Systematics of the Neopelminae (Aves: Passeriformes: Pipridae) with description of a new genus.

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Evolutionary dynamics of the elevational diversity gradient in passerine birds.

Low-elevation regions harbour the majority of the world's species diversity compared to high-elevation areas. This global gradient suggests that lowland species have had more time to diversify, or that net diversification rates have been higher in the lowlands. However, highlands seem to be cradles of diversity as they contain many young endemics, suggesting that their rates of speciation are exceptionally fast.

Dense Geographic and Genomic Sampling Reveals Paraphyly and a Cryptic Lineage in a Classic Sibling Species Complex.

Incomplete or geographically biased sampling poses significant problems for research in phylogeography, population genetics, phylogenetics, and species delimitation. Despite the power of using genome-wide genetic markers in systematics and related fields, approaches such as the multispecies coalescent remain unable to easily account for unsampled lineages. The Empidonax difficilis/Empidonax occidentalis complex of small tyrannid flycatchers (Aves: Tyrannidae) is a classic example of widely distributed species with limited phenotypic geographic variation that was broken into two largely cryptic (or "sibling") lineages following extensive study.

First steps towards assessing the evolutionary history and phylogeography of a widely distributed Neotropical grassland bird (Motacillidae: ).

Grasslands in southern South America are extensive ecosystems which harbor a unique biodiversity; however, studies on the evolution of their taxa are scarce. Here we studied the phylogeography and population history of the Correndera Pipit (), a grassland specialist bird with a large breeding distribution in southern South America, with the goals of investigating its phylogeographic history and relate it to the historical development of South American grasslands. The mitochondrial NADH dehydrogenase subunit II gene (ND2) was sequenced in 66 individuals from 19 localities and the intron 9 of the sex-linked gene for aconitase (ACOI9) was sequenced from a subset of those individuals, including all five subspecies of , as well as the closely related .

Detecting the Dependence of Diversification on Multiple Traits from Phylogenetic Trees and Trait Data.

Species diversification may be determined by many different variables, including the traits of the diversifying lineages. The state-dependent speciation and extinction (SSE) framework contains methods to detect the dependence of diversification on these traits. For the analysis of traits with multiple states, MuSSE (multiple-states dependent speciation and extinction) was developed.

Extensive gene flow characterizes the phylogeography of a North American migrant bird: Black-headed Grosbeak (Pheucticus melanocephalus).

We describe range-wide phylogeographic variation in the Black-headed Grosbeak (Pheucticus melanocephalus), a songbird that is widely distributed across North American scrublands and forests. Phylogenetic analysis of mitochondrial DNA (mtDNA, n=424) revealed three geographically structured clades. One widespread clade occurs throughout the Rocky Mountains, Great Basin, and Mexican Plateau, a second clade is found on the Pacific coast and in coastal ranges; and, a third in the Sierra Madre del Sur of Oaxaca and Guerrero.

High latitudes and high genetic diversity: phylogeography of a widespread boreal bird, the gray jay (Perisoreus canadensis).

We describe range-wide phylogeographic variation in gray jays (Perisoreus canadensis), a boreal Nearctic corvid that occurs today primarily in recently glaciated regions. Phylogenetic analysis of mitochondrial DNA (1041 base pairs ND2 gene; N=205, 50 localities) revealed four reciprocally monophyletic groups. One widespread clade occurs across the North American boreal zone, from Newfoundland to Alaska and southwest into Utah.