Ecology

Ceballos, G. et al. Accelerated modern human – induced species losses: entering the sixth mass extinction. Sci. Adv. 1, e1400253, https://doi.org/10.1126/sciadv.1400253 (2015).ADS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Hoffmann, M. et al. The impact of conservation on the status of the world’s vertebrates. Science 330, 1503–1509, https://doi.org/10.1126/science.1194442 (2010).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Whittaker, R. J. et al. Conservation biogeography: assessment and prospect. Divers. Distrib. 11, 3–23, https://doi.org/10.1111/j.1366-9516.2005.00143.x (2005).Article 

Google Scholar 
Dirzo, R. & Raven, P. H. Global state of biodiversity and loss. Annu. Rev. Env. Resour. 28, 137–167, https://doi.org/10.1146/annurev.energy.28.050302.105532 (2003).Article 

Google Scholar 
Dinerstein, E. et al. An ecoregion-based approach to protecting half the terrestrial realm. BioScience 67, 534–545, https://doi.org/10.1093/biosci/bix014 (2017).Article 
PubMed 
PubMed Central 

Google Scholar 
Brito, J. C. et al. Unravelling biodiversity, evolution and threats to conservation in the Sahara-Sahel. Biol. Rev. 89, 215–231, https://doi.org/10.1111/brv.12049 (2014).Article 
PubMed 

Google Scholar 
Sampaio, M. et al. Beyond the comfort zone: amphibian diversity and distribution in the West Sahara-Sahel using mtDNA and nuDNA barcoding and spatial modelling. Conserv. Genet. 22(2), 233–248, https://doi.org/10.1007/s10592-021-01331-8 (2021).Article 

Google Scholar 
Velo-Antón, G. et al. DNA barcode reference library for the West Sahara-Sahel reptiles, figshare, https://doi.org/10.6084/m9.figshare.20338335 (2022).Carranza, S., Arnold, E. N., Geniez, P., Roca, J. & Mateo, J. A. Radiation, multiple dispersal and parallelism in the skinks, Chalcides and Sphenops (Squamata: Scincidae), with comments on Scincus and Scincopus and the age of the Sahara Desert. Mol. Phyl. Evol. 46, 1071–1094, https://doi.org/10.1016/j.ympev.2007.11.018 (2008).CAS 
Article 

Google Scholar 
Gonçalves, D. V. et al. Phylogeny of North African Agama lizards (Reptilia: Agamidae) and the role of the Sahara desert in vertebrate speciation. Mol. Phyl. Evol. 64, 582–591, https://doi.org/10.1016/j.ympev.2012.05.007 (2012).Article 

Google Scholar 
Gonçalves, D. V. et al. The role of climatic cycles and trans-Saharan migration corridors in species diversification: biogeography of Psammophis schokari group in North Africa. Mol. Phyl. Evol. 118, 64–74, https://doi.org/10.1016/j.ympev.2017.09.009 (2018).Article 

Google Scholar 
Gonçalves, D. V. et al. Assessing the role of aridity-induced vicariance and ecological divergence in species diversification in North-West Africa using Agama lizards. Biol. J. Linn. Soc. 124, 363–380, https://doi.org/10.1093/biolinnean/bly055 (2018).Article 

Google Scholar 
Metallinou, M. et al. Conquering the Sahara and Arabian deserts: Systematics and biogeography of Stenodactylus geckos (Reptilia: Gekkonidae). BMC Evol. Biol. 12, 258, https://doi.org/10.1186/1471-2148-12-258 (2012).Article 
PubMed 
PubMed Central 

Google Scholar 
Metallinou, M. et al. Species on the rocks: Systematics and biogeography of the rock-dwelling Ptyodactylus geckos (Squamata: Phyllodactylidae) in North Africa and Arabia. Mol. Phyl. Evol. 85, 208–220, https://doi.org/10.1016/j.ympev.2015.02.010 (2015).Article 

Google Scholar 
Kapli, P. et al. Historical biogeography of the lacertid lizard Mesalina in North Africa and the Middle East. J. Biogeog. 42, 267–279, https://doi.org/10.1111/jbi.12420 (2015).Article 

Google Scholar 
Tamar, K., Geniez, P., Brito, J. C. & Crochet, P. A. Systematic revision of Acanthodactylus busacki (Squamata: Lacertidae) with a description of a new species from Morocco. Zootaxa 4276(3), 357–386, https://doi.org/10.11646/ZOOTAXA.4276.3.3 (2017).Article 

Google Scholar 
Velo-Antón, G., Martínez-Freiría, F., Pereira, P., Crochet, P.-A. & Brito, J. C. Living on the edge: ecological and genetic connectivity of the Spiny-footed lizard, Acanthodactylus aureus, confirms the Atlantic Sahara desert as biogeographic corridor and centre of lineage diversification. J. Biogeog. 45, 1031–1042, https://doi.org/10.1111/jbi.13176 (2018).Article 

Google Scholar 
Vale, C. G., Pimm, S. L. & Brito, J. C. Overlooked mountain rock pools in deserts are critical local hotspots of biodiversity. PLoS ONE 10, e0118367, https://doi.org/10.1371/journal.pone.0118367 (2015).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Brito, J. C. et al. Conservation Biogeography of the Sahara-Sahel: additional protected areas are needed to secure unique biodiversity. Divers. Distrib. 22, 371–384, https://doi.org/10.1111/ddi.12416 (2016).Article 

Google Scholar 
Hawlitschek, O. et al. Comprehensive DNA barcoding of the herpetofauna of Germany. Mol. Ecol. Res. 16, 242–253, https://doi.org/10.1111/1755-0998.12416 (2016).CAS 
Article 

Google Scholar 
Hebert, P. D. N., Cywinska, A., Ball, S. L. & Jeremy, R. Biological Identifications through DNA Barcodes. P. Roy. Soc. Lond. B Bio. 270, 313–321, https://doi.org/10.1098/rspb.2002.2218 (2003).CAS 
Article 

Google Scholar 
Murphy, R. W. et al. Cold Code: the global initiative to DNA barcode amphibians and nonavian reptiles. Mol. Ecol. Res. 13, 161–167, https://doi.org/10.1111/1755-0998.12050 (2013).CAS 
Article 

Google Scholar 
Vasconcelos, R. et al. Unexpectedly high levels of cryptic diversity uncovered by a complete DNA barcoding of reptiles of the Socotra Archipelago. PLoS ONE 11, e0149985, https://doi.org/10.1371/journal.pone.0149985 (2016).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Krishnamurthy, P. K. & Francis, R. A. A critical review on the utility of DNA barcoding in biodiversity conservation. Biodiv. Conserv. 21, 1901–1919, https://doi.org/10.1007/s10531-012-0306-2 (2012).Article 

Google Scholar 
DeSalle, R. & Amato, G. The expansion of conservation genetics. Nat. Rev. Genet. 5, 702–12, https://doi.org/10.7312/amat12832-006 (2004).CAS 
Article 
PubMed 

Google Scholar 
Campos, J. C. & Brito, J. C. Mapping underrepresented land cover heterogeneity in arid regions: the Sahara-Sahel example. ISPRS J. Photogramm 146, 211–220, https://doi.org/10.1016/j.isprsjprs.2018.09.012 (2018).Article 

Google Scholar 
Brito, J. C. et al. Armed conflicts and wildlife decline: Challenges and recommendations for effective conservation policy in the Sahara‐Sahel. Conserv. Lett. 11(5), e12446, https://doi.org/10.1111/conl.12446 (2018).Article 

Google Scholar 
Weiss, D. J. et al. A global map of travel time to cities to assess inequalities in accessibility in 2015. Nature 553, 333–336, https://doi.org/10.1038/nature25181 (2018).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Geniez, P., Mateo, J. A. & Bons, J. A checklist of the amphibians and reptiles of Western Sahara (Amphibia, Reptilia). Herpetozoa 133, 149–63 (2000).
Google Scholar 
Geniez, P., Mateo, J. A., Geniez, M. & Pether, J. The Amphibians and Reptiles of the Western Sahara. An Atlas and Field Guide. Chimaira Editions (2004). Available at https://doi.org/10.1643/0045-8511(2007)2007[772:TAAROT]2.0.CO;2Trape, J. – F. & Mané, Y. Guide des Serpents d’Afrique Occidentale: Savane et Désert. IRD éditions (2006).Trape, J.-F., Trape, S. & Chirio, L. Lézards, Crocodiles et Tortues d’Afrique Occidentale et du Sahara. IRD éditions (2012).Dabney, J. et al. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl. Acad. Sci. USA 110, 15758–15763, https://doi.org/10.1073/pnas.1314445110 (2013).ADS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Nagy, Z. T., Sonet, G., Glaw, F. & Vences, M. First large-scale DNA barcoding assessment of reptiles in the biodiversity hotspot of Madagascar, based on newly designed COI primers. PLoS ONE 7, e34506, https://doi.org/10.1371/journal.pone.0034506 (2012).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Folmer, O., Black, M., Hoeh, W., Lutz, R. & Vrijenhoek, R. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol. 3, 294–299 (1994).CAS 
PubMed 

Google Scholar 
Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids. Res. 32, 1792–1797, https://doi.org/10.1093/nar/gkh340 (2004).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Kimura, M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16, 111–120, https://doi.org/10.1007/BF01731581 (1980).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Brown, S. D. et al. Spider: An R package for the analysis of species identity and evolution, with particular reference to DNA barcoding. Mol. Ecol. Res. 12, 562–565, https://doi.org/10.1111/j.1755-0998.2011.03108.x (2012).ADS 
Article 

Google Scholar 
Meier, R., Shiyang, K., Vaidya, G. & Ng, P. K. L. DNA barcoding and taxonomy in diptera: a tale of high intraspecific variability and low identification success. Syst. Biol. 55, 715–728, https://doi.org/10.1080/10635150600969864 (2006).Article 
PubMed 

Google Scholar 
Pizzigalli, C. et al. Phylogeographic diversification of the Mesalina olivieri species complex (Squamata: Lacertidae) with the description of a new species and a new subspecies endemic from North West Africa. J. Zool. Syst. Evol. Res. 59, 2321–2349, https://doi.org/10.1111/jzs.12516 (2021).Article 

Google Scholar 
Mediannikov, O., Trape, S. & Trape, J.-F. A molecular study of the genus Agama (Squamata: Agamidae) in West Africa, with description of two new species and a review of the taxonomy, geographic distribution, and ecology of currently recognized species. Russ. J. Herpetol. 19, 115–142, https://doi.org/10.30906/1026-2296-2012-19-2-115-142 (2012).Article 

Google Scholar 
Wagner, P., Wilms, T. M., Bauer, A. & Böhme, W. Studies on African Agama. V. On the origin of Lacerta agama Linnaeus, 1758 (Squamata: Agamidae). Bonn. zool. Beitr. 56, 215–223 (2009).
Google Scholar  More

