in

Inter-annual variability patterns of reef cryptobiota in the central Red Sea across a shelf gradient

  • Knowlton, N. et al. in Life in the World’s Oceans 65–78 (Wiley-Blackwell, 2010).

  • Fisher, R. et al. Species richness on coral reefs and the pursuit of convergent global estimates. Curr. Biol. 25, 500–505. https://doi.org/10.1016/j.cub.2014.12.022 (2015).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Brandl, S. J., Goatley, C. H. R., Bellwood, D. R. & Tornabene, L. The hidden half: Ecology and evolution of cryptobenthic fishes on coral reefs. Biol. Rev. 93, 1846–1873. https://doi.org/10.1111/brv.12423 (2018).

    Article 
    PubMed 

    Google Scholar 

  • Appeltans, W. et al. The magnitude of global marine species diversity. Curr. Biol. 22, 2189–2202. https://doi.org/10.1016/j.cub.2012.09.036 (2012).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Carvalho, S. et al. Beyond the visual: Using metabarcoding to characterize the hidden reef cryptobiome. Proc. R. Soc. B Biol. Sci. https://doi.org/10.1098/rspb.2018.2697 (2019).

    Article 

    Google Scholar 

  • Kramer, M. J., Bellwood, O., Fulton, C. J. & Bellwood, D. R. Refining the invertivore: Diversity and specialisation in fish predation on coral reef crustaceans. Mar. Biol. 162, 1779–1786. https://doi.org/10.1007/s00227-015-2710-0 (2015).

    CAS 
    Article 

    Google Scholar 

  • Brandl, S. J. et al. Demographic dynamics of the smallest marine vertebrates fuel coral reef ecosystem functioning. Science 364, 1189–1192. https://doi.org/10.1126/science.aav3384 (2019).

    ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Kramer, M. J., Bellwood, D. R. & Bellwood, O. Cryptofauna of the epilithic algal matrix on an inshore coral reef, Great Barrier Reef. Coral Reefs 31, 1007–1015. https://doi.org/10.1007/s00338-012-0924-x (2012).

    ADS 
    Article 

    Google Scholar 

  • Rocha, L. A. et al. Specimen collection: An essential tool. Science 344, 814–815. https://doi.org/10.1126/science.344.6186.814 (2014).

    ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Berumen, M. L. et al. The status of coral reef ecology research in the Red Sea. Coral Reefs 32, 737–748. https://doi.org/10.1007/s00338-013-1055-8 (2013).

    ADS 
    Article 

    Google Scholar 

  • Paknia, O., Sh, H. R. & Koch, A. Lack of well-maintained natural history collections and taxonomists in megadiverse developing countries hampers global biodiversity exploration. Org. Divers. Evol. 15, 619–629. https://doi.org/10.1007/s13127-015-0202-1 (2015).

    Article 

    Google Scholar 

  • Knowlton, N. & Leray, M. Censusing marine life in the twentyfirst Century. Genome 58, 238–238 (2015).

    Google Scholar 

  • Yu, D. W. et al. Biodiversity soup: Metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring. Methods Ecol. Evol. 3, 613–623. https://doi.org/10.1111/j.2041-210X.2012.00198.x (2012).

    Article 

    Google Scholar 

  • Ransome, E. et al. The importance of standardization for biodiversity comparisons: A case study using autonomous reef monitoring structures (ARMS) and metabarcoding to measure cryptic diversity on Mo’orea coral reefs, French Polynesia. PLoS ONE https://doi.org/10.1371/journal.pone.0175066 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Coker, D. J., DiBattista, J. D., Sinclair-Taylor, T. H. & Berumen, M. L. Spatial patterns of cryptobenthic coral-reef fishes in the Red Sea. Coral Reefs 37, 193–199. https://doi.org/10.1007/s00338-017-1647-9 (2018).

    ADS 
    Article 

    Google Scholar 

  • Pearman, J. K. et al. Cross-shelf investigation of coral reef cryptic benthic organisms reveals diversity patterns of the hidden majority. Sci. Rep. 8, 8090. https://doi.org/10.1038/s41598-018-26332-5 (2018).

    ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Pearman, J. K. et al. Disentangling the complex microbial community of coral reefs using standardized Autonomous Reef Monitoring Structures (ARMS). Mol. Ecol. 28, 3496–3507. https://doi.org/10.1111/mec.15167 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Selkoe, K. A. et al. The DNA of coral reef biodiversity: Predicting and protecting genetic diversity of reef assemblages. Proc. R. Soc. B-Biol. Sci. https://doi.org/10.1098/rspb.2016.0354 (2016).

    Article 

    Google Scholar 

  • DiBattista, J. D. et al. Digging for DNA at depth: Rapid universal metabarcoding surveys (RUMS) as a tool to detect coral reef biodiversity across a depth gradient. PeerJ https://doi.org/10.7717/peerj.6379 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • DiBattista, J. D. et al. Assessing the utility of eDNA as a tool to survey reef-fish communities in the Red Sea. Coral Reefs 36, 1245–1252. https://doi.org/10.1007/s00338-017-1618-1 (2017).

    ADS 
    Article 

    Google Scholar 

  • Nester, G. M. et al. Development and evaluation of fish eDNA metabarcoding assays facilitate the detection of cryptic seahorse taxa (family: Syngnathidae). Environ. DNA 2, 614–626 (2020).

    Article 

    Google Scholar 

  • West, K. M. et al. eDNA metabarcoding survey reveals fine-scale coral reef community variation across a remote, tropical island ecosystem. Mol. Ecol. 29, 1069–1086. https://doi.org/10.1111/mec.15382 (2020).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • DiBattista, J. D. et al. Environmental DNA can act as a biodiversity barometer of anthropogenic pressures in coastal ecosystems. Sci. Rep. https://doi.org/10.1038/s41598-020-64858-9 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Worm, B. et al. Impacts of biodiversity loss on ocean ecosystem services. Science 314, 787–790. https://doi.org/10.1126/science.1132294 (2006).

    ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Spalding, M. et al. Mapping the global value and distribution of coral reef tourism. Mar. Policy 82, 104–113. https://doi.org/10.1016/j.marpol.2017.05.014 (2017).

    Article 

    Google Scholar 

  • Thomsen, P. F. & Willerslev, E. Environmental DNA – An emerging tool in conservation for monitoring past and present biodiversity. Biol. Cons. 183, 4–18. https://doi.org/10.1016/j.biocon.2014.11.019 (2015).

    Article 

    Google Scholar 

  • Hughes, T. P. et al. Spatial and temporal patterns of mass bleaching of corals in the Anthropocene. Science 359, 80–83. https://doi.org/10.1126/science.aan8048 (2018).

    ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Monroe, A. A. et al. In situ observations of coral bleaching in the central Saudi Arabian Red Sea during the 2015/2016 global coral bleaching event. PLoS ONE https://doi.org/10.1371/journal.pone.0195814 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Roth, F. et al. Coral reef degradation affects the potential for reef recovery after disturbance. Mar. Environ. Res. 142, 48–58. https://doi.org/10.1016/j.marenvres.2018.09.022 (2018).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Foster, T. & Gilmour, J. P. Seeing red: Coral larvae are attracted to healthy-looking reefs. Mar. Ecol. Prog. Ser. 559, 65–71. https://doi.org/10.3354/meps11902 (2016).

    ADS 
    CAS 
    Article 

    Google Scholar 

  • Karcher, D. B. et al. Nitrogen eutrophication particularly promotes turf algae in coral reefs of the central Red Sea. PeerJ https://doi.org/10.7717/peerj.8737 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Pancrazi, I., Ahmed, H., Cerrano, C. & Montefalcone, M. Synergic effect of global thermal anomalies and local dredging activities on coral reefs of the Maldives. Marine Pollut. Bull. https://doi.org/10.1016/j.marpolbul.2020.111585 (2020).

    Article 

    Google Scholar 

  • Vercelloni, J. et al. Forecasting intensifying disturbance effects on coral reefs. Glob. Change Biol. 26, 2785–2797. https://doi.org/10.1111/gcb.15059 (2020).

    ADS 
    Article 

    Google Scholar 

  • González-Barrios, F. J., Cabral-Tena, R. A. & Alvarez-Filip, L. Recovery disparity between coral cover and the physical functionality of reefs with impaired coral assemblages. Glob. Change Biol. 27, 640–651. https://doi.org/10.1111/gcb.15431 (2020).

