Phylogeography, color variation, and hybridization in an Andean tanager, Superciliaried Hemispingus (Aves: Thlypopsis superciliaris)

Abstract

Natural history collections are invaluable libraries of Earth’s biodiversity. Museum specimens frequently span temporal, geographic, and taxonomic scales and afford unparalleled insights into environmental, organismal, and genomic change through time. In this dissertation, I show how museum specimens, particularly of birds, can be used to document diverse axes of biological change through time. In Chapter 1, I review how museum specimens of vertebrates, including birds, are sensitive indicators of environmental change in the Anthropocene. The remainder of my dissertation is dedicated to illustrating how data derived from both historical and modern museum specimens can be integrated to understand the evolution of an intriguing pattern of geographic color variation where disjunct populations are similar in coloration while intervening populations differ in coloration. This pattern of color variation, known as ‘leapfrog’ geographic variation, is particularly prevalent among bird species distributed along the verdant slopes of the Andes mountains in western South America. Although the leapfrog pattern was formally described nearly four decades ago, the evolutionary forces which have driven its origin and maintenance remain largely unstudied. In Chapter 2, I examine the evolution of a classic leapfrog color pattern in Superciliaried Hemispingus (Thlypopsis superciliaris), a species of Andean tanager whose northern and southern populations exhibit strikingly similar yellow plumage despite being geographically separated by gray-colored populations in the Peruvian Andes. Combining two seasons of fieldwork, detailed color measurements of 155 individuals and whole genome sequencing of 106 individuals, I show that yellow populations are not each other’s closest relatives and conclude that the leapfrog pattern likely evolved via a single transition from yellow to gray plumage coloration in an ancestral central population. Using over 16 million single nucleotide polymorphisms (SNPs), I then illustrate that the leapfrog pattern appears to have persisted to the present despite a complicated history of gene flow between yellow and gray populations, suggesting a role of sexual selection in maintaining the leapfrog pattern. In Chapter 3, I present the discovery of a hybrid zone between southern yellow and gray populations of T. superciliaris. I characterize the hybrid zone using color measurements and genome-wide SNPs, finding that a small number of genomic loci, including the mitochondrial genome, are moving from the yellow to gray population faster than the genome-wide average. Finally, I take advantage of genomic admixture and recombination in the hybrid zone to identify a putative, yet novel genomic basis for yellow plumage coloration. Specifically, I find that a small genomic region approximately 15 kilobases upstream of the 6-pyruvoyltetrahydropterin synthase gene (PTS) is strongly associated with yellow plumage coloration.