Challenges in polyploid phylogenetic reconstruction: A case story from the arctic‐alpine Cerastium alpinum complex
Abstract Here we illustrate and discuss the major challenges involved in reticulate phylogenetic reconstruction, with special reference to single‐ and low‐copy nuclear data (the RNA polymerase genes) produced for the polyploid Cerastium alpinum group and close relatives. The dynamic nature of polypl...
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crwiley:10.1002/tax.602004 2024-06-02T08:02:26+00:00 Challenges in polyploid phylogenetic reconstruction: A case story from the arctic‐alpine Cerastium alpinum complex Brysting, Anne K. Mathiesen, Cecilie Marcussen, Thomas 2011 http://dx.doi.org/10.1002/tax.602004 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1002%2Ftax.602004 https://onlinelibrary.wiley.com/doi/pdf/10.1002/tax.602004 en eng Wiley http://onlinelibrary.wiley.com/termsAndConditions#vor TAXON volume 60, issue 2, page 333-347 ISSN 0040-0262 1996-8175 journal-article 2011 crwiley https://doi.org/10.1002/tax.602004 2024-05-03T10:41:39Z Abstract Here we illustrate and discuss the major challenges involved in reticulate phylogenetic reconstruction, with special reference to single‐ and low‐copy nuclear data (the RNA polymerase genes) produced for the polyploid Cerastium alpinum group and close relatives. The dynamic nature of polyploid genomes paves the way for evolutionary novelty, and is obviously an important clue for the evolutionary success of polyploid plants, but at the same time it also creates problems in reconstructing the evolutionary history of polyploids. Nascent allopolyploids will hold two homoeologous copies of every gene that is initially single‐copy in the parental species; however, immediately after the polyploidization event, modification of the polyploid genome starts, involving gene silencing, pseudogenization and divergence of duplicated genes. Identifying the signatures of reticulation, especially when dealing with old polyploids, may thus be a huge challenge. Sorting of ancestral/diploid variation in the polyploids and additional gene losses and duplications not associated with polyploidy may further complicate the case. Besides these general problems related to incongruent gene and organism lineage phylogenies, there are also several methodological challenges connected with retrieving sequence information from polyploids, such as polymerase errors, differential amplification of homoeologs (PCR selection), generation of chimeric sequences during PCR, and selection of shorter and more common fragments and insertion of incorrect fragments during the cloning reaction. Article in Journal/Newspaper Arctic Wiley Online Library Arctic TAXON 60 2 333 347 |
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English |
description |
Abstract Here we illustrate and discuss the major challenges involved in reticulate phylogenetic reconstruction, with special reference to single‐ and low‐copy nuclear data (the RNA polymerase genes) produced for the polyploid Cerastium alpinum group and close relatives. The dynamic nature of polyploid genomes paves the way for evolutionary novelty, and is obviously an important clue for the evolutionary success of polyploid plants, but at the same time it also creates problems in reconstructing the evolutionary history of polyploids. Nascent allopolyploids will hold two homoeologous copies of every gene that is initially single‐copy in the parental species; however, immediately after the polyploidization event, modification of the polyploid genome starts, involving gene silencing, pseudogenization and divergence of duplicated genes. Identifying the signatures of reticulation, especially when dealing with old polyploids, may thus be a huge challenge. Sorting of ancestral/diploid variation in the polyploids and additional gene losses and duplications not associated with polyploidy may further complicate the case. Besides these general problems related to incongruent gene and organism lineage phylogenies, there are also several methodological challenges connected with retrieving sequence information from polyploids, such as polymerase errors, differential amplification of homoeologs (PCR selection), generation of chimeric sequences during PCR, and selection of shorter and more common fragments and insertion of incorrect fragments during the cloning reaction. |
format |
Article in Journal/Newspaper |
author |
Brysting, Anne K. Mathiesen, Cecilie Marcussen, Thomas |
spellingShingle |
Brysting, Anne K. Mathiesen, Cecilie Marcussen, Thomas Challenges in polyploid phylogenetic reconstruction: A case story from the arctic‐alpine Cerastium alpinum complex |
author_facet |
Brysting, Anne K. Mathiesen, Cecilie Marcussen, Thomas |
author_sort |
Brysting, Anne K. |
title |
Challenges in polyploid phylogenetic reconstruction: A case story from the arctic‐alpine Cerastium alpinum complex |
title_short |
Challenges in polyploid phylogenetic reconstruction: A case story from the arctic‐alpine Cerastium alpinum complex |
title_full |
Challenges in polyploid phylogenetic reconstruction: A case story from the arctic‐alpine Cerastium alpinum complex |
title_fullStr |
Challenges in polyploid phylogenetic reconstruction: A case story from the arctic‐alpine Cerastium alpinum complex |
title_full_unstemmed |
Challenges in polyploid phylogenetic reconstruction: A case story from the arctic‐alpine Cerastium alpinum complex |
title_sort |
challenges in polyploid phylogenetic reconstruction: a case story from the arctic‐alpine cerastium alpinum complex |
publisher |
Wiley |
publishDate |
2011 |
url |
http://dx.doi.org/10.1002/tax.602004 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1002%2Ftax.602004 https://onlinelibrary.wiley.com/doi/pdf/10.1002/tax.602004 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
TAXON volume 60, issue 2, page 333-347 ISSN 0040-0262 1996-8175 |
op_rights |
http://onlinelibrary.wiley.com/termsAndConditions#vor |
op_doi |
https://doi.org/10.1002/tax.602004 |
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TAXON |
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60 |
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333 |
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347 |
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1800746927636086784 |