Fluorescence in situ hybridization (FISH) maps chromosomal homologies between the dusky titi and squirrel monkey

Characterization of Satellite DNAs in Squirrel Monkeys genus Saimiri (Cebidae, Platyrrhini)

The genus Saimiri is a decades-long taxonomic and phylogenetic puzzle to which cytogenetics has contributed crucial data. All Saimiri species apparently have a diploid number of 2n = 44 but vary in the number of chromosome arms. Repetitive sequences such as satellite DNAs are potentially informative cytogenetic markers because they display high evolutionary rates. Our goal is to increase the pertinent karyological data by more fully characterizing satellite DNA sequences in the Saimiri genus. We were able to identify two abundant satellite DNAs, alpha (~340 bp) and CapA (~1,500 bp), from short-read clustering of sequencing datasets from S. boliviensis. The alpha sequences comprise about 1% and the CapA 2.2% of the S. boliviensis genome. We also mapped both satellite DNAs in S. boliviensis, S. sciureus, S. vanzolinii, and S. ustus. The alpha has high interspecific repeat homogeneity and was mapped to the centromeres of all analyzed species. CapA is associated with non-pericentromeric heterochromatin and its distribution varies among Saimiri species. We conclude that CapA genomic distribution and its pervasiveness across Platyrrhini makes it an attractive cytogenetic marker for Saimiri and other New World monkeys.

Evolution of the Human Chromosome 13 Synteny: Evolutionary Rearrangements, Plasticity, Human Disease Genes and Cancer Breakpoints

The history of each human chromosome can be studied through comparative cytogenetic approaches in mammals which permit the identification of human chromosomal homologies and rearrangements between species. Comparative banding, chromosome painting, Bacterial Artificial Chromosome (BAC) mapping and genome data permit researchers to formulate hypotheses about ancestral chromosome forms. Human chromosome 13 has been previously shown to be conserved as a single syntenic element in the Ancestral Primate Karyotype; in this context, in order to study and verify the conservation of primate chromosomes homologous to human chromosome 13, we mapped a selected set of BAC probes in three platyrrhine species, characterised by a high level of rearrangements, using fluorescence in situ hybridisation (FISH). Our mapping data on Saguinus oedipus, Callithrix argentata and Alouatta belzebul provide insight into synteny of human chromosome 13 evolution in a comparative perspective among primate species, showing rearrangements across taxa. Furthermore, in a wider perspective, we have revised previous cytogenomic literature data on chromosome 13 evolution in eutherian mammals, showing a complex origin of the eutherian mammal ancestral karyotype which has still not been completely clarified. Moreover, we analysed biomedical aspects (the OMIM and Mitelman databases) regarding human chromosome 13, showing that this autosome is characterised by a certain level of plasticity that has been implicated in many human cancers and diseases.

Terminal 13p deletion in squirrel monkey (Saimiri sciureus) with differentiated phenotype

BACKGROUND

The taxonomic classification of squirrel monkeys is often controversial issue offering many different information. The classification of captive animals is difficult due to the phenotypic similarities between the presented species, which is observed mainly in coat coloration.

METHODS

The objective of this study was to analyze the chromosome pattern of one squirrel monkey with off standard physical characteristics, which is kept in the Laboratory Animals Breeding Center in Rio de Janeiro State, Brazil, and try to establish some correlations. Chromosomes were obtained using lymphocyte culture technique.

RESULTS AND CONCLUSIONS

Evaluation of G bands showed a terminal deletion in one chromosome of pair 13. The association of the results found with the different phenotypic characteristics led us to classify it as a Saimiri sciureus specimen with a structural chromosomal change, possibly allowing the expression of hemizygous alleles.

Evolutionary insight on localization of 18S, 28S rDNA genes on homologous chromosomes in Primates genomes

We explored the topology of 18S and 28S rDNA units by fluorescence in situ hybridization (FISH) in the karyotypes of thirteen species representatives from major groups of Primates and Tupaia minor (Günther, 1876) (Scandentia), in order to expand our knowledge of Primate genome reshuffling and to identify the possible dispersion mechanisms of rDNA sequences. We documented that rDNA probe signals were identified on one to six pairs of chromosomes, both acrocentric and metacentric ones. In addition, we examined the potential homology of chromosomes bearing rDNA genes across different species and in a wide phylogenetic perspective, based on the DAPI-inverted pattern and their synteny to human. Our analysis revealed an extensive variability in the topology of the rDNA signals across studied species. In some cases, closely related species show signals on homologous chromosomes, thus representing synapomorphies, while in other cases, signal was detected on distinct chromosomes, leading to species specific patterns. These results led us to support the hypothesis that different mechanisms are responsible for the distribution of the ribosomal DNA cluster in Primates.

Comprehensive characterization of evolutionary conserved breakpoints in four New World Monkey karyotypes compared to Chlorocebus aethiops and Homo sapiens

Comparative cytogenetic analysis in New World Monkeys (NWMs) using human multicolor banding (MCB) probe sets were not previously done. Here we report on an MCB based FISH-banding study complemented with selected locus-specific and heterochromatin specific probes in four NWMs and one Old World Monkey (OWM) species, i.e. in Alouatta caraya (ACA), Callithrix jacchus (CJA), Cebus apella (CAP), Saimiri sciureus (SSC), and Chlorocebus aethiops (CAE), respectively. 107 individual evolutionary conserved breakpoints (ECBs) among those species were identified and compared with those of other species in previous reports. Especially for chromosomal regions being syntenic to human chromosomes 6, 8, 9, 10, 11, 12 and 16 previously cryptic rearrangements could be observed. 50.4% (54/107) NWM-ECBs were colocalized with those of OWMs, 62.6% (62/99) NWM-ECBs were related with those of Hylobates lar (HLA) and 66.3% (71/107) NWM-ECBs corresponded with those known from other mammalians. Furthermore, human fragile sites were aligned with the ECBs found in the five studied species and interestingly 66.3% ECBs colocalized with those fragile sites (FS). Overall, this study presents detailed chromosomal maps of one OWM and four NWM species. This data will be helpful to further investigation on chromosome evolution in NWM and hominoids in general and is prerequisite for correct interpretation of future sequencing based genomic studies in those species.

