Biodiversity Science ›› 2017, Vol. 25 ›› Issue (4): 355-363.doi: 10.17520/biods.2017037


• Reviews • Previous Article     Next Article

Biodiversity science and macroecology in the era of big data

Jian Zhang*()   

  1. School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241
  • Received:2017-02-15 Accepted:2017-04-07 Online:2017-04-20
  • Zhang Jian

High-quality biodiversity data are the scientific basis for understanding the origin and maintenance of biodiversity and dealing with its extinction risk. Currently, we identify at least seven knowledge shortfalls or gaps in biodiversity science, including the lack of knowledge on species descriptions, species geographic distributions, species abundance and population dynamics, evolutional history, functional traits, interactions between species and the abiotic environment, and biotic interactions. The arrival of the current era of big data offers a potential solution to address these shortfalls. Big data mining and its applications have recently become the frontier of biodiversity science and macroecology. It is a challenge for ecologists to utilize and effectively analyze the ever-growing quantity of biodiversity data. In this paper, I review several biodiversity-related studies over global, continental, and regional scales, and demonstrate how big data approaches are used to address biodiversity questions. These examples include forest cover changes, conservation ecology, biodiversity and ecosystem functioning, and the effect of climate change on biodiversity. Furthermore, I summarize the current challenges facing biodiversity data collection, data processing and data analysis, and discuss potential applications of big data approaches in the fields of biodiversity science and macroecology.

Key words: big data science, conservation biology, biodiversity informatics, macrosystems ecology, citizen science

Fig. 1

The number of papers between 2008 and 2016 using “big data” as the topic in the Web of Science Core database"

Table 1

Definitions for seven main shortfalls (or gaps) of current biodiversity knowledge (Adopted from Hortal et al, 2015)"

