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Demographic analysis of cyanobacteria based on the mutation rates estimated from an ancient ice core. Heredity (Edinb) 2018; 120:562-573. [PMID: 29302050 DOI: 10.1038/s41437-017-0040-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 11/12/2017] [Accepted: 11/20/2017] [Indexed: 12/15/2022] Open
Abstract
Despite the crucial role of cyanobacteria in various ecosystems, little is known about their evolutionary histories, especially microevolutionary dynamics, because of the lack of knowledge regarding their mutation rates. Here we directly estimated cyanobacterial mutation rates based on ancient DNA analyses of ice core samples collected from Kyrgyz Republic that dates back to ~12,500 cal years before present. We successfully sequenced the 16S rRNA and 16S-23S internal transcribed spacer (ITS) region. Two cyanobacterial operational taxonomic units (OTUs) were detected from the ancient ice core samples, and these OTUs are shared with those from the modern glacier surface. The mutation rate of ITS region was estimated by comparing ancient and modern populations, and were at the magnitude of 10-7substitutions/sites/year. By using a model selection framework, we also demonstrated that the ancient sequences from the ice sample were not contaminated from modern samples. Bayesian demographic analysis based on coalescent theory revealed that cyanobacterial population sizes increased over Asia regions during the Holocene. Thus, our results enhance our understanding of the enigmatic timescale of cyanobacterial microevolution, which has the potential to elucidate the environmental responses of cyanobacteria to the drastic climatic change events of the Quaternary.
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Osman SAM, Yonezawa T, Nishibori M. Origin and genetic diversity of Egyptian native chickens based on complete sequence of mitochondrial DNA D-loop region. Poult Sci 2016; 95:1248-56. [PMID: 26994197 DOI: 10.3382/ps/pew029] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 01/08/2016] [Indexed: 11/20/2022] Open
Abstract
Domestic chickens (Gallus gallus) play a significant role, ranging from food and entertainment to religion and ornamentation. However, the details on their domestication process are still controversial, especially the origin and evolution of African chickens. Egypt is thought to be important place for this event because of its geographic location as well as its long history of civilization. However, the genetic component and structure of Egyptian native chicken (ENC) have not been studied so far. The aim of this study is to clarify the origin and evolution of African chickens through assessing the genetic diversities and structure of five ENC breeds using the mitochondrial D-loop sequences. Our results suggest there is genetic differentiation between the pure native breeds and the improved native breeds. The latter breeds were established by the hybridization of the pure native and the exotic breeds. The pure native breeds were estimated to be established about 800 years ago. Subsequently, we extensively analyzed the D-loop sequences from the ENC as well as the globally collected chickens (2,010 individuals in total). Our phylogenetic tree among the regional populations shows African chickens can be separated to two distinct clades. The first clade consists of North African (Egypt), Central African (Sudan and Cameroon), European, and West (and Central) Asian chickens. The second clade consists of East African (Kenya, Malawi, and Zimbabwe) and Pacific chickens. It suggests the dual origins of African native chickens. The first group was probably originated from South Asia, and then migrated to West Asia, and finally arrived to Africa thorough Egypt. The second group migrated from Pacific to East Africa via Indian Ocean probably by Austronesian people. This dual origin hypothesis as well as estimated divergence times in this study is harmonious with the archaeological and historical evidences. Our migration analysis suggests there is limited gene flow within African continent. These obtained findings are important for the better understanding of the diversity and uniqueness of African native chickens.
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Affiliation(s)
- Sayed A-M Osman
- Laboratory of Animal Genetics, Department of Bioresource Science, Graduate School of Biosphere Science, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima 739-8528, Japan Department of Genetics, Faculty of Agriculture, Minia University, El Minia 61517, Egypt
| | - Takahiro Yonezawa
- School of Life Sciences, Fudan University, SongHu Rd. 2005, Shanghai 200438, China The Institute of Statistical Mathematics, Midori-cho 10-3, Tachikawa, Tokyo 190-8562, Japan
| | - Masahide Nishibori
- Laboratory of Animal Genetics, Department of Bioresource Science, Graduate School of Biosphere Science, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima 739-8528, Japan
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Burgstaller JP, Johnston IG, Jones NS, Albrechtová J, Kolbe T, Vogl C, Futschik A, Mayrhofer C, Klein D, Sabitzer S, Blattner M, Gülly C, Poulton J, Rülicke T, Piálek J, Steinborn R, Brem G. MtDNA segregation in heteroplasmic tissues is common in vivo and modulated by haplotype differences and developmental stage. Cell Rep 2014; 7:2031-2041. [PMID: 24910436 DOI: 10.1016/j.celrep.2014.05.020] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 03/11/2014] [Accepted: 05/12/2014] [Indexed: 12/21/2022] Open
Abstract
The dynamics by which mitochondrial DNA (mtDNA) evolves within organisms are still poorly understood, despite the fact that inheritance and proliferation of mutated mtDNA cause fatal and incurable diseases. When two mtDNA haplotypes are present in a cell, it is usually assumed that segregation (the proliferation of one haplotype over another) is negligible. We challenge this assumption by showing that segregation depends on the genetic distance between haplotypes. We provide evidence by creating four mouse models containing mtDNA haplotype pairs of varying diversity. We find tissue-specific segregation in all models over a wide range of tissues. Key findings are segregation in postmitotic tissues (important for disease models) and segregation covering all developmental stages from prenatal to old age. We identify four dynamic regimes of mtDNA segregation. Our findings suggest potential complications for therapies in human populations: we propose "haplotype matching" as an approach to avoid these issues.
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Affiliation(s)
- Joerg Patrick Burgstaller
- Biotechnology in Animal Production, Department for Agrobiotechnology, IFA Tulln, 3430 Tulln, Austria.,Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Iain G Johnston
- Department of Mathematics, Imperial College London, London SW7 2AZ, United Kingdom
| | - Nick S Jones
- Department of Mathematics, Imperial College London, London SW7 2AZ, United Kingdom
| | - Jana Albrechtová
- Research Facility Studenec, Academy of Sciences of the Czech Republic, Květná 8, 60365 Brno, Czech Republic
| | - Thomas Kolbe
- Biomodels Austria, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria.,Department for Agrobiotechnology, IFA Tulln, University of Natural Resources and Applied Life Sciences, Tulln 3430, Austria
| | - Claus Vogl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Andreas Futschik
- Department of Statistics, University of Vienna, 1010 Vienna, Austria
| | - Corina Mayrhofer
- Biotechnology in Animal Production, Department for Agrobiotechnology, IFA Tulln, 3430 Tulln, Austria.,Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Dieter Klein
- VetCore Facility for Research, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Sonja Sabitzer
- VetCore Facility for Research, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Mirjam Blattner
- VetCore Facility for Research, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Christian Gülly
- Center for Medical Research, Medical University of Graz, 8010 Graz, Austria
| | - Joanna Poulton
- Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Oxford OX3 9DU, United Kingdom
| | - Thomas Rülicke
- Institute of Laboratory Animal Science, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Jaroslav Piálek
- Research Facility Studenec, Academy of Sciences of the Czech Republic, Květná 8, 60365 Brno, Czech Republic
| | - Ralf Steinborn
- VetCore Facility for Research, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Gottfried Brem
- Biotechnology in Animal Production, Department for Agrobiotechnology, IFA Tulln, 3430 Tulln, Austria.,Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
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