PSMC (pairwise sequentially Markovian coalescent) analysis of RAD (restriction site associated DNA) sequencing data
The pairwise sequentially Markovian coalescent (PSMC) method uses the genome sequence of a single individual to estimate demographic history covering a time span of thousands of generations. Although originally designed for whole-genome data, we here use simulations to investigate its applicability...
Published in: | Molecular Ecology Resources |
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Online Access: | https://pure.au.dk/portal/da/publications/psmc-pairwise-sequentially-markovian-coalescent-analysis-of-rad-restriction-site-associated-dna-sequencing-data(ff63b3a2-ca8a-4555-8a73-db78f6b87796).html https://doi.org/10.1111/1755-0998.12606 |
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ftuniaarhuspubl:oai:pure.atira.dk:publications/ff63b3a2-ca8a-4555-8a73-db78f6b87796 2023-05-15T16:29:58+02:00 PSMC (pairwise sequentially Markovian coalescent) analysis of RAD (restriction site associated DNA) sequencing data Liu, Shenglin Hansen, Michael M. 2017-07 https://pure.au.dk/portal/da/publications/psmc-pairwise-sequentially-markovian-coalescent-analysis-of-rad-restriction-site-associated-dna-sequencing-data(ff63b3a2-ca8a-4555-8a73-db78f6b87796).html https://doi.org/10.1111/1755-0998.12606 eng eng info:eu-repo/semantics/restrictedAccess Liu , S & Hansen , M M 2017 , ' PSMC (pairwise sequentially Markovian coalescent) analysis of RAD (restriction site associated DNA) sequencing data ' , Molecular Ecology Resources , vol. 17 , no. 4 , pp. 631-641 . https://doi.org/10.1111/1755-0998.12606 demographic history pairwise sequentially Markovian coalescent (PSMC) RAD sequencing three-spined stickleback whole-genome sequencing WHOLE-GENOME SEQUENCES POPULATION GENOMICS HISTORY STICKLEBACKS REVEAL NUCLEOTIDE SIGNATURES EVOLUTION DISCOVERY IMPACT article 2017 ftuniaarhuspubl https://doi.org/10.1111/1755-0998.12606 2020-07-18T21:58:13Z The pairwise sequentially Markovian coalescent (PSMC) method uses the genome sequence of a single individual to estimate demographic history covering a time span of thousands of generations. Although originally designed for whole-genome data, we here use simulations to investigate its applicability to reference genome-aligned restriction site associated DNA (RAD) data. We find that RAD data can potentially be used for PSMC analysis, but at present with limitations. The key factor is the proportion (p) of the genome that the RAD data covers. In our simulations, a proportion of 10% can still retain a substantial amount of coalescent information, whereas for 1% estimation becomes unreliable. The performance depends strongly on mutation rate (mu) and recombination rate (r) and is proportional to mu*p/r. When the value of this term is low, increasing the amount of data and number of iterations helps restoring the power of the estimation. We subsequently analyse one whole-genome-sequenced and 17 RAD-sequenced three-spined sticklebacks (Gasterosteus aculeatus) from a lake in Greenland. The whole-genome sequence suggests a relatively recent expansion and decline within ca. 4000-40 000 generations ago, possibly reflecting postglacial expansion and founding of the lake population. RAD data, where chromosomes from 10 individuals are combined, identify a similar pattern. Our study provides guidance about the use of PSMC analysis and suggests measures that can improve its utility for RAD data. Finally, the study shows that RAD loci in general contain coalescent information that can be used for developing more targeted methods. Article in Journal/Newspaper Greenland Aarhus University: Research Greenland Molecular Ecology Resources 17 4 631 641 |
institution |
Open Polar |
collection |
Aarhus University: Research |
op_collection_id |
ftuniaarhuspubl |
language |
English |
topic |
demographic history pairwise sequentially Markovian coalescent (PSMC) RAD sequencing three-spined stickleback whole-genome sequencing WHOLE-GENOME SEQUENCES POPULATION GENOMICS HISTORY STICKLEBACKS REVEAL NUCLEOTIDE SIGNATURES EVOLUTION DISCOVERY IMPACT |
spellingShingle |
