Comparative molecular cytogenetic studies in the order Carnivora: mapping chromosomal rearrangements onto the phylogenetic tree

We have made a set of chromosome-specific painting probes for the American mink by degenerate oligonucleotide primed-PCR (DOP-PCR) amplification of flow-sorted chromosomes. The painting probes were used to delimit homologous chromosomal segments among human, red fox, dog, cat and eight species of the family Mustelidae, including the European mink, steppe and forest polecats, least weasel, mountain weasel, Japanese sable, striped polecat, and badger. Based on the results of chromosome painting and G-banding, comparative maps between these species have been established. The integrated map demonstrates a high level of karyotype conservation among mustelid species. Comparative analysis of the conserved chromosomal segments among mustelids and outgroup species revealed 18 putative ancestral autosomal segments that probably represent the ancestral chromosomes, or chromosome arms, in the karyotype of the most recent ancestor of the family Mustelidae. The proposed 2n = 38 ancestral Mustelidae karyotype appears to have been retained in some modern mustelids, e.g., Martes, Lutra, Ictonyx, and Vormela. The derivation of the mustelid karyotypes from the putative ancestral state resulted from centric fusions, fissions, the addition of heterochromatic arms, and occasional pericentric inversions. Our results confirm many of the evolutionary conclusions suggested by other data and strengthen the topology of the carnivore phylogenetic tree through the inclusion of genome-wide chromosome rearrangements.     

Phylogenetic implications of the 38 putative ancestral chromosome segments for four canid species.

Chromosome homologies between the Japanese raccoon dog (Nectereutes procyonoides viverrinus, 2n = 39 + 2-4 B chromosomes) and domestic dog (Canis familiaris, 2n = 78) have been established by hybridizing a complete set of canine paint probes onto high-resolution G-banded chromosomes of the raccoon dog. Dog chromosomes 1, 13, and 19 each correspond to two raccoon dog chromosome segments, while the remaining 35 dog autosomes each correspond to a single segment. In total, 38 dog autosome paints revealed 41 conserved segments in the raccoon dog. The use of dog painting probes has enabled integration of the raccoon dog chromosomes into the previously established comparative map for the domestic dog, Arctic fox (Alopex lagopus), and red fox (Vulpes vulpes). Extensive chromosome arm homologies were found among chromosomes of the red fox, Arctic fox, and raccoon dog. Contradicting previous findings, our results show that the raccoon dog does not share a single biarmed autosome in common with the Arctic fox, red fox, or domestic cat. Comparative analysis of the distribution patterns of conserved chromosome segments revealed by dog paints in the genomes of the canids, cats, and human reveals 38 ancestral autosome segments. These segments could represent the ancestral chromosome arms in the karyotype of the most recent ancestor of the Canidae family, which we suggest could have had a low diploid number, based on comparisons with outgroup species.     

The ancestral carnivore karyotype (2n = 38) lives today in ringtails

Chromosome painting was used to investigate the conservation of high-resolution longitudinal 4',6-diamidino-2-phenylindole (DAPI)/G bands in Carnivore chromosomes. Cat (Felis catus) and raccoon dog (Nyctereutes procyonoides) painting probes were hybridized to the ringtail (Bassaricus astutus), dwarf mongoose (Helogale parvula), and Malagasy civet (Fossa fossa) to identify homologous chromosome elements. The patterns of chromosome segment homology among Carnivore species allowed us to reconstruct and propose the disposition of a high-resolution banded ancestral carnivore karyotype (ACK). Three bi-armed chromosomes consistently found among Caniformia species are represented as 6 homologous acrocentric chromosomes among Feliformia species of Carnivora. However, reexamination of the most basal of Feliformia species, the African palm civet Nandinia, revealed the presence of the 3 heretofore Caniformia bi-armed chromosomes. Because these 3 bi-armed chromosomes are found in both Caniformia and Feliformia lineages, they are presumed ancestral for all Carnivora, suggesting that the ACK chromosome number would be 38, rather than the previously supposed 42. Banded chromosomes of the ACK are used to evaluate the consistency between recently determined molecular phylogenetic relationships and postulated cytogenetic dynamics in the same Carnivore species.     

