TTWG [Turtle Taxonomy Working Group; Rhodin, A. G. J. et al.] Turtles of the World. Annotated Checklist and Atlas of Taxonomy, Synonymy, Distribution, and Conservation Status (8th Ed.) (Chelonian Research Foundation and Turtle Conservancy, Chelonian Research Monographs 7, 2017).
TEWG [Turtle Extinctions Working Group; Rhodin, A. G. J. et al.] Turtles and Tortoises of the World During the Rise and Global Spread of Humanity: First Checklist and Review of Extinct Pleistocene and Holocene Chelonians (IUCN/SSC Tortoise and Freshwater Turtle Specialist Group, Chelonian Research Monographs 5, 2015).
Clausen, C. J., Cohen, A. D., Emiliani, C., Holman, J. A. & Stipp, J. J. Little Salt Spring, Florida: A unique underwater site. Science 203, 609–614 (1979).
Holman, J. A. & Clausen, C. J. Fossil vertebrates associated with Paleo-Indian artifact at Little Salt Spring, Florida. J. Vertebr. Paleontol. 4, 146–154 (1984).
Cantalamessa, G. et al. A new vertebrate fossiliferous site from the Late Quaternary at San José on the north coast of Ecuador: Preliminary note. J. South Am. Earth Sci. 14, 331–334 (2001).
Aguilera Socorro, O. Tesoros paleontológicos de Venezuela. El Cuaternario del Estado Falcón (Ministerio de la Cultura, Instituto del Patrimonio Cultural, Caracas, 2006).
Zacarías, G. G., de la Fuente, M. S., Fernández, M. S. & Zurita, A. E. Nueva especie de tortuga terrestre gigante del género Chelonoidis Fitzinger, 1835 (Cryptodira: Testudinidae), del miembro inferior de la Formación Toropí/Yupoí (Pleistoceno tardío/Lujanense), Bella Vista, Corrientes, Argentina. Ameghiniana 50, 298–318 (2013).
Zacarías, G. G., de la Fuente, M. S. & Zurita, A. E. Testudinoidea Fitzinger (Testudines: Cryptodira) de la Formación Toropí/Yupoí (ca. 58–28 ka) en la Provincia de Corrientes, Argentina: Taxonomía y aspectos paleoambientales. Rev. Bras. Paleontol. 17, 389–404 (2014).
Torres Chiriboga, F. J. Histología ósea de una tortuga gigante del Pleistoceno (Testudinidae) de Ecuador continental, con comentarios del origen de las tortugas de Galápagos (Disertación previa, Pontificia Universidad Católica del Ecuador, Quito, 2016).
Cadena, E. A. & Román-Carrión, J. L. A review of the fossil record of Ecuador, with insights about its challenges and future development. Ameghiniana 55, 571–591 (2018).
Franz, R., Albury, N. A. & Steadman, D. W. Extinct tortoises from the Turks and Caicos Islands. Florida Mus. Nat. Hist. Bull. 58, 1–38 (2020).
Williams, E. E. Testudo cubensis and the evolution of Western Hemisphere tortoises. Bull. Am. Mus. Nat. Hist. 95, 1–36 (1950).
Williams, E. E. A new fossil tortoise from Mona Island, West Indies, and a tentative arrangement of the tortoises of the world. Bull. Am. Mus. Nat. Hist. 99, 545–560 (1952).
Auffenberg, W. Notes on West Indian tortoises. Herpetologica 23, 34–44 (1967).
Franz, R. & Woods, C. A. A fossil tortoise from Hispaniola. J. Herpetol. 17, 79–81 (1983).
Franz, R. & Franz, S. A new fossil land tortoise in the genus Chelonoidis (Testudines: Testudinidae) from the northern Bahamas, with an osteological assessment of other Neotropical tortoises. Florida Mus. Nat. Hist. Bull. 49, 1–44 (2009).
Steadman, D. W. et al. Exceptionally well preserved late Quaternary plant and vertebrate fossils from a blue hole on Abaco, The Bahamas. Proc. Natl. Acad. Sci. USA 104, 19897–19902 (2007).