In this picture, I’m face to face with an anaesthetized 250-kilogram male grizzly bear (Ursus arctos horribilis), which was caught near Sparwood and Elkford in Canada. With help from conservation inspector Joe Caravetta, who is sitting next to me, and my field technician Laura Smit, I’m putting a GPS-enabled collar on the bear so that we can track his movements.The first time I worked with a bear this size, it was absolutely exhilarating, a real adrenaline rush. I thought, “My whole head could fit inside this animal’s jaws.” Over time, it has become fairly routine. I learnt to trust the anaesthetic — a mix of drugs given using an air-powered dart gun — and we constantly monitor the bears’ vital signs.While I’m attaching the collar, Laura collects hair samples for genetic studies. We measure the bear’s temperature and oxygen levels, and take hair samples to get an idea of his diet. We weigh him, which is quite a challenge: we use a custom-made tarpaulin with handles to wrap him up like a bear taco. We attach the handles to a hanging scale and, with a rope over a tree branch, winch him up. This particular bear is eight years old and has 29% body fat, which is very healthy for spring.Ultimately, the collars will help us to reduce conflict between bears and the people who live in the area — I’ve seen bears rip shed doors off to get to livestock, and peel open an outdoor freezer like a can of sardines.At times, it’s chaos for both humans and bears, and people react by shooting the bear — the most common cause of death for younger ones. Tracking bears with collars will help us to find solutions.From tracking the bears, we’ve learnt that they are adapting their habits to avoid people, and they become more nocturnal as they get older. We’ve helped local communities to adapt, too: we’ve launched cost-share initiatives for electrical fencing, which is a really effective bear deterrent. More

Stanier, R. Y. & Van Niel, C. B. Arch. Mikrobiol. 42, 17–35 (1962).CAS 
Article 

Google Scholar 
Schavemaker, P. E. & Muñoz-Gómez, S. A. Nat. Ecol. Evol. https://doi.org/10.1038/s41559-022-01833-9 (2022).Article 

Google Scholar 
Lane, N. & Martin, W. F. Nature 467, 929–934 (2010).CAS 
Article 

Google Scholar 
Lynch, M. & Marinov, G. K. PNAS 112, 15690–15695 (2015).CAS 
Article 

Google Scholar 
Cavalier-Smith, T. & Chao, E. E. Protoplasma 257, 621–753 (2020).CAS 
Article 

Google Scholar 
Zachar, I. & Szathmáry, E. Biol. Direct 12, 19 (2017).Article 

Google Scholar 
Cavalier-Smith, T. Cold Spring Harb. Perspect. Biol. 6, 1–31 (2014).Article 

Google Scholar 
de Duve, C. Nat. Rev. Genet. 8, 395–403 (2007).Article 

Google Scholar 
Shiratori, T., Suzuki, S., Kakizawa, Y. & Ishida, K. Nat. Commun. 10, 5529 (2019).Article 

Google Scholar 
Martin, W. F., Tielens, A. G. M., Mentel, M., Garg, S. G. & Gould, S. B. Microbiol. Mol. Biol. Rev. 81, 8–17 (2017).Article 

Google Scholar 
Jékely, G. Biol. Direct 2, 3 (2007).Article 

Google Scholar 
Stanier, R. Y. Some aspects of the biology of cells and their possible evolutionary significance. Organization and Control in Prokaryotic and Eukaryotic Cells. In Proc. 20th Symposium of the Society for General Microbiology (eds Charles, H. P. & Knight, B. C. J. G) 20, 1–38 (Cambridge University Press, Cambridge, 1970).Zachar, I., Szilágyi, A., Számadó, S. & Szathmáry, E. PNAS USA 115, E1504–E1510 (2018).CAS 
PubMed 
PubMed Central 

Google Scholar 
Burns, J. A., Pittis, A. A. & Kim, E. Nat. Ecol. Evol. 2, 697–704 (2018).Article 

Google Scholar 
Bremer, N., Tria, F. D. K., Skejo, J., Garg, S. G. & Martin, W. F. Genome Biol. Evol. 14, evac079 (2022).Article 

Google Scholar 
Imachi, H. et al. Nature 577, 519–525 (2020).CAS 
Article 

Google Scholar 
Zachar, I. & Boza, G. Cell. Mol. Life Sci. 77, 3503–3523 (2020).CAS 
Article 

Google Scholar 
Devos, D. P. Mol. Biol. Evol. 38, 3531–3542 (2021).CAS 
Article 

Google Scholar  More

Effects of grid spacing on habitat hydraulic complexity metricsThe sensitivity of the habitat hydraulic complexity metrics to Δs was examined by calculating the metrics for Δs = 0.06, 0.12, 0.18, and 0.24 m (for M4, Δs = Δx = Δy). Figure 3 shows the variation of the metrics with grid spacing for scenarios with boulders. A preliminary assessment of no-boulder scenarios (S1-L and S1-H) showed that all the metrics decreased by increasing the grid spacing. However, because the metrics are mostly used in complex rather than non-obstructed and 1-D flows, the plots only include scenarios with boulder placement to highlight the effects of grid spacing on the metrics in complex flows. All the metrics generally decreased as Δs increased. At the low flow rate, by changing the Δs from the smallest to largest, i.e., 0.06 m to 0.024, the mean decreases in the M1, M2, and M4 metrics (averaged over all the scenarios with boulders) were 45.1, 9.9, and 74.7%, respectively. At the high flow rate, these reductions were 34.8, 14.7, and 82.5% for M1, M2, and M4, respectively. Table 2 shows the p-values associated with the changes in the metrics due to increasing Δs from 0.06 to 0.24 m for all scenarios. The table indicates that changes in M1 and M4 were statistically significant while for M2 they were not (p-values  > 0.05 for all scenarios except for S2-H). This result indicated the considerable influence of grid spacing on M1 and M4 metrics in the reaches with boulder placement. Additionally, the differences in the reported average reductions due to changing the flow rate were less than 10%, indicating an insubstantial effect of flow rate on the habitat hydraulic complexity metrics’ sensitivity to the grid spacing. The significant sensitivity of the metrics M1 and M4 to the grid spacing in this study is contrary to the findings of a previous study in which an insignificant correlation was found between the habitat hydraulic complexity metrics and Δs29. This difference can be attributed to different topographic features in the studied reaches. In the previous findings, measurements were mainly taken around the bends and reaches with no significant obstruction29, in which a more uniform flow with smaller velocity gradients is expected. However, in this study, the systematic boulder placement generated more complex flow patterns with noticeable velocity gradients. Therefore, due to the variations of flow velocities in the zone studied, substantially different values for the metrics are anticipated by computing the metrics over different spatial scales.Figure 3Variation of the habitat hydraulic complexity metrics with grid spacing (Δs) for scenarios with boulder placement. (a) kinetic energy gradient metric, M1, (b) normalized kinetic energy gradient metric, M2, (c) modified recirculation metric M4.Full size imageTable 2 p-values associated with changing the grid spacing from 0.06 to 0.24 m.Full size tableStatistical distribution of habitat hydraulic complexity metricsTable 3 lists the mean, minimum, maximum, and standard deviations of the habitat hydraulic complexity metrics (Δs = 0.06 m) for all the scenarios. To complement the results from Table 3 and assess whether the influences of solely changing the boulder concentration or flow rate on the metrics were statistically significant, Table 4 shows p-values associated with changing flow rate from low to high for a given boulder concentration, and Table 5 shows p-values associated with gradually increasing the boulder concentration for a given flow rate.Table 3 The statistical parameters of the habitat hydraulic complexity metrics in the detailed measurement zone.Full size tableTable 4 p-values from a t-test associated with changes in flow rate for a given boulder concentration.Full size tableTable 5 p-values from a t-test associated with changes in boulder concertation for a given flow rate.Full size tableFor metric M1, the mean M1 values for scenarios incorporating boulders showed the same order of magnitude as values from previous studies for reaches with single and multiple boulders27 but they were about one order of magnitude larger than calculated values in the confluence of two rivers11. Using a larger grid spacing in the study in the confluence of two rivers11 can be the reason for this difference. For a scenario at the higher flow rate, the mean M1 was on average (averaged for all the scenarios) 36% greater than its counterpart at the lower flow rate and this change in M1 values was statistically significant with p  More

Pecl, G. T. et al. Biodiversity redistribution under climate change: Impacts on ecosystems and human well-being. Science (80-) https://doi.org/10.1126/science.aai9214 (2017).Article 

Google Scholar 
Walther, G. R. et al. Ecological responses to recent climate change. Nature 416, 389–395 (2002).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Thuiller, W. et al. Consequences of climate change on the tree of life in Europe. Nature 470, 531–534 (2011).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Zimmermann, N. E., Edwards, T. C. Jr., Graham, C. H., Pearman, P. B. & Svenning, J. New trends in species distribution modelling. Ecography (Cop.) 33, 985–989 (2010).Article 

Google Scholar 
Norberg, A. et al. A comprehensive evaluation of predictive performance of 33 species distribution models at species and community levels. Ecol. Monogr. 89, e01370 (2019).Article 

Google Scholar 
Smeraldo, S. et al. Generalists yet different: Distributional responses to climate change may vary in opportunistic bat species sharing similar ecological traits. Mamm. Rev. 51, 571–584 (2021).Article 

Google Scholar 
Sohlström, E. H. et al. Future climate and land-use intensification modify arthropod community structure. Agric. Ecosyst. Environ. 327, 107830 (2022).Article 
CAS 

Google Scholar 
Araújo, M. B. & New, M. Ensemble forecasting of species distributions. Trends Ecol. Evol. 22, 42–47 (2007).PubMed 
Article 

Google Scholar 
Stohlgren, T. J. et al. Ensemble habitat mapping of invasive plant species. Risk Anal. Int. J. 30, 224–235 (2010).Article 

Google Scholar 
Meller, L. et al. Ensemble distribution models in conservation prioritization: from consensus predictions to consensus reserve networks. Divers. Distrib. 20, 309–321 (2014).PubMed 
PubMed Central 
Article 

Google Scholar 
Dubuis, A. et al. Improving the prediction of plant species distribution and community composition by adding edaphic to topo-climatic variables. J. Veg. Sci. 24, 593–606 (2013).Article 

Google Scholar 
Walthert, L. & Meier, E. S. Tree species distribution in temperate forests is more influenced by soil than by climate. Ecol. Evol. 7, 9473–9484 (2017).PubMed 
PubMed Central 
Article 

Google Scholar 
Figueiredo, F. O. G. et al. Beyond climate control on species range: The importance of soil data to predict distribution of Amazonian plant species. J. Biogeogr. 45, 190–200 (2018).Article 

Google Scholar 
Arar, A., Nouidjem, Y., Bounar, R., Tabet, S. & Kouba, Y. Potential future changes of the geographic range size of Juniperus phoenicea in Algeria based on present and future climate change projections. Contemp. Probl. Ecol. 13, 429–441 (2020).Article 

Google Scholar 
Coudun, C., Gégout, J., Piedallu, C. & Rameau, J. Soil nutritional factors improve models of plant species distribution: An illustration with Acer campestre (L.) in France. J. Biogeogr. 33, 1750–1763 (2006).Article 

Google Scholar 
Buri, A. et al. What are the most crucial soil variables for predicting the distribution of mountain plant species? A comprehensive study in the Swiss Alps. J. Biogeogr. 47, 1143–1153 (2020).Article 

Google Scholar 
Buri, A. et al. Soil factors improve predictions of plant species distribution in a mountain environment. Prog. Phys. Geogr. 41, 703–722 (2017).Article 

Google Scholar 
Mod, H. K., Scherrer, D., Luoto, M. & Guisan, A. What we use is not what we know: environmental predictors in plant distribution models. J. Veg. Sci. 27, 1308–1322 (2016).Article 

Google Scholar 
Scherrer, D. & Guisan, A. Ecological indicator values reveal missing predictors of species distributions. Sci. Rep. 9, 1–8 (2019).ADS 
CAS 
Article 

