Origin and cross-century dynamics of an avian hybrid zone.

BACKGROUND: Characterizations of the dynamics of hybrid zones in space and time can give insights about traits and processes important in population divergence and speciation. We characterized a hybrid zone between tanagers in the genus Ramphocelus (Aves, Thraupidae) located in southwestern Colombia. We evaluated whether this hybrid zone originated as a result of secondary contact or of primary differentiation, and described its dynamics across time using spatial analyses of molecular, morphological, and coloration data in combination with paleodistribution modeling. RESULTS: Models of potential historical distributions based on climatic data and genetic signatures of demographic expansion suggested that the hybrid zone likely originated following secondary contact between populations that expanded their ranges out of isolated areas in the Quaternary. Concordant patterns of variation in phenotypic characters across the hybrid zone and its narrow extent are suggestive of a tension zone, maintained by a balance between dispersal and selection against hybrids. Estimates of phenotypic cline parameters obtained using specimens collected over nearly a century revealed that, in recent decades, the zone appears to have moved to the east and to higher elevations, and may have become narrower. Genetic variation was not clearly structured along the hybrid zone, but comparisons between historical and contemporary specimens suggested that temporal changes in its genetic makeup may also have occurred. CONCLUSIONS: Our data suggest that the hybrid zone likey resulted from secondary contact between populations. The observed changes in the hybrid zone may be a result of sexual selection, asymmetric gene flow, or environmental change.

Variation in positively selected major histocompatibility complex class I loci in rufous-collared sparrows (Zonotrichia capensis).

The major histocompatibility complex (MHC) is a highly variable family of genes involved in parasite recognition and the initiation of adaptive immune system responses. Variation in MHC loci is maintained primarily through parasite-mediated selection or disassortative mate choice. To characterize MHC diversity of rufous-collared sparrows (Zonotrichia capensis), an abundant South American passerine, we examined allelic and nucleotide variation in MHC class I exon 3 using pyrosequencing. Exon 3 comprises a substantial portion of the peptide-binding region (PBR) of class I MHC and thus plays an important role in intracellular pathogen defense. We identified 98 putatively functional alleles that produce 56 unique protein sequences across at least 6 paralogous loci. Allelic diversity per individual and exon-wide nucleotide diversity were relatively low; however, we found specific amino acid positions with high nucleotide diversity and signatures of positive selection (elevated d N /d S ) that may correspond to the PBR. Based on the variation in physicochemical properties of amino acids at these "positively selected sites," we identified ten functional MHC supertypes. Spatial variation in nucleotide diversity and the number of MHC alleles, proteins, and supertypes per individual suggests that environmental heterogeneity may affect patterns of MHC diversity. Furthermore, populations with high MHC diversity have higher prevalence of avian malaria, consistent with parasite-mediated selection on MHC. Together, these results provide a framework for subsequent investigations of selective agents acting on MHC in Z. capensis.

Reconstructing the phylogeny of "Buarremon" brush-finches and near relatives (Aves, Emberizidae) from individual gene trees.

Gene trees are often assumed to be equivalent to species trees, but processes such as incomplete lineage sorting can generate incongruence among gene topologies and analyzing multilocus data in concatenated matrices can be prone to systematic errors. Accordingly, a variety of new methods have been developed to estimate species trees using multilocus data sets. Here, we apply some of these methods to reconstruct the phylogeny of Buarremon and near relatives, a group in which phylogenetic analyses of mitochondrial DNA sequences produced results that were inconsistent with relationships implied by a taxonomy based on variation in external phenotype. Gene genealogies obtained for seven loci (one mitochondrial, six nuclear) were varied, with some supporting and some rejecting the monophyly of Buarremon. Overall, our species-tree analyses tended to support a monophyletic Buarremon, but due to lack of congruence between methodologies, resolution of the phylogeny of this group remains uncertain. More generally, our study indicates that the number of individuals sampled can have an important effect on phylogenetic reconstruction, that the use of seven markers does not guarantee obtaining a strongly-supported species tree, and that methods for species-tree reconstruction can produce different results using the same data; these are important considerations for researchers using these new phylogenetic approaches in other systems.

Phylogenetic conservatism and antiquity of a tropical specialization: army-ant-following in the typical antbirds (Thamnophilidae).

One of the most novel foraging strategies in Neotropical birds is army-ant-following, in which birds prey upon arthropods and small vertebrates flushed from the forest floor by swarm raids of the army-ant Eciton burchellii. This specialization is most developed in the typical antbirds (Thamnophilidae) which are divisible into three specialization categories: (1) those that forage at swarms opportunistically as army-ants move through their territories (occasional followers), (2) those that follow swarms beyond their territories but also forage independently of swarms (regular followers), and (3) those that appear incapable of foraging independently of swarms (obligate followers). Although army-ant-following is one of the great spectacles of tropical forests, basic questions about its evolution remain unaddressed. Using a strongly resolved molecular phylogeny of the typical antbirds, we found that army-ant-following is phylogenetically conserved, with regular following having evolved only three times, and that the most likely evolutionary progression was from least (occasional) to more (regular) to most (obligate) specialized, with no reversals from the obligate state. Despite the dependence of the specialists on a single ant species, molecular dating indicates that army-ant-following has persisted in antbirds since the late Miocene. These results provide the first characterization of army-ant-following as an ancient and phylogenetically conserved specialization.