Phylogenetic assessment of introns and SINEs within the Y chromosome using the cat family felidae as a species tree.
The cat family Felidae was used as a species tree to assess the phylogenetic performance of genes, and their embedded SINE elements, within the nonrecombining region of the Y chromosome (NRY). Genomic segments from single-copy X-Y homologs SMCY, UBE1Y, and ZFY (3,604 bp) were amplified in 36 species of cat. These genes are located within the X-degenerate region of the NRY and are thought to be molecular "fossils" that ceased conventional recombination with the X chromosome early within the placental mammal evolution. The pattern and tempo of evolution at these three genes is significant in light of the recent, rapid evolution of the family over approximately 12 Myr and provides exceptional support for each of the eight recognized felid lineages, as well as clear diagnostic substitutions identifying nearly all species. Bootstrap support and Bayesian posterior probabilities are uniformly high for defining each of the eight monophyletic lineages. Further, the preferential use of specific target-site motifs facilitating SINE insertion is empirically supported by sequence analyses of SINEs embedded within the three genes. Target-site insertion is thought to explain the contradiction between intron phylogeny and results of the SMCY SINE phylogeny that unites distantly related species. Overall, our data suggest X-degenerate genes within the NRY are singularly powerful markers and offer a valuable patrilineal perspective in species evolution. (+info)
Characterization of sucrose-negative Pasteurella multocida variants, including isolates from large-cat bite wounds.
To validate the identification of Pasteurella multocida-like bacteria negative for acid formation from sucrose, including isolates from bite wounds caused by large cats, 17 strains were phenotypically and genotypically characterized. Phylogenetic analysis of partially sequenced rpoB and infB genes showed the monophyly of the strains characterized and the reference strains of P. multocida. The sucrose-negative strains formed two groups, one related to reference strains of P. multocida and the other related to a separate species-like group (taxon 45 of Bisgaard). DNA-DNA hybridization further documented the species-like nature of this group. Ribotyping showed the heterogeneity of all strains except four strains that shared the same ribotype and that were isolated from bovine lungs. Phylogenetic analysis by 16S rRNA sequence comparison showed the monophyly of the strains characterized and the reference strains of P. multocida. Two strains isolated from leopard bite wounds were related to the type strain of P. dagmatis; however, they represented a new taxon (taxon 46 of Bisgaard), in accordance with their distinct phenotypic and genotypic identifications. The present study documents that sucrose-negative strains of P. multocida-like bacteria belong to two genotypically distinct groups. The study further confirms the phenotypic heterogeneity of P. multocida strains and documents two new species-like taxa of Pasteurella related to P. multocida. Until diagnostic tools have been further elaborated, special care should be taken in the identification of Pasteurella-like bacteria isolated from bite wounds caused by large cats. The evidence of phenotypic and genotypic divergence calls for the further development of PCR tests and DNA sequencing to document doubtful isolates. (+info)
Cementum on Smilodon sabers.
The maxillary canines of Smilodon californicus Bovard, 1907 have a deeply curved cementoenamel junction. The gingiva of modern cats is attached to the tooth at the cementoenamel junction and provides tactile and other dental information to the animal. The presence of cementum at the cervix of the maxillary canines, also called sabers, would indicate that the gingiva in Smilodon was attached in this region. Such an attachment would be advantageous, providing stability and sensory input for the large tooth. Also, gingiva at the cervix would impact the manner in which the teeth were used. Previous study using scanning electron microscopy of dental casts was indirect. The purpose of this study was to confirm by direct methods the presence of cementum at the cervix of Smilodon californicus sabers. Parts of three Smilodon californicus sabers were sectioned and examined with light and scanning electron microscopy (EDS). In addition, percent weight of calcium and phosphorus was measured in enamel, dentin, and cementum using electron dispersive spectroscopy. Cementum was identified in the cervical region of each saber. Spectroscopy confirmed that the tissue is calcified and the mineral is hydroxyapatite. Percent calcium and percent phosphorus of individual tissues were highly variable between specimens. However, the ratios of calcium to phosphorus were not significantly different from the hydroxyapatite standard. In the future, bite models will have to take the presence of soft tissues into account. (+info)
Seroprevalence and genomic divergence of circulating strains of feline immunodeficiency virus among Felidae and Hyaenidae species.
Feline immunodeficiency virus (FIV) infects numerous wild and domestic feline species and is closely related to human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV). Species-specific strains of FIV have been described for domestic cat (Felis catus), puma (Puma concolor), lion (Panthera leo), leopard (Panthera pardus), and Pallas' cat (Otocolobus manul). Here, we employ a three-antigen Western blot screening (domestic cat, puma, and lion FIV antigens) and PCR analysis to survey worldwide prevalence, distribution, and genomic differentiation of FIV based on 3,055 specimens from 35 Felidae and 3 Hyaenidae species. Although FIV infects a wide variety of host species, it is confirmed to be endemic in free-ranging populations of nine Felidae and one Hyaenidae species. These include the large African carnivores (lion, leopard, cheetah, and spotted hyena), where FIV is widely distributed in multiple populations; most of the South American felids (puma, jaguar, ocelot, margay, Geoffroy's cat, and tigrina), which maintain a lower FIV-positive level throughout their range; and two Asian species, the Pallas' cat, which has a species-specific strain of FIV, and the leopard cat, which has a domestic cat FIV strain in one population. Phylogenetic analysis of FIV proviral sequence demonstrates that most species for which FIV is endemic harbor monophyletic, genetically distinct species-specific FIV strains, suggesting that FIV transfer between cat species has occurred in the past but is quite infrequent today. (+info)
The late Miocene radiation of modern Felidae: a genetic assessment.
