complotypes, which may lead to the discovery of new risk factors for common diseases and progress towards precision medicines for treating complement-associated diseases in Indigenous and non-Indigenous populations. Herein, the disease profiles suggestive of a common complement CFHR3-1Δ control haplotype are examined.
Background: Population genomic studies of individuals of Indigenous ancestry have been extremely limited comprising <0.5% of participants in international genetic databases and genome-wide association studies, contributing to a “genomic gap” that limits their access to personalised medicine. While Indigenous Australians face a high burden of chronic disease and associated medication exposure, corresponding genomic and drug safety datasets are sorely lacking.
Methods: To address this, we conducted a pharmacogenomic study of almost 500 individuals from a founder Indigenous Tiwi population. Whole genome sequencing was performed using short-read Illumina Novaseq6000 technology. We characterised the pharmacogenomics (PGx) landscape of this population by analysing sequencing results and associated pharmacological treatment data.
Results: We observed that every individual in the cohort carry at least one actionable genotype and 77% of them carry at least three clinically actionable genotypes across 19 pharmacogenes. Overall, 41% of the Tiwi cohort were predicted to exhibit impaired CYP2D6 metabolism, with this frequency being much higher than that for other global populations. Over half of the population predicted an impaired CYP2C9, CYP2C19, and CYP2B6 metabolism with implications for the processing of commonly used analgesics, statins, anticoagulants, antiretrovirals, antidepressants, and antipsychotics. Moreover, we identified 31 potentially actionable novel variants within Very Important Pharmacogenes (VIPs), five of which were common among the Tiwi. We further detected important clinical implications for the drugs involved with cancer pharmacogenomics such as thiopurines and tamoxifen, immunosuppressants like tacrolimus and certain antivirals used in the hepatitis C treatment due to potential differences in their metabolic processing.
Conclusion: The pharmacogenomic profiles generated in our study demonstrate the utility of pre-emptive PGx testing and have the potential to help guide the development and application of precision therapeutic strategies tailored to Tiwi Indigenous patients. Our research provides valuable insights on pre-emptive PGx testing and the feasibility of its use in ancestrally diverse populations, emphasizing the need for increased diversity and inclusivity in PGx investigations.
Admixture, the genetic merging of parental populations resulting in mixed ancestry, has occurred frequently throughout the course of human history. Numerous admixture events have occurred between human populations across the world, which have shaped genetic ancestry in modern humans. For example, populations in the Americas are often mosaics of different ancestries due to recent admixture events as part of European colonization. Admixed individuals also often have introgressed DNA from Neanderthals and Denisovans that may have come from multiple ancestral populations, which may affect how archaic ancestry is distributed across an admixed genome. In this study, we analyzed admixed populations from the Americas to assess whether the proportion and location of admixed segments due to recent admixture impact an individual's archaic ancestry. We identified a positive correlation between non-African ancestry and archaic alleles, as well as a slight enrichment of Denisovan alleles in Indigenous American segments relative to European segments in admixed genomes. We also identify several genes as candidates for adaptive introgression, based on archaic alleles present at high frequency in admixed American populations but low frequency in East Asian populations. These results provide insights into how recent admixture events between modern humans redistributed archaic ancestry in admixed genomes.
What shapes the distribution of nucleotide diversity along the genome? Attempts to answer this question have sparked debate about the roles of neutral stochastic processes and natural selection in molecular evolution. However, the mechanisms of evolution do not act in isolation, and integrative models that simultaneously consider the influence of multiple factors on diversity are lacking; without them, confounding factors lurk in the estimates. Here we present a new statistical method that jointly infers the genomic landscapes of genealogies, recombination rates and mutation rates. In doing so, our model captures the effects of genetic drift, linked selection and local mutation rates on patterns of genomic variation. We then formalize a causal model of how these micro-evolutionary mechanisms interact, and cast it as a linear regression to estimate their individual contributions to levels of diversity along the genome. Our analyses reclaim the well-established signature of linked selection in Drosophila melanogaster, but we estimate that the mutation landscape is the major driver of the genome-wide distribution of diversity in this species. Furthermore, our simulation results suggest that in many evolutionary scenarios the mutation landscape will be a crucial factor shaping diversity, depending notably on the genomic window size. We argue that incorporating mutation rate variation into the null model of molecular evolution will lead to more realistic inferences in population genomics.
Butterflies and moths (Lepidoptera) are one of the most ecologically diverse and speciose insect orders, with more than 157,000 described species. However, the abundance and diversity of Lepidoptera are declining worldwide at an alarming rate. As few Lepidoptera are explicitly recognised as at risk globally, the need for conservation is neither mandated nor well-evidenced. Large-scale biodiversity genomics projects that take advantage of the latest developments in long-read sequencing technologies offer a valuable source of information. We here present a comprehensive, reference-free, whole-genome, multiple sequence alignment of 88 species of Lepidoptera. We show that the accuracy and quality of the alignment is influenced by the contiguity of the reference genomes analysed. We explored genomic signatures that might indicate conservation concern in these species. In our dataset, which is largely from Britain, many species, in particular moths, display low heterozygosity and a high level of inbreeding, reflected in medium (0.1 - 1 Mb) and long (> 1 Mb) runs of homozygosity. Many species with low inbreeding display a higher masked load, estimated from the sum of rejected substitution scores at heterozygous sites. Our study shows that the analysis of a single diploid genome in a comparative phylogenetic context can provide relevant genetic information to prioritise species for future conservation investigation, particularly for those with an unknown conservation status.
