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PubMed1993

Conservative genome size and rapid chromosomal evolution in the South American tuco-tucos (Rodentia: Ctenomyidae).

Genome size (the amount of DNA per cell) was measured by flow-cytometric analysis in seven species of a chromosomally variable rodent genus: Ctenomys boliviensis, C. conoveri, C. frater, C. leucodon, C. lewisi, C. opimus, and C. steinbachi. The mean genome size of these species was 7.19 pg DNA and little inter- and intra-specific variation was observed. Genome size was not correlated with diploid number, suggesting that chromosomal evolution at this level is independent of total DNA content. A hypothetical taxonomic unit optimization procedure was carried out using genome size change on a Wagner tree derived from allozyme data. Allozyme evolution and genome size change are linked by a weak, but significant, negative correlation suggestive of preferential genic evolution in the absence of genome size evolution.

Animals↗
PubMed2006

Chromosomal mechanisms underlying the karyotype evolution of the oriental voles (Muridae, Eothenomys).

We have investigated the karyotype relationships of two oriental voles, i.e. the Yulong vole (Eothenomys proditor, 2n = 32) and the large oriental vole (Eothenomys miletus, 2n = 56) as well as the Clarke's vole (Microtus clarkei, 2n = 52), by a combined approach of cross-species chromosome painting and high-resolution G-banding comparison. Chromosome-specific painting probes were generated from flow-sorted chromosomes of E. proditor and hybridized onto metaphases of E. proditor, E. miletus and M. clarkei, leading to the establishment of genome-wide comparative chromosome maps. Our results demonstrate that Robertsonian translocations (centric fusions) have played a major role in the karyotype evolution of oriental voles with no obvious evidence for the involvement of tandem fusions as proposed previously and that the genome organizations of vole species are highly conserved. The comparative chromosome maps of these three vole species belonging to two phylogenetically distinct genera provide a framework for future studies on the karyotype evolution in voles.

Animals↗
PubMed1997

Comparative linkage mapping of genes on sheep chromosome 3 provides evidence of chromosomal rearrangements in the evolution of the Bovidae.

Three genes--parathyroid hormone-like hormone (PTHLH), insulin-like growth factor 1 (IGF 1), and retinoic acid receptor gamma (RARG)--have been mapped to sheep (Ovis aries) chromosome 3 (OAR 3). The order and genetic distances between loci on OAR 3 are similar to those on cattle (Bos taurus) chromosome 5, as expected from their close evolutionary relationship. The OAR 3 linkage map shows conserved synteny with human chromosome 12, but there are at least two rearrangements in gene order between the species.

Animals↗
PubMed1982

Primary structure of the chromosomal origins (oriC) of Enterobacter aerogenes and Klebsiella pneumoniae: comparisons and evolutionary relationships.

The nucleotide sequences of the Enterobacter aerogenes and Klebsiella pneumoniae DNA replication origins (oriC) were determined and compared with those of Escherichia coli and Salmonella typhimurium. Four interrelated, 9-base-pair repeats were identified from the conserved regions within the minimal origin. Evolutionary rates calculated from the minimal origin sequences yielded a quantitative phylogenic tree which agreed with the taxonomic classification of these genera.

Base Sequence↗
PubMed1999

Mosquito genomes: structure, organization, and evolution.

