{"id":45368977,"url":"https://github.com/cjabradshaw/cyprushippoelephant","last_synced_at":"2026-02-21T15:20:00.042Z","repository":{"id":203889708,"uuid":"710630678","full_name":"cjabradshaw/CyprusHippoElephant","owner":"cjabradshaw","description":"Demographic models predicting the effect of human hunting on now-extinct dwarf hippopotamus and dwarf elephant in 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Demographic models predicting the effect of human hunting on now-extinct dwarf hippopotamus 🦛 and dwarf elephant 🐘 in Cyprus 🇨🇾\n\u003ca href=\"https://www.ucy.ac.cy/migrate/\"\u003e\u003cimg align=\"right\" src=\"www/MigratelogoShad.png\" width=\"200\" style=\"margin-top: 20px\"\u003e\u003c/a\u003e\n\u003ca href=\"https://zenodo.org/doi/10.5281/zenodo.10561469\"\u003e\u003cimg src=\"https://zenodo.org/badge/DOI/10.5281/zenodo.10561469.svg\" alt=\"DOI\"\u003e\u003c/a\u003e\n\nPart of the \u003ca href=\"https://www.ucy.ac.cy/migrate/\"\u003eMIGRATE\u003c/a\u003e (\u003cstrong\u003eM\u003c/strong\u003eodell\u003cstrong\u003ei\u003c/strong\u003eng Demo\u003cstrong\u003egr\u003c/strong\u003eaphy and \u003cstrong\u003eA\u003c/strong\u003edaptation in the Initial Peopling of the Eastern M\u003cstrong\u003ee\u003c/strong\u003editerranean Islandscape) project, under the auspices of the European Union Research and Innovation Foundation for Research, Technological Development and Innovation \"Restart 2016-2020\".\n\u003cbr\u003e\n\u003cbr\u003e\n\u003cstrong\u003elead investigator\u003c/strong\u003e: Dr \u003ca href=\"https://www.ucy.ac.cy/directory/en/profile/tmouts01\"\u003eTheodora Moutsiou\u003c/a\u003e\u003cbr\u003e\n\u003cstrong\u003ekey personnel\u003c/strong\u003e: Dr \u003ca href=\"https://scholar.google.com.au/citations?user=BU25ogMAAAAJ\u0026hl=en\"\u003eChristian Reepmeyer\u003c/a\u003e, Associate Professor \u003ca href=\"https://www.ucy.ac.cy/directory/en/profile/demest\"\u003eStella Demesticha\u003c/a\u003e, Prof \u003ca href=\"https://www.presidency.gov.cy/cypresidency/cypresidency.nsf/All/FBA917CB5206BC95C225896B0023FAFD?OpenDocument\"\u003eVasiliki Kassianidou\u003c/a\u003e, Dr \u003ca href=\"https://www.cut.ac.cy/faculties/fet/ceg/staff/athos.agapiou/?languageId=1\"\u003eAthos Agapiou\u003c/a\u003e, Dr \u003ca href=\"https://www.researchgate.net/profile/Zomenia-Zomeni\"\u003eZomenia Zomeni\u003c/a\u003e, Professor \u003ca href=\"https://globalecologyflinders.com/people/#DIRECTOR\"\u003eCorey Bradshaw\u003c/a\u003e\u003cbr\u003e\n\u003cstrong\u003ecollaborators\u003c/strong\u003e: Dr \u003ca href=\"https://globalecologyflinders.com/people/#COORDINATOR\"\u003eFrédérik Saltré\u003c/a\u003e, Dr \u003ca href=\"https://qcnr.usu.edu/directory/envs/faculty/crabtree-stefani\"\u003eStefani Crabtree\u003c/a\u003e\n\u003cbr\u003e\n## Project overview\nProject \u003ca href=\"https://www.ucy.ac.cy/migrate/\"\u003eMIGRATE\u003c/a\u003e seeks to offer novel insights into population dynamics and range shifts that resulted in dispersals from the Eastern Mediterranean mainland to the island of \u003ca href=\"https://www.google.com/maps/place/Cyprus/@35.1670135,32.765821,9z/\"\u003eCyprus\u003c/a\u003e