Google Scholar 
Boulos, L. Flora of Egypt, Vol. 1. vol. 1 (Al Hadara Publishing, 1999).Farjon, A. & Filer, D. An atlas of the world’s conifers: An analysis of their distribution, biogeography, diversity and conservation status. (Brill, 2013).Allen, DJ. Juniperus phoenicea. The IUCN red list of threatened species 2017: e.T16348983A99965052. https://doi.org/10.2305/IUCN.UK.2017-2.RLTS. T16348983A99965052.en. Downloaded on 19 May 2020El-Bana, M., Shaltout, K., Khalafallah, A. & Mosallam, H. Ecological status of the Mediterranean Juniperus phoenicea L. relicts in the desert mountains of North Sinai Egypt. Flora-Morphol. Distrib. Funct. Ecol. Plants 205, 171–178 (2010).Article 

Google Scholar 
Moustafa, A. et al. Ecological Prominence of Juniperus phoenicea L. Growing in Gebel Halal, North Sinai Egypt. Catrina Int. J. Environ. Sci. 15, 11–23 (2016).
Google Scholar 
Farahat, E. A. Age structure and static life tables of the endangered Juniperus phoenicea L. in North Sinai Mountains, Egypt. J. Mt. Sci. 17, 2170–2178 (2020).Article 

Google Scholar 
El-Wahab, A. Condition assessment of plant diversity of Gebel Maghara, North Sinai, Egypt. Catrina Int. J. Environ. Sci. 3, 21–40 (2008).
Google Scholar 
Youssef, A. M., Morsy, A. A., Mosallam, H. A. & Hashim, A. M. Vegetation and soil relationships in some wadis from the North-Central part of Sinai Peninsula Egypt. Minia Sci. Bull. 25, 1–28 (2014).
Google Scholar 
Fisher, M. Decline in the juniper woodlands of Raydah Reserve in southwestern Saudi Arabia: A response to climate changes?. Glob. Ecol. Biogeogr. Lett. 6, 379–386 (1997).Article 

Google Scholar 
Salvà-Catarineu, M. et al. Past, present, and future geographic range of the relict Mediterranean and Macaronesian Juniperus phoenicea complex. Ecol. Evol. 11, 5075–5095 (2021).PubMed 
PubMed Central 
Article 

Google Scholar 
Quevedo, L., Rodrigo, A. & Espelta, J. M. Post-fire resprouting ability of 15 non-dominant shrub and tree species in Mediterranean areas of NE Spain. Ann. For. Sci. 64(8), 883–890 (2007).Article 

Google Scholar 
Trabucco, A. & Zomer, R. J. Global aridity index (global-aridity) and global potential evapo-transpiration (global-PET) geospatial database. CGIAR Consort. Spat. Inf. 89, 1–2 (2009).
Google Scholar 
Hengl, T. et al. SoilGrids1km—Global soil information based on automated mapping. PLoS One 9, e105992 (2014).ADS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Kennedy, C. M., Oakleaf, J. R., Theobald, D. M., Baruch-Mordo, S. & Kiesecker, J. Documentation for the global human modification of terrestrial systems (2020).Naimi, B. & Araújo, M. B. sdm: a reproducible and extensible R platform for species distribution modelling. Ecography (Cop.) 39, 368–375 (2016).Article 

Google Scholar 
Naimi, B. usdm: Uncertainty analysis for species distribution models. R Packag. Version 1, 1–12 (2015).
Google Scholar 
Guisan, A., Thuiller, W. & Zimmermann, N. E. In Habitat Suitability and Distribution Models: With Applications in R. (Cambridge University Press, 2017).Dakhil, M. A. et al. Global invasion risk assessment of Prosopis juliflora at biome level : Does soil matter?. Biology 10, 203 (2021).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Iturbide, M., Bedia, J. & Gutiérrez, J. M. Background sampling and transferability of species distribution model ensembles under climate change. Glob. Planet. Change 166, 19–29 (2018).ADS 
Article 

Google Scholar 
Barbet-Massin, M., Jiguet, F., Albert, C. H. & Thuiller, W. Selecting pseudo-absences for species distribution models: How, where and how many?. Methods Ecol. Evol. 3, 327–338 (2012).Article 

Google Scholar 
Zhang, Z., Mammola, S., Xian, W. & Zhang, H. Modelling the potential impacts of climate change on the distribution of ichthyoplankton in the Yangtze Estuary, China. Divers. Distrib. 26, 126–137 (2020).Article 

Google Scholar 
Thuiller, W., Guéguen, M., Renaud, J., Karger, D. N. & Zimmermann, N. E. Uncertainty in ensembles of global biodiversity scenarios. Nat. Commun. 10, 1–9 (2019).CAS 
Article 

Google Scholar 
Breiner, F. T., Nobis, M. P., Bergamini, A. & Guisan, A. Optimizing ensembles of small models for predicting the distribution of species with few occurrences. Methods Ecol. Evol. 9, 802–808 (2018).Article 

Google Scholar 
Liu, C., Newell, G. & White, M. On the selection of thresholds for predicting species occurrence with presence-only data. Ecol. Evol. 6, 337–348 (2016).PubMed 
Article 

Google Scholar 
Haider, S. M., Benscoter, A. M., Pearlstine, L., D’Acunto, L. E. & Romañach, S. S. Landscape-scale drivers of endangered Cape Sable Seaside Sparrow (Ammospiza maritima mirabilis) presence using an ensemble modeling approach. Ecol. Modell. 461, 109774 (2021).Article 

Google Scholar 
Allouche, O., Tsoar, A. & Kadmon, R. Assessing the accuracy of species distribution models: Prevalence, kappa and the true skill statistic (TSS). J. Appl. Ecol. 43, 1223–1232 (2006).Article 

Google Scholar 
Franklin, J. Mapping Species Distributions: Spatial Inference and Prediction (Cambridge University Press, 2010).Book 

Google Scholar 
Kabiel, H. F., Hegazy, A. K., Lovett-Doust, L., Al-Rowaily, S. L. & Al Borki, A. E. N. S. Ecological assessment of populations of Juniperus phoenicea L. in the Al-Akhdar mountainous landscape of Libya. Arid L. Res. Manag. 30, 269–289 (2016).Article 

Google Scholar 
Camarero, J. J. et al. Dieback and mortality of junipers caused by drought: Dissimilar growth and wood isotope patterns preceding shrub death. Agric. For. Meteorol. 291, 108078 (2020).ADS 
Article 

Google Scholar 
Sánchez-Salguero, R. & Camarero, J. J. Greater sensitivity to hotter droughts underlies juniper dieback and mortality in Mediterranean shrublands. Sci. Total Environ. 721, 137599 (2020).ADS 
PubMed 
Article 
CAS 

Google Scholar 
Cramer, W. et al. Climate change and interconnected risks to sustainable development in the Mediterranean. Nat. Clim. Chang. 8, 972–980 (2018).ADS 
Article 

Google Scholar 
Forzieri, G. et al. Ensemble projections of future streamflow droughts in Europe. Hydrol. Earth Syst. Sci. 18, 85–108 (2014).ADS 
Article 

Google Scholar 
González-Hidalgo, J. C. et al. High-resolution spatio-temporal analyses of drought episodes in the western Mediterranean basin (Spanish mainland, Iberian Peninsula). Acta Geophys. 66, 381–392 (2018).ADS 
Article 

Google Scholar 
Stockhecke, M. et al. Millennial to orbital-scale variations of drought intensity in the Eastern Mediterranean. Quat. Sci. Rev. 133, 77–95 (2016).ADS 
Article 

Google Scholar 
Navarro Cerrillo, R. M. et al. Can habitat prediction models contribute to the restoration and conservation of the threatened tree Abies pinsapo Boiss. in Southern Spain?. New For. 52, 89–112 (2021).Article 

Google Scholar  More

Brooke, S. & Young, C. M. In situ measurement of survival and growth of Lophelia pertusa in the northern Gulf of Mexico. Mar. Ecol. Prog. Ser. 397, 153–161 (2009).ADS 

Google Scholar 
Reyes, J., Santodomingo, N. & Florez, P. Corales Escleractinios de Colombia. (Invemar Serie de Publicaciones Especiales, 2010).Alonso, D. et al. Behind the scenes for the designation of the Corales de Profundidad national natural park of Colombia. Front. Mar. Sci. 8, 1147 (2021).
Google Scholar 
Hughes, J. A., Menot, L. & Levin, L. Habitat classification and mapping on deep continental margins. Research and Consultancy Report, No 54. COMARGE Workshop (2008).Rogers, A. The biology, ecology and vulnerability of deep-water coral reefs. International Union for Conservation of Nature and Natural Resources (2004).Maier, C., Hegeman, J., Weinbauer, M. G. & Burg, D. Calcification of the cold-water coral Lophelia pertusa under ambient and reduced pH. Biogeosciences 1, 1671–1680 (2009).ADS 

Google Scholar 
DeLeo, D. M., Glazier, A., Herrera, S., Barkman, A. & Cordes, E. E. Transcriptomic responses of deep-sea corals experimentally exposed to crude oil and dispersant. Front. Mar. Sci. 8, 1–17 (2021).
Google Scholar 
Buddemeier, R., Kleypas, J. A. & Aronson, R. B. Potential contributions of climate change to stresses on coral reef ecosystems. Coral Reefs Global Clim. Change 15, 17789 (2004).
Google Scholar 
Schmidt, C. A. et al. Faster crystallization during coral skeleton formation correlates with resilience to ocean acidification. J. Am. Chem. Soc. 144, 1332–1341 (2022).CAS 
PubMed 
PubMed Central 

Google Scholar 
Bors, E. K. et al. Patterns of deep-sea genetic connectivity in the New Zealand Region: Implications for management of benthic ecosystems. PLoS One 7, 11047 (2012).
Google Scholar 
Hernández-Ávila, I. Patterns of deep-water coral diversity in the Caribbean basin and adjacent southern waters: An approach based on records from the R/V Pillsbury Expeditions. PLoS ONE 9, 11 (2014).
Google Scholar 
Alonso, D. et al. Corales de Profundidad: descripción de comunidades coralinas y fauna asociada. (Serie de Publicaciones Generales del Invemar, 2015).Frade, P. R. et al. Semi-permeable species boundaries in the coral genus Madracis: the role of introgression in a brooding coral system. Mol. Phylogenet. Evol. 57, 1072–1090 (2010).CAS 
PubMed 

Google Scholar 
Locke, J. M. & Coates, K. A. What are the costs of bad taxonomic practices: and what is Madracis mirabilis? Proc. 11th Int. Coral Reef Symp. 7, 1348–1351 (2008).
Google Scholar 
Palumbi, S. R. The Ecology of Marine Protected Areas. in Marine Community Ecology (eds. Bertness, M., Gaines, S. & Hay, M.) 509–530 (Sinauer Press, Inc, 2001).Jones, G. P., Srinivasan, M. & Almany, G. R. Population connecivity and conservation of marine biodiversity. Oceanography 20, 100 (2007).
Google Scholar 
Fogarty, M. J. & Botsford, L. W. Population connectivity and spatial management of marine fisheries. Oceanography 20, 112–123 (2007).
Google Scholar 
Gillis, L. G. et al. Potential for landscape-scale positive interactions among tropical marine ecosystems. Mar. Ecol. Prog. Ser. 503, 289–303 (2014).ADS 

