Data from: Relieving efforts in palm-tree tissue sampling for population genetics analyses
Data files
Sep 28, 2026 version files 756.32 KB
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README.md
14.96 KB
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Root_Stats.htm
691.64 KB
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Roots_Data.txt
22.34 KB
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Roots_Data.xlsx
27.38 KB
Abstract
The young leaves are the main source of nucleic acids for population genetic studies in palm trees; however, access to this tissue may be limited by specific features of each species. Using root tissues as an alternative source of nucleic acids could facilitate sampling in large populations. This study tests root tissue viability as an alternative nucleic acid source (root vs. leaf) and explores different protocols (tissue storage and DNA purification methods) to obtain high-quality DNA samples. The results showed no significant differences in DNA concentration and quality for the comparisons of tissue source (leaf vs. root) and DNA purification method (manual vs. kit). For tissue storage method, DNA concentration was significantly higher for root tissues stored in 70% and 90% alcohol solutions versus those obtained from leaf tissue; however, for the quality parameters, no differences were found. Results showed the effective potential of using root tissue as an alternative source for nucleic acids, which could facilitate population sampling of palm-tree species for future studies; this methodological alternative could be applied to other plant systems with similar sampling challenges.
Overview
This dataset contains the raw experimental data, tabulated data, and complete statistical output supporting the article:
Espinoza-Ulloa, S. A. (2021). Relieving efforts in palm-tree tissue sampling for population genetics analyses. Ecology and Evolution, 11(12), 7946–7950.
Article DOI: 10.1002/ece3.7624
Dryad DOI: 10.5061/dryad.ht76hdrfj
The study evaluated the use of palm root tissue as an alternative to young leaf tissue for DNA extraction in population genetic studies. Root tissue provides a potentially more accessible sampling source, particularly for tall palms in which collecting young leaves from the crown may be difficult.
The experiment compared DNA obtained from leaf and root tissues under different preservation treatments and using two DNA extraction methods. DNA quantity and purity were evaluated from spectrophotometric measurements.
Four palm species were included:
- Ceroxylon echinulatum
- Ceroxylon ventricosum
- Prestoea acuminata
- Phoenix dactylifera
Two individuals from each species were included in the experiment.
Description of the data and file structure
The dataset contains three files:
.
├── Root_Stats.htm
├── Roots_Data.txt
└── Roots_Data.xlsx
Roots_Data.txt and Roots_Data.xlsx contain the experimental observations. The two files provide the dataset in plain-text and spreadsheet formats, respectively.
The dataset contains 240 observations and 13 variables. A total of 80 experimental samples are represented, with three spectrophotometric readings (L1, L2, and L3) per sample.
The experimental structure combines:
- 4 palm species;
- 2 sampled individuals per species;
- tissue source;
- preservation treatment;
- 2 DNA extraction methods; and
- 3 spectrophotometric readings per extracted sample.
There are no missing observations in the archived dataset.
Files and variables
File: Roots_Data.txt
Description:
Tab-delimited plain-text version of the experimental dataset used for statistical analyses.
Variable names in this file use underscores instead of spaces to facilitate import into statistical software.
The file contains the following 13 variables:
Species
Description: Palm species from which the tissue sample was obtained.
Type: Categorical
Values:
Ceroxylon_equinulatum— Ceroxylon echinulatumCeroxylon_ventricosum— Ceroxylon ventricosumPrestoea_acuminata— Prestoea acuminataPhoenix_dactylifera— Phoenix dactylifera
Each species is represented by two sampled individuals.
Tissue_Source
Description: Biological tissue used for DNA extraction.
Type: Categorical
Values:
Leaf— young leaf tissueRoot— root tissue
Leaf tissue preserved in silica gel represents the conventional tissue-sampling approach against which the alternative root treatments were compared.
Treatment
Description: Preservation treatment applied to the tissue before DNA extraction.
Type: Categorical
Values:
Silica_Gel— tissue preserved using silica gelWater— root tissue stored in distilled waterETOH_70%— root tissue stored in 70% ethanolETOH_90%— root tissue stored in 90% ethanol
Leaf samples were preserved using silica gel. Root samples were evaluated using silica gel, distilled water, 70% ethanol, and 90% ethanol.
Groups_Source._x_Treat.
Description: Combined categorical variable representing the interaction between tissue source and preservation treatment.
