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Award Detail

Awardee:CARNEGIE INSTITUTE
Doing Business As Name:Carnegie Institute
PD/PI:
  • Zhe-Xi Luo
  • (412) 622-6578
  • luoz@carnegiemnh.org
Co-PD(s)/co-PI(s):
  • John R Wible
  • Timothy J Gaudin
  • Guillermo W Rougier
Award Date:09/15/2006
Estimated Total Award Amount: $ 349,106
Funds Obligated to Date: $ 349,106
  • FY 2008=$114,435
  • FY 2009=$32,276
  • FY 2006=$187,122
  • FY 2010=$15,273
Start Date:10/01/2006
End Date:09/30/2012
Transaction Type:Grant
Agency:NSF
Awarding Agency Code:4900
Funding Agency Code:4900
CFDA Number:47.074
Primary Program Source:490100 NSF RESEARCH & RELATED ACTIVIT
Award Title or Description:ATOL: Collaborative Research: Resolving Mammalian Phylogeny with Genomic and Morphological Approaches
Federal Award ID Number:0629959
DUNS ID:072165699
Parent DUNS ID:072165699
Program:ASSEMBLING THE TREE OF LIFE
Program Officer:
  • Simon Malcomber
  • (703) 292-8227
  • smalcomb@nsf.gov

Awardee Location

Street:4400 Forbes Avenue
City:Pittsburgh
State:PA
ZIP:15213-4080
County:Pittsburgh
Country:US
Awardee Cong. District:18

Primary Place of Performance

Organization Name:CARNEGIE INSTITUTE
Street:4400 FORBES AVE
City:PITTSBURGH
State:PA
ZIP:15213-4007
County:Pittsburgh
Country:US
Cong. District:18

Abstract at Time of Award

AToL: Collaborative Research: Resolving Mammalian Phylogeny with Genomic and Morphological Approaches Novacek, Michael J., American Museum of Natural History, EF 0629811 Murphy, William J., Texas A & M Research Foundation, EF 0629849 O'Leary, Maureen A., SUNY Stony Brook, EF 0629836 Luo, Zhe-Xi, Carnegie Institute, EF 0629959 Springer, Mark, Univ. California, Riverside, EF 0629860 Abstract Only a few of the myriad biological groups now thriving on this planet have fossil records that chronicle their evolutionary past. One of these few is Mammalia, known from about 5,000 extant species distributed among 1135 living genera, including our own human lineage, and more than 4,000 extinct genera, a four-to-one ratio of fossil genera to living genera that can hardly be matched elsewhere in the biota. Mammals display a spectacular range in size, form, and adaptations. They are closely linked to human health, welfare, and experience. No tree of all life could be regarded as complete without a comprehensive phylogeny of Mammalia. This conviction has inspired a surge of work in paleontology, comparative anatomy, and molecular biology. Despite these significant gains, many aspects of mammalian phylogeny are unresolved or highly controversial, even at some of the major branching points on the mammalian tree. PIs propose to examine species exemplars for 135 extant families, the majority of some 350 extinct families, and to extend this sample to a generic-level data set of 500 extant and nearly 500 extinct genera for combined analysis of genes and morphology. Their molecular team will continue to sample taxa toward a goal of covering 95% of all living genera outside the murids (rats, mice, and kin) and sciurids (squirrels). For character evidence, PIs plan to sample 30Kb in gene sequences from 34 genes for at least one exemplar of all living families. For the larger generic-level phases of the project, they will sample at least 6Kb of sequence. Morphologists will collect a projected 2,000 characters. Completion of a broad scale phylogeny for mammals will provide a model system in evolutionary and comparative biology with numerous applications in conservation and wildlife management, human health, biomedicine, and other areas. In addition, PIs intend to compile an integrated and image rich database for mammalian characters and convert it into a powerful toolkit for conservation management, education, and outreach through training programs and web resources.

