Recent genomic analyses of evolutionary radiations suggest that ancestral or standing genetic variation may facilitate rapid diversification, particularly in cases involving convergence in ecological traits. Likewise, lateral transfer of alleles via hybridization may also facilitate adaptive convergence, but little is known about the role of ancestral variation in examples of explosive diversification that primarily involve the evolution of species recognition traits. Here, we show that genomic regions distinguishing sympatric species in an extraordinary radiation of small finches called munias (genus Lonchura) have phylogenetic histories that are discordant with each other, with the overall pattern of autosomal differentiation among species, and with sex-linked and mitochondrial components of the genome. Genome-wide data for 11 species sampled in Australia and Papua New Guinea indicate substantial autosomal introgression between sympatric species, but also identify a limited number of divergent autosomal regions, several of which overlap known colour genes (ASIP, EDN3, IGSF11, KITLG, MC1R and SOX10). Phylogenetic analysis of these outlier regions shows that different munia species have acquired unique combinations of alleles across a relatively small set of phenotypically relevant genes. Our results demonstrate that the recombination of ancestral genetic variation across multiple loci may be an important mechanism for generating phenotypic novelty and diversity.

Parasites that exploit multiple hosts often experience diversifying selection for host-specific adaptations. This can result in multiple strains of host specialists coexisting within a single parasitic species. A long-standing conundrum is how such sympatric host races can be maintained within a single parasitic species in the face of interbreeding among conspecifics specializing on different hosts. Striking examples are seen in certain avian brood parasites such as cuckoos, many of which show host-specific differentiation in traits such as host egg mimicry. Exploiting a Zambian egg collection amassed over several decades and supplemented by recent fieldwork, we show that the brood parasitic Greater Honeyguide Indicator indicator exhibits host-specific differentiation in both egg size and egg shape. Genetic analysis of honeyguide eggs and chicks show that two highly divergent mitochondrial DNA lineages are associated with ground-and tree-nesting hosts, respectively, indicating perfect fidelity to two mutually exclusive sets of host species for millions of years. Despite their age and apparent adaptive diversification, however, these ancient lineages are not cryptic species; a complete lack of differentiation in nuclear genes shows that mating between individuals reared by different hosts is sufficiently frequent to prevent speciation. These results indicate that host specificity is maternally inherited, that host-specific adaptation among conspecifics can be maintained without reproductive isolation, and that host specificity can be remarkably ancient in evolutionary terms.coevolution | gentes | phylogeography | W chromosome hypothesis S pecies interactions can be powerful generators of evolutionary diversity (1, 2). In host-parasite relationships, different hosts can exert divergent selection for parasitic specialization. Although this sometimes results in speciation in the parasitic lineage (3-5), in other cases multiple strains of host specialists coexist within a single parasitic species. A textbook example is seen in avian brood parasites such as cuckoos, in which the individuals of a single parasitic species specialize on different hosts and show phenotypic differentiation in traits such as host egg mimicry (6, 7). How phenotypically distinct host races [also known as "gentes" in the context of avian brood parasitism (8)] can evolve and be maintained over evolutionary time in the face of interbreeding among conspecifics has long remained paradoxical (9-12).Genetic data have provided important insights by allowing a test of whether lineages of parasitic females consistently specialize on particular host species. Studies of the common cuckoo Cuculus canorus (13) and the shiny cowbird Molothrus bonariensis (14), both of which show host-specific phenotypic differentiation in egg traits (7, 15), have revealed subtle genetic differentiation in mitochondrial DNA (mtDNA) haplotype frequencies in relation to host use. These results are potentially consistent with the long-standing hypothesis that egg mimicry might ...

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Gloger’s rule is a classic ecogeographical principle that, in its simplest version, predicts animals should be darker in warmer and wetter climates. In a rarely tested more complex version, it also predicts animals should be more rufous in warmer and drier climates. The Variable Antshrike (Thamnophilus caerulescens) is a widely distributed South American passerine that presents an impressive amount of plumage color variation and occupies a wide variety of climatic conditions. Moreover, genetic and vocal evidence indicate ongoing hybridization in south-central Bolivia among 3 populations with very distinct plumages. We collected color data from 232 specimens from throughout this species’ distribution to test the predictions of Gloger’s rule. We found a negative correlation between brightness and precipitation, consistent with the simple version of Gloger’s rule. In contrast, we found that birds were darker in cooler climates, contrary to the simple version of Gloger’s rule, but consistent with recent findings in other taxa. We found support for both predictions of the complex Gloger’s rule and suggest it might be driven by background matching. We conclude by concurring with a recent suggestion that the simple version of Gloger’s rule should be reformulated exclusively in terms of humidity.