Lineage diversification and hybridization in the Cayratia japonicaCayratia tenuifolia species complex

https://doi.org/10.1016/j.ympev.2014.01.027Get rights and content

Highlights

  • Phylogenetic relationships in the Cayratia japonicaCayratia tenuifolia species complex were resolved.

  • Accessions from Australia and Asia formed distinct monophyletic clades.

  • Details of cryptic divergences and hybridizations in the Asian group were revealed.

  • Major divergences within the Asian clade likely occurred in the Tertiary era.

Abstract

The Cayratia japonicaCayratia tenuifolia species complex (Vitaceae) is distributed from temperate to tropical East Asia, Southeast Asia, India, and Australia. The spatiotemporal diversification history of this complex was assessed through phylogenetic and biogeographic analyses. Maximum parsimony, neighbor-joining, and maximum likelihood methods were used to analyze sequences of one nuclear (AS1) and two plastid regions (trnL-F and trnC-petN). Bayesian dating analysis was conducted to estimate the divergence times of clades. The likelihood method LAGRANGE was used to infer ancestral areas. The Asian C. japonica and C. tenuifolia should be treated as an unresolved complex, and Australian C. japonica is distinct from the Asian C. japonicaC. tenuifolia species complex and should be treated as separate taxa. The Asian C. japonicaC. tenuifolia species complex was estimated to have diverged from its closest relatives during the Late Eocene (35.1 million years ago [Ma], 95% highest posterior densities [HPD] = 23.3–47.3 Ma) and most likely first diverged in mid-continental Asia. This complex was first divided into a northern clade and a southern clade during the middle Oligocene (27.3 Ma; 95% HPD = 17.4–38.1 Ma), which is consistent with a large southeastward extrusion of the Indochina region relative to South China along the Red River. Each of the northern and southern clades then further diverged into multiple subclades through a series of dispersal and divergence events following significant geological and climatic changes in East and Southeast Asia during the Miocene. Multiple inter-lineage hybridizations among four lineages were inferred to have occurred following this diversification process, which caused some Asian lineages to be morphologically cryptic.

Introduction

The Sino-Japanese floristic region in temperate Asia has remarkably rich biodiversity compared to other temperate floristic regions worldwide. The high species richness of the region is explained by its climatic diversity, complex topography, complex geological history, and the absence of major extinctions during Quaternary glaciations (Qian and Ricklefs, 2000, Harrison et al., 2001, Milne and Abbott, 2002, Milne, 2006, Qiu et al., 2011). Adjacent to temperate Asia, tropical Asia (Indo-Burma and Sundaland) is also known for high biodiversity (Myers et al., 2000). In addition to the high rates of endemics in these floristic regions, some species are widely distributed across the regions. Those species have previously received little attention; however, recent advances in molecular analyses have made it possible to reveal hidden lineages within a species (e.g., Qiu et al., 2011). Phylogeographic analyses of such species may reveal how they spread across floristic regions and help to clarify the geological histories of temperate and tropical Asia.

Cayratia Jussieu (Vitaceae) comprises over 60 species, occurring mainly in tropical and subtropical Asia, Africa, Australasia, and the Pacific islands (Wen, 2007, Lu et al., 2013). Cayratia japonica (Thunb.) Gagnep. is distributed from the temperate to tropical regions of East Asia, Southeast Asia, India, and Australia (Jackes, 1987, Ohba, 1999, Hui and Wen, 2007). Two intraspecific varieties are recognized in China: C. japonica var. pseudotrifolia (W.T. Wang) C.L. Li and C. japonica var. mollis (Wallich ex M.A. Lawson) Momiyama (Hui and Wen, 2007). Cayratia tenuifolia (Wight & Arn.) Gagnep. occurs in the Japanese islands of Kyushu and the Ryukyus, as well as in Taiwan, the Malay Peninsula, and Borneo. It was morphologically distinguished from C. japonica by differences in dentate leaflet margins (Hatusima and Amano, 1967, Hatusima, 1971) and was treated as a synonym of C. japonica var. dentata (Makino) Honda (Makino, 1909, Ohba, 1999). Okada et al. (2007) suggested that C. tenuifolia might be distinguished from C. japonica by differences in the color of the floral disc at anthesis: specifically, yellow in C. tenuifolia and orange in C. japonica.