Publications Produced as a Result of this Research

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Gomez, R.O.; Baez, A.M.; Rougier, G.W. "An anilioid snake from the Upper Cretaceous of northern Patagonia." Cretaceous Research, v.29, 2008, p.481. doi:10.1016/j.cretres.2008.01.002 

Wible, JR; Rougier, GW; Novacek, MJ; Asher, RJ "Cretaceous eutherians and Laurasian origin for placental mammals near the K/T boundary" NATURE, v.447, 2007, p.1003. doi:10.1038/nature0585  View record at Web of Science

Rougier, Guillermo W.; Apesteguia, Sebastian; Gaetano, Leandro C. "Highly specialized mammalian skulls from the Late Cretaceous of South America" NATURE, v.479, 2011, p.98-102.

Luo, ZX; Chen, PJ; Li, G; Chen, M "A new eutriconodont mammal and evolutionary development in early mammals" NATURE, v.446, 2007, p.288. doi:10.1038/nature0562  View record at Web of Science

O?Leary, M.A.; Bloch,J.I.; Flynn, J.J.; Gaudin, T.J.; Giallombardo, A.; Giannini, N.P.; Goldberg, S.L.; Kraatz, B.P.; Luo, Z.-X.; Meng, J.; Ni, X.; Novacek, M.J.; Perini, F.P.; Randall, Z.; Rougier, G.W.; Sargis, E.S.; Silcox, M.T.; Simmons, N.B.; et al. "The placental mammal ancestor and the post-KPg radiation of placentals" Science, v.339, 2013, p.662-667. doi:10.1126/science.1229237 

Chen, M.; Luo, Z.-X. "Morphology of dentition and postcranial skeleton of Akidolestes." Acta Geologica Sinica (Chinese Edition), v.82, 2008, p.155.

Rougier, G.W.; Corbitt, C. "The fringes of mammalness, the platypus and monotreme biology." Journal of Mammalian Evolution, v.15, 2008, p.289. doi:10.1017/s10914-008-9078-6 

Giannini, N.; Macrini, T.E.; Wible, J.R.; Rowe, T.B.; Simmons, N.B. "The internal nasal skeleton of the bat Pteropus lylei K. Andersen, 1908 (Chiroptera: Pteropodidae)" Annals of Carnegie Museum, v.81, 2012, p.1-17. doi:http://dx.doi.org/10.2992/007.081.0101 

MARTINELLI, A. G.; ROUGIER, G.W. "On Chaliminia musteloides (Eucynodontia: Tritheledontidae) from the Late Triassic of Argentina, and a phylogeny of Ictidosauria." Journal of Vertebrate Paleontology, v.27, 2007, p..

Rougier, G.W.; Chornogubsky, L.; Casadio, S.; Paez Arango, N.; Giallombardo, A. "Mammals from the Allen Formation, Late Cretaceous, Argentina." Cretaceous Research, v.30, 2009, p.223. doi:10.1016/j.cretres.2008.07.006 

Martinelli, A.; Forasiepi, A.M.; Rougier, G.W. "Australosfenidos, parientes de los enigmaticos monotremas." Ciencia Hoy, v.18, 2008, p.52.

Wible, J.R.; Spaulding, M. "Reexamination of the Carnivora malleus (Mammalia, Placentalia)" PLoS One, v.7, 2012, p.1-18. doi:10.1371/journal.pone.0050485 

ROUGIER, G.W.; FORASIEPI, A.M. ; MARTINELLI, A.G.; NOVACEK, M.J. "New Jurassic Mammals from Patagonia, Argentina: a reappraisal of Australosphenidan morphology and interrelationships." American Museum Novitates 3566, v.3566, 2007, p..

