Skip to main content

Advertisement

Log in

Niche evolution in Australian terrestrial mammals? Clarifying scale-dependencies in phylogenetic and functional drivers of co-occurrence

  • Original Paper
  • Published:
Evolutionary Ecology Aims and scope Submit manuscript

Abstract

Interactive forces between competition and habitat filtering drive many biogeographic patterns over evolutionary time scales. However, the responsiveness of assemblages to these two forces is highly influenced by spatial scale, forming complex patterns of niche separation. We explored these spatial dependencies by quantifying the influence of phylogeny and functional traits in shaping present day native terrestrial mammal assemblages at multiple scales, principally by identifying the spatial scales at which niche evolution operates. We modelled the distribution of 53 native terrestrial mammal species across New South Wales, Australia. Using predicted distributions, we estimated the range overlap between each pair of species at increasing grain sizes (~0.8, 5.1, 20, 81, 506, 2,025, 8,100 km2). We employed a decision tree to identify how interactions among functional traits and phylogenetic relatedness translated to levels of sympatry at increasing spatial scales. We found that Australian terrestrial mammals displayed phylogenetic over-dispersion that was inversely related to spatial scale, suggesting that ecological processes were more influential than biogeographic sympatry patterns in defining assemblages of species. While the contribution of phylogenetic relatedness to patterns of co-occurrence decreased as spatial scale increased, the reverse was true for habitat preferences. At the same time, functional traits also operated at different scales, as dietary preferences dominated at local spatial scales (<10 km2) while body mass has a stronger effect at larger spatial scales. Our findings show that ecological and evolutionary processes operate at different scales and that Australian terrestrial mammals diverged slower along their micro-scale niche compared to their macro-scale niche. By combining phylogenetic and niche methods through the modelling of species distributions, we assessed whether specific traits were related to a particular niche. More importantly, conducting multi-scale spatial analysis avoids categorical assignment of traits-to-niches, providing a clearer relationship between traits and a species ecological niche and a more precise scaling for the axes of niche evolution.

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

Access this article

Subscribe and save

Springer+
from $39.99 /Month
  • Starting from 10 chapters or articles per month
  • Access and download chapters and articles from more than 300k books and 2,500 journals
  • Cancel anytime
View plans

Buy Now

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

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

Explore related subjects

Discover the latest articles and news from researchers in related subjects, suggested using machine learning.

References

  • Abrams PA, Rueffler C (2009) Coexistence and limiting similarity of consumer species competing for a linear array of resources. Ecology 90:812–822

    Article  PubMed  Google Scholar 

  • Ackerly DD, Schwilk DW, Webb CO (2006) Niche evolution and adaptive radiation: testing the order of trait divergence. Ecology 87:S50–S61

    Article  PubMed  CAS  Google Scholar 

  • Australian Faunal Directory (2009) Australian biological resources study. Australian Government, Department of the Environment, Water, Heritage and the Arts, Canberra

    Google Scholar 

  • Bininda-Emonds ORP, Cardillo M, Jones KE, MacPhee RDE, Beck RMD, Grenyer R, Price SA, Vos RA, Gittleman JL, Purvis A (2007) The delayed rise of present-day mammals. Nature 446:507–512

    Article  PubMed  CAS  Google Scholar 

  • Bino G, Ramp D, Kingsford RT (2012) Improving bioregional frameworks for conservation by including mammal distributions. Austral Ecol. doi:10.1111/j.1442-9993.2012.02423.x

  • Blackburn TM, Petchey OL, Cassey P, Gaston KJ (2005) Functional diversity of mammalian predators and extinction in island birds. Ecology 86:2916–2923

    Article  Google Scholar 

  • Blanckenhorn WU (2000) The evolution of body size: what keeps organisms small? Q Rev Biol 75:385–407

    Article  PubMed  CAS  Google Scholar 

  • Blomberg SP, Garland T, Ives AR (2003) Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution 57:717–745

    PubMed  Google Scholar 

  • Bohning-Gaese K, Oberrath R (1999) Phylogenetic effects on morphological, life-history, behavioural and ecological traits of birds. Evol Ecol Res 1:347–364

    Google Scholar 

  • Boitani L, Sinibaldi I, Corsi F, De Biase A, Carranza I, Ravagli M, Reggiani G, Rondinini C, Trapanese P (2008) Distribution of medium- to large-sized African mammals based on habitat suitability models. Biodiversity Conserv 17:605–621

