Evolution of Australian Cryptocarya (Lauraceae) based on nuclear and plastid phylogenetic trees: evidence of recent landscape-level disjunctions
Marlien van der Merwe A D , Darren M. Crayn B , Andrew J. Ford C , Peter H. Weston A and Maurizio Rossetto A
+ Author Affiliations
- Author Affiliations
A National Herbarium of New South Wales, The Royal Botanic Garden Sydney, Mrs Macquaries Road, Sydney, NSW 2000, Australia.
B Australian Tropical Herbarium, James Cook University, McGregor Road, Smithfield, Qld 4878, Australia.
C CSIRO Land and Water, Tropical Forest Research Centre, Atherton, Qld 4883, Australia.
D Corresponding author. Email: marlien.vandermerwe@rbgsyd.nsw.gov.au
Australian Systematic Botany 29(2) 157-166 https://doi.org/10.1071/SB16023
Submitted: 25 May 2016 Accepted: 25 August 2016 Published: 17 October 2016
Abstract
Species-level relationships within the pantropical, largely rainforest genus Cryptocarya R.Br (Lauraceae) and allied groups have long been problematic. Here, we utilise nuclear RPB2 and plastid trnL–trnF sequence data to reconstruct the phylogenetic relationships among Australian Cryptocarya species. We relate our findings to the previous two disparate attempts to resolve species-level relationships on the basis of traditional taxonomic tools. Our results showed that an early diversification gave rise to two lineages present in Australia and globally. The loss of cataphylls (bract-like leaves in seedlings) seems to be a derived state only found in the larger of these two clades. Ruminate cotyledons is another potentially informative character; however, it is highly likely that this condition arose through convergent or parallel evolution. Little or no molecular variation was observed between many species, which suggests recent diversification. Furthermore, the close relationships between species from two geographically disjunct centres of rainforest diversity within Australia suggests that loss of between-region connectivity is recent. A global revision of the group, incorporating molecular analyses and seedling and fruit morphology, is needed to untangle the complex evolutionary relationships within this genus.
Additional keywords: Australian rainforest flora, cataphylls, diversification, laurels, ribbed endocarp, ruminate cotyledons, RPB2, trnL–F.
References
Biffin E, Craven LA, Crisp MD, Gadek PA (2006) Molecular systematics of Syzygium and allied genera (Myrtaceae): evidence from the chloroplast genome. Taxon 55, 79–94.| Molecular systematics of Syzygium and allied genera (Myrtaceae): evidence from the chloroplast genome.Crossref | GoogleScholarGoogle Scholar |
Brown R (1810) Cryptocarya. In ‘Prodromus florae Novae Hollandiae et Insulae Van-Diemen, exhibens characteres plantarum. Londini: typis R. Taylor et socii’.
Byrne M, Steane D, Joseph L, Yeates D, Jordan GJ, Crayn D, Aplin K, Cantrill D, Cook LG, Crisp MD, Keogh JS, Melville J, Moritz C, Porch N, Sniderman JMK, Sunnucks P, Weston PH (2011) Decline of a biome: evolution, contraction, fragmentation, extinction and invasion of the Australian mesic zone biota. Journal of Biogeography 38, 1635–1656.
| Decline of a biome: evolution, contraction, fragmentation, extinction and invasion of the Australian mesic zone biota.Crossref | GoogleScholarGoogle Scholar |
Chanderbali AS, van der Werff H, Renner SS (2001) Phylogeny and historical biogeography of Lauraceae: evidence from the chloroplast and nuclear genomes. Annals of the Missouri Botanical Garden 88, 104–134.
| Phylogeny and historical biogeography of Lauraceae: evidence from the chloroplast and nuclear genomes.Crossref | GoogleScholarGoogle Scholar |
Christophel DC, Rowett ALI (1996) ‘Leaf and Cuticle Atlas of Australian Leafy Lauraceae. Flora of Australia, Supplementary Series Number 6.’ (Australian Biological Resources Study: Canberra)
Cooper WA (2013) Cryptocarya cercophylla W.E.Cooper (Lauraceae), a new species from Queensland’s Wet tropics. Austrobaileya 9, 75–79.
