Article
Evolutionary Biology
Zhou Wu, Chiara Bortoluzzi, Martijn F. L. Derks, Langqing Liu, Mirte Bosse, Sipke Joost Hiemstra, Martien A. M. Groenen, Richard P. M. A. Crooijmans
Summary: This study demonstrates the heterogeneity of the bantam trait in Dutch chickens and reveals the underlying genetic causes. Multiple genetic variants and genes associated with the bantam phenotype were identified through genome-wide association studies, including HMGA2 and PRDM16, genes involved in body growth and stature.
EVOLUTIONARY APPLICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Kejun Wang, Haifei Hu, Yadong Tian, Jingyi Li, Armin Scheben, Chenxi Zhang, Yiyi Li, Junfeng Wu, Lan Yang, Xuewei Fan, Guirong Sun, Donghua Li, Yanhua Zhang, Ruili Han, Ruirui Jiang, Hetian Huang, Fengbin Yan, Yanbin Wang, Zhuanjian Li, Guoxi Li, Xiaojun Liu, Wenting Li, David Edwards, Xiangtao Kang
Summary: The study of chicken pan-genome has revealed the evolutionary processes of genome construction, showing the factors influencing gene expression levels and gene presence/absence variations. Through PAV-based genome-wide association studies, multiple candidate mutations related to growth, meat quality, etc. have been identified.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
G. Ozan Bozdag, Seyed Alireza Zamani-Dahaj, Thomas C. Day, Penelope C. Kahn, Anthony J. Burnetti, Dung T. Lac, Kai Tong, Peter L. Conlin, Aishwarya H. Balwani, Eva L. Dyer, Peter J. Yunker, William C. Ratcliff
Summary: This study investigates the evolution of multicellular organisms using a long-term experiment with snowflake yeast as the model system. The results show that snowflake yeast evolved to be macroscopic in anaerobic conditions, while remaining microscopic in aerobic conditions. This research provides insights into how simple groups of cells overcome biophysical limitations through gradual multicellular evolution.
Article
Agriculture, Dairy & Animal Science
Zeinab Asgari, Alireza Ehsani, Ali Akbar Masoudi, Rasoul Vaez Torshizi
Summary: The study utilized Bayes C pi methodology to identify SNPs associated with body weight in a crossbred chicken population from 2 to 8 weeks of age. The most important chromosomes containing QTLs associated with observed traits were found to be GGA1 and GGA4. Different genetic regions were responsible for body weight in early and late ages.
ITALIAN JOURNAL OF ANIMAL SCIENCE
(2021)
Article
Agriculture, Dairy & Animal Science
Eunjin Cho, Sunghyun Cho, Minjun Kim, Thisarani Kalhari Ediriweera, Dongwon Seo, Seung-Sook Lee, Jihye Cha, Daehyeok Jin, Young-Kuk Kim, Jun Heon Lee
Summary: Genetic analysis has great potential in differentiating between different species and breeds of livestock. In this study, the optimal combinations of SNP markers for discriminating the Yeonsan Ogye chicken breed were identified using high-density SNP array data. Machine learning algorithms were utilized to select significant SNP markers, achieving 100% accuracy.
JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Jinxin Zhang, Changsheng Nie, Xinye Zhang, Xiurong Zhao, Yaxiong Jia, Jianlin Han, Yu Chen, Liang Wang, Xueze Lv, Weifang Yang, Kaiyang Li, Jianwei Zhang, Zhonghua Ning, Haigang Bao, Junying Li, Chunjiang Zhao, Lujiang Qu
Summary: In this study, whole-genome resequencing was performed to investigate the genetic mechanisms underlying the rumplessness trait in Piao chicken, a Chinese indigenous breed. A 4174 bp deletion located in the upstream region of the IRX1 gene on chromosome 2 was found to be associated with the rumplessness phenotype. Tailbone CT scan revealed that the rumplessness phenotype has not been completely fixed in Piao chicken breed. This study provides insights into the genetic characteristics of Piao chicken.
Article
Multidisciplinary Sciences
Mark Pagel, Ciara O'Donovan, Andrew Meade
Summary: Macroevolution poses challenges to evolutionary theory due to abrupt changes and long stagnation periods. This study introduces a statistical model that considers directional changes and evolvability changes to account for this uneven evolutionary landscape. In mammals, both processes independently contribute to macroevolution, with increased evolvability being more common than reduced evolutionary potentials. Large or sudden phenotypic changes can be statistically explained as biased random walks, bridging the gap between macroevolution and gradualist microevolution. This study emphasizes the importance of considering multiple evolutionary processes simultaneously.
