Article
Genetics & Heredity
Ryan Joseph Daniels, Maria Eugenia D'Amato, Mpasi Lesaoana, Mohaimin Kasu, Karen Ehlers, Paballo Abel Chauke, Puseletso Lecheko, Sam Challis, Kirk Rockett, Francesco Montinaro, Miguel Gonzalez-Santos, Cristian Capelli
Summary: Using contemporary individuals as proxies for ancient communities is necessary but controversial in anthropology. The distinction between Cape KhoeSan and eastern KhoeSan remains unclear in southern Africa due to changing ethnicity labels and the decimation of most communities. Genetic analysis suggests that the Baphuthi, who had a nomadic lifestyle and shared heritage with the KhoeSan, have genetic affinities with early-arriving southern Bantu-speaking communities rather than a unique eastern KhoeSan ancestry. The references to San and Bushman in historic literature may reflect non-sedentary polities instead of ethnic/biological distinctions.
AMERICAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Multidisciplinary Sciences
Sam Tallman, Maria das Dores Sungo, Silvio Saranga, Sandra Beleza
Summary: This study presents a collection of 350 whole genome sequences from Angola and Mozambique, providing insights into significant demographic events in African history and shedding light on the complexity of the Bantu Expansion. The generated reference panels improve imputation accuracy in African Americans and Brazilians.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Shaohua Fan, Jeffrey P. Spence, Yuanqing Feng, Matthew E. B. Hansen, Jonathan Terhorst, Marcia H. Beltrame, Alessia Ranciaro, Jibril Hirbo, William Beggs, Neil Thomas, Thomas Nyambo, Sununguko Wata Mpoloka, Gaonyadiwe George Mokone, Alfred Njamnshi, Charles Folkunang, Dawit Wolde Meskel, Gurja Belay, Yun S. Song, Sarah A. Tishkoff
Summary: By conducting whole-genome sequencing of indigenous African populations, we identified numerous unreported variants and observed evidence of ancient population structure and introgression events from highly diverged ''ghost'' populations. We also found signatures of local adaptation for traits related to skin color, immune response, height, and metabolic processes.
Article
Agriculture, Dairy & Animal Science
Felix J. M. King, Cuthbert B. Banga, Carina Visser
Summary: The study on native Mozambican cattle populations revealed low genetic diversity and varying degrees of admixture among the populations, as well as a decrease in effective population size over time. These findings will aid in formulating management and conservation strategies for indigenous Mozambican cattle populations.
TROPICAL ANIMAL HEALTH AND PRODUCTION
(2021)
Article
Multidisciplinary Sciences
Byeongyong Ahn, Mingue Kang, Hyoim Jeon, Jong-Seok Kim, Hao Jiang, Jihong Ha, Chankyu Park
Summary: To investigate the ancestry and phylogenetic relationships of native Korean dog breeds, we analyzed the nucleotide variations in whole-genome sequences of 205 canid individuals. Our results revealed that different Korean dog breeds have genetic associations with various ancestral populations. We also found evidence of ancient admixture of European ancestry in East Asian dog breeds.
Article
Biochemistry & Molecular Biology
Maike L. Morrison, Nicolas Alcala, Noah A. Rosenberg
Summary: In model-based inference of population structure, individuals are assigned membership coefficients in statistical clusters generated by clustering algorithms. Different groups of individuals can have distinct patterns of variability in their membership coefficients, which are difficult to capture using a single numerical value. We introduce a method that measures the variability of membership coefficients in a predefined group, using an analogy between individual membership coefficient vectors and population allele frequency vectors. Our approach makes use of a normalized F-ST statistic and can be used to compare and analyze inferred population structures.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Agronomy
Phanchita Vejchasarn, Jeremy R. Shearman, Usawadee Chaiprom, Yotwarit Phansenee, Arissara Suthanthangjai, Jirapong Jairin, Varapong Chamarerk, Tatpong Tulyananda, Chainarong Amornbunchornvej
Summary: The study identified five subpopulations in the population structure of Thai rice, grouping individuals based on location. Each subpopulation exhibits unique genetic patterns, agronomic traits, and environmental conditions. This research can serve as a valuable reference for breeders and researchers interested in Thai rice.
