Genomic distribution of heterochromatic sequences in equids: implications to rapid chromosomal evolution.

We describe a molecular model for rapid chromosomal evolution that proposes tandemly repeated DNA sequences as a driving force. A prediction of this model is that when extensive rearrangements of euchromatin have been facilitated by heterochromatin, genomes will be characterized by tandemly repeated sequences that have actively changed chromosomal fields by intragenomic movement. Alternatively, it is proposed that in conservative chromosomal lineage each class of tandemly repeated sequences will be restricted to a specific chromosomal field. To provide baseline data to test this model we examined four classes of tandemly repeated elements in six species of equids (Equus). Distribution of these sequences among species, as determined from slot blot analysis, and restriction site variation, shown by Southern blot hybridization, document that these sequences are in an evolutionarily dynamic state, and in situ hybridization documents extensive intragenomic movement among nonhomologous chromosomes and chromosomal fields. These data are interpreted as being compatible with the predictions of this model. Although this is clearly not the sole molecular factor driving chromosomal evolution, the model appears to be viable as an explanation of certain patterns of chromosomal evolution such as karyotypic megaevolution and some types of karyotypic orthoselection.     

Cytogenetic evidence for a complex of species within the taxon Anopheles maculatus (Diptera: Culicidae)

Two largely independent studies of chromosomes from natural populations of Anopheles maculatus provide evidence for several genetic species within the taxon. (1) Polytene chromosome variation shows four different rearrangements of arm 2 and three rearrangements of the X chromosome. There is strong evidence for three species. Two allopatric populations represent either dramatic geographic variation for two independent inversion systems within one of the genetic species, or represent two additional species. Their species status remains unresolved by this work. (2) Heterochromatic variation occurs in both X and Y chromosomes as revealed by Giemsa-banding of mitotic chromosomes from larval brains. The distribution and association of these various sex chromosomes give further evidence of a species complex. A preliminary correlation of these two kinds of chromosomal variation is given.     

The origin of a Robertsonian chromosomal translocation in house mice inferred from linked microsatellite markers

The western European house mouse, Mus domesticus, includes many distinct Robertsonian (Rb) chromosomal races. Two competing hypotheses may explain the distribution of Rb translocations found in different populations: they may have arisen independently multiple times, or they may have arisen once and been spread through long-distance dispersal. We investigated the origin of the Rb 5.15 translocation using six microsatellite loci linked to the centromeres of chromosomes 5 and 15 in 84 individuals from three Rb populations and four neighboring standard-karyotype populations. Microsatellite variation on the 5.15 metacentric chromosomes was significantly reduced relative to the amount of variation found on acrocentric chromosomes 5 and 15, suggesting that linked microsatellite loci can track specific mutational events. Phylogenetic analyses resulted in trees which are consistent with multiple origins of the 5.15 metacentric chromosomes found in the three Rb populations. These results suggest that cytologically indistinguishable mutations have arisen independently in natural populations of house mice.     

The evolution of hypervariable sex and supernumerary (B) chromosomes in the relict New Zealand frog,Leiopelma hochstetteri

Chromosomes exhibiting elevated levels of differentiation are termed hypervariable but no proposed mechanisms are sufficient to account for such enhanced evolutionary divergence. Both hypervariable sex and supernumerary (B) chromosomes were investigated in the endemic New Zealand frog, Leiopelma hochstetteri, which is chromosomally polymorphic both within and between populations and has sufficiently elevated variation that different populations can be identified solely by their C-banded karyotypes. This frog is further distinguished by the univalent, female-specific W-chromosome (0W/00 sex determination) uniquely possessed by North Island populations. This sex chromosome exhibited variation in morphology, size, and heterochromatin distribution, sufficient to resolve 11 different types, including isochromosomes. Five of the 12 populations examined also had supernumerary chromosomes that varied in number (up to 15 per individual) and morphology. Specific variations seen among the hypervariable chromosomes could have resulted from heterochromatinisation, chromosome fusions, loss-of-function mutations, deletions, and/or duplications. Frogs of the same species from Great Barrier Island, however, had neither supernumeraries nor the female-specific chromosome. The 0W/00 sex chromosome system must have been derived after the isolation of Great Barrier Island from North Island populations by raised sea levels between 14 000 and 8000 years ago. Furthermore, biochemical divergence between populations is minor and therefore the chromosomal variation seen is comparatively recent in origin. The one characteristic common to all known hypervariable chromosomes is curtailment or lack of recombination. Their accelerated evolution therefore is possible via the mechanism of Muller's ratchet, either alone or in concert with other factors.     

