In this study, we sought to fill knowledge gaps surrounding the species of the genus Sicalis on two main aspects: (I) reconstructing the phylogenetic relationships of ten of the twelve species described for this genus and (II) realizing a phylogeographic analysis with S. flaveola, seeking to identify if the subspecies described correspond to genetically different populations, thereby assisting in the taxonomic revision and conservation of this species. The phylogeny of the genus Sicalis was performed with a larger number of individuals and more collection sites than study previously published. Furthermore, the temporal process of diversification of the species of this genus was investigated by molecular dating. In the second chapter, we seek to identify the phylogeographic pattern in S. flaveola investigating the distribution of genetic lineages of the five subspecies described: S. f. flaveola, S. f. valida, S. f. koenigi, S. f. brasiliensis and S. f. pelzelni), and identify management units (MUs) present in this species. Both studies were based on analysis of two molecular markers: a segment of mtDNA (ND2; 1041 bp) and a segment of nuclear genome (FIB5; 569 bp). As previously noted, the phylogenetic reconstructions indicate that Sicalis genus is polyphyletic, since S. citrina grouped in distinct clade from other species of the genus. Moreover, with the exception of S. citrina, all species of this genus were also recovered as polyphyletic, possibly due to misidentification or eventually hybridization events. Based on molecular dating, it is observed that the genus Sicalis had originated about 15 million years ago in the Miocene, while most speciation events within this genus yet occurred in Pliocene. The phylogeographical analyzes indicate that the five subspecies of S. flaveola can be divided into three haplogroups: Group I: S. f. brasiliensis from the north and south; Group II: S. f. pelzelni from the north, S. f. flaveola and S. f. valida and Group III: S. f. pelzelni from the south and S. f. koenigi). S. f. brasiliensis seems to be the oldest group, which possibly left expansion events in opposite directions (north and south) giving rise to Groups II and III, respectively. S. f. brasiliensis showed a monophyletic group, while S. f. pelzelni seems to be poliphyletic. S. f. valida and S. f. flaveola are not genetically distinguishable. Thus, our data highlight the need for comprehensive taxonomic revision of the species of this genus, including in subspecies levels. And yet, the absence of agreement between the genetic and morphological data suggests that management and conservation measures for S. flaveola should be taken with caution, especially the release back into the nature birds seized by the organization responsible to combat wildlife crimes.
