Inferring True Species Richness and Complete Abundance Distribution in Six Reef-fish Communities from Red-sea, Using the Numerical Extrapolation of Incomplete Samplings

Main Article Content

Jean Beguinot

Abstract

Even when ecological communities are incompletely sampled (which is most frequent in practice, at least for species-rich assemblages including many rare species), it remains possible to retrieve much more information than could be expected first, by applying numerical extrapolation to incomplete field data. Indeed, recently developed procedures of numerical extrapolation of partial samplings now allow to estimate, with fair accuracy, not only the number of the still unrecorded species but, moreover, the distribution of abundances of each of these unrecorded species, thereby making available the full range of the Species Abundance Distribution, despite dealing with incomplete data only. In turn, this allows to address a series of descriptive and functional aspects of the internal organization of species assemblages, which otherwise would have required disposing of truly exhaustive samplings.

This approach is applied, here, to the previously reported partial samplings of six neighboring reef-fish communities from Tiran Island, Red Sea, with the goal of better understanding their internal organization in relation to their respective environments.

In practice, the numerical completion contributes to avoid erroneous interpretations that would likely stem from considering only the incomplete field data. This point is especially relevant when studying reef-associated communities because accurate understanding of their organization will help guiding and refining at best the protective measures required by these particularly vulnerable communities.

Keywords:
Coral reef, species diversity, rank abundance distribution, evenness, unevenness, hierarchical structuration, Gulf of Aquaba.

Article Details

How to Cite
Beguinot, J. (2019). Inferring True Species Richness and Complete Abundance Distribution in Six Reef-fish Communities from Red-sea, Using the Numerical Extrapolation of Incomplete Samplings. Asian Journal of Environment & Ecology, 11(3), 1-21. https://doi.org/10.9734/ajee/2019/v11i330136
Section
Original Research Article

References

Cam E, Nichols JD, Saue JR, Hines, JE. On the estimation of species richness based on the accumulation of previously unrecorded species. Ecography. 2002;25: 102-108.

Rajakaruna H, Drake DAR, Chan FT, Bailey SA. Optimizing performance of nonparametric species richness estimators under constrained sampling. Ecology and Evolution. 2016;6:7311-7322.

Chen Y, Shen TJ. Rarefaction and extrapolation of species richness using an area-based Fisher’s logseries. Ecology and Evolution. 2017;7:10066-10078.

May RM. Patterns of species abundance and diversity. In Cody M.L. & Diamond J.M. Ecology and Evolution of Communities. 1975; The Belknap Press of Harvard University. 1975;81-120.

McGill BJ, Etienne RS, Gray JS et al. Species abundance distributions: moving beyond single prediction theories to integration within an ecological framework. Ecology Letters. 2007;10:995-1015.

Ulrich W, Ollik M, Ugland KI. A meta-analysis of species-abundance distributions. Oikos. 2010;119:1149-1155.

Komonen A, Elo M. Ecological response hides behind the species abundance distribution: Community response to low-intensity disturbance in managed grasslands. Ecology and Evolution. 2017; 7:8558-8566.

Wang X, Ellwood F, Ai D, Zhang R & Wang G. Species abundance distributions as a proxy for the niche-neutrality continuum. Journal of Plant Ecology. 2017; rtx 013.

Wells JW. Coral reefs: 609-632; in J.W. Hedspeth editor, Treatise on marine ecology and paleoecology. Geological Society of America. Mem. 1957;67.

Glynn PW. High complexity food webs in low-diversity eastern Pacific reef-coral communities. Ecosystems. 2004;7:358-367.

Goren M. & Spanier E. The communities of benthic fish in Foul Bay (Tiran Island, Red Sea). Oceanologica Acta. 1985;8(4): 471-478.

Willis A Rarefaction, alpha diversity and statistics. bioRxiv; 2017.
DOI: 10.1101/231878

Rumohr H, Karakassis I, Jensen JN. Estimating species richness, abundance and diversity with 70 macro-benthic replicates in the Western Baltic Sea. Marine Ecology Progress Series. 2001; 214:103-110.

Fontaine B, Bouchet P et al. The European union’s 2010 target: Putting rare species in focus. Biodiversity and Conservation. 2007;139:167-185.

Flöder S, Jaschinski S, Wells G, Burns CW. Dominance and compensatory growth in phytoplankton communities under salinity stress. Journal of Experimental Marine Biology and Ecology. 2010;395: 223-231.

