Some Current and Former Projects

I currently have several different research projects, many done in collaboration with others. Below are some of the types of projects that I (and my students) are or have worked 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. (There are links to PDFs for older some publications, but not more recent pubs).

BUILDING TAXON-RICH AVIAN PHYLOGENIES

Building a phylogeny of all (or most) avian species is a beneficial tool for avian comparative studies. I have been involved in several projects that have had the goal of resolving higher level relationships in birds (SEE BELOW). More recently, the goal has been to build species-rich phylogenies, such as is being done by the OpenWings group. Publications encompassing all birds from this includes Burleigh et al. 2015, Oliveros et al. 2019, Kimball et al. 2019), though we have also focused on dense sampling with some groups (e.g., Kimball et al. 2021, Leite et al. 2021, Salter et al. 2022, Zhao et al. 2025).

TRAIT EVOLUTION

I began doing phylogenetics as a way to understand trait evolution – gains and losses of traits, understanding what might drive trait evolution, etc. Over the years, I and collaborators have looked at such things as the distribution of intraspecific brood parasitism in galliforms (Krakauer and Kimball 2009), several papers on secondary sexual trait evolution (e.g., Kimball and Braun 2008, Sun et al. 2014, Hosner et al. 2020, Shogren et al. 2022, Zhao et al. 2024), biogeography (e.g., Hosner et al. 2015, Wang et al. 2017, Hosner et al. 2017).

Although I primarily work on birds, I have also been involved in some fun collaborations that have estimated phylogenies to look at trait evolution. Much of this has been with Drs. Christine Miller and Michale Forthman (Emberts et al. 2020, Forthman et al. 2023, Miller et al. 2024).

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.

My former graduate stduent, Joni Wright, looked at the evolution of chemoreceptors in New World vultures (Cathartidae), focusing on olfactory receptors (e.g., Wright et al. 2025). Understanding patterns of change in a large gene family such as the olfactory receptor family should provide insights both into the relative importance of olfaction to a species (e.g., species that rely heavily on olfaction might be expected to have more types of receptors) and as to the dynamics of change in gene families (since these appear to duplicate and be lost quite rapidly).

I am also interested in visual systems (e.g., White et al. 2022). 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. However, preliminary analyses of rhodopsin sequences from multiple independent comparisons of nocturnal and diurnal species suggests that birds have altered rhodopsin sequences in response to lifestyle, in contrast to several other lineages.

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 had an NSF grant to elucidate phylogenetic relationships among  galliform species. We have a lot of papers out from this work (Wang et al. 2013, Kimball and Braun 2014, Meicklejohn et al. 2014, Sun et al. 2014, Meikleohn et al. 2014, Persons et al. 2016, Hosner et al. 2016, Meiklejohn et al. 2016, Hosner et al. 2016, Wang et al. 2017a, b, Chen et al. 2021, Kimball et al. 2021a, b).

AVIAN HIGHER LEVEL 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. Former graduate student Kin Han looked at parentage and group relatedness in this population (Han et al. 2015) using microsatellites developed by a former student, Sarah Haas (Haas et al. 2009, 2010). Kin is primarily interested in population genetics, and that was also part of her research (Han et al. 2019).

OTHER PROJECTS

There are always a number of projects ongoing in the lab, often on things that are of interest but do not become large, multi paper projects (but may at some point…). These include things such as:

Evolution of sex chromosomes (Kimball and Braun 2022)

Hybridization and evolution of paradise flycatchers

Distribution of paired ovaries in birds of prey