Article

A genomic history of Aboriginal Australia

Authors:
  • Griffith University, Nathan
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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

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... The advantages of this system, in addition to its universality, is that it allows for relatively simple qualitative and quantitative analysis. This is important, as there is increasing interest in mapping human diversity in different ways, using quantitative techniques (Stinchcombe and Hoekstra, 2008;Malaspinas et al., 2016;Matsumura et al., 2019); the abundance of dental remains provides an additional source of information. In addition, there is growing interest among geneticists to map phenotypic variation against genetic variation (Zichello et al., 2018), and to develop a better understanding of genotypephenotype relationships. ...
... The first is Sahul-Pacific. The genomic evidence (Malaspinas et al., 2016) would suggest an age of colonization of Australia and New Guinea around 48 Ka (i.e. the split date for Sahul populations from Sunda ones). However, there is strong evidence for colonization as early 65 Ka (Clarkson et al., 2017). ...
... The same pattern can be observed in the Geographical Level 2 (Continental Groups), where Australia & Melanesia (Sahul) are very similar to South East Asia, and Africa is similar when Canonical Variable 3 is included (Figure 7.4). Together these are perhaps strong support for a southern dispersal, as is indicated by some genetic evidence(Malaspinas et al., 2016). ...
Thesis
This dissertation is an investigation of post-canine tooth root morphology in a global sample of modern humans. Tooth roots are variable in number, shape and orientation, and internal canal form and number do not necessarily covary with external morphology. However, this variation is poorly understood in anthropological and biological contexts. This is, in part, due to the inaccessibility of tooth roots for metric and morphological assessment. Early studies relied on x-rays, which are problematic when visualizing root structures, which are often curved or layered one on top of another. Computed tomography (CT) allows for clear visualization of tooth roots, and has revealed a previously unknown, complex combination of external and internal morphologies. Using CT scans from a global sample of humans (n = 945) a novel phenotype system is developed comprised of five elements: Root presence/absence (E1), canal root presence/absence (E2), canal location (E3), external root morphology (E4), and canal morphology and configuration (E5). Together, these five elements capture the external and internal morphology of the tooth root complex and are used to carry out four objectives: (1) to test and describe patterns of variation and divergence between root and canal number in individual teeth and between populations; (2) to develop a predictive model of tooth root morphology based on canal count and configuration; (3) to identify and define the total tooth root phenotypic set of the human sample; (4) to investigate if and how the total phenotypic set can delineate and define geographic and population structure in our sample. Novel statistical approaches are developed and used to ascertain complex patterning. Results indicate that there are clear differences between patterns of root to canal number both within and between teeth of the maxilla and mandible, and that these patterns are different between populations; that root canal number and orientation are powerful predictors of external root morphology; that the combined phenotype elements capture variation within and between populations; and that the combined phenotype elements can accurately identify and delineate population substructures. These findings are discussed in terms of evolutionary and developmental biology and biomechanics, and population structure and diversity.
... Several layers of genetic, paleoanthropology, and paleoclimatology evidence point to 70-60 ka as the most likely time window for the major colonization of Eurasia by Homo sapiens. For several millennia, however, the human population OoA did not expand much from a demographic perspective, with the divergence between Eastern and Western Eurasian populations inferred not earlier than 45-40 ka from modern DNA data (Soares et al. 2012;Schiffels and Durbin 2014;Pagani et al. 2015Pagani et al. , 2016Malaspinas et al. 2016;Bergström et al. 2020;Choin et al. 2021). We can imagine that, after leaving Africa (Pagani 2019), the ancestors of all non-Africans lived somewhere on the new continent, interbred with Neanderthals (Green et al. 2010), and persisted as a single population for at least 15 thousand years (conservatively, the time between the OoA bottleneck and the split between European and East Asian populations, marking the beginning of a broader expansion) and later diffused from this "population Hub" ultimately colonizing all of Eurasia and further. ...
... Given the relatively simple population tree needed to explain the post-OoA Eurasian population movements using aDNA samples available to date, and benefiting from the basal position of Zlatý Kůň, we tried to add Oceanian populations (using modern Papuans from Skoglund et al. 2015) within the emerging picture to resolve a long-lasting debate on their topological position with respect to East and West Eurasians. Starting from the topologies proposed in Malaspinas et al. (2016) and Choin et al. (2021), we first tried to place Papuans as the most basal branch along with the non-African subtree, allowing for the documented Denisova admixture (Reich et al. 2011;Meyer et al. 2012). We avoided including the sampled Denisova aDNA within the population tree to eliminate attractions from yet uncharacterized, deep splits along the hominin branch (Hajdinjak et al. 2021), and opted for letting qpGraph infer Denisova as a basal split along the archaic human lineage. ...
... Notably, all the acceptable solutions for the placement of Papuans within the broader OoA tree encompass a Denisova contribution and confirm Zlatý Kůňas the most basal human genome among the ones ever found OoA. Taken together with a lower bound of the final settlement of Sahul at 37 ka (the date of the deepest population splits estimated by Malaspinas et al. 2016), it is reasonable to describe Papuans as either an almost even mixture between East Asians and a lineage basal to West and East Asians occurred sometimes between 45 and 38 ka, or as a sister lineage of East Asians with or without a minor basal OoA or xOoA contribution. We here chose to parsimoniously describe Papuans as a simple sister group of Tianyuan, cautioning that this may be just one out of six equifinal possibilities. ...
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The population dynamics that followed the Out of Africa (OoA) expansion and the whereabouts of the early migrants before the differentiation that ultimately led to the formation of Oceanian, West and East Eurasian macropopulations have long been debated. Shedding light on these events may, in turn, provide clues to better understand the cultural evolution in Eurasia between 50 and 35 ka. Here, we analyze Eurasian Paleolithic DNA evidence to provide a comprehensive population model and validate it in light of available material culture. Leveraging on our integrated approach we propose the existence of a Eurasian population Hub, where Homo sapiens lived between the OoA and the broader colonization of Eurasia, which was characterized by multiple events of expansion and local extinction. A major population wave out of Hub, of which Ust'Ishim, Bacho Kiro, and Tianyuan are unadmixed representatives, is broadly associated with Initial Upper Paleolithic lithics and populated West and East Eurasia before or around 45 ka, before getting largely extinct in Europe. In this light, we suggest a parsimonious placement of Oase1 as an individual related to Bacho Kiro who experienced additional Neanderthal introgression. Another expansion, started before 38 ka, is broadly associated with Upper Paleolithic industries and repopulated Europe with sporadic admixtures with the previous wave (GoyetQ116-1) and more systematic ones, whereas moving through Siberia (Yana, Mal'ta). Before these events, we also confirm Zlatý Kůň as the most basal human lineage sequenced to date OoA, potentially representing an earlier wave of expansion out of the Hub.
... Using the normalized Population Branch Statistic (PBSn1) [14], we identified, for Kalenjin and Oromo, respectively, 297 and 352 genes linked to highly differentiated genomic regions (Fig 3; S1 Dataset). We submitted these lists to an enrichment analysis [15] to recover phenotypes or traits showing enriched gene-sets. ...
... For estimating the peaks of genomic differentiation, we used the Population Branch Statistic (PBS) [12], in its standardized version, PBSn1, as described by Malaspinas et al. [14]. This statistic, which is based on the classical F ST statistic, uses allele frequency data to estimate the degree of genetic differentiation specific to a population of interest, or focal population, in relation to two reference populations, generally one closely related to the focal population and another more distantly related [12,13]. ...
... Those combinations were excluded because the Amhara have the highest level of Eurasian ancestry (47.82-54.70%) [76], and spurious results can emerge in PBSn1 when the two reference populations are closer to each other than to the focal population [14]. On the other hand, thanks to this level of mixing, the Amhara themselves act as good controls for Eurasian ancestry. ...
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Since the 1960s, East African athletes, mainly from Kenya and Ethiopia, have dominated long-distance running events in both the male and female categories. Further demographic studies have shown that two ethnic groups are overrepresented among elite endurance runners in each of these countries: the Kalenjin, from Kenya, and the Oromo, from Ethiopia, raising the possibility that this dominance results from genetic or/and cultural factors. However, looking at the life history of these athletes or at loci previously associated with endurance athletic performance, no compelling explanation has emerged. Here, we used a population approach to identify peaks of genetic differentiation for these two ethnicities and compared the list of genes close to these regions with a list, manually curated by us, of genes that have been associated with traits possibly relevant to endurance running in GWAS studies, and found a significant enrichment in both populations (Kalenjin, P = 0.048, and Oromo, P = 1.6x10 ⁻⁵ ). Those traits are mainly related to anthropometry, circulatory and respiratory systems, energy metabolism, and calcium homeostasis. Our results reinforce the notion that endurance running is a systemic activity with a complex genetic architecture, and indicate new candidate genes for future studies. Finally, we argue that a deterministic relationship between genetics and sports must be avoided, as it is both scientifically incorrect and prone to reinforcing population (racial) stereotyping.
