Organelle DNA phylogeography of Cycas taitungensis, a relict species in Taiwan

The phylogegraphic pattern of Cycas taitungensis, an endemic species with t wo remaining populations in Taiwan, was investigated based on genetic varia bility and phylogeny of the atpB-rbcL noncoding spacer of chloroplast DNA ( cpDNA) and the ribosomal DNA (rDNA) internal transcribed spacer (ITS) of mi tochondrial DNA (mtDNA). High levels of genetic variation at both organelle loci, due to frequent intramolecular recombination, and low levels of gene tic differentiation were detected in the relict gymnosperm. The apportionme nt of genetic variation within and between populations agreed with a migran t-pool model, which describes a migratory pattern with colonists recruited from a random sample of earlier existing populations. Phylogenies obtained from cpDNA and mtDNA were discordant according to neighbour-joining analyse s. In total four chlorotypes (clades I-IV) and five mitotypes (clades A-E) were identified based on minimum spanning networks of each locus. Significa nt linkage disequilibrium in mitotype-chlorotype associations excluded the possibility of the recurrent homoplasious mutations as the major force caus ing phylogenetic inconsistency. The most abundant chlorotype I was associat ed with all mitotypes and the most abundant mitotype C with all chlorotypes ; no combinations of rare mitotypes with rare chlorotypes were found. Accor ding to nested clade analyses, such nonrandom associations may be ascribed to relative ages among alleles associated with the geological history throu gh which cycads evolved. Nested in networks as interior nodes coupled with wide geographical distribution, the most dominant cytotypes of CI and El ma y represent ancestral haplotypes of C. taitungensis with a possible long ex istence prior to the Pleistocene glacial maximum. In contrast, rare chlorot ypes and mitotypes with restricted and patchy distribution may have relativ ely recent origins. Newly evolved genetic elements of mtDNA, with a low fre quency, were likely to be associated with the dominant chlorotype, and vice versa, resulting in the nonrandom mitotype-chlorotype associations. Paraph yly of CI and EI cytotypes, leading to the low level of genetic differentia tion between cycad populations, indicated a short period for isolation, whi ch allowed low possibilities of the attainment of coalescence at polymorphi c ancestral alleles.