Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions, local adaptation and geographic structure

© 2015 The Authors. Recent advances in sequencing allow population-genomic data to be generated for virtually any species. However, approaches to analyse such data lag behind the ability to generate it, particularly in nonmodel species. Linkage disequilibrium (LD, the nonrandom association of allele...

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Main Authors: Petri Kemppainen, Christopher G. Knight, Devojit K. Sarma, Thaung Hlaing, Anil Prakash, Yan Naung Maung Maung, Pradya Somboon, Jagadish Mahanta, Catherine Walton
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Published: 2018
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http://cmuir.cmu.ac.th/jspui/handle/6653943832/44888
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Institution: Chiang Mai University
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spelling th-cmuir.6653943832-448882018-04-25T07:57:24Z Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions, local adaptation and geographic structure Petri Kemppainen Christopher G. Knight Devojit K. Sarma Thaung Hlaing Anil Prakash Yan Naung Maung Maung Pradya Somboon Jagadish Mahanta Catherine Walton Agricultural and Biological Sciences © 2015 The Authors. Recent advances in sequencing allow population-genomic data to be generated for virtually any species. However, approaches to analyse such data lag behind the ability to generate it, particularly in nonmodel species. Linkage disequilibrium (LD, the nonrandom association of alleles from different loci) is a highly sensitive indicator of many evolutionary phenomena including chromosomal inversions, local adaptation and geographical structure. Here, we present linkage disequilibrium network analysis (LDna), which accesses information on LD shared between multiple loci genomewide. In LD networks, vertices represent loci, and connections between vertices represent the LD between them. We analysed such networks in two test cases: a new restriction-site-associated DNA sequence (RAD-seq) data set for Anopheles baimaii, a Southeast Asian malaria vector; and a well-characterized single nucleotide polymorphism (SNP) data set from 21 three-spined stickleback individuals. In each case, we readily identified five distinct LD network clusters (single-outlier clusters, SOCs), each comprising many loci connected by high LD. In A. baimaii, further population-genetic analyses supported the inference that each SOC corresponds to a large inversion, consistent with previous cytological studies. For sticklebacks, we inferred that each SOC was associated with a distinct evolutionary phenomenon: two chromosomal inversions, local adaptation, population-demographic history and geographic structure. LDna is thus a useful exploratory tool, able to give a global overview of LD associated with diverse evolutionary phenomena and identify loci potentially involved. LDna does not require a linkage map or reference genome, so it is applicable to any population-genomic data set, making it especially valuable for nonmodel species. 2018-01-24T04:49:32Z 2018-01-24T04:49:32Z 2015-01-01 Journal 17550998 1755098X 2-s2.0-84938989827 10.1111/1755-0998.12369 https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=84938989827&origin=inward http://cmuir.cmu.ac.th/jspui/handle/6653943832/44888
institution Chiang Mai University
building Chiang Mai University Library
country Thailand
collection CMU Intellectual Repository
topic Agricultural and Biological Sciences
spellingShingle Agricultural and Biological Sciences
Petri Kemppainen
Christopher G. Knight
Devojit K. Sarma
Thaung Hlaing
Anil Prakash
Yan Naung Maung Maung
Pradya Somboon
Jagadish Mahanta
Catherine Walton
Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions, local adaptation and geographic structure
description © 2015 The Authors. Recent advances in sequencing allow population-genomic data to be generated for virtually any species. However, approaches to analyse such data lag behind the ability to generate it, particularly in nonmodel species. Linkage disequilibrium (LD, the nonrandom association of alleles from different loci) is a highly sensitive indicator of many evolutionary phenomena including chromosomal inversions, local adaptation and geographical structure. Here, we present linkage disequilibrium network analysis (LDna), which accesses information on LD shared between multiple loci genomewide. In LD networks, vertices represent loci, and connections between vertices represent the LD between them. We analysed such networks in two test cases: a new restriction-site-associated DNA sequence (RAD-seq) data set for Anopheles baimaii, a Southeast Asian malaria vector; and a well-characterized single nucleotide polymorphism (SNP) data set from 21 three-spined stickleback individuals. In each case, we readily identified five distinct LD network clusters (single-outlier clusters, SOCs), each comprising many loci connected by high LD. In A. baimaii, further population-genetic analyses supported the inference that each SOC corresponds to a large inversion, consistent with previous cytological studies. For sticklebacks, we inferred that each SOC was associated with a distinct evolutionary phenomenon: two chromosomal inversions, local adaptation, population-demographic history and geographic structure. LDna is thus a useful exploratory tool, able to give a global overview of LD associated with diverse evolutionary phenomena and identify loci potentially involved. LDna does not require a linkage map or reference genome, so it is applicable to any population-genomic data set, making it especially valuable for nonmodel species.
format Journal
author Petri Kemppainen
Christopher G. Knight
Devojit K. Sarma
Thaung Hlaing
Anil Prakash
Yan Naung Maung Maung
Pradya Somboon
Jagadish Mahanta
Catherine Walton
author_facet Petri Kemppainen
Christopher G. Knight
Devojit K. Sarma
Thaung Hlaing
Anil Prakash
Yan Naung Maung Maung
Pradya Somboon
Jagadish Mahanta
Catherine Walton
author_sort Petri Kemppainen
title Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions, local adaptation and geographic structure
title_short Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions, local adaptation and geographic structure
title_full Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions, local adaptation and geographic structure
title_fullStr Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions, local adaptation and geographic structure
title_full_unstemmed Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions, local adaptation and geographic structure
title_sort linkage disequilibrium network analysis (ldna) gives a global view of chromosomal inversions, local adaptation and geographic structure
publishDate 2018
url https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=84938989827&origin=inward
http://cmuir.cmu.ac.th/jspui/handle/6653943832/44888
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