Skip to main content
Log in

Unravelling fish community assembly in shallow lakes: Insights from functional and phylogenetic diversity

  • Original Research
  • Published:
Reviews in Fish Biology and Fisheries Aims and scope Submit manuscript

Abstract

Global biodiversity loss has increased interest in identifying the patterns and mechanisms that shape community assembly. Growing empirical evidence indicates that investigating functional and phylogenetic diversity beyond purely taxonomic considerations may provide different but complementary information about community assembly. However, such multifaceted studies on community assembly from both functional and phylogenetic perspectives are rare in the context of fish assemblages in lakes. We examined patterns of functional and phylogenetic alpha diversity in fishes and explored the relationships between these patterns and their environmental drivers across broad environmental gradients in 30 shallow lakes. Furthermore, we examined community assembly mechanisms using null models to quantify the relative importance of deterministic and stochastic assembly processes. Our results revealed no clear patterns among multiple biodiversity components and their environmental drivers, and no single component could be used as a reliable proxy for another; these results suggest that accounting for functional and phylogenetic diversity can help to explain fish community variation. Null models revealed that both deterministic and stochastic assembly processes occurred simultaneously, with stochastic processes being responsible for the majority of fish community assembly processes in most of our study lakes. Taken together, these results highlight the importance of evaluating both functional and phylogenetic alpha diversity when identifying patterns of community assembly.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

Data availability

Data can be made available on reasonable request.

References

  • Alahuhta J, Erős T, Kärnä OM, Soininen J, Wang J, Heino J (2019) Understanding environmental change through the lens of trait-based, functional, and phylogenetic biodiversity in freshwater ecosystems. Environ Rev 27(2):263–273

    Article  Google Scholar 

  • Archer E, Archer ME (2020) Package ‘rfPermute’

  • Arrington DA, Winemiller KO, Layman CA (2005) Community assembly at the patch scale in a species rich tropical river. Oecologia 144:157–167

    Article  PubMed  Google Scholar 

  • Bannar-Martin KH, Kremer CT, Ernest SM, Leibold MA, Auge H, Chase J et al (2018) Integrating community assembly and biodiversity to better understand ecosystem function: the community assembly and the functioning of ecosystems (CAFE) approach. Ecol Lett 21(2):167–180

    Article  PubMed  Google Scholar 

  • Beguería S, Pueyo Y (2009) A comparison of simultaneous autoregressive and generalized least squares models for dealing with spatial autocorrelation. Glob Ecol Biogeogr 18(3):273–279

    Article  Google Scholar 

  • Blanchet S, Helmus MR, Brosse S, Grenouillet G (2014) Regional vs local drivers of phylogenetic and species diversity in stream fish communities. Freshwater Biol 59(3):450–462

    Article  Google Scholar 

  • Breiman L (2001) Random Forests. Mach Learn 45:5–32

    Article  Google Scholar 

  • Cadotte M, Albert CH, Walker SC (2013) The ecology of differences: assessing community assembly with trait and evolutionary distances. Ecol Lett 16(10):1234–1244

    Article  PubMed  Google Scholar 

  • Caruso T, Taormina M, Migliorini M (2012) Relative role of deterministic and stochastic determinants of soil animal community: a spatially explicit analysis of oribatid mites. J Anim Ecol 81(1):214–221

    Article  PubMed  Google Scholar 

  • Chapin Iii FS, Zavaleta ES, Eviner VT, Naylor RL, Vitousek PM, Reynolds HL et al (2000) Consequences of changing biodiversity. Nature 405(6783):234–242

    Article  Google Scholar 

  • Chapman PM, Tobias JA, Edwards DP, Davies RG (2018) Contrasting impacts of land-use change on phylogenetic and functional diversity of tropical forest birds. J Appl Ecol 55(4):1604–1614

    Article  Google Scholar 

  • Chase JM (2010) Stochastic community assembly causes higher biodiversity in more productive environments. Science 328(5984):1388–1391

