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A genomic history of Aboriginal Australia
Abstract
The population history of Aboriginal Australians remains largely uncharacterized. Here we generate high-coverage genomes for 83 Aboriginal Australians (speakers of Pama-Nyungan languages) and 25 Papuans from the New Guinea Highlands. We find that Papuan and Aboriginal Australian ancestors diversified 25-40 thousand years ago (kya), suggesting pre-Holocene population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania). However, all of the studied Aboriginal Australians descend from a single founding population that differentiated ∼10-32 kya. We infer a population expansion in northeast Australia during the Holocene epoch (past 10,000 years) associated with limited gene flow from this region to the rest of Australia, consistent with the spread of the Pama-Nyungan languages. We estimate that Aboriginal Australians and Papuans diverged from Eurasians 51-72 kya, following a single out-of-Africa dispersal, and subsequently admixed with archaic populations. Finally, we report evidence of selection in Aboriginal Australians potentially associated with living in the desert. © 2016 Macmillan Publishers Limited, part of Springer Nature. All rights reserved
Supplementary resource (1)
... Rasmussen et al. (2011) suggested that Aboriginal Australians are descendants of an early modern human dispersal into East Asia ~62-75 Kya. Later, Malaspinas et al. (2016) conducted a comprehensive study of 83 genomes of Aboriginal Australians from eight populations, in addition to 25 Papuan genomes. The authors provided evidence suggesting that Aboriginal Australians were part of a single Out-of-Africa event and estimated the divergence time between Eurasians and Australo-Papuans at 51-72 Kya. ...
... Until the recent articles by Reis et al. (2023) and Silcocks et al. (2023), which include a sample of NPN-speaking Tiwi people, published accounts of genomic variation among Indigenous Australians were confined to PN speakers (e.g., Malaspinas et al. 2016). These studies also included a sample of Yolngu from Galiwin'ku on Elcho Island in northeast Arnhem Land. ...
... For this study, 81 samples that were aligned to hg19 and filtered for PCR duplicate reads (Binary Alignment/Mapping files) were obtained from the Malaspinas et al. (2016) study, including Western Central Desert (WCD; n = 13), Cairns (CAI; n = 6), Weipa (WPA; n = 6), Pilbara (PIL; n = 3), Wongatha (WON; n = 6), Northern Gold Field (NGA; n = 6), Birdsville (BDV; n = 6), Riverine (RIV; n = 6), Papuan (n = 11), African (n = 10), European (n = 4), and East Asian (n = 4) ( Table S1). All-site genotype calling was performed for each of the 81 samples, and subsequently, indels were removed using an inhouse awk script. ...
Objectives
About 300 Aboriginal languages were spoken in Australia, classified into two groups: Pama‐Nyungan (PN), comprised of one language Family, and Non‐Pama‐Nyungan (NPN) with more than 20 language Families. The Yolngu people belong to the larger PN Family and live in Arnhem Land in northern Australia. They are surrounded by groups who speak NPN languages. This study, using nuclear genomic and mitochondrial DNA data, was undertaken to shed light on the origins of the Yolngu people and their language. The nuclear genomic sequences of Yolngu people were compared to those of other Indigenous Australians, as well as Papuan, African, East Asian, and European people.
Materials and Methods
With the agreement of Indigenous participants, samples were collected from 13 Yolngu individuals and 4 people from neighboring NPN speakers, and their nuclear genomes were sequenced to a 30× coverage. Using the short‐read DNA BGISEQ‐500 technology, these sequences were mapped to a reference genome and identified ~24.86 million Single Nucleotide Variants (SNVs). The Yolngu SNVs were then compared to those of 36 individuals from 10 other Indigenous populations/locations across Australia and four worldwide populations using multidimensional scaling, population structure, F3 statistics, and phylogenetic analyses.
Results
Using the above methods, we infer that Yolngu speakers are closely related to neighboring NPN speakers, followed by the Weipa population. No European or East Asian admixture was detected in the genomes of the Yolngu speakers studied here, which contrasts with the genomes of many other PN speakers that have been studied. Our results show that Yolngu speakers are more closely related to other PN speakers in the northeast of Australia than to those in central and Western Australia studied here. Yolngu and the other Australian populations from this study share Papuans as an out‐group.
Discussion
The study presented here provides an account of the nuclear and mitochondrial genomic diversity within the PN Yolngu Aboriginal population. The results show the Yolngu sample and their NPN neighbors have a strong genetic relationship. They also offer evidence of ancestral links between the Yolngu and PN‐speaking populations in Cape York. From earlier fingerprint studies, consistent with the genomic results shown here, we consider a movement of people from the east into northeast Arnhem Land, associated with the flooding of the Sahul Shelf, estimated to have occurred between about 11 and 8 Kya ago. Several Yolngu myths point to such a movement. It is suggested that the spread of the PN language or its speakers may have influenced the population structure of the Yolngu. Further genomic studies, with larger samples, of populations to the east of the Yolngu around the Gulf of Carpentaria into Cape York are required to test this hypothesis. Our results imply that PN did not spread with the movement of people across the continent; rather, the PN languages diffused among the different populations. It seems clear that the languages dispersed and not the people. The low level of relatedness detected between the Yolngu people and the people of the central arid desert of Australia suggests a long period of separation with different patterns of migration. Beyond Australia, Yolngu are most closely related to the Papuan people of New Guinea.
... Shui Tao (Fig. 0 (2015( , 2016( ), and Pakistan (2017. ...
... During the last few decades, great progress has been made in several domains, particularly palaeogenetics, which have revealed the complex ancestry of early Eurasians. This progress -including the identication o a ghost lineage 1 of Eurasians in the Middle East -is providing important new biogeographical hypotheses (Malaspinas et al. 2016). ...
... 1 Ghost lineage is the ancestral population of all non-Africans that admixed with Neanderthals that has left no fossil evidence but genomic evidence (Malaspinas et al. 2016) 2 Marine isotope stages (MIS) or oxygen isotope stages are alternating cold and warm climate episodes. The database uses core drillings rom dierent parts o the world to reconstruct past climate and is used widely in archaeology. ...
... F3 analyses were performed before and after masking the ancestry. 25 26 2.6 | mtDNA analyses 27 Mitochondrial DNA (mtDNA) analyses were carried out using the following samples: 28 Yolngu (n=13) and NPN (n=4) from this study, in addition to 25 mitochondrial genomes 29 from PN speakers, including PIL (n=3), CAI (n=3), WPA (n=2), NGA (n=1), WON (n=1), 30 RIV (n=1), WCD (n=12), and BDV (n=2) from Malaspinas et al. (2016) and Wright et al. 31 (2018). MtDNA sequences were obtained from BAM files of each sample and processed in 32 two steps. ...
... Birdsville (Malaspinas et al., 2016;Wright et al., 2018) In addition, we performed analyses of kinship relatedness among the 110 samples used. 17 ...
... Over the last decade, considerable attention has been paid to estimates of genomic 20 variation in Aboriginal Australians. This includes reports of whole genome sequence 21 variation, as well as partial and complete mitochondrial genomes (Malaspinas et al. 2016;22 Nagle et al., 2017a, b;Tobler et al., 2017;Wright et al., 2018;Reis et al., 2023;Silcocks et 23 al., 2023). Y chromosome variation among Aboriginal Australians has also been investigated 24 over the last decade (e.g. ...
Objectives: About 300 Aboriginal languages were spoken in Australia. These were classified into two groups: Pama-Nyungan (PN), comprised of one language Family, and Non-Pama-Nyungan (NPN) with more than 20 language Families. The Yolngu people belong to the larger PN Family and live in Arnhem Land in northern Australia. They are surrounded by groups who speak NPN languages. This study, using nuclear genomic and mitochondrial DNA data, was undertaken to shed light on the origins of the Yolngu people and their language. The nuclear genomic sequences of Yolngu people were compared to those of other Indigenous Australians, as well as Papuan, African, East Asian and European people.
Materials and methods: With the agreement of Indigenous participants, samples were collected from 13 Yolngu individuals and 4 people from neighbouring NPN speakers and their nuclear genomes sequenced to a 30✕ coverage. Using the short-read DNA BGISEQ-500 technology, these sequences were mapped to a reference genome and identified ~24.86 million Single Nucleotide Variants (SNVs). The Yolngu SNVs were then compared to those of 36 individuals from 10 other Indigenous populations/locations across Australia and four worldwide populations using multidimensional scaling, population structure, F3 statistics and phylogenetic analyses.
Results: Using the above methods, we infer that Yolngu speakers are closely related to neighbouring NPN speakers, followed by the Weipa population. No European or East Asian admixture was detected in the genomes of the Yolngu speakers studied here, which contrasts with the genomes of many other PN speakers that have been studied. Our results show that Yolngu speakers are more closely related to other PN speakers in the northeast of Australia than to those in central and western Australia studied here. Yolngu and the other Australian populations from this study share Papuans as an out-group.
Discussion: The study presented here provides an account of the nuclear and mitochondrial genomic diversity within the PN Yolngu Aboriginal population. The results show the Yolngu sample and their NPN neighbours have a strong genetic relationship. They also offer evidence of ancestral links between the Yolngu and PN-speaking populations in Cape York. From earlier fingerprint studies, consistent with the genomic results shown here, we suggest that there was a movement of people from the east into northeast Arnhem Land, associated with the flooding of the Sahul Shelf, and that this occurred between about 11 Kya and 8 Kya ago. Several Yolngu myths point to such a movement. It is suggested that the spread of the PN language or its speakers may have influenced the population structure of the Yolngu. Further genomic studies, with larger samples, of populations to the east of the Yolngu around the Gulf of Carpentaria into Cape York are required to test this hypothesis. Our results imply that PN did not spread with the movement of people across the continent, rather, the PN languages diffused among the different populations. It seems clear that the languages dispersed and not the people. The low level of relatedness detected between the Yolngu people and the people of the central arid desert of Australia suggests a long period of separation with different patterns of migration. Beyond Australia, Yolngu are most closely related to the Papuan people of New Guinea.
... We use different SMC-based methods throughout this study. These methods include: (1) MSMC2 used as a reference method (Malaspinas et al., 2016), (2) SMCtheo is an extension of the PSMC' (Li and Durbin, 2011;Schiffels and Durbin, 2014) accounting for any number of heritable theoretical markers, and (3) eSMC2 which is equivalent to SMCtheo but accounting only for SNPs markers (Sellinger et al., 2021) (to avoid any bias in implementation differences between SMCtheo and MSMC2). All methods are hidden Markov models (HMM) derived from the pairwise sequentially Markovian coalescent (PSMC') (Schiffels and Durbin, 2014) and assume neutral evolution and a panmictic population. ...
... The hidden states of these methods are the coalescence time of a sample of size two at a position on the sequence. From the distribution of the hidden states along the genome, all methods can infer population size variation through time as well as the recombination rate (Schiffels and Durbin, 2014;Malaspinas et al., 2016;Sellinger et al., 2021). ...
... In the event of recombination, there is a break in the current genealogy and the coalescence time consequently takes a new value according to the model parameters (Marjoram and Wall, 2006;Schiffels and Durbin, 2014). A detailed description of the algorithm can be found in Malaspinas et al., 2016;Sellinger et al., 2020. ...
With the availability of high-quality full genome polymorphism (SNPs) data, it becomes feasible to study the past demographic and selective history of populations in exquisite detail. However, such inferences still suffer from a lack of statistical resolution for recent, for example bottlenecks, events, and/or for populations with small nucleotide diversity. Additional heritable (epi)genetic markers, such as indels, transposable elements, microsatellites, or cytosine methylation, may provide further, yet untapped, information on the recent past population history. We extend the Sequential Markovian Coalescent (SMC) framework to jointly use SNPs and other hyper-mutable markers. We are able to (1) improve the accuracy of demographic inference in recent times, (2) uncover past demographic events hidden to SNP-based inference methods, and (3) infer the hyper-mutable marker mutation rates under a finite site model. As a proof of principle, we focus on demographic inference in Arabidopsis thaliana using DNA methylation diversity data from 10 European natural accessions. We demonstrate that segregating single methylated polymorphisms (SMPs) satisfy the modeling assumptions of the SMC framework, while differentially methylated regions (DMRs) are not suitable as their length exceeds that of the genomic distance between two recombination events. Combining SNPs and SMPs while accounting for site- and region-level epimutation processes, we provide new estimates of the glacial age bottleneck and post-glacial population expansion of the European A. thaliana population. Our SMC framework readily accounts for a wide range of heritable genomic markers, thus paving the way for next-generation inference of evolutionary history by combining information from several genetic and epigenetic markers.
