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Many coastal foundation plant species thrive across a range of environmental conditions, often displaying dramatic phenotypic variation in response to environmental variation. We characterized the response of propagules from six populations of the foundation species Rhizophora mangle L. to full factorial combinations of two levels of salinity (15 ppt and 45 ppt) reflecting the range of salinity measured in the field populations, and two levels of nitrogen (N; no addition and amended at approximately 3 mg N per pot each week) equivalent to comparing ambient N to a rate of addition of 75 kg per hectare per year. The response to increasing salinity included significant changes, i.e., phenotypic plasticity, in succulence and root to shoot biomass allocation. Propagules also showed plasticity in maximum photosynthetic rate and root to shoot allocation in response to N amendment, but the responses depended on the level of salinity and varied by population of origin. In addition, propagules from different populations and maternal families within populations differed in survival and all traits measured except photosynthesis. Variation in phenotypes, phenotypic plasticity and propagule survival within and among R. mangle populations may contribute to adaptation to a complex mosaic of environmental conditions and response to climate change. 

This record contains supplementary information for the article "Inheritance of DNA methylation differences in the mangrove Rhizophora mangle" published in Evolution&Development. It contains the barcodes (barcodes.txt), the reference contigs (contigs.fasta.gz), the annotation of the reference contigs (mergedAnnot.csv.gz), the SNPs (snps.vcf.gz), the methylation data (methylation.txt.gz), and the experimental design (design.txt). All data are unfiltered. Short reads are available on SRA (PRJNA746695). Note that demultiplexing of the pooled reads (SRX11452376) will fail because the barcodes are already removed and the header information is lost during SRA submission. Instead, use the pre-demultiplexed reads that are as well linked to PRJNA746695.

 

Table S13 (TableS13_DSSwithGeneAnnotation.offspringFams.csv.gz):

Differential cytosine methylation between families using the mother data set. The first three columns fragment number ("chr"), the position within the fragment ("pos"), and the sequence context ("context"). Columns with the pattern FDR_<X>_vs_<Y> contain false discovery rates of a test comparing population X with population Y. Average DNA methylation levels for each population are given in the columns "AC", "FD", "HI", "UTB", "WB", and "WI". The remaining columns contain the annotation of the fragment, for example whether it matches to a gene and if yes, the gene name ID and description are provided.

 

Anthropogenic changes to the environment challenge animal populations to adapt to new conditions and unique threats. While the study of adaptation has focused on genetic variation, epigenetic mechanisms may also be important. DNA methylation is sensitive to environmental stressors, such as parasites and pesticides, which may affect gene expression and phenotype. We studied the effects of an invasive ectoparasite,Philornis downsi, on DNA methylation of Galápagos mockingbirds (Mimus parvulus). We used the insecticide permethrin to manipulateP. downsipresence in nests of free‐living mockingbirds and tested for effects of parasitism on nestling mockingbirds using epiGBS, a reduced‐representation bisulfite sequencing (RRBS) approach. To distinguish the confounding effects of insecticide exposure, we conducted a matching experiment exposing captive nestling zebra finches (Taeniopygia guttata) to permethrin. We used zebra finches because they were the closest model organism to mockingbirds that we could breed in controlled conditions. We identified a limited number of differentially methylated cytosines (DMCs) in parasitized versus nonparasitized mockingbirds, but the number was not more than expected by chance. In contrast, we saw clear effects of permethrin on methylation in captive zebra finches. DMCs in zebra finches paralleled documented effects of permethrin exposure on vertebrate cellular signaling and endocrine function. Our results from captive birds indicate a role for epigenetic processes in mediating sublethal nontarget effects of pyrethroid exposure in vertebrates. Environmental conditions in the field were more variable than the laboratory, which may have made effects of both parasitism and permethrin harder to detect in mockingbirds. RRBS approaches such as epiGBS may be a cost‐effective way to characterize genome‐wide methylation profiles. However, our results indicate that ecological epigenetic studies in natural populations should consider the number of cytosines interrogated and the depth of sequencing in order to have adequate power to detect small and variable effects.

 

Despite the severe impacts of theDeepwater Horizonoil spill, the foundation plant speciesSpartina alternifloraproved resilient to heavy oiling, providing an opportunity to identify mechanisms of response to the anthropogenic stress of crude oil exposure. We assessed plants from oil‐affected and unaffected populations using a custom DNA microarray to identify genomewide transcription patterns and gene expression networks that respond to crude oil exposure. In addition, we used T‐DNA insertion lines of the model grassBrachypodium distachyonto assess the contribution of four novel candidate genes to crude oil response. Responses inS. alterniflorato hydrocarbon exposure across the transcriptome as well as xenobiotic specific response pathways had little overlap with those previously identified in the model plantArabidopsis thaliana. Among T‐DNA insertion lines ofB. distachyon, we found additional support for two candidate genes, one (ATTPS21) involved in volatile production, and the other (SUVH5) involved in epigenetic regulation of gene expression, that may be important in the response to crude oil. The architecture of crude oil response inS. alterniflorais unique from that of the model speciesA. thaliana,suggesting that xenobiotic response may be highly variable across plant species. In addition, further investigations of regulatory networks may benefit from more information about epigenetic response pathways.