RESUMEN
f-statistics have emerged as a first line of analysis for making inferences about demographic history from genome-wide data. Not only are they guaranteed to allow robust tests of the fits of proposed models of population history to data when analyzing full genome sequencing data-that is, all single nucleotide polymorphisms (SNPs) in the individuals being analyzed-but they are also guaranteed to allow robust tests of models for SNPs ascertained as polymorphic in a population that is an outgroup in a phylogenetic sense to all groups being analyzed. True "outgroup ascertainment" is in practice impossible in humans because our species has arisen from a substructured ancestral population that does not descend from a homogeneous ancestral population going back many hundreds of thousands of years into the past. However, initial studies suggested that non-outgroup-ascertainment schemes might produce robust enough results using f-statistics, and that motivated widespread fitting of models to data using non-outgroup-ascertained SNP panels such as the "Affymetrix Human Origins array" which has been genotyped on thousands of modern individuals from hundreds of populations, or the "1240k" in-solution enrichment reagent which has been the source of about 70% of published genome-wide data for ancient humans. In this study, we show that while analyses of population history using such panels work well for studies of relationships among non-African populations and one African outgroup, when co-modeling more than one sub-Saharan African and/or archaic human groups (Neanderthals and Denisovans), fitting of f-statistics to such SNP sets is expected to frequently lead to false rejection of true demographic histories, and failure to reject incorrect models. Analyzing panels of SNPs polymorphic in archaic humans, which has been suggested as a solution for the ascertainment problem, has limited statistical power and retains important biases. However, by carrying out simulations of diverse demographic histories, we show that bias in inferences based on f-statistics can be minimized by ascertaining on variants common in a union of diverse African groups; such ascertainment retains high statistical power while allowing co-analysis of archaic and modern groups.
Asunto(s)
Pueblo Africano , Demografía , Filogenia , Polimorfismo de Nucleótido Simple , Animales , Humanos , Población Negra/genética , Mapeo Cromosómico , Genotipo , Hombre de Neandertal/genética , Polimorfismo de Nucleótido Simple/genética , Pueblo Africano/genética , Demografía/historia , Variación Biológica Poblacional/genética , Modelos Estadísticos , SesgoRESUMEN
Much of the American Arctic was first settled 5,000 years ago, by groups of people known as Palaeo-Eskimos. They were subsequently joined and largely displaced around 1,000 years ago by ancestors of the present-day Inuit and Yup'ik1-3. The genetic relationship between Palaeo-Eskimos and Native American, Inuit, Yup'ik and Aleut populations remains uncertain4-6. Here we present genomic data for 48 ancient individuals from Chukotka, East Siberia, the Aleutian Islands, Alaska, and the Canadian Arctic. We co-analyse these data with data from present-day Alaskan Iñupiat and West Siberian populations and published genomes. Using methods based on rare-allele and haplotype sharing, as well as established techniques4,7-9, we show that Palaeo-Eskimo-related ancestry is ubiquitous among people who speak Na-Dene and Eskimo-Aleut languages. We develop a comprehensive model for the Holocene peopling events of Chukotka and North America, and show that Na-Dene-speaking peoples, people of the Aleutian Islands, and Yup'ik and Inuit across the Arctic region all share ancestry from a single Palaeo-Eskimo-related Siberian source.