... To test whether we could reduce the stochasticity issue mentioned above we ran ten independent runs for the first panel of Figure 5 and plotted both the independent runs and the average MSMC curves. While we found that the fit to the expected curve improved, there still were differences, particularly for k = 6 as can be seen in Figure S5 and S6 Given that the MSMC2 method was introduced as an improvement on the PSMC and MSMC methods [48,66] we also applied the MSMC2 method to genomic data generated under several scenarios and sampling schemes. In Figure 7 we compare the PSMC, MSMC and MSMC2 curves obtained for a diploid genome (k = 2) sampled in one deme of an n-island model with different migration rates. ...
... In Figure 8 we plot the results of MSMC2 for the same sampling schemes as in Figure 3. Compared to the results obtained with the MSMC method the figures show much less stochasticity, as expected given that the method appears to use all pairwise comparisons among haploid genomes [48,66], but the stepwise curves differ significantly from the expected 12 . CC-BY-NC-ND 4.0 International license made available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. ...
... The MSMC2 method was introduced as an improvement over the PSMC and MSMC methods [48,66]. However, we found that MSMC2 produces additional curves that do not correspond to the expected k 2 × IICR k in the general case, even though they may approximate the IICR 2 in the recent past when all individuals are sampled in the same deme. ...
Reconstructing the demographic history of populations and species is one of the greatest challenges facing population geneticists. [50] introduced, for a sample of size k = 2 haploid genomes, a time- and sample-dependent parameter which they called the IICR (inverse instantaneous coalescence rate). Here we extend their work to larger sample sizes and focus on T k , the time to the first coalescence event in a haploid sample of size k where k ≥ 2. We define the IICR k as the Inverse Instantaneous Coalescence Rate among k lineages. We show that (i) under a panmictic population is equivalent to N e , (ii) the IICR k can be obtained by either simulating T k values or by using the Q -matrix approach of [61] and we provide the corresponding Python and R scripts. We then study the properties of the under a limited set of n -island and stepping-stone models. We show that (iii) in structured models the is dependent on the sample size and on the sampling scheme, even when the genomes are sampled in the same deme. For instance, we find that plots for individuals sampled in the same deme will be shifted towards recent times with a lower plateau as k increases. We thus show that (iv) the cannot be used to represent “the demographic history” in a general sense, (v) the can be estimated from real or simulated genomic data using the PSMC/MSMC methods [44, 65] (vi) the MSMC2 method produces smoother curves that infer something that is not the , but are close to the in the recent past when all samples are obtained from the same deme. Altogether we argue that the PSMC, MSMC and MSMC2 plots are not expected to be identical even when the genomes are sampled from the same deme, that none can be said to represent the “demographic history of populations” and that they should be interpreted with care. We suggest that the PSMC, MSMC and MSMC2 could be used together with the to identify the signature of population structure, and to develop new strategies for model choice.
... Wallacean Genetic Landscape. To place the Wallacean populations within a broader global context and uncover genetic structure within Wallacea and West Papua, we combined our Indonesian and Melanesian samples with 438 additional high-coverage genomes from global human populations (13,34,35). After removing nine closely related individuals (1st and 2nd-degree relatives) and The distinctive dual ancestry countergradient reported in previous genetic studies of Wallacea ( 12 -15 ) is also a defining feature in both the PCA and ancestry decomposition analysis of our considerably larger grouping of 270 Wallacean individuals ( Figs. 2A and SI Appendix, S2 ). ...
... Previously published data from refs. 13,19,29,34,35 were also used in this study. ...
The tropical archipelago of Wallacea was first settled by anatomically modern humans (AMH) by 50 thousand years ago (kya), with descendent populations thought to have remained genetically isolated prior to the arrival of Austronesian seafarers around 3.5 kya. Modern Wallaceans exhibit a longitudinal countergradient of Papuan- and Asian-related ancestries widely considered as evidence for mixing between local populations and Austronesian seafarers, though converging multidisciplinary evidence suggests that the Papuan-related component instead comes primarily from back-migrations from New Guinea. Here, we reconstruct Wallacean population genetic history using more than 250 newly reported genomes from 12 Wallacean and three West Papuan populations and confirm that the vast majority of Papuan-related ancestry in Wallacea (~75 to 100%) comes from prehistoric migrations originating in New Guinea and only a minor fraction is attributable to the founding AMH settlers. Mixing between Papuan and local Wallacean lineages appears to have been confined to the western and central parts of the archipelago and likely occurred contemporaneously with the widespread introduction of genes from Austronesian seafarers—which now comprise between ~40 and 85% of modern Wallacean ancestry—though dating historical admixture events remains challenging due to mixing continuing into the Historical Period. In conjunction with archaeological and linguistic records, our findings point to a dynamic Wallacean population history that was profoundly reshaped by the spread of Papuan genes, languages, and culture in the past 3,500 y.
... Various estimates of effective population size (N e ) for the pre-colonial Indigenous population have been calculated using mitochondrial (mtDNA) and Y-chromosome DNA (Y-DNA) 45,47 . However, census population size (N c ; i.e., number of individuals censused in a population) rarely equals N e because of deviation from random breeding 46 . ...
... Nonetheless, we took the range of N e derived from mtDNA from Tobler et al. 45 (their Extended Data Fig. 7) and doubled it (assuming an equal sex ratio) to infer total N e (i.e., because mtDNA-based analyses of N e estimate the female component of the population 64 ). Likewise, we took the N e range of all mitochondrial genomes and all Y chromosomes from Malaspinas et al. 47 (their Fig. S12.2C,D), added them, and took the resultant full range to infer total N e . ...
Estimating the size of Indigenous populations in Australia prior to European colonial invasion is essential to truth-telling and reconciliation. Robust estimates of the population dynamics of pre-colonial Indigenous Australians are poor due to lethal diseases, frontier violence, and no systematic censuses. We review ethnographic observations, archaeological and genetic reconstructions, and modelled carrying capacity, to infer Indigenous population size prior to colonial invasion. This allows an estimate of the number of excess deaths in post-colonial times. Congruency of the modelled (not historical accounts) estimates suggests a bootstrapped pre-colonial median of 2.51 million, or 0.33 people km-2. For a median pre-colonial population of 2.51 million, ~ 32,500 excess deaths year-1 (2.39 million deaths in total) would have had to occur over the late 18th and early 19th Centuries from colonial invasion-related mortality. These findings highlight the major impacts of invasion experienced by Indigenous Australians, and demonstrate their survival, resilience, and recovery over the past 235 years.
... By contrast, in individuals with high consanguinity (for example, the Paiter Suruí from southern Amazon 48 and the Punjabi from Pakistan 49 ), a large proportion of ROH are long: the two Paiter Suruí individuals carry more than 76% ROH ≥ 12 cM (>335 cM) and Punjabi-2 bears 18 cM out of 30 cM in ROH ≥ 12 cM. We observed that the Ancient Rapanui ROH distribution is similar to that of a present-day Rapanui genome (P2077) 45 . Nevertheless, the latter carries longer ROH than the ancient individuals (38 cM of the genome in ≥20 cM runs). ...
... Ancient Rapanui sequencing data are available for population history research and not for public posting, medical research or commercial purposes. Publicly available data were obtained from the following sources-access granted by aut hors 5,7,[32][33][34]39,45,90,107 ; publicly available data in the European Nucleotide Archive: PRJEB22217 (ref. (those that do not include an age range) symbols and colours correspond to their language family following 57 , e.g., NaDene, and for ancient Native American populations, they correspond to their sampling location and age. ...
Rapa Nui (also known as Easter Island) is one of the most isolated inhabited places in the world. It has captured the imagination of many owing to its archaeological record, which includes iconic megalithic statues called moai¹. Two prominent contentions have arisen from the extensive study of Rapa Nui. First, the history of the Rapanui has been presented as a warning tale of resource overexploitation that would have culminated in a major population collapse—the ‘ecocide’ theory2–4. Second, the possibility of trans-Pacific voyages to the Americas pre-dating European contact is still debated5–7. Here, to address these questions, we reconstructed the genomic history of the Rapanui on the basis of 15 ancient Rapanui individuals that we radiocarbon dated (1670–1950 ce) and whole-genome sequenced (0.4–25.6×). We find that these individuals are Polynesian in origin and most closely related to present-day Rapanui, a finding that will contribute to repatriation efforts. Through effective population size reconstructions and extensive population genetics simulations, we reject a scenario involving a severe population bottleneck during the 1600s, as proposed by the ecocide theory. Furthermore, the ancient and present-day Rapanui carry similar proportions of Native American admixture (about 10%). Using a Bayesian approach integrating genetic and radiocarbon dates, we estimate that this admixture event occurred about 1250–1430 ce.
... MSMC2 (Malaspinas et al. 2016) was used to reconstruct the demographic history of the more distant past. As the method can analyse at most eight haplotypes, we selected and utilised the four individuals with the highest sequencing coverage from each population. ...
Effective population size (Ne) is a quantity of central importance in evolutionary biology and population genetics, but often notoriously challenging to estimate. Analyses of Ne are further complicated by the many interpretations of the concept and the alternative approaches to quantify Ne utilising different properties of the data. Each method is also informative over different time scales, suggesting that a combination of approaches should allow piecing together the entire continuum of Ne, spanning from the recent to more distant past. To test this in practice, we inferred the Ne continuum for 45 populations of nine‐spined sticklebacks (Pungitius pungitius) using whole‐genome data with both LD‐ and coalescent‐based methods. Our results show that marine populations exhibit the highest Ne values in contemporary, recent, and historical times, followed by coastal and freshwater populations. The results also demonstrate the impact of both recent and historical gene flow on Ne estimates and show that simple summary statistics are informative in comprehending the events in the very recent past and aid in more accurate estimation of NeC, the contemporary Ne, as well as in reconstruction and interpretation of recent demographic histories. Although our sample size for each large population is limited, we found that GONE can provide reasonable Ne estimates. However, due to challenges in detecting subtle genetic drift in large populations, these estimates may represent the lower bound of Ne. Finally, we show that combining GONE and CurrentNe2, both sensitive to population structure, with MSMC2 provides a meaningful interpretation of Ne dynamics over time.
... Rather than restricting coalescence between lineages of different colors, as in the case of inversions (Peischl et al., 2013), MSMC-IM expects fewer coalescence events to happen between lineages from different populations, as these events reflect migration. MSMC-IM uses the SMC-based method MSMC2 (Malaspinas et al., 2016;Wang et al., 2020) to infer three separate rates of coalescence: within each population and between the two populations. It then uses these three histories to fit an isolation-migration model (IM; based on Hobolth et al., 2011). ...
Genomes contain the mutational footprint of an organism's evolutionary history, shaped by diverse forces including ecological factors, selective pressures, and life history traits. The sequentially Markovian coalescent (SMC) is a versatile and tractable model for the genetic genealogy of a sample of genomes, which captures this shared history. Methods that utilize the SMC, such as PSMC and MSMC, have been widely used in evolution and ecology to infer demographic histories. However, these methods ignore common biological features, such as gene flow events and structural variation. Recently, there have been several advancements that widen the applicability of SMC-based methods: inclusion of an isolation with migration model, integration with the multi-species coalescent, incorporation of ecological variables (such as selfing and dormancy), inference of dispersal rates, and many computational advances in applying these models to data. We give an overview of the SMC model and its various recent extensions, discuss examples of biological discoveries through SMC-based inference, and comment on the assumptions, benefits and drawbacks of various methods.
... Indigenous students spoke confidently and knowledgeably about the natural landscape, recognising the duality of their role as being part of but also wardens of the natural environment in which they lived. While this intricate connection with the land may be expected to emerge as central to the cultural identities of Australian Indigenous peoples, who are among the oldest living cultures in the world (Malaspinas et al., 2016), more surprising perhaps was the importance of familiarity with natural spaces captured in children's photos in the English study. While Indigenous people have lived off and remained in close contact with the land for many centuries, more recent cultures like that of the United Kingdom may be considered more disconnected from nature. ...