Chromosome evolution in new world monkeys (Platyrrhini)

During the last decades, New World monkey (NWM, Platyrrhini, Anthropoideae) comparative cytogenetics has shed light on many fundamental aspects of genome organisation and evolution in this fascinating, but also highly endangered group of neotropical primates. In this review, we first provide an overview about the evolutionary origin of the inferred ancestral NWM karyotype of 2n = 54 chromosomes and about the lineage-specific chromosome rearrangements resulting in the highly divergent karyotypes of extant NWM species, ranging from 2n = 16 in a titi monkey to 2n = 62 in a woolly monkey. Next, we discuss the available data on the chromosome phylogeny of NWM in the context of recent molecular phylogenetic analyses. In the last part, we highlight some recent research on the molecular mechanisms responsible for the large-scale evolutionary genomic changes in platyrrhine monkeys.

Centromere repositioning in mammals

The evolutionary history of chromosomes can be tracked by the comparative hybridization of large panels of bacterial artificial chromosome clones. This approach has disclosed an unprecedented phenomenon: 'centromere repositioning', that is, the movement of the centromere along the chromosome without marker order variation. The occurrence of evolutionary new centromeres (ENCs) is relatively frequent. In macaque, for instance, 9 out of 20 autosomal centromeres are evolutionarily new; in donkey at least 5 such neocentromeres originated after divergence from the zebra, in less than 1 million years. Recently, orangutan chromosome 9, considered to be heterozygous for a complex rearrangement, was discovered to be an ENC. In humans, in addition to neocentromeres that arise in acentric fragments and result in clinical phenotypes, 8 centromere-repositioning events have been reported. These 'real-time' repositioned centromere-seeding events provide clues to ENC birth and progression. In the present paper, we provide a review of the centromere repositioning. We add new data on the population genetics of the ENC of the orangutan, and describe for the first time an ENC on the X chromosome of squirrel monkeys. Next-generation sequencing technologies have started an unprecedented, flourishing period of rapid whole-genome sequencing. In this context, it is worth noting that these technologies, uncoupled from cytogenetics, would miss all the biological data on evolutionary centromere repositioning. Therefore, we can anticipate that classical and molecular cytogenetics will continue to have a crucial role in the identification of centromere movements. Indeed, all ENCs and human neocentromeres were found following classical and molecular cytogenetic investigations.

Chromosome painting in two genera of South American monkeys: species identification, conservation, and management

Cytogenetic studies showed that a number of New World primate taxa, particularly the genera Alouatta, Aotus, and Callicebus, have highly derived karyotypes. Cytogenetics in these primates, at every level of analysis, has contributed to the recognition of species and revealed that their number was certainly underestimated by researchers relying solely on traditional morphological data. Further attention was drawn to Alouatta and Aotus because they are characterized by translocations of the Y chromosome to autosomes, generating multiple sex chromosome systems. Here we present a report on the hybridization of human chromosome-specific paints on metaphases from 4 individuals originally assigned to Alouatta caraya and 1 individual of Aotuslemurinus. This is only the third karyotype studied with chromosome painting out of more than 10 known karyomorphs in Aotus. The banded chromosomes matched those of karyotype II as defined by Ma et al. [1976a], and we were able to more precisely assign the origin of the sample to A. l. griseimembra. Our results on the Argentinean Alouatta caraya samples were generally comparable to the banding and hybridization pattern of previous studies of A. caraya including the presence of an X(1)X(1)X(2)X(2)/X(1)X(2)Y(1)Y(2) sex chromosome system. The karyotype of the Brazilian Alouatta sample labeled as A. caraya differs from the 3 Argentinean samples by at least 10 chromosome rearrangements. The diploid number, G banding, and hybridization pattern of this female cell line was almost identical to previous painting results on Alouatta guariba guariba. Therefore we must conclude that this cell line is actually from an A. guariba guariba individual. The contribution of cytogenetic tools in identifying species or in this case assigning individuals or cell lines to their precise taxonomic allocation is stressed. Gathering further molecular cytogenetic data on New World primates should be conservation and management priorities.

Genomic mapping of human chromosome paints on the threatened masked Titi monkey (Callicebus personatus)

Callicebus is a complex genus of neotropical primates thought to include 29 or more species. Currently, the genus is divided into 5 species groups: donacophilus, cupreus, moloch, torquatus and personatus. However, the phylogenetic relationships among the species are still poorly understood. This genus is karyotypically diverse and shows extensive variation in diploid number (2n = 16 to 50). To foster a better understanding of the chromosomal diversities and phylogenetic relationships among the species of Callicebus, we performed a chromosome-painting analysis on the Callicebus personatus genome using human probes, and compared the resulting hybridization map to those of previously mapped titi species. We detected 38 hybridization signals per haploid autosomal set of C. personatus. Few ancestral syntenies were conserved without rearrangement, but 4 human associations (HSA20/13, 3c/8b, 1b/1c and 21/3a/15a/14) were demonstrated to be apomorphic traits for C. persona tus. G-banding suggested that these associations are shared with C. nigrifrons and C. coimbrai (personatus group), while C. personatus is linked with C. pallescens (donacophilus group) by 2 synapomorphies: HSA10b/11 (submetacentric) and an inversion of HSA1a.

