Biochemical Polymorphisms and Genetic Relationships in Rodents of the Genera Oryzomys and Oligoryzomys (Sigmodontinae) from Brazil

An electrophoretic analysis of 12 allozyme systems (14 loci, 40 alleles) was performed in the rodent genera Oryzomys and Oligoryzomys, in order to determine the levels of genetic variability within and among populations and species. One hundred and fifty-five individuals from 16 populations of Oryzomys russatus, Or. angouya, Oligoryzomys flavescens, and O1. nigripes species were trapped in nine Brazilian localities. Genetic divergence among populations, as well as the interpopulational gene diversity, was higher in Oryzomys than in Oligoryzomys. The dendrogram of the phenetic relationships among the 16 populations of these four species displays three clusters: the first one joins the O1. flavescens populations with those of O1. nigripes; the second groups the populations of Or. russatus, and the last assembles the populations of Or. angouya. The genetic parameters analyzed reveal that the species belonging to the genus Oryzomys are genetically more structured than those of Oligoryzomys, the latter presenting lower levels of intrademe genetic differentiation (G(ST)')     

Molecular phylogeny of the genus Oryzomys (Rodentia: Sigmodontinae) based on cytochrome b DNA sequences

The genus Oryzomys comprises 40 species arranged in several species groups. To test the monophyly of three Oryzomys species groups ("capito," nitidus, and subflavus), we analyzed, by distance, parsimony, and maximum-likelihood (ML), 801 bp of the mitochondrial gene cytochrome b. Our results did not sustain the monophyly of Oryzomys nor of the nitidus and subflavus species groups. Within the "capito" species group, O. perenensis appeared as a valid species, as a sister branch of the clade formed by O. megacephalus and O. laticeps. Within the nitidius species group, only the association between O. nitidus and O. lamia was well supported.The subflavus species group split into two clades: one with O. subflavus karyomorphotypes and another grouping O. angouya with species of different genera in the parsimony, distance, and ML trees.     

Genetic differentiation in populations of the yellow-necked mouse,Apodemus flavicollis,harbouring B chromosomes in different frequencies

Two alternative models are used to explain maintenance of polymorphism of B chromosomes (Bs) in populations of a great number of species. The parasitic model suggests deleterious effects of Bs on fitness of carriers, while the heterotic model assumes that, in the absence of drive, equilibrium is produced by beneficial effects of Bs at low numbers. In order to determine the potential contribution of Bs to genetic differentiation and diversity, four populations of Apodemus flavicollis, differing in frequency of Bs (from 0.23 to 0.38) and settled in ecologically different habitats, were analyzed by 471 AFLP markers. Although numerous loci were demonstrated to be population specific, none of them was associated with individuals with Bs. AMOVA showed that the presence of Bs does not affect population differentiation, pointing to greater genetic similarity of Bs to A chromosomes. The greatest genetic diversity (0.241) was found in the population settled in optimal conditions for this species featured by the lowest frequency of animals with Bs (0.23). We found that the majority of loci marked as loci under directional selection, are characteristic of either a population with lower or one with a higher frequency of Bs. Several loci detected as outliers were associated with environmental variables that could directly and/or indirectly influence population dynamics of A. flavicollis. Thus, we suggest that the different frequency of Bs carriers in populations is related to adaptive differentiation to diverse habitats, which is in accordance with the heterotic model of Bs maintenance.     

The distribution of B chromosomes across species

In this review we look at the broad picture of how B chromosomes are distributed across a wide range of species. We review recent studies of the factors associated with the presence of Bs across species, and provide new analyses with updated data and additional variables. The major obstacle facing comparative studies of B chromosome distribution is variation among species in the intensity of cytogenetic study. Because Bs are, by definition, not present in all individuals of a species, they may often be overlooked in species that are rarely studied. We give examples of corrections for differences in study effort, and show that after a variety of such corrections, strong correlations remain. Several major biological factors are associated with the presence of B chromosomes. Among flowering plants, Bs are more likely to occur in outcrossing than in inbred species, and their presence is also positively correlated with genome size and negatively with chromosome number. They are no more frequent in polyploids than in diploids, nor in species with multiple ploidies. Among mammals, Bs are more likely to occur in species with karyotypes consisting of mostly acrocentric chromosomes. We find no evidence for an association with chromosome number or genome size in mammals, although the sample for genome size is small. The associations with breeding system and acrocentric chromosomes were both predicted in advance, but those with genome size and chromosome number were discovered empirically and we can offer only tentative explanations for the very strong associations we have uncovered. Our understanding of why B chromosomes are present in some species and absent in others is still in its infancy, and we suggest several potential avenues for future research.     

