Microsatellite variation and evolutionary history of PCDHX/Y gene pair within the Xq21.3/Yp11.2 hominid-specific homology block

To better understand the evolutionary dynamics of repetitive sequences in human sex chromosomes, we have analyzed seven new X/Y homologous microsatellites located within PCDHX/Y, one of the two recently described gene pairs in the Xq21.3/Yp11.2 hominid-specific homology block, in samples from Portugal and Mozambique. Sharp differences were observed on X/Y allele distributions, concerning both the presence of private alleles and a different modal repeat length for X-linked and Y-linked markers, and this difference was statistically significant. Higher diversity was found in X-linked microsatellites than in their Y chromosome counterparts; when comparing populations, Mozambicans showed more allele diversity for the X chromosome, but the contrary was true for the Y chromosome microsatellites. Evolutionary patterns, relying on intragenic PCDHX/Y SNPs, also revealed distinct scenarios for X and Y chromosomes. Greater microsatellite diversity was displayed by African X chromosomes within the most common haplotypes shared by both populations, whereas higher microsatellite diversity was found in Portugal for the ancestral Y chromosome haplotype. The most frequent PCDHY haplotype in Portuguese was the derived one, and it was not found in Mozambicans. TMRCA estimated by the rho parameter resulted in 13,700 years (7,500-20,000 years), which is consistent with a recent, post-Out-of-Africa origin for this haplotype. In conclusion, the newly described microsatellite loci generally displayed greater X-linked to Y-linked diversity and this pattern was also detected with slower evolving markers, with a remarkable differentiation between populations observed for Y chromosome haplotypes and, thus, greater divergence among Y chromosomes in human populations.     

A novel poly(A)-binding protein gene (PABPC5) maps to an X-specific subinterval in the Xq21.3/Yp11.2 homology block of the human sex chromosomes

The gene-poor human-specific Xq21.3/Yp11.2 block of homology exhibits 99% nucleotide identity, with the exception of an internal X-specific region containing the marker DXS214. This paper describes the characterization of a novel gene (PABPC5) from this X-specific subinterval that belongs to the poly(A)-binding protein gene family. The genomic structure of PABPC5 covers 4061 bp of an uninterrupted open reading frame (ORF) and a 5'UTR spanning across two exons and associated with a CpG island; the potential 382-amino-acid protein contains four RNA recognition motif domains. PABPC5 has 73% nucleotide identity with PABPC4 over 1801 bp of the ORF. At the protein level, 60% identity and 75% similarity are obtained in the comparison with human PABPC4, as well as human, mouse, and Xenopus PABPC1. RT-PCR indicates that PABPC5 is expressed in fetal brain and in a range of adult tissues. Conservation of the PABPC5 ORF and genomic structure is shown in primates and rodents. The close proximity of this gene to translocation breakpoints associated with premature ovarian failure makes it a potential candidate for this condition.     

The evolutionary conservation of the human chitotriosidase gene in rodents and primates

Chitinases have been identified in a variety of organisms ranging from prokaryotes to eukaryotes, known to specifically degrade chitin, an abundant polymer of N-acetylglucosamine. Recently a human chitinolytic enzyme called CHIT1 was discovered. CHIT1 is expressed by activated macrophages and hydrolyzes artificial chitotrioside substrates, but its specific function in humans is unknown, since it is generally believed that man completely lacks endogenous chitin and endogenous substrates for chitinases. An intriguing question is whether the chitotriosidase activity is just an evolutionary remnant or it has a physiological function in man. To test these hypotheses we utilized a "phylogenomic" approach performing accurate sequence analyses of this gene, coding for CHIT1, in rodents and primates. Inspecting the sequences available in public databases, we determined that this gene is conserved in rodents (mouse and rat) and primates (chimpanzee, gorilla, orangutan, gibbon, baboon, a common marmoset and black macaque). Moreover we found that a 24-base pair duplication that determines an enzymatically inactive human protein is not present in primates, suggesting that this polymorphism was created during human evolution. These results indicate that chitotriosidase is conserved across the evolutionary scale. Such conservation of the CHIT1 gene argues in favour of an important biological role.     

Characterization of DXZ4 conservation in primates implies important functional roles for CTCF binding,array expression and tandem repeat organization on the X chromosome

Background  

Comparative sequence analysis is a powerful means with which to identify functionally relevant non-coding DNA elements through conserved nucleotide sequence. The macrosatellite DXZ4 is a polymorphic, uninterrupted, tandem array of 3-kb repeat units located exclusively on the human X chromosome. While not obviously protein coding, its chromatin organization suggests differing roles for the array on the active and inactive X chromosomes.     