... They settled a wide range of environments, from the savannah dry lands in the south to the tropical forests in the north, deep inlands and the coasts. Currently the descendants of this exceptional chapter of human history have among the highest genetic and cultural diversity in the world (Attenborough et al., 2005;Bergstrom et al., 2017;Malaspinas et al., 2016). Within their genetic diversity, almost 3-4% come from an extinct hominin, Denisovan (Reich et al., 2011), which might have settled Sahul before modern humans (Choin et al., 2021;Jacobs et al., 2019). ...
... However, few examples of genetic adaptation are documented. The genomes of Indigenous Australians show signs of natural selection in genes related to thermoregulation, a physiological feature driven by the extreme temperatures in the Australian desert (Malaspinas et al., 2016). In Vanuatu, an archipelago located east of north Australia, genes related to metabolism and pregnancy were found to be under selection (Choin et al., 2021). ...
... In Oceania, the median age of SNPs restricted to the continent at a frequency of 0.25 is 78, 795YBP (IQR: 47,075YBP,Figures 1B,S4,and S5). This median age is older than in other non-African groups, like Europeans (41,079 YBP, IQR: 26,068-72,236 YBP, Figure S4) and East Asians (38,171 YBP, IQR:26,322-70,503 YBP, Figure S4), which coincides with previous reports on the Oceanian genetic divergence from Africa (Brucato et al., 2021;Malaspinas et al., 2016;Pagani et al., 2016). However, as with other continental groups, the vast majority of the Oceanian-specific SNPs appeared between 10,000YBP and 20,000YBP ( Figure S6). ...
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As human populations left Asia to first settle in Oceania around 50,000 years ago, they entered a territory ecologically separated from the Old World for millions of years. We analyzed genomic data of 239 modern Oceanian individuals to detect and date signals of selection specific to this region. Combining both relative and absolute dating approaches, we identified a strong selection pattern between 52,000 and 54,000 years ago in the genomes of descendants of the first settlers of Sahul. This strikingly corresponds to the dates of initial settlement as inferred from archaeological evidence. Loci under selection during this period, some showing enrichment in Denisovan ancestry, overlap genes involved in the immune response and diet, especially based on plants. Pathogens and natural resources, especially from endemic plants, therefore appear to have acted as strong selective pressures on the genomes of the first settlers of Sahul.
... A complicating factor, however, was that Denisovans, early archaic hominins from Siberia [27,31,32] and the Tibetan Plateau [33,34], contributed up to 5% of their ancestry to populations living in Southeast Asia and Australasia island nations [27,32,35]. Because much smaller proportions of Denisovan ancestry were found in mainland Asian populations (0.05%-2%), the deep divergences observed genetically were potentially explained by archaic admixture rather than an earlier dispersal of modern humans [11,[35][36][37][38]. [40] examined the likelihood of a single dispersal model versus a multiple dispersal model by comparing the observed joint frequency spectrum to the expected joint frequency spectrum using fastsimcoal2 (Box 1). They found that accounting for Denisovan admixture led to better support for the single dispersal model, while excluding Denisovan admixture led to better support for the multiple dispersal model [40]. ...
... Because much smaller proportions of Denisovan ancestry were found in mainland Asian populations (0.05%-2%), the deep divergences observed genetically were potentially explained by archaic admixture rather than an earlier dispersal of modern humans [11,[35][36][37][38]. [40] examined the likelihood of a single dispersal model versus a multiple dispersal model by comparing the observed joint frequency spectrum to the expected joint frequency spectrum using fastsimcoal2 (Box 1). They found that accounting for Denisovan admixture led to better support for the single dispersal model, while excluding Denisovan admixture led to better support for the multiple dispersal model [40]. Collectively, these studies showed that after accounting for archaic admixture from Neanderthals and Denisovans, Australasians consistently grouped closely with mainland Asian populations, supporting a single dispersal model. ...
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L.L. Cavalli-Sforza spearheaded early efforts to study the genetic history of humans, recognizing the importance of sampling diverse populations worldwide. He supported research on human evolutionary genetics in Asia, with research on human dispersal into Asia and genetic distances between present-day East Asians in the late 20th century. Since then, great strides have been made in understanding the genetic history of humans in Asia, through large-scale genomic sequencing of present-day humans and targeted sequencing of DNA from ancient humans. In this review, I survey the genetic prehistory of humans in Asia, based on research using sequence data from humans who lived in Asia as early as 45,000 years ago. Genetic studies comparing present-day Australasians and Asians show that they likely derived from a single dispersal out of Africa, rapidly differentiating into three main lineages: one that persists partially in South Asia, one that is primarily found today in Australasia, and one that is widely represented across Siberia, East Asia, and Southeast Asia. Studies of ancient DNA from human remains in Asia dating from as far back as 45,000 years has greatly increased our understanding of the population dynamics leading to the current Asian populations. Based on "Jin L, Underhill PA, Doctor V, Davis RW, Shen P, Cavalli-Sforza LL, Oefner PJ. Distribution of haplotypes from a chromosome 21 region distinguishes multiple prehistoric human migrations. Proc Natl Acad Sci U S A. 1999;96(7):3796-3800”.
... Intriguingly, the Orang Asli Negrito (Jehai sub-tribe) showed a shared genetic drift with ancient genomes from Hoabinhian ancestry (McColl et al., 2018), suggesting that they are genetically closer to the ancestors of Hoabinhian huntergatherers who occupied northern parts of Peninsular Malaysia during the late Pleistocene (Bellwood, 2007). What puzzles us, however, is that the divergence between Eurasian and Australian aborigines (Malaspinas et al., 2016) predates the divergence between Eurasian and Orang Asli Negrito (Yew et al., 2018a), thus complicates the peopling history in Peninsular Malaysia. ...
... (ii) The pre-historical migrations of the Negrito into this landmass remain fragmentary. If the Orang Asli Negrito were postulated to be the direct descendants of the modern human out of Africa and that the divergence time between Australia aborigines and Eurasia occurred 65 kya (Malaspinas et al., 2016;Clarkson et al., 2017), we would then anticipate the divergence time between Orang Asli Negrito and Eurasia to have overlapped with the Australian aborigines if not earlier. However, our inferred time of divergence was younger than the Australia aborigines-Eurasia divergence time. ...
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Southeast Asia (SEA) has one of the longest records of modern human habitation out-of-Africa. Located at the crossroad of the mainland and islands of SEA, Peninsular Malaysia is an important piece of puzzle to the map of peopling and migration history in Asia, a question that is of interest to many anthropologists, archeologists, and population geneticists. This review aims to revisit our understanding to the population genetics of the natives from Peninsular Malaysia and Borneo over the past century based on the chronology of the technology advancement: 1) Anthropological and Physical Characterization; 2) Blood Group Markers; 3) Protein Markers; 4) Mitochondrial and Autosomal DNA Markers; and 5) Whole Genome Analysis. Subsequently some missing gaps of the study are identified. In the later part of this review, challenges of studying the population genetics of natives will be elaborated. Finally, we conclude our review by reiterating the importance of unveiling migration history and genetic diversity of the indigenous populations as a steppingstone towards comprehending disease evolution and etiology.
... A total of~1 M SNPs were retained. We used the scikit-allel package to compute PBSn1 [21] score for each available position with the allele.pbs function with window size = 1, window step = 1 and normed = True. ...
... We computed the normalized version [21] of Population Branch Statistic-PBS [25] to identify putative signs of selection in the Kho, using Punjabi and Yoruba samples from 1000 Genomes Project as reference. We averaged the PBS score over 50-Kb windows and annotated the top results with PBS score based on the confidence percentile cut-off threshold ≥ 99.9% and 99.5%shown as red and blue dash lines in Manhattan plot (Fig. 3, Table S6). ...
... A total of~1 M SNPs were retained. We used the scikit-allel package to compute PBSn1 [21] score for each available position with the allele.pbs function with window size = 1, window step = 1 and normed = True. ...
... We computed the normalized version [21] of Population Branch Statistic-PBS [25] to identify putative signs of selection in the Kho, using Punjabi and Yoruba samples from 1000 Genomes Project as reference. We averaged the PBS score over 50-Kb windows and annotated the top results with PBS score based on the confidence percentile cut-off threshold ≥ 99.9% and 99.5%shown as red and blue dash lines in Manhattan plot (Fig. 3, Table S6). ...
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Northern Pakistan is home to many diverse ethnicities and languages. The region acted as a prime corridor for ancient invasions and population migrations between Western Eurasia and South Asia. Kho, one of the major ethnic groups living in this region, resides in the remote and isolated mountainous region in the Chitral Valley of the Hindu Kush Mountain range. They are culturally and linguistically distinct from the rest of the Pakistani population groups and their genetic ancestry is still unknown. In this study, we generated genome-wide genotype data of ~1 M loci (Illumina WeGene array) for 116 unrelated Kho individuals and carried out comprehensive analyses in the context of worldwide extant and ancient anatomically modern human populations across Eurasia. The results inferred that the Kho can trace a large proportion of their ancestry to the population who migrated south from the Southern Siberian steppes during the second millennium BCE ~110 generations ago. An additional wave of gene flow from a population carrying East Asian ancestry was also identified in the Kho that occurred ~60 generations ago and may possibly be linked to the expansion of the Tibetan Empire during 7th to 9th centuries CE (current era) in the northwestern regions of the Indian sub-continent. We identified several candidate regions suggestive of positive selection in the Kho, that included genes mainly involved in pigmentation, immune responses, muscular development, DNA repair, and tumor suppression.
