Ecological speciation in sympatric palms: 1. Gene expression, selection and pleiotropy

Abstract

Ecological speciation requires divergent selection, reproductive isolation and a genetic mechanism to link the two. We examined the role of gene expression and coding sequence evolution in this process using two species of Howea palms that have diverged sympatrically on Lord Howe Island, Australia. These palms are associated with distinct soil types and have displaced flowering times, representing an ideal candidate for ecological speciation. We generated large amounts of RNA-Seq data from multiple individuals and tissue types collected on the island from each of the two species. We found that differentially expressed loci as well as those with divergent coding sequences between Howea species were associated with known ecological and phenotypic differences, including response to salinity, drought, pH and flowering time. From these loci, we identified potential 'ecological speciation genes' and further validate their effect on flowering time by knocking out orthologous loci in a model plant species. Finally, we put forward six plausible ecological speciation loci, providing support for the hypothesis that pleiotropy could help to overcome the antagonism between selection and recombination during speciation with gene flow.

Arbuscular mycorrhizal fungi promote coexistence and niche divergence of sympatric palm species on a remote oceanic island

“…Thus, the reduction in AMF in H. forsteriana on volcanic soil may place it at a substantial disadvantage compared with H. belmoreana . Plant RNA sequence data from a previous study (Dunning et al ., ) have indicated that adaptive divergence between Howea species may be linked to the difference in AMF abundance uncovered here. Specifically, mycorrhizal‐associated genes show signs of adaptive divergence between H. forsteriana and H. belmoreana .…”

“…Therefore, soil has clearly played a key role in speciation and remains important for species coexistence. A large transcriptomic study found that only three loci were differentially expressed between the roots of H. forsteriana on volcanic vs calcareous soils, but they were of unknown function (Dunning et al ., ). Previous studies of the soil itself have focused on its chemical composition, pH, salinity and soil water content (Savolainen et al ., ; Papadopulos et al ., ); although these abiotic factors differ between the soil types, they offer limited explanatory power regarding the selective pressures that operate on the two species when occupying the same soil type (Papadopulos et al ., ).…”

Developing a new variety of kentia palms (Howea forsteriana): up-regulation of cytochrome b561 and chalcone synthase is associated with red colouration of the stems

“…note that differential expression for only two isoforms, Cyt b 561 and CHs (in bold), was significant in both qPCr and rna-seq analyses. "ID" refers to the unique sequence identifier in the reference transcriptome of Dunning et al (2016). seedling applied for the green-stemmed kentia palm (LHI nursery, pers.…”

“…Primer sequences are 17-24 bp long, have a Tm of 53-65 °C, and whenever possible, primer pairs differed less than two degrees in their Tm (Table S1). The pentatricopeptide repeat-containing protein (PP442) gene of H. forsteriana was used as reference for qPCR following Dunning et al (2016). Quantitative PCR reactions were carried out in a LightCycler® 480 Instrument (Roche), using 1 × Power SYBR Green PCR Master Mix (Applied Biosystems).…”

Ecological speciation in sympatric palms: 3. Genetic map reveals genomic islands underlying species divergence in Howea

“…To assign transcripts from the Howea reference transcriptome (Dunning et al. ) to genomic scaffolds, BLASTn was used with max_target_seqs = 1 and an E ‐value cutoff of 1 × 10 −20 . Only the highest scoring match for each transcript was retained.…”