Type: Categorical
Values:
LS— Leaf + Silica GelRW— Root + WaterR70— Root + 70% EthanolR90— Root + 90% EthanolRS— Root + Silica Gel
This variable defines the five tissue-source/preservation combinations compared in the statistical analyses.
DNA_Extraction_Method
Description: Method used to extract DNA from the preserved tissue.
Type: Categorical
Values:
Kit— commercial DNA extraction kitManual— manual plant DNA extraction protocol
The commercial extraction method corresponds to the PureLink Plant Total DNA Purification Kit (Invitrogen). The manual method was based on a plant DNA extraction protocol described in the associated publication.
Sample
Description: Unique identifier for each experimental DNA sample.
Type: Categorical/string
There are 80 unique sample identifiers.
Sample identifiers encode the sampled species/individual, tissue-preservation treatment, and DNA extraction method.
Examples include:
Ce1_HSG_KCe1_A_MCv2_E70_KPa1_RSG_M
The general structure is:
[Individual]_[Treatment]_[Extraction method]
The first component identifies the species and sampled individual, for example:
Ce1,Ce2— Ceroxylon echinulatum, individuals 1 and 2Cv1,Cv2— Ceroxylon ventricosum, individuals 1 and 2Pa1,Pa2— Prestoea acuminata, individuals 1 and 2Pd1,Pd2— Phoenix dactylifera, individuals 1 and 2
Treatment codes used within the sample identifier include:
HSG— leaf tissue preserved in silica gelA— root tissue preserved in waterE70— root tissue preserved in 70% ethanolE90— root tissue preserved in 90% ethanolRSG— root tissue preserved in silica gel
The final component indicates DNA extraction method:
K— KitM— Manual
Thus, for example, Ce1_E70_K identifies a sample from Ceroxylon echinulatum individual 1, consisting of root tissue preserved in 70% ethanol and processed using the commercial extraction kit.
Read
Description: Identifier of the replicate spectrophotometric measurement performed on an extracted DNA sample.
Type: Categorical
Values:
L1L2L3
Each of the 80 experimental DNA samples has three readings, resulting in 240 observations in the dataset.
These values represent repeated instrument readings of the corresponding extracted DNA sample rather than independent biological samples.
Concentration_(ng/ul)
Description: Estimated DNA concentration obtained from the spectrophotometric measurement.
Type: Numeric, continuous
Unit: ng/µL
Used as the primary measurement of DNA yield.
Absorbance_at_260_nm
Description: Spectrophotometric absorbance measured at a wavelength of 260 nm.
Type: Numeric, continuous
Absorbance at 260 nm is primarily associated with nucleic-acid absorption and contributes to the estimation of DNA concentration and purity ratios.
Absorbance_at_280_nm
Description: Spectrophotometric absorbance measured at a wavelength of 280 nm.
Type: Numeric, continuous
This measurement is used together with absorbance at 260 nm to calculate the A260/A280 purity ratio.
Ratio_A260/A280
Description: Ratio between absorbance measured at 260 nm and 280 nm.
Type: Numeric, continuous
This variable was used as an indicator of DNA purity and potential contamination by proteins or other compounds absorbing at approximately 280 nm.
Absorbance_at_230_nm
Description: Spectrophotometric absorbance measured at a wavelength of 230 nm.
Type: Numeric, continuous
This measurement is used together with absorbance at 260 nm to calculate the A260/A230 purity ratio.
Ratio_A260/A230
Description: Ratio between absorbance measured at 260 nm and 230 nm.
Type: Numeric, continuous
This variable provides an additional measure of DNA purity and can indicate contamination by compounds absorbing at approximately 230 nm.
File: Roots_Data.xlsx
Description:
Spreadsheet representation of the same experimental dataset provided in Roots_Data.txt.
The spreadsheet contains 240 observations and 13 variables. Variable names are presented in a more human-readable format using spaces rather than underscores.
The columns are:
SpeciesTissue SourceTreatmentGroups Source. x Treat.DNA Extraction MethodSampleReadConcentration (ng/ul)Absorbance at 260 nmAbsorbance at 280 nmRatio A260/A280Absorbance at 230 nmRatio A260/A230
Species and treatment labels in the spreadsheet similarly use spaces rather than underscores (e.g., Ceroxylon echinulatum, Silica Gel, ETOH 70%).
The .xlsx file is intended primarily for convenient human inspection and spreadsheet-based use, whereas the tab-delimited .txt version is suitable for direct import into statistical and scripting environments.