    Article  CAS  PubMed  Google Scholar 

  • Chase JM, Kraft NJ, Smith KG, Vellend M, Inouye BD (2011) Using null models to disentangle variation in community dissimilarity from variation in α-diversity. Ecosphere 2(2):1–11

    Article  Google Scholar 

  • Clarke KR, Warwick RM (1998) A taxonomic distinctness index and its statistical properties. J Appl Ecol 35(4):523–531

    Article  Google Scholar 

  • Crozier RH, Dunnett LJ, Agapow PM (2005) Phylogenetic biodiversity assessment based on systematic nomenclature. Evol Bioinf 1:11–36

    Article  Google Scholar 

  • Daniel J, Gleason JE, Cottenie K, Rooney RC (2019) Stochastic and deterministic processes drive wetland community assembly across a gradient of environmental filtering. Oikos 128(8):1158–1169

    Article  Google Scholar 

  • de Bello F, Šmilauer P, Diniz-Filho JAF, Carmona CP, Lososová Z, Herben T, Götzenberger L (2017) Decoupling phylogenetic and functional diversity to reveal hidden signals in community assembly. Methods Ecol Evol 8(10):1200–1211

    Article  Google Scholar 

  • Dini-Andreote F, Stegen JC, Van Elsas JD, Salles JF (2015) Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession. Proc Natl Acad Sci USA 112(11):E1326–E1332

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dormann CF, McPherson MJ, Araújo MB, Bivand R, Bolliger J, Carl G et al (2007) Methods to account for spatial autocorrelation in the analysis of species distributional data: a review. Ecography 30(5):609–628

    Article  Google Scholar 

  • Dormann CF, Elith J, Bacher S, Buchmann C, Carl G, Carré G et al (2013) Collinearity: a review of methods to deal with it and a simulation study evaluating their performance. Ecography 36:27–46

    Article  Google Scholar 

  • Emerson BC, Gillespie RG (2008) Phylogenetic analysis of community assembly and structure over space and time. Trends Ecol Evol 23(11):619–630

    Article  PubMed  Google Scholar 

  • Englund G, Johansson F, Olofsson P, Salonsaari J, Öhman J (2009) Predation leads to assembly rules in fragmented fish communities. Ecol Lett 12(7):663–671

    Article  PubMed  Google Scholar 

  • Evans JS, Murphy MA (2019) Package ‘rfUtilities’

  • Farnon Ellwood MD, Manica A, Foster WA (2009) Stochastic and deterministic processes jointly structure tropical arthropod communities. Ecol Lett 12(4):277–284

    Article  Google Scholar 

  • Froese R, Pauly D (2020) FishBase. http://www.fishbase.org

  • Gajdzik L, Parmentier E, Michel LN, Sturaro N, Soong K, Lepoint G, Frédérich B (2018) Similar levels of trophic and functional diversity within damselfish assemblages across Indo-Pacific coral reefs. Funct Ecol 32(5):1358–1369

    Article  Google Scholar 

  • Gerhold P, Cahill JF Jr, Winter M, Bartish IV, Prinzing A (2015) Phylogenetic patterns are not proxies of community assembly mechanisms (they are far better). Funct Ecol 29:600–614

    Article  Google Scholar 

  • Giam X, Olden JD (2016) Environment and predation govern fish community assembly in temperate streams. Global Ecol Biogeogr 25(10):1194–1205

    Article  Google Scholar 

  • Gillespie R (2004) Community assembly through adaptive radiation in Hawaiian spiders. Science 303(5656):356–359

    Article  CAS  PubMed  Google Scholar 

  • Gomes LC, Bulla CK, Agostinho AA, Vasconcelos LP, Miranda LE (2012) Fish assemblage dynamics in a Neotropical floodplain relative to aquatic macrophytes and the homogenizing effect of a flood pulse. Hydrobiologia 685(1):97–107

    Article  Google Scholar 

  • Gotelli NJ, Graves GR (1996) Null models in ecology. Smithsonian Institution Press, Washington, DC

