Heterochromatin variation and spermatogenesis in Nesokia

A probable role of heterochromatin variation in male meiosis has been evaluated using fertile and infertile Indian mole rat males (Nesokia) with polymorphic X and/or Y chromosomes. A comprehensive study of tubular histology, meiotic progression, and X-Y chromosome pairing was undertaken. Despite heterochromatin variation, spermatogenesis was found to be complete in all individuals. Patterns of X-Y synaptonemal complex pairing varied considerably from extensive synapsis in individuals with a normal heterochromatin complement, through end-to-end synapsis, to X and Y univalents in those with different degrees of loss of heterochromatin. Changes in the gonadal histology corresponding to heterochromatin variation were also observed. Loss of some coding DNA sequences in polymorphic X-chromosomes otherwise located at specific sites in the X-chromosome heterochromatin have been linked directly to modifications of the reproductive process. This is thought to be mediated by an altered X-chromosome activity during spermatogenesis or regulation of other locus/loci involved in fertility or reproduction.     

Heterochromatin

The properties of heterochromatin are reconsidered in the context of our present understanding of gene silencing, telomeric and centromeric properties, position-effect variegation and X-chromosome inactivation. It is proposed that the chromatin in heterochromatic chromosomal regions is generally similar in its molecular composition to that in silenced chromosomal regions. Heterochromatic appearance hence reflects not a particular quality of the respective chromosomal regions but only a specific kind of chromatin packaging comparable to that required for the inactivation of genes. This packaging may be initiated by particular signals in the DNA but can be propagated over more extended chromosomal regions by the formation of multiprotein complexes that interact with histones and possibly cell-specific additional components (RNA or proteins) that determine the status of the chromosome in a particular cell type. Received: 15 November 1998 / Accepted: 8 December 1998     

The tribal radiation of the family Bovidae (Artiodactyla) and the evolution of the mitochondrial cytochrome b gene

The nucleotide sequence of the complete mitochondrial cytochrome b gene has been determined and compared for 51 species of the family Bovidae and 10 potential pecoran and tragulid outgroups. A detailed saturation analysis at each codon position relative to the maximum parsimony procedure indicates that all transitions on third codon positions do not accumulate in a similar fashion: C-T are more saturated than A-G substitutions. The same trend is observed for second positions but not for first positions where A-G and C-T transitions exhibit roughly the same levels of saturation. Maximum parsimony reconstructions were weighted according to these observations. Maximum parsimony, maximum likelihood, and distance phylogenetic reconstructions all depict a major split within Bovidae. The subfamily Bovinae includes four multifurcating tribes and subtribes: Boselaphini, Tragelaphini, cattle-Bovini (Bos and Bison), and buffalo-Bovini (Bubalus and Syncerus). Its sister group is the subfamily Antilopinae, i.e., all non-Bovinae taxa, represented by seven lineages: Antilopini (including Saiga), Caprini sensu lato (i. e., Caprinae including Pantholops), Hippotragini, Alcelaphini, Reduncini (including Pelea), Aepyceros possibly linked to Neotragus, and Cephalophini possibly linked to Oreotragus (the suni and the klipspringer being members of a polyphyletic Neotragini). These various tribes and major lineages were produced by two noteworthy explosive radiations, which occurred simultaneously between 12.0 and 15.3 MY (Middle Miocene) in the subfamilies Bovinae and Antilopinae.     

The validity of horn ring counts to determine the age of Scottish feral goats (Capra (domestic))

The use of horn ring counts to age species in the tribes Caprini and Rupricaprini (Bovidae) has been well documented. Few studies have, however, tested the validity of the method. This paper compares the number of horn rings with age in years for individually known Scottish feral goats (Capra (domestic)). For all age-sex classes, except females older than two years, the number of horn rings corresponded exactly to the age in years. The discrepancies amongst older females were attributed to difficulties in counting their horn rings due to the small size of the horn and wear.     