Bracken M, Low N. Realistic losses of rare species disproportionately impact higher trophic levels. Ecology Letters. 2012;15: 461-467.

Mouillot D, Bellwood DR, Baraloto C, Chave J, Galzin R, Harmelin-Vivien M, Kulbicki M, Lavergne S, Lavorel S, Mouquet N, Paine CET, Renaud J & Thuiller W. Rare species support vulnerable functions in high-diversity ecosystems. PLoS Biol. 2013;11(5): e1001569.

Jain M, Flynn DFB, Prager CM, Hart GM, DeVan CM, Ahrestani FS, Palmer MI, Bunker DE, Knops JHM, Jouseau CF & Naeem S. The importance of rare species: A trait-based assessment of rare species contribution to functional diversity and possible ecosystem function in tall-grass prairies. Ecology and Evolution. 2014;4(1):104-112.

Ignatiades L, Gotsis-Skretas O. The contribution of rare species to coastal phytoplankton assemblages. Marine Ecology. 2014;35:132-145.

Low-Decarie E, Kolber M, Homme P, Lofano A, Dumbrell A, Gonzalez A & Bell G. Community rescue in experimental communities. Proceedings of the National Academy of Sciences USA. 2015;112(46): 14307-14312.

Leitao RP, Zuanon J, Villéger S, Williams SE, Baraloto C, Fortunel C, Mendonça FP, Mouillot D. Rare species contribute disproportionately to the functional structure of species assemblages. Proceedings of The Royal Society B. 2016; 283:0084.
DOI: 10.1098/rspb.2016.0084

Violle C, Thuillier W, Mouquet N, Munoz F, Kraft NJB, Cadotte MW, Livingstone SW & Mouillot D. Functional rarity: the ecology of outliers. Trends in Ecology; 2017.
DOI: 10.1016/j.tree.2017.02.002

Cao Y, Williams DD & Williams NE. How important are rare species in aquatic community ecology and bioassessment? Limnology and Oceanography. 1998; 43(7):1403-1409.

Bellier E, Grotan V, Engen S, Schartau AK, Diserud OH, Finstad AG. Combining counts and incidence data: An efficient approach for estimating the log-normal species abundance distribution and diversity indices. Oecologia; 2012.
DOI: 10.1007/s00442-012-2311-2

Cam E, Nichols JD, Sauer JR & Hines JE. On the estimation of species richness based on the accumulation of previously unrecorded species. Ecography. 2002;25: 102-108.

Rajakaruna H, Drake DAR, Chan FT & Bailey SA. Optimizing performance of nonparametric species richness estimators under constrained sampling. Ecology and Evolution. 2016;6:7311-7322.

Connolly SR, Hughes TP & Bellwood DR. A unified model explains commonness and rarity on coral reefs. Ecology Letters. 2017; 20:477-486.

Chen Y, Shen TJ. Rarefaction and extrapolation of species richness using an area-based Fisher’s logseries. Ecology and Evolution. 2017;7:10066-10078.

Kery M, Royle JA. Inference about species richness and community structure using species-specific occupancy models in the National Swiss Breeding Bird survey MUB. Proceedings of the EURING Technical Meeting and Workshop, Dunedin, New Zealand; 2007.

McGill BJ, Etienne RS, Gray JS et al. Species abundance distributions: Moving beyond single prediction theories to integration within an ecological framework. Ecology Letters. 2007;10:995-1015.

Ulrich W, Ollik M, Ugland KI. A meta-analysis of species-abundance distributions. Oikos. 2010;119:1149-1155.

Komonen A, Elo M. Ecological response hides behind the species abundance distribution: Community response to low-intensity disturbance in managed grasslands. Ecology and Evolution. 2017; 7:8558-8566.

Wang X, Ellwood F, AI D, Zhang R, Wang G. Species abundance distributions as a proxy for the niche-neutrality continuum. Journal of Plant Ecology. 2017;rtx:013.

Béguinot J. Theoretical derivation of a bias-reduced expression for the extrapolation of the species accumulation curve and the associated estimation of total species richness. Advances in Research. 2016;7(3):1-16.
DOI:10.9734/AIR/2016/26387

Béguinot J. Extrapolation of the Species Accumulation curve associated to “Chao” estimator of the number of unrecorded species: A mathematically consistent derivation. Annual Research & Review in Biology. 2016;11(4):1-19.
DOI:10.9734/ARRB/2016/30522;

Chao A, Hsieh T, Chazdon RL, Colwell RK & Gotelli NJ. Unveiling the species-rank abundance distribution by generalizing the Good-Turing sample coverage theory. Ecology. 2015;96(5):1189-1201.