    Google Scholar 

  • Hardy OJ, Senterre B (2007) Characterizing the phylogenetic structure of communities by an additive partitioning of phylogenetic diversity. J Ecol 95(3):493–506

    Article  Google Scholar 

  • Heino J, Tolonen KT (2017a) Ecological drivers of multiple facets of beta diversity in a lentic macroinvertebrate metacommunity. Limnol Oceanogr 62(6):2431–2444

    Article  Google Scholar 

  • Heino J, Tolonen KT (2017b) Untangling the assembly of littoral macroinvertebrate communities through measures of functional and phylogenetic alpha diversity. Freshwater Biol 62(7):1168–1179

    Article  CAS  Google Scholar 

  • Heino J, Alahuhta J, Bini LM, Cai Y, Heiskanen AS, Hellsten S et al (2021) Lakes in the era of global change: moving beyond single-lake thinking in maintaining biodiversity and ecosystem services. Biol Rev 96:89–106

    Article  PubMed  Google Scholar 

  • Hill MJ, Heino J, White JC, Ryves DB, Wood PJ (2019) Environmental factors are primary determinants of different facets of pond macroinvertebrate alpha and beta diversity in a human-modified landscape. Biol Conserv 237:348–357

    Article  Google Scholar 

  • HilleRisLambers J, Adler PB, Harpole WS, Levine JM, Mayfield MM (2012) Rethinking community assembly through the lens of coexistence theory. Annu Rev Ecol Evol Syst 43:227–248

    Article  Google Scholar 

  • Hou X, Feng L, Tang J, Song XP, Liu J, Zhang Y et al (2020) Anthropogenic transformation of Yangtze Plain freshwater lakes: patterns drivers and impacts. Remote Sens Environ 248:111998

    Article  Google Scholar 

  • Hubbell SP (2001) The unified neutral theory of biodiversity and biogeography. Princeton University Press, Princeton

    Google Scholar 

  • Ingram T, Shurin JB (2009) Trait-based assembly and phylogenetic structure in northeast Pacific rockfish assemblages. Ecology 90(9):2444–2453

    Article  PubMed  Google Scholar 

  • Ishwaran H, Kogalur U (2014) Random forests for survival, regression and classification (RF-SRC), R package version 1.6. URL http://CRAN.R-project.org/package=randomForestSRC

  • Jackson DA, Harvey HH (1997) Qualitative and quantitative sampling of lake fish communities. Can J Fish Aquat Sci 54:2807–2813

    Article  Google Scholar 

  • Jackson DA, Somers KM, Harvey HH (1992) Null models and fish communities: evidence of nonrandom patterns. Am Nat 139(5):930–951

    Article  Google Scholar 

  • Jeppesen E, Søndergaard M, Søndergaard M, Christoffersen K (2012) The structuring role of submerged macrophytes in lakes. Springer

  • Jia Y, Kennard MJ, Liu Y, Sui X, Chen Y, Li K, Wang G, Chen Y (2019a) Understanding invasion success of Pseudorasbora parva in the Qinghai-Tibetan Plateau: insights from life-history and environmental filters. Sci Total Environ 694:133739

    Article  CAS  PubMed  Google Scholar 

  • Jia Y, Chen K, Sun H, Chen Y (2019b) Climate, habitat and human disturbance driving the variation of life-history traits of the invasive goldfish Carassius auratus (Linnaeus, 1758) in a Tibetan Plateau river. Aquat Invasions 14:724–737

    Article  Google Scholar 

  • Jia Y, Kennard MJ, Liu Y, Sui X, Li K, Wang G, Chen Y (2020) Human disturbance and long-term changes in fish taxonomic, functional and phylogenetic diversity in the Yellow River, China. Hydrobiologia 847:3711–3725

