RESEARCH PROJECTS
I currently have several
different research
projects, many done in collaboration with others. Below are a handful
of
the core projects that I am currently working on. Graduate
students in the lab work on projects unrelated to my core projects, and
the diverse range of those projects can be found in Lab Group
information. Some undergraduate students are working with me on the
projects listed below, but others are working on different projects.
These are also listed in the Lab Group information.
EARLYBIRD
The “Early Bird” tree
of life project, funded by
the NSF, is
a large-scale, cooperative effort among five institutions in the U.S.
to determine the evolutionary relationships among all major groups of
birds.
The primary investigators are Shannon Hackett (Field Museum of Natural
History), Mike Braun (Smithsonian Institution), Fred Sheldon (Louisiana
State University), Bill Moore (Wayne State University), and three
researchers at the University of Florida: Rebecca Kimball, Edward
Braun, and David Steadman (Florida Museum of Natural History; providing
the paleontological and
morphological expertise). The project has generated a large amount of
sequence data for all major avian lineages from multiple genes. We have
recently published (Hackett et al. 2008, Science) an analysis of 169
avian species for 19 loci (representing about 25kb per species, and a
final alignment across all taxa of about 52kb). We have several other
publications that have arisen from this project (Yuri et al. 2008,
Chojnowski et al. 2008, Kimball and Braun 2008).
We are working on additional publications from this data, examining a
wide range of questions in phylogenetics, molecular evolution, and
addressing questions about the evolution of specific traits. In
addition to analyses using the initial data set, we have also been
increasing the size of our dataset by adding in more species and new
loci.
In the Kimball and Braun labs, we
developed 7 loci
for use in the initial analyses (though sequencing for two of these
regions was shared across other labs). For each region, we sequenced a
region of the total gene, and obtained a mixture of intron and exon
data. The genes we worked on were alpha-crystallin (1kb), aldolase B (2
kb), clathrin heavy chain (1.5 kb), dimerization co-factor of
hepatocyte nuclear factor alpha (1 kb), eukaryotic elongation factor (2
kb), high mobility 17 protein (1.5 kb), and rhodopsin (1.8 kb). We have
developed additional loci that are in progress, and these new regions
primarily focus on intron data with little or no exon sequence. For
some of these we have amplified and sequenced up to 200 species, while
others have been sequence from a subset of 40-60 species.
GALLIFORM
EVOLUTION
I have
long been interested in gallforms, a group of
birds including (among others) chickens, pheasants, turkeys, grouse,
quail, and guineafowl. This
group contains
species that are sexually dimorphic with
highly specialized ornamental plumage and/or specialized fleshy traits,
as well as monomorphic species with little or no ornamentation -- thus
raising many interesting questions about the evolutionary patterns of
such traits. I have some some behavioral work in
the red junglefowl, but most of my research on galliforms has been on
phylogeny. Initially my phylogenetic research used mitochondrial
sequences, particularly cytochrome b
(and with control region sequences collected by my collaborator, Ettore
Randi). This type of data resolved some relationships within the
phasianids, particularly among closely related species (congeners and
closely related genera). However, many unknown relationships remained.
For a number of years I have been primarily using nuclear data
(particularly intron data) to address these questions. Some of the
introns initially developed for the galliforms formed the basis for
some of our EarlyBird loci, though we have developed other introns that
we have only examined in the galliforms. In addition to using this
nuclear intron data to examine phylogenetic relationships, we also hope
to compare the patterns of molecular evolution among the introns. I am
hoping that
integrating the more rapidly evolving mitochondrial data with the more
slowly evolving nuclear intron data will provide a well-resolved
phylogeny. In addition, combining multiple unlinked regions may help
provide more robust estimates of branch lengths for comparative
analyses and molecular clock estimates.
I have primarily focused on pheasants,
though it is
clear that understanding the evolution of the pheasants (and the
associated ornamental traits) will require understanding evolution of
the partridges and quail as well. I hope to expand the taxon sampling
to include more of these type of species, allowing me to better address
questions about the evolution of sexual dimorphism and ornamentation in
this group.
BROWN-HEADED
NUTHATCHES
Brown-headed
nuthatches occur in the southeastern
United States, and are known to breed cooperatively. Although the first
publications about this mating system came out in the 1950's, this
species has remained poorly studied. Jim Cox
at
Tall Timbers Research
Station (TTRS) has been working for several years on a population of
nuthatches, where he has been able to identify a large number of
territories, band a number of adults and nestlings, and begin to obtain
patterns about group composition and dispersal. We are currently using
microsatellite loci developed by a former MS student,
Sarah
Haas (with some help from current student, Jordan Smith), to
genotype family groups from the past three years to determine
patterns of relatedness within groups.
Sarah Haas did research on genetic spatial structure, looking
intesively on relationships within the TTRS population as well as
across several additional populations in Florida and Georgia. This
species is declining across its range, but particularly in some states
such as FL. It has been suggested to be a poor disperser, possibly
quite habitat restricted, and this may lead to small, isolated
populations in areas of heavy development (like much of central and
southern FL). We are interested in continuing to examine the population
genetics of thsi species.
