Ecological niche differentiation mediates near-complete premating reproductive isolation within the Gladiolus carneus (Iridaceae) species complex
Data files
Sep 12, 2025 version files 50.40 MB
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1._G._carneus_morphology_2020_-_2023.csv
63.10 KB
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10._G._carneus_ecogeographic_binary.csv
29.53 MB
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11._G._carneus_phenology_binary.csv
6.91 KB
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12._G._carneus_pollinator_binary.csv
234 B
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2._G._carneus_spectra_new_spec.csv
14.54 MB
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3._G._carneus_spectra_old_spec.csv
5.91 MB
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4._Eristalis_spectral_sensitivities.csv
15.66 KB
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5._G._carneus_inat_occurance.csv
49.10 KB
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6._G._carneus_flowering_times.csv
75.55 KB
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7._G._carneus_visitation_rates.csv
2.61 KB
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8._G._carneus_pollen_deposition.csv
6.31 KB
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9._G._carneus_tube_length___flower_gape_morphology.csv
30.85 KB
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Gladiolus_carneus_Ecological_Niche_Differentiation.Rmd
152.89 KB
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README.md
13 KB
Abstract
Ecological niche differentiation is well associated with intraspecific divergence of functional traits, which may lead to the evolution of premating reproductive isolation. However, the link between the ecological niches, trait divergence, and premating isolation remains poorly understood. This is particularly pertinent in hyper-diverse areas such as the Cape Floristic Region (CFR) of South Africa, where fine-scale ecological heterogeneity has been hypothesised as a major driver of speciation. Using the polymorphic geophyte Gladiolus carneus, endemic to the CFR, we test whether ecological niche differentiation mediates premating reproductive isolation. We first tested whether putative ecotypes of G. carneus were distinct based on their floral and vegetative morphology. Next, we documented each putative ecotype’s abiotic niche, flowering phenology, and pollination niche and further tested whether any resulting niche differentiation causes premating reproductive isolation. Seven distinct ecotypes were identified. Using niche modelling and multivariate analyses, we found that these ecotypes occupied distinct abiotic niches, resulting in strong ecogeographic isolation. They also had distinct flowering times, causing varying strengths of phenological isolation. For the pollinator niche, we found that all sampled populations were pollinated by one of three highly effective functional pollinators; however, at the ecotypic level, there were no consistent trends leading to varying strengths in pollinator-mediated isolation. Across all ecotypes, ecogeographic isolation was the strongest gene flow barrier, which, combined with phenological and pollinator-mediated isolation, caused near-complete premating reproductive isolation. These results suggest that ecological niche differentiation between G. carneus ecotypes may be contributing to incipient speciation within the species complex and further suggest that ecological niche differentiation may be a major driver of speciation in the hyper-diverse Cape Floristic Region.
Dataset DOI: 10.5061/dryad.0cfxpnwf5
Description of the data and file structure
This file ‘README.txt’ was generated on 07/08/2025
GENERAL INFORMATION:
- Author Information: Katharine L. Khoury, Shelley Edwards, and Ethan Newman
- Date of data collection: 2020 to 2024
DATA AND FILES
Our dataset has been collected to investigate whether ecological niche differentiation mediates premating reproductive isolation in the Gladiolus carneus species complex. We tested (1) whether putative ecotypes of G. carneus are morphologically distinct from one another; (2) whether they occupy distinct abiotic, phenological, and pollinator niches; and (3) whether differences in these ecological niches result in premating reproductive isolation.
File 1: 1._G.carneus_morphology_2020-_2023.csv
Description: All morphological measurements from all G. carneus ecotypes.
(A) Number of variables: 18
(B) Number of rows: 650
(C) Variable list:
Date: Date of the measurement
Variety: G. carneus ecotype
Site: Site of the measurement
tube_length: tube length (mm)
flower_gape: flower gape (mm)
petal_size: petal size (mm)
flower_width: flower width (mm)
style_length: style length (mm)
flower_depth: flower depth (mm)
inflourescence_height_cm: inflorescence height (cm)
inflourescence_display_mm: inflorescence height (mm)
total_flowers: total number of buds, open and senesced flowers
no_leaves: total number of leaves
length_longest_leaf_cm: leaf length (cm)
width_longest_leaf: leaf width (mm)
nectar_volume_ul: nectar volume (ul)
nectar_conc: nectar concentration (%)
nectar_welling: the height of the nectar welling in the corolla (mm)
(D) Missing data codes: NA
(E) Abbreviations used: None
(F) Other relevant information: None
File 2: 2._G._carneus_spectra_new_spec.csv
Description: Spectral measurements of G. carneus ecotypes taken from 2022 and 2023. Files 2 to 4 include all spectral data from the G. carneus ecotypes and the Eristalis tenax spectral sensitivities used in the fly colour vision models.