at a critical period (Late Pleistocene, 45-12 ka) through stochastic spatial modelling. This advanced modelling will  enhance our understanding of timing, and climatic and social factors important in the initial colonisation of Cyprus. The proposed project aims to establish new research domains in the field of Cypriot archaeology extending traditional chronological frontiers beyond the Holocene (current Warm Period), encompassing innovative and interdisciplinary methodologies at the forefront of archaeological research.\n\n## Papers arising\n- Bradshaw, CJA, C Reepmeyer, F Saltré, A Agapiou, V Kassinadiou, S Demesticha, Z Zomeni, M Polidorou, T Moutsiou. 2024. \u003ca href=\"http://doi.org/10.1073/pnas.2318293121\"\u003eDemographic models predict end-Pleistocene arrival and rapid expansion of pre-agropastoralist humans in Cyprus\u003c/a\u003e. \u003cem\u003e\u003cstrong\u003eProceedings of the National Academy of Sciences of the USA\u003c/strong\u003e\u003c/em\u003e 121:e2318293121. doi:10.1073/pnas.2318293121 (see also \u003ca href=\"https://github.com/cjabradshaw/CyprusHumanPleistocene\"\u003erelated Github repository\u003c/a\u003e)\n- Moutsiou T. 2021. \u003ca href=\"http://doi.org/10.1016/j.quaint.2020.09.012\"\u003eClimate, environment and cognition in the colonisation of the Eastern Mediterranean islands during the Pleistocene\u003c/a\u003e.  \u003cem\u003e\u003cstrong\u003eQuaternary International\u003c/strong\u003e\u003c/em\u003e 577:1-14\n- Moutsiou T, C Reepmeyer, V Kassianidou, Z Zomeni, A Agapiou A. 2021. \u003ca href=\"http://doi.org/10.1371/journal.pone.0258370\"\u003eModelling the Pleistocene colonisation of Eastern Mediterranean islandscapes\u003c/a\u003e. \u003cem\u003e\u003cstrong\u003ePLoS One\u003c/strong\u003e\u003c/em\u003e 16:e0258370\n\n## Focal manuscript\nBradshaw, CJA, F Saltré, SA Crabtree, C Reepmeyer, T Moutsiou. \u003ca href=\"http://doi.org/10.1098/rspb.2024.0967\"\u003eSmall populations of palaeolithic humans in Cyprus hunted endemic megafauna to extinction\u003c/a\u003e. \u003cem\u003eProceedings of the Royal Society B\u003c/em\u003e 291: 20240967. doi:10.1098/rspb.2024.0967\u003cbr\u003e\n\u003cbr\u003e\nand (now out-of-date) preprint:\u003cbr\u003e\n\u003cbr\u003e\nBradshaw, CJA, F Saltré, SA Crabtree, C Reepmeyer, T Moutsiou. \u003ca href=\"http://doi.org/10.21203/rs.3.rs-3889827/v1\"\u003eMechanisms of hunting native megafauna to extinction by Palaeolithic humans on Cyprus\u003c/a\u003e. \u003cem\u003eResearch Square\u003c/em\u003e (preprint) doi:10.21203/rs.3.rs-3889827/v1\n\n## Abstract\nThe hypothesised main drivers of megafauna extinctions in the late Quaternary have wavered between over-exploitation by humans and environmental change, with recent investigations demonstrating more nuanced synergies between these drivers depending on taxon, spatial scale, and region. However, most studies still rely on comparing archaeologically based chronologies of timing of initial human arrival into naïve ecosystems and palaeontologically inferred dates of megafauna extinctions. Conclusions