File: Root_Stats.htm
Description:
HTML export containing the complete IBM SPSS Statistics output generated from the experimental dataset.
The analyses use three principal dependent variables:
- DNA concentration (
Concentration) - A260/A280 ratio (
A260A280) - A260/A230 ratio (
A260A230)
The archived output includes descriptive and inferential analyses examining the effects of the major experimental factors.
Tissue source
DNA concentration, A260/A280, and A260/A230 were summarized and compared according to tissue source:
- Leaf
- Root
The output includes:
- mean;
- sample count;
- standard deviation;
- variance; and
- ANOVA statistics.
The analysis contains 48 leaf observations and 192 root observations, for a total of 240 measurements.
DNA extraction method
The three response variables were also summarized and compared according to DNA extraction method:
- Kit
- Manual
Descriptive statistics and ANOVA results are included.
Tissue source × preservation treatment
A General Linear Model (GLM) was used to compare the five combined tissue-source/preservation groups:
LS— Leaf + Silica GelRW— Root + WaterR70— Root + 70% EthanolR90— Root + 90% EthanolRS— Root + Silica Gel
Each group contains 48 spectrophotometric observations.
The GLM evaluates:
- DNA concentration;
- A260/A280; and
- A260/A230.
The archived SPSS output includes descriptive statistics, tests of between-subject effects, estimated marginal means, observed statistical power, and multiple-comparison procedures.
Post-hoc comparisons include:
- Tukey HSD;
- Least Significant Difference (LSD); and
- Bonferroni-adjusted comparisons.
The significance criterion used in the archived analysis was α = 0.05.
Species
A General Linear Model was also used to evaluate differences among the four palm species:
- Ceroxylon echinulatum
- Ceroxylon ventricosum
- Phoenix dactylifera
- Prestoea acuminata
Each species contributes 60 spectrophotometric observations to the complete dataset.
The archived output includes descriptive statistics, tests of between-subject effects, estimated marginal means, observed power, and Tukey, LSD, and Bonferroni post-hoc comparisons.
Experimental structure
The five experimental tissue/preservation groups can be summarized as follows:
| Group | Tissue source | Preservation treatment |
|---|---|---|
LS |
Leaf | Silica gel |
RW |
Root | Distilled water |
R70 |
Root | 70% ethanol |
R90 |
Root | 90% ethanol |
RS |
Root | Silica gel |
Each tissue/preservation combination was processed using both DNA extraction methods:
| Extraction code | Method |
|---|---|
K |
Commercial extraction kit |
M |
Manual DNA extraction |
The complete data structure is therefore:
4 species
└── 2 individuals per species
└── 5 tissue/preservation groups
└── 2 DNA extraction methods
└── 3 spectrophotometric readings
This produces:
4 × 2 × 5 × 2 × 3 = 240 observations
corresponding to 80 extracted DNA samples and 240 spectrophotometric measurements.
Data quality and missing values
All 240 observations contain recorded values for all 13 variables in the archived dataset.
No missing values are present in Roots_Data.txt or Roots_Data.xlsx.
The SPSS statistical output likewise reports 240 included cases and no excluded cases for the principal response variables.
Users conducting secondary analyses should note that L1, L2, and L3 are repeated spectrophotometric measurements of the same extracted DNA sample rather than independent biological replicates.
Potential uses of the dataset
The dataset can be reused to investigate:
- DNA yield from leaf versus root tissue;
- effects of root-preservation methods on DNA quantity and purity;
- differences between manual and commercial DNA extraction methods;
- interspecific variation in DNA extraction performance;
- relationships among DNA concentration and spectrophotometric purity measurements; and
- methodological approaches for reducing field-sampling effort in palms and other difficult-to-sample plant species.
The hierarchical structure of the dataset should be considered when performing alternative statistical analyses, particularly because multiple spectrophotometric readings correspond to the same extracted DNA sample.
Access information
Dataset
Espinoza-Ulloa, S. A.
Relieving efforts in palm-tree tissue sampling for population genetics analyses: Dataset and analyses.
Dryad Digital Repository.
DOI: 10.5061/dryad.ht76hdrfj
Associated publication
Espinoza-Ulloa, S. A. (2021).
Relieving efforts in palm-tree tissue sampling for population genetics analyses.
Ecology and Evolution, 11(12), 7946–7950.
DOI: 10.1002/ece3.7624
Other publicly accessible locations of the data
The dataset is publicly available through the Dryad Digital Repository at the DOI provided above.