Synteny of human chromosomes 14 and 15 in the platyrrhines (Primates, Platyrrhini)

In order to study the intra- and interspecific variability of the 14/15 association in Platyrrhini, we analyzed 15 species from 13 genera, including species that had not been described yet. The DNA libraries of human chromosomes 14 and 15 were hybridized to metaphases of Alouatta guariba clamitans, A. caraya, A. sara, Ateles paniscus chamek, Lagothrix lagothricha, Brachyteles arachnoides, Saguinus midas midas, Leontopithecus chrysomelas, Callimico goeldii, Callithrix sp., Cebus apella, Aotus nigriceps, Cacajao melanocephalus,Chiropotes satanas and Callicebus caligatus. The 14/15 hybridization pattern was present in 13 species, but not in Alouatta sara that showed a 14/15/14 pattern and Aotus nigriceps that showed a 15/14/15/14 pattern. In the majority of the species, the HSA 14 homologue retained synteny for the entire chromosome, whereas the HSA 15 homologue displayed fragmented segments. Within primates, the New World monkeys represent the taxon with the highest variability in chromosome number (2n = 16 to 62). The presence of the HSA 14/15 association in all species and subspecies studied herein confirms that this association is the ancestral condition for platyrrhines and that this association has been retained in most platyrrhines, despite the occurrence of extensive inter- and intrachromosomal rearrangements in this infraorder of Primates.

Phylogenetic studies of the genus Cebus (Cebidae-Primates) using chromosome painting and G-banding

BACKGROUND

Chromosomal painting, using whole chromosome probes from humans and Saguinus oedipus, was used to establish karyotypic divergence among species of the genus Cebus, including C. olivaceus, C. albifrons, C. apella robustus and C. apella paraguayanus. Cytogenetic studies suggested that the species of this genus have conservative karyotypes, with diploid numbers ranging from 2n = 52 to 2n = 54.

RESULTS

Banding studies revealed morphological divergence among some chromosomes, owing to variations in the size of heterochromatic blocks. This analysis demonstrated that Cebus species have five conserved human associations (i.e., 5/7, 2/16, 10/16, 14/15, 8/18 and 3/21) when compared with the putative ancestral Platyrrhini karyotype.

CONCLUSION

The autapomorphies 8/15/8 in C. albifrons and 12/15 in C. olivaceus explain the changes in chromosome number from 54 to 52. The association 5/16/7, which has not previously been reported in Platyrrhini, was also found in C. olivaceus. These data corroborate previous FISH results, suggesting that the genus Cebus has a very similar karyotype to the putative ancestral Platyrrhini.

Primate chromosome evolution: ancestral karyotypes, marker order and neocentromeres

In 1992 the Japanese macaque was the first species for which the homology of the entire karyotype was established by cross-species chromosome painting. Today, there are chromosome painting data on more than 50 species of primates. Although chromosome painting is a rapid and economical method for tracking translocations, it has limited utility for revealing intrachromosomal rearrangements. Fortunately, the use of BAC-FISH in the last few years has allowed remarkable progress in determining marker order along primate chromosomes and there are now marker order data on an array of primate species for a good number of chromosomes. These data reveal inversions, but also show that centromeres of many orthologous chromosomes are embedded in different genomic contexts. Even if the mechanisms of neocentromere formation and progression are just beginning to be understood, it is clear that these phenomena had a significant impact on shaping the primate genome and are fundamental to our understanding of genome evolution. In this report we complete and integrate the dataset of BAC-FISH marker order for human syntenies 1, 2, 4, 5, 8, 12, 17, 18, 19, 21, 22 and the X. These results allowed us to develop hypotheses about the content, marker order and centromere position in ancestral karyotypes at five major branching points on the primate evolutionary tree: ancestral primate, ancestral anthropoid, ancestral platyrrhine, ancestral catarrhine and ancestral hominoid. Current models suggest that between-species structural rearrangements are often intimately related to speciation. Comparative primate cytogenetics has become an important tool for elucidating the phylogeny and the taxonomy of primates. It has become increasingly apparent that molecular cytogenetic data in the future can be fruitfully combined with whole-genome assemblies to advance our understanding of primate genome evolution as well as the mechanisms and processes that have led to the origin of the human genome.

Chromosomal instability in Afrotheria: fragile sites, evolutionary breakpoints and phylogenetic inference from genome sequence assemblies

BACKGROUND

Extant placental mammals are divided into four major clades (Laurasiatheria, Supraprimates, Xenarthra and Afrotheria). Given that Afrotheria is generally thought to root the eutherian tree in phylogenetic analysis of large nuclear gene data sets, the study of the organization of the genomes of afrotherian species provides new insights into the dynamics of mammalian chromosomal evolution. Here we test if there are chromosomal bands with a high tendency to break and reorganize in Afrotheria, and by analyzing the expression of aphidicolin-induced common fragile sites in three afrotherian species, whether these are coincidental with recognized evolutionary breakpoints.

RESULTS

We described 29 fragile sites in the aardvark (OAF) genome, 27 in the golden mole (CAS), and 35 in the elephant-shrew (EED) genome. We show that fragile sites are conserved among afrotherian species and these are correlated with evolutionary breakpoints when compared to the human (HSA) genome. Inddition, by computationally scanning the newly released opossum (Monodelphis domestica) and chicken sequence assemblies for use as outgroups to Placentalia, we validate the HSA 3/21/5 chromosomal synteny as a rare genomic change that defines the monophyly of this ancient African clade of mammals. On the other hand, support for HSA 1/19p, which is also thought to underpin Afrotheria, is currently ambiguous.

