Article
Biochemistry & Molecular Biology
Wibhu Kutanan, Dang Liu, Jatupol Kampuansai, Metawee Srikummool, Suparat Srithawong, Rasmi Shoocongdej, Sukrit Sangkhano, Sukhum Ruangchai, Pittayawat Pittayaporn, Leonardo Arias, Mark Stoneking
Summary: The study revealed genetic structure among different ethnolinguistic groups in Thailand and Laos, with heterogeneity in certain language families and populations reflecting population interactions and genetic drift. Some Thai groups show admixture from South Asia, likely associated with intensive international trade networks around 600-1000 years ago.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Ecology
Zheng Ren, Meiqing Yang, Xiaoye Jin, Qiyan Wang, Yubo Liu, Hongling Zhang, Jingyan Ji, Chuan-Chao Wang, Jiang Huang
Summary: This study provides a detailed analysis of the genome characteristics and admixture history of Tai-Kadai-speaking populations in southern China. The study reveals genetic substructure within these populations and their genetic affinity with other groups. These findings are important for understanding population dynamics in southern China.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Nian Wang, Laura J. Kelly, Hugh A. McAllister, Jasmin Zohren, Richard J. A. Buggs
Summary: This study utilized RAD sequences to generate genome-wide sequence reads for 27 diploid and 36 polyploid Betula species, and reconstructed the evolutionary relationships among these species using supermatrix and species tree methods. The research identified the complex reticulate origins of the majority of polyploid taxa in the genus Betula, leading to the proposal of splitting Betula into two subgenera based on differences in seed-wing morphology.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Ecology
Jingbin Zhou, Xianpeng Zhang, Xin Li, Jie Sui, Shuang Zhang, Hua Zhong, Qiuxi Zhang, Xiaoming Zhang, He Huang, Youfeng Wen
Summary: In this study, the genetic structure and demographic history of Han individuals in Liaoning Province were investigated using various population genetic analysis methods. The results showed genetic similarities between Liaoning Han people and other northern Han populations, as well as Liaoning Manchu people. The main ancestral sources of Liaoning Han people were millet farmers in the Yellow River Basin and the West Liao River Basin, and hunter-gatherers in the Mongolian Plateau and the Amur River Basin. The study also supported the northern origin hypothesis and revealed significant genetic influences from northern East Asian populations, as well as population admixture between Tungusic Manchu people and Han people.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Julen Aizpurua-Iraola, Aaron Gimenez, Annabel Carballo-Mesa, Francesc Calafell, David Comas
Summary: The Roma, the largest ethnic minority in Europe, have genetic and cultural diversity influenced by founder lineages. The study reveals that over 60% of the mtDNA pool of Iberian Roma originated from South Asia, with TMRCA predating their arrival in Spain. Additionally, no evidence of genetic substructure within the Roma population in the Iberian Peninsula was found.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Jun Inoue
Summary: Comparative genome-scale analyses are used to examine evidence for whole-genome duplication and horizontal gene transfer, but face challenges in inferring all gene histories and conducting detailed analysis within orthogroups.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Plant Sciences
Meng-Ge Wang, Guang-Lin He, Xing Zou, Peng-Yu Chen, Zheng Wang, Ren-Kuan Tang, Xiao-Min Yang, Jing Chen, Mei-Qing Yang, Ying-Xiang Li, Jing Liu, Fei Wang, Jing Zhao, Jian-Xin Guo, Rong Hu, Lan-Hai Wei, Gang Chen, Hui-Yuan Yeh, Chuan-Chao Wang
Summary: The study reveals the genetic history of the population in South China, showing genetic affinities between inland Tai-Kadai-speaking people and coastal Austronesian-speaking people as well as between southwestern Han Chinese and Neolithic Yellow River basin farmers. Genetic differentiations are identified among Tai-Kadai people from South China and Southeast Asia, as well as between northern and southern inland Chinese Tai-Kadai people. The findings suggest a common origin of the Austronesian and Tai-Kadai groups.
JOURNAL OF SYSTEMATICS AND EVOLUTION
(2023)
Article
Genetics & Heredity
Ke He, Chun-hong Liang, Ying Zhu, Peter Dunn, Ayong Zhao, Piotr Minias
Summary: This study explores the macroevolutionary patterns in the avian Major Histocompatibility Complex (MHC) architecture and provides evidence for important transitions in the genomic arrangement of the MHC region during bird evolution.
FRONTIERS IN GENETICS
(2022)
Article
Ecology
Chun-Wei Chang, Takeshi Miki, Masayuki Ushio, Po-Ju Ke, Hsiao-Pei Lu, Fuh-Kwo Shiah, Chih-hao Hsieh
Summary: A novel approach for reconstructing high-dimensional interaction Jacobian networks without specific model assumptions was proposed in this study, which successfully identified important species and revealed mechanisms governing the dynamical stability of a bacterial community. The method overcame the challenge of high dimensionality in large natural dynamical systems.