demographic history pairwise sequentially Markovian coalescent (PSMC) RAD sequencing three-spined stickleback whole-genome sequencing WHOLE-GENOME SEQUENCES POPULATION GENOMICS HISTORY STICKLEBACKS REVEAL NUCLEOTIDE SIGNATURES EVOLUTION DISCOVERY IMPACT Liu, Shenglin Hansen, Michael M. PSMC (pairwise sequentially Markovian coalescent) analysis of RAD (restriction site associated DNA) sequencing data |
topic_facet |
demographic history pairwise sequentially Markovian coalescent (PSMC) RAD sequencing three-spined stickleback whole-genome sequencing WHOLE-GENOME SEQUENCES POPULATION GENOMICS HISTORY STICKLEBACKS REVEAL NUCLEOTIDE SIGNATURES EVOLUTION DISCOVERY IMPACT |
description |
The pairwise sequentially Markovian coalescent (PSMC) method uses the genome sequence of a single individual to estimate demographic history covering a time span of thousands of generations. Although originally designed for whole-genome data, we here use simulations to investigate its applicability to reference genome-aligned restriction site associated DNA (RAD) data. We find that RAD data can potentially be used for PSMC analysis, but at present with limitations. The key factor is the proportion (p) of the genome that the RAD data covers. In our simulations, a proportion of 10% can still retain a substantial amount of coalescent information, whereas for 1% estimation becomes unreliable. The performance depends strongly on mutation rate (mu) and recombination rate (r) and is proportional to mu*p/r. When the value of this term is low, increasing the amount of data and number of iterations helps restoring the power of the estimation. We subsequently analyse one whole-genome-sequenced and 17 RAD-sequenced three-spined sticklebacks (Gasterosteus aculeatus) from a lake in Greenland. The whole-genome sequence suggests a relatively recent expansion and decline within ca. 4000-40 000 generations ago, possibly reflecting postglacial expansion and founding of the lake population. RAD data, where chromosomes from 10 individuals are combined, identify a similar pattern. Our study provides guidance about the use of PSMC analysis and suggests measures that can improve its utility for RAD data. Finally, the study shows that RAD loci in general contain coalescent information that can be used for developing more targeted methods. |
format |
Article in Journal/Newspaper |
author |
Liu, Shenglin Hansen, Michael M. |
author_facet |
Liu, Shenglin Hansen, Michael M. |
author_sort |
Liu, Shenglin |
title |
PSMC (pairwise sequentially Markovian coalescent) analysis of RAD (restriction site associated DNA) sequencing data |
title_short |
PSMC (pairwise sequentially Markovian coalescent) analysis of RAD (restriction site associated DNA) sequencing data |
title_full |
PSMC (pairwise sequentially Markovian coalescent) analysis of RAD (restriction site associated DNA) sequencing data |
title_fullStr |
PSMC (pairwise sequentially Markovian coalescent) analysis of RAD (restriction site associated DNA) sequencing data |
title_full_unstemmed |
PSMC (pairwise sequentially Markovian coalescent) analysis of RAD (restriction site associated DNA) sequencing data |
title_sort |
psmc (pairwise sequentially markovian coalescent) analysis of rad (restriction site associated dna) sequencing data |
publishDate |
2017 |
url |
https://pure.au.dk/portal/da/publications/psmc-pairwise-sequentially-markovian-coalescent-analysis-of-rad-restriction-site-associated-dna-sequencing-data(ff63b3a2-ca8a-4555-8a73-db78f6b87796).html https://doi.org/10.1111/1755-0998.12606 |
geographic |
Greenland |
geographic_facet |
Greenland |
genre |
Greenland |
genre_facet |
Greenland |
op_source |
Liu , S & Hansen , M M 2017 , ' PSMC (pairwise sequentially Markovian coalescent) analysis of RAD (restriction site associated DNA) sequencing data ' , Molecular Ecology Resources , vol. 17 , no. 4 , pp. 631-641 . https://doi.org/10.1111/1755-0998.12606 |
op_rights |
info:eu-repo/semantics/restrictedAccess |
op_doi |
https://doi.org/10.1111/1755-0998.12606 |
container_title |
Molecular Ecology Resources |
container_volume |
17 |
container_issue |
4 |
container_start_page |
631 |
op_container_end_page |
641 |
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1766019676334194688 |