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Biogeography of the Phalaenopsis amabilis species complex inferred from nuclear and plastid DNAs.

Tsai CC, Chou CH, Wang HV, Ko YZ, Chiang TY, Chiang YC - BMC Plant Biol. (2015)

Bottom Line: Demographic growth associated with the climatic oscillations in the Würm glacial period followed the species splits.Nevertheless, a subsequent population slowdown occurred in the late LGM due to extinction of regional populations.The reduction of suitable habitats resulted in geographic fragmenttation of the remaining taxa.

View Article: PubMed Central - PubMed

Affiliation: Crop Improvement Division, Kaohsiung District Agricultural Improvement Station, Pingtung, 900, Taiwan. tsaicc@mail.kdais.gov.tw.

ABSTRACT

Background: Phalaenopsis is one of the important commercial orchids in the world. Members of the P. amabilis species complex represent invaluable germplasm for the breeding program. However, the phylogeny of the P. amabilis species complex is still uncertain. The Phalaenopsis amabilis species complex (Orchidaceae) consists of subspecies amabilis, moluccana, and rosenstromii of P. amabilis, as well as P. aphrodite ssp. aphrodite, P. ap. ssp. formosana, and P. sanderiana. The aims of this study were to reconstruct the phylogeny and biogeographcial patterns of the species complex using Neighbor Joining (NJ), Maxinum Parsimony (MP), Bayesian Evolutionary Analysis Sampling Trees (BEAST) and Reconstruct Ancestral State in Phylogenies (RASP) analyses based on sequences of internal transcribed spacers 1 and 2 from the nuclear ribosomal DNA and the trnH-psbA spacer from the plastid DNA.

Results: A pattern of vicariance, dispersal, and vicariance + dispersal among disjunctly distributed taxa was uncovered based on RASP analysis. Although two subspecies of P. aphrodite could not be differentiated from each other in dispersal state, they were distinct from P. amabilis and P. sanderiana. Within P. amabilis, three subspecies were separated phylogenetically, in agreement with the vicariance or vicariance + dispersal scenario, with geographic subdivision along Huxley's, Wallace's and Lydekker's Lines. Molecular dating revealed such subdivisions among taxa of P. amabilis complex dating back to the late Pleistocene. Population-dynamic analyses using a Bayesian skyline plot suggested that the species complex experienced an in situ range expansion and population concentration during the late Last Glacial Maximum (LGM).

Conclusions: Taxa of the P. amabilis complex with disjunct distributions were differentiated due to vicariance or vicariance + dispersal, with events likely occurring in the late Pleistocene. Demographic growth associated with the climatic oscillations in the Würm glacial period followed the species splits. Nevertheless, a subsequent population slowdown occurred in the late LGM due to extinction of regional populations. The reduction of suitable habitats resulted in geographic fragmenttation of the remaining taxa.

No MeSH data available.


Phylogenetic relationships using Neighbor joining (NJ) and Maxinum Pasimony (MP) methods of the 39 accessions in the P. amabilis species complex, plus the three outgroups P. schilleriana, P. stuartiana and P. philippinensis, obtained from sequence comparisons of (a) the ITS region of nrDNA and (b) the cpDNA trnH-psbA spacer sequence and generated by MEGA 6.0 and Phylip 3.65. Numbers at nodes represent bootstrap values over 50 % of NJ and MP between major lineages
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Fig2: Phylogenetic relationships using Neighbor joining (NJ) and Maxinum Pasimony (MP) methods of the 39 accessions in the P. amabilis species complex, plus the three outgroups P. schilleriana, P. stuartiana and P. philippinensis, obtained from sequence comparisons of (a) the ITS region of nrDNA and (b) the cpDNA trnH-psbA spacer sequence and generated by MEGA 6.0 and Phylip 3.65. Numbers at nodes represent bootstrap values over 50 % of NJ and MP between major lineages

Mentions: Genealogy was reconstructed based on the ITS1 and ITS2 and plastid DNA haplotypes of the P. amabilis complex, rooted at three species of the P. schilleriana complex, including P. schilleriana, P. stuartiana, and P. philippinensis (Fig. 2). In the ITS1 and ITS2 sequences, a total of 13 variable sites (nucleotide substitutions) and 7 indels were found among the species/subspecies of the P. amabilis complex. Based on the phylogenetic tree, the six taxa of the P. amabilis complex were closely related with high bootstrap supporting in both NJ and MP phylogenetic trees (Figs. 2a). Phalaenopsis aphrodite ssp. aphrodite and P. aphrodite ssp. formosana clustered together. Subspecies of P. aphrodite are not distinguishable from each other, whereas they were separable from other members of the P. amabilis complex. Subspecies of P. amabilis, except for the Palawan populations, and P. sanderiana formed a clade. Within the P. amabilis/P. sanderiana clade, two subclades were identified, rooted by P. amabilis ssp. amabilis from Palawan. The first subclades showed distinct geographic subdivision, including P. sanderiana, P. amabilis ssp. amabilis from Java and ssp. moluccana from Molucca island. Nevertheless, P. amabilis ssp. amabilis from Timor and P. amabilis ssp. rosentromii cannot be distinguished from each other. The other subclade included all P. amabilis ssp. amabilis from Mentawai Island, Sabah (Borneo) and the one from Palawan (Fig. 2a).Fig. 2


Biogeography of the Phalaenopsis amabilis species complex inferred from nuclear and plastid DNAs.

