Abstract
No central online repository exists for the collection of animal images; hence it remains unclear how extensively species have been illustrated in the published literature or online. Here we compiled a list of more than 8000 reptile species (out of 11,341) that have photos in one of six popular online repositories, namely iNaturalist (6,349 species), the Reptile Database (5,144), Flickr (4,386), CalPhotos (3,071), Wikimedia (2,952), and Herpmapper (2,571). These sites have compiled over one million reptile photos, with some species represented by tens of thousands of images. Despite the number of images, many species have only one or a few images. This suggests that a considerable fraction of morphological and geographic variation is under documented or difficult to access. We highlight prominent gaps in amphisbaenians, lizards, and snakes, with geographic hotspots for species without images in Central Africa, Pacific Islands, and the Andes Mountains. We present a list of ~3,000 species without photos in any of the six databases and ask the community to fill the gaps by depositing images on one of these sites (preferably with minimal copyright restrictions).
References
Allain, S. (2019) Mining Flickr: a method for expanding the known distribution of invasive species. Herpetological Bulletin, 148, 11–14.
https://doi.org/10.33256/hb148.1114
Auliya, M., Altherr, S., Ariano-Sanchez, D., Baard, E.H., Brown, C., Brown, R.M., Cantu, J., Gentile, G., Gildenhuys, P., Henningheim, E., Hintzmann, J., Kanari, K., Krvavac, M., Lettink, M., Lippert, J., Luiselli, L., Nilson, G., Nguyen, T.Q., Nijman, V., Parham, J.F., Pasachnik, S.A., Pedrono, M., Rauhaus, A., Rueda Córdova, D., Sanchez, M.E., Schepp, U., van Schingen, M., Schneeweiss, N., Segniagbeto, G.H., Somaweera, R., Sy, E.Y., Türkozan, O., Vinke, S., Vinke, T., Vyas, R., Williamson, S. & Ziegler, T. (2016) Trade in live reptiles, its impact on wild populations, and the role of the European market. Biological Conservation, 204, 103–119.
https://doi.org/10.1016/j.biocon.2016.05.017
Austen, G.E., Bindemann, M., Griffiths, R.A. & Roberts, D.L. (2016) Species identification by experts and non-experts: comparing images from field guides. Scientific Reports, 6, 33634.
https://doi.org/10.1038/srep33634
Austen, G.E., Bindemann, M., Griffiths, R.A. & Roberts, D.L. (2018) Species identification by conservation practitioners using online images: accuracy and agreement between experts. PeerJ, 6, e4157.
https://doi.org/10.7717/peerj.4157
Botella, C., Joly, A., Bonnet, P., Monestiez, P. & Munoz, F. (2018) Species distribution modeling based on the automated identification of citizen observations. Applications in Plant Sciences, 6, e1029.
https://doi.org/10.1002/aps3.1029
Chang, W. (2015) downloader: Download files over HTTP and HTTPS. Available from: https://CRAN.R-project.org/package=downloader (accessed 31 October 2020)
Drury, J.P., Barnes, M., Finneran, A.E., Harris, M. & Grether, G.F. (2019) Continent-scale phenotype mapping using citizen scientists’ photographs. Ecography, 42, 1436–1445.
https://doi.org/10.1111/ecog.04469
Dylewski, Ł., Mikula, P., Tryjanowski, P., Morelli, F. & Yosef, R. (2017) Social media and scientific research are complementary—YouTube and shrikes as a case study. The Science of Nature, 104, 48.
https://doi.org/10.1007/s00114-017-1470-8
Egloff, W., Agosti, D., Kishor, P., Patterson, D. & Miller, J. (2017) Copyright and the use of images as biodiversity data. Research Ideas and Outcomes, 3, e12502.
https://doi.org/10.3897/rio.3.e12502
Farnsworth, E.J., Chu, M., Kress, W.J., Neill, A.K., Best, J.H., Pickering, J., Stevenson, R.D., Courtney, G.W., VanDyk, J.K. & Ellison, A.M. (2013) Next-generation field guides. BioScience, 63, 891–899.
https://doi.org/10.1525/bio.2013.63.11.8
Fernandes, R.F., Scherrer, D. & Guisan, A. (2018) Effects of simulated observation errors on the performance of species distribution models. Diversity and Distributions, 25.3, 1–14.