Chromosomal evolution of the Canidae. I. Species with high diploid numbers

The Giemsa banding patterns of seven canid species, including the grey wolf (Canis lupus), the maned wolf (Chrysocyon brachyurus), the bush dog (Speothos venaticus), the crab-eating fox (Cerdocyon thous), the grey fox (Urocyon cinereoargenteus), the bat-eared fox (Otocyon megalotis), and the fennec (Fennecus zerda), are presented and compared. Relative to other members of Canidae, these species have high diploid complements (2n greater than 64) consisting of largely acrocentric chromosomes. They show a considerable degree of chromosome homoeology, but relative to the grey wolf, each species is either missing chromosomes or has unique chromosomal additions and rearrangements. Differences in chromosome morphology among the seven species were used to reconstruct their phylogenetic history. The results suggest that the South American canids are closely related to each other and are derived from a wolf-like progenitor. The fennec and the bat-eared fox seem to be recent derivatives of a lineage that branched early from the wolf-like canids and which also includes the grey fox.     

A complete comparative chromosome map for the dog, red fox, and human and its integration with canine genetic maps

Cross-species reciprocal chromosome painting was used to delineate homologous chromosomal segments between domestic dog, red fox, and human. Whole sets of chromosome-specific painting probes for the red fox and dog were made by PCR amplification of flow-sorted chromosomes from established cell cultures. Based on their hybridization patterns, a complete comparative chromosome map of the three species has been built. Thirty-nine of the 44 synteny groups from the published radiation hybrid map and 33 of the 40 linkage groups in the linkage map of the dog have been assigned to specific chromosomes by fluorescence in situ hybridization and PCR-based genotyping. Each canine chromosome has at least one DNA marker assigned to it. The human-canid map shows that the canid karyotypes are among the most extensively rearranged karyotypes in mammals. Twenty-two human autosomal paints delineated 73 homologous regions on 38 canine autosomes, while paints from 38 dog autosomes detected 90 homologous segments in the human genome. Of the 22 human autosomes, only the syntenies of three chromosomes (14, 20, and 21) have been maintained intact in the canid genome. The dog-fox map and DAPI banding comparison demonstrate that the remarkable karyotype differences between fox (2n = 34 + 0-8 Bs) and dog (2n = 78) are due to 26 chromosomal fusion events and 4 fission events. It is proposed that the more easily karyotyped fox chromosomes can be used as a common reference and control system for future gene mapping in the DogMap project and CGH analysis of canine tumor DNA.     

Comparative chromosome painting in carnivora and pholidota

The order of Carnivora has been very well characterized with over 50 species analyzed by chromosome painting and with painting probe sets made for 9 Carnivora species. Representatives of almost all families have been studied with few exceptions (Otariidae, Odobenidae, Nandiniidae, Prionodontidae). The patterns of chromosome evolution in Carnivora are discussed here. Overall, many Carnivora species retained karyotypes that only slightly differ from the ancestral carnivore karyotype. However, there are at least 3 families in which the ancestral carnivore karyotype has been severely rearranged - Canidae, Ursidae and Mephitidae. Here we report chromosome painting of yet another Carnivora species with a highly rearranged karyotype, Genetta pardina. Recurrent rearrangements make it difficult to define the ancestral chromosomal arrangement in several instances. Only 2 species of pangolins (Pholidota), a sister order of Carnivora, have been studied by chromosome painting. Future use of whole-genome sequencing data is discussed in the context of solving the questions that are beyond resolution of conventional banding techniques and chromosome painting.     