Humans have no close living relatives and so it is of interest to human ethologists to try and model the characteristics of the last common ancestor (LCA) of humans and chimpanzees. This can be done by examining similarities in the behaviour of these species and also by considering their behavioural differences. This analysis indicates that the LCA was a self-aware, tool-using, hunter-gathering, hand-assisted arboreal biped. It is suggested that the human line's most likely point of origin was in the flooded/swamp forests of what became the Congo basin following the uplifting of the East African Rift region during the mid-to-late Miocene. It is proposed that this subsidence created the conditions for the LCA line to divide based on propensity to engage with water and that this is still reflected in the behaviour of chimpanzees and humans today. COMMENTARY Tinbergen's four questions of Form, Function, Ontogeny, Phylogeny, the 'what does it look like, 'what does it do' , how does it change within an individual's lifetime' , 'how do other closely related species solve homologous problems' questions (Hendrie, 2022, after Tinbergen, 1963) are undoubtedly Ethology's most powerful tools. They provide guidance for systematic study that is missing from disciplines like Psychology and elevate what would otherwise be an interesting technique for analysing behaviour into a scientific discipline. Whilst answers to the first three questions can be obtained by direct observation, answering questions about phylogeny is less straightforward for those studying humans as there are no close relatives of our species still in existence. Comparisons with chimpanzees (Pan troglodytes) are commonly made on the basis of there being a 96% overlap between genomes (The Chimpanzee Sequencing and Analysis Consortium, 2005). Whilst this is clearly of importance for biomedical studies etc, it is of lesser relevance when considering behaviour as behaviour is not predicted by genetic relatedness. There is for example, significant genetic overlap between humans and simple animals like sponges (Gaiti et al, 2017). A significant proportion of the human genome also derives from endogenous retroviruses (Nelson et al, 2003) and other hominins, such as Denisovans/Neanderthals (e.g. Malaspinas et al, 2016) and whilst bonobos (Pan paniscus) are Hendrie, C. (2023). The Last Common Ancestor. Human Ethology, 38, 02-07.
Understanding what determines species and population differences in levels of genetic diversity has important implications for our understanding of evolution, as well as for the conservation and management of wild populations. Previous comparative studies have emphasized the roles of linked selection, life-history trait variation and genomic properties, rather than pure demography, as important determinants of genetic diversity. However, these findings are based on coarse estimates across a range of highly diverged taxa, and it is unclear how well they represent the processes within individual species. We assessed genome-wide genetic diversity (pi) in 45 nine-spined stickleback (Pungitius pungitius) populations and found that pi varied 15-fold among populations (pi min approx. 0.00015, pi max approx 0.0023) whereas estimates of recent effective population sizes varied 122-fold. Analysis of inbreeding coefficients (F ROH) estimated from runs of homozygosity revealed strong negative association between pi and F ROH. Genetic diversity was also negatively correlated with mean body size and longevity, but these associations were not statistically significant after controlling for demographic effects (F ROH). The results give strong support for the view that populations' demographic features, rather than life history differences, are the chief determinants of genetic diversity in the wild.
This chapter describes the current understanding of climate and human variation using global and local approaches, and considers the emerging topics of epigenetic analyses and climate change. It characterizes stresses, describes human biological variation, and presents evidence for modes of adaptation. Anthropologists operationalize climate broadly to include temperature and humidity, ultraviolet radiation (UVR) intensity, and altitude above sea level. Thermoneutrality refers to the ambient temperature at which a nude, inactive adult maintains core temperature without engaging behavioral and biological thermoregulation. UVR penetrates the outer layers of the skin, where melanin and other molecules either reflect or absorb radiation. Climate change will alter the water supply for human and agricultural use, including precipitation, ground, and surface sources; “the quantity and quality of our water are woven into the intersections between human health, culture, and human biology, just as they are for food”.
Data from recent years have substantially changed scientific understanding of Middle and Late Pleistocene human evolution. For many paleoanthropologists, there could be at least six species coexisting in the later Pleistocene. The Evolutionary Species Concept (ESC) extends these morphological patterns over time, identifying an evolutionary lineage that has its own unique evolutionary fate. The Biological Species Concept defines species based on reproductive isolation. Species diversity in mammals is tied to body mass, with larger forms exhibiting less taxonomic diversity. African post‐Erectine humans are represented by remains from a geographically diverse series of sites. It is difficult to determine the ultimate origin of the Heidelbergs. Neandertals are the best known and most intensely studied fossil humans. Neandertals and higher latitude archaic Asians are adapted for life in the cold but not just in terms of anatomy.
Introduction
There is a considerable and ongoing health gap experienced by First Nations Australians. Physiotherapists play an integral role in the health care of this population; however, little is known about new graduate preparedness and training needs to work in a First Nations context.
Objective
To explore the perceptions of new graduate physiotherapists regarding their preparedness and training needs for working with First Nation Australians.
Methods
Qualitative telephone, semi-structured interviews of new graduate physiotherapists (n = 13) who have worked with First Nations Australians in the last two years. Inductive, reflexive thematic analysis was used.