Asunto(s)
Migración Humana/historia , Inuk/clasificación , Inuk/genética , Filogenia , Filogeografía , África , Alaska , Alelos , Regiones Árticas , Asia Sudoriental , Canadá , Europa (Continente) , Genoma Humano/genética , Haplotipos , Historia Antigua , Humanos , Análisis de Componente Principal , Siberia/etnologíaRESUMEN
The great ethnolinguistic diversity found today in mainland Southeast Asia (MSEA) reflects multiple migration waves of people in the past. Maritime trading between MSEA and India was established at the latest 300 BCE, and the formation of early states in Southeast Asia during the first millennium CE was strongly influenced by Indian culture, a cultural influence that is still prominent today. Several ancient Indian-influenced states were located in present-day Thailand, and various populations in the country are likely to be descendants of people from those states. To systematically explore Indian genetic heritage in MSEA populations, we generated genome-wide SNP data (using the Affymetrix Human Origins array) for 119 present-day individuals belonging to 10 ethnic groups from Thailand and co-analyzed them with published data using PCA, ADMIXTURE, and methods relying on f-statistics and on autosomal haplotypes. We found low levels of South Asian admixture in various MSEA populations for whom there is evidence of historical connections with the ancient Indian-influenced states but failed to find this genetic component in present-day hunter-gatherer groups and relatively isolated groups from the highlands of Northern Thailand. The results suggest that migration of Indian populations to MSEA may have been responsible for the spread of Indian culture in the region. Our results also support close genetic affinity between Kra-Dai-speaking (also known as Tai-Kadai) and Austronesian-speaking populations, which fits a linguistic hypothesis suggesting cladality of the two language families.
Asunto(s)
Pueblo Asiatico/genética , Etnicidad/genética , Asia Sudoriental/etnología , Variación Genética/genética , Genética de Población/métodos , Haplotipos/genética , Humanos , India/etnología , Lenguaje , Polimorfismo de Nucleótido Simple/genética , Tailandia/etnologíaRESUMEN
The human parasite Trypanosoma brucei does not synthesize heme de novo and instead relies entirely on heme supplied by its vertebrate host or its insect vector, the tsetse fly. In the host bloodstream T. brucei scavenges heme via haptoglobin-hemoglobin (HpHb) receptor-mediated endocytosis occurring in the flagellar pocket. However, in the procyclic developmental stage, in which T. brucei is confined to the tsetse fly midgut, this receptor is apparently not expressed, suggesting that T. brucei takes up heme by a different, unknown route. To define this alternative route, we functionally characterized heme transporter TbHrg in the procyclic stage. RNAi-induced down-regulation of TbHrg in heme-limited culture conditions resulted in slower proliferation, decreased cellular heme, and marked changes in cellular morphology so that the cells resemble mesocyclic trypomastigotes. Nevertheless, the TbHrg KO developed normally in the tsetse flies at rates comparable with wild-type cells. T. brucei cells overexpressing TbHrg displayed up-regulation of the early procyclin GPEET and down-regulation of the late procyclin EP1, two proteins coating the T. brucei surface in the procyclic stage. Light microscopy of immunostained TbHrg indicated localization to the flagellar membrane, and scanning electron microscopy revealed more intense TbHrg accumulation toward the flagellar pocket. Based on these findings, we postulate that T. brucei senses heme levels via the flagellar TbHrg protein. Heme deprivation in the tsetse fly anterior midgut might represent an environmental stimulus involved in the transformation of this important human parasite, possibly through metabolic remodeling.
Asunto(s)
Hemo/metabolismo , Proteínas de Transporte de Membrana/metabolismo , Proteínas Protozoarias/metabolismo , Trypanosoma brucei brucei/metabolismo , Moscas Tse-Tse/parasitología , Secuencia de Aminoácidos , Animales , Transporte Biológico , Proliferación Celular , Regulación hacia Abajo , Flagelos/metabolismo , Regulación del Desarrollo de la Expresión Génica , Estadios del Ciclo de Vida , Microscopía Electrónica de Rastreo , Interferencia de ARN , Reacción en Cadena en Tiempo Real de la Polimerasa , Receptores de Superficie Celular/metabolismo , TransgenesRESUMEN
Trypanosoma brucei has a complex life cycle during which its single mitochondrion is subjected to major metabolic and morphological changes. While the procyclic stage (PS) of the insect vector contains a large and reticulated mitochondrion, its counterpart in the bloodstream stage (BS) parasitizing mammals is highly reduced and seems to be devoid of most functions. We show here that key Fe-S cluster assembly proteins are still present and active in this organelle and that produced clusters are incorporated into overexpressed enzymes. Importantly, the cysteine desulfurase Nfs, equipped with the nuclear localization signal, was detected in the nucleolus of both T. brucei life stages. The scaffold protein Isu, an interacting partner of Nfs, was also found to have a dual localization in the mitochondrion and the nucleolus, while frataxin and both ferredoxins are confined to the mitochondrion. Moreover, upon depletion of Isu, cytosolic tRNA thiolation dropped in the PS but not BS parasites.
