Chromosomal evolution in Malagasy lemurs. VIII. Chromosome banding studies of Lepilemur ruficaudatus, L leucopus, and L septentrionalis

The karyotypes of three Lepilemuridae species, Lepilemur ruficaudatus, L leucopus, and L septentrionalis, are described and compared. An almost complete analogy of chromosome banding is exhibited. Several complex chromosomal rearrangements, especially end-to-end translocations, have occurred in the evolution of these species. The chromosomal data indicate that the species studied are well separated. In addition, their common chromosomal characters show that they constitute a clearly distinct family among the lemurs.     

Reorganization of the X chromosome in voles of the genus Microtus

Comparative chromosomal analysis is a powerful tool in the investigation of the mechanisms of chromosomal evolution. The accuracy of the analysis depends on the availability of region-specific markers to follow the fate of the particular chromosomal region through the evolution of species. We have assigned 12 unique sequences to the euchromatic part of the vole X chromosome, which serve as reliable markers of chromosomal segments. Together with region-specific libraries and GTG banding, these markers allow us to delineate the homologous regions of the X chromosomes in five species of the genus Microtus. We found that X chromosomes of these species differ by numerous rearrangements and all rearrangements are clustered at specific breakpoints. Moreover, these breakpoints were found to colocalise with repetitive and/or duplicated DNA sequences. We suggest that clusters of repeated and/or duplicated DNA sequences have played a crucial role in the formation of rearrangement hot spots during evolution of the X chromosome in the subgenus Microtus.     

Chromosome comparison among five species of platyrrhini (Alouatta caraya,Aotus azarae,Callithrix jacchus,Cebus apella,andSaimiri sciureus)

Karyotypes of 82 individuals from five Platyrrhini species (Alouatta caraya, Aotus azarae, Callithrix jacchus, Cebus apella, andSaimiri sciureus) were studied and compared using a G-banding technique. Cytogenetic analysis showed full chromosome or full arm homologies among these geographically neighbouring species. A small number of chromosomal rearrangements (inversions, deletions, and translocations) could be detected among these taxa. These five species are closely related in chromosomal evolution. An interesting correspondance was found betweenCebus apella chromosomes and those of the other four species.Alouatta caraya andCebus apella are the closest species.Callithrix jacchus andAotus azarae would have the most separated karyotypes.     

Polytene chromosome relationships of five species of the Anopheles dirus complex in Thailand.

Photographic maps and rearrangements of each salivary gland polytene chromosome arm of Anopheles nemophilous (species F) and of An. dirus species A, B, C, and D of the Dirus group from natural populations in Thailand are presented. Structural conformation of heterokaryotypes and comparison of chromosome banding sequences reveal 10 paracentric inversions. The data on fixed inversion of 3Rb and inversion polymorphism of the X chromosome shared by these species were used to construct a phylogeny of the five members of the An. dirus complex, thereby outlining their patterns of speciation through chromosomal rearrangements.     

Genome evolution among cruciferous plants: a lecture from the comparison of the genetic maps of three diploid species--Capsella rubella, Arabidopsis lyrata subsp. petraea, and A. thaliana

Comparative mapping in cruciferous plants is ongoing, and recently two additional genetic maps of diploid Capsella and Arabidopsis lyrata subsp. petraea have been presented. We compared both maps with each other using the sequence map and genomic data resources from Arabidopsis thaliana as a reference. The ancestors of the species pair Capsella-Arabidopsis diverged from one another approximately 10-14 million years ago (mya), whereas Arabidopsis thaliana and Arabidopsis lyrata have been separated since roughly 5-6 mya. Our analysis indicated that among diploid Capsella and Arabidopsis lyrata all eight genetic linkage groups are totally colinear to each other, with only two inversions significantly differentiating these two species.By minimizing the number of chromosomal rearrangements during genome evolution, we presented a model of chromosome evolution involving all three species. From this scenario, it is obvious that Arabidopsis thaliana underwent a dramatic genome reconstruction, with a base chromosome number reduction from five to eight and with approximately 1.3 chromosomal rearrangements per million years. In contrast, the terminal lineage leading to Capsella has only undergone less than 0.09 rearrangements per million years. This is the same rate as calculated for Arabidopsis lyrata since its separation from the Capsella lineage 10-14 mya. These results are in strong contrast to all overestimated rates calculated from comparisons of the systems Arabidopsis thaliana and Brassica, and our data demonstrate the problematic nature of both model systems.     