The associated peer-reviewed publication is openly available through Ecology and Evolution.
Data derived from the following sources
The archived data were generated directly from the tissue sampling, preservation, DNA extraction, and spectrophotometric measurements described in the associated publication.
The dataset was not derived from an external data source.
Recommended citation
Users reusing these data are encouraged to cite the Dryad dataset and the associated publication.
Dataset
Espinoza-Ulloa, S. A. Relieving efforts in palm-tree tissue sampling for population genetics analyses: Dataset and analyses. Dryad Digital Repository. DOI: 10.5061/dryad.ht76hdrfj.
Associated article
Espinoza-Ulloa, S. A. (2021). Relieving efforts in palm-tree tissue sampling for population genetics analyses. Ecology and Evolution, 11(12), 7946–7950. DOI: 10.1002/ece3.7624.
Due to the fact that the present study will have applications in future studies of several Andean palm-tree species (Arecaceae), four different species of easy access were selected in the surroundings of Quito city (Ecuador) in order to obtain a proxy of possible variations between species. The species were as follows: (a) Phoenix dactylifera, (b) Ceroxylon echinulatum, (c) Ceroxylon ventricosum, and (d) Prestoea acuminata. These species are easily found in the Ecuadorian Andean urban and rural landscapes (between 1,800 and 2,500 m.a.s.l.). All these species are conspicuous stem palm trees that commonly exceed 10 m in height, and their roots are placed underground.
For sampling, two individuals were selected per species. The tissue collection for each individual was carried out (a) climbing along the stem to obtain young leaf tissue and (b) using a shovel to dig about 30 cm in the stem base to obtain root tissue (Figure S1). Leaf tissue was stored directly in a single bag with Silica Gel, following the most commonly used protocol for leaf tissue sampling (control sample). For root tissue sampling, eight roots per individual were pruned at 5 cm from the tip (Figure 1), and two pruned roots were placed into each tissue storage treatment. Four storage treatments for root tissues (T1 to T4) were used as follows: (T1) Silica Gel dehydration (rationale: standardized method for plant tissue sampling), (T2) distilled water (rationale: maintain hydrated and alive the tissue as is possible), (T3) 70% ethanol solution (EtOH 70%; rationale: dehydration by alcohol in a liquid solution), and (T4) 90% ethanol solution (EtOH 90%; rationale: stronger dehydration by alcohol in a liquid solution). All samples were processed after 2 weeks of storage.
Each stored tissue underwent two DNA extraction methods: (a) DNA extraction manual method for plant tissues based on Doyle and Doyle (1987, with modifications) and (b) commercial method using PureLink® Plant Total DNA Purification Kit (Invitrogen™). Each extraction started with 100 mg of macerated tissue. The final DNA extraction solutions were evaluated using NanoDrop™ 1000 Spectrophotometer (Thermo Fisher Scientific). Three readings for each processed sample were taken.
DNA concentration and quality were compared between tissue sources, storage treatments, and DNA extraction methods. The concentration was measured as DNA nanograms contained in one microliter. The quality parameters are based on the A260/A280 and A260/A230 ratios, where A260 is the absorbance at 260 nm that would be marking the presence of aromatic bases (nucleotides/DNA/RNA), A280 is the absorbance at 280 nm that would recognize contaminants such as proteins and phenolic compounds, and A230 would identify residual contaminants of many organic compounds such as phenol, TRIzol, salts, among others. In this way, the A260/A280 ratio would be linked to factors related to the nature and processing of the tissue, while the A260/A230 ratio would be linked to the reagents and residues produced by the extraction protocol used (Matlock, 2015).
Finally, using all DNA extractions obtained, a positive–negative PCR test was performed. The PCR test was performed with two microsatellite loci developed for Oenocarpus bataua (Ob01and OB11; Montufar et al., 2007) that had previously been tested and had positive results for all species used in this study. The amplification parameters for the used loci were the same described in their source paper.
For the statistical analyses, a multifactor ANOVA (general linear model) was performed to observe the statistical differences between the analyzed factors. The factors analyzed were as follows: (a) species, (b) source (leaf vs. root), (c) storage treatment, and (d) extraction method. Additionally, a Tukey post hoc test was performed to compare the results obtained by each storage treatment versus the results obtained for the leaf, in order to determine the best storage treatment and how much it differs from the result of a standard protocol.