Asunto(s)
Liasas de Carbono-Azufre/metabolismo , Núcleo Celular/metabolismo , Mitocondrias/metabolismo , Proteínas Asociadas a Matriz Nuclear/metabolismo , Proteínas Protozoarias/metabolismo , Trypanosoma brucei brucei/enzimología , Transporte Activo de Núcleo Celular , Secuencia de Aminoácidos , Liasas de Carbono-Azufre/química , Liasas de Carbono-Azufre/genética , Ferredoxinas/metabolismo , Proteínas de Unión a Hierro/metabolismo , Proteínas Mitocondriales/metabolismo , Datos de Secuencia Molecular , Señales de Localización Nuclear , Proteínas Asociadas a Matriz Nuclear/química , Proteínas Asociadas a Matriz Nuclear/genética , Unión Proteica , Multimerización de Proteína , Proteínas Protozoarias/química , Proteínas Protozoarias/genética , Trypanosoma brucei brucei/genética , Trypanosoma brucei brucei/metabolismo , FrataxinaRESUMEN
Ferredoxins are highly conserved proteins that function universally as electron transporters. They not only require Fe-S clusters for their own activity, but are also involved in Fe-S formation itself. We identified two homologues of ferredoxin in the genome of the parasitic protist Trypanosoma brucei and named them TbFdxA and TbFdxB. TbFdxA protein, which is homologous to other eukaryotic mitochondrial ferredoxins, is essential in both the procyclic (= insect-transmitted) and bloodstream (mammalian) stage, but is more abundant in the active mitochondrion of the former stage. Depletion of TbFdxA caused disruption of Fe-S cluster biogenesis and lowered the level of intracellular haem. However, TbFdxB, which is present exclusively within kinetoplastid flagellates, was non-essential for the procyclic stage, and double knock-down with TbFdxA showed this was not due to functional redundancy between the two homologues. Heterologous expressions of human orthologues HsFdx1 and HsFdx2 fully rescued the growth and Fe-S-dependent enzymatic activities of TbFdxA knock-down. In both cases, the genuine human import signals allowed efficient import into the T. brucei mitochondrion. Given the huge evolutionary distance between trypanosomes and humans, ferredoxins clearly have ancestral and highly conserved function in eukaryotes and both human orthologues have retained the capacity to participate in Fe-S cluster assembly.
Asunto(s)
Ferredoxinas/metabolismo , Trypanosoma brucei brucei/enzimología , Trypanosoma brucei brucei/metabolismo , Análisis por Conglomerados , Transporte de Electrón , Ferredoxinas/genética , Técnicas de Silenciamiento del Gen , Prueba de Complementación Genética , Humanos , Filogenia , Transporte de Proteínas , Homología de Secuencia de Aminoácido , Trypanosoma brucei brucei/genéticaRESUMEN
The Yamnaya archaeological complex appeared around 3300BCE across the steppes north of the Black and Caspian Seas, and by 3000BCE reached its maximal extent from Hungary in the west to Kazakhstan in the east. To localize the ancestral and geographical origins of the Yamnaya among the diverse Eneolithic people that preceded them, we studied ancient DNA data from 428 individuals of which 299 are reported for the first time, demonstrating three previously unknown Eneolithic genetic clines. First, a "Caucasus-Lower Volga" (CLV) Cline suffused with Caucasus hunter-gatherer (CHG) ancestry extended between a Caucasus Neolithic southern end in Neolithic Armenia, and a steppe northern end in Berezhnovka in the Lower Volga. Bidirectional gene flow across the CLV cline created admixed intermediate populations in both the north Caucasus, such as the Maikop people, and on the steppe, such as those at the site of Remontnoye north of the Manych depression. CLV people also helped form two major riverine clines by admixing with distinct groups of European hunter-gatherers. A "Volga Cline" was formed as Lower Volga people mixed with upriver populations that had more Eastern hunter-gatherer (EHG) ancestry, creating genetically hyper-variable populations as at Khvalynsk in the Middle Volga. A "Dnipro Cline" was formed as CLV people bearing both Caucasus Neolithic and Lower Volga ancestry moved west and acquired Ukraine Neolithic hunter-gatherer (UNHG) ancestry to establish the population of the Serednii Stih culture from which the direct ancestors of the Yamnaya themselves were formed around 4000BCE. This population grew rapidly after 3750-3350BCE, precipitating the expansion of people of the Yamnaya culture who totally displaced previous groups on the Volga and further east, while admixing with more sedentary groups in the west. CLV cline people with Lower Volga ancestry contributed four fifths of the ancestry of the Yamnaya, but also, entering Anatolia from the east, contributed at least a tenth of the ancestry of Bronze Age Central Anatolians, where the Hittite language, related to the Indo-European languages spread by the Yamnaya, was spoken. We thus propose that the final unity of the speakers of the "Proto-Indo-Anatolian" ancestral language of both Anatolian and Indo-European languages can be traced to CLV cline people sometime between 4400-4000 BCE.