Extensive polymorphism and chromosomal characteristics of ribosomal DNA in a loach fish, Cobitis vardarensis (Ostariophysi, Cobitidae) detected by different banding techniques and fluorescence in situ hybridization (FISH)

When surveying the karyotype diversity of European loaches of the genus Cobitis to identify species involved in hybrid polyploid complexes, an extensive polymorphism in number and location of NORs was discovered in C. vardarensis using Ag-staining, C-banding, CMA₃-fluorescence and fluorescence in situ hybridization (FISH). This species had 2n=50, the karyotype contained 13 pairs of metacentric, 10 pairs of submetacentric and two pairs of subtelocentric chromosomes. The NOR-bearing chromosomes included one medium-sized metacentric pair with a large CMA₃-positive heterochromatic pericentromeric block, one small metacentric as well as one large submetacentric pairs. Ribosomal sites were always located in telomeres of these chromosomes. Each of the pair of NOR-bearing chromosomes occurred in three variants – (1) presence and/or (2) absence of NORs on both homologues and (3) heterozygous combination where only one of the homologues bears NORs. Altogether, 10 different NOR cytotypes from 27 theoretically possible ones were discovered among 20 indviduals examined. The number of NORs ranged from two to five per specimen. The results regarding the number and locations of NORs as revealed by banding techniques were confirmed using FISH with rDNA probe. NOR sites were of CMA₃-positive, suggesting that ribosomal sites are associated with GC-rich DNA. Very similar structural polymorphism with multiple NORs is expressed in the Danubian loach C. elongatoides indicating a close relationship between both species.     

The odd-even effect in mitotically unstable B chromosomes in grasshoppers

The odd-even effect, by which B chromosomes are more detrimental in odd numbers, has been reported in plants and animals. In grasshoppers, there are only a few reports of this effect and all were referred to as traits related to the formation of aberrant meiotic products (AMPs). Here we review the existing information about B chromosome effects on AMPs, chiasma frequency and the number of active nucleolus organizer regions (NORs) per cell. Polysomy for A chromosomes and B chromosomes are two kinds of chromosome polymorphism frequently found in grasshoppers. In some aspects, e.g. meiotic behaviour and mitotic instability leading to individual mosaicism (in the case of mitotically unstable Bs), polysomic As show similar characteristics to B chromosomes. In fact, polysomy is regarded as one of the main mechanisms for B chromosome origin. Here we review some features of meiotic behaviour in known cases of polysomy and mitotically unstable Bs in grasshoppers, in looking for possible causes for the odd-even effect. In all these traits, the odd-even effect was apparent, although its appearance was not universal in any case, with variation among species or populations within the same species. The equational division and lagging of the extra chromosomes, when univalents, could favour the appearance of abnormal meiotic products, and the formation of bivalents, when there are two or more extra chromosomes, inhibits this process. Therefore, the odd-even effect might be a consequence of the concomitant operation of both aspects of extra chromosome meiotic behaviour. The possibility that the odd-even effect might result from an increase in cell stress generated by odd numbers is suggested.     

The B chromosomes in Brachycome

This review presents a historical account of studies of B chromosomes in the genus Brachycome Cass. (synonym: Brachyscome) from the earliest cytological investigations carried out in the late 1960s though to the most recent molecular analyses. Molecular analyses provide insights into the origin and evolution of the B chromosomes (Bs) of Brachycome dichromosomatica, a species which has Bs of two different sizes. The larger Bs are somatically stable whereas the smaller, or micro, Bs are somatically unstable. Both B types contain clusters of ribosomal RNA genes that have been shown unequivocally to be inactive in the case of the larger Bs. The large Bs carry a family of tandem repeat sequences (Bd49) that are located mainly at the centromere. Multiple copies of sequences related to this repeat are present on the A chromosomes (As) of related species, whereas only a few copies exist in the A chromosomes of B. dichromosomatica. The micro Bs share DNA sequences with the As and the larger Bs, and they also have B-specific repeats (Bdm29 and Bdm54). In some cases repeat sequences on the micro Bs have been shown to occur as clusters on the A chromosomes in a proportion of individuals within a population. It is clear that none of these B types originated by simple excision of segments from the A chromosomes.     