(A) Number of columns: 710
(B) Number of rows: 3649
(C) Variable list:
Wavelength: wavelength measurement
Individual spectral measurements: the reflectance at a particular wavelength
(D) Missing data codes: None
(E) Abbreviations used: Naming system for spectral measurements
Ecotype: The G. carneus ecotype from which the measurement was taken.
[number]: The number associated with each G. carneus individual
morphology: The part of the flower from which the measurement was taken (tepal - tepal, Mcentre - centre of the median tepal, Mguide - guide of the median tepal, Lcentre - centre of the lateral tepal, Lguide - guide of the lateral tepal)
(F) Other relevant information: NA
File 3: 3._G._carneus_spectra_old_spec.csv
Description: Spectral measurements of G. carneus ecotypes taken from 2020. Files 2 to 4 include all spectral data from the G. carneus ecotypes and the Eristalis tenax spectral sensitivities used in the fly colour vision models.
(A) Number of columns: 552
(B) Number of rows: 2049
(C) Variable list:
Wavelength: wavelength measurement
Individual spectral measurements: the reflectance at a particular wavelength
(D) Missing data codes: None
(E) Abbreviations used: Naming system for spectral measurements
Ecotype: The G. carneus ecotype from which the measurement was taken.
[number]: The number associated with each G. carneus individual
morphology: The part of the flower from which the measurement was taken (tepal - tepal, Mcentre - centre of the median tepal, Mguide - guide of the median tepal, Lcentre - centre of the lateral tepal, Lguide - guide of the lateral tepal)
(F) Other relevant information: NA
File 4: 4._Eristalis_spectral_sensitivities.csv
Description: Eristalis tenax spectral sensitivities. Files 2 to 4 include all spectral data from the G. carneus ecotypes and the Eristalis tenax spectral sensitivities used in the fly colour vision models.
(A) Number of columns: 5
(B) Number of rows: 402
(C) Variable list:
Wavelength: wavelength
Individual Receptor Sensitivities: The efficiency of detection for a particular wavelength of light. Four receptors are given - R7p, R7y, R8p, R8y
(D) Missing data codes: None
(E) Abbreviations used: None
(F) Other relevant information: This data set was provided by Adrian Dyer.
File 5: 5._G._carneus_inat_occurance.csv
Description: File 5 includes all occurrence data for all G. carneus ecotypes mined from iNaturalist observations. These observations were used to quantify the fundamental and realised niches of the G. carneus ecotypes.
(A) Number of variables: 5
(B) Number of rows: 1247
(C) Variable list:
quality_grade: the quality of the observation, which was either research (iNat research grade) or own (provided by KLK)
latitude: latitudinal coordinates
longitude: longitudinal coordinates
positional_accuracy: the accuracy (m) of the observation
field:varieties: G. carneus ecotype
(D) Missing data codes: None
(E) Abbreviations used: G. carneus ecotypes
AL - albidus
BL - blandus
CL - callistus
HA - high-altitude
LB - langeberg
MC - macowanianus
PS - prismatosiphon
(F) Other relevant information: None
File 6: 6._G._carneus_flowering_times.csv
Description: File 6 includes all phenological flowering data for all G. carneus ecotypes mined from iNaturalist observations. The data were used to quantify the phenological niche of the ecotypes.
(A) Number of variables: 8
(B) Number of rows: 1231
(C) Variable list:
date_observed: the full observation date
day: the day of the month of the observation
month: the month of the observation (1 - 12)
year: the year of the observation
day_num: the day of the year (1 - 365) of the observation
degrees: the day of the year converted to degrees
radians: the day of the year converted to radians
Varieties: the G. carneus ecotypes
(D) Missing data codes: None
(E) Abbreviations used: None
(F) Other relevant information: None
File 7: 7._G._carneus_visitation_rates.csv
Description: Visitation rates of functional pollinators at G. carneus populations. Files 7 and 8 contain visitation rates and pollen deposition of the functional pollinators at G. carneus populations. This data was used to quantify the pollinator niche for each population and ecotype.
(A) Number of variables: 7
(B) Number of rows: 36
(C) Variable list:
Date: the date of the observations
Variety: G. carneus ecotype
Site: The site of the observations. The first letter indicates the ecotype.
Func_pollinator: the functional pollinators
Visits.flower.hour: the number of visits/flower/hour
No_flowers_obs: the total flowers observed at the site
Decminal_hours: total hours observed at the site
(D) Missing data codes: None
(E) Abbreviations used: Functional pollinators
MTFs - medium-tongued flies
LTFs - long-tongued flies
(F) Other relevant information: None
File 8: 8._G._carneus_pollen_deposition.csv
Description: Pollen deposition on functional pollinators at G. carneus populations. Files 7 and 8 contain visitation rates and pollen deposition of the functional pollinators at G. carneus populations. This data was used to quantify the pollinator niche for each population and ecotype.
(A) Number of variables: 18
(B) Number of rows: 51
(C) Variable list:
Date_Collected: Date the pollinator was caught
Variety: the G. carneus ecotype
Site: The site of the observations. The first letter indicates the ecotype.