With levels of mental health difficulties among young people rising and policymakers focusing on the state's role in promoting young people's wellbeing, educational institutions have become positioned on the front line as key sites to identify and implement wellbeing interventions. This paper draws on a series of policy analyses and qualitative studies with young people and educators, leading to recognition for the importance of a relational approach to wellbeing. We outline the case for an identity‐based approach to school wellbeing support, arguing that this reflects a novel point of departure from the largely individualistic approach reflected in the prevailing policy positions of many countries in the Global North, including the United Kingdom, Australia and the United States. The paper advances an original relational approach, which we call Connected Belonging, that links identity‐building and affirmation to wellbeing through strengthening students' sense of belonging across the different arenas of their daily lives: school, social life, local community and wider society. Connected Belonging's focus on building connection across these social domains provides young people with identity resources such as trust and validation, ultimately generating a meaningful sense of belonging. We argue that policymakers need to find ways to adapt current strategies and schooling regimes to ensure that school leaders have space and opportunity to engage with wellbeing policy and practice. Given the clear links between students' wellbeing, their engagement with school life and educational achievement, we highlight, as a priority, policy directions that counter the impetus towards competition and academic results and instead foster collaboration and broader notions of success.
... The genetic history of Aboriginal Australians reveals a single founding population~10-32 thousand years ago, suggesting a potential selection signal related to desert habitation [1]. Indigenous people, who make up 3.8% of the Australian population (n = 984,000) [2], exhibit high genetic distinctiveness and genetic variation [3][4][5]. ...
The genetic distinctiveness of Indigenous Australian populations is well established, yet the Tiwi population remains underrepresented in genetic research. Due to their prolonged geographic isolation, these populations are prone to increased runs of homozygosity (ROH). We investigated the genetic diversity of the Tiwi population, isolated from mainland Australia for decades, based on ROH and their associations with clinical traits. We analyzed 455 whole genome sequences to identify population structure via PCA and performed a comparison with UK Biobank, Melanesian, and Polynesian cohorts. ROH assessment and genome-wide and regional measures of homozygosity were used to explore associations between clinical traits and autozygosity. Our analysis revealed distinct genetic characteristics of the Tiwi population that aligned closely with those of the Melanesian cohort. Tiwi individuals exhibited an increased burden of ROH, particularly in LINC0109 , FMLN1 , and RPL17P45 genes on chromosomes 2, 17, and 18, respectively, indicating prolonged isolation and genetic drift. A positive correlation was observed between genomic F ROH and albumin-to-creatinine ratio (ACR) levels, suggesting a potential link between autozygosity and renal health markers. Furthermore, regional autozygosity association analysis revealed an association between elevated ACR and a region in FTO , implicating its role in obesity, kidney disease, and cardiovascular conditions. Importantly, we found that this association is strong under the recessive model. This research lays a robust foundation for further exploration of ROH mapping and its implications for disease susceptibility within Indigenous communities worldwide.
... Ancestors of First Nations began arriving from south-east Asia 50,000-65,000 BC (Clarkson et al., 2017;Malaspinas et al., 2016) 1600s Exploration by the Dutch to Australia previously named "New Holland" and Tasmania previously named "Van Dieman's Land" (Martins, 2022) ...
In the drive to embrace more inclusive, equitable, and respectful approaches to research, academics are increasingly encouraged to engage with diverse and alternate knowledges, including with First Nations and Indigenous Communities. Yet for those working at the intersection of different worldviews—known as the “cultural interface”—the experience can be accompanied by feelings of discomfort. We recognise discomfort as a personal, inner emotion of vulnerability that alerts us to unspoken, difficult conversations; to challenged beliefs and assumptions; and to the limits of our own knowledge. As a group of academics working at the cultural interface, we identify common themes across our collective experiences of discomfort, including fragility and guilt, helplessness, fear, ignorance, shame, challenged conceptions of time, and finally connection and relationality. By openly discussing and confronting our experiences of discomfort, we demonstrate that immersion in discomfort is a journey that provides opportunities for learning, understanding, and fostering co‐governing partnerships with integrity.
... While the reconstruction of stratospheric ozone in the past is not available, the tropospheric ozone burden during the LIG was estimated based on a record of the clumped isotope composition of O2 in the East Antarctic ice core (Yan et al. 2022), indicating a reduction in the tropospheric ozone burden by nearly 9 % compared with the PI conditions. It has been 315 inferred that the dispersal of modern humans had not yet occurred during the LIG (Liu et al. 2015;Malaspinas et al. 2016;Groucutt et al. 2018), which makes the LIG an ideal period for reconstructing the tropospheric ozone under a smaller impact from the influence of humans (Yan et al. 2022). The important factor affecting the amount of tropospheric ozone is the concentration of methane. ...
The climates of the mid-Holocene (MH) and Last Interglacial (LIG) are characterised by warm periods caused by astronomical forcing and climate feedback. One potential feedback is variation in the stratospheric ozone, the influence of which would extend down to the troposphere, potentially affecting the climate. However, understanding the role of changes in the stratospheric ozone during past warm interglacial periods is limited to MH conditions. Here, we employ MRI-ESM2.0, an Earth system model with an iterative ozone model, and simulate the climate and atmospheric ozone during the MH and LIG. We show that the vertical and seasonal changes of stratospheric ozone in the LIG exhibited a stronger variation in the stratospheric ozone near the South Pole compared to that in the MH, indicating that both obliquity and precession forcings affect the stratospheric ozone distributions. We further show that its impact on the zonal mean surface air temperature is small, while it may affect surface air temperature regionally. These results advance the understanding of the dynamics of atmospheric ozone to astronomical forcing during the warm interglacials.
... Another mechanism that can facilitate the occupation of diverse habitats is genetic adaptation, just as local adaptation has contributed to genetic population differentiation in humans (31) despite great behavioral flexibility (32,33). In fact, humans have evolved local genetic adaptations to environmental pressures that differ between forest and savannah habitats, including pathogens (34)(35)(36), such as malaria (37,38); diet (39)(40)(41); solar exposure (42); and climatic variables, such as temperature and water availability (43,44). Culture can also promote genetic adaptations, similar to human adaptations to diet and zoonotic diseases associated with animal domestication (41,45). ...
How populations adapt to their environment is a fundamental question in biology. Yet, we know surprisingly little about this process, especially for endangered species, such as nonhuman great apes. Chimpanzees, our closest living relatives, are particularly notable because they inhabit diverse habitats, from rainforest to woodland-savannah. Whether genetic adaptation facilitates such habitat diversity remains unknown, despite it having wide implications for evolutionary biology and conservation. By using newly sequenced exomes from 828 wild chimpanzees (388 postfiltering), we found evidence of fine-scale genetic adaptation to habitat, with signatures of positive selection in forest chimpanzees in the same genes underlying adaptation to malaria in humans. This work demonstrates the power of noninvasive samples to reveal genetic adaptations in endangered populations and highlights the importance of adaptive genetic diversity for chimpanzees.
... However, such biological effect would most likely need to be present for both medical and surgical admissions. Further, the fact that we are observing this effect for two entirely distinct populations (Australian Indigenous and African-American) that are far apart in terms of ancestral lineages (Tishkoff et al, 2009;Malaspinas et al, 2016) makes this explanation less likely. Therefore, this effect is more likely to be a consequence of social differences between groups, since the minority groups on both continents are known to be disadvantaged in their socioeconomic positions. ...
The new era of large-scale data collection and analysis presents an opportunity for diagnosing and understanding the causes of health inequities. In this study, we describe a framework for systematically analyzing health disparities using causal inference. The framework is illustrated by investigating racial and ethnic disparities in intensive care unit (ICU) outcome between majority and minority groups in Australia (Indigenous vs. Non-Indigenous) and the United States (African-American vs. White). We demonstrate that commonly used statistical measures for quantifying inequity are insufficient, and focus on attributing the observed disparity to the causal mechanisms that generate it. We find that minority patients are younger at admission, have worse chronic health, are more likely to be admitted for urgent and non-elective reasons, and have higher illness severity. At the same time, however, we find a protective direct effect of belonging to a minority group, with minority patients showing improved survival compared to their majority counterparts, with all other variables kept equal. We demonstrate that this protective effect is related to the increased probability of being admitted to ICU, with minority patients having an increased risk of ICU admission. We also find that minority patients, while showing improved survival, are more likely to be readmitted to ICU. Thus, due to worse access to primary health care, minority patients are more likely to end up in ICU for preventable conditions, causing a reduction in the mortality rates and creating an effect that appears to be protective. Since the baseline risk of ICU admission may serve as proxy for lack of access to primary care, we developed the Indigenous Intensive Care Equity (IICE) Radar, a monitoring system for tracking the over-utilization of ICU resources by the Indigenous population of Australia across geographical areas.
... This reduction in diversity is mostly marked among extant non-African human populations. The origin of this bottleneck, genetically dated around $80-70 ka, is related to the last outof-Africa event, which is at the origin of the diversity of non-African recent human populations (Malaspinas et al., 2016;Mallick et al., 2016). ...
... Aboriginal and Torres Strait Islander peoples collectively represent the longest continuing cultures on the planet, having thrived on the Australian continent for countless generations and tens of thousands of years [1,2]. The ongoing harms of colonisation following European invasion less than three centuries ago shape socio-economic experiences and health outcomes for Aboriginal and Torres Strait Islander people [3]. ...
Background
The siloed nature of the health and social service system threatens access for clients engaging numerous organisations. Many Aboriginal and Torres Strait Islander people face adverse circumstances which contribute to multiple health and social needs. Effective relationships between health and social services are integral to coordinated service provision to meet the diverse needs of Aboriginal and Torres Strait Islander clients. Place-specific insights into inter-agency relationships are needed to inform targeted strategies that bolster service coordination to benefit Aboriginal and Torres Strait Islander people.
Methods
This study sought to understand experiences of inter-agency partnerships among health and social service providers on Kaurna Country in northern Adelaide using semi-structured interviews and yarning circles to explore partnership actions, outcomes, enablers, challenges, and identify strategies to strengthen partnerships. Fifty-nine service providers (78% female, 62% Aboriginal) participated including six from non-government organisations, 17 from Aboriginal community-controlled services and 36 from government organisations.
Results
A content analysis identified partnership actions such as client advocacy, referrals, sharing information, case management meetings and collaborative tender submissions which were seen to improve client access, navigation and outcomes and strengthen worker connectedness and job satisfaction. Motivated workers, listening to Aboriginal people, shared goals and values, and partnership agreements (e.g., memorandum of understanding, service contracts) were identified enablers of partnerships. Racism and ignorance, lack of networking events, communication breakdown, red tape and administrative barriers, competition between services, short-term funding, high turnover of staff and a focus on key performance indicators rather than community needs were among the challenges. Effective partnerships to benefit Aboriginal communities in northern Adelaide was reported to require aligned intersectoral strategic intentions, reforms to service commissioning processes, sustainable funding, regular network events for management and frontline workforce, Aboriginal practitioner-led service coordination approaches and a network of Aboriginal and Torres Strait Islander workers across organisations.
Conclusions
This study identified key leverage points for action on inter-agency partnerships to benefit Aboriginal and Torres Strait Islander communities on Kaurna Country. System drivers such as funded inter-agency networks and reforms to commissioning of services must support organisational- and practitioner-level enablers to strengthen partnerships between health and social services across northern Adelaide.
... In their study of Indigenous Australian populations' genomic adaptations, Malaspinas et al. (2016) identified "genomic regions showing high differentiation associated with different ecological regions within Australia" (p. 213). ...
Humans living off-world will face numerous physical, psychological and social challenges and are likely to suffer negative health effects due to their lack of evolutionary adaptation to space environments. While some of the necessary adaptations may develop naturally over many generations, genetic technologies could be used to speed this process along, potentially improving the wellbeing of early space settlers and their offspring. With broad support, such a program could lead to significant genetic modification of off-world communities, for example, to limit radiation damage on body systems or prevent bone and muscle loss in reduced gravity conditions. Given the extreme stressors of living off-world, and the need to have a healthy workforce to support a fledgling human settlement, those in favour of using genetic technologies to enhance settlers might even claim there is a moral imperative to protect their health in the face of the unique threats of space travel, especially for children born in settlements who did not take on these risks voluntarily. For some, this might simply be an extension of procreative beneficence. However, ethical concerns arise regarding the risks of embracing a eugenicist agenda and the potential impacts on the rights of future settlers to refuse such genetic enhancements for themselves or their children.
