Human Population Genetics and Genomics最新文献

{"title":"In Memory of António Amorim (1952 – 2024)","authors":"","doi":"10.47248/hpgg2404020006","DOIUrl":"https://doi.org/10.47248/hpgg2404020006","url":null,"abstract":"","PeriodicalId":393324,"journal":{"name":"Human Population Genetics and Genomics","volume":"103 29","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140985941","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Medieval genomes from eastern Mongolia share a stable genetic profile over a millennium","authors":"Juhyeon Lee, Takehiro Sato, Atsushi Tajima, T. Amgalantugs, Batmunkh Tsogtbaatar, Shigeki Nakagome, Toshihiko Miyake, Noriyuki Shiraishi, Choongwon Jeong, Takashi Gakuhari","doi":"10.47248/hpgg2404010004","DOIUrl":"https://doi.org/10.47248/hpgg2404010004","url":null,"abstract":"Recent archaeogenomic studies in Mongolia have elucidated the genetic origins of people from the Xiongnu and Mongol eras, but left the Medieval period between them only tangentially explored. Due to this dearth of ancient genomes, the dynamic history of Medieval Mongolia with the rise and fall of numerous polities still lacks a genomic perspective. To fill in this knowledge gap, here we report whole-genome sequences of nine ancient individuals from eastern Mongolia, who were excavated from two nearby cemeteries, Gurvan Dov and Tavan Khailaast. They are distributed from the Xiongnu-Xianbei period (ca. 200 CE) to the Mongol era (ca. 1,400 CE), forming a local time transect encompassing nearly 1,200 years. Remarkably, despite the long-time span, all nine individuals derive most of their ancestry (85–100%) from the eastern Eurasian lineages and show low heterogeneity in their genetic composition. This is in contrast to the general pattern observed in previously published Medieval genomes from central Mongolia, who showed higher heterogeneity and overall less eastern Eurasian ancestry, thus calling for a comprehensive archaeogenetic survey of Medieval Mongolia to fully capture the dynamic genetic history in this period.","PeriodicalId":393324,"journal":{"name":"Human Population Genetics and Genomics","volume":"65 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140085350","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tales from the end of the world: three decades of paleogenetic research in Patagonia","authors":"Constanza de la Fuente Castro, Josefina Motti, Valeria Arencibia, Pierre Luisi","doi":"10.47248/hpgg2404010003","DOIUrl":"https://doi.org/10.47248/hpgg2404010003","url":null,"abstract":"Patagonia is a region that has fascinated researchers for centuries considering the evidence of early human occupation, its geographical and environmental variability, and the diversity of human adaptations. From an archaeological and bioanthropological perspective, the region has been the focus of many studies addressing a wide range of questions, from a broad scale, such as the peopling of the Americas, to a local scale concerning the diversity and interactions of human populations. For three decades, paleogenetic studies have contributed to the understanding of population dynamics in the region: first using uniparental markers, particularly mitochondrial DNA in a much larger proportion; and more recently including genome-wide data for ancient individuals. In this work, we revise these studies considering three themes: (1) the first stages of migration into the region; (2) the diversification and interactions of populations during the Middle and Late Holocene; and (3) the link between present-day and ancient populations. While genetic evidence from the early peopling stages is either absent or scarce, making it difficult to evaluate the relative contributions of early South American lineages in the first Patagonian populations, evidence from later periods (from Middle Holocene onwards) is consistent with a single migration wave with founding events and genetic drift acting on small groups during their migration southward. After the initial occupation, the population dynamics seem to have been characterised by the relative isolation of different groups, leading to their differentiation. While there is evidence of some degree of gene flow between groups, the genetic structure in the region is generally associated with geography, subsistence systems, and languages. After European contact, paleogenetic data supports a relative genetic continuity in the region. We finish this review with a fourth theme in which we reflect on the current state and direction of the field in Patagonia, highlighting research lines that will benefit from the implementation of state-of-the-art paleogenomic approach, as well as legal and ethical considerations that would allow to move forward into a more collaborative and inclusive field.","PeriodicalId":393324,"journal":{"name":"Human Population Genetics and Genomics","volume":"67 13","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139959872","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of ancient DNA imputation: a simulation study","authors":"Mariana Escobar-Rodríguez, K. Veeramah","doi":"10.47248/hpgg2404010002","DOIUrl":"https://doi.org/10.47248/hpgg2404010002","url":null,"abstract":"Ancient genomic data is becoming increasingly available thanks to recent advances in high-throughput sequencing technologies. Yet, post-mortem degradation of endogenous ancient DNA often results in low depth of coverage and subsequently high levels of genotype missingness and uncertainty. Genotype imputation is a potential strategy for increasing