Shedlock2009chap52.Pdf

Amniotes (Amniota)

Andrew M. Shedlock* and Scott V. Edwards overlaps with a widely cited value of 310 Ma, based on Department of Organismic and Evolutionary Biology, Museum the approximate methods of Benton (3) and employed of Comparative Zoology, 26 Oxford Street, Harvard University, by Kumar and Hedges (4) to calibrate a comprehensive Cambridge, MA 02138, USA molecular timescale for vertebrate evolution. 7 e amni- *To whom correspondence should be addressed (shedlock@oeb. ote timetree considered here includes six terminal taxa: harvard.edu) Mammalia (mammals), Sphenodontia (the tuatara), Squamata (lizards and snakes), Testudines (turtles), Abstract Crocodylia (alligators and crocodiles), and Aves (birds). A combination of molecular and fossil evidence suggests Amniota is a remarkably diverse clade of tetrapod ver- that the major lineages of living reptiles likely originated tebrates comprising more than 23,000 living species of in the Permian and Triassic (3–5) although exact diver- mammals, non-avian reptiles, and birds adapted to a wide gence time estimates vary among the molecular studies variety of primarily terrestrial habitats. Our most recent used in the present synthesis. common amniote ancestor probably lived ~325 million ConP icting phylogenetic results from diB erent mor- years ago (Ma), and molecular data suggest that the major phological and molecular data sets have clouded the lineages of living reptiles arose in the Permian and Triassic picture of amniote macroevolution and have slowed the (299–200 Ma), when land areas were coalesced into a single process of establishing a clear consensus of views between supercontinent, Pangaea. Confl icting morphological and paleontologists and molecular systematists. Synapsids molecular results for the origin of turtles has been particu- (mammals) are accepted to be the closest relatives of larly challenging to resolve, although most recent analyses diapsid reptiles. Turtles lack temporal holes in the skull, place turtles with birds and crocodilians. however, and have been viewed as the only surviving ana- psid amniotes. Based on this and other characters, they Amniota is a clade noted for the extraordinary ecological and taxonomic diversity of its more than 23,000 living species, comprising mammals and reptiles, includ- ing birds. 7 e taxon is named for the characteristic egg structure in which the amnion membrane forms a P uid- A lled cavity that surrounds the developing embryo. 7 e amniote egg is considered one of the key adaptations in the evolution of vertebrate terrestrial life history (Fig. 1). 7 is shared-derived character is generally accepted to be one of several key adaptations for enduring the terrestrial life adopted by our amniote ancestors, thereby facilitat- ing the remarkable evolutionary success of the group. Considerable debate has been focused on precisely when our most recent common amniote ancestor lived (1). Tightly constrained radiometric analysis of fossils places the divergence between the A rst undisputed synapsids (mammals which have only one temporal fenestration in the skull) and diapsids (reptiles with two temporal fenestrations) at 306.1 ± 8.5 Ma. 7 is dating technique generally exhibits about 1% error ( 2). 7 e upper bound Fig. 1 An amniote, the Rough Greensnake (Opheodrys aestivus), of this narrow estimate for bird–mammal divergence hatching from an egg. Photo credit: S. B. Hedges.

A. M. Shedlock and S. V. Edwards. Amniotes (Amniota). Pp. 375–379 in e Timetree of Life, S. B. Hedges and S. Kumar, Eds. (Oxford University Press, 2009).

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Testudines 4 Crocodylia 5 2 Aves

Squamata Archosauria 1 3 Sphenodontia

Mammalia Lepidosauria

C P Tr J Cretaceous Pg Ng PALEOZOIC MESOZOIC CZ 300 250 200150 100 50 0 Million years ago Fig. 2 A timetree of amniotes. The divergence times are from Table 1. Abbreviations: C (Carboniferous), CZ (Cenozoic), J (Jurassic), Ng (Neogene), P (Permian), Pg (Paleogene), and Tr (Triassic).

