Diversity indices, particularly the Shannon-Wiener index, have extensively been used in analyzing patterns of diversity at different geographic and ecological scales. These indices have serious conceptual and statistical problems which make comparisons of species richness or species abundances across communities nearly impossible. There is often no a single statistical method that retains all information needed to answer even a simple question. However, multivariate analyses could be used instead of diversity indices, such as cluster analyses or multiple regressions. More complex multivariate analyses, such as Canonical Correspondence Analysis, provide very valuable information on environmental variables associated to the presence and abundance of the species in a community. in addition, particular hypotheses associated to changes in species richness across localities, or change in abundance of one, or a group of species can be tested using univariate, bivariate, and/or rarefaction statistical tests. The rarefaction method has proved to be robust to standardize all samples to a common size. Even the simplest method as reporting the number of species per taxonomic category possibly provides more information than a diversity index value. Rev. Biol.

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After establishing secondary contact, recently diverged populations may remain reproductively isolated or hybridize to a varying extent depending on factors such as hybrid fitness and the strength of assortative mating. Replicated contact zones between hybridizing taxa offer a unique opportunity to explore how different factors interact to shape patterns of hybridization. Here, we used genomic and phenotypic data from three independent contact zones between subspecies of the Variable Seedeater (Sporophila corvina), to examine how coloration and genetic divergence shape patterns of hybridization. We found that plumage coloration has limited introgression across contact zones, but the degree of plumage divergence does not explain overall patterns of introgression. Across two parallel contact zones between populations with divergent phenotypes (entirely black vs. pied plumage) populations hybridized extensively across one contact zone but not the other, suggesting that plumage divergence is not sufficient to maintain reproductive isolation. Where subspecies hybridized, hybrid zones were wide and formed by later-generation hybrids, suggesting that hybrids present similar or higher fitness than parental subspecies. Moreover, contemporary gene flow has played an important role in shaping patterns of genetic diversity between populations. Overall, our results demonstrate that divergence in plumage coloration is important in reducing gene flow but insufficient in maintaining reproductive isolation in this clade, and that other factors such as divergence in song and time since secondary contact may also play an important role in driving patterns of reduced hybridization and gene flow.

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Black plumage is expected to absorb and retain more heat and provide better protection against UV radiation compared with lighter plumages. Black plumage is common in species of the genera Turdus and Platycichla that inhabit highlands across different regions of the world. Considering this geographical recurrent pattern we tested the hypothesis that black plumage in these two genera has evolved as a co‐adaptive response to inhabiting highlands, reconstructing ancestral character states for plumage and altitudinal distribution using maximum‐likelihood methods, and a Pagel's multistate discrete method. For these analyses, we used a phylogeny based on mitochondrial and nuclear DNA regions that included 60 of the 66 recognized species in the genera Turdus and Platycichla. We found that black‐plumage coloration evolved independently on eight occasions within these two genera, and species with black plumage occur more often at highlands. Our results support the hypothesis that black‐plumage is adaptative in highlands; but, studies in other bird groups with black‐plumage inhabiting at the same elevations will provide evidence for this adaptive hypothesis or if the evolution of black‐plumage in other groups is explained by other evolutionary forces.

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