Results
Five themes were generated: 1) limitations of pre-professional training; 2) benefits of work integrated learning; 3) ‘on the job’ development; 4) intrapersonal factors and efforts; and 5) insights into improving training.
Conclusion
New graduate physiotherapists perceive that their preparedness to work in a First Nations health context is supported by practical and varied learning experiences. At the pre-professional level, new graduates benefit from work integrated learning and opportunities that evoke critical self-reflection. At the professional level, new graduates express a need for ‘on the job’ development, peer supervision, and tailored professional development, that focuses on the unique perspectives of the specific community in which they work.
Motivation
Structure methods are highly used population genetic methods for classifying individuals in a sample fractionally into discrete ancestry components.
Contribution
We introduce a new optimization algorithm of the classical Structure model in a maximum likelihood framework. Using analyses of real data we show that the new optimization algorithm finds higher likelihood values than the state-of-the-art method in the same computational time. We also present a new method for estimating population trees from ancestry components using a Gaussian approximation. Using coalescence simulations modeling populations evolving in a tree-like fashion, we explore the adequacy of the Structure model and the Gaussian assumption for identifying ancestry components correctly and for inferring the correct tree. In most cases, ancestry components are inferred correctly, although sample sizes and times since admixture can influence the inferences. Similarly, the popular Gaussian approximation tends to perform poorly when branch lengths are long, although the tree topology is correctly inferred in all scenarios explored. The new methods are implemented together with appropriate visualization tools in the computer package Ohana.
Availability
Ohana is publicly available at https://github.com/jade-cheng/ohana . Besides its source code and installation instructions, we also provide example workflows in the project wiki site.
Contact
jade.cheng@birc.au.dk
This Encyclopaedia is the first significant authoritative and comprehensive reference on all apects of Australian Aboriginal and Torres Strait Islander history, society and culture. Containing some 2000 clearly written and informative entries by over 200 authors from all parts of Australia, and illustrated with around 1000 colour and black and white photographs, maps and drawings, this work is an indispensable resource for government and community organisations, schools, tertiary institutions, libraries and for the home.
Entries range across all major subject categories (Ancient History, Art, Economy, Education, Food, Health, Land Ownership, Language, Law, LIterature, media, Music, Politics, Recent History, Sport) and also cover current topics contemporary art and music, mining and royalties, land rights, deaths in custody, housing, legal services and language maintenance, as well as including biographies, historical sketches of significant places, and profiles of the approximately 500 indigenous "tribal" peoples of Australia. These 500 groups are divided into 18 geographic regions which form an additional framework of organisation to the subject groupings.
There are in addition many appendices with, for example statistical information and timelines. There is a comprehensive index in addition to the cross-linkings between every entry and every other entry. Finally there is an extensive bibliography of some 1800 items.
The maps of the tribal groupings were also combined into a single large wall map "Aboriginal Australia" which includes the regions and an extensive index of synonyms to tribal/langage names.
The Encyclopaedia itself was also released in an electronic interactive form (on a CD Rom, for both Windows and Apple systems) which contained all the above and also added music and film material.
The Encyclopaedia was well received by Aboriginal people, and Charles Perkins, David Mowaljarlai, and Galarrwuy Yunupingu all wrote endorsements for the cover.
Readable link: http://rdcu.be/kt5n
High-coverage whole-genome sequence studies have so far focused on a limited number of geographically restricted populations or been targeted at specific diseases, such as cancer. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history and refuelled the debate on the mutation rate in humans. Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets. We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long- and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record, and admixture between AMHs and Neanderthals predating the main Eurasian expansion, our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago.
Significance
This report is the first publication, to our knowledge, to report the complete mitochondrial genome of an ancient Aboriginal Australian. In addition, it also provides important evidence about the reliability of the only previous publication of this kind. The paper attained international significance, although its conclusions have remained controversial. Using second generation DNA sequencing methods, we provide strong evidence that the DNA sequences reported by Adcock et al. were, indeed, contamination. Our manuscript is also important, because the research was planned and conducted and is published with the support of the Barkindji, Ngiyampaa, and Muthi Muthi indigenous groups.
Australia was one of the earliest regions outside Africa to be colonized by fully modern humans, with archaeological evidence for human presence by 47,000 years ago (47 kya) widely accepted [1, 2]. However, the extent of subsequent human entry before the European colonial age is less clear. The dingo reached Australia about 4 kya, indirectly implying human contact, which some have linked to changes in language and stone tool technology to suggest substantial cultural changes at the same time [3]. Genetic data of two kinds have been proposed to support gene flow from the Indian subcontinent to Australia at this time, as well: first, signs of South Asian admixture in Aboriginal Australian genomes have been reported on the basis of genome-wide SNP data [4]; and second, a Y chromosome lineage designated haplogroup C(∗), present in both India and Australia, was estimated to have a most recent common ancestor around 5 kya and to have entered Australia from India [5]. Here, we sequence 13 Aboriginal Australian Y chromosomes to re-investigate their divergence times from Y chromosomes in other continents, including a comparison of Aboriginal Australian and South Asian haplogroup C chromosomes. We find divergence times dating back to ∼50 kya, thus excluding the Y chromosome as providing evidence for recent gene flow from India into Australia.