Chromosomal evolution of the Canidae. II. Divergence from the primitive carnivore karyotype

The Giemsa-banding patterns of chromosomes from the arctic fox (Alopex lagopus), the red fox (Vulpes vulpes), the kit fox (Vulpes macrotis), and the raccoon dog (Nyctereutes procyonoides) are compared. Despite their traditional placement in different genera, the arctic fox and the kit fox have an identical chromosome morphology and G-banding pattern. The red fox has extensive chromosome arm homoeology with these two species, but has only two entire chromosomes in common. All three species share some chromosomes with the raccoon dog, as does the high diploid-numbered grey wolf (Canis lupus, 2n = 78). Moreover, some chromosomes of the raccoon dog show partial or complete homoeology with metacentric feline chromosomes which suggests that these are primitive canid chromosomes. We present the history of chromosomal rearrangements within the Canidae family based on the assumption that a metacentric-dominated karyotype is primitive for the group.     

New insights into the karyotypic relationships of Chinese muntjac (Muntiacus reevesi), forest musk deer (Moschus berezovskii) and gayal (Bos frontalis)

To investigate the karyotypic relationships between Chinese muntjac (Muntiacus reevesi), forest musk deer (Moschus berezovskii) and gayal (Bos frontalis), a complete set of Chinese muntjac chromosome-specific painting probes has been assigned to G-banded chromosomes of these three species. Sixteen autosomal probes (i.e. 6-10, 12-22) of the Chinese muntjac each delineated one pair of conserved segments in the forest musk deer and gayal, respectively. The remaining six autosomal probes (1-5, and 11) each delineated two to five pairs of conserved segments. In total, the 22 autosomal painting probes of Chinese muntjac delineated 33 and 34 conserved chromosomal segments in the genomes of forest musk deer and gayal, respectively. The combined analysis of comparative chromosome painting and G-band comparison reveals that most interspecific homologous segments show a high degree of conservation in G-banding patterns. Eleven chromosome fissions and five chromosome fusions differentiate the karyotypes of Chinese muntjac and forest musk deer; twelve chromosome fissions and six fusions are required to convert the Chinese muntjac karyotype to that of gayal; one chromosome fission and one fusion separate the forest musk deer and gayal. The musk deer has retained a highly conserved karyotype that closely resembles the proposed ancestral pecoran karyotype but shares none of the rearrangements characteristic for the Cervidae and Bovidae. Our results substantiate that chromosomes 1-5 and 11 of Chinese muntjac originated through exclusive centromere-to-telomere fusions of ancestral acrocentric chromosomes.     

Cytogenetic characterization and description of an XX/XY1Y2 sex chromosome system in catfish Harttia carvalhoi (Siluriformes, Loricariidae)

Karyotypic and cytogenetic characteristics of catfish Harttia carvalhoi (Paraíba do Sul River basin, S?o Paulo State, Brazil) were investigated using differential staining techniques (C-banding, Ag-staining) and fluorescent in situ hybridization (FISH) with 18S and 5S rDNA probes. The diploid chromosome number of females was 2n = 52 and their karyotype was composed of nine pairs of metacentric, nine pairs of submetacentric, four pairs of subtelocentric and four pairs of acrocentric chromosomes. The diploid chromosome number of males was invariably 2n = 53 and their karyotype consisted of one large unpaired metacentric, eight pairs of metacentric, nine pairs of submetacentric, four pairs of subtelocentric, four pairs of acrocentric plus two middle-sized acrocentric chromosomes. The differences between female and male karyotypes indicated the presence of a sex chromosome system of XX/XY1Y2 type, where the X is the largest metacentric and Y1 and Y2 are the two additional middle-sized acrocentric chromosomes of the male karyotype. The major rDNA sites as revealed by FISH with an 18S rDNA probe were located in the pericentromeric region of the largest pair of acrocentric chromosomes. FISH with a 5S rDNA probe revealed two sites: an interstitial site located in the largest pair of acrocentric chromosomes, and a pericentromeric site in a smaller metacentric pair of chromosomes. Translocations or centric fusions in the ancestral 2n = 54 karyotype is hypothesized for the origin of such multiple sex chromosome systems where females are fixed translocation homozygotes whereas males are fixed translocation heterozygotes. The available cytogenetic data for representatives of the genus Harttia examined so far indicate large kayotype diversity.     