A great deal of information has been accumulated on chromosome numbers and heterochromatin distribution as well as on genome size and organization in the mosquito family Culicidae. A number of trends in genome evolution emerge when these data are reviewed in light of recent cladistic phylogenies of Culicidae and its sister families. Anophelinae have heteromorphic sex chromosomes and a small genome size, and repetitive elements are distributed in a long-period interspersion pattern. In contrast, Culicinae have homomorphic sex chromosomes, and repetitive DNA is organized in a short-period interspersion pattern. There has been a general increase in genome size during the evolution of culicine tribes. The organization of the ancestral culicid genome remains uncertain awaiting studies on genome organization in Chaoboridae-Corethrellidae taxa. The most parsimonious hypothesis for the evolution of sex chromosomes and genome organization in Culicidae would be that homomorphic sex chromosomes and a long-period interspersion pattern was ancestral in lineages leading to Toxorhynchitinae and Culcinae. Larger genomes developed in subsequent culicine lineages through accumulation of short-period interspersed repetitive elements. Heteromorphic sex chromosomes evolved early in the evolution of Anophelinae, and a long-period interspersion pattern was retained. The alternative scenario proposed by Rao and Rai (1987a) is that Culicidae arose from a chaoborid Mochlonyx-like ancestor with heteromorphic sex chromosomes and possibly short-period interspersion. This scenario would require the loss of heteromorphic sex chromosomes in the lineage leading to Toxorhynchitinae and Culicinae and the "shedding" of repetitive elements in the lineage leading to Anophelinae. Several interesting patterns have emerged from studies of C-banding, and the distribution of heterochromatin in Culicidae and phylogenies derived from these studies are supported by the modern cladistic analyses. Recent intensive multipoint linkage map studies suggest that recombination frequencies per genome have remained relatively constant over the course of culicid evolution such that Anophelinae, with a relatively small genome size, has a linkage map of similar size to Aedini. As a consequence, taxa in Anophelinae have higher amounts of recombination per haploid genome size than Culicinae. Although several key questions have yet to be addressed, the Culicidae remain one of the best-studied systems of genome evolution in animals.

Animals↗
PubMed1982

The chromosomal origin of replication (oriC) of Erwinia carotovora.

The chromosomal DNA replication origin (oriC) of the plant pathogen Erwinia carotovora has been isolated and sequenced. The minimal E. carotovora oriC regional functional in Escherichia coli is a 374 base pair region located on a 7.9 kilobase pair SalI fragment which also contains a functional asnA gene. Differences between the nucleotide sequence of the minimal origin regions of E. carotovora and those of E. coli and Salmonella typhimurium are clustered nucleotide substitutions, with regions of complete homology, up to 19 base pairs long, between the three origins. Nine GATC sites are found in the minimal origin, and all are conserved. In contrast, the region toward asnA from the minimal origin shows little clustering and the differences occur mainly every third nucleotide, suggesting that this region is a protein coding region.

Base Sequence↗
PubMed1997

The genes of the lysosomal cysteine proteinases cathepsin B, H, L, and S map to different mouse chromosomes.

The mouse genes for the lysosomal cysteine proteinases cathepsin B, H, L, and S were mapped to Chromosomes (Chrs) 14, 9, 13, and 3, respectively. Two of the DNA probes used in this study detected an additional, independently segregating locus. The cathepsin B-specific probe hybridized to a locus on Chr 2, and the cathepsin H probe to a locus on the X Chr. These loci either correspond to pseudogenes or to cathepsin B- and cathepsin H-related genes. The four cysteine proteinases mapped in this study lie within known regions of conserved synteny between mouse and human chromosomes, when compared with the corresponding positions of their human homologs. Assuming that the genes of the cysteine proteinase gene family arose from a common ancestral gene, our results suggest that these four cysteine proteinases had been dispersed over different chromosomes before separation of mouse and human in evolution.

Animals↗
PubMed1998

Vertebrate genome evolution and the zebrafish gene map.