Although initial studies suggested that Denisovan ancestry was found only in modern human populations from island Southeast Asia and Oceania, more recent studies have suggested that Denisovan ancestry may be more widespread. However, the geographic extent of Denisovan ancestry has not been determined, and moreover the relationship between the Denisovan ancestry in Oceania and that elsewhere has not been studied. Here we analyze genome-wide SNP data from 2493 individuals from 221 worldwide populations, and show that there is a widespread signal of a very low level of Denisovan ancestry across Eastern Eurasian and Native American (EE/NA) populations. We also verify a higher level of Denisovan ancestry in Oceania than that in EE/NA; the Denisovan ancestry in Oceania is correlated with the amount of New Guinea ancestry, but not the amount of Australian ancestry, indicating that recent gene flow from New Guinea likely accounts for signals of Denisovan ancestry across Oceania. However, Denisovan ancestry in EE/NA populations is equally correlated with their New Guinea or their Australian ancestry, suggesting a common source for the Denisovan ancestry in EE/NA and Oceanian populations. Our results suggest that Denisovan ancestry in EE/NA is derived either from common ancestry with, or gene flow from, the common ancestor of New Guineans and Australians, indicating a more complex history involving East Eurasians and Oceanians than previously suspected.
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Neanderthals are thought to have disappeared in Europe approximately 39,000-41,000 years ago but they have contributed 1-3% of the DNA of present-day people in Eurasia. Here we analyse DNA from a 37,000-42,000-year-old modern human from Peştera cu Oase, Romania. Although the specimen contains small amounts of human DNA, we use an enrichment strategy to isolate sites that are informative about its relationship to Neanderthals and present-day humans. We find that on the order of 6-9% of the genome of the Oase individual is derived from Neanderthals, more than any other modern human sequenced to date. Three chromosomal segments of Neanderthal ancestry are over 50 centimorgans in size, indicating that this individual had a Neanderthal ancestor as recently as four to six generations back. However, the Oase individual does not share more alleles with later Europeans than with East Asians, suggesting that the Oase population did not contribute substantially to later humans in Europe.
A colonization model is proposed to explain the timing of human occupation in different regions of the arid zone and the reasons for inferred demographic changes through time. A biogeographic approach views changes in human economy and technology against the backdrop of climatic oscillations of the last 40,000 years. This model stands in strong contrast to that of the ‘conservative desert culture’ proposed by Gould, which has become untenable as data from arid zone excavations are increasingly argued to reflect significant changes in human economy, technology and demography through time. The results of regional survey and excavation from the Pilbara and sandy deserts of north-west Australia, from central Australia, the Flinders Ranges and adjacent dunefields and from semi-arid Queensland suggest that the occupation of the arid zone from the late Pleistocene on is likely to have been a highly dynamic process. The notion of a stable human adaptation to the diverse landforms and environments of the arid zone finds little support in the archaeological record.
We present the high-quality genome sequence of a 45,000-year-old modern human male from Siberia. This individual derives from a population that lived before—or simultaneously with—the separation of the populations in western and eastern Eurasia and carries a similar amount of Neanderthal ancestry as present-day Eurasians. However, the genomic segments of Neanderthal ancestry are substantially longer than those observed in present-day individuals, indicating that Neanderthal gene flow into the ancestors of this individual occurred 7,000–13,000 years before he lived. We estimate an autosomal mutation rate of 0.4 3 10 29 to 0.6 3 10 29 per site per year, a Y chromosomal mutation rate of 0.7 3 10 29 to 0.9 3 10 29 per site per year based on the additional substitutions that have occurred in present-day non-Africans compared to this genome, and a mitochondrial mutation rate of 1.8 3 10 28 to 3.2 3 10 28 per site per year based on the age of the bone.
Background
Comparisons of maternally-inherited mitochondrial DNA (mtDNA) and paternally-inherited non-recombining Y chromosome (NRY) variation have provided important insights into the impact of sex-biased processes (such as migration, residence pattern, and so on) on human genetic variation. However, such comparisons have been limited by the different molecular methods typically used to assay mtDNA and NRY variation (for example, sequencing hypervariable segments of the control region for mtDNA vs. genotyping SNPs and/or STR loci for the NRY). Here, we report a simple capture array method to enrich Illumina sequencing libraries for approximately 500 kb of NRY sequence, which we use to generate NRY sequences from 623 males from 51 populations in the CEPH Human Genome Diversity Panel (HGDP). We also obtained complete mtDNA genome sequences from the same individuals, allowing us to compare maternal and paternal histories free of any ascertainment bias.
Results
We identified 2,228 SNPs in the NRY sequences and 2,163 SNPs in the mtDNA sequences. Our results confirm the controversial assertion that genetic differences between human populations on a global scale are bigger for the NRY than for mtDNA, although the differences are not as large as previously suggested. More importantly, we find substantial regional variation in patterns of mtDNA versus NRY variation. Model-based simulations indicate very small ancestral effective population sizes (<100) for the out-of-Africa migration as well as for many human populations. We also find that the ratio of female effective population size to male effective population size (Nf/Nm) has been greater than one throughout the history of modern humans, and has recently increased due to faster growth in Nf than Nm.
Conclusions
The NRY and mtDNA sequences provide new insights into the paternal and maternal histories of human populations, and the methods we introduce here should be widely applicable for further such studies.