Deleterious mutations at the mitochondrial ND3 gene in South American marsh rats (Holochilus).

Statistical analyses of DNA sequences have revealed patterns of nonneutral evolution in mitochondrial DNA of mice, humans, and Drosophila. Here we report patterns of mitochondrial sequence evolution in South American marsh rats (genus Holochilus). We sequenced the complete mitochondrial ND3 gene in 82 Holochilus brasiliensis and 21 H. vulpinus to test the neutral prediction that the ratio of nonsynonymous to synonymous nucleotide changes is the same within and between species. Within H. brasiliensis we observed a greater number of amino acid polymorphisms than expected based on interspecific comparisons. This contingency table analysis suggests that many amino acid polymorphisms are mildly deleterious. Several tests of the frequency distribution also revealed departures from a neutral, equilibrium model, and these departures were observed for both nonsynonymous and synonymous sites. In general, an excess of rare sites was observed, consistent with either a recent selective sweep or with populations not at mutation-drift equilibrium.     

SUPERNUMERARY CHROMOSOMES IN SAXIFRAGA VIRGINIENSIS (SAXIFRAGACEAE)

Acetocarmine squashes of root tips have demonstrated that 2n = 20 and 38 in Saxifraga virginiensis. These contrast with the earlier reported count of 2n = 28 for this species. In several populations supernumerary chromosomes were detected. Both intrapopulational and interpopulational variation in supernumerary chromosome number were detected, with the largest number of supernumerary chromosomes observed being six. Because these supernumerary chromosomes are equal in size to many of the smaller A chromosomes during mitotic metaphase, the presence of supernumerary chromosomes in this species could not be ascertained by analysis of mitotic metaphase preparations alone. During mitotic prophase, however, the supernumerary chromosomes of S. virginiensis are highly heterochromatic, appearing more densely coiled and darkly stained than the A chromosomes. This characteristic facilitated the recognition of supernumerary chromosomes in this species. The similarity in size of A and supernumerary chromosomes during mitotic metaphase and the observation of six supernumerary chromosomes in one population suggest that the count of 2n = 28 reported earlier for S. virginiensis may actually be a misinterpretation of 2n = 20 plus 8 supernumerary chromosomes. Furthermore, these findings and the observation of this same supernumerary chromosome phenomenon in other species of Saxifraga raise the possibility that some of the many disparate chromosome counts attributed to aneuploidy in the large genus Saxifraga may also be the result of misinterpretations of supernumerary chromosomes as A chromosomes.     

Genic differentiation and origin of Robertsonian populations of the house mouse (Mus musculus domesticus Rutty)

This paper examines the relation between chromosomal and nuclear-gene divergence in 28 wild populations of the house mouse semi-species, Mus musculus domesticus, in Western Europe and North Africa. Besides describing the karyotypes of 15 of these populations and comparing them to those of 13 populations for which such information was already known, it reports the results of an electrophoretic survey of proteins encoded by 34 nuclear loci in all 28 populations. Karyotypic variation in this taxon involves only centric (or Robertsonian) fusions which often differ in arm combination and number between chromosomal races. The electrophoretic analysis showed that the amount of genic variation within Robertsonian (Rb) populations was similar to that for all-acrocentric populations, i.e. bearing the standard karyotype. Moreover, divergence between the two types of populations was extremely low. These results imply that centric fusions in mice have not modified either the level or the nature of genic variability. The genetic similarity between Rb and all-acrocentric populations is not attributed to the persistence of gene flow, since multiple fusions cause marked reproductive isolation. Rather, we attribute this extreme similarity to the very recent origin of chromosomal races in Europe. Furthermore, genic diversity measures suggest that geographically separated Rb populations have in situ and independent origins. Thus, Rb translocations are probably not unique events, but originated repeatedly. Two models are presented to explain how the rapid fixation of a series of chromosomal rearrangements can occur in a population without lowering variability in the nuclear genes. The first model assumes that chromosomal mutation rates are between 10(-3) and 10(-4) and that populations underwent a series of transient bottlenecks in which the effective population size did not fall below 35. In the second model, genic variability is restored following severe bottlenecks, through gene flow and recombination.     

