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1. Space-filling and benthic competition on coral reefs

   https://doi.org/10.7717/peerj.11213  

   George, Emma E.; Mullinix, James A.; Meng, Fanwei; Bailey, Barbara A.; Edwards, Clinton; Felts, Ben; Haas, Andreas F.; Hartmann, Aaron C.; Mueller, Benjamin; Roach, Ty N. F.; et al (June 2021, PeerJ)

   Reef-building corals are ecosystem engineers that compete with other benthic organisms for space and resources. Corals harvest energy through their surface by photosynthesis and heterotrophic feeding, and they divert part of this energy to defend their outer colony perimeter against competitors. Here, we hypothesized that corals with a larger space-filling surface and smaller perimeters increase energy gain while reducing the exposure to competitors. This predicted an association between these two geometric properties of corals and the competitive outcome against other benthic organisms. To test the prediction, fifty coral colonies from the Caribbean island of Curaçao were rendered using digital 3D and 2D reconstructions. The surface areas, perimeters, box-counting dimensions (as a proxy of surface and perimeter space-filling), and other geometric properties were extracted and analyzed with respect to the percentage of the perimeter losing or winning against competitors based on the coral tissue apparent growth or damage. The increase in surface space-filling dimension was the only significant single indicator of coral winning outcomes, but the combination of surface space-filling dimension with perimeter length increased the statistical prediction of coral competition outcomes. Corals with larger surface space-filling dimensions (D_s> 2) and smaller perimeters displayed more winning outcomes, confirming the initial hypothesis. We propose that the space-filling property of coral surfaces complemented with other proxies of coral competitiveness, such as life history traits, will provide a more accurate quantitative characterization of coral competition outcomes on coral reefs. This framework also applies to other organisms or ecological systems that rely on complex surfaces to obtain energy for competition. 

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2. Three competitors in three dimensions: photogrammetry reveals rapid overgrowth of coral during multispecies competition with sponges and algae

   https://doi.org/10.3354/meps13579  

   Olinger, LK; Chaves-Fonnegra, A; Enochs, IC; Brandt, ME (January 2021, Marine Ecology Progress Series)

   null (Ed.)

   Competition for limited space is an important driver of benthic community structure on coral reefs. Studies of coral-algae and coral-sponge interactions often show competitive dominance of algae and sponges over corals, but little is known about the outcomes when these groups compete in a multispecies context. Multispecies competition is increasingly common on Caribbean coral reefs as environmental degradation drives loss of reef-building corals and proliferation of alternative organisms such as algae and sponges. New methods are needed to understand multispecies competition, whose outcomes can differ widely from pairwise competition and range from coexistence to exclusion. In this study, we used 3D photogrammetry and image analyses to compare pairwise and multispecies competition on reefs in the US Virgin Islands. Sponges ( Desmapsamma anchorata, Aplysina cauliformis ) and macroalgae ( Lobophora variegata ) were attached to coral ( Porites astreoides ) and arranged to simulate multispecies (coral-sponge-algae) and pairwise (coral-sponge, coral-algae) competition. Photogrammetric 3D models were produced to measure surface area change of coral and sponges, and photographs were analyzed to measure sponge-coral, algae-coral, and algae-sponge overgrowth. Coral lost more surface area and was overgrown more rapidly by the sponge D. anchorata in multispecies treatments, when the sponge was also in contact with algae. Algae contact may confer a competitive advantage to the sponge D. anchorata, but not to A. cauliformis , underscoring the species-specificity of these interactions. This first application of photogrammetry to study competition showed meaningful losses of living coral that, combined with significant overgrowths by competitors detected from image analyses, exposed a novel outcome of multispecies competition. 