Wible, J.R. "The ear region of the aardvark Orycteropus afer Pallas, 1766 (Mammalia, Afrotheria, Tubulidentata)" Annals of Carnegie Museum, v.80, 2012, p.115-146. doi:http://dx.doi.org/10.2992/007.080.0202 

Rougier, G.W.; Forasiepi, A.M.; Hill, R.V.; Novacek, M.J. "New mammalian remains from the Late Cretaceous La Colonia Formation, Patagonia, Argentina." Acta Palaeontologica Polonica, v.54, 2009, p.195.

Rougier, G.W.; Wible, J.R.; Beck, R.M.D.; Apesteguía, S. "The Miocene mammal Necrolestes demonstrates survival of a Mesozoic non-therian lineage into the late Cenozoic of South America" Proceedings of the National Academy of Sciences USA, v.109, 2012, p.20053-58. doi:10.1073/pnas.1212997109 

Saint-Andr�©, P.-A.; Pujos, F.; Cartelle, C.; DeIuliis, G.;Gaudin, T.G.;McDonald, H.G.; Quispe, B.M. "Presentation preliminaire de deux nouveaux paresseux terrestres (Mammalia, Xenarthra, Mylodontidae) du Neogene de l'Altiplano bolivien." Geodiversitas, v.32, 2010, p.255.

Wible JR "On the treeshrew skull (Mammalia, Placentalia, Scandentia)." Annals of Carnegie Museum, v.79, 2011, p.149. doi:10.2992/007.079.0301 

Gaudin, T.J.; Eichler, S.E.; Brinson, J.S. "New records of the nine-banded armadillo, Dasypus novemcinctus (Mammalia, Xenarthra, Dasypodidae), in southeast Tennessee." Journal of the Tennessee Academy of Science, v.85, 2010, p.27.

Gaudin, T.J. "Endless forms most beautiful and most wonderful: South American mammals." Journal of Mammalian Evolution, v.16, 2009, p.307.

Rougier, G.W.; Forasiepi, A.M.; Hill, R. V.; Novacek, M.J. "New mammalian remains from the Late Cretaceous La Colonia Formation, Patagonia, Argentina." Acta Palaeontologica Polonica, v.54, 2009, p.195.

CHEN, M.; LUO, Z.-X. "Morphology of dentition and postcranial skeleton of Akidolestes" Acta Geologica Sinica (Chinese Edition), v.82, 2008, p.155.

Ruf, I.; Luo, Z.-X.; Wible, J.R.; Martin, T. "Petrosal anatomy and inner ear structure of the Late Jurassic mammal Henkelotherium and the ear region characters of basal therian mammals." Journal of Anatomy, v.214, 2009, p.679. doi:10.1111/j.1469-7580.2009.10059x 

Gaetano, L.; Rougier, G.W. "First amphilestid from South America: a molariform from the Jurassic Cañadon Asfalto Formation, Patagonia, Argentina" Journal of Mammalian Evolution, v.19, 2012, p.235-248.

Xiao, S.-H.; Yang, Q.; Luo, Z.-X. "A golden age of paleontology in China? A SWOT analysis." Palaeontologia Electronica, v.13, 2010, p.3E:4p.

Luo, Z.-X. "Journal Club." Nature, v.465, 2010, p.669.

Wible, J.R.; Rougier, G.W.; Novacek, M. J.; Asher, R.J. "The eutherian mammal Maelestes gobiensis from the Late Cretaceous of Mongolia and the phylogeny of Cretaceous Eutheria." Bulletin of the American Museum of Natural, v.327, 2009, p.1.

