Biodiversity Science ›› 2017, Vol. 25 ›› Issue (2): 175-181.doi: 10.17520/biods.2016183

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• Orginal Article • Previous Article     Next Article

Phylogenetic diversity and its application in floristics and biodiversity conservation

Xiuqin Ci, Jie Li*()   

  1. Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223
  • Received:2016-07-12 Accepted:2016-10-16 Online:2017-03-06
  • Li Jie E-mail:jieli@xtbg.ac.cn

The application of phylogenetic relationships helps us to understand species composition and species distribution patterns, which provide a scientific basis for the effective protection and sustainable use of biological diversity. Phylogenetic diversity (PDfaith), based on branch lengths of the phylogenetic tree, is the most basic measurement index. Many indices are derived from PDfaith, which makes difficult to choose the most appropriate parameters. The most effective and feasible way is to select suitable indices based on specific research questions, and some examples have been presented in plant phylofloristics and biodiversity conservation. DNA sequences have rapidly accumulated particularly through the global DNA barcoding project, which provides a standardized mass data, and can be used to reconstruct mega-phylogeny. But studies conducted around the phylogenetic diversity require more information, specifically data on species distribution, environmental factors, and climatic data. In addition, some fundamental questions need to be verified, such as the relationship between phylogenetic diversity and ecosystem functions.

Key words: evolutional history, DNA barcoding, megaphylogeny, biodiversity, flora, conservation