Hastings, A. K., Krigbaum, J., Steadman, D. W. & Albury, N. A. Domination by reptiles in a terrestrial food web of the Bahamas prior to human occupation. J. Herpetol. 48, 380–388 (2014).
Kehlmaier, C. et al. Tropical ancient DNA reveals relationships of the extinct Bahamian giant tortoise Chelonoidis alburyorum. Proc. R. Soc. B 284, 20162235 (2017).
Steadman, D. W. et al. The paleoecology and extinction of endemic tortoises in the Bahamian Archipelago. Holocene 30, 420–427 (2020).
Albury, N. A., Franz, R., Rimoli, P., Lehman, P. & Rosenberger, A. L. Fossil land tortoises (Testudines: Testudinidae) from the Dominican Republic, West Indies, with a description of a new species. Am. Mus. Novit. 3904, 1–28 (2018).
Fulton, T. L. & Shapiro, B. Setting up an ancient DNA laboratory. In Ancient DNA: Methods and Protocols. Methods in Molecular Biology, Vol. 1963 (eds Shapiro, B. et al.), 1–13 (Humana Press, Totowa, 2019).
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 (2013).
Gansauge, M.-T. & Meyer, M. Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA. Nat. Protoc. 8, 737–748 (2013).
Korlević, P. et al. Reducing microbial and human contamination in DNA extractions from ancient bones and teeth. Biotechniques 58, 87–93 (2015).
Maricic, T., Whitten, M. & Pääbo, S. Multiplexed DNA sequence capture of mitochondrial genomes using PCR products. PLoS One 5, e14004 (2010).
Horn, S. Target enrichment via DNA hybridization capture. In Ancient DNA: Methods and Protocols. Methods in Molecular Biology, Vol. 840 (eds Shapiro, B. & Hofreiter, M.), 177–188 (Springer, Berlin, 2012).
Jiang, H., Lei, R., Ding, S. W. & Zhu, S. Skewer: A fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinform. 15, 182 (2014).
Bushnell, B., Rood, J. & Singer, E. BBMerge—accurate paired shotgun read merging via overlap. PLoS One 12, e0185056 (2017).
Wingett, S. W. & Andrews, S. FastQ Screen: A tool for multi-genome mapping and quality control [version 2; referees: 4 approved]. F1000Research 7, 1338 (2018).
Hahn, C., Bachmann, L. & Chevreux, B. Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach. Nucleic Acids Res. 41, 1–9 (2013).
Milne, I. et al. Using Tablet for visual exploration of second-generation sequencing data. Brief. Bioinform. 14, 193–202 (2013).
Quinlan, A. R. & Hall, I. M. BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).
Kehlmaier, C. et al. Ancient mitogenomics clarifies radiation of extinct Mascarene giant tortoises. Sci. Rep. 9, 17487 (2019).
Poulakakis, N. et al. Colonization history of Galapagos giant tortoises: Insights from mitogenomes support the progression rule. J. Zool. Syst. Evol. Res. 58, 1262–1275 (2020).
Thompson, J. D., Higgins, D. G. & Gibson, T. J. Clustal W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673–4680 (1994).
Hall, T. A. BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41, 95–98 (1999).
Bernt, M. et al. MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol. Phylogenet. Evol. 69, 313–319 (2013).
Kumar, S., Stecher, G., Knyaz, C. & Tamura, K. MEGA X: Molecular Evolutionary Genetic Analysis across computing platforms. Mol. Biol. Evol. 35, 1547–1549 (2018).
Stamatakis, A. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).
Ronquist, F. et al. MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 61, 539–542 (2012).
Lanfear, R., Frandsen, P. B., Wright, A. M., Senfeld, T. & Calcott, B. PartitionFinder 2: New methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Mol. Biol. Evol. 34, 772–773 (2016).
Rambaut, A., Drummond, A. J., Xie, D., Baele, G. & Suchard, M. A. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst. Biol. 5, 901–904 (2018).