Ruf, I.; Luo, Z.-X.; Wible, J.R.; Martin, T. "Petrosal anatomy and inner ear structure of the Late Jurassic mammal Henkelotherium and the ear region characters of basal therian mammals." Journal of Anatomy, v.214, 2009, p.679. doi:10.1111/j.1469-7580.2009.01059.x 

Xu, X.; Luo Z.-X.; Rong, J-Y "Recent advances in Chinese palaeontology." Proceedings of Royal Society B (Biological Sciences), v.277, 2009, p.161. doi:10.1098/rspb.2009.1668 

Ji, Q.; Luo, Z.-X.; Zhang, Z.-L.; Yuan, C.-X. ; Xu, L. "Evolutionary development of the middle ear in Mesozoic therian mammals." Science, v.326, 2009, p.278. doi:10.1126/science.1187501 

Gao, C.-L.; Wilson, G. P.; Luo, Z.-X.; Maga, A. M.; Meng, Q.-J.; Wang, X.-R. "A new mammal skull from the Lower Cretaceous of China with implications for the evolution of obtuse angled molars and amphilestid eutriconodonts." Proceedings of Royal Society (London) Series B (Biological Sciences), v.277, 2009, p.237. doi:10.1098/rspb.2009.1014 

Smith, M.B.; Gaudin, T.J.; Wilson, T.P. "Geographic distribution. Ambystoma opacum (Marbled Salamander). New County Record, Hamilton Co., TN." Herpetological Review, v.38, 2007, p.347.

Botha, J.; Gaudin, T.J. "A new pangolin (Mammalia: Pholidota) from the Pliocene of Langebaanweg, South Africa." Journal of Vertebrate Paleontology, v.27(2), 2007, p.484.

Wible, J.R. "On the cranial osteology of the Lagomorpha." Bulletin of Carnegie Museum of Natural History, v.39, 2007, p.213.

Gelfo, J.N.; Ortiz-Jaureguizar, E.; Rougier, G.W. "New remains and species of the "condylarth" genus Escribania (Mammalia:Didolodontidae) from the early Paleocene of Patagonia, Argentina." Earth and Environmental Transactions of the Royal Society of Edinburgh, v.98(2), 2007, p.127.

Sterli, J.; de la Fuente, M.S.; Rougier, G.W. "Anatomy and relationships of Palaeochersis talampayensis, a Late Triassic turtle from Argentina" Palaeontographica Albeitung A, v.281, 2007, p.1.

Macrini, T.A.; Rougier, G.W.; Rowe, T. "Digital cranial endocast from Vincelestes neuquenianus, a Cretaceous theriiform mammal." Anatomical Record Part A, v.290, 2007, p.874.

Apesteguia, S.; Rougier, G.W. "A Late Campanian sphenodontid maxilla from northern Patagonia." American Museum Novitates, v.3581, 2007, p.1.

Wible, J.R.; Rougier, G.W.; Asher, A.; Novacek, M.J. "Cretaceous eutherians and laurasian origin for placental mammals near K/T boundary." Nature, v.447, 2007, p.1003.

Luo, Z.-X. "Natural history of human's most distant relatives: Echidna - Extraordinary egg-laying mammal." Journal of Mammalian Evolution, v.14, 2007, p.283.

Luo, Z.-X.; Chen, P.-J.; Li, G.; Chen, M. "A new eutriconodont mammal and evolutionary development of early mammals." Nature, v.446, 2007, p.288.

Luo, Z.-X.; Martin, T. "Analysis of molar structure and phylogeny of docodontan genera." Bulletin of Carnegie Museum of Natural History, v.39, 2007, p.27.

SMITH, M.B.; GAUDIN, T.J.; WILSON, T.P. "Geographic distribution. Ambystoma opacum (Marbled Salamander). New County Record, Hamilton Co., TN" Herpetological Review, v.38, 2007, p.347.

Luo, Z.-X.; Ji, Q.; Yuan, C.-X. "Convergent dental evolution in pseudotribosphenic and tribosphenic mammals." Nature, v.450, 2007, p.93.

BOTHA, J.; GAUDIN, T.J. "A new pangolin (Mammalia: Pholidota) from the Pliocene of Langebaanweg, South Africa" Journal of Vertebrate Paleontology, v.2, 2007, p.484.

Luo, Z.-X. "Transformation and diversification in the early mammalian evolution." Nature, v.450, 2007, p.1011.