RESUMEN
Thailand is a country where over 60 languages from five language families (Austroasiatic, Austronesian, Hmong-Mien, Kra-Dai, and Sino-Tibetan) are spoken. The Kra-Dai language family is the most prevalent, and Thai, the official language of the country, belongs to it. Previous genome-wide studies on Thailand populations revealed a complex population structure and put some hypotheses forward concerning the population history of the country. However, many published populations have not been co-analyzed, and some aspects of population history were not explored adequately. In this study, we employ new methods to re-analyze published genome-wide genetic data on Thailand populations, with a focus on 14 Kra-Dai-speaking groups. Our analyses reveal South Asian ancestry in Kra-Dai-speaking Lao Isan and Khonmueang, and in Austroasiatic-speaking Palaung, in contrast to a previous study in which the data were generated. We support the admixture scenario for the formation of Kra-Dai-speaking groups from Thailand who harbor both Austroasiatic-related ancestry and Kra-Dai-related ancestry from outside of Thailand. We also provide evidence of bidirectional admixture between Southern Thai and Nayu, an Austronesian-speaking group from Southern Thailand. Challenging some previously reported genetic analyses, we reveal a close genetic relationship between Nayu and Austronesian-speaking groups from Island Southeast Asia (ISEA).
Asunto(s)
Pueblo Asiatico , Asiático , Lenguaje , Humanos , Asiático/etnología , Asiático/genética , Pueblo Asiatico/etnología , Pueblo Asiatico/genética , Tailandia , Asia Sudoriental/etnología , Estudio de Asociación del Genoma CompletoRESUMEN
f -statistics have emerged as a first line of analysis for making inferences about demographic history from genome-wide data. These statistics can provide strong evidence for either admixture or cladality, which can be robust to substantial rates of errors or missing data. f -statistics are guaranteed to be unbiased under "SNP ascertainment" (analyzing non-randomly chosen subsets of single nucleotide polymorphisms) only if it relies on a population that is an outgroup for all groups analyzed. However, ascertainment on a true outgroup that is not co-analyzed with other populations is often impractical and uncommon in the literature. In this study focused on practical rather than theoretical aspects of SNP ascertainment, we show that many non-outgroup ascertainment schemes lead to false rejection of true demographic histories, as well as to failure to reject incorrect models. But the bias introduced by common ascertainments such as the 1240K panel is mostly limited to situations when more than one sub-Saharan African and/or archaic human groups (Neanderthals and Denisovans) or non-human outgroups are co-modelled, for example, f 4 -statistics involving one non-African group, two African groups, and one archaic group. Analyzing panels of SNPs polymorphic in archaic humans, which has been suggested as a solution for the ascertainment problem, cannot fix all these problems since for some classes of f -statistics it is not a clean outgroup ascertainment, and in other cases it demonstrates relatively low power to reject incorrect demographic models since it provides a relatively small number of variants common in anatomically modern humans. And due to the paucity of high-coverage archaic genomes, archaic individuals used for ascertainment often act as sole representatives of the respective groups in an analysis, and we show that this approach is highly problematic. By carrying out large numbers of simulations of diverse demographic histories, we find that bias in inferences based on f -statistics introduced by non-outgroup ascertainment can be minimized if the derived allele frequency spectrum in the population used for ascertainment approaches the spectrum that existed at the root of all groups being co-analyzed. Ascertaining on sites with variants common in a diverse group of African individuals provides a good approximation to such a set of SNPs, addressing the great majority of biases and also retaining high statistical power for studying population history. Such a "pan-African" ascertainment, although not completely problem-free, allows unbiased exploration of demographic models for the widest set of archaic and modern human populations, as compared to the other ascertainment schemes we explored.
