Current Projects

I currently have several different research projects, many done in collaboration with others. Below are the primary projects that I (and my students) are working on.  Some graduate students in the lab work on projects unrelated to my core projects, and the diverse range of those projects can be found in the People section.

• Galliform Evolution
• Evolution of Sensory Systems
• Avian Phylogenetics and Comparative Studies
• Cooperative breeding Brown-headed Nuthatches
• Hybridization in Paradise Flycatchers
• Other projects – evolution of runx2 and sex chromosomes

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 (Kimball et al. 1997a, Kimball et al. 1997b, Ligon et al. 1998, Furlow et al. 1998), but most of my research on galliforms has been on to elucidate evolutionary relationships (Kimball et al. 1997, 1999, 2001, 2006, 2011, Kimball and Braun 2008, Randi et al. 2000, 2001, Armstrong et al. 2001, Crowe et al. 2006) and to understand trait evolution, particularly sexually dimoprhic traits (Kimball et al. 2011, Kimball and Braun 2008).

Along with Ed Braun (Univ. Florida), we have an NSF grant to elucidate phylogenetic relationships among all (hopefully) galliform species. We are using a combination of next-gen sequencing of ultra-conserved elements as well as sequencing of more traditional markers (introns and mitochondrial regions). We have several papers out from this work (Wang et al. 2013, Kimball and Braun 2014, Meicklejohn et al. 2014, Sun et al. in press), and others that are in progress.

EVOLUTION OF SENSORY SYSTEMS

Sensory systems are critical to help organisms interact with their environment. Therefore, understanding how these systems evolve can provide insights into how organisms may adapt to changing environments. I am working with one of my graduate students, Joni Wright, to look at the evolution of chemoreceptors in New World vultures (Cathartidae). So far, we have focused on olfactory receptors, the largest gene family in vertebrates. Turkey vultures are known to locate food using olfactory cues, while black vultures do not appear to rely on olfaction. Using a red-tailed hawk as an outgroup, we estimate turkey vultures have ~1600, black vultures have ~900, while the outgroup has <400 (chickens have ~500). Thus, this gene family varies substantially in size within the Cathartidae. We are examining additional cathartids, and also exploring other chemoreceptors in this group (TAAR’s, T1R’s and T2R’s).

I am also interested in visual systems. 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 multiple independent comparisons of nocturnal and diurnal species to determine whether there has been convergent evolution at key amino acid residues. Overall, it does not appear that birds have altered rhodopsin sequences in response to lifestyle, in contrast to several other lineages.

AVIAN PHYLOGENETICS

Currently, I am working with Gordon Burleigh and Edward Braun to produce a phylogeny that comprises ~70% of all avian species (called “Bigbird”). We are using this phylogeny to address a variety of questions such as patterns of diversification across birds, the evolution of sexual size dimorphism, and to identify
correlates of speciation.

An earlier project was “Early bird”, involving Edward Braun, Shannon Hackett, Mike Braun, Fred Sheldon, Bill Moore and David Steadman, to resolve basal avian relationships (Hackett et al. 2008, Harshman et al. 2008, Chojnowski et al. 2008; see also Wang et al. 2012, Smith et al. 2013 and Kimball et al. 2013).

This study also yielded insights into molecular evolution and rare genomic changes (Yuri et al. 2008, Braun et al. 2011, Han et al. 2011, Yuri et al. 2013), and provided good resources for future molecular phylogenetic studies in birds (Kimball et al. 2009; see also Wang et al. 2012).

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. My graduate student Kin Han is looking at parentage and group relatedness in this population using microsatellites developed by a former student, Sarah Haas (Haas et al. 2009, 2010). Kin is primarily interested in population genetics, and she is also sampling nuthatches from multiple populations in Florida and throughout the range to look at patterns of dispersal and the affects of fragmentation on this species.

HYBRIDIZATION IN PARADISE FLYCATCHERS

The African Paradise Flycatcher Terpsiphone viridis) and the Red-bellied Paradise Flycatcher (T. rufiventer) are both distributed in Africa with regions of sympatry. Hybridization between these species has been suggested to occur due to habitat destruction that has led the species to breed in the same areas. However, high levels of plumage variation within the species makes it difficult to separate out whether hybridization is occurring regularly. Working with Caitlin Wildes, a former undergraduate in my lab, and John Bates, Field Museum of Natural History, we have been collecting microsatellite and sequence data to examine this issue. Our initial results suggest that hybridization may be occurring regularly and throughout the entire range of T. rufiventer.

OTHER PROJECTS

A former undergraduate, Reid Green, sequenced runx2. This gene is involved in laying down cartilage prior to bone deposition, and the number of alanines and glutamines in this exon correlates with snout length in canids. Reid sequences this in shorebirds (Scolopacidae) and found a correlation between bill length and runx2. Interestingly, in some other groups with bill length variation, there does not appear to be a relationship.

Another former undergraduate, Carly Ferguson, sequenced ATP5A1 which is located on the sex chromosomes in birds. Previous research had suggested that this locus had ceased recombining independently in several different groups of birds. We have now sequenced this from many different avian species, and have identified 13 independent cessation of recombination at this locus. Interestingly, there are an almost similar number of cases where the gene appears to be still undergoing recombination.