Béguinot J. How to extrapolate Species Abundance Distributions with minimum bias when dealing with incomplete species inventories. Advances in Research. 2018; 13(4):1-24.
DOI: 10.9734/AIR/2018/39002

Béguinot J. Numerical extrapolation of the species abundance distribution unveils the true species richness and the hierarchical structuring of a partially sampled marine gastropod community in the Andaman Islands (India). Asian Journal of Environment and Ecology. 2018;6(4):1–23.
DOI: 10.9734/AJEE/2018/41293

Heip CHR, Herman PMJ & Soetaert K. Indices of diversity and evenness. Océanis. 1998;24(4):61-87.

Strong WL. Assessing species abundance unevenness within and between plant communities. Community Ecology. 2002; 3(2):237-246.
DOI: 10.1556/COMEC.3.2002.2.9

Grzès IM. Ant species richness and evenness increase along a metal pollution gradient in the Boleslaw zinc smelter area. Pedobiologia. 2009;53:65-73.

Loreau M. Species abundance patterns and the structure of ground-beetle communities. Ann. Zool. Fennici. 1992;28: 49-56.

Magurran AE, Henderson PA. Explaining the excess of rare species in natural species abundance distributions. Nature. 2003;422:714-716.

Connolly SR, Hughes TP, Bellwood DR & Karlson RH - Community structure of corals and reef fishes at multiple scales. Science. 2005;309:1363-1365.

Ulrich W, Soliveres S, Thomas AD, Dougill AJ, Maestre FT - Environmental correlates of species rank-abundance distributions in global drylands. Europe PMC Funders Group. 2016;20:56-64.

Béguinot J. The hierarchical structuring of species abundances within communities: Disentangling the intensity of the underlying structuring process behind the apparent unevenness pattern. Advances in Research. 2018;16(1):1-12.
DOI: 10.9734/AIR/2018/43918

Béguinot J. Disentangling and quantifying the functional determinants of species abundance unevenness in ecological communities. Advances in Research. 2019;19(1):1-14.
DOI: 10.9734/AIR/2019/v19i130114

DeBenedictis PA. On the correlations between certain diversity indices. The American Naturalist. 1973;107: 295-302.

Stirling G, Wilsey B. Empirical relationships between species richness, evenness and proportional diversity. The American Naturalist. 2001;158(3):286- 299.

Smith B, Wilson JB. A consumer’s guide to evenness indices. Oikos. 1996;76:70-82.

Loiseau N, Gaertner JC. Indices for assessing coral reef fish biodiversity: The need for a change in habits. Ecology and Evolution. 2015;5(18):4018-4027.

Buzas MA, Hayek LAC. On richness and evenness within and between communities. Paleobiology. 2005;31(2): 199-220.

MacArthur RH. On the relative abundance of bird species. Proceedings of the National Academy of Sciences U.S.A. 1957;43:293-295.

Wilson JB. Would we recognize a Broken-Stick community if we found one? Oikos. 1993;67(1):181-183.

Su Q. A relationship between species richness and evenness that depends on specific relative abundance distribution. Peer J. 2018;6:e4951.

Lande R, DeVries PJ, Walla TR When species accumulation curves intersect: implications for ranking diversity using small samples. Oikos. 2000;89(3):601-605.

Béguinot J. Least-biased estimations of true species richness of butterfly fauna in sub-urban sites around Jhansi (India) and the range of inter-annual variation of species richness. Asian Journal of Environment & Ecology. 2017;2(1):1-12. DOI:10.9734/AJEE/2017/32040; .

Béguinot J. Inter-annual variations of true species richness in a subtropical butterfly assemblage: An estimation based on least-biased extrapolations of species accumulation curves. Asian Journal of Biology. 2017;2(4):1-16.
DOI: 10.9734/AJOB/2017/33876;

Béguinot J. Extrapolation of total species richness from incomplete inventories: Application to the Gastropod fauna associated to coral reefs in ‘Mannar Gulf Biosphere Reserve’, India. Asian Journal of Environment and Ecology. 2017;4(3):1-14.
DOI: 109734/AJEE/2017/36831;

.

