105 million years ago 44 million years ago
Research
Research

esearch. Our research explores connections between biological evolution and Earth history in all organisms and time periods. Because time itself is of great utility in drawing these connections, we often use molecular clocks in combination with morphology, phylogeny, geology, and the fossil record to uncover historical patterns and reveal the mechanisms of change. We study, among other topics, speciation, adaptive radiation, lineage diversification, historical biogeography, and mass extinction. Of particular interest are global changes in the planetary environment such as continental breakup, climate change, and extraterrestrial impacts, and their effect on the evolution of life. Research topics in the lab have included the early evolution of life, vertebrate evolution, historical biogeography, primate evolution, and biodiversity & conservation. A large component of our work is computational (bioinformatics), involving the analysis of sequence data from many genes or complete genomes. Another component involves field work and collection of new DNA sequences as needed for particular questions. This laboratory is part of NASA's Astrobiology Institute. For examples of representative studies, see below. For other articles including the most recent, see complete list of publications.

CLICK IMAGE for trailer on our work in Haiti. 1-hour movie showing at film festivals (2014)


Early Evolution of Life

In this research program, we investigate how the planetary environment has influenced the early evolution of life and how biological processes changed the environment. For example, the geologic record suggests that oxygen levels increased substantially about 2.3 billion years ago (Ga), and then again about 600 million years ago (Ma).From Hedges et al. (2004)From Hedges et al. (2004) These were times of major environmental change for our planet, but their relationship with biological evolution is poorly understood.Cyanobacteria are believed to be responsible for the early rise in oxygen, but when did they originate and when did they evolve oxygenic photosynthesis? Complex multicellular life apparently arose after the Great Oxidation event, but how long after? How did eukaryotes evolve? When did plants, animals, and fungi originate and when did they colonize land? How did the colonization of land by complex life affect the biosphere? We have touched on some of these questions in our previous work (see selected publications) but are actively seeking more and better data to achieve greater precision and a fuller understanding of the early evolution of life. (figure from Hedges et al., 2004).

Selected publications:

  • Hedges, S. B. Life. Pp. 89-98 in The Timetree of Life, S. B. Hedges and S. Kumar, Eds. (Oxford University Press, New York, 2009). E-print
  • Hedges, S. B., and Kumar, S. Discovering the timetree of life. Pp. 3-18 in The Timetree of Life, S. B. Hedges and S. Kumar, Eds. (Oxford University Press, New York, 2009).
  • Battistuzzi, F.U., and S.B. Hedges. 2009. A major clade of prokaryotes with ancient adaptations to life on land. Mol. Biol. Evol. 26:335–344. E-print
  • Hedges, S. B., F. U. Battistuzzi, and J. E. Blair. 2006. Molecular timescale of evolution in the Proterozoic. Pp. 00-00 in S. Xiao and A. J. Kaufman (Eds.), Neoproterozoic Geobiology and Paleobiology, Springer, New York. (in press)
  • Blair, J. E., P. Shah, and S. B. Hedges. 2005. Evolutionary sequence analysis of complete eukaryote genomes. BMC Bioinformatics 4:53. E-print
  • Battistuzzi, F. U., A. Feijão, and S. B. Hedges. 2004. A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land. BMC Evol. Biol. 4:44. E-print
  • Hedges, S. B., J. E. Blair, M. L. Venturi, and J. L. Shoe. 2004. A molecular timescale of eukaryote evolution and the rise of complex multicellular life. BMC Evol. Biol. 4:2. E-print
  • Hedges, S. B. 2002. The origin and evolution of model organisms. Nature Reviews Genetics 3:838-849. E-print
  • Heckman, D. S., D. M. Geiser, B. R. Eidell, R. L. Stauffer, N. L. Kardos, and S. B. Hedges. 2001. Molecular evidence for the early colonization of land by fungi and plants. >Science 293:1129-1133. E-print

