F. García

Distribution of intrachromosomal telomeric sequences (ITS) on Macaca fascicularis (Primates) chromosomes and their implication for chromosome evolution

Abstract. The intrachromosomal location of the telomeric sequence in the crab-eating macaque, Macaca fascicularis (F. Cercopithecidae, Catarrhini) has been analysed by fluorescent in situ hybridisation with a long synthetic (TTAGGG)n probe. A total of 237 metaphases was analysed. As expected, all telomeres hybridised with the probe and 90 intrachromosomal loci with different hybridisation frequencies were also detected. The chromosomal location of interstitial telomeric sequences in M. fascicularis and in Homo sapiens was then compared, 37 sites (41.11%) being found to be conserved. Some of these sequences can be derived from rearrangements, such as inversions (MFA13q23) or fusions (MFA2p13 and MFA13p12), that have taken place during karyotype evolution.

Evolutionary breakpoints are co-localized with fragile sites and intrachromosomal telomeric sequences in primates

The concentration of evolutionary breakpoints in primate karyotypes in some particular regions or chromosome bands suggests that these chromosome regions are more prone to breakage. This is the first extensive comparative study which investigates a possible relationship of two genetic markers (intrachromosomal telomeric sequences [TTAGGG]n, [ITSs] and fragile sites [FSs]), which are implicated in the evolutionary process as well as in chromosome rearrangements. For this purpose, we have analyzed: (a) the cytogenetic expression of aphidicolin-induced FSs in Cebus apella and Cebus nigrivittatus (F. Cebidae, Platyrrhini) and Mandrillus sphinx (F. Cercopithecidae, Catarrhini), and (b) the intrachromosomal position of telomeric-like sequences by FISH with a synthetic (TTAGGG)n probe in C. apella chromosomes. The multinomial FSM statistical model allowed us to determinate 53 FSs in C. apella, 16 FSs in C. nigrivittatus and 50 FSs in M. sphinx. As expected, all telomeres hybridized with the probe, and 55 intrachromosomal loci were also detected in the Cebus apella karyotype. The χ2 test indicates that the coincidence of the location of Cebus and Mandrillus FSs with the location of human FSs is significant (P < 0.005). Based on a comparative cytogenetic study among different primate species we have identified (or described) the chromosome bands in the karyotypes of Papionini and Cebus species implicated in evolutionary reorganizations. More than 80% of these evolutionary breakpoints are located in chromosome bands that express FSs and/or contain ITSs.

Fragile sites in human and Macaca fascicularis chromosomes are breakpoints in chromosome evolution.

We have analysed the expression of aphidicolin-induced common fragile sites at two different aphidicolin concentrations (0.1 µmol/L and 0.2 µmol/L) in three female and one male crab-eating macaques (Macaca fascicularis, Cercopithecidae, Catarrhini). A total of 3948 metaphases were analysed: 1754 in cultures exposed to 0.1 µmol/L aphidicolin, 1261 in cultures exposed to 0.2 µmol/L aphidicolin and 933 in controls. The number of breaks and gaps detected ranged from 439 in cultures exposed to 0.1 µmol/L aphidicolin to 2061 in cultures exposed to 0.2 µmol/L aphidicolin. The use of a multinomial FSM statistical model allowed us to identify 95 fragile sites in the chromosomes of M. fascicularis, of which only 16 are expressed in all four specimens. A comparative study between the chromosomes of M. fascicularis and man has demonstrated that 38 human common fragile sites (50%) are found in the equivalent location in M. fascicularis. The analysis of the rearrangements that have taken place during chromosome evolution has revealed that the breakpoints involved in these rearrangements correspond significantly (p < 0.025) to the location of M. fascicularis fragile sites.

Evolution of recombination in eutherian mammals: insights into mechanisms that affect recombination rates and crossover interference

Recombination allows faithful chromosomal segregation during meiosis and contributes to the production of new heritable allelic variants that are essential for the maintenance of genetic diversity. Therefore, an appreciation of how this variation is created and maintained is of critical importance to our understanding of biodiversity and evolutionary change. Here, we analysed the recombination features from species representing the major eutherian taxonomic groups Afrotheria, Rodentia, Primates and Carnivora to better understand the dynamics of mammalian recombination. Our results suggest a phylogenetic component in recombination rates (RRs), which appears to be directional, strongly punctuated and subject to selection. Species that diversified earlier in the evolutionary tree have lower RRs than those from more derived phylogenetic branches. Furthermore, chromosome-specific recombination maps in distantly related taxa show that crossover interference is especially weak in the species with highest RRs detected thus far, the tiger. This is the first example of a mammalian species exhibiting such low levels of crossover interference, highlighting the uniqueness of this species and its relevance for the study of the mechanisms controlling crossover formation, distribution and resolution.

Conservation of aphidicolin-induced fragile sites in Papionini (Primates) species and humans

Fragile sites are considered structural features of mammalian chromosomes and a commonly repeated hypothesis is that they are evolutionarily conserved. We tested this hypothesis by establishing the subchromosomal homology of regions harbouring fragile sites in the chromosomes of humans, Macaca fascicularis (MFA) and Mandrillus sphinx (MSP). We delineated the interspecific homology of chromosome bands expressing aphidicolin-induced fragile sites of homologues to human chromosomes 1, 3, 5, 7, 18 and X by the comparative FISH of human BAC and YAC clones. Notably, two YAC clones known to span human chromosome regions containing fragile sites were shown to also span fragile sites in macaques and mandrills. The present comparative BAC/YAC mapping data represent, up to now, the most precise evidence of fragile site conservation during primate evolution.