Chromosome analysis of 82 species of Scarabaeoidea (Coleoptera), with special focus on NOR localization

The aim of this study was the identification of the ancestral location of the nucleolus organizer region (NOR) in the Scarabaeoidea superfamily, and its evolutive trends in the karyotypes. For this purpose, the mitotic and meiotic chromosomes at pachynema of 82 species belonging to 4 families and 8 subfamilies, including 49 species without any published data, were examined after Giemsa staining, C-banding and NOR staining. It could be perceived that most karyotypes are composed of 18 nonacrocentric autosomes, an acrocentric X and a punctiform Y. NORs are frequently located on the X independent of its morphology. In contrast, autosomal NORs are frequently on the rare acrocentric short arms. Thus, it could be shown that the ancestral karyotype was very probably composed of 18 metacentric/submetacentric autosomes, an NOR carrier acrocentric X and a punctiform Y. The NOR translocation on autosomes parallels the passage to their acrocentric morphology. It is proposed that the frequent location of the NOR on the X of beetles, and possibly other insects, is made possible by their mode of dosage compensation of the X chromosome, consisting in the overexpression of the unique X of the males.     

Contributions to the cytotaxonomy of the Commelinaceae. Chromosome evolution in Tradescantia section Cymbispatha

The five species of Tradescantia section Cymbispatha studied, including one species T. poelliae D. R. Hunt, have chromosome numbers of In = 12, 14, 16, 22, 28, 30 and 36 and karyotypes of acrocentric, metacentric or telocentric chromosomes, or mixtures of both acrocentric and metacentric chromosomes. The numbers of major chromosome arms of these cytotypes give a nombre fondamentaP series of 14, 28, 42 and 56 which, in combination with meiotic analyses, indicates plants which, in genetical terms at least, are diploid, tetraploid, hexaploid and octoploid. This series has evolved from a 2 n = 14 acrocentric or telocentric karyotype by a combination of Robertsonian fusion and polyploidy. Pseudo-iso-chromosomes are sometimes formed in this evolutionary development and can persist as stable members of normal complements.     

Contributions to the cytotaxonomy of the Commelinaceae. Chromosome evolution in Tradescantia section Cymbispatha

The five species of Tradescantia section Cymbispatha studied, including one species T. poelliae D. R. Hunt, have chromosome numbers of In = 12, 14, 16, 22, 28, 30 and 36 and karyotypes of acrocentric, metacentric or telocentric chromosomes, or mixtures of both acrocentric and metacentric chromosomes. The numbers of major chromosome arms of these cytotypes give a nombre fondamentaP series of 14, 28, 42 and 56 which, in combination with meiotic analyses, indicates plants which, in genetical terms at least, are diploid, tetraploid, hexaploid and octoploid. This series has evolved from a 2 n = 14 acrocentric or telocentric karyotype by a combination of Robertsonian fusion and polyploidy. Pseudo-iso-chromosomes are sometimes formed in this evolutionary development and can persist as stable members of normal complements.     

Comparative cytogenetics of the African elephant (Loxodonta africana) and Asiatic elephant (Elephas maximus)

G- and C-banded karyotypes of the two extant species of the mammalian order Proboscidea are presented for the first time. Chromosome complements were 2n = 56 in both Loxodonta africana and Elephas maximus. Comparisons between the species demonstrated a high level of chromosome band homology, with 26 conserved autosomal pairs. The normal diploid karyotype of L. africana had 25 acrocentric/telocentric and two metacentric/submetacentric autosomal pairs. E. maximus differed by having one less acrocentric and one additional submetacentric pair due to either a heterochromatic arm addition or deletion involving autosomal pair 27. Several acrocentric autosomes of L. africana exhibited small short arms that were absent in homologous chromosomes of E. maximus. The X chromosomes in both species were large submetacentric elements and were homologous. However, the small acrocentric Y chromosomes differed; in E. maximus it was slightly larger and had more distinct G-bands than its counterpart in L. africana. Extant Elephantidae appear to be relatively conservative in their rates of chromosomal change compared to some other mammalian families. The high-quality banded karyotypes presented here should prove useful as references in future chromosome analyses of elephant populations and in comparative cytogenetic studies with other ungulate orders.     