In chordate phylogeny, changes in the nervous system, jaws, and appendages transformed meek filter feeders into fearsome predators. Gene duplication is thought to promote such innovation. Vertebrate ancestors probably had single copies of genes now found in multiple copies in vertebrates and gene maps suggest that this occurred by polyploidization. It has been suggested that one genome duplication event occurred before, and one after the divergence of ray-finned and lobe-finned fishes. Holland et al., however, have argued that because various vertebrates have several HOX clusters, two rounds of duplication occurred before the origin of jawed fishes. Such gene-number data, however, do not distinguish between tandem duplications and polyploidization events, nor whether independent duplications occurred in different lineages. To investigate these matters, we mapped 144 zebrafish genes and compared the resulting map with mammalian maps. Comparison revealed large conserved chromosome segments. Because duplicated chromosome segments in zebrafish often correspond with specific chromosome segments in mammals, it is likely that two polyploidization events occurred prior to the divergence of fish and mammal lineages. This zebrafish gene map will facilitate molecular identification of mutated zebrafish genes, which can suggest functions for human genes known only by sequence.

Animals↗
PubMed2001

Genetic heterogeneity and clonal evolution in neuroblastoma.

Tumour heterogeneity and clonal evolution at the genetic level may explain the development of malignant or resistant disease during clinical progression of neuroblastoma (NB). In this report we use 1p allelic analysis and DNA ploidy to evaluate clonal heterogeneity and clonal selection in vivo. We studied a total of 69 tumours from 29 patients with NB. To evaluate tumour heterogeneity and clonal evolution in vivo we used a panel of polymorphic allelic markers mapping to chromosome 1. 33 tumours from 12 patients (group 1) were obtained from different sites during the same surgery or at sequential surgeries without intervening chemotherapy to evaluate genetic heterogeneity. Paired samples from 10 patients (group 2) were used to evaluate clonal selection before and after chemotherapy. In 6 cases paired tumours and derived cell lines were studied. Analysis of DNA ploidy changes by karyotype, FISH and flow cytometry was performed in 15 tumours from 6 multiply recurred local-regional (LR) NB patients. Allelotype study revealed that 66% (8/12) of group 1 samples were heterogeneous, with distinct allelic patterns in tumour samples separated by time or location. In group 2 allelic patterns were different in post-chemotherapy specimens in 60% (6/10). DNA ploidy analysis showed that pre-chemotherapy samples contained 2 distinct ploidy clones, one diploid and one triploid, whereas all post-chemotherapy tumor samples were 100% diploid. These findings suggest that NB exhibits a high degree of clonal heterogeneity and clonal evolution occurs during the course of therapy and clinical progression.

Chromosomes, Human, Pair 1↗
PubMed1976

Translocations of acrocentric chromosomes and their implications in the evolution of sheep (Ovis).

Cytogenetic evidence suggests that the caprids (sheep and goats) evolved from a common ancestor with a 2n=60 karyotype. Although goats (Capra) retained the primitive 2n=60 karyotype, sheep (Ovis) underwent a sequential reduction in the number of chromosomes by means of acrocentric translocation. The formation of the first metacentric autosome (M1) occurred in the aoudad (Ammotragus) and urial (O. vignei), resulting in a 2n=58 karyotype. The G-bands are homologous, which implies both genotypes arose from a common ancestor, possibly a rupicaprid. Based on G-bands, acrocentric chromosomes 1 and 7 of the 2n=60 karyotype formed the M1. The X chromosome, which is the second longest acrocentric in the 2n=60 karyotype, became the longest acrocentric in Ammotragus and Ovis (2n=58). The second pair of metacentrics to evolve, which is ranked in the M3 position of the 2n=54 karotype, resulted from the translocations of acrocentric chromosomes 4 and 14 or 15 in the 2n=60 karyotype. The M2 was the third pair of metacentrics to be formed and resulted from the translocations of acrocentric chromosomes 3 and 12 or 13 in the 2n=60 karyotype. The G-bands of all 2n=54 karyotypes are homologous, which indicates origin from a common ancestor. Evidence is presented that suggests a prezygotic selection is bringing about a reduction in diploid chromosome numbers. The possible roles of fission and fusion in the karyotypic evolution of Ovis are discussed.

Animals↗
PubMed1994

The karyotype of Alligator mississippiensis, and chromosomal mapping of the ZFY/X homologue, Zfc.

