Multilocus data of a manakin species reveal cryptic diversification moulded by vicariance

Abstract

We used molecular tools and a multilocus approach to investigate the phylogeography of Lepidothrix coronata across most of its ample range. We sequenced six DNA fragments to produce phylogenies, molecular dating estimates, analyses of the dynamics of the demographic history of the species and a biogeographic analysis to estimate the events and changes in the ancestral distribution of the species. The results indicated the presence of four well‐established lineages, with high levels of divergence. These lineages are delineated by well‐defined geographic barriers, with one lineage, restricted to the west of the Andes, being the first to diverge from the complex. The other three lineages are exclusive to the Amazonian distribution of the species, with two being found north of the Amazon River, and the third, south of the Amazon. Some of the relationships found between these lineages were distinct from those described in previous studies. Important disagreements were found between the mtDNA phylogeny and that of the multilocus analysis, in relation to the lineages located to the west of the Andes. We propose that past introgression events may have influenced shifts in the relationships between lineages, despite the fact that the groups were well defined in both the phylogenies. The biogeographic analysis indicates that the lineages arose through successive vicariance events, which had a primary role in the diversification of the group. Two or three genetically structured subclades were also found within each Amazonian lineage, although these subclades are not isolated by an obvious geographic barrier.

Genomic phylogeography of the White-crowned ManakinPseudopipra pipra(Aves: Pipridae) illuminates a continental-scale radiation out of the Andes

“…Both the Solimóes and Japurá rivers seem to have undergone recent changes due to sedimentation dynamics and channel reorganization (Ruokolainen et al, 2019), and such processes likely affected upland forest bird populations. The pattern of introgression in the western Napo Pseudopipra lineage may be temporally congruent with a similar pattern described for Lepidothrix coronata, with a split across the upper Solimões around 1-1.5 Ma, and hypothesized introgression from Northeastern lineages (Reis et al, 2020).…”

“…We hypothesize that introgression has introduced more recently derived variation from the Guiana Shield + Northern Amazon clade D into an older, differentiated, population of the Southern Amazonian clade, pulling the phylogenetic affinity toward the northern clade. A similar scenario may have occurred in another manakin lineage, Lepidothrix coronata , in which nuclear and mitochondrial markers seem to show contrasting topologies regarding the western Amazonian Napo lineage (Reis et al, 2020).…”

“…While the higher level phylogeny and taxonomy of manakins has received significant attention (also see Tello et al, 2009), work exploring intraspecific genetic variation within manakins has been restricted to relatively few species (e.g. Brumfield et al, 2008; Capurucho et al, 2013; Cheviron et al, 2006; Cheviron et al, 2005; Francisco et al, 2007; Gubili et al, 2016; Luna et al, 2017; McDonald, 2003; Reis et al, 2020).…”

Pleistocene climatic fluctuations promoted alternative evolutionary histories in Phytelephas aequatorialis, an endemic palm from western Ecuador

“…Such north-south phylogeographic breaks have been reported in other tropical rain forests because of differences in past and current climate and in geological history, including those from western Amazonia (Escobar et al, 2018;Jimenez-Vasquez et al, 2017;Reis et al, 2020;Roncal et al, 2015;Symula et al, 2003), eastern…”

Integrative taxonomy of Flatbill Flycatchers (Tyrannidae) reveals a new species from the Amazonian lowlands

“…Carneiro et al, 2012;Moncrieff et al, 2017;Portes et al, 2013;Whitney & Cohn-Haft, 2013;Whittaker et al, 2013). Moreover, recent studies have proposed that several taxa (including many polytypic species) with wide distributions across the Amazon basin are in fact complexes of multiple species (Aleixo et al, 2013;Batista et al, 2013;Rodrigues et al, 2013;Thom & Aleixo, 2015;Cerqueira et al, 2016;Ferreira et al, 2017;Reis et al, 2019;Schultz et al, 2017;Smith et al, 2017). These cryptic taxa usually represent allopatric populations with strong genetic differentiation, distinct vocal parameters, but which are very similar in external morphology.…”