Skip to main content

Advertisement

SpringerLink
Log in

Phylogeography and conservation genetics of Hygrophila pogonocalyx (Acanthaceae) based on atpB–rbcL noncoding spacer cpDNA

  • Original Article
  • Published:
Journal of Plant Research Aims and scope Submit manuscript

Abstract

Genetic variation in the atpB–rbcL intergenic spacer region of chloroplast DNA (cpDNA) was investigated in Hygrophila pogonocalyx Hayata (Acanthaceae), an endangered and endemic species in Taiwan. In this aquatic species, seed dispersal from capsules via elasticity is constrained by gravity and is thereby confined within populations, resulting in limited gene flow between populations. In this study, a total of 849 bp of the cpDNA atpB–rbcL spacer were sequenced from eight populations of H. pogonocalyx. Nucleotide diversity in the cpDNA is low (θ=0.00343±0.00041). The distribution of genetic variation among populations agrees with an “isolation-by-distance” model. Two geographically correlated groups, the western and eastern regions, were identified in a neighbor-joining tree and a minimum-spanning network. Phylogeographical analyses based on the cpDNA network suggest that the present-day differentiation between western and eastern groups of H. pogonocalyx resulted from past fragmentation. The differentiation between eastern and western populations may be ascribed to isolation since the formation of the Central Mountain Range about 5 million years ago, which is consistent with the rate estimates based on a molecular clock of cpDNA.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Avise JC (2000) Phylogeography: the history and formation of species. Harvard University Press, Cambridge

    Google Scholar 

  • Avise JC, Arnold J, Ball RM, Bermingham E, Lamb T, Neigel JE, Reeb CA, Saunders NC (1987) Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annu Rev Ecol Syst 18:489–522

    Google Scholar 

  • Bermingham E, Avise JC (1986) Molecular zoogeography of freshwater fishes in the southeastern United States. Genetics 113:939–965

    CAS  Google Scholar 

  • Birky CW Jr (1995) Uniparental inheritance of mitochondrial and chloroplast genes: mechanisms and evolution. Proc Natl Acad Sci USA 92:11331–11338

    Google Scholar 

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

    Article  Google Scholar 

  • Chiang TY (2000) Lineage sorting accounting for the disassociation between chloroplast and mitochondrial lineages in oaks of southern France. Genome 43:1090–1094

    CAS  PubMed  Google Scholar 

  • Chiang TY, Schaal BA (2000a) The internal transcribed spacer 2 region of the nuclear ribosomal DNA and the phylogeny of the moss family Hylocomiaceae. Plant Syst Evol 224:127–137

    CAS  Google Scholar 

  • Chiang TY, Schaal BA (2000b) Molecular evolution of the atpB–rbcL noncoding spacer of chloroplast DNA in the moss family Hylocomiaceae. Bot Bull Acad Sin 41:85–92

    CAS  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. Bot Bull Acad Sin 39:245–250

    CAS  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. Mol Ecol 10:2697–2710

    Article  CAS  PubMed  Google Scholar 

  • Chiang TY, Hung KH, Hsu TW, Wu WL (2004) Lineage sorting and phylogeography in Lithocarpus formosanus and L. dodonaeifolius (Fagaceae) from Taiwan. Ann MO Bot Gard 91:207–222

    Google Scholar 

  • Cruzan MB, Templeton AR (2000) Paleoecology and coalescence: phylogeographic analysis of hypotheses from the fossil record. Trends Ecol Evol 15:491–496

    PubMed  Google Scholar 

  • Doyle JJ, Doyle JL (1987) A rapid isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15

    Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

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

    Google Scholar 

  • Felsenstein J (1993) PHYLIP (Phylogeny Inference Package) version 3.6a2. Distributed by the author. Department of Genetics, University of Washington, Seattle

  • Frankham R, Ballou JD, Briscoe DA (2002) Introduction to conservation genetics. Cambridge University Press, Cambridge, pp 175–196

    Google Scholar 

  • Futuyma DJ (1998) Evolutionary biology, 3rd edn. Sinauer, Sunderland

    Google Scholar 

  • Ge XJ, Chiang YC, Chou CH, Chiang TY (2002) Nested clade analysis of Dunnia sinensis (Rubiaceae), a monotypic genus from China based on organelle DNA sequences. Conserv Genet 3:351–362

    CAS  Google Scholar 

  • Grassly NC, Holmes EC (1997) A likelihood method for the detection of selection and recombination using nucleotide sequences. Mol Biol Evol 9:366–369

    Google Scholar 

  • Hamrick JL, Godt MJ (1989) Allozyme diversity in plant species. In: Brown AHD, Clegg MT, Kahler AL, Weir BS (eds) Plant population genetics, breeding and genetic resources. Sinauer, Sunderland, pp 43–63