CONCLUSION

We provide evidence that (i) the evolutionary breakpoints that characterise human syntenies detected in the basal Afrotheria correspond at the chromosomal band level with fragile sites, (ii) that HSA 3p/21 was in the amniote ancestor (i.e., common to turtles, lepidosaurs, crocodilians, birds and mammals) and was subsequently disrupted in the lineage leading to marsupials. Its expansion to include HSA 5 in Afrotheria is unique and (iii) that its fragmentation to HSA 3p/21 + HSA 5/21 in elephant and manatee was due to a fission within HSA 21 that is probably shared by all Paenungulata.

Phylogenomics of species from four genera of New World monkeys by flow sorting and reciprocal chromosome painting

Background

The taxonomic and phylogenetic relationships of New World monkeys (Platyrrhini) are difficult to distinguish on the basis of morphology and because diagnostic fossils are rare. Recently, molecular data have led to a radical revision of the traditional taxonomy and phylogeny of these primates. Here we examine new hypotheses of platyrrhine evolutionary relationships by reciprocal chromosome painting after chromosome flow sorting of species belonging to four genera of platyrrhines included in the Cebidae family: Callithrix argentata (silvered-marmoset), Cebuella pygmaea (pygmy marmoset), Callimico goeldii (Goeldi's marmoset) and Saimiri sciureus (squirrel monkey). This is the first report of reciprocal painting in marmosets.

Results

The paints made from chromosome flow sorting of the four platyrrhine monkeys provided from 42 to 45 hybridization signals on human metaphases. The reciprocal painting of monkey probes on human chromosomes revealed that 21 breakpoints are common to all four studied species. There are only three additional breakpoints. A breakpoint on human chromosome 13 was found in Callithrix argentata, Cebuella pygmaea and Callimico goeldii, but not in Saimiri sciureus. There are two additional breakpoints on human chromosome 5: one is specific to squirrel monkeys, and the other to Goeldi's marmoset.

Conclusion

The reciprocal painting results support the molecular genomic assemblage of Cebidae. We demonstrated that the five chromosome associations previously hypothesized to phylogenetically link tamarins and marmosets are homologous and represent derived chromosome rearrangements. Four of these derived homologous associations tightly nest Callimico goeldii with marmosets. One derived association 2/15 may place squirrel monkeys within the Cebidae assemblage. An apparently common breakpoint on chromosome 5q33 found in both Saimiri and Aotus nancymae could be evidence of a phylogenetic link between these species. Comparison with previous reports shows that many syntenic associations found in platyrrhines have the same breakpoints and are homologous, derived rearrangements showing that the New World monkeys are a closely related group of species. Our data support the hypothesis that the ancestral karyotype of the Platyrrhini has a diploid number of 2n = 54 and is almost identical to that found today in capuchin monkeys; congruent with a basal position of the Cebidae among platyrrhine families.

Evolutionary history of chromosome 11 featuring four distinct centromere repositioning events in Catarrhini

Panels of BAC clones used in FISH experiments allow a detailed definition of chromosomal marker arrangement and orientation during evolution. This approach has disclosed the centromere repositioning phenomenon, consisting in the activation of a novel, fully functional centromere in an ectopic location, concomitant with the inactivation of the old centromere. In this study, appropriate panels of BAC clones were used to track the chromosome 11 evolutionary history in primates and nonprimate boreoeutherian mammals. Chromosome 11 synteny was found to be highly conserved in both primate and boreoeutherian mammalian ancestors. Amazingly, we detected four centromere repositioning events in primates (in Old World monkeys, in gibbons, in orangutans, and in the Homo-Pan-Gorilla (H-P-G) clade ancestor), and one in Equidae. Both H-P-G and Lar gibbon novel centromeres were flanked by large duplicons with high sequence similarity. Outgroup species analysis revealed that this duplicon was absent in phylogenetically more distant primates. The chromosome 11 ancestral centromere was probably located near the HSA11q telomere. The domain of this inactivated centromere, in humans, is almost devoid of segmental duplications. An inversion occurred in chromosome 11 in the common ancestor of H-P-G. A large duplicon, again absent in outgroup species, was found located adjacent to the inversion breakpoints. In Hominoidea, almost all the five largest duplicons of this chromosome appeared involved in significant evolutionary architectural changes.

Evolutionary Formation of New Centromeres in Macaque

A systematic fluorescence in situ hybridization comparison of macaque and human synteny organization disclosed five additional macaque evolutionary new centromeres (ENCs) for a total of nine ENCs. To understand the dynamics of ENC formation and progression, we compared the ENC of macaque chromosome 4 with the human orthologous region, at 6q24.3, that conserves the ancestral genomic organization. A 250-kilobase segment was extensively duplicated around the macaque centromere. These duplications were strictly intrachromosomal. Our results suggest that novel centromeres may trigger only local duplication activity and that the absence of genes in the seeding region may have been important in ENC maintenance and progression.

Chromosome painting between human and lorisiform prosimians: evidence for the HSA 7/16 synteny in the primate ancestral karyotype

Multidirectional chromosome painting with probes derived from flow-sorted chromosomes of humans (Homo sapiens, HSA, 2n = 46) and galagos (Galago moholi, GMO, 2n = 38) allowed us to map evolutionarily conserved chromosomal segments among humans, galagos, and slow lorises (Nycticebus coucang, NCO, 2n = 50). In total, the 22 human autosomal painting probes detected 40 homologous chromosomal segments in the slow loris genome. The genome of the slow loris contains 16 sytenic associations of human homologues. The ancient syntenic associations of human chromosomes such as HSA 3/21, 7/16, 12/22 (twice), and 14/15, reported in most mammalian species, were also present in the slow loris genome. Six associations (HSA 1a/19a, 2a/12a, 6a/14b, 7a/12c, 9/15b, and 10a/19b) were shared by the slow loris and galago. Five associations (HSA 1b/6b, 4a/5a, 11b/15a, 12b/19b, and 15b/16b) were unique to the slow loris. In contrast, 30 homologous chromosome segments were identified in the slow loris genome when using galago chromosome painting probes. The data showed that the karyotypic differences between these two species were mainly due to Robertsonian translocations. Reverse painting, using galago painting probes onto human chromosomes, confirmed most of the chromosome homologies between humans and galagos established previously, and documented the HSA 7/16 association in galagos, which was not reported previously. The presence of the HSA 7/16 association in the slow loris and galago suggests that the 7/16 association is an ancestral synteny for primates. Based on our results and the published homology maps between humans and other primate species, we propose an ancestral karyotype (2n = 60) for lorisiform primates.

