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Australian Journal of Botany Australian Journal of Botany Society
Southern hemisphere botanical ecosystems
RESEARCH ARTICLE

Demographic history and niche conservatism of tropical rainforest trees separated along an altitudinal gradient of a biogeographic barrier

Rohan Mellick A C , Peter D. Wilson A B and Maurizio Rossetto A
+ Author Affiliations
- Author Affiliations

A National Herbarium of NSW, The Royal Botanic Gardens and Domain Trust, Sydney, NSW 2000, Australia.

B Department of Biological Sciences, Macquarie University, Sydney, NSW 2019, Australia.

C Corresponding author. Email: rohan.mellick@csiro.au

Australian Journal of Botany 62(5) 438-450 https://doi.org/10.1071/BT14103
Submitted: 14 May 2014  Accepted: 12 September 2014   Published: 16 October 2014

Abstract

The genetic disjunctions and distributions of long-lived species provide valuable signatures of past demographic response to environmental change. Here we use genetic markers to study two Elaeocarpus species from the Australian Wet Tropics to understand changes in palaeodistribution and demography associated with environmental change on either side of the Black Mountain Corridor (BMC). Contrasting the genetic structure of species with different distributions along altitudinal gradients is important to explore some of the environmental drivers of adaptive evolution. Using coalescent-based molecular and environmental niche models, we investigate the demographic history of two long-lived, altitudinally differentiated species that were previously identified as genetically divergent across the BMC. The origin of the genetic disjunction across the BMC is inferred to have occurred during the last glacial cycle in relation to 13 combined molecular histories of both plastid and nuclear loci. Interestingly, whereas midland populations show a dynamic history of expansion and contraction, the highland populations do not. Molecular history and environmental niche models show the populations north of the BMC have remained relatively stable over time in response to environmental change. Populations south of the BMC have been more dynamic in response to environmental change. These differences are likely to highlight the topographical character and environmental heterogeneity of areas separated by the BMC.

Additional keywords: ancestral gene flow, Australian Wet Tropics, Black Mountain Corridor, Elaeocarpus, molecular history, niche conservatism, palaeodistribution modelling, population expansion and contraction.


References

Adam P (1992) ‘Australian rainforests.’ (Oxford University Press: Oxford, UK)

Barker R, Vestjens W (1989) ‘The food of Australian birds 2. Passerines.’ (CSIRO Publishing: Melbourne)

Beaumont LJ, Hughes L, Poulsen M (2005) Predicting species distributions: use of climatic parameters in BIOCLIM and its impact on predictions of species’ current and future distributions. Ecological Modelling 186, 251–270.
Predicting species distributions: use of climatic parameters in BIOCLIM and its impact on predictions of species’ current and future distributions.Crossref | GoogleScholarGoogle Scholar |

Bedia J, Busqué J, Gutiérrez JM (2011) Predicting plant species distribution across an alpine rangeland in northern Spain. A comparison of probabilistic methods. Applied Vegetation Science 14, 415–432.
Predicting plant species distribution across an alpine rangeland in northern Spain. A comparison of probabilistic methods.Crossref | GoogleScholarGoogle Scholar |

Beerli P (2006) Comparison of Bayesian and maximum-likelihood inference of population genetic parameters. Bioinformatics 22, 341–345.
Comparison of Bayesian and maximum-likelihood inference of population genetic parameters.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD28XhtFaisbo%3D&md5=b5bc1cd66233b5ce04c9c38ba0b11b6cCAS | 16317072PubMed |

Beerli P, Felsenstein J (2001) Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proceedings of the National Academy of Sciences of the United States of America 98, 4563–4568.
Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD3MXjtVagtLY%3D&md5=c0d80834c9030bac418aef0ec4690fbbCAS | 11287657PubMed |

Beerli P, Palczewski M (2010) Unified framework to evaluate panmixia and migration direction among multiple sampling locations. Genetics 185, 313–326.
Unified framework to evaluate panmixia and migration direction among multiple sampling locations.Crossref | GoogleScholarGoogle Scholar | 20176979PubMed |