    Google Scholar 

  • Hanski IA, Gilpin ME (1997) Metapopulation biology: ecology, genetics, and evolution. Academic, Orlando

    Google Scholar 

  • Hawkins JA, Harris SA (1998) RAPD characterization of two neotropical hybrid legumes. Plant Syst Evol 213:11–34

    Google Scholar 

  • Hedrick PW (1983) Genetics of populations. Science Book International, Boston

    Google Scholar 

  • Hewitt GM (2000) The genetic legacy of the Quaternary ice ages. Nature 405:907–913

    Article  CAS  PubMed  Google Scholar 

  • Hoelzer GA, Wallman J, Melnick DJ (1998) The effects of social structure, geographical structure, and population size on the evolution of mitochondrial DNA. II. Molecular clocks and the lineage sorting period. J Mol Evol 47:21–31

    CAS  PubMed  Google Scholar 

  • Hsieh CF, Huang TC (1974) The Acanthaceous plants of Taiwan. Taiwania 19:19–57

    Google Scholar 

  • Huang JC, Wang WK, Chiang TY (2001a) Population differentiation and phylogeography of Hygrophila pogonocalyx based on RAPDs fingerprint. Aquat Bot 70:269–280

    CAS  Google Scholar 

  • Huang S, Chiang YC, Schaal BA, Chou CH, Chiang TY (2001b) Organelle DNA phylogeography of Cycas taitungensis, a relict species in Taiwan. Mol Ecol 10:2669–2681

    Article  CAS  PubMed  Google Scholar 

  • Hudson RR (1990) Gene genealogies and the coalescent process. In: Futuyma DJ, Antonovices J (eds) Oxford survey of evolutionary biology. Oxford University Press, New York, pp 1–44

    Google Scholar 

  • IUCN (International Union for Conservation of Nature and Natural Resources) (1997) Red list of threatened plants. IUCN, Gland, Switzerland

    Google Scholar 

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

    Google Scholar 

  • Kanno M, Yokoyama J, Suyama Y, Ohyama M, Itoh T, Suzuki M (2003) Geographical distribution of two haplotypes of chloroplast DNA in four oak species (Quercus) in Japan. J Plant Res 116:311–317

    Google Scholar 

  • Kim HN, Harada K, Yamazaki T (1996) Isozyme polymorphism and genetic structure of a liverwort Conocephallum conicum. Genes Genet Syst 71:225–235

    CAS  Google Scholar 

  • Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

    CAS  PubMed  Google Scholar 

  • Kubo T, Satoh Y, Muro T, Kinoshita T, Mikami T (1995) Physical and gene organization of mitochondrial DNA from the fertile cytoplasm of sugarbeet (Beta vulgaris L). Curr Genet 28:235–241

    CAS  PubMed  Google Scholar 

  • Kumar S, Tamura K, Jakobsen IB, Nei M (2001) MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17:1244–1245

    Article  CAS  PubMed  Google Scholar 

  • Li WH (1997) Molecular evolution. Sinauer, Sunderland

    Google Scholar 

  • Liu TK, Chen YG, Chen WS, Jiang SH (2000) Rates of cooling and denudation of the Early Penglai Orogeny, Taiwan, as assessed by fission track constraints. Tectonophysics 320:69–82

    CAS  Google Scholar 

  • Lonsdale DM, Brears T, Hodge TP, Melville SE, Rottmann WH (1988) The plant mitochondrial genome: homologous recombinations as a mechanism for generating heterogeneity. Phil Trans R Soc Lond B Biol Sci 319:49–163

    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

    CAS  PubMed  Google Scholar 

  • Manen JF, Natali A (1995) Comparison of the evolution of ribulose-1, 5-biphosphate carboxylase (rbcL) and atpB–rbcL noncoding spacer sequences in a recent plant group, the tribe Rubieae (Rubiaceae). J Mol Evol 41:920–927

    CAS  PubMed  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

    CAS  PubMed  Google Scholar 

  • McCauley DE (1994) Contrasting the distribution of chloroplast DNA and allozyme polymorphisms among local populations of Silene alba: implications for studies of gene flow in plants. Proc Natl Acad Sci USA 91: 8127–8131

    Google Scholar 

  • McCauley DE (1995) The use of chloroplast DNA polymorphism in studies of gene flow in plants. Trends Ecol Evol 10:198–202

    Article  Google Scholar 

  • Moore WS (1995) Inferring phylogenies from mtDNA variation: mitochondrial-gene tree versus nuclear-gene trees. Evolution 49:718–726

    Google Scholar 

  • Moritz C (1994) Defining ‘evolutionarily significant units’ for conservation. Trends Ecol Evol 9:373–375

    Article  Google Scholar 

  • Moritz C (1995) Uses of molecular phylogenies for conservation. Phil Trans R Soc Lond B Biol Sci 349:113–118