... Indeed, despite some phenotypic similarities between Africans and Australian Aborigines, they are the most genetically distinct groups on earth. This is because all humans evolved initially in Africa, but Aborigine evolution has subsequently been distinct for about 37,000 years (Malaspinas et al. 2016). In sum, the genes that account for the slight variance in the visual appearance of different groups (e.g., eye shape or skin colour) are controlled by a very small set of genes, meaning that humans are far more fundamentally alike genetically than different. ...
Laypeople reason that different races share 68% of their genes. In fact, the Human Genome Project indicates that humans, regardless of race, share 99.9% of our genetic material and that only 1/200th of 1% has been used to group people into the five classically conceived races. We reasoned that information about shared genetics might compel participants to extend their ingroup to include those formerly in the outgroup. In three studies, we showed participants an 11‐min video with this information and compared this to a music video. In Study 1, we examined 123 European New Zealanders and found that attitudes towards individuals in other countries (measured by questions such as How much do you believe in being loyal to all mankind?) improved significantly from pre‐ to post‐test compared to a music video detailing the effect of music on a child's brain. In Study 2, we replicated this effect with a group of 93 European participants in the United Kingdom. In Study 3, we replicated this effect again with a group of 150 participants from the United Kingdom and showed that the effect is independent of age, political orientation, need for cognitive control and submissiveness.
... The debate within the fields of physical anthropology and human evolutionary genetics centers on whether these traits have developed as adaptations to diverse local environments or through other evolutionary processes. Recent advances in the analysis of genomic data from various populations have emerged as a crucial method for addressing these pivotal questions [24][25][26][27][28]. ...
Background
High-quality genomic datasets from under-representative populations are essential for population genetic analysis and medical relevance. Although the Tujia are the most populous ethnic minority in southwestern China, previous genetic studies have been fragmented and only partially reveal their genetic diversity landscape. The understanding of their fine-scale genetic structure and potentially differentiated biological adaptive features remains nascent.
Objectives
This study aims to explore the demographic history and genetic architecture related to the natural selection of the Tujia people, focusing on a meta-Tujia population from the central regions of the Yangtze River Basin.
Results
Population genetic analyses conducted on the meta-Tujia people indicate that they occupy an intermediate position in the East Asian North-South genetic cline. A close genetic affinity was identified between the Tujia people and neighboring Sinitic-speaking populations. Admixture models suggest that the Tujia can be modeled as a mixture of northern and southern ancestries. Estimates of f3/f4 statistics confirmed the presence of ancestral links to ancient Yellow River Basin millet farmers and the BaBanQinCen-related groups. Furthermore, population-specific natural selection signatures were explored, revealing highly differentiated functional variants between the Tujia and southern indigenous populations, including genes associated with hair morphology (e.g., EDAR) and skin pigmentation (e.g., SLC24A5). Additionally, both shared and unique selection signatures were identified among ethnically diverse but geographically adjacent populations, highlighting their extensive admixture and the biological adaptations introduced by this admixture.
Conclusions
The study unveils significant population movements and genetic admixture among the Tujia and other ethno-linguistically diverse East Asian groups, elucidating the differentiated adaptation processes across geographically diverse populations from the current genetic landscape.
... Understanding these genetic underpinnings of desert adaptation not only contributes to our comprehension of evolutionary biology, but it also holds promise for insights into how these adaptations may be leveraged to address challenges posed by water scarcity and climate change in other organisms, including humans, and in other ecosystems. Studies of desert mammals have provided evidence of positive selection on genes related to food storage [4,6], water reabsorption [5][6][7][8], osmoregulation [1,[9][10][11], fat metabolism [1,3,[12][13][14], thyroid-induced metabolism [15], and salt regulation [16]. These genetic insights suggest ...
The harsh and dry conditions of desert environments have resulted in genomic adaptations, allowing for desert organisms to withstand prolonged drought, extreme temperatures, and limited food resources. Here, we present a comprehensive exploration of gene expression across five tissues (kidney, liver, lung, gastrointestinal tract, and hypothalamus) and 19 phenotypic measurements to explore the whole-organism physiological and genomic response to water deprivation in the desert-adapted cactus mouse (Peromyscus eremicus). The findings encompass the identification of differentially expressed genes and correlative analysis between phenotypes and gene expression patterns across multiple tissues. Specifically, we found robust activation of the vasopressin renin-angiotensin-aldosterone system (RAAS) pathways, whose primary function is to manage water and solute balance. Animals reduced food intake during water deprivation, and upregulation of PCK1 highlights the adaptive response to reduced oral intake via its actions aimed at maintained serum glucose levels. Even with such responses to maintain water balance, hemoconcentration still occurred, prompting a protective downregulation of genes responsible for the production of clotting factors while simultaneously enhancing angiogenesis which is thought to maintain tissue perfusion. In this study, we elucidate the complex mechanisms involved in water balance in the desert-adapted cactus mouse, P. eremicus. By prioritizing a comprehensive analysis of whole-organism physiology and multi-tissue gene expression in a simulated desert environment, we describe the complex response of regulatory processes.
... Our ancestors survived through ice ages, sea-level changes and significant seismic events, and still we have endured. First Nations cultures are the oldest continuous cultures in the world and have existed on the Australian continent and adjacent islands for over 60,000 years (Malaspinas et al, 2016). During this time, given that culture is not innate, these many cultures were taught to subsequent generations of children and adults through complex and specific pedagogical processes developed to support their growth, wellbeing and learning outcomes. ...
... To place the Wallacean populations within a broader global context and uncover genetic structure within Wallacea and West Papua, we combined our Indonesian and Melanesian samples with 438 additional high coverage genomes from global human populations (13,34,35). After removing 11 closely related individuals (1st and 2nd-degree relatives; see Methods), we submitted the resulting dataset of 844 individuals to Principal Components Analysis (PCA; performed using smartsnp v1.1.0; ...
The tropical archipelago of Wallacea was first settled by anatomically modern humans (AMH) by 50 thousand years ago (kya), with descendent populations thought to have remained genetically isolated prior to the arrival of Austronesian seafarers around 3.5 kya. Modern Wallaceans exhibit a longitudinal countergradient of Papuan- and Asian-related ancestries widely considered as evidence for mixing between local populations and Austronesian seafarers, though converging multidisciplinary evidence suggests that the Papuan-related component instead comes primarily from back-migrations from New Guinea. Here, we reconstruct Wallacean population genetic history using more than 250 newly reported genomes from 12 Wallacean and three West Papuan populations and confirm that the vast majority of Papuan-related ancestry in Wallacea (∼75–100%) comes from prehistoric migrations originating in New Guinea and only a minor fraction is attributable to the founding AMH settlers. Mixing between Papuan and local Wallacean lineages appear to have been confined to the western and central parts of the archipelago and likely occurred contemporaneously with the widespread introduction of genes from Austronesian seafarers—which now comprise between ∼40–85% of modern Wallacean ancestry—though dating historical admixture events remains challenging due to mixing continuing into the Historical Period. In conjunction with archaeological and linguistic records, our findings point to a dynamic Wallacean population history that was profoundly reshaped by the spread of Papuan genes, languages, and culture in the past 3,500 years.
... The fossil record indicates repeated Homo sapiens presence in Eurasia from Marine Isotope Stage (MIS) 8 (300-243 ka) onwards [1][2][3][4] , reaching mainland Southeast Asia by MIS5a (82-71 ka) 5 and Sumatra by early MIS4 (~68 ka) 6 . However, genetic evidence indicates that over 90% of non-African ancestry is derived from a single late dispersal during MIS4 (71-57 ka), reaching Sahul (the combined continent of Australia and New Guinea at times of lowered sea level) in MIS3 (57-29 ka) [7][8][9][10][11][12] . A trace of an earlier dispersal may survive in the genomes of some Papuans 13 , while the archaeological site of Madjedbebe shows humans had already reached Australia in late MIS4 (~65 ka) 14 . ...
Archaeological evidence attests multiple early dispersals of Homo sapiens out of Africa, but genetic evidence points to the primacy of a single dispersal 70-40 ka. Laili in Timor-Leste is on the southern dispersal route between Eurasia and Australasia and has the earliest record of human occupation in the eastern Wallacean archipelago. New evidence from the site shows that, unusually in the region, sediment accumulated in the shelter without human occupation, in the window 59–54 ka. This was followed by an abrupt onset of intensive human habitation beginning ~44 ka. The initial occupation is distinctive from overlying layers in the aquatic focus of faunal exploitation, while it has similarities in material culture to other early Homo sapiens sites in Wallacea. We suggest that the intensive early occupation at Laili represents a colonisation phase, which may have overwhelmed previous human dispersals in this part of the world.
This paper explores Great Basin arid-zone hunter–forager rock art as signalling behaviour. The rock art in Lincoln County, Nevada, is the focus, and this symbolic repertoire is analysed within its broader archaeological and ethnographic contexts. This paper mobilises an explicitly theoretical approach which integrates human behavioural ecology (HBE) and the precepts of information exchange theory (IET), generating assumptions about style and signalling behaviour based on hunter–forager mobility patterns. An archaeological approach is deployed to contextualise two characteristic regional motifs—the Pahranagat solid-bodied and patterned-bodied anthropomorphs. Contemporary Great Basin Native American communities see Great Basin rock writing through a shamanistic ritual explanatory framework, and these figures are understood to be a powerful spirit figure, the Water Baby, and their attendant shamans’ helpers. This analysis proposes an integrated model to understand Great Basin symbolic behaviours through the Holocene: taking a dialogical approach to travel backward from the present to meet the archaeological past. The recursive nature of rock art imagery and its iterative activation by following generations allows for multiple interpretive frameworks to explain Great Basin hunter–forager and subsequent horticulturalist signalling behaviours over the past ca. 15,000 years.
Genome sequencing of 1537 individuals from 139 ethnic groups reveals the genetic characteristics of understudied populations in North Asia and South America. Our analysis demonstrates that West Siberian ancestry, represented by the Kets and Nenets, contributed to the genetic ancestry of most Siberian populations. West Beringians, including the Koryaks, Inuit, and Luoravetlans, exhibit genetic adaptation to Arctic climate, including medically relevant variants. In South America, early migrants split into four groups—Amazonians, Andeans, Chaco Amerindians, and Patagonians—~13,900 years ago. Their longest migration led to population decline, whereas settlement in South America’s diverse environments caused instant spatial isolation, reducing genetic and immunogenic diversity. These findings highlight how population history and environmental pressures shaped the genetic architecture of human populations across North Asia and South America.
Population branch statistics, which estimate the degree of genetic differentiation along a focal population’s lineage, have been used as an alternative to FST-based genome-wide scans for identifying loci associated with local selective sweeps. Beyond the population branch statistic (PBS), the normalized PBSn1 adjusts focal branch length with respect to outgroup branch lengths at the same locus, whereas population branch excess (PBE) incorporates median branch lengths at other loci. PBSn1 and PBE were proposed to be more specific to local selective sweeps as opposed to geographically ubiquitous selection. However, the accuracy and statistical power of branch statistics have not been systematically assessed. To do so, we simulate genomes in representative large and small populations with varying proportions of sites evolving under genetic drift or (approximated) background selection, with local selective sweeps or geographically parallel selective sweeps. We then assess the probability that local selective sweep loci are correctly identified as outliers by FST and by each of the branch statistics. We find that branch statistics consistently outperform FST at identifying local sweeps. Particularly when parallel sweeps are introduced, PBSn1 and PBE correctly identify local sweeps among their top outliers more frequently than PBS. Additionally, we evaluate versions of these statistics based on maximal site differentiation within a window, finding that site-based PBE and PBSn1 are particularly effective at identifying local soft sweeps. These results validate the greater specificity of the rescaled branch statistics PBE and PBSn1 to detect population-specific positive selection, supporting their use in genomic studies focused on local adaptation.
