Mitochondrial genes are placed on one molecule, which implies that they should carry consistent phylogenetic information. Following this advantage, we present a well-supported phylogeny based on mitochondrial genomes from almost 300 representatives of Passeriformes, the most numerous and differentiated Aves order. The analyses resolved the phylogenetic position of paraphyletic Basal and Transitional Oscines. Passerida occurred divided into two groups, one containing Paroidea and Sylvioidea, whereas the other, Passeroidea and Muscicapoidea. Analyses of mitogenomes showed four types of rearrangements including a duplicated control region (CR) with adjacent genes. Mapping the presence and absence of duplications onto the phylogenetic tree revealed that the duplication was the ancestral state for passerines and was maintained in early diverged lineages. Next, the duplication could be lost and occurred independently at least four times according to the most parsimonious scenario. In some lineages, two CR copies have been inherited from an ancient duplication and highly diverged, whereas in others, the second copy became similar to the first one due to concerted evolution. The second CR copies accumulated over twice as many substitutions as the first ones. However, the second CRs were not completely eliminated and were retained for a long time, which suggests that both regions can fulfill an important role in mitogenomes. Phylogenetic analyses based on CR sequences subjected to the complex evolution can produce tree topologies inconsistent with real evolutionary relationships between species. Passerines with two CRs showed a higher metabolic rate in relation to their body mass.

The Yellow-shouldered Amazon (Amazona barbadensis) is the sole parrot of the genus Amazona that inhabits only dry forests. Its population has been dropping; therefore it has been the topic of many studies and conservation efforts. However, the phylogenetic relationship of this species to potential relatives classified within the Yellow-Headed Amazon (YHA) complex are still not clear. Therefore, we used more extensive data sets, including the newly sequenced mitochondrial genome of A. barbadensis, to conduct phylogenetic analyses. Various combinations of genes and many phylogenetic approaches showed that A. barbadensis clustered significantly with A. ochrocephala ochrocephala from Colombia and Venezuela, which created the Northern South American (NSA) lineage, clearly separated from two other lineages within the YHA complex, the Central (CA) and South American (SA). Tree topology tests and exclusion of rapidly evolving sites provided support for a NSA+SA grouping. We propose an evolutionary scenario for the YHA complex and its colonization of the American mainland. The NSA lineage likely represents the most ancestral lineage, which derived from Lesser Antillean Amazons and colonized the northern coast of Venezuela about a million years ago. Then, Central America was colonized through the Isthmus of Panama, which led to the emergence of the CA lineage. The southward expansion to South America and the origin of the SA lineage happened almost simultaneously. However, more intensive or prolonged gene flow or migrations have led to much weaker geographic differentiation of genetic markers in the SA than in the CA lineage.

Sexing of birds is indispensable for scientific, breeding and conservation programs but is difficult in many species and is particularly problematic in the case of nestlings showing no sexual dimorphism. Most useful and efficient methods of sex determination are based on unique features of the Z and W sex chromosomes detected via PCR to distinguish males (ZZ) and females (ZW). During the last twenty-five years researchers searched for the universal marker capable of sexing a maximally wide spectrum of species in a single PCR assay. We screened the phylogenetically representative set of 135 Psittaciformes species including 59 species sexed for the first time. Two known (P2P8, CHD1iA) PCR markers and four additional W/Z polymorphisms (CHD1iE, CHD1i16, CHD1i9 and NIPBLi16) located within the Chromo Helicase DNA binding CHD1 or the Nipped-B homolog NIPBL genes were applied. We present the electrophoretic patterns obtained for the PCR products of the analyzed markers including most typical and atypical patterns allowing sex determination, as well as those obtained when the given marker failed in sexing. Technical aspects of molecular sex determination are discussed: the optimization of amplification conditions, direct PCR and potential misinterpretations. A truly universal marker has not been found, and therefore, we propose a sexing strategy based on multiple CHD1i16, NIPBLi16, CHD1i9 and CHD1iE markers. This new strategy confirms the sex of a given bird with at least two markers detecting independent Z/W polymorphisms, reduces the number of necessary PCR reactions and minimizes the risk of sex misidentification.