RESUMEN
Our understanding of population history in deep time has been assisted by fitting admixture graphs (AGs) to data: models that specify the ordering of population splits and mixtures, which along with the amount of genetic drift and the proportions of mixture, is the only information needed to predict the patterns of allele frequency correlation among populations. The space of possible AGs relating populations is vast, and thus most published studies have identified fitting AGs through a manual process driven by prior hypotheses, leaving the majority of alternative models unexplored. Here, we develop a method for systematically searching the space of all AGs that can incorporate non-genetic information in the form of topology constraints. We implement this findGraphs tool within a software package, ADMIXTOOLS 2, which is a reimplementation of the ADMIXTOOLS software with new features and large performance gains. We apply this methodology to identify alternative models to AGs that played key roles in eight publications and find that in nearly all cases many alternative models fit nominally or significantly better than the published one. Our results suggest that strong claims about population history from AGs should only be made when all well-fitting and temporally plausible models share common topological features. Our re-evaluation of published data also provides insight into the population histories of humans, dogs, and horses, identifying features that are stable across the models we explored, as well as scenarios of populations relationships that differ in important ways from models that have been highlighted in the literature.
Asunto(s)
Genética de Población , Hominidae , Humanos , Perros , Animales , Caballos , Frecuencia de los Genes , Programas Informáticos , Flujo Genético , Modelos GenéticosRESUMEN
Although a broad range of methods exists for reconstructing population history from genome-wide single nucleotide polymorphism data, just a few methods gained popularity in archaeogenetics: principal component analysis (PCA); ADMIXTURE, an algorithm that models individuals as mixtures of multiple ancestral sources represented by actual or inferred populations; formal tests for admixture such as f3-statistics and D/f4-statistics; and qpAdm, a tool for fitting two-component and more complex admixture models to groups or individuals. Despite their popularity in archaeogenetics, which is explained by modest computational requirements and ability to analyze data of various types and qualities, protocols relying on qpAdm that screen numerous alternative models of varying complexity and find "fitting" models (often considering both estimated admixture proportions and p-values as a composite criterion of model fit) remain untested on complex simulated population histories in the form of admixture graphs of random topology. We analyzed genotype data extracted from such simulations and tested various types of high-throughput qpAdm protocols ("rotating" and "non-rotating", with or without temporal stratification of target groups and proxy ancestry sources, and with or without a "model competition" step). We caution that high-throughput qpAdm protocols may be inappropriate for exploratory analyses in poorly studied regions/periods since their false discovery rates varied between 12% and 68% depending on the details of the protocol and on the amount and quality of simulated data (i.e., >12% of fitting two-way admixture models imply gene flows that were not simulated). We demonstrate that for reducing false discovery rates of qpAdm protocols to nearly 0% it is advisable to use large SNP sets with low missing data rates, the rotating qpAdm protocol with a strictly enforced rule that target groups do not pre-date their proxy sources, and an unsupervised ADMIXTURE analysis as a way to verify feasible qpAdm models. Our study has a number of limitations: for instance, these recommendations depend on the assumption that the underlying genetic history is a complex admixture graph and not a stepping-stone model.