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3. Scaling the effects of ocean acidification on coral growth and coral–coral competition on coral community recovery

   https://doi.org/10.7717/peerj.11608  

   Evensen, Nicolas R.; Bozec, Yves-Marie; Edmunds, Peter J.; Mumby, Peter J. (January 2021, PeerJ)

   Ocean acidification (OA) is negatively affecting calcification in a wide variety of marine organisms. These effects are acute for many tropical scleractinian corals under short-term experimental conditions, but it is unclear how these effects interact with ecological processes, such as competition for space, to impact coral communities over multiple years. This study sought to test the use of individual-based models (IBMs) as a tool to scale up the effects of OA recorded in short-term studies to community-scale impacts, combining data from field surveys and mesocosm experiments to parameterize an IBM of coral community recovery on the fore reef of Moorea, French Polynesia. Focusing on the dominant coral genera from the fore reef, Pocillopora , Acropora , Montipora and Porites , model efficacy first was evaluated through the comparison of simulated and empirical dynamics from 2010–2016, when the reef was recovering from sequential acute disturbances (a crown-of-thorns seastar outbreak followed by a cyclone) that reduced coral cover to ~0% by 2010. The model then was used to evaluate how the effects of OA (1,100–1,200 µatm pCO 2 ) on coral growth and competition among corals affected recovery rates (as assessed by changes in % cover y −1 ) of each coral population between 2010–2016. The model indicated that recovery rates for the fore reef community was halved by OA over 7 years, with cover increasing at 11% y −1 under ambient conditions and 4.8% y −1 under OA conditions. However, when OA was implemented to affect coral growth and not competition among corals, coral community recovery increased to 7.2% y −1 , highlighting mechanisms other than growth suppression (i.e., competition), through which OA can impact recovery. Our study reveals the potential for IBMs to assess the impacts of OA on coral communities at temporal and spatial scales beyond the capabilities of experimental studies, but this potential will not be realized unless empirical analyses address a wider variety of response variables representing ecological, physiological and functional domains. 

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4. A biodiversity dataset graph: DataONE

   https://doi.org/10.5281/zenodo.3277312  

   Poelen, Jorrit H. (January 2019, Zenodo)