    Article  Google Scholar 

  • Bradley RD, Baker RJ (2001) A test of the genetic species concept: cytochrome-b sequences and mammals. J Mammal 82:960–973

    Article  Google Scholar 

  • Bray JR, Curtis JT (1957) An ordination of the Upland Forest Communities of Southern Wisconsin. Ecol Monogr 27:325–349

    Article  Google Scholar 

  • Breiman L (2001) Random forests. Mach Learn 45:5–32

    Article  Google Scholar 

  • Burnham KP, Anderson DR (2002) Model selection and multimodel inference: a practical information–theoretic approach. Springer, New York

    Google Scholar 

  • Cardillo M (2011) Phylogenetic structure of mammal assemblages at large geographical scales: linking phylogenetic community ecology with macroecology. Philos Trans R Soc B 366:2545–2553

    Article  Google Scholar 

  • Cavender-Bares J, Keen A, Miles B (2006) Phylogenetic structure of floridian plant communities depends on taxonomic and spatial scale. Ecology 87:S109–S122

    Article  PubMed  Google Scholar 

  • Cavender-Bares J, Kozak KH, Fine PV, Kembel SW (2009) The merging of community ecology and phylogenetic biology. Ecol Lett 12:693–715

    Article  PubMed  Google Scholar 

  • Clarke K, Warwick R (2001) Change in marine communities: an approach to statistical analysis and interpretation, 2nd edn. PRIMER-E, Plymouth

    Google Scholar 

  • Cooper N, Rodríguez J, Purvis A (2008) A common tendency for phylogenetic overdispersion in mammalian assemblages. Proc R Soc B Biol Sci 275:2031–2037

    Article  Google Scholar 

  • Cornwell WK, Schwilk DW, Ackerly DD (2006) A trait-based test for habitat filtering: convex hull volume. Ecology 87:1465–1471

    Article  PubMed  Google Scholar 

  • Crisp MD, Arroyo MTK, Cook LG, Gandolfo MA, Jordan GJ, McGlone MS, Weston PH, Westoby M, Wilf P, Linder HP (2009) Phylogenetic biome conservatism on a global scale. Nature 458:754–756

    Article  PubMed  CAS  Google Scholar 

  • Cutler DR, Edwards TC Jr, Beard KH, Cutler A, Hess KT, Gibson J, Lawler JJ (2007) Random forests for classification in ecology. Ecology 88:2783–2792

    Article  PubMed  Google Scholar 

  • Davidson AD, Hamilton MJ, Boyer AG, Brown JH, Ceballos G (2009) Multiple ecological pathways to extinction in mammals. Proc Natl Acad Sci USA 106:10702–10705

    Article  PubMed  CAS  Google Scholar 

  • De’ath G, Fabricius KE (2000) Classification and regression trees: a powerful yet simple technique for ecological data analysis. Ecology 81:3178–3192

    Article  Google Scholar 

  • DECCW (2009) The atlas of NSW wildlife. The NSW Department of Environment, Climate Change and Water, Sydney

    Google Scholar 

  • Diamond JM (1975) Assembly of species communities. In: Cody ML, Diamond JM (eds) Ecology and evolution of communities. Belknap Press of Harvard University Press, Cambridge, pp 342–444

    Google Scholar 

  • Diamond JM (1986) Evolution of ecological segregation in the New Guinea montane avifauna. In: Diamond JM, Case TJ (eds) Community Ecol. Harper and Row, Cambridge, pp 98–125

    Google Scholar 

  • Efron B, Tibshirani R (1997) Improvements on cross-validation: the.632 + bootstrap method. J Am Stat Assoc 92:548–560

    Google Scholar 

  • Elton C (1946) Competition and the structure of ecological communities. J Anim Ecol 15:54–68

    Article  Google Scholar 

  • Emerson BC, Gillespie RG (2008) Phylogenetic analysis of community assembly and structure over space and time. Trends Ecol Evol 23:619–630

    Article  PubMed  Google Scholar 

  • Flynn DFB, Gogol-Prokurat M, Nogeire T, Molinari N, Richers BT, Lin BB, Simpson N, Mayfield MM, DeClerck F (2009) Loss of functional diversity under land use intensification across multiple taxa. Ecol Lett 12:22–33