Mapping genomic rearrangements in titi monkeys by chromosome flow sorting and multidirectional in-situ hybridization

We developed chromosome painting probes for Callicebus pallescens from flow-sorted chromosomes and used multidirectional chromosome painting to investigate the genomic rearrangements in C. cupreus and C. pallescens. Multidirectional painting provides information about chromosomal homologies at the subchromosomal level and rearrangement break points, allowing chromosomes to be used as cladistic markers. Chromosome paints of C. pallescens were hybridized to human metaphases and 43 signals were detected. Then, both human and C. pallescens probes were hybridized to the chromosomes of another titi monkey, C. cupreus. The human chromosome paints detected 45 segments in the haploid karyotype of C. cupreus. We found that all the syntenic associations proposed for the ancestral platyrrhine karyotype are present in C. cupreus and in C. pallescens. The rearrangements differentiating C. pallescens from C. cupreus re one inversion, one fission and three fusions (two tandem and one Robertsonian)that occurred on the C. cupreus lineage. Our results support the hypothesis that karyological evolution in titi monkeys has resulted in reduction in diploid number and that species with higher diploid numbers (with less derived, more ancestral karyotypes)are localized in the centre of the geographic range of the genera, while more derived species appear to occupy the periphery.

The primates of the Neotropics: genomes and chromosomes

The classification of neotropical primates has been controversial. Different arrangements have been proposed, depending on taxonomic criteria and on the traits selected for phylogenetic reconstructions. These include gross morphologic characters, karyotypic attributes and DNA sequence data of nuclear and mitochondrial genes and of repetitive genomic components. These approaches have substantially clarified the main intergeneric relationships although several intrageneric arrangements still remain to be elucidated. In this review, we compare karyologic and molecular data of this speciose group.

Comparative chromosome painting in Aotus reveals a highly derived evolution

The genus Aotus represents a highly diverse group with an especially intricate taxonomy. No standard cytogenetic nomenclature for the genus has yet been established. So far, cytogenetic studies have characterized 18 different karyotypes with diploid numbers ranging from 46 to 58 chromosomes. By combining G-banding comparisons and molecular cytogenetic techniques, we were able to describe the most likely pattern of chromosome evolution and phylogenetic position of two Aotus karyomorphs (KMs) from Venezuela: Aotus nancymai (KM3, 2n=54) and Aotus sp. (KM9, 2n=50). All of the proposed Platyrrhini ancestral associations (2/16, 3/21, 5/7, 8/18, 10/16, 14/15) were found in the Aotus KMs studied, except 2/16 and 10/16. In addition, some derived chromosomal associations were also detected in both KMs (1/3, 1/16, 2/12, 2/20, 3/14, 4/15, 5/15, 7/11, 9/15, 9/17, 10/11, and 10/22). Although some of these associations have been found in other New World monkeys, our results suggest that Aotus species have undergone a highly derived chromosomal evolution. The homologies between these two Aotus KMs and human chromosomes were established, indicating that KM3 has a more derived karyotype than KM9 with respect to the ancestral Platyrrhini karyotype.

Chromosome painting comparison of Leontopithecus chrysomelas (Callitrichine, Platyrrhini) with man and its phylogenetic position

Using human probes of whole chromosomes, the homoeologies between human and Leontopithecus chrysomelas (Platyrrhini) karyotypes were established. Thirty-three conserved segments were observed between the two species. Intrachromosomal rearrangements between the two species were identified using hybridization of chromosome arm probes of human chromosomes 1 and 3. We also used chromosomal data to investigate phylogenetic relationships of Callitrichines. These data were encoded using Cebus capucinus , a species which kept fairly ancestral chromosomes, as reference. Two equi-parsimonious trees, including reversion or convergence events, were obtained. The monophyly of Callitrichines is confirmed. They share nine chromosomal rearrangements at least. The Cebuella-Callithrix group forms a clade sharing five rearrangements at least. According to the tree considered, the Tamarins, Leontopithecus and Saguinus share two chromosomal rearrangements restricted to these two taxa or none. Callimico accumulated seven chromosomal rearrangements unshared with other taxa, at least. To avoid convergence and reversion events, we propose the hypothesis of a network (or populational) evolution. Six chromosomal rearrangements would have occurred during the period of this network evolution. Finally, the karyotype of the last common ancestor to all Callitrichines has been reconstructed. It possessed 48 chromosomes.

Multi-directional chromosome painting maps homologies between species belonging to three genera of New World monkeys and humans

We mapped chromosomal homologies in two species of Chiropotes (Pitheciini, Saki Monkeys) and one species of Aotus (Aotinae, Owl Monkey) by multi-directional chromosome painting. Human chromosome probes were hybridized to Chiropotes utahicki, C. israelita and Aotus nancymae metaphases. Wooly Monkey chromosome paints were also hybridized to Owl Monkey metaphases. We established Owl Monkey chromosome paint probes by flow sorting and reciprocally hybridized them to human chromosomes. The karyotypes of the Bearded Saki Monkeys studied here are close to the hypothesized ancestral platyrrhine karytoype, while that of the Owl Monkey appears to be highly derived. The A. nancymae karyotype is highly shuffled and only three human syntenic groups were found conserved coexisting with 17 derived human homologous associations. A minimum of 14 fissions and 13 fusions would be required to derive the A. nancymae karyotype from that of the ancestral New World primate karyotype. An inversion between homologs to segments of human 10 and 16 suggests a link between Callicebus and Chiropotes, while the syntenic association of 10/11 found in Aotus and Callicebus suggests a link between these two genera. Future molecular cytogenetic work will be needed to determine whether these rearrangements represent synapomorphic chromosomal traits.