   {"Abstract":["A biodiversity dataset graph: DataONE<\/p>\n\nThe intended use of this archive is to facilitate meta-analysis of the Data Observation Network for Earth (DataONE, [1]). DataONE is a distributed infrastructure that provides information about earth observation data. <\/p>\n\nThis dataset provides versioned snapshots of the DataONE network as tracked by Preston [2] between 17 October 2018 and 7 July 2019.  <\/p>\n\nThe archive consists of 256 individual parts (e.g., preston-00.tar.gz, preston-01.tar.gz, ...) to allow for parallel file downloads. The archive contains three types of files: index files, provenance files and data files. Only two index and provenance files are included and have been individually included in this dataset publication. Index files provide a way to links provenance files in time to eestablish a versioning mechanism. Provenance files describe how, when and where the DataONE meta-data files were retrieved. For more information, please visit https://preston.guoda.bio or https://doi.org/10.5281/zenodo.1410543).  <\/p>\n\nTo retrieve and verify the downloaded DataONE biodiversity dataset graph, first concatenate all the downloaded preston-*.tar.gz files (e.g., cat preston-*.tar.gz > preston.tar.gz). Then, extract the archives into a "data" folder. Alternatively, you can use the preston[2] command-line tool to "clone" this dataset using:<\/p>\n\n$$ java -jar preston.jar clone --remote https://zenodo.org/record/3277312/files<\/p>\n\nAfter that, verify the index of the archive by reproducing the following result:<\/p>\n\n$$ java -jar preston.jar history\n<0659a54f-b713-4f86-a917-5be166a14110> <http://purl.org/pav/hasVersion> <hash://sha256/8c67e0741d1c90db54740e08d2e39d91dfd73566ea69c1f2da0d9ab9780a9a9f> .\n<hash://sha256/3ed3acaca7ac57f546d0b8877c1927ab5e08c23eccaa8219600c59c77a72c685> <http://purl.org/pav/previousVersion> <hash://sha256/8c67e0741d1c90db54740e08d2e39d91dfd73566ea69c1f2da0d9ab9780a9a9f> .\n<hash://sha256/857753997a7595a1b372b05641b58a25d9408b7ff08d557ce1fe8b73e4bd383f> <http://purl.org/pav/previousVersion> <hash://sha256/3ed3acaca7ac57f546d0b8877c1927ab5e08c23eccaa8219600c59c77a72c685> .\n<hash://sha256/7ee0376f4c3f7aeeda36927a5211395e5da8201e810e8c7e638a0fe23d001e88> <http://purl.org/pav/previousVersion> <hash://sha256/857753997a7595a1b372b05641b58a25d9408b7ff08d557ce1fe8b73e4bd383f> .\n<hash://sha256/68b4974d8ab7c4c7a7a4305065839b60ba460aaa862590b34c67877738feba90> <http://purl.org/pav/previousVersion> <hash://sha256/7ee0376f4c3f7aeeda36927a5211395e5da8201e810e8c7e638a0fe23d001e88> .\n<hash://sha256/060a76d56255bf9482c951748c91291fddeeb20f180632132be1344e081b2372> <http://purl.org/pav/previousVersion> <hash://sha256/68b4974d8ab7c4c7a7a4305065839b60ba460aaa862590b34c67877738feba90> .\n<hash://sha256/29357bdfab4548025f8a5743301f5c3c9146fa436c39e3c9e019fb9409ac9c42> <http://purl.org/pav/previousVersion> <hash://sha256/060a76d56255bf9482c951748c91291fddeeb20f180632132be1344e081b2372> .\n<hash://sha256/3669cd95100d1d533eb8953ff4ec5092cbd8addb8879b3e6262191148a8a3ebb> <http://purl.org/pav/previousVersion> <hash://sha256/29357bdfab4548025f8a5743301f5c3c9146fa436c39e3c9e019fb9409ac9c42> .