Paraphyly of organelle DNAs in Cycas Sect. Asiorientales due to ancient ancestral polymorphisms

Abstract

BackgroundThis study addresses the apportionment of genetic diversity between Cycas revoluta and C. taitungensis, species that constitute the section Asiorientales and represent a unique, basal lineage of the Laurasian genus Cycas. Fossil evidence indicates divergence of the section from the rest of Cycas at least 30 million years ago. Geographically, C. taitungensis is limited to Taiwan whereas C. revoluta is found in the Ryukyu Archipelago and on mainland China.ResultsThe phylogenies of ribosomal ITS region of mtDNA and the intergenic spacer between atpB and rbcL genes of cpDNA were reconstructed. Phylogenetic analyses revealed paraphyly of both loci in the two species and also in the section Asiorientales. The lack of reciprocal monophyly between these long isolated sections is likely due to persistent shared ancestral polymorphisms. Molecular dating estimated that mt- and cp DNA lineages coalesced to the most recent common ancestors (TMRCA) about 327 (mt) and 204 MYA (cp), corresponding with the divergence of cycad sections in the Mesozoic.ConclusionFates of newly derived mutations of cycads follow Klopfstein et al.'s surfing model where the majority of new mutations do not spread geographically and remain at low frequencies or are eventually lost by genetic drift. Only successful 'surfing mutations' reach very high frequencies and occupy a large portion of a species range. These mutations exist as dominant cytotypes across populations and species. Geographical subdivision is lacking in both species, even though recurrent gene flow by both pollen and seed is severely limited. In total, the contrasting levels between historical and ongoing gene flow, large population sizes, a long lifespan, and slow mutation rates in both organelle DNAs have all likely contributed to the unusually long duration of paraphyly in cycads.

Patterns of chloroplast DNA variation in Cycas debaoensis (Cycadaceae): conservation implications

“…In seed plants, evolutionary rates are estimated at 1.01 9 10 -9 substitutions per site per year for synonymous sites of cpDNAs (Graur and Li 2000). These values approximate the evolutionary rates of introns and noncoding spacers of organelle DNAs (Chiang et al 2009). …”

Morphometric and geographical variation in theCeratozamia mexicanaBrongn. (Zamiaceae) complex: evolutionary and taxonomic implications

“…Either through the lens of 'classical' population genetics (Gonz alez-Astorga et al, 2003b, 2005, 2006 or through phylogeography (Huang et al, 2001;Chiang et al, 2009;Kyoda & Setoguchi, 2010;Zhan et al, 2011;Guti errez-Ortega, Kajita & Molinar-Freaner, 2014;Nolasco-Soto et al, 2015), the results of further work in this direction will allow the construction of ancestor-descendant hypotheses involving known populations, as well as the assessment of demographic history and genetic differentiation between these populations. In accordance with our population-genetic research programme, evolutionary inferences derived from these phylogeographical interventions will constitute the starting point in species recognition and circumscription.…”

Temperate origin and diversification via southward colonization in Fatsia (Araliaceae), an insular endemic genus of the West Pacific Rim

“…Chen and Cycas revoluta Thunb. Chiang et al 2009), and Gentiana L. species (Chen 2000), display a pattern of colonization from the Asian continent eastward to Taiwan, and subsequently to the islands of the Ryukyu Archipelagos. Compared to ancestral populations on the mainland, one expects island populations to maintain lower genetic variability as the result of smaller population sizes and numbers due to habitat limitation on islands as well as genetic bottlenecks associated with colonization.…”