BackgroundThe Neotropical avifauna is more diverse than that of any other biogeographic region, but our understanding of patterns of regional divergence is limited. Critical examination of this issue is currently constrained by the limited genetic information available. This study begins to address this gap by assembling a library of mitochondrial COI sequences, or DNA barcodes, for Argentinian birds and comparing their patterns of genetic diversity to those of North American birds.Methodology and Principal FindingsFive hundred Argentinian species were examined, making this the first major examination of DNA barcodes for South American birds. Our results indicate that most southern Neotropical bird species show deep sequence divergence from their nearest-neighbour, corroborating that the high diversity of this fauna is not based on an elevated incidence of young species radiations. Although species ages appear similar in temperate North and South American avifaunas, patterns of regional divergence are more complex in the Neotropics, suggesting that the high diversity of the Neotropical avifauna has been fueled by greater opportunities for regional divergence. Deep genetic splits were observed in at least 21 species, though distribution patterns of these lineages were variable. The lack of shared polymorphisms in species, even in species with less than 0.5M years of reproductive isolation, further suggests that selective sweeps could regularly excise ancestral mitochondrial polymorphisms.ConclusionsThese findings confirm the efficacy of species delimitation in birds via DNA barcodes, even when tested on a global scale. Further, they demonstrate how large libraries of a standardized gene region provide insight into evolutionary processes.

A fundamental question in evolutionary genetics concerns the extent to which adaptive phenotypic convergence is attributable to convergent or parallel changes at the molecular sequence level. Here we report a comparative analysis of hemoglobin (Hb) function in eight phylogenetically replicated pairs of high- and low-altitude waterfowl taxa to test for convergence in the oxygenation properties of Hb, and to assess the extent to which convergence in biochemical phenotype is attributable to repeated amino acid replacements. Functional experiments on native Hb variants and protein engineering experiments based on site-directed mutagenesis revealed the phenotypic effects of specific amino acid replacements that were responsible for convergent increases in Hb-O2 affinity in multiple high-altitude taxa. In six of the eight taxon pairs, high-altitude taxa evolved derived increases in Hb-O2 affinity that were caused by a combination of unique replacements, parallel replacements (involving identical-by-state variants with independent mutational origins in different lineages), and collateral replacements (involving shared, identical-by-descent variants derived via introgressive hybridization). In genome scans of nucleotide differentiation involving high- and low-altitude populations of three separate species, function-altering amino acid polymorphisms in the globin genes emerged as highly significant outliers, providing independent evidence for adaptive divergence in Hb function. The experimental results demonstrate that convergent changes in protein function can occur through multiple historical paths, and can involve multiple possible mutations. Most cases of convergence in Hb function did not involve parallel substitutions and most parallel substitutions did not affect Hb-O2 affinity, indicating that the repeatability of phenotypic evolution does not require parallelism at the molecular level.

Selection acted repeatedly on regions that may regulate the expression of genes underlying coloration differences in seedeaters.

We assessed relationships between acoustic frequency, body mass, and habitat in tinamous. This monophyletic group of primitive birds comprises c. 47 ground dwelling species whose habitats range from dense humid forest to open grasslands. The relationship between frequency and body mass was found to be negative, while the songs of open‐habitat species exhibited higher frequencies and a wider bandwidth than the closed‐habitat ones. Residual variation in song frequency, after controlling for the effect of body mass and phylogeny, tends to differ among habitats. However, a statistical test of this pattern was not possible because of the existence of only five pairs of sister species differing in habitat. In spite of this, positive contrasts of bandwidth were associated with positive contrasts of habitat, confirming that songs of open‐habitat species have a wider bandwidth than those of their more closed habitat relatives. © 2002 The Linnean Society of London, Biological Journal of the Linnean Society, 2002, 77, 423–430.

Adaptive radiations have helped shape how we view animal speciation, particularly classic examples such as Darwin's finches, Hawaiian fruitflies and African Great Lakes cichlids. These 'island' radiations are comparatively recent, making them particularly interesting because the mechanisms that caused diversification are still in motion. Here, we identify a new case of a recent bird radiation within a continentally distributed species group; the capuchino seedeaters comprise 11 Sporophila species originally described on the basis of differences in plumage colour and pattern in adult males. We use molecular data together with analyses of male plumage and vocalizations to understand species limits of the group. We find marked phenotypic variation despite lack of mitochondrial DNA monophyly and few differences in other putatively neutral nuclear markers. This finding is consistent with the group having undergone a recent radiation beginning in the Pleistocene, leaving genetic signatures of incomplete lineage sorting, introgressive hybridization and demographic expansions. We argue that this apparent uncoupling between neutral DNA homogeneity and phenotypic diversity is expected for a recent group within the framework of coalescent theory. Finally, we discuss how the ecology of open habitats in South America during the Pleistocene could have helped promote this unique and ongoing radiation.

Much of our knowledge of the evolution of reproductive isolation comes from studies of Drosophila . This body of work has revealed the following patterns: (1) reproductive isolation increases with phylogenetic distance between hybridizing species; (2) reproductive isolation is greater between sympatric than allopatric species with the same level of divergence; and (3) hybrid crosses conform to Haldane's rule. We tested for the existence of these patterns in ducks (subfamily Anatinae, sensu Livezey, 1997b) based on 1037 hybrids of known parentage. Our analyses of the number of interspecific crosses in relation to phylogenetic distance found a significant deviation between the observed and expected distribution of crosses controlling for the topology of the Anatinae phylogeny. In particular, we found both an excess of hybrid crosses among closely related species and a scarcity among distantly related species. The number of hybrid males also decreased with increasing phylogenetic distance between parental species, although the number of hybrid females remained low and constant. Sympatric species produced higher numbers of hybrid males than allopatric ones, despite no difference in phylogenetic distance among parental species in compared groups. The number of hybrid males exceeded the number of hybrid females, consistent with Haldane's rule. This was evident even though the analysis was restricted to a reduced set of phylogenetically independent crosses. However, the pattern was no longer significant after correction for the number of hybrid males by the male-biased sex ratio of adult ducks.

Abstract. The study of the patterns of reproductive isolation in relation to species divergence is critical for the understanding of the process of speciation. Comparative analyses of this kind were previously conducted in Drosophila, Lepidoptera, frogs, ducks, and birds in general. In the present study, we used information from the literature to analyze hybrid inviability in relation to species divergence in pigeons and doves. Four main patterns arose from this analysis:(1) as in the other groups studied, F 1 hybrid inviability gradually increases as species diverge, the time needed to reach total inviability being higher in birds than in the other groups; (2) as expected, the presence of geographic overlap does not influence the evolution of postzygotic isolation; (3) the percentage of unhatched eggs does not differ between hybrids of the first generation and the backcrosses, but it increases in the second hybrid generation; and (4) pigeons and doves follow Haldane's rule, as found in the other groups studied so far. The similarity between the results of this and previous studies contributes to the growing evidence suggesting that the patterns of the evolution of postzygotic isolation, and the process of speciation in general, are shared among animal groups.

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