The Ancestral Carnivore Karyotype As Substantiated by Comparative Chromosome Painting of Three Pinnipeds,the Walrus,the Steller Sea Lion and the Baikal Seal (Pinnipedia,Carnivora)

Karyotype evolution in Carnivora is thoroughly studied by classical and molecular cytogenetics and supplemented by reconstructions of Ancestral Carnivora Karyotype (ACK). However chromosome painting information from two pinniped families (Odobenidae and Otariidae) is noticeably missing. We report on the construction of the comparative chromosome map for species from each of the three pinniped families: the walrus (Odobenus rosmarus, Odobenidae–monotypic family), near threatened Steller sea lion (Eumetopias jubatus, Otariidae) and the endemic Baikal seal (Pusa sibirica, Phocidae) using combination of human, domestic dog and stone marten whole-chromosome painting probes. The earliest karyological studies of Pinnipedia showed that pinnipeds were characterized by a pronounced karyological conservatism that is confirmed here with species from Phocidae, Otariidae and Odobenidae sharing same low number of conserved human autosomal segments (32). Chromosome painting in Pinnipedia and comparison with non-pinniped carnivore karyotypes provide strong support for refined structure of ACK with 2n = 38. Constructed comparative chromosome maps show that pinniped karyotype evolution was characterized by few tandem fusions, seemingly absent inversions and slow rate of genome rearrangements (less then one rearrangement per 10 million years). Integrative comparative analyses with published chromosome painting of Phoca vitulina revealed common cytogenetic signature for Phoca/Pusa branch and supports Phocidae and Otaroidea (Otariidae/Odobenidae) as sister groups. We revealed rearrangements specific for walrus karyotype and found the chromosomal signature linking together families Otariidae and Odobenidae. The Steller sea lion karyotype is the most conserved among three studied species and differs from the ACK by single fusion. The study underlined the strikingly slow karyotype evolution of the Pinnipedia in general and the Otariidae in particular.     

High chromosomal polymorphism and heterozygosity in Cyclocephala tridentata from Guadeloupe: chromosome comparison with some other species of Dynastinae (Coleoptera: Scarabaeidae)

Very distinct karyotypes have been observed in two Cyclocephala species from Guadeloupe, considered as very close and possibly vicariant: C. insulicola with only metacentric and C. tridentata tridentata with many acrocentric autosomes. This prompted us to study the karyotype of a few other neotropical Dynastinae belonging to four of the eight existing tribes, to find out which one of these two species had the most divergent chromosomes from their ancestral condition. In the four additional species studied, i.e., Cyclocephalamaffafa, Strategus syphax, Ligyrus cuniculus and Megasoma actaeon, a karyotype composed of 20 chromosomes, including 18 meta- or submetacentric autosomes was found, as it was in C. insulicola. Thus, the karyotype of C. t. tridentata, in which most of the 18 autosomes were acrocentric, is apomorphic. In addition, it was highly polymorphic, with six different karyotypes observed among the ten specimens studied. All had one to four heterozygous chromosome pairs formed by one acrocentric and one submetacentric carrying a large juxta-centromeric heterochromatic component. This heterozygosity did not seem to impair either meiotic synapsis or chiasma formation and chromosome segregation. Such high rates of chromosome heterozygosity and polymorphism are infrequent and never described in beetles. This suggests that C. t. tridentata undergoes an active process of chromosome evolution. A possible relationship with insularity and/or pesticide exposure is briefly discussed.     

Adult male emigration and a female-based social organization in swift foxes, Vulpes velox

Members of the family Canidae are distinguished from other carnivore families by pair bonding and male care of the young. Because of the importance of food provisioning and territorial defence by males, social structure among canids is shared or even dominated by males. However, small, insectivorous species of canids show little male parental care, although whether social structure differs from other canids is unknown. We combined data from three independent research projects on a small canid, the swift fox, to help elucidate the social organization of this species. Based on data on movements of 35 adult mated pairs and the fate of litters, we found that adult females maintained territories and family structure, whereas adult males tended to emigrate. This is the first evidence of a female-based social organization among any canid species. This type of social organization probably resulted from the decreased importance of territorial defence and food provisioning by males, as their diet is primarily insectivorous during summer when young are weaned. Our results, along with others, indicate that variations in social structure among canid species are strongly influenced by the importance of food provisioning and territorial defence by males.     