are traditionally placed as the closest relatives of all other relationship of crocodilians and birds to the exclusion living reptiles (5, 7, 8). However, a recent morphological of turtles (11). reevaluation of skull characters (9), and essentially all Despite considerable debate on the subject, few stud- molecular genetic studies, indicates that turtles should ies have presented average divergence time estimations be nested within diapsids despite their apparent anapsid across major branches of the amniote tree based on a skull morphology. Based on a growing body of genomic calibrated clock analysis of numerous genes. Two highly evidence (6, 10–14), it appears that turtles exhibit a sec- visible studies within the last decade have set the foun- ondary loss of skull fenestration or reversal to an ances- dation for an ongoing debate about integrating fossils tral condition. and genes to estimate divergence times among major Molecular data sets have not completely clariA ed the amniote clades. Kumar and Hedges (4) published their amniote picture, however, since diB erent genes and landmark comprehensive molecular timescale for ver- sampling schemes have in some cases placed turtles tebrate evolution based on protein clock calibrations of within archosaurs, as the closest relative of crocodil- 658 nuclear genes and 207 vertebrate species. A point ians (6, 10, 13, 15), and in other cases, as the closest estimate of 310 Ma for the bird–mammal divergence, relative of an archosaur clade that includes crocodilians derived from radiometric dating of fossil evidence, was and birds (11, 12, 14, 16). Statistical evaluation of phylo- employed to externally calibrate the protein clock. Time genetic signal in these studies (10) has revealed that estimates based on statistical tests of rate constancy mitochondrial genome data have tended to separate (17, 18) were averaged across multiple genes and taxo- turtles from archosaurs, whereas concatenated nuclear nomic groups and presented with 95% conA dence inter- gene sequences under potentially strong selection such vals. Published dates relevant for the amniote timetree as globin genes, lactate dehydrogenase (LDH), and ribo- included a Permian average estimate for the origin of somal RNAs have tended to group turtles with croco- Lepidosaria at ~276 ± 54.4 Ma, and a bird–crocodilian dilians. 7 e a1 nity of turtles and crocodilians has also split at ~222 ± 52.5 Ma. been observed in evaluating short DNA word motifs Less than a year later, similar methods were focused embedded in more than 84 million basepairs (Mbp) of speciA cally on the Reptilia. Hedges and Poling (6) genomic sequence for amniotes (13). 7 eearliest turtles analyzed combinations of 23 nuclear and two mitochon- appear ~223 Ma in the fossil record (3), which is within drial genes, including globulins, LDH, rRNAs, alpha- the interval of both older and younger molecular clock c r y s t a l l i n e , alpha-enolase, and cyt b, to infer a molecular estimates for the time of their origin. 7 e most recent phylogeny of reptiles. As with previous analyses, the comprehensive eB ort to resolve the relationships of the 310 synapsid–diapsid split date was used to anchor the major groups of amniotes used more than 5100 amino molecular clock. 7 e paper unconventionally joined acids from mostly single-copy nuclear DPLA and turtles with crocodilians and suggested a more distant GAG genes within a maximum likelihood framework, relationship between the tuatara and squamates based and presented strong statistical support for a close on a subset of amino acid data available for Sphenodon.

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Table 1. Divergence times (Ma) and their confi dence/credibility intervals (CI) among amniotes (Amniota).

Timetree Estimates Node Time Refs. (4, 25) Refs. (6, 27) Refs. (12, 21, 23) Ref. (15) Ref. (20)(a) Time CI Time CI Time CI Time CI Time CI

1324.5– – 323(27)343–305326(21)354–311–––– 2 274.9 276 383–169 245 269–221 285 – 250 267–233 285 296–274 3271.5––––––––268280–256 4230.7225(25) 238–205 – – – – 152 176–128 265 278–252 5 219.2 222 325–119 258(27) 279–238 196(23) 294–98 214 259–169 201 216–186

Timetree Estimates (Continued) Node Time Ref. (20)(b) Ref. (22) Ref. (24) Ref. (26) Ref. (27) Time CI Time Time Time CI Time CI

1324.5–– – –––– – 2274.9289302–276–294–––– 3271.5275292–258––––– – 4230.7273291–255191278–––– 5 219.2 194 218–170 175 254 259 282–236 258 279–238