New species typically evolve over several million years. However, rates of speciation and ecological diversification vary by orders of magnitude across the tree of life, with the fastest shown by some adaptive radiations. Eight hundred endemic species of cichlid fishes emerged and formed entire food webs in Lake Victoria and nearby lakes in East Africa. According to Victorias paleolimnological history, five hundred may have arisen within the past 16,700 years, but molecular phylogenies estimated a much older origin. We reconstruct the age and demography of all Lake Victoria region radiations from whole genomes. We show that indeed, in Lake Victoria all trophic guilds diverged <16,700 years ago, corresponding to between 537 and nearly 30000 speciation events per species per million years, the fastest speciation rate in metazoans. Cichlid radiations in lakes Edward, Albert and Kivu too began <20,000 years ago, an order of magnitude faster than previously thought. Evolutionary transitions between trophic levels led to divergence in effective population sizes as predicted by the trophic pyramid of numbers concept and replicated across three parallel food web radiations. Our results demonstrate that classical theory of trophic interactions in ecologically assembled food webs applies equally to food webs that assembled through rapid adaptive radiation.
Multiple methods of demography inference are based on the ancestral recombination graph. This powerful approach uses observed mutations to model local genealogies changing along chromosomes by historical recombination events. However, inference of underlying genealogies is difficult in regions with high recombination rate relative to mutation rate due to the lack of mutations representing genealogies. Despite the prevalence of high-recombining genomic regions in some organisms, such as birds, its impact on demography inference based on ancestral recombination graphs has not been well studied. Here, we use population genomic simulations to investigate the impact of high-recombining regions on demography inference based on ancestral recombination graphs. We demonstrate that inference of effective population size and the time of population split events is systematically affected when high-recombining regions cover wide breadths of the chromosomes. Excluding high-recombining genomic regions can practically mitigate this impact, and population genomic inference of recombination maps is informative in defining such regions, yet the estimated values of local recombination rate may not be utilized for this decision. Finally, we confirm the relevance of our findings in empirical analysis by contrasting demography inferences applied for a bird species, the Eurasian blackcap (Sylvia atricapilla), using different parts of the genome with high and low recombination rates. Our results suggest that demography inference methods based on ancestral recombination graphs should be carried out with caution when applied in species whose genomes contain long stretches of high-recombining regions.
Infections have imposed strong selection pressures throughout human evolution, making the study of natural selection's effects on immunity genes highly complementary to disease-focused research. This review discusses how ancient DNA studies, which have revolutionized evolutionary genetics, increase our understanding of the evolution of human immunity. These studies have shown that interbreeding between modern humans and Neanderthals or Denisovans has influenced present-day immune responses, particularly to viruses. Additionally, ancient genomics enables the tracking of how human immunity has evolved across cultural transitions, highlighting strong selection since the Bronze Age in Europe (<4,500 years) and potential genetic adaptations to epidemics raging during the Middle Ages and the European colonization of the Americas. Furthermore, ancient genomic studies suggest that the genetic risk for noninfectious immune disorders has gradually increased over millennia because alleles associated with increased risk for autoimmunity and inflammation once conferred resistance to infections. The challenge now is to extend these findings to diverse, non-European populations and to provide a more global understanding of the evolution of human immunity.
It was recently reported that a severe ancient bottleneck occurred around 900 thousand years ago in the ancestry of African populations, while this signal is absent in non-African populations. Here, we present evidence to show that this finding is likely a statistical artifact.
Currently, there is limited empirically published Australian studies on effective rehabilitative programs in youth justice. This study used a mixed-methods approach to evaluate the Healthy Relationships program which was designed to challenge attitudes relating to intimate partner violence for male adolescents in detention in Western Australia. Paired group analyses compared pre and post measures of attitudes towards intimate partner violence and traditional gender roles and stereotypes for the total sample (N = 65). Given the significant overrepresentation of First Nations youth in detention, additional analyses were also run separately for this group (n = 51). Participation in the Healthy Relationships program was expected to reduce participant endorsement of attitudes supporting intimate partner violence and endorsement of attitudes supporting traditional gender roles and stereotypes. Results supported our expectations for the total sample and the First Nations youth sample, indicating significant improvements across all outcomes following program participation. Qualitative analysis of participant program feedback further supported the quantitative results and identified the importance of the therapeutic alliance and incentives-based learning approaches. The findings contribute to the “what works” literature and provide insights into factors that improve positive treatment outcomes for youth in detention. Suggestions for program improvements and future research directions are discussed.
Gene flow from Neanderthals has shaped genetic and phenotypic variation in modern humans. We generated a catalog of Neanderthal ancestry segments in more than 300 genomes spanning the past 50,000 years. We examined how Neanderthal ancestry is shared among individuals over time. Our analysis revealed that the vast majority of Neanderthal gene flow is attributable to a single, shared extended period of gene flow that occurred between 50,500 to 43,500 years ago, as evidenced by ancestry correlation, colocalization of Neanderthal segments across individuals, and divergence from the sequenced Neanderthals. Most natural selection—positive and negative—on Neanderthal variants occurred rapidly after the gene flow. Our findings provide new insights into how contact with Neanderthals shaped modern human origins and adaptation.
The archaeology of the island of New Guinea is ancient and surprising, yet it is highly fragmentary in space and time. Consequently, archaeology provides only local and fleeting glimpses of social life in the distant past. In this review, we consider several key themes, such as initial colonization at least 55,000 years ago, the emergence of agriculture by at least 7,000–6,400 years ago, and social diversification in the last few thousand years. We build our discussions around robust archaeological records that convey a coherent impression of what people were doing in the past. We also highlight the ways in which archaeology can be repurposed to address contemporary issues, including social and environmental problems, and flag how a distinctive New Guinean archaeology could be rooted in a vegecultural conception of social life and time.
As an alternative to a recent coastal southern route followed by modern humans to colonize Eurasia after an Out of Africa around 60 Kya, and under the premise that the evolutionary rate based coalescent ages slowdown going backwards in time, I propose a new model based on phylogenetic and phylogeographic analyses of uniparental markers in present and past modern human populations across Eurasia and Australasia. The archaeological record favors a northern route that reached China around 120 kya and then descended latitudinally reaching Southeast Asia and islands around 70-60 kya. These ages coincide with the basal split of the mtDNA macrohaplogroup L3’4* and the origin of the Y- chromosome macrohaplogroup CT* and the subsequent splits in Eurasia of mtDNA haplogroups M and N and Y-chromosome C, D and F clades respectively. Roughly at the same time modern humans arrived in Australasia other groups retreated southwest returning to Africa carrying with them mtDNA L3 and Y-Chromosome E lineages. Southeast Asia and Southwest-Central Asia were the subsequent demographic centers for the respective colonization of East and northern Asia and Europe. Across the Ganges-Brahmaputra and the Indus valleys, South Asia was colonized from both migratory centers.
Papua New Guinea (PNG) hosts distinct environments mainly represented by the ecoregions of the Highlands and Lowlands that display increased altitude and a predominance of pathogens, respectively. Since its initial peopling approximately 50,000 years ago, inhabitants of these ecoregions might have differentially adapted to the environmental pressures exerted by each of them. However, the genetic basis of adaptation in populations from these areas remains understudied. Here, we investigated signals of positive selection in 62 highlanders and 43 lowlanders across 14 locations in the main island of PNG using whole-genome genotype data from the Oceanian Genome Variation Project (OGVP) and searched for signals of positive selection through population differentiation and haplotype-based selection scans. Additionally, we performed archaic ancestry estimation to detect selection signals in highlanders within introgressed regions of the genome. Among highland populations we identified candidate genes representing known biomarkers for mountain sickness (SAA4, SAA1, PRDX1, LDHA) as well as candidate genes of the Notch signaling pathway (PSEN1, NUMB, RBPJ, MAML3), a novel proposed pathway for high altitude adaptation in multiple organisms. We also identified candidate genes involved in oxidative stress, inflammation, and angiogenesis, processes inducible by hypoxia, as well as in components of the eye lens and the immune response. In contrast, candidate genes in the lowlands are mainly related to the immune response (HLA-DQB1, HLA-DQA2, TAAR6, TAAR9, TAAR8, RNASE4, RNASE6, ANG). Moreover, we find two candidate regions to be also enriched with archaic introgressed segments, suggesting that archaic admixture has played a role in the local adaptation of PNG populations.
Although it is well known that the ancestors of modern humans and Neanderthals admixed, the effects of gene flow on the Neanderthal genome are not well understood. We develop methods to estimate the amount of human-introgressed sequences in Neanderthals and apply it to whole-genome sequence data from 2000 modern humans and three Neanderthals. We estimate that Neanderthals have 2.5 to 3.7% human ancestry, and we leverage human-introgressed sequences in Neanderthals to revise estimates of Neanderthal ancestry in modern humans, show that Neanderthal population sizes were significantly smaller than previously estimated, and identify two distinct waves of modern human gene flow into Neanderthals. Our data provide insights into the genetic legacy of recurrent gene flow between modern humans and Neanderthals.
Chestnut plants (Castanea) are important nut fruit trees worldwide. However, little is known regarding the genetic relationship and evolutionary history of different species within the genus. How modern chestnut plants have developed local adaptation to various climates remains a mystery. The genomic data showed that Castanea henryi first diverged in the Oligocene ~31.56 million years ago, followed by Castanea mollissima, and the divergence between Castanea seguinii and Castanea crenata occurred in the mid-Miocene. Over the last 5 million years, the population of chestnut plants has continued to decline. A combination of selective sweep and environmental association studies was applied to investigate the genomic basis of chestnut adaptation to different climates. Twenty-two candidate genes were associated with temperature and precipitation. We also revealed the molecular mechanism by which CmTOE1 interacts with CmZFP8 and CmGIS3 to promote the formation of non-glandular trichomes for adaptation to low temperature and high altitudes. We found a significant expansion of CER1 genes in Chinese chestnut (C. mollissima) and verified the CmERF48 regulation of CmCER1.6 adaptation to drought environments. These results shed light on the East Asian chestnut plants as a monophyletic group that had completed interspecific differentiation in the Miocene, and provided candidate genes for future studies on adaptation to climate change in nut trees.
Ongoing advances in population genomic methodologies have recently made it possible to study millions of loci across hundreds of genomes at a relatively low cost, by leveraging a combination of low-coverage shotgun sequencing and innovative genotype imputation methods. This approach has the potential to provide economical access to genotype information that is similar to most widely used low-cost genotyping approach, i.e. SNP panels, while avoiding potential issues related to loci being ascertained in distantly related populations. Nonetheless, adoption of imputation methods has been constrained by the lack of suitable reference panels of phased genomes, as performance degrades when panel individuals are distantly related to the target populations. Recent advances in imputation algorithms now allow genetic information from the target population to be used in the imputation process, however, potentially mitigating the lack of a suitable reference panel. Here we assess the performance of the recently released GLIMPSE imputation software on a set of 250 low coverage genomes (~3x) from populations from Island Southeast Asia and Near Oceania that are poorly represented in publicly available datasets, comparing the use of imputed genotypes against other common genotype calling methods for a range of standard population genomic analyses. We find that imputation performance and inference both greatly improved when genetic information from the 250 target individuals was leveraged, with comparable results to pseudo-haploid calls that trade off improved precision with reduced accuracy. Our study shows that imputed genotypes are a cost effective and robust basis for population genomic studies of groups, especially those that are poorly represented in publicly available data.
Population branch statistics, which estimate the branch lengths of focal populations with respect to two outgroups, have been used as an alternative to F ST -based genome-wide scans for identifying loci associated with local selective sweeps. In addition to the original population branch statistic (PBS), there are subsequently proposed branch rescalings: normalized population branch statistic (PBSn1), which adjusts focal branch length with respect to outgroup branch lengths at the same locus, and population branch excess (PBE), which also incorporates median branch lengths at other loci. PBSn1 and PBE have been proposed to be less sensitive to allele frequency divergence generated by background selection or geographically ubiquitous positive selection rather than local selective sweeps. However, the accuracy and statistical power of branch statistics have not been systematically assessed. To do so, we simulate genomes in representative large and small populations with varying proportions of sites evolving under genetic drift or background selection (approximated using variable N e ), local selective sweeps, and geographically parallel selective sweeps. We then assess the probability that local selective sweep loci are correctly identified as outliers by F ST and by each of the branch statistics. We find that branch statistics consistently outperform F ST at identifying local sweeps. When background selection and/or parallel sweeps are introduced, PBSn1 and especially PBE correctly identify local sweeps among their top outliers at a higher frequency than PBS. These results validate the greater specificity of rescaled branch statistics such as PBE to detect population-specific positive selection, supporting their use in genomic studies focused on local adaptation.