Diagrammatic representation for chromosomal mutagenesis studies IV. Radiation-induced rearrangements in Ateles sp. (Primate,Platyrhini)

In order to study the induction of rearrangements by γ-rays in relation to chromosomal size and morphology, experiments were conducted in an Ateles, a species with a rather unusual karyotype among primates. It possesses some very large chromosomes, which tend to be too rarely affected, especially by intrachanges like inversions. Both their large size and their characteristic banding pattern suggest that this low involvement is not due to difficulty of analysis. This suggests very strongly that chromosomal involvement in rearrangements is not a function of size. The possible role of other factors involved in chromosomal rearrangements like chromosome position during interphase are discussed.     

Numerous small rearrangements of gene content,order and orientation differentiate grass genomes

Comparative genetic mapping has indicated that the grass family (Poaceae) exhibits extensive chromosomal collinearity. In order to investigate microcollinearity in these genomes, several laboratories have begun to undertake comparative DNA sequence analyses of orthologous chromosome segments from various grass species. Five different regions have now been investigated in detail, with four regions sequenced for maize, rice and sorghum, plus two for wheat and one for barley. In all five of these segments, gene rearrangements were observed in at least one of the comparisons. Most of the detected rearrangements are small, involving the inversion, duplication, translocation or deletion of DNA segments that contain only 1-3 genes. Even closely related species, like barley and wheat or maize and sorghum, exhibit approximately 20% alterations in gene content or orientation. These results indicate that thousands of small genetic rearrangements have occurred in several grass lineages since their divergence from common ancestors. These rearrangements have largely been missed by genetic mapping and will both complicate and enrich the use of comparative genetics in the grasses.     

Chromosome numbers, genome sizes, cell volumes and evolution of snake-head fish (family Channidae)

Chromosome number, C-value and cell volume studies were carried out on three species of the genus Channa , viz., C. punctatus, C. striatus and C. gachua . The chromosome number, karyotypic structure and DNA content per cell along with cell volume are reported and described. A series of chromosomal rearrangements are established in three different karyotypes along with polyploidy. Both pericentric inversion and Robertsonian fusion played a major role in chromosome rearrangements. The nuclear DNA content of these three species is within 19-29% of the present-day placental mammals, and is thus lower than the median amount for fishes in general and teleosts in particular. Their lower DNA content suggests that the three species of the family Channidae are highly specialized, and this is supported by their known morphologic, reproductive, behavioural and ecological characteristics.
The evolutionary significance of these chromosomal rearrangements, their origin and their mode of establishment are discussed. A probable phylogenetic model based on karyotype, C-value and chromosomal rearrangements of the genus is presented.     

Geographic patterns of chromosomal variation in South American marsh rats, Holochilus brasiliensis and H. vulpinus.

Karyotypes were prepared from 146 individuals, representing nine populations evenly spaced along a 2,000-km north-south transect in Paraguay and Argentina, to determine the nature, extent, and pattern of chromosomal variation in Holochilus brasiliensis chacarius and H. vulpinus. Two distinct patterns of chromosomal variation characterized these two species. In H. brasiliensis, the diploid number (2n) ranged from 48 to 56 and the nombre fondamental (NF) from 57 to 63. Four classes of chromosomal variation were found in populations of H. brasiliensis: whole-arm Robertsonian (Rb) translocations, including Rb changes with monobrachial homology, variation in the number and kind of supernumerary (B) chromosomes, centromeric rearrangements (putative pericentric inversions), and variation in the amount of euchromatin. The amount of structural variation was uniformly high in all populations of H. brasiliensis sampled, and all rearrangements appeared to be in Hardy-Weinberg proportions, corroborating the hypothesis that chromosomal rearrangements are not strongly underdominant in this species. In H. vulpinus, 2n ranged from 35 to 39 and NF from 57 to 61. Two classes of variation were found in this species: variation in the number, but not the kind, of supernumerary chromosomes and variation in the amount of euchromatin.     

