A phylogenomic analysis of turtles

Crawford, Nicholas G.; Parham, James F.; Sellas, Anna B.; Faircloth, Brant C.; Glenn, Travis C.; Papenfuss, Theodore J.; Henderson, James; Hansen, Madison H.; Simison, W. Brian

doi:10.1016/j.ympev.2014.10.021

Cited by 267 publications

(269 citation statements)

References 63 publications

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“…The ecological driver for this convergence in many instances may have been sexual selection [20,42]. Our results imply that red retinal oil droplets themselves were present in the common ancestor of the archelosaurs (archosaurs and turtles) [31], so that red oil droplets had a single origin in tetrapods ( figure 3). An alternative would be if CYP2J19 originally arose for a different function than red oil droplets, but this is unlikely because no other functions for ketocarotenoids have been described.…”

Section: Discussionmentioning

confidence: 62%

“…Previous work has shown that there are two lineages of avian CYP2J loci, CYP2J19 and CYP2J40 (31), whereas humans and other mammals have a single CYP2J locus, CYP2J2. CYP2R1 and CYP2D6 are single-copy CYP families that are closely related to CYP2J and were used as outgroups (31). Nucleotide sequences were aligned in MEGA v. 6 [60] using MUSCLE [61].…”

Section: Materials and Methods (A) Data Mining And Phylogenetic Analysmentioning

confidence: 99%

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Seeing red to being red: conserved genetic mechanism for red cone oil droplets and co-option for red coloration in birds and turtles

et al. 2016

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Avian ketocarotenoid pigments occur in both the red retinal oil droplets that contribute to colour vision and bright red coloration used in signalling. Turtles are the only other tetrapods with red retinal oil droplets, and some also display red carotenoid-based coloration. Recently, the CYP2J19 gene was strongly implicated in ketocarotenoid synthesis in birds. Here, we investigate CYP2J19 evolution in relation to colour vision and red coloration in reptiles using genomic and expression data. We show that turtles, but not crocodiles or lepidosaurs, possess a CYP2J19 orthologue, which arose via gene duplication before turtles and archosaurs split, and which is strongly and specifically expressed in the ketocarotenoid-containing retina and red integument. We infer that CYP2J19 initially functioned in colour vision in archelosaurs and conclude that red ketocarotenoid-based coloration evolved independently in birds and turtles via gene regulatory changes of CYP2J19. Our results suggest that red oil droplets contributed to colour vision in dinosaurs and pterosaurs.

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Section: Discussionmentioning

confidence: 62%

Section: Materials and Methods (A) Data Mining And Phylogenetic Analysmentioning

confidence: 99%

Seeing red to being red: conserved genetic mechanism for red cone oil droplets and co-option for red coloration in birds and turtles

et al. 2016

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“…Subsequent cladistic analyses supported the distinct nature of pan-chelydrids and placed this clade as sister either to all other extant cryptodires (e.g., Gaffney et al 1991;Hirayama et al 2000;Tong et al 2009) or to testudinoids and trionychoids (e.g., Brinkman and Wu 1999;Joyce 2007). A series of increasingly well-sampled analyses that utilize molecular data (e.g., Shaffer et al 1997;Krenz et al 2005;Parham et al 2006;Barley et al 2010;Crawford et al 2015), however, have more recently revived the sister group relationship between chelydrids and kinosternoids to the exclusion of P. megacephalum. This resulting "superfamilial" clade is named Chelydroidea following Baur (1893), who was the first to recognize this exact arrangement (Knauss et al 2011).…”

Section: Introductionmentioning

confidence: 93%

A Review of the Fossil Record of Turtles of the CladePan-Chelydridae

Joyce¹

2016

Bulletin of the Peabody Museum of Natural History

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Turtles of the total clade Pan-Chelydridae have a relatively sparse fossil record that reaches back to the Late Cretaceous (Santonian). The clade was only present in North America during the Cretaceous but spread along unclear routes to Asia and Europe during the Paleocene, only to go extinct on those continents by the end of the Pliocene. Final dispersal to South America took place at some time during the late Neogene. The ecology of stem chelydrids seems to have been similar to that of the extant Chelydra serpentina, although more primitive representatives were more molluscivorous as inferred from their broader triturating surfaces. Current phylogenies only recognize five internested clades: Pan-Chelydridae, Chelydridae, Chelydropsis, Chelydra and Macrochelys. A taxonomic review of the group concludes that of 31 named fossil taxa, 8 are nomina valida, 10 are nomina invalida, 9 are nomina dubia, 1 is a nomen nudum and 1 is a regular, unavailable name.