Article
Biochemistry & Molecular Biology
Kylie M. Cairns, Mathew S. Crowther, Heidi G. Parker, Elaine A. Ostrander, Mike Letnic
Summary: Admixture between canid species is a concern in wildlife management. By genotyping 402 wild dingoes and comparing them with domestic dogs using SNP genotyping, the study reveals at least five distinct dingo populations in Australia and limited evidence of dog admixture in wild dingoes. These findings challenge previous reports and support the use of genome-wide SNP genotyping to inform dingo management policy and legislation.
Article
Multidisciplinary Sciences
Mark Lipson, Elizabeth A. Sawchuk, Jessica C. Thompson, Jonas Oppenheimer, Christian A. Tryon, Kathryn L. Ranhorn, Kathryn M. de Luna, Kendra A. Sirak, Inigo Olalde, Stanley H. Ambrose, John W. Arthur, Kathryn J. W. Arthur, George Ayodo, Alex Bertacchi, Jessica Cerezo-Roman, Brendan J. Culleton, Matthew C. Curtis, Jacob Davis, Agness O. Gidna, Annalys Hanson, Potiphar Kaliba, Maggie Katongo, Amandus Kwekason, Myra F. Laird, Jason Lewis, Audax Z. P. Mabulla, Fredrick Mapemba, Alan Morris, George Mudenda, Raphael Mwafulirwa, Daudi Mwangomba, Emmanuel Ndiema, Christine Ogola, Flora Schilt, Pamela R. Willoughby, David K. Wright, Andrew Zipkin, Ron Pinhasi, Douglas J. Kennett, Fredrick Kyalo Manthi, Nadin Rohland, Nick Patterson, David Reich, Mary E. Prendergast
Summary: Genetic and archaeological evidence suggest major demographic changes in sub-Saharan Africa during the Late Pleistocene and early Holocene. This study presents ancient DNA data from eastern and south-central Africa, revealing a geographically structured mixture of three highly divergent source populations.
Article
Biochemical Research Methods
Pablo Librado, Ludovic Orlando
Summary: This article presents "Struct-f4", an automated solution for characterizing and summarizing the genetic ancestry profile of individuals, assessing their genetic affinities, identifying admixture sources, and quantifying admixture levels.
Article
Multidisciplinary Sciences
Ezequiel Koile, Simon J. Greenhill, Damian E. Blasi, Remco Bouckaert, Russell D. Gray
Summary: The Bantu expansion, which transformed sub-Saharan Africa in terms of language, economy, and culture, was reconstructed using a break-away geographical diffusion model with augmented geographic data. The findings suggest an expansion of the Bantu language family through Central African tropical forests over 4000 years ago, predating the opening of the Sangha River Interval.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Tianyi Wang, Wei Wang, Guangmao Xie, Zhen Li, Xuechun Fan, Qingping Yang, Xichao Wu, Peng Cao, Yichen Liu, Ruowei Yang, Feng Liu, Qingyan Dai, Xiaotian Feng, Xiaohong Wu, Ling Qin, Fajun Li, Wanjing Ping, Lizhao Zhang, Ming Zhang, Yalin Liu, Xiaoshan Chen, Dongju Zhang, Zhenyu Zhou, Yun Wu, Hassan Shafiey, Xing Gao, Darren Curnoe, Xiaowei Mao, E. Andrew Bennett, Xueping Ji, Melinda A. Yang, Qiaomei Fu
Summary: The study reveals the presence of ancient East Asian ancestry in southern China's Guangxi region, as well as a history of admixture with deep Asian ancestry related to Southeast Asia and local ancestry. Historical populations in Guangxi dating back to 1,500 to 500 years ago are closely related to Tai-Kadai and Hmong-Mien speakers, indicating interactions between East and Southeast Asia.
Article
Genetics & Heredity
Shuichi Kitada, Reiichiro Nakamichi, Hirohisa Kishino
Summary: Population structure is influenced by history, and F-ST values provide insights into both the current structure and evolutionary history. Overlaying F-ST estimates on maps and trees can help to better understand population structure and expansion history.
G3-GENES GENOMES GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Jonas Meisner, Anders Albrechtsen
Summary: HaploNet is a method for performing dimensionality reduction and clustering of genetic data, which can cluster haplotypes in a highly scalable manner to infer global population structure and estimate ancestry proportions.