Chromosomal rearrangements differentiating the ryegrass genome from the Triticeae, oat, and rice genomes using common heterologous RFLP probes

An restriction fragment length polymorphism (RFLP)-based genetic map of ryegrass (Lolium) was constructed for comparative mapping with other Poaceae species using heterologous anchor probes. The genetic map contained 120 RFLP markers from cDNA clones of barley (Hordeum vulgare L.), oat (Avena sativa L.), and rice (Oryza sativa L.), covering 664 cM on seven linkage groups (LGs). The genome comparisons of ryegrass relative to the Triticeae, oat, and rice extended the syntenic relationships among the species. Seven ryegrass linkage groups were represented by 10 syntenic segments of Triticeae chromosomes, 12 syntenic segments of oat chromosomes, or 16 syntenic segments of rice chromosomes, suggesting that the ryegrass genome has a high degree of genome conservation relative to the Triticeae, oat, and rice. Furthermore, we found ten large-scale chromosomal rearrangements that characterize the ryegrass genome. In detail, a chromosomal rearrangement was observed on ryegrass LG4 relative to the Triticeae, four rearrangements on ryegrass LGs2, 4, 5, and 6 relative to oat, and five rearrangements on ryegrass LGs1, 2, 4, 5, and 7 relative to rice. Of these, seven chromosomal rearrangements are reported for the first time in this study. The extended comparative relationships reported in this study facilitate the transfer of genetic knowledge from well-studied major cereal crops to ryegrass.     

Diagrammatic representation for chromosomal mutagenesis studies. IV. Radiation-induced rearrangements in Ateles sp. (Primate, Platyrhini)

In order to study the induction of rearrangements by gamma-rays in relation to chromosomal size and morphology, experiments were conducted in an Ateles, a species with a rather unusual karyotype among primates. It possesses some very large chromosomes, which tend to be too rarely affected, especially by intrachanges like inversions. Both their large size and their characteristic banding pattern suggest that this low involvement is not due to difficulty of analysis. This suggests very strongly that chromosomal involvement in rearrangements is not a function of size. The possible role of other factors involved in chromosomal rearrangements like chromosome position during interphase are discussed.     

A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi

Background  

Gene loss, inversions, translocations, and other chromosomal rearrangements vary among species, resulting in different rates of structural genome evolution. Major chromosomal rearrangements are rare in most eukaryotes, giving large regions with the same genes in the same order and orientation across species. These regions of macrosynteny have been very useful for locating homologous genes in different species and to guide the assembly of genome sequences. Previous analyses in the fungi have indicated that macrosynteny is rare; instead, comparisons across species show no synteny or only microsyntenic regions encompassing usually five or fewer genes. To test the hypothesis that chromosomal evolution is different in the fungi compared to other eukaryotes, synteny was compared between species of the major fungal taxa.     

Chromosomal characteristics of ribosomal DNA in two extant species of North American mudminnows Umbra pygmaea and U. limi (Euteleostei: Umbridae)

The locations and chromosomal characteristics of ribosomal DNA (rDNA) sites in the karyotypes of two extant North American species of mudminnows, Umbra pygmaea and U. limi (2n = 22, NF = 44), were analyzed sequentially by conventional Giemsa staining, Ag staining, CMA(3) fluorescence and fluorescence in situ hybridization (FISH). The nucleolar organizer regions (NORs) were located in the fourth chromosomal pair in both species (pericentromeric region in U. pygmaea and subtelomeric in U. LIMI). These sites were strongly CMA(3)-positive suggesting that the rDNA sites in these species are associated with GC-rich DNA. FISH with a rDNA probe gave consistently positive signals in the same regions detected by Ag-staining and CMA(3)-fluorescence. However, both species also had additional CMA(3)-positive/Ag-negative heterochromatic blocks at pericentrometric regions of several chromosomal pairs (three in U. pygmaea and five in U. limi). FISH revealed additional rDNA clusters in both species. It is hypothesized that a paracentric inversion of the chromosome arm carrying the NORs might be one of the rearrangements differentiating the karyotypes of two North American species. The presence of additional rDNA sites is indicative of more complex rearrangements. The pericentromeric NOR phenotype of Umbra pygmaea is similar to that seen in U. krameri and in the distantly related genus Esox.     