RESUMEN
IscA/Isa proteins function as alternative scaffolds for the assembly of Fe-S clusters and/or provide iron for their assembly in prokaryotes and eukaryotes. Isa are usually non-essential and in most organisms are confined to the mitochondrion. We have studied the function of TbIsa1 and TbIsa2 in Trypanosoma brucei, where the requirement for both of them to sustain cell growth depends on the life cycle stage. The TbIsa proteins are abundant in the procyclic form, which contains an active organelle. Both proteins are indispensable for growth, as they are required for the assembly of Fe-S clusters in mitochondrial aconitase, fumarase and succinate dehydrogenase. Reactive oxygen species but not iron accumulate in the procyclic mitochondrion upon ablation of the TbIsa proteins, but their depletion does not influence the assembly of Fe-S clusters in cytosolic proteins. In the bloodstream form, which has a downregulated mitochondrion, the TbIsa proteins are non-essential. The Isa2 orthologue of the anaerobic protist Blastocystis partially rescued the growth and enzymatic activities of TbIsa1/2 knock-down. Rescues of single knock-downs as well as heterologous rescues with human Isa orthologues partially recovered the activities of aconitase and fumarase. These results show that the Isa1 and Isa2 proteins of diverse eukaryotes have overlapping functions.
Asunto(s)
Eliminación de Gen , Prueba de Complementación Genética , Mitocondrias/enzimología , Proteínas Mitocondriales/metabolismo , Proteínas Protozoarias/metabolismo , Trypanosoma brucei brucei/crecimiento & desarrollo , Blastocystis/genética , Supervivencia Celular , Humanos , Mitocondrias/metabolismo , Proteínas Mitocondriales/genética , Proteínas Protozoarias/genética , Trypanosoma brucei brucei/genética , Trypanosoma brucei brucei/metabolismoRESUMEN
Indian cultural influence is remarkable in present-day Mainland Southeast Asia (MSEA), and it may have stimulated early state formation in the region. Various present-day populations in MSEA harbor a low level of South Asian ancestry, but previous studies failed to detect such ancestry in any ancient individual from MSEA. In this study, we discovered a substantial level of South Asian admixture (ca. 40-50%) in a Protohistoric individual from the Vat Komnou cemetery at the Angkor Borei site in Cambodia. The location and direct radiocarbon dating result on the human bone (95% confidence interval is 78-234 calCE) indicate that this individual lived during the early period of Funan, one of the earliest states in MSEA, which shows that the South Asian gene flow to Cambodia started about a millennium earlier than indicated by previous published results of genetic dating relying on present-day populations. Plausible proxies for the South Asian ancestry source in this individual are present-day populations in Southern India, and the individual shares more genetic drift with present-day Cambodians than with most present-day East and Southeast Asian populations.
Asunto(s)
ADN Antiguo , Genética de Población , Humanos , Cambodia , Personas del Sur de Asia , Pueblo AsiaticoRESUMEN
Resistance to African trypanosomes in humans relies in part on the high affinity targeting of a trypanosome lytic factor 1 (TLF1) to a trypanosome haptoglobin-hemoglobin receptor (HpHbR). While TLF1 avoidance by the inactivation of HpHbR contributes to Trypanosoma brucei gambiense human infectivity, the evolutionary trade-off of this adaptation is unknown, as the physiological function of the receptor remains to be elucidated. Here we show that uptake of hemoglobin via HpHbR constitutes the sole heme import pathway in the trypanosome bloodstream stage. T. b. gambiense strains carrying the inactivating mutation in HpHbR, as well as genetically engineered T. b. brucei HpHbR knock-out lines show only trace levels of intracellular heme and lack hemoprotein-based enzymatic activities, thereby providing an uncommon example of aerobic parasitic proliferation in the absence of heme. We further show that HpHbR facilitates the developmental progression from proliferating long slender forms to cell cycle-arrested stumpy forms in T. b. brucei. Accordingly, T. b. gambiense was found to be poorly competent for slender-to-stumpy differentiation unless a functional HpHbR receptor derived from T. b. brucei was genetically restored. Altogether, we identify heme-deficient metabolism and disrupted cellular differentiation as two distinct HpHbR-dependent evolutionary trade-offs for T. b. gambiense human infectivity.