    ADS 
    Article 

    Google Scholar 

  • Rice, M. M., Ezzat, L. & Burkepile, D. E. Corallivory in the anthropocene: Interactive effects of anthropogenic stressors and corallivory on coral reefs. Front. Marine Sci. https://doi.org/10.3389/fmars.2018.00525 (2019).

    Article 

    Google Scholar 

  • Lin, Y.-J. et al. Long-term ecological changes in fishes and macro-invertebrates in the world’s warmest coral reefs. Sci. Total Environ. 750, 142254. https://doi.org/10.1016/j.scitotenv.2020.142254 (2021).

    ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Loreau, M. & de Mazancourt, C. Biodiversity and ecosystem stability: A synthesis of underlying mechanisms. Ecol. Lett. 16, 106–115. https://doi.org/10.1111/ele.12073 (2013).

    Article 
    PubMed 

    Google Scholar 

  • Cardinale, B. J. et al. Biodiversity loss and its impact on humanity. Nature 486, 59–67. https://doi.org/10.1038/nature11148 (2012).

    ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Handley, L. L. How will the “molecular revolution’ contribute to biological recording?. Biol. J. Lin. Soc. 115, 750–766. https://doi.org/10.1111/bij.12516 (2015).

    Article 

    Google Scholar 

  • Ducklow, H. W., Doney, S. C. & Steinberg, D. K. Contributions of long-term research and time-series observations to marine ecology and biogeochemistry. Ann. Rev. Mar. Sci. 1, 279–302. https://doi.org/10.1146/annurev.marine.010908.163801 (2009).

    Article 
    PubMed 

    Google Scholar 

  • Hughes, B. B. et al. Long-term studies contribute disproportionately to ecology and policy. Bioscience 67, 271–281. https://doi.org/10.1093/biosci/biw185 (2017).

    Article 

    Google Scholar 

  • Kraft, N. J. B. et al. Community assembly, coexistence and the environmental filtering metaphor. Funct. Ecol. 29, 592–599. https://doi.org/10.1111/1365-2435.12345 (2015).

    Article 

    Google Scholar 

  • Leibold, M. A. et al. The metacommunity concept: A framework for multi-scale community ecology. Ecol. Lett. 7, 601–613. https://doi.org/10.1111/j.1461-0248.2004.00608.x (2004).

    Article 

    Google Scholar 

  • Vellend, M. The Theory of Ecological Communities (MPB-57). (Princeton University Press, 2016).

  • Condon, R. H. et al. Recurrent jellyfish blooms are a consequence of global oscillations. Proc. Natl. Acad. Sci. U.S.A. 110, 1000–1005. https://doi.org/10.1073/pnas.1210920110 (2013).

    ADS 
    Article 
    PubMed 

    Google Scholar 

  • Boero, F., Kraberg, A. C., Krause, G. & Wiltshire, K. H. Time is an affliction: Why ecology cannot be as predictive as physics and why it needs time series. J. Sea Res. 101, 12–18. https://doi.org/10.1016/j.seares.2014.07.008 (2015).

    ADS 
    Article 

    Google Scholar 

  • Pearman, J. K., Anlauf, H., Irigoien, X. & Carvalho, S. Please mind the gap – Visual census and cryptic biodiversity assessment at central Red Sea coral reefs. Mar. Environ. Res. 118, 20–30. https://doi.org/10.1016/j.marenvres.2016.04.011 (2016).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • David, R. et al. Lessons from photo analyses of autonomous reef monitoring structures as tools to detect (bio-)geographical, spatial, and environmental effects. Mar. Pollut. Bull. 141, 420–429. https://doi.org/10.1016/j.marpolbul.2019.02.066 (2019).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Pennesi, C. & Danovaro, R. Assessing marine environmental status through microphytobenthos assemblages colonizing the autonomous reef monitoring structures (ARMS) and their potential in coastal marine restoration. Mar. Pollut. Bull. 125, 56–65. https://doi.org/10.1016/j.marpolbul.2017.08.001 (2017).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Chang, J. J. M., Ip, Y. C. A., Bauman, A. G. & Huang, D. MinION-in-ARMS: Nanopore sequencing to expedite barcoding of specimen-rich macrofaunal samples from Autonomous Reef Monitoring Structures. Front. Marine Sci. https://doi.org/10.3389/fmars.2020.00448 (2020).