https://doi.org/10.1111/ddi.12868
Flickr Development Team (2019) Flickr API. Flickr. Available from: https://www.flickr.com/services/api/ (accessed 31 October 2020)
Gibbon, G.E.M., Bindemann, M. & Roberts, D.L. (2015) Factors affecting the identification of individual mountain bongo antelope. PeerJ, 3, e1303.
https://doi.org/10.7717/peerj.1303
Heberle, H., Meirelles, G.V., da Silva, F.R., Telles, G.P. & Minghim, R. (2015) InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams. BMC Bioinformatics, 16, 169.
https://doi.org/10.1186/s12859-015-0611-3
Hedges, S.B., Dudley, J. & Kumar, S. (2006) TimeTree: A public knowledge-base of divergence times among organisms. Bioinformatics, 22, 2971–2972.
https://doi.org/10.1093/bioinformatics/btl505
Hijmans, R.J. (2020) raster: Geographic data analysis and modeling. Available from: https://CRAN.R-project.org/package=raster (accessed 31 October 2020)
Jarić, I., Correia, R.A., Brook, B.W., Buettel, J.C., Courchamp, F., Di Minin, E., Firth, J.A., Gaston, K.J., Jepson, P., Kalinkat, G., Ladle, R., Soriano-Redondo, A., Souza, A.T. & Roll, U. (2020) iEcology: Harnessing large online resources to generate ecological insights. Trends in Ecology & Evolution, S016953472030077X.
https://doi.org/10.1016/j.tree.2020.03.003
Jiménez-Valverde, A., Peña-Aguilera, P., Barve, V. & Burguillo-Madrid, L. (2019) Photo-sharing platforms key for characterising niche and distribution in poorly studied taxa. In: Leather, S. & Stewart, A. (Eds.), Insect Conservation and Diversity, icad.12351. https://doi.org/10.1111/icad.12351
Joly, A., Goeau, H., Deneu, B., Cole, E., de Castaneda, R.R., Bolon, I., Durso, A., Lorieul, T., Glotin, H., Eggel, I., Vellinga, W.-P. & Muller, H. (2020) Overview of LifeCLEF 2020: a system-oriented evaluation of automated species identification and species distribution Prediction. Lecture Notes in Computer Science, 25, 342–363
https://doi.org/10.1007/978-3-030-58219-7_23
Kassambara, A. (2018) ggpubr: “ggplot2” based publication ready plots. Available from: https://CRAN.R-project.org/package=ggpubr (accessed 31 October 2020)
Keyes, O., Jacobs, J., Schmidt, D., Greenaway, M., Rudis, B., Pinto, A., Khezrzadeh, M., Meilstrup, P., Costello, A.M., Bezanson, J., Meilstrup, P. & Jiang, X. (2019) urltools: Vectorised tools for URL handling and parsing. Available from: https://cran.r-project.org/package=urltools (accessed 31 October 2020)
Kidd, L.R., Gregg, E.A., Bekessy, S.A., Robinson, J.A. & Garrard, G.E. (2018) Tweeting for their lives: Visibility of threatened species on twitter. Journal for Nature Conservation, 46, 106–109.
https://doi.org/10.1016/j.jnc.2018.10.001
Kosmala, M., Wiggins, A., Swanson, A. & Simmons, B. (2016) Assessing data quality in citizen science. Frontiers in Ecology and the Environment, 14, 551–560.
https://doi.org/10.1002/fee.1436
Kumar, S. & Hedges, S.B. (2011) Timetree2: Species divergence times on the iPhone. Bioinformatics, 27, 2023–2024.
https://doi.org/10.1093/bioinformatics/btr315
Kumar, S., Stecher, G., Suleski, M. & Hedges, S.B. (2017) TimeTree: A resource for timelines, timetrees, and divergence times. Molecular biology and evolution, 34, 1812–1819.
https://doi.org/10.1093/molbev/msx116
Lang, D.T. & The CRAN Team (2018) RCurl: General Network (HTTP/FTP/...) Client interface for R. Available from: https://CRAN.R-project.org/package=RCurl (accessed 31 October 2020)
Mahendiran, M., Parthiban, M., Azeez, P.A. & Nagarajan, R. (2018) In situ measurements of animal morphological features: A non-invasive method. In: Fisher, D. (Ed.), Methods in Ecology and Evolution, 9, pp. 613–623.