NATURE COMMUNICATIONS
(2022)
Article
Zoology
Marcelo H. Cassini
Summary: The study delves into the evolutionary relationships between sexual characteristics in mammals, proposing a reversed causal link and using phylogenetic confirmatory path analysis to test different models. The key finding reveals that a shift from closed to open habitats triggers the evolutionary pathway toward polygyny, leading to a series of evolutionary changes and ultimately resulting in niche separation and sexual size dimorphism between sexes.
Article
Multidisciplinary Sciences
Haoxuan Liu, Jianzhi Zhang
Summary: The study reveals that the mutation rate substantially exceeds the drift barrier in various organisms, indicating that stabilizing selection plays a key role in maintaining the mutation rate above the drift barrier, and the formation of mutation spectrum is also selectively preserved. These findings suggest the possibility of alleviating mutagenesis in various organisms through genome editing.
NATURE COMMUNICATIONS
(2021)
Article
Biotechnology & Applied Microbiology
Youngbeom Cho, Jae-Yoon Kim, Namshin Kim
Summary: This study examines the genome of the ancient chicken breed OGYE from the Korean Peninsula and identifies selection signatures resulting from environmental pressures. The research reveals the unique genetic diversity of OGYE and emphasizes the importance of sustainable management and breeding strategies for livestock on the Korean Peninsula.
Article
Biology
Tim Janicke, Salome Fromonteil
Summary: The study found that sexual size dimorphism (SSD) based on length measurements was correlated with the sex difference in the opportunity for sexual selection but showed a weak and statistically non-significant relationship with the sex difference in the Bateman gradient. This suggests that pre-copulatory sexual selection plays a limited role in the evolution of SSD across a broad phylogenetic context.
Article
Ecology
Anna M. Hewett, Martin A. Stoffel, Lucy Peters, Susan E. Johnston, Josephine M. Pemberton
Summary: The distribution of runs of homozygosity (ROH) in a wild population of red deer is shaped by selection, recombination, and population history. Population history and local recombination rate have been found to have an effect on ROH distribution by comparing populations and using different map types. Genetic drift resulting from a historical population bottleneck is the most likely cause of the observed ROH distribution in this population, with selection possibly playing a minor role.
Article
Biotechnology & Applied Microbiology
Xiaodong Lian, Haipeng Zhang, Chao Jiang, Fan Gao, Liu Yan, Xianbo Zheng, Jun Cheng, Wei Wang, Xiaobei Wang, Xia Ye, Jidong Li, Langlang Zhang, Zhiqian Li, Bin Tan, Jiancan Feng
Summary: The genome of temperature-sensitive semi-dwarf peach cultivar 'Zhongyoutao 14' was sequenced and analyzed to identify candidate genes controlling tree size, flower characteristics, and other agronomic traits. Additionally, a genome-wide association study revealed loci associated with fruit traits. The findings will advance genomic research and breeding efforts in peach.
PLANT BIOTECHNOLOGY JOURNAL
(2022)
Article
Multidisciplinary Sciences
Jaim Sivan, Itay Tesler, Shlomo Hadad, Abraham Allan Degen, Eli Geffen, Michael Kam
Summary: The morphological constraint hypothesis suggests that male snakes usually have longer tails than females to accommodate reproductive organs. In this study, the hypothesis was tested intraspecifically on Cerastes vipera, showing that males have relatively longer tails due to the length of the hemipenes pocket. This is the first report to support the MCH intraspecifically, and further studies are needed to determine if these relations are widespread among snake families or specifically within C. vipera.
SCIENTIFIC REPORTS
(2023)
Article
Biology
Shengnan Chen, Ying Jiang, Long Jin, Wenbo Liao
Summary: Testis asymmetry in anuran species was studied to test the packaging and compensation hypotheses. The results showed a positive correlation between testes size asymmetry and livers mass, supporting the packaging hypothesis; and a positive relationship between postcopulatory sperm competition and the degree of testes asymmetry, supporting the role of sexual selection. However, no effect of developmental stress on testes size asymmetry was found, inconsistent with the compensation hypothesis.
