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Robert K Wayne - One of the best experts on this subject based on the ideXlab platform.
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Anchoring the dog to its relatives reveals new evolutionary breakpoints across 11 species of the Canidae and provides new clues for the role of B chromosomes
Chromosome Research, 2011Co-Authors: Shannon E. Duke Becker, Robert K Wayne, Alexander S Graphodatsky, Rachael Thomas, Vladimir A. Trifonov, Matthew BreenAbstract:The emergence of genome-integrated molecular cytogenetic resources allows for comprehensive comparative analysis of gross karyotype architecture across related species. The identification of evolutionarily conserved chromosome segment (ECCS) boundaries provides deeper insight into the process of chromosome evolution associated with speciation. We evaluated the genome-wide distribution and relative orientation of ECCSs in three wild canid species with diverse karyotypes (red fox, Chinese raccoon dog, and gray fox). Chromosome-specific panels of dog genome-integrated bacterial artificial chromosome (BAC) clones spaced at ∼10-Mb intervals were used in fluorescence in situ hybridization analysis to construct integrated physical genome maps of these three species. Conserved evolutionary breakpoint regions (EBRs) shared between their karyotypes were refined across these and eight additional wild canid species using targeted BAC panels spaced at ∼1-Mb intervals. Our findings suggest that the EBRs associated with speciation in the Canidae are compatible with recent phylogenetic groupings and provide evidence that these breakpoints are also recurrently associated with spontaneous canine cancers. We identified several regions of domestic dog sequence that share homology with canid B chromosomes, including additional cancer-associated genes, suggesting that these supernumerary elements may represent more than inert passengers within the cell. We propose that the complex karyotype rearrangements associated with speciation of the Canidae reflect unstable chromosome regions described by the fragile breakage model.
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isolation and molecular evolution of the selenocysteine trna cf trsp and rnase p rna cf rpph1 genes in the dog family Canidae
Molecular Biology and Evolution, 2005Co-Authors: Carolyne Bardeleben, Rachael L Moore, Robert K WayneAbstract:: In an effort to identify rapidly evolving nuclear sequences useful for phylogenetic analyses of closely related species, we isolated two genes transcribed by RNA polymerase III (pol III), the selenocysteine tRNA gene (TRSP) and an RNase P RNA (RPPH1) gene from the domestic dog (Canis familiaris). We focus on genes transcribed by pol III because their coding regions are small (generally 100-300 base pairs [bp]) and their essential promoter elements are located within a couple of hundred bps upstream of the coding region. Therefore, we predicted that regions flanking the coding region and outside of the promoter elements would be free of constraint and would evolve rapidly. We amplified TRSP from 23 canids and RPPH1 from 12 canids and analyzed the molecular evolution of these genes and their utility as phylogenetic markers for resolving relationships among species in Canidae. We compared the rate of evolution of the gene-flanking regions to other noncoding regions of nuclear DNA (introns) and to the mitochondrial encoded COII gene. Alignment of TRSP from 23 canids revealed that regions directly adjacent to the coding region display high sequence variability. We discuss this pattern in terms of functional mechanisms of transcription. Although the flanking regions evolve no faster than introns, both genes were found to be useful phylogenetic markers, in part, because of the synapomorphic indels found in the flanking regions. Gene trees generated from the TRSP and RPPH1 loci were generally in agreement with the published mtDNA phylogeny and are the first phylogeny of Canidae based on nuclear sequences.
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molecular systematics of the Canidae
Systematic Biology, 1997Co-Authors: Robert K Wayne, Eli Geffen, Derek J Girman, Klaus-peter Koepfli, Charles R. MarshallAbstract:Despite numerous systematic studies, the relationships among many species within the dog family, Canidae, remain unresolved. Two problems of broad evolutionary significance are the origins of the taxonomically rich canid fauna of South America and the development in three species of the trenchant heel, a unique meat-cutting blade on the lower first molar. The first problem is of interest because the fossil record provides little evidence for the origins of divergent South American species such as the maned wolf and the bush dog. The second issue is problematic because the trenchant heel, although complex in form, may have evolved independently to assist in the processing of meat. We attempted to resolve these two issues and five other specific taxo- nomic controversies by phylogenetic analysis of 2,001 base pairs of mitochondrial DNA (mtDNA) sequence data from 23 canid species. The mtDNA tree topology, coupled with data from the fossil record, and estimates of rates of DNA sequence divergence suggest at least three and possibly four North American invasions of South America. This result implies that an important chapter in the evolution of modern canids remains to be discovered in the fossil record and that the South American canid endemism is as much the result of extinction outside of South America as it is due to speciation within South America. The origin of the trenchant heel is not well resolved by our data, although the maximum parsimony tree is weakly consistent with a single origin followed by multiple losses of the character in several extant species. A combined analysis of the mtDNA data and published morphological data provides unexpected support for a monophyletic South American canid clade. However, the homogeneity partition tests indicate significant heterogeneity between the two data sets. (Canidae; combined analysis; mtDNA; phylogeny; South America; trenchant heel.)