\n<hash://sha256/8dc1663299359d271cb1b4c14ad521d0f1be67743689dd18016543dc1e097efb> <http://purl.org/pav/previousVersion> <hash://sha256/3669cd95100d1d533eb8953ff4ec5092cbd8addb8879b3e6262191148a8a3ebb> .\n<hash://sha256/dc4903e8afee651db1d9bf509f20503bf9c8e89679c4bcffb46d5b97440cb6de> <http://purl.org/pav/previousVersion> <hash://sha256/8dc1663299359d271cb1b4c14ad521d0f1be67743689dd18016543dc1e097efb> .<\/p>\n\nTo check the integrity of the extracted archive, confirm that each line produce by the command "preston verify" produces lines as shown below, with each line including "CONTENT_PRESENT_VALID_HASH". Depending on hardware capacity, this may take a while.<\/p>\n\n$ java -jar preston.jar verify\nhash://sha256/e55c1034d985740926564e94decd6dc7a70f779a33e7deb931553739cda16945    file:/home/preston/preston-dataone/data/e5/5c/e55c1034d985740926564e94decd6dc7a70f779a33e7deb931553739cda16945    OK    CONTENT_PRESENT_VALID_HASH    21580\nhash://sha256/d0ddcc2111b6134a570bcc7d89375920ef4d754130cecc0727c79d2b05a9f81f    file:/home/preston/preston-dataone/data/d0/dd/d0ddcc2111b6134a570bcc7d89375920ef4d754130cecc0727c79d2b05a9f81f    OK    CONTENT_PRESENT_VALID_HASH    2035\nhash://sha256/472de9d1c9fd7e044aac409abfbfff9f12c6b69359df995d431009580ffb0f53    file:/home/preston/preston-dataone/data/47/2d/472de9d1c9fd7e044aac409abfbfff9f12c6b69359df995d431009580ffb0f53    OK    CONTENT_PRESENT_VALID_HASH    1935\nhash://sha256/b29879462cd43862129c5cf9b149c41ecd33ffef284a4dbea4ac1c0f90108687    file:/home/preston/preston-dataone/data/b2/98/b29879462cd43862129c5cf9b149c41ecd33ffef284a4dbea4ac1c0f90108687    OK    CONTENT_PRESENT_VALID_HASH    1553<\/p>\n\nNote that a copy of the java program "preston", preston.jar, is included in this publication. The program runs on java 8+ virtual machine using "java -jar preston.jar", or in short "preston". <\/p>\n\nFiles in this data publication:<\/p>\n\nREADME - this file<\/p>\n\npreston.jar - executable java jar containing preston[2] v0.1.1.<\/p>\n\npreston-[00-ff].tar.gz - preston archives containing DataONE meta-data files, their provenance and a provenance index.<\/p>\n\n2a5de79372318317a382ea9a2cef069780b852b01210ef59e06b640a3539cb5a - preston index file\n2aecaf289def0e23a27058bf7715f226ef9189905f0be13228174825633125cf - preston index file\n3d38b70198e448674be6a63d14b9817f3a956f48bba7418fa7baa086a56c05b7 - preston index file\n66ad3e5e904740f1e835ac6718dda4279e0c24b204ea0d1113cda1352a5072ba - preston index file\n8bf062872ce958545d361e9d53a552ffb025ac29ab875caad1157c0995d34f66 - preston index file\nd9378616636be3686bbabd5bf29d50f0ef0e5ceb5ddd7dfce47f7e755b596b7d - preston index file\nda26fa6e7371385ed3f61af9a766221c833060d59dfd4869bbd7110f95f288db - preston index file\ne4103a75627857de3ee2e317429108611c244fc448c01d1d7bf652115c3b8a55 - preston index file\neb368fedb8f100210dd968edcf80f4d13cab3dd64135a6ab744102cf15e68c94 - preston index file\nff92b6c06ae5286bd2f1db679e0fcc4da294acb9bc01b2e9522378d99218c2e3 - preston index file<\/p>\n\n[1] DataONE, https://www.dataone.org\n[2] https://preston.guoda.bio, https://doi.org/10.5281/zenodo.1410543 . DataONE was crawled via Preston with "preston update -u https://dataone.org".<\/p>\n\nThis work is funded in part by grant NSF OAC 1839201 from the National Science Foundation<\/p>"]} 