Significance
Current consensus indicates that modern humans originated from an ancestral African population between ∼100–200 ka. The ensuing dispersal pattern is controversial, yet has important implications for the demographic history and genetic/phenotypic structure of extant human populations. We test for the first time to our knowledge the spatiotemporal dimensions of competing out-of-Africa dispersal models, analyzing in parallel genomic and craniometric data. Our results support an initial dispersal into Asia by a southern route beginning as early as ∼130 ka and a later dispersal into northern Eurasia by ∼50 ka. Our findings indicate that African Pleistocene population structure may account for observed plesiomorphic genetic/phenotypic patterns in extant Australians and Melanesians. They point to an earlier out-of-Africa dispersal than previously hypothesized.
Inference of individual ancestry coefficients, which is important for population genetic and association studies, is commonly performed using computer-intensive likelihood algorithms. With the availability of large population genomic data sets, fast versions of likelihood algorithms have attracted considerable attention. Reducing the computational burden of estimation algorithms remains, however, a major challenge. Here, we present a fast and efficient method for estimating individual ancestry coefficients based on sparse non-negative matrix factorization algorithms. We implemented our method in the computer program sNMF, and applied it to human and plant data sets. The performances of sNMF were then compared to the likelihood algorithm implemented in the computer program ADMIXTURE. Without loss of accuracy, sNMF computed estimates of ancestry coefficients with run-times approximately 10 to 30 times shorter than those of ADMIXTURE.
The hormone thyroxine that regulates mammalian metabolism is carried and stored in the blood by thyroxine-binding globulin (TBG). We demonstrate here that the release of thyroxine from TBG occurs by a temperature-sensitive mechanism and show how this will provide a homoeostatic adjustment of the concentration of thyroxine to match metabolic needs, as with the hypothermia and torpor of small animals. In humans, a rise in temperature, as in infections, will trigger an accelerated release of thyroxine, resulting in a predictable 23% increase in the concentration of free thyroxine at 39°C. The in vivo relevance of this fever-response is affirmed in an environmental adaptation in aboriginal Australians. We show how two mutations incorporated in their TBG interact in a way that will halve the surge in thyroxine release, and hence the boost in metabolic rate that would otherwise occur as body temperatures exceed 37°C. The overall findings open insights into physiological changes that accompany variations in body temperature, as notably in fevers.
Neandertal Shadows in Us
Non-African modern humans carry a remnant of Neandertal DNA from interbreeding events that have been postulated to have occurred as humans migrated out of Africa. While the total amount of Neandertal sequence is estimated to be less than 3% of the modern genome, the specific retained sequences vary among individuals. Analyzing the genomes of more than 600 Europeans and East Asians, Vernot and Akey (p. 1017 , published online 29 January) identified Neandertal sequences within modern humans that taken together span approximately 20% of the Neandertal genome. Some Neandertal-derived sequences appear to be under positive selection in humans, including several genes associated with skin phenotypes.
We sequenced the genomes of a ~7,000 year old farmer from Germany and eight
~8,000 year old hunter-gatherers from Luxembourg and Sweden. We analyzed these and other
ancient genomes1–4 with 2,345 contemporary humans to show that most
present Europeans derive from at least three highly differentiated populations: West
European Hunter-Gatherers (WHG), who contributed ancestry to all Europeans but not to Near
Easterners; Ancient North Eurasians (ANE) related to Upper Paleolithic Siberians3, who contributed to both Europeans and Near
Easterners; and Early European Farmers (EEF), who were mainly of Near Eastern origin but
also harbored WHG-related ancestry. We model these populations’ deep relationships
and show that EEF had ~44% ancestry from a “Basal Eurasian”
population that split prior to the diversification of other non-African lineages.
We present a high-quality genome sequence of a Neanderthal woman from Siberia. We show that her parents were related at the level of half-siblings and that mating among close relatives was common among her recent ancestors. We also sequenced the genome of a Neanderthal from the Caucasus to low coverage. An analysis of the relationships and population history of available archaic genomes and 25 present-day human genomes shows that several gene flow events occurred among Neanderthals, Denisovans and early modern humans, possibly including gene flow into Denisovans from an unknown archaic group. Thus, interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene. In addition, the high-quality Neanderthal genome allows us to establish a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neanderthals and Denisovans.
Human pygmy populations inhabit different regions of the world, from Africa to Melanesia. In Asia, short-statured populations are often referred to as "negritos." Their short stature has been interpreted as a consequence of thermoregulatory, nutritional, and/or locomotory adaptations to life in tropical forests. A more recent hypothesis proposes that their stature is the outcome of a life history trade-off in high-mortality environments, where early reproduction is favored and, consequently, early sexual maturation and early growth cessation have coevolved. Some serological evidence of deficiencies in the growth hormone/insulin-like growth factor axis have been previously associated with pygmies' short stature. Using genome-wide single-nucleotide polymorphism genotype data, we first tested whether different negrito groups living in the Philippines and Papua New Guinea are closely related and then investigated genomic signals of recent positive selection in African, Asian, and Papuan pygmy populations. We found that negritos in the Philippines and Papua New Guinea are genetically more similar to their nonpygmy neighbors than to one another and have experienced positive selection at different genes. These results indicate that geographically distant pygmy groups are likely to have evolved their short stature independently. We also found that selection on common height variants is unlikely to explain their short stature and that different genes associated with growth, thyroid function, and sexual development are under selection in different pygmy groups.
