Biology subjects

Silveira, L. F.

Publications and source records attributed to Silveira, L. F..

3 recordsLinked to original sources

bioRxiv2026

Plumage diversity without differential expression of pigmentation genes in a rapid avian radiation

Uncovering the molecular basis of reproductive traits is key to understanding species divergence. Capuchino Seedeaters ( Sporophila ), a radiation of genetically similar birds differing mainly in male reproductive plumage color, can be leveraged to study how such traits evolve. Outlier scans identified candidate pigmentation variants primarily in noncoding sequence, implying regulatory changes. However, RNA-seq of growing feather follicles generally did not show differential expression of pigmentation genes among different colors, with only ASIP downregulated in crown feathers. Gene expression patterns instead varied by body region. The largest difference between dimorphic sexes was the upregulation of the carotenoid-degrading gene BCO2 in males, accompanied by lower carotenoid content in male feathers. An improved genome annotation assigned 9.5% of candidate variants into coding and untranslated sequence. This suggests species-diagnostic variants lie within transcribed sequence and could act post-transcriptionally, rather than through transcript abundance, leading to a revised hypothesis for plumage divergence in this radiation.

genomics↗

bioRxiv2025

A multiscale physicochemical characterization of melanin-based feather coloration in the rapid Capuchino Seedeater radiation

Melanin-based plumage coloration in birds is shaped by pigment composition as well as melanosome morphology and distribution, however, the ways in which these factors together modulate observable color remain poorly understood. We investigate this relationship in the Capuchino Seedeaters (genus Sporophila), whose recent, rapid radiation driven by sexual selection resulted in 12 species with diverse coloration patterns. Using scanning electron microscopy (SEM) and micro-computed tomography ({micro}CT), combined with a novel application of Fontana-Masson stain to image melanosomes at high resolution, we characterize melanosome distribution and morphology in several variably colored plumage patches across Capuchino species. Melanosome morphologies followed patch-specific patterns that did not directly correlate with coloration: crown feather melanosomes were larger, more elongated, and had greater percent eumelanin content than those in belly, throat, or dorsum/rump patches. We also observed that dorsal patches had more total melanin than ventral ones, with pigment and coloration patterns suggesting possible signaling and photoprotective roles. More generally, we show how the patch-specific coloration of male Capuchinos is accompanied by differences in melanosome morphology and melanin composition and abundance. Our work highlights the challenges that remain in understanding how the nanoscale mechanisms of melanin-based pigmentation translate into macroscale plumage coloration.

evolutionary biology↗

bioRxiv2019

Systematics, biogeography and diversification of Scytalopus tapaculos (Rhinocryptidae), an enigmatic radiation of Neotropical montane birds

We studied the phylogeny, biogeography and diversification of suboscine birds in the genus Scytalopus (Rhinocryptidae), a widespread, speciose, and taxonomically challenging group of Neotropical birds. We analyzed nuclear (exons, regions flanking ultraconserved elements) and mitochondrial (ND2) DNA sequence data for a taxonomically and geographically comprehensive sample of specimens collected from Costa Rica to Patagonia and eastern Brazil. We found that Scytalopus is a monophyletic group sister to Eugralla, and consists of three main clades roughly distributed in (1) the Southern Andes, (2) eastern Brazil, and (3) the Tropical Andes and Central America. The clades from the Southern Andes and Eastern Brazil are sister to each other. Despite their confusing overall uniformity in plumage coloration, body shape and overall appearance, rates of species accumulation through time in Scytalopus since the origin of the clade in the Late Miocene are unusually high compared to those of other birds, suggesting rapid non-adaptive diversification in the group which we attribute to their limited dispersal abilities making them speciation-prone and their occurrence in a complex landscape with numerous barriers promoting allopatric differentiation. Divergence times among species and downturns in species accumulation rates in recent times suggest that most speciation events in Scytalopus predate climatic oscillations of the Pleistocene. Our analyses identified various cases of strong genetic structure within species and lack of monophyly of taxa, flagging populations which likely merit additional study to establish their taxonomic status. In particular, detailed analyses of species limits are due in S. parvirostris, S. latrans, S. speluncae, the S. atratus complex, and the Southern Andes clade.

evolutionary biology↗