P M Borodin - One of the best experts on this subject based on the ideXlab platform.
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inheritance of litter size at birth in farmed arctic foxes alopex lagopus Canidae carnivora
Heredity, 2007Co-Authors: Tatiana I Axenovich, Irina V Zorkoltseva, Ilya R Akberdin, S V Beketov, S N Kashtanov, I A Zakharov, P M BorodinAbstract:Inheritance of litter size at birth in farmed arctic foxes ( Alopex lagopus , Canidae, Carnivora)
Lei Chen - One of the best experts on this subject based on the ideXlab platform.
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Composition and diversity of Canidae fecal flora
Acta Ecologica Sinica, 2012Co-Authors: Hong-hai Zhang, Lei ChenAbstract:Abstract Canidae fecal flora reflects the distal gut microbial community structure. Cuon alpinus was captured on Qilian Mountain in Gansu province of China, and other animals, including Canis lupus , Vulpes vulpes , Vulpes corsac and Nyctereutes procyonoides , were captured at the nearby Dalai Lake Nature Reserve in Inner Mongolia. Fecal samples were collected 2 h after defecation from five healthy unrelated adult animals of each species. None of the animals had recently fed or been administered any drugs or additives that could influence the composition or diversity of the fecal flora. Using traditional culture-dependent methods, we investigated the composition and diversity of the fecal flora of these five Canidae species. Gram-positive spore bacilli, gram-positive having no spore bacilli, gram-positive coccobacteria, gram-negative coccobacteria and gram-negative bacilli were first identified through microscopic observation and then formal identification tests were carried out, including oxygen needing, methyl red and Acetyl methyl methanol test, catalase, gelatin liquefaction, KNO 3 reduction, indole, fermentation of saccharides and mellows, sodium citrate and NaCl-phily and so on. Based on the results of these physiological and biochemical tests, along with the morphological description, species from approximately 19–21 genera were identified in the feces. The number of genera in the feces was 22 in C. lupus , 19 in C. alpinus , 21 in N. procyonoides , 21 in V. corsac and 19 in V. vulpes , as well as some unidentified strains. Although, some strains were endemic to the Canidae gut, there were some differences in the community among individuals and species. The Canidae fecal flora comprised 10 10 –10 11 colony forming units/g of feces (wet weight). The amount of bacteria reached 1.442 × 10 11 cfu/g in C. lupus , 8.330 × 10 10 cfu/g in V. vulpes , 8.170 × 10 10 cfu/g in V. corsac , 8.620 × 10 10 cfu/g in N. procyonoides and 1.485 × 10 11 cfu/g in C. alpinus . The amount of bacteria was significantly different among species ( P C. lupus: P = 0.19; V. vulpes : P = 0.898; V. corsac : P = 0.315; N. procyonoides : P = 0.074; C. alpinus: P = 0.197). The percentage of shared species among different Canidaes was 65–80%, with the highest percentage between V. vulpes and V. corsac , and the lowest between C. lupus and C. alpinus . Although the proportion of shared species between V. vulpes and C. alpinus was 78.95%, the amount of bacteria was markedly different. There was no correlation between the amount and the diversity of bacteria. The most common microbes were Escherichia , Enterobacter , Streptococcus , Proteus , Enterococcus and Lactobacillus . Of these, Escherichia and Enterobacter can be considered as beneficial strains and they were found in all the Canidaes. Our findings suggest that, despite some differences, there is high similarity in the dominant fecal bacteria of different Canidaes.
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the complete mitochondrial genome of dhole cuon alpinus phylogenetic analysis and dating evolutionary divergence within Canidae
Molecular Biology Reports, 2011Co-Authors: Hong-hai Zhang, Lei ChenAbstract:The dhole (Cuon alpinus) is the only existent species in the genus Cuon (Carnivora: Canidae). In the present study, the complete mitochondrial genome of the dhole was sequenced. The total length is 16672 base pairs which is the shortest in Canidae. Sequence analysis revealed that most mitochondrial genomic functional regions were highly consistent among canid animals except the CSB domain of the control region. The difference in length among the Canidae mitochondrial genome sequences is mainly due to the number of short segments of tandem repeated in the CSB domain. Phylogenetic analysis was progressed based on the concatenated data set of 14 mitochondrial genes of 8 canid animals by using maximum parsimony (MP), maximum likelihood (ML) and Bayesian (BI) inference methods. The genera Vulpes and Nyctereutes formed a sister group and split first within Canidae, followed by that in the Cuon. The divergence in the genus Canis was the latest. The divarication of domestic dogs after that of the Canis lupus laniger is completely supported by all the three topologies. Pairwise sequence divergence data of different mitochondrial genes among canid animals were also determined. Except for the synonymous substitutions in protein-coding genes, the control region exhibits the highest sequence divergences. The synonymous rates are approximately two to six times higher than those of the non-synonymous sites except for a slightly higher rate in the non-synonymous substitution between Cuon alpinus and Vulpes vulpes. 16S rRNA genes have a slightly faster sequence divergence than 12S rRNA and tRNA genes. Based on nucleotide substitutions of tRNA genes and rRNA genes, the times since divergence between dhole and other canid animals, and between domestic dogs and three subspecies of wolves were evaluated. The result indicates that Vulpes and Nyctereutes have a close phylogenetic relationship and the divergence of Nyctereutes is a little earlier. The Tibetan wolf may be an archaic pedigree within wolf subspecies. The genetic distance between wolves and domestic dogs is less than that among different subspecies of wolves. The domestication of dogs was about 1.56–1.92 million years ago or even earlier.
