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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]

Background Repetitive short interspersed elements (SINEs) are retrotransposons ubiquitous in mammalian genomes and are highly informative markers to identify species and phylogenetic associations. Of these, SINEs unique to the order Carnivora (CanSINEs) yield novel insights on genome evolution in domestic dogs and cats, but less is known about their role in related carnivores. In particular, genome-wide assessment of CanSINE evolution has yet to be completed across the Feliformia (cat-like) suborder of Carnivora. Within Feliformia, the cat family Felidae is composed of 37 species and numerous subspecies organized into eight monophyletic lineages that likely arose 10 million years ago. Using the Felidae family as a reference phylogeny, along with representative taxa from other families of Feliformia, the origin, proliferation and evolution of CanSINEs within the suborder were assessed. Results We identified 93 novel intergenic CanSINE loci in Feliformia. Sequence analyses separated Feliform CanSINEs into two subfamilies, each characterized by distinct RNA polymerase binding motifs and phylogenetic associations. Subfamily I CanSINEs arose early within Feliformia but are no longer under active proliferation. Subfamily II loci are more recent, exclusive to Felidae and show evidence for adaptation to extant RNA polymerase activity. Further, presence/absence distributions of CanSINE loci are largely congruent with taxonomic expectations within Feliformia and the less resolved nodes in the Felidae reference phylogeny present equally ambiguous CanSINE data. SINEs are thought to be nearly impervious to excision from the genome. However, we observed a nearly complete excision of a CanSINEs locus in puma (Puma concolor). In addition, we found that CanSINE proliferation in Felidae frequently targeted existing CanSINE loci for insertion sites, resulting in tandem arrays. Conclusions We demonstrate the existence of at least two SINE families within the Feliformia suborder, one of which is actively involved in insertional mutagenesis. We find SINEs are powerful markers of speciation and conclude that the few inconsistencies with expected patterns of speciation likely represent incomplete lineage sorting, species hybridization and SINEmediated genome rearrangement. [ABSTRACT FROM AUTHOR]