Kevin J. Burns

PHYLOGENETIC RELATIONSHIPS AND MORPHOLOGICAL DIVERSITY IN DARWIN'S FINCHES AND THEIR RELATIVES

Abstract Despite the importance of Darwins finches to the development of evolutionary theory, the origin of the group has only recently been examined using a rigorous, phylogenetic methodology that includes many potential outgroups. Knowing the evolutionary relationships of Darwins finches to other birds is important for understanding the context from which this adaptive radiation arose. Here we show that analysis of mitochondrial DNA sequence data from the cytochrome b gene confirm that Darwins finches are monophyletic. In addition, many taxa previously proposed as the sister taxon to Darwins finches can be excluded as their closest living relative. Darwins finches are part of a well‐supported monophyletic group of species, all of which build a domed nest. All but two of the non‐Darwins finches included in this clade occur on Caribbean islands and most are Caribbean endemics. These close relatives of Darwins finches show a diversity of bill types and feeding behaviors similar to that observed among Darwins finches themselves. Recent studies have shown that adaptive evolution in Darwins finches occurred relatively quickly. Our data show that among the relatives of Darwins finches, the evolution of bill diversity was also rapid and extensive.

A PHYLOGENETIC PERSPECTIVE ON THE EVOLUTION OF SEXUAL DICHROMATISM IN TANAGERS (THRAUPIDAE) : THE ROLE OF FEMALE VERSUS MALE PLUMAGE

The evolution of sexual dichromatism in tanagers (family Thraupidae) was studied from a phylogenetic perspective using a molecular‐based phylogeny. Mapping patterns of sexual dimorphism in plumage onto the phylogeny reveals that changes in female plumage occur more frequently than changes in male plumage. Possible explanations for this pattern include sexual selection acting on female plumage and natural selection for background matching. The results of this study and other recent phylogenetic and comparative studies suggest that factors affecting female plumage are important in shaping patterns of sexual dimorphism.

Going to Extremes: Contrasting Rates of Diversification in a Recent Radiation of New World Passerine Birds

Recent analyses suggest that a few major shifts in diversification rate may be enough to explain most of the disparity in diversity among vertebrate lineages. At least one significant increase in diversification rate appears to have occurred within the birds; however, several nested lineages within birds have been identified as hyperdiverse by different studies. A clade containing the finches and relatives (within the avian order Passeriformes), including a large radiation endemic to the New World that comprises ~8% of all bird species, may be the true driver of this rate increase. Understanding the patterns and processes of diversification of this diverse lineage may go a long way toward explaining the apparently rapid diversification rates of both passerines and of birds as a whole. We present the first multilocus phylogenetic analyses of this endemic New World radiation of finch relatives that include sampling of all recognized genera, a relaxed molecular clock analysis of its divergence history, and an analysis of its broad-scale diversification patterns. These analyses recovered 5 major lineages traditionally recognized as avian families, but identified an additional 10 relatively ancient lineages worthy of recognition at the family level. Time-calibrated diversification analyses suggested that at least 3 of the 15 family-level lineages were significantly species poor given the entire groups background diversification rate, whereas at least one-the tanagers of family Thraupidae-appeared significantly more diverse. Lack of an age-diversity relationship within this clade suggests that, due to rapid initial speciation, it may have experienced density-dependent ecological limits on its overall diversity.

A comprehensive multilocus phylogeny for the wood-warblers and a revised classification of the Parulidae (Aves)

The birds in the family Parulidae-commonly termed the New World warblers or wood-warblers-are a classic model radiation for studies of ecological and behavioral differentiation. Although the monophyly of a core wood-warbler clade is well established, no phylogenetic hypothesis for this group has included a full sampling of wood-warbler species diversity. We used parsimony, maximum likelihood, and Bayesian methods to reconstruct relationships among all genera and nearly all wood-warbler species, based on a matrix of mitochondrial DNA (5840 nucleotides) and nuclear DNA (6 loci, 4602 nucleotides) characters. The resulting phylogenetic hypotheses provide a highly congruent picture of wood-warbler relationships, and indicate that the traditional generic classification of these birds recognizes many non-monophyletic groups. We recommend a revised taxonomy in which each of 14 genera (Seiurus, Helmitheros, Mniotilta, Limnothlypis, Protonotaria, Parkesia, Vermivora, Oreothlypis, Geothlypis, Setophaga, Myioborus, Cardellina, Basileuterus, Myiothlypis) corresponds to a well-supported clade; these nomenclatural changes also involve subsuming a number of well-known, traditional wood-warbler genera (Catharopeza, Dendroica, Ergaticus, Euthlypis, Leucopeza, Oporornis, Parula, Phaeothlypis, Wilsonia). We provide a summary phylogenetic hypothesis that will be broadly applicable to investigations of the historical biogeography, processes of diversification, and evolution of trait variation in this well studied avian group.