Bell KL, Moritz C, Moussalli A, Yeates DK (2007) Comparative phylogeography and speciation of dung beetles from the Australian Wet Tropics rainforest. Molecular Ecology 16, 4984–4998.
Comparative phylogeography and speciation of dung beetles from the Australian Wet Tropics rainforest.Crossref | GoogleScholarGoogle Scholar | 17927709PubMed |

Bell RC, MacKenzie JB, Hickerson MJ, Chavarría KL, Cunningham M, Williams S, Moritz C (2012) Comparative multi-locus phylogeography confirms multiple vicariance events in co-distributed rainforest frogs. Proceedings of the Royal Society B: Biological Sciences 279, 991–999.
Comparative multi-locus phylogeography confirms multiple vicariance events in co-distributed rainforest frogs.Crossref | GoogleScholarGoogle Scholar | 21900325PubMed |

Biffin E, Hill RS, Lowe AJ (2010) Did kauri (Agathis: Araucariaceae) really survive the Oligocene drowning of New Zealand? Systematic Biology 59, 594–601.
Did kauri (Agathis: Araucariaceae) really survive the Oligocene drowning of New Zealand?Crossref | GoogleScholarGoogle Scholar | 20530131PubMed |

Biffin E, Conran J, Lowe A (2011) Podocarp evolution: a molecular phylogenetic perspective. In ‘Ecology of the Podocarpaceae in tropical forests’. (Eds BL Turner, LA Cernusak) pp. 1–20. Smithsonian Contributions to Botany No. 95. (Smithsonian Institution Scholarly Press: Washington, DC)

Bresson C, Vitasse Y, Kremer A, Delzon S (2011) To what extent is altitudinal variation of functional traits driven by genetic adaptation in European oak and beech? Tree Physiology 31, 1164–1174.
To what extent is altitudinal variation of functional traits driven by genetic adaptation in European oak and beech?Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38Xit1ymsrs%3D&md5=fea79af25dc83b14735ec994db4f3687CAS | 21908436PubMed |

Brown JL (2014) SDMtoolbox: a python-based GIS toolkit for landscape genetic, biogeographic and species distribution model analyses. Methods in Ecology and Evolution 5, 694–700.
SDMtoolbox: a python-based GIS toolkit for landscape genetic, biogeographic and species distribution model analyses.Crossref | GoogleScholarGoogle Scholar |

Busby JR (1991) BIOCLIM-a bioclimate analysis and prediction system. Plant Protection Quarterly 6, 8–9.

Crayn DM, Rossetto M, Maynard DJ (2006) Molecular phylogeny and dating reveals an Oligo-Miocene radiation of dry-adapted shrubs (Tremandraceae) from rainforest tree progenitors (Elaeocarpaceae) in Australia. American Journal of Botany 93, 1328–1342.
Molecular phylogeny and dating reveals an Oligo-Miocene radiation of dry-adapted shrubs (Tremandraceae) from rainforest tree progenitors (Elaeocarpaceae) in Australia.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD28XhtFGrtb3J&md5=aa202269ed46ad21dc9395232ebb26d2CAS | 21642198PubMed |

Dormann CF, Elith J, Bacher S, Buchmann C, Carl G, Carré G, Marquéz JRG, Gruber B, Lafourcade B, Leitão PJ, Münkemüller T, McClean Dormann CF, Elith J, Bacher S, Buchmann C, Carl G, Carré G, Marquéz JRG, Gruber B, Lafourcade B, Leitão PJ, Münkemüller T, McClean (2013) Collinearity: a review of methods to deal with it and a simulation study evaluating their performance. Ecography 36, 27–46.
Collinearity: a review of methods to deal with it and a simulation study evaluating their performance.Crossref | GoogleScholarGoogle Scholar |

