UC Berkeley

This dissertation aims to understand the patterns and processes involved in the origin, maintenance, and diversification of montane birds in Nuclear Central America. Nuclear Central America, the region between the Isthmus of Tehuantepec and the Nicaraguan Depression, is an understudied tropical, but highly biodiverse region. We assemble genetic, morphological, and climatic datasets to uncover biogeographic and evolutionary processes across a spatial and temporal continuum. We report genomic data from 850 individuals representing ten bird species from the mountains of Nuclear Central America, and using these data we detect several new biogeographic breaks. This dissertation constitutes the first study incorporating genomic data to understand evolutionary processes underpinning bird diversity in Nuclear Central America.

Chapter 1 reveals that historical and contemporary processes have fueled in situ diversification within Nuclear Central America. We study Lampornis viridipallens and L. sybillae integrating phylogeography, landscape genetics, ecological niche modeling, and morphological measurements to understand diversification across the species-population interface. Mitochondrial and microsatellite data indicate that L. viridipallens and L. sybillae diverged in allopatry during the early Pleistocene on either side of the Honduras Depression. This divergence was followed or accompanied by ecological niche divergence. Within L. viridipallens, dry valleys that separate mountain ranges are geographic barriers promoting isolation in this hummingbird species restricted to cloud forests. Moreover, environmental variables are much more critical for facilitating gene flow and population connectivity than straight-line geographic distance.

Chapter 2 highlights the importance of assessing multiple processes to understand the origin and maintenance of biodiversity, especially in topographically complex regions such as the Neotropics. We investigate the phylogeography and genetic basis of phenotype-genotype discordance in Atlapetes albinucha across its geographic range, from Mexico to Colombia. We assemble mitochondrial and genomic data of 73 individuals, including the yellow and gray phenotypes of the species. Our analyses show that allopatric divergence results in high geographic genetic structure. Additionally, we included two individuals with intermediate phenotypes. Ours is the first report of hybridization between the two plumage color phenotypes. We describe the environment where the barrier between the yellow and gray phenotypes occurs (biogeographic barrier east to Altos de Chiapas). We find that high precipitation and low elevation limit the geographic range of both phenotypes and provide a different environment in the hybrid zone. Furthermore, our genomic data suggests UDP-glucuronosyltransferase as a candidate gene explaining the presence-absence of yellow color in the ventral feathers of A. albinucha.

Chapter 3 investigates that the evolutionary and biogeographic history of Saucerottia hummingbirds and sets the biological stage for understanding the genetic basis of structural color variation in hummingbird plumage. We integrate mitochondrial and genomic data of 128 individuals, including representation from Mexico to Guyana, to understand phylogenetic relationships and the geographic distribution of genetic variation. Additionally, we examine and describe the physical structure of rufous, blue, and intermediately colored tail feathers. Our results demonstrate that shallow divergence and mixed ancestry in Saucerottia provide similar genetic backgrounds across species. Evolutionary labile tail coloration occurs across multiple species pairs differing mainly in structural coloration. Geographically detailed sampling within Nuclear Central America uncovers divergence consistent with the geographic distribution of tail color variants. We also identify various candidate genes related to the melanin biosynthesis pathway that may underlie variation in structural coloration.

Chapter 4 reports that the current mountain bird assemblage in Nuclear Central America results from common biogeographic history and species idiosyncratic evolutionary paths. Through a comparative phylogeographic approach, we examine mitochondrial and genomic data of 676 individuals comprising the bird species: Lampornis viridipallens, L. sybillae, Henicorhina leucophrys, Basileuterus belli, Myioborus miniatus, Chlorospingus flavopectus, and Arremon brunneinucha. Phylogenetic analyses support the role of Nuclear Central America as the interconnection between the avian fauna of North and South America. Additionally, high levels of population genetic structure among different mountain ranges within Nuclear Central America suggest in situ diversification. We show that the isolating effect of the Motagua-Polochic-Jocotán Fault System is not homogenous along its extent and that the biogeographic barrier east to Altos de Chiapas is essential to isolating montane populations from one another.