We introduce a flexible and robust simulation-based framework to infer demographic parameters from the site frequency spectrum (SFS) computed on large genomic datasets. We show that our composite-likelihood approach allows one to study evolutionary models of arbitrary complexity, which cannot be tackled by other current likelihood-based methods. For simple scenarios, our approach compares favorably in terms of accuracy and speed with [Formula: see text], the current reference in the field, while showing better convergence properties for complex models. We first apply our methodology to non-coding genomic SNP data from four human populations. To infer their demographic history, we compare neutral evolutionary models of increasing complexity, including unsampled populations. We further show the versatility of our framework by extending it to the inference of demographic parameters from SNP chips with known ascertainment, such as that recently released by Affymetrix to study human origins. Whereas previous ways of handling ascertained SNPs were either restricted to a single population or only allowed the inference of divergence time between a pair of populations, our framework can correctly infer parameters of more complex models including the divergence of several populations, bottlenecks and migration. We apply this approach to the reconstruction of African demography using two distinct ascertained human SNP panels studied under two evolutionary models. The two SNP panels lead to globally very similar estimates and confidence intervals, and suggest an ancient divergence (>110 Ky) between Yoruba and San populations. Our methodology appears well suited to the study of complex scenarios from large genomic data sets.
The first colonization of the Greater Australian continent, known as Sahul, indicated that humans had modern cognitive ability. Such modern human abilities probably emerged earlier in Africa. I will argue that the only way we can identify what constitutes modern human behavior is to look at the record in Australia-the first place colonized only by modern humans. I place this argument within recent theorizing about cognitive evolution. © 2010 by The Wenner-Gren Foundation for Anthropological Research. All rights reserved.
The Australian region spans some 60° of latitude and 50° of longitude and displays considerable regional climate variability both today and during the Late Quaternary. A synthesis of marine and terrestrial climate records, combining findings from the Southern Ocean, temperate, tropical and arid zones, identifies a complex response of climate proxies to a background of changing boundary conditions over the last 35,000 years. Climate drivers include the seasonal timing of insolation, greenhouse gas content of the atmosphere, sea level rise and ocean and atmospheric circulation changes. Our compilation finds few climatic events that could be used to construct a climate event stratigraphy for the entire region, limiting the usefulness of this approach. Instead we have taken a spatial approach, looking to discern the patterns of change across the continent.
We present the first proposal of detailed internal subgrouping and higher-order structure of the Pama-Nyungan family of Australian languages. Previous work has identified more than twenty-five primary subgroups in the family, with little indication of how these groups might fit together. Some work has assumed that reconstruction of higher nodes in the tree was impossible, either because extensive internal borrowing has obscured more remote relations, or because the languages are not sufficiently well attested (see, for example, Bowern & Koch 2004b, Dixon 1997). With regard to the first objection, work by Alpher and Nash (1999) and Bowern and colleagues (2011) shows that loan levels are not high enough to obscure vertical transmission for all but a few languages. New data remove the second objection. Here we use Bayesian phylogenetic inference to show that the Pama-Nyungan tree has a discernible internal subgrouping. We identify four major divisions within the family and discuss the implications of this grouping for future work on the family.*
Neanderthals were a group of archaic hominins that occupied most of Europe and parts of Western Asia from roughly 30-300 thousand years ago (Kya). They coexisted with modern humans during part of this time. Previous genetic analyses that compared a draft sequence of the Neanderthal genome with genomes of several modern humans concluded that Neanderthals made a small (1-4%) contribution to the gene pools of all non-African populations. This observation was consistent with a single episode of admixture from Neanderthals into the ancestors of all non-Africans when the two groups coexisted in the Middle East 50-80 Kya. We examined the relationship between Neanderthals and modern humans in greater detail by applying two complementary methods to the published draft Neanderthal genome and an expanded set of high-coverage modern human genome sequences. We find that, consistent with the recent finding of Meyer et al. (2012), Neanderthals contributed more DNA to modern East Asians than to modern Europeans. Furthermore we find that the Maasai of East Africa have a small but significant fraction of Neanderthal DNA. Because our analysis is of several genomic samples from each modern human population considered, we are able to document the extent of variation in Neanderthal ancestry within and among populations. Our results combined with those previously published show that a more complex model of admixture between Neanderthals and modern humans is necessary to account for the different levels of Neanderthal ancestry among human populations. In particular, at least some Neanderthal-modern human admixture must postdate the separation of the ancestors of modern European and modern East Asian populations.
Despite a massive endeavour, the problem of modern human origins not only remains unresolved, but is usually reduced to “Out of Africa” versus multiregional evolution. Not all would agree, but evidence for a single recent origin is accumulating. Here, we want to go beyond this debate and explore within the “Out of Africa” framework an issue that has not been fully addressed: the mechanism by which modern human diversity has developed. We believe there is no clear rubicon of modern Homo sapiens, and that multiple dispersals occurred from a morphologically variable population in Africa. Pre-existing African diversity is thus crucial to the way human diversity developed outside Africa. The pattern of diversity—behavioural, linguistic, morphological and genetic—can be interpreted as the result of dispersals, colonisation, differentiation and subsequent dispersals overlaid on former population ranges. The first dispersals would have originated in Africa from where two different geographical routes were possible, one through Ethiopia/Arabia towards South Asia, and one through North Africa/Middle East towards Eurasia.
