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Background  The thin-spined porcupine, also known as the bristle-spined rat,  Chaetomys subspinosus  (Olfers, 1818), the only member of its genus, figures among Brazilian endangered species. In addition to being threatened, it is poorly known, and even its taxonomic status at the family level has long been controversial. The genus  Chaetomys  was originally regarded as a porcupine in the family Erethizontidae, but some authors classified it as a spiny-rat in the family Echimyidae. Although the dispute seems to be settled in favor of the erethizontid advocates, further discussion of its affinities should be based on a phylogenetic framework. In the present study, we used nucleotide-sequence data from the complete mitochondrial cytochrome  b  gene and karyotypic information to address this issue. Our molecular analyses included one individual of  Chaetomys subspinosus  from the state of Bahia in northeastern Brazil, and other hystricognaths.    Results  All topologies recovered in our molecular phylogenetic analyses strongly supported  Chaetomys subspinosus  as a sister clade of the erethizontids. Cytogenetically,  Chaetomys subspinosus  showed 2n = 52 and FN = 76. Although the sexual pair could not be identified, we assumed that the X chromosome is biarmed. The karyotype included 13 large to medium metacentric and submetacentric chromosome pairs, one small subtelocentric pair, and 12 small acrocentric pairs. The subtelocentric pair 14 had a terminal secondary constriction in the short arm, corresponding to the nucleolar organizer region (Ag-NOR), similar to the erethizontid  Sphiggurus villosus , 2n = 42 and FN = 76, and different from the echimyids, in which the secondary constriction is interstitial.    Conclusion  Both molecular phylogenies and karyotypical evidence indicated that  Chaetomys  is closely related to the Erethizontidae rather than to the Echimyidae, although in a basal position relative to the rest of the Erethizontidae. The high levels of molecular and morphological divergence suggest that  Chaetomys  belongs to an early radiation of the Erethizontidae that may have occurred in the Early Miocene, and should be assigned to its own subfamily, the Chaetomyinae.

The taxonomic status of the endangered thin-spined porcupine, Chaetomys subspinosus (Olfers, 1818), based on molecular and karyologic data