The impact of chromosome sorting and painting on the comparative analysis of primate genomes

Chromosome sorting by flow cytometry is the main source of chromosome-specific DNA for the production of painting probes. These probes have been used for cross-species in situ hybridization in the construction of comparative maps, in the study of karyotype evolution and phylogenetics, in delineating territories in interphase nuclei, and in the analysis of chromosome breakpoints. We review here the contributions that this technology has made to the analysis of primate genomes.

Evolutionary conserved chromosomal segments in the human karyotype are bounded by unstable chromosome bands

In this paper an ancestral karyotype for primates, defining for the first time the ancestral chromosome morphology and the banding patterns, is proposed, and the ancestral syntenic chromosomal segments are identified in the human karyotype. The chromosomal bands that are boundaries of ancestral segments are identified. We have analyzed from data published in the literature 35 different primate species from 19 genera, using the order Scandentia, as well as other published mammalian species as out-groups, and propose an ancestral chromosome number of 2n = 54 for primates, which includes the following chromosomal forms: 1(a+c(1)), 1(b+c(2)), 2a, 2b, 3/21, 4, 5, 6, 7a, 7b, 8, 9, 10a, 10b, 11, 12a/22a, 12b/22b, 13, 14/15, 16a, 16b, 17, 18, 19a, 19b, 20 and X and Y. From this analysis, we have been able to point out the human chromosome bands more "prone" to breakage during the evolutionary pathways and/or pathology processes. We have observed that 89.09% of the human chromosome bands, which are boundaries for ancestral chromosome segments, contain common fragile sites and/or intrachromosomal telomeric-like sequences. A more in depth analysis of twelve different human chromosomes has allowed us to determine that 62.16% of the chromosomal bands implicated in inversions and 100% involved in fusions/fissions correspond to fragile sites, intrachromosomal telomeric-like sequences and/or bands significantly affected by X irradiation. In addition, 73% of the bands affected in pathological processes are co-localized in bands where fragile sites, intrachromosomal telomeric-like sequences, bands significantly affected by X irradiation and/or evolutionary chromosomal bands have been described. Our data also support the hypothesis that chromosomal breakages detected in pathological processes are not randomly distributed along the chromosomes, but rather concentrate in those important evolutionary chromosome bands which correspond to fragile sites and/or intrachromosomal telomeric-like sequences.

New insights into the evolution of chromosome 1

A complex low-repetitive human DNA probe (BAC RP11-35B4) together with two microdissection-derived region-specific probes of the multicolor banding (MCB) probe-set for chromosome 1 were used to re-analyze the evolution of human chromosome 1 in comparison to four ape species. BAC RP11-35B4 derives from 1q21 and contains 143 kb of non-repetitive DNA; however, it produces three specific FISH signals in 1q21, 1p12 and 1p36.1 of Homo sapiens (HSA). Human chromosome 1 was studied in comparison to its homologues in Hylobates lar (HLA), Pongo pygmaeus (PPY), Gorilla gorilla (GGO) and Pan troglodytes (PTR). A duplication of sequences homologous to human 1p36.1 could be detected in PPY plus an additional signal on PPY 16q. The region homologous to HSA 1p36.1 is also duplicated in HLA, and split onto chromosomes 7q and 9p; the region homologous to HSA 1q21/1p12 is present as one region on 5q. Additionally, the breakpoint of a small pericentric inversion in the evolution of human chromosome 1 compared to other great ape species could be refined. In summary, the results obtained here are in concordance with previous reports; however, there is evidence for a deletion of regions homologous to human 1p34.2-->p34.1 during evolution in the Pongidae branch after separation of PPY.

Fluorescence in situ hybridization to chromosomes as a tool to understand human and primate genome evolution

For the last 15 years molecular cytogenetic techniques have been extensively used to study primate evolution. Molecular probes were helpful to distinguish mammalian chromosomes and chromosome segments on the basis of their DNA content rather than solely on morphological features such as banding patterns. Various landmark rearrangements have been identified for most of the nodes in primate phylogeny while chromosome banding still provides helpful reference maps. Fluorescence in situ hybridization (FISH) techniques were used with probes of different complexity including chromosome painting probes, probes derived from chromosome sub-regions and in the size of a single gene. Since more recently, in silico techniques have been applied to trace down evolutionarily derived chromosome rearrangements by searching the human and mouse genome sequence databases. More detailed breakpoint analyses of chromosome rearrangements that occurred during higher primate evolution also gave some insights into the molecular changes in chromosome rearrangements that occurred in evolution. Hardly any "fusion genes" as known from chromosome rearrangements in cancer cells or dramatic "position effects" of genes transferred to new sites in primate genomes have been reported yet. Most breakpoint regions have been identified within gene poor areas rich in repetitive elements and/or low copy repeats (segmental duplications). The progress in various molecular and molecular-cytogenetic approaches including the recently launched chimpanzee genome project suggests that these new tools will have a significant impact on the further understanding of human genome evolution.