    Article  CAS  Google Scholar 

  • Jia YT, Jiang YH, Liu YH, Sui XY, Feng X, Zhu R, Chen YF (2021) Understanding trophic structure variation in fish assemblages of subtropical shallow lakes: Combined effects of ecosystem size, productivity, and disturbance. Ecol Indic 129:107924

    Article  Google Scholar 

  • Jiang X, Zheng P, Cao L, Pan B (2021) Effects of long-term floodplain disconnection on multiple facets of lake fish biodiversity: decline of alpha diversity leads to a regional differentiation through time. Sci Total Eenviron 763:144177

    Article  CAS  Google Scholar 

  • Keck F, Kahlert M (2019) Community phylogenetic structure reveals the imprint of dispersal-related dynamics and environmental filtering by nutrient availability in freshwater diatoms. Sci Rep 9(1):1–8

    Article  Google Scholar 

  • Kembel SW, Cowan PD, Helmus MR, Cornwell WK, Morlon H, Ackerly D et al (2010) Picante: R tools for integrating phylogenies and ecology. Bioinformatics 26(11):1463–1464

    Article  CAS  PubMed  Google Scholar 

  • Laliberté E, Legendre P, Shipley B, Laliberté ME (2014) Package ‘FD’. Measuring functional diversity from multiple traits, and other tools for functional ecology

  • Lepori F, Malmqvist B (2009) Deterministic control on community assembly peaks at intermediate levels of disturbance. Oikos 118(471):479

    Google Scholar 

  • Li D, Olden JD, Lockwood JL, Record S, McKinney ML, Baiser B (2020) Changes in taxonomic and phylogenetic diversity in the Anthropocene. Proc R Soc London Ser B 287(1929):20200777

    Google Scholar 

  • Liaw A, Wiener M (2002) Classification and regression by randomForest. R News 2:18–22

    Google Scholar 

  • Liu X, Wang H (2018a) Effects of loss of lateral hydrological connectivity on fish functional diversity. Conserv Biol 32(6):1336–1345

    Article  PubMed  Google Scholar 

  • Liu X, Wang H (2018b) Contrasting patterns and drivers in taxonomic versus functional diversity, and community assembly of aquatic plants in subtropical lakes. Biodivers Conserv 27(12):3103–3118

    Article  Google Scholar 

  • Lopes TM, Cunha ER, Silva JCB, Behrend RD, Gomes LC (2015) Dense macrophytes influence the horizontal distribution of fish in floodplain lakes. Environ Biol Fishes 98(7):1741–1755

    Article  Google Scholar 

  • Losos JB (2008) Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species. Ecol Lett 11(10):995–1003

    Article  PubMed  Google Scholar 

  • Ma R, Yang G, Duan H, Jiang J, Wang S, Feng X, Li A, Kong F, Xue B, Wu J, Li S (2011) China’s lakes at present: number, area and spatial distribution. Sci China Earth Sci 54:283–289

    Article  CAS  Google Scholar 

  • Macarthur R, Levins R (1967) The limiting similarity, convergence, and divergence of coexisting species. Am Nat 101:377–385

    Article  Google Scholar 

  • Måren IE, Kapfer J, Aarrestad PA, Grytnes JA, Vandvik V (2018) Changing contributions of stochastic and deterministic processes in community assembly over a successional gradient. Ecology 99(1):148–157

    Article  PubMed  Google Scholar 

  • Mazel F, Pennell MW, Cadotte MW, Diaz S, Dalla Riva GV, Grenyer R et al (2018) Prioritizing phylogenetic diversity captures functional diversity unreliably. Nat Commun 9(1):1–9

    Article  CAS  Google Scholar 

  • Mercier L, Darnaude AM, Bruguier O, Vasconcelos RP, Cabral HN, Costa MJ et al (2011) Selecting statistical models and variable combinations for optimal classification using otolith microchemistry. Ecol Appl 21(4):1352–1364

    Article  PubMed  Google Scholar 

  • Middelboe AL, Markager S (1997) Depth limits and minimum light requirements of freshwater macrophytes. Freshwater Biol 37(3):553–568