1 Abellán P, Sánchez-Fernández D, Picazo F, Millán A, Lobo JM, Ribera I (2013) Preserving the evolutionary history of freshwater biota in Iberian National Parks. Biological Conservation, 162, 116-126.
2 Ahrendsen DL, Aust SK, Kellar PR (2015) Biodiversity assessment using next-generation sequencing: comparison of phylogenetic and functional diversity between Nebraska grasslands. Plant Systematics and Evolution, 302, 89-108.
3 APG IV (2016) An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Botanical Journal of the Linnean Society, 181, 1-20.
4 Arroyo-Rodríguez V, Cavender-Bares J, Escobar F, Melo FPL, Tabarelli M, Santos BA (2012) Maintenance of tree phylogenetic diversity in a highly fragmented rain forest. Journal of Ecology, 100, 702-711.
5 Athayde EA, Cancian LF, Verdade LM, Morellato LPC (2015) Functional and phylogenetic diversity of scattered trees in an agricultural landscape: implications for conservation. Agriculture Ecosystems and Environment, 199, 272-281.
6 Buerki S, Callmander MW, Bachman S, Moat J, Labat J-N, Forest F (2015) Incorporating evolutionary history into conservation planning in biodiversity hotspots. Philosophical Transactions of the Royal Society B: Biological Sciences, 370, 20140014.
7 Cadotte MW (2013) Experimental evidence that evolutionarily diverse assemblages result in higher productivity. Proceedings of the National Academy of Sciences, USA, 110, 8996-9000.
8 Cadotte MW, Cardinale BJ, Oakley TH (2008) Evolutionary history and the effect of biodiversity on plant productivity. Proceedings of the National Academy of Sciences, USA, 105, 17012-17017.
9 Cadotte MW, Dinnage R, Tilman D (2012) Phylogenetic diversity promotes ecosystem stability. Ecology, 93, S223-S233.
10 Cardinale BJ, Venail P, Gross K, Oakley TH, Narwani A, Allan E, Flombaum P, Joshi J, Reich PB, Tilman D, van Ruijven J (2015) Further re-analyses looking for effects of phylogenetic diversity on community biomass and stability. Functional Ecology, 29, 1607-1610.
11 Cavender-Bares J, Keen A, Miles B (2006) Phylogenetic structure of Floridian plant communities depends on taxonomic and spatial scale. Ecology, 87, 109-122.
12 Cavender-Bares J, Kozak KH, Fine PVA, Kembel SW (2009) The merging of community ecology and phylogenetic biology. Ecology Letters, 12, 693-715.
13 Chen ZD, Yang T, Lin L, Lu LM, Li HL, Sun M, Liu B, Chen M, Niu YT, Ye JF, Cao ZY, Liu HM, Wang XM, Wang W, Zhang JB, Meng Z, Cao W, Li JH, Wu SD, Zhao HL, Liu ZJ, Du ZY, Wang QF, Guo J, Tan XX, Su JX, Zhang LJ, Yang LL, Liao YY, Li MH, Zhang GQ, Chung SW, Zhang J, Xiang KL, Li RQ, Soltis DE, Soltis PS, Zhou SL, Ran JH, Wang XQ, Jin XH, Chen YS, Gao TG, Li JH, Zhang SZ, Lu AM, China Phylogeny Consortium (2016) Tree of life for the genera of Chinese vascular plants. Journal of Systematics and Evolution, 54, 277-306.
14 Chiu CH, Jost L, Chao A (2014) Phylogenetic beta diversity, similarity, and differentiation measures based on Hill numbers. Ecological Monographs, 84, 21-44.
15 Costion CM, Edwards W, Ford AJ, Metcalfe DJ, Cross HB, Harrington MG, Richardson JE, Hilbert DW, Lowe AJ, Crayn DM (2015) Using phylogenetic diversity to identify ancient rain forest refugia and diversification zones in a biodiversity hotspot. Diversity and Distributions, 21, 279-289.
16 Daru BH, le Roux PC (2016) Marine protected areas are insufficient to conserve global marine plant diversity. Global Ecology and Biogeography, 25, 324-334.
17 Davies TJ, Buckley LB (2012) Exploring the phylogenetic history of mammal species richness. Global Ecology and Biogeography, 21, 1096-1105.
18 Davies TJ, Fritz SA, Grenyer R, Orme CD, Bielby J, Bininda-Emonds OR, Cardillo M, Jones KE, Gittleman JL, Mace GM, Purvis A (2008) Phylogenetic trees and the future of mammalian biodiversity. Proceedings of the National Academy of Sciences, USA, 105, 11556-11563.
19 Dinnage R, Cadotte MW, Haddad NM, Crutsinger GM, Tilman D (2012) Diversity of plant evolutionary lineages promotes arthropod diversity. Ecology Letters, 15, 1308-1317.
20 Faith DP (1992) Conservation evaluation and phylogenetic diversity. Biological Conservation, 61, 1-10.
21 Faith DP (2015) Phylogenetic diversity, functional trait diversity and extinction: avoiding tipping points and worst-case losses. Philosophical Transactions of the Royal Society B: Biological Sciences, 370, 200140011.
22 Faith DP, Richards Z (2012) Climate change impacts on the Tree of Life: changes in phylogenetic diversity illustrated for Acropora Corals. Biology, 1, 906-932.
23 Faith DP, Baker AM (2006) Phylogenetic diversity (PD) and biodiversity conservation: some bioinformatics challenges. Evolutionary Bioinformatics Online, 2, 121-128.
24 Fine PVA, Kembel SW (2011) Phylogenetic community structure and phylogenetic turnover across space and edaphic gradients in western Amazonian tree communities. Ecography, 34, 552-565.