WIBLE, J.R. "On the cranial osteology of the Lagomorpha" Bulletin of Carnegie Museum of Natural History, v.39, 2007, p.213.

STERLI, J.; de la FUENTE, M.S.; ROUGIER, G.W. "Anatomy and relationships of Palaeochersis talampayensis, a Late Triassic turtle from Argentina" Palaeontographica Albeitung A, v.281, 2007, p.1.

Novacek, MJ; AToL Mammal Morphology Team "A team-based approach yields a new matrix of 4,500 morphological characters for mammalian phylogeny." Journal of Vertebrate Paleontology, v.28(supp, 2008, p.121A.

GELFO, J.N.; ORTIZ-JAUREGUIZAR, E.; ROUGIER, G.W. "New remains and species of the ?condylarth? genus Escribania (Mammalia:Didolodontidae) from the Early Paleocene of Patagonia, Argentina" Earth and Environmental Transactions of the Royal Society of Edinburgh, v.98, 2007, p.127.

You, H.-L.; Luo, Z.-X. "Dinosaurs from the Lower Cretaceous Gonpoquan Basin in Jiuquan Area, Gansu Province, China." Acta Geologica Sinica (Chinese Edition), v.82(1), 2008, p.139.

MACRINI, T.A.; ROUGIER, G.W.; ROWE, T. "Digital cranial endocast from Vincelestes neuquenianus, a Cretaceous theriiform mammal" Anatomical Record Part A, v.290, 2007, p.874.

Gaudin, T.J.; Emry, R.J.; Wible, J.R. "The phylogeny of living and extinct pangolins (Mammalia, Pholidota) and associated taxa: a morphology based analysis." Journal of Mammalian Evolution, v.16, 2009, p.235. doi:10.1007/s10914-009-9119-9 

ASPESTEGUIA, S.; ROUGIER, G.W. "A Late Campanian sphenodontid maxilla" American Museum Novitates, v.3581, 2007, p.1.

LUO, Z.-X.; MARTIN, T. "Analysis of molar structure and phylogeny of docodontan genera" Bulletin of Carnegie Museum of Natural History, v.39, 2007, p.27.

LUO, Z.-X.; Ji, Q.; YUAN, C.-X. "Convergent dental evolution in pseudotribosphenic and tribosphenic mammals" Nature, v.450, 2007, p.93.

Ruf, I.; Luo, Z.-X.; Martin, T. "Re-investigation of the basicranium of Haldanodon exspectatus (Docodonta, Mammaliaformes)" Journal of Vertebrate Paleontology, v.33, 2013, p.382-400.

You, H.-L.; Luo, Z.-X. "Dinosaurs from the Lower Cretaceous Gonpoquan Basin in Jiuquan Area, Gansu Province, China." Acta Geologica Sinica (Chinese Edition), v.82, 2008, p.139.

Luo, Zhe-Xi; Ruf, Irina; Martin, Thomas "The petrosal and inner ear of the Late Jurassic cladotherian mammal Dryolestes leiriensis and implications for ear evolution in therian mammals" ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, v.166, 2012, p.433-463.

Wible, J.R. "On the cranial osteology of the Hispaniolan solenodon, Solenodon paradoxus Brandt, 1833 (Mammalia, Lipotyphla, Solenodontidae)." Annals of Carnegie Museum, v.77, 2008, p.321. doi:10.2992/0097-4463-77.3.321 

LUO, Z.-X. "Transformation and diversification in the early mammalian evolution" Nature, v.450, 2007, p.1011.

Z.X. Luo "Developmental Patterns in Mesozoic Evolution of Mammal Ears" Annual Review of Ecology, Evolution, and Systematics, v.42, 2011, p.355-380.

