Evolution of the cryptic FMR1 CGG repeat.

We have sequenced the 5' untranslated region of the orthologous FMR1 gene from 44 species of mammals. The CGG repeat is present in each species, suggesting conservation of the repeat over 150 million years of mammalian radiation. Most mammals possess small contiguous repeats (mean number of repeats = 8.0 +/- 0.8), but in primates, the repeats are larger (mean = 20.0 +/- 2.3) and more highly interrupted. Parsimony analysis predicts that enlargement of the FMR1 CGG repeat beyond 20 triplets has occurred in three different primate lineages. In man and gorilla, AGG interruptions occur with higher-order periodicity, suggesting that historical enlargement has involved incremental and vectorial addition of larger arrays demarcated by an interruption. Our data suggest that replication slippage and unequal crossing over have been operative during the evolution of this repeat.

Phylogeny of horse chromosome 5q in the genus Equus and centromere repositioning.

Horses, asses and zebras belong to the genus Equus and are the only extant species of the family Equidae in the order Perissodactyla. In a previous work we demonstrated that a key factor in the rapid karyotypic evolution of this genus was evolutionary centromere repositioning, that is, the shift of the centromeric function to a new position without alteration of the order of markers along the chromosome. In search of previously undiscovered evolutionarily new centromeres, we traced the phylogeny of horse chromosome 5, analyzing the order of BAC markers, derived from a horse genomic library, in 7 Equus species (E. caballus, E. hemionus onager, E. kiang, E. asinus, E. grevyi, E. burchelli and E. zebra hartmannae). This analysis showed that repositioned centromeres are present in E. asinus (domestic donkey, EAS) chromosome 16 and in E. burchelli (Burchell's zebra, EBU) chromosome 17, confirming that centromere repositioning is a strikingly frequent phenomenon in this genus. The observation that the neocentromeres in EAS16 and EBU17 are in the same chromosomal position suggests that they may derive from the same event and therefore, E. asinus and E. burchelli may be more closely related than previously proposed; alternatively, 2 centromere repositioning events, involving the same chromosomal region, may have occurred independently in different lineages, pointing to the possible existence of hot spots for neocentromere formation. Our comparative analysis also showed that, while E. caballus chromosome 5 seems to represent the ancestral configuration, centric fission followed by independent fusion events gave rise to 3 different submetacentric chromosomes in other Equus lineages.

Resolution of the early placental mammal radiation using Bayesian phylogenetics.

Molecular phylogenetic studies have resolved placental mammals into four major groups, but have not established the full hierarchy of interordinal relationships, including the position of the root. The latter is critical for understanding the early biogeographic history of placentals. We investigated placental phylogeny using Bayesian and maximum-likelihood methods and a 16.4-kilobase molecular data set. Interordinal relationships are almost entirely resolved. The basal split is between Afrotheria and other placentals, at about 103 million years, and may be accounted for by the separation of South America and Africa in the Cretaceous. Crown-group Eutheria may have their most recent common ancestry in the Southern Hemisphere (Gondwana).

Conservation genomics: applying whole genome studies to species conservation efforts.

Studies of complete genomes are leading to a new understanding of the biology of mammals and providing ongoing insights into the fundamental aspects of the organization and evolution of biological systems. Comparison of primate genomes can identify aspects of their organization, regulation and function that appeared during the primate radiation, but without comparison to more evolutionarily distant mammals and other vertebrates, highly conserved aspects of genome architecture will not be accurately identified nor will the lineage-specific changes be identified as such. Many species of primates face risks of extinction; yet the knowledge of their genomes will provide a deeper understanding of primate adaptations, human origins, and provide the framework for discoveries anticipated to improve human medicine. The great apes, the closest relatives of the human species, are among the most vulnerable and most important for human medical studies. However, apes are not the only species whose genomic information will enrich humankind. Comparative genomic studies of endangered species can benefit conservation efforts on their behalf. Increased knowledge of genome makeup and variation in endangered species finds conservation application in population evaluation monitoring and management, understanding phylozoogeography, can enhance wildlife health management, identify risk factors for genetic disorders, and provide insights into demographic management of small populations in the wild and in captivity.

Homologous fission event(s) implicated for chromosomal polymorphisms among five species in the genus Equus.

The genus Equus is unusual in that five of the ten extant species have documented centric fission (Robertsonian translocation) polymorphisms within their populations, namely E. hemionus onager, E. hemionus kulan, E. kiang, E. africanus somaliensis, and E. quagga burchelli. Here we report evidence that the polymorphism involves the same homologous chromosome segments in each species, and that these chromosome segments have homology to human chromosome 4 (HSA4). Bacterial artificial chromosome clones containing equine genes SMARCA5 (ECA2q21 homologue to HSA4q31. 21) and UCHL1 (ECA3q22 homologue to HSA4p13) were mapped to a single metacentric chromosome and two unpaired acrocentrics by FISH mapping for individuals possessing odd numbers of chromosomes. These data suggest that the polymorphism is either ancient and conserved within the genus or has occurred recently and independently within each species. Since these species are separated by 1-3 million years of evolution, this polymorphism is remarkable and worthy of further investigations.

