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Research Spending & Results

Award Detail

Awardee:AMERICAN MUSEUM OF NATURAL HISTORY, THE
Doing Business As Name:American Museum Natural History
PD/PI:
  • Michael J Novacek
  • (212) 769-5805
  • novacek@amnh.org
Co-PD(s)/co-PI(s):
  • Nancy B Simmons
  • John Flynn
  • Robert J Asher
  • Jin Meng
Award Date:09/15/2006
Estimated Total Award Amount: $ 861,587
Funds Obligated to Date: $ 861,587
  • FY 2006=$282,141
  • FY 2009=$182,866
  • FY 2008=$278,735
  • FY 2010=$117,845
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:0629811
DUNS ID:061202768
Parent DUNS ID:061202768
Program:ASSEMBLING THE TREE OF LIFE
Program Officer:
  • Simon Malcomber
  • (703) 292-8227
  • smalcomb@nsf.gov

Awardee Location

Street:Central Park West at 79th St
City:New York
State:NY
ZIP:10024-0000
County:
Country:US
Awardee Cong. District:08

Primary Place of Performance

Organization Name:American Museum Natural History
Street:Central Park West at 79th St
City:New York
State:NY
ZIP:10024-0000
Country:US
Cong. District:08

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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Simmons, N. B. "Taking wing: uncovering the evolutionary origins of bats" Scientific American, v., 2008, p.96.

Y.-Q. Wang, J. Meng, X.-J. Ni, and C.-K. Li "Major events of Paleocene mammal radiation in China" Geological Journal, v.42, 2007, p.415.

Asher RJ, Maree S, Bronner G, Bennett NC, Bloomer P, Czechowski P, Meyer M, Hofreiter M "A phylogenetic estimate for golden moles (Mammalia, Afrotheria, Chrysochloridae)" BMC Evolutionary Biology, v.10, 2010, p.69.

Giallombardo, A., and the ATOL Mammalia Morphology Team "Postcanine teeth homologies in Mammalia" Journal of Vertebrate Paleontology, SVP Program and Abstracts Book 2010, v., 2010, p.96A.

Giallombardo, A., and the ATOL Mammalia Morphology Team "Postcanine teeth homologies in Mammalia" Journal of Vertebrate Paleontology, SVP Program and Abstracts Book 2010, v., 2010, p.96A.

Habersetzer, J, N. Simmons, K. Seymour, G. Gunnell, and E. Schlosser-Strum "Die evolution des fluges und der echoortung" Biol. Unserer Zeit, v.38, 2008, p.246.

Finarelli, J.A., and J.J. Flynn "Brain-size evolution and sociality in Carnivora" Proceedings of the National Academy of Sciences USA, v., 2009, p.1. doi:10.1073_pnas.0901780106 

Y.-M. Hu, J. Meng, and J. M. Clark "A new Late Jurassic docodont (Mammalia) from northeastern Xinjiang, China" Vertebrata PalAsiatica, v.45, 2007, p.173.

S.-D. Bi, J. Meng, and W.-Y. Wu "A new species of Megacricetodon (Cricetidae?, Rodentia, Mammalia) from the middle Miocene of northern Junggar Basin, China" American Museum Novitates, v.3602, 2008, p.1.

S.-D. Bi, J. Meng, and W.-Y. Wu "A new species of Megacricetodon (Cricetidae?, Rodentia, Mammalia) from the middle Miocene of northern Junggar Basin, China" American Museum Novitates, v.3602, 2008, p.1.

N.B. Simmons, K. L. Seymour, J. Habersetzer, and G. F. Gunnell "Primitive Early Eocene bat from Wyoming and the evolution of flight and echolocation" Nature, v.451, 2008, p.818.

Giannini, N. P., and Simmons, N. B. "Element homology and the evolution of dental formulae megachiropteran bats (Mammalia: Chiroptera: Pteropodidae)" American Museum Novitates, v.3559, 2007, p..

Flynn, J.J., R. Charrier, D.A. Croft, P.B. Gans, T.M. Herriott, J.A. Wertheim, and A.R. Wyss "Chronologic implications of new Miocene mammals from the Cura-Mall­ín and Trapa Trapa Formations, Laguna del Laja area, south central Chile" Journal of South American Earth Sciences, v.26, 2008, p.412. doi:10.1016/j.jsames.2008.05.006 

J. Meng, Y.-Q. Wang, X.-J. Ni, K. C., Beard, C.-K. Sun, Q. Li, X. Jin. B. Bai "New Stratigraphic data from the Erlian Basin: definitions, divisions and correlations of Paleogene stratigraphic units in Inner Mongolia" American Museum Novitates, v.3570, 2007, p.1.

Kammerer, C., J.J. Flynn, L. Ranivoharimanana, and A.R. Wyss "New material of Menadon besairiei (Cynodontia: Traversodontidae) from the Triassic of Madagascar" Journal of Vertebrate Paleontology, v.28, 2008, p.445.