Knowledge shortfalls
Aspect of biodiversity
物种 Species 缺乏对世界上很多现存和已灭绝物种描述的知识。Lack of knowledge about the description of most of living and extinct species on Earth. Brown & Lomolino, 1998; Brito, 2010
Wallacean shortfall 地理分布
Geographic distribution
缺乏有关大多数物种在各个时间尺度上的地理分布的知识。Lack of knowledge about the geographic distribution of most species at all scales most of the time. Lomolino, 2004
Prestonian shortfall 种群 Populations 缺乏在时空尺度上的物种多度和种群动态的知识。Lack of knowledge about species abundance and population dynamics in space and time. Cardoso et al, 2011
Darwinian shortfall 进化 Evolution 缺乏关于生命之树以及物种和它们的性状进化的信息。Lack of knowledge about the tree of life and the evolution of species and their traits. Diniz-Filho et al, 2013
Raunkiaeran shortfall 功能性状和生态功能
Functional traits and
ecological functions
缺乏物种的性状及其生态功能的知识。Lack of knowledge about species’ traits and their ecological functions. Hortal et al, 2015
Hutchinsonian shortfall 非生物耐性因子
Abiotic tolerances
缺乏物种如何应对和忍耐非生物因子的知识。Lack of knowledge about the responses and tolerances of species to abiotic conditions. Cardoso et al, 2011
Eltonian shortfall 生态的相互作用
Ecological interactions
缺乏物种相互作用及其影响个体存活和适合度的知识。Lack of knowledge on species’ interactions and these interactions’ effects on individual survival and fitness. Hortal et al, 2015
1 ABMI (Alberta Biodiversity Monitoring Institute) (2016) Alberta Wall-to-Wall Vegetation Layer Including “Backfilled” Vegetation in Human Footprints (Version 6). http: (accessed on 2017-03-22)
2 Asner GP, Martin RE, Knapp DE, Tupayachi R, Anderson CB, Sinca F, Vaughn NR, Llactayo W (2017) Airborne laser-guided imaging spectroscopy to map forest trait diversity and guide conservation. Science, 355, 385-389.
3 Bechtold WA, Patterson PL (2005) The Enhanced Forest Inventory and Analysis Program: National Sampling Design and Estimation Procedures. General Techinical Report, SRS-80. USDA Forest Service, Southern Research Station, Asheville, NC.
4 Brown JH (1995) Macroecology. Chicago University Press, Chicago.
5 Brown JH, Lomolino MV (1998) Biogeography. Sinauer Press, Sunderland, Massachusetts.
6 Brito D (2010) Overcoming the Linnean shortfall: data deficiency and biological survey priorities. Basic and Applied Ecology, 11, 709-713.
7 Cardoso P, Erwin TL, Borges PA, New TR (2011) The seven impediments in invertebrate conservation and how to overcome them. Biological Conservation, 144, 2647-2655.
8 Diniz-Filho JAF, Loyola RD, Raia P, Mooers AO, Bini LM (2013) Darwinian shortfalls in biodiversity conservation. Trends in Ecology and Evolution, 28, 689-695.
9 Dai SQ, Zhao B (2016) Trends and challenges of ecosystem observations in the age of big data. Biodiversity Science, 24, 85-94. (in Chinese with English abstract)
[戴圣骐, 赵斌 (2016) 大数据时代下的生态系统观测发展趋势与挑战. 生物多样性, 24, 85-94.]
10 Dobson LL, La Sorte FA, Manne LL, Hawkins BA (2015) The diversity and abundance of North American bird assemblages fail to track changing productivity. Ecology, 96, 1105-1114.
11 Enquist BJ, Condit R, Peet RK, Schildhauer M, Thiers BM (2017) Cyberinfrastructure for an integrated botanical information network to investigate the ecological impacts of global climate change on plant biodiversity. PeerJ, 4, e2615v2.
12 Falchi F, Cinzano P, Duriscoe D, Kyba CCM, Elvidge CD, Baugh K, Portnov BA, Rybnikova NA, Furgoni R (2016) The new world atlas of artificial night sky brightness. Science Advances, 2, e1600377.
13 Fei S, Guo Q, Potter K (2016) Macrosystems ecology: novel methods and new understanding of multi-scale patterns and processes. Landscape Ecology, 31, 1-6.
14 Gantz J, Reinsel D (2012) The Digital Universe in 2020: Big Data, Bigger Digital Shadows, and Biggest Growth in the Far East. IDC (International Data Corporation), Framingham.
15 Gaston KJ, Visser ME, Hölker F (2015) The biological impacts of artificial light at night: the research challenge. Philosophical Transactions of the Royal Society B: Biological Sciences, 370, 20140133.