25 Flynn DFB, Mirotchnick N, Jain M, Palmer MI, Naeem S (2011) Functional and phylogenetic diversity as predictors of biodiversity-ecosystem-function relationships. Ecology, 92, 1573-1581.
26 Forest F, Grenyer R, Rouget M, Davies TJ, Cowling RM, Faith DP, Balmford A, Manning JC, Procheş Ş, van der Bank M, Reeves G, Hedderson TAJ, Savolainen V (2007) Preserving the evolutionary potential of floras in biodiversity hotspots. Nature, 445, 757-760.
27 Frishkoff LO, Karp DS, M’Gonigle LK, Mendenhall CD, Zook J, Kremen C, Hadly EA, Daily GC (2014) Loss of avian phylogenetic diversity in neotropical agricultural systems. Science, 345, 1343-1346.
28 Ge XJ (2015) Application of DNA barcoding in phylofloristics study. Biodiversity Science, 23, 295-296.
(in Chinese) [葛学军 (2015) DNA条形码在植物系统发育区系学研究中的应用. 生物多样性, 23, 295-296.]
29 González-Orozco CE, Mishler BD, Miller JT, Laffan SW, Knerr N, Unmack P, Georges A, Thornhill AH, Rosauer DF, Gruber B (2015) Assessing biodiversity and endemism using phylogenetic methods across multiple taxonomic groups. Ecology and Evolution, 5, 5177-5192.
30 Harrison S, Cornell H (2008) Toward a better understanding of the regional causes of local community richness. Ecology Letters, 11, 969-979.
31 Helmus MR, Bland TJ, Williams CK, Ives AR (2007) Phylogenetic measures of biodiversity. The American Naturalist, 169, E68-E83.
32 Honorio Coronado EN, Dexter KG, Pennington RT, Chave J, Lewis SL, Alexiades MN, Alvarez E, Alves de Oliveira A, Amaral IL, Araujo-Murakami A, Arets EJMM, Aymard GA, Baraloto C, Bonal D, Brienen R, Cerón C, Cornejo Valverde F, Di Fiore A, Farfan-Rios W, Feldpausch TR, Higuchi N, Huamantupa-Chuquimaco I, Laurance SG, Laurance WF, López-Gonzalez G, Marimon BS, Marimon-Junior BH, Monteagudo Mendoza A, Neill D, Palacios Cuenca W, Peñuela Mora MC, Pitman NCA, Prieto A, Quesada CA, Ramirez Angulo H, Rudas A, Ruschel AR, Salinas Revilla N, Salomão RP, Segalin de Andrade A, Silman MR, Spironello W, ter Steege H, Terborgh J, Toledo M, Valenzuela Gamarra L, Vieira ICG, Vilanova TE, Vos V, Phillips OL (2015) Phylogenetic diversity of Amazonian tree communities. Diversity and Distributions, 21, 1295-1307.
33 Isaac NJB, Turvey ST, Collen B, Waterman C, Baillie JEM (2007) Mammals on the EDGE: conservation priorities based on threat and phylogeny. PLoS ONE, 2, e296.
34 Jetz W, Thomas GH, Joy JB, Hartmann K, Mooers AO (2012) The global diversity of birds in space and time. Nature, 491, 444-448.
35 Kembel SW, Hubbell SP (2006) The phylogenetic structure of a neotropical forest tree community. Ecology, 87, S86-S99.
36 Knapp S, Kühn I, Schweiger O, Klotz S (2008) Challenging urban species diversity: contrasting phylogenetic patterns across plant functional groups in Germany. Ecology Letters, 11, 1054-1064.
37 Laity T, Laffan SW, González-Orozco CE, Faith DP, Rosauer DF, Byrne M, Miller JT, Crayn D, Costion C, Moritz CC, Newport K (2015) Phylodiversity to inform conservation policy: an Australian example. Science of the Total Environment, 534, 131-143.
38 Li R, Kraft NJB, Yang J, Wang Y (2015) A phylogenetically informed delineation of floristic regions within a biodiversity hotspot in Yunnan, China. Scientific Reports, 5, 9396.
39 Mishler BD, Knerr N, González-Orozco CE, Thornhill AH, Laffan SW, Miller JT (2014) Phylogenetic measures of biodiversity and neo- and paleo-endemism in Australian Acacia. Nature Communications, 5, 4473.
40 Mouquet N, Devictor V, Meynard CN, Munoz F, Bersier L-F, Chave J, Couteron P, Dalecky A, Fontaine C, Gravel D, Hardy OJ, Jabot F, Lavergne S, Leibold M, Mouillot D, Münkemüller T, Pavoine S, Prinzing A, Rodrigues ASL, Rohr RP, Thébault E, Thuiller W (2012) Ecophylogenetics: advances and perspectives. Biological Reviews, 87, 769-785.
41 Pavoine S, Bonsall M (2011) Measuring biodiversity to explain community assembly: a unified approach. Biological Reviews, 86, 792-812.
42 Pio DV, Engler R, Linder HP, Monadjem A, Cotterill FPD, Taylor PJ, Schoeman MC, Price BW, Villet MH, Eick G, Salamin N, Guisan A (2014) Climate change effects on animal and plant phylogenetic diversity in southern Africa. Global Change Biology, 20, 1538-1549.
43 Pollock LJ, Rosauer DF, Thornhill AH, Kujala H, Crisp MD, Miller JT, McCarthy MA (2015) Phylogenetic diversity meets conservation policy: small areas are key to preserving eucalypt lineages. Philosophical Transactions of the Royal Society B: Biological Sciences, 370, 20140007.
44 Posadas P, Miranda Esquivel DR, Crisci JV (2001) Using phylogenetic diversity measures to set priorities in conservation: an example from southern South America. Conservation Biology, 15, 1325-1334.