D.A. Croft, J.J. Flynn, and A.R. Wyss "A new basal glyptodontid and other Xenarthra of the early Miocene Chucal Fauna, northern Chile" Journal of Vertebrate Paleontology, v.27 (4), 2007, p.781.

Hu, Y.-M, J. Meng, Li C.-K., and Wang, Y.-Q. "A new basal eutherian mammal from the Early Cretaceous Jehol Biota, Liaoning, China" Proceedings of the Royal Society B., v., 2009, p.. doi:10.1098/rspb.2009.0203 

O?Leary, M., Bloch, J., Flynn, J., Gaudin, T., Giallombardo, A., Giannini, N., Goldberg, S., Kraatz, B., Luo, Z.-X., Meng, J., Ni, X., Novacek, M., Perini, F., Randall, Z., Rougier, G.,Sargis, E., Silcox, M., Simmons, N., Spaulding, M., Velazco, et al. "Phylogenetic reconstruction of the post K-Pg placental ancestor and a transformation of the scale of phylophenomics" Science, v.339, 2013, p.662-667.

Hu, Y.-M, J. Meng, Li C.-K., and Wang, Y.-Q. "A new basal eutherian mammal from the Early Cretaceous Jehol Biota, Liaoning, China" Proceedings of the Royal Society B., v.277, 2010, p.229. doi:10.1098/rspb.2009.0203 

Wible, J. R., G. W. Rougier, M. J. Novacek, and R. J. Asher "Cretaceous eutherians and Laurasian origin for placental mammals near" Nature, v.447, 2007, p..

Ni, X.-J., J. Meng, K. Christopher Beard, Y.-Q. Wang, D. L. Gebo, C.-K. Li "A new tarkadectine primate from Inner Mongolia, China" Proceedings of the Royal Society B., v., 2009, p.. doi:10.1098/rspb.2009.0173 

J. Meng, C.-K. Li, Y.-Q. Wang, X.-J. Ni "A new Eocene rodent from the lower Arshanto Formation in the Nuhetingboerhe (Camp Margetts) area, Inner Mongolia" American Museum Novitates, v.3569, 2007, p.1.

Ni, X.-J., J. Meng, K. Christopher Beard, Y.-Q. Wang, D. L. Gebo, C.-K. Li "A new tarkadectine primate from Inner Mongolia, China" Proceedings of the Royal Society B., v.277, 2010, p.247. doi:10.1098/rspb.2009.0173 

D.A. Croft, J.J. Flynn, and A.R. Wyss "The Tinguiririca Fauna of Chile and the early stages of ?modernization? of South American mammal faunas" Arquivos do Museu Nacional, Rio de Janeiro (Brasil), v.66 (1), 2008, p..

N.P. Giannini and N. B. Simmons "The chiropteran premaxilla: a reanalysis of morphological variation and its phylogenetic interpretation" American Museum Novitates, v.3585, 2007, p.1.

K.E. Sears, A. Goswami, J.J. Flynn, and L.A. Niswander "The correlated evolution of Runx2 tandem repeats, transcriptional activity, and facial length in Carnivora" Evolution and Development, v.9 (6), 2007, p.555.

D.A. Croft, J.J. Flynn, and A.R. Wyss "The Tinguiririca Fauna of Chile and the early stages of "modernization" of South American mammal faunas" Arquivos do Museu Nacional, Rio de Janeiro (Brasil), v.66 (1), 2008, p..

X.-J. Ni, K. C., Beard, J. Meng, Y.-Q. Wang and D. Gebo "Discovery of the first early Cenozoic euprimate (Mammalia) from Inner Mongolia" American Museum Novitates, v.3571, 2007, p.1.

C-K. Li, J. Meng, and Y.-Q. Wang "Dawsonolagus, a primitive lagomorph from the Eocene Arshanto Formation, Inner Mongolia, China" Bulletin of the Carnegie Museum, v.39, 2007, p.97.

Kraatz, B. P., Badamgarav, D., and Bibi, F. "Gomphos ellae, a new mimotonid from the Middle Eocene of Mongolia and its implications for the origin of Lagomorpha" Journal of Vertebrate Paleontology, v.29, 2009, p.576.

M.J. Novacek and 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 (sup, 2008, p.121A.

M. Spaulding "The impact of postcranial characters on reconstructing the phylogeny of Carnivoramorpha" Journal of Vertebrate Paleontology, v.27 (3), 2007, p.151A.

J. Meng, X.-J. Ni, C.-K Li. K.C. Beard, D.L. Gebo, Y.-Q. Wang and H.-J. Wang "New material of Alagomyidae (Mammalia, Glires) from the Late Paleocene Subeng locality, Inner Mongolia" American Museum Novitates, v.3597, 2007, p.1.

Giannini, N. P., and N. B. Simmons "Element homology and the evolution of dental formulae in megachiropteran bats" American Museum Novitates, v.3559, 2007, p.1.