Drummond, A. J., Suchard, M. A., Xie, D. & Rambaut, A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29, 1969–1973 (2012).
Woods, R. et al. Rapid size change associated with intra-island evolutionary radiation in extinct Caribbean “island shrews”. BMC Evol. Biol. 29, 106 (2020).
Geist, D., Snell, H. L., Snell, H. M., Goddard, C. & Kurz, M. Paleogeography of the Galápagos Islands and biogeographical implications. In The Galápagos: A Natural Laboratory for the Earth Sciences, Vol. 204 (eds Harpp, K., Mittelstaedt, E., d’Ozouville, N. & Graham, D.) 145–166 (American Geophysical Union, New York, 2014).
Hearty, P. J., Kindler, P., Cheng, H. & Edwards, R. A +20 m middle Pleistocene sea-level highstand (Bermuda and the Bahamas) due to partial collapse of Antarctic ice. Geology 27, 375–378 (1999).
Bowen, D. Sea level ∼400 000 years ago (MIS 11): Analogue for present and future sea-level? Clim. Past 6, 19–29 (2010).
Steadman, D. W. & Franklin, J. Origin, paleoecology, and extirpation of bluebirds and crossbills in the Bahamas across the last glacial-interglacial transition. Proc. Natl. Acad. Sci. USA 114, 9924–9929 (2017).
Fritz, U., Široký, P., Kami, H. & Wink, M. Environmentally caused dwarfism or a valid species—Is Testudo weissingeri Bour, 1996 a distinct evolutionary lineage? New evidence from mitochondrial and nuclear genomic markers. Mol. Phylogenet. Evol. 37, 389–401 (2005).
Fritz, U. et al. Phenotypic plasticity leads to incongruence between morphology-based taxonomy and genetic differentiation in western Palaearctic tortoises (Testudo graeca complex; Testudines, Testudinidae). Amphibia-Reptilia 28, 97–121 (2007).
Fritz, U. et al. Mitochondrial phylogeography and subspecies of the wide-ranging sub-Saharan leopard tortoise Stigmochelys pardalis (Testudines: Testudinidae)—a case study for the pitfalls of pseudogenes and GenBank sequences. J. Zool. Syst. Evol. Res. 48, 348–359 (2010).
Fritz, U. et al. Northern genetic richness and southern purity, but just one species in the Chelonoidis chilensis complex. Zool. Scr. 41, 220–232 (2012).
Carlson, L. A. & Keegan, W. F. Resource depletion in the prehistoric northern West Indies. In Voyages of Discovery (ed. Fitzpatrick, S. M.) 85–107 (Praeger, Westport, 2004).
Keegan, W. F. Taino Indian Myth and Practice: The Arrival of the Stranger King (University Press of Florida, Gainesville, 2007).
Oswald, J. A. et al. Ancient DNA and high-resolution chronometry reveal a long-term human role in the historical diversity and biogeography of the Bahamian hutia. Sci. Rep. 10, 1373 (2020).
Loire, E. & Galtier, N. Lacking conservation genomics in the giant Galápagos tortoise. bioRxiv 101980, 1–14 (2017).
Fontaine, M. C. A genomic perspective is needed for the re-evaluation of species boundaries, evolutionary trajectories, and conservation strategies of the Galápagos giant tortoises. PCI Evol. Biol. 100031, 1–3 (2017).
Vargas-Ramírez, M., Maran, J. & Fritz, U. Red- and yellow-footed tortoises (Chelonoidis carbonaria, C. denticulata) in South American savannahs and forests: Do their phylogeographies reflect distinct habitats? Org. Divers. Evol. 10, 161–172 (2010).
Blake, S. et al. Seed dispersal by Galápagos tortoises. J. Biogeogr. 39, 1961–1972 (2012).
Walton, R. et al. In the land of giants: Habitat use and selection of the Aldabra giant tortoise on Aldabra Atoll. Biodiv. Conserv. 28, 3183–3198 (2019).
Source: Ecology - nature.com