Insect_Family: Family-level identification of the pollinator
Func_pollinator: the functional pollinator designation
Polliantor_species: Species-level identification of the pollinator
Ext_proboscis_length: the extended proboscis length of the pollinator (mm)
body_length: the body length of the pollinator (mm)
thorax_width: the thorax width of the pollinator (mm)
thorax_depth: the thorax depth of the pollinator (mm)
Visitor - whether the pollinator was observed visiting flowering G. carneus individuals (Y) or whether it was caught in the surrounding environment (N)
Glad_thorax_pollendep: number of G. carneus pollen grains on the thorax of the pollinator.
Glad_head_pollendep: number of G. carneus pollen grains on the head of the pollinator.
Glad_abdomin_pollendep: number of G. carneus pollen grains on the abdomen of the pollinator.
Glad_total_pollen: total number of G. carneus pollen grains on the pollinator.
foreign_thorax_pollendep: number of foreign pollen grains on the thorax of the pollinator.
foreign_head_pollendep: number of foreign pollen grains on the head of the pollinator.
foreign_abdomin_pollendep: number of foreign pollen grains on the abdomen of the pollinator.
(D) Missing data codes: NA
(E) Abbreviations used: Functional pollinators
MTFs - medium-tongued flies
LTFs - long-tongued flies
(F) Other relevant information: Pollen loads on each part of the pollinator were only counted to 1000 grains.
File 9: 9._G._carneus_tube_length___flower_gape_morphology.csv
Description: Measurements of tube length and flower gape for G. carneus populations, which are used to test for correlations between pollinator and floral morphology.
(A) Number of variables: 5
(B) Number of rows: 650
(C) Variable list:
Date: the date of the measurement
Variety: the G. carneus ecotype
Site: The site of the observations. The first letter indicates the ecotype.
tube_length: tube length (mm)
flower_gape: flower gape (mm)
(D) Missing data codes: NA
(E) Abbreviations used: None
(F) Other relevant information: None
File 10: 10._G._carneus_ecogeographic_binary.csv
Description: Binary occurrence records for G. carneus ecotypes used to calculate ecogeographic isolation. Files 10 to 12 contain the data used to calculate ecogeographic, phenological, pollinator isolation, and total premating reproductive isolation.
(A) Number of columns: 8
(B) Number of rows: 1 048 576
(C) Variable list:
id: the ID of a specific place in the niche model predictions.
Individual G. carneus ecotypes: binary occurrence predictions of the ecotypes, with 1 indicating the prediction was above the ETSS threshold, 0 indicating the prediction was below the ETSS threshold, and NA indicating there was no predicted niche.
(D) Missing data codes: NA
(E) Abbreviations used: None
(F) Other relevant information: All NA values are converted to 0 in the R script to facilitate the calculation of ecogeographic isolation.
File 11: Name: 11._G._carneus_phenology_binary.csv
Description: Binary phenological records for G. carneus ecotypes used to calculate phenological isolation. Files 10 to 12 contain the data used to calculate ecogeographic, phenological, pollinator isolation, and total premating reproductive isolation.
(A) Number of columns: 8
(B) Number of rows: 366
(C) Variable list:
day_num: the day of the year
Individual G. carneus ecotypes: binary occurrence predictions of the ecotypes, with 1 indicating the flowering individuals were documented and 0 indicating no flowering individuals were documented.
(D) Missing data codes: None
(E) Abbreviations used: None
(F) Other relevant information: None
File 12: 12._G._carneus_pollinator_binary.csv
Description: Binary pollinator records for G. carneus ecotypes used to calculate pollinator isolation. Files 10 to 12 contain the data used to calculate ecogeographic, phenological, pollinator isolation, and total premating reproductive isolation.
(A) Number of variables: 7
(B) Number of rows: 7
(C) Variable list:
FuncPollinator: the functional pollinator
Individual G. carneus ecotypes: binary records showing whether a particular functional pollinator was documented for an ecotype, with 1 indicating that the functional pollinator was documented, and 0 indicating the functional pollinator was not documented
(D) Missing data codes: None
(E) Abbreviations used: None
(F) Other relevant information: Blandus is missing from the data set due to a lack of pollinator data
File 13: Gladiolus_carneus_Ecological_Niche_Differentiation.Rmd
Description: The annotated R code used to analyse all of the data.
Code/software
All R scripts used to analyse the data have been included in an R Markdown document. All data analysis was conducted in R v.4.1.2.
Access information
Other publicly accessible locations of the data:
- Worldclim (https://www.worldclim.org/data/worldclim21.html)
- Cramer MD, Wootton LM, van Mazijk R, Verboom GA. 2019. New regionally modelled soil layers improve prediction of vegetation type relative to that based on global soil models. Diversity & Distributions 25: 1736–1750. doi:10.1111/ddi.12973