Selfish DNA and breeding system in flowering plants

In many species, some individuals carry one or more B chromosomes: extra, or supernumerary chromosomes not part of the normal complement. In most well-studied cases, Bs lower the fitness of their carrier and persist in populations only because of accumulation mechanisms analogous to meiotic drive. It has been suggested that such genomic parasites are expected to persist only in outcrossed sexual species, in which uninfected lines of descent can be continuously reinfected; in inbred or asexual species, all selection is between lines of descent, and the genomic parasites are either lost or must evolve into commensals or mutualists. Here we present a simple population genetic model of the effect of outcrossing rate on the frequency of B chromosomes, and find that outcrossing facilitates the spread of parasitic Bs, but inhibits the spread of mutualists. Data compiled from the literature on breeding system and B chromosomes of British plants indicate that Bs are much more likely to be reported from obligately outcrossed species than inbred species. These results support the ideas that most B chromosomes are parasitic, and that breeding systems play a central role in the biology of selfish genes.     

The mammalian model for population studies of B chromosomes: the wood mouse (Apodemus)

The presence of B chromosomes was reported in six species of the genus Apodemus (A. peninsulae, A. agrarius, A. sylvaticus, A. flavicollis, A. mystacinus, A. argenteus). High frequencies of Bs were recorded particularly in A. peninsulae and A. flavicollis. The origin of Bs in Apodemus seems to be rather ancient, and it is possible that the supernumerary elements, and/or a tendency for their appearance, were inherited from the common ancestor of the extant species. We have not found any correlated changes between frequencies of Bs and the level of protein polymorphism and/or heterozygosity assessed in electrophoretic studies. No measurable effect of Bs on overall genetic variability was thus revealed in studied populations. The pattern of evolutionary dynamics of Bs can be distinctly different between geographical populations, and both the parasitic and the heterotic models can be applied to explain the maintenance of Bs in different populations. Further studies are desirable to improve our understanding of the complicated evolutionary dynamics of Bs in the Apodemus species. An essential condition for success in this respect is much more detailed information on inheritance and the molecular structure of Bs.     

B chromosomes and genome size in flowering plants.

B chromosomes are extra chromosomes found in some, but not all, individuals within a species, often maintained by giving themselves an advantage in transmission, i.e. they drive. Here we show that the presence of B chromosomes correlates to and varies strongly and positively with total genome size (excluding the Bs and corrected for ploidy) both at a global level and via a comparison of independent taxonomic contrasts. B chromosomes are largely absent from species with small genomes; however, species with large genomes are studied more frequently than species with small genomes and Bs are more likely to be reported in well-studied species. We controlled for intensity of study using logistic regression. This regression analysis also included effects of degree of outbreeding, which is positively associated with Bs and genome size, and chromosome number, which is negatively associated with Bs and genome size, as well as variable ploidy (more than one ploidy level in a species). Genome size, breeding system and chromosome number all contribute independently to the distribution of B chromosomes, while variable ploidy does not have a significant effect. The genome size correlates are consistent with reduced selection against extra DNA in species with large genomes and with increased generation of B sequences from large A genomes.     