... Several studies have shown that admixture in humans has often involved multiple admixture pulses from two or more source populations. 8,51,[67][68][69][70][71] We thus estimated the detection performance of F adm and LAD under admixture models that are more complex than the single admixture pulse. We found that the power to detect adaptive admixture is only moderately reduced under a two-pulse admixture model or a constant, continuous admixture model: the true positive rate (TPR) decreases by <11% at a FPR ¼ 5%, relative to the single pulse model (Figures S6A and S6B). ...
... Notably, we found that power is marginally affected when admixture has been recurrent, a feature that is convenient given the difficulty to distinguish between single-pulse, doublepulse, or more complex admixture models from the genetic data. 8,51,[67][68][69][70][71] Furthermore, F adm is more powerful than LAD when selection occurs in the admixed population only and when the divergence time between source populations is low (T div ¼ 500 generations), whereas LAD is more powerful than F adm when source sample sizes are low (i.e., n ¼ 20) and when the true and proxy source populations are distantly related (i.e., F ST R 0.01; Table S4). The latter result is consistent with the known robustness of LAI to cases where the populations used as reference sources are poor proxies of the true source populations. ...
Article
Admixture has been a pervasive phenomenon in human history, extensively shaping the patterns of population genetic diversity. There is increasing evidence to suggest that admixture can also facilitate genetic adaptation to local environments, i.e., admixed populations acquire beneficial mutations from source populations, a process that we refer to as “adaptive admixture.” However, the role of adaptive admixture in human evolution and the power to detect it remain poorly characterized. Here, we use extensive computer simulations to evaluate the power of several neutrality statistics to detect natural selection in the admixed population, assuming multiple admixture scenarios. We show that statistics based on admixture proportions, Fadm and LAD, show high power to detect mutations that are beneficial in the admixed population, whereas other statistics, including iHS and FST, falsely detect neutral mutations that have been selected in the source populations only. By combining Fadm and LAD into a single, powerful statistic, we scanned the genomes of 15 worldwide, admixed populations for signatures of adaptive admixture. We confirm that lactase persistence and resistance to malaria have been under adaptive admixture in West Africans and in Malagasy, North Africans, and South Asians, respectively. Our approach also uncovers other cases of adaptive admixture, including APOL1 in Fulani nomads and PKN2 in East Indonesians, involved in resistance to infection and metabolism, respectively. Collectively, our study provides evidence that adaptive admixture has occurred in human populations whose genetic history is characterized by periods of isolation and spatial expansions resulting in increased gene flow.
... The presence of schizophrenia in indigenous Australians, a population that seems to have been genetically isolated for about 50,000 years [72], could perhaps provide a minimum age for schizophrenia [13]. ...
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Ever since the first detailed descriptions of shamans by pioneering anthropologists of the 19th century, researchers have pondered the similarities between shamanism and schizophrenia. Where some theorists have seen compelling parallels, others have dismissed such similarities as coincidence. This review draws upon the latest knowledge in medical genetics, evolutionary science, religious studies, psychology, anthropology and medical history, in order to catalogue all of the possible links between the institution of shamanism and the medical condition of schizophrenia. Major discrepancies between the two phenomena are also examined. It is concluded that schizophrenia could have possibly originated in Upper Paleolithic shamanism-a constitutional behavioral trait that may have once been adaptive for modern hominids.
... Several rainforest tribal populations scattered throughout the tropical areas of Asia and Oceania are thought to be descended from the original inhabitants of Asia, including the Melanesians, the Aboriginal Australians, and the Negritos currently found in the Andaman Islands, Peninsular Malaysia, and the Philippine Islands (Bae et al. 2017). This hypothesis was first proposed based on morphological features of these people and has received substantial attention in recent years due to mounting evidence from anthropologic and genetic studies (Oppenheimer 2009;Malaspinas et al. 2016;Mondal et al. 2016;Skoglund et al. 2016;Yelmen et al. 2019;Wang et al. 2021). The arrival of Austroasiatic and Austronesian farmers from the north during the Late Paleolithic and Neolithic era forced the early inhabitants into separate areas, which added to the complex demographic history of these peoples (Bellwood 2007;Jinam et al. 2012;Lipson et al. 2014). ...
Article
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Tropical indigenous peoples in Asia (TIA) attract much attention for their unique appearance, while their genetic history and adaptive evolution remain mysteries. We conducted a comprehensive study to characterize the genetic distinction and connection of broad geographical TIAs. Despite the diverse genetic makeup and large inter-area genetic differentiation between the TIA groups, we identified a basal Asian ancestry (bASN) specifically shared by these populations. The bASN ancestry was relatively enriched in ancient Asian human genomes dated as early as ∼50,000 years before the present, and diminished in more recent history. Notably, the bASN ancestry is unlikely to be derived from archaic hominins. Instead, we suggest it may be better modeled as a survived lineage of the initial peopling of Asia. Shared adaptations inherited from the ancient Asian ancestry were detected among the TIA groups (e.g., LIMS1 for hair morphology, and COL24A1 for bone formation), and they are enriched in neurological functions either at an identical locus (e.g., NKAIN3), or different loci in an identical gene (e.g., TENM4). The bASN ancestry could also have formed the substrate of the genetic architecture of the dark pigmentation observed in the TIA peoples. We hypothesize that phenotypic convergence of the dark pigmentation in TIAs could have resulted from parallel (e.g., DDB1/DAK) or genetic convergence driven by admixture (e.g., MTHFD1 and RAD18), new mutations (e.g., STK11), or notably purifying selection (e.g., MC1R). Our results provide new insights into the initial peopling of Asia and an advanced understanding of the phenotypic convergence of the TIA peoples.
... This way poses thinking about origins of stories (Phillips & Bunda, 2018). The story of Yarning as a communication and knowledge sharing process is an ancient one, as Australian Indigenous people have one of the oldest continuing cultures in the world (Malaspinas et al., 2016). A further part of Yarning's story is that it has also been conceptualised as a research method (Bessarab & Ng'andu, 2010). ...
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Internationally within academia settler-colonial processes occur in various ways alongside a growth in the use of research methods conceived with Indigenous knowledges. However, most research environments and practices are built upon and privilege dominant non-Indigenous settler-colonial knowledge systems. It is within this power imbalance and contested space that Yarning research method is being applied and interpreted. Underpinned by an Indigenous Research Paradigm, we employed storying ways to examine researcher experiences of settler-colonialism and the Yarning research method. The story outlines challenges and pitfalls that researchers can fall into and critically examines how researchers can fail to recognise the depth of Indigenous knowledge embedded within the practice. This story is gifted by creating an imagined narrative interview with a character called Settler-Colonisation, whereby we identify a litany of settler-colonial processes impacting Yarning research. Scrutinising the epistemological and methodological practices and processes enacted in academia is imperative for better-informed application of Indigenous research methods and create sustainable research more generally.
... To develop a fully resolved picture of chrY diversity in this region, we sequenced 14 new male samples ( fig. 1 and supplementary table S1, Supplementary Material online) on the Illumina platform, and combined these with 26 chrY sequences from Papua New Guinea (Brucato et al. 2021) and 112 chrY sequences from ISEA (Jacobs et al. 2019) that were not previously analyzed for their chrY diversity. We then combined this new data set with all available chrY sequences from the region, supplemented with samples from a broader geographic and phylogenetic context taken from previously published full chrY studies on neighboring East Asia, Mainland Southeast Asia, and other world regions (Abecasis et al. 2010;Drmanac et al. 2010;Wong et al.2013;Carmi et al. 2014;Ball et al. 2014;Karmin et al. 2015;Bergström et al. 2016;Ilum€ ae et al. 2016;Malaspinas et al. 2016;Mallick et al. 2016;Poznik et al. 2016;Vernot et al. 2016;Zheng-Bradley et al. 2017;Hudjashov et al. 2018;Bergström et al. 2020;Byrska-Bishop 2021 Sequencing, Mapping, and Genotyping All newly generated chrY sequences were generated using the Illumina technology (Illumina, San Diego, CA, USA) on the HiSeq instrument (PCR-free protocol) with 30Â genomewide coverage. We employed a series of filters and sequence masks to limit the data set to high quality variant calls, resulting in 9.7 Mb of complete chrY sequence per sample. ...