Significance Statement
Population branch statistics are widely used in genome-wide scans to identify loci associated with local adaptation. This study finds that branch statistics are more accurate than F ST at identifying local selective sweeps under a wide range of demographic parameters and models of evolution. It also demonstrates that certain branch statistics have improved ability to distinguish local adaptation from other models of natural selection.
Encompassing regions that were amongst the first inhabited by humans following the out-of-Africa expansion, hosting populations with the highest levels of archaic hominid introgression, and including Pacific islands that are the most isolated inhabited locations on the planet, Oceania has a rich, but understudied, human genomic landscape. Here we describe the first region-wide analysis of genome-wide data from population groups spanning Oceania and its surroundings, from island and peninsular southeast Asia to Papua New Guinea, east across the Pacific through Melanesia, Micronesia, and Polynesia, and west across the Indian Ocean to related island populations in the Andamans and Madagascar. In total we generate and analyze genome-wide data from 981 individuals from 92 different populations, 58 separate islands, and 30 countries, representing the most expansive study of Pacific genetics to date. In each sample we disentangle the Papuan and more recent Austronesian ancestries, which have admixed in various proportions across this region, using ancestry-specific analyses, and characterize the distinct patterns of settlement, migration, and archaic introgression separately in these two ancestries. We also focus on the patterns of clinically relevant genetic variation across Oceania--a landscape rippled with strong founder effects and island-specific genetic drift in allele frequencies--providing an atlas for the development of precision genetic health strategies in this understudied region of the world.
Motivation
Structure methods are highly used population genetic methods for classifying individuals in a sample fractionally into discrete ancestry components.
Contribution
We introduce a new optimization algorithm of the classical Structure model in a maximum likelihood framework. Using analyses of real data we show that the new optimization algorithm finds higher likelihood values than the state-of-the-art method in the same computational time. We also present a new method for estimating population trees from ancestry components using a Gaussian approximation. Using coalescence simulations modeling populations evolving in a tree-like fashion, we explore the adequacy of the Structure model and the Gaussian assumption for identifying ancestry components correctly and for inferring the correct tree. In most cases, ancestry components are inferred correctly, although sample sizes and times since admixture can influence the inferences. Similarly, the popular Gaussian approximation tends to perform poorly when branch lengths are long, although the tree topology is correctly inferred in all scenarios explored. The new methods are implemented together with appropriate visualization tools in the computer package Ohana.
Availability
Ohana is publicly available at https://github.com/jade-cheng/ohana . Besides its source code and installation instructions, we also provide example workflows in the project wiki site.
Contact
jade.cheng@birc.au.dk
This Encyclopaedia is the first significant authoritative and comprehensive reference on all apects of Australian Aboriginal and Torres Strait Islander history, society and culture. Containing some 2000 clearly written and informative entries by over 200 authors from all parts of Australia, and illustrated with around 1000 colour and black and white photographs, maps and drawings, this work is an indispensable resource for government and community organisations, schools, tertiary institutions, libraries and for the home.
Entries range across all major subject categories (Ancient History, Art, Economy, Education, Food, Health, Land Ownership, Language, Law, LIterature, media, Music, Politics, Recent History, Sport) and also cover current topics contemporary art and music, mining and royalties, land rights, deaths in custody, housing, legal services and language maintenance, as well as including biographies, historical sketches of significant places, and profiles of the approximately 500 indigenous "tribal" peoples of Australia. These 500 groups are divided into 18 geographic regions which form an additional framework of organisation to the subject groupings.
There are in addition many appendices with, for example statistical information and timelines. There is a comprehensive index in addition to the cross-linkings between every entry and every other entry. Finally there is an extensive bibliography of some 1800 items.
The maps of the tribal groupings were also combined into a single large wall map "Aboriginal Australia" which includes the regions and an extensive index of synonyms to tribal/langage names.
The Encyclopaedia itself was also released in an electronic interactive form (on a CD Rom, for both Windows and Apple systems) which contained all the above and also added music and film material.
The Encyclopaedia was well received by Aboriginal people, and Charles Perkins, David Mowaljarlai, and Galarrwuy Yunupingu all wrote endorsements for the cover.
Readable link: http://rdcu.be/kt5n
High-coverage whole-genome sequence studies have so far focused on a limited number of geographically restricted populations or been targeted at specific diseases, such as cancer. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history and refuelled the debate on the mutation rate in humans. Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets. We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long- and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record, and admixture between AMHs and Neanderthals predating the main Eurasian expansion, our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago.
Significance
This report is the first publication, to our knowledge, to report the complete mitochondrial genome of an ancient Aboriginal Australian. In addition, it also provides important evidence about the reliability of the only previous publication of this kind. The paper attained international significance, although its conclusions have remained controversial. Using second generation DNA sequencing methods, we provide strong evidence that the DNA sequences reported by Adcock et al. were, indeed, contamination. Our manuscript is also important, because the research was planned and conducted and is published with the support of the Barkindji, Ngiyampaa, and Muthi Muthi indigenous groups.
Australia was one of the earliest regions outside Africa to be colonized by fully modern humans, with archaeological evidence for human presence by 47,000 years ago (47 kya) widely accepted [1, 2]. However, the extent of subsequent human entry before the European colonial age is less clear. The dingo reached Australia about 4 kya, indirectly implying human contact, which some have linked to changes in language and stone tool technology to suggest substantial cultural changes at the same time [3]. Genetic data of two kinds have been proposed to support gene flow from the Indian subcontinent to Australia at this time, as well: first, signs of South Asian admixture in Aboriginal Australian genomes have been reported on the basis of genome-wide SNP data [4]; and second, a Y chromosome lineage designated haplogroup C(∗), present in both India and Australia, was estimated to have a most recent common ancestor around 5 kya and to have entered Australia from India [5]. Here, we sequence 13 Aboriginal Australian Y chromosomes to re-investigate their divergence times from Y chromosomes in other continents, including a comparison of Aboriginal Australian and South Asian haplogroup C chromosomes. We find divergence times dating back to ∼50 kya, thus excluding the Y chromosome as providing evidence for recent gene flow from India into Australia.
Although initial studies suggested that Denisovan ancestry was found only in modern human populations from island Southeast Asia and Oceania, more recent studies have suggested that Denisovan ancestry may be more widespread. However, the geographic extent of Denisovan ancestry has not been determined, and moreover the relationship between the Denisovan ancestry in Oceania and that elsewhere has not been studied. Here we analyze genome-wide SNP data from 2493 individuals from 221 worldwide populations, and show that there is a widespread signal of a very low level of Denisovan ancestry across Eastern Eurasian and Native American (EE/NA) populations. We also verify a higher level of Denisovan ancestry in Oceania than that in EE/NA; the Denisovan ancestry in Oceania is correlated with the amount of New Guinea ancestry, but not the amount of Australian ancestry, indicating that recent gene flow from New Guinea likely accounts for signals of Denisovan ancestry across Oceania. However, Denisovan ancestry in EE/NA populations is equally correlated with their New Guinea or their Australian ancestry, suggesting a common source for the Denisovan ancestry in EE/NA and Oceanian populations. Our results suggest that Denisovan ancestry in EE/NA is derived either from common ancestry with, or gene flow from, the common ancestor of New Guineans and Australians, indicating a more complex history involving East Eurasians and Oceanians than previously suspected.
© 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.
Neanderthals are thought to have disappeared in Europe approximately 39,000-41,000 years ago but they have contributed 1-3% of the DNA of present-day people in Eurasia. Here we analyse DNA from a 37,000-42,000-year-old modern human from Peştera cu Oase, Romania. Although the specimen contains small amounts of human DNA, we use an enrichment strategy to isolate sites that are informative about its relationship to Neanderthals and present-day humans. We find that on the order of 6-9% of the genome of the Oase individual is derived from Neanderthals, more than any other modern human sequenced to date. Three chromosomal segments of Neanderthal ancestry are over 50 centimorgans in size, indicating that this individual had a Neanderthal ancestor as recently as four to six generations back. However, the Oase individual does not share more alleles with later Europeans than with East Asians, suggesting that the Oase population did not contribute substantially to later humans in Europe.
A colonization model is proposed to explain the timing of human occupation in different regions of the arid zone and the reasons for inferred demographic changes through time. A biogeographic approach views changes in human economy and technology against the backdrop of climatic oscillations of the last 40,000 years. This model stands in strong contrast to that of the ‘conservative desert culture’ proposed by Gould, which has become untenable as data from arid zone excavations are increasingly argued to reflect significant changes in human economy, technology and demography through time. The results of regional survey and excavation from the Pilbara and sandy deserts of north-west Australia, from central Australia, the Flinders Ranges and adjacent dunefields and from semi-arid Queensland suggest that the occupation of the arid zone from the late Pleistocene on is likely to have been a highly dynamic process. The notion of a stable human adaptation to the diverse landforms and environments of the arid zone finds little support in the archaeological record.
We present the high-quality genome sequence of a 45,000-year-old modern human male from Siberia. This individual derives from a population that lived before—or simultaneously with—the separation of the populations in western and eastern Eurasia and carries a similar amount of Neanderthal ancestry as present-day Eurasians. However, the genomic segments of Neanderthal ancestry are substantially longer than those observed in present-day individuals, indicating that Neanderthal gene flow into the ancestors of this individual occurred 7,000–13,000 years before he lived. We estimate an autosomal mutation rate of 0.4 3 10 29 to 0.6 3 10 29 per site per year, a Y chromosomal mutation rate of 0.7 3 10 29 to 0.9 3 10 29 per site per year based on the additional substitutions that have occurred in present-day non-Africans compared to this genome, and a mitochondrial mutation rate of 1.8 3 10 28 to 3.2 3 10 28 per site per year based on the age of the bone.
Background
Comparisons of maternally-inherited mitochondrial DNA (mtDNA) and paternally-inherited non-recombining Y chromosome (NRY) variation have provided important insights into the impact of sex-biased processes (such as migration, residence pattern, and so on) on human genetic variation. However, such comparisons have been limited by the different molecular methods typically used to assay mtDNA and NRY variation (for example, sequencing hypervariable segments of the control region for mtDNA vs. genotyping SNPs and/or STR loci for the NRY). Here, we report a simple capture array method to enrich Illumina sequencing libraries for approximately 500 kb of NRY sequence, which we use to generate NRY sequences from 623 males from 51 populations in the CEPH Human Genome Diversity Panel (HGDP). We also obtained complete mtDNA genome sequences from the same individuals, allowing us to compare maternal and paternal histories free of any ascertainment bias.
Results
We identified 2,228 SNPs in the NRY sequences and 2,163 SNPs in the mtDNA sequences. Our results confirm the controversial assertion that genetic differences between human populations on a global scale are bigger for the NRY than for mtDNA, although the differences are not as large as previously suggested. More importantly, we find substantial regional variation in patterns of mtDNA versus NRY variation. Model-based simulations indicate very small ancestral effective population sizes (<100) for the out-of-Africa migration as well as for many human populations. We also find that the ratio of female effective population size to male effective population size (Nf/Nm) has been greater than one throughout the history of modern humans, and has recently increased due to faster growth in Nf than Nm.
Conclusions
The NRY and mtDNA sequences provide new insights into the paternal and maternal histories of human populations, and the methods we introduce here should be widely applicable for further such studies.
Significance
Current consensus indicates that modern humans originated from an ancestral African population between ∼100–200 ka. The ensuing dispersal pattern is controversial, yet has important implications for the demographic history and genetic/phenotypic structure of extant human populations. We test for the first time to our knowledge the spatiotemporal dimensions of competing out-of-Africa dispersal models, analyzing in parallel genomic and craniometric data. Our results support an initial dispersal into Asia by a southern route beginning as early as ∼130 ka and a later dispersal into northern Eurasia by ∼50 ka. Our findings indicate that African Pleistocene population structure may account for observed plesiomorphic genetic/phenotypic patterns in extant Australians and Melanesians. They point to an earlier out-of-Africa dispersal than previously hypothesized.
Inference of individual ancestry coefficients, which is important for population genetic and association studies, is commonly performed using computer-intensive likelihood algorithms. With the availability of large population genomic data sets, fast versions of likelihood algorithms have attracted considerable attention. Reducing the computational burden of estimation algorithms remains, however, a major challenge. Here, we present a fast and efficient method for estimating individual ancestry coefficients based on sparse non-negative matrix factorization algorithms. We implemented our method in the computer program sNMF, and applied it to human and plant data sets. The performances of sNMF were then compared to the likelihood algorithm implemented in the computer program ADMIXTURE. Without loss of accuracy, sNMF computed estimates of ancestry coefficients with run-times approximately 10 to 30 times shorter than those of ADMIXTURE.
