Geographic drivers of avian diversification in the Philippine archipelago

I investigate the relative roles of different classes of geographical barriers in the diversification of the Philippine avifauna, by inferring the evolutionary relationships of 20 avian groups with DNA sequence data. In chapter one, I reconstruct the historical biogeography of the Aethopyga sunbirds. In chapter two, I examine the distribution of genetic variation and plumage patterns in Robsonius ground-warblers, and described a new species. In chapter 3, I reconstruct the evolutionary history and ecological niches of eight co-distributed polytypic species of Philippine birds, and infer that a paleoclimate barrier dove diversification. In chapter four, I use molecular markers and plumage characters to reassess conservative species limits in 19 avian species or species groups in the Mindanao Island group of the Philippines. In addition to permanent marine barriers, long understood to isolate insular lineages, I provide evidence that periodic marine barriers, periodic climatic barriers, and complex topography isolate and promote diversification in Philippine birds. Populations inhabiting island groups (bounded by deep-water barriers) are frequently paraphyletic, contrary to the perception that deep-water barriers are the most important geographic isolating feature in insular systems. I document two small avian radiations, the Robsonius in Luzon, and Aethopyga in Mindanao, are exceptions to the paradigm that birds do not diversify within single islands. Congruence of molecular markers and plumage characters support that avian taxonomy in the Philippines is extremely conservative, and most Philippines species would be more appropriately treated as sets of allopatric evolutionary lineages, rather than widespread polytypic species

A Molecular Phylogeny of Black-Tyrants (Tyrannidae: Knipolegus) Reveals Strong Geographic Patterns and Homoplasy in Plumage and Display Behavior

This is the Publisher's version, also available from http://www.bioone.org/doi/abs/10.1525/auk.2012.11101.We present the first molecular phylogenetic hypothesis for Knipolegus (black-tyrants), a widespread genus of South American tyrant-flycatchers, based on nuclear and mitochondrial DNA sequences. Bayesian and maximum-likelihood analyses support three clades within Knipolegus, one confined to northern South America, one confined to southeast Brazil, and one confined to the Southern Cone and southern Andes. Within each clade, two or more species are broadly sympatric or parapatric, overlapping in general distribution but differing in habitat specialization. Maximum-likelihood ancestral state reconstructions using an equal-rate stochastic model support a single origin of austral migration in the southern group. Contrasting with these strong geographic patterns, ancestral state reconstructions of plumage and display evolution were more complex, with multiple inferred character-state changes. Ancestral state reconstructions suggest a sexually dimorphic ancestor of Knipolegus, and sexually similar plumages are the result of three independent character-state changes: one in male plumage and two in female plumage. Ancestral state reconstructions support the conclusion that flight displays with mechanical sounds originated in the Knipolegus ancestor, and loss of mechanical sounds in flight displays occurred twice

Birds (Aves), Serrania Sadiri, Parque Nacional Madidi, Depto. La Paz, Bolivia

We surveyed the Serrania Sadiri for birds at elevations between 500-950m for a combined total of 15 days in three different months. The area surveyed was along the Tumupasa/San Jose de Uchupiamones trail at the edge of Parque Nacional Madidi in Depto. La Paz, Bolivia. We report observations of 231 species of birds detected by sight and sound, including many outlying ridge specialists. We report and present photographs of a new species for Depto. La Paz (Caprimulgis nigrescens), the second Bolivian localities for Porphyrolaema prophyrolae ereicapillus, and Basileuterus chrysogaster, and five new species records for Parque Nacional Madidi

Rethinking phylogeographic structure and historical refugia in the rufous-capped babbler Cyanoderma ruficeps in light of range-wide genetic sampling and paleodistributional reconstructions

Combining ecological niche modeling with phylogeography has become a popular approach to understand how historical climate changes have created and maintained population structure. However, methodological choices in geographic extents and environmental layer sets employed in modeling may affect results and interpretations profoundly. Here, we infer range-wide phylogeographic structure and model ecological niches of Cyanoderma ruficeps, and compare results to previous studies that examined this species across mainland China and Taiwan only. Use of dense taxon sampling of closely related species as outgroups question C. ruficeps monophyly. Furthermore, previously unsampled C. ruficeps populations from central Vietnam were closely related to disjunct western populations (Nepal, Tibet, Myanmar, Yunnan), rather than to geographically proximate populations in northern Vietnam and eastern China. Phylogeographic structure is more complex than previously appreciated; niche model projections to Last Glacial Maximum climate scenarios identified larger areas of suitable conditions than previous studies, but potential distributional limits differed markedly between climate models employed and were dependent upon interpretation of non-analogous historical climate scenarios. Previously identified population expansion across central China may result from colonization from refugial distributions during the Last Interglacial, rather than the Last Glacial Maximum, as previously understood

La Filogeografía de Robsonius (Passeriformes: Locustellidae) Revela una Especie No Descripta del Noreste de Luzón, Filipinas