    Article  PubMed  Google Scholar 

  • Freckleton RP, Jetz W (2009) Space versus phylogeny: disentangling phylogenetic and spatial signals in comparative data. Proc R Soc B Biol Sci 276:21–30

    Article  Google Scholar 

  • Freckleton RP, Harvey PH, Pagel M (2002) Phylogenetic analysis and comparative data: a test and review of evidence. Am Nat 160:712–726

    Article  PubMed  CAS  Google Scholar 

  • Fritz SA, Bininda-Emonds ORP, Purvis A (2009) Geographical variation in predictors of mammalian extinction risk: big is bad, but only in the tropics. Ecol Lett 12:538–549

    Article  PubMed  Google Scholar 

  • Gleason HA (1917) The structure and development of the plant association. Bull Torrey Bot Club 44:463–481

    Google Scholar 

  • González AL, Fariña JM, Kay AD, Pinto R, Marquet PA (2011) Exploring patterns and mechanisms of interspecific and intraspecific variation in body elemental composition of desert consumers. Oikos 120:1247–1255

    Article  Google Scholar 

  • Graham CH, Ron SR, Santos JC, Schneider CJ, Moritz C (2004) Integrating phylogenetics and environmental niche models to explore speciation mechanisms in dendrobatid frogs. Evolution 58:1781–1793

    PubMed  Google Scholar 

  • Guisan A, Thuiller W (2005) Predicting species distribution: offering more than simple habitat models. Ecol Lett 8:993–1009

    Article  Google Scholar 

  • Harmon LJ, Glor RE (2010) Poor statistical performance of the Mantel test in phylogenetic comparative analyses. Evolution 64:2173–2178

    PubMed  Google Scholar 

  • Hastie T, Tibshirani R, Friedman J (2009) The elements of statistical learning: data mining, inference and prediction. Springer, New York

    Book  Google Scholar 

  • Holt RD (2009) Bringing the Hutchinsonian niche into the 21st century: ecological and evolutionary perspectives. Proc Natl Acad Sci 106:19659–19665

    Article  PubMed  CAS  Google Scholar 

  • Hutchinson GE (1957) Population studies—animal ecology and demography—concluding remarks. Cold Spring Harb Symp Quant Biol 22:415–427

    Article  Google Scholar 

  • Ingram T (2011) Speciation along a depth gradient in a marine adaptive radiation. Proc R Soc B Biol Sci 278:613–618

    Article  Google Scholar 

  • Jablonski D, Sepkoski JJ (1996) Paleobiology, community ecology, and scales of ecological pattern. Ecology 77:1367–1378

    Article  PubMed  CAS  Google Scholar 

  • Jackson SM (2003) Australian mammals: biology and captive management. CSIRO Publishing, Melbourne

    Google Scholar 

  • Jenkins DG, Brescacin CR, Duxbury CV, Elliott JA, Evans JA, Grablow KR, Hillegass M, Lyon BN, Metzger GA, Olandese ML, Pepe D, Silvers GA, Suresch HN, Thompson TN, Trexler CM, Williams GE, Williams NC, Williams SE (2007) Does size matter for dispersal distance? Glob Ecol Biogeogr 16:415–425

    Article  Google Scholar 

  • Johnson CN, Isaac JL (2009) Body mass and extinction risk in Australian marsupials: the ‘critical weight range’ revisited. Austral Ecol 34:35–40

    Article  Google Scholar 

  • Jones MJ, Fielding A, Sullivan M (2006) Analysing extinction risk in parrots using decision trees. Biodiversity Conserv 15:1993–2007

    Article  Google Scholar 

  • Justice CO, Vermote E, Townshend JRG, Defries R, Roy DP, Hall DK, Salomonson VV, Privette JL, Riggs G, Strahler A, Lucht W, Myneni RB, Knyazikhin Y, Running SW, Nemani RR, Wan ZM, Huete AR, van Leeuwen W, Wolfe RE, Giglio L, Muller JP, Lewis P, Barnsley MJ (1998) The moderate resolution imaging spectroradiometer (MODIS): land remote sensing for global change research. IEEE Trans Geosci Remote 36:1228–1249

    Article  Google Scholar 

  • Kembel SW, Cowan PD, Helmus MR, Cornwell WK, Morlon H, Ackerly DD, Blomberg SP, Webb CO (2010) Picante: R tools for integrating phylogenies and ecology. Bioinformatics 26:1463–1464