Vertebrate Evolution

We are also interested in the major transitions and adaptive radiations in vertebrate evolution, and how they relate to Earth's history. For example, the fossil record has suggested that most lineage splitting among orders of modern birds and placental mammals took place in the early Cenozoic (~65-60 million years ago, Ma) as a result of the mass extinction at the end of the Cretaceous and subsequent ecological changes.However, in the mid-1990's we analyzed protein sequences from hundreds of genes and found evidence that the lineage splitting may have been related to continental drift in the mid-Cretaceous (~100 Ma) rather than later niche-filling in the early Cenozoic (see selected publications). Although this hypothesis continues to be debated, our later studies (also in collaboration with Sudhir Kumar of Arizona State University) and those of others have found similar results. Also, the definition in 1997 of an African clade of mammals (Afrotheria), from the labs of Springer, Stanhope, and de Jong, lent support to the hypothesis that continental breakup was an important factor.In other studies we have found intriguing relationships for lampreys and hagfishes, caecilians, turtles, squamates (lizards, snakes, and amphisbaenians), and flamingos.

Selected publications:

  • Vidal, N, Marin J, Morini M, Donnellan S, Branch WR, Thomas R, Vences M, Wynn A, Cruaud C, & Hedges SB. 2010. Blindsnake evolutionary tree reveals long history on Gondwana. Biology Letters 6:558-561. E-print Supp
  • Hedges, S. B. Vertebrates (Vertebrata). Pp. 309-314 in The Timetree of Life, S. B. Hedges and S. Kumar, Eds. (Oxford University Press, New York, 2009).
  • Fry, B.G., N. Vidal, J. A. Norman, F. J. Vonk, H. Scheib, R. Ramjan, S. Kuruppu, K. Fung, S. B. Hedges, M. K. Richardson, W. C. Hodgson, V. Ignjatovic, R. Summerhayes, and E. Kochva. 2006. Early evolution of the venom system in lizards and snakes. Nature 439:584-588. E-print
  • Vidal, N., and S. B. Hedges. 2005. The phylogeny of squamate reptiles (lizards, snakes, and amphisbaenians) inferred from nine nuclear protein-coding genes. C. R. Biologies 328:1000-1008. E-print
  • Vidal, N. and S. B. Hedges. 2004. Molecular evidence for a terrestrial origin of snakes. Proc. R. Soc. Lond. B (Suppl.)271:S226-S229. E-print
  • Hedges, S. B. 2000. Molecular evidence for the early history of living vertebrates. Pp. 119-134 in P. E. Ahlberg (Ed.) Major events in early vertebrate evolution: palaeontology, phylogeny, genetics and development. Taylor and Francis, London. E-print
  • Hedges, S. B., and L. L. Poling. 1999. A molecular phylogeny of reptiles. Science 283:998-1001. E-print
  • Stanhope, M. J., V. G. Waddell, O. Madsen, W. de Jong, S. B. Hedges, G. Cleven, D. Kao, and M. S. Springer. 1998. Molecular evidence for multiple origins of Insectivora and for a new order of endemic African insectivore mammals. Proc. Nat. Acad. Sci. (USA) 95:9967-9972. E-print
  • Kumar S., and S. B. Hedges. 1998. A molecular timescale for vertebrate evolution. Nature 392:917-920. E-print
  • Feller, A. E. and S. B. Hedges. 1998. Molecular evidence for the early history of living amphibians. Molec. Phylogenet. Evol. 9:509-516. E-print
  • Hedges, S. B., P. H. Parker, C. G. Sibley, and S. Kumar. 1996. Continental breakup and the ordinal diversification of birds and mammals. Nature 381:226-229. E-print

Historical Biogeography

Understanding the connections between Earth's history and biological evolution also is the central question of historical biogeography. Our focus in this research program is on a geologically complex and species-rich region of the World: the islands of the West Indies. The Antillean island arc formed in the mid-Cretaceous (~100 Ma) much further west of its present location. As the arc moved eastward along with the Caribbean geologic plate, opportunities appeared for island-hopping and land-to-land connections between various islands and the mainland. Species can arise when such connections disappear (vicariance) or by colonists floating on flotsam across water gaps to invade new territories (dispersal). The biotic history of the West Indies almost certainly included the operation of both mechanisms, but it is of interest to know whether one or the other predominated. Thus far, our systematic and biogeographic work on West Indian vertebrates, using molecular clocks, phylogenies, morphology, and other data, has supported an origin by overwater dispersal for most groups, but with some notable exceptions.

