Article
Genetics & Heredity
Zhouping Cui, Jian Zhang, Zhihui Sun, Bingzheng Liu, Chong Zhao, Yaqing Chang
Summary: Sex-specific markers were identified in sea urchin through 2b-RAD-seq and genome survey, suggesting the existence of a female heterogametic and male homogametic ZW/ZZ sex determination system. These results provide a solid foundation for further research on the sex determination mechanism of sea urchin and potential applications in sex-control breeding.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Amanda K. Navine, Kristina L. Paxton, Eben H. Paxton, Patrick J. Hart, Jeffrey T. Foster, Nancy McInerney, Robert C. Fleischer, Elin Videvall
Summary: Hawaiian honeycreepers, specifically the amakihi species, show some level of immunity to avian malaria. Examining their cloacal microbiomes has revealed potential microbes, such as Escherichia and Lactobacillus species, that could mitigate malaria severity and be candidates for future probiotic research. This study highlights the importance of innovative conservation strategies and the potential role of gut microbiota in enhancing malaria immunity in endangered species.
Article
Biochemistry & Molecular Biology
Kate D. Lee, Craig D. Millar, Patricia Brekke, Annabel Whibley, John G. Ewen, Melanie Hingston, Amy Zhu, Anna W. Santure
Summary: Next-generation sequencing technology has revolutionized ecological and evolutionary genetics, enabling cost-effective identification of genome-wide variation. In this study, researchers developed a 50K SNP chip for the threatened species hihi by combining RAD-seq and WGS data, demonstrating its utility in identifying SNPs for genotyping and revealing high rates of linkage disequilibrium in the hihi genome, indicative of population bottleneck events.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Endocrinology & Metabolism
Ya-Lun Han, Zhi-Hui Sun, Shuai Chang, Bin Wen, Jian Song, Ran-Tao Zuo, Ya-Qing Chang
Summary: A sex-related SNP was identified in sea urchin, which is located in the spata4 gene specifically expressed in males. Knocking down spata4 in males led to downregulation of other testis differentiation genes. The study also revealed a non-1:1 sex ratio in the S. intermedius population and dynamic changes in gene expression related to sex differentiation and estrogen metabolism after a 58-day estradiol feeding experiment.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Article
Environmental Sciences
Yu Li, Jianhua Chen, Guangpeng Feng, Qingyun Wang, Rulong Xia, Chao Song, Haihua Wang, Yanping Zhang
Summary: In this study, the genetic diversity of Coilia nasus was investigated using 2b-RAD simplified genome sequencing technology. The results showed that the genetic purity of the populations was low and needs to be improved. The populations exhibited high genetic diversity, indicating strong adaptability and potential for distribution and resource growth. Moderate genetic differentiation was observed among the populations, suggesting a common spawning ground for these migratory species and the need to protect the gene purity of C. nasus.
Article
Genetics & Heredity
A. Gilles, Y. Thevenin, F. Dione, J. -F Martin, B. Barascud, R. Chappaz, N. Pech
Summary: This study demonstrates the early stages of hybridization between divergent lineages and predicts the emergence of future hybrid zones in the wild, generating a wide spectrum of hybrids that are a potential source of important evolutionary novelties.
FRONTIERS IN GENETICS
(2022)
Article
Multidisciplinary Sciences
Bailing Chen, Yulong Li, Meilin Tian, Hao Su, Wei Sun, Yunfeng Li
Summary: This study utilized the 2b-RAD method to sequence R. esculentum and constructed a linkage map. Several quantitative trait loci associated with umbrella diameter and body weight were identified. Additionally, candidate growth-related genes were found in QTL regions, with one gene potentially playing a significant role in controlling the growth of R. esculentum.
SCIENTIFIC REPORTS
(2022)
Article
Biodiversity Conservation
Long Jin, Wen Bo Liao, Juha Merila
Summary: Amphibians require both terrestrial and aquatic environments to complete their life cycles. Genetic differentiation studies along geographical clines in Microhyla fissipes populations in China revealed significant differentiation related to temperature and precipitation variations.
DIVERSITY AND DISTRIBUTIONS
(2022)
Article
Plant Sciences
Anfei Fang, Zhuangyuan Fu, Zexiong Wang, Yuhang Fu, Yubao Qin, Zhenxu Bai, Ze Tan, Junsong Cai, Yuheng Yang, Yang Yu, Wenxian Sun, Chaowei Bi
Summary: This study analyzed the genetic diversity and population structure of Ustilaginoidea virens isolates from the Sichuan-Chongqing region in China using novel molecular markers and a previously reported marker. The findings revealed gene flow among different populations and identified six genetic groups. Significant genetic differentiation was observed among different geographical populations. The study also found differences in genetic composition between isolates collected from different areas and identified genetic recombination in some isolates. These findings have important implications for the management of rice false smut and resistance breeding.