Asunto(s)
Lipoproteínas HDL , Trypanosoma brucei gambiense , Humanos , Trypanosoma brucei gambiense/genética , Trypanosoma brucei gambiense/metabolismo , Lipoproteínas HDL/metabolismo , Evolución Biológica , Hemo/metabolismo , Diferenciación Celular/genéticaRESUMEN
Fe/S clusters are part of the active site of many enzymes and are essential for cell viability. In eukaryotes the cysteine desulfurase Nfs (IscS) donates the sulfur during Fe/S cluster assembly and was thought sufficient for this reaction. Moreover, Nfs is indispensable for tRNA thiolation, a modification generally required for tRNA function and protein synthesis. Recently, Isd11 was discovered as an integral part of the Nfs activity at an early step of Fe/S cluster assembly. Here we show, using a combination of genetic, molecular, and biochemical approaches, that Isd11, in line with its strong association with Nfs, is localized in the mitochondrion of T. brucei. In addition to its involvement in Fe/S assembly, Isd11 also partakes in both cytoplasmic and mitochondrial tRNA thiolation, whereas Mtu1, another protein proposed to collaborate with Nfs in tRNA thiolation, is required for this process solely within the mitochondrion. Taken together these data place Isd11 at the center of these sulfur transactions and raises the possibility of a connection between Fe/S metabolism and protein synthesis, helping integrate two seemingly unrelated pathways.
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Proteínas Hierro-Azufre/metabolismo , Proteínas Protozoarias/metabolismo , ARN Protozoario/metabolismo , ARN de Transferencia/metabolismo , Compuestos de Sulfhidrilo/metabolismo , Trypanosoma brucei brucei/metabolismo , Aconitato Hidratasa/metabolismo , Citosol/metabolismo , Fumarato Hidratasa/metabolismo , Potencial de la Membrana Mitocondrial , Mitocondrias/metabolismo , Proteínas Mitocondriales/metabolismo , Fenotipo , Estabilidad Proteica , Interferencia de ARN , Trypanosoma brucei brucei/citología , Trypanosoma brucei brucei/enzimología , Trypanosoma brucei brucei/crecimiento & desarrolloRESUMEN
The Maniq and Mlabri are the only recorded nomadic hunter-gatherer groups in Thailand. Here, we sequenced complete mitochondrial (mt) DNA genomes and ~2.364 Mbp of non-recombining Y chromosome (NRY) to learn more about the origins of these two enigmatic populations. Both groups exhibited low genetic diversity compared to other Thai populations, and contrasting patterns of mtDNA and NRY diversity: there was greater mtDNA diversity in the Maniq than in the Mlabri, while the converse was true for the NRY. We found basal uniparental lineages in the Maniq, namely mtDNA haplogroups M21a, R21 and M17a, and NRY haplogroup K. Overall, the Maniq are genetically similar to other negrito groups in Southeast Asia. By contrast, the Mlabri haplogroups (B5a1b1 for mtDNA and O1b1a1a1b and O1b1a1a1b1a1 for the NRY) are common lineages in Southeast Asian non-negrito groups, and overall the Mlabri are genetically similar to their linguistic relatives (Htin and Khmu) and other groups from northeastern Thailand. In agreement with previous studies of the Mlabri, our results indicate that the Malbri do not directly descend from the indigenous negritos. Instead, they likely have a recent origin (within the past 1,000 years) by an extreme founder event (involving just one maternal and two paternal lineages) from an agricultural group, most likely the Htin or a closely-related group.