Human chromosome 16 conservation in primates

A study was made of the organization of the chromosome orthologous to HSA16 in primates using a panel of 8 BAC probes spanning human chromosome 16. The probes were used in FISH experiments on great apes and on representatives of the Old World monkeys, New World monkeys, and lemurs. The domestic cat was used as an outgroup. The results indicate that 16p and 16q were separate chromosomes in a primate ancestor. They fused in a Catarrhini ancestor giving rise to the present day form found in HSA, great apes, and Old World monkeys. Several rearrangements were found in New World monkeys.

Chromosomal studies in Callicebus donacophilus pallescens, with classic and molecular cytogenetic approaches: multicolour FISH using human and Saguinus oedipus painting probes

This paper presents the karyotype of Callicebus donacophilus pallescens for the first time. The analysis included G-, C-, NOR-banding techniques and FISH with chromosome painting probes from Saguinus oedipus and Homo sapiens. The results were compared with the karyotypes of Callicebus moloch donacophilus and C. moloch previously published. These three karyotypes display the same diploid number (2n = 50) but diverge about the number of biarmed and acrocentric chromosomes. The acrocentrics 14 and 15 from C. m. donacophilus and C. moloch have undergone an in-tandem fusion originating a large acrocentric (pair 10) in C. d. pallescens. The major submetacentric pair (pair 1) from C. d. donacophilus and C. moloch have undergone fission originating two acrocentric pairs in C. d. pallescens (pairs 15 and 22). Herein was evidence that, in spite of the high interspecific variation among Callicebus, most of the chromosomes remained conserved.

Chromosome painting in Callicebus lugens, the species with the lowest diploid number (2n=16) known in primates

Cytogenetic studies have shown that New World primates are karyologically diverse and highly derived. The genus Callicebus is the best example of this karyological diversity, with diploid numbers ranging from 2n=50 to 2n=16. We report on Callicebus lugens, which has the lowest diploid number (2n=16) yet found in the primate order and represents a striking example of extreme karyotypic shuffling. To better understand the genomic rearrangements that have resulted in this extremely low diploid number, we mapped chromosome homologies between C. lugens and humans by in situ hybridization. The total number of hybridization signals was 42, excluding the Y chromosome, with a total of 34 syntenic associations not found in humans. This species has one of the most derived karyotypes among the Platyrrhini. Fusion has been the predominant mode of karyological evolution, although fissions and inversions have also transformed the C. lugens karyotype. Remarkably in such a highly rearranged karyotype, the synteny of 11 human chromosomes (4, 5, 9, 12, 13, 14, 17, 18, 20, 21, and X) was maintained intact, even if most of these human-homologous gene clusters were translocated. Other human syntenies, such as homologues to human chromosomes 10 and 16, were highly fragmented. Comparisons of the C. lugens-human homology map with those of other New World primates have not yet helped establish a phylogenic arrangement between congeneric species or link Callicebus with any other genus.

The phylogeny of howler monkeys (Alouatta, Platyrrhini): reconstruction by multicolor cross-species chromosome painting

We performed multidirectional chromosome painting in a comparative cytogenetic study of the three howler monkey species Alouatta fusca, A. caraya and A. seniculus macconnelli (Atelinae, Platyrrhini) in order to reconstruct phylogenetic relationships within this genus. Comparative genome maps between these species were established by multicolor fluorescence in-situ hybridization (FISH) employing human, Saguinus oedipus and Lagothrix lagothricha chromosome-specific probes. The three species included in this study and previously analyzed howler monkey species were subjected to a phylogenetic analysis on the basis of a data matrix comprised of 98 discrete molecular cytogenetic characters. The results revealed that howler monkeys represent the genus with the most extensive karyotype diversity within Platyrrhini so far analyzed with high levels of intraspecific chromosomal variability. Two different multiple sex chromosome systems were identified. The phylogenetic analysis indicated that Alouatta is a monophyletic clade which can be derived from a proposed ancestral Atelinae karyotype of 2n = 62 chromosomes by a chromosome fusion, a fission, a Y-autosomal translocation and a pericentric inversion. Following these suggestions, the genus Alouatta can be divided into two distinct species groups: the first includes A. caraya and A. belzebul, the second A. s. macconnelli, A. sara, A. s. arctoidea and A. fusca.

Chromosomal homologies between Cebus and Ateles (primates) based on ZOO-FISH and G-banding comparisons

ZOO-FISH (Fluorescent "in vitro" hybridization) was used to establish the chromosomal homology between humans (HSA) and Cebus nigrivitatus (CNI) and Ateles belzebuth hybridus (ABH). These two species belong to different New World monkey families (Cebidae and Atelidae, respectively) which differ greatly in chromosome number and in chromosome morphology. The molecular results were followed by a detailed banding analysis. The ancestral karyotype of Cebus was then determined by a comparison of in situ hybridization results, as well as chromosomal morphology and banding in other Platyrrhini species. The karyotypes of the four species belonging to the genus Cebus differ from each other by three inversions and one fusion as well as in the location and amounts of heterochromatin. Results obtained by ZOO-FISH in ABH are in general agreement with previous gene-mapping and in situ hybridization data in Ateles, which show that spider monkeys have highly derived genomes. The chromosomal rearrangements detected between HSA and ABH on a band-to-band basis were 27 fusions/fissions, 12 centromeric shifts, and six pericentric inversions. The ancestral karyotype of Cebus was then compared with that of Ateles. The rearrangements detected were 20 fusions/fissions, nine centromeric shifts, and five inversions. Atelidae species are linked by a fragmentation of chromosome 4 into three segments forming an association of 4/15, while Ateles species are linked by 13 derived associations. The results also helped clarify the content of the ancestral platyrrhine karyotype and the mode of chromosomal evolution in these primates. In particular, associations 2/16 and 5/7 should be included in the ancestral karyotype of New World monkeys.