arising from comparing chronologies also depend on the reliability of dated evidence, dating uncertainties, and correcting for the low probability of preservation (Signor-Lipps effect). While some models have been developed to test the susceptibility of megafauna to theoretical offtake rates, none has explicitly linked human energetic needs, prey choice, and hunting efficiency to examine the plausibility of human-driven extinctions. Using the island of Cyprus in the terminal Pleistocene as an ideal test case because of its late human settlement (~ 14.2 ka–13.2 ka), small area (~ 11,000 km\u003csup\u003e2\u003c/sup\u003e), and low megafauna diversity (2 species), we developed stochastic models of megafauna population dynamics, with offtake dictated by human energetic requirements, prey choice, and hunting-efficiency functions to test whether the human population at the end of the Pleistocene could have caused the extinction of dwarf hippopotamus (\u003cem\u003ePhanourios minor\u003c/em\u003e) and dwarf elephants (\u003cem\u003ePalaeoloxodon cypriotes\u003c/em\u003e). Our models reveal not only that the estimated human population sizes (\u003cem\u003eN\u003c/em\u003e = 3,000–7,000) in Late Pleistocene Cyprus could have easily driven both species to extinction within \u003c 1,000 years, the model predictions match the observed, Signor-Lipps-corrected chronological sequence of megafauna extinctions inferred from the palaeontological record (\u003cem\u003eP. minor\u003c/em\u003e at ~ 12 ka–11.1 ka, followed by \u003cem\u003eP. cypriotes\u003c/em\u003e at ~ 10.3 ka–9.1 ka).\n\n\u003cstrong\u003eΠαλαιολιθικοί ανθρώπινοι πληθυσμοί στην Κύπρο και οι μηχανισμοί κυνηγιού της εγγενούς μεγαλοπανίδας εώς την εξαφάνιση\u003c/strong\u003e\nΟι κύριες υποθέσεις που έχουν διατυπωθεί αναφορικά με τους πρωταρχικούς παράγοντες εξαφάνισης της μεγαλοπανίδας στο τέλος του Τεταρτογενούς αφορούν είτε στην υπερεκμετάλλευση από τον άνθρωπο ή στην περιβαλλοντική αλλαγή. Πρόσφατες έρευνες καταδεικνύουν ελαφρώς διαφοροποιημένες συνέργειες μεταξύ αυτών των παραγόντων ανάλογα με την ταξινομική βαθμίδα, την χωρική κλίμακα και την περιοχή. Ωστόσο, οι περισσότερες μελέτες εξακολουθούν να βασίζονται στη σύγκριση χρονολογιών της αρχικής ανθρώπινης άφιξης σε παρθένα οικοσυστήματα σύμφωνα με αρχαιολογικά δεδομένα και παλαιοντολογικά συναγόμενες ημερομηνίες εξαφανίσεων της μεγαλοπανίδας. Τα συμπεράσματα που προκύπτουν από τη σύγκριση χρονολογιών εξαρτώνται επιπλέον από την αξιοπιστία των χρονολογημένων στοιχείων, τις αβεβαιότητες χρονολόγησης και τη διόρθωση για την χαμηλή πιθανότητα διατήρησης (φαινόμενο Signor-Lipps). Παρόλο που διάφορα μοντέλα έχουν αναπτυχθεί για να διερευνήσουν την ευαισθησία της μεγαλοπανίδας σε θεωρητικά ποσοστά απόληψης, κανένα δεν έχει συνδέσει ρητά τις ανθρώπινες ενεργειακές ανάγκες, την επιλογή θηραμάτων και την αποτελεσματικότητα του κυνηγιού για να εξετάσει την αξιοπιστία των εξαφανίσεων ως ανθρωπογενές φαινόμενο. Το νησί της Κύπρου στο τέλος του Πλειστόκαινου αποτελεί ιδανική περίπτωση διερεύνησης του φαινομένου της εξαφάνισης της εγγενούς μεγαλοπανίδας λόγω της ύστερης ανθρώπινης εγκατάστασης (~ 14,200 χ.