Google Scholar 
Griffiths, S. M. et al. A Galaxy-based bioinformatics pipeline for optimised, streamlined microsatellite development from Illumina next-generation sequencing data. Conserv. Genet. Resour. 8, 481–486 (2016).PubMed 
PubMed Central 

Google Scholar 
Botsford, L. W. et al. Connectivity and resilience of coral reef metapopulations in marine protected areas: Matching empirical efforts to predictive needs. Coral Reefs 28, 327–337 (2009).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Palumbi, S. R. Population genetics, demographic connectivity, and the desing of marine reserves. Ecol. Appl. 13, 146–158 (2003).
Google Scholar 
Ridgway, T., Riginos, C., Davis, J. & Hoegh-Guldberg, O. Genetic connectivity patterns of Pocillopora verrucosa in southern African Marine Protected Areas. Mar. Ecol. Prog. Ser. 354, 161–168 (2008).ADS 

Google Scholar 
Hemond, E. M. & Vollmer, S. V. Genetic diversity and connectivity in the threatened staghorn coral (Acropora cervicornis) in Florida. PLoS One 5, 1140 (2010).
Google Scholar 
Goodbody-Gringley, G., Woollacott, R. M. & Giribet, G. Population structure and connectivity in the Atlantic scleractinian coral Montastraea cavernosa (Linnaeus, 1767). Mar. Ecol. 33, 32–48 (2012).ADS 
CAS 

Google Scholar 
Montoya-Maya, P. H., Macdonald, A. H. H. & Schleyer, M. H. Cross-amplification and characterization of microsatellite loci in Acropora austera from the south-western Indian Ocean. Genet. Mol. Res. 13, 1244–1250 (2014).CAS 
PubMed 

Google Scholar 
Le Goff-Vitry, M., Pybus, O. G. & Roger, N. Genetic structure of the deep-sea coral. Mol. Ecol. 13, 537–549 (2004).CAS 
PubMed 

Google Scholar 
Zeng, C., Rowden, A. A., Clark, M. R. & Gardner, J. P. A. Population genetic structure and connectivity of deep-sea stony corals (Order Scleractinia) in the New Zealand region: Implications for the conservation and management of vulnerable marine ecosystems. Evol. Appl. 10, 1040–1054 (2017).CAS 
PubMed 
PubMed Central 

Google Scholar 
Addamo, A. M., García-Jiménez, R., Taviani, M. & Machordom, A. Development of microsatellite markers in the deep-sea cup coral desmophyllum dianthus by 454 sequencing and cross-species amplifications in scleractinia order. J. Hered. 106, 322–330 (2015).CAS 
PubMed 

Google Scholar 
Morrison, C. L., Springmann, M. J., Shroades, K. M. & Stone, R. P. Development of twelve microsatellite loci in the red tree corals Primnoa resedaeformis and Primnoa pacifica. Conserv. Genet. Resour. 7, 763–765 (2015).
Google Scholar 
Baranets, V., Forsman, Z. H. & Karl, S. A. Microsatellite loci for the plate-and-pillar coral, Porities rus. Conserv. Genet. Resour. 3, 519–521 (2011).
Google Scholar 
Gang, H. et al. Evaluating the reliability of microsatellite genotyping from low-quality DNA templates with a polynomial distribution model. Chin. Sci. Bull. 56, 2523–2530 (2011).
Google Scholar 
Taberlet, P. et al. Reliable genotyping of samples with very low DNA quantities using PCR. Nucleic Acids Res. 24, 3189–3194 (1996).CAS 
PubMed 
PubMed Central 

Google Scholar 
Casado-Amezúa, P. et al. Development of microsatellite markers as a molecular tool for conservation studies of the Mediterranean reef builder coral cladocora caespitosa (Anthozoa, Scleractinia). J. Hered. 102, 622–626 (2011).PubMed 

Google Scholar 
Nakajima, Y. et al. Microsatellite markers for multiple Pocillopora genetic lineages offer new insights about coral populations. Sci. Rep. 7, 1–8 (2017).ADS 

Google Scholar 
Jenkins, T. L. & Stevens, J. R. Assessing connectivity between MPAs: Selecting taxa and translating genetic data to inform policy. Mar. Policy 94, 165–173 (2018).
Google Scholar 
Flot, J. F., Magalon, H., Cruaud, C., Couloux, A. & Tillier, S. Patterns of genetic structure among Hawaiian corals of the genus Pocillopora yield clusters of individuals that are compatible with morphology. Comptes Rendus Biol. 331, 239–247 (2008).
Google Scholar 
Benzoni, F. et al. Morphological and genetic divergence between Mediterranean and Caribbean populations of Madracis pharensis (Heller 1868) (Scleractinia, Pocilloporidae): Too much for one species? Zootaxa 4471, 473–492 (2018).PubMed 

Google Scholar 
Filatov, M. V., Frade, P. R., Bak, R. P. M., Vermeij, M. J. A. & Kaandorp, J. A. Comparison between colony morphology and molecular phylogeny in the Caribbean Scleractinian Coral Genus Madracis. PLoS One 8, 1104 (2013).
Google Scholar 
Althaus, F. et al. Impacts of bottom trawling on deep-coral ecosystems of seamounts are long-lasting. Mar. Ecol. Prog. Ser. 397, 279–294 (2009).ADS 

Google Scholar 
Alonso, D. et al. Caracterización de las comunidades coralinas del Parque Nacional Natural Corales de Profundidad en el Caribe colombiano: una aproximación a la conservación de su biodiversidad. (2014).Cairns, S. D., Jaap, W. C. & Lang, J. Scleractinia (Cnidaria) of the Gulf of Mexico. (2009).Werding, B. & Erhardt, H. Un encuentro de Madracis Myriaster (Milne-Edwards & Haime) (Scleractinia) en la Bahia de Santa Marta. Colombia. Bull. Mar. Coast. Res. 9, 415 (1977).
Google Scholar 
Blacket, M. J., Robin, C., Good, R. T., Lee, S. F. & Miller, A. D. Universal primers for fluorescent labelling of PCR fragments-an efficient and cost-effective approach to genotyping by fluorescence. Mol. Ecol. Resour. 12, 456–463 (2012).CAS 
PubMed 

Google Scholar 
Culley, T. M. et al. An efficient technique for primer development and application that integrates fluorescent labeling and multiplex PCR. Appl. Plant Sci. 1, 1300027 (2013).
Google Scholar 
Holleley, C. E. & Geerts, P. G. Multiplex Manager 1.0: A cross-platform computer program that plans and optimizes multiplex PCR. Biotechniques 46, 511–517 (2009).CAS 
PubMed 

Google Scholar 
Covarrubias-pazaran, A. G., Diaz-Garcia, L., Schlautman, B., Salazar, W. & Zalapa, J. Fragman: An R package for fragment analysis. BMC Genet. 17, 1–8 (2016).
Google Scholar 
Alberto, F. MsatAllele_1.0: An R package to visualize the binning of microsatellite alleles. J. Hered. 100, 394–397 (2013).
Google Scholar 
Kamvar, Z. N., Tabima, J. F. & Grunwald, N. J. Poppr: An R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. PeerJ 2014, 1–14 (2014).
Google Scholar  More

Kiers, E. T., Palmer, T. M., Ives, A. R., Bruno, J. F. & Bronstein, J. L. Mutualisms in a changing world: an evolutionary perspective. Ecol. Lett. 13, 1459–1474 (2010).Article 

Google Scholar 
Idjadi, J. & Edmunds, P. Scleractinian corals as facilitators for other invertebrates on a Caribbean reef. Mar. Ecol. Prog. Ser. 319, 117–127 (2006).Article 

Google Scholar 
Norström, A., Nyström, M., Lokrantz, J. & Folke, C. Alternative states on coral reefs: beyond coral–macroalgal phase shifts. Mar. Ecol. Prog. Ser. 376, 295–306 (2009).Article 

Google Scholar 
Richardson, L. E., Graham, N. A. J., Pratchett, M. S., Eurich, J. G. & Hoey, A. S. Mass coral bleaching causes biotic homogenization of reef fish assemblages. Glob. Chang. Biol. 24, 3117–3129 (2018).PubMed 
Article 

Google Scholar 
Wilson, S. K., Graham, N. A. J., Pratchett, M. S., Jones, G. P. & Polunin, N. V. C. Multiple disturbances and the global degradation of coral reefs: are reef fishes at risk or resilient? Glob. Chang. Biol. 12, 2220–2234 (2006).Article 

Google Scholar 
Apprill, A. The role of symbioses in the adaptation and stress responses of marine organisms. Ann. Rev. Mar. Sci. 12, 291–314 (2020).Alberdi, A., Aizpurua, O., Bohmann, K., Zepeda-Mendoza, M. L. & Gilbert, M. T. P. Do Vertebrate gut metagenomes confer rapid ecological adaptation? Trends Ecol. Evol. 31, 689–699 (2016).PubMed 
Article 

Google Scholar 
Voolstra, C. R. & Ziegler, M. Adapting with microbial help: microbiome flexibility facilitates rapid responses to environmental change. BioEssays 42, e2000004 (2020).Webster, N. S. & Reusch, T. B. H. Microbial contributions to the persistence of coral reefs. ISME J. 11, 2167–2174 (2017).PubMed 
PubMed Central 
Article 

Google Scholar 
Wilkins, L. G. E. et al. Host-associated microbiomes drive structure and function of marine ecosystems. PLoS Biol. 17, e3000533 (2019).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Ley, R. E. et al. Evolution of mammals and their gut microbes. Science 320, 1647–1651 (2008).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Ley, R. E., Lozupone, C. A., Hamady, M., Knight, R. & Gordon, J. I. Worlds within worlds: evolution of the vertebrate gut microbiota. Nat. Rev. Microbiol. 6, 776–788 (2008).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Egerton, S., Culloty, S., Whooley, J., Stanton, C. & Ross, R. P. The gut microbiota of marine fish. Front. Microbiol. 9, 873 (2018).PubMed 
PubMed Central 
Article 

Google Scholar 
Llewellyn, M. S., Boutin, S., Hoseinifar, S. H. & Derome, N. Teleost microbiomes: the state of the art in their characterization, manipulation and importance in aquaculture and fisheries. Front. Microbiol. 5, 1–1 (2014).Article 

Google Scholar 
Tarnecki, A. M., Burgos, F. A., Ray, C. L. & Arias, C. R. Fish intestinal microbiome: diversity and symbiosis unravelled by metagenomics. J. Appl. Microbiol. 123, 2–17 (2017).CAS 
PubMed 
Article 

Google Scholar 
Wang, A. R., Ran, C., Ringø, E. & Zhou, Z. G. Progress in fish gastrointestinal microbiota research. Rev. Aquac. 10, 626–640 (2018).Article 

Google Scholar 
Legrand, T. P. R. A., Wynne, J. W., Weyrich, L. S. & Oxley, A. P. A. A microbial sea of possibilities: current knowledge and prospects for an improved understanding of the fish microbiome. Rev. Aquac. 12, 1101–1134 (2019).Rawls, J. F., Mahowald, M. A., Ley, R. E. & Gordon, J. I. Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection. Cell 127, 423–433 (2006).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Shade, A. & Handelsman, J. Beyond the Venn diagram: the hunt for a core microbiome. Environ. Microbiol. 14, 4–12 (2012).CAS 
PubMed 
Article 

