Genomic inference of a severe human bottleneck during the Early to Middle Pleistocene transition
Creators
- 1. CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences
- 2. College of Artificial Intelligence and Big Data for Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences; Jinan, China
- 3. Natural History Museum, University of Florence; Florence, Italy
- 4. Department of Environmental Biology, Sapienza University of Rome
- 5. Key Laboratory of Brain Functional Genomics of Ministry of Education, School of Life Science, East China Normal University
- 6. Department of Biostatistics, School of Public Health, University of Texas Health Science Center at Houston
Description
The demographic history has been a foundation of human evolutionary studies for more than a century. We developed a novel method referred to as the fast infinitesimal time coalescent (FitCoal) process. This method allows the accurate calculation of the composite likelihood of a site frequency spectrum and provides the precise inference of recent and ancient demographic history.
FitCoal has been developed as a free plug-in of eGPS software while FitCoal can also be download and run as an independent Java package. If you are familiar with DOS/Linux or need batch processing, you can run FitCoal on command lines. You need to install Java environment first. The recommended JAVA version is 1.8 or the latest. Users can visit https://www.java.com/ to download the JAVA for free. Please note that the openJDK is not supported.
If you need Graphical User Interface (GUI), please download and install the eGPS software. Then copy the FitCoal to the eGPS plug-in directory (…/egps/config/plugin) and restart eGPS. You can find FitCoal under the plug-in menu.