FISH analysis comparing genome organization in the domestic horse (Equus caballus) to that of the Mongolian wild horse (E. przewalskii).

Przewalski's wild horse (E. przewalskii, EPR) has a diploid chromosome number of 2n = 66 while the domestic horse (E. caballus, ECA) has a diploid chromosome number of 2n = 64. Discussions about their phylogenetic relationship and taxonomic classification have hinged on comparisons of their skeletal morphology, protein and mitochondrial DNA similarities, their ability to produce fertile hybrid offspring, and on comparison of their chromosome morphology and banding patterns. Previous studies of GTG-banded karyotypes suggested that the chromosomes of both equids were homologous and the difference in chromosome number was due to a Robertsonian event involving two pairs of acrocentric chromosomes in EPR and one pair of metacentric chromosomes in ECA (ECA5). To determine which EPR chromosomes were homologous to ECA5 and to confirm the predicted chromosome homologies based on GTG banding, we constructed a comparative gene map between ECA and EPR by FISH mapping 46 domestic horse-derived BAC clones containing genes previously mapped to ECA chromosomes. The results indicated that all ECA and EPR chromosomes were homologous as predicted by GTG banding, but provide new information in that the EPR acrocentric chromosomes EPR23 and EPR24 were shown to be homologues of the ECA metacentric chromosome ECA5.

Karyotypic relationships of horses and zebras: results of cross-species chromosome painting.

Complete sets of chromosome-specific painting probes, derived from flow-sorted chromosomes of human (HSA), Equus caballus (ECA) and Equus burchelli (EBU) were used to delineate conserved chromosomal segments between human and Equus burchelli, and among four equid species, E. przewalskii (EPR), E. caballus, E. burchelli and E. zebra hartmannae (EZH) by cross-species chromosome painting. Genome-wide comparative maps between these species have been established. Twenty-two human autosomal probes revealed 48 conserved segments in E. burchelli. The adjacent segment combinations HSA3/21, 7/16p, 16q/19q, 14/15, 12/22 and 4/8, presumed ancestral syntenies for all eutherian mammals, were also found conserved in E. burchelli. The comparative maps of equids allow for the unequivocal characterization of chromosomal rearrangements that differentiate the karyotypes of these equid species. The karyotypes of E. przewalskii and E. caballus differ by one Robertsonian translocation (ECA5 = EPR23 + EPR24); numerous Robertsonian translocations and tandem fusions and several inversions account for the karyotypic differences between the horses and zebras. Our results shed new light on the karyotypic evolution of Equidae.

Molecular basis of albinism in the rhesus monkey.

Sequence analysis of the tyrosinase (TYR) coding region from one albino rhesus monkey (Macaca mulatta) family revealed that the two monkeys with phenotype similar to human TYR-negative oculocutaneous albinism (OCA) were homozygous for a missense mutation (S184TER) in exon 1 at codon 184. The offspring of one of the albino monkey ("Kangkang") are all heterozygous for the S184TER mutation, but the S184TER mutation was not observed in 93 control individuals. We conclude that the point mutation is responsible and sufficient to generate the albino rhesus monkey phenotype. The rough age of the S184TER nonsense mutation may be about 0.8 million years using a rate of 0.16% per million years.

Cytogenetic analysis shows extensive genomic rearrangements between red howler (Alouatta seniculus, Linnaeus) subspecies.

A comparison of the G-banded karyotypes of two red howler subspecies, Alouatta seniculus arctoidea and A. s. sara, showed that they differed by at least 14 chromosomal rearrangements. Genomic reshuffling is so great that homologs between subspecies could not be found for some chromosome, while the assignment of homology for other chromosomes remains uncertain. The two red howlers, however, share an unusual X1X2Y1Y2/ X1X1X2X2 sex-chromosome system that resulted from a Y-autosome translocation, probably in a common ancestor. The great chromosomal variability resulting from rapid chromosomal evolution in howlers indicates that cytogenetic data could make an important contribution to resolving phylogenetic and conservation problems in this group of highly conspicuous New World Monkeys. © 1995 Wiley-Liss, Inc.

Sequence variation and genetic diversity in the giant panda.

About 336-444 bp mitochondrial D-loop region and tRNA gene were sequenced for 40 individuals of the giant panda which were collected from Mabian, Meigu, Yuexi, Baoxing, Pingwu, Qingchuan, Nanping and Baishuijiang, respectively. 9 haplotypes were found in 21 founders. The results showed that the giant panda has low genetic variations, and that there is no notable genetic isolation among geographical populations. The ancestor of the living giant panda population perhaps appeared in the late Pleistocene, and unfortunately, might have suffered bottleneck attacks. Afterwards, its genetic diversity seemed to recover to some extent.

[Mitochondrial DNA sequence evolution and conservation relevance of snub-nosed langurs].