Google Scholar 
Sullam, K. E. et al. Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis. Mol. Ecol. 21, 3363–3378 (2012).PubMed 
Article 

Google Scholar 
Ainsworth, T. D. et al. The coral core microbiome identifies rare bacterial taxa as ubiquitous endosymbionts. ISME J. 9, 2261–2274 (2015).CAS 
Article 

Google Scholar 
Hernandez-Agreda, A., Leggat, W., Bongaerts, P. & Ainsworth, T. D. The microbial signature provides insight into the mechanistic basis of coral success across reef habitats. MBio. 7, e00560–16 (2016).PubMed 
PubMed Central 
Article 

Google Scholar 
Roeselers, G. et al. Evidence for a core gut microbiota in the zebrafish. ISME J. 5, 1595–1608 (2011).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Clements, K. D., Angert, E. R., Montgomery, W. L. & Choat, J. H. Intestinal microbiota in fishes: what’s known and what’s not. Mol. Ecol. 23, 1891–1898 (2014).PubMed 
Article 

Google Scholar 
Jones, J. et al. The microbiome of the gastrointestinal tract of a range-shifting marine herbivorous fish. Front. Microbiol. 9, 2000 (2018).PubMed 
PubMed Central 
Article 

Google Scholar 
Miyake, S., Ngugi, D. K. & Stingl, U. Diet strongly influences the gut microbiota of surgeonfishes. Mol. Ecol. 24, 656–672 (2015).PubMed 
Article 

Google Scholar 
Ngugi, D. K. et al. Genomic diversification of giant enteric symbionts reflects host dietary lifestyles. Proc. Natl Acad. Sci. USA 114, E7592–E7601 (2017).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Degregori, S., Casey, J. M. & Barber, P. H. Nutrient pollution alters the gut microbiome of a territorial reef fish. Mar. Pollut. Bull. 169, 112522 (2021).CAS 
PubMed 
Article 

Google Scholar 
Gómez, G. D. & Balcázar, J. L. A review on the interactions between gut microbiota and innate immunity of fish. FEMS Immunol. Med. Microbiol. 52, 145–154 (2008).PubMed 
Article 
CAS 

Google Scholar 
Butt, R. L. & Volkoff, H. Gut microbiota and energy homeostasis in fish. Front. Endocrinol. 10, 9 (2019).Article 

Google Scholar 
Hughes, T. P. et al. Spatial and temporal patterns of mass bleaching of corals in the Anthropocene. Science 359, 80–83 (2018).CAS 
PubMed 
Article 

Google Scholar 
Bellwood, D. R. et al. Evolutionary history of the butterflyfishes (f: Chaetodontidae) and the rise of coral feeding fishes. J. Evol. Biol. 23, 335–349 (2010).CAS 
PubMed 
Article 

Google Scholar 
Berumen, M., S., M. & McCormick, M. Within-reef differences in diet and body condition of coral-feeding butterflyfishes (Chaetodontidae). Mar. Ecol. Prog. Ser. 287, 217–227 (2005).Article 

Google Scholar 
Pratchett, M. S. Dietary overlap among coral-feeding butterflyfishes (Chaetodontidae) at Lizard Island, northern Great Barrier Reef. Mar. Biol. 148, 373–382 (2005).Article 

Google Scholar 
Nagelkerken, I., van der Velde, G., Wartenbergh, S. L. J., Nugues, M. M. & Pratchett, M. S. Cryptic dietary components reduce dietary overlap among sympatric butterflyfishes (Chaetodontidae). J. Fish. Biol. 75, 1123–1143 (2009).CAS 
PubMed 
Article 

Google Scholar 
Bouchon & Harmelin-Vivien Impact of coral degradation on a chaetodontid fish assemblage, Moorea, French Polynesia. Fifth Int. Coral Tahiti 5, 427–432 (1985).
Google Scholar 
Graham, N. A. J. Ecological versatility and the decline of coral feeding fishes following climate driven coral mortality. Mar. Biol. 153, 119–127 (2007).Article 

Google Scholar 
Pratchett, M. S., Wilson, S. K. & Baird, A. H. Declines in the abundance of Chaetodon butterflyfishes following extensive coral depletion. J. Fish. Biol. 69, 1269–1280 (2006).Article 

Google Scholar 
Birkeland & Neudecker. Foraging behavior of two Caribbean Chaetodontids: Chaetodon capistratus and C. aculeatus. Copeia 1981, 169–178 (1981).Gore, M. A. Factors affecting the feeding behavior of a coral reef fish, Chaetodon capistratus. Bull. Mar. Sci. 35, 211–220 (1984).
Google Scholar 
Liedke, A. M. R. et al. Resource partitioning by two syntopic sister species of butterflyfish (Chaetodontidae). J. Mar. Biol. Assoc. UK 98, 1767–1773 (2018).CAS 
Article 

Google Scholar 
Altieri, A. H. et al. Tropical dead zones and mass mortalities on coral reefs. Proc. Natl Acad. Sci. USA 114, 3660–3665 (2017).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Zaneveld, J. R., McMinds, R. & Vega Thurber, R. Stress and stability: applying the Anna Karenina principle to animal microbiomes. Nat. Microbiol. 2, 17121 (2017).CAS 
PubMed 
Article 

Google Scholar 
Neave, M. J., Apprill, A., Ferrier-Pagès, C. & Voolstra, C. R. Diversity and function of prevalent symbiotic marine bacteria in the genus Endozoicomonas. Appl. Microbiol. Biotechnol. 100, 8315–8324 (2016).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Ricaboni, D., Mailhe, M., Khelaifia, S., Raoult, D. & Million, M. Romboutsia timonensis, a new species isolated from human gut. N. Microbes N. Infect. 12, 6–7 (2016).CAS 
Article 

Google Scholar 
Zhang, L. et al. Characterization of the microbial community structure in intestinal segments of yak (Bos grunniens). Anaerobe 61, 102115 (2020).Gerritsen, J. et al. A comparative and functional genomics analysis of the genus Romboutsia provides insight into adaptation to an intestinal lifestyle. Preprint at bioRxiv https://doi.org/10.1101/845511 (2019).Fernández-Cadena, J. C. et al. Detection of sentinel bacteria in mangrove sediments contaminated with heavy metals. Mar. Pollut. Bull. 150, 110701 (2020).Williams, B., Landay, A. & Presti, R. M. Microbiome alterations in HIV infection a review. Cell. Microbiol. 18, 645–651 (2016).CAS 
PubMed 
Article 

Google Scholar 
Ahmed, H. I., Herrera, M., Liew, Y. J. & Aranda, M. Long-term temperature stress in the Coral Model Aiptasia supports the ‘Anna Karenina principle’ for bacterial microbiomes. Front. Microbiol. 10, 975 (2019).Beatty, D. S. et al. Variable effects of local management on coral defenses against a thermally regulated bleaching pathogen. Sci. Adv. 5, eaay1048 (2019).Zaneveld, J. R. et al. Overfishing and nutrient pollution interact with temperature to disrupt coral reefs down to microbial scales. Nat. Commun. 7, 11833 (2016).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Ma, Q. et al. Impact of microbiota on central nervous system and neurological diseases: the gut-brain axis. J. Neuroinflammation 16, 53 (2019).Pita, L., Rix, L., Slaby, B. M., Franke, A. & Hentschel, U. The sponge holobiont in a changing ocean: from microbes to ecosystems. Microbiome 6, 46 (2018).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Johnson, K. V. A. & Foster, K. R. Why does the microbiome affect behaviour? Nat. Rev. Microbiol. 16, 647–655 (2018).CAS 
PubMed 
Article 

Google Scholar 
Werbner, M. et al. Social-stress-responsive microbiota induces stimulation of self-reactive effector T helper cells. mSystems 4, e00292-18 (2019).Keith, S. A. et al. Synchronous behavioural shifts in reef fishes linked to mass coral bleaching. Nat. Clim. Chang. 8, 986–991 (2018).Article 

Google Scholar 
Thompson, C. A., Matthews, S., Hoey, A. S. & Pratchett, M. S. Changes in sociality of butterflyfishes linked to population declines and coral loss. Coral Reefs 38, 527–537 (2019).Article 

Google Scholar 
Almany, G. R. Differential effects of habitat complexity, predators and competitors on abundance of juvenile and adult coral reef fishes. Oecologia 141, 105–113 (2004).PubMed 
Article 

Google Scholar 
Clinchy, M., Sheriff, M. J. & Zanette, L. Y. Predator-induced stress and the ecology of fear. Funct. Ecol. 27, 56–65 (2013).Article 

Google Scholar 
Bolnick, D. I., Svanbäck, R., Araújo, M. S. & Persson, L. Comparative support for the niche variation hypothesis that more generalized populations also are more heterogeneous. Proc. Natl Acad. Sci. USA 104, 10075–10079 (2007).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Svanbäck, R. & Bolnick, D. I. Intraspecific competition drives increased resource use diversity within a natural population. Proc. R. Soc. B Biol. Sci. 274, 839–844 (2007).Article 

Google Scholar 
Neudecker, S. Foraging patterns of Chaetodontid and Pomacanthis fishes at St. Croix (U.S. Virgin Islands). Proc. Fifth International Coral Reef Symposium. 415–414 (1985).Lasker, H. Prey preferences and browsing pressure of the butterflyfish Chaetodon capistratus on Caribbean gorgonians. Mar. Ecol. Prog. Ser. 21, 213–220 (1985).Article 

Google Scholar 
Cole, A. J., Pratchett, M. S. & Jones, G. P. Diversity and functional importance of coral-feeding fishes on tropical coral reefs. Fish Fish. 9, 286–307 (2008).Article 

Google Scholar 
Pratchett, M. S., Wilson, S. K., Berumen, M. L. & McCormick, M. I. Sublethal effects of coral bleaching on an obligate coral feeding butterflyfish. Coral Reefs 23, 352–356 (2004).Article 

Google Scholar 
Fishelson, L., Montgomery, W. L. & Myrberg, A. A. A unique symbiosis in the gut of tropical herbivorous surgeonfish (Acanthuridae: teleostei) from the red sea. Science 229, 49–51 (1985).Article 

Google Scholar 
Miyake, S., Ngugi, D. K. & Stingl, U. Phylogenetic diversity, distribution, and cophylogeny of giant bacteria (Epulopiscium) with their surgeonfish hosts in the Red Sea. Front. Microbiol. 7, 285 (2016).PubMed 
PubMed Central 
Article 

Google Scholar 
Choat, J. H., Robbins, W. & Clements, K. The trophic status of herbivorous fishes on coral reefs II. Mar. Biol. 145, 445–454 (2004).Article 

Google Scholar 
Elifantz, H., Horn, G., Ayon, M., Cohen, Y. & Minz, D. Rhodobacteraceae are the key members of the microbial community of the initial biofilm formed in Eastern Mediterranean coastal seawater. FEMS Microbiol. Ecol. 85, 348–357 (2013).CAS 
PubMed 
Article 

Google Scholar 
Pujalte, M. J., Lucena, T., Ruvira, M. A., Arahal, D. R. & Macián, M. C. In The Prokaryotes: Alphaproteobacteria and Betaproteobacteria (Springer, 2014).Glasl, B., Herndl, G. J. & Frade, P. R. The microbiome of coral surface mucus has a key role in mediating holobiont health and survival upon disturbance. ISME J. 10, 2280–2292 (2016).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Sunagawa, S. et al. Bacterial diversity and White Plague Disease-associated community changes in the Caribbean coral Montastraea faveolata. ISME J. 3, 512–521 (2009).CAS 
PubMed 
Article 