Differential gene flow of mitochondrial and nuclear DNA markers among chromosomal races of Australian morabine grasshoppers (Vandiemenella, viatica species group)

Recent theoretical developments have led to a renewed interest in the potential role of chromosomal rearrangements in speciation. Australian morabine grasshoppers (genus Vandiemenella, viatica species group) provide an excellent study system to test this potential role of chromosomal rearrangements because they show extensive chromosomal variation and formed the basis of a classic chromosomal speciation model. There are three chromosomal races, viatica19, viatica17, and P24(XY), on Kangaroo Island, South Australia, forming five parapatric populations with four putative contact zones among them. We investigate the extent to which chromosomal variation among these populations may be associated with barriers to gene flow. Population genetic and phylogeographical analyses using 15 variable allozyme loci and the elongation factor-1alpha (EF-1alpha) gene indicate that the three races represent genetically distinct taxa. In contrast, analyses of the mitochondrial cytochrome c oxidase subunit I (COI) gene show the presence of three distinctive and geographically localized groups that do not correspond with the distribution of the chromosomal races. These discordant population genetic patterns are likely to result from introgressive hybridization between the chromosomal races and range expansions/contractions. Overall, these results suggest that reduction of nuclear gene flow may be associated with chromosomal variation, or underlying genetic variation linked with chromosomal variation, whereas mitochondrial gene flow appears to be independent of this variation in these morabine grasshoppers. The identification of an intact contact zone between P24(XY) and viatica17 offers considerable potential for further investigation of molecular mechanisms that maintain distinct nuclear genomes among the chromosomal races.     

Conservation and reorganization of loci on the mammalian X chromosome: a molecular framework for the identification of homologous subchromosomal regions in man and mouse

By means of cross-reacting molecular probes, some 18 loci specific for the X chromosome of both man and mouse have been localized on the mouse X chromosome using an interspecific mouse cross involving the inbred SPE/Pas strain derived from Mus spretus. Comparison of the localizations of these loci on the mouse X with their positions on the human X chromosome suggests that intrachromosomal rearrangements involving at least five X chromosome breakage events must have occurred during the period of evolutionary divergence separating primates from rodents. Within the five blocks of chromosomal material so defined, there is for the moment little or no evidence that either chromosomal inversion events or extensive rearrangements have occurred. These data confirm the remarkable evolutionary conservation of the X chromosome apparent in mammalian species, compared to autosomal synteny groups in which both inter- and intrachromosomal rearrangement events appear to have occurred frequently. The breakage events described here for the X chromosome should therefore provide a minimal estimate for the frequency of chromosomal rearrangement events, such as breakage and inversion, which have affected autosomal synteny groups during the evolutionary period separating man from mouse. The definition of the number of chromosome breakage events by which the X chromosomes of these species differ, together with their localization, provides a framework for the use of interspecies mouse crosses for further detailed mapping of particular subchromosomal regions of the human X chromosome and for defining loci in the mouse homologous to those implicated in human congenital diseases.     

Chromosomal evolution in Malagasy lemurs: X. chromosomal banding studies of Propithecus diadema edwardsi and Indri indri and phylogenic relationships between all the species of the Indriidae

The R-banded karyotypes of two Indriidae, Propithecus diadema and Indri indri, are described and compared with each other and with those of the other species of this family, previously reported, Avahi laniger and Propithecus verreauxi. These comparisons show that 30 chromosomal rearrangements, including 21 Robertsonian translocations and eight pericentric inversions, differentiate these karyotypes. A phylogenic diagram is proposed, showing the early separation of Avahi and the relatively late divergence of the three other species. A populational evolution has occurred between the three other species, but Indri is clearly separated from the two other species by at least five complex rearrangements, although it shares four Robertsonian translocations with P. verreauxi but not P. diadema.     