the information available in ancient DNA samples and thus improving the power of downstream population genetic analyses. However, the performance of genotype imputation on ancient genomes under different conditions has not yet been fully explored, with all previous work primarily using an empirical approach of downsampling high coverage paleogenomes. While these studies have provided invaluable insights into best practices for imputation, they rely on a fairly limited number of existing high coverage samples with significant temporal and geographical biases. \u0000As an alternative, we used a coalescent simulation approach to generate genomes with characteristics of ancient DNA in order to more systematically evaluate the performance of two popular imputation software, BEAGLE and GLIMPSE, under variable divergence times between the target sample and reference haplotypes, as well as different depths of coverage and reference sample size. Our results suggest that for genomes with coverage <=0.1x imputation performance is poor regardless of the strategy employed. Beyond 0.1x coverage imputation is generally improved as the size of the reference panel increases, and imputation accuracy decreases with increasing divergence between target and reference populations. It may thus be preferable to compile a smaller set of less diverged reference samples than a larger more highly diverged dataset. In addition, the imputation accuracy may plateau beyond some level of divergence between the reference and target populations. While accuracy at common variants is similar regardless of divergence time, rarer variants are better imputed on less diverged target samples. Furthermore, both imputation software, but particularly GLIMPSE, overestimate high genotype probability calls, especially at low coverages. Our results provide insight into optimal strategies for ancient genotype imputation under a wide set of scenarios, complementing previous empirical studies based on imputing downsampled high-coverage ancient genomes.","PeriodicalId":393324,"journal":{"name":"Human Population Genetics and Genomics","volume":"8 19","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139381362","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"GRUPS-rs, a high-performance ancient DNA genetic relatedness\u0000estimation software relying on pedigree simulations","authors":"Maël Lefeuvre, Michael David Martin, Flora Jay, Marie-Claude Marsolier, Céline Bon","doi":"10.47248/hpgg2404010001","DOIUrl":"https://doi.org/10.47248/hpgg2404010001","url":null,"abstract":"Background: The study of fine-grain genetic kinship ties (parents, siblings, cousins, etc.) from ancient remains is now gaining significant interest within the field of paleogenetics, as a means of deciphering the social organization of past societies. However, kinship analyses are in practice often quite difficult to apply within paleogenetic studies, and may carry a high degree of uncertainty in the results they provide, especially when applied on low coverage and/or highly degraded samples, or when studying poorly characterized populations. To overcome these challenges, most of the available kinship estimation methods either refrain from inferring ties beyond the second degree (e.g., half-siblings), and/or rely on the use of a cohort of individuals to obtain a satisfactory statistical significance. Thus, the current state of the art remains intrinsically limited when attempting to estimate kinship on a small number of individuals, or when trying to detect more distant relationships (e.g., cousins).\u0000Methods:Here, we present GRUPS-rs:an update and complete reimplementation of GRUPS (Get Relatedness Using Pedigree Simulations), an ancient DNA kinship estimation software based on the methods originally developed in (Martin et al. 2017).GRUPS-rs both computes an estimate of relatedness from randomly sampled pseudo-haploidized variant calls, and leverages high-definition pedigree simulations to bypass the use of a cohort of individuals.\u0000Results: We highlight that GRUPS and GRUPS-rs are especially suitable to perform kinship analysis on a restricted number of ancient samples, and can provide a sufficient statistical significance to estimate genetic relatedness past the second degree, while taking into account user-defined contamination and sequencing error estimates. Importantly, GRUPS-rs offers an estimated 14000-fold speed-up in runtime performance compared to its predecessor — allowing the joint estimation of kinship between dozens of individuals in a matter of minutes — and is now bundled with a user-friendly Shiny interface, in which users can interactively visualize their results.\u0000Conclusions: The GRUPS kinship estimation method is now fully operational in its \"GRUPS-rs\" implementation, whose use is particularly recommended when analyzing a restricted number of low coverage DNA samples.","PeriodicalId":393324,"journal":{"name":"Human Population Genetics and Genomics","volume":"78 11","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139387154","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Acknowledgement to Reviewers of Human Population Genetics and Genomics","authors":"","doi":"10.47248/hpgg2303040009","DOIUrl":"https://doi.org/10.47248/hpgg2303040009","url":null,"abstract":"","PeriodicalId":393324,"journal":{"name":"Human Population Genetics and Genomics","volume":"50 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139166523","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An ancient genome