Restricted gene flow at specific parts of the shrew genome in chromosomal hybrid zones

The species and races of the shrews of the Sorex araneus group exhibit a broad range of chromosomal polymorphisms. European taxa of this group are parapatric and form contact or hybrid zones that span an extraordinary variety of situations, ranging from absolute genetic isolation to almost free gene flow. This variety seems to depend for a large part on the chromosome composition of populations, which are primarily differentiated by various Robertsonian fusions of a subset of acrocentric chromosomes. Previous studies suggested that chromosomal rearrangements play a causative role in the speciation process. In such models, gene flow should be more restricted for markers on chromosomes involved in rearrangements than on chromosomes common in both parent species. In the present study, we address the possibility of such differential gene flow in the context of two genetically very similar but karyotypically different hybrid zones between species of the S. araneus group using microsatellite loci mapped to the chromosome arm level. Interspecific genetic structure across rearranged chromosomes was in general larger than across common chromosomes. However, the difference between the two classes of chromosomes was only significant in the hybrid zone where the complexity of hybrids is expected to be larger. These differences did not distinguish populations within species. Therefore, the rearranged chromosomes appear to affect the reproductive barrier between karyotypic species, although the strength of this effect depends on the complexity of the hybrids produced.     

Unusually extensive karyotype reorganization in four congeneric Gerbillus species (Muridae: Gerbillinae)

Comparative analysis of the G- and C-banding patterns in four morphologically poorly differentiated Gerbillus species (G. pyramidum, G. perpallidus, G. tarabuli and G. occiduus) was carried out. These gerbils have similar karyotype morphology with 2n and NF equal to 38/76, 40/76, 40/78 and 40/80, respectively. Our study revealed that possibly 70 Robertsonian (Rb) fusions, two pericentric inversions, one tandem translocation and at least 13 non-identified rearrangements have occurred during the karyotypic evolution of these species. The number of chromosomal changes by which any of these species differ from each other ranges from 33 to 49. One Rb fusion was common to two of the species, with only a single autosome-gonosome translocation shared by all four, suggesting a monophyletic origin of these karyotypically highly divergent species. Based on the chromosomal data obtained here, the systematic and geographic implications for these North African species are also discussed.     

Genetic characterization of the yeast Pichia anomala (strain K), an antagonist of postharvest diseases of apple

AIMS: To obtain information about the genomic organization of Pichia anomala (strain K) and about its genomic diversity at species and intraspecies level. METHODS AND RESULTS: The PFGE karyotype of strain K was composed of four bands ranging in size from 1.1 to 3.2 Mb. The number of chromosomes was estimated at six since bands 2 and 3 seemed to result from the comigration of two chromosomes with similar size. A comparison of strain K and Hansenulawingeii migration profiles led to the estimate of K strain genome size at 11.7 Mb. Comparison with isogenic strains, resulting from the sporulation of strain K, highlighted some major karyotypic differences. Two segregants (KH6 and KH7) showed supernumerary chromosomes and one (KH9) displayed chromosomal length polymorphism. This genomic instability was confirmed by molecular hybridization with four probes, consisting of URA3, LEU2, PAEXG1 and PAEXG2 genes of P. anomala. URA3 and LEU2 probes showed second hybridization signals on supernumerary chromosomes of strain KH7 and on chromosome 6 of strain K for LEU2 only. Karyotypic comparison of seven non-isogenic P. anomala strains revealed chromosomal length polymorphism, a sign of intraspecies variation. CONCLUSIONS: This work has supplied information about genome size and chromosome number of strain K of P. anomala. The strain seems to be aneuploid because of the presence of supernumerary chromosomes and additional hybridization signals for URA3 and LEU2 probes in the chromosomal profile of some segregants. The work also highlighted genomic diversity within the P. anomala species. SIGNIFICANCE AND IMPACT OF THE STUDY: Results obtained here increase information about the aneuploidy of P. anomala (strain K). Information about the genomic diversity of the segregants will be of great interest for further studies on strain K mode of action. The genome size and chromosomal profile of P. anomala presented here are different from the results obtained elsewhere for Hansenula anomala, while Hansenula is included as a synonym of Pichia. This warrants further studies to investigate this taxonomic relationship.     