Molecular cytotaxonomy of New World monkeys (Platyrrhini) - comparative analysis of five species by multi-color chromosome painting gives evidence for a classification of Callimico goeldii within the family of Callitrichidae

Chromosome rearrangements are considered as "rare genomic changes" and can provide useful markers and even landmarks for reconstructing phylogenies complementary to DNA sequence data and bio-morphological comparisons. Here, we applied multi-directional chromosome painting to reconstruct the chromosome phylogeny and evolutionary relationships among the New World monkey (Platyrrhini) species Callithrix argentata, Cebuella pygmaea, Saguinus oedipus, Callithrix jacchus and Callimico goeldii. The results clarified several aspects of New Wold monkey phylogeny. In particular the phylogenetic position of C. goeldii was elucidated, which has been controversially discussed and variously classified in the family Callitrichidae, in the family Cebidae or in its own family Callimiconidae. Comparative genome maps were established by multi-color fluorescence in situ hybridization (FISH) with human, S. oedipus and Lagothrix lagothricha chromosome- specific DNA probes. From these data we reconstructed the putative ancestral karyotype of all Callitrichidae. Various derived chromosomal syntenies are shared by all five species and cytogenetically define Callitrichidae - including Callimico goeldii -- as a distinctive group within the Platyrrhini. C. pygmaea and C. argentata share identical chromosomal syntenies from which S. oedipus and C. jacchus differ by single independent translocations. A common derived chromosomal change links Callimico with the marmosets to the exclusion of the tamarins, however, it has further diverged from an ancestral marmoset karyotype by at least four apomorphic rearrangements. Saimiri sciureus, representing the Cebinae, exclusively shares a derived syntenic association with all Callithrichidae, defining the genus Saimiri as a sister group.

Evolutionary conservation of chromosome territory arrangements in cell nuclei from higher primates

We demonstrate that the nuclear topological arrangement of chromosome territories (CTs) has been conserved during primate evolution over a period of about 30 million years. Recent evidence shows that the positioning of chromatin in human lymphocyte nuclei is correlated with gene density. For example, human chromosome 19 territories, which contain mainly gene-dense and early replicating chromatin, are located toward the nuclear center, whereas chromosome 18 territories, which consist mainly of gene-poor and later replicating chromatin, is located close to the nuclear border. In this study, we subjected seven different primate species to comparative analysis of the radial distribution pattern of human chromosome 18- and 19-homologous chromatin by three-dimensional fluorescence in situ hybridization. Our data demonstrate that gene-density-correlated radial chromatin arrangements were conserved during higher-primate genome evolution, irrespective of the major karyotypic rearrangements that occurred in different phylogenetic lineages. The evolutionarily conserved positioning of homologous chromosomes or chromosome segments in related species supports evidence for a functionally relevant higher-order chromatin arrangement that is correlated with gene-density.

Chromosome painting reveals that galagos have highly derived karyotypes

The differences in chromosome number between Otolemur crassicaudatus (2n = 62) and Galago moholi (2n = 38) are dramatic. However, the total number of signals given by hybridizing human chromosome paints to galago metaphases is similar: 42 in O. crassicaudatus and 38 G. moholi. Many human chromosome homologs are found fragmented in each species, and numerous translocations have resulted in chromosomal syntenies or hybridization associations which differ from those found in humans. Only 7 human autosomes showed conserved synteny in O. crassicaudatus, and 9 in G. moholi. Both galago species have numerous associations or syntenies not found in humans: O. crassicaudatus has 11, and G. moholi has 21. The phylogenetic line leading to the last common ancestor of the two galago species accumulated 6 synapomorphic fissions and 5 synapomorphic fusions. Since the divergence of the two galago species, 10 Robertsonian translocations have further transformed the G. moholi karyotype, and 2 fissions have been incorporated into the O. crassicaudatus karyotype. Comparison with other primates, tree shrews, and other mammals shows that both galagos have karyotypes which are a mixture of derived and conserved chromosomes, and neither has a karyotype close to that of the proposed ancestor of all primates. Am J Phys Anthropol 117:319-326, 2002. Published 2002 Wiley-Liss, Inc.

Reciprocal chromosome painting between a New World primate, the woolly monkey, and humans

We employed fluorescence-activated chromosome sorting (FACS) to construct chromosome paint sets for the woolly monkey (Lagothrix lagotricha) and then FISH to reciprocally paint human and woolly monkey metaphases. Reciprocal chromosome painting between humans and the woolly monkey allowed us to assign subchromosomal homologies between these species. The reciprocal painting data between humans and the woolly monkey also allow a better interpretation of the chromosomal difference between humans and platyrrhines, and refine hypotheses about the genomic rearrangements that gave origin to the genome of New World monkeys. Paints of woolly monkey chromosomes were used to paint human metaphases and forty-five clear signals were detected. Paints specific to each human chromosome were used to paint woolly monkey metaphases. The 23 human paints gave 39 clear signals on the woolly monkey karyotype. The woolly monkey chromosomes painted by human paints produced 7 associations of segments homologous to human chromosomes or human chromosome segments: 2/16, 3/21, 4/15, 5/7, 8/18, 10/16 and 14/15. A derived translocation between segments homologous to human chromosomes 4 and 15 is a synapomorphic marker linking all Atelines. These species may also be linked by fragmentation of homologs to human 1, 4, and 15.

Evolution of mammalian genome organization inferred from comparative gene mapping

Comparative genome analyses, including chromosome painting in over 40 diverse mammalian species, ordered gene maps from several representatives of different mammalian and vertebrate orders, and large-scale sequencing of the human and mouse genomes are beginning to provide insight into the rates and patterns of chromosomal evolution on a whole-genome scale, as well as into the forces that have sculpted the genomes of extant mammalian species.