Note: Node times in the timetree represent the mean of time estimates from different studies. Estimates are presented from an analysis of nine nuclear genes examined within a comprehensive analysis of 658 nuclear genes (4); 23 nuclear and nine mitochondrial protein-coding genes (6), 11 nuclear protein- coding genes (23); nuclear LDH-A, LDH-B, and alpha-enolase genes (15); 11 mitochondrial protein-coding genes (24); 12 protein-coding genes, two rRNA genes, and 19 tRNAs from mitochondria (25); 11 protein-coding genes and 19 tRNAs from mitochondria (12), 11 protein-coding genes and unspecifi ed RNA genes from mitochondria (22); 325 protein-coding genes (21), mitochondrial genomes (26, 27), and the nucleotide (a) and amino acid sequences (b) of the nuclear RAG1 gene (20).

Squamates were estimated to have diverged from other the phylogenetic position of turtles (15). 7 e study adds reptiles ~245 ± 12.2 Ma, birds from the crocodilian + considerable additional LDH-A, LDH-B, and alpha- turtle clade ~228 ± 10.3 Ma, and turtles from crocodil- enolase protein sequences to the available data matrix ians ~207 ± 20.5 Ma. 7 ese results diB er from previous and employs the average distance methods and 310 Ma average dates published for the vertebrate timescale (4) synapsid–diapsid clock calibration of Kumar and Hedges by suggesting a younger Triassic vs. Permian time frame (4). Strong statistical support was provided for a turtle– for the origin of squamate lizards, and a slightly older crocodilian relationship to the exclusion of birds, with an time for the bird–crocodilian split. 7 ese divergence time exceptionally recent Upper Jurassic average divergence estimates cannot be reconciled with fossil evidence that time estimate for turtles from crocodilians of only 152 provides a minimum age estimate of at least ~223 Ma for Ma, some 71 million years younger than the oldest fossil the oldest known turtles (3), but suggest that a number turtle. No data were presented for Sphenodon, highlight- of key innovations during amniote evolution occurred ing the overall lack of published divergence time esti- within a roughly 40 million period of the Triassic. 7 e mates for this unique “living fossil.” study also posed a challenge for paleontologists to recon- Rest et al. (12) examined 11 protein-coding genes and cile the derived position of turtles among amniotes and 19 tRNAs from the mitochondrial genomes of all major set a methodological framework for expanded applica- amniote lineages, emphasizing the importance of sam- tion of molecular clock analyses to a variety of questions pling the tuatara to accurately reconstructing reptile regarding vertebrate evolution. phylogeny. 7 e study employed advances in Bayesian Several additional studies warrant summary here for model-based methods of inference and resolved turtles their contributions to establishing the amniote timetree. as the sister group to archosaurs with 100% statistical 7 e A rst is speciA cally aimed at attempting to resolve support. Adopting a maximum likelihood approach to