Elith J, Graham CH, Anderson RP, Dudik M, Ferrier S, Guisan A, Hijmans RJ, Huettmann F, Leathwick JR, Lehmann A, Li J, Lohmann LG, Loiselle BA, Manion G, Moritz C, Nakamura M, Nakazawa Y, Overton JM, Peterson AT, Phillips SJ, Richardson K, Scachetti-Pereira R, Schapire RE, Soberon J, Williams S, Wisz MS, Zimmermann NE (2006) Novel methods improve prediction of species’ distributions from occurrence data. Ecography 29, 129–151.
Novel methods improve prediction of species’ distributions from occurrence data.Crossref | GoogleScholarGoogle Scholar |

Elith J, Phillips SJ, Hastie T, Dudík M, Chee YE, Yates CJ (2011) A statistical explanation of MaxEnt for ecologists. Diversity & Distributions 17, 43–57.
A statistical explanation of MaxEnt for ecologists.Crossref | GoogleScholarGoogle Scholar |

Gallant JC Dowling TI Read AM Wilson N Tickle P Inskeep C 2011 1 second SRTM derived Digital elevation models user guide. Geoscience Australia www.ga.gov.au/topographic-mapping/digital-elevation-data.html.

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. (University of Chicago Press: Chicago, IL)

Gugger PF, Ikegami M, Sork VL (2013) Influence of late Quaternary climate change on present patterns of genetic variation in valley oak, Quercus lobata Nee. Molecular Ecology 22, 3598–3612.
Influence of late Quaternary climate change on present patterns of genetic variation in valley oak, Quercus lobata Nee.Crossref | GoogleScholarGoogle Scholar | 23802553PubMed |

Hasegawa M, Kishino H, Yano T (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 22, 160–174.
Dating of the human-ape splitting by a molecular clock of mitochondrial DNA.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaL2MXmtFSns7g%3D&md5=7b8e8cb1450d6b13e18f0c827b2800ddCAS | 3934395PubMed |

Hewitt GM (1996) Some genetic consequences of ice ages, and their role in divergence and speciation. Biological Journal of the Linnean Society. Linnean Society of London 58, 247–276.
Some genetic consequences of ice ages, and their role in divergence and speciation.Crossref | GoogleScholarGoogle Scholar |

Hey J (2010) Isolation with migration models for more than two populations. Molecular Biology and Evolution 27, 905–920.
Isolation with migration models for more than two populations.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3cXjslalt7s%3D&md5=05a03b893c7c87a0cb4911e577d5bf00CAS | 19955477PubMed |

Hijmans RJ, Cameron SE, Parra JL, Jones PG, Jarvis A (2005) Very high resolution interpolated climate surfaces for global land areas. International Journal of Climatology 25, 1965–1978.
Very high resolution interpolated climate surfaces for global land areas.Crossref | GoogleScholarGoogle Scholar |

Hill RS (1994) The history of selected Australian taxa. In ‘History of the Australian vegetation: Cretaceous to Recent’. (Ed. RS Hill) pp. 390–419. (Cambridge University Press: Cambridge, UK)

Ho SYW, Shapiro B (2011) Skyline-plot methods for estimating demographic history from nucleotide sequences. Molecular Ecology Resources 11, 423–434.
Skyline-plot methods for estimating demographic history from nucleotide sequences.Crossref | GoogleScholarGoogle Scholar |

Hugall A, Moritz C, Moussalli A, Stanisic J (2002) Reconciling paleodistribution models and comparative phylogeography in the Wet Tropics rainforest land snail Gnarosophia bellendenkerensis (Brazier 1875). Proceedings of the National Academy of Sciences of the United States of America 99, 6112–6117.
Reconciling paleodistribution models and comparative phylogeography in the Wet Tropics rainforest land snail Gnarosophia bellendenkerensis (Brazier 1875).Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD38XjslWnsrk%3D&md5=6854a0db39e868a6d9918673ccfca84fCAS | 11972064PubMed |

