Experimental and genetic analysis of selfing reveals no reinforcement in Phlox cuspidata
Data files
Jan 09, 2024 version files 41.03 KB
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A-S_distance.csv
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Fis.csv
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Flower_size.csv
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Fruit_set.csv
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Internode.csv
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README.md
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Selfing_rate.csv
Abstract
Reinforcement is the process through which prezygotic reproductive barriers evolve in sympatry due to selection against hybridization between co-occurring, closely related species. The role of self-fertilization in reinforcement and reproductive isolation is uncertain in part because its efficiency as a barrier against heterospecific mating can depend on the timing of autonomous selfing.
To investigate whether increased autonomous selfing has evolved as a mechanism for reinforcement, we compared Phlox cuspidata populations across their native Texas range using both estimates of genetic diversity and experimental manipulation with morphological measurements. Specifically, we investigated patterns of variation in floral traits and timing of selfing between individuals from allopatric populations of P. cuspidata and from populations sympatric with the closely related species, P. drummondii.
We infer intermediate rates of selfing across field-collected individuals with no significant difference between allopatric and sympatric populations. Among greenhouse grown plants, we find no differences in timing of selfing or other floral traits including anther dehiscence timing, anther-stigma distances, autonomous selfing rate and self-seed count between allopatric and sympatric populations. However, our statistical analyses indicate that P. cuspidata individuals sympatric with P drummondii seem to have generally larger flowers compared to allopatric individuals.
Despite strong evidence of costly hybridization with P. drummondii, we find no evidence of trait divergence due to reinforcement in P. cuspidata. Although we document nearly complete autonomous self-seed set in the greenhouse, estimates of selfing rates from genetic data imply realized selfing is much lower in nature suggesting an opportunity for reinforcing selection to act on this trait.
README
This folder contains the data and code for the article titled: Experimental and genetic analyses of selfing reveals no reinforcement in Phlox cuspidata
Comments and requests should be addressed to Bushra Shahid: bushra.shahid@usys.ethz.ch. All material is free of use, but please cite the paper whenever appropriate.
The folder named Data contains six .csv files and an R file for the final version of the manuscript.
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Summary
The manuscript aimed to investigate whether increased autonomous selfing has evolved as a mechanism for reinforcement, we compared Phlox cuspidata populations across their native Texas range using both estimates of genetic diversity and experimental manipulation with morphological measurements. Specifically, we investigated patterns of variation in floral traits and timing of selfing between individuals from allopatric populations of P. cuspidata and from populations sympatric with the closely related species, P. drummondii.
We infer intermediate rates of selfing across field-collected individuals with no significant difference between allopatric and sympatric populations. Among greenhouse grown plants, we find no differences in timing of selfing or other floral traits including anther dehiscence timing, anther-stigma distances, autonomous selfing rate and self-seed count between allopatric and sympatric populations. However, our statistical analyses indicate that P. cuspidata individuals sympatric with P drummondii tend to have significantly bigger flowers compared to allopatric individuals.
Description of the data and file structure
The individual CSV files contain quantitative trait values for 6 traits measured using Phlox cuspidata individuals from sympatric and allopatric populations (categorical). The "Pop" refers to the population (categorical), "Pot_ID" is the pot number for each potted plant in the experiment (categorical). the "ID" (categorical) is a unique number given to each indiviudal consisting of their population, mom ID and offspring number ^.
The files are as follows:
1. Flower_size: Contains flower length and diameter values in cm (continuous) for a minimum of 3 flowers on each individual sampled. The columns include the
- Pot_Id (categorical)
- a unique ID (categorical)
- Mom ID (categorical)
- Population (categorical)
- Length 1-3 in cm (continuous)
- Diameter 1-3 in cm (continuous)
2. Internode: Contains the internode length in cm (continuous) as measured between the second and third internode on each sample. The columns include the
- Pot_Id (categorical)
- a unique ID (categorical)
- Mom ID (categorical)
- Population (categorical)
- Internode length in cm (continuous).
3. A-S_distance: Contains the lengths in cm (continuous) of each of 5 anthers (A1-5) and the pistil (P) on Stage 0 (bud the day before it opens) and Stage 1 (day 1 of an open flower) for each sample. There are 2 replicates per sample for reproducibility. These values were used to obtain the minimum distance between the anther and stigma in cm. The columns include
- Pot_Id (categorical)
- a unique ID (categorical)
- Mom ID (categorical)
- Population (categorical)
- Replicate number (categorical)
- anther length of Stage0 A1-5 and Stage1A1-5 and pistil lengths in Stage 0 and Stage 1 (all continuous).
4. Fruit_set: Contains the number of fruit set (discrete) on the respective stages (Day 0 to 4) for each sample. The columns include
- Pot_Id (categorical)
- a unique ID (categorical)
- Population (categorical)
- fruit set in the 5 days (discrete).
5. Selfing rate: Contains the number of fruits (discrete) and seed set (discrete) after bagging known number of fruits (discrete). Also contains a column called selfing rate (continuous) which was estimated using the proportion of flowers that set fruit. The columns include
- Pot_Id (categorical)
- a unique ID (categorical)
- Population (categorical)
- the selfing rate (continuous)
- number of fruits set (discrete)
- number of seeds produced by the said number of fruits (discrete).
6. Fis: Contains the inbreeding coefficient and genetic selfing rate values for the populations. The columns include
- population (categorical)
- selfing rate (s) (continuous)
- Fis inbreeding coefficient (continuous)
- minor allele frequency (MAF)
- zone (categorical)
- lat and long values (continuous)
- number of individuals (discrete).
Code/Software
An R script is provided which was used to create models and plots for each of the trait trait values listed above along with genetic selfing rates.
Packages used included tidyverse, lmerTest, ggeffects and dplyr.