    Article  Google Scholar 

  • Miller ET, Farine DR, Trisos CH (2017) Phylogenetic community structure metrics and null models: a review with new methods and software. Ecography 40(4):461–477

    Article  Google Scholar 

  • Mori AS, Isbell F, Seidl R (2018) β-diversity, community assembly, and ecosystem functioning. Trends Ecol Evol 33(7):549–564

    Article  PubMed  Google Scholar 

  • Münkemüller T, De Bello F, Meynard CN, Gravel D, Lavergne S, Mouillot D et al (2012) From diversity indices to community assembly processes: a test with simulated data. Ecography 35(5):468–480

    Article  Google Scholar 

  • Oksanen J, Blanchet F, Kindt R, Legendre P, Ohara B (2016) Vegan: community ecology package. R Package 2:3–3

    Google Scholar 

  • Orrock JL, Watling JI (2010) Local community size mediates ecological drift and competition in metacommunities. Proc R Soc B 277:2185–2191

    Article  PubMed  PubMed Central  Google Scholar 

  • Park DS, Razafindratsima OH (2019) Anthropogenic threats can have cascading homogenizing effects on the phylogenetic and functional diversity of tropical ecosystems. Ecography 42(1):148–161

    Article  Google Scholar 

  • Pavoine S, Bonsall MB (2011) Measuring biodiversity to explain community assembly: a unified approach. Biol Rev 86(4):792–812

    Article  CAS  PubMed  Google Scholar 

  • Pecuchet L, Törnroos A, Lindegren M (2016) Patterns and drivers of fish community assembly in a large marine ecosystem. Mar Ecol Prog Ser 546:239–248

    Article  Google Scholar 

  • Post DM, Pace ML, Hairston NG (2000) Ecosystem size determines food-chain length in lakes. Nature 405:1047–1049

    Article  CAS  PubMed  Google Scholar 

  • Powell JR, Karunaratne S, Campbell CD, Yao H, Robinson L, Singh BK (2015) Deterministic processes vary during community assembly for ecologically dissimilar taxa. Nat Commun 6(1):1–10

    Article  CAS  Google Scholar 

  • Purschke O, Schmid BC, Sykes MT, Poschlod P, Michalski SG, Durka W et al (2013) Contrasting changes in taxonomic, phylogenetic and functional diversity during a long-term succession: insights into assembly processes. J Ecol 101(4):857–866

    Article  Google Scholar 

  • Qian H, Cao Y, Li D, Chu C, Sandel B, Wang X (2020) Geographic patterns and environmental correlates of phylogenetic relatedness and diversity for freshwater fish assemblages in North America. Ecography 43(12):1814–1824

    Article  Google Scholar 

  • Ricotta C, Bacaro G, Marignani M, Godefroid S, Mazzoleni S (2012) Computing diversity from dated phylogenies and taxonomic hierarchies: does it make a difference to the conclusions? Oecologia 170(2):501–506

    Article  PubMed  Google Scholar 

  • Roa-Fuentes CA, Heino J, Cianciaruso MV, Ferraz S, Zeni JO, Casatti L (2019) Taxonomic, functional, and phylogenetic β-diversity patterns of stream fish assemblages in tropical agroecosystems. Freshwater Biol 64(3):447–460

    Article  Google Scholar 

  • Schindler DE, Scheuerell MD (2002) Habitat coupling in lake ecosystems. Oikos 98:177–189

    Article  Google Scholar 

  • Søndergaard M, Lauridsen TL, Johansson LS, Jeppesen E (2017) Nitrogen or phosphorus limitation in lakes and its impact on phytoplankton biomass and submerged macrophyte cover. Hydrobiologia 795(1):35–48

    Article  CAS  Google Scholar 

  • Spasojevic MJ, Suding KN (2012) Inferring community assembly mechanisms from functional diversity patterns: the importance of multiple assembly processes. J Ecol 100(3):652–661