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“…Major contributions to this topic include Gaffney (1984), Gaffney and Meylan (1988), Joyce (2007), Gaffney et al (2007), Danilov and Parham (2008), Sterli (2008Sterli ( , 2010, Joyce et al (2009Joyce et al ( , 2013, Barley et al (2010), Gaffney and Jenkins (2010), Sterli and de la Fuente (2013), and Crawford et al (2015).…”

Section: E2 Conservation Biology Of Freshwater Turtles and Tortoisesmentioning

confidence: 99%

Turtles and Tortoises of the World During the Rise and Global Spread of Humanity: First Checklist and Review of Extinct Pleistocene and Holocene Chelonians.

Rhodin¹,

Thomson²,

Georgalis³

et al. 2015

Chelonian Research Monographs

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ABsTrAcT. -We provide a first checklist and review of all recognized taxa of the world's extinct Pleistocene and Holocene (Quaternary) turtles and tortoises that existed during the early rise and global expansion of humanity, and most likely went extinct through a combination of earlier hominin (e.g., Homo erectus, H. neanderthalensis) and later human (H. sapiens) exploitation, as well as being affected by concurrent global or regional climatic and habitat changes. This checklist complements the broader listing of all modern and extant turtles and tortoises by the Turtle Taxonomy Working Group (2014). We provide a comprehensive listing of taxonomy, names, synonymies, and stratigraphic distribution of all chelonian taxa that have gone extinct from approximately the boundary between the Late Pliocene and Early Pleistocene, ca. 2.6 million years ago, up through 1500 AD, at the beginning of modern times. We also provide details on modern turtle and tortoise taxa that have gone extinct since 1500 AD. This checklist currently includes 100 fossil turtle and tortoise taxa, including 84 named and apparently distinct species, and 16 additional taxa that appear to represent additional valid species, but are only identified to genus or family. Modern extinct turtles and tortoises include 8 species, 3 subspecies, and 1 unnamed taxon, for 12 taxa. Of the extinct fossil taxa, terrestrial tortoises of the family Testudinidae (including many large-bodied island forms) are the most numerous, with 60 taxa. When the numbers for fossil tortoises are combined with the 61 modern (living and extinct) species of tortoises, of the 121 tortoise species that have existed at some point since the beginning of the Pleistocene, 69 (57.0%) have gone extinct. This likely reflects the high vulnerability of these large and slow terrestrial (often insular) species primarily to human exploitation. The other large-bodied terrestrial turtles, the 000e.2 Conservation Biology of Freshwater Turtles and Tortoises • Chelonian Research Monographs, No. 5As an addition to the annual checklist of extant modern turtle taxa (Turtle Taxonomy Working Group [TTWG] 2014), we here present an annotated checklist of extinct Pleistocene and Holocene turtle and tortoise species that existed in relatively recent times, prior to 1500 AD, during the history of the rise and global spread of humanity and concurrent global climatic and habitat changes. These species, recorded from archaeological and paleontological sites from the Pleistocene and Holocene epochs (Quaternary period), approximately the last 2.6 million years, are currently considered to be valid, and not synonymous with modern (post-1500 AD) taxa.These fossil species, including some unnamed taxa of indeterminate or undescribed generic or specific allocation, represent the majority of the chelonian diversity that has gone extinct relatively recently. Many of these taxa were likely extirpated by anthropogenic exploitation over the relatively long prehistory of earlier hominin (e.g., Homo erectus, H. neanderthalensi...

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A phylogenomic analysis of turtles

Cited by 267 publications

References 63 publications

Seeing red to being red: conserved genetic mechanism for red cone oil droplets and co-option for red coloration in birds and turtles

Seeing red to being red: conserved genetic mechanism for red cone oil droplets and co-option for red coloration in birds and turtles

A Review of the Fossil Record of Turtles of the CladePan-Chelydridae

Turtles and Tortoises of the World During the Rise and Global Spread of Humanity: First Checklist and Review of Extinct Pleistocene and Holocene Chelonians.

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