Béguinot J. The full hierarchical structuration of species abundances reliably inferred from the numerical extrapolation of still partial samplings: A case study with marine snail communities in Mannar Gulf (India). Asian Journal of Environment and Ecology. 2018;7(3):1-27. DOI: 109734/AJEE/2018/36831

Béguinot J. Analyzing the role of environmental stresses on species richness and the process of hierarchical structuring of species abundances in marine Gastropods communities at Suva (Fiji Islands). International Journal of Environment and Climate Change. 2018; 8(3):200-233.
DOI: 109734/IJECC/2018/44913

Béguinot J. Inferring total species richness and the exhaustive hierarchical structuring of species abundances in tropical Sea Stars communities (Asteroidea), using numerical extrapolation of partial inventories. Asian Journal of Environment and Ecology. 2018;8(2):1-25.
DOI: 109734/AJEE/2018/46272

Béguinot J. Comparing the complete hierarchical structuration of species abundances in reef fish communities according to coral morphology, using the numerical extrapolation of only incomplete inventories. Asian Journal of Environment and Ecology. 2018;8(1):1-20.
DOI: 109734/AJEE/2018/45402

Béguinot J. Influence of Coral Architecture on Species Richness and the Hierarchical Structuration of Species Abundances in Reef Fish Communities: A Case Study in the Eastern Tropical Pacific. Asian Journal of Environment & Ecology. 2019;8(3):1- 21.
DOI: 10.9734/AJEE/2018/V8I330075

Béguinot J. Influence of fishing activity on the total species richness and the abundance unevenness in reef fish communities: A case study in a Brazilian tropical coral complex. International Journal of Environment and Climate Change. 2019;9(1):58-76.
DOI: 109734/IJECC/2019/v9i130097

Béguinot J. Influence of Coral-reef complexity on Species Richness and the Hierarchical Structuration of Species Abundances in Reef Fish Communities: A Case Study in south-east Brazil. Asian Journal of Environment & Ecology. 2019; 9(3):1-20.
DOI: 10.9734/AJEE/2019/v9i330098

Baselga A. Partitioning the turnover and nestedness components of beta diversity. Global Ecology and Biogeography. 2010; 19:134-143.

Rattray A, Andrello M, Asnaghi V, Bevilacqua S et al. Geographic distance, water circulation and environmental condition shape the biodiversity of Mediterranean rocky coast. Marine Ecology Progress Series. 2016;553:1-11.

Béguinot J. Influence of environmental heterogeneity on the species composition, species richness and species abundances unevenness in reef-associated Conus communities (Neogastropoda) from Papua New-Guinea. Asian Journal of Environment & Ecology. 2019;10(3):1-21. DOI: 10.9734/AJEE/2019/v10i330116

Béguinot J. Variations in total species richness and the unevenness of species abundance distribution between two distant Conus communities (Neogastropoda): A case study in Mannar Gulf (India). Asian Journal of Environment & Ecology. 2019;9(4):1-18.
DOI: 10.9734/AJEE/2019/v9i430102

Béguinot J. An algebraic derivation of Chao’s estimator of the number of species in a community highlights the condition allowing Chao to deliver centered estimates. ISRN Ecology; 2014.
[Article ID: 847328]
DOI:10.1155/2014/847328;

Béguinot J. When reasonably stop sampling? How to estimate the gain in newly recorded species according to the degree of supplementary sampling effort. Annual Research & Review in Biology. 2015;7(5): 300-308.
DOI: 10.9734/ARRB/2015/18809;

O’Hara RB. Species richness estimators: How many species can dance on the head of a pin? Journal of Animal Ecology. 2005; 74:375-386.

Gotelli NJ, Colwell RK. Estimating species richness. pp. 39-54 in: Biological Diversity: Frontiers in Measurement and Assessment. A.E. Magurran and B.J. McGill (eds.). Oxford University Press, Oxford. 2010;345.

Gotelli NJ, Chao A. Measuring and estimating species richness, species diversity, biotic similarity from sampling data. In: Levin S.A. (ed.) Encyclopedia of Biodiversity. 2013; second edition. Waltham, MA: Academic Press. 2013;5: 195-211.

Brose U, Martinez ND, Williams RJ. Estimating species richness: Sensitivity to sample coverage and insensitivity to spatial patterns. Ecology. 2003;84(9): 2364-2377.