Recent studies of ancient genomes have suggested that gene flow from archaic hominin groups to the ancestors of modern humans occurred on two separate occasions during the modern human expansion out of Africa. At the same time, decreasing levels of human genetic diversity have been found at increasing distance from Africa as a consequence of human expansion out of Africa. We analyzed the signal of archaic ancestry in modern human populations, and we investigated how serial founder models of human expansion affect the signal of archaic ancestry using simulations. For descendants of an archaic admixture event, we show that genetic drift coupled with ascertainment bias for common alleles can cause artificial but largely predictable differences in similarity to archaic genomes. In genotype data from non-Africans, this effect results in a biased genetic similarity to Neandertals with increasing distance from Africa. However, in addition to the previously reported gene flow between Neandertals and non-Africans as well as gene flow between an archaic human population from Siberia ("Denisovans") and Oceanians, we found a significant affinity between East Asians, particularly Southeast Asians, and the Denisova genome--a pattern that is not expected under a model of solely Neandertal admixture in the ancestry of East Asians. These results suggest admixture between Denisovans or a Denisova-related population and the ancestors of East Asians, and that the history of anatomically modern and archaic humans might be more complex than previously proposed.
It has recently been shown that ancestors of New Guineans and Bougainville Islanders have inherited a proportion of their ancestry from Denisovans, an archaic hominin group from Siberia. However, only a sparse sampling of populations from Southeast Asia and Oceania were analyzed. Here, we quantify Denisova admixture in 33 additional populations from Asia and Oceania. Aboriginal Australians, Near Oceanians, Polynesians, Fijians, east Indonesians, and Mamanwa (a "Negrito" group from the Philippines) have all inherited genetic material from Denisovans, but mainland East Asians, western Indonesians, Jehai (a Negrito group from Malaysia), and Onge (a Negrito group from the Andaman Islands) have not. These results indicate that Denisova gene flow occurred into the common ancestors of New Guineans, Australians, and Mamanwa but not into the ancestors of the Jehai and Onge and suggest that relatives of present-day East Asians were not in Southeast Asia when the Denisova gene flow occurred. Our finding that descendants of the earliest inhabitants of Southeast Asia do not all harbor Denisova admixture is inconsistent with a history in which the Denisova interbreeding occurred in mainland Asia and then spread over Southeast Asia, leading to all its earliest modern human inhabitants. Instead, the data can be most parsimoniously explained if the Denisova gene flow occurred in Southeast Asia itself. Thus, archaic Denisovans must have lived over an extraordinarily broad geographic and ecological range, from Siberia to tropical Asia.
We present an Aboriginal Australian genomic sequence obtained from a 100-year-old lock of hair donated by an Aboriginal man from southern Western Australia in the early 20th century. We detect no evidence of European admixture and estimate contamination levels to be below 0.5%. We show that Aboriginal Australians are descendants of an early human dispersal into eastern Asia, possibly 62,000 to 75,000 years ago. This dispersal is separate from the one that gave rise to modern Asians 25,000 to 38,000 years ago. We also find evidence of gene flow between populations of the two dispersal waves prior to the divergence of Native Americans from modern Asian ancestors. Our findings support the hypothesis that present-day Aboriginal Australians descend from the earliest humans to occupy Australia, likely representing one of the oldest continuous populations outside Africa.
Serum urate concentrations are highly heritable and elevated serum urate is a key risk factor for gout. Genome-wide association
studies (GWAS) of serum urate in African American (AA) populations are lacking. We conducted a meta-analysis of GWAS of serum
urate levels and gout among 5820 AA and a large candidate gene study among 6890 AA and 21 708 participants of European ancestry
(EA) within the Candidate Gene Association Resource Consortium. Findings were tested for replication among 1996 independent
AA individuals, and evaluated for their association among 28 283 EA participants of the CHARGE Consortium. Functional studies
were conducted using 14C-urate transport assays in mammalian Chinese hamster ovary cells. In the discovery GWAS of serum urate, three loci achieved
genome-wide significance (P< 5.0 × 10−8): a novel locus near SGK1/SLC2A12 on chromosome 6 (rs9321453, P= 1.0 × 10−9), and two loci previously identified in EA participants, SLC2A9 (P= 3.8 × 10−32) and SLC22A12 (P= 2.1 × 10−10). A novel rare non-synonymous variant of large effect size in SLC22A12, rs12800450 (minor allele frequency 0.01, G65W), was identified and replicated (beta −1.19 mg/dl, P= 2.7 × 10−16). 14C-urate transport assays showed reduced urate transport for the G65W URAT1 mutant. Finally, in analyses of 11 loci previously
associated with serum urate in EA individuals, 10 of 11 lead single-nucleotide polymorphisms showed direction-consistent association
with urate among AA. In summary, we identified and replicated one novel locus in association with serum urate levels and experimentally
characterize the novel G65W variant in URAT1 as a functional allele. Our data support the importance of multi-ethnic GWAS
in the identification of novel risk loci as well as functional variants.