    Article  PubMed  CAS  Google Scholar 

  • Kingsford RT, Brandis K, Thomas RF, Crighton P, Knowles E, Gale E (2004) Classifying landform at broad spatial scales: the distribution and conservation of wetlands in New South Wales. Australia. Mar. Freshw. Res. 55:17–31

    Article  Google Scholar 

  • Kodandaramaiah U, Konvicka M, Tammaru T, Wahlberg N, Gotthard K (2012) Phylogeography of the threatened butterfly, the woodland brown < i > Lopinga achine (Nymphalidae: Satyrinae): implications for conservation. J Insect Conserv 16:305–313

    Article  Google Scholar 

  • Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and clustal X version 2.0. Bioinformatics 23:2947–2948

    Article  PubMed  CAS  Google Scholar 

  • Leathwick JR, Elith J, Hastie T (2006) Comparative performance of generalized additive models and multivariate adaptive regression splines for statistical modelling of species distributions. Ecol Model 199:188–196

    Article  Google Scholar 

  • Liaw A, Wiener M (2002) Classification and Regression by randomForest. R News 2:18–22

    Google Scholar 

  • Losos JB (2008) Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species. Ecol Lett 11:995–1003

    Article  PubMed  Google Scholar 

  • Losos JB (2009) Lizards in an evolutionary tree: the ecology of adaptive radiation in anoles. University of California Press, Berkeley

    Google Scholar 

  • Losos JB, Leal M, Glor RE, De Queiroz K, Hertz PE, Rodriguez Schettino L, Lara AC, Jackman TR, Larson A (2003) Niche lability in the evolution of a Caribbean lizard community. Nature 424:542–545

    Article  PubMed  CAS  Google Scholar 

  • Lovette IJ, Hochachka WM (2006) Simultaneous effects of phylogenetic niche conservatism and competition on avian community structure. Ecology 87:14–28

    Article  Google Scholar 

  • Macarthur R, Levins R (1967) The limiting similarity, convergence, and divergence of coexisting species. Am Nat 101:377–385

    Article  Google Scholar 

  • Menkhorst PW, Knight F (2004) A field guide to the mammals of Australia. Oxford University Press, Melbourne

    Google Scholar 

  • Millar JS, Hickling GJ (1991) Body size and the evolution of mammalian life histories. Funct Ecol 5:588–593

    Article  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 

  • Münkemüller T, Bugmann H, Johst K (2009) Hutchinson revisited: patterns of density regulation and the coexistence of strong competitors. J Theor Biol 259:109–117

    Article  PubMed  Google Scholar 

  • Nix H (1986) A biogeographic analysis of Australian Elapid snakes. In: Longmore R (ed) Snakes: atlas of Elapid snakes of Australia. Bureau of Flora and Fauna, Canberra, pp 4–10

    Google Scholar 

  • Olden JD, Lawler JJ, Poff NL (2008) Machine learning methods without tears: a primer for ecologists. Q Rev Biol 83:171–193

    Article  PubMed  Google Scholar 

  • Paradis E, Claude J, Strimmer K (2004) APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20:289–290

    Article  PubMed  CAS  Google Scholar 

  • Parson W, Pegoraro K, Niederstatter H, Foger M, Steinlechner M (2000) Species identification by means of the cytochrome b gene. Int J Leg Med 114:23–28

    Article  CAS  Google Scholar 

  • Peters RH (1983) The ecological implications of body size. Cambridge University Press, Cambridge

    Book  Google Scholar 

  • Rice NH, Martinez-Meyer E, Peterson AT (2003) Ecological niche differentiation in the Aphelocoma jays: a phylogenetic perspective. Biol J Linn Soc 80:369–383

    Article  Google Scholar 

  • Ricklefs RE (2004) A comprehensive framework for global patterns in biodiversity. Ecol Lett 7:1–15

    Article  Google Scholar 

  • Rodríguez MÁ, López-Sañudo IL, Hawkins BA (2006) The geographic distribution of mammal body size in Europe. Glob Ecol Biogeogr 15:173–181

    Article  Google Scholar 

  • Rosenzweig ML (1995) Species diversity in space and time. Cambridge University Press, Cambridge

    Book  Google 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 Distrib 16:343–353

    Article  Google Scholar 

  • Sibly RM, Brown JH (2007) Effects of body size and lifestyle on evolution of mammal life histories. Proc Natl Acad Sci USA 104:17707–17712

