Francesca Bigoni

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.

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.

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

BackgroundThe 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 (Goeldis marmoset) and Saimiri sciureus (squirrel monkey). This is the first report of reciprocal painting in marmosets.ResultsThe 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 Goeldis marmoset.ConclusionThe 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.

Chromosome Painting Shows That Pygathrix nemaeus Has the Most Basal Karyotype Among Asian Colobinae

We mapped the chromosomal homology of Pygathrix namaeus (douc) with human and other primates by in situ hybridization of human chromosome paints. The synteny of 3 human chromosomes (1, 2, 19) is fragmented in the douc karyotype and the 23 human probes (autosomes plus X) provided 26 signals. There are associations between human chromosomes 14/15, 21/22, and 1/19. Human chromosomes 1 and 19 are divided in two segments and associated on douc chromosomes 8 and 10. The fragmentation and association of human chromosomes 1 and 19 is best explained as the result of a reciprocal translocation, which occurs in all documented Asian colobines studied, but not in the African species Colobus guereza. However, the homologs to douc chromosome 10 in all other Asian documented colobines show an additional pericentric inversion. Our results indicate that Pygathrix nemeus is karyologically the most conservative colobine species yet studied and that this species probably diverged early after the separation of Asian and African Colobinae. The data reinforce the monophyly of the Colobinae and their division into an African and an Asian clade.

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 ncestral karyotypes)are localized in the centre of the geographic range of the genera, while more derived species appear to occupy the periphery

Reciprocal painting between humans, De Brazza’s and patas monkeys reveals a major bifurcation in the Cercopithecini phylogenetic tree

We report on reciprocal painting between humans and two Cercopithecini species, Erythrocebus patas (patas monkey) and Cercopithecus neglectus (De Brazza’s monkey). Both human and monkeys chromosome-specific probes were made by degenerate oligonucleotide primed PCR (DOP-PCR) from flow sorted chromosomes. Metaphases of both monkey species were first hybridized with human chromosome-specific probes and then human metaphases were hybridized with chromosome paints from each monkey species. The human paint probes detected 34 homologous segments on the C. neglectus karyotype, while the C. neglectus probes, including the Y, revealed 41 homologous segments on the human karyotype. The probes specific for human chromosomes detected 29 homologous segments in the E. patas karyotype, while the patas monkey probes painted 34 segments on the human karyotype. We tested various hypotheses of Cercopithecini phylogeny and taxonomy developed by morphologists, molecular biologists and cytogeneticists. Our hybridization data confirm that fissions (both Robertsonian and non-Robertsonian) are the main mechanism driving the evolutionary trend in Cercopithecini toward higher diploid numbers and strongly suggest an early phylogenetic bifurcation in Cercopithecini. One branch leads to Cercopithecus neglectus/Cercopithecus wolfi while the other line leads to Erythrocebus patas/Chlorocebus aethiops. Allenopithecus nigroviridis may have diverged prior to this major phylogenetic node.

Sexual selection and the evolution of behavior, morphology, neuroanatomy and genes in humans and other primates

Explaining human evolution means developing hypotheses about the occurrence of sex differences in the brain. Neuroanatomy is significantly influenced by sexual selection, involving the cognitive domain through competition for mates and mate choice. Male neuroanatomy emphasizes subcortical brain areas and visual-spatial skills whereas that of females emphasizes the neocortex and social cognitive areas. In primate species with high degrees of male competition, areas of the brain dealing with aggression are emphasized. Females have higher mirror neuron activity scores than males. Hundreds of genes differ in expression profiles between males and females. Sexually selected differences in gene expression can produce neuroanatomical sex differences. A feedback system links genes, gene expression, hormones, morphology, social structure and behavior. Sex differences, often through female choice, can be rapidly modulated by socialization. Human evolution is a dramatic case of how a trend toward pair bonding and monogamy lowered male competition and increased female choice as a necessary step in releasing the cognitive potential of our species.

Chromosome Painting of the Pygmy Tree Shrew Shows that No Derived Cytogenetic Traits Link Primates and Scandentia

We hybridized human chromosome paints on metaphases of the pygmy tree shrew (Tupaia minor, Scandentia). The lack of the ancestral mammalian 4/8 association in both Primates and Scandentia was long considered a cytogenetic landmark that phylogenetically linked these mammalian orders. However, our results show that the association 4/8 is present in Tupaia along with not previously reported associations for 1/18 and 7/10. Altogether there are 11 syntenic associations of human chromosome segments in the pygmy tree shrew karyotype: 1/18, 2/21, 3/21, 4/8, 7/10, 7/16, 11/20, 12/22 (twice), 14/15 and 16/19. Our data remove any cytogenetic evidence that Scandentia has a preferential phylogenetic relationship with Primates.

Evolutionary Molecular Cytogenetics of Catarrhine Primates: Past, Present and Future

The catarrhine primates were the first group of species studied with comparative molecular cytogenetics. Many of the fundamental techniques and principles of analysis were initially applied to comparisons in these primates, including interspecific chromosome painting, reciprocal chromosome painting and the extensive use of cloned DNA probes for evolutionary analysis. The definition and importance of chromosome syntenies and associations for a correct cladistics analysis of phylogenomic relationships were first applied to catarrhines. These early chromosome painting studies vividly illustrated a striking conservation of the genome between humans and macaques. Contemporarily, it also revealed profound differences between humans and gibbons, a group of species more closely related to humans, making it clear that chromosome evolution did not follow a molecular clock. Chromosome painting has now been applied to more that 60 primate species and the translocation history has been mapped onto the major taxonomic divisions in the tree of primate evolution. In situ hybridization of cloned DNA probes, primarily BAC-FISH, also made it possible to more precisely map breakpoints with spanning and flanking BACs. These studies established marker order and disclosed intrachromosomal rearrangements. When applied comparatively to a range of primate species, they led to the discovery of evolutionary new centromeres as an important new category of chromosome evolution. BAC-FISH studies are intimately connected to genome sequencing, and probes can usually be assigned to a precise location in the genome assembly. This connection ties molecular cytogenetics securely to genome sequencing, assuring that molecular cytogenetics will continue to have a productive future in the multidisciplinary science of phylogenomics.

The Ancestral Genomes in Primate Phylogeny and Origins: A Molecular Cytogenetic Perspective

Over the last decade molecular techniques have become powerful tools in cytogenetics, and it is now generally accepted that cytogenetic reconstructions of phylogeny should be based on molecular techniques. Banding has often led to incorrect assignments of homology or comparisons of only highly conserved chromosomes. In particular, new syntenic associations have often gone undetected by banding (Stanyon et al., 2000).