Comparative mapping studies of X-linked genes in mammals have provided insights into the evolution of the X chromosome. Many reptiles including the American alligator, Alligator mississippiensis, do not appear to possess heteromorphic sex chromosomes, and sex is determined by the incubation temperature of the egg during embryonic development. Mapping of homologues of mammalian X-linked genes in reptiles could lead to a greater understanding of the evolution of vertebrate sex chromosomes. One of the genes used in the mammalian mapping studies was ZFX, an X-linked copy of the human ZFY gene which was originally isolated as a candidate for the mammalian testis-determining factor (TDF). ZFX is X-linked in eutherians, but maps to two autosomal locations in marsupials and monotremes, close to other genes associated with the eutherian X. The alligator homologue of the ZFY/ZFX genes, Zfc, has been isolated and described previously. A detailed karyotype of A. mississippiensis is presented, together with chromosomal in situ hybridisation data localising the Zfc gene to chromosome 3. Further chromosomal mapping studies using eutherian X-linked genes may reveal conserved chromosomal regions in the alligator that have become part of the eutherian X chromosome during evolution.

Alligators and Crocodiles↗
PubMed1997

A third neurofibromatosis type 1 (NF1) pseudogene at chromosome 15q11.2.

Sequences related to the neurofibromatosis type 1 (NF1) gene have been identified on several human chromosomes. In the centromeric region of chromosomes 14 and 15, two NF1 pseudogenes have been described. Sequence comparison between NF1-related exons amplified from two yeast artificial chromosome clones hybridizing to chromosomal region 15q11.2 and published NF1-related sequences localized at 15q11.2 suggested that a third NF1 pseudogene resides in this chromosomal region. The previous localization of an NF1-related locus to the telomeric part of chromosome 15 could not be confirmed by us. Our findings further support pericentromeric spreading of partial NF1 gene copies at chromosome 15q11.2 during evolution.

Base Sequence↗
PubMed2002

Chromosome painting refines the history of genome evolution in hares and rabbits (order Lagomorpha).

Fluorescence in situ hybridization (FISH) was used to define homologous segments among representatives of 7 of the 11 recognized leporid genera. Chromosome painting using 22 rabbit chromosome-specific paints derived from flow-sorted chromosomes revealed that at least 18 fusions and six fissions differentiate the extant karyotypes from the presumed ancestral state (2n = 48). The riverine rabbit, Bunolagus monticularis, has the most derived karyotype, differing from the ancestor by seven fusions and five fissions, followed by Pronolagus rupestris, with four fusions and one fission. These findings are consistent with the proposed Palaeolaginae/Leporinae dichotomy in the lagomorphs. The molecular cytogenetic data allow for a refinement of the structural changes that have shaped genome evolution in this group of mammals and underscore the rapid radiation of the Leporidae suggested by mitochondrial DNA sequence data.

Animals↗
PubMed1995

The reduction principle for recombination under density-dependent selection.

In diploid random mating populations with constant viability selection, genetic modifiers of recombination, introduced near equilibria that exhibit genetic association, invade if they reduce recombination. In this study we combine ecological and standard populations genetics in a haploid multilocus model that includes density-dependent regulation of population size and weak density-dependent differential selection among the multilocus genotypes. An allele that affects recombination among the genes contributing to the ecological selection, introduced near a stable equilibrium of the ecological-genetic system, invades if it reduces a weighted average of the recombination rates among pairs of loci under selection. This generalizes the Reduction Principle for the evolution of recombination (M. W. Feldman and U. Liberman, Proc. Nat. Acad. Sci. USA 83, 4824-4827, 1986; L. A. Zhivotovsky, W. M. Feldman, and F. B. Christiansen, Theor. Popul. Biol. 44, 225-245, 1993). It is also shown that the stronger the extent of density-dependence, the weaker the selection for reduced recombination.

Alleles↗
PubMed1992

Comparative analysis of the mitochondrial genomes of Chlamydomonas eugametos and Chlamydomonas moewusii.