Hughes L (2000) Biological consequences of global warming: is the signal already apparent? Trends in Ecology & Evolution 15, 56–61.
Biological consequences of global warming: is the signal already apparent?Crossref | GoogleScholarGoogle Scholar |

Jones RC, Rossetto M,, McNally J (2002) Isolation of microsatellite loci from a rainforest tree, Elaeocarpus grandis (Elaeocarpaceae), and amplification across closely related taxa. Molecular Ecology Notes 2, 179–181.
Isolation of microsatellite loci from a rainforest tree, Elaeocarpus grandis (Elaeocarpaceae), and amplification across closely related taxa.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD38Xls1artro%3D&md5=289524c7efae8e8f973d19eb8f24c263CAS |

Kimura M, Ohta T (1978) Stepwise mutation model and distribution of allelic frequencies in a finite population. Proceedings of the National Academy of Sciences, USA 75, 2868–2872.
Stepwise mutation model and distribution of allelic frequencies in a finite population.Crossref | GoogleScholarGoogle Scholar | 1:STN:280:DyaE1c3gt1SksQ%3D%3D&md5=8a17ec0eadad54c4868c2ed5cb3a4bf2CAS |

Liu C, Berry PM, Dawson TP, Pearson RG (2005) Selecting thresholds of occurrence in the prediction of species distributions. Ecography 28, 385–393.
Selecting thresholds of occurrence in the prediction of species distributions.Crossref | GoogleScholarGoogle Scholar |

Matthews ML, Endress PK (2002) Comparative floral structure and systematics in Oxalidales (Oxalidaceae, Connaraceae, Brunelliaceae, Cephalotaceae, Cunoniaceae, Elaeocarpaceae, Tremandraceae). Botanical Journal of the Linnean Society 140, 321–381.
Comparative floral structure and systematics in Oxalidales (Oxalidaceae, Connaraceae, Brunelliaceae, Cephalotaceae, Cunoniaceae, Elaeocarpaceae, Tremandraceae).Crossref | GoogleScholarGoogle Scholar |

Mellick R, Lowe A, Rossetto M (2011) Consequences of long- and short-term fragmentation on the genetic diversity and differentiation of a late successional rainforest conifer. Australian Journal of Botany 59, 351–362.
Consequences of long- and short-term fragmentation on the genetic diversity and differentiation of a late successional rainforest conifer.Crossref | GoogleScholarGoogle Scholar |

Mellick R, Lowe A, Allen C, Hill RS, Rossetto M (2012) Palaeodistribution modelling and genetic evidence highlight differential post-glacial range shifts of a rain forest conifer distributed across a latitudinal gradient. Journal of Biogeography 39, 2292–2302.
Palaeodistribution modelling and genetic evidence highlight differential post-glacial range shifts of a rain forest conifer distributed across a latitudinal gradient.Crossref | GoogleScholarGoogle Scholar |

Mellick R, Wilson PD, Rossetto M (2013a) Post-Glacial spatial dynamics in a rainforest biodiversity hot spot. Diversity 5, 124–138.
Post-Glacial spatial dynamics in a rainforest biodiversity hot spot.Crossref | GoogleScholarGoogle Scholar |

Mellick R, Rossetto M, Allen C, Wilson PD, Hill RS, Lowe A (2013b) Intraspecific divergence associated with a biogeographic barrier and climatic models show future threats and long-term decline of a rainforest conifer. The Open Conservation Biology Journal 7, 1–10.
Intraspecific divergence associated with a biogeographic barrier and climatic models show future threats and long-term decline of a rainforest conifer.Crossref | GoogleScholarGoogle Scholar |

Moritz C, Patton JL, Schneider CJ, Smith TB (2000) Diversification of rainforest faunas: an integrated molecular approach. Annual Review of Ecology and Systematics 31, 533–563.
Diversification of rainforest faunas: an integrated molecular approach.Crossref | GoogleScholarGoogle Scholar |