Tsai CC, Chou CH, Wang HV, Ko YZ, Chiang TY, Chiang YC - BMC Plant Biol. (2015)

Phylogenetic relationships using Neighbor joining (NJ) and Maxinum Pasimony (MP) methods of the 39 accessions in the P. amabilis species complex, plus the three outgroups P. schilleriana, P. stuartiana and P. philippinensis, obtained from sequence comparisons of (a) the ITS region of nrDNA and (b) the cpDNA trnH-psbA spacer sequence and generated by MEGA 6.0 and Phylip 3.65. Numbers at nodes represent bootstrap values over 50 % of NJ and MP between major lineages
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4537552&req=5

Fig2: Phylogenetic relationships using Neighbor joining (NJ) and Maxinum Pasimony (MP) methods of the 39 accessions in the P. amabilis species complex, plus the three outgroups P. schilleriana, P. stuartiana and P. philippinensis, obtained from sequence comparisons of (a) the ITS region of nrDNA and (b) the cpDNA trnH-psbA spacer sequence and generated by MEGA 6.0 and Phylip 3.65. Numbers at nodes represent bootstrap values over 50 % of NJ and MP between major lineages
Mentions: Genealogy was reconstructed based on the ITS1 and ITS2 and plastid DNA haplotypes of the P. amabilis complex, rooted at three species of the P. schilleriana complex, including P. schilleriana, P. stuartiana, and P. philippinensis (Fig. 2). In the ITS1 and ITS2 sequences, a total of 13 variable sites (nucleotide substitutions) and 7 indels were found among the species/subspecies of the P. amabilis complex. Based on the phylogenetic tree, the six taxa of the P. amabilis complex were closely related with high bootstrap supporting in both NJ and MP phylogenetic trees (Figs. 2a). Phalaenopsis aphrodite ssp. aphrodite and P. aphrodite ssp. formosana clustered together. Subspecies of P. aphrodite are not distinguishable from each other, whereas they were separable from other members of the P. amabilis complex. Subspecies of P. amabilis, except for the Palawan populations, and P. sanderiana formed a clade. Within the P. amabilis/P. sanderiana clade, two subclades were identified, rooted by P. amabilis ssp. amabilis from Palawan. The first subclades showed distinct geographic subdivision, including P. sanderiana, P. amabilis ssp. amabilis from Java and ssp. moluccana from Molucca island. Nevertheless, P. amabilis ssp. amabilis from Timor and P. amabilis ssp. rosentromii cannot be distinguished from each other. The other subclade included all P. amabilis ssp. amabilis from Mentawai Island, Sabah (Borneo) and the one from Palawan (Fig. 2a).Fig. 2

Bottom Line: Demographic growth associated with the climatic oscillations in the Würm glacial period followed the species splits.Nevertheless, a subsequent population slowdown occurred in the late LGM due to extinction of regional populations.The reduction of suitable habitats resulted in geographic fragmenttation of the remaining taxa.

View Article: PubMed Central - PubMed

Affiliation: Crop Improvement Division, Kaohsiung District Agricultural Improvement Station, Pingtung, 900, Taiwan. tsaicc@mail.kdais.gov.tw.

ABSTRACT

Background: Phalaenopsis is one of the important commercial orchids in the world. Members of the P. amabilis species complex represent invaluable germplasm for the breeding program. However, the phylogeny of the P. amabilis species complex is still uncertain. The Phalaenopsis amabilis species complex (Orchidaceae) consists of subspecies amabilis, moluccana, and rosenstromii of P. amabilis, as well as P. aphrodite ssp. aphrodite, P. ap. ssp. formosana, and P. sanderiana. The aims of this study were to reconstruct the phylogeny and biogeographcial patterns of the species complex using Neighbor Joining (NJ), Maxinum Parsimony (MP), Bayesian Evolutionary Analysis Sampling Trees (BEAST) and Reconstruct Ancestral State in Phylogenies (RASP) analyses based on sequences of internal transcribed spacers 1 and 2 from the nuclear ribosomal DNA and the trnH-psbA spacer from the plastid DNA.

Results: A pattern of vicariance, dispersal, and vicariance + dispersal among disjunctly distributed taxa was uncovered based on RASP analysis. Although two subspecies of P. aphrodite could not be differentiated from each other in dispersal state, they were distinct from P. amabilis and P. sanderiana. Within P. amabilis, three subspecies were separated phylogenetically, in agreement with the vicariance or vicariance + dispersal scenario, with geographic subdivision along Huxley's, Wallace's and Lydekker's Lines. Molecular dating revealed such subdivisions among taxa of P. amabilis complex dating back to the late Pleistocene. Population-dynamic analyses using a Bayesian skyline plot suggested that the species complex experienced an in situ range expansion and population concentration during the late Last Glacial Maximum (LGM).

Conclusions: Taxa of the P. amabilis complex with disjunct distributions were differentiated due to vicariance or vicariance + dispersal, with events likely occurring in the late Pleistocene. Demographic growth associated with the climatic oscillations in the Würm glacial period followed the species splits. Nevertheless, a subsequent population slowdown occurred in the late LGM due to extinction of regional populations. The reduction of suitable habitats resulted in geographic fragmenttation of the remaining taxa.

No MeSH data available.