Google Scholar 
Roder, C. et al. Bacterial profiling of White Plague Disease in a comparative coral species framework. ISME J. 8, 31–39 (2014).CAS 
PubMed 
Article 

Google Scholar 
Morrow, K. M., Moss, A. G., Chadwick, N. E. & Liles, M. R. Bacterial associates of two caribbean coral species reveal species-specific distribution and geographic variability. Appl. Environ. Microbiol. 78, 6438–6449 (2012).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Chiarello, M. et al. Exceptional but vulnerable microbial diversity in coral reef animal surface microbiomes. Proc. R. Soc. B Biol. Sci. 287, 20200642 (2020).Article 

Google Scholar 
Sunagawa, S., Woodley, C. M. & Medina, M. Threatened corals provide underexplored microbial habitats. PLoS ONE 5, e9554 (2010).Zhang, C. et al. Ecological robustness of the gut microbiota in response to ingestion of transient food-borne microbes. ISME J. 10, 2235–2245 (2016).PubMed 
PubMed Central 
Article 

Google Scholar 
Uren Webster, T. M. et al. Environmental plasticity and colonisation history in the Atlantic salmon microbiome: a translocation experiment. Mol. Ecol. 29, 886–898 (2020).PubMed 
PubMed Central 
Article 

Google Scholar 
Fietz, K. et al. Mind the gut: genomic insights to population divergence and gut microbial composition of two marine keystone species. Microbiome 6, 82 (2018).PubMed 
PubMed Central 
Article 

Google Scholar 
Smith, C. C., Snowberg, L. K., Caporaso, J. G., Knight, R. & Bolnick, D. I. Dietary input of microbes and host genetic variation shape among-population differences in stickleback gut microbiota. ISME J. 9, 2515 (2015).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Uren Webster, T. M., Consuegra, S., Hitchings, M. & Garcia de Leaniz, C. Interpopulation variation in the Atlantic salmon microbiome reflects environmental and genetic diversity. Appl. Environ. Microbiol. 84, e00691-18 (2018).Fiore, C. L., Labrie, M., Jarett, J. K. & Lesser, M. P. Transcriptional activity of the giant barrel sponge, Xestospongia muta holobiont: molecular evidence for metabolic interchange. Front. Microbiol. 6, 364 (2015).Neave, M. J., Michell, C. T., Apprill, A. & Voolstra, C. R. Endozoicomonas genomes reveal functional adaptation and plasticity in bacterial strains symbiotically associated with diverse marine hosts. Sci. Rep. 7, 40579 (2017).Pogoreutz, C. et al. Dominance of Endozoicomonas bacteria throughout coral bleaching and mortality suggests structural inflexibility of the Pocillopora verrucosa microbiome. Ecol. Evol. 8, 2240–2252 (2018).PubMed 
PubMed Central 
Article 

Google Scholar 
Reverter, M., Sasal, P., Tapissier-Bontemps, N., Lecchini, D. & Suzuki, M. Characterisation of the gill mucosal bacterial communities of four butterflyfish species: a reservoir of bacterial diversity in coral reef ecosystems. FEMS Microbiol. Ecol. 93 (2017).Parris, D. J., Brooker, R. M., Morgan, M. A., Dixson, D. L. & Stewart, F. J. Whole gut microbiome composition of damselfish and cardinalfish before and after reef settlement. PeerJ 4, e2412 (2016).PubMed 
PubMed Central 
Article 

Google Scholar 
Reese, E. S. Coevolution of corals and coral feeding fishes of the family Chaetodontidae. In Proc. 3rd International Coral Reef Symposium, 267–274 (Rosenstiel School of Marine and Atmospheric Science, Miami, Florida., 1977).Hammer, T. J. & Bowers, M. D. Gut microbes may facilitate insect herbivory of chemically defended plants. Oecologia 179, 1–14 (2015).Kohl, K. D., Weiss, R. B., Cox, J., Dale, C. & Denise Dearing, M. Gut microbes of mammalian herbivores facilitate intake of plant toxins. Ecol. Lett. 17, 1238–1246 (2014).PubMed 
Article 

Google Scholar 
Emslie, M. J., Pratchett, M. S., Cheal, A. J. & Osborne, K. Great Barrier Reef butterflyfish community structure: the role of shelf position and benthic community type. Coral Reefs 29, 705–715 (2010).Article 

Google Scholar 
Noble, M. M., Pratchett, M. S., Coker, D. J., Cvitanovic, C. & Fulton, C. J. Foraging in corallivorous butterflyfish varies with wave exposure. Coral Reefs 33, 351–361 (2014).Article 

Google Scholar 
Greb, L. et al. Ökologie und Sedimentologie eines rezenten Rampensystems an der Karibikküste von Panamá (Inst. für Geologie und Paläontologie, Stuttgart, 1996).Aronson, R., Hilbun, N., Bianchi, T., Filley, T. & McKee, B. Land use, water quality, and the history of coral assemblages at Bocas del Toro, Panamá. Mar. Ecol. Prog. Ser. 504, 159–170 (2014).Article 

Google Scholar 
Collin, R., D’Croz, L., Gondola, P. & Del Rosario, J. B. Climate and hydrological factors affecting variation in chlorophyll concentration and water clarity in the Bahia Almirante, Panama. Smithson. Contrib. Mar. Sci. 323–334 (2009).D’Croz, L., Rosario, J. B.del. & Gondola, P. The effect of fresh water runoff on the distribution of dissolved inorganic nutrients and plankton in the Bocas del Toro Archipelago, Caribbean Panamá. Caribb. J. Sci. 41, 414–429 (2005).
Google Scholar 
Seemann, J. et al. Assessing the ecological effects of human impacts on coral reefs in Bocas del Toro, Panama. Environ. Monit. Assess. 186, 1747–1763 (2014).CAS 
PubMed 
Article 

Google Scholar 
Guzmán, H. M., Barnes, P. A. G., Lovelock, C. E. & Feller, I. C. A site description of the CARICOMP mangrove, seagrass and coral reef sites in Bocas del Toro, Panamá. Caribb. J. Sci. 41, 430–440 (2005).
Google Scholar 
Beijbom, O. et al. Towards automated annotation of benthic survey images: variability of human experts and operational modes of automation. PLoS ONE 10, e0130312 (2015).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Rocha, L. A., Jogan, J., Király, G., Feráková, V. & Bernhardt, K.-G. Chaetodon capistratus. The IUCN Red List of Threatened Species. https://doi.org/10.2305/IUCN.UK.2010-4.RLTS.T165695A6094300.en (2010).Froese, R. & D. P. E. FishBase. FishBase. 2019. www.fishbase.org (2020)Smith, L. C. National Audubon Society Field Guide to Tropical Marine Fishes Caribbean, Gulf of Mexico, Florida, Bahamas, Bermuda (Alfred A. Knopf, 1997).Nguyen, B. N. et al. Environmental DNA survey captures patterns of fish and invertebrate diversity across a tropical seascape. Sci. Rep. 10, 1–14 (2020).Article 
CAS 

Google Scholar 
Parada, A. E., Needham, D. M. & Fuhrman, J. A. Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ. Microbiol. 18, 1403–1414 (2016).CAS 
PubMed 
Article 

Google Scholar 
Apprill, A., McNally, S., Parsons, R. & Weber, L. Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton. Aquat. Microb. Ecol. 75, 129–137 (2015).Article 

Google Scholar 
Weber, L. et al. EMP 16S Illumina amplicon protocol. https://doi.org/10.17504/protocols.io.nuudeww (2018).R Core Team. R: a language and environment for statistical computing. (R Foundation for Statistical Computing, Vienna, Austria, 2019).
Google Scholar 
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. J. 17, 10 (2011).Article 

Google Scholar 
Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581 (2016).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261–5267 (2007).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2013).CAS 
PubMed 
Article 

Google Scholar 
Wright, E. S. Using DECIPHER v2.0 to analyze big biological sequence data in R. R. J. 8, 352–359 (2016).Article 

Google Scholar 
Schliep, K., Potts, A. J., Morrison, D. A. & Grimm, G. W. Intertwining phylogenetic trees and networks. Methods Ecol. Evol. 8, 1212–1220 (2017).Article 

Google Scholar 
Weiss, S. et al. Normalization and microbial differential abundance strategies depend upon data characteristics. Microbiome 5, 27 (2017).PubMed 
PubMed Central 
Article 

Google Scholar 
McMurdie, P. J. & Holmes, S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One 8, e61217 (2013).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Astudillo-García, C. et al. Evaluating the core microbiota in complex communities: a systematic investigation. Environ. Microbiol. 19, 1450–1462 (2017).PubMed 
Article 

Google Scholar 
Dufrêne, M. & Legendre, P. Species assemblages and indicator species: the need for a flexible asymmetrical approach. Ecol. Monogr. 67, 345–366 (1997).
Google Scholar 
Roberts, D. W. labdsv: ordination and multivariate analysis for ecology. (2019).Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).CAS 
PubMed 
Article 

Google Scholar 
Leray, M. & Knowlton, N. Random sampling causes the low reproducibility of rare eukaryotic OTUs in Illumina COI metabarcoding. PeerJ 5, e3006 (2017).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Hill, M. O. Diversity and evenness: a unifying notation and its consequences. Ecology 54, 427–432 (1973).Article 

Google Scholar 
Alberdi, A. & Gilbert, M. T. P. A guide to the application of Hill numbers to DNA‐based diversity analyses. Mol. Ecol. Resour. 19, 1755–0998.13014 (2019).
Google Scholar 
Jost, L. Entropy and diversity. Oikos 113, 363–375 (2006).Article 

Google Scholar 
Chiu, C. H. & Chao, A. Estimating and comparing microbial diversity in the presence of sequencing errors. PeerJ 2016, e1634 (2016).Article 
CAS 

Google Scholar 
Oksanen, J. et al. Community Ecology Package. Vienna R Found. Stat. Comput. https://doi.org/10.4135/9781412971874.n145 (2012).Chen, J. et al. Associating microbiome composition with environmental covariates using generalized UniFrac distances. Bioinformatics 28, 2106–2113 (2012).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Lozupone, C. A., Hamady, M., Kelley, S. T. & Knight, R. Quantitative and qualitative diversity measures lead to different insights into factors that structure microbial communities. Appl. Environ. Microbiol. 73, 1576–1585 (2007).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Jaccard, P. The distribution of the flora in the alpine zone.1. N. Phytol. 11, 37–50 (1912).Article 

Google Scholar 
Anderson, M. J., Ellingsen, K. E. & McArdle, B. H. Multivariate dispersion as a measure of beta diversity. Ecol. Lett. 9, 683–693 (2006).PubMed 
Article 

Google Scholar 
Bray, J. R. & Curtis, J. T. An ordination of the upland forest communities of Southern Wisconsin. Ecol. Monogr. 27, 325–349 (1957).Article 

Google Scholar 
Anderson, M. J. A new method for non-parametric multivariate analysis of variance. Austral Ecol. 26, 32–46 (2001).
Google Scholar 
Anderson, M. J. & Walsh, D. C. I. PERMANOVA, ANOSIM, and the Mantel test in the face of heterogeneous dispersions: what null hypothesis are you testing? Ecol. Monogr. 83, 557–574 (2013).Article 