Rampant gene exchange across a strong reproductive barrier between the annual sunflowers, Helianthus annuus and H. petiolaris

Plant species may remain morphologically distinct despite gene exchange with congeners, yet little is known about the genomewide pattern of introgression among species. Here we analyze the effects of persistent gene flow on genomic differentiation between the sympatric sunflower species Helianthus annuus and H. petiolaris. While the species are strongly isolated in testcrosses, genetic distances at 108 microsatellite loci and 14 sequenced genes are highly variable and much lower (on average) than for more closely related but historically allopatric congeners. Our analyses failed to detect a positive association between levels of genetic differentiation and chromosomal rearrangements (as reported in a prior publication) or proximity to QTL for morphological differences or hybrid sterility. However, a significant increase in differentiation was observed for markers within 5 cM of chromosomal breakpoints. Together, these results suggest that islands of differentiation between these two species are small, except in areas of low recombination. Furthermore, only microsatellites associated with ESTs were identified as outlier loci in tests for selection, which might indicate that the ESTs themselves are the targets of selection rather than linked genes (or that coding regions are not randomly distributed). In general, these results indicate that even strong and genetically complex reproductive barriers cannot prevent widespread introgression.     

Comparative mapping and rapid karyotypic evolution in the genus helianthus

Comparative genetic linkage maps provide a powerful tool for the study of karyotypic evolution. We constructed a joint SSR/RAPD genetic linkage map of the Helianthus petiolaris genome and used it, along with an integrated SSR genetic linkage map derived from four independent H. annuus mapping populations, to examine the evolution of genome structure between these two annual sunflower species. The results of this work indicate the presence of 27 colinear segments resulting from a minimum of eight translocations and three inversions. These 11 rearrangements are more than previously suspected on the basis of either cytological or genetic map-based analyses. Taken together, these rearrangements required a minimum of 20 chromosomal breakages/fusions. On the basis of estimates of the time since divergence of these two species (750,000-1,000,000 years), this translates into an estimated rate of 5.5-7.3 chromosomal rearrangements per million years of evolution, the highest rate reported for any taxonomic group to date.     

A comparison of five hybrid zones of the weta Hemideina thoracica (Orthoptera: Anostostomatidae): degree of cytogenetic differentiation fails to predict zone width

Abstract Tension zones are maintained by the interaction between selection against hybrids and dispersal of individuals. Investigating multiple hybrid zones within a single species provides the opportunity to examine differences in zone structure on a background of differences in extrinsic factors (e.g., age of the zone, ecology) or intrinsic factors (e.g., chromosomes). The New Zealand tree weta Hemideina thoracica comprises at least eight distinct chromosomal races with diploid numbers ranging from 2n = 11 (XO) to 2n = 23 (XO). Five independent hybrid zones were located that involve races differing from one another by a variety of chromosomal rearrangements. The predicted negative correlation between extent of karyotypic differentiation (measured in terms of both percent of genome and number of rearrangements) and zone width was not found. Conversely, the widest zones were those characterized by two chromosome rearrangements involving up to 35% of the genome. The narrowest zone occurred where the two races differ by a single chromosome rearrangement involving approximately 2% of the genome. The five estimates of chromosomal cline width ranged from 0.5 km to 47 km. A comparative investigation of cline width for both chromosomal and mitochondrial markers revealed a complex pattern of zone characteristics. Three of the five zones in this study showed cline concordance for the nuclear and cytoplasmic markers, and at two of the zones the clines were also coincident. Zones with the widest chromosomal clines had the widest mitochondrial DNA clines. It appears that, even within a single species, the extent of karyotypic differentiation between pairs of races is not a good predictor of the level of disadvantage suffered by hybrids.