Chromosomal evolution in Primates: Tentative phylogeny from Microcebus murinus (Prosimian) to man

Summary The karyotypes of more than 60 species of Primates are studied and compared, with the use of almost all existing banding techniques. There is a very close analogy of chromosome banding between the Simians studied and man. The quantitative or qualitative variations detected all involve the heterochromatin. It is very likely that all the euchromatin (nonvariable R and Q bands) is identical in all the species.Approximately 70% of the bands are common to the Simians and to the Lemurs (Prosimians). In the remaining 30%, technical difficulties prevented a valuable comparison, but this does not exclude the possibility that a complete analogy may exist.Thus, it is very likely that chromosomal evolutions of the Simians, and probably of all the Primates, has occurred without duplication or deficiency of the euchromatin.Approximately 150 rearrangements could be identified and related to the human chromosomes. The types of rearrangements vary from one group (suborder, family, genus) to another. For instance, Robertsonian translocations are preponderant among the Lemuridae (44/57) but are nonexistent among the Pongidae. Chromosome fissions are very frequent among the Cercopithecidae (10/23), but were not found elsewhere, and pericentric inversions are preponderant in the evolution of Pongidae and man (17/28).This suggests that the chromosomal evolution may be directed by the genic constitution (favouring the occurrence of a particular type of rearrangement, by enzymatic reaction), by the chromosomal morphology (the probability that Robertsonian translocations will be formed depends at least partially on the number of acrocentrics), and by the reproductive behaviour of the animals.Reconstitution of the sequence of the chromosomal rearrangements allowed us to propose a fairly precise genealogy of many Primates, giving the positions of the Catarrhines, the Platyrrhines, and the Prosimians. It was also possible to reconstruct the karyotypes of ancestors that died out several dozen million years ago.The possible role of chromosomal rearrangements in evolution is discussed. It appears necessary to consider different categories of rearrangements separately, depending on their behaviour. The nonfavoured rearrangements, such as pericentric inversions, need to occur in an isolated small population for implanting, by an equivalent of genic derivation.The favoured rearrangements, e.g., Robertsonian translocations, may occur and diffuse in panmictic populations, and accumulate. Their role of gametic barrier could be much more progressive.For discrimination between these two categories, it was necessary to differentiate the selective advantage or disadvantage of the rearrangement itself. It was not possible to show that chromosomal rearrangements play a direct role in modification of the phenotype by position effect.Comparison of the rearrangements that have occurred during evolution and those detected in the human population shows a strong correlation for some of them. In particular, a large proportion of pericentric inversions can be regarded as reverse mutations, because they reproduce ancestral chromosomes.     

Different types of plant chromatin associated with modified histones H3 and H4 and methylated DNA

Eukaryotic chromosomes are organized into two large and distinct domains, euchromatin and heterochromatin, which are cytologically characterized by different degrees of chromatin compaction during interphase/prophase and by post-synthesis modifications of histones and DNA methylation. Typically, heterochromatin remains condensed during the entire cell cycle whereas euchromatin is decondensed at interphase. However, a fraction of the euchromatin can also remain condensed during interphase and appears as early condensing prophase chromatin. 5S and 45S rDNA sites and telomere DNA were used to characterize these regions in metaphase and interphase nuclei. We investigated the chromosomal distribution of modified histones and methylated DNA in the early and late condensing prophase chromatin of two species with clear differentiation between these domains. Both species, Costus spiralis and Eleutherine bulbosa, additionally have a small amount of classical heterochromatin detected by CMA/DAPI staining. The distribution of H4 acetylated at lysine 5 (H4K5ac), H3 phosphorylated at serine 10 (H3S10ph), H3 dimethylated at lysine 4 or 9 (H3K4me2, H3K9me2), and 5-methylcytosine was compared in metaphase, prophase, and interphase cells by immunostaining with specific antibodies. In both species, the late condensing prophase chromatin was highly enriched in H4K5ac and H3K4me2 whereas the early condensing chromatin was very poor in these marks. H3K9me2 was apparently uniformly distributed along the chromosomes whereas the early condensing chromatin was slightly enriched in 5-methylcytosine. Signals of H3S10ph were restricted to the pericentromeric region of all chromosomes. Notably, none of these marks distinguished classical heterochromatin from the early condensing euchromatin. It is suggested that the early condensing chromatin is an intermediate type between classical heterochromatin and euchromatin.     

Chromosomal polymorphisms due to heterochromatin growth and pericentric inversions in white-bellied rat,Niviventer confucianus,from China

Different cytogenetic techniques were used to analyze the chromosomes of white-bellied rat, Niviventer confucianus from Mt. Tai and Jinan, Shandong Province and Ningshan, Shaanxi Province of China. Shandong populations have 2n = 46 chromosomes with 4 metacentric, 2 subtelocentric, 16 telocentric pairs of autosomes and the submetacentric X and telocentric Y. The chromosomal arm number (NF) of the two populations was 56. Shaanxi population has 2n = 46 chromosomes with 4 metacentric, 1 submetacentric, 1 subtelocentric and 16 telocentric pairs of autosomes and the submetacentric X and telocentric Y. The karyotype of Ningshan population showed NF = 58. As the result of the comparison of C- and G-banding patterns, and compare with other species in the genus Niviventer, we suppose that the chromosomal evolution of Niviventer involved in pericentric inversion and heterochromatin growth. The submetacentric chromosomes of Shaanxi population would be originated from the growth of heterochromatin of the subtelocentric chromosome of Shandong population.     