45 Potter KM, Woodall CW (2014) Does biodiversity make a difference? Relationships between species richness, evolutionary diversity, and aboveground live tree biomass across U. S. forests. Forest Ecology and Management, 321, 117-129.
46 Qian H, Jiang L (2014) Phylogenetic community ecology: integrating community ecology and evolutionary biology. Journal of Plant Ecology, 7, 97-100.
47 Qian H, Swenson NG, Zhang JL (2013) Phylogenetic beta diversity of angiosperms in North America. Global Ecology and Biogeography, 22, 1152-1161.
48 Rodrigues ASL, Gaston KJ (2002) Maximising phylogenetic diversity in the selection of networks of conservation areas. Biological Conservation, 105, 103-111.
49 Rodrigues ASL, Brooks TM, Gaston KJ (2005) Integrating phylogenetic diversity in the selection of priority areas for conservation: does it make a difference? In: Phylogeny and Conservation (eds Purvis A, Gittleman JL, Brooks TM), pp. 101-199. Cambridge University Press, Cambridge.
50 Rosauer DF, Laffan SW, Crisp MD, Donnellan SC, Cook LG (2009) Phylogenetic endemism: a new approach for identifying geographical concentrations of evolutionary history. Molecular Ecology, 18, 4061-4072.
51 Sarkar S, Pressey RL, Faith DP, Margules CR, Fuller T, Stoms DM, Moffett A, Wilson KA, Williams KL, Williams PH, Andelman S (2006) Biodiversity conservation planning tools: present status and challenges for the future. Annual Review of Environment and Resources, 31, 123-159.?
52 Sechrest W, Brooks TM, da Fonseca GAB, Konstant WR, Mittermeier RA, Purvis A, Rylands AB, Gittleman JL (2002) Hotspots and the conservation of evolutionary history. Proceedings of the National Academy of Sciences, USA, 99, 2067-2071.
53 Shapcott A, Forster PI, Guymer GP, McDonald WJF, Faith DP, Erickson D, Kress WJ (2015) Mapping biodiversity and setting conservation priorities for SE Queensland’s rainforests using DNA barcoding. PLoS ONE, 10, e0122164.
54 Srivastava DS, Cadotte MW, MacDonald AM, Marushia RG, Mirotchnick N (2012) Phylogenetic diversity and the functioning of ecosystems. Ecology Letters, 15, 637-648.
55 Swenson NG, Umana MN (2014) Phylofloristics: an example from the Lesser Antilles. Journal of Plant Ecology, 7, 166-175.
56 Thornhill AH, Mishler BD, Knerr NJ, González-Orozco CE, Costion CM, Crayn DM, Laffan SW, Miller JT (2016) Continental-scale spatial phylogenetics of Australian angiosperms provides insights into ecology, evolution and conservation. Journal of Biogeography, 43, 2085-2098
57 Tucker CM, Cadotte MW (2013) Unifying measures of biodiversity: understanding when richness and phylogenetic diversity should be congruent. Diversity and Distributions, 19, 845-854.
58 Tucker CM, Cadotte MW, Carvalho SB, Davies TJ, Ferrier S, Fritz SA, Grenyer R, Helmus MR, Jin LS, Mooers AO, Pavoine S, Purschke O, Redding DW, Rosauer DF, Winter M, Mazel F (2016) A guide to phylogenetic metrics for conservation, community ecology and macroecology. Biological Reviews, doi: 10.1111/brv.12252.
59 Vane-Wright RI, Humphries CJ, Williams PH (1991) What to protect? Systematics and the agony of choice. Biological Conservation, 55, 235-254.
60 Wang L, Young SS, Wang W, Ren G, Xiao W, Long Y, Li J, Zhu J (2016) Conservation priorities of forest ecosystems with evaluations of connectivity and future threats: implications in the Eastern Himalaya of China. Biological Conservation, 195, 128-135.
61 Webb CO, Donoghue MJ (2005) Phylomatic: tree assembly for applied phylogenetics. Molecular Ecology Notes, 5, 181-183.
62 Winter M, Devictor V, Schweiger O (2013) Phylogenetic diversity and nature conservation: where are we? Trends in Ecology and Evolution, 28, 199-204.
63 Winter M, Schweiger O, Klotz S, Nentwig W, Andriopoulos P, Arianoutsou M, Basnou C, Delipetrou P, Didziulis V, Hejda M, Hulme PE, Lambdon PW, Pergl J, Pysek P, Roy DB, Kühn I (2009) Plant extinctions and introductions lead to phylogenetic and taxonomic homogenization of the European flora. Proceedings of the National Academy of Sciences, USA, 106, 21721-21725.
64 Zanne AE, Tank DC, Cornwell WK, Eastman JM, Smith SA, FitzJohn RG, McGlinn DJ, O’Meara BC, Moles AT, Reich PB, Royer DL, Soltis DE, Stevens PF, Westoby M, Wright IJ, Aarssen L, Bertin RI, Calaminus A, Govaerts R, Hemmings F, Leishman MR, Oleksyn J, Soltis PS, Swenson NG, Warman L, Beaulieu JM (2014) Three keys to the radiation of angiosperms into freezing environments. Nature, 506, 89-92.
65 Zhang J, Nielsen SE, Stolar J, Chen Y, Thuiller W (2015) Gains and losses of plant species and phylogenetic diversity for a northern high-latitude region. Diversity and Distributions, 21, 1441-1454.
66 Zhang JL, Swenson NG, Chen SB, Liu XJ, Li ZS, Huang JH, Mi XC, Ma KP (2013) Phylogenetic beta diversity in tropical forests: implications for the roles of geographical and environmental distance. Journal of Systematic Evolution, 51, 71-85.
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