Article
Multidisciplinary Sciences
Dong-Dong Wu, Cui-Ping Yang, Ming-Shan Wang, Kun-Zhe Dong, Da-Wei Yan, Zi-Qian Hao, Song-Qing Fan, Shu-Zhou Chu, Qiu-Shuo Shen, Li-Ping Jiang, Yan Li, Lin Zeng, He-Qun Liu, Hai-Bing Xie, Yun-Fei Ma, Xiao-Yan Kong, Shu-Li Yang, Xin-Xing Dong, Ali Esmailizadeh, David M. Irwin, Xiao Xiao, Ming Li, Yang Dong, Wen Wang, Peng Shi, Hai-Peng Li, Yue-Hui Ma, Xiao Gou, Yong-Bin Chen, Ya-Ping Zhang
NATIONAL SCIENCE REVIEW
(2020)
Article
Biochemistry & Molecular Biology
Ming-Shan Wang, Sheng Wang, Yan Li, Yadvendradev Jhala, Mukesh Thakur, Newton O. Otecko, Jing-Fang Si, Hong-Man Chen, Beth Shapiro, Rasmus Nielsen, Ya-Ping Zhang, Dong-Dong Wu
MOLECULAR BIOLOGY AND EVOLUTION
(2020)
Article
Cell Biology
Ming-Shan Wang, Mukesh Thakur, Min-Sheng Peng, Yu Jiang, Laurent Alain Francois Frantz, Ming Li, Jin-Jin Zhang, Sheng Wang, Joris Peters, Newton Otieno Otecko, Chatmongkon Suwannapoom, Xing Guo, Zhu-Qing Zheng, Ali Esmailizadeh, Nalini Yasoda Hirimuthugoda, Hidayat Ashari, Sri Suladari, Moch Syamsul Arifin Zein, Szilvia Kusza, Saeed Sohrabi, Hamed Kharrati-Koopaee, Quan-Kuan Shen, Lin Zeng, Min-Min Yang, Ya-Jiang Wu, Xing-Yan Yang, Xue-Mei Lu, Xin-Zheng Jia, Qing-Hua Nie, Susan Joy Lamont, Emiliano Lasagna, Simone Ceccobelli, Humpita Gamaralalage Thilini Nisanka Gunwardana, Thilina Madusanka Senasige, Shao-Hong Feng, Jing-Fang Si, Hao Zhang, Jie-Qiong Jin, Ming-Li Li, Yan-Hu Liu, Hong-Man Chen, Cheng Ma, Shan-Shan Dai, Abul Kashem Fazlul Haque Bhuiyan, Muhammad Sajjad Khan, Gamamada Liyanage Lalanie Pradeepa Silva, Thi-Thuy Le, Okeyo Ally Mwai, Mohamed Nawaz Mohamed Ibrahim, Megan Supple, Beth Shapiro, Olivier Hanotte, Guojie Zhang, Greger Larson, Jian-Lin Han, Dong-Dong Wu, Ya-Ping Zhang
Article
Agriculture, Dairy & Animal Science
X. Guo, Z. -C. Wang, S. Wang, H. -F. Li, C. Suwannapoom, J. -X. Wang, C. Zhang, Y. Shao, M. -S. Wang, R. -S. Jiang
Article
Genetics & Heredity
Yun-Mei Wang, Saber Khederzadeh, Shi-Rong Li, Newton Otieno Otecko, David M. Irwin, Mukesh Thakur, Xiao-Die Ren, Ming-Shan Wang, Dong-Dong Wu, Ya-Ping Zhang
Summary: Piao chicken, a rare Chinese native poultry breed, lacks primary tail structures and the molecular mechanisms underlying tail absence in this breed remain unclear. This study employed comparative transcriptomic and genomic analyses to uncover potential genetic underpinnings of rumplessness in Piao chicken, revealing biological factors involved in tail development and genomic regions under strong positive selection. Candidate genes associated with rumplessness and the hypothesis that strong selection pressures on regulatory elements may lead to tail truncation were also discussed.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2021)
Article
Evolutionary Biology
Quan-Kuan Shen, Min-Sheng Peng, Adeniyi C. Adeola, Ling Kui, Shengchang Duan, Yong-Wang Miao, Nada M. Eltayeb, Jacqueline K. Lichoti, Newton O. Otecko, Maria Giuseppina Strillacci, Erica Gorla, Alessandro Bagnato, Olaogun S. Charles, Oscar J. Sanke, Philip M. Dawuda, Agboola O. Okeyoyin, John Musina, Peter Njoroge, Bernard Agwanda, Szilvia Kusza, Hojjat Asadollahpour Nanaei, Rana Pedar, Ming-Min Xu, Yuan Du, Lotanna M. Nneji, Robert W. Murphy, Ming-Shan Wang, Ali Esmailizadeh, Yang Dong, Sheila C. Ommeh, Ya-Ping Zhang
Summary: The domestication of the helmeted guinea fowl in West Africa around 1,300-5,500 years ago was revealed, with selective signals scanning functional genes related to behavior and locomotion changes. The recent breeding of Italian domestic guinea fowl unveiled the pleiotropy and linkage in genes affecting plumage color and fertility.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Biology