Smith, M.B.; Aborn, D.A.; Gaudin, T.J.; Tucker, J.C. "Mammalian predator distribution around a transmission line." Southeastern Naturalist, v.7, 2008, p.289. doi:10.1656/1528-7092(2008)7[289:MPDAAT]2.0.CO;2 

YOU, H.-L.; LUO, Z.-X. "Dinosaurs from the Lower Cretaceous Gonpoquan Basin in Jiuquan Area, Gansu Province, China" Acta Geologica Sinica (Chinese Edition), v.82, 2008, p.139.

Spaulding, M.; Flynn, J.J. "Phylogeny of the Carnivoramorpha: the impact of postcranial characters" Journal of Systematic Palaeontology, v.10, 2012, p.653-677. doi:10.1080/14772019.2011.630681 

Smith, M.B.; Conley, J.; Nelson, C.; Gaudin, T.J. "First record of the water shrew, Sorex palustris, from Graham County, North Carolina." Journal of the North Carolina Academy of Science, v.124, 2008, p.61.


Project Outcomes Report

Disclaimer

This Project Outcomes Report for the General Public is displayed verbatim as submitted by the Principal Investigator (PI) for this award. Any opinions, findings, and conclusions or recommendations expressed in this Report are those of the PI and do not necessarily reflect the views of the National Science Foundation; NSF has not approved or endorsed its content.

In 2005 Science magazine identified discovery of the Tree of Life as one of the 125 most important science questions still unanswered.  The mammal part of this Tree, the group to which humans belong, has been actively debated by scholars, including the relationships and times of origin of major groups. Debates include such basic questions as whether or not primates and rodents lived at the same time as the non-avian dinosaurs.  Mammals have an enormously rich fossil record that provides critical data impacting this debate. 

We conducted the largest research effort to date using new computer infrastructure and cutting edge team-based approaches to build an unprecedented dataset of phenomic (e.g., anatomical, developmental) data on living and fossil mammals.  We combined this with genomic data to create a synthetic Tree of Life for mammals and to reconstruct scientifically the ‘look’ of the common ancestor of all placental mammals.  We discovered that when all data are integrated it becomes clear that placental mammals (those giving live birth after long gestation) evolved much later than would be predicted by the use of molecular data alone and that groups like primates and rodents appeared after the extinction of the non-avian dinosaurs.  This means that placental mammal evolution fit what is called an “Explosive Model” whereby groups like whales, primates, carnivores and bats originated and speciated after the Cretaceous-Paleogene boundary some 65 million years ago when 75% of species when extinct following an asteroid impact and major volcanic eruptions.

The significance of our research was reported on the front page of the New York Times and over 75 other media outlets internationally.  We estimate that the research was read by over 114 million people worldwide, and the reconstruction of the placental ancestor proved to be an enormously effective means of generating public interest in the significance of science, systematics, and evolutionary biology.

More than a dozen US institutions and 30 collaborating scientists from four continents collaborated on this project, which was published as a long article in Science (O’Leary et al. 2013), one of the highest impact science journals.  Accompanying the printed article is our new online dataset of mammal comparative anatomy in the NSF supported database MorphoBank.  This dataset is available to scientists, educators and the public via the web, and documents in words and pictures thousands of anatomical features for 86 fossil and modern species.

Specifically during this project, we answered three main questions:

     1) “When did the placental mammals first appear and begin to diversify?” Placental mammals originated  after the extinction of the non-avian dinosaurs, but within 200,000 to 400,000 years after the mass extinction event, contrary to some prior hypotheses based on genetic data alone that suggested placentals evolved much earlier.

     2) “What are the relationships among the major groups of living and extinct mammals?” Our analyses showed that phenomic data are particularly powerful for building the Tree of Life and combined with genetic data give a fuller picture of evolution. Phenomic data were essential to determining some major groupings in this tree, including determining the closest relatives of our own group the Primates (tree shrews and “flying lemurs”).

     3)“What were the biological attributes of the placental mammal ancestor?”  Using an algorithm to trace features on the mammal tree permitted a “full-body” and life-history reconstruction of the placental ancestor as a small (less than half a ...

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