Using Ancestry Informative Markers (AIMs) to Detect Fine Structures Within Gorilla Populations
The knowledge of ancestral origin is monumental in conservation of endangered animals since it can aid in preservation of population level genetic integrity and prevent inbreeding among related individuals. Despite maintenance of studbook, the biogeographical affiliation of most captive gorillas is...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2019-02-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2019.00043/full |
| _version_ | 1818291597165461504 |
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| author | Ranajit Das Ria Roy Neha Venkatesh |
| author_facet | Ranajit Das Ria Roy Neha Venkatesh |
| author_sort | Ranajit Das |
| collection | DOAJ |
| description | The knowledge of ancestral origin is monumental in conservation of endangered animals since it can aid in preservation of population level genetic integrity and prevent inbreeding among related individuals. Despite maintenance of studbook, the biogeographical affiliation of most captive gorillas is largely unknown, which has constrained management of captive gorillas aiming at maximizing genetic diversity at the population level. In recent years, ancestry informative markers (AIMs) has been successfully employed for the inference of genomic ancestry in a wide range of studies in evolutionary genetics, biomedical research, genetic stock identification, and introgression analysis and forensic analyses. In this study, we sought to derive the AIMs yielding the most cohesive and faithful understanding of biogeographical affiliation of query gorillas. To this end, we compared three commonly used AIMs-determining methods namely, Infocalc, FST, and Smart Principal Component Analysis (SmartPCA) with ADMIXTURE, using gorilla genome data available through Great Ape Genome Project database. Our findings suggest that the SNPs that were detected by at least three of the four AIMs-determining approaches (N = 1,531), is likely most suitable for delineation of gorilla AIMs. It recapitulated the finer structure within western lowland gorilla genomes with high degree of precision. We further have validated the robustness of our results using a randomized negative control containing the same number of SNPs. To the best of our knowledge, this is the first report of an AIMs panel for gorillas that may aid in developing cost-effective resources for large-scale demographic analyses, and greatly help in conservation of this charismatic mega-fauna. |
| first_indexed | 2024-12-13T02:46:35Z |
| format | Article |
| id | doaj.art-32501923b9204066a331c13f43b2835c |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-13T02:46:35Z |
| publishDate | 2019-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-32501923b9204066a331c13f43b2835c2022-12-22T00:02:10ZengFrontiers Media S.A.Frontiers in Genetics1664-80212019-02-011010.3389/fgene.2019.00043422887Using Ancestry Informative Markers (AIMs) to Detect Fine Structures Within Gorilla PopulationsRanajit Das0Ria Roy1Neha Venkatesh2Manipal Centre for Natural Sciences, Manipal Academy of Higher Education, Manipal, IndiaDepartment of Biotechnology Engineering, Sahrdaya College of Engineering and Technology, Kodakara, IndiaDepartment of Genetics, University of Mysore, Mysore, IndiaThe knowledge of ancestral origin is monumental in conservation of endangered animals since it can aid in preservation of population level genetic integrity and prevent inbreeding among related individuals. Despite maintenance of studbook, the biogeographical affiliation of most captive gorillas is largely unknown, which has constrained management of captive gorillas aiming at maximizing genetic diversity at the population level. In recent years, ancestry informative markers (AIMs) has been successfully employed for the inference of genomic ancestry in a wide range of studies in evolutionary genetics, biomedical research, genetic stock identification, and introgression analysis and forensic analyses. In this study, we sought to derive the AIMs yielding the most cohesive and faithful understanding of biogeographical affiliation of query gorillas. To this end, we compared three commonly used AIMs-determining methods namely, Infocalc, FST, and Smart Principal Component Analysis (SmartPCA) with ADMIXTURE, using gorilla genome data available through Great Ape Genome Project database. Our findings suggest that the SNPs that were detected by at least three of the four AIMs-determining approaches (N = 1,531), is likely most suitable for delineation of gorilla AIMs. It recapitulated the finer structure within western lowland gorilla genomes with high degree of precision. We further have validated the robustness of our results using a randomized negative control containing the same number of SNPs. To the best of our knowledge, this is the first report of an AIMs panel for gorillas that may aid in developing cost-effective resources for large-scale demographic analyses, and greatly help in conservation of this charismatic mega-fauna.https://www.frontiersin.org/article/10.3389/fgene.2019.00043/fullancestry informative marker (AIM)gorilla ancestryconservation genetic managementadmixtureinformativeness of SNPs |
| spellingShingle | Ranajit Das Ria Roy Neha Venkatesh Using Ancestry Informative Markers (AIMs) to Detect Fine Structures Within Gorilla Populations Frontiers in Genetics ancestry informative marker (AIM) gorilla ancestry conservation genetic management admixture informativeness of SNPs |
| title | Using Ancestry Informative Markers (AIMs) to Detect Fine Structures Within Gorilla Populations |
| title_full | Using Ancestry Informative Markers (AIMs) to Detect Fine Structures Within Gorilla Populations |
| title_fullStr | Using Ancestry Informative Markers (AIMs) to Detect Fine Structures Within Gorilla Populations |
| title_full_unstemmed | Using Ancestry Informative Markers (AIMs) to Detect Fine Structures Within Gorilla Populations |
| title_short | Using Ancestry Informative Markers (AIMs) to Detect Fine Structures Within Gorilla Populations |
| title_sort | using ancestry informative markers aims to detect fine structures within gorilla populations |
| topic | ancestry informative marker (AIM) gorilla ancestry conservation genetic management admixture informativeness of SNPs |
| url | https://www.frontiersin.org/article/10.3389/fgene.2019.00043/full |
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