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Pueblo Asiatico/genética , Cromosomas Humanos Y , ADN Mitocondrial/genética , Variación Genética , Migrantes , ADN Mitocondrial/química , Haplotipos , Humanos , Análisis de Secuencia de ADN , TailandiaRESUMEN
Southeast Asia is home to rich human genetic and linguistic diversity, but the details of past population movements in the region are not well known. Here, we report genome-wide ancient DNA data from 18 Southeast Asian individuals spanning from the Neolithic period through the Iron Age (4100 to 1700 years ago). Early farmers from Man Bac in Vietnam exhibit a mixture of East Asian (southern Chinese agriculturalist) and deeply diverged eastern Eurasian (hunter-gatherer) ancestry characteristic of Austroasiatic speakers, with similar ancestry as far south as Indonesia providing evidence for an expansive initial spread of Austroasiatic languages. By the Bronze Age, in a parallel pattern to Europe, sites in Vietnam and Myanmar show close connections to present-day majority groups, reflecting substantial additional influxes of migrants.
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Genoma Humano , Migración Humana/historia , Lenguaje/historia , Agricultura/historia , Asia Sudoriental , Pueblo Asiatico/genética , ADN Antiguo , Variación Genética , Historia Antigua , Humanos , Datación RadiométricaRESUMEN
In a recent interdisciplinary study, Das et al. have attempted to trace the homeland of Ashkenazi Jews and of their historical language, Yiddish (Das et al. 2016 Localizing Ashkenazic Jews to Primeval Villages in the Ancient Iranian Lands of Ashkenaz. Genome Biol Evol. 8:1132-1149). Das et al. applied the geographic population structure (GPS) method to autosomal genotyping data and inferred geographic coordinates of populations supposedly ancestral to Ashkenazi Jews, placing them in Eastern Turkey. They argued that this unexpected genetic result goes against the widely accepted notion of Ashkenazi origin in the Levant, and speculated that Yiddish was originally a Slavic language strongly influenced by Iranian and Turkic languages, and later remodeled completely under Germanic influence. In our view, there are major conceptual problems with both the genetic and linguistic parts of the work. We argue that GPS is a provenancing tool suited to inferring the geographic region where a modern and recently unadmixed genome is most likely to arise, but is hardly suitable for admixed populations and for tracing ancestry up to 1,000 years before present, as its authors have previously claimed. Moreover, all methods of historical linguistics concur that Yiddish is a Germanic language, with no reliable evidence for Slavic, Iranian, or Turkic substrata.
Asunto(s)
Evolución Molecular , Genética de Población/métodos , Migración Humana , Judíos/genética , Población/genética , Genética de Población/normas , Genoma Humano , Humanos , LinajeRESUMEN
The Kets, an ethnic group in the Yenisei River basin, Russia, are considered the last nomadic hunter-gatherers of Siberia, and Ket language has no transparent affiliation with any language family. We investigated connections between the Kets and Siberian and North American populations, with emphasis on the Mal'ta and Paleo-Eskimo ancient genomes, using original data from 46 unrelated samples of Kets and 42 samples of their neighboring ethnic groups (Uralic-speaking Nganasans, Enets, and Selkups). We genotyped over 130,000 autosomal SNPs, identified mitochondrial and Y-chromosomal haplogroups, and performed high-coverage genome sequencing of two Ket individuals. We established that Nganasans, Kets, Selkups, and Yukaghirs form a cluster of populations most closely related to Paleo-Eskimos in Siberia (not considering indigenous populations of Chukotka and Kamchatka). Kets are closely related to modern Selkups and to some Bronze and Iron Age populations of the Altai region, with all these groups sharing a high degree of Mal'ta ancestry. Implications of these findings for the linguistic hypothesis uniting Ket and Na-Dene languages into a language macrofamily are discussed.