Moritz C, Hoskin CJ, MacKenzie JB, Phillips BL, Tonione M, Silva N, VanDerWal J, Williams SE, Graham CH (2009) Identification and dynamics of a cryptic suture zone in tropical rainforest. Proceedings. Biological Sciences 276, 1235–1244.
Identification and dynamics of a cryptic suture zone in tropical rainforest.Crossref | GoogleScholarGoogle Scholar | 1:STN:280:DC%2BD1M3jsFWmug%3D%3D&md5=cbfde610c2ddac450fba02f0d5b1a2f4CAS |

Nielsen R, Wakeley J (2001) Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics 158, 885–896.

Oza AU, Lovett KE, Williams SE, Moritz C (2012) Recent speciation and limited phylogeographic structure in Mixophyes frogs from the Australian Wet Tropics. Molecular Phylogenetics and Evolution 62, 407–413.

Phillips SJ, Anderson RP, Schapire RE (2006) Maximum entropy modeling of species geographic distributions. Ecological Modelling 190, 231–259.
Maximum entropy modeling of species geographic distributions.Crossref | GoogleScholarGoogle Scholar |

Posada D, Crandall KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14, 817–818.
MODELTEST: testing the model of DNA substitution.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaK1MXktlCltw%3D%3D&md5=9e1ffdf58cb1ecee7487a523ff5c6773CAS | 9918953PubMed |

Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155, 945–959.

R Core Team (2013) ‘R: a language and environment for statistical computing.’ (R Foundation for Statistical Computing: Vienna)

Raes N, ter Steege H (2007) A null-model for significance testing of presence-only species distribution models. Ecography 30, 727–736.
A null-model for significance testing of presence-only species distribution models.Crossref | GoogleScholarGoogle Scholar |

Rossetto M, Gross CL, Jones R, Hunter J (2004a) The impact of clonality on an endangered tree (Elaeocarpus williamsianus) in a fragmented rainforest. Biological Conservation 117, 33–39.
The impact of clonality on an endangered tree (Elaeocarpus williamsianus) in a fragmented rainforest.Crossref | GoogleScholarGoogle Scholar |

Rossetto M, Jones R, Hunter J (2004b) Genetic effects of rainforest fragmentation in an early successional tree (Elaeocarpus grandis). Heredity 93, 610–618.
Genetic effects of rainforest fragmentation in an early successional tree (Elaeocarpus grandis).Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2cXhtVWgtb7J&md5=a4326e780dc3b3de2cee931d6985772bCAS | 15367910PubMed |

Rossetto M, Crayn D, Ford A, Ridgeway P, Rymer P (2007) The comparative study of range-wide genetic structure across related, co-distributed rainforest trees reveals contrasting evolutionary histories. Australian Journal of Botany 55, 416–424.
The comparative study of range-wide genetic structure across related, co-distributed rainforest trees reveals contrasting evolutionary histories.Crossref | GoogleScholarGoogle Scholar |

Rossetto M, Kooyman R, Sherwin W, Jones R (2008) Dispersal limitations, rather than bottlenecks or habitat specificity, can restrict the distribution of rare and endemic rainforest trees. American Journal of Botany 95, 321–329.
Dispersal limitations, rather than bottlenecks or habitat specificity, can restrict the distribution of rare and endemic rainforest trees.Crossref | GoogleScholarGoogle Scholar | 21632357PubMed |

Rossetto M, Crayn D, Ford A, Mellick R, Sommerville K (2009) The influence of environment and life-history traits on the distribution of genes and individuals: a comparative study of 11 rainforest trees. Molecular Ecology 18, 1422–1438.
The influence of environment and life-history traits on the distribution of genes and individuals: a comparative study of 11 rainforest trees.Crossref | GoogleScholarGoogle Scholar | 1:STN:280:DC%2BD1M3osVGktA%3D%3D&md5=548d4251f2bd6bfe65082f13b1e3e46fCAS | 19284473PubMed |

Rozefelds AC, Christophel DC (1996) Elaeocarpus (Elaeocarpaceae) endocarps from the Oligo-Miocene of eastern Australia. Papers and Proceedings of the Royal Society of Tasmania 130, 41–48.