    Article  Google Scholar 

  • Wang J, Legendre P, Soininen J, Yeh CF, Graham E, Stegen J et al (2020a) Temperature drives local contributions to beta diversity in mountain streams: stochastic and deterministic processes. Global Ecol Biogeogr 29(3):420–432

    Article  Google Scholar 

  • Wang K, Yan H, Peng X, Hu H, Zhang H, Hou D et al (2020b) Community assembly of bacteria and archaea in coastal waters governed by contrasting mechanisms: a seasonal perspective. Mol Ecol 29(19):3762–3776

    Article  CAS  PubMed  Google Scholar 

  • Wang SM, Dou HS (1998) Lakes in China. Science, Beijing

  • Webb CO (2000) Exploring the phylogenetic structure of ecological communities: an example for rain forest trees. Am Nat 156(2):145–155

    Article  PubMed  Google Scholar 

  • Webb CO, Ackerly DD, McPeek MA, Donoghue MJ (2002) Phylogenies and community ecology. Ann Rev Ecol Evol Syst 33(1):475–505

    Article  Google Scholar 

  • Wiegand T, Uriarte M, Kraft NJ, Shen G, Wang X, He F (2017) Spatially explicit metrics of species diversity, functional diversity, and phylogenetic diversity: insights into plant community assembly processes. Annu Rev Ecol Evol Syst 48:329–351

    Article  Google Scholar 

  • Wiens JJ, Donoghue MJ (2004) Historical biogeography, ecology and species richness. Trends Ecol Evol 19(12):639–644

    Article  PubMed  Google Scholar 

  • Willig MR, Kaufman DM, Stevens RD (2003) Latitudinal gradients of biodiversity: pattern, process, scale, and synthesis. Annu Rev Ecol Evol Syst 34:273–309

    Article  Google Scholar 

  • Winter M, Devictor V, Schweiger O (2013) Phylogenetic diversity and nature conservation: Where are we? Trends Ecol Evol 28(4):199–204

    Article  PubMed  Google Scholar 

  • Ye S, Li Z, Lek-Ang S, Feng G, Lek S, Cao W (2006) Community structure of small fishes in a shallow macrophytic lake (Niushan Lake) along the middle reach of the Yangtze River. China Aquat Living Resour 19(4):349–359

    Article  Google Scholar 

  • Zhang X, Liu X, Wang H (2015) Effects of water level fluctuations on lakeshore vegetation of three subtropical floodplain lakes. China Hydrobiol 747(1):43–52

    Article  Google Scholar 

  • Zhang C, Ding C, Ding L, Chen L, Hu J, Tao J, Jiang X (2019) Large-scale cascaded dam constructions drive taxonomic and phylogenetic differentiation of fish fauna in the Lancang River. China Rev Fish Biol Fisheries 29(4):895–916

    Article  Google Scholar 

Download references

Acknowledgements

This research was financially supported by the National Natural Science Foundation of China (Grant no. 31720103905); the Major Science and Technology Program for Water Pollution Control and Treatment (Grant No. 2017ZX07302-002); and the Key Laboratory of Plateau Aquatic Organism and Environment of Qinghai Province (Grant No. KLPA2013-01; KLPA2016-01; KLPA2017-01).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Yifeng Chen.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (DOC 58 KB)

Appendices

Appendix 1

See Table

Table 4 References used in compiling database for the fishes in our studied lakes

4.

Appendix 2

See Table

Table 5 Species list and functional traits used in our study

5.

Appendix 3

See Fig. 

Fig. 7
figure 7

Spearman’s correlation coefficients between environmental variables

7.

Appendix 4

See Table

Table 6 Variance inflation factor values for each environmental variable included in our study

6.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Jia, Y., Jiang, Y., Liu, Y. et al. Unravelling fish community assembly in shallow lakes: Insights from functional and phylogenetic diversity. Rev Fish Biol Fisheries 32, 623–644 (2022). https://doi.org/10.1007/s11160-021-09688-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11160-021-09688-2

Keywords

Navigation