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      Adaptive molecular evolution of the two-pore channel 1 geneTPC1in the karst-adapted genusPrimulina(Gesneriaceae)

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      Annals of Botany
      Oxford University Press (OUP)

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          Abstract

          <p class="first" id="d2130035e165"> <b>Background and Aims</b> Limestone karst areas possess high floral diversity and endemism. The genus <i>Primulina</i>, which contributes to the unique calcicole flora, has high species richness and exhibit specific soil-based habitat associations that are mainly distributed on calcareous karst soils. The adaptive molecular evolutionary mechanism of the genus to karst calcium-rich environments is still not well understood. The Ca <sup>2+</sup>-permeable channel TPC1 was used in this study to test whether its gene is involved in the local adaptation of <i>Primulina</i> to karst high-calcium soil environments. </p><p id="d2130035e179"> <b>Methods</b> Specific amplification and sequencing primers were designed and used to amplify the full-length coding sequences of <i>TPC1</i> from cDNA of 76 <i>Primulina</i> species. The sequence alignment without recombination and the corresponding reconstructed phylogeny tree were used in molecular evolutionary analyses at the nucleic acid level and amino acid level, respectively. Finally, the identified sites under positive selection were labelled on the predicted secondary structure of TPC1. </p><p id="d2130035e190"> <b>Key Results</b> Seventy-six full-length coding sequences of <i>Primulina TPC1</i> were obtained. The length of the sequences varied between 2220 and 2286 bp and the insertion/deletion was located at the 5′ end of the sequences. No signal of substitution saturation was detected in the sequences, while significant recombination breakpoints were detected. The molecular evolutionary analyses showed that <i>TPC1</i> was dominated by purifying selection and the selective pressures were not significantly different among species lineages. However, significant signals of positive selection were detected at both <i>TPC1</i> codon level and amino acid level, and five sites under positive selective pressure were identified by at least three different methods. </p><p id="d2130035e204"> <b>Conclusions</b> The Ca <sup>2+</sup>-permeable channel <i>TPC1</i> may be involved in the local adaptation of <i>Primulina</i> to karst Ca <sup>2+</sup>-rich environments. Different species lineages suffered similar selective pressure associated with calcium in karst environments, and episodic diversifying selection at a few sites may play a major role in the molecular evolution of <i>Primulina TPC1</i>. </p>

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          Most cited references43

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          TreeView: an application to display phylogenetic trees on personal computers.

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            Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology.

            Datamonkey is a popular web-based suite of phylogenetic analysis tools for use in evolutionary biology. Since the original release in 2005, we have expanded the analysis options to include recently developed algorithmic methods for recombination detection, evolutionary fingerprinting of genes, codon model selection, co-evolution between sites, identification of sites, which rapidly escape host-immune pressure and HIV-1 subtype assignment. The traditional selection tools have also been augmented to include recent developments in the field. Here, we summarize the analyses options currently available on Datamonkey, and provide guidelines for their use in evolutionary biology. Availability and documentation: http://www.datamonkey.org.
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              Statistical methods for detecting molecular adaptation.

              The past few years have seen the development of powerful statistical methods for detecting adaptive molecular evolution. These methods compare synonymous and nonsynonymous substitution rates in protein-coding genes, and regard a nonsynonymous rate elevated above the synonymous rate as evidence for darwinian selection. Numerous cases of molecular adaptation are being identified in various systems from viruses to humans. Although previous analyses averaging rates over sites and time have little power, recent methods designed to detect positive selection at individual sites and lineages have been successful. Here, we summarize recent statistical methods for detecting molecular adaptation, and discuss their limitations and possible improvements.
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                Author and article information

                Journal
                Annals of Botany
                Ann Bot
                Oxford University Press (OUP)
                0305-7364
                1095-8290
                December 14 2016
                December 30 2016
                : 118
                : 7
                : 1257-1268
                Article
                10.1093/aob/mcw168
                5155596
                27582362
                c2e3c6a4-c98c-4dba-b2c5-ad1eb6339813
                © 2016
                History

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