Reply to Claramunt et al.: Robustness of the Cretaceous radiation of crown aves.

Autor: Wu S; Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, Jiangsu International Joint Center of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China., Rheindt FE; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore., Zhang J; School of Computer and Communication Engineering, Changsha University of Science & Technology, Changsha, Hunan 410114, China., Wang J; Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, Jiangsu International Joint Center of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China., Zhang L; Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, Jiangsu International Joint Center of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China., Quan C; School of Earth Science and Resources, Chang'an University, Xi'an, Shaanxi 710054, China., Li Z; Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China., Wang M; Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China., Wu F; Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China., Qu Y; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China., Edwards SV; Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138., Zhou Z; Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China., Liu L; Department of Statistics & Institute of Bioinformatics, University of Georgia, Athens, GA 30606.

Publikováno v: Proceedings of the National Academy of Sciences of the United States of America [Proc Natl Acad Sci U S A] 2024 Sep 24; Vol. 121 (39), pp. e2412448121. Date of Electronic Publication: 2024 Sep 16.

Practical guidance and workflows for identifying fast evolving non-coding genomic elements using PhyloAcc.

Autor: Thomas GWC; Informatics Group, Harvard University, Cambridge, MA, USA., Gemmell P; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.; Department of Statistics, Harvard University, Cambridge, MA, USA., Shakya SB; Informatics Group, Harvard University, Cambridge, MA, USA.; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.; Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA., Hu Z; Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA., Liu JS; Department of Statistics, Harvard University, Cambridge, MA, USA., Sackton TB; Informatics Group, Harvard University, Cambridge, MA, USA., Edwards SV; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.; Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA.

Publikováno v: Integrative and comparative biology [Integr Comp Biol] 2024 May 30. Date of Electronic Publication: 2024 May 30.

Boom-bust population dynamics drive rapid genetic change.

Autor: Stringer EJ; Centre for Conservation Ecology and Genomics, Institute for Applied Ecology, University of Canberra, Canberra ACT 2617, Australia., Gruber B; Centre for Conservation Ecology and Genomics, Institute for Applied Ecology, University of Canberra, Canberra ACT 2617, Australia., Sarre SD; Centre for Conservation Ecology and Genomics, Institute for Applied Ecology, University of Canberra, Canberra ACT 2617, Australia., Wardle GM; Desert Ecology Research Group, School of Life and Environmental Sciences, The University of Sydney, Sydney NSW 2006, Australia., Edwards SV; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138., Dickman CR; Desert Ecology Research Group, School of Life and Environmental Sciences, The University of Sydney, Sydney NSW 2006, Australia., Greenville AC; Desert Ecology Research Group, School of Life and Environmental Sciences, The University of Sydney, Sydney NSW 2006, Australia., Duncan RP; Centre for Conservation Ecology and Genomics, Institute for Applied Ecology, University of Canberra, Canberra ACT 2617, Australia.

Publikováno v: Proceedings of the National Academy of Sciences of the United States of America [Proc Natl Acad Sci U S A] 2024 Apr 30; Vol. 121 (18), pp. e2320590121. Date of Electronic Publication: 2024 Apr 15.

slimr: An R package for tailor-made integrations of data in population genomic simulations over space and time.

Autor: Dinnage R; Institute of Environment, Department of Biological Sciences, Florida International University, Miami, Florida, USA.; Centre for Conservation Ecology and Genomics, Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia., Sarre SD; Centre for Conservation Ecology and Genomics, Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia., Duncan RP; Centre for Conservation Ecology and Genomics, Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia., Dickman CR; Desert Ecology Research Group, School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia., Edwards SV; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.; Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, USA., Greenville AC; Desert Ecology Research Group, School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia., Wardle GM; Desert Ecology Research Group, School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia., Gruber B; Centre for Conservation Ecology and Genomics, Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia.

Publikováno v: Molecular ecology resources [Mol Ecol Resour] 2024 Apr; Vol. 24 (3), pp. e13916. Date of Electronic Publication: 2023 Dec 20.

Gene flow and an anomaly zone complicate phylogenomic inference in a rapidly radiated avian family (Prunellidae).

Autor: Jiang Z; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China., Zang W; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China., Ericson PGP; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, Stockholm, SE-104 05, Sweden., Song G; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China., Wu S; Jiangsu International Joint Center of Genomics, Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu, China., Feng S; Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, 310058, China.; Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou, 311121, China.; Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, 314102, China., Drovetski SV; National Museum of Natural History, Smithsonian Institution, Washington, DC, 20004, USA.; Present address: U.S. Geological Survey, Eastern Ecological Science Center at Patuxent Research Refuge, Laurel, MD, 20708, USA., Liu G; Chinese Academy of Forestry, Institute of Ecological Conservation and Restoration, Beijing, 100091, China., Zhang D; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China., Saitoh T; Yamashina Institute for Ornithology, Abiko, Chiba, Japan., Alström P; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.; Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, 752 36, Uppsala, Sweden., Edwards SV; Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA., Lei F; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China., Qu Y; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China. quyh@ioz.ac.cn.; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China. quyh@ioz.ac.cn.; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, Stockholm, SE-104 05, Sweden. quyh@ioz.ac.cn.

Publikováno v: BMC biology [BMC Biol] 2024 Feb 27; Vol. 22 (1), pp. 49. Date of Electronic Publication: 2024 Feb 27.