1
|
Huang CJ, Chu FH, Huang YS, Tu YC, Hung YM, Tseng YH, Pu CE, Hsu CT, Chao CH, Chou YS, Liu SC, You YT, Hsu SY, Hsieh HC, Wang CT, Chen CT. SSR individual identification system construction and population genetics analysis for Chamaecyparis formosensis. Sci Rep 2022; 12:4126. [PMID: 35260700 PMCID: PMC8904461 DOI: 10.1038/s41598-022-07870-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 02/03/2022] [Indexed: 12/25/2022] Open
Abstract
Chamaecyparis formosensis is an endemic species of Taiwan, threatened from intensive use and illegal felling. An individual identification system for C. formosensis is required to provide scientific evidence for court use and deter illegal felling. In this study, 36 polymorphic simple sequence repeat markers were developed. By applying up to 28 non-linked of the developed markers, it is calculated that the cumulative random probability of identity (CPI) is as low as 1.652 × 10–12, and the identifiable population size is up to 60 million, which is greater than the known C. formosensis population size in Taiwan. Biogeographical analysis data show that C. formosensis from four geographic areas belong to the same genetic population, which can be further divided into three clusters: SY (Eastern Taiwan), HV and GW (Northwestern Taiwan), and MM (Southwestern Taiwan). The developed system was applied to assess the provenance of samples with 88.44% accuracy rate and therefore can serve as a prescreening tool to reduce the range required for comparison. The system developed in this study is a potential crime-fighting tool against illegal felling.
Collapse
Affiliation(s)
- Chiun-Jr Huang
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, 10617, Taiwan. .,Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan. .,Department of Forensic Science, Investigation Bureau, Ministry of Justice, New Taipei City, 23149, Taiwan.
| | - Fang-Hua Chu
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, 10617, Taiwan
| | - Yi-Shiang Huang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Yu-Ching Tu
- Department of Forensic Science, Investigation Bureau, Ministry of Justice, New Taipei City, 23149, Taiwan
| | - Yu-Mei Hung
- Department of Forensic Science, Investigation Bureau, Ministry of Justice, New Taipei City, 23149, Taiwan
| | - Yu-Hsin Tseng
- Department of Life Sciences, National Chung Hsing University, Taichung, 402, Taiwan
| | - Chang-En Pu
- Department of Forensic Science, Investigation Bureau, Ministry of Justice, New Taipei City, 23149, Taiwan
| | - Cheng Te Hsu
- Hualien Forest District Office, Forestry Bureau, Council of Agriculture, Hualien, 97051, Taiwan
| | - Chi-Hsiang Chao
- Department of Forensic Science, Investigation Bureau, Ministry of Justice, New Taipei City, 23149, Taiwan
| | - Yu-Shyang Chou
- Department of Forensic Science, Investigation Bureau, Ministry of Justice, New Taipei City, 23149, Taiwan
| | - Shau-Chian Liu
- Department of Applied Science, National Taitung University, Taitung, 95092, Taiwan
| | - Ya Ting You
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Shuo-Yu Hsu
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, 10617, Taiwan
| | - Hsiang-Chih Hsieh
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, 10617, Taiwan
| | - Chieh-Ting Wang
- The Experimental Forest, National Taiwan University, No. 12, Sec. 1, Qianshan Rd., Nantou County, 55750, Taiwan
| | - Chi-Tsong Chen
- Department of Forensic Science, Investigation Bureau, Ministry of Justice, New Taipei City, 23149, Taiwan.
| |
Collapse
|
3
|
Weng YM, Kavanaugh DH, Schoville SD. Drainage basins serve as multiple glacial refugia for alpine habitats in the Sierra Nevada Mountains, California. Mol Ecol 2020; 30:826-843. [PMID: 33270315 DOI: 10.1111/mec.15762] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 11/19/2020] [Accepted: 11/26/2020] [Indexed: 12/13/2022]
Abstract
The evolutionary histories of alpine species are often directly associated with responses to glaciation. Deep divergence among populations and complex patterns of genetic variation have been inferred as consequences of persistence within glacier boundaries (i.e., on nunataks), while shallow divergence and limited genetic variation are assumed to result from expansion from large refugia at the edge of ice shields (i.e., massifs de refuge). However, for some species, dependence on specific microhabitats could profoundly influence their spatial and demographic response to glaciation, and such a simple dichotomy may obscure the localization of actual refugia. In this study, we use the Nebria ingens complex (Coleoptera: Carabidae), a water-affiliated ground beetle lineage, to test how drainage basins are linked to their observed population structure. By analysing mitochondrial COI gene sequences and genome-wide single nucleotide polymorphisms, we find that the major drainage systems of the Sierra Nevada Mountains in California best explain the population structure of the N. ingens complex. In addition, we find that an intermediate morphotype within the N. ingens complex is the product of historical hybridization of N. riversi and N. ingens in the San Joaquin basin during glaciation. This study highlights the importance of considering ecological preferences in how species respond to climate fluctuations and provides an explanation for discordances that are often observed in comparative phylogeographical studies.
Collapse
Affiliation(s)
- Yi-Ming Weng
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
| | - David H Kavanaugh
- Department of Entomology, California Academy of Sciences, San Francisco, CA, USA
| | - Sean D Schoville
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
| |
Collapse
|