Article
Plant Sciences
Qingqing Yu, Yao Ling, Yanli Xiong, Wenda Zhao, Yi Xiong, Zhixiao Dong, Jian Yang, Junming Zhao, Xinquan Zhang, Xiao Ma
Summary: This study proposed the use of high-throughput RAD-seq to distinguish 11 Italian ryegrass varieties based on their genetic background. The results showed significant differences among the tested varieties, with a heterogeneous genetic background for all of them. The analysis also revealed that the variety 'Changjiang No.2' had the best intra-variety consistency. The study suggests that RAD-seq could be an effective method for variety distinction in Italian ryegrass and potentially for other allogamous species.
Article
Plant Sciences
Ademola Aina, Ana Luisa Garcia-Oliveira, Christopher Ilori, Peter L. Chang, Muyideen Yusuf, Olaniyi Oyatomi, Michael Abberton, Daniel Potter
Summary: This study focused on the genetic diversity of African Yam Bean (AYB) accessions, analyzing 93 accessions from IITA genebank using 3722 SNP markers. The results showed substantial genetic variability and grouped the accessions into three to four main clusters, with majority sharing similar phenotypes. The study also successfully associated agronomic traits with genetic clusters, providing insights for AYB breeding programs.
Article
Plant Sciences
Hui Li, Li Chang, Huijuan Tang, Mingbao Luan, Gen Pan, Siqi Huang, Jiang Hui, Yena Wu, Anguo Chen
Summary: This study found that fiber yield and quality are controlled by multiple genes and correlated with traits such as plant height, fresh bast weight, and dry bast weight. QTL mapping was used to successfully map SNP markers onto 18 different linkage groups and identify 6 QTLs related to fiber yield and quality. This is the first study to map QTLs for fiber yield and quality, providing valuable insights into the molecular genetic basis of these traits.
SOUTH AFRICAN JOURNAL OF BOTANY
(2023)
Article
Agronomy
Noriyuki Onoue, Atsushi Kono, Akifumi Azuma, Ryusuke Matsuzaki, Atsushi J. Nagano, Akihiko Sato
Summary: Inbreeding depression reduces the yield potential of a persimmon population. This study examined the effects of inbreeding on yield-related traits using sequence-based genotyping. The results showed that inbreeding depression occurs in persimmon, and employing an F-M method helps increase the chance of developing high-yielding hybrid cultivars.
Article
Fisheries
Mahdieh Rahbar, Majidreza Khoshkholgh, Sajad Nazari
Summary: The study used RAD-seq approach to investigate the genetic variability and population structure of Caspian kutum populations in Iran. The results revealed significant genetic variation and identified several SNP markers that can be used for monitoring and understanding the genetic variation in this endangered species.
FISHERIES RESEARCH
(2023)
Article
Plant Sciences
Bishnu Maya Bashyal, Gaurav Kumar Yadav, Pooja Parmar, Sunil Kumar Sunani, Shweta Aggarwal, S. Gopala Krishnan, Atul Kumar, Najam Waris Zaidi, Rashmi Aggarwal
Summary: A high-quality genome of Ustilaginoidea virens was sequenced, revealing numerous variants and important genes. This high-quality genome will provide valuable insights into the biology and pathogenesis of U. virens.