The chromosome number of C. japonica has been reported as 2n = 40 in China (Huang et al., 1988). Both C. japonica and C. tenuifolia contain diploids (2n = 2x = 40) and triploids (2n = 3x = 60) in Japan (Okada et al., 2003, Okada et al., 2005, Okada et al., 2007, Tsukaya et al., 2012). Consistent with triploids in other species, the triploids of C. japonica and C. tenuifolia have low fertilities and rarely bear fruit. Moreover, the diploid C. japonica of Honshu, Japan, has variable pollen fertility (31–97%; Okada et al., 2003) and is often unable to produce seeds. Both C. japonica and C. tenuifolia readily propagate vegetatively, and thus some individuals of the species were assumed to spread through vegetative clones in Japan (Okada et al., 2003).

In a previous study, we explored the origins of triploids of C. japonica and C. tenuifolia in Japan using the single-copy nuclear gene ASYMMETRIC LEAVES 1 (AS1) (Tsukaya et al., 2012). According to the phylogenetic investigation, alleles were divided into three distinct lineages, the majority of which were shared by C. japonica and C. tenuifolia. These results suggested that the two species were not phylogeneticaly distinct from each other and may be members of a species complex (Tsukaya et al., 2012). In addition, the majority of diploids and all triploids were heterozygous for the AS1 genotypes and consisted of two alleles with distinct lineages, suggesting that lineage diversifications were followed by lineage admixtures through hybridizations. Furthermore, triploids of each species originated from independent hybridizations.

Only a few studies have examined this species complex in other regions. In Australia, C. japonica is found along the east coast of Queensland (Jackes, 1987). Although phylogenetic relationships between Australasian C. japonica and other Australian species of Vitaceae were investigated (Rossetto et al., 2001, Rossetto et al., 2007), the analysis did not include the Asian C. japonica. The phylogenetic relationship between C. japonica in Australia and Asia has not yet been examined.

In this study, we used expanded taxon sampling and additional molecular markers to determine the phylogenetic relationships among the C. japonica–C. tenuifolia species complex across most of its distribution. Details of divergences and hybridizations among major lineages were assessed. Divergence times of the main lineages and the ancestral area of the species complex were estimated, and the divergence history of this clade was also investigated. The species complex is widely distributed across temperate to tropical regions from East Asia to Australia and provides an appropriate model system for determining the origins of intraspecies complex lineages.

Section snippets

Materials and determinations of ploidy levels

Cayratia japonica and C. tenuifolia were treated as members of the C. japonicaC. tenuifolia species complex in the present study, as suggested by Tsukaya et al. (2012). We collected 116 accessions of the C. japonicaC. tenuifolia species complex from native habitats in Australia, China, Japan, Korea, Taiwan, Indonesia, Malaysia, and Myanmar (details of accessions are shown in Supplementary Table 1). Both C. japonica var. pseudotrifolia and C. japonica var. mollis were included (Supplementary

Haplotypes of cpDNA (trnL-F and trnC-petN) and phylogeny

Nucleotide sequences of trnL-F and trnC-petN were determined for 112 accessions (Supplementary Table 1). Four nucleotide sequences were obtained from GenBank (Supplementary Table 1, ID Nos. 112–115). In total, 27 unique trnL-F types (trnLF-1–trnLF-27) and 20 unique trnC-petN types (trnCpetN-1–trnCpetN-20) were identified. Accession numbers of these types are listed in Supplementary Table 3. The combined trnL-F and trnC-petN produced 34 unique haplotypes (HT1–HT34), which are provided in

