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.Current research topics in
the lab include theearly evolution of life,
vertebrate evolution,
historical biogeography, and
primate evolution. A large component of our work is computational (bioinformatics), involving the
analysis of sequence data from many genes or complete genomes. Another component involves collection of new DNA sequences as needed for particular questions. This laboratory is part of NASA's
Astrobiology Institute. For examples of recent
studies, see below. For other articles, see complete list of
publications.
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 about 2.3
billion years ago (Ga).This was a major environmental change for our planet (the “Great
Oxidation Event”), but its relationship with biological evolution is poorly
understood.Cyanobacteria are
believed to be responsible for that 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:
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
Hedges,
S. B. 2002. The origin and evolution of model organisms. Nature
Reviews Genetics 3:838-849.
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.
Battistuzzi, F. U., A. Feijăo, 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
Blair, J. E., P. Shah, and S. B.
Hedges. 2005. Evolutionary sequence analysis of complete eukaryote genomes.
BMC Bioinformatics4:53.
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)
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:
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
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
Kumar S., and S. B.
Hedges. 1998. A molecular timescale for vertebrate evolution. Nature
392:917-920.
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
Hedges, S. B., and L. L.
Poling. 1999. A molecular phylogeny of reptiles. Science 283:998-1001.
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
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.
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
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. A field component involves expeditions to
remote regions of the islands and discovery of new species (~50 thus far), and a laboratory
component involves molecular phylogenetic studies (see also our two
Caribbean databases, Caribherp & Caribmap).
Selected publications:
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
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. 1996. Historical biogeography of West Indian vertebrates.
Ann. Rev. Ecol. Syst.27:163-196.
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. 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
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
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. 2006. Paleogeography of the Antilles and origin of West Indian terrestrial
vertebrates. Annals of the Missouri Botanical Garden 93:231-244.
Hedges, S. Blair. 2006. An
overview of the evolution and conservation of West Indian amphibians and
reptiles. Applied Herpetology
3:281-292. 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., and S. B.
Hedges. 1998. A molecular timescale for vertebrate evolution. Nature
392:917-920.
Hedges, S. B. 2000. A
start for population genomics. Nature 408:652-653.
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. 2002.
The origin and evolution of model organisms. Nature Reviews
Genetics 3:838-849.
E-print
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
Our
research explores connections between biological evolution and Earth history
in all organisms and time periods.
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.
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. A field component involves expeditions to
remote regions of the islands and discovery of new species (~50 thus far), and a laboratory
component involves molecular phylogenetic studies (see also our two
Caribbean databases, 
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.