Phylogenetics and diversification of tanagers (Passeriformes: Thraupidae), the largest radiation of Neotropical songbirds

Thraupidae is the second largest family of birds and represents about 4% of all avian species and 12% of the Neotropical avifauna. Species in this family display a wide range of plumage colors and patterns, foraging behaviors, vocalizations, ecotypes, and habitat preferences. The lack of a complete phylogeny for tanagers has hindered the study of this evolutionary diversity. Here, we present a comprehensive, species-level phylogeny for tanagers using six molecular markers. Our analyses identified 13 major clades of tanagers that we designate as subfamilies. In addition, two species are recognized as distinct branches on the tanager tree. Our topologies disagree in many places with previous estimates of relationships within tanagers, and many long-recognized genera are not monophyletic in our analyses. Our trees identify several cases of convergent evolution in plumage ornaments and bill morphology, and two cases of social mimicry. The phylogeny produced by this study provides a robust framework for studying macroevolutionary patterns and character evolution. We use our new phylogeny to study diversification processes, and find that tanagers show a background model of exponentially declining diversification rates. Thus, the evolution of tanagers began with an initial burst of diversification followed by a rate slowdown. In addition to this background model, two later, clade-specific rate shifts are supported, one increase for Darwins finches and another increase for some species of Sporophila. The rate of diversification within these two groups is exceptional, even when compared to the overall rapid rate of diversification found within tanagers. This study provides the first robust assessment of diversification rates for the Darwins finches in the context of the larger group within which they evolved.

Closely related bird species demonstrate flexibility between beak morphology and underlying developmental programs

The astonishing variation in the shape and size of bird beaks reflects a wide range of dietary specializations that played an important role in avian diversification. Among Darwin’s finches, ground finches (Geospiza spp.) have beaks that represent scaling variations of the same shape, which are generated by alterations in the signaling pathways that regulate growth of the two skeletal components of the beak: the prenasal cartilage (pnc) and the premaxillary bone (pmx). Whether this developmental mechanism is responsible for variation within groups of other closely related bird species, however, has remained unknown. Here, we report that the Caribbean bullfinches (Loxigilla spp.), which are closely related to Darwin’s finches, have independently evolved beaks of a novel shape, different from Geospiza, but also varying from each other only in scaling. However, despite sharing the same beak shape, the signaling pathways and tissues patterning Loxigilla beaks differ among the three species. In Loxigilla noctis, as in Geospiza, the pnc develops first, shaped by Bmp4 and CaM signaling, followed by the development of the pmx, regulated by TGFβIIr, β-catenin, and Dkk3 signaling. In contrast, beak morphogenesis in Loxigilla violacea and Loxigilla portoricensis is generated almost exclusively by the pmx through a mechanism in which Ihh and Bmp4 synergize to promote expansion of bone tissue. Together, our results demonstrate high flexibility in the relationship between morphology and underlying developmental causes, where different developmental programs can generate identical shapes, and similar developmental programs can pattern different shapes.

MOLECULAR PHYLOGENETICS OF THE GENUS PIRANGA: IMPLICATIONS FOR BIOGEOGRAPHY AND THE EVOLUTION OF MORPHOLOGY AND BEHAVIOR

Species in the genus Piranga vary in degree of sexual dimorphism, plumage coloration, morphology, song, migratory patterns, and geographic distribution. To study these aspects of Piranga biology in an evolutionary context, I constructed a phylogeny for this genus using cytochrome-b sequence data. Parsimony and maximum-likelihood analyses of DNA data reveal three possible phylogenies for species in this genus. All three trees iden- tify a clade containing P rubriceps, P leucoptera, and R erythrocephala and a clade containing R rubra, P ludoviciana, R olivacea, R bidentata, and P flava. The trees differ in the placement of R roseogularis. Morphology, song, and plumage data did not agree with these phylogenies. Levels of sequence divergence and the phylogeny of haplotypes are consistent with the idea that P flava as currently described contains more than one evolutionary unit. Mapping the evolution of seasonal migration onto the DNA trees indicates that migration evolved once