Charles R. Marshall - One of the best experts on this subject based on the ideXlab platform.
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molecular systematics of the Canidae
Systematic Biology, 1997Co-Authors: Robert K Wayne, Eli Geffen, Derek J Girman, Klaus-peter Koepfli, Charles R. MarshallAbstract:Despite numerous systematic studies, the relationships among many species within the dog family, Canidae, remain unresolved. Two problems of broad evolutionary significance are the origins of the taxonomically rich canid fauna of South America and the development in three species of the trenchant heel, a unique meat-cutting blade on the lower first molar. The first problem is of interest because the fossil record provides little evidence for the origins of divergent South American species such as the maned wolf and the bush dog. The second issue is problematic because the trenchant heel, although complex in form, may have evolved independently to assist in the processing of meat. We attempted to resolve these two issues and five other specific taxo- nomic controversies by phylogenetic analysis of 2,001 base pairs of mitochondrial DNA (mtDNA) sequence data from 23 canid species. The mtDNA tree topology, coupled with data from the fossil record, and estimates of rates of DNA sequence divergence suggest at least three and possibly four North American invasions of South America. This result implies that an important chapter in the evolution of modern canids remains to be discovered in the fossil record and that the South American canid endemism is as much the result of extinction outside of South America as it is due to speciation within South America. The origin of the trenchant heel is not well resolved by our data, although the maximum parsimony tree is weakly consistent with a single origin followed by multiple losses of the character in several extant species. A combined analysis of the mtDNA data and published morphological data provides unexpected support for a monophyletic South American canid clade. However, the homogeneity partition tests indicate significant heterogeneity between the two data sets. (Canidae; combined analysis; mtDNA; phylogeny; South America; trenchant heel.)
John A Finarelli - One of the best experts on this subject based on the ideXlab platform.
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testing hypotheses of the evolution of encephalization in the Canidae carnivora mammalia
Paleobiology, 2008Co-Authors: John A FinarelliAbstract:Evolutionary trends observed over large clades have the potential to mask underlying trends that occur within their constituent subclades. A recent study of encephalization in the Caniformia (Carnivora, Mammalia) found evidence for an abrupt increase in median log-encephalization quotients (logEQs), indicating higher brain volume relative to body mass, at the end-Miocene, but gradual increase in the variance of logEQs. In this study, new endocranial volume estimates for fossil taxa in the well-sampled caniform subclade Canidae are reported. Using the encephalization data for the Canidae, hypotheses of evolution in encephalization allometries were tested with respect to canid phylogeny. The Akaike Information Criterion and likelihood ratios recovered support for a preferred hypothesis of the evolution of canid encephalization, which proposed two distinct allometric relationships: (1) a plesiomorphic grade of encephalization in the subfamilies Hesperocyoninae and Borophaginae and the paraphyletic canine genus Leptocyon , and (2) an apomorphic grade in the crown radiation of Caninae. This defines a shift in to higher encephalization, but without an associated change in the variance around the allometry. Increased canid encephalization coincides with a reorganization of the brain and the observed trend may reflect the evolution of complex social behavior in this clade.
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mechanisms behind active trends in body size evolution of the Canidae carnivora mammalia
The American Naturalist, 2007Co-Authors: John A FinarelliAbstract:Abstract: Clade‐level interactions can impart trends on observed characters. In this study, origination and extinction events were compiled for the three subfamilies of the Canidae (dogs): Hesperocyoninae, Borophaginae, and Caninae. These events were binned into 2‐million‐year time slices, and median body masses were calculated for each time slice. Originations and extinctions were classified as “large” or “small” relative to these median values. Likelihood ratios demonstrate that originations were significantly biased from random in four time slices, while extinctions were never significantly different from random. Two models were chosen by the Akaike Information Criterion to describe the evolutionary dynamics of canid body size. Both proposed a consistent, significant bias toward larger originations, punctuated by episodic “pulses” of increased bias toward larger originations and a Quaternary “pulse” favoring smaller originations, tracking the Quaternary diversification of foxlike canids. These pulses c...
