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The canid genus Lycalopex comprises six recently diversified South American species whose evolutionary relationships have been remarkably challenging to resolve. We analyzed 6000 bp of mitochondrial DNA (mtDNA) from 55 Lycalopex individuals (L. sechurae = 4, L. culpaeus = 7, L.griseus = 8, L.gymnocercus = 17, L.vetulus = 13 and L. fulvipes = 6), and nine specimens from the closely related species Cerdocyon thous, Chrysocyon brachyurus and Speothos venaticus, to reconstruct their phylogenetic relationships, estimate the support for species-level monophyly, and date their divergences. In addition, we also sequenced seven nuclear segments from the same taxa. Three different phylogenetic approaches converged on the same mitochondrial topology with strong support for most nodes. All species were confirmed to be monophyletic for mtDNA, except for one intriguing case in which two L. vetulus individuals carried L. gymnocercus haplotypes, potentially implying a case of interspecies admixture. L. vetulus was the first species to diverge (ca. 1.2 Mya), followed by L. sechurae and then L. gymnocercus. The most internal group comprised L. griseus and the sister-species L. culpaeus and L. fulvipes, which diverged around 430,000 years ago in southern Argentina or Chile. The analysis of nuclear markers revealed several examples of intra-specific variation coupled with lack of species monophyly, consistent with pervasive incomplete lineage sorting and/or hybridization in this recent radiation. Our results provide robust mitochondrial resolution of this challenging radiation, and illustrate the difficulty of attaining similar success with traditional nuclear markers. [ABSTRACT FROM AUTHOR]

The vertebrate toll-like receptor (TLRs) supergene family is a first-line immune defense against viral and non-viral pathogens. Here, comparative evolutionary-genomics of 79 vertebrate species (8 mammals, 48 birds, 11 reptiles, 1 amphibian, and 11 fishes) revealed differential gain/loss of 26 TLRs, including 6 (TLR3, TLR7, TLR8, TLR14, TLR21, and TLR22) that originated early in vertebrate evolution before the diversification of Agnatha and Gnathostomata. Subsequent dynamic gene gain/loss led to lineage-specific diversification with TLR repertoires ranging from 8 subfamilies in birds to 20 in fishes. Lineage-specific loss of TLR8-9 and TLR13 in birds and gains of TLR6 and TLR10-12 in mammals and TLR19-20 and TLR23-27 in fishes. Among avian species, 5–10% of the sites were under positive selection (PS) (omega 1.5–2.5) with radical amino-acid changes likely affecting TLR structure/functionality. In non-viral TLR4 the 20 PS sites (posterior probability PP > 0.99) likely increased ability to cope with diversified ligands (e.g., lipopolysaccharide and lipoteichoic). For viral TLR7, 23 PS sites (PP > 0.99) possibly improved recognition of highly variable viral ssRNAs. Rapid evolution of the TLR supergene family reflects the host–pathogen arms race and the coevolution of ligands/receptors, which follows the premise that birds have been important vectors of zoonotic pathogens and reservoirs for viruses. [ABSTRACT FROM AUTHOR]