Biased-corrected richness estimates for the Amazonian tree flora.
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
23 06 2020
23 06 2020
Historique:
received:
21
11
2019
accepted:
19
05
2020
entrez:
25
6
2020
pubmed:
25
6
2020
medline:
16
1
2021
Statut:
epublish
Résumé
Amazonian forests are extraordinarily diverse, but the estimated species richness is very much debated. Here, we apply an ensemble of parametric estimators and a novel technique that includes conspecific spatial aggregation to an extended database of forest plots with up-to-date taxonomy. We show that the species abundance distribution of Amazonia is best approximated by a logseries with aggregated individuals, where aggregation increases with rarity. By averaging several methods to estimate total richness, we confirm that over 15,000 tree species are expected to occur in Amazonia. We also show that using ten times the number of plots would result in an increase to just ~50% of those 15,000 estimated species. To get a more complete sample of all tree species, rigorous field campaigns may be needed but the number of trees in Amazonia will remain an estimate for years to come.
Identifiants
pubmed: 32576943
doi: 10.1038/s41598-020-66686-3
pii: 10.1038/s41598-020-66686-3
pmc: PMC7311553
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
10130Références
ter Steege, H. et al. Hyperdominance in the Amazonian tree flora. Science 342, 1243092, https://doi.org/10.1126/science.1243092 (2013).
doi: 10.1126/science.1243092
pubmed: 24136971
Fung, T., Villain, L. & Chisholm, R. A. Analytical formulae for computing dominance from species-abundance distributions. Journal of Theoretical Biology 386, 147–158, https://doi.org/10.1016/j.jtbi.2015.09.011 (2015).
doi: 10.1016/j.jtbi.2015.09.011
pubmed: 26409166
Ricklefs, R. E. How tree species fill geographic and ecological space in eastern North America. Annals of Botany 115, 949–959, https://doi.org/10.1093/aob/mcv029 (2015).
doi: 10.1093/aob/mcv029
pubmed: 25851139
pmcid: 4407066
Cardoso, D. et al. Amazon plant diversity revealed by a taxonomically verified species list. Proceedings of the National Academy of Sciences 114, 10695–10700, https://doi.org/10.1073/pnas.1706756114 (2017).
doi: 10.1073/pnas.1706756114
Harte, J. & Kitzes, J. Inferring regional-scale species diversity from small-plot censuses. Plos One 10, e0117527, https://doi.org/10.1371/journal (2015).
doi: 10.1371/journal
pubmed: 25706536
pmcid: 4338294
ter Steege, H. et al. Estimating species richness in hyper-diverse large tree communities. Ecology 98, 1444–1454, https://doi.org/10.1002/ecy.1813 (2017).
doi: 10.1002/ecy.1813
pubmed: 28419434
ter Steege, H. et al. The discovery of the Amazonian tree flora with an updated checklist of all known tree taxa. Scientific Reports 6, 29549, https://doi.org/10.1038/srep29549 (2016).
doi: 10.1038/srep29549
pubmed: 27406027
pmcid: 4942782
ter Steege, H. et al. Towards a dynamic list of Amazonian tree species. Scientific Reports 9, 3501, https://doi.org/10.1038/s41598-019-40101-y (2019).
doi: 10.1038/s41598-019-40101-y
pubmed: 30837572
pmcid: 6401171
ter Steege, H. & al, e. Amazon Tree Diversity Network, http://atdn.myspecies.info/ (2019).
Ulrich, W. & Ollik, M. Limits to the estimation of species richness: the use of relative abundance distributions. Diversity and Distributions 11, 265–273 (2005).
doi: 10.1111/j.1366-9516.2005.00127.x
Baldridge, E., Harris, D. J., Xiao, X. & White, E. P. An extensive comparison of species-abundance distribution models. PeerJ 4, e2823, https://doi.org/10.7717/peerj.2823 (2016).
doi: 10.7717/peerj.2823
pubmed: 28028483
pmcid: 5183127
Tovo, A. et al. Upscaling species richness and abundances in tropical forests. Science Advances 3, e1701438, https://doi.org/10.1126/sciadv.1701438 (2017).
doi: 10.1126/sciadv.1701438
pubmed: 29057324
pmcid: 5647133
Bulmer, M. G. On fitting the Poisson lognormal distribution to species abundance data. Biometrics 30, 101–110 (1974).
doi: 10.2307/2529621
Engen, S., Lande, R., Walla, T. & DeVries, P. J. Analyzing spatial structure of communities using the two‐dimensional Poisson lognormal species abundance model. The American Naturalist 160, 60–73, https://doi.org/10.1086/340612 (2002).
doi: 10.1086/340612
pubmed: 18707499
Duque, A. et al. Insights into regional patterns of Amazonian forest structure, diversity, and dominance from three large terra-firme forest dynamics plots. Biodiversity and Conservation 26, 669–686, https://doi.org/10.1007/s10531-016-1265-9 (2017).
doi: 10.1007/s10531-016-1265-9
Chao, A., Colwell, R. K., Lin, C.-W. & Gotelli, N. J. Sufficient sampling for asymptotic minimum species richness estimators. Ecology 90, 1125–1133, https://doi.org/10.1890/07-2147.1 (2009).
doi: 10.1890/07-2147.1
pubmed: 19449706
Branco, M., Figueiras, F. G. & Cermeño, P. Assessing the efficiency of non-parametric estimators of species richness for marine microplankton. Journal of Plankton Research 40, 230–243, https://doi.org/10.1093/plankt/fby005 (2018).
doi: 10.1093/plankt/fby005
Ulrich, W., Kusumoto, B., Fattorini, S. & Kubota, Y. Factors influencing the precision of species richness estimation in Japanese vascular plants. Diversity and Distributions, https://doi.org/10.1111/ddi.13049 (2020).
