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A molecular phylogeny of the Old World cypresses (Cupressus: Cupressaceae): evidence from nuclear and chloroplast DNA sequences

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Abstract

Studies of phylogenetic relationships among cypresses of the Old World (Cupressus; Cupressaceae) have been plagued by unresolved relationships, poor branch support, and conflict between data sets and methods of analysis. In this study, we combined 5.4 kb of aligned DNA sequence and 157 binary characters with previously published data in examining phylogenetic relationships among Cupressus species. Bayesian and parsimony analysis of the combined data or of the nuclear data alone always recovered three principal clades of Cupressus; however, tests of phylogenetic incongruence could not distinguish between competing relationships among the three principal Cupressus lineages. In contrast, incongruence tests often found statistically significant conflict between the nuclear and plastid data, particularly with respect to the placement of C. chengiana. Consistent with previous studies and prevailing taxonomic opinion, we find C. darjeelingensis more closely related to cypresses of the New World (Hesperocyparis). In contrast, we placed accessions of C. assamica and C. tonkinensis, two putatively Old World species suggested to be misidentified New World taxa by some authors, within well-supported Old World clades. Statistical analysis of genetic distances suggests instances in which taxa recognized as distinct species by some authors are identical or nearly so and may best be considered a single taxon. Conversely, we identify instances in which infraspecific taxa are more distantly related to one another than those traditionally recognized as distinct species. Factors confounding cypress taxonomies, including poor morphological differentiation, misidentification, and the use of accessions of questionable provenance, are discussed.

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Acknowledgements

We thank Bob Adams for providing leaf tissue and helpful comments on the manuscript. We also thank an anonymous reviewer for many comments helpful in improving the manuscript. This work was funded in part by a Research Enhancement Grant awarded to RGT through the College of Arts and Sciences, Lamar University. Support from the Lamar University Department of Biology is gratefully acknowledged.

Funding

This study was funded by a Research Enhancement (REG2011) from Lamar University to RGT.

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Authors and Affiliations

  1. Biology Department, Lamar University, P.O. Box 10037, Beaumont, TX, 77710, USA

    Randall G. Terry

  2. Department of Health and Biomedical Sciences, University of Texas-Rio Grande Valley, One West Blvd., Brownsville, TX, 78520, USA

    Andrea E. Schwarzbach

  3. San Diego Botanic Garden, P.O. Box 230005, Encinitas, CA, 92023, USA

    Jim A. Bartel

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  1. Randall G. Terry
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  2. Andrea E. Schwarzbach
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Correspondence to Randall G. Terry.

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Handling Editor: Jürg Schönenberger.

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Online Resource 1. Combined nuclear and chloroplast DNA data with binary characters in Nexus format.

Online Resource 2. Nuclear or chloroplast DNA data (depending on exclusion set) with binary characters in Nexus format.

Online Resource 3. Nuclear and chloroplast DNA data with binary characters used in distance analyses.

Online Resource 4. Voucher and source information for outgroups and a listing of outgroup and non-ingroup taxa used in the various analyses presented here.

Online Resource 5. Features of the parsimony analyses and trees presented in this study.

Online Resource 6. Output from analysis of the nuclear data.

Online Resource 7. Output from analysis of the nuclear and chloroplast data combined.

Online Resource 8. Topologies used to generate constraints, the analyses constrained, and results from parsimony-based and maximum likelihood-based tests of topological incongruence.

Online Resource 9. Output from analysis of the chloroplast data.

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Terry, R.G., Schwarzbach, A.E. & Bartel, J.A. A molecular phylogeny of the Old World cypresses (Cupressus: Cupressaceae): evidence from nuclear and chloroplast DNA sequences. Plant Syst Evol 304, 1181–1197 (2018). https://doi.org/10.1007/s00606-018-1540-1

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