Evidence from DNA that the mysterious 'linh duong' (Pseudonovibos spiralis) is not a new bovid

In 1993, several horns of an unknown mammal were collected in the south of Vietnam. Due to the unusual characteristics of its horns, the 'linh duong', as named by Vietnamese hunters, was quickly described as belonging to a new monospecific genus of bovid, i.e. Pseudonovibos spiralis Peter & Feiler, 1994. The taxonomic status of Pseudonovibos was a highly controversial subject, and it has been suggested that this enigmatic species may be related to three different groups of Bovidae: Antilopini (gazelles), Bovini (cattle, bisons, buffaloes), and Caprini sensu lato (goats, sheep and allies). To assess the phylogenetic relationships of the linh duong within the family Bovidae, two different DNA markers, the nuclear lactoferrin and the mitochondrial cytochrome b genes, were sequenced from bone samples of four trophies collected during 1925 in Indochina. Results show that the mysterious horns of linh duong belong to domestic cattle (Bos taurus). Thus, the linh duong is not a new mammal and the scientific name Pseudonovibos spiralis should be abandoned.     

Heterochromatin and chromosome variation in cultivated species ofTulipa subg.Leiostemones (Liliaceae)

The chromosomes of several cultivatedTulipa species of subg.Leiostemones were examined in conventionally stained and C-banded preparations. The heterochromatin content varied from almost none to 45%. Several chromosome types were recognized with respect to chromosome morphology and heterochromatin distribution, and groups of species with common chromosome characteristics could be identified. These karyological relationships are discussed with respect to the groups formed on the basis of floral and bulb charateristics.     

Quercus ilex browse utilization by Caprini in Sierra de Cazorla and Segura (Spain)

The impact of domestic and wild Caprini browsing on Quercus ilex has been examined in an area of the Sierra de Cazorla. Vegetation as a herbivore food supply, herbivore feeding regime and density in the study area during six sampling periods throughout two years, has been quantified. Wild Caprini show diets similar to the available vegetation, whereas domestic Caprini tend more towards the trophic specialities (browsing or grazing) of their genus. Nevertheless, this tendency was more pronounced in domestic goats than in sheep. A hypothetical estimate of Q. ilex intake by each species under the study conditions was carried out. It was found that domestic Caprini have a greater impact on the holm oak than wild Caprini, density and feeding-niche deviations being the main factors responsible for this situation.Abbreviations DM= dry matter     

Molecular phylogeny of musk deer: a genomic view with mitochondrial 16S rRNA and cytochrome b gene

The phylogenetic status of the infra order Pecora is controversial, even though it is supported by paleontological, morphological, and molecular evidence. We analyzed two mitochondrial genes (i.e., 16S rRNA and cytochrome b) to resolve the phylogenetic position of pecoran species, i.e., the Bovidae, Cervidae, and Moschidae endemic to the Indian subcontinent. We used phylogenetic analysis based on different algorithms, including neighbor joining, maximum parsimony, Bayesian inference, maximum likelihood, minimum evolution, median joining network, along with multidimensional scaling, and DNA word analysis. Our results established the basal position of Tragulidae and the monophyly of the infra order Pecora within the Suborder Ruminantia. Our results also demonstrated that Bovidae, Cervidae, and Moschidae are allied with the placement of musk deer as more closely related to bovids than to cervids. Molecular dating based on sequence analysis shows that the radiation of Pecora occurred during the early Oligocene and that the majority of the pecoran families radiated and dispersed rapidly during the Oligocene/Miocene transition.     

The species and chromosomal distribution of the centromeric alpha-satellite I sequence from sheep in the tribe Caprini and other Bovidae

The evolution of chromosomes in species in the family Bovidae includes fusion and fission of chromosome arms (giving different numbers of acrocentric and metacentric chromosomes with a relatively conserved total number of arms) and evolution in both DNA sequence and copy number of the pericentromeric alpha-satellite I repetitive DNA sequence. Here, a probe representing the sheep alpha-satellite I sequence was isolated and hybridized to genomic DNA digests and metaphase chromosomes from various Bovidae species. The probe was highly homologous to the centromeric sequence in all species in the tribe Caprini, including sheep (Ovis aries), goat (Capra hircus) and the aoudad or Barbary sheep (Amnotragus lervia), but showed no detectable hybridization to the alpha-satellite I sequence present in the tribe Bovini and at most very weak to species in the tribes Hippotragini, Alcelaphini or Aepycerotini. The sex chromosomes of sheep, goat and aoudad did not contain detectable alpha-satellite I sequence; in sheep, one of the three metacentric autosomal chromosomes does not carry the sequence, while in aoudad, it is essentially absent in three large autosomal pairs as well as the large metacentric chromosome pair. The satellite probes can be used as robust chromosome and karyotype markers of evolution among tribes and increase the resolution of the evolutionary tree at the base of the Artiodactyla.     