Article
Island Southeast Asia (ISEA) and Oceania host one of the world's richest assemblages of human phenotypic, linguistic, and cultural diversity. Despite this, the region's male genetic lineages are globally among the last to remain unresolved. We compiled ∼9.7 Mb of Y chromosome (chrY) sequence from a diverse sample of over 380 men from this region, including 152 first reported here. The granularity of this data set allows us to fully resolve and date the regional chrY phylogeny. This new high-resolution tree confirms two main population bursts: multiple rapid diversifications following the region's initial settlement ∼50 kya, and extensive expansions <6 kya. Notably, ∼40-25 kya the deep rooting local lineages of C-M130, M-P256, and S-B254 show almost no further branching events in ISEA, New Guinea, and Australia, matching a similar pause in diversification seen in maternal mitochondrial DNA lineages. The main local lineages start diversifying ∼25 kya, at the time of the last glacial maximum. This improved chrY topology highlights localized events with important historical implications, including pre-Holocene contact between Mainland and ISEA, potential interactions between Australia and the Papuan world, and a sustained period of diversification following the flooding of the ancient Sunda and Sahul continents as the insular landscape observed today formed. The high-resolution phylogeny of the chrY presented here thus enables a detailed exploration of past isolation, interaction, and change in one of the world's least understood regions.
... Various methods have been developed for inferring demographic histories from the SFS [31][32][33][34] including the program fastsimcoal2, which uses a composite likelihood based framework to robustly infer demographic parameters under complex demographic scenarios [35]. Estimating the SFS requires high-resolution data from multiple individuals, so SFS-based demographic inference was historically limited to species for which large genomic datasets were available [36,37]. However, the emergence of reduced representation sequencing approaches such as restriction site associated DNA (RAD) sequencing [38] has meant that population genomic data can now be generated at reasonable cost for practically any species. ...
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Much debate surrounds the importance of top-down and bottom-up effects in the Southern Ocean, where the harvesting of over two million whales in the mid twentieth century is thought to have produced a massive surplus of Antarctic krill. This excess of krill may have allowed populations of other predators, such as seals and penguins, to increase, a top-down hypothesis known as the ‘krill surplus hypothesis’. However, a lack of pre-whaling population baselines has made it challenging to investigate historical changes in the abundance of the major krill predators in relation to whaling. Therefore, we used reduced representation sequencing and a coalescent-based maximum composite likelihood approach to reconstruct the recent demographic history of the Antarctic fur seal, a pinniped that was hunted to the brink of extinction by 18th and 19th century sealers. In line with the known history of this species, we found support for a demographic model that included a substantial reduction in population size around the time period of sealing. Furthermore, maximum likelihood estimates from this model suggest that the recovered, post-sealing population at South Georgia may have been around two times larger than the pre-sealing population. Our findings lend support to the krill surplus hypothesis and illustrate the potential of genomic approaches to shed light on long-standing questions in population biology.
... We used MSMC2 to estimate changes in effective population sizes (N e ) with the multiple sequentially Markovian coalescent model (Malaspinas et al. 2016, Schiffels andWang 2020), using the PSMC mode with one individual per run. While demographic history can be inferred from a single individual, sufficient sample coverage is necessary to maintain accuracy in analyses (Nadachowska-Brzyska et al. 2016). ...
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Genetic variation is a fundamental component of biodiversity, and studying population structure, gene flow and demographic history can help guide conservation strategies for many species. Like other aerial insectivores, the purple martin Progne subis is in decline, and yet their genetic background remains largely unknown. To address this knowledge gap, we assessed population structure in the nominate eastern subspecies (P. s. subis) with relation to natal dispersal and examined historical genetic patterns in all three subspecies (P. s. subis, P. s. arboricola, P. s. hesperia) across their North American breeding range by estimating effective population sizes over time. We used next‐generation sequencing strategies for genomic analyses, integrating whole‐genome resequencing data with continent‐wide band encounter records to examine natal dispersal. We documented population structure across P. s. subis, with the highest differentiation between the northern (Alberta) and more southern colonies and following patterns of isolation‐by‐distance. Consistent with spatial patterns of genetic differentiation, we also found greater longitudinal than latitudinal natal dispersal distances, signifying potential latitudinal constraints on gene flow. Earlier contractions in effective population sizes in the western P. s. arboricola and P. s. hesperia compared to the eastern P. s. subis subspecies suggest these subspecies originated from two different glacial refugia. Together, these findings support latitudinal distinction in P. s. subis, and elucidate the origin of subspecies differentiation, highlighting the importance of conserving populations across the range to maximize genetic diversity and adaptive potential in the purple martin.
... This proposal will clearly require more extensive investigation. The Indigenous Australians are part of this lineage, and their settlement history has now been elaborated in some detail (Malaspinas et al. 2016). Much the same can be said for PNG (Bergström et al. 2017), with the exception of the north coast settlements and offshore islands, which have extensive AN admixture, as has long been known. ...
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The Austronesian Diaspora is a 5,000-year account of how a small group of Taiwanese farmers expanded to occupy territories reaching halfway around the world. Reconstructing their detailed history has spawned many academic contests across many disciplines. An outline orthodox version has eventually emerged but still leaves many unanswered questions. The remarkable power of whole-genome technology has now been applied to people across the entire region. This review gives an account of this era of genetic investigation and discusses its many achievements, including revelation in detail of many unexpected patterns of population movement and the significance of this information for medical genetics.
... S3, 496 Supplementary Material online). We generated a consensus genome for each sample 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 19 520 from the Chinese wolf, IW01, Tibetan wolf, and dhole into 250kb, 500kb and 1,000kb 521 windows across autosomes and constructed phylogenies for each window using 543 We used the multiple sequential Markovian coalescent (MSMC2) model to infer the 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 available tools from the MSMC-tool package (https://github.com/stschiff/msmc-tools). 549 We ran MSMC for each pair of genomes using default settings and the time when the 550 relative cross coalescent rate (RCCR) was dropped to 50% as an approximate estimate 551 of the splitting time (Malaspinas, et al. 2016). For each calculation, four haplotypes 552 were analyzed, and estimations were scaled using a generation time (g) of 3 years and and dog and other wolves. ...
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The gray wolf (Canis lupus) is among the few large carnivores that survived the Late Pleistocene megafaunal extinctions. Thanks to their complex history of admixture and extensive geographic range, the number of gray wolf subspecies and their phylogenetic relationships remain poorly understood. Here, we perform whole-genome sequencing of a gray wolf collected from peninsular India that was phenotypically distinct from gray wolves outside India. Genomic analyses reveal that the Indian gray wolf is an evolutionarily distinct lineage that diverged from other extant gray wolf lineages ∼110 thousand years ago. Demographic analyses suggest that the Indian wolf population declined continuously decline since separating from other gray wolves and, today, has exceptionally low genetic diversity. We also find evidence for pervasive and mosaic gene flow between the Indian wolf and African canids including African wolf, Ethiopian wolf, and African wild dog despite their current geographical separation. Our results support the hypothesis that the Indian subcontinent was a Pleistocene refugium and center of diversification and further highlight the complex history of gene flow that characterized the evolution of gray wolves.
... The out-of-Africa event, during which a relatively small group of anatomically modern humans spread from East Africa into Eurasia [1], was a defining moment in the evolution of modern humans. Although paleoanthropology has detected several older waves of Middle Pleistocene migrations from Africa to Eurasia [2], genetic studies show that contemporary non-sub-Saharans are descendants of an ancestral population that spread from Africa only about 60 ka (thousands of years ago) [3]. Leaving aside the long-term isolation of Khoisan populations in southern Africa and of the Pygmies in the tropical rain forests of central Africa, the out-of-Africa event is nowadays considered to be the most significant restriction of gene flow between two groups of anatomically modern humans: the sub-Saharans and non-sub-Saharans had been separated by the Sahara Desert throughout most of prehistory. ...
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African history has been significantly influenced by the Sahara, which has represented a barrier for migrations of all living beings, including humans. Major exceptions were the gene flow events that took place between North African and sub-Saharan populations during the so-called African Humid Periods, especially in the Early Holocene (11.5 to 5.5 thousand years ago), and more recently in connection with trans-Saharan commercial routes. In this study, we describe mitochondrial DNA (mtDNA) diversity of human populations from both sides of the Sahara Desert, i.e., both from North Africa and the Sahel/Savannah belt. The final dataset of 7213 mtDNA sequences from 134 African populations encompasses 470 newly collected and 6743 previously published samples, which were analyzed using descriptive methods and Bayesian statistics. We completely sequenced 26 mtDNAs from sub-Saharan samples belonging to the Eurasian haplogroup N1. Analyses of these N1 mitogenomes revealed their possible routes to the Sahel, mostly via Bab el-Mandab. Our results indicate that maternal gene flow must have been important in this circum-Saharan space, not only within North Africa and the Sahel/Savannah belt but also between these two regions.
... This could include domestic pigs, where episodic admixture of pig lineages from different geographic regions may have occurred, as indicated by the mtDNA signatures of present-day Philippine pig populations. Although some suggest advanced navigation techniques would be needed to connect distant islands (Arenas et al., 2020), archaic fossil suggest that humans have started navigating around 60,000 years ago (Stringer, 2000;Balme, 2013;Malaspinas et al., 2016;Norman et al., 2018;Arenas et al., 2020) that may have indeed initiated these processes. This hypothesis was further supported by contemporary mtDNA studies as earlier revealed the expansion of modern humans that has occurred through long-distance dispersal events (Arenas et al., 2020). ...