Using DNA extracted from a finger bone found in Denisova Cave in southern Siberia, we have sequenced the genome of an archaic hominin to about 1.9-fold coverage. This individual is from a group that shares a common origin with Neanderthals. This population was not involved in the putative gene flow from Neanderthals into Eurasians; however, the data suggest that it contributed 4-6% of its genetic material to the genomes of present-day Melanesians. We designate this hominin population 'Denisovans' and suggest that it may have been widespread in Asia during the Late Pleistocene epoch. A tooth found in Denisova Cave carries a mitochondrial genome highly similar to that of the finger bone. This tooth shares no derived morphological features with Neanderthals or modern humans, further indicating that Denisovans have an evolutionary history distinct from Neanderthals and modern humans.
Aboriginal people have been in Australia for at least 40,000 years, speaking about 250 languages. Through examination of published and unpublished materials on each of the individual languages, Professor Dixon surveys the ways in which the languages vary typologically and presents a profile of this long-established linguistic area. The areal distribution of most features is illustrated with more than 30 maps, showing that the languages tend to move in cyclic fashion with respect to many of the parameters. There is also an index of languages and language groups. Professor Dixon, a pioneering scholar in the field, brings an interesting perspective to this diverse and complex material.
Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans.
Some present-day humans derive up to ∼5% [1] of their ancestry from archaic Denisovans, an even larger proportion than the ∼2% from Neanderthals [2]. We developed methods that can disambiguate the locations of segments of Denisovan and Neanderthal ancestry in present-day humans and applied them to 257 high-coverage genomes from 120 diverse populations, among which were 20 individual Oceanians with high Denisovan ancestry [3]. In Oceanians, the average size of Denisovan fragments is larger than Neanderthal fragments, implying a more recent average date of Denisovan admixture in the history of these populations (p = 0.00004). We document more Denisovan ancestry in South Asia than is expected based on existing models of history, reflecting a previously undocumented mixture related to archaic humans (p = 0.0013). Denisovan ancestry, just like Neanderthal ancestry, has been deleterious on a modern human genetic background, as reflected by its depletion near genes. Finally, the reduction of both archaic ancestries is especially pronounced on chromosome X and near genes more highly expressed in testes than other tissues (p = 1.2 × 10(-7) to 3.2 × 10(-7) for Denisovan and 2.2 × 10(-3) to 2.9 × 10(-3) for Neanderthal ancestry even after controlling for differences in level of selective constraint across gene classes). This suggests that reduced male fertility may be a general feature of mixtures of human populations diverged by >500,000 years.
This book is an introduction to the archaeology of Australia from prehistoric times to the eighteenth century AD. It is the only up-to-date textbook on the subject and is designed for undergraduate courses, based on the author's considerable experience of teaching at the Australian National University. Lucidly written, it shows the diversity and colourfulness of the history of humanity in the southern continent. The Archaeology of Ancient Australia demonstrates with an array of illustrations and clear descriptions of key archaeological evidence from Australia a thorough evaluation of Australian prehistory. Readers are shown how this human past can be reconstructed from archaeological evidence, supplemented by information from genetics, environmental sciences, anthropology, and history. The result is a challenging view about how varied human life in the ancient past has been.
Published ages of >50 ka for occupation at Madjedbebe (Malakunanja II) in Australia's north have kept the site prominent in discussions about the colonisation of Sahul. The site also contains one of the largest stone artefact assemblages in Sahul for this early period. However, the stone artefacts and other important archaeological components of the site have never been described in detail, leading to persistent doubts about its stratigraphic integrity. We report on our analysis of the stone artefacts and faunal and other materials recovered during the 1989 excavations, as well as the stratigraphy and depositional history recorded by the original excavators. We demonstrate that the technology and raw materials of the early assemblage are distinctive from those in the overlying layers. Silcrete and quartzite artefacts are common in the early assemblage, which also includes edge-ground axe fragments and ground haematite. The lower flaked stone assemblage is distinctive, comprising a mix of long convergent flakes, some radial flakes with faceted platforms, and many small thin silcrete flakes that we interpret as thinning flakes. Residue and use-wear analysis indicate occasional grinding of haematite and woodworking, as well as frequent abrading of platform edges on thinning flakes. We conclude that previous claims of extensive displacement of artefacts and post-depositional disturbance may have been overstated. The stone artefacts and stratigraphic details support previous claims for human occupation 50-60 ka and show that human occupation during this time differed from later periods. We discuss the implications of these new data for understanding the first human colonisation of Sahul.
Copyright © 2015 Elsevier Ltd. All rights reserved.
The availability of complete human genome sequences from populations across the world has given rise to new population genetic inference methods that explicitly model ancestral relationships under recombination and mutation. So far, application of these methods to evolutionary history more recent than 20,000-30,000 years ago and to population separations has been limited. Here we present a new method that overcomes these shortcomings. The multiple sequentially Markovian coalescent (MSMC) analyzes the observed pattern of mutations in multiple individuals, focusing on the first coalescence between any two individuals. Results from applying MSMC to genome sequences from nine populations across the world suggest that the genetic separation of non-African ancestors from African Yoruban ancestors started long before 50,000 years ago and give information about human population history as recent as 2,000 years ago, including the bottleneck in the peopling of the Americas and separations within Afri