Phylogenetic analyses and improved resolution of the family Bovidae based on complete mitochondrial genomes

Efforts have been made to investigate the phylogeny of the family Bovidae; however, the relationships within this group still remain controversial. To further our understanding of the relationships, we sequenced the mitochondrial genome of the Himalayan goral, Naemorhedus goral, an IUCN Redlist near threatened conservation dependent species. Then we conducted molecular phylogenetic relationships of the Bovidae based on Bayesian and Maximum Likelihood methods. The results indicate that the basal divergence within the Bovidae is between the Bovinae and a strongly supported clade of the remaining Bovidae species. The two Neotragus species (the suni and pygmy antelope) clustered with the impala, Aepyceros melampus (Aepycerotinae), and together they formed the most basal of the non-Bovinae. All the genera of the Antilopinae clustered together except Neotragus, which suggested that the Antilopinae was a paraphyletic subfamily. The present study confirmed a close relationship between the genera Capricornis and Naemorhedus while supporting their designation as separate genera and suggested that the Capricornis-Naemorhedus-Ovibos clade (serows, gorals, and the muskox) should be placed in the Caprinae. Bison, Bos, and Tragelaphus (bison & cattle and kudus and nyalas) were paraphyletic. The very close relationship between Bison and Bos suggested that Bos and Bison should be integrated into a single Bos genus. Saiga and Pantholops (the Chiru or Tibetan Antelope), unique genera which have sometimes been lumped together, were placed in different groups: Saiga within the Antilopinae and Pantholops at the base of the Caprinae. Our results also supported a new taxonomy which places the three species of Hemitragus into three monospecific genera: the genus Hemitragus is restricted to the Himalayan tahr, and two new genera are created: Arabitragus for the Arabian tahr and Nilgiritragus for the Nilgiri tahr.     

Ammotragus europaeus : une nouvelle espèce de Caprini (Bovidae, Mammalia) du Pléistocène inférieur à la grotte du Vallonnet (France)

Ammotragus europaeus: a new species of Caprini (Bovidae, Mammalia) from the Early Pleistocene site of Vallonnet (France). A new species of the genus Ammotragus is described from the assemblage III of Vallonnet cave (Roquebrune-Cap-Martin, Alpes-Maritimes, France). These remains were interpreted as Ovis, but the re-study of the dental collection from the site and a first study of a partial braincase with the basal internal region of the horn-core pedicels, the parietals, the temporals, and the basisphenoid bones, show anatomical differences with the Caprini genera Ovis, Capra, and Hemitragus and the Ovibovini genus Soergelia. At the opposite, anatomical similarities of the Vallonnet material to the extant North-African Caprini genus Ammotragus are observed. The age of Vallonnet cave is dated by palaeomagnetic techniques at about 1.0 Ma. Teeth remains similar to the Vallonnet species have been found at Fuente Nueva-3 (Orce, Andalusia, Spain). To cite this article: P.-É. Moullé et al., C. R. Palevol 3 (2004).     

Phylogenetic relationships and the primitive X chromosome inferred from chromosomal and satellite DNA analysis in Bovidae

The early phylogeny of the 137 species in the Bovidae family is difficult to resolve; knowledge of the evolution and relationships of the tribes would facilitate comparative mapping, understanding chromosomal evolution patterns and perhaps assist breeding and domestication strategies. We found that the study of the presence and organization of two repetitive DNA satellite sequences (the clone pOaKB9 from sheep, a member of the 1.714 satellite I family and the pBtKB5, a 1.715 satellite I clone from cattle) on the X and autosomal chromosomes by in situ hybridization to chromosomes from 15 species of seven tribes, was informative. The results support a consistent phylogeny, suggesting that the primitive form of the X chromosome is acrocentric, and has satellite I sequences at its centromere. Because of the distribution of the ancient satellite I sequence, the X chromosome from the extant Tragelaphini (e.g. oryx), rather than Caprini (sheep), line is most primitive. The Bovini (cow) and Tragelaphini tribes lack the 1.714 satellite present in the other tribes, and this satellite is evolutionarily younger than the 1.715 sequence, with absence of the 1.714 sequence being a marker for the Bovini and Tragelaphini tribes (the Bovinae subfamily). In the other tribes, three (Reduncini, Hippotragini and Aepycerotini) have both 1.714 and 1.715 satellite sequences present on both autosomes and the X chromosome. We suggest a parallel event in two lineages, leading to X chromosomes with the loss of 1.715 satellite from the Bovini, and the loss of both 1.714 and 1.715 satellites in a monophyletic Caprini and Alcelaphini lineage. The presence and X chromosome distribution of these satellite sequences allow the seven tribes to be distributed to four groups, which are consistent with current diversity estimates, and support one model to resolve points of separation of the tribes.     