Derived cytogenetic traits, multiple NORs and B chromosomes in the compact karyotype of Canthigaster figueiredoi (Tetraodontiformes)

The Tetraodontiformes are one of the main irradiation lineages of Teleosts representing a highly specialized group. Among its families, Tetraodontidae has the lowest DNA/cell content of the vertebrates, and for this reason has been used as a model group for genomic evolution studies. Seeking to widen the cytogenetic database of this family, we performed a chromosomal analysis of the species Canthigaster figueiredoi using conventional staining, Ag-NORs, C-banding, base-specific fluorochromes DAPI-CMA(3), and in situ hybridization with 18S rDNA probe. This species has 2n=36 (10 m+6sm+20a; FN=52). Multiple Ag-NORs (CMA(3)(+)) sites were detected on the four chromosome pairs. Heterochromatic blocks (CMA(3)(+)) were present in the centromeric regions of most of the pairs, extending on the short arm of some chromosomes. A GC-positive polymorphic heterochromatic region was identified in some of the individuals, in one or both of the homologs of the 6th pair. The presence of heteromorphic B microchromosomes was detected in the karyotype of one female, exhibiting intra-individual variation of 0-3 Bs. The occurrence of heterochromatic polymorphisms, multiple NORs, and B chromosomes in C. figueiredoi are very infrequent events in marine fish. They are probably associated to the accentuated restructuring and genomic reduction suffered by this family.     

B染色体起源的研究进展

B染色体(简写为Bs)起源的传统观点是认为它起源于携带者所在物种的基因组.目前又发现了许多新的证据来推测Bs的起源.它可能具有两种起源:种内起源和种间起源(起源于另一物种的基因组),且有证据表明同一物种的Bs可能是多次起源,同时对Bs的起源机制也作了总结.认为B8起源的研究已取得了一定的进展,但要给Bs起源下一个确切的结论仍需要大量的实验证据.     

Single-cell quantitative RT-PCR analysis of Cpt1b and Cpt2 gene expression in mouse antral oocytes and in preimplantation embryos

Among crustacean Decapoda numerical chromosome variability is frequent, and it has been hypothesized that the presence of supernumerary chromosomes accounts for this variability. Thanks to the improvement of cytogenetic analysis by chromosomal banding techniques, supernumerary B chromosomes (Bs) have been demonstrated in Nephrops norvegicus, Homarus americanus,Palinurus elephas and P. mauritanicus, belonging to different crustacean families. In all four species Bs were variable in number, mainly heterochromatic and undigested by various endonucleases, and in meiosis they showed non-Mendelian segregation. Compared to the other chromosomes of the complement, the Bs are very small in almost all species, but some of them were very large in N. norvegicus.     

B chromosomes in populations of mammals

B chromosomes (Bs) have been found in 55 out of 4629 living species of mammals. The summarized data show great variability in types of mammalian Bs, including differences in size, shape and molecular composition. This variability extends to the origin, mode of transmission and population dynamics. In general, B chromosomes in mammals do not differ from Bs found in other animal or plant species, but some peculiarities do exist. Most species in which Bs are found are widespread. Some data support the view that Bs may contribute to the successful expansion of some of these species, but it is possible that Bs are just more easily scored in them due to their frequent occurrence. Most of these species are also characterized by cycling fluctuations of abundance and characteristic social organization that produce conditions favorable for Bs to spread. All areas of research on Bs in mammals suffer from lack of data, emphasizing the necessity for intensified research on the molecular structure and ways of maintenance of Bs in populations.     

Prevalence of B chromosomes in Orthoptera is associated with shape and number of A chromosomes

We analyze the prevalence of B chromosomes in 1,601 species of orthopteran insects where chromosome number and shape are known. B chromosomes have been reported in 191 of these species. Bs are not uniformly distributed among orthopteran superfamilies, with evident hotspots in the Pyrgomorphoidea (32.3% of species carrying Bs), Grylloidea (14.9%), Acridoidea (14.6%) and Tetrigoidea (14.3%). As expected under the theory of centromeric drive, we found a correlation between B chromosome presence and A chromosome shape-Bs are more frequent in karyotypes with more acrocentric A chromosomes. We also found that Bs are less common in species with high chromosome numbers and appear to be most common at the modal chromosome number (2n = 24). Study effort, measured for each genus, was not associated with B prevalence, A chromosome shape or A chromosome number. Our results thus provide support for centromeric drive as an important and prevalent force in the karyotypic evolution of Orthoptera, just as it appears to be in mammals. We suggest that centromeric drive may provide a mechanistic explanation for White's principle of karyotypic orthoselection.     