Article
Biochemistry & Molecular Biology
Daniel T. Ksepka, Amy M. Balanoff, N. Adam Smith, Gabriel S. Bever, Bhart-Anjan S. Bhullar, Estelle Bourdon, Edward L. Braun, J. Gordon Burleigh, Julia A. Clarke, Matthew W. Colbert, Jeremy R. Corfield, Federico J. Degrange, Vanesa L. De Pietri, Catherine M. Early, Daniel J. Field, Paul M. Gignac, Maria Eugenia Leone Gold, Rebecca T. Kimball, Soichiro Kawabe, Louis Lefebvre, Jesus Marugan-Lobon, Carrie S. Mongle, Ashley Morhardt, Mark A. Norell, Ryan C. Ridgely, Ryan S. Rothman, R. Paul Scofield, Claudia P. Tambussi, Christopher R. Torres, Marcel van Tuinen, Stig A. Walsh, Akinobu Watanabe, Lawrence M. Witmer, Alexandra K. Wright, Lindsay E. Zanno, Erich D. Jarvis, Jeroen B. Smaers
Article
Multidisciplinary Sciences
David Jebb, Zixia Huang, Martin Pippel, Graham M. Hughes, Ksenia Lavrichenko, Paolo Devanna, Sylke Winkler, Lars S. Jermiin, Emilia C. Skirmuntt, Aris Katzourakis, Lucy Burkitt-Gray, David A. Ray, Kevin A. M. Sullivan, Juliana G. Roscito, Bogdan M. Kirilenko, Liliana M. Davalos, Angelique P. Corthals, Megan L. Power, Gareth Jones, Roger D. Ransome, Dina K. N. Dechmann, Andrea G. Locatelli, Sebastien J. Puechmaille, Olivier Fedrigo, Erich D. Jarvis, Michael Hiller, Sonja C. Vernes, Eugene W. Myers, Emma C. Teeling
Letter
Marine & Freshwater Biology
Phillip A. Morin, Alana Alexander, Mark Blaxter, Susana Caballero, Olivier Fedrigo, Michael C. Fontaine, Andrew D. Foote, Shigehiro Kuraku, Brigid Maloney, Morgan L. McCarthy, Michael R. McGowen, Jacquelyn Mountcastle, Mariana F. Nery, Morten Tange Olsen, Patricia E. Rosel, Erich D. Jarvis
MARINE MAMMAL SCIENCE
(2020)
Article
Biochemistry & Molecular Biology
Phillip A. Morin, Frederick I. Archer, Catherine D. Avila, Jennifer R. Balacco, Yury V. Bukhman, William Chow, Olivier Fedrigo, Giulio Formenti, Julie A. Fronczek, Arkarachai Fungtammasan, Frances M. D. Gulland, Bettina Haase, Mads Peter Heide-Jorgensen, Marlys L. Houck, Kerstin Howe, Ann C. Misuraca, Jacquelyn Mountcastle, Whitney Musser, Sadye Paez, Sarah Pelan, Adam Phillippy, Arang Rhie, Jacqueline Robinson, Lorenzo Rojas-Bracho, Teri K. Rowles, Oliver A. Ryder, Cynthia R. Smith, Sacha Stevenson, Barbara L. Taylor, Jonas Teilmann, James Torrance, Randall S. Wells, Andrew J. Westgate, Erich D. Jarvis
Summary: The vaquita is the most critically endangered marine mammal, with fewer than 19 remaining in the wild. Research has shown that its genome has a stable historical population size and low heterozygosity, potentially allowing for the purging of highly deleterious alleles and maintaining the necessary diversity for population health.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Biochemistry & Molecular Biology
Jing Liu, Zongji Wang, Jing Li, Luohao Xu, Jiaqi Liu, Shaohong Feng, Chunxue Guo, Shengchan Chen, Zhanjun Ren, Jinpeng Rao, Kai Wei, Yuezhou Chen, Erich D. Jarvis, Guojie Zhang, Qi Zhou
Summary: Emus and other ratites have slower genome evolution rates compared to other birds, making them useful for reconstructing ancestral avian or vertebrate karyotype evolution. The study's findings show that ratites have fewer intra and inter-chromosomal changes than other birds since diverging from turtles. The distinct structure of the emu W chromosome, with highly heterochromatic and recently evolved regions, suggests important early steps in sex chromosome evolution.
Article
Multidisciplinary Sciences
Yang Zhou, Linda Shearwin-Whyatt, Jing Li, Zhenzhen Song, Takashi Hayakawa, David Stevens, Jane C. Fenelon, Emma Peel, Yuanyuan Cheng, Filip Pajpach, Natasha Bradley, Hikoyu Suzuki, Masato Nikaido, Joana Damas, Tasman Daish, Tahlia Perry, Zexian Zhu, Yuncong Geng, Arang Rhie, Ying Sims, Jonathan Wood, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, Qiye Li, Huanming Yang, Jian Wang, Stephen D. Johnston, Adam M. Phillippy, Kerstin Howe, Erich D. Jarvis, Oliver A. Ryder, Henrik Kaessmann, Peter Donnelly, Jonas Korlach, Harris A. Lewin, Jennifer Graves, Katherine Belov, Marilyn B. Renfree, Frank Grutzner, Qi Zhou, Guojie Zhang
Summary: The study of egg-laying mammals' genomes offers insights into mammalian evolution, highlighting ancestral and lineage-specific genomic changes in monotremes and mammals. Unique chromosome complex in monotremes may have originated from ancestral chromosome configuration, and differences in specific genes underlie ecological adaptations of monotremes compared to therians.