    Article 

    Google Scholar 

  • Hazeri, G. et al. Latitudinal species diversity and density of cryptic crustacean (Brachyura and Anomura) in micro-habitat Autonomous Reef Monitoring Structures across Kepulauan Seribu, Indonesia. Biodivers. J. Biol. Divers. 20 (2019).

  • Al-Rshaidat, M. M. D. et al. Deep COI sequencing of standardized benthic samples unveils overlooked diversity of Jordanian coral reefs in the northern Red Sea. Genome 59, 724–737. https://doi.org/10.1139/gen-2015-0208 (2016).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Pearman, J. K. et al. Pan-regional marine benthic cryptobiome biodiversity patterns revealed by metabarcoding Autonomous Reef Monitoring Structures. Mol. Ecol. https://doi.org/10.1111/mec.15692 (2020).

    Article 
    PubMed 

    Google Scholar 

  • Leray, M. & Knowlton, N. DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity. Proc. Natl. Acad. Sci. U.S.A. 112, 2076–2081. https://doi.org/10.1073/pnas.1424997112 (2015).

    ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Obst, M. et al. A marine biodiversity observation network for genetic monitoring of hard-bottom communities (ARMS-MBON). Front. Marine Sci. https://doi.org/10.3389/fmars.2020.572680 (2020).

    Article 

    Google Scholar 

  • Hughes, T. P. et al. Ecological memory modifies the cumulative impact of recurrent climate extremes. Nat. Clim. Chang. 9, 40–43. https://doi.org/10.1038/s41558-018-0351-2 (2019).

    ADS 
    Article 

    Google Scholar 

  • Hughes, T. P., Kerry, J. T. & Simpson, T. Large-scale bleaching of corals on the Great Barrier Reef. Ecology 99, 501–501. https://doi.org/10.1002/ecy.2092 (2018).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Furby, K. A., Bouwmeester, J. & Berumen, M. L. Susceptibility of central Red Sea corals during a major bleaching event. Coral Reefs 32, 505–513. https://doi.org/10.1007/s00338-012-0998-5 (2013).

    ADS 
    Article 

    Google Scholar 

  • Froehlich, C. Y. M., Klanten, O. S., Hing, M. L., Dowton, M. & Wong, M. Y. L. Uneven declines between corals and cryptobenthic fish symbionts from multiple disturbances. Sci. Rep. https://doi.org/10.1038/s41598-021-95778-x (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Bellwood, D. R. et al. Coral recovery may not herald the return of fishes on damaged coral reefs. Oecologia 170, 567–573. https://doi.org/10.1007/s00442-012-2306-z (2012).

    ADS 
    Article 
    PubMed 

    Google Scholar 

  • Archana, A. & Baker, D. M. Multifunctionality of an urbanized coastal marine ecosystem. Front. Marine Sci. https://doi.org/10.3389/fmars.2020.557145 (2020).

    Article 

    Google Scholar 

  • Servis, J. A., Reid, B. N., Timmers, M. A., Stergioula, V. & Naro-Maciel, E. Characterizing coral reef biodiversity: Genetic species delimitation in brachyuran crabs of Palmyra Atoll Central Pacific. Mitochondrial DNA Part A 31, 178–189. https://doi.org/10.1080/24701394.2020.1769087 (2020).

    CAS 
    Article 

    Google Scholar 

  • Chaves-Fonnegra, A. et al. Bleaching events regulate shifts from corals to excavating sponges in algae-dominated reefs. Glob. Change Biol. 24, 773–785. https://doi.org/10.1111/gcb.13962 (2018).

    ADS 
    Article 

    Google Scholar 

  • Perry, C. T. & Morgan, K. M. Post-bleaching coral community change on southern Maldivian reefs: Is there potential for rapid recovery?. Coral Reefs 36, 1189–1194. https://doi.org/10.1007/s00338-017-1610-9 (2017).

    ADS 
    Article 

    Google Scholar 

  • DeCarlo, T. M. The past century of coral bleaching in the Saudi Arabian central Red Sea. PeerJ https://doi.org/10.7717/peerj.10200 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Cortés, J. et al. in Coral Reefs of the Eastern Tropical Pacific: Persistence and Loss in a Dynamic Environment (eds Peter W. Glynn, Derek P. Manzello, & Ian C. Enochs) 203–250 (Springer Netherlands, 2017).

  • Enochs, I. C. & Manzello, D. P. Species richness of motile cryptofauna across a gradient of reef framework erosion. Coral Reefs 31, 653–661. https://doi.org/10.1007/s00338-012-0886-z (2012).