16 Hampton SE, Strasser CA, Tewksbury JJ, Gram WK, Budden AE, Batcheller AL, Duke CS, Porter JH (2013) Big data and the future of ecology. Frontiers in Ecology and the Environment, 11, 156-162.
17 Hansen MC, Potapov PV, Moore R, Hancher M, Turubanova SA, Tyukavina A, Thau D, Stehman SV, Goetz SJ, Loveland TR, Kommareddy A, Egorov A, Chini L, Justice CO, Townshend JRG (2013) High-resolution global maps of 21st-century forest cover change. Science, 342, 850-853.
18 Heffernan JB, Soranno PA, Angilletta MJ, Buckley LB, Gruner DS, Keitt TH, Kellner JR, Kominoski JS, Rocha AV, Xiao J, Harms TK, Goring SJ, Koenig LE, McDowell WH, Powell H, Richardson AD, Stow CA, Vargas R, Weathers KC (2014) Macrosystems ecology: understanding ecological patterns and processes at continental scales. Frontiers in Ecology and the Environment, 12, 5-14.
19 Hey T, Tansley S, Tolle K (translated by Pan XF, Zhang XL) (2012) The Fourth Paradigm: Data-Intensive Scientific Discovery. Science Press, Beijing. (in Chinese)
[潘教峰, 张晓林等(译) (2012) 第四范式: 数据密集型科学发现. 科学出版社, 北京.]
20 Hinchliff CE, Smith SA, Allman JF, Burleigh JG, Chaudhary R, Coghill LM, Crandall KA, Deng J, Drew BT, Gazis R, Gude K, Hibbett DS, Katz LA, Laughinghouse HD, McTavish EJ, Midford PE, Owen CL, Ree RH, Rees JA, Soltis DE, Williams T, Cranston KA (2015) Synthesis of phylogeny and taxonomy into a comprehensive tree of life. Proceedings of the National Academy of Sciences, USA, 112, 12764-12769.
21 Hortal J, Bello F, Diniz-Filho JAF, Lewinsohn TM, Lobo JM, Ladle RJ (2015) Seven shortfalls that beset large-scale knowledge of biodiversity. Annual Review of Ecology, Evolution, and Systematics, 46, 523-549.
22 Houlahan JE, McKinney ST, Anderson TM, McGill BJ (2017) The priority of prediction in ecological understanding. Oikos, 26, 1-7.
23 Hu HJ, Jiang ZG, Wang ZW (2003) Macroecology: concept and progresses. Acta Ecologica Sinica, 23, 1192-1199. (in Chinese with English abstract)
[胡慧建, 蒋志刚, 王祖望 (2003) 宏生态学(Macroecology)及其研究. 生态学报, 23, 1192-1199.]
24 Ibisch PL, Hoffmann MT, Kreft S, Pe’er G, Kati V, Biber- Freudenberger L, DellaSala DA, Vale MM, Hobson PR, Selva N (2016) A global map of roadless areas and their conservation status. Science, 354, 1423-1427.
25 Jetz W, Thomas GH, Joy JB, Hartmann K, Mooers AO (2012) The global diversity of birds in space and time. Nature, 491, 444-448.
26 Jones MB, Schildhauer MP, Reichman OJ, Bowers S (2006) The new bioinformatics: integrating ecological data from the gene to the biosphere. Annual Review of Ecology, Evolution, and Systematics, 37, 519-544.
27 Keitt TH, Stanley HE (1998) Dynamics of North American breeding bird populations. Nature, 393, 257-260.
28 LaDeau SL, Kilpatrick AM, Marra PP (2007) West Nile virus emergence and large-scale declines of North American bird populations. Nature, 447, 710-713.
29 Lawton JH (1999) Are there general laws in ecology? Oikos, 84, 177-192.
30 Liang JJ, Crowther TW, Picard N, Wiser S, Zhou M, Alberti G, Schulze ED, McGuire AD, Bozzato F, Pretzsch H, de-Miguel S, Paquette A, Hérault B, Scherer-Lorenzen M, Barrett CB, Glick HB, Hengeveld GM, Nabuurs GJ, Pfautsch S, Viana H, Vibrans AC, Ammer C, Schall P, Verbyla D, Tchebakova N, Fischer M, Watson JV, Chen HYH, Lei X, Schelhaas MJ, Lu H, Gianelle D, Parfenova EI, Salas C, Lee E, Lee B, Kim HS, Bruelheide H, Coomes DA, Piotto D, Sunderland T, Schmid B, Gourlet-Fleury S, Sonké B, Tavani R, Zhu J, Brandl S, Vayreda J, Kitahara F, Searle EB, Neldner VJ, Ngugi MR, Baraloto C, Frizzera L, Bałazy R, Oleksyn J, Zawiła-Niedźwiecki T, Bouriaud O, Bussotti F, Finér L, Jaroszewicz B, Jucker T, Valladares F, Jagodzinski AM, Peri PL, Gonmadje C, Marthy W, O’Brien T, Martin EH, Marshall AR, Rovero F, Bitariho R, Niklaus PA, Alvarez-Loayza P, Chamuya N, Valencia R, Mortier F, Wortel V, Engone-Obiang NL, Ferreira LV, Odeke DE, Vasquez RM, Lewis SL, Reich PB (2016) Positive biodiversity-productivity relationship predominant in global forests. Science, 354, aaf8957.
31 Liu XJ, Ma KP (2015) Plant functional traits—concepts, applications and future directions. Scientia Sinica Vitae, 45, 325-339. (in Chinese with English abstract)