Article
Multidisciplinary Sciences
Anoushka Joglekar, Andrey Prjibelski, Ahmed Mahfouz, Paul Collier, Susan Lin, Anna Katharina Schlusche, Jordan Marrocco, Stephen R. Williams, Bettina Haase, Ashley Hayes, Jennifer G. Chew, Neil I. Weisenfeld, Man Ying Wong, Alexander N. Stein, Simon A. Hardwick, Toby Hunt, Qi Wang, Christoph Dieterich, Zachary Bent, Olivier Fedrigo, Steven A. Sloan, Davide Risso, Erich D. Jarvis, Paul Flicek, Wenjie Luo, Geoffrey S. Pitt, Adam Frankish, August B. Smit, M. Elizabeth Ross, Hagen U. Tilgner
Summary: The study revealed variations in alternative RNA splicing across different brain regions, with unclear single-cell resolution of such differences. Certain genes can be influenced by multiple cell types, allowing regional identity to occasionally override cell-type specificity. Through spatial transcriptomics and long-read sequencing, a deeper understanding of brain integration of molecular and cellular complexities is achieved.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Jing Li, Jilin Zhang, Jing Liu, Yang Zhou, Cheng Cai, Luohao Xu, Xuelei Dai, Shaohong Feng, Chunxue Guo, Jinpeng Rao, Kai Wei, Erich D. Jarvis, Yu Jiang, Zhengkui Zhou, Guojie Zhang, Qi Zhou
Summary: Utilizing long-read sequencing and multiplatform scaffolding techniques, we resolved the genome assembly issues in ducks and found extensive overlap in chromosome features between ducks and chickens. The duck W chromosome shares similarities with the human Y chromosome in terms of chromosome structure and suppression of homologous recombination.
Article
Behavioral Sciences
Ha Na Choe, Jeevan Tewari, Kevin W. Zhu, Matthew Davenport, Hiroaki Matsunami, Erich D. Jarvis
Summary: Sex hormones impact brain development and behavior coordination. In zebra finches, song learning is limited to males, with estrogen treatment preventing atrophy in females. Sex-specific gene expression in song nuclei differs between males and females.
HORMONES AND BEHAVIOR
(2021)
Article
Zoology
Amanda D. Melin, Joseph D. Orkin, Mareike C. Janiak, Alejandro Valenzuela, Lukas Kuderna, Frank Marrone, Hasinala Ramangason, Julie E. Horvath, Christian Roos, Andrew C. Kitchener, Chiea Chuen Khor, Weng Khong Lim, Jessica G. H. Lee, Patrick Tan, Govindhaswamy Umapathy, Muthuswamy Raveendran, R. Alan Harris, Ivo Gut, Marta Gut, Esther Lizano, Tilo Nadler, Dietmar Zinner, Minh D. Le, Sivakumara Manu, Clement J. Rabarivola, Alphonse Zaramody, Nicole Andriaholinirina, Steig E. Johnson, Erich D. Jarvis, Olivier Fedrigo, Dongdong Wu, Guojie Zhang, Kyle Kai-How Farh, Jeffrey Rogers, Tomas Marques-Bonet, Arcadi Navarro, David Juan, Paramjit S. Arora, James P. Higham
Summary: The global pandemic of the novel coronavirus COVID-19 is not only a threat to human health, but also poses potential risks to nonhuman primates, especially lemurs. Conservation efforts should focus on understanding and limiting the exposure of lemurs to SARS-CoV-2, as some species are at high risk, including the endangered aye-aye.