Article
Biochemistry & Molecular Biology
Ornob Alam, Rafal M. Gutaker, Cheng-Chieh Wu, Karen A. Hicks, Kyle Bocinsky, Cristina Cobo Castillo, Stephen Acabado, Dorian Fuller, Jade A. d'Alpoim Guedes, Yue-Ie Hsing, Michael D. Purugganan
Summary: The dispersal of rice after domestication had significant social and cultural impacts on South, East, and Southeast Asia. The origins of indigenous rice varieties in Taiwan and the northern Philippines differ, with genetic evidence suggesting complex origins and admixture with populations from northeast Asia and mainland Southeast Asia. Positive selection acting on different genomic regions in rice subpopulations indicates local adaptation during the spread of japonica rice.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biotechnology & Applied Microbiology
Joao Almeida, Joao M. Alves, Monica Valecha, Sonia Prado-Lopez, Pilar Alvarino, Miguel M. Fonseca, David Posada, Andres Perez-Figueroa, Jose Manuel Cameselle-Teijeiro, Debora Chantada
Summary: This study found that single-cell mitochondrial genomes in both normal and tumor cells of colorectal cancer patients can carry various mitochondrial haplotypes. Moreover, intra-cellular heteroplasmy that exists before tumor development can be maintained in specific tumor cell subpopulations. Somatic mutations in single cells do not seem to play a prominent role in tumorigenesis in these colorectal cancer patients.
Article
Ecology
Sandra Oliveira, Kathrin Naegele, Selina Carlhoff, Irina Pugach, Toetik Koesbardiati, Alexander Hubner, Matthias Meyer, Adhi Agus Oktaviana, Masami Takenaka, Chiaki Katagiri, Delta Bayu Murti, Rizky Sugianto Putri, Mahirta, Fiona Petchey, Thomas Higham, Charles F. W. Higham, Sue O'Connor, Stuart Hawkins, Rebecca Kinaston, Peter Bellwood, Rintaro Ono, Adam Powell, Johannes Krause, Cosimo Posth, Mark Stoneking
Summary: Genome-wide data from 16 ancient individuals from islands in present-day Eastern Indonesia and Timor-Leste reveal diverse sources of admixture and support multiple dispersals into the Wallacea region. The study provides insights into the demographic movements and admixture timings in this region and suggests that the Neolithic dispersals in Island Southeast Asia involved the spread of multiple genetic ancestries.
NATURE ECOLOGY & EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Cesar Fortes-Lima, Petr Triska, Martina Cizkova, Eliska Podgorna, Mame Yoro Diallo, Carina M. Schlebusch, Viktor Cerny
Summary: The study reveals fine-scale population structure and complex admixture patterns among populations in the Sahel/Savannah belt, with the Rashaayda Arabic-speaking population showing lack of gene flow from African groups, and Western Sahelian populations exhibiting signatures of selection in various genetic regions.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Omar Alva, Anais Leroy, Margit Heiske, Veronica Pereda-Loth, Lenka Tisseyre, Anne Boland, Jean-Francois Deleuze, Jorge Rocha, Carina Schlebusch, Cesar Fortes-Lima, Mark Stoneking, Chantal Radimilahy, Jean-Aime Rakotoarisoa, Thierry Letellier, Denis Pierron
Summary: Madagascar, one of the last land masses to be colonized by humans, has shown genetic and linguistic evidence of a mixture between African and Asian populations in the past millennium. The admixture coincides with rapid population growth and landscape changes, as well as the extinction of endemic large-bodied vertebrates.
Article
Multidisciplinary Sciences
Mark Stoneking, Leonardo Arias, Dang Liu, Sandra Oliveira, Irina Pugach, Jae Joseph Russell B. Rodriguez
Summary: Nearly 20 years ago, Jared Diamond and Peter Bellwood examined the evidence of the spread of farming and large language families through the demographic expansions of farmers. Advances in genomic data analysis have revolutionized our understanding of human dispersals during the Holocene. This article provides an overview of Holocene dispersals based on genomic evidence and concludes that they have a complex history. Further research is needed to investigate the factors and social circumstances that have influenced the variation and complexity of these dispersals.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Anthropology
Maryna Steyn, Anja Meyer, Rita Peyroteo-Stjerna, Cecile Jolly, Carina Schlebusch, Larry Barham, Marlize Lombard
Summary: This article reevaluates the human remains from Mumbwa Caves in South Africa, revealing that the poorly preserved remains represent at least 16 individuals. The analysis of radiocarbon dating and stable isotope shows that the individuals were buried between the late tenth and early twentieth century CE, with most dates clustering between the early sixteenth and the late nineteenth century. The isotope values suggest that these individuals lived in agricultural communities rather than the Stone Age as previously suggested.