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5. A biodiversity dataset graph: Biodiverity Heritage Library (BHL)

   https://doi.org/10.5281/zenodo.3849560  

   Poelen, Jorrit (January 2020, Zenodo)

   {"Abstract":["A biodiversity dataset graph: BHL<\/p>\n\nThe intended use of this archive is to facilitate (meta-)analysis of the Biodiversity Heritage Library (BHL). The Biodiversity Heritage Library improves research methodology by collaboratively making biodiversity literature openly available to the world as part of a global biodiversity community.<\/p>\n\nThis dataset provides versioned snapshots of the BHL network as tracked by Preston [2] between 2019-05-19 and 2020-05-09 using "preston update -u https://biodiversitylibrary.org".<\/p>\n\nThe archive consists of 256 individual parts (e.g., preston-00.tar.gz, preston-01.tar.gz, ...) to allow for parallel file downloads. The archive contains three types of files: index files, provenance logs and data files. In addition, index files have been individually included in this dataset publication to facilitate remote access. Index files provide a way to links provenance files in time to establish a versioning mechanism. Provenance files describe how, when, what and where the BHL content was retrieved. For more information, please visit https://preston.guoda.bio or https://doi.org/10.5281/zenodo.1410543 .  <\/p>\n\nTo retrieve and verify the downloaded BHL biodiversity dataset graph, first concatenate all the downloaded preston-*.tar.gz files (e.g., cat preston-*.tar.gz > preston.tar.gz). Then, extract the archives into a "data" folder. Alternatively, you can use the preston[2] command-line tool to "clone" this dataset using:<\/p>\n\n$$ java -jar preston.jar clone --remote https://zenodo.org/record/3849560/files<\/p>\n\nAfter that, verify the index of the archive by reproducing the following provenance log history:<\/p>\n\n$$ java -jar preston.jar history\n<0659a54f-b713-4f86-a917-5be166a14110> <http://purl.org/pav/hasVersion> <hash://sha256/89926f33157c0ef057b6de73f6c8be0060353887b47db251bfd28222f2fd801a> .\n<hash://sha256/41b19aa9456fc709de1d09d7a59c87253bc1f86b68289024b7320cef78b3e3a4> <http://purl.org/pav/previousVersion> <hash://sha256/89926f33157c0ef057b6de73f6c8be0060353887b47db251bfd28222f2fd801a> .\n<hash://sha256/7582d5ba23e0d498ca4f55c29408c477d0d92b4fdcea139e8666f4d78c78a525> <http://purl.org/pav/previousVersion> <hash://sha256/41b19aa9456fc709de1d09d7a59c87253bc1f86b68289024b7320cef78b3e3a4> .\n<hash://sha256/a70774061ccded1a45389b9e6063eb3abab3d42813aa812391f98594e7e26687> <http://purl.org/pav/previousVersion> <hash://sha256/7582d5ba23e0d498ca4f55c29408c477d0d92b4fdcea139e8666f4d78c78a525> .\n<hash://sha256/007e065ba4b99867751d688754aa3d33fa96e6e03133a2097e8a368d613cd93a> <http://purl.org/pav/previousVersion> <hash://sha256/a70774061ccded1a45389b9e6063eb3abab3d42813aa812391f98594e7e26687> .\n<hash://sha256/4fb4b4d8f1ae2961311fb0080e817adb2faa746e7eae15249a3772fbe2d662a1> <http://purl.org/pav/previousVersion> <hash://sha256/007e065ba4b99867751d688754aa3d33fa96e6e03133a2097e8a368d613cd93a> .\n<hash://sha256/67cc329e74fd669945f503917fbb942784915ab7810ddc41105a82ebe6af5482> <http://purl.org/pav/previousVersion> <hash://sha256/4fb4b4d8f1ae2961311fb0080e817adb2faa746e7eae15249a3772fbe2d662a1> .\n<hash://sha256/e46cd4b0d7fdb51ea789fa3c5f7b73591aca62d2d8f913346d71aa6cf0745c9f> <http://purl.org/pav/previousVersion> <hash://sha256/67cc329e74fd669945f503917fbb942784915ab7810ddc41105a82ebe6af5482> .\n<hash://sha256/9215d543418a80510e78d35a0cfd7939cc59f0143d81893ac455034b5e96150a> <http://purl.org/pav/previousVersion> <hash://sha256/e46cd4b0d7fdb51ea789fa3c5f7b73591aca62d2d8f913346d71aa6cf0745c9f> .\n<hash://sha256/1448656cc9f339b4911243d7c12f3ba5366b54fff3513640306682c50f13223d> <http://purl.org/pav/previousVersion> <hash://sha256/9215d543418a80510e78d35a0cfd7939cc59f0143d81893ac455034b5e96150a> .