Ming-Shan Wang, Jin-Jin Zhang, Xing Guo, Ming Li, Rachel Meyer, Hidayat Ashari, Zhu-Qing Zheng, Sheng Wang, Min-Sheng Peng, Yu Jiang, Mukesh Thakur, Chatmongkon Suwannapoom, Ali Esmailizadeh, Nalini Yasoda Hirimuthugoda, Moch Syamsul Arifin Zein, Szilvia Kusza, Hamed Kharrati-Koopaee, Lin Zeng, Yun-Mei Wang, Ting-Ting Yin, Min-Min Yang, Ming-Li Li, Xue-Mei Lu, Emiliano Lasagna, Simone Ceccobelli, Humpita Gamaralalage Thilini Nisanka Gunwardana, Thilina Madusanka Senasig, Shao-Hong Feng, Hao Zhang, Abul Kashem Fazlul Haque Bhuiyan, Muhammad Sajjad Khan, Gamamada Liyanage Lalanie Pradeepa Silva, Le Thi Thuy, Okeyo A. Mwai, Mohamed Nawaz Mohamed Ibrahim, Guojie Zhang, Kai-Xing Qu, Olivier Hanotte, Beth Shapiro, Mirte Bosse, Dong-Dong Wu, Jian-Lin Han, Ya-Ping Zhang
Summary: Despite having higher genetic diversity, modern domestic chickens experienced a significant population size decline during early domestication compared to their wild counterparts. This led to an increase in deleterious mutations in chicken genomes, challenging modern breeding programs to effectively eliminate these genetic loads. Positive selection was found to decrease the incidence but increase the frequency of deleterious SNPs in domestic chicken genomes.
Article
Evolutionary Biology
Ming-Shan Wang, Mukesh Thakur, Yadvendradev Jhala, Sheng Wang, Yellapu Srinivas, Shan-Shan Dai, Zheng-Xi Liu, Hong-Man Cheng, Richard E. Green, Klaus-Peter Koepfli, Beth Shapiro
Summary: The study reveals that the Indian gray wolf is an evolutionarily distinct lineage that diverged from other gray wolf lineages approximately 110 thousand years ago. The Indian wolf population has continuously declined since separating from other gray wolves and has exceptionally low genetic diversity. Additionally, there is evidence for pervasive gene flow between the Indian wolf and African canids.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Immunology
Suyun Liang, Ming-Shan Wang, Bo Zhang, Yulong Feng, Jing Tang, Ming Xie, Wei Huang, Qi Zhang, Dabing Zhang, Shuisheng Hou
Summary: By comparing the genomes and transcriptomes of resistant and susceptible duck flocks, the study identified a strong association of NOD1 with the susceptibility of ducks to Duck viral hepatitis. Further experiments revealed that NOD1 expression influenced the number of DHAV-3 genomic copies in duck hepatocytes, providing a potential target for future investigations into the pathogenesis of DVH.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Ecology
Ming-Shan Wang, Gemma G. R. Murray, Daniel Mann, Pamela Groves, Alisa O. Vershinina, Megan A. Supple, Joshua D. Kapp, Russell Corbett-Detig, Sarah E. Crump, Ian Stirling, Kristin L. Laidre, Michael Kunz, Love Dalen, Richard E. Green, Beth Shapiro
Summary: This study reveals a massive admixture event between polar bears and brown bears approximately 100,000 years ago, during a period of climate change-induced overlap in their ranges. The gene flow was largely unidirectional, with polar bear genes being incorporated into the genomes of brown bears. These findings highlight the complex reticulate paths that evolution can take within a regime of radically shifting climate.
NATURE ECOLOGY & EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Xiangxiang Hu, Sing-Wai Wong, Kaixin Liang, Tai-Hsien Wu, Sheng Wang, Lufei Wang, Jie Liu, Mitsuo Yamauchi, Brian L. Foster, Jenny P. -Y. Ting, Baohong Zhao, Henry C. Tseng, Ching-Chang Ko
Summary: Degenerative diseases affecting the nervous and skeletal systems, such as neurodegenerative diseases and Paget's disease of bone, are influenced by the protein OPTN. OPTN and NRF2 show an age-related increase, and OPTN can interact with NRF2 and KEAP1 to up-regulate antioxidant response. Deletion of OPTN leads to increased oxidative stress and osteoclastogenesis, which can be attenuated by curcumin. These findings suggest the therapeutic potential of antioxidants for PDB.
