Contrasting patterns of DNA variation in natural populations of two related conifers, Cryptomeria japonica and Taxodium distichum (Cupressaceae sensu lato)

Abstract

We investigated DNA variation within and between two closely related conifers, Cryptomeria japonica and Taxodium distichum, at nuclear loci encoding ferredoxin, glutamyl-tRNA reductase, lycopene beta cyclase, and phosphoribosylanthranilate transferase. Average nucleotide diversity at silent sites was estimated to be 0.0035 (SE 0.0012) in C. japonica and 0.0058 (SE 0.0006) in T. distichum . One population in C. japonica was differentiated from the others but generally there was not much differentiation among populations or varieties within the two species. However, the two species seemed to differ in frequency spectra of DNA polymorphisms. Excesses of intermediate-frequency variants were found in C. japonica, whereas excesses of both rare and high-frequency variants were found in T. distichum , which suggested different histories of population structures in the two species. Deviations from the standard neutral expectations in DNA polymorphisms were found by applications of neutrality tests. The results show that actions of selection to respective loci seem to differ between the two species, indicating differences of interaction among evolutionary factors.

Amounts and patterns of nucleotide variation within and between two Japanese conifers, sugi (Cryptomeria japonica) and hinoki (Chamaecyparis obtusa) (Cupressaceae sensu lato)

“…For example, using this test, Smith and EyreWalker (2002) found that rates of replacement substitution were higher than expected across loci in Drosophila and estimated that 45% of replacement substitutions were due to positive selection. In our study, a higher than expected frequency of replacement polymorphism was found at the CC2188 locus, and a similar pattern has been found at the Lcyb locus in a previous study (Kado et al 2006). However, these patterns can be more readily explained by substitutions with nearly neutral variants at replacement sites (Ohta 1992) rather than positive selection.…”

“…Notably, cypress tends to have higher than expected frequencies of singleton polymorphisms (Kado et al 2006), and hinoki tends to have relatively small numbers of alleles (this study). These patterns seem to reflect differences in historical population structures among the species rather than differences in the effects of natural selection on them.…”

“…However, these patterns can be more readily explained by substitutions with nearly neutral variants at replacement sites (Ohta 1992) rather than positive selection. Significant excesses of replacement substitution were found only at the mature protein region in the Ferr locus (Kado et al 2006). Therefore, the contribution of positive selection to replacement substitutions seems to be lower in cupressaceous species than in Drosophila.…”

“…In previous studies, we investigated nucleotide variations in sugi (Cryptomeria japonica), which is the most widely planted tree species in Japan, and its closest relative, cypress (Taxodium distichum), as a reference species (Kado et al 2003(Kado et al , 2006. In the study presented here, we turned our attention to hinoki (Chamaecycparis obtusa), the second most widely planted tree species in Japan.…”