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estimating divergence times under a relaxed molecular periods of amniote cladogenesis: (1) the divergence and clock assumption and multiple fossil calibration points early diversiA cation of lepidosaurs between ~270 and (19), the authors reported a divergence time well into the 275 Ma and (2) the origin of turtles and subsequent Permian for the origin of Lepidosauria. divergence of crocodilians and birds between roughly Most recently, Hugall et al. (20) analyzed the nuclear ~230 and 220 Ma. Young amniote lineages would have gene RAG1 across 88 taxa spanning all major tetrapod emerged into a relatively unconstrained evolutionary clades. 7 e study supported the close relationship of landscape before extensive Pangean supercontinental turtles to a monophyletic Archosauria and employed breakup. A combination of favorable environmental and model-based rate-smoothing methods to estimate diver- biogeographic forces likely facilitated successful tetra- gence times in amniotes. Results highlighted an ancient pod invasion into a variety of open terrestrial niches dur- Permian origin for the tuatara estimated at ~268–275 ing the Triassic, exempliA ed today by the extraordinary Ma and revealed slower molecular evolutionary rates in ecological, phenotypic, and taxonomic diversity of living archosaurs and especially turtles that tend to underesti- amniotes. mate divergence times for these groups without using appropriate fossil calibration points. Comparison with other molecular clock studies underscored the bias Acknowledgments toward inP ated divergence time estimates created by sat- Support for the preparation of this manuscript was urated mitochondrial gene sequence data. provided by Harvard University and in part by a U.S. Seven other studies also present molecular time esti- National Science Foundation grant to S.V.E. mates for at least one node in the amniote tree of life (21–27). 7 e genes examined in each of these studies are listed in the caption for Table 1 and the average time References estimates from all 12 investigations considered here are 1. S. B. Hedges, S. Kumar, Trends Genet. 20, 242 (2004). reP ected by the topology in Fig. 2. Based on this litera- 2. J. Remane et. al., Eds., International Stratigraphic Chart ture synthesis, the amniote common ancestor is dated (International Union of Geological Sciences: Inter- at 325 Ma, with the origin of lepidosaurs taking place in national Commission on Stratigraphy, Paris, 2002). the mid-Permian ~275 Ma, and the divergence of sphe- 3. M. J. Benton, Vertebrate Paleontology (Chapman & Hall, nodontids from squamates at 272 Ma, distinguishing the New York, 1997). living tuatara as a remarkably ancient evolutionary relict. 4. S. Kumar, S. B. Hedges, Nature 392, 917 (1998). Turtles are estimated to have diverged from archosaurs 5. R. R. Reisz, Trends Ecol. Evol. 12, 218 (1997). in the early Triassic some 231 Ma, whereas crocodylians 6. S. B. Hedges, L. L. Poling, Science 283, 998 (1999). subsequently split from birds as recently as 219 Ma. It 7. J. Gauthier, A. G. Kluge, T. Rowe, Cladistics 4, 105 (1988). 8. M. S. Y. Lee, Zool. J. Linn. Soc. 120, 197 (1997). must be noted that conA dence intervals on the estimates 9. O. Rieppel, R. R. Reisz, Ann. Rev. Ecol. Syst. 30, 1 (1999). summarized in Table 1 are not available for several stud- 10. Y. Cao, M. D. Sorenson, Y. Kumazawa, D. P. Mindell, ies (12, 22, 24) or vary widely among studies depending M. Hasegawa, Gene 259, 139 (2000). on the number of genes investigated, the nature of the 11. N. Iwabe et al., Mol. Biol. Evol. 22, 810 (2005). gene sequence data analyzed, and taxonomic sampling 12. J. R. Rest et al., Mol. Phylogenet. Evol. 29, 289 (2003). (e.g., 4 vs. 20). 7 e results in Fig. 2 should therefore be 13. A. M. Shedlock et al., Proc. Natl. Acad. Sci. U.S.A. 104, interpreted cautiously within narrow time frames of 2767 (2007). amniote evolutionary history. 14. R. Zardoya, A. Meyer, Proc. Natl. Acad. Sci. U.S.A. 95, In summary, the amniote timetree paints a mixed 14226 (1998). portrait of organismal evolution among major tetrapod 15. H. Mannen, S. S.-L. Li, Mol. Phylogenet. Evol. 13, 144 lineages that underwent a number of key vertebrate inno- (1999). 16. Y. Kumazawa, M. Nishida, Mol. Biol. Evol. 16, 784 (1999). vations adapted for the rigors of terrestrial life. 7 e late 17. F. Tajima, Genetics 135, 599 (1993). Permian mass extinction was due presumably to wide- 18. N. Takezaki, A. Rzhetsky, M. Nei, Mol. Biol. Evol. 12, 823 spread stressful environmental conditions produced by (1995). unfavorable ocean–atmosphere chemical interactions 19. M. J. Sanderson, Mol. Biol. Evol. 14, 1218 (1997). (28). Fossil diversity indicates a protracted biological 20. A. F. Hugall, R. Foster, M. S. Lee, Syst. Biol. 56, 543 recovery through the lower Triassic ~250 Ma ( 29) that (2007). falls between molecular time estimates for two major 21. J. E. Blair, S. B. Hedges, Mol. Biol. Evol. 22, 2275 (2005).

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