Comparative cytogenetic analysis of sex chromosomes in several Canidae species using zoo-FISH

Sex chromosome differentiation began early during mammalian evolution. The karyotype of almost all placental mammals living today includes a pair of heterosomes: XX in females and XY in males. The genomes of different species may contain homologous synteny blocks indicating that they share a common ancestry. One of the tools used for their identification is the Zoo-FISH technique. The aim of the study was to determine whether sex chromosomes of some members of the Canidae family (the domestic dog, the red fox, the arctic fox, an interspecific hybrid: arctic fox x red fox and the Chinese raccoon dog) are evolutionarily conservative. Comparative cytogenetic analysis by Zoo-FISH using painting probes specific to domestic dog heterosomes was performed. The results show the presence of homologous synteny covering the entire structures of the X and the Y chromosomes. This suggests that sex chromosomes are conserved in the Canidae family. The data obtained through Zoo-FISH karyotype analysis append information obtained using other comparative genomics methods, giving a more complete depiction of genome evolution.     

Comparative genomics: tracking chromosome evolution in the family ursidae using reciprocal chromosome painting

The Ursidae family includes eight species, the karyotype of which diverges somewhat, in both chromosome number and morphology, from that of other families in the order Carnivora. The combination of consensus molecular phylogeny and high-resolution trypsin G-banded karyotype analysis has suggested that ancestral chromosomal fissions and at least two fusion events are associated with the development of the different ursid species. Here, we revisit this hypothesis by hybridizing reciprocal chromosome painting probes derived from the giant panda (Ailuropoda melanoleuca), domestic cat (Felis catus), and man (Homo sapiens) to representative bear species karyotypes. Comparative analysis of the different chromosome segment homologies allowed reconstruction of the genomic composition of a putative ancestral bear karyotype based upon the recognition of 39 chromosome segments defined by painting as the smallest conserved evolutionary unit segments (pSCEUS) among these species. The different pSCEUS combinations occurring among modern bear species support and extend the postulated sequence of chromosomal rearrangements and provide a framework to propose patterns of genome reorganization among carnivores and other mammal radiations.     

伞形科3个种5个居群的核型分析

对伞形科前胡属(PeucedanumL.)2个种以及羌活属(NotopterygiumH.Boiss.)1个种3个居群的染色体数目和核型进行了研究。研究表明,它们的染色体数目均为2n=22,核型公式可分别表示为长前胡:2n=2x=22=22 m(1 SAT),属1A型;松潘前胡:2n=2x=22=20 m 2 sm,属2A型;宽叶羌活的3个居群分别是:马边大风顶居群1为2n=2x=22=6 m 12 sm 4 st,属2A型;马边大风顶居群2为2n=2x=22=12 m 4 sm 6 st,属2B型;屏山老君山居群为2n=2x=22=4 m 14 sm 4 st,属2A型。其中长前胡和松潘前胡的染色体数目和核型为首次报道。     

Karyotypic analysis of the gobiid fish genus Quietula Jordan and Evermann

The karyotypes of the two species of the gobiid fish genus Quietula, Q. y-cauda (Jenkins & Evermann) and Q. guaymasiae (Jenkins & Evermann), are reported for the first time. The karyotypes contained equal numbers of chromosomes (2 n =42) but differed in chromosome morphology. Quietula y-cauda has 42 acrocentric chromosomes. Quietula guaymasiae has six metacentric, four submetacentric, and 32 acrocentric chromosomes. It is suggested the karyotype of Q. guaymasiae might have been derived from that of Q. y-cauda. In addition, from comparison of the species' karyotypes of the genera Quietula and Gillichthys , it is possible the karyotype of Q. y-cauda might have been derived from that of Gillichthys mirabilis.