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Nested clade analysis of Dunnia sinensis (Rubiaceae), a monotypic genus from China based on organelle DNA sequences

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Abstract

Dunnia sinensis, a monotypic genus of theRubiaceae endemic to the southeast mainlandChina, is an endangered species due to habitatdestruction over the past decades. Informationon levels and apportionment of geneticvariation across populations and geographicalregions is fundamental to conservation. In thepresent study, we used organelle DNA variationand nested phylogeographic analyses to test theisolation-by-distance model in this specieswith wind-mediated seed-dispersal and todistinguish ongoing gene flow from historicalprocesses. As expected, low levels of geneticvariation were detected at the ribosomal ITSregion of mtDNA (θ = 0.0019± 0.0002) and the atpB-rbcLintergenic spacer of cpDNA (θ =0.0022 ± 0.0009) in the rare species. Sixand seven haplotypes of mt- and cpDNA wereidentified from 125 individuals, respectively,according to the reconstructed neighbor-joiningtrees. Both data sets suggested consistentphylogenies that recovered two differentiatedlineages corresponding to western (Yangchun)and eastern (four others populations) portionsof the range. Hierarchical analyses of themolecular variance (AMOVA) of mt- and cpDNAindicated that molecular variance wasattributable to the difference between regions(Φct = 0.911 and 0.771 for mt- and cpDNA,respectively) in D. sinensis. Based ongeographic distributions of haplotypes in thehaplotype networks, significant geneticdifferentiation between the two geographicregions, which can be seen as evolutionarilyconservation units, was associated withhistorical fragmentation. In contrast, limitedgene flow with occasional long-range dispersalshaped the apportionment of organelle DNAalleles among populations of the easternregion, within which two incompletely isolatedphylogeographic groups can be recognized asconservation units for management.

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References

  • Bossart JL, Prowell DP (1998) Genetic estimates of population structure and gene flow, limitations, lessons and new directions. Trends in Ecology and Evolution, 13, 202–206.

    Google Scholar 

  • Caron H, Dumas S, Marque G, Messier C, Bandou E, Petit RJ, Kremer A (2000) Spatial and temporal distribution of chloroplast DNA polymorphism in a tropical tree species. Molecular Ecology, 9, 1089–1098.

    Google Scholar 

  • Chao S, Sederoff R, Levings III CS (1984) Nucleotide sequence and evolution of the 18S ribosomal RNA gene in maize mitochondria. Nucleic Acids Research, 12, 6629–6644.

    Google Scholar 

  • Chiang TY (2000) Lineage sorting accounting for the disassociation between chloroplast and Mictochondrial lineages in oaks of southern France. Genome, 43, 1–5.

    Google Scholar 

  • Chiang TY, Schaal BA (1999) Phylogeography of North American populations of the moss species Hylocomium splendens based on the nucleotide sequence of internal transcribed spacer 2 of nuclear ribosomal DNA. Molecular Ecology, 8, 1037–1042.

    Google Scholar 

  • Chiang TY, Schaal BA, Peng CI (1998) Universal primers for amplification and sequencing a noncoding spacer between atpB and rbcL genes of chloroplast DNA. Botanical Bulletin of Academia Sinica, 39, 245–250.

    Google Scholar 

  • Chiang TY, Chiang YC, Chen YJ, Chou CH, Havanond S, Hong TN, Huang S (2001) Phylogeography of Kandelia candel in east Asiatic mangroves based on nucleotide variation of chloroplast and mitochondrial DNAs. Molecular Ecology, 10, 2697–2710.

    Google Scholar 

  • Crandall KA, Templeton AR (1993) Empirical tests of some predictions from coalescent theory with applications to intraspecific phylogeny reconstruction. Genetics, 134, 959–969.

    Google Scholar 

  • Donnelly P, Tavare S (1986) The ages of alleles and a coalescent. Advances in Applied Probability, 18, 1–19.

    Google Scholar 

  • Dumolin-Lapegue S, Demesure B, Fineschi S, Le Corre V, Petit RJ (1997) Phylogeographic structure of the white oaks throughout the European continent. Genetics, 146, 1475–1487.

    Google Scholar 

  • Dumolin-Lapègue S, Pemonge MH, Petit RJ (1998) Association between chloroplast and mitochondrial lineages in oaks. Molecular Biology and Evolution, 15, 1321–1331.

