Phylogeny-Based Measurements at Global and Regional Scales

  • Shawn W. Laffan


The purpose of this chapter is to describe a number of methodological issues, considerations and opportunities when applying phylogeny-based measures at regional to global scales, a process recently labelled as “spatial phylogenetics”. These are divided into four sections: (1) the nature of the source data; (2) issues and effects of spatial aggregation; (3) some useful properties of phylogenetic diversity, endemism and rarity across landscapes; and (4) how to develop analysis tools that will complete in reasonable time for large data sets. The focus of the discussion is on measures of phylogenetic diversity, endemism and rarity, but the issues, considerations and opportunities raised have general application to other related indices across landscape and global scales.


  1. Amboni MPM, Laffan SW (2012) The effect of species geographical distribution estimation methods on richness and phylogenetic diversity estimates. Int J Geogr Inf Sci 26(11):2097–2109. Scholar
  2. Bloomfield NJ, Knerr N, Encinas-Viso F (2018) A comparison of network and clustering methods to detect biogeographical regions. Ecography 41(1):1–10. Scholar
  3. Cadotte MW, Davies JT (2010) Rarest of the rare: advances in combining evolutionary distinctiveness and scarcity to inform conservation at biogeographical scales. Divers Distrib 16(3):376–385. Scholar
  4. Carta A, Pierini B, Roma-Marzio F, Bedini G, Peruzzi L (2017) Phylogenetic measures of biodiversity uncover pteridophyte centres of diversity and hotspots in Tuscany. Plant Biosyst:1–9.
  5. Cassis G, Laffan SW, Ebach MC (2017) Biodiversity and bioregionalisation perspectives on the historical biogeography of Australia. In: Ebach MC (ed) Handbook of Australasian biogeography. CRC Press, pp 1–16.
  6. Chapman AD (1998) Quality control and validation of point-sourced environmental resource data. In: Lowell K, Jaton A (eds) Third international symposium on spatial accuracy assessment: land information uncertainty in natural resources. Ann Arbor Press, Chelsea, pp 409–418Google Scholar
  7. Crisp MD, Laffan SW, Linder P, Monro A (2001) Endemism in the Australian flora. J Biogeogr 28(2):183–198CrossRefGoogle Scholar
  8. Di Virgilio G, Laffan SW, Nielsen SV, Chapple DG (2017) Does range-restricted evolutionary history predict extinction risk? A case study in lizards. J Biogeogr 44(3):605–614. Scholar
  9. Faith DP (1992) Conservation evaluation and phylogenetic diversity. Biol Conserv 61(1):1–10. Scholar
  10. Franklin J (2010) Mapping species distributions: spatial inference and prediction. Cambridge University Press, Cambridge, UKGoogle Scholar
  11. Gallagher RV (2016) Correlates of range size variation in the Australian seed- plant flora. J Biogeogr 43(7):1287–1298. Scholar
  12. González-Orozco CE, Laffan SW, Knerr N, Miller JT (2013) A biogeographic regionalisation of Australian Acacia species. J Biogeogr 40:2156–2166CrossRefGoogle Scholar
  13. González-Orozco CE, Ebach MC, Laffan SW, Thornhill AH, Knerr N, Schmidt- Lebuhn A, Cargill CC, Clements M, Nagalingum N, Mishler BD, Miller JT (2014a) Quantifying phytogeographical regions of Australia using geospatial turnover in species composition. PLoS One 9(3):e92558CrossRefPubMedPubMedCentralGoogle Scholar
  14. González-Orozco CE, Thornhill AH, Knerr N, Laffan S, Miller JT (2014b) Biogeographical regions and phytogeography of the eucalypts. Divers Distrib 20(1):46–58. Scholar
  15. González-Orozco CE, Mishler BD, Miller JT, Laffan SW, Knerr N, Unmack P, Georges A, Thornhill A, Rosauer DF, Gruber B (2015) Assessing biodiversity and endemism using phylogenetic methods across multiple taxonomic groups. Ecol Evol 5(22):5177–5192. Scholar
