Diversification and species limits in scale-backed antbirds (Willisornis: Thamnophilidae), an Amazonian endemic lineage

Abstract

The genus Willisornis is endemic to the Amazon Basin, inhabiting upland terra firme forest, with two species and seven subspecies currently recognized. Despite numerous systematic studies, a taxonomically-dense sampled phylogeny for Willisornis is still lacking, which, combined with evidence of paraphyly and gene flow between its recognized species, underscores the uncertainty concerning species limits and evolutionary history of the genus. Here we present phylogenies and population genetic analyses, including all currently recognized Willisornis taxa, relating them to patterns of plumage variation, and reconstructing the spatiotemporal context of diversification in the genus. Our analyses have uncovered 13 independent genetic lineages in the genus, and the monophyly of all currently named taxa, which also showed robust plumage diagnoses. However, deeply coalesced genetic lineages were also found within most Willisornis taxa, for which no consistent variation in plumage was found. The diversification of the genus Willisornis is related to hydrographic and climate change cycles across Amazonia since the Plio-Pleistocene, with most genetic lineages originating in the past one million years. Based on our findings, we recommend the recognition of a total of six species in Willisornis (one of which polytypic) based on the congruency between deeply coalesced lineages and consistent plumage diagnoses.

Comparative Phylogeography of Birds Across the Tocantins–Araguaia Interfluve Reveals a New Biogeographic Suture in the Amazon Far East

“…In Willisornis vidua, BAE populations clustered in a wellsupported clade along with those from the northernmost part of the TAI, whereas XAE specimens did not cluster in a single clade, but with some of them being closely related to several individuals occurring throughout most of the TAI, as also supported by the haplotype networks (Supplementary Figure 9). These two genetically structured W. vidua populations within the TAI are apparently parapatric, and no evidence of widespread gene flow between them has been recovered so far (see Quaresma et al, 2022). Preliminary phylogeographic analyses focusing on T. andrei showed a similar north-south replacement across the TAI involving distinct phylogroups and haplotype network arrangements clustering with the BAE or XAE clades (Supplementary Figure 10).…”

Whole genomes show contrasting trends of population size changes and genomic diversity for an Amazonian endemic passerine over the late quaternary

“…We estimated species trees with SNPs to verify the phylogenetic relationships among the Willisornis lineages and reconstruct their diversification timing and spatial patterns. Quaresma et al (2022) delimited these lineages, but their modest genetic sampling that included only two mitochondrial and two nuclear genes did not resolve the basal relationships within Willisornis with high statistical support. We assigned individuals into lineages/species following Quaresma et al (2022) results and tested whether WGS data would provide a fully resolved time tree for Willisornis (Table 1).…”

“…We converted .bam files to .fasta using the mpileup function from SAMtools (Danecek et al, 2021), BCFTools (Danecek et al, 2021), TA B L E 1 Genetic diversity metrics for Willisornis individuals classified into different taxa according to Quaresma et al (2022) and in different groups according to the areas of Endemism and geographic regions of the Amazon. (Quaresma et al, 2022). We used 34 free atomic time intervals (parapattern = 4 + 30*2 + 4 + 6 + 10), as recommended for birds (Nadachowska-Brzyska et al, 2015.…”

“…(3) Did southern and eastern populations of species associated with humid terra-firme Amazonian rainforest originate more recently and over shorter periods [see Quaresma et al, 2022;Silva et al, 2019],…”

Fine scale patterns of genetic structure in three species of forest birds reveal no population structure and dynamic history within an Amazonian area of endemism

“…Oneillornis salvini is restricted to the Inambari Area of Endemism IAE (Willis 1968; Cracraft 1985) while L. coronata occurs in the western part of the Amazon basin (Moncrieff et al, 2022). Although W. poecilinotus is known to occur throughout the Amazon basin, currently ve sub-species are recognized (Gill et al, 2021), with W. p. griseiventris and W. p. gutturalis occurring in the IAE (Quaresma et al, 2022). Yet only W. p. griseiventris occur in the Purus-Madeira inter uvium.…”