An improved phylogeny of the Andean tit-tyrants (Aves, Tyrannidae): More characters trump sophisticated analyses

Abstract

The phylogeny of the flycatcher genus Anairetes was previously inferred using short fragments of mitochondrial DNA and parsimony and distance-based methods. The resulting topology spurred taxonomic revision and influenced understanding of Andean biogeography. More than a decade later, we revisit the phylogeny of Anairetes tit-tyrants using more mtDNA characters, seven unlinked loci (3 mitochondrial genes, 6 nuclear loci), more closely related outgroup taxa, partitioned Bayesian analyses, and two coalescent species-tree approaches (Bayesian estimation of species trees, BEST; Bayesian evolutionary analysis by sampling trees, *BEAST). Of these improvements in data and analyses, the fourfold increase in mtDNA characters was both necessary and sufficient to incur a major shift in the topology and near-complete resolution. The species-tree analyses, while theoretically preferable to concatenation or single gene approaches, yielded topologies that were compatible with mtDNA but with weaker statistical resolution at nodes. The previous results that had led to taxonomic and biogeographic reappraisal were refuted, and the current results support the resurrection of the genus Uromyias as the sister clade to Anairetes. The sister relationship between these two genera corresponds to an ecological dichotomy between a depauperate humid cloudforest clade and a diverse dry-tolerant clade that has diversified along the latitudinal axis of the Andes. The species-tree results and the concatenation results each reaffirm the primacy of mtDNA to provide phylogenetic signal for avian phylogenies at the species and subspecies level. This is due in part to the abundance of informative characters in mtDNA, and in part to its lower effective population size that causes it to more faithfully track the species tree.

Differential high‐altitude adaptation and restricted gene flow across a mid‐elevation hybrid zone in Andean tit‐tyrant flycatchers

“…Previous research suggests that the ancestor of the genus Anairetes was restricted to high elevations and it therefore may have been genetically adapted to cold, hypoxic environments (DuBay & Witt ). If this is the case, the respiratory differences that we observed between A. nigrocristatus and A. reguloides most likely reflect ‘low‐altitude adaptation’ in the latter species, implying the secondary loss of high‐altitude adapted alleles.…”

“…We sequenced 82 individuals for Cyt b , 79 individuals for Myo2, 80 individuals for IRF2 and 79 individuals for MUSK across the transect (Table S1, Supporting information). We used primers and PCR amplification conditions as described by DuBay & Witt (), and used PCR and sequencing protocols described by Johnson et al . ().…”

“…Diversification within the clade appears to have occurred by allopatric isolation along the latitudinal axis of the Andean ridge, with A. reguloides in the south and A . nigrocristatus in the north (DuBay & Witt ). Subsequent range expansion led to latitudinal overlap of the two taxa in central Peru, with A. reguloides apparently restricted to lower elevations only where it overlaps A. nigrocristatus (Schulenberg et al .…”

The role of the \"Cordillera Blanca\" (Ancash, Peru) in the evolutionary history of sigmodontinae rodents in northern Peru

“…This shows the basin acting as a barrier to support the Riverine Barrier hypothesis (Wallace, 1854;Patton et al, 1994). These results are congruent with Pacheco (2002), Pacheco (2018), andDuBay (2012), who subtly mention the presence of the Santa River as a possible geographic barrier. One example of another taxon with the same patterns is the bird Atlapetes rufigenis (García-Moreno & Fjeldså, J.…”

Origin of elevational replacements in a clade of nearly flightless birds – most diversity in tropical mountains accumulates via secondary contact following allopatric speciation

“…Funk et al, 2016;Hua, 2016), parapatric speciation along mountain slopes appears to be rare. In contrast to data discussed above, several studies do suggest that species replacing each other along elevational gradients may be closely related (Bates & Zink, 1994;Hall, 2005;DuBay & Witt, 2012), yet evidence that these replacements do not reflect separate colonization events of elevation belts or lowland-highland vicariance resulting from uplift processes (Brumfield & Edwards, 2007;Ribas et al, 2007;Santos et al, 2009) is lacking. To our knowledge, the clearest example of parapatric speciation in mountains involves sister species in the plant genus Senecio occurring on Mount Etna, Italy, which differ strikingly in ecology and phenotype despite experiencing extensive gene flow (Chapman et al, 2013;Osborne et al, 2013;Chapman et al, 2016).…”