[刘晓娟, 马克平 (2015) 植物功能性状研究进展. 中国科学: 生命科学, 45, 325-339.]
32 Lomolino MV (2004) Conservation biogeography. In: Frontiers of Biogeography: New Directions in the Geography of Nature (eds Lomolino MV, Heaney LR), pp. 293-296. Sinauer Press, Sunderland, Massachusetts.
33 Ma KP (2014) Rapid development of biodiversity informatics in China. Biodiversity Science, 22, 251-252. (in Chinese)
[马克平 (2014) 生物多样性信息学在中国快速发展. 生物多样性, 22, 251-252.]
34 Ma KP (2016) Hot topics for biodiversity science. Biodiversity Science, 24, 1-2. (in Chinese)
[马克平 (2016) 生物多样性科学的热点问题. 生物多样性, 24, 1-2.]
35 Ma KP (2017) Mapping Asia Plants: a cyberinfrastructure for plant diversity in Asia. Biodiversity Science, 25, 1-2. (in Chinese)
[马克平 (2017) 亚洲生物多样性数字化计划. 生物多样性, 25, 1-2.]
36 Mayer-Schönberger V, Cukier K (2013) Big Data: A Revolution that Will Transform How We Live, Work, and Think. Houghton Mifflin Harcourt, Boston.
37 Mayor S, Cahill J, He F, Sólymos P, Boutin S (2012) Regional boreal biodiversity peaks at intermediate human disturbance. Nature Communications, 3, 1142.
38 Meyer C, Kreft H, Guralnick R, Jetz W (2015) Global priorities for an effective information basis of biodiversity distributions. Nature Communications, 6, 8221.
39 Meyer C, Weigelt P, Kreft H (2016) Multidimensional biases, gaps and uncertainties in global plant occurrence information. Ecology Letters, 19, 992-1006.
40 Pennisi E (2005) What determines species diversity? Science, 309, 90.
41 Roughgarden J (2009) Is there a general theory of community ecology? Biology & Philosophy, 24, 521-529.
42 Soberon J, Peterson T (2004) Biodiversity informatics: managing and applying primary biodiversity data. Philosophical Transactions of the Royal Society B: Biological Sciences, 359, 689-698.
43 Soranno PA, Schimel DS (2014) Macrosystems ecology: big data, big ecology. Frontiers in Ecology and the Environment, 12, 3.
44 Stralberg D, Matsuoka SM, Hamann A, Bayne EM, Sólymos P, Schmiegelow F, Wang X, Cumming SG, Song SJ (2015) Projecting boreal bird responses to climate change: the signal exceeds the noise. Ecological Applications, 25, 52-69.
45 Sun H, Deng T, Chen YS, Zhou Z (2017) Current research and development trends in floristic geography. Biodiversity Science, 25, 111-122. (in Chinese with English abstract)
[孙航, 邓涛, 陈永生, 周卓 (2017) 植物区系地理研究现状及发展趋势. 生物多样性, 25, 111-122.]
46 Sutherland WJ, Adams WM, Aronson RB, Aveling R, Blackburn TM, Broad S, Ceballos G, Côté IM, Cowling RM, Dafonseca GAB, Dinerstein E, Ferraro PJ, Fleishman E, Gascon C, Hunter Jr M, Hutton J, Kareiva P, Kuria A, MacDonald DW, Mackinnon K, Madgwick FJ, Mascia MB, Mcneely J, Milner-Gulland EJ, Moon S, Morley CG, Nelson S, Osborn D, Pai M, Parsons ECM, Peck LS, Possingham H, Prior SV, Pullin AS, Rands MRW, Ranganathan J, Redford KH, Rodriguez JP, Seymour F, Sobel J, Sodhi NS, Stott A, Vance-Borland K, Watkinson AR (2009) One hundred questions of importance to the conservation of global biological diversity. Conservation Biology, 23, 557-567.
47 Terborgh JW (2015) Toward a trophic theory of species diversity. Proceedings of the National Academy of Sciences, USA, 112, 11415-11422.
48 Violle C, Reich PB, Pacala SW, Enquist BJ, Kattge J (2014) The emergence and promise of functional biogeography. Proceedings of the National Academy of Sciences, USA, 111, 13690-13696.
49 Wang LS, Chen B, Ji LQ, Ma KP (2010) Progress in biodiversity informatics. Biodiversity Science, 18, 429-443. (in Chinese with English abstract)
[王利松, 陈彬, 纪力强, 马克平 (2010) 生物多样性信息学研究进展. 生物多样性, 18, 429-443.]
50 Wu JG, Shen WJ (2002) The sciences of complexity and ecological applications. In: Lectures in Modern Ecology (II): From Basic Ecology to Environmental Issues (eds Wu JG, Han XG, Huang JH), pp. 6-15. China Science and Technology Press, Beijing. (in Chinese)
[邬建国, 申卫军 (2002) 复杂性科学及其生态学应用. 见: 现代生态学讲座 (二): 基础研究与环境问题(邬建国, 韩兴国, 黄建辉主编), 6-15页. 中国科学技术出版社, 北京.]