Article
Computer Science, Artificial Intelligence
Yutong Sha, Yuchi Qiu, Peijie Zhou, Qing Nie
Summary: TIGON is a dynamic and unbalanced optimal transport algorithm that can reconstruct dynamic trajectories, population growth, and gene regulatory networks. It uses a deep learning method to tackle the high-dimensional optimal transport problem and has demonstrated robustness and accuracy in predicting cell state transition and population growth.
NATURE MACHINE INTELLIGENCE
(2023)
Article
Physics, Multidisciplinary
Irem Topal, Deniz Eroglu
Summary: Reconstructing network dynamics from data is crucial for predicting changes in complex systems such as neuron networks. Previous research has shown that reconstruction is possible under strong constraints, but here we present a recovery scheme that blends theoretical model reduction and sparse recovery to ease unrealistic constraints for real-world applications. By learning dynamics and connectivity, our technique can detect critical transitions for parameter changes in realistic neuronal systems.
PHYSICAL REVIEW LETTERS
(2023)
Article
Evolutionary Biology
Catherine Beliveau, Patrick Gagne, Sandrine Picq, Oksana Vernygora, Christopher Keeling, Kristine Pinkney, Daniel Doucet, Fayuan Wen, J. Spencer Johnston, Halim Maaroufi, Brian Boyle, Jerome Laroche, Ken Dewar, Nikoleta Juretic, Gwylim Blackburn, Audrey Nisole, Bryan Brunet, Marcelo Brandao, Lisa Lumley, Jun Duan, Guoxing Quan, Christopher J. Lucarotti, Amanda D. Roe, Felix A. H. Sperling, Roger C. Levesque, Michel Cusson
Summary: Insects, such as the spruce budworm, have developed antifreeze proteins (AFPs) to survive harsh winter conditions. A study on the genome of the budworm found that the genes responsible for AFPs were present in other related species as well, suggesting a common origin. The study also identified a zonadhesin-like protein that may have served as a precursor to tortricid AFPs.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Zhiyu Yang, Peristera Paschou, Petros Drineas
Summary: The emergence of genome-wide association studies (GWAS) has created great opportunities for genetic research and worldwide collaboration. Using GWAS summary statistics, methods have been developed to overcome data access barriers and save computational resources. In this study, we compare the performance of different methods and introduce a novel framework called ReACt. We find that METAL and ReACt are significantly faster than ASSET, and ReACt performs comparable to existing methods for case-case GWAS. Additionally, ReACt allows for the calculation of polygenic risk scores (PRS) based on summary statistics. This work demonstrates the power of GWAS summary-statistics-based methodologies and provides a unified framework for researchers to explore the genetics of complex diseases.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Shamam Waldman, Daniel Backenroth, Eadaoin Harney, Stefan Flohr, Nadia C. Neff, Gina M. Buckley, Hila Fridman, Ali Akbari, Nadin Rohland, Swapan Mallick, Inigo Olalde, Leo Cooper, Ariel Lomes, Joshua Lipson, Jorge Cano Nistal, Jin Yu, Nir Barzilai, Inga Peter, Gil Atzmon, Harry Ostrer, Todd Lencz, Yosef E. Maruvka, Maike Lammerhirt, Alexander Beider, Leonard Rutgers, Virginie Renson, Keith M. Prufer, Stephan Schiffels, Harald Ringbauer, Karin Sczech, Shai Carmi, David Reich
Summary: We obtained genome-wide data from 33 Ashkenazi Jews dating back to the 14th century, and found that they are genetically similar to modern Ashkenazi Jews but show more variability in their Eastern European-related ancestry. The study also reveals that the ancient Ashkenazi Jewish community had already experienced a significant reduction in size, indicating substructure in medieval Ashkenazi Jews.
Article
Biochemistry & Molecular Biology
Igor Segota, Jeramie D. Watrous, Edward D. Kantz, Shriram Nallamshetty, Saumya Tiwari, Susan Cheng, Mohit Jain, Tao Long
Summary: The human gut microbiome is associated with health and disease. Researchers have used 16S amplicon sequencing to study the human microbiome, but it has limited ability to identify microbes at the species level. The Reference-based Exact Mapping (RExMap) technology developed in this study allows mapping of microbial species from standard 16S sequencing data. RExMap analysis of 16S data captures a significant portion of microbial species identified by whole-genome shotgun sequencing, and reveals the landscape of gut microbial species across populations and geography.
NUCLEIC ACIDS RESEARCH
(2023)