https://doi.org/10.1111/2041-210X.12898
Maritz, R.A. & Maritz, B. (2020) Sharing for science: high-resolution trophic interactions revealed rapidly by social media. PeerJ, 8, e9485.
https://doi.org/10.7717/peerj.9485
Marshall, B.M. & Strine, C.T. (2019a) Exploring snake occurrence records: Spatial biases and marginal gains from accessible social media. PeerJ, 7, e8059.
https://doi.org/10.7717/peerj.8059
Marshall, B.M. & Strine, C.T. (2019b) Supplementary information for Marshall & Strine 2019: Code, data and packages. PeerJ, 7, e8059.
https://doi.org/10.7717/peerj.8059
Marshall, B.M., Strine, C. & Hughes, A.C. (2020) Thousands of reptile species threatened by under-regulated global trade. Nature Communications, 11, 4738.
https://doi.org/10.1038/s41467-020-18523-4
McClain, C.R. (2019) Likes, comments, and shares of marine organism imagery on Facebook. PeerJ, 7, e6795.
https://doi.org/10.7717/peerj.6795
Measey, J., Basson, A., Rebelo, A.D., Nunes, A.L., Vimercati, G., Louw, M. & Mohanty, N.P. (2019) Why have a pet amphibian? Insights from YouTube. Frontiers in Ecology and Evolution, 7, 52.
https://doi.org/10.3389/fevo.2019.00052
Miranda, E.B.P., Ribeiro, R.P. & Strüssmann, C. (2016) The ecology of human-anaconda conflict: a study using internet videos. Tropical Conservation Science 9, 43–77.
https://doi.org/10.1177/194008291600900105
Miralles, A., Bruy, T., Wolcott, K., Scherz, M.D., Begerow, D., Beszteri, B., Bonkowski, M., Felden, J., Gemeinholzer, B., Glaw, F., Glöckner, F.O., Hawlitschek, O., Kostadinov, I., Nattkemper, T.W., Printzen, C., Renz, J., Rybalka, N., Stadler, M., Weibulat, T., Wilke, T., Renner, S.S. & Vences, M. (2020) Repositories for Taxonomic Data: Where We Are and What is Missing. Systematic biology, 69, 1231–1253
https://doi.org/10.1093/sysbio/syaa026
Murphy, J.C., Jowers, M.J., Lehtinen, R.M., Charles, S.P., Colli, G.R. Jr., A.K.P., Hendry, C.R. & Pyron, R.A. (2016) Cryptic, sympatric diversity in Tegu Lizards of the Tupinambis teguixin group (Squamata, Sauria, Teiidae) and the description of three new species. PLOS ONE, 11, e0158542.
https://doi.org/10.1371/journal.pone.0158542
Ooms, J. (2014) The jsonlite Package: A practical and consistent mapping between JSON data and R objects. arXiv, 1403.2805. [published online]
Otsuka, R. & Yamakoshi, G. (2020) Analyzing the popularity of YouTube videos that violate mountain gorilla tourism regulations. In: Lau, E.H. (Ed.), PLOS ONE, 15, e0232085.
https://doi.org/10.1371/journal.pone.0232085
Paradis, E. & Schliep, K. (2019) ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics, 35, 526–528.
Pebesma, E. (2018) Simple features for r: Standardized support for spatial vector data. The R Journal, 10, 439–446. https://doi.org/10.32614/RJ-2018-009
Pedersen, T.L. & Crameri, F. (2018) scico: Colour Palettes Based on the Scientific Colour-Maps.
https://cran.r-project.org/web/packages/scico/index.html
Poisot, T., Mounce, R. & Gravel, D. (2013) Moving toward a sustainable ecological science: don’t let data go to waste! Ideas in Ecology and Evolution, 6 (2), 11–19.