Article
Multidisciplinary Sciences
Yong Shao, Long Zhou, Fang Li, Lan Zhao, Bao-Lin Zhang, Feng Shao, Jia-Wei Chen, Chun-Yan Chen, Xupeng Bi, Xiao-Lin Zhuang, Hong-Liang Zhu, Jiang Hu, Zongyi Sun, Xin Li, Depeng Wang, Iker Rivas-Gonzalez, Sheng Wang, Yun-Mei Wang, Wu Chen, Gang Li, Hui-Meng Lu, Yang Liu, Lukas F. K. Kuderna, Kyle Kai-How Farh, Peng-Fei Fan, Li Yu, Ming Li, Zhi-Jin Liu, George P. Tiley, Anne D. Yoder, Christian Roos, Takashi Hayakawa, Tomas Marques-Bonet, Jeffrey Rogers, Peter D. Stenson, David N. Cooper, Mikkel Heide Schierup, Yong-Gang Yao, Ya-Ping Zhang, Wen Wang, Xiao-Guang Qi, Guojie Zhang, Dong-Dong Wu
Summary: Comparative analysis of primate genomes is crucial for understanding human genetic architecture and primate evolution. This study analyzed the genomes of 50 primate species, including previously underrepresented groups. The results revealed varying rates of genomic rearrangement and gene evolution across primate lineages, with many genes under positive selection playing important roles in primate adaptations.
Article
Multidisciplinary Sciences
Bao-Lin Zhang, Wu Chen, Zefu Wang, Wei Pang, Meng -Ting Luo, Sheng Wang, Yong Shao, Wen-Qiang He, Yuan Deng, Long Zhou, Jiawei Chen, Min -Min Yang, Yajiang Wu, Lu Wang, Hugo Fernandez-Bellon, Sandra Molloy, Helene Meunler, Fanelie Wanert, Lukas Kuderna, Tomas Marques-Bonet, Christian Roos, Xiao-Guang Qi, Ming Li, Zhiji Liu, Mikkel Heide Schierup, David N. Cooper, Jianquan Liu, Yong-Tang Zheng, Guojie Zhang, Dong-Dong Wu
Summary: Through phylogenomic analysis of 12 macaque species, we discovered that the fascicularis group originated from an ancient hybridization event between the sinica and silenus groups around 3.45 to 3.56 million years ago. The X chromosomes and low-recombination regions showed equal contributions from each parental lineage, suggesting their importance in maintaining hybrid integrity. We also identified reproduction-associated genes and confirmed susceptibility to HIV-1 infection in all extant Western silenus species. Our study provides new insights into macaque evolution and highlights a rare hybrid speciation event in primates.
Article
Zoology
Lin Zeng, He-Qun Liu, Xiao-Long Tu, Chang-Mian Ji, Xiao Gou, Ali Esmailizadeh, Sheng Wang, Ming-Shan Wang, Ming-Cheng Wang, Xiao-Long Li, Hadi Charati, Adeniyi C. Adeola, Rahamon Akinyele Moshood Adedokun, Olatunbosun Oladipo, Sunday Charles Olaogun, Oscar J. Sanke, Mangbon F. Godwin, Sheila Cecily Ommeh, Bernard Agwanda, Jacqueline Kasiiti Lichoti, Jian-Lin Han, Hong-Kun Zheng, Chang-Fa Wang, Ya-Ping Zhang, Laurent A. F. Frantz, Dong-Dong Wu
Summary: Donkeys and kiangs on the Tibetan Plateau have adapted to high-altitude conditions through different biological pathways, with donkeys mainly involving the EGLN1 gene and kiangs mainly involving the EPAS1 gene. There is no evidence of interspecific gene flow between the two species.
ZOOLOGICAL RESEARCH
(2021)
Article
Zoology
Xing Guo, Xin-Xin He, Hong Chen, Zhi-Cheng Wang, Hui-Fang Li, Jiang-Xian Wang, Ming-Shan Wang, Run-Shen Jiang
Summary: Although mallards and Chinese spot-billed ducks have been proposed as potential wild ancestors of domestic ducks, a study analyzing 118 whole genomes suggests that domestic ducks may have originated from a different, currently unspecified wild duck population. Additionally, the study reveals pervasive introgression patterns among duck populations, and shows that domestic ducks separated from mallard and Chinese spot-billed ducks much earlier than previously thought, challenging the existing theories of duck domestication.
ZOOLOGICAL RESEARCH
(2021)