鱼类染色体的荧光显带研究

应用GC碱基特异性荧光染料色霉素A,辅以AT减基特异性荧光染料Hoechst33258,DAPI或喹吖因对鲤鱼,鲫鱼,大鳞副泥鳅和的有丝分裂染色体及黄鳝的有丝分裂和减数分裂染色体进行了荧光显带研究,结果发现,色霉素A3可以特异性地显示鱼类有丝分裂及减数分裂各个时期核仁组织区NORS的存在,Hoechst33258,DAPI或喹吖因则使这些区域（NORs)淡染,大鳞副泥鳞的染色体NORs 分布位置具有性别,根据实验结果,对有关鱼类染色体的荧光染色研究及其应用进行了讨论。     

Chromosome banding in amphibia

In the chromosomes of 12 frog species of the suborder Diplasiocoela (Amphibia, Anura), the constitutive heterochromatin and the nucleolus organizer regions (NORs) have been specifically stained. On most of the chromosomes, aside from the centric heterochromatin, telomeric and interstitial C-bands were also found. The various C-bands display a very variable reaction to alkaline pretreatment; this indicates heterogeneity in the constitutive heterochromatin. Sex chromosomes could not be identified in any of the species studied. The number and chromosomal positions of the NORs vary quite strongly between species and between families. In 4 species of the genus Rana, there were, aside from the standard-NORs in chromosome pair 10, between 4 and 14 extra, small NORs detectable in the smaller chromosome pairs. As possible causal mechanism of these additional small NORs the reintegration of amplified rDNA during amphibian oogenesis is suggested. Q- or G-bands could only be recognized in mitotic prophase chromosomes. The strong spiralization of metaphase chromosomes prevents the differential demonstration of Q- or G-bands in the euchromatic regions.     

Cytogenetic analysis of the neotropical spider Nephilengys cruentata (Araneomorphae, Tetragnathidae): standard staining nors, C-bands and base-specific fluorochromes.

The aim of this work is to characterize Nephilengys cruentata in relation to the diploid number, chromosome morphology, type of sex determination chromosome system, chromosomes bearing the Nucleolar Organizer Regions (NORs), C-banding pattern, and AT or GC repetitive sequences. The chromosome preparations were submitted to standard staining (Giemsa), NOR silver impregnation, C-banding technique, and base-specific fluorochrome staining. The analysis of the cells showed 2n = 24 and 2n = 26 chromosomes in the embryos, and 2n = 26 in the ovarian cells, being all the chromosomes acrocentric. The long arm of the pairs 1, 2 and 3 showed an extensive negative heteropycnotic area when the mitotic metaphases were stained with Giemsa. The sexual chromosomes did not show differential characteristics that allowed to distinguish them from the other chromosomes of the complement. Considering the diploid numbers found in N. cruentata and the prevalence of X1X2 sex determination chromosome system in Tetragnathidae, N. cruentata seems to possess 2n = 24 = 22 + X1X2 in the males, and 2n = 26 = 22 + X1X1X2X2 in the females. The pairs 1, 2 and 3 showed NORs which are coincident with the negative heteropycnotic patterns. Using the C-banding technique, the pericentromeric region of the chromosomes revealed small quantity or even absence of constitutive heterochromatin, differing of the C-banding pattern described in other species of spiders. In N. cruentata the fluorochromes DAPI/DA, DAPI/MM and CMA3/DA revealed that the constitutive heterochromatin is rich in AT bases and the NORs possess repetitive sequences of GC bases.     

B chromosomes and Robertsonian fusions of Dichroplus pratensis (Acrididae): intraspecific support for the centromeric drive theory

We tested the centromeric drive theory of karyotypic evolution in the grasshopper Dichroplus pratensis, which is simultaneously polymorphic for eight Robertsonian fusions and two classes of B chromosomes. A logistic regression analysis performed on 53 natural populations from Argentina revealed that B chromosomes are more probably found in populations with a higher proportion of acrocentric chromosomes, as the theory predicts. Furthermore, frequencies of B-carrying individuals are significantly negatively correlated with the mean frequency of different Robertsonian fusions per individual. No significant correlations between presence/absence or frequency of Bs, and latitude or altitude of the sampled populations, were found. We thus provide the first intraspecific evidence supporting the centromeric drive theory in relation to the establishment of B chromosomes in natural populations.