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The Philippines is a mega-diverse country that lies at the crossroads of past human migrations in the Asia-Pacific region and is believed to have never been connected to the Asian continent, even during the major sea-level subsidence of the Quaternary. As a result, the history of pig dispersal in the Philippines remains controversial, due to limited molecular studies and absence of archaeological evidence of pig domestication. This study provides the first comprehensive analysis of 184 complete mitochondrial DNA D-loop region from Philippine pigs to elucidate their early dispersal history by performing a phylogenetic comparison with wild boars and domestic pigs worldwide. The results showed a demographic signal of the ancestry of Philippine pigs that had a close genetic relationship with those from the mainland Southeast Asia and Northeast Asia, suggesting gene flow that may have resulted from human migration and trade. Here we have suggested two possible dispersal routes. One parallels the Neolithic expansion in Island Southeast Asia and Oceania via Northeast Asia, the other from the mainland Southeast Asia, into Palawan and Sulu Archipelago as early as prehistoric times via the Sundaic Region. Despite geographic barriers to migration, numerous genetic lineages have persisted across the Philippine islands, even justifying the recognition of a Philippine Lanyu subclade. The prehistoric population history suggests a demographic expansion that coincided with the interglacial periods of the Pleistocene and may have spread from the southern regions into the eastern and central regions of the Philippines. The intriguing signal of discrepancy discovered between the ancestral pattern and distribution range of the numerous endemic Philippine wild pigs opens a challenging new approach to illuminate complexity among these animals. Our study has contributed significantly towards completing the sparse molecular studies on Philippine pigs, an essential for creating win-win conservation measures.
... MSMC (Schiffels and Durbin 2014) version 2 (MSMC2: https://github.com/stschiff/msmc2; Schiffels and Wang 2020;Malaspinas et al. 2016) was used to estimate changes in N e as well as the divergence time of subspecies. During the MSMC/MSMC2 analysis, we performed estimations using phased haplotype sequences as input. ...
Article
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For more than 100 years, house mice (Mus musculus) have been used as a key animal model in biomedical research. House mice are genetically diverse, yet their genetic background at the global level has not been fully understood. Previous studies have suggested that they originated in South Asia and diverged into three major subspecies, almost simultaneously, approximately 110,000-500,000 years ago; however, they have spread across the world with the migration of modern humans in prehistoric and historic times (∼10,000 years ago to the present day) and have undergone secondary contact, which has complicated the genetic landscape of wild house mice. In this study, we sequenced the whole-genome sequences of 98 wild house mice collected from Eurasia, particularly East Asia, Southeast Asia, and South Asia. Although wild house mice were found to consist of three major genetic groups corresponding to the three major subspecies, individuals representing admixtures between subspecies were more prevalent in East Asia than has been previously recognized. Furthermore, several samples exhibited an incongruent pattern of genealogies between mitochondrial and autosomal genomes. Using samples that likely retained the original genetic components of subspecies with the least admixture, we estimated the pattern and timing of divergence among the subspecies. The estimated divergence time of the three subspecies was 187,000-226,000 years ago. These results will help us to understand the genetic diversity of wild mice on a global scale, and the findings will be particularly useful in future biomedical and evolutionary studies involving laboratory mice established from such wild mice.
... To infer the demographic history of the populations, we used the Markovian coalescent MSMC2 (v2.1.1) 101 . Coalescence analyses use a backwardin-time algorithm, starting from the current generation and randomly building back the lineage of genomes. ...
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The fungus Blumeria graminis f. sp. tritici causes wheat powdery mildew disease. Here, we study its spread and evolution by analyzing a global sample of 172 mildew genomes. Our analyses show that B.g. tritici emerged in the Fertile Crescent during wheat domestication. After it spread throughout Eurasia, colonization brought it to America, where it hybridized with unknown grass mildew species. Recent trade brought USA strains to Japan, and European strains to China. In both places, they hybridized with local ancestral strains. Thus, although mildew spreads by wind regionally, our results indicate that humans drove its global spread throughout history and that mildew rapidly evolved through hybridization.
... Specifically, we divided the SNP data set in 100 blocks with an equal number of SNPs, from which we created 100 bootstrapped-SFS and performed 50 independent runs of the software for each, with 250,000 simulations. Due to computational constraints we reduced the number of EM cycles to 10, an approach used previously and characterized as conservative (Malaspinas et al., 2016). The highest likelihood run for each bootstrapped replicate was used to calculate the 95% CI of the inferred parameters. ...
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The study of insular populations was key in the development of evolutionary theory. The successful colonisation of an island depends on the geographic context, and specific characteristics of the organism and the island, but also on stochastic processes. As a result, apparently identical islands may harbour populations with contrasting histories. Here, we use whole genome sequences of 65 barn owls to investigate the patterns of inbreeding and genetic diversity of insular populations in the eastern Mediterranean Sea. We focus on Crete and Cyprus, islands with similar size, climate and distance to mainland, that provide natural replicates for a comparative analysis of the impacts of microevolutionary processes on isolated populations. We show that barn owl populations from each island have a separate origin, Crete being genetically more similar to other Greek islands and mainland Greece, and Cyprus more similar to the Levant. Further, our data show that their respective demographic histories following colonisation were also distinct. On the one hand, Crete harbours a small population and maintains very low levels of gene flow with neighbouring populations. This has resulted in low genetic diversity, strong genetic drift, increased relatedness in the population and remote inbreeding. Cyprus, on the other hand, appears to maintain enough gene flow with the mainland to avoid such an outcome. Our work provides a comparative population genomic analysis of the effects of neutral processes on a classical island‐mainland model system. It provides empirical evidence for the role of stochastic processes in determining the fate of diverging isolated populations.
... Since the original Cambridge Reference Sequence was published 40 years ago 9 , the field of human mtDNA phylogenetics has increasingly shown that non-African lineages are a subset, or small clade nested within a much older and hyper-diverse African phylogeny 6,8,10,11 . That same pattern of ancient African origins and subsequent Out-of-Africa (OOA) expansion some 70-50 thousand years ago (kya) has since been corroborated by Y-DNA 12,13 , autosomal DNA [14][15][16] , patterns of archaic introgression [17][18][19] , and African fossils [20][21][22] . Although the uniparental mtDNA and Y-DNA loci have a coalescence time of 250-150 kya, archaeological, nuclear, and genome-wide datasets suggest the possibility of a much older (500-300 kya) origin for modern humans [23][24][25] . ...
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Archaeological and genomic evidence suggest that modern Homo sapiens have roamed the planet for some 300–500 thousand years. In contrast, global human mitochondrial (mtDNA) diversity coalesces to one African female ancestor (“Mitochondrial Eve”) some 145 thousand years ago, owing to the ¼ gene pool size of our matrilineally inherited haploid genome. Therefore, most of human prehistory was spent in Africa where early ancestors of Southern African Khoisan and Central African rainforest hunter-gatherers (RFHGs) segregated into smaller groups. Their subdivisions followed climatic oscillations, new modes of subsistence, local adaptations, and cultural-linguistic differences, all prior to their exodus out of Africa. Seven African mtDNA haplogroups (L0–L6) traditionally captured this ancient structure—these L haplogroups have formed the backbone of the mtDNA tree for nearly two decades. Here we describe L7, an eighth haplogroup that we estimate to be ~ 100 thousand years old and which has been previously misclassified in the literature. In addition, L7 has a phylogenetic sublineage L7a*, the oldest singleton branch in the human mtDNA tree (~ 80 thousand years). We found that L7 and its sister group L5 are both low-frequency relics centered around East Africa, but in different populations (L7: Sandawe; L5: Mbuti). Although three small subclades of African foragers hint at the population origins of L5'7, the majority of subclades are divided into Afro-Asiatic and eastern Bantu groups, indicative of more recent admixture. A regular re-estimation of the entire mtDNA haplotype tree is needed to ensure correct cladistic placement of new samples in the future.
... During the Last Glaciation until ca. 11,700 cal yr BP, the Gulf of Carpentaria was a freshwater lake within a land bridge connecting Australia to New Guinea that is considered to have played a central role in the subsequent dispersal of people throughout Australia (Malaspinas et al. 2016;McConvell 1996). Specifically, the effect of the breaching of the Arafura Sill by sea-level rise allowed ocean water in 11,700 cal yr BP and the attainment of full marine conditions by approximately 10,000 cal yr BP (Sloss et al. 2018). ...
... During the Last Glaciation until ca. 11,700 cal yr BP, the Gulf of Carpentaria was a freshwater lake within a land bridge connecting Australia to New Guinea that is considered to have played a central role in the subsequent dispersal of people throughout Australia (Malaspinas et al. 2016;McConvell 1996). Specifically, the effect of the breaching of the Arafura Sill by sea-level rise allowed ocean water in 11,700 cal yr BP and the attainment of full marine conditions by approximately 10,000 cal yr BP (Sloss et al. 2018). ...
... The Population Branching Statistic (PBS), which harnesses the differences in pairwise F st values between three populations, was estimated with the function allel.pbs of the scikit-allel python package (https:// zenodo.org/badge/latestdoi/7890/cggh/scikit-allel) using a window_size of 1 and setting the normed option as True, which normalised the PBS as in [96]. We focused on differences between Southern (Abruzzo, Calabria, East Sicily, West Sicily, Sicily, Apulia) and Northern Italy (Lombardy, Tuscany) using the Han Chinese in Beijing (CHB) population as an outgroup. ...