Phylogenetic diversity and the conservation biogeography of African primates

Aim Phylogenetics has an important role in conservation biogeography. However, there are few data on the phylogenetic diversity of African primates. The phylogenetic diversity (PD) of a species is a measure of its taxonomic distinctness and can be estimated by looking at the phylogenetic relationships among taxa. Species‐specific metrics on PD can then be used to determine conservation priorities at various biogeographical scales. We used PD metrics to rank 55 African primate species according to their conservation priorities at the country level and within six African biogeographical regions. We also addressed the following question: are there differences in conservation rankings between the IUCN Red List and our PD metrics? Location Africa. Methods We created a consensus phylogeny for all African primate clades based on genetic studies. Analyses of species distributions were determined using presence/absence scores at two levels: country and biogeographical region. A node‐based method that standardizes for widespread taxa and endemicity was used to calculate PD indices. Hierarchical cluster analysis was used to convert one of the standardized, phylogenetic indices into three clusters that could be ranked and compared with the main IUCN conservation rankings of endangered, vulnerable, and lower risk. Results At the country and region levels, the top‐priority species in terms of PD are Pan paniscus, Macaca sylvanus, Arctocebus calabarensis, Gorilla beringei, Arctocebus aureus, Allenopithecus nigroviridis, Gorilla gorilla, Procolobus verus, Cercopithecus solatus, Cercocebus galeritus, Colobus angolensis, Theropithecus gelada, Galagoides zanzibaricus, Galagoides granti, and Procolobus (Piliocolobus) badius. Geographic rankings were highest for the Democratic Republic of the Congo (country level) and Central Africa (region level). Although there were no overall differences between IUCN conservation ranks and the PD rankings, there were significant differences between the two systems for vulnerable and endangered primate taxa. Main conclusions There are few ecological and behavioural data on populations of some of the African primates that represent the highest levels of phylogenetic diversity. Studies of primate taxa with high PD rankings should focus on identifying sites suitable for intensive studies of population densities, feeding ecology, and reproductive behaviour. We suggest that PD metrics can serve as an important, complementary data set in the IUCN ranking system for primates.     

Vigilance and social organization in two species of primates

Animals that live in groups may accrue anti-predator benefits by virtue of their association with other individuals. While a number of factors (e.g. habitat quality, group geometry, dominance rank) have been shown to affect the relationship between group living and individual rates of visual vigilance, sociality and vigilance have not been studied specifically in terms of the two competing demands they impose upon an individual's visual time. Two captive groups each of tamarins, Saguinus labiatus, and squirrel monkeys, Saimiri sciureus, were used in three related experiments to determine whether they looked at the social or non-social environment while they engated in a simulated foraging task. The tamarins, whose social behaviour is quite pacific and cooperative relative to the more hierarchical squirrel monkeys, looked at the non-social environment when they visually interrupted their foraging. Squirrel monkeys, however, looked more often at group mates. Detection of predators is probably more likely when an individual directs its attention not to conspecifics, but to the environment. Hence, social organizations in which individuals must pay social attention in order to monitor threats and avoid aggression may reduce individual rates of vigilance for predators. Failure to consider various targets of attention may well overestimate vigilance for predators by including other sorts of attentional phenomena in the measurement of vigilance.     

N-terminal sequence of human leukocyte glycoprotein Mo1: conservation across species and homology to platelet IIb/IIIa

Mo1 and gp160-gp93 are two surface membrane glycoprotein heterodimers present on granulocytes and monocytes derived from humans and guinea pigs, respectively. We purified both antigens and found that their alpha subunits had identical N-termini which were significantly homologous to the alpha subunit of the human adhesion platelet glycoprotein IIb/IIIa.     

YAC contigs mapping the human COL4A5 and COL4A6 genes and DXS118 within Xq21.3–q22

Sequence-tagged sites (STSs) were developed for three loci of uncertain X chromosomal localization (DXS122, DXS137, and DXS174) and were used to seed YAC contigs. Two contigs now total about 3.3 Mb formatted with 34 STSs. One contains DXS122 and DXS174 within 250 kb on single YACs; it is placed in Xq21.3–q22.1 by FISH analysis, which is consistent with somatic cell hybrid panel analyses and with the inclusion of a probe that detects polymorphism at the DXS118 locus already assigned to that general region. The other contig, which contains DXS137, is in Xq22.2 by FISH, consistent with cell hybrid analyses and with the finding that it covers the human COL4A5 and COL4A6 genes known to be in that vicinity. In addition to extending the cloned coverage of this portion of the X chromosome, these materials should aid, for example, in the further analysis of Alport syndrome.     

Genetic linkage analysis places locus DXS250 between locus DXYS1 and locus DXS3 in Xq21.3.

The locus DXS250, which is linked to the Allan-Herndon type of X-linked mental retardation, maps between DXS3 and DXYS1 in a panel of 40 families established by the Centre d'Etude du Polymorphisme Humain, Paris.