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

ABSTRACT: BACKGROUND:This 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. RESULTS:The 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. CONCLUSION:Fates 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.

SUBMITTER: Chiang YC

PROVIDER: S-EPMC3224665 | biostudies-literature | 2009 Jul

REPOSITORIES: biostudies-literature

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

Chiang Yu-Chung YC Hung Kuo-Hsiang KH Moore Shann-Jye SJ Ge Xue-Jun XJ Huang Shong S Hsu Tsai-Wen TW Schaal Barbara A BA Chiang Ty T

BMC evolutionary biology 20090710

<h4>Background</h4>This 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.<h4>Results</h4>The phy ...[more]

PMID: 19589178

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Project description:Two datasets, the geologic record and the genetic content of extant organisms, provide complementary insights into the history of how key molecular components have shaped or driven global environmental and macroevolutionary trends. Changes in global physico-chemical modes over time are thought to be a consistent feature of this relationship between Earth and life, as life is thought to have been optimizing protein functions for the entirety of its approximately 3.8 billion years of history on the Earth. Organismal survival depends on how well critical genetic and metabolic components can adapt to their environments, reflecting an ability to optimize efficiently to changing conditions. The geologic record provides an array of biologically independent indicators of macroscale atmospheric and oceanic composition, but provides little in the way of the exact behaviour of the molecular components that influenced the compositions of these reservoirs. By reconstructing sequences of proteins that might have been present in ancient organisms, we can downselect to a subset of possible sequences that may have been optimized to these ancient environmental conditions. How can one use modern life to reconstruct ancestral behaviours? Configurations of ancient sequences can be inferred from the diversity of extant sequences, and then resurrected in the laboratory to ascertain their biochemical attributes. One way to augment sequence-based, single-gene methods to obtain a richer and more reliable picture of the deep past, is to resurrect inferred ancestral protein sequences in living organisms, where their phenotypes can be exposed in a complex molecular-systems context, and then to link consequences of those phenotypes to biosignatures that were preserved in the independent historical repository of the geological record. As a first step beyond single-molecule reconstruction to the study of functional molecular systems, we present here the ancestral sequence reconstruction of the beta-carbonic anhydrase protein. We assess how carbonic anhydrase proteins meet our selection criteria for reconstructing ancient biosignatures in the laboratory, which we term palaeophenotype reconstruction.This article is part of the themed issue 'Reconceptualizing the origins of life'.

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

Publications

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

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