Abstract
BackgroundTropical trees undergo severe stress through seasonal drought and flooding, and the ability of these species to respond may be a major factor in their survival in tropical ecosystems, particularly in relation to global climate change. Aquaporins are involved in the regulation of water flow and have been shown to be involved in drought response; they may therefore play a major adaptive role in these species. We describe genetic diversity in the PIP sub-family of the widespread gene family of Aquaporins in five Neotropical tree species covering four botanical families.ResultsPIP Aquaporin subfamily genes were isolated, and their DNA sequence polymorphisms characterised in natural populations. Sequence data were analysed with statistical tests of standard neutral equilibrium and demographic scenarios simulated to compare with the observed results. Chloroplast SSRs were also used to test demographic transitions. Most gene fragments are highly polymorphic and display signatures of balancing selection or bottlenecks; chloroplast SSR markers have significant statistics that do not conform to expectations for population bottlenecks. Although not incompatible with a purely demographic scenario, the combination of all tests tends to favour a selective interpretation of extant gene diversity.ConclusionsTropical tree PIP genes may generally undergo balancing selection, which may maintain high levels of genetic diversity at these loci. Genetic variation at PIP genes may represent a response to variable environmental conditions.
Highlights
Tropical trees undergo severe stress through seasonal drought and flooding, and the ability of these species to respond may be a major factor in their survival in tropical ecosystems, in relation to global climate change
Among protein classes involved in response to drought, and the regulation of water balance in general, aquaporins are a good candidate starting point for the exploration of genetic diversity in natural populations of non-model species such as Neotropical rainforest trees, as they are ubiquitous, well known and the focus of in-depth functional studies in plants in general [13] and trees in particular [14]
We chose for this study plasma membrane intrinsic proteins (PIPs), which are grouped in two subfamilies (PIP1 and PIP2)
Summary
Amplifications with universal primers allowed the cloning of 1-5 different genes per species (Table 1). As further evidence that single genes are amplified by each primer pair, non-synonymous polymorphisms, when occurring, mostly caused replacements between amino acids of similar structure and chemical properties, and in no case were stop-codon mutations detected. This led us to conclude that the amplicons correspond to separate, functional gene loci. Details of the distribution of these polymorphisms in coding and non-coding regions, and between synonymous and non-synonymous sites within the latter, are provided in Table 3 (note that the total number of SNPs in Table 3 sums to more than 79 because they are reported at the population level, not the species level, for the species for which two populations have been analysed). The calculation of neutral confidence intervals for mutation-drift equilibrium statistics
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