Differential Accumulation of Heterochromatin as a Cause for Karyotype Variation in Phalaenopsis Orchids

Karyotypes of nine Phalaenopsis species and the closely relatedDoritis pulcherrima were compared based on Feulgen- and DAPI-stainedsomatic metaphase chromosomes prepared from root tips. All specieshad the same chromosome number (2n = 2x = 38), but their karyotypesdiffered markedly in absolute chromosome size, relative chromosomesize, and the position of the centromere. Both genome size andthe amount of constitutive heterochromatin (CH) varied widelyamong the species studied, and there was a positive correlationbetween these two parameters. The distribution of CH in thegenomes was non-random: one or both arms of long chromosomesusually possessed large blocks of CH, while the small chromosomescontained little or no CH. DAPI-staining revealed that mostCH regions are rich in AT base pairs. We suggest that differentialaccumulation of CH is a major cause for karyotype variationin Phalaenopsis orchids. Copyright 2001 Annals of Botany Company Phalaenopsis, Doritis pulcherrima, karyotype differentiation, constitutive heterochromatin, total chromosome volume, nuclear DNA content     

Evolution of the Mitochondrial Genome in Mammals Living at High Altitude: New Insights from a Study of the Tribe Caprini (Bovidae,Antilopinae)

Organisms living at high altitude are exposed to severe environmental stress associated with decreased oxygen pressure, cold temperatures, increased levels of UV radiation, steep slopes, and scarce food supplies, which may have imposed important selective constraints on the evolution of the mitochondrial genome. Within mammals, the tribe Caprini is of particular interest for studying the evolutionary effects of life at high altitude, as most species live in mountain regions, where they developed morphological and physiological adaptations for climbing. In this report, we analyzed the complete mitochondrial genome of 24 ruminants, including 20 species of Caprini. The phylogenetic analyses based on 16,117 nucleotides suggested the existence of a new large clade, here named subtribe Caprina, containing all genera, but Pantholops (Pantholopina), Capricornis, Naemorhedus, and Ovibos (Ovibovina). The alignment of the control region showed that all Caprini have between two and four tandem repeats of ~75 bp in the RS2 region, and that several of these copies emerged from recent and independent duplication events. We proposed therefore that the maintenance of at least two RS2 repeats in the control region of Caprini is positively selected, probably for producing a higher number of D-loop strands 3′-ending at different locations. The analyses of base composition at third-codon positions of protein-coding genes revealed that Caprini have the highest percentage of A nucleotide and the lowest percentage of G nucleotide, a pattern which suggests increased rates of cytosine deamination (C→T transitions) on the H strand of mtDNA. Two nonexclusive hypotheses related to high-altitude life can explain such a mutational pattern: more severe oxidative stress (ROS) and higher metabolic rates. By comparing the relative rates of nonsynonymous and synonymous substitutions in protein-coding genes, we identified that Caprini have higher levels of adaptive variation in the ATPase complex. In addition, we detected several changes in mitochondrial genes that should be tested for their potential role in mountain adaptation. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Essential Genes in Autosomal Heterochromatin of Drosophila Melanogaster

We are taking two approaches to understanding the structure, function and regulation of essential genes within Drosophilaheterochromatin. In the first, we have undertaken a genetic and molecular characterization of essential genes within proximal 3L heterochromatin. The expression of such ‘resident’ genes within a heterochromatic environment is paradoxical and poorly understood, given that the same environment can inactivate euchromatic sequences (position effect variegation, or PEV). A second approach involves the study of the local chromosomal environment of heterochromatic (het) genes, as assayed both biochemically, and via the effects of genetic modifiers of PEV, the latter being putative components important for het