Google Scholar 
Martinez Arbizu, P. pairwiseAdonis: pairwise multilevel comparison using adonis. R package version 0.3. https://github.com/pmartinezarbizu/pairwiseAdonis (2019).Roesch, L. F. W. et al. Pime: a package for discovery of novel differences among microbial communities. Mol. Ecol. Resour. 20, 415–428 (2020).CAS 
PubMed 
Article 

Google Scholar 
Breiman, L. Random forests. Mach. Learn. 45, 5–32 (2001).Article 

Google Scholar 
Klaus, J. S., Janse, I., Heikoop, J. M., Sanford, R. A. & Fouke, B. W. Coral microbial communities, zooxanthellae and mucus along gradients of seawater depth and coastal pollution. Environ. Microbiol. 9, 1291–1305 (2007).CAS 
PubMed 
Article 

Google Scholar 
Ward, R. J. et al. Gastrointestinal Bacterial Symbionts: Reproductive Strategy and Community Structure. Thesis, Cornell Univ. (2009).Séré, M. G. et al. Bacterial communities associated with Porites White Patch Syndrome (PWPS) on three Western Indian Ocean (WIO) coral reefs. PLoS ONE 8, e83746 (2013).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Moran, D., Turner, S. J. & Clements, K. D. Ontogenetic development of the gastrointestinal microbiota in the marine herbivorous fish Kyphosus sydneyanus. Microb. Ecol. 49, 590–597 (2005).CAS 
PubMed 
Article 

Google Scholar 
Mausz, M., Schmitz-Esser, S. & Steiner, G. Identification and comparative analysis of the endosymbionts of Loripes lacteus and Anodontia fragilis (Bivalvia: Lucinidae). (University of Vienna, 2008).Bano, N., DeRae Smith, A., Bennett, W., Vasquez, L. & Hollibaugh, J. T. Dominance of mycoplasma in the guts of the long-jawed mudsucker, Gillichthys mirabilis, from five California salt marshes. Environ. Microbiol. 9, 2636–2641 (2007).CAS 
PubMed 
Article 

Google Scholar 
Frade, P. R., Roll, K., Bergauer, K. & Herndl, G. J. Archaeal and Bacterial Communities associated with the surface mucus of Caribbean corals differ in their degree of host specificity and community turnover over reefs. PLoS ONE 11, e0144702 (2016).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Turnbaugh, P. J. et al. A core gut microbiome in obese and lean twins. Nature 457, 480–484 (2009).CAS 
PubMed 
Article 

Google Scholar 
Ley, R. E., Turnbaugh, P. J., Klein, S. & Gordon, J. I. Microbial ecology: human gut microbes associated with obesity. Nature 444, 1022–1023 (2006).CAS 
PubMed 
Article 

Google Scholar 
Kimes, N. E. et al. The Montastraea faveolata microbiome: ecological and temporal influences on a Caribbean reef-building coral in decline. Environ. Microbiol. 15, 2082–2094 (2013).PubMed 
Article 

Google Scholar 
Smriga, S., Sandin, S. A. & Azam, F. Abundance, diversity, and activity of microbial assemblages associated with coral reef fish guts and feces. FEMS Microbiol. Ecol. 73, no–no (2010).Article 
CAS 

Google Scholar 
Zhang, X. et al. Effects of dietary supplementation of Ulva pertusa and non-starch polysaccharide enzymes on gut microbiota of Siganus canaliculatus. J. Oceanol. Limnol. 36, 438–449 (2018).CAS 
Article 

Google Scholar 
Klaus, J. S., Janse, I. & Fouke, B. W. Coral black band disease microbial communities and genotypic variability of the dominant cyanobacteria (CD1C11). Bull. Mar. Sci. 87, 795–821 (2011).Article 

Google Scholar 
Lu, J., Santo Domingo, J. W., Hill, S. & Edge, T. A. Microbial diversity and host-specific sequences of Canada goose feces. Appl. Environ. Microbiol. 75, 5919–5926 (2009).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Ueki, A., Goto, K., Ohtaki, Y., Kaku, N. & Ueki, K. Description of Anaerotignum aminivorans gen. Nov., sp. nov., a strictly anaerobic, amino-acid-decomposing bacterium isolated from a methanogenic reactor, and reclassification of Clostridium propionicum, Clostridium neopropionicum and Clostridium lactatifermentans as species of the genus Anaerotignum. Int. J. Syst. Evol. Microbiol. 67, 4146–4153 (2017).CAS 
PubMed 
Article 

Google Scholar 
Bowman, K. S., Rainey, F. A. & Moe, W. M. Production of hydrogen by Clostridium species in the presence of chlorinated solvents. FEMS Microbiol. Lett. 290, 188–194 (2008).PubMed 
Article 
CAS 

Google Scholar 
Bueno de Mesquita, C. P., Sartwell, S. A., Schmidt, S. K. & Suding, K. N. Growing‐season length and soil microbes influence the performance of a generalist bunchgrass beyond its current range. Ecology 101, e03095 (2020).Clever, F. et al. The gut microbiome variability of a butterflyfish increases on severely degraded Caribbean reefs. Dryad Datasets. https://doi.org/10.5061/dryad.m905qfv28 (2022).Clever, F. & Scott, J. J. R code for reproducing the statistical analyses and figures of ‘The gut microbiome variability of a butterflyfish increases on severely degraded Caribbean reefs’. Commun. Biol. https://github.com/bocasbiome/web/ (2022). More

Stocker, T. F. et al. Climate Change 2013: The Physical Science Basis. Contribution of Working Group I to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change (eds T.F. Stocker et al.) Ch. TS, 33–115 (Cambridge University Press, 2013).Doney, S. C., Fabry, V. J., Feely, R. A. & Kleypas, J. A. Ocean acidification: The other CO2 problem. Ann. Rev. Mar. Sci. 1, 169–192 (2009).PubMed 
Article 

Google Scholar 
Albright, R. et al. Carbon dioxide addition to coral reef waters suppresses net community calcification. Nature 555, 516–519 (2018).ADS 
PubMed 
Article 

Google Scholar 
Chen, C.-T.A. et al. Deep oceans may acidify faster than anticipated due to global warming. Nat. Clim. Chang. 7, 890–894 (2017).ADS 
Article 

Google Scholar 
Guinotte, J. M. et al. Will human-induced changes in seawater chemistry alter the distribution of deep-sea scleractinian corals?. Front. Ecol. Environ. 4, 141–146 (2006).Article 

Google Scholar 
Figuerola, B. et al. A review and meta-analysis of potential impacts of ocean acidification on marine calcifiers from the southern ocean. Front. Mar. Sci. 8, 584445 (2021).Article 

Google Scholar 
Ries, J. B. Skeletal mineralogy in a high-CO2 world. J. Exp. Mar. Biol. Ecol. 403, 54–64 (2011).Article 

Google Scholar 
Blackmon, P. D. & Todd, R. Mineralogy of some foraminifera as related to their classification and ecology. J. Paleontol. 33, 1–15 (1959).
Google Scholar 
Oliver, W. A. Jr. The relationship of the scleractinian corals to the rugose corals. Paleobiology 6, 146–160 (1980).Article 

Google Scholar 
Sinclair, D. J. et al. Reproducibility of trace element profiles in a specimen of the deep-water bamboo coral Keratoisis sp. Geochim. Cosmochim. Acta 75, 5101–5121 (2011).ADS 
Article 

Google Scholar 
Liu, Y.-W., Sutton, J. N., Ries, J. B. & Eagle, R. A. Regulation of calcification site pH is a polyphyletic but not always governing response to ocean acidification. Sci. Adv. 6, eaax1314 (2020).ADS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Cornwall, C. E. et al. Understanding coralline algal responses to ocean acidification: Meta-analysis and synthesis. Glob. Change Biol. 28, 362–374 (2022).Article 

Google Scholar 
Al-Horani, F. A., Al-Moghrabi, S. M. & de Beer, D. Microsensor study of photosynthesis and calcification in the scleractinian coral, Galaxea fascicularis: Active internal carbon cycle. J. Exp. Mar. Biol. Ecol. 288, 1–15 (2003).Article 

Google Scholar 
Al-Horani, F. A., Al-Moghrabi, S. M. & de Beer, D. The mechanism of calcification and its relation to photosynthesis and respiration in the scleractinian coral Galaxea fascicularis. Mar. Biol. 142, 419–426 (2003).Article 

Google Scholar 
Le Goff, C. et al. In vivo pH measurement at the site of calcification in an octocoral. Sci. Rep. 7, 11210 (2017).ADS 
PubMed 
PubMed Central 
Article 

Google Scholar 
McCulloch, M. et al. Resilience of cold-water scleractinian corals to ocean acidification: Boron isotopic systematics of pH and saturation state up-regulation. Geochim. Cosmochim. Acta 87, 21–34 (2012).ADS 
Article 

Google Scholar 
Gilbert, P. U. P. A. et al. Biomineralization: Integrating mechanism and evolutionary history. Sci. Adv. 8, eabl9653 (2022).PubMed 
PubMed Central 
Article 

Google Scholar 
Donald, H. K., Ries, J. B., Stewart, J. A., Fowell, S. E. & Foster, G. L. Boron isotope sensitivity to seawater pH change in a species of Neogoniolithon coralline red alga. Geochim. Cosmochim. Acta 217, 240–253 (2017).ADS 
Article 

Google Scholar 
Krief, S. et al. Physiological and isotopic responses of scleractinian corals to ocean acidification. Geochim. Cosmochim. Acta 74, 4988–5001 (2010).ADS 
Article 

Google Scholar 
Hönisch, B. et al. Assessing scleractinian corals as recorders for paleo-pH: Empirical calibration and vital effects. Geochim. Cosmochim. Acta 68, 3675–3685 (2004).ADS 
Article 

Google Scholar 
Anagnostou, E., Williams, B., Westfield, I., Foster, G. L. & Ries, J. B. Calibration of the pH-δ11B and temperature-Mg/Li proxies in the long-lived high-latitude crustose coralline red alga Clathromorphum compactum via controlled laboratory experiments. Geochim. Cosmochim. Acta 254, 142–155 (2019).ADS 
Article 

Google Scholar 
Cornwall, C. E., Comeau, S. & McCulloch, M. T. Coralline algae elevate pH at the site of calcification under ocean acidification. Glob. Change Biol. 23, 4245–4256 (2017).ADS 
Article 

Google Scholar 
Rosenthal, Y., Lear, C. H., Oppo, D. W. & Linsley, B. K. Temperature and carbonate ion effects on Mg/Ca and Sr/Ca ratios in benthic foraminifera: Aragonitic species Hoeglundina elegans. Paleoceanography 21, PA1007 (2006).ADS 
Article 

Google Scholar 
Gori, A. et al. Physiological response of the cold-water coral Desmophyllum dianthus to thermal stress and ocean acidification. PeerJ 4, e1606 (2016).PubMed 
PubMed Central 
Article 

Google Scholar 
Gagnon, A. C., Gothmann, A. M., Branson, O., Rae, J. W. B. & Stewart, J. A. Controls on boron isotopes in a cold-water coral and the cost of resilience to ocean acidification. Earth Planet. Sci. Lett. 554, 116662 (2021).Article 