The hormone thyroxine that regulates mammalian metabolism is carried and stored in the blood by thyroxine-binding globulin (TBG). We demonstrate here that the release of thyroxine from TBG occurs by a temperature-sensitive mechanism and show how this will provide a homoeostatic adjustment of the concentration of thyroxine to match metabolic needs, as with the hypothermia and torpor of small animals. In humans, a rise in temperature, as in infections, will trigger an accelerated release of thyroxine, resulting in a predictable 23% increase in the concentration of free thyroxine at 39°C. The in vivo relevance of this fever-response is affirmed in an environmental adaptation in aboriginal Australians. We show how two mutations incorporated in their TBG interact in a way that will halve the surge in thyroxine release, and hence the boost in metabolic rate that would otherwise occur as body temperatures exceed 37°C. The overall findings open insights into physiological changes that accompany variations in body temperature, as notably in fevers.
Neandertal Shadows in Us
Non-African modern humans carry a remnant of Neandertal DNA from interbreeding events that have been postulated to have occurred as humans migrated out of Africa. While the total amount of Neandertal sequence is estimated to be less than 3% of the modern genome, the specific retained sequences vary among individuals. Analyzing the genomes of more than 600 Europeans and East Asians, Vernot and Akey (p. 1017 , published online 29 January) identified Neandertal sequences within modern humans that taken together span approximately 20% of the Neandertal genome. Some Neandertal-derived sequences appear to be under positive selection in humans, including several genes associated with skin phenotypes.
We sequenced the genomes of a ~7,000 year old farmer from Germany and eight
~8,000 year old hunter-gatherers from Luxembourg and Sweden. We analyzed these and other
ancient genomes1–4 with 2,345 contemporary humans to show that most
present Europeans derive from at least three highly differentiated populations: West
European Hunter-Gatherers (WHG), who contributed ancestry to all Europeans but not to Near
Easterners; Ancient North Eurasians (ANE) related to Upper Paleolithic Siberians3, who contributed to both Europeans and Near
Easterners; and Early European Farmers (EEF), who were mainly of Near Eastern origin but
also harbored WHG-related ancestry. We model these populations’ deep relationships
and show that EEF had ~44% ancestry from a “Basal Eurasian”
population that split prior to the diversification of other non-African lineages.
We present a high-quality genome sequence of a Neanderthal woman from Siberia. We show that her parents were related at the level of half-siblings and that mating among close relatives was common among her recent ancestors. We also sequenced the genome of a Neanderthal from the Caucasus to low coverage. An analysis of the relationships and population history of available archaic genomes and 25 present-day human genomes shows that several gene flow events occurred among Neanderthals, Denisovans and early modern humans, possibly including gene flow into Denisovans from an unknown archaic group. Thus, interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene. In addition, the high-quality Neanderthal genome allows us to establish a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neanderthals and Denisovans.
Human pygmy populations inhabit different regions of the world, from Africa to Melanesia. In Asia, short-statured populations are often referred to as "negritos." Their short stature has been interpreted as a consequence of thermoregulatory, nutritional, and/or locomotory adaptations to life in tropical forests. A more recent hypothesis proposes that their stature is the outcome of a life history trade-off in high-mortality environments, where early reproduction is favored and, consequently, early sexual maturation and early growth cessation have coevolved. Some serological evidence of deficiencies in the growth hormone/insulin-like growth factor axis have been previously associated with pygmies' short stature. Using genome-wide single-nucleotide polymorphism genotype data, we first tested whether different negrito groups living in the Philippines and Papua New Guinea are closely related and then investigated genomic signals of recent positive selection in African, Asian, and Papuan pygmy populations. We found that negritos in the Philippines and Papua New Guinea are genetically more similar to their nonpygmy neighbors than to one another and have experienced positive selection at different genes. These results indicate that geographically distant pygmy groups are likely to have evolved their short stature independently. We also found that selection on common height variants is unlikely to explain their short stature and that different genes associated with growth, thyroid function, and sexual development are under selection in different pygmy groups.
We introduce a flexible and robust simulation-based framework to infer demographic parameters from the site frequency spectrum (SFS) computed on large genomic datasets. We show that our composite-likelihood approach allows one to study evolutionary models of arbitrary complexity, which cannot be tackled by other current likelihood-based methods. For simple scenarios, our approach compares favorably in terms of accuracy and speed with [Formula: see text], the current reference in the field, while showing better convergence properties for complex models. We first apply our methodology to non-coding genomic SNP data from four human populations. To infer their demographic history, we compare neutral evolutionary models of increasing complexity, including unsampled populations. We further show the versatility of our framework by extending it to the inference of demographic parameters from SNP chips with known ascertainment, such as that recently released by Affymetrix to study human origins. Whereas previous ways of handling ascertained SNPs were either restricted to a single population or only allowed the inference of divergence time between a pair of populations, our framework can correctly infer parameters of more complex models including the divergence of several populations, bottlenecks and migration. We apply this approach to the reconstruction of African demography using two distinct ascertained human SNP panels studied under two evolutionary models. The two SNP panels lead to globally very similar estimates and confidence intervals, and suggest an ancient divergence (>110 Ky) between Yoruba and San populations. Our methodology appears well suited to the study of complex scenarios from large genomic data sets.
The first colonization of the Greater Australian continent, known as Sahul, indicated that humans had modern cognitive ability. Such modern human abilities probably emerged earlier in Africa. I will argue that the only way we can identify what constitutes modern human behavior is to look at the record in Australia-the first place colonized only by modern humans. I place this argument within recent theorizing about cognitive evolution. © 2010 by The Wenner-Gren Foundation for Anthropological Research. All rights reserved.
The Australian region spans some 60° of latitude and 50° of longitude and displays considerable regional climate variability both today and during the Late Quaternary. A synthesis of marine and terrestrial climate records, combining findings from the Southern Ocean, temperate, tropical and arid zones, identifies a complex response of climate proxies to a background of changing boundary conditions over the last 35,000 years. Climate drivers include the seasonal timing of insolation, greenhouse gas content of the atmosphere, sea level rise and ocean and atmospheric circulation changes. Our compilation finds few climatic events that could be used to construct a climate event stratigraphy for the entire region, limiting the usefulness of this approach. Instead we have taken a spatial approach, looking to discern the patterns of change across the continent.
We present the first proposal of detailed internal subgrouping and higher-order structure of the Pama-Nyungan family of Australian languages. Previous work has identified more than twenty-five primary subgroups in the family, with little indication of how these groups might fit together. Some work has assumed that reconstruction of higher nodes in the tree was impossible, either because extensive internal borrowing has obscured more remote relations, or because the languages are not sufficiently well attested (see, for example, Bowern & Koch 2004b, Dixon 1997). With regard to the first objection, work by Alpher and Nash (1999) and Bowern and colleagues (2011) shows that loan levels are not high enough to obscure vertical transmission for all but a few languages. New data remove the second objection. Here we use Bayesian phylogenetic inference to show that the Pama-Nyungan tree has a discernible internal subgrouping. We identify four major divisions within the family and discuss the implications of this grouping for future work on the family.*
Neanderthals were a group of archaic hominins that occupied most of Europe and parts of Western Asia from roughly 30-300 thousand years ago (Kya). They coexisted with modern humans during part of this time. Previous genetic analyses that compared a draft sequence of the Neanderthal genome with genomes of several modern humans concluded that Neanderthals made a small (1-4%) contribution to the gene pools of all non-African populations. This observation was consistent with a single episode of admixture from Neanderthals into the ancestors of all non-Africans when the two groups coexisted in the Middle East 50-80 Kya. We examined the relationship between Neanderthals and modern humans in greater detail by applying two complementary methods to the published draft Neanderthal genome and an expanded set of high-coverage modern human genome sequences. We find that, consistent with the recent finding of Meyer et al. (2012), Neanderthals contributed more DNA to modern East Asians than to modern Europeans. Furthermore we find that the Maasai of East Africa have a small but significant fraction of Neanderthal DNA. Because our analysis is of several genomic samples from each modern human population considered, we are able to document the extent of variation in Neanderthal ancestry within and among populations. Our results combined with those previously published show that a more complex model of admixture between Neanderthals and modern humans is necessary to account for the different levels of Neanderthal ancestry among human populations. In particular, at least some Neanderthal-modern human admixture must postdate the separation of the ancestors of modern European and modern East Asian populations.
Despite a massive endeavour, the problem of modern human origins not only remains unresolved, but is usually reduced to “Out of Africa” versus multiregional evolution. Not all would agree, but evidence for a single recent origin is accumulating. Here, we want to go beyond this debate and explore within the “Out of Africa” framework an issue that has not been fully addressed: the mechanism by which modern human diversity has developed. We believe there is no clear rubicon of modern Homo sapiens, and that multiple dispersals occurred from a morphologically variable population in Africa. Pre-existing African diversity is thus crucial to the way human diversity developed outside Africa. The pattern of diversity—behavioural, linguistic, morphological and genetic—can be interpreted as the result of dispersals, colonisation, differentiation and subsequent dispersals overlaid on former population ranges. The first dispersals would have originated in Africa from where two different geographical routes were possible, one through Ethiopia/Arabia towards South Asia, and one through North Africa/Middle East towards Eurasia.
Recent studies of ancient genomes have suggested that gene flow from archaic hominin groups to the ancestors of modern humans occurred on two separate occasions during the modern human expansion out of Africa. At the same time, decreasing levels of human genetic diversity have been found at increasing distance from Africa as a consequence of human expansion out of Africa. We analyzed the signal of archaic ancestry in modern human populations, and we investigated how serial founder models of human expansion affect the signal of archaic ancestry using simulations. For descendants of an archaic admixture event, we show that genetic drift coupled with ascertainment bias for common alleles can cause artificial but largely predictable differences in similarity to archaic genomes. In genotype data from non-Africans, this effect results in a biased genetic similarity to Neandertals with increasing distance from Africa. However, in addition to the previously reported gene flow between Neandertals and non-Africans as well as gene flow between an archaic human population from Siberia ("Denisovans") and Oceanians, we found a significant affinity between East Asians, particularly Southeast Asians, and the Denisova genome--a pattern that is not expected under a model of solely Neandertal admixture in the ancestry of East Asians. These results suggest admixture between Denisovans or a Denisova-related population and the ancestors of East Asians, and that the history of anatomically modern and archaic humans might be more complex than previously proposed.
It has recently been shown that ancestors of New Guineans and Bougainville Islanders have inherited a proportion of their ancestry from Denisovans, an archaic hominin group from Siberia. However, only a sparse sampling of populations from Southeast Asia and Oceania were analyzed. Here, we quantify Denisova admixture in 33 additional populations from Asia and Oceania. Aboriginal Australians, Near Oceanians, Polynesians, Fijians, east Indonesians, and Mamanwa (a "Negrito" group from the Philippines) have all inherited genetic material from Denisovans, but mainland East Asians, western Indonesians, Jehai (a Negrito group from Malaysia), and Onge (a Negrito group from the Andaman Islands) have not. These results indicate that Denisova gene flow occurred into the common ancestors of New Guineans, Australians, and Mamanwa but not into the ancestors of the Jehai and Onge and suggest that relatives of present-day East Asians were not in Southeast Asia when the Denisova gene flow occurred. Our finding that descendants of the earliest inhabitants of Southeast Asia do not all harbor Denisova admixture is inconsistent with a history in which the Denisova interbreeding occurred in mainland Asia and then spread over Southeast Asia, leading to all its earliest modern human inhabitants. Instead, the data can be most parsimoniously explained if the Denisova gene flow occurred in Southeast Asia itself. Thus, archaic Denisovans must have lived over an extraordinarily broad geographic and ecological range, from Siberia to tropical Asia.