Asian C. japonica–C. tenuifolia species complex

Phylogenetic analysis of cpDNA revealed a set of well-resolved and highly supported clades within the monophyletic Asian C. japonicaC. tenuifolia species complex (Fig. 1, e.g., CP1.1 and CP1.2). However, we observed no morphological distinctions among the lineages, and thus the diversification was cryptic. According to the AS1 analysis, the Asian lineage was divided into seven subclades (subclades A–G; Fig. 3). Four different heterozygous genotypes composed of two alleles in the different

Conclusions

We performed phylogenetic analysis of the C. japonicaC. tenuifolia species complex using the nuclear-encoded AS1 and two cpDNA loci. Three major conclusions emerged from this analysis. First, distinct monophyly of Asian and Australian lineages was determined (Fig. 1, Fig. 3). Second, two major lineages of cpDNA diverged in mid-continental Asia during the Tertiary (Clade-CP1.1 and Clade-CP1.2). The extrusion of Indochina from southeastern China during the Oligo–Miocene might have been

Acknowledgments

This study was supported by a Grant-in-Aid for Scientific Research from the Japan Society for the Promotion of Science. We express our thanks to Dr. D. Li (Kunming Institute of Botany) for arranging our field study in Yunnan, China. We also thank the Secretariat of Permission for Foreign Research, the Ministry of Research and Technology, Republic of Indonesia (RISTEK), the Indonesian Institute of Science (LIPI), and the Betung Kerihun National Park office for allowing this study to take place

References (61)

  • D. Darriba et al.

    JModelTest 2: more models, new heuristics and parallel computing

    Nat. Methods

    (2012)
  • A.J. Drummond et al.

    A Rough Guide to BEAST 1.4

    (2007)
  • J.S. Farris

    The retention index and the rescaled consistency index

    Cladistics

    (1989)
  • J. Felsenstein

    Confidence limits on phylogenies: an approach using the bootstrap

    Evolution

    (1985)
  • R. Hall

    Reconstructing Cenozoic SE Asia

  • R. Hall

    Plate tectonics of Cenozoic SE Asia and the distribution of land and sea

  • R. Hall

    Southeast Asia’s changing palaeogeography

    Blumea

    (2009)
  • S.P. Harrison et al.

    Palaeovegetation: diversity of temperate plants in East Asia

    Nature

    (2001)
  • Hatusima, S., 1971. Flora of the Ryukyus. Okinawa Seibutsu Kyouiku Kenkyukai, Naha (in...
  • Hatusima, S., Amano, T., 1967. Flora of Okinawa. Okinawa Association of Biology Education (in...
  • D.D. Hinsinger et al.

    The phylogeny and biogeographic history of Ashes (Fraxinus, Oleaceae) highlight the roles of migration and vicariance in the diversification of temperate trees

    PLoS ONE

    (2013)
  • T.W. Hsu et al.

    Cayratia maritima B.R. Jackes (Vitaceae), a new addition to the flora of Taiwan

    Bot. Bull. Acad. Sin. (Taiwan)

    (1999)
  • S.F. Huang et al.

    Plant chromosome counts (4)

    Subtrop. Forest Sci. Technol.

    (1988)
  • R. Hui et al.

    Cayratia

  • N. Ishikawa et al.

    Molecular evidence of reticulate evolution in the subgenus Plantago (Plantaginaceae)

    Am. J. Bot.

    (2009)
  • B.R. Jackes

    Revision of the Australian Vitaceae, 2. Cayratia Juss

    Austrobaileya

    (1987)
  • G. Jobb et al.

    TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics

    BMC Evol. Biol.

    (2004)
  • R. Kass et al.

    Bayes factors

    J. Am. Stat. Assoc.

    (1995)
  • K. Kizaki et al.

    Paleogeography of the Ryukyu Islands

    Marine Sci. Monthly

    (1977)
  • A.G. Kluge et al.

    Quantitative phyletics and the evolution of Anurans

    Syst. Zool.

    (1969)
  • View full text