The classification and phylogenetic relationships of the snub-nosed langurs (Rhinopithecus) are still open questions. We have sequenced a mitochondrial cytochrome b gene fragment from R. roxellana, R. bieti, R. avunculus and Presbytis phayrei. There are 47 sites (19%) characterized by variation. A series of evolutionary trees with concordant topology has been derived by using parsimony, maximum likelihood and distance methods, which may have resolved the evolutionary relationships of the three golden monkey species. R. bieti is more closely related to R. avunculus than to R. roxellana. The divergence among those three species occurred about 2-6 million years ago. Our results suggest that Rhinopithecus is a valid genus, and avunculus should be placed into this genus. Our non-invasive genetic analysis provided useful information for the genetic management of the captive population at the Kunming Institute of Zoology.

[The relationship among human, gorilla, chimpanzee and orangutan].

The phylogeny of hominoid is still an open question. The contrary point is which relationship is more closed related between human and gorilla and human and chimpanzee. Tyrosinase is the essential enzyme in melanogenesis. The mutation of tyrosinase gene causes albinism. The five exons of tyrosinase gene were sequenced for gorilla, chimpanzee, orangutan and gibbon in hominoid. Combined with the human tyrosinase gene sequence, the gene tree was constructed using parsimony method. The results show that the relationship between human and gorilla is more closed related than between human and chimpanzee.

Genome sequence, comparative analysis, and population genetics of the domestic horse.

We report a high-quality draft sequence of the genome of the horse (Equus caballus). The genome is relatively repetitive but has little segmental duplication. Chromosomes appear to have undergone few historical rearrangements: 53% of equine chromosomes show conserved synteny to a single human chromosome. Equine chromosome 11 is shown to have an evolutionary new centromere devoid of centromeric satellite DNA, suggesting that centromeric function may arise before satellite repeat accumulation. Linkage disequilibrium, showing the influences of early domestication of large herds of female horses, is intermediate in length between dog and human, and there is long-range haplotype sharing among breeds.

Karyotypic evolution of a novel cervid satellite DNA family isolated by microdissection from the Indian muntjac Y-chromosome.

A minilibrary was constructed from DOP-PCR products using microdissected Y-chromosomes of Indian muntjac as DNA templates. Two microclones designated as IM-Y4-52 and IM-Y5-7 were obtained from negative screening of all three cervid satellite DNAs (satellites I, II, and IV). These two microclones were 295 and 382 bp in size, respectively, and shared approximately 70% sequence homology. Southern blot analysis showed that the IM-Y4-52 clone was repetitive in nature with an approximately 0.32-kb register in HaeIII digest. Sequence comparison revealed no similarities to DNA sequences deposited in the GenBank database, suggesting that the microclone sequences were from a novel satellite DNA family designated as cervid satellite V. A subclone of an Indian muntjac BAC clone which screened positive for IM-Y4-52 had a 3,325-bp insert containing six intact monomers, four deleted monomers, and two partial monomers. The consensus sequence of the monomer was 328 bp in length and shared more than 80% sequence homology with every intact monomer. A zoo blot study using IM-Y4-52 as a probe showed that the strong hybridization with EcoRI digested male genomic DNA of Indian muntjac, Formosan muntjac, Chinese muntjac, sambar deer, and Chinese water deer. Female genomic DNA of Indian muntjac, Chinese water deer, and Formosan muntjac also showed positive hybridization patterns. Satellite V was found to specifically localize to the Y heterochromatin region of the muntjacs, sambar deer, and Chinese water deer and to chromosome 3 of Indian muntjac and the X-chromosome of Chinese water deer.

Chromosomal polymorphism in Equus hemionus.

The first cytogenetic studies of the Turkmenian kulan, Equus hemionus kulan, are reported, and a polymorphism in diploid chromosome number is described. Chromosome fusion is apparently involved in the alterations of the karyotype of E. hemionus kulan (2n = 55, 54) when compared to the karyotype of the onager, E. hemionus onager (2n = 56). Additionally, the rearrangement involved has been identified in animals unrelated through captive breeding; inheritance of the fusion chromosomes has also been observed.

Genetic studies of blood markers in Przewalski's horses.

Ninety-six Przewalski's horses (Equus przewalskii) were blood typed using systems of inherited blood variants known to be highly effective for parentage testing of domestic horses (E. caballus). Sixteen red cell antigenic factors detected using sera prepared by alloimmunization of domestic horses were shown to be inherited in six systems (A, C, D, P, Q, and U) and in the same patterns as domestic horses. Family data confirmed autosomal, codominant inheritance at five loci of serum protein variants (Al, Tf, Xk, Pi, and Es) and three loci of red cell proteins (PGM, PHI, and Hb). One serum protein locus (Gc) and two red cell protein loci (PGD and CA) appeared to be monomorphic. Despite the narrow genetic base and high inbreeding coefficients of captive Przewalski's horses, average heterozygosity calculated over 18 loci was estimated to be 0.320 +/- 0.05, which was similar to that found in five breeds of domestic horses.