Phylogenetic trees of genus Oncidium Sw. based on analysis of DNA sequences - Open Research Data - Bridge of Knowledge

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Phylogenetic trees of genus Oncidium Sw. based on analysis of DNA sequences

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Description

Genus Oncidium Sw. is widely regarded as a polyphiletic, and the taxonomic boundaries between him and such genera as Odontoglossum Kunth. or Miltonia Lindley remain blurred. The goal of the study was to determine the phylogenetic relationships within the genus Oncidium s.lato based on the DNA sequences analysis. The correlation between molecular data and geographical distribution of the studied species was also examined. Two markers were used for the analysis: the ITS sequence derived from the nuclear genome and the matK gene that is part of mitochondrial DNA. Sequences were obtained by DNA isolation from frozen leaves, polymerase chain reaction (PCR) and sequencing. For their analysis in the PAUP* program, a feature-based parsimony (MP) method was used, and for assessing the reliability of the resulting trees, the non-parametric bootstrap method. The ITS MP search resulted in 10 000 trees (CI=0.49; RI=0.631). The aligned matrix resulted in 814 characters of which 433 were parsimony informative. The matK MP search resulted in 10 000 trees (CI=0.505; RI=0.714). The aligned matrix resulted in 1359 characters of which 358 were parsimony informative. 

This dataset contains two image files with phylogenetic trees - the first one based on ITS analysis of 190 species and the second one based on the matK analysis of 154 species. The upper numbers above branches are the Fitch values and lower numbers are the bootstrap values. The information about geographical distribution is added.  The dataset includes also two NEXUS files (for ITS and for matK) with DNA sequences.

 
Illustration of the publication

Dataset file

Oncidium phylogenetic analysis (3).zip
3.5 MB, S3 ETag 63c677c2d274139e3513c17953e88245-1, downloads: 64
The file hash is calculated from the formula
hexmd5(md5(part1)+md5(part2)+...)-{parts_count} where a single part of the file is 512 MB in size.

Example script for calculation:
https://github.com/antespi/s3md5
download file Oncidium phylogenetic analysis (3).zip

File details

License:
Creative Commons: by 4.0 open in new tab
CC BY
Attribution
Software:
PAUP*

Details

Year of publication:
2020
Verification date:
2021-01-04
Dataset language:
Polish
Fields of science:
  • biological sciences (Natural sciences)
DOI:
DOI ID 10.34808/ea8p-3z78 open in new tab
Verified by:
Gdańsk University of Technology

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Version this document has several versions

DOI 10.34808/7waa-aq49 represents the latest version of the data.

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