Abstract
Phytochromes play a key role in allowing plants to monitor their surrounding environment and, conversely, adaptation to local environments has driven the evolutionary history of phytochromes. As a result of natural selection, polymorphisms in phytochrome genes would thus be expected to exhibit locus-specific phylogeographic structure. To evaluate this hypothesis, we conducted a phylogeographic investigation based on four nuclear genes, including two phytochrome genes (PHYB and PHYE) using 155 samples of Arcterica nana from the entire range of the Japanese archipelago. Bayesian clustering revealed geographic differentiation between northern and southern Japan when all four genes were included. However, this geographic differentiation is inconsistent with previously reported genetic structure of genome-wide polymorphisms based on amplified fragment length polymorphisms, as these did not show geographic differentiation throughout the Japanese archipelago. In contrast, the north-south differentiation was not apparent when PHYE was excluded. This indicates that PHYE alone could be responsible for the north-south differentiation (FCT = 0.15, P <0.001). Furthermore, a single nonsynonymous polymorphism (C360T) strongly contributed to geographic differentiation (FCT = 0.57, P <0.001) and its corresponding amino acid replacement (P120L) was significantly under positive selection based on maximum likelihood analysis (P = 0.98). Consequently, the locus-specific geographic differentiation in PHYE could be caused by natural selection, suggesting the involvement of PHYE in local adaptation between populations of A. nana in northern and southern Japan. This finding is consistent with a previous study on Cardamine nipponica, indicating the importance of PHYE for local adaptation in Japanese alpine plants.
| Original language | English |
|---|---|
| Pages (from-to) | 2779-2791 |
| Number of pages | 13 |
| Journal | Molecular Ecology |
| Volume | 19 |
| Issue number | 13 |
| DOIs | |
| Publication status | Published - Jul 2010 |
| Externally published | Yes |
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Keywords
- Japanese archipelago
- latitudinal cline
- local adaptation
- phylogeography
- phytochrome
ASJC Scopus subject areas
- Ecology, Evolution, Behavior and Systematics
- Genetics
- Medicine(all)
Cite this
Natural selection on PHYE by latitude in the Japanese archipelago : Insight from locus specific phylogeographic structure in Arcterica nana (Ericaceae). / Ikeda, Hajime; Setoguchi, Hiroaki.
In: Molecular Ecology, Vol. 19, No. 13, 07.2010, p. 2779-2791.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Natural selection on PHYE by latitude in the Japanese archipelago
T2 - Insight from locus specific phylogeographic structure in Arcterica nana (Ericaceae)
AU - Ikeda, Hajime
AU - Setoguchi, Hiroaki
PY - 2010/7
Y1 - 2010/7
N2 - Phytochromes play a key role in allowing plants to monitor their surrounding environment and, conversely, adaptation to local environments has driven the evolutionary history of phytochromes. As a result of natural selection, polymorphisms in phytochrome genes would thus be expected to exhibit locus-specific phylogeographic structure. To evaluate this hypothesis, we conducted a phylogeographic investigation based on four nuclear genes, including two phytochrome genes (PHYB and PHYE) using 155 samples of Arcterica nana from the entire range of the Japanese archipelago. Bayesian clustering revealed geographic differentiation between northern and southern Japan when all four genes were included. However, this geographic differentiation is inconsistent with previously reported genetic structure of genome-wide polymorphisms based on amplified fragment length polymorphisms, as these did not show geographic differentiation throughout the Japanese archipelago. In contrast, the north-south differentiation was not apparent when PHYE was excluded. This indicates that PHYE alone could be responsible for the north-south differentiation (FCT = 0.15, P <0.001). Furthermore, a single nonsynonymous polymorphism (C360T) strongly contributed to geographic differentiation (FCT = 0.57, P <0.001) and its corresponding amino acid replacement (P120L) was significantly under positive selection based on maximum likelihood analysis (P = 0.98). Consequently, the locus-specific geographic differentiation in PHYE could be caused by natural selection, suggesting the involvement of PHYE in local adaptation between populations of A. nana in northern and southern Japan. This finding is consistent with a previous study on Cardamine nipponica, indicating the importance of PHYE for local adaptation in Japanese alpine plants.
AB - Phytochromes play a key role in allowing plants to monitor their surrounding environment and, conversely, adaptation to local environments has driven the evolutionary history of phytochromes. As a result of natural selection, polymorphisms in phytochrome genes would thus be expected to exhibit locus-specific phylogeographic structure. To evaluate this hypothesis, we conducted a phylogeographic investigation based on four nuclear genes, including two phytochrome genes (PHYB and PHYE) using 155 samples of Arcterica nana from the entire range of the Japanese archipelago. Bayesian clustering revealed geographic differentiation between northern and southern Japan when all four genes were included. However, this geographic differentiation is inconsistent with previously reported genetic structure of genome-wide polymorphisms based on amplified fragment length polymorphisms, as these did not show geographic differentiation throughout the Japanese archipelago. In contrast, the north-south differentiation was not apparent when PHYE was excluded. This indicates that PHYE alone could be responsible for the north-south differentiation (FCT = 0.15, P <0.001). Furthermore, a single nonsynonymous polymorphism (C360T) strongly contributed to geographic differentiation (FCT = 0.57, P <0.001) and its corresponding amino acid replacement (P120L) was significantly under positive selection based on maximum likelihood analysis (P = 0.98). Consequently, the locus-specific geographic differentiation in PHYE could be caused by natural selection, suggesting the involvement of PHYE in local adaptation between populations of A. nana in northern and southern Japan. This finding is consistent with a previous study on Cardamine nipponica, indicating the importance of PHYE for local adaptation in Japanese alpine plants.
KW - Japanese archipelago
KW - latitudinal cline
KW - local adaptation
KW - phylogeography
KW - phytochrome
UR - http://www.scopus.com/inward/record.url?scp=77954268850&partnerID=8YFLogxK
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U2 - 10.1111/j.1365-294X.2010.04700.x
DO - 10.1111/j.1365-294X.2010.04700.x
M3 - Article
VL - 19
SP - 2779
EP - 2791
JO - Molecular Ecology
JF - Molecular Ecology
SN - 0962-1083
IS - 13
ER -