Google Scholar 
Cairns, S. D. Global diversity of the Stylasteridae (Cnidaria: Hydrozoa: Athecatae). PLoS ONE 6, e21670 (2011).ADS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Cairns, S. D. Deep-water corals: An overview with special reference to diversity and distribution of deep-water scleractinian corals. Bull. Mar. Sci. 81, 311–322 (2007).
Google Scholar 
Samperiz, A. et al. Stylasterid corals: A new paleotemperature archive. Earth Planet. Sci. Lett. 545, 116407 (2020).Article 

Google Scholar 
Cairns, S. D. & Macintyre, I. G. Phylogenetic implications of calcium carbonate mineralogy in the Stylasteridae (Cnidaria: Hydrozoa). Palaios, 96–107 (1992).Anagnostou, E., Huang, K. F., You, C. F., Sikes, E. L. & Sherrell, R. M. Evaluation of boron isotope ratio as a pH proxy in the deep sea coral Desmophyllum dianthus: Evidence of physiological pH adjustment. Earth Planet. Sci. Lett. 349–350, 251–260 (2012).ADS 
Article 

Google Scholar 
Rae, J. W. B. et al. CO2 storage and release in the deep Southern Ocean on millennial to centennial timescales. Nature 562, 569–573 (2018).ADS 
PubMed 
Article 

Google Scholar 
Farmer, J. R., Hönisch, B., Robinson, L. F. & Hill, T. M. Effects of seawater-pH and biomineralization on the boron isotopic composition of deep-sea bamboo corals. Geochim. Cosmochim. Acta 155, 86–106 (2015).ADS 
Article 

Google Scholar 
Sutton, J. N. et al. δ11B as monitor of calcification site pH in divergent marine calcifying organisms. Biogeosciences 15, 1447–1467 (2018).ADS 
Article 

Google Scholar 
Heinemann, A. et al. Conditions of Mytilus edulis extracellular body fluids and shell composition in a pH-treatment experiment: Acid-base status, trace elements and δ11B. Geochem. Geophys. Geosyst. 13, 1–17 (2012).Article 

Google Scholar 
Rae, J. W. B., Foster, G. L., Schmidt, D. N. & Elliott, T. Boron isotopes and B/Ca in benthic foraminifera: Proxies for the deep ocean carbonate system. Earth Planet. Sci. Lett. 302, 403–413 (2011).ADS 
Article 

Google Scholar 
Auscavitch, S. R. et al. Distribution of deep-water scleractinian and stylasterid corals across abiotic environmental gradients on three seamounts in the Anegada Passage. PeerJ 8, e9523 (2020).PubMed 
PubMed Central 
Article 

Google Scholar 
DeCarlo, T. M., Holcomb, M. & McCulloch, M. T. Reviews and syntheses: Revisiting the boron systematics of aragonite and their application to coral calcification. Biogeosciences 15, 2819–2834 (2018).ADS 
Article 

Google Scholar 
McCulloch, M. T., D’Olivo, J. P., Falter, J., Holcomb, M. & Trotter, J. A. Coral calcification in a changing world and the interactive dynamics of pH and DIC upregulation. Nat. Commun. 8, 15686 (2017).ADS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Henehan, M. J. et al. Calibration of the boron isotope proxy in the planktonic foraminifera Globigerinoides ruber for use in palaeo-CO2 reconstruction. Earth Planet. Sci. Lett. 364, 111–122 (2013).ADS 
Article 

Google Scholar 
Rink, S., Kühl, M., Bijma, J. & Spero, H. Microsensor studies of photosynthesis and respiration in the symbiotic foraminifer Orbulina universa. Mar. Biol. 131, 583–595 (1998).Article 

Google Scholar 
Fietzke, J. & Wall, M. Distinct fine-scale variations in calcification control revealed by high-resolution 2D boron laser images in the cold-water coral Lophelia pertusa. Sci. Adv. 8, eabj4172 (2022).PubMed 
PubMed Central 

Google Scholar 
Drake, J. L. et al. How corals made rocks through the ages. Glob. Change Biol. 26, 31–53 (2020).ADS 
Article 

Google Scholar 
Blamart, D. et al. Correlation of boron isotopic composition with ultrastructure in the deep-sea coral Lophelia pertusa: Implications for biomineralization and paleo-pH. Geochem. Geophys. Geosyst. 8, Q12001 (2007).ADS 
Article 

Google Scholar 
Jurikova, H. et al. Boron isotope composition of the cold-water coral Lophelia pertusa along the Norwegian margin: Zooming into a potential pH-proxy by combining bulk and high-resolution approaches. Chem. Geol. 513, 143–152 (2019).ADS 
Article 

Google Scholar 
NOAA Deep Sea Coral Research & Technology Program. NOAA National Database for Deep-Sea Corals and Sponges (version 20201021-0), https://deepseacoraldata.noaa.gov/ (2017).Dickson, A. G. Thermodynamics of the dissociation of boric acid in synthetic seawater from 273.15 to 318.15 K. Deep Sea Res. Part A Oceanogr. Res. Pap. 37, 755–766 (1990).ADS 
Article 

Google Scholar 
Stewart, J. A., Anagnostou, E. & Foster, G. L. An improved boron isotope pH proxy calibration for the deep-sea coral Desmophyllum dianthus through sub-sampling of fibrous aragonite. Chem. Geol. 447, 148–160 (2016).ADS 
Article 

Google Scholar 
Mavromatis, V., Montouillout, V., Noireaux, J., Gaillardet, J. & Schott, J. Characterization of boron incorporation and speciation in calcite and aragonite from co-precipitation experiments under controlled pH, temperature and precipitation rate. Geochim. Cosmochim. Acta 150, 299–313 (2015).ADS 
Article 

Google Scholar 
Holcomb, M., DeCarlo, T. M., Gaetani, G. A. & McCulloch, M. Factors affecting B/Ca ratios in synthetic aragonite. Chem. Geol. 437, 67–76 (2016).ADS 
Article 

Google Scholar 
DeCarlo, T. M., Gaetani, G. A., Holcomb, M. & Cohen, A. L. Experimental determination of factors controlling U/Ca of aragonite precipitated from seawater: Implications for interpreting coral skeleton. Geochim. Cosmochim. Acta 162, 151–165 (2015).ADS 
Article 

Google Scholar 
Reeder, R. J., Nugent, M., Lamble, G. M., Tait, C. D. & Morris, D. E. Uranyl Incorporation into Calcite and Aragonite: XAFS and Luminescence Studies. Environ. Sci. Technol. 34, 638–644 (2000).ADS 
Article 

Google Scholar 
Anagnostou, E. et al. Seawater nutrient and carbonate ion concentrations recorded as P/Ca, Ba/Ca, and U/Ca in the deep-sea coral Desmophyllum dianthus. Geochim. Cosmochim. Acta 75, 2529–2543 (2011).ADS 
Article 

Google Scholar 
Chen, S., Littley, E. F. M., Rae, J. W. B., Charles, C. D. & Adkins, J. F. Uranium distribution and incorporation mechanism in deep-sea corals: Implications for seawater [CO32–] proxies. Front. Earth Sci. 9, 159 (2021).ADS 

Google Scholar 
Inoue, M., Suwa, R., Suzuki, A., Sakai, K. & Kawahata, H. Effects of seawater pH on growth and skeletal U/Ca ratios of Acropora digitifera coral polyps. Geophys. Res. Lett. 38, L12809 (2011).ADS 

Google Scholar 
Gothmann, A. M. & Gagnon, A. C. The primary controls on U/Ca and minor element proxies in a cold-water coral cultured under decoupled carbonate chemistry conditions. Geochim. Cosmochim. Acta 315, 38–60 (2021).ADS 
Article 

Google Scholar 
Mass, T. et al. Cloning and characterization of four novel coral acid-rich proteins that precipitate carbonates in vitro. Curr. Biol. 23, 1126–1131 (2013).PubMed 
Article 

Google Scholar 
Rogers, A. D. Advances in Marine Biology, Vol. 79 (ed Sheppard, C.) 137–224 (Academic Press, 2018).Rodolfo-Metalpa, R. et al. Coral and mollusc resistance to ocean acidification adversely affected by warming. Nat. Clim. Chang. 1, 308–312 (2011).ADS 
Article 

Google Scholar 
Hoarau, L. et al. Unexplored refugia with high cover of scleractinian Leptoseris spp. and hydrocorals Stylaster flabelliformis at lower mesophotic depths (75–100 m) on lava flows at Reunion Island (Southwestern Indian Ocean). Diversity 13, 141 (2021).Article 

Google Scholar 
Lindner, A., Cairns, S. D. & Cunningham, C. W. From offshore to onshore: Multiple origins of shallow-water corals from deep-sea ancestors. PLoS ONE 3, e2429 (2008).ADS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Stewart, J. A. et al. Refining trace metal temperature proxies in cold-water scleractinian and stylasterid corals. Earth Planet. Sci. Lett. 545, 116412 (2020).Article 

Google Scholar 
Seacarb: Seawater Carbonate Chemistry. R package version 3.0.6 .http://CRAN.R-project.org/package=seacarb (2015).Lueker, T. J., Dickson, A. G. & Keeling, C. D. Ocean pCO2 calculated from dissolved inorganic carbon, alkalinity, and equations for K1 and K2: Validation based on laboratory measurements of CO2 in gas and seawater at equilibrium. Mar. Chem. 70, 105–119 (2000).Article 

Google Scholar 
Lee, K. et al. The universal ratio of boron to chlorinity for the North Pacific and North Atlantic oceans. Geochim. Cosmochim. Acta 74, 1801–1811 (2010).ADS 
Article 

Google Scholar 
Olsen, A. et al. The Global Ocean Data Analysis Project version 2 (GLODAPv2)—An internally consistent data product for the world ocean. Earth Syst. Sci. Data 8, 297–323 (2016).ADS 
Article 

Google Scholar 
Hemming, N. G. & Hanson, G. N. Boron isotopic composition and concentration in modern marine carbonates. Geochim. Cosmochim. Acta 56, 537–543 (1992).ADS 
Article 

Google Scholar 
Zeebe, R. E. & Wolf-Gladrow, D. A. CO2 in Seawater: Equilibrium, Kinetics, Isotopes Vol. 65 (Elsevier, 2001).
Google Scholar 
Foster, G. L., Pogge von Strandmann, P. A. E. & Rae, J. W. B. Boron and magnesium isotopic composition of seawater. Geochem. Geophys. Geosyst. 11, Q08015 (2010).ADS 
Article 

Google Scholar 
Klochko, K., Kaufman, A. J., Yao, W., Byrne, R. H. & Tossell, J. A. Experimental measurement of boron isotope fractionation in seawater. Earth Planet. Sci. Lett. 248, 276–285 (2006).ADS 
Article 

Google Scholar 
Stewart, J. A. et al. NIST RM 8301 boron isotopes in marine carbonate (simulated coral and foraminifera solutions): Inter-laboratory δ11B and trace element ratio value assignment. Geostand. Geoanal. Res. 45, 77–96 (2020).Article 

Google Scholar 
Foster, G. L. Seawater pH, pCO2 and [CO32−] variations in the Caribbean Sea over the last 130 kyr: A boron isotope and B/Ca study of planktic foraminifera. Earth Planet. Sci. Lett. 271, 254–266 (2008).ADS 
Article 

Google Scholar 
Schlitzer, R. Ocean Data View, Version 4.6.5 http://odv.awi.de, (2021). More