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Southern Italy was characterised by a complex prehistory that started with different Palaeolithic cultures, later followed by the Neolithization and the demic dispersal from the Pontic-Caspian Steppe during the Bronze Age. Archaeological and historical evidences point to a link between Southern Italians and the Balkans still present in modern times. To shed light on these dynamics, we analysed around 700 South Mediterranean genomes combined with informative ancient DNAs. Our findings revealed high affinities of South-Eastern Italians with modern Eastern Peloponnesians, and a closer affinity of ancient Greek genomes with those from specific regions of South Italy than modern Greek genomes. The higher similarity could be associated with a Bronze Age component ultimately originating from the Caucasus with high Iranian and Anatolian Neolithic ancestries. Furthermore, extremely differentiated allele frequencies among Northern and Southern Italy revealed putatively adapted SNPs in genes involved in alcohol metabolism, nevi features and immunological traits.
... MBE scenarios above. This procedure has been defined as conservative (Malaspinas et al. 2016), and is expected to produce quite large CIs. We accepted this trade-off as our main goal was to determine the best demographic topology, accepting uncertainty on specific parameter values. ...
Article
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The combined actions of climatic variations and landscape barriers shape the history of natural populations. When organisms follow their shifting niches, obstacles in the landscape can lead to the splitting of populations, on which evolution will then act independently. When two such populations are reunited, secondary contact occurs in a broad range of admixture patterns, from narrow hybrid zones to the complete dissolution of lineages. A previous study suggested that barn owls colonized the Western Palearctic after the last glaciation in a ring-like fashion around the Mediterranean Sea, and conjectured an admixture zone in the Balkans. Here, we take advantage of whole-genome sequences of 94 individuals across the Western Palearctic to reveal the complex history of the species in the region using observational and modeling approaches. Even though our results confirm that two distinct lineages colonized the region, one in Europe and one in the Levant, they suggest that it predates the last glaciation and identify a secondary contact zone between the two in Anatolia. We also show that barn owls re-colonized Europe after the glaciation from two distinct glacial refugia: a previously identified western one in Iberia and a new eastern one in Italy. Both glacial lineages now communicate via eastern Europe, in a wide and permeable contact zone. This complex history of populations enlightens the taxonomy of Tyto alba in the region, highlights the key role played by mountain ranges and large water bodies as barriers and illustrates the power of population genomics in uncovering intricate demographic patterns.
... We estimated the maximum likelihood values for scenarios I, II, and III, independently, after performing 1,000,000 simulations, 65 conditional maximization cycles, and 100 optimization runs starting from random initial conditions. We used approaches described in Choin et al. (2021) and Malaspinas et al. (2016) to optimize the fit between the expected and observed SFS (supplementary fig. S31, Supplementary Material online). ...
... MSMC, l'extension de PSMC (Schiffels and Durbin 2014), utilise le temps de la première coalescence entre n individus, il a besoin de données phasées.Ces méthodes sont gourmandes en calcul (à ce jour, MSMC ne peut pas déduire l'histoire démographique de plus de 10 individus) et regroupent la diversité sur des fenêtres de 100 pb, supposées former un seul locus à deux états, hétérozygote ou homozygote. Le MSMC2 (Malaspinas et al. 2016) permet d'utiliser l'information portée par plus individus en mesurant l'IICR entre chaque paires de génome haploïde. ...
Thesis
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L'impact des activités industrielles humaines conduit à une érosion importante de la biodiversité. Cependant, 94% des espèces décrites ne possèdent pas de statut de conservation, pourtant indispensable à la mise en place de politiques de conservation. En effet, les méthodes utilisées pour attribuer ces statuts sont généralement qualitatives et ne peuvent s’appliquer de manière rigoureuse à l’ensemble des espèces. Nous avons proposé une méthodologie quantitative utilisant les alignements multiples de génomes échantillonnés dans une population donnée pour en inférer l’histoire démographique récente, détectant notamment les changements soudains de taille de population. Nous avons utilisé à la fois l'information issue des polymorphismes, résumée par leur spectre de fréquence, et celle issue de leur liaison génétique, résumée par la distribution des longueurs de segments d’ADN non recombinés, ou compatibles avec une seule généalogie. Nous avons démontré que ces deux sources d’informations n’étaient pas affectées de la même manière par les différents paramètres du scénario démographique considéré. Il est donc possible de gagner en précision en combinant ces deux informations, aussi bien pour sélectionner un scénario que pour en inférer les paramètres. Nous nous sommes également intéressés à un modèle d’évolution moléculaire plus général que le coalescent standard autorisant les multifurcations dans les généalogies et avons démontré que l’utilisation de ce modèle permettait d’expliquer une plus grande partie de la diversité observée.
... We estimated the maximum likelihood values for scenarios I, II, and III, independently, after performing 1,000,000 simulations, 65 conditional maximization cycles, and 100 optimization runs starting from random initial conditions. We used approaches described in Choin et al. (2021) and Malaspinas et al. (2016) to optimize the fit between the expected and observed SFS (supplementary fig. S31, Supplementary Material online). ...
Article
Domestic sheep and their wild relatives harbor substantial genetic variants that can form the backbone of molecular breeding, but their genome landscapes remain understudied. Here, we present a comprehensive genome resource for wild ovine species, landraces and improved breeds of domestic sheep, comprising high-coverage (∼16.10×) whole-genomes of 810 samples from 7 wild species and 158 diverse domestic populations. We detected, in total, ∼121.2 million single nucleotide polymorphisms (SNPs), ∼61 million of which are novel. Some display significant (P < 0.001) differences in frequency between wild and domestic species, or are private to continent-wide or individual sheep populations. Retained or introgressed wild gene variants in domestic populations have contributed to local adaptation, such as the variation in the HBB associated with plateau adaptation. We identified novel and previously reported targets of selection on morphological and agronomic traits such as stature, horn, tail configuration and wool fineness. We explored the genetic basis of wool fineness and unveiled a novel mutation (chr25: T7068586C) in the 3'-UTR of IRF2BP2 as plausible causal variant for fleece fiber diameter. We reconstructed pre-historical migrations from the Near Eastern domestication center to South-and-Southeast Asia, and found two main waves of migrations across the Eurasian Steppe and the Iranian Plateau in the Early and Late Bronze Ages. Our findings refine our understanding of genome variation as shaped by continental migrations, introgression, adaptation and selection of sheep.
... The first two issues were addressed by another method known as Multiple Sequentially Markovian Coalescent (MSMC; Schiffels and Durbin, 2014) and its successor MSMC2 (Malaspinas et al., 2016;Schiffels and Wang, 2020) which use transitions based on SMC'. MSMC can analyze more than a pair of haplotypes, but only tracks the first coalescence time between any pair of haplotypes in the sample. ...
Thesis
Genetic sequences carry a wealth of information. Scientists and statisticians have utilized genetic variation data to answer a wide range of questions in evolutionary biology and epidemiology. With the advent of high throughput sequencing, the availability of genetic sequence data has exploded this century. While the unprecedented amount of genetic data available presents an opportunity to garner a deeper understanding about viruses and humans, making use of large volumes of genetic data is still a challenging problem. In what is to follow, we present three methods that tackle various problems analyzing genetic variation data. First, we introduce the framework known as the sequentially Markov coalescent (SMC), which enables likelihood based inference using hidden Markov models (HMMs) where the latent variables represent genealogies. While genealogies are continuous, HMMs are discrete, requiring SMC based methods to discretize genealogies. This discretization often leads to biased and noisy estimates of the population size history. We introduce a method that avoids the need for discretization leading to Bayesian and frequentist inference procedures that are faster and less biased than its predecessors. Additionally, while coalescent HMMs based on SMC can be decoded in linear time, there does not yet exist a linear time EM algorithm for coalescent HMMs based on SMC', the more accurate approximation. We present a linear time EM algorithm based on SMC'. Advantages of this method include increased accuracy, computation time, uncertainty quantification, and ability to incorporate regularization. Lastly, we present a new approach for estimating transmission and recovery rates of viruses using genetic sequence data. With the outbreak of the SARS-CoV-2, there are millions of genomic sequences available to analyze, but few methods to exploit the information contained in these sequences. By integrating recent advances in Bayesian inference and differentiable programming with phylodynamics, we provide a method capable of estimating transmission, recovery, and sampling of pathogens using thousands of sequences. We apply our method to SARS-CoV-2 data and find that our estimates of the effective reproductive number closely match other estimates from methods based on public health data.
... To maximize the SNP discovery and phasing power, we used approximately 900 complete genomes in a multi-sample calling pipeline. In addition to the newly generated genomes, these included complete genome sequences from SGDP 12 and IGDP 6 projects, Malaspinas et al., 13 Vernot et al., 14 Lan et al., 15 and the HiSeqX Diversity Cohort of Polaris project (web resources) as well as approximately 100 unpublished genome sequences from Estonia and Papua. SNP calling was performed on the combined dataset and published genomes were analyzed from raw reads exactly as they were for the new sequence data. ...