PHYLOGEOGRAPHY OF THE CALIFORNIA THRASHER (TOXOSTOMA REDIVIVUM) BASED ON NESTED-CLADE ANALYSIS OF MITOCHONDRIAL-DNA VARIATION

Abstract Distribution of genealogical lineages within a species is likely the result of a complicated series of ecological and historical events. Nested-clade analysis is specifically designed as an objective phylogeographic approach for inferring evolutionary processes on a spatial and temporal scale for small subclades within a larger set of intraspecific relationships. Here, we use nested-clade analysis as well as other phylogeographic methods to investigate the evolutionary history of California Thrasher (Toxostoma redivivum) populations. Inferences resulting from nested clade analysis suggest a history that includes past fragmentation, range expansion, and isolation-by-distance. Along with root information, those inferences enable the construction of a biogeographic scenario for this species involving general southern ancestry, an early north–south division, northward range expansion, and a southward back-expansion into an already populated southern region. Isolation-by-distance is also identified, particularly in southern California, indicating that gene flow between localities does occur but is restricted. Many conclusions drawn from this study are concordant with geologic data as well as phylogeographic scenarios drawn for other codistributed California taxa.

Comparison of Target-Capture and Restriction-Site Associated DNA Sequencing for Phylogenomics: A Test in Cardinalid Tanagers (Aves, Genus: Piranga)

Restriction-site associated DNA sequencing (RAD-seq) and target capture of specific genomic regions, such as ultraconserved elements (UCEs), are emerging as two of the most popular methods for phylogenomics using reduced-representation genomic data sets. These two methods were designed to target different evolutionary timescales: RAD-seq was designed for population-genomic level questions and UCEs for deeper phylogenetics. The utility of both data sets to infer phylogenies across a variety of taxonomic levels has not been adequately compared within the same taxonomic system. Additionally, the effects of uninformative gene trees on species tree analyses (for target capture data) have not been explored. Here, we utilize RAD-seq and UCE data to infer a phylogeny of the bird genus Piranga The group has a range of divergence dates (0.5-6 myr), contains 11 recognized species, and lacks a resolved phylogeny. We compared two species tree methods for the RAD-seq data and six species tree methods for the UCE data. Additionally, in the UCE data, we analyzed a complete matrix as well as data sets with only highly informative loci. A complete matrix of 189 UCE loci with 10 or more parsimony informative (PI) sites, and an approximately 80% complete matrix of 1128 PI single-nucleotide polymorphisms (SNPs) (from RAD-seq) yield the same fully resolved phylogeny of Piranga We inferred non-monophyletic relationships of Piranga lutea individuals, with all other a priori species identified as monophyletic. Finally, we found that species tree analyses that included predominantly uninformative gene trees provided strong support for different topologies, with consistent phylogenetic results when limiting species tree analyses to highly informative loci or only using less informative loci with concatenation or methods meant for SNPs alone.

New insights into New World biogeography: An integrated view from the phylogeny of blackbirds, cardinals, sparrows, tanagers, warblers, and allies

ABSTRACT Understanding the biogeographic origins and temporal sequencing of groups within a region or of lineages within an ecosystem can yield important insights into evolutionary dynamics and ecological processes. Fifty years ago, Ernst Mayr generated comprehensive—if limited—inferences about the origins of the New World avifaunas, including the importance of pre-Isthmian dispersal between North and South America. Since then, methodological advances have improved our ability to address many of the same questions, but the phylogenies upon which such analyses should be based have been incompletely sampled or fragmentary. Here, we report a near-species-level phylogeny of the diverse (~832 species) New World clade Emberizoidea—the group that includes the familiar sparrows, cardinals, blackbirds, wood-warblers, tanagers, and their close relatives—to our knowledge the largest essentially complete (≥95%) phylogenetic hypothesis for any group of organisms. Biogeographic analyses based on this tree suggest initial dispersal into the New World via Beringia, with rapid subsequent diversification, including early dispersal of 1 lineage (the tanagers, Thraupidae) into South America. We found substantial dispersal between North and South America prior to closure of the Isthmus of Panama, but with a notable increase afterward, with a directional bias from north to south. With much greater detail and historical rigor, these analyses largely confirm Mayrs speculations based on taxonomy, resolving outstanding ambiguity regarding the continental origins of some groups such as the Emberizidae and Icteridae. The phylogeny reported here will be a resource of broad utility for addressing additional evolutionary and ecological questions with this diverse group.