Modern felid species descend from relatively recent (<11 million years ago) divergence and speciation events that produced successful predatory carnivores worldwide but that have confounded taxonomic classifications. A highly resolved molecular phylogeny with divergence dates for all living cat species, derived from autosomal, X-linked, Y-linked, and mitochondrial gene segments (22,789 base pairs) and 16 fossil calibrations define eight principal lineages produced through at least 10 intercontinental migrations facilitated by sea-level fluctuations. A ghost lineage analysis indicates that available felid fossils underestimate (i.e., unrepresented basal branch length) first occurrence by an average of 76%, revealing a low representation of felid lineages in paleontological remains. The phylogenetic performance of distinct gene classes showed that Y-chromosome segments are appreciably more informative than mitochondrial DNA, X-linked, or autosomal genes in resolving the rapid Felidae species radiation. (+info)
Transitional cell carcinoma in fishing cats (Prionailurus viverrinus): pathology and expression of cyclooxygenase-1, -2, and p53.
A high prevalence of urinary bladder transitional-cell carcinoma (TCC) has been noted in captive fishing cats (Prionailurus viverrinus). Of the 91 adult deaths between 1995 and 2004, 12 (13%) were attributed to TCC. To help elucidate mechanisms of carcinogenesis, archival sections of urinary bladder from 14 fishing cats were examined histologically and immunohistochemically for p53, cyclooxygenase (COX)-1, and COX-2 expression. Ten cats had TCC, and 4 were unaffected. The average age at death was 10.8 years in affected individuals and 10.5 years in unaffected individuals. There was no sex predilection. Fishing cat TCCs were characterized histologically as papillary and infiltrating (n = 6), nonpapillary and infiltrating (n = 3), or carcinoma in situ (n = 1). Glandular and squamous metaplasia, necrosis, and lymphatic invasion were prominent histologic features. Two individuals had documented metastasis. p53 nuclear immunolabeling was detected in 4/10 (40%) TCCs. In two cases, immunolabeling was limited to less than 10% of the neoplastic cellular population and was comparable to staining of normal fishing cat bladder. Therefore, p53 gene mutation did not appear to be an essential component of TCC carcinogenesis in examined fishing cats. COX-1 immunohistochemistry was negative in all cases. All TCCs had some degree of COX-2 cytoplasmic immunolabeling, which was exclusively within the invasive portions of the neoplasms. Papillary portions were uniformly negative. COX-2 overexpression was a prominent feature in the majority of the examined fishing cat TCCs, suggesting that COX-2-mediated mechanisms of carcinogenesis are important in this species and that COX-inhibiting drugs may be of therapeutic benefit. (+info)
Molecular evidence for species-level distinctions in clouded leopards.
Among the 37 living species of Felidae, the clouded leopard (Neofelis nebulosa) is generally classified as a monotypic genus basal to the Panthera lineage of great cats. This secretive, mid-sized (16-23 kg) carnivore, now severely endangered, is traditionally subdivided into four southeast Asian subspecies (Figure 1A). We used molecular genetic methods to re-evaluate subspecies partitions and to quantify patterns of population genetic variation among 109 clouded leopards of known geographic origin (Figure 1A, Tables S1 ans S2 in the Supplemental Data available online). We found strong phylogeographic monophyly and large genetic distances between N. n. nebulosa (mainland) and N. n. diardi (Borneo; n = 3 individuals) with mtDNA (771 bp), nuclear DNA (3100 bp), and 51 microsatellite loci. Thirty-six fixed mitochondrial and nuclear nucleotide differences and 20 microsatellite loci with nonoverlapping allele-size ranges distinguished N. n. nebulosa from N. n. diardi. Along with fixed subspecies-specific chromosomal differences, this degree of differentiation is equivalent to, or greater than, comparable measures among five recognized Panthera species (lion, tiger, leopard, jaguar, and snow leopard). These distinctions increase the urgency of clouded leopard conservation efforts, and if affirmed by morphological analysis and wider sampling of N. n. diardi in Borneo and Sumatra, would support reclassification of N. n. diardi as a new species (Neofelis diardi). (+info)
Geographical variation in the clouded leopard, Neofelis nebulosa, reveals two species.
The clouded leopard, Neofelis nebulosa, is an endangered semiarboreal felid with a wide distribution in tropical forests of southern and southeast Asia, including the islands of Sumatra and Borneo in the Indonesian archipelago. In common with many larger animal species, it displays morphological variation within its wide geographical range and is currently regarded as comprising of up to four subspecies. It is widely recognized that taxonomic designation has a major impact on conservation planning and action. Given that the last taxonomic revision was made over 50 years ago, a more detailed examination of geographical variation is needed. We describe here the results of a morphometric analysis of the pelages of 57 clouded leopards sampled throughout the species' range. We conclude that there are two distinct morphological groups, which differ primarily in the size of their cloud markings. These results are supported by a recent genetic analysis. On that basis, we give diagnoses for the distinction of two species, one in mainland Asia (N. nebulosa) and the other in Indonesia (N. diardi). The implications for conservation that arise from this new taxonomic arrangement are discussed. (+info)