Condit, R. et al. Spatial patterns in the distribution of tropical tree species. Science 288, 1414, https://doi.org/10.1126/science.288.5470.1414 (2000).
doi: 10.1126/science.288.5470.1414
pubmed: 10827950
Plotkin, J. B. & Muller-Landau, H. C. Sampling the species composition of a landscape. Ecology 83, 3344–3356, https://doi.org/10.1890/0012-9658 (2002).
doi: 10.1890/0012-9658
Plotkin, J. B. et al. Species-area curves, spatial aggregation, and habitat specialization in tropical forests. Journal of Theoretical Biology 207, 81–99, https://doi.org/10.1006/jtbi.2000.2158 (2000).
doi: 10.1006/jtbi.2000.2158
pubmed: 11027481
ter Steege, H. et al. Estimating the global conservation status of over 15,000 Amazonian tree species. Science Advances 1, e1500936, https://doi.org/10.1126/sciadv.1500936 (2015).
doi: 10.1126/sciadv.1500936
pubmed: 26702442
pmcid: 4681336
McGill, B. J. et al. Species abundance distributions: moving beyond single prediction theories to integration within an ecological framework. Ecology Letters 10, 995–1015 (2007).
doi: 10.1111/j.1461-0248.2007.01094.x
Green, J. L. & Plotkin, J. B. A statistical theory for sampling species abundances. Ecology Letters 10, 1037–1045 (2007).
doi: 10.1111/j.1461-0248.2007.01101.x
Hanski, I. Dynamics of regional distribution: the core and satellite species hypothesis. Oikos 87, 210–221 (1982).
doi: 10.2307/3544021
Magurran, A. E. & Henderson, P. A. Explaining the excess of rare species in natural species abundance distributions. Nature 422, 714–716 (2003).
doi: 10.1038/nature01547
Baker, T. R. et al. Maximising Synergy among Tropical Plant Systematists, Ecologists, and Evolutionary Biologists. Trends in Ecology & Evolution 32, 258–267, https://doi.org/10.1016/j.tree.2017.01.007 (2017).
doi: 10.1016/j.tree.2017.01.007
Hopkins, M. J. G. Are we close to knowing the plant diversity of the Amazon? Anais da Academia Brasileira de Ciências 91, e20190396, https://doi.org/10.1590/0001-3765201920190396. (2019).
doi: 10.1590/0001-3765201920190396.
pubmed: 31531554
Elias, T. S. The Complete Trees of North America. Field Guide and Natural History. (Times Mirror Magazines., 1980).
Kunin, W. E. et al. Upscaling biodiversity: estimating the species–area relationship from small samples. Ecological Monographs 88, 170–187, https://doi.org/10.1002/ecm.1284 (2018).
doi: 10.1002/ecm.1284
Jabot, F. & Chave, J. Analyzing tropical forest tree species abundance distributions using a nonneutral model and through approximate Bayesian inference. The American Naturalist 178, E37–47 (2011).
doi: 10.1086/660829
Environmental Systems Research Institute. ESRI Data & Maps 1999 - An ESRI White Paper. (Environmental Systems Research Institute, Redlands, US, 1999).
Soares-Filho, B. S. et al. Modelling conservation in the Amazon basin. Nature 440, 520–523, doi:http://www.nature.com/nature/journal/v440/n7083/suppinfo/nature04389_S1.html (2006).
Soares-Filho, B. S. et al. LBA-ECO LC-14 Modeled Deforestation Scenarios, Amazon Basin: 2002–2050, https://daac.ornl.gov/cgi-bin/dsviewer.pl?ds_id=1153 (2013).
Shuttle Radar Propulsion Mission. NASA Jet Propulsion Laboratory, http://www2.jpl.nasa.gov/srtm/ (2009).
Fisher, R. A., Corbet, A. S. & Williams, C. B. The relation between the number of species and the number of individuals in a random sample of an animal population. Journal of Animal Ecology 12, 42–58 (1943).
doi: 10.2307/1411
Saether, B. E., Engen, S. & Grøtan, V. Species diversity and community similarity in fluctuating environments: parametric approaches using species abundance distributions. The Journal of Animal Ecology 82, 721–738 (2013).
doi: 10.1111/1365-2656.12068
Pielou, E. C. Mathematical Ecology. (John Wiley and Sons, 1977).
Preston, F. W. The commonness, and rarity of species. Ecology 29, 254–283, https://doi.org/10.2307/1930989 (1948).
doi: 10.2307/1930989
Prado, P. I., Miranda, M. D. & Chalom, A. sads: Maximum likelihood models for species abundance distributions. (CRAN network, https://CRAN.R-project.org/package=sads , 2018).
Csilléry, K., Blum, M. G. B., Gaggiotti, O. E. & François, O. Approximate Bayesian Computation (ABC) in practice. Trends in Ecology & Evolution 25, 410–418, https://doi.org/10.1016/j.tree.2010.04.001 (2010).
doi: 10.1016/j.tree.2010.04.001
Csilléry, K., François, O. & Blum, M. G. B. abc: an R package for approximate Bayesian computation (ABC). Methods in Ecology and Evolution 3, 475–479, https://doi.org/10.1111/j.2041-210X.2011.00179.x (2012).
doi: 10.1111/j.2041-210X.2011.00179.x