Karyotype differentiation in Chromaphyosemion killifishes (Cyprinodontiformes, Nothobranchiidae). III: extensive karyotypic variability associated with low mitochondrial haplotype differentiation in C. bivittatum

We investigated chromosomal evolution in the African killifish species Chromaphyosemion bivittatum using a combination of cytogenetic and phylogenetic methods. Specimens from five populations were examined by conventional Giemsa staining as well as sequential chromosome banding with 4',6-diamidino-2-phenylindole (DAPI), chromomycin A(3) (CMA(3)), AgNO(3)-staining and C-banding. The cytogenetic analysis revealed variability in 2n ranging from 2n = 29 to 2n = 36 and in NF ranging from NF = 38 to NF = 44. Two populations showed an extensive chromosomal polymorphism (2n = 29-34, NF = 44 and 2n = 32-34, NF = 38-42, respectively). Karyotypic variability within and among populations was mainly due to Robertsonian translocations and heterochromatin additions, and chromosome banding patterns suggested that both types of chromosomal rearrangements were related to the presence of AT-rich heterochromatin. A phylogenetic analysis of the partial mitochondrial (mt) cytochrome b gene, using specimens from eleven populations, revealed a low degree of haplotype differentiation, which suggested a relatively recent divergence of the populations examined. This finding conformed to the low degree of morphological differentiation observed among C. bivittatum populations and might indicate fast chromosomal evolution. The high karyotypic variability may be caused by an elevated chromosomal mutation rate as well as certain aspects of the mating system and population dynamics of C. bivittatum facilitating the fixation of new chromosomal variants.     

A CYTOGENETIC STUDY OF CLARKIA UNGUICULATA II. SUPERNUMERARY CHROMOSOMES

Mooring , John S. (Washington State U., Pullman.) A cytogenetic study of Clarkia unguiculata. II. Supernumerary chromosomes. Amer. Jour. Bot. 47(10): 847–854. Illus. 1960.—Supernumerary chromosomes morphologically comparable to those of the basic complement occur in high frequency in wild populations of this onagraceous annual plant. This paper evaluates the role that these supernumerary chromosomes play in the population dynamics of this species. The results of crossing plants with various numbers of supernumeraries showed that these chromosomes often increased in number in the seed parent. Examination of microsporocytes showed that almost 30% of the 491 plants determined had 1 or more supernumerary chromosomes. Studies of natural populations revealed that the frequency of individuals with supernumeraries varied from 0 to 79% in different populations, and also that in 1 population their frequency varied significantly in different years. It is concluded that supernumerary chromosomes in this species are adaptive under at least certain conditions. It is speculated that they are components of polygenic systems which increase tolerance to environmental extremes.     

B chromosomes, translocation between B and autosomes, and C-heterochromatin polymorphism of the grasshopper Podisma sapporensis Shir. (Orthoptera, Acrididae) in Hokkaido, northern Japan.

Seven categories of B chromosomes found in the brachypterus grasshopper Podisma sapporensis from Hokkaido populations differ in structure, size, and C-band content. The interchange between B and one autosome from M3 and sporadically M7 was observed in most of the populations examined. Such an interaction between standard and non-standard chromosomal set provides an insight into the integration of supernumerary chromosome. In addition, C-heterochromatin polymorphism was also identified in male karyotypes in some populations. These facts indicate P. sapporensis is a highly polymorphic species from the cytogenetic point of view.     