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Lack of diversity in human genomics limits our understanding of the genetic underpinnings of complex traits, hinders precision medicine, and contributes to health disparities. To map genetic effects on gene regulation in the underrepresented Indonesian population, we have integrated genotype, gene expression, and CpG methylation data from 115 participants across three island populations that capture the major sources of genomic diversity in the region. In a comparison with European datasets, we identify eQTLs shared between Indonesia and Europe as well as population-specific eQTLs that exhibit differences in allele frequencies and/or overall expression levels between populations. By combining local ancestry and archaic introgression inference with eQTLs and methylQTLs, we identify regulatory loci driven by modern Papuan ancestry as well as introgressed Denisovan and Neanderthal variation. GWAS colocalization connects QTLs detected here to hematological traits, and further comparison with European datasets reflects the poor overall transferability of GWAS statistics across diverse populations. Our findings illustrate how population-specific genetic architecture, local ancestry, and archaic introgression drive variation in gene regulation across genetically distinct and in admixed populations and highlight the need for performing association studies on non-European populations.
... After we selected 8,053 references from our 90 MYORIGINS v3 populations (Table 2), we needed to hierarchically group them into more inclusive super-populations for chromosome painting (see Overview). We used several methods to generate a putative population tree of human life: TreeMix [63], Speedymix (e.g., Appendix A), hierarchical clustering on pairwise "# , and scientific literature [63][64][65][66][67][68]. The super-population groupings are shown in Fig. 7. ...
Technical Report
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FamilyTreeDNA team is excited to introduce MYORIGINS V3, our new tool for estimating population ancestry. Population ancestry is the proportion of DNA you have inherited from each ancestral population. Depending upon how much admixture occurred between your ancestors, you may have inherited DNA from one or perhaps many populations. We have updated many aspects of our pipeline, including: (1) An increase in number of reference populations from 24 to 90, (2) Improvements in precision and accuracy using our newest methodological advancements, (3) A chromosome painting: you may learn the chromosomal location of each population segment; this information may be genealogically valuable.
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Recent research on the phylogeny of Neanderthals recognises a division within Neanderthal groups around 150ka suggesting a population turnover is likely to have occurred in the Caucasus. For instance, Neanderthal remains dated ca. 100ka associated with fully fledged Levallois lithic industry were con-firmed in the Azokh 1 Cave, at the Lesser Caucasus. This exciting finding, however, raises the questions of whether the Neanderthals impacted on the Southern Caspian Corridor (SCC), which is a geo-ecologi-cal continuum of the Caucasus. What role did SSC play in the world of hominin expansion?In his expedition to Iran during 1960s, McBurney considered SCC provided the closest and fastest route connecting Europe and Caucasus to the Central Asia and Siberia and any hominin movement from the west might be expected to pass this region en route to the east. In his excavation at Ke’Aram Cave located in SCC he documented Middle Palaeolithic )MP( artefacts reminiscent of the Zagros Mousterian which are seen to be closely related to the Teshik Tash Cave in Central Asia. McBurney’s conclusion allows this research to hypothesize that the SCC, with the dual role of biogeographical corridor of expansion and habitat, witnessed a series of human evolutionary events that occurred at least in the Marine Isotope Stages (MIS) 5 and 4. It aims to go further to suggest that SCC as a potential place of admixture of Ne-anderthals and Anatomically Modern Humans. The exceptional physiogeographic condition of the SCC provided a milder climatic condition making this region highly attractive as a glacial refugium during the cold episodes of MIS 5 and 4 for different hominins. Thereby this research also hypothesizes that con-temporaneous MP assemblages from western- and eastern-most areas of the corridor represent a high degree of cultural affinity.For testing these hypotheses, I conducted a survey on the unknown areas of the southern Caspian Sea shore, especially south-eastern parts. This survey led to the discovery of several Palaeolithic sites, includ-ing Kiyasar 1 Rockshelter. I also re-analysed the lithic assemblage from KeAram Cave. The location of the newly discovered Palaeolithic sites together with the techno-typological analysis of the lithic assem-blages revealed a different settlement pattern and lithic techno-complex than what is known from the Palaeolithic period in other parts of the Iranian Plateau.In the second step, I compared lithics from SCC to the data from Azokh 1 cave in the Lesser Caucasus as western- and from Teshik Tash cave as eastern-most site of the SCC using chaîne opératoire as well as attribute analytical methods. All lithics have been carefully compared to the Zagros MP assemblages, where stratified Zagros Mousterian artefacts are associated with the Neanderthal remains, to trace any possible cultural exchange between these sites. No affinities to the Zagros Mousterian, have been ob-served in these assemblages.For the third step of the project, in 2019, I excavated Sorheh Rockshelter located in the Alborz Moun-tains. Sorheh is located at the elevation of 1904 asl, in an unknown region for the Palaeolithic research. Five charcoal samples from Sorheh were 14C dated between 24 to 39 kya cal. BP. Despite of the time span, the lithic industry has no affinity to the yet-known Upper Palaeolithic (UP) cultures from the Iranian Plateau. The most significant point of the lithics from Sorheh is the strong use of Levallois technology. Preliminary inter-regional comparisons bear no resemblances to the MP of the Zagros and the Iranian Central Plateau sites, but more affinities to the Caucasus. More data are needed from Sorheh to under-stand the nature of the deeper archaeological layers and find out why the Levallois technology persisted until so late, at the time that in other regions of the Iranian Plateau, well-developed bladelet industry of the UP had been already developed.The new data from survey in south-eastern SCC and excavation in Sorheh Rockshelter in the Alborz Mountains, demonstrate the complex picture of human settlement dynamics in one of the strategic re-gions in the Iranian Plateau. Continuing research in Sorheh and the promising sites of the SCC will make it possible to determine its role in the expansion of hominins from Europe towards Central Asia and their possible admixture in this refugium.
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Southeast Asia comprises 11 countries that span mainland Asia across to numerous islands that stretch from the Andaman Sea to the South China Sea and Indian Ocean. This region harbors an impressive diversity of history, culture, religion and biology. Indigenous people of Malaysia display substantial phenotypic, linguistic, and anthropological diversity. Despite this remarkable diversity which has been documented for centuries, the genetic history and structure of indigenous Malaysians remain under-studied. To have a better understanding about the genetic history of these people, especially Malaysian Negritos, we sequenced whole genomes of 15 individuals belonging to five indigenous groups from Peninsular Malaysia and one from North Borneo to high coverage (30X). Our results demonstrate that indigenous populations of Malaysia are genetically close to East Asian populations. We show that present-day Malaysian Negritos can be modeled as an admixture of ancient Hoabinhian hunter-gatherers and Neolithic farmers. We observe gene flow from South Asian populations into the Malaysian indigenous groups, but not into Dusun of North Borneo. Our study proposes that Malaysian indigenous people originated from at least three distinct ancestral populations related to the Hoabinhian hunter-gatherers, Neolithic farmers and Austronesian speakers.
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Behavioral genetics in dogs has focused on modern breeds, which are isolated subgroups with distinctive physical and, purportedly, behavioral characteristics. We interrogated breed stereotypes by surveying owners of 18,385 purebred and mixed-breed dogs and genotyping 2155 dogs. Most behavioral traits are heritable [heritability (h2) > 25%], and admixture patterns in mixed-breed dogs reveal breed propensities. Breed explains just 9% of behavioral variation in individuals. Genome-wide association analyses identify 11 loci that are significantly associated with behavior, and characteristic breed behaviors exhibit genetic complexity. Behavioral loci are not unusually differentiated in breeds, but breed propensities align, albeit weakly, with ancestral function. We propose that behaviors perceived as characteristic of modern breeds derive from thousands of years of polygenic adaptation that predates breed formation, with modern breeds distinguished primarily by aesthetic traits.
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The precise genetic origins of the first Neolithic farming populations in Europe and Southwest Asia, as well as the processes and the timing of their differentiation, remain largely unknown. Demogenomic modeling of high-quality ancient genomes reveals that the early farmers of Anatolia and Europe emerged from a multiphase mixing of a Southwest Asian population with a strongly bottlenecked western hunter-gatherer population after the last glacial maximum. Moreover, the ancestors of the first farmers of Europe and Anatolia went through a period of extreme genetic drift during their westward range expansion, contributing highly to their genetic distinctiveness. This modeling elucidates the demographic processes at the root of the Neolithic transition and leads to a spatial interpretation of the population history of Southwest Asia and Europe during the late Pleistocene and early Holocene.