Selected publications:

  • Hedges, S.B. 2010. Molecular clocks, flotsam, and Caribbean islands. Pp. 353–354 in Cox, C. B. & P. D. Moore, Biogeography: an ecological and evolutionary Approach. 8th Edition (John Wiley & Sons, Inc., Hoboken, New Jersey). E-print
  • Vidal, N, Marin J, Morini M, Donnellan S, Branch WR, Thomas R, Vences M, Wynn A, Cruaud C, & Hedges SB. 2010. Blindsnake evolutionary tree reveals long history on Gondwana. Biology Letters 6:558-561. E-print Supp
  • Hedges, S. Blair. 2006. An overview of the evolution and conservation of West Indian amphibians and reptiles. Applied Herpetology 3:281-292. E-print
  • Hedges, S. B. 2006.Paleogeography of the Antilles and origin of West Indian terrestrial vertebrates. Annals of the Missouri Botanical Garden 93:231-244.
  • Smith, M. L., S. B. Hedges, W. Buck, A. Hemphill, S. Inchaustegui, M. Ivie, D. Martina, M. Maunder, and J. F. Ortega. 2005. Caribbean Islands. Pp 112-118 in R. A. Mittermeier, P. R. Gil, M. Hoffman, J. Pilgrim, T. Brooks, C. G. Mittermeier, J. Lamoreux, and G. A. B. da Fonseca (eds.), Hotspots revisited: Earth's biologically richest and most endangered terrestrial ecoregions. Mexico City: CEMEX. E-print
  • Hedges, S. B., and R. Thomas. 2001. At the lower size limit in amniotes: a new diminutive lizard from the West Indies. Caribbean J. Sci. 37:168-173. E-print
  • Hedges, S. B. 2001. Caribbean biogeography: an overview. Pp 15-33 In C. A. Woods and F. E. Sergile (eds.), Biogeography of the West Indies: patterns and perspectives. CRC Press, Boca Raton, Florida. E-print
  • Schubart, C., R. Diesel, and S. B. Hedges. 1998. Rapid evolution to terrestrial life in Jamaican crabs. Nature 393:363-365. E-print
  • Hedges, S. B. 1996. Historical biogeography of West Indian vertebrates. Ann. Rev. Ecol. Syst. 27:163-196. E-print
  • Estrada, A. R., and S. B. Hedges. 1996. At the lower size limit in tetrapods: a new diminutive frog from Cuba (Leptodactylidae: Eleutherodactylus). Copeia 1996:852-859. E-print
  • Hedges, S. B., C. A. Hass, and L. R. Maxson. 1992. Caribbean biogeography: Molecular evidence for dispersal in West Indian terrestrial vertebrates. Proc. Natl. Acad. Sci. (U.S.A.) 89:1909-1913. E-print

Primate Evolution

In this research program, we focus on the evolutionary history of our closest relatives to better understand the sequence of events leading to the origin of modern humans. In particular, we would like to know the relationship between environmental and organismal change in primates during the Cenozoic. Although the primate fossil record in general is poor, an accurate timescale from molecular clocks can help to constrain divergence events and relationships of fossil taxa. For example, we recently refined the molecular timescale of human and ape evolution, in collaboration with Alan Walker (see selected publications).Our most recent study, in collaboration with Sudhir Kumar, led to the development of a new method for determining confidence limits on molecular time estimates. Our estimate of the divergence time between humans and chimpanzees (4.5-6.5 Ma) is compatible with most interpretations of the hominoid fossil record, but suggests that some traits of humans, such as bipedalism, evolved relatively quickly. Additional data from ongoing ape genome projects will help to further refine this timescale and better constrain evolutionary hypotheses.