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

K.E. Sears, J.A. Finarelli, J.J. Flynn, and A.R. Wyss "Morphometric estimators of body mass and diet in New World monkeys (Platyrrhini, Anthropoidea, Primates), with consideration of the Miocene-aged Chilecebus carrascoensis" American Museum Novitates, v.3617, 2008, p.1.

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

Giallombardo, A. "New Cretaceous mammals from Mongolia and the early diversification of Eutheria" Ph.D. Dissertation, Columbia University, New York, v., 2009, p.377.

Spaulding M, O'Leary MA, Gatesy J "Relationships of Cetacea (Artiodactyla) Among Mammals: Increased Taxon Sampling Alters Interpretations of Key Fossils and Character Evolution" PLoS ONE, v.4(9), 2009, p.e7062. doi:10.1371/journal.pone.0007062 

Giannini, N. P., F. C. Almeida, N. B. Simmons "Phylogenetic relationships of harpionycterine megabats" Bulletin of the American Museum of Natural History, v.331, 2009, p.183.

Rougier, G.W., Forasiepi, A.M., Hill, R.V., and Novacek. M.J. "New mammalian remains from the Late Cretaceous La Colonia Formation, Patagonia, Argentina" Acta Palaeontologica Polonica, v.54 (2), 2009, p.195.

Almeida, F., N.P. Giannini, R. DeSalle, and N. B. Simmons "The phylogenetic relationships of cynopterine fruit bats (Chiroptera: Pteropodidae: Cynopterinae)" Molecular Phylogenetics and Evolution, v.53, 2009, p.772.

A.A. Carlini, M.R. Ciancio, J.J. Flynn, G.J. Scillato-Yané, and A.R. Wyss "The phylogenetic and biostratigraphic significance of new armadillos (Mammalia, Xenarthra, Dasypodidae, Euphractinae) from the Tinguirirican (Early Oligocene) of Chile" Journal of Systematic Palaeontology, v.7, 2009, p.489. doi:10.1017/S1477201908002708 

M. Spaulding, J.J. Flynn, and L. Grande "A new mammalian carnivore from the Green River Formation, possibly possessing a prehensile tail" Journal of Vertebrate Paleontology, v.28, 2008, p.146A.

M. Spaulding and J.J. Flynn "Anatomy of the postcranial skeleton of "Miacis" uintensis (Mammalia: Carnivoramorpha)" Journal of Vertebrate Paleontology, v.29, 2009, p.1212.

S.-Y. Ting, J. Meng, Q. Li, Y.-Q. Wang, Y.-S. Tong, J. A. Shiebout, P. L. Koch, W. C. Clyde, and G. J. Bowen "Ganungulatum xincunliense, an artiodactyls-like mammal (Ungulata, Mammalia) from the Paleocene, Chijiang Basin, Jiangxi, China" Vertebrata PalAsiatica, v.45, 2007, p.278.

O'Leary, M.A., Spaulding, M., Parent, S., and Gatesy, J. "Instability of pivotal fossil clades in cetartiodactylan phylogeny and evolution of the ear region and ankle" Journal of Vertebrate Paleontology, v.28, 2008, p.122A.

D.M. Boyer, G.V.R. Prasad, D.W. Krause, M. Godinot, A. Goswami, O. Verma, and J.J. Flynn "New postcrania of Deccanolestes from the Late Cretaceous of India and their bearing on the evolutionary and biogeographic history of euarchontan mammals" Naturwissenschaften, v.97, 2010, p.365.

B.J. Shockey and J.J. Flynn "Morphological diversity in the postcranial skeleton of Casamayoran (?middle to late Eocene) Notoungulata and foot posture in notoungulates" American Museum Novitates, v.3601, 2007, p.1.

T. Macrini, J.J. Flynn, D.A. Croft, and A.R. Wyss "Inner ear of a notoungulate placental mammal: anatomical description and examination of potentially phylogenetically informative characters" Journal of Anatomy, v.216, 2010, p.600.

Maridet, O., W.-Y. Wu, J. Ye, S.-D. Bi, X.-J. Ni, and J. Meng "Eucricetodon (Rodentia, Mammalia) from the Late Oligocene of the Junggar basin, Northern Xinjiang, China" American Museum Novitates, v.3665, 2009, p.1.

J.A. Finarelli and J.J. Flynn "The evolution of encephalization in caniform carnivorans" Evolution, v.61 (7), 2007, p.1758. doi:10.1111/j.1558-5646.2007.00131.x 

Meng, J., B. P. Kraatz, Y.-Q. Wang, X.-J. Ni, D. L. Gebo, K. C. Beard "A new species of Gomphos (Glires, Mammalia) from the Eocene of the Erlian Basin, Nei-Mongol, China" American Museum Novitates, v.3670, 2009, p.1.


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 pound),...

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