\n<hash://sha256/7ee6b16b7a5e9b364776427d740332d8552adf5041d48018eeb3c0e13ccebf27> <http://purl.org/pav/previousVersion> <hash://sha256/1448656cc9f339b4911243d7c12f3ba5366b54fff3513640306682c50f13223d> .\n<hash://sha256/34ccd7cf7f4a1ea35ac6ae26a458bb603b2f6ee8ad36e1a58aa0261105d630b1> <http://purl.org/pav/previousVersion> <hash://sha256/7ee6b16b7a5e9b364776427d740332d8552adf5041d48018eeb3c0e13ccebf27> .<\/p>\n\nTo check the integrity of the extracted archive, confirm that each line produce by the command "preston verify" produces lines as shown below, with each line including "CONTENT_PRESENT_VALID_HASH". Depending on hardware capacity, this may take a while.<\/p>\n\n$ java -jar preston.jar verify\nhash://sha256/e0c131ebf6ad2dce71ab9a10aa116dcedb219ae4539f9e5bf0e57b84f51f22ca    file:/home/preston/preston-bhl/data/e0/c1/e0c131ebf6ad2dce71ab9a10aa116dcedb219ae4539f9e5bf0e57b84f51f22ca    OK    CONTENT_PRESENT_VALID_HASH    49458087    hash://sha256/e0c131ebf6ad2dce71ab9a10aa116dcedb219ae4539f9e5bf0e57b84f51f22ca\nhash://sha256/1a57e55a780b86cff38697cf1b857751ab7b389973d35113564fe5a9a58d6a99    file:/home/preston/preston-bhl/data/1a/57/1a57e55a780b86cff38697cf1b857751ab7b389973d35113564fe5a9a58d6a99    OK    CONTENT_PRESENT_VALID_HASH    25745    hash://sha256/1a57e55a780b86cff38697cf1b857751ab7b389973d35113564fe5a9a58d6a99\nhash://sha256/85efeb84c1b9f5f45c7a106dd1b5de43a31b3248a211675441ff584a7154b61c    file:/home/preston/preston-bhl/data/85/ef/85efeb84c1b9f5f45c7a106dd1b5de43a31b3248a211675441ff584a7154b61c    OK    CONTENT_PRESENT_VALID_HASH    519892    hash://sha256/85efeb84c1b9f5f45c7a106dd1b5de43a31b3248a211675441ff584a7154b61c\nhash://sha256/251e5032afce4f1e44bfdc5a8f0316ca1b317e8af41bdbf88163ab5bd2b52743    file:/home/preston/preston-bhl/data/25/1e/251e5032afce4f1e44bfdc5a8f0316ca1b317e8af41bdbf88163ab5bd2b52743    OK    CONTENT_PRESENT_VALID_HASH    787414    hash://sha256/251e5032afce4f1e44bfdc5a8f0316ca1b317e8af41bdbf88163ab5bd2b52743<\/p>\n\nNote that a copy of the java program "preston", preston.jar, is included in this publication. The program runs on java 8+ virtual machine using "java -jar preston.jar", or in short "preston".<\/p>\n\nFiles in this data publication:<\/p>\n\n--- start of file descriptions ---<\/p>\n\n-- description of archive and its contents (this file) --\nREADME<\/p>\n\n-- executable java jar containing preston[2] v0.1.15. --\npreston.jar<\/p>\n\n-- preston archives containing BHL data files, associated provenance logs and a provenance index --\npreston-[00-ff].tar.gz<\/p>\n\n-- individual provenance index files --\n2a5de79372318317a382ea9a2cef069780b852b01210ef59e06b640a3539cb5a\n2b1104cb7749e818c9afca78391b2d0099bbb0a32f2b348860a335cd2f8f6800\n4081bc59dff58d63f6a86c623cb770f01e9a355a42495b205bcb538cd526190f\n47a2816f8b5600b24487093adcddfea12434cc4f270f3ab09d9215fbdd546cd2\n6f99a1388823fca745c9e22ac21e2da909a219aa1ace55170fa9248c0276903c\n7ae46d7cd9b5a0f5889ba38bac53c82e591b0bdf8b605f5e48c0dce8fb7b717f\n82903464889fea7c53f53daedf4e41fa31092f82619edeb3415eb2b473f74af3\n9e8c86243df39dd4fe82a3f814710eccf73aa9291d050415408e346fa2b09e70\na8308fbf4530e287927c471d881ce0fc852f16543d46e1ee26f1caba48815f3a\nbcec6df2ea7f74e9a6e2830d0072e6b2fbe65323d9ddb022dd6e1349c23996e2\ncfe47c25ec0210ac73c06b407beb20d9c58355cb15bae427fdc7541870ca2e4e\nf73fc9e70bce8f21f0c96b8ef0903749d8f223f71343ab5a8910968f99c9b8b6<\/p>\n\n--- end of file descriptions ---<\/p>\n\n\nReferences<\/p>\n\n[1] Biodiversity Heritage Library (BHL, https://biodiversitylibrary.org) accessed from 2019-05-19 to 2020-05-09 with provenance hash://sha256/34ccd7cf7f4a1ea35ac6ae26a458bb603b2f6ee8ad36e1a58aa0261105d630b1.\n[2] https://preston.guoda.bio, https://doi.org/10.5281/zenodo.1410543 .<\/p>\n\n\nThis work is funded in part by grant NSF OAC 1839201 from the National Science Foundation.<\/p>"]} 

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