We report the cloning and physical mapping of the mitochondrial genome of Chlamydomonas eugametos together with a comparison of the overall sequence structure of this DNA with the mitochondrial genome of Chlamydomonas moewusii, its closely related and interfertile relative. The C. eugametos mitochondrial DNA (mtDNA) has a 24 kb circular map and is thus 2 kb larger than the 22 kb circular mitochondrial genome of C. moewusii. Restriction mapping and heterologous, fragment hybridization experiments indicate that the C. eugametos and C. moewusii mtDNAs are colinear. Nine cross-hybridizing restriction fragments common to the C. eugametos and C. moewusii mtDNAs, and spanning the entirely of these genomes, show length differences between homologous fragments which vary from 0.1 to 2.3 kb. A 600 bp subfragment of C. moewusii mtDNA, within one of these conserved fragments, showed no hybridization with the C. eugametos mtDNA. Of the 73 restriction sites identified in the C. eugametos and C. moewusii mtDNAs, five are specific to C. moewusii, eight are specific to C. eugametos and 30 are common to both species. Hybridization experiments with gene probes derived from protein-coding and ribosomal RNA-coding regions of wheat and Chlamydomonas reinhardtii mtDNAs support the view that the small and large subunit ribosomal RNA-coding regions of the C. eugametos and C. moewusii mtDNAs are interrupted and interspersed with each other and with protein-coding regions, as are the ribosomal RNA-coding regions of C. reinhardtii mtDNA; however, the specific arrangement of these coding elements in the C. eugametos and C. moewusii mtDNAs appears different from that of C. reinhardtii mtDNA.

Animals↗
PubMed1989

Deletions in processed pseudogenes accumulate faster in rodents than in humans.

The relative rates of point nucleotide substitution and accumulation of gap events (deletions and insertions) were calculated for 22 human and 30 rodent processed pseudogenes. Deletion events not only outnumbered insertions (the ratio being 7:1 and 3:1 for human and rodent pseudogenes, respectively), but also the total length of deletions was greater than that of insertions. Compared with their functional homologs, human processed pseudogenes were found to be shorter by about 1.2%, and rodent pseudogenes by about 2.3%. DNA loss from processed pseudogenes through deletion is estimated to be at least seven times faster in rodents than in humans. In comparison with the rate of point substitutions, the abridgment of pseudogenes during evolutionary times is a slow process that probably does not retard the rate of growth of the genome due to the proliferation of processed pseudogenes.

Animals↗
PubMed1981

Evolutionary tree for apes and humans based on cleavage maps of mitochondrial DNA.

The high rate of evolution of mitochondrial DNA makes this molecule suitable for genealogical research on such closely related species as humans and apes. Because previous approaches failed to establish the branching order of the lineages leading to humans, gorillas, and chimpanzees, we compared human mitochondrial DNA to mitochondrial DNA from five species of ape (common chimpanzee, pygmy chimpanzee, gorilla, orangutan, and gibbon). About 50 restriction endonuclease cleavage sites were mapped in each mitochondrial DNA, and the six maps were aligned with respect to 11 invariant positions. Differences among the maps were evident at 121 positions. Both conserved and variable sites are widely dispersed in the mitochondrial genome. Besides site differences, ascribed to point mutations, there is evidence for one rearrangement: the gorilla map is shorter than the other owing to the deletion of 95 base pairs near the origin of replication. The parsimony method of deriving all six maps from a common ancestor produced a genealogical tree in which the common and pygmy chimpanzee maps are the most closely related pair; the closest relative of this pair is the gorilla map; most closely related to this trio is the human map. This tree is only slightly more parsimonious than some alternative trees. Although this study has given a magnified view of the genetic differences among humans and apes, the possibility of a three-way split among the lineages leading to humans, gorillas, and chimpanzees still deserves serious consideration.

Animals↗