1. I have since come to value chickens as valuable for studying phylogenetic networks within a fairly tractable empirical system ². There is the difficult problem of overlapping cycles in a network, caused by introgression between Gallus gallus and G. varius and between G. gallus and G. sonneratii. Network analyses can miss this from the overlapping cycles, but it is evident when observing the entire gene distribution of gene tree topologies.

Tiley GP, Kimball RT, Braun EL, Burleigh JG. 2018. Comparison of the Chinese bamboo partridge and red Junglefowl genome sequences highlights the importance of demography in genome evolution. BMC Genomics 19:336. ↩
Tiley GP, Pandey A, Kimball RT, Braun EL, Burleigh JG. 2020. Whole genome phylogeny of Gallus: introgression and data-type efects. Avian Research 11:1-15. ↩

"> 1. I have since come to value chickens as valuable for studying phylogenetic networks within a fairly tractable empirical system ². There is the difficult problem of overlapping cycles in a network, caused by introgression between Gallus gallus and G. varius and between G. gallus and G. sonneratii. Network analyses can miss this from the overlapping cycles, but it is evident when observing the entire gene distribution of gene tree topologies.

Tiley GP, Kimball RT, Braun EL, Burleigh JG. 2018. Comparison of the Chinese bamboo partridge and red Junglefowl genome sequences highlights the importance of demography in genome evolution. BMC Genomics 19:336. ↩
Tiley GP, Pandey A, Kimball RT, Braun EL, Burleigh JG. 2020. Whole genome phylogeny of Gallus: introgression and data-type efects. Avian Research 11:1-15. ↩

"> 1. I have since come to value chickens as valuable for studying phylogenetic networks within a fairly tractable empirical system ². There is the difficult problem of overlapping cycles in a network, caused by introgression between Gallus gallus and G. varius and between G. gallus and G. sonneratii. Network analyses can miss this from the overlapping cycles, but it is evident when observing the entire gene distribution of gene tree topologies.

Tiley GP, Kimball RT, Braun EL, Burleigh JG. 2018. Comparison of the Chinese bamboo partridge and red Junglefowl genome sequences highlights the importance of demography in genome evolution. BMC Genomics 19:336. ↩
Tiley GP, Pandey A, Kimball RT, Braun EL, Burleigh JG. 2020. Whole genome phylogeny of Gallus: introgression and data-type efects. Avian Research 11:1-15. ↩

" />

Chicken Evolution

Translational Research between Molecular Evolution and Agriculture

I always liked chickens and enjoyed the chance to get involved with some genomics work for them ¹. I have since come to value chickens as valuable for studying phylogenetic networks within a fairly tractable empirical system ². There is the difficult problem of overlapping cycles in a network, caused by introgression between Gallus gallus and G. varius and between G. gallus and G. sonneratii. Network analyses can miss this from the overlapping cycles, but it is evident when observing the entire gene distribution of gene tree topologies.

I am currently working on raising funding for investigating mutation rate variation at the population level among chicken breeds. Large-scale mutation analyses among populations can further elucidate the functional genetic basis of traits desirable for agriculture and supply chains. Similar to studies of abiotic stress in plants, such investigations are necessary now so we can meet the moment when climate change creates an environment no longer suitable for the current profit-maximizing traits of commercial broilers.

Tiley GP, Kimball RT, Braun EL, Burleigh JG. 2018. Comparison of the Chinese bamboo partridge and red Junglefowl genome sequences highlights the importance of demography in genome evolution. BMC Genomics 19:336. ↩
Tiley GP, Pandey A, Kimball RT, Braun EL, Burleigh JG. 2020. Whole genome phylogeny of Gallus: introgression and data-type efects. Avian Research 11:1-15. ↩