    ADS 
    Article 

    Google Scholar 

  • Timmers, M. A. et al. Biodiversity of coral reef cryptobiota shuffles but does not decline under the combined stressors of ocean warming and acidification. Proc. Natl. Acad. Sci. 118, e2103275118. https://doi.org/10.1073/pnas.2103275118 (2021).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Khalil, M. T., Bouwmeester, J. & Berumen, M. L. Spatial variation in coral reef fish and benthic communities in the central Saudi Arabian Red Sea. PeerJ https://doi.org/10.7717/peerj.3410 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Roik, A. et al. Year-long monitoring of physico-chemical and biological variables provide a comparative baseline of coral reef functioning in the central Red Sea. PLoS ONE https://doi.org/10.1371/journal.pone.0163939 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Largier, J. L. Considerations in estimating larval dispersal distances from oceanographic data. Ecol. Appl. 13, S71–S89 (2003).

    Article 

    Google Scholar 

  • Volkov, I., Banavar, J. R., Hubbell, S. P. & Maritan, A. Patterns of relative species abundance in rainforests and coral reefs. Nature 450, 45–49. https://doi.org/10.1038/nature06197 (2007).

    ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Alsaffar, Z., Cúrdia, J., Borja, A., Irigoien, X. & Carvalho, S. Consistent variability in beta-diversity patterns contrasts with changes in alpha-diversity along an onshore to offshore environmental gradient: The case of Red Sea soft-bottom macrobenthos. Mar. Biodivers. 49, 247–262. https://doi.org/10.1007/s12526-017-0791-3 (2017).

    Article 

    Google Scholar 

  • Alsaffar, Z. et al. The role of seagrass vegetation and local environmental conditions in shaping benthic bacterial and macroinvertebrate communities in a tropical coastal lagoon. Sci. Rep. https://doi.org/10.1038/s41598-020-70318-1 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Rocha, L. A. et al. Mesophotic coral ecosystems are threatened and ecologically distinct from shallow water reefs. Science 361, 281–284. https://doi.org/10.1126/science.aaq1614 (2018).

    ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Soininen, J., Lennon, J. J. & Hillebrand, H. A multivariate analysis of beta diversity across organisms and environments. Ecology 88, 2830–2838. https://doi.org/10.1890/06-1730.1 (2007).

    Article 
    PubMed 

    Google Scholar 

  • Chust, G. et al. Dispersal similarly shapes both population genetics and community patterns in the marine realm. Sci. Rep. https://doi.org/10.1038/srep28730 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Gianuca, A. T., Declerck, S. A. J., Lemmens, P. & De Meester, L. Effects of dispersal and environmental heterogeneity on the replacement and nestedness components of beta-diversity. Ecology 98, 525–533. https://doi.org/10.1002/ecy.1666 (2017).

    Article 
    PubMed 

    Google Scholar 

  • Enochs, I. C., Toth, L. T., Brandtneris, V. W., Afflerbach, J. C. & Manzello, D. P. Environmental determinants of motile cryptofauna on an eastern Pacific coral reef. Mar. Ecol. Prog. Ser. 438, 105-U127. https://doi.org/10.3354/meps09259 (2011).

    ADS 
    Article 

    Google Scholar 

  • Hughes, T. P. et al. Coral reefs in the anthropocene. Nature 546, 82–90. https://doi.org/10.1038/nature22901 (2017).

    ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Fabricius, K. E. Effects of terrestrial runoff on the ecology of corals and coral reefs: Review and synthesis. Mar. Pollut. Bull. 50, 125–146. https://doi.org/10.1016/j.marpolbul.2004.11.028 (2005).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Chaidez, V., Dreano, D., Agusti, S., Duarte, C. M. & Hoteit, I. Decadal trends in Red Sea maximum surface temperature. Sci. Rep. https://doi.org/10.1038/s41598-018-25731-y (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hubbell, S. P. in Monographs in Population Biology. The unified neutral theory of biodiversity and biogeography Vol. 32 Monographs in Population Biology i-xiv, 1–375 (2001).

  • Dornelas, M., Connolly, S. R. & Hughes, T. P. Coral reef diversity refutes the neutral theory of biodiversity. Nature 440, 80–82. https://doi.org/10.1038/nature04534 (2006).

    ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Baselga, A. Partitioning the turnover and nestedness components of beta diversity. Glob. Ecol. Biogeogr. 19, 134–143. https://doi.org/10.1111/j.1466-8238.2009.00490.x (2010).

    Article 

    Google Scholar 

  • Legendre, P. Interpreting the replacement and richness difference components of beta diversity. Glob. Ecol. Biogeogr. 23, 1324–1334. https://doi.org/10.1111/geb.12207 (2014).

    Article 

    Google Scholar 

  • Hollander, M. & Wolfe, D. A. Nonparametric statistical methods. Ergonomics 18, 701–702 (1975).

    Google Scholar 

  • Kohler, K. E. & Gill, S. M. Coral point count with excel extensions (CPCe): A visual basic program for the determination of coral and substrate coverage using random point count methodology. Comput. Geosci. 32, 1259–1269. https://doi.org/10.1016/j.cageo.2005.11.009 (2006).

    ADS 
    Article 

    Google Scholar 

  • Geller, J., Meyer, C., Parker, M. & Hawk, H. Redesign of PCR primers for mitochondrial cytochrome c oxidase subunit I for marine invertebrates and application in all-taxa biotic surveys. Mol. Ecol. Resour. 13, 851–861. https://doi.org/10.1111/1755-0998.12138 (2013).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Hao, X., Jiang, R. & Chen, T. Clustering 16S rRNA for OTU prediction: A method of unsupervised Bayesian clustering. Bioinformatics 27, 611–618. https://doi.org/10.1093/bioinformatics/btq725 (2011).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581. https://doi.org/10.1038/nmeth.3869 (2016).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2020).

  • Ranwez, V., Harispe, S., Delsuc, F. & Douzery, E. J. P. MACSE: Multiple alignment of coding SEquences accounting for frameshifts and stop codons. PLoS ONE https://doi.org/10.1371/journal.pone.0022594 (2011).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Machida, R. J., Leray, M., Ho, S. L. & Knowlton, N. Data Descriptor: Metazoan mitochondrial gene sequence reference datasets for taxonomic assignment of environmental samples. Sci. Data https://doi.org/10.1038/sdata.2017.27 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261–5267. https://doi.org/10.1128/aem.00062-07 (2007).

    ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Generate High-Resolution Venn and Euler Plots v. 1.6.20 (2018).

  • Ginestet, C. ggplot2: Elegant graphics for data analysis. J. R. Stat. Soc. Ser. Stat. Soc. 174, 245–245. https://doi.org/10.1111/j.1467-985X.2010.00676_9.x (2011).

    Article 

    Google Scholar 

  • McMurdie, P. J. & Holmes, S. phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE https://doi.org/10.1371/journal.pone.0061217 (2013).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Anderson, M. J. A new method for non-parametric multivariate analysis of variance. Austral Ecol. 26, 32–46. https://doi.org/10.1111/j.1442-9993.2001.01070.pp.x (2001).

    Article 

    Google Scholar 

  • Hervé, M. Testing and plotting procedures for biostatistics v. 0.9-79. Retrieved from https://cran.r-project.org/web/packages/RVAideMemoire/index.html (2021).

  • De Caceres, M. & Legendre, P. Associations between species and groups of sites: Indices and statistical inference. Ecology 90, 3566–3574. https://doi.org/10.1890/08-1823.1 (2009).

    Article 
    PubMed 

    Google Scholar 

  • Legendre, P. & Anderson, M. J. Distance-based redundancy analysis: Testing multispecies responses in multifactorial ecological experiments. Ecol. Monogr. 69, 1–24. https://doi.org/10.1890/0012-9615(1999)069[0001:dbratm]2.0.co;2 (1999).

    Article 

    Google Scholar 

  • Roberts, D. Ordination and multivariate analysis for ecology v. 2.0-1. Retrieved from http://ecology.msu.montana.edu/labdsv/R (2019).

  • Dray, S., Bauman, D., Blanchet, G., Borcard, D., Clappe, S., Guenard, G. & Wagner, H. Adespatial: Multivariate multiscale spatial analysis v. 0.3-13. Retrieved from https://cran.r-project.org/package=adespatial (2021).


  • Source: Ecology - nature.com

    Spatial structure of city population growth

    Condition- and context-dependent variation of sexual dimorphism across lizard populations at different spatial scales