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@article{980073,
author = {Marcussen, Thomas and Jakobsen, Kjetill S. and Danihelka, Jiří and Ballard, Harvey E. and Blaxland, Kim and Brysting, Anne K. and Oxelman, Bengt},
article_number = {1},
doi = {http://dx.doi.org/10.1093/sysbio/syr096},
keywords = {Allopolyploidy; BEAST; homoeolog loss; low-copy nuclear gene; PADRE; single-molecule PCR; species network; Viola},
language = {eng},
issn = {1063-5157},
journal = {Systematic Biology},
title = {Inferring species networks from gene trees in high-polyploid North American and Hawaiian violets (Viola, Violaceae)},
url = {http://sysbio.oxfordjournals.org/content/61/1/107.full.pdf+html?sid=2c61b0d9-3607-44ea-ae91-f832e99482db},
volume = {61},
year = {2012}
}
TY - JOUR
ID - 980073
AU - Marcussen, Thomas - Jakobsen, Kjetill S. - Danihelka, Jiří - Ballard, Harvey E. - Blaxland, Kim - Brysting, Anne K. - Oxelman, Bengt
PY - 2012
TI - Inferring species networks from gene trees in high-polyploid North American and Hawaiian violets (Viola, Violaceae)
JF - Systematic Biology
VL - 61
IS - 1
SP - 107-126
EP - 107-126
PB - Oxford University Press
SN - 10635157
KW - Allopolyploidy
KW - BEAST
KW - homoeolog loss
KW - low-copy nuclear gene
KW - PADRE
KW - single-molecule PCR
KW - species network
KW - Viola
UR - http://sysbio.oxfordjournals.org/content/61/1/107.full.pdf+html?sid=2c61b0d9-3607-44ea-ae91-f832e99482db
N2 - The phylogenies of allopolyploids take the shape of networks and cannot be adequately represented as bifurcating trees. Especially for high polyploids the signatures of gene homoeolog loss, deep coalescence, and polyploidy may become confounded, with the result that gene trees may be congruent with more than one species network. Herein, we obtained the most parsimonious species network by objective comparison of competing scenarios involving polyploidization and homoeolog loss in a high-polyploid lineage of violets (Viola, Violaceae) mostly or entirely restricted to North America, Central America, or Hawaii. We amplified homoeologs of the low-copy nuclear gene, glucose-6-phosphate isomerase (GPI), by single-molecule polymerase chain reaction (PCR)and the chloroplast trnL-F region by conventional PCR for 51 species and subspecies. Topological incongruence among GPI homoeolog subclades, owing to deep coalescence and two instances of putative loss (or lack of detection) of homoeologs, were reconciled by applying the maximum tree topology for each subclade. The most parsimonious species network and the fossil-based calibration of the homoeolog tree favored monophyly of the high polyploids, which has resulted from allodecaploidization 9–14 Ma, involving sympatric ancestors from the extant Viola sections Chamaemelanium (diploid), Plagiostigma (paleotetraploid), and Viola (paleotetraploid). Although two of the high-polyploid lineages (Boreali-Americanae, Pedatae) remained decaploid, recurrent polyploidization with tetraploids of section Plagiostigma within the last 5 Ma has resulted in two 14-ploid lineages (Mexicanae, Nosphinium) and one 18-ploid lineage (Langsdorffianae). This implies a more complex phylogenetic and biogeographic origin of the Hawaiian violets (Nosphinium) than that previously inferred from rDNA data and illustrates the necessity of considering polyploidy in phylogenetic and biogeographic reconstruction.
ER -
MARCUSSEN, Thomas, Kjetill S. JAKOBSEN, Jiří DANIHELKA, Harvey E. BALLARD, Kim BLAXLAND, Anne K. BRYSTING and Bengt OXELMAN. Inferring species networks from gene trees in high-polyploid North American and Hawaiian violets (Viola, Violaceae). \textit{Systematic Biology}. Oxford University Press, 2012, vol.~61, No~1, p.~107-126. ISSN~1063-5157. Available from: https://dx.doi.org/10.1093/sysbio/syr096.
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