Molecular data and distribution dynamics indicate a recent and incomplete separation of manakins species of the genus Antilophia (Aves: Pipridae) in response to Holocene climate change

Abstract

To determine a hypothetical scenario that accounts for the diversification of the two species of the genus Antilophia, we conducted multilocus molecular comparisons and species distribution modeling for the two taxa, which have distinct male plumage coloration patterns and allopatric geographic distributions, despite the high degree of genetic similarity indicated by recent studies. Three mitochondrial and three nuclear fragments were analyzed. The results indicate clear differences in the genetic diversity of the two species, but with ample sharing of haplotypes in all the markers analyzed, reflecting the absence of reciprocal monophyly, presumably due to the relatively recent and still incomplete separation of the two species. The paleoclimatic distribution models, together with the observed genetic profile indicate a recent process of divergence by geographic isolation in the ancestral populations of the two species. This scenario coincides with the recent climatic events of the South American dry diagonal, which involves the gallery forests of the Cerrado biome and the cloud forest enclaves of the seasonal tropical dry forest of the Caatinga between the late Pleistocene and the mid Holocene.

Integrative Taxonomy of Birds: The Nature and Delimitation of Species

“…For instance, Johnson et al (2005) suggested that the Cape Verde Kite Milvus fasciicauda "does not exist," because cytochrome b sequences of that species were nested phylogenetically within those of the Red Kite M. milvus. This ignores not only that these species are still diagnosable by plumage characters (Hazevoet 1995) but also that non-monophyly may simply result from incomplete lineage sorting due to recent speciation-a common phenomenon in bird species (reviewed by Funk and Omland 2003; McKay and Zink 2010) of which new examples are still being discovered (Päckert et al 2012;Luna et al 2017). Appeals to defining criteria will no doubt continue to be made in the taxonomic literature but should be resisted, because it results in unnecessary confusion and instability.…”

Recent chapters of Neotropical history overlooked in phylogeography: Shallow divergence explains phenotype and genotype uncoupling in Antilophia manakins

“…The Araripe manakin differs from the Helmeted manakin by the mostly white—instead of black—male plumage. Intriguingly, despite such a remarkable plumage difference, phylogenetic trees and haplotype networks based on mitochondrial and intron data (Luna et al., ; Rêgo et al., ) did not show clear genetic differentiation between the two species (Figure ). The ranges of these species are embedded in a large stretch of open vegetation ecosystems with poor vertical, but strong horizontal stratification known as the Open Diagonal (from here OD), which includes the relatively humid Cerrado and dry vegetation types of Caatinga .…”

“…Geographic distribution and sampled localities (colour dots) of the Helmeted ( Antilophia galeata ) and Araripe ( Antilophia bokermanni ) manakins (a), sNMF estimates of population structure based on ultraconserved elements (b) and mitochondrial and nuclear haplotype networks from Luna et al., (c). The orange and blue dots represent the sampled localities of the Helmeted and Araripe manakins, respectively.…”

“…Reproduction of the manakin drawings was kindly authorized by the editorial board of the Handbook of birds of the world alive (del Hoyo, Elliott, Sargatal, Christie, & Juana, ). Figure modified from Luna et al., [Colour figure can be viewed at wileyonlinelibrary.com]…”

“…Here, we ask if the Araripe and Helmeted manakins are discernible from each other based on a subgenomic data set, and we explore the demographic history and possible biogeographic events that may have led to the origin of this complex. Building on the work of previous studies (Luna et al., ; Rêgo et al., ), we test two main scenarios (implemented in a series of models) to explain the contrast between the apparent lack of population genetic structure and conspicuous phenotypic divergence in this system. Specifically, we use coalescent simulations to test (a) if the two species are connected by gene flow; under that scenario, observed phenotypic variation could likely be maintained by a small number of loci under selection, which leads to a prediction that even a large SNP data set would be unable to recover neutral population structure matching observed phenotypic variation; and (b) if divergence is too recent for small DNA sequence data sets to detect, despite limited or absent gene flow; here, previous Sanger data sets and our next‐generation sequencing (NGS) data set would differ in their ability to identify population structure driven by neutral processes, leading to the prediction that only a large SNP data set would recover population structure matching phenotypic variation.…”