Rozefelds AC, Christophel DC (2002) Cenozoic Elaeocarpus (Elaeocarpaceae) fruits from Australia. Alcheringa: An Australasian Journal of Palaeontology 26,
Cenozoic Elaeocarpus (Elaeocarpaceae) fruits from Australia.Crossref | GoogleScholarGoogle Scholar |

Saatchi S, Buermann W, Ter Steege H, Mori S, Smith TB (2008) Modeling distribution of Amazonian tree species and diversity using remote sensing measurements. Remote Sensing of Environment 112, 2000–2017.
Modeling distribution of Amazonian tree species and diversity using remote sensing measurements.Crossref | GoogleScholarGoogle Scholar |

Schauble CS, Moritz C (2001) Comparative phylogeography of two open forest frogs from eastern Australia. Biological Journal of the Linnean Society. Linnean Society of London 74, 157–170.

Schlötterer C (2000) Evolutionary dynamics of microsatellite DNA. Chromosoma 109, 365–371.
Evolutionary dynamics of microsatellite DNA.Crossref | GoogleScholarGoogle Scholar | 11072791PubMed |

Schneider CJ, Cunningham M, Moritz C (1998) Comparative phylogeography and the history of endemic vertebrates in the Wet Tropics rainforests of Australia. Molecular Ecology 7, 487–498.
Comparative phylogeography and the history of endemic vertebrates in the Wet Tropics rainforests of Australia.Crossref | GoogleScholarGoogle Scholar |

Scoble J, Lowe AJ (2010) A case for incorporating phylogeography and landscape genetics into species distribution modelling approaches to improve climate adaptation and conservation planning. Diversity & Distributions 16, 343–353.
A case for incorporating phylogeography and landscape genetics into species distribution modelling approaches to improve climate adaptation and conservation planning.Crossref | GoogleScholarGoogle Scholar |

Strasburg J, Sherman NA, Wright KM, Moyle LC, Willis JH, Rieseberg LH (2012) What can patterns of differentiation across plant genomes tell us about adaptation and speciation? Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 367, 364–373.
What can patterns of differentiation across plant genomes tell us about adaptation and speciation?Crossref | GoogleScholarGoogle Scholar | 22201166PubMed |

VanDerWal J, Shoo LP, Graham C, Williams SE (2009) Selecting pseudo-absence data for presence-only distribution modeling: how far should you stray from what you know? Ecological Modelling 220, 589–594.
Selecting pseudo-absence data for presence-only distribution modeling: how far should you stray from what you know?Crossref | GoogleScholarGoogle Scholar |

Warren DL, Seifert SN (2011) Ecological niche modeling in Maxent: the importance of model complexity and the performance of model selection criteria. Ecological Applications 21, 335–342.
Ecological niche modeling in Maxent: the importance of model complexity and the performance of model selection criteria.Crossref | GoogleScholarGoogle Scholar | 21563566PubMed |

Webb LJ, Tracey JG (1981) Australian rainforests: patterns and change. In ‘Ecological biogeography of Australia’. (Ed. A Keast) pp. 607–94. (W. Junk: The Hague, The Netherlands)

Wilford J (2012) A weathering intensity index for the Australian continent using airborne gammaray spectrometry and digital terrain analysis. Geoderma 183–184, 124–142.
A weathering intensity index for the Australian continent using airborne gammaray spectrometry and digital terrain analysis.Crossref | GoogleScholarGoogle Scholar |

Williams KJ, Belbin L, Austin MP, Steinc JL, Ferrier S (2012) Which environmental variables should I use in my biodiversity model? International Journal of Geographical Information Science 26, 2009–2047.
Which environmental variables should I use in my biodiversity model?Crossref | GoogleScholarGoogle Scholar |