  16. González-Orozco CE, Pollock LJ, Thornhill AH, Mishler BD, Knerr N, Laffan SW, Miller JT, Rosauer DF, Faith DP, Nipperess DA, Kujala H, Linke S, Butt N, Külheim C, Crisp MD, Gruber B (2016) Phylogenetic approaches reveal biodiversity threats under climate change. Nat Clim Chang 6:1110. Scholar
  17. Graham CH, Storch D, Machac A (2018) Phylogenetic scale in ecology and evolution. Glob Ecol Biogeogr 27(2):175–187. Scholar
  18. Guedes TB, Sawaya RJ, Zizka A, Laffan S, Faurby S, Pyron RA, Bérnils RS, Jansen M, Passos P, Prudente ALC, Cisneros-Heredia DF, Braz HB, Nogueira CC, Antonelli A (2018) Patterns, biases and prospects in the distribution and diversity of Neotropical snakes. Glob Ecol Biogeogr 27(1):14–21. Scholar
  19. Guerin GR, Ruokolainen L, Lowe AJ (2015) A georeferenced implementation of weighted endemism. Methods Ecol Evol 6(7):845–852. Scholar
  20. Hallgren W, Beaumont L, Bowness A, Chambers L, Graham E, Holewa H, Laffan S, Mackey B, Nix H, Vanderwal J, Warren R, Weis G (2016) The biodiversity and climate change virtual laboratory: where ecology meets big data. Environ Model Softw 76:182–186CrossRefGoogle Scholar
  21. Haque MM, Nipperess DA, Gallagher RV, Beaumont LJ (2017) How well documented is Australia's flora? Understanding spatial bias in vouchered plant specimens. Austral Ecol 42(6):690–699. Scholar
  22. IUCN (2018) The IUCN red list of threatened species, version 2018–1. Accessed 06 April 2018
  23. Jasiewicz J, Niesterowicz J, Stepinski T (2016) Multi-resolution, pattern-based segmentation of very large raster datasets. In: Miller JA, O'Sullivan D, Wiegand N (eds) International conference on GIScience short paper proceedings, 2016. Scholar
  24. 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(11):1463–1464. Scholar
  25. Knuth DE (1974) Computer programming as an art. Commun ACM 17(12):667–673. Scholar
  26. Kooyman R, Rossetto M, Laffan SW (2012) Cleaning and reconciling Australian Virtual Herbarium records for the ‘woody’ Australian rain forest vegetation: a test case. Are the error bars larger than the mountains? Cunninghamia 12(3):177–180CrossRefGoogle Scholar
  27. Kooyman RM, Rossetto M, Sauquet H, Laffan SW (2013) Landscape patterns in rainforest phylogenetic signal: isolated islands of refugia or structured continental distributions? PLoS One 8(12):e80685CrossRefPubMedPubMedCentralGoogle Scholar
  28. Laffan SW, Crisp MD (2003) Assessing endemism at multiple spatial scales, with an example from the Australian vascular flora. J Biogeogr 30(4):511–520CrossRefGoogle Scholar
  29. Laffan SW, Lubarsky E, Rosauer DF (2010) Biodiverse, a tool for the spatial analysis of biological and related diversity. Ecography 33(4):643–647CrossRefGoogle Scholar
  30. Laffan SW, Ramp D, Roger E (2013) Using endemism to assess representation of protected areas – the family Myrtaceae in the Greater Blue Mountains World Heritage Area. J Biogeogr 40(3):570–578. Scholar
  31. Laffan SW, Rosauer DF, Di Virgilio G, Miller JT, González-Orozco CE, Knerr N, Thornhill AH, Mishler BD (2016) Range-weighted metrics of species and phylogenetic turnover can better resolve biogeographic transition zones. Methods Ecol Evol 7(5):580–588. Scholar
  32. Laity T, Laffan SW, González-Orozco C, Faith DP, Rosauer DF, Byrne M, Miller JT, Crayn D, Costion C, Moritz C, Newport K (2015) Phylodiversity to in form conservation policy: an Australian example. Sci Total Environ 534:131–143. Scholar
  33. López-Aguirre C, Hand SJ, Laffan SW, Archer M (2018) Phylogenetic diversity, types of endemism and the evolutionary history of New World bats. Ecography 41:1–12.
  34. Millar TR, Heenan PB, Wilton AD, Smissen RD, Breitwieser I (2017) Spatial distribution of species, genus and phylogenetic endemism in the vascular flora of New Zealand, and implications for conservation. Aust Syst Bot 30(2):134–147. Scholar