    Article  PubMed  CAS  Google Scholar 

  • Silvertown J, Dodd M, Gowing D, Lawson C, McConway K (2006) Phylogeny and the hierarchical organization of plant diversity. Ecology 87:S39–S49

    Article  PubMed  Google Scholar 

  • Stern H, de Hoedt G, Ernst J (2000) Objective classification of Australian climates. Aust Meteorol Mag 49:87–96

    Google Scholar 

  • Steyerberg EW, Harrell FE, Borsboom GJJM, Eijkemans MJC, Vergouwe Y, Habbema JDF (2001) Internal validation of predictive models: efficiency of some procedures for logistic regression analysis. J Clin Epidemiol 54:774–781

    Article  PubMed  CAS  Google Scholar 

  • Strahan R (1984) Complete book of Australian mammals. Angus & Robertson Publishers, London

    Google Scholar 

  • Streelman TJ, Danley PD (2003) The stages of vertebrate evolutionary radiation. Trends Ecol Evol 18:126–131

    Article  Google Scholar 

  • Sutherland GD, Harestad AS, Price K, Lertzman KP (2000) Scaling of natal dispersal distances in terrestrial birds and mammals. Conserv Ecol 4:16

    Google Scholar 

  • Swenson NG, Enquist BJ, Pither J, Thompson J, Zimmerman JK (2006) The problem and promise of scale dependency in community phylogenetics. Ecology 87:2418–2424

    Article  PubMed  Google Scholar 

  • R Development Core Team (2010) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0. URL http://www.R-project.org. Accessed 14 Mar 2011: R Foundation for Statistical Computing

  • Tofts R, Silvertown J (2000) A phylogenetic approach to community assembly from a local species pool. Proc R Soc Lond B Biol 267:363–369

    Article  CAS  Google Scholar 

  • Vamosi SM, Heard SB, Vamosi JC, Webb CO (2009) Emerging patterns in the comparative analysis of phylogenetic community structure. Mol Ecol 18:572–592

    Article  PubMed  CAS  Google Scholar 

  • Van der Vaart AW (1998) Asymptotic statistics. Cambridge University Press, Cambridge

    Book  Google Scholar 

  • Warren DL, Glor RE, Turelli M (2010) ENMTools: a toolbox for comparative studies of environmental niche models. Ecography 33:607–611

    Article  Google Scholar 

  • Webb CO (2000) Exploring the phylogenetic structure of ecological communities: an example for rain forest trees. Am Nat 156:145–155

    Article  PubMed  Google Scholar 

  • Webb CO, Ackerly DD, McPeek MA, Donoghue MJ (2002) Phylogenies and community ecology. Annu Rev Ecol Syst 33:475–505

    Article  Google Scholar 

  • Weiher E, Keddy PA (1995) The assembly of experimental wetland plant communities. Oikos 73:323–335

    Article  Google Scholar 

  • Wiens JJ (2012) Perspective: why biogeography matters: historical biogeography vs. phylogeography and community phylogenetics for inferring ecological and evolutionary processes. Front Biogeogr 4:128–135

    Google Scholar 

  • Wiens JJ, Graham CH (2005) Niche conservatism: integrating evolution, ecology, and conservation biology. Annu Rev Ecol Evol Syst 36:519–539

    Article  Google Scholar 

Download references

Acknowledgments

This research was part of Australian Research Council Linkage Project LP0774833 titled “Managing for ecosystem change in the GBMWHA”. We thank the following partner organizations for their support: the Blue Mountains World Heritage Institute, the Blue Mountains City Council, the New South Wales Department of Environment and Climate Change (DECCW), the New South Wales Department of Primary Industries and the Hawkesbury-Nepean Catchment and Management Authority. GB was supported by an Australian Postgraduate Award. We are grateful to DECCW for the provision of Atlas data. We thank Evan Webster for providing valuable technical support. We are especially thankful for the anonymous comments from two anonymous reviewers and the Editor in Chief Prof. John A Endler.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Gilad Bino.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 687 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Bino, G., Ramp, D. & Kingsford, R.T. Niche evolution in Australian terrestrial mammals? Clarifying scale-dependencies in phylogenetic and functional drivers of co-occurrence. Evol Ecol 27, 1159–1173 (2013). https://doi.org/10.1007/s10682-013-9631-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10682-013-9631-5

Keywords

Profiles

  1. Gilad Bino