Multilocus assessment of population differentiation in Baja California birds: implications for community assembly and conservation

This dissertation is an assessment of biological diversification at the community, species, and population levels from large continental scales in the Americas to small regions between Mexico and the U.S. using birds as a study system. In Chapter 1, I calculate when the avian community of the Baja California peninsula diverged from the mainland using mitochondrial and nuclear DNA sequences. I discovered that even though birds fly and could have arrived to the peninsula in independent dispersal waves, genetic estimates correspond to few events of diversification that correspond to historical barriers to gene flow and more recent ecologic scenarios. Additionally, I find evidence for recognizing four peninsular lineages as valid species, doubling the number of endemic birds in Baja California. Chapter 2 is a collaboration with Keith Barker. In it, we explore the continental diversification of wrens in the genus Campylorhynchus solving all evolutionary relationships by sequencing 23 genes and multiple individuals per lineage, developing a new metric for comparing all sorts of phylogenetic trees, and clarifying biogeographic and behavioral evolution aspects in the Neotropics. In Chapter 3, me and collaborators Kelly Barr, Craig Farquhar, and Robert Zink merge historic fire ecology and population genetics to understand how and when the black-capped vireo ( Vireo atricapilla), went from being a historically common bird to being considered currently as endangered in its breeding grounds in the oak savannas of Oklahoma, Texas and northern Mexico. Five online supplementary files (OSFs) accompany this dissertation: the first file includes voucher numbers, geographic information, substitution models, used primers, and full likelihood values in Chapter 1 (OSF 1); the second file contains Bayesian trees ivand taxon pair distributions in Chapter 1 (OSF 2); the third file includes voucher numbers, evolutionary models, recombination tests, and primers used in Chapter 2 (OSF 3); the fourth file includes the randomization design in Chapter 2 (OSF 4); and the fifth file includes geographic information for all samples, primers, and multilocus phylogeny of vireos used in Chapter 3 (OSF 5).