    Google Scholar 

  • Moritz C, Faith DP (1998) Comparative phylogeography and the identification of genetically divergent areas for conservation. Mol Ecol 7:419–429

    Article  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Noruis MJ (1994) SPSS for Windows, version 6.0. Prentice Hall, Englewood Cliffs

  • Ohsako T, Ohnishi O (2000) Intra- and interspecific phylogeny of wild Fagopyrum (Polygonaceae) species based on nucleotide sequences of noncoding regions in chloroplast DNA. Am J Bot 87:573–582

    CAS  PubMed  Google Scholar 

  • Orive ME, Asmussen MA (2000) The effects of pollen and seed migration on nuclear-dicytoplasmic systems. II. A new method for estimating plant gene flow from joint nuclear-cytoplasmic data. Genetics 155:833–854

    CAS  PubMed  Google Scholar 

  • Ouborg NJ, Piquot Y, Groenendael JMVan (1999) Population genetics, molecular markers and the study of dispersal of plants. J Ecol 87:551–568

    Article  Google Scholar 

  • Peng CI, Liu SL, Chiang TY (1999) Conservation of Ludwigia × taiwanensis (Onagraceae) in Taiwan. Endem Spec Res 1:73–78

    Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Provan J, Powell W, Hollingsworth PM (2001) Chloroplast microsatellites: new tools for studies in plant ecology and evolution. Trends Ecol Evol 16:142–147

    PubMed  Google Scholar 

  • Ray N, Currat M, Excoffier L (2003) Intra-deme molecular diversity in spatially expanding populations. Mol Biol Evol 20:76–86

    CAS  PubMed  Google Scholar 

  • Rozas J, Rozas R (1999) DnaSP version 3.0: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15:174–175

    Article  CAS  PubMed  Google Scholar 

  • Sanderson MJ (2002) r8s: Analysis of rates (“r8s”) of evolution (and other stuff), version 1.5. Section of Evolution and Ecology, University of California, Davis. Distributed at http://ginger.ucdavis.edu/r8s/

  • Sarich VM, Wilson AC (1973) Generation time and genomic evolution in primates. Science 179:1144–1147

    CAS  PubMed  Google Scholar 

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

    Google Scholar 

  • Templeton AR (1998) Nested clade analyses of phylogeographic data: testing hypotheses about gene flow and population history. Mol Ecol 7:381–397

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Teng LS (1990) Geotectonic evolution of late Cenozoic arc-continent collision in Taiwan. Tectonophysics 183:57–76

    Article  Google Scholar 

  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24:4876–4882

    Article  Google Scholar 

  • Wang WK, Huang JC, Chiang TY (2000) Ecology and conservation of Hygrophila pogonocalyx, endemic species of Taiwan. Quart Nat Conserv 31:54–58

    Google Scholar 

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

    Article  PubMed  Google Scholar 

  • Wu CI, Li WH (1985) Evidence for higher rates of nucleotide substitution in rodents than in man. Proc Natl Acad Sci USA 82:1741–1745

    CAS  PubMed  Google Scholar 

  • Wu JC, Chiang TY, Shiue WK, Wang SY, Sheen IJ (1999) Recombination of hepatitis D virus RNA sequences and its implications. Mol Biol Evol 16:1622–1632

    CAS  PubMed  Google Scholar 

  • Zuckerkandl E, Pauling L (1965) Evolutionary divergence and convergence in proteins. In: Bryson V, Vogel HJ (eds) Evolving genes and proteins. Academic, New York, pp 97–166

    Google Scholar 

Download references

Acknowledgments

Financial support for this project was provided by the National Science Council and the Council of Agriculture, Taiwan. The authors thank Mei-Jane Fang of Academia Sinica for the technical assistance with nucleotide sequencing. We are indebted to two anonymous reviewers for their critical comments.

Author information

Authors and Affiliations

  1. Division of Botany, Taiwan Endemic Species Research Institute, Chi-Chi, Taiwan, 551

    Jao-Ching Huang

  2. Department of Life Sciences, Cheng-Kung University, Tainan, Taiwan, 701

    Wei-Kuang Wang & Tzen-Yuh Chiang

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

    Ching-I Peng

Authors
  1. Jao-Ching Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Wei-Kuang Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ching-I Peng
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Tzen-Yuh Chiang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Tzen-Yuh Chiang.

Additional information

Huang JC and Wang WK equally contributed to this work.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Huang, JC., Wang, WK., Peng, CI. et al. Phylogeography and conservation genetics of Hygrophila pogonocalyx (Acanthaceae) based on atpB–rbcL noncoding spacer cpDNA. J Plant Res 118, 1–11 (2005). https://doi.org/10.1007/s10265-004-0185-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10265-004-0185-z

Keywords

Search

Navigation