Supernumerary chromosomal elements in lymphocytes cultured from phenotypically normal human adult males

In a group of phenotypically normal men there were approximately 0.24% of metaphase lymphocytes with extra chromosomal elements along with the regular 46 chromosomes. They ranged in size from small acrocentric-acentric elements to elements longer than any chromosome arm. These elements have been referred to as supernumerary chromosomal elements. No significant effects due to donor's age, smoking history, season, storage of blood samples prior to culture, or culture medium, were found either in the frequency of supernumerary elements per cell or in the frequency of cells with supernumerary elements. Furthermore, the same subject did not consistently exhibit supernumerary elements. Furthermore, the same subject did not consistently exhibit supernumerary elements when sampled during four successive quarters of the year. Some of these elements in pairs were identified by G-banding technique as translocation chromosomes bearing long arms of chromosome number 2 and presumptive short arms of chromosome 8, acentric long arms of chromosome 4, and iso-acentric chromosomes for the long arms of chromosome 5. Presumably, more than one type of cytogenetic event occurred in their formation. Circumstantial evidence has been presented to show that the means of elimination of these supernumerary elements is a process of chromosomal disintegration.     

Trends of karyotypical evolution in the pearl cichlid,Geophagus brasiliensis,from southern Brazil

Chromosomal rearrangements such as inversions can facilitate speciation even in the presence of gene flow. The present study aims to analyze the karyotypic variation in six populations of Geophagus brasiliensis from southern Brazil. All specimens showed 2n = 48 chromosomes, but three karyotypes were found to have one, two or three pairs of submetacentric chromosomes. Although G. brasiliensis did not exhibit variation in the diploid number, it presented a wide interpopulational variation mainly regarding the karyotype formula and specific chromosomal markers. Differences in the location of the major and minor rDNA loci were observed among the populations. Moreover, different patterns were observed in the distribution of the constitutive heterochromatin, presenting intra- and interpopulational variation. This supports the hypothesis that this taxon represents a complex species or that cryptic species are included in this group, indicating a possibleprocess of sympatric speciation. By potentially restricting gene flow between heterokaryotypes, the segregating chromosome rearrangements we describe for G. brasiliensis may play a role in diversification in this species complex.     

REDUCED GENE FLOW AT PERICENTROMERIC LOCI IN A HYBRID ZONE INVOLVING CHROMOSOMAL RACES OF THE HOUSE MOUSE MUS MUSCULUS DOMESTICUS

The West European house mouse, Mus musculus domesticus, is a particularly suitable model to investigate the role of chromosomal rearrangements in reproductive isolation. In fact, it exhibits a broad range of chromosomal polymorphism due to Robertsonian (Rb) fusions leading to various types of contact zones between different chromosomal races. In the present study, we analyzed a parapatric contact in central Italy between the Cittaducale chromosomal race (CD: 2n= 22) and the surrounding populations with standard karyotype (2n= 40) to understand if Rb fusions play a causative role in speciation. One hundred forty‐seven mice from 17 localities were genotyped by means of 12 microsatellite loci. A telomeric and a pericentromeric locus situated on six chromosome arms (four Rbs and one telocentric) were selected to detect differences in the amount of gene flow for each locus in different chromosomal positions. The analyses performed on the two subsets of loci show differences in the level of gene flow, which is more restricted near the centromeres of Rb chromosomes. This effect is less pronounced in the homozygotes populations settled at the border of the hybrid zone. We discuss the possible cause of the differential porosity of gene flow in Rbs considering “hybrid dysfunctions” and “suppressed recombination” models.     

Comparative genomics, marker density and statistical analysis of chromosome rearrangements

Estimates of the number of chromosomal breakpoints that have arisen (e.g., by translocation and inversion) in the evolutionary past between two species and their common ancestor can be made by comparing map positions of marker loci. Statistical methods for doing so are based on a random-breakage model of chromosomal rearrangement. The model treats all modes of chromosome rearrangement alike, and it assumes that chromosome boundaries and breakpoints are distributed randomly along a single genomic interval. Here we use simulation and numerical analysis to test the validity of these model assumptions. Mean estimates of numbers of breakpoints are close to those expected under the random-breakage model when marker density is high relative to the amount of chromosomal rearrangement and when rearrangements occur by translocation alone. But when marker density is low relative to the number of chromosomes, and when rearrangements occur by both translocation and inversion, the number of breakpoints is underestimated. The underestimate arises because rearranged segments may contain markers, yet the rearranged segments may, nevertheless, be undetected. Variances of the estimate of numbers of breakpoints decrease rapidly as markers are added to the comparative maps, but are less influenced by the number or type of chromosomal rearrangement separating the species. Variances obtained with simulated genomes comprised of chromosomes of equal length are substantially lower than those obtained when chromosome size is unconstrained. Statistical power for detecting heterogeneity in the rate of chromosomal rearrangement is also investigated. Results are interpreted with respect to the amount of marker information required to make accurate inferences about chromosomal evolution.