AFRICAN ARCHAEOLOGICAL REVIEW
(2023)
Review
Genetics & Heredity
Viktor Cerny, Edita Priehodova, Cesar Fortes-Lima
Summary: This review focuses on the Sahel/Savannah belt in Africa, where the interaction between pastoralism and agriculture, two alternative subsistence systems, is examined. By analyzing lactase persistence, a trait associated with pastoral lifestyle, it is found that current pastoralists are distinguished from farmer neighbors. However, most other genetic polymorphisms do not show such clear differentiation, suggesting a common origin and/or extensive gene flow. Understanding the genetic affinity and ecological symbiosis between the subsistence systems can shed light on the population history of this African region.
Article
Biology
Riaan F. F. Rifkin, Surendra Vikram, Jaime Alcorta, Jean-Baptiste Ramond, Don A. A. Cowan, Mattias Jakobsson, Carina M. M. Schlebusch, Marlize Lombard
Summary: By analyzing metagenome libraries derived from the sequencing of a Later Stone Age hunter-gatherer child who lived near Ballito Bay, South Africa, about 2000 years ago, ancient DNA sequences homologous to the flea-borne typhus-like pathogen Rickettsia felis were identified, and an ancient R. felis genome was reconstructed. This provides ancient genomic evidence for the presence of Rickettsia felis in human remains from 2000 years ago, reframing previous hypotheses of R. felis as a novel or emergent pathogen in modern humans.
COMMUNICATIONS BIOLOGY
(2023)
Article
Genetics & Heredity
Marcela Sandoval-Velasco, Anuradha Jagadeesan, Jazmin Ramos-Madrigal, Maria C. Avila-Arcos, Cesar A. Fortes-Lima, Judy Watson, Erna Johannesdottir, Diana I. Cruz-Davalos, Shyam Gopalakrishnan, J. Victor Moreno-Mayar, Jonas Niemann, Gabriel Renaud, Katharine A. Robson Brown, Helena Bennett, Andrew Pearson, Agnar Helgason, M. Thomas P. Gilbert, Hannes Schroeder
Summary: This article highlights the crucial role of St Helena in suppressing the transatlantic slave trade. The study conducted ancient DNA analyses on 20 individuals whose remains were recovered on the island, revealing that they most likely originated from different source populations between northern Angola and Gabon. The majority of the individuals were male, supporting documented gender bias in the latter phase of the transatlantic slave trade.
AMERICAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Biodiversity Conservation
Sandra Oliveira, Cesar Capinha, Jorge Rocha
Summary: The highly invasive Aedes albopictus mosquito continues to spread worldwide, driven by international trade and its role as a vector for diseases such as Zika and dengue. A model based on trade volumes, climate similarity, and geographic distance predicts that this species might enter all assessed countries by 2035.
JOURNAL OF APPLIED ECOLOGY
(2023)
Article
Agriculture, Dairy & Animal Science
Shijun Li, Xiaojian Zhang, Xinyu Dong, Ruiyang Guo, Jiuhong Nan, Jingwei Yuan, Carina M. Schlebusch, Zheya Sheng
Summary: This study systematically evaluated the population structure and demography of current Tibetan chicken populations, revealing complex genetic histories and a clear separation into 4 sub-populations. Two high altitude associated genes were found in all 4 sub-populations, indicating similar responses to selection pressures. These results have important implications for future genetic analyses on chickens and other domestic animals in Tibet.
Review
Multidisciplinary Sciences
Maria C. Avila-Arcos, Maanasa Raghavan, Carina Schlebusch
Summary: Ancient DNA research has provided valuable insights into the history of our species, particularly in regions beyond the continental level and the histories of oppressed peoples.
Review
Anthropology
Anne-Maria Fehn, Beatriz Amorim, Jorge Rocha
Summary: The diversity of southern African populations is the result of three major pre-historic settlement layers associated with different linguistic groups: early foragers speaking Kx'a and Tuu languages, Late Stone Age pastoralists associated with Khoe-Kwadi languages, and Iron Age Bantu-speaking farmers. By combining linguistic and genetic data, this review provides evidence for the origins, migration routes, and internal diversification patterns of these three layers. The study highlights the impact of admixture and social interactions in shaping southern Africa as a zone of high contact between different communities, leading to the formation of new ethnic identities.
JOURNAL OF ANTHROPOLOGICAL SCIENCES
(2022)