    Google Scholar 

  • Desplanque BF, Viard J, Bernard D, Forcioli P, Saumitou-Laprade J, Cuguen H, van Dijk H (2000) The linkage disequilibrium between chloroplast DNA and mitochondrial DNA haplotypes in Beta vulgaris ssp. maritima (L.), the usefulness of both genomes for population genetic studies. Molecular Ecology, 9, 141–154.

    Google Scholar 

  • El Mousadik A, Petit RJ (1996) Chloroplast DNA phylogeography of the argan tree of Morocco. Molecular Ecology, 5, 547–555.

    Google Scholar 

  • Excoffier L (1993) Analysis of Molecular Variance. Version 1.5.5. Genetics and Biometry Laboratory, University of Geneva.

  • Excoffier L, Smouse PE (1994) Using allele frequencies and geographic subdivision to reconstruct gene trees within a species, molecular variance parsimony. Genetics, 136, 343–359.

    Google Scholar 

  • Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes, Application to human mitochondrial DNA restriction data. Genetics, 131, 479–491.

    Google Scholar 

  • Felsenstein J (1985) Confidence limits on phylogenies, an approach using the bootstrap. Evolution, 39, 783–791.

    Google Scholar 

  • Fauron CMR, Moore B, Casper M (1995) Maize as a model on higher plant mitochondrial genome plasticity. Plant Science, 112, 11–32.

    Google Scholar 

  • Fu LG (1992) The Red Book of Chinese Plants – Rare and Endangered Plants. Science Press, Beijing.

    Google Scholar 

  • Ge XJ (1998) The identity of Dunnia assamica (Hook. f.) Ridsd. (Rubiaceae). Journal of Tropical and Subtropical Botany, 6, 47–48.

    Google Scholar 

  • Golding GB (1987) The detection of deleterious selection using ancestors inferred from a phylogenetic history. Genetic Research, 49, 71–82.

    Google Scholar 

  • Harris SA, Ingram R (1991) Chloroplast DNA and biosystematics, the effects of intraspecific diversity and plasmid transmission. Taxon, 40, 393–421.

    Google Scholar 

  • Hewitt GM (1996) Some genetic consequences of ice ages, and their role in divergence and speciation. Biological Journal of Linnean Society, 58, 247–276.

    Google Scholar 

  • Hewitt GM (1999) Post-glacial re-colonization of European biota. Biological Journal of Linnean Society, 68, 247–276.

    Google Scholar 

  • Hillis DM, Bull JJ (1993) An empirical test of bootstrapping as a method assessing confidence in phylogenetic analysis. Systematic Biology, 41, 182–192.

    Google Scholar 

  • Huang S, Chiang YC, Schaal BA, Chou CH, Chiang TY (2001) Organelle DANs phylogeography of Cycas taitungensis, a relict species in Taiwan. Molecular Ecology, 10, 2669–2681.

    Google Scholar 

  • Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Mammalian Protein Metabolism (ed. Munroled HN), pp. 31–132. Academic Press, New York.

    Google Scholar 

  • Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16, 111–120.

    Google Scholar 

  • King RA, Ferris C (1998) Chloroplast DNA phylogeography of Alnus glutinosa (L.) Gaertn. Molecular Ecology, 7, 1151–1161.

    Google Scholar 

  • Kumar S, Tamura K, Nei M (1993) MEGA, Molecular Evolutionary Genetics Analysis. Version 1.01. The Pennsylvania State University, University Park, PA 16802.

    Google Scholar 

  • Lu SY, Peng CI, Cheng YP, Hong KH, Chiang TY (2001) Chloroplast DNA phylogeography of Cunninghamia konishii (Cupressaceae), an endemic conifer of Taiwan. Genome, 44, 797–807.

    Google Scholar 

  • Luo H, van Coppenolle B, Seguin M, Boutry M (1995) Mitochondrial DNA polymorphism and phylogenetic relationships in Hevea brasiliensis. Molecular Breeding, 1, 51–63.

    Google Scholar 

  • Manicacci D, Couvet D, Belhassen E, Gouyon PH, Atlan A (1996) Founder effects and sex ratio in the gyndioeciuos Thymus vulgaris L. Molecular Ecology, 5, 63–72.

    Google Scholar 

  • Maskas SD, Cruzan MB (2000) Patterns of intraspecific diversification in the Piriqueta caroliniana complex in southeastern North America and Bahamas. Evolution, 54, 815–827.

    Google Scholar 

  • Moritz C (1994) Defining ‘Evolutionarily Significant Units’ for conservation. Trends in Ecology and Evolution, 9, 373–375.