perspective on the dynamic history of the prehistoric Jomon people in and around the Japanese archipelago","authors":"Gichan Jeong, Haechan Gill, Hyungmin Moon, Choongwon Jeong","doi":"10.47248/hpgg2303040008","DOIUrl":"https://doi.org/10.47248/hpgg2303040008","url":null,"abstract":"The Jomon people were prehistoric residents of the Japanese archipelago who occupied the region from ca. 16,500 to 2,300 years before present (BP). While recent accumulation of ancient genomes and genome-wide data of the Jomons has substantially enhanced \u0000our understanding of their genetic profiles and contribution to present-day populations, their genetic history in the Jomon-period archipelago, spanning over 14,000 years in time and 2,000 km in distance, remains scarcely investigated. Here we report multiple findings illuminating the Jomon genetic history based on the analysis of the genetic relationship between published ancient genome-wide data of 23 Jomon and Jomon-like individuals. First, the Initial Jomon individual from Shikoku, dated to ca. 9,000 BP, forms a common outgroup to the remaining later Jomon individuals, suggesting a population turnover in western Japan. Second, genetically Jomon-like individuals outside the Jomon archaeological context, found in the Miyako Island in Ryukyu and the Yokjido island in the southern coast of Korea, show the closest genetic affinity with the Late Jomon individual from Shikoku, narrowing down their sources in space and time. This study highlights a dynamic history of the Jomon people in and out of the Japanese archipelago and calls for a large-scale investigation of the ancient Jomon genomes.","PeriodicalId":393324,"journal":{"name":"Human Population Genetics and Genomics","volume":"10 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138981671","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The importance of gene flow in human evolution","authors":"Alan R. Templeton","doi":"10.47248/hpgg2303030005","DOIUrl":"https://doi.org/10.47248/hpgg2303030005","url":null,"abstract":"By the latter half of the 20th century, there were three dominant models of human evolution. All three accepted an African origin of humans at the Homo erectus stage, with H. erectus expanding out of Africa and colonizing Eurasia near the beginning of the Pleistocene. The candelabra model had H. erectus splitting into mostly isolated geographical lineages that independently evolved into the modern African, European and Asian “races”. The out-of-Africa replacement model starts out like the candelabra model, but then posits that Homo sapiens first evolved in Africa and then expanded out of Africa in the late Pleistocene and replaced all of the archaic Eurasian populations without interbreeding with them. Neither of these models assign an important role to gene flow (genetic interchange). In contrast, the multiregional model regarded the human populations in Africa and Eurasia as experiencing gene flow throughout the Pleistocene and evolving as a single human lineage with some local differentiation. Studies on mitochondrial DNA in the 1980’s claimed to support the out-of-Africa replacement model and to falsify both the candelabra and multiregional models by mistakenly equating the two. In fact, the mitochondrial DNA studies were fully compatible with both the replacement and multiregional models. The first statistically significant discrimination between these two models appeared in 2002 and revealed a hybrid model in which there was a mid-Pleistocene and a late Pleistocene expansion of humans out of Africa that resulted in limited genetic interchange with Eurasians rather than complete replacement. Moreover, significant gene flow and population movements led to genetic interchange throughout the mid-Pleistocene to the present. Studies on genomic data and ancient DNA have strongly confirmed these inferences. Moreover, our modern species of humans was forged in an African multiregional metapopulation rather than arising from one local area of Africa. Thus, gene flow has played a dominant role in human evolution since the mid-Pleistocene whereas splits and isolation have not. This undercuts the idea that human races are biologically real categories or separate branches on an evolutionary tree.","PeriodicalId":393324,"journal":{"name":"Human Population Genetics and Genomics","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130932232","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mutation Rate (Under)estimation through Mendelian Incompatibilities","authors":"António Amorim","doi":"10.47248/hpgg2303020004","DOIUrl":"https://doi.org/10.47248/hpgg2303020004","url":null,"abstract":"","PeriodicalId":393324,"journal":{"name":"Human Population Genetics and Genomics","volume":"60 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116956803","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An anthropologist’s point of view","authors":"J. Marks","doi":"10.47248/hpgg2303020003","DOIUrl":"https://doi.org/10.47248/hpgg2303020003","url":null,"abstract":"The historical relationship between the cognate fields of biological anthropology and human population genetics is complicated. Of Cavalli-Sforza’s contributions to this dialogue, The Human Genome Diversity Project has had some of the most interesting cultural reverberations to the present day.","PeriodicalId":393324,"journal":{"name":"Human Population Genetics and Genomics","volume":"5 18","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"120841249","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}