PLANT PHYLOGENETICS
The plant phylogenetic work I have been
involved in
has primarily been done in collaboration with a botanist, Dan Crawford
(currently at Univ. of Kansas), and several other collaborators (Don
Les, Univ. Connecticut, and Tim Lowrey, Univ. of New Mexico). Much of
the plant research in my lab is under the guise of the Director. Although
I am not a botanist, I have enjoyed working on plants. Rather than
approaching the data with a single question (as I have sometimes done
with other researach), working on plants requires me to really focus on
the patterns I see in the data, and sometimes that has allowed me to
detect patterns I might have missed otherwise (a useful skill to
develop). As with my avian research, my interest in plants is the
ability to look at general evolutionary patterns. As such, I have
addressed some of the same questions in plants that I have addressed in
birds (e.g., biogeography, evolution of reproductive characters).
One of the key plant projects I am working on is a
phylogeny of the African and Madagascar genus Brachylaena, and
the relationship
between Brachylaena
and
Tarchonanthus.
This group of
composites is interesting as they are dioecious (most composites are
monoecious) and are not only woody but can grow into enormous trees.
Results I have obtained with Dan Crawford and Tim Lowrey suggest that
this genus evolved in Africa (though we are just collecting some
additional outgroup sequences to be certain this is most likely),
dispersed to and radiated
within Madagascar, and
then one species
dispersed back to Africa relatively recently. Our results also suggest Tarchonanthus may
nest within,
rather than sister to, Brachylaena.
(Photos courtesy of Tim Lowrey)
Another project I have begun is to
develop five
different (and hopefully unlinked) nuclear markers in the genus Coreocarpus.
Previous research I
have done in this genus suggests that lineage sorting or hybridization
is occurring in this group (chloroplast phylogenies differ from those
generated using nuclear ITS data). Timing of the divergences are such
that lineage sorting is possible, though the probable small population
sizes in this group suggest short coalescence times and a low
likelihood of lineage sorting. A previous biosystematic study indicated
hybridization was unlikely to occur between most of the species in the
genus, suggesting that if hybridization accounts for the
incongruence, it may have occurred prior to the evolution of
reproductive barriers between some of the species. Syki Duong helped
with the initial data collection for this project, but currently my
graduate student Deena Westbrook is finishing the data collection as
part of her interest in understanding patterns of evolution due to
hybridization and lineage sorting.
Dan Crawford and I also have data from
quite a few
species of Mexican and South American species in the genus Coreopsis for both
nuclear ITS and
chloroplast data. Coreopsis
is a large, non-monophyletic genus. Taxonomy of the South American
species is poorly resolved, and several key questions about this group
remain to be answsered. In particular, there are questions about the
evolution of one group, the Pseudoagarista, which share similar
reproductive traits but do not form a monophyletic group using nuclear
ITS data (Kim et al. 1999). We hope to better resolve these
relationships as we try to obtain additional samples (particularly from
the Mexican taxa).
MISCELLANEOUS
OTHER PROJECTS
In addition to the primary projects in
the lab, there are a number of smaller or preliminary projects going on
as well.
Paradise
Flycatchers (Terpsiphone):
The African Paradise
Flycatcher (Terpsiphone viridis) and
the Red-bellied Paradise Flycatcher (T.
rufiventer) are both distributed in Africa
with regions of sympatry. Although the species
prefer different habitats (open woodland vs. forest), there have been
reports
of hybridization between the two species. The two species, particularly
the
African Paradise Flycatcher, also exhibit a large degree of plumage
variability
(from males that are rust and gray to those that are black and white)
across
their ranges. Such variation has the potential to confound detection of
hybrids
based on plumage patterns. To determine whether hybridization was
occurring, I
examined sequence data from both the mitochondria from
multiple accessions of Terpsiphone
viridis and T. rufiventer
collected
in a variety of locations. The results of my initial sampling indicate
there is
not reciprocal monophyly between the species. Although the species are
largely
separated by habitat, these results do suggest that hybridization
between the
two species may have occurred multiple times. However, there are
alternative
explanations for the data that I am examining. We have
recently
begun collecting data from nuclear introns for this group, and are
working with John Bates (Field Museum of Natural History) on
development of microsatellite loci.
Patterns
of rhodopsin in
nocturnal and diurnal birds: Similar
adaptations may sometimes arise independently in
response to similar ecological conditions. Such convergence has been
observed
in visual pigments (opsins) in a variety of vertebrate lineages such as
fish,
birds, and mammals. The opsins form a gene family of visual pigments,
of which
there are five different opsins in birds. Rhodopsin, found in the rod
cells, is
responsible for day/night vision while the other four visual pigments
are
responsible for color vision. I have collected rhodopsin sequences from
a
wide
range of avian orders (including paleognathes and a diversity of
neognathe
orders) to get multiple independent comparisons of nocturnal and
diurnal species.
Absorbance of opsins can be estimated from amino acid sequences,
allowing us to
compare absorbance of rhodopsin between diurnal and nocturnal species.
I also
looked for specific amino acid substitutions in key sites, such as near
the
retinal-binding pocket between the diurnal and nocturnal species.
Overall, it does not appear that birds have altered rhodopsin sequences
in response to lifestyle, in contrast to several other lineages.