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+c1), 1(b+c2), 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.

Radiation and speciation of spider monkeys, genus Ateles, from the cytogenetic viewpoint

The chromosomes of 22 animals of four subspecies of the genus Ateles (A. paniscus paniscus, A. p. chamek, A. belzebuth hybridus, and A. b. marginatus) were compared using G/C banding and NOR (nucleolar organizer region) staining methods. The cytogenetic data of Ateles in the literature were also used to clarify the phylogenetic relationships of the species and subspecies and to infer the routes of radiation and speciation of these taxa. Chromosomes 6 and 7 that showed more informative geographic variation and the apomorphic form 4/12, exclusively in A. p. paniscus, are the keys for understanding the evolution, radiation, and specification of the Ateles taxa. The ancestral populations of the genus originated in the southwestern Amazon Basin (the occurrence area of A. paniscus chamek) and spread in the Amazon Basin and westward, crossing the Andes and colonizing Central America and northwesternmost regions of South America. The evolutionary history of the northern South American taxa is interpreted using the model of biogeographical evolution postulated by Haffer [Science 185:131–137, 1969]. Ateles paniscus paniscus is the genetically most differentiated form and probably derives from A. belzebuth hybridus. Based on the karyotype differences, the populations of Ateles can be divided into four different group. These findings indicate the necessity of a more coherent taxonomic arrangement for the taxa of Ateles. Am. J. Primatol. 42:167–178, 1997.

Chromosomal homologies between humans and Cebus apella (Primates) revealed by ZOO-FISH.

The chromosome reorganizations that arose during primate evolution have usually been detected by use of banding patterns. The ZOO-FISH technique allows more precise characterization of the chromosome homologies between humans and other non-human primates. This technique is useful when the phylogenetic distance between the species is large and chromosome homologies are difficult to detect by comparing G bands (Sherlock et al. 1996). The genusCebus(Cebidae, Platyrrhini) has been widely studied from a cytogenetic point of view (Garcia et al. 1983; Matayoshi et al. 1986; Mudry 1990; Ponsa ` et al. 1995). Results obtained by comparing the Gor R-banding patterns of this genus and those of other primates allowed us to establish the hypothesis that Cebus maintained a primitive karyotype (Dutrillaux and Couturier 1981; Clemente et al. 1990). For this reason, comparison between C bus and the human karyotype is especially interesting. Homologies betweenCebus capucinusand human chromosomes have been established by comparing their R-banding patterns (Dutrillaux 1979) and by the ZOO-FISH technique (Richard et al. 1996). Comparison between the G-banding pattern of Cebus apellaand the human karyotype was also carried out by Clemente et al. (1987) and Borrell (1995). Using ZOO-FISH, we have confirmed the homologies for human Chromosomes (Chrs) 2, 3, 9, and 14 in C. apella(Garcia et al. 1999). Correspondence to: M. Garcia Calde ́s; e-mail: IBCE1@cc.uab.es

Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx

BackgroundGenomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective conservation. The Iberian lynx (Lynx pardinus) is the most endangered felid and a unique example of a species on the brink of extinction.ResultsWe generate the first annotated draft of the Iberian lynx genome and carry out genome-based analyses of lynx demography, evolution, and population genetics. We identify a series of severe population bottlenecks in the history of the Iberian lynx that predate its known demographic decline during the 20th century and have greatly impacted its genome evolution. We observe drastically reduced rates of weak-to-strong substitutions associated with GC-biased gene conversion and increased rates of fixation of transposable elements. We also find multiple signatures of genetic erosion in the two remnant Iberian lynx populations, including a high frequency of potentially deleterious variants and substitutions, as well as the lowest genome-wide genetic diversity reported so far in any species.ConclusionsThe genomic features observed in the Iberian lynx genome may hamper short- and long-term viability through reduced fitness and adaptive potential. The knowledge and resources developed in this study will boost the research on felid evolution and conservation genomics and will benefit the ongoing conservation and management of this emblematic species.

Characterization of constitutive heterochromatin in Cebus apella (Cebidae, Primates) and Pan troglodytes (Hominidae, Primates): comparison to human chromosomes.

Using G bands, some homologies between the chromosomes of Cebus apella (CAP) and human chromosomes are difficult to establish. To solve this problem, we analyzed these homologies by fluorescence in situ hybridization using human whole chromosome probes (ZOO‐FISH). The results indicated that 1) the human probe for chromosome 2 partially hybridizes with CAP chromosomes 13 and 5, 2) the human probe for chromosome 3 partially hybridizes with CAP chromosomes 18 and 20, 3) the human probe for chromosome 9 partially hibridizes with CAP chromosome 19, and 4) the human probe for chromosome 14 hybridizes with the p‐terminal and q‐terminal regions of CAP chromosome 6. However, none of the human probes employed hybridized with the heterochromatic regions of CAP chromosomes. For this reason, we characterized the heterochromatic regions of CAP chromosomes and of the chromosomes of Pan troglodytes (PTR), to allow comparison between CAP, PTR, and human chromosomes using in situ digestion of fixed chromosomes with the restriction enzymes AluI, HaeIII, and RsaI and by fluorescent staining with DA/DAPI. The results show that 1) centromeric heterochromatin is heterogeneous in the three species studied and 2) noncentromeric heterochromatin is homogeneous within each of the three species, but is different for each species. Thus, centromeric heterochromatin undergoes a higher degree of variability than noncentromeric heterochromatin. Am. J. Primatol. 49:205–221, 1999.