    Google Scholar 

  • Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight DNA. Nucleic Acids Research, 8, 4321–4325.

    Google Scholar 

  • Nei M, Tajima F (1983) Maximum likelihood estimation of the number of nucleotide substitutions from restriction sites data. Genetics, 105, 207–217.

    Google Scholar 

  • Posada D, Crandall KA, Templeton AR (2000) GeoDis, a program for the cladistic nested analysis of the geographical distribution of genetic haplotypes. Molecular Ecology, 9, 487–488.

    Google Scholar 

  • Ridsdale CE (1978) The taxonomic position of Dunnia (Rubiaceae). Blumea, 24, 367–368.

    Google Scholar 

  • Ronfort J, Saumitou-Laprade P, Cuguen J, Couvet D (1995) Mitochondrial DNA diversity and male sterility in natural populations of Daucus carota ssp carota. Theoretical Applied Genetics, 91, 150–159.

    Google Scholar 

  • Rozas J, Rozas R (1999) DnaSP version 3, an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics, 15, 174–175.

    Google Scholar 

  • Schaal BA, Olsen KM (2000) Gene genealogies and population variation in plants. Proceedings of National Academy of Sciences of the United States of America, 97, 7024–7029.

    Google Scholar 

  • Schaal BA, Hayworth DA, Olsen KM, Rauscher JT, Smith WA (1998) Phylogeographic studies in plants, problems and prospects. Molecular Ecology, 7, 465–474.

    Google Scholar 

  • Schnabel A, Asmussen JA (1989) Definition and properties of disequilibrium within nuclear-mitochondrial-chloroplast and other nuclear-dicytoplasmic systems. Genetics, 123, 199–215.

    Google Scholar 

  • Senda M, Onodera Y, Mikami T (1998) Recombination events across the atpA-associated repeated sequences in the mitochondrial genomes of beets. Theoretical and Applied Genetics, 96, 964–968.

    Google Scholar 

  • Slatkin M (1993) Isolation by distance in equilibrium and nonequilibrium populations. Evolution, 47, 264–279.

    Google Scholar 

  • Stern DB, Palmer JD (1984) Recombination sequences in plant mitochondrial genomes, diversity and homologies to known mitochondrial genes. Nucleic Acids Research, 12, 6141–6157.

    Google Scholar 

  • Templeton AR (1998) Nested clade analyses of phylogeographic data, Testing hypotheses about gene flow and population history. Molecular Ecology, 7, 381–397.

    Google Scholar 

  • Templeton AR, Routman E, Phillips CA (1995) Separating population structure from population history, a cladistic analysis the geographical distribution of mitochondrial DNA haplotypes in the tiger salamander, Ambystoma tigrinum. Genetics, 140, 767–782.

    Google Scholar 

  • Whitlock MC, MaCauley D (1999) Indirect measures of gene flow and migration, Fst ≠ 1/(4Nm + 1). Heredity, 82, 117–125.

    Google Scholar 

  • Xia X (1999) Data Analysis in Molecular Biology and Evolution. Version 3. 5. 19. Department of Ecology and Biodiversity, University of Hong-Kong.

  • Yesodi V, Izhar S, Hauschner H, Tabib Y, Firon N (1997) Homologous recombination invloving cox2 is responsible for a mutation in the cmS-specific mitochondrial locus of Petunia. Molecular & General Genetics, 255, 106–114.

    Google Scholar 

Download references

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Authors and Affiliations

  1. South China Institute of Botany, Chinese Academy of Sciences, Guangzhou, 510650, P.R. China

    X.-J. Ge

  2. Department of Biology, Taiwan Normal University, Taipei

    Y.-C. Chiang

  3. Institute of Botany, Academia Sinica, Taipei, Taiwan, 115

    C.-H. Chou

  4. Departmet of Biology, Cheng-Kung University, Tainan, Taiwan, 701 (Author for correspondence: Fax

    T.-Y. Chiang

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  1. X.-J. Ge
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  2. Y.-C. Chiang
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  3. C.-H. Chou
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  4. T.-Y. Chiang
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Correspondence to T.-Y. Chiang.

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Ge, XJ., Chiang, YC., Chou, CH. et al. Nested clade analysis of Dunnia sinensis (Rubiaceae), a monotypic genus from China based on organelle DNA sequences. Conservation Genetics 3, 351–362 (2002). https://doi.org/10.1023/A:1020579617678

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