  35. Mishler BD, Knerr N, González-Orozco CE, Thornhill A, Laffan SW, Miller JT (2014) Phylogenetic measures of biodiversity and neo- and paleo-endemism in Australian Acacia. Nat Commun 5:4473. Scholar
  36. Nagalingum NS, Knerr N, Laffan SW, González-Orozco CE, Thornhill AH, Miller JT, Mishler B (2015) Continental scale patterns and predictors of fern richness and phylogenetic diversity. Front Genet 6:132CrossRefPubMedPubMedCentralGoogle Scholar
  37. Newbold T (2010) Applications and limitations of museum data for conservation and ecology, with particular attention to species distribution models. Prog Phys Geogr 34(1):3–22. Scholar
  38. Openshaw S (1983) The modifiable areal unit problem, vol 38. Concepts and techniques in modern geography. Geo Books, NorwichGoogle Scholar
  39. Rosauer DF, Jetz W (2014) Phylogenetic endemism in terrestrial mammals. Glob Ecol Biogeogr 24(2):168–179. Scholar
  40. Rosauer DF, Laffan SW, Crisp MD, Donnellan SC, Cook LG (2009) Phylogenetic endemism: a new approach to identifying geographical concentrations of evolutionary history. Mol Ecol 18:4061–4072CrossRefPubMedGoogle Scholar
  41. Rosauer DF, Catullo RA, VanDerWal J, Moussalli A, Hoskin CJ, Moritz C (2015) Lineage range estimation method reveals fine-scale endemism linked to Pleistocene stability in Australian rainforest herpetofauna. PLoS One 10(5):e0126274. Scholar
  42. Rosauer DF, Byrne M, Blom MPK, Coates DJ, Donnellan S, Doughty P, Keogh JS, Kinloch J, Laver RJ, Myers C, Oliver PM, Potter S, Rabosky DL, Afonso Silva AC, Smith J, Moritz C (2018) Real-world conservation planning for evolutionary diversity in the Kimberley, Australia, sidesteps uncertain taxonomy. Conserv. Lett:e12438.
  43. Rossetto M, Kooyman RM, Yap S, Laffan SW (2015) From ratites to rats: the size of fleshy fruits shapes species distributions and continental rainforest assembly. Proc R Soc B 282:20151998CrossRefPubMedGoogle Scholar
  44. Scherson RA, Thornhill AH, Urbina-Casanova R, Freyman WA, Pliscoff PA, Mishler BD (2017) Spatial phylogenetics of the vascular flora of Chile. Mol Phylogenet Evol 112:88–95. Scholar
  45. Schmidt-Lebuhn AN, Knerr NJ, Miller JT, Mishler BD (2015) Phylogenetic diversity and endemism of Australian daisies (Asteraceae). J Biogeogr 42(6):1114–1122. Scholar
  46. Thornhill AH, Mishler BD, Knerr N, González-Orozco CE, Costion C, Crayn D, Laffan SW, Miller JT (2016) Continental-scale spatial phylogenetics of Australian angiosperms provides insights into ecology, evolution and conservation. J Biogeogr 43(11):2085–2098. Scholar
  47. Thornhill AH, Baldwin BG, Freyman WA, Nosratinia S, Kling MM, Morueta-Holme N, Madsen TP, Ackerly DD, Mishler BD (2017) Spatial phylogenetics of the native California flora. BMC Biol 15(1):96. Scholar
  48. Van Niel KP, Austin MP (2007) Predictive vegetation modeling for conservation: impact of error propagation from digital elevation data. Ecol Appl 17(1):266–280.[0266:PVMFCI]2.0.CO;2CrossRefPubMedGoogle Scholar
  49. Van Niel KP, Laffan SW, Lees BG (2004) Error and uncertainty in environmental variables for predictive vegetation modelling. J Veg Sci 15:747–756CrossRefGoogle Scholar
  50. Vilhena DA, Antonelli A (2015) A network approach for identifying and delimiting biogeographical regions. Nat Commun 6:6848. Scholar
  51. Webb CO, Ackerly DD, Kembel SW (2008) Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics 24(18):2098–2100. Scholar
  52. Williams N, Stewart A, Papadopoulos P (2017) Virtualizing Lifemapper software infrastructure for biodiversity expedition. Concurr Comput Pract Experience 29(13):e4137-n/a. Scholar

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© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.School of Biological, Earth and Environmental SciencesUniversity of New South WalesSydneyAustralia

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