AMERICAN JOURNAL OF PRIMATOLOGY
(2021)
Correction
Multidisciplinary Sciences
Shaohong Feng, Josefin Stiller, Yuan Deng, Joel Armstrong, Qi Fang, Andrew Hart Reeve, Duo Xie, Guangji Chen, Chunxue Guo, Brant C. Faircloth, Bent Petersen, Zongji Wang, Qi Zhou, Mark Diekhans, Wanjun Chen, Sergio Andreu-Sanchez, Ashot Margaryan, Jason Travis Howard, Carole Parent, George Pacheco, Mikkel-Holger S. Sinding, Lara Puetz, Emily Cavill, Angela M. Ribeiro, Leopold Eckhart, Jon Fjeldsa, Peter A. Hosner, Robb T. Brumfield, Les Christidis, Mads F. Bertelsen, Thomas Sicheritz-Ponten, Dieter Thomas Tietze, Bruce C. Robertson, Gang Song, Gerald Borgia, Santiago Claramunt, Irby J. Lovette, Saul J. Cowen, Peter Njoroge, John Philip Dumbacher, Oliver A. Ryder, Jerome Fuchs, Michael Bunce, David W. Burt, Joel Cracraft, Guanliang Meng, Shannon J. Hackett, Peter G. Ryan, Knud Andreas Jonsson, Ian G. Jamieson, Rute R. da Fonseca, Edward L. Braun, Peter Houde, Siavash Mirarab, Alexander Suh, Bengt Hansson, Suvi Ponnikas, Hanna Sigeman, Martin Stervander, Paul B. Frandsen, Henriette van der Zwan, Rencia van der Sluis, Carina Visser, Christopher N. Balakrishnan, Andrew G. Clark, John W. Fitzpatrick, Reed Bowman, Nancy Chen, Alison Cloutier, Timothy B. Sackton, Scott V. Edwards, Dustin J. Foote, Subir B. Shakya, Frederick H. Sheldon, Alain Vignal, Andre E. R. Soares, Beth Shapiro, Jacob Gonzalez-Solis, Joan Ferrer-Obiol, Julio Rozas, Marta Riutort, Anna Tigano, Vicki Friesen, Love Dalen, Araxi O. Urrutia, Tamas Szekely, Yang Liu, Michael G. Campana, Andre Corvelo, Robert C. Fleischer, Kim M. Rutherford, Neil J. Gemmell, Nicolas Dussex, Henrik Mouritsen, Nadine Thiele, Kira Delmore, Miriam Liedvogel, Andre Franke, Marc P. Hoeppner, Oliver Krone, Adam M. Fudickar, Borja Mila, Ellen D. Ketterson, Andrew Eric Fidler, Guillermo Friis, Angela M. Parody-Merino, Phil F. Battley, Murray P. Cox, Nicholas Costa Barroso Lima, Francisco Prosdocimi, Thomas Lee Parchman, Barney A. Schlinger, Bette A. Loiselle, John G. Blake, Haw Chuan Lim, Lainy B. Day, Matthew J. Fuxjager, Maude W. Baldwin, Michael J. Braun, Morgan Wirthlin, Rebecca B. Dikow, T. Brandt Ryder, Glauco Camenisch, Lukas F. Keller, Jeffrey M. DaCosta, Mark E. Hauber, Matthew I. M. Louder, Christopher C. Witt, Jimmy A. McGuire, Joann Mudge, Libby C. Megna, Matthew D. Carling, Biao Wang, Scott A. Taylor, Glaucia Del-Rio, Alexandre Aleixo, Ana Tereza Ribeiro Vasconcelos, Claudio V. Mello, Jason T. Weir, David Haussler, Qiye Li, Huanming Yang, Jian Wang, Fumin Lei, Carsten Rahbek, M. Thomas P. Gilbert, Gary R. Graves, Erich D. Jarvis, Benedict Paten, Guojie Zhang
Editorial Material
Multidisciplinary Sciences
Erich D. Jarvis
Article
Evolutionary Biology
Xuankun Li, Emily Ellis, David Plotkin, Yume Imada, Masaya Yago, Jacqueline Heckenhauer, Timothy P. Cleland, Rebecca B. Dikow, Torsten Dikow, Caroline G. Storer, Akito Y. Kawahara, Paul B. Frandsen
Summary: The research team presents a new annotated genome assembly of Neomicropteryx cornuta, offering valuable insights into the early evolution of Amphiesmenoptera. The highly contiguous genome assembly provides important resources for studying ecological and evolutionary transitions in the group. The study demonstrates high recovery of universal single copy orthologs and provides genome annotation of 15,643 genes.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Ecology
Marek L. Borowiec, Rebecca B. Dikow, Paul B. Frandsen, Alexander McKeeken, Gabriele Valentini, Alexander E. White
Summary: This review summarizes the use of deep learning in ecology and evolution, discussing its applications, limitations, and possible future developments in these fields.
METHODS IN ECOLOGY AND EVOLUTION
(2022)
Article
Linguistics
Julia Hyland Bruno, Erich D. Jarvis, Mark Liberman, Ofer Tchernichovski
Summary: The study examines the similarities and differences between vocal learning bird species and humans across various levels, suggesting that the cultural transmission of vocal repertoires is a natural outcome of vocal learning evolution. The balance between genetic constraints and social environment features allows for the propagation of cultural learning in both birdsong and human vocal culture.
ANNUAL REVIEW OF LINGUISTICS, VOL 7
(2021)