Selected publications:

  • Kumar, S., A. Filipski, V. Swarna, A. Walker & S. B. Hedges. 2005. Placing confidence limits on the molecular age of the human-chimpanzee divergence. Proc. Natl. Acad. Sci. 102:18842-18847. E-print
  • Hedges, S. B. 2002. The origin and evolution of model organisms. Nature Reviews Genetics 3:838-849. E-print
  • Stauffer, R. L., A. Walker, O. Ryder, M. Lyons-Weiler, and S. B. Hedges. 2001. Human and ape molecular clocks and constraints on paleontological hypotheses. J. Heredity 92:469-474. E-print
  • Hedges, S. B. 2000. A start for population genomics. Nature 408:652-653. E-print
  • Kumar S., and S. B. Hedges. 1998. A molecular timescale for vertebrate evolution. Nature 392:917-920.

Biodiversity & Conservation

Another major aspect of research in the lab involves the discovery, characterization, and organization of biodiversity at all levels, including prokaryotes and eukaryotes. This includes not only systematic and taxonomic research but also ecology, natural history, and conservation biology. In the course of this work, about 80 species have been discovered and described, as well as many genera, families, and other higher taxa. Field work is mostly confined to Caribbean islands and to amphibians and reptiles, but laboratory research has included all major groups of organisms. The lab PI is intimately involved with conservation in the region and is a Red List Authority for the IUCN. Recent work in Haiti has involved rescue missions for critically endangered frogs, for captive breeding. A lab website (Caribnature) is devoted to the conservation of biodiversity on Caribbean islands. See also the other Caribbean web sites developed by the lab: Caribherp, Caribmap.

NPR interview on Haiti's pending mass extinctions

Selected publications:

  • Vidal, N, Marin J, Morini M, Donnellan S, Branch WR, Thomas R, Vences M, Wynn A, Cruaud C, & Hedges SB. 2010. Blindsnake evolutionary tree reveals long history on Gondwana. Biology Letters 6:558-561. E-print Supp
  • Battistuzzi, F.U., and S.B. Hedges.2009. A major clade of prokaryotes with ancient adaptations to life on land. Mol. Biol. Evol. 26:335–344. E-print Supplementary data
  • Hedges, S. B. 2008. Threatened amphibians of the West Indies. Pp. 104–105 in Stuart, S.N., Hoffmann, M., Chanson, J.S., Cox, N.A., Berridge, R., Ramani, P. and Young B.E.(Ed.), Threatened Amphibians of the World. Lynx Ediciones, with IUCN - The World Conservation Union, Conservation International, and NatureServe, Barcelona.
  • Hedges, S. B. 2008. At the lower limit of size in snakes: two new species of threadsnakes (Squamata: Leptotyphlopidae: Leptotyphlops) from the Lesser Antilles. Zootaxa 1841:1–30. E-print
  • Hedges, S. B., W. E. Duellman, and M. P. Heinicke. 2008. New World direct-developing frogs (Anura: Terrarana): molecular phylogeny, classification, biogeography, and conservation. Zootaxa 1737:1–182. E-print
  • Thomas, R. and S. B. Hedges. 2007. Eleven new species of snakes of the genus Typhlops (Serpentes: Typhlopidae) from Hispaniola and Cuba. Zootaxa 1400:1-26. E-print
  • Hedges, S. B., and R. Thomas. 2001. At the lower size limit in amniotes: a new diminutive lizard from the West Indies. Caribbean J. Sci. 37:168-173. E-print
  • Estrada, A. R., and S. B. Hedges. 1996. At the lower size limit in tetrapods: a new diminutive frog from Cuba (Leptodactylidae: Eleutherodactylus). Copeia 1996:852-859. E-print
  • Hedges, S. B. 1993. Global amphibian declines: a perspective from the Caribbean. Biodiversity and Conservation 2:290-303. E-print
Sphaerodactylus ariasae Tetracheilostoma carlae Eleutherodactylus iberia

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