α.σ.–13,200 χ.α.σ.), της μικρής έκτασης του νησιού (~ 11,000 χμ\u003csup\u003e2\u003c/sup\u003e) και της χαμηλής ποικιλότητας της μεγαλοπανίδας (2 είδη). Για το σκοπό αυτό, αναπτύξαμε στοχαστικά μοντέλα της δυναμικής του πληθυσμού της μεγαλοπανίδας, με απόληψη που υπαγορεύεται από τις ανθρώπινες ενεργειακές απαιτήσεις, την επιλογή θηράματος και τις λειτουργίες απόδοσης κυνηγιού ώστε να εξετάσουμε εάν ο ανθρώπινος πληθυσμός στο τέλος του Πλειστόκαινου θα μπορούσε να είχε προκαλέσει την εξαφάνιση του νάνου ιπποπόταμου (\u003cem\u003ePhanourios minor\u003c/em\u003e) και των νάνων ελεφάντων (\u003cem\u003ePalaeoloxodon cypriotes\u003c/em\u003e). Τα μοντέλα μας αποκαλύπτουν ότι τα εκτιμώμενα μεγέθη ανθρώπινου πληθυσμού (\u003cem\u003eN\u003c/em\u003e = 3,000–7,000) στην Κύπρο του Ύστερου Πλειστόκαινου θα μπορούσαν εύκολα να οδηγήσουν και τα δύο είδη σε εξαφάνιση εντός \u003c 1,000 ετών. Επιπλέον, οι προβλέψεις των μοντέλων μας ταιριάζουν με την παρατηρούμενη, διορθωμένη με Signor-Lipps, χρονική ακολουθία των εξαφανίσεων της μεγαλοπανίδας όπως προκύπτει από το παλαιοντολογικό αρχείο (\u003cem\u003ePhanourios minor\u003c/em\u003e σε ~ 12,000–11,100 χ.α.σ. και \u003cem\u003ePalaeoloxodon cypriotes\u003c/em\u003e σε ~ 10,300–9,100 χ.α.σ.).\n\nThe code presented in this repository tests how palaeolithic peoples could have hunted dwarf hippopotamus (\u003cem\u003ePhanourios minor\u003c/em\u003e 🦛) and dwarf elephants (\u003cem\u003ePalaeoloxodon cypriotes\u003c/em\u003e 🐘) to extinction in the Late Pleistocene.\n\n## \u003ca href=\"https://github.com/cjabradshaw/CyprusHippoElephant/tree/main/scripts\"\u003eScripts\u003c/a\u003e\nR code by Corey Bradshaw (\u003ca href=\"http://github.com/cjabradshaw\"\u003e@cjabradshaw\u003c/a\u003e) and Frédérik Saltré (\u003ca href=\"http://github.com/fredsaltre\"\u003e@fredsaltre\u003c/a\u003e)\n\n### Cohort-based models\n- \u003ccode\u003edwarf hippo \u0026 elephant extinction dates.R\u003c/code\u003e: estimates Signor-Lipps-corrected extinction window for both megafauna species\n- \u003ccode\u003ebase hippo \u0026 elephant model.R\u003c/code\u003e: stochastic, age-structured demographic projection models for both megafauna species\n- \u003ccode\u003eofftake hippo \u0026 elephant model.R\u003c/code\u003e: stochastic models simulating incrementing offtake rates for both megafauna species (requires running 'base' models first)\n- \u003ccode\u003emeat equivalents hippo \u0026 elephant model.R\u003c/code\u003e: stochastic models simulating how incrementing population sizes of humans translates to loss of individuals of both megafauna species (requires running 'base' models first)\n- \u003ccode\u003edwarf hippo \u0026 elephant model gsa.R\u003c/code\u003e: global sensitivity analysis using Latin hypercube sampling of stochastic, age-structured demographic projection models for both megafauna species\n\n### \u003ca href=\"https://github.com/cjabradshaw/CyprusHippoElephant/tree/main/scripts/source\"\u003eSource functions\u003c/a\u003e\n- \u003ccode\u003ematrixOperators.r\u003c/code\u003e: functions for manipulating matrices for population projections\n- \u003ccode\u003equalityRating.r\u003c/code\u003e: applies quality rating to radiocarbon age estimates\n- \u003ccode\u003eendRating.r\u003c/code\u003e: chooses final quality rating for radiocarbon age estimates\n\n## \u003ca href=\"https://github.com/cjabradshaw/CyprusHippoElephant/tree/main/data\"\u003eData\u003c/a\u003e\n- \u003cem\u003ephanourios.txt\u003c/em\u003e: radiocarbon dates for \u003cem\u003ePhanourios minor\u003c/em\u003e 🦛 from \u003ca href=\"http://doi.org/10.1371/journal.pone.0134429\"\u003eZazzo et al.\u003c/a\u003e (2020: \u003cem\u003ePLoS One\u003c/em\u003e 10:0134429)\n- \u003cem\u003epalaeoloxodon.txt\u003c/em\u003e: radiocarbon dates for \u003cem\u003ePalaeoloxodon cypriotes\u003c/em\u003e 🐘 from Wigand, PE \u0026 Simmons, AH (1999: The dating of Akrotiri \u003cem\u003eAetokremnos\u003c/em\u003e, in \u003ca href=\"https://link.springer.com/book/10.1007/b109876\"\u003e\u003cem\u003eFaunal Extinction in an Island Society. Pygmy Hippopotamus Hunters of Cyprus\u003c/em\u003e\u003c/a\u003e. AH Simmons, ed. Kluwer Academic Publishers, New York. pp. 193-215)\n- \u003cem\u003eqx-Nicolaou.csv\u003c/em\u003e: life-table estimates of age-specific survival for \u003cem\u003ePhanourios minor\u003c/em\u003e 🦛 from \u003ca href=\"http://doi.org/10.1016/j.quaint.2020.09.016\"\u003eNicolaou et al.\u003c/a\u003e (2020: \u003cem\u003eQuat Int\u003c/em\u003e 568:55-64)\n- \u003cem\u003essdHuman.csv\u003c/em\u003e: stable-stage distribution of paleaolithic humans 🧑‍🤝‍🧑 from \u003ca href=\"http://doi.org/10.1073/pnas.2318293121\"\u003eBradshaw et al.\u003c/a\u003e (2024: doi:10.1073/pnas.2318293121)\n\n## R (v4.3.2) libraries\n- \u003ca href=\"https://github.com/FredSaltre/CRIWM/\"\u003e\u003ccode\u003eRextinct\u003c/code\u003e\u003c/a\u003e (approach described in this \u003ca href=\"https://doi.org/10.1016/j.quageo.2023.101489\"\u003epaper\u003c/a\u003e): install via Github – \u003ccode\u003edevtools::install_github(\"FredSaltre/CRIWM/Rextinct\")\u003c/code\u003e\n- \u003ca href=\"https://dplyr.tidyverse.org/\"\u003e\u003ccode\u003edplyr\u003c/code\u003e\u003c/a\u003e (v1.1.4), \u003ca href=\"https://plotly.com/r/\"\u003e\u003ccode\u003eplotly\u003c/code\u003e\u003c/a\u003e (v4.10.4), \u003ca href=\"https://rpkgs.datanovia.com/ggpubr/\"\u003e\u003ccode\u003eggpubr\u003c/code\u003e\u003c/a\u003e (v0.6.0), \u003ca href=\"https://cran.r-project.org/web/packages/truncnorm/truncnorm.pdf\"\u003e\u003ccode\u003etruncnorm\u003c/code\u003e\u003c/a\u003e (v1.0-9), \u003ca href=\"https://cran.r-project.org/web/packages/doSNOW/doSNOW.pdf\"\u003e\u003ccode\u003edoSNOW\u003c/code\u003e\u003c/a\u003e (v1.0.20), \u003ca href=\"https://cran.r-project.org/web/packages/iterators/iterators.pdf\"\u003e\u003ccode\u003eiterators\u003c/code\u003e\u003c/a\u003e (v1.0.14), \u003ca href=\"https://cran.r-project.org/web/packages/snow/snow.pdf\"\u003e\u003ccode\u003esnow\u003c/code\u003e\u003c/a\u003e (v0.4-4), \u003ca href=\"https://cran.r-project.org/web/packages/foreach/vignettes/foreach.html\"\u003e\u003ccode\u003eforeach\u003c/code\u003e\u003c/a\u003e (v1.5.2), \u003ca href=\"https://cran.r-project.org/web/packages/lhs/vignettes/lhs_basics.html\"\u003e\u003ccode\u003elhs\u003c/code\u003e\u003c/a\u003e (v1.1.6), \u003ca href=\"https://cran.r-project.org/web/packages/data.table/vignettes/datatable-intro.html\"\u003e\u003ccode\u003edata.table\u003c/code\u003e\u003c/a\u003e (v1.15.4), \u003ca href=\"https://cran.r-project.org/web/packages/dismo/dismo.pdf\"\u003e\u003ccode\u003edismo\u003c/code\u003e\u003c/a\u003e (v1.3-14), \u003ca href=\"https://cran.r-project.org/web/packages/gbm/gbm.pdf\"\u003e\u003ccode\u003egbm\u003c/code\u003e\u003c/a\u003e (v2.1.9)\n\n### Acknowledgements\nCo-financed by the \u003ca href=\"https://ec.europa.eu/regional_policy/funding/erdf_en\"\u003eEuropean Regional Development Fund\u003c/a\u003e and the Republic of Cyprus through the \u003ca href=\"https://www.research.org.cy/en/\"\u003eResearch and Innovation Foundation\u003c/a\u003e (EXCELLENCE/0421/0050) for the project \u003ca href=\"https://www.ucy.ac.cy/migrate/\"\u003eModelling Demography and Adaptation in the Initial Peopling of the Eastern Mediterranean Islandscape\u003c/a\u003e (MIGRATE, 2022-2024). Funding provided to CJAB and FS by the \u003ca href=\"https://www.arc.gov.au\"\u003eAustralian Research Council\u003c/a\u003e \u003ca href=\"https://EpicAustralia.org.au\"\u003eCentre of Excellence for Australian Biodiversity and Heritage\u003c/a\u003e (CE170100015). Χάρη και στα θρυλικά λουκάνικα της Λυσού.\n\u003cbr\u003e\n\u003cp\u003e\u003ca href=\"https://www.ucy.ac.cy\"\u003e\u003cimg align=\"bottom-left\" src=\"www/UCypruslogo.png\" alt=\"UCyprus logo\" height=\"40\" style=\"margin-top: 20px\"\u003e\u003c/a\u003e \u0026nbsp; \u003ca href=\"http://www.dainst.org\"\u003e\u003cimg align=\"bottom-left\" src=\"www/DAIlogo.png\" alt=\"DAI logo\" height=\"55\" style=\"margin-top: 20px\"\u003e\u003c/a\u003e \u0026nbsp; \u0026nbsp; \u003ca href=\"https://www.flinders.edu.au\"\u003e\u003cimg align=\"bottom-left\" src=\"www/Flinders_University_Logo_Horizontal_RGB_Master.png\" alt=\"Flinders University logo\" height=\"30\" style=\"margin-top: 20px\"\u003e\u003c/a\u003e \u0026nbsp; \u003ca href=\"https://globalecologyflinders.com\"\u003e\u003cimg align=\"bottom-left\" src=\"www/GEL Logo Kaurna New Transp-2.png\" alt=\"GEL logo\" height=\"55\" style=\"margin-top: 20px\"\u003e\u003c/a\u003e \u0026nbsp; \u0026nbsp; \u003ca href=\"https://epicaustralia.org.au\"\u003e\u003cimg align=\"bottom-left\" src=\"www/CabahFCL.jpg\" alt=\"CABAH logo\" height=\"40\" style=\"margin-top: 20px\"\u003e\u003c/a\u003e \u0026nbsp; \u0026nbsp; \u003ca href=\"https://www.santafe.edu/\"\u003e\u003cimg align=\"bottom-left\" src=\"www/SFI logo.png\" alt=\"Santa Fe Institute logo\" height=\"45\" style=\"margin-top: 20px\"\u003e\u003c/a\u003e\u003c/p\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcjabradshaw%2Fcyprushippoelephant","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcjabradshaw%2Fcyprushippoelephant","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcjabradshaw%2Fcyprushippoelephant/lists"}