51 Yang WJ, Ma KP, Kreft H (2013) Geographical sampling bias in a large distributional database and its effects on species richness-environment models. Journal of Biogeography, 40, 1415-1426.
52 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.
53 Zhang J, Chen SB, Chen B, Du YJ, Huang XL, Pan XB, Zhang Q (2013) Citizen science: integrating scientific research, ecological conservation and public participation. Biodiversity Science, 21, 738-749. (in Chinese with English abstract)
[张健, 陈圣宾, 陈彬, 杜彦君, 黄晓磊, 潘绪斌, 张强 (2013) 公众科学: 整合科学研究, 生态保护和公众参与. 生物多样性, 21, 738-749.]
54 Zhang J, Huang S, Hogg E, Lieffers V, Qin Y, He F (2014a) Estimating spatial variation in Alberta forest biomass from a combination of forest inventory and remote sensing data. Biogeosciences, 11, 2793-2808.
55 Zhang J, Kissling WD, He F (2013) Local forest structure, climate and human disturbance determine regional distribution of boreal bird species richness in Alberta, Canada. Journal of Biogeography, 40, 1131-1142.
56 Zhang J, Mayor SJ, He F (2014b) Does disturbance regime change community assembly of angiosperm plant communities in the boreal forest? Journal of Plant Ecology, 7, 188-201.
57 Zhang J, Nielsen SE, Chen Y, Georges D, Qin Y, Wang SS, Svenning JC, Thuiller W (2017) Extinction risk of North American seed plants elevated by climate and land-use change. Journal of Applied Ecology, 54, 303-312.
58 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.
[1] Wenying Zhuang Yi Li Huandi Zheng Zhaoqing Zeng Xincun Wang. (2020) Threat status of macro-ascomycetes in China and analysis of its threatening factors . Biodiv Sci, 28(1): 0-0.
[2] Fenglin Zhang,Xin Wang,Jian Zhang. (2018) Biodiversity information resources. II. Environmental data . Biodiv Sci, 26(1): 53-65.
[3] Shitao Xu,Xiqiang Song,Peng Ling,Yuanjun Chen,Mingxun Ren. (2018) The University Forests of Japan and implications for biodiversity conservation and national park development in China . Biodiv Sci, 26(1): 96-104.
[4] Hui Shang, Yuehong Yan. (2017) Natural hybridization and biodiversity conservation . Biodiv Sci, 25(6): 683-688.
[5] Xin Wang, Fenglin Zhang, Jian Zhang. (2017) Biodiversity information resources. I. Species distribution, catalogue, phylogeny, and life history traits . Biodiv Sci, 25(11): 1223-1238.
[6] Shengqi Dai,Bin Zhao. (2016) Trends and challenges of ecosystem observations in the age of big data . Biodiv Sci, 24(1): 85-94.
[7] Xile Zhou,Xianchun Zhang,Jiuqiong Sun,Yuehong Yan. (2016) Diversity and distribution of lycophytes and ferns in China . Biodiv Sci, 24(1): 102-107.
[8] Kwangtsao Shao,Han Lee,Yungchang Lin,Kunchi Lai. (2014) A review of marine biodiversity information resources . Biodiv Sci, 22(3): 253-263.
[9] Lisong Wang,Vincent S Smith,Hongrui Zhang,Xianchun Zhang. (2014) Scratchpads 2.0: a virtual research environment for biodiversity sciences in the Internet era . Biodiv Sci, 22(3): 264-276.
[10] Jian Zhang,Shengbin Chen,Bin Chen,Yanjun Du,Xiaolei Huang,Xubin Pan,Qiang Zhang. (2013) Citizen science: integrating scientific research, ecological conservation and public participation . Biodiv Sci, 21(6): 738-749.
[11] Lisong Wang, Lina Zhao, Haining Qin. (2012) A preliminary assessment of extinction risk from six species in the genus Pternopetalum based on herbarium specimen data . Biodiv Sci, 20(6): 761-768.
[12] Kunchi Lai, Youhua Cheng, Yuehchih Chen, Yousheng Li, Kwangtsao Shao. (2012) Applying cluster analysis and Google Maps in the study of large-scale species occurrence data . Biodiv Sci, 20(1): 76-85.
[13] Kwangtsao Shao, Kunchi Lai, Yungchang Lin, Chihjen Ko, Han Lee, Lingya Hung, Yuehchih Chen, Leesea Chen. (2010) Experience and strategy of biodiversity data integration in Taiwan . Biodiv Sci, 18(5): 444-453.
[14] Zheping Xu, Jinzhong Cui, Haining Qin, Keping Ma. (2010) On the architecture of biodiversity e-Science infrastructure in China . Biodiv Sci, 18(5): 480-488.
[15] Jing Chen, Baowei Zhang, Keping Ma, Zhigang Jiang. (2009) Bibliometric analysis of status quo of conservation biology in China . Biodiv Sci, 17(4): 423-429.
Full text