Summary: 1. Methods that assess patterns of phylogenetic relatedness, as well as character distribution and evolution, allow one to infer the ecological processes involved in community assembly. Assuming niche conservatism, assemblages should shift from phylogenetic clustering to evenness with decreasing geographic scale because the relative importance of mechanisms that shape assemblages is hypothesized to be scale‐dependent. Whereas habitat filtering is more likely to act at regional scales because of increased habitat heterogeneity that allows sorting of ecologically similar species in contrasting environments, competition is more likely to act at local scales because low habitat heterogeneity provides few opportunities for niche partitioning. 2. We used species lists to assess assemblage composition, data on ecologically‐relevant traits, and a molecular phylogeny, to examine the phylogenetic structure of antbird (Thamnophilidae) assemblages at three different geographical scales: regional (ecoregions), intermediate (100‐ha plots) and local (mixed‐flocks). In addition, we used patterns of phylogenetic beta diversity and beta diversity to separate the factors that structure antbird assemblages at regional scales. 3. Contrary to previous findings, we found a shift from phylogenetic evenness to clustering with decreasing geographical scale. We argue that this does not reject the hypothesis that habitat filtering is the predominant force in regional community assembly, because analyses of trait evolution and structure indicated a lack of niche conservatism in antbirds. 4. In some cases, phylogenetic evenness at regional scales can be an effect of historical biogeographic processes instead of niche‐based processes. However, regional patterns of beta diversity and phylogenetic beta diversity suggested that phylogenetic structure in our study cannot be explained by the history of speciation and dispersal of antbirds, further supporting the habitat‐filtering hypothesis. 5. Our analyses suggested that competitive interactions might not play an important role locally, which would provide a plausible explanation for the high alpha diversity of antbirds in Amazonia. 6. Finally, we emphasize the importance of including trait information in studies of phylogenetic community structure to adequately assess the mechanisms that determine species co‐existence.

Phylogenetic relationships among the Tyrannides were assessed using over 4000 base pairs of nuclear recombination activating 1 (RAG-1) and 2 (RAG-2) DNA sequence data from about 93% of all described genera, which represents the most complete assessment of relationships for this diverse New World radiation to date. With this sampling we propose a significantly expanded interpretation of higher-level relationships within the group. The Tyrannides are shown to be comprised of six major lineages, all of which represent traditional family-level taxa (sensu Fitzpatrick, 2004a and Snow, 2004a,b ; del Hoyo et al., 2004 ): (i) manakins (Pipridae); (ii) cotingas (Cotingidae); (iii) the sharpbill (Oxyruncus) + onychorhynchine flycatchers (Onychorhynchini); (iv) tityrines (Tityridae); (v) rhynchocycline flycatchers (Rhynchocyclidae); and (vi) the tyrant flycatchers (Tyrannidae). In addition, the RAG data recovered isolated lineages with uncertain relationships, including Neopipo, Platyrinchus, Piprites, and Tachuris. The Pipridae are the sister-group to all the other Tyrannides. Within the latter, the clade ((Oxyruncidae + Tityridae) + Cotingidae) is the sister-group of the Tyrannoidea. Within the Tyrannoidea, the Rhynchocyclidae and their allies are sisters to Neopipo + Tyrannidae. Using our phylogenetic hypothesis, we propose the first comprehensive phylogenetic classification that attempts to achieve isometry between the tree and a classification scheme using subordination and phyletic sequencing. This study thus provides a phylogenetic framework for understanding the evolution of this diverse New World assemblage, and identifies many avenues for further systematic study. © The Willi Hennig Society 2009.

The infraorder Furnariides is a diverse group of suboscine passerine birds comprising a substantial component of the Neotropical avifauna. The included species encompass a broad array of morphologies and behaviours, making them appealing for evolutionary studies, but the size of the group (ca. 600 species) has limited well‐sampled higher‐level phylogenetic studies. Using DNA sequence data from the nuclear RAG‐1 and RAG‐2 exons, we undertook a phylogenetic analysis of the Furnariides sampling 124 (more than 88%) of the genera. Basal relationships among family‐level taxa differed depending on phylogenetic method, but all topologies had little nodal support, mirroring the results from earlier studies in which discerning relationships at the base of the radiation was also difficult. In contrast, branch support for family‐rank taxa and for many relationships within those clades was generally high. Our results support the Melanopareidae and Grallariidae as distinct from the Rhinocryptidae and Formicariidae, respectively. Within the Furnariides our data contradict some recent phylogenetic hypotheses and suggest that further study is needed to resolve these discrepancies. Of the few genera represented by multiple species, several were not monophyletic, indicating that additional systematic work remains within furnariine families and must include dense taxon sampling. We use this study as a basis for proposing a new phylogenetic classification for the group and in the process erect new family‐group names for clades having high branch support across methods.

We compared mitochondrial DNA sequences of portions of the cytochrome b (cyt b) and the NADH dehydrogenase subunit 2 (ND2) genes from samples of ten bird species that occur in both extremes of the Cerrado region (eastern Bolivia and Amapá, Brazil). The species include a wide sampling of taxa from several avian families: Tinamidae (1), Apodidae (1), Dendrocolaptidae (1), Furnariidae (1), Thamnophilidae (1), Tyrannidae (1), Turdidae (1), and Emberizidae (3). The taxa also exhibit a variety of distribution patterns in Neotropical open lands. Levels of genetic divergence within all taxa were low compared to comparable intraspecific values in many other widespread birds. In particular, these data suggest that there is much less genetic differentiation within these Cerrado birds than exists in birds of neighboring Amazonian forest. We suggest this implies the non-mutually exclusive possibilities that these open country birds have maintained higher levels of gene flow than forest understory birds, and that the Cerrado may have expanded to parts of its present-day distribution fairly rapidly. These data also suggest that hypothesized forest connections between Amazonia and Atlantic forest did not isolate open country bird populations from one another to a great extent.