This is the publisher's version, also available electronically from http://www.bioone.org/doi/abs/10.1525/cond.2013.120124The Robsonius ground-warblers are forest birds endemic to the Luzon Island complex in the Philippine archipelago. Their systematic relationships have long remained ambiguous; until recently they were included in the timaliid genus Napothera. Two Robsonius species are currently recognized on the basis of plumage differences: R. rabori from northern Luzon in the Cordillera Central and the northern Sierra Madre, and R. sorsogonensis from southern Luzon and Catanduanes Island. Recent specimen collections, including the first adult specimen from the Cordillera Central, establish plumage differences between populations of R. rabori in the Cordillera Central and Sierra Madre and reveal a third diagnosable population within Luzon. These differences have gone unnoticed because R. rabori (sensu stricto) had been known only from the juvenile holotype. Molecular phylogenetic data further support the hypothesis that three highly divergent taxa occur across the Luzon Island complex: Robsonius rabori is known only from the northern Cordillera Central in Ilocos Norte; an undescribed taxon (formerly included in R. rabori) occurs in the northern Sierra Madre in Cagayan, Isabela, Aurora, and Nueva Vizcaya provinces; and R. sorsogonensis occurs in southern Luzon (Bulacan and Laguna provinces), the Bicol Peninsula, and on Catanduanes Island. The existence of three putatively allopatric species within the Luzon island complex highlights the role of in situ diversification in island systems, and brings attention to the need for forest conservation to protect geographically restricted populations throughout the Luzon Island complex

A genome-wide assessment of stages of elevational parapatry in Bornean passerine birds reveals no introgression: implications for processes and patterns of speciation

Topographically complex regions often contain the close juxtaposition of closely related species along elevational gradients. The evolutionary causes of these elevational replacements, and thus the origin and maintenance of a large portion of species diversity along elevational gradients, are usually unclear because ecological differentiation along a gradient or secondary contact following allopatric diversification can produce the same pattern. We used reduced representation genomic sequencing to assess genetic relationships and gene flow between three parapatric pairs of closely related songbird taxa (Arachnothera spiderhunters, Chloropsis leafbirds, and Enicurus forktails) along an elevational gradient in Borneo. Each taxon pair presents a different elevational range distribution across the island, yet results were uniform: little or no gene flow was detected in any pairwise comparisons. These results are congruent with an allopatric “species-pump” model for generation of species diversity and elevational parapatry of congeners on Borneo, rather than in situ generation of species by “ecological speciation” along an elevational gradient

Tectonic collision and uplift of Wallacea triggered the global songbird radiation

Songbirds (oscine passerines) are the most species-rich and cosmopolitan bird group, comprising almost half of global avian diversity. Songbirds originated in Australia, but the evolutionary trajectory from a single species in an isolated continent to worldwide proliferation is poorly understood. Here, we combine the first comprehensive genome-scale DNA sequence data set for songbirds, fossil-based time calibrations, and geologically informed biogeographic reconstructions to provide a well-supported evolutionary hypothesis for the group. We show that songbird diversification began in the Oligocene, but accelerated in the early Miocene, at approximately half the age of most previous estimates. This burst of diversification occurred coincident with extensive island formation in Wallacea, which provided the first dispersal corridor out of Australia, and resulted in independent waves of songbird expansion through Asia to the rest of the globe. Our results reconcile songbird evolution with Earth history and link a major radiation of terrestrial biodiversity to early diversification within an isolated Australian continent

Acknowledging uncertainty in evolutionary reconstructions of ecological niches

Reconstructing ecological niche evolution can provide insight into the biogeography and diversification of evolving lineages. However, comparative phylogenetic methods may infer the history of ecological niche evolution inaccurately because (a) species' niches are often poorly characterized; and (b) phylogenetic comparative methods rely on niche summary statistics rather than full estimates of species' environmental tolerances. Here, we propose a new framework for coding ecological niches and reconstructing their evolution that explicitly acknowledges and incorporates the uncertainty introduced by incomplete niche characterization. Then, we modify existing ancestral state inference methods to leverage full estimates of environmental tolerances. We provide a worked empirical example of our method, investigating ecological niche evolution in the New World orioles (Aves: Passeriformes: Icterus spp.). Temperature and precipitation tolerances were generally broad and conserved among orioles, with niche reduction and specialization limited to a few terminal branches. Tools for performing these reconstructions are available in a new R package called nichevol

Acknowledging uncertainty in evolutionary reconstructions of ecological niches

Reconstructing ecological niche evolution can provide insight into the biogeography and diversification of evolving lineages. However, comparative phylogenetic methods may infer the history of ecological niche evolution inaccurately because (a) species' niches are often poorly characterized; and (b) phylogenetic comparative methods rely on niche summary statistics rather than full estimates of species' environmental tolerances. Here, we propose a new framework for coding ecological niches and reconstructing their evolution that explicitly acknowledges and incorporates the uncertainty introduced by incomplete niche characterization. Then, we modify existing ancestral state inference methods to leverage full estimates of environmental tolerances. We provide a worked empirical example of our method, investigating ecological niche evolution in the New World orioles (Aves: Passeriformes: Icterus spp.). Temperature and precipitation tolerances were generally broad and conserved among orioles, with niche reduction and specialization limited to a few terminal branches. Tools for performing these reconstructions are available in a new R package called nichevol