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The Pleistocene archaeological record of mainland Southeast Asia (MSEA) is difficult to interpret, due to a sparsity of dated sites and a lithic record that is ill-suited to typological analysis. These challenges are compounded by the poorly constrained effects of tropical environments upon the deposition, preservation and degradation of archaeological cave sediments. These uncertainties restrict the interpretative potential of archaeological investigations, but the development of a rigorous, geoarchaeological framework of interpretation that is tailored to tropical cave sites offers an opportunity to improve research outcomes in MSEA and in tropical zones worldwide. Con Moong Cave (henceforth CMC), a Pleistocene archaeological site in North Vietnam, provided a small-scale example with which to explore the effects of tropical conditions upon archaeological site formation processes, and the potential of micro-geoarchaeological methods to overcome the difficulties of site interpretation in tropical zones. Research at CMC produced a depositional history for the site that revealed a correlation between sedimentation, the intensity of human occupation and changes in regional precipitation, as recognised in speleothem records in the published literature. Mineral suites from CMC’s guano deposits did not conform to established models of guano-driven diagenetic change and suggested that fluctuating hydrological conditions had led to diachronous episodes of mineral authigenesis. A shortage of reference data relevant to these processes meant it was not possible to conclusively relate these results to sedimentary palaeoenvironments or to understand their effects on assemblage taphonomy. Geo-ethnoarchaeological experiments were conducted to generate such a dataset, to enable hypothesis testing of the models of environmental changes at CMC and provide an assessment of the effects of tropical climates on sediment diagenesis.
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With a growing number of available de novo sequenced genomes, protocols for their applications to population genetics will benefit our understanding of the human genome. Here we detail analytic steps to apply an example de novo reference genome to map and detect variants of short-read sequences from corresponding populations and to discover variants of disease-relevant genes. Using this protocol, we can improve variant discovery, better investigate population-specific genome properties, and evaluate the potential of sequenced genomes in medical studies. For complete details on the use and execution of this protocol, please refer to Lou et al. (2022).
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Archaeologists and anthropologists have long been interested in the study of past human interaction. In the Indo-Pacific, research has focused on the age and processes by which islands were settled and the role that intermediary communities played in these histories. Torres Strait, on Australia’s northern border, represents one such frontier zone. For millennia this 48,000 km2 area (containing at least 274 islands) separated predominately horticultural and pottery-using Melanesians and hunter-gatherer Australians, a contrast considered by some to be ‘starker and more perplexingly than anywhere else in the world’ (Walker 1972:405). Mirroring archaeological explanations and theoretical interests elsewhere, Coral Sea chronicles have transitioned between those prioritising large-scale migration to narratives of entanglement on the periphery of ancient globalisations. This paper develops the theme of entanglement, exploring distinctive regionally diverging histories of innovation and interaction occurring in Western, Central and Eastern Torres Strait. We suggest that traditional histories, involving the wandering trackways of Culture Heroes, provide useful insights into the deep history of human interactions, thereby helping us to understand patterns observed in the archaeological and linguistic record.
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The prospect that First Nations Australians were in contact with cultures beyond Australia prior to European arrival has fascinated theorists for over a century. Early views tended to see Aboriginal culture as too primitive to have independently developed 'higher level' cultural traits. Once this view was abandoned, further enquiry into external contact largely ceased. However, it has been gradually recognised that transformations occurred within Australia not only independently but also through external elements arriving from the north (Macassans and Papuans). This paper offers perhaps the first comprehensive overview of a less studied potential conduit: the eastern seaboard of Australia. Given the vast scale of the eastern seaboard (and its geographic position directly opposite the seafaring cultures of the Pacific Basin it is surprising that the notion of contact between these two realms has received such limited attention. The east coast is a potentially very large target for contact. Queensland and New South Wales mainland and island coastlines comprise in excess of 15,000 km. The Pacific Basin is similarly a huge potential source for contact, covering over one-third of the world's surface, and containing over 20,000 islands. Our paper first considers the contrast between studies of the eastern and western edges of the Pacific Basin, and then the means (and evidence) by which 'contact' is normally discerned. We next consider the potential for contact based on ocean currents and similar factors. The bulk of the paper assesses specific source regions and purported evidence of contact from these regions: Papua New Guinea, Island Melanesia, Polynesia and two islands between these areas (Norfolk and Lord Howe). Our study concludes that evidence for Pacific-Australian contact ought to be relatively abundant, given the size of the source area (the Pacific Basin) and the target area (the eastern seaboard). Instead, contact must have been very limited and sporadic, as most evidence has been either inconclusive or requires further substantiation. Equally, the impact of these cultures on the development of Australian First Nations seems to have been negligible. On the other hand, this review accumulated enough evidence to suggest there was considerable potential for such contacts. We conclude that archaeological frameworks should be developed to investigate purported and possible Pacific-Eastern seaboard contacts.
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May, A. (2021c): History and future of life on Earth - a synthesis of natural sciences and theology. - Dialogo, vol. 8 (1): p. 233-251; Constanta, Romania. "A synthesis of research results of modern natural sciences and fundamental statements of the Christian faith is attempted. The creation of the universe is addressed. Four important events in the history of the Earth as well as the diversity of living beings are shortly discussed. There are good reasons to believe that the universe was created by a transcendent superior being, which we call God, and that this superior being intervened in evolution and Earth history to promote the development of intelligent life. Furthermore, it can be concluded that intelligent life is very rare in the universe. This is the explanation for the “Fermi paradox”. Intelligent life on planet Earth has cosmic significance. The overabundance of this universe inspires the hope for participating in the fulfilled eternity of the Creator in transcendence. Prehistoric humans had long had hope for life after biological death. While scientific speculation about the end of the universe prophesies scenarios of destruction, the Christian faith says that humanity is destined to be united with Jesus Christ. Furthermore, all evolution will be completed with the Creator in transcendence. Then the whole of creation will “obtain the freedom of the glory of the children of God”. From the first primitive living cell, an abundance of the most diverse living beings has evolved. Comparably, humanity has differentiated into a plethora of different cultures. This entire abundance will find its unification and fulfilment in transcendence with the Creator of the universe, without its diversity being erased."
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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
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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.
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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.
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The publication in 2001 by Adcock et al. [Adcock GJ, et al. (2001) Proc Natl Acad Sci USA 98(2):537-542] in PNAS reported the recovery of short mtDNA sequences from ancient Australians, including the 42,000-y-old Mungo Man [Willandra Lakes Hominid (WLH3)]. This landmark study in human ancient DNA suggested that an early modern human mitochondrial lineage emerged in Asia and that the theory of modern human origins could no longer be considered solely through the lens of the "Out of Africa" model. To evaluate these claims, we used second generation DNA sequencing and capture methods as well as PCR-based and single-primer extension (SPEX) approaches to reexamine the same four Willandra Lakes and Kow Swamp 8 (KS8) remains studied in the work by Adcock et al. Two of the remains sampled contained no identifiable human DNA (WLH15 and WLH55), whereas the Mungo Man (WLH3) sample contained no Aboriginal Australian DNA. KS8 reveals human mitochondrial sequences that differ from the previously inferred sequence. Instead, we recover a total of five modern European contaminants from Mungo Man (WLH3). We show that the remaining sample (WLH4) contains ∼1.4% human DNA, from which we assembled two complete mitochondrial genomes. One of these was a previously unidentified Aboriginal Australian haplotype belonging to haplogroup S2 that we sequenced to a high coverage. The other was a contaminating modern European mitochondrial haplotype. Although none of the sequences that we recovered matched those reported by Adcock et al., except a contaminant, these findings show the feasibility of obtaining important information from ancient Aboriginal Australian remains.
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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.
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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. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
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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.
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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.
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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.
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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.
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Despite broad consensus on Africa as the main place of origin for anatomically modern humans, their dispersal pattern out of the continent continues to be intensely debated. In extant human populations, the observation of decreasing genetic and phenotypic diversity at increasing distances from sub-Saharan Africa has been interpreted as evidence for a single dispersal, accompanied by a series of founder effects. In such a scenario, modern human genetic and phenotypic variation was primarily generated through successive population bottlenecks and drift during a rapid worldwide expansion out of Africa in the Late Pleistocene. However, recent genetic studies, as well as accumulating archaeological and paleoanthropological evidence, challenge this parsimonious model. They suggest instead a "southern route" dispersal into Asia as early as the late Middle Pleistocene, followed by a separate dispersal into northern Eurasia. Here we test these competing out-of-Africa scenarios by modeling hypothetical geographical migration routes and assessing their correlation with neutral population differentiation, as measured by genetic polymorphisms and cranial shape variables of modern human populations from Africa and Asia. We show that both lines of evidence support a multiple-dispersals model in which Australo-Melanesian populations are relatively isolated descendants of an early dispersal, whereas other Asian populations are descended from, or highly admixed with, members of a subsequent migration event.
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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.
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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.
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Anatomically modern humans overlapped and mated with Neandertals such that non-African humans inherit ~1-3% of their genomes from Neandertal ancestors. We identified Neandertal lineages that persist in the DNA of modern humans, in whole-genome sequences from 379 European and 286 East Asian individuals, recovering over 15 Gb of introgressed sequence that spans ~20% of the Neandertal genome (FDR = 5%). Analyses of surviving archaic lineages suggests that there were fitness costs to hybridization, admixture occurred both before and subsequent to divergence of non-African modern humans, and Neandertals were a source of adaptive variation for loci involved in skin phenotypes. Our results provide a new avenue for paleogenomics studies, allowing substantial amounts of population-level DNA sequence information to be obtained from extinct groups even in the absence of fossilized remains.
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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.
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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.
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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.
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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.
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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.
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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.
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