https://doi.org/10.4033/iee.2013.6b.14.f
R Core Team (2020) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. Available from: https://www.r-project.org/ (accessed 31 October 2020)
R Studio Team (2020) RStudio: Integrated Development Environment for R. RStudio, Inc., Boston, MA. Available from: http://www.rstudio.com/ (accewssed 10 November 2020)
Roll, U., Feldman, A., Novosolov, M., Allison, A., Bauer, A.M., Bernard, R., Böhm, M., Castro-Herrera, F., Chirio, L., Collen, B., Colli, G.R., Dabool, L., Das, I., Doan, T.M., Grismer, L.L., Hoogmoed, M., Itescu, Y., Kraus, F., LeBreton, M., Lewin, A., Martins, M., Maza, E., Meirte, D., Nagy, Z.T., de C. Nogueira, C., Pauwels, O.S.G., Pincheira-Donoso, D., Powney, G.D., Sindaco, R., Tallowin, O.J.S., Torres-Carvajal, O., Trape, J.-F., Vidan, E., Uetz, P., Wagner, P., Wang, Y., Orme, C.D.L., Grenyer, R. & Meiri, S. (2017) The global distribution of tetrapods reveals a need for targeted reptile conservation. Nature Ecology & Evolution, 1, 1677–1682.
https://doi.org/10.1038/s41559-017-0332-2
Roll, U., Mittermeier, J.C., Diaz, G.I., Novosolov, M., Feldman, A., Itescu, Y., Meiri, S. & Grenyer, R. (2016) Using Wikipedia page views to explore the cultural importance of global reptiles. Biological Conservation, 204, 42–50.
https://doi.org/10.1016/j.biocon.2016.03.037
Ross, N. (2020) fasterize: Fast polygon to raster conversion. Available from: https://CRAN.R-project.org/package=fasterize (accessed 31 October 2020)
Slowikowski, K. (2018) ggrepel: Automatically Position Non-Overlapping Text Labels with “ggplot2.” Available from: https://CRAN.R-project.org/package=ggrepel (accessed 31 October 2020)
Wäldchen, J., Rzanny, M., Seeland, M. & Mäder, P. (2018) Automated plant species identification—Trends and future directions. In: Bucksch, A. (Ed.), PLOS Computational Biology, 14, e1005993.
https://doi.org/10.1371/journal.pcbi.1005993
Wickham, H. (2016) ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag, New York. Available from: https://cran.r-project.org/web/packages/ggplot2/index.html (accessed 31 October 2020)
Wickham, H. (2019a) rvest: Easily Harvest (Scrape) Web Pages. Available from: https://CRAN.R-project.org/package=rvest (accessed 31 October 2020)
Wickham, H. (2019b) stringr: Simple, consistent wrappers for common string operations. Available from: https://CRAN.R-project.org/package=stringr (accessed 31 October 2020)
Wickham, H., François, R., Henry, L. & Müller, K. (2019) dplyr: A Grammar of Data Manipulation. Available from: https://CRAN.R-project.org/package=dplyr (accessed 31 October 2020)
Wickham, H. & Henry, L. (2019) tidyr: Easily Tidy Data with “spread()” and “gather()” Functions. Available from: https://CRAN.R-project.org/package=tidyr (accessed 31 October 2020)
Wickham, H., Hester, J. & Ooms, J. (2018) xml2: Parse XML. Available from: https://CRAN.R-project.org/package=xml2 (accessed 31 October 2020)
Wilke, C.O. (2019) cowplot: Streamlined plot theme and plot annotations for “ggplot2.” Available from: https://CRAN.R-project.org/package=cowplot (accessed 31 October 2020)
Yu, G., Lam, T.T.-Y., Zhu, H. & Guan, Y. (2018) Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution, 35, 3041–3043.
https://doi.org/10.1093/molbev/msy194
Yu, G., Smith, D., Zhu, H., Guan, Y. & Lam, T.T.-Y. (2017) ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution, 8, 28–36.
https://doi.org/10.1111/2041-210X.12628
Zhu, W., Drewes, J. & Gegenfurtner, K.R. (2013) Animal detection in natural images: Effects of color and image database. PLOS ONE, 8, 1–14.
https://doi.org/10.1371/journal.pone.0075816
Ziegler, T., Rauhaus, A. & Vences, M. (2020) Welt-Zooerstzucht des Kryptischen Goldtejus (Tupinambis cryptus) im Terrarium des Kölner Zoos. Elaphe, 2020 (1), 22–31