Crayn DM, Costion C, Harrington MG (2015) The Sahul–Sunda floristic exchange: dated molecular phylogenies document Cenozoic intercontinental dispersal dynamics. Journal of Biogeography 42, 11–24.
| The Sahul–Sunda floristic exchange: dated molecular phylogenies document Cenozoic intercontinental dispersal dynamics.Crossref | GoogleScholarGoogle Scholar |
Denton AL, McConaughy BL, Hall BD (1998) Usefulness of RNA polymerase II coding sequences for estimation of green plant phylogeny. Molecular Biology and Evolution 15, 1082–1085.
| Usefulness of RNA polymerase II coding sequences for estimation of green plant phylogeny.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaK1cXlt1ejtr4%3D&md5=725cd11f74c8d8136a7a6a3a39607986CAS | 9718735PubMed |
Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19, 11–15.
Drinnan AN, Crane PC, Friis EM, Pedersen KR (1990) Lauraceous flowers from the Potomac group (mid-Cretaceous) of eastern North America. Botanical Gazette 151, 370–384.
| Lauraceous flowers from the Potomac group (mid-Cretaceous) of eastern North America.Crossref | GoogleScholarGoogle Scholar |
Floyd A (2010) Chapter 12: the flora. In ‘Remnants of Gondwana’. (Eds R Kitching, R Braithwaite, J Cavanaugh) pp. 135–146. (Surrey Beatty: Sydney)
Greenwood DR, Christophel DC (2005) The origins and tertiary history of Australian ‘Tropical’ rainforests. In ‘Tropical Rainforests Past, Present and Future’. (Eds E Bermingham, CW Dick, C Moritz) pp. 336–373. (The University of Chicago Press: Chicago, IL, USA)
Harrington MG, Gadek PA (2004) Molecular systematics of the Acmena alliance (Myrtaceae): phylogenetic analyses and evolutionary implications with reference to Australian taxa. Australian Systematic Botany 17, 63–72.
| Molecular systematics of the Acmena alliance (Myrtaceae): phylogenetic analyses and evolutionary implications with reference to Australian taxa.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2cXitFCgt74%3D&md5=e9278358f325ce4f15d2c14f80db7a8eCAS |
Hill RS (1988) Australian Tertiary angiosperm and gymnosperm leaf remains: an updated catalogue. Alcheringa 12, 207–219.
| Australian Tertiary angiosperm and gymnosperm leaf remains: an updated catalogue.Crossref | GoogleScholarGoogle Scholar |
Hocknull SA, Zhao JX, Feng YX, Webb GE (2007) Responses of Quaternary rainforest vertebrates to climate change in Australia. Earth and Planetary Science Letters 264, 317–331.
| Responses of Quaternary rainforest vertebrates to climate change in Australia.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2sXhtlahsbzF&md5=d5ec55604f424a48b7f926cec60d846aCAS |
Huang J-F, Li L, van der Werff H, Li H-W, Rohwer JG, Crayn DM, Meng H-H, van der Merwe M, Conran JG, Li J (2016) Origins and evolution of cinnamon and camphor: a phylogenetic and historical biogeographical analysis of the Cinnamomum group (Lauraceae). Molecular Phylogenetics and Evolution 96, 33–44.
| Origins and evolution of cinnamon and camphor: a phylogenetic and historical biogeographical analysis of the Cinnamomum group (Lauraceae).Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC2MXitV2ktr%2FP&md5=6a94f4694eadf97b500f75c15e581fbfCAS | 26718058PubMed |
Huelsenbeck JP, Ronquist F (2001) MrBAYES: Bayesian inference of phylogeny. Bioinformatics 17, 754–755.
| MrBAYES: Bayesian inference of phylogeny.Crossref | GoogleScholarGoogle Scholar | 1:STN:280:DC%2BD3MvotV2isw%3D%3D&md5=b8644e64d679ca4a9de09f610a1cf0f1CAS | 11524383PubMed |
Hyland BPM (1983) A revision of Syzygium and allied genera (Myrtaceae) in Australia. Australian Journal of Botany 13, 1–164.
| A revision of Syzygium and allied genera (Myrtaceae) in Australia.Crossref | GoogleScholarGoogle Scholar |
Hyland BPM (1989) A revision of Lauraceae in Australia (excluding Cassytha). Australian Systematic Botany 2, 135–367.
| A revision of Lauraceae in Australia (excluding Cassytha).Crossref | GoogleScholarGoogle Scholar |
Katoh K, Misawa K, Kuma K, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research 30, 3059–3066.
| MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD38XlslOqu7s%3D&md5=4238d11c94502d8eb467f976d1dafc4dCAS | 12136088PubMed |
Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Mentjies P, Drummond A (2012) Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28, 1647–1649.
| Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.Crossref | GoogleScholarGoogle Scholar | 22543367PubMed |
Kershaw AP, van der Kaars S, Moss PT (2003) Late Quaternary Milankovich-scale climatic change and variability and its impact on monsoonal Australasia. Marine Geology 201, 81–95.
| Late Quaternary Milankovich-scale climatic change and variability and its impact on monsoonal Australasia.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD3sXns12nu7g%3D&md5=5ff3dbd428850ec2c3e5036ca108099dCAS |
Kimoto Y, Utami N, Tobe H (2006) Embryology of Eusideroxylon (Cryptocaryeae, Lauraceae) and character evolution in the family. Botanical Journal of the Linnean Society 150, 187–201.
| Embryology of Eusideroxylon (Cryptocaryeae, Lauraceae) and character evolution in the family.Crossref | GoogleScholarGoogle Scholar |
Kooyman RM, Rossetto M, Sauquet H, Laffan SW (2013) Landscape patterns in rainforests phylogenetic signal: isolated islands of refugia or structured continental distributions? PLoS One 8, e80685
| Landscape patterns in rainforests phylogenetic signal: isolated islands of refugia or structured continental distributions?Crossref | GoogleScholarGoogle Scholar | 24312493PubMed |
Le Cussan J, Hyland BPM (2007) Lauraceae. In ‘Flora of Australia, Vol. 2, Winteraceae to Platanaceae’. (Ed. AJG Wilson) pp. 106–223. (ABRS/CSIRO Publishing: Melbourne)
Li L, Li J, Rohwer JG, van der Werff H, Wang ZH, Li HW (2011) Molecular phylogenetic analysis of the Persea group (Lauraceae) and its biogeographic implications on the evolution of tropical and subtropical amphi-Pacific disjunctions. American Journal of Botany 98, 1520–1536.
| Molecular phylogenetic analysis of the Persea group (Lauraceae) and its biogeographic implications on the evolution of tropical and subtropical amphi-Pacific disjunctions.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3MXhtlSks73I&md5=aca61a23f0afba4175dcc384f6617f7aCAS | 21860056PubMed |
Little SA, Stuckey RA, Penner B (2009) Anatomy and development of fruits of Lauraceae from the middle Eocene Princeton chert. American Journal of Botany 96, 637–651.
| Anatomy and development of fruits of Lauraceae from the middle Eocene Princeton chert.Crossref | GoogleScholarGoogle Scholar | 21628220PubMed |
Miller MA, Pfeiffer W, Schwartz T (2010) Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In ‘Proceedings of the Gateway Computing Environments Workshop (GCE)’, 14 November 2010, New Orleans, LA, USA. pp. 1–8. Available at http://www.phylo.org/portal2/ [Verified 21 September 2016]
Pillon Y (2012) Time and tempo of diversification in the flora of New Caledonia. Botanical Journal of the Linnean Society 170, 288–298.
| Time and tempo of diversification in the flora of New Caledonia.Crossref | GoogleScholarGoogle Scholar |
Richardson JE, Costion C, Muellner AN (2012) The Malesian floristic interchange: plant migration patterns across Wallace’s line. In ‘Biotic Evolution and Environmental Change in Southeast Asia’. (Eds D Gower, K Johnson, JE Richardson, B Rosen, L Rüber, S Williams) pp. 138–163. (Cambridge University Press: Cambridge, UK)
Rohwer JG (1993) Lauraceae. In ‘The Families and Genera of Vascular Plants’. (Eds K Kubitzki, JG Rohwer, V Bittrich) Vol. 2, pp. 366–391. (Springer-Verlag: Berlin)
Rohwer JG, De Moraes PLR, Rudolph B, van der Werff H (2014) A phylogenetic analysis of the Cryptocarya group (Lauraceae), and relationships of Dahlgrenodendron, Sinopora, Triadodaphne, and Yasunia. Phytotaxa 158, 111–132.
| A phylogenetic analysis of the Cryptocarya group (Lauraceae), and relationships of Dahlgrenodendron, Sinopora, Triadodaphne, and Yasunia.Crossref | GoogleScholarGoogle Scholar |
Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572–1574.
| MrBayes 3: Bayesian phylogenetic inference under mixed models.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD3sXntlKms7k%3D&md5=ebb7f79ca3abc332a555ac1fa9492884CAS | 12912839PubMed |
Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP (2012) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61, 539–542.
| MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space.Crossref | GoogleScholarGoogle Scholar | 22357727PubMed |
Rossetto M, Kooyman R, Yap JS, Laffan SW (2015a) From ratites to rats: the size of fleshy fruits shapes species’ distributions and continental rainforest assembly. Proceedings of the Royal Society of London – B. Biological Sciences 282, 20 151 998
| From ratites to rats: the size of fleshy fruits shapes species’ distributions and continental rainforest assembly.Crossref | GoogleScholarGoogle Scholar |
Rossetto M, McPherson H, Siow J, Kooyman R, van der Merwe M, Wilson PD (2015b) Where did all the trees come from? A novel multispecies approach reveals the impacts of biogeographical history and functional diversity on rain forest assembly. Journal of Biogeography 42, 2172–2186.
| Where did all the trees come from? A novel multispecies approach reveals the impacts of biogeographical history and functional diversity on rain forest assembly.Crossref | GoogleScholarGoogle Scholar |
Sniderman JMK, Jordan GJ (2011) Extent and timing of floristic exchange between Australian and Asian rain forests. Journal of Biogeography 38, 1445–1455.
| Extent and timing of floristic exchange between Australian and Asian rain forests.Crossref | GoogleScholarGoogle Scholar |
Song Y, Dong W, Liu B, Xu C, Yao X, Gao J, Corlett RT (2015) Comparative analysis of complete chloroplast genome sequences of two tropical trees Machilus yunnanensis and Machilus balansae in the family Lauraceae. Frontiers in Plant Science 6, 662
| Comparative analysis of complete chloroplast genome sequences of two tropical trees Machilus yunnanensis and Machilus balansae in the family Lauraceae.Crossref | GoogleScholarGoogle Scholar | 26379689PubMed |
Stamatakis A, Ludwig T, Meier H (2005) RAxML–III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 21, 456–463.
| RAxML–III: a fast program for maximum likelihood-based inference of large phylogenetic trees.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2MXhsFSgu7s%3D&md5=63b918f7fa798b769043365a537011e5CAS | 15608047PubMed |
Taberlet P, Gielly L, Pautou G, Bouvet J (1991) Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Molecular Biology 17, 1105–1109.
| Universal primers for amplification of three non-coding regions of chloroplast DNA.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaK38Xhslel&md5=6d2f79284cf4d62f47d3c274de5bebcfCAS | 1932684PubMed |
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution 30, 2725–2729.
| MEGA6: molecular evolutionary genetics analysis version 6.0.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3sXhvVKhurzP&md5=f96b9a6ff756fc575d7627d1961f5101CAS | 24132122PubMed |
The Angiosperm Phylogeny Group (2009) An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Botanical Journal of the Linnean Society 161, 105–121.
| An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III.Crossref | GoogleScholarGoogle Scholar |
Vadala AJ, Greenwood DR (2001) Australian Paleogene vegetation and environments: evidence from Palaeo Gondwanan elements in the fossil records of Lauraceae and Proteaceae. In ‘Faunal and Floral Migrations and Evolution in SE Asia–Australasia’. (Eds I Metcalfe, JMB Smith, M Morwood, I Davidson) pp. 201–226. (A.A Balkema Publishers: Lisse, Netherlands)
van der Werff H (1992) Proposal to conserve 2813 Cryptocarya against Ravensara (Lauraceae). Taxon 41, 129–130.
| Proposal to conserve 2813 Cryptocarya against Ravensara (Lauraceae).Crossref | GoogleScholarGoogle Scholar |
van der Werff H, Richter HG (1996) Toward an improved classification of Lauraceae. Annals of the Missouri Botanical Garden 83, 409–418.
| Toward an improved classification of Lauraceae.Crossref | GoogleScholarGoogle Scholar |
Wang Z, Li J, Conran J, Li H (2010) Phylogeny of the Southeast Asian endemic genus Neocinnamomum H.Liu (Lauraceae). Plant Systematics and Evolution 290, 173–184.
| Phylogeny of the Southeast Asian endemic genus Neocinnamomum H.Liu (Lauraceae).Crossref | GoogleScholarGoogle Scholar |