We present an Aboriginal Australian genomic sequence obtained from a 100-year-old lock of hair donated by an Aboriginal man from southern Western Australia in the early 20th century. We detect no evidence of European admixture and estimate contamination levels to be below 0.5%. We show that Aboriginal Australians are descendants of an early human dispersal into eastern Asia, possibly 62,000 to 75,000 years ago. This dispersal is separate from the one that gave rise to modern Asians 25,000 to 38,000 years ago. We also find evidence of gene flow between populations of the two dispersal waves prior to the divergence of Native Americans from modern Asian ancestors. Our findings support the hypothesis that present-day Aboriginal Australians descend from the earliest humans to occupy Australia, likely representing one of the oldest continuous populations outside Africa.
Serum urate concentrations are highly heritable and elevated serum urate is a key risk factor for gout. Genome-wide association
studies (GWAS) of serum urate in African American (AA) populations are lacking. We conducted a meta-analysis of GWAS of serum
urate levels and gout among 5820 AA and a large candidate gene study among 6890 AA and 21 708 participants of European ancestry
(EA) within the Candidate Gene Association Resource Consortium. Findings were tested for replication among 1996 independent
AA individuals, and evaluated for their association among 28 283 EA participants of the CHARGE Consortium. Functional studies
were conducted using 14C-urate transport assays in mammalian Chinese hamster ovary cells. In the discovery GWAS of serum urate, three loci achieved
genome-wide significance (P< 5.0 × 10−8): a novel locus near SGK1/SLC2A12 on chromosome 6 (rs9321453, P= 1.0 × 10−9), and two loci previously identified in EA participants, SLC2A9 (P= 3.8 × 10−32) and SLC22A12 (P= 2.1 × 10−10). A novel rare non-synonymous variant of large effect size in SLC22A12, rs12800450 (minor allele frequency 0.01, G65W), was identified and replicated (beta −1.19 mg/dl, P= 2.7 × 10−16). 14C-urate transport assays showed reduced urate transport for the G65W URAT1 mutant. Finally, in analyses of 11 loci previously
associated with serum urate in EA individuals, 10 of 11 lead single-nucleotide polymorphisms showed direction-consistent association
with urate among AA. In summary, we identified and replicated one novel locus in association with serum urate levels and experimentally
characterize the novel G65W variant in URAT1 as a functional allele. Our data support the importance of multi-ethnic GWAS
in the identification of novel risk loci as well as functional variants.
Using DNA extracted from a finger bone found in Denisova Cave in southern Siberia, we have sequenced the genome of an archaic hominin to about 1.9-fold coverage. This individual is from a group that shares a common origin with Neanderthals. This population was not involved in the putative gene flow from Neanderthals into Eurasians; however, the data suggest that it contributed 4-6% of its genetic material to the genomes of present-day Melanesians. We designate this hominin population 'Denisovans' and suggest that it may have been widespread in Asia during the Late Pleistocene epoch. A tooth found in Denisova Cave carries a mitochondrial genome highly similar to that of the finger bone. This tooth shares no derived morphological features with Neanderthals or modern humans, further indicating that Denisovans have an evolutionary history distinct from Neanderthals and modern humans.
Aboriginal people have been in Australia for at least 40,000 years, speaking about 250 languages. Through examination of published and unpublished materials on each of the individual languages, Professor Dixon surveys the ways in which the languages vary typologically and presents a profile of this long-established linguistic area. The areal distribution of most features is illustrated with more than 30 maps, showing that the languages tend to move in cyclic fashion with respect to many of the parameters. There is also an index of languages and language groups. Professor Dixon, a pioneering scholar in the field, brings an interesting perspective to this diverse and complex material.
Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans.
Some present-day humans derive up to ∼5% [1] of their ancestry from archaic Denisovans, an even larger proportion than the ∼2% from Neanderthals [2]. We developed methods that can disambiguate the locations of segments of Denisovan and Neanderthal ancestry in present-day humans and applied them to 257 high-coverage genomes from 120 diverse populations, among which were 20 individual Oceanians with high Denisovan ancestry [3]. In Oceanians, the average size of Denisovan fragments is larger than Neanderthal fragments, implying a more recent average date of Denisovan admixture in the history of these populations (p = 0.00004). We document more Denisovan ancestry in South Asia than is expected based on existing models of history, reflecting a previously undocumented mixture related to archaic humans (p = 0.0013). Denisovan ancestry, just like Neanderthal ancestry, has been deleterious on a modern human genetic background, as reflected by its depletion near genes. Finally, the reduction of both archaic ancestries is especially pronounced on chromosome X and near genes more highly expressed in testes than other tissues (p = 1.2 × 10(-7) to 3.2 × 10(-7) for Denisovan and 2.2 × 10(-3) to 2.9 × 10(-3) for Neanderthal ancestry even after controlling for differences in level of selective constraint across gene classes). This suggests that reduced male fertility may be a general feature of mixtures of human populations diverged by >500,000 years.
This book is an introduction to the archaeology of Australia from prehistoric times to the eighteenth century AD. It is the only up-to-date textbook on the subject and is designed for undergraduate courses, based on the author's considerable experience of teaching at the Australian National University. Lucidly written, it shows the diversity and colourfulness of the history of humanity in the southern continent. The Archaeology of Ancient Australia demonstrates with an array of illustrations and clear descriptions of key archaeological evidence from Australia a thorough evaluation of Australian prehistory. Readers are shown how this human past can be reconstructed from archaeological evidence, supplemented by information from genetics, environmental sciences, anthropology, and history. The result is a challenging view about how varied human life in the ancient past has been.
Published ages of >50 ka for occupation at Madjedbebe (Malakunanja II) in Australia's north have kept the site prominent in discussions about the colonisation of Sahul. The site also contains one of the largest stone artefact assemblages in Sahul for this early period. However, the stone artefacts and other important archaeological components of the site have never been described in detail, leading to persistent doubts about its stratigraphic integrity. We report on our analysis of the stone artefacts and faunal and other materials recovered during the 1989 excavations, as well as the stratigraphy and depositional history recorded by the original excavators. We demonstrate that the technology and raw materials of the early assemblage are distinctive from those in the overlying layers. Silcrete and quartzite artefacts are common in the early assemblage, which also includes edge-ground axe fragments and ground haematite. The lower flaked stone assemblage is distinctive, comprising a mix of long convergent flakes, some radial flakes with faceted platforms, and many small thin silcrete flakes that we interpret as thinning flakes. Residue and use-wear analysis indicate occasional grinding of haematite and woodworking, as well as frequent abrading of platform edges on thinning flakes. We conclude that previous claims of extensive displacement of artefacts and post-depositional disturbance may have been overstated. The stone artefacts and stratigraphic details support previous claims for human occupation 50-60 ka and show that human occupation during this time differed from later periods. We discuss the implications of these new data for understanding the first human colonisation of Sahul.
Copyright © 2015 Elsevier Ltd. All rights reserved.
The availability of complete human genome sequences from populations across the world has given rise to new population genetic inference methods that explicitly model ancestral relationships under recombination and mutation. So far, application of these methods to evolutionary history more recent than 20,000-30,000 years ago and to population separations has been limited. Here we present a new method that overcomes these shortcomings. The multiple sequentially Markovian coalescent (MSMC) analyzes the observed pattern of mutations in multiple individuals, focusing on the first coalescence between any two individuals. Results from applying MSMC to genome sequences from nine populations across the world suggest that the genetic separation of non-African ancestors from African Yoruban ancestors started long before 50,000 years ago and give information about human population history as recent as 2,000 years ago, including the bottleneck in the peopling of the Americas and separations within Africa, East Asia and Europe.
The Australian continent holds some of the earliest archaeological evidence for the expansion of modern humans out of Africa, with initial occupation at least 40,000 y ago. It is commonly assumed that Australia remained largely isolated following initial colonization, but the genetic history of Australians has not been explored in detail to address this issue. Here, we analyze large-scale genotyping data from aboriginal Australians, New Guineans, island Southeast Asians and Indians. We find an ancient association between Australia, New Guinea, and the Mamanwa (a Negrito group from the Philippines), with divergence times for these groups estimated at 36,000 y ago, and supporting the view that these populations represent the descendants of an early "southern route" migration out of Africa, whereas other populations in the region arrived later by a separate dispersal. We also detect a signal indicative of substantial gene flow between the Indian populations and Australia well before European contact, contrary to the prevailing view that there was no contact between Australia and the rest of the world. We estimate this gene flow to have occurred during the Holocene, 4,230 y ago. This is also approximately when changes in tool technology, food processing, and the dingo appear in the Australian archaeological record, suggesting that these may be related to the migration from India.
Population mixture is an important process in biology. We present a suite of methods for learning about population mixtures, implemented in a software package called ADMIXTOOLS, that support formal tests for whether mixture occurred, and make it possible to infer proportions and dates of mixture. We also describe the development of a new single nucleotide polymorphism (SNP) array consisting of 629,433 sites with clearly documented ascertainment that was specifically designed for population genetic analyses, and that we genotyped in 934 individuals from 53 diverse populations. To illustrate the methods, we give a number of examples where they provide new insights about the history of human admixture. The most striking finding is a clear signal of admixture into northern Europe, with one ancestral population related to present day Basques and Sardinians, and the other related to present day populations of northeast Asia and the Americas. This likely reflects a history of admixture between Neolithic migrants and the indigenous Mesolithic population of Europe, consistent with recent analyses of ancient bones from Sweden and the sequencing of the genome of the Tyrolean 'Iceman'.
It is now possible to make direct measurements of the mutation rate in modern humans using next-generation sequencing. These measurements reveal a value that is approximately half of that previously derived from fossil calibration, and this has implications for our understanding of demographic events in human evolution and other aspects of population genetics. Here, we discuss the implications of a lower-than-expected mutation rate in relation to the timescale of human evolution.
The genetic history of a group of populations is usually analyzed by reconstructing a tree of their origins. Reliability of the reconstruction depends on the validity of the hypothesis that genetic differentiation of the populations is mostly due to population fissions followed by independent evolution. If necessary, adjustment for major population admixtures can be made. Dating the fissions requires comparisons with paleoanthropological and paleontological dates, which are few and uncertain. A method of absolute genetic dating recently introduced uses mutation rates as molecular clocks; it was applied to human evolution using microsatellites, which have a sufficiently high mutation rate. Results are comparable with those of other methods and agree with a recent expansion of modern humans from Africa. An alternative method of analysis, useful when there is adequate geographic coverage of regions, is the geographic study of frequencies of alleles or haplotypes. As in the case of trees, it is necessary to summarize data from many loci for conclusions to be acceptable. Results must be independent from the loci used. Multivariate analyses like principal components or multidimensional scaling reveal a number of hidden patterns and evaluate their relative importance. Most patterns found in the analysis of human living populations are likely to be consequences of demographic expansions, determined by technological developments affecting food availability, transportation, or military power. During such expansions, both genes and languages are spread to potentially vast areas. In principle, this tends to create a correlation between the respective evolutionary trees. The correlation is usually positive and often remarkably high. It can be decreased or hidden by phenomena of language replacement and also of gene replacement, usually partial, due to gene flow.
The human history of Oceania comprises two extremes: the initial colonizations of Near Oceania, one of the oldest out-of-Africa migrations, and of Remote Oceania, the most recent expansion into unoccupied territories. Genetic studies, mostly using uniparentally inherited DNA, have shed some light on human origins in Oceania, particularly indicating that Polynesians are of mixed East Asian and Near Oceanian ancestry. Here, we use ∼1 million single nucleotide polymorphisms (SNPs) to investigate the demographic history of Oceania in a more detailed manner.
We developed a new approach to account for SNP ascertainment bias, used approximate Bayesian computation simulations to choose the best-fitting model of population history, and estimated demographic parameters. We find that the ancestors of Near Oceanians diverged from ancestral Eurasians ∼27 thousand years ago (kya), suggesting separate initial occupations of both territories. The genetic admixture in Polynesian history between East Asians (∼87%) and Near Oceanians (∼13%) occurred ∼3 kya, prior to the colonization of Polynesia. Fijians are of Polynesian (∼65%) and additional Near Oceanian (∼35%) ancestry not found in Polynesians, with this admixture occurring considerably after the initial settlement of Remote Oceania. Our data support a greater contribution of East Asian women than men in the admixture history of Remote Oceania and highlight population substructure in Polynesia and New Guinea.
Despite the inherent ascertainment bias, genome-wide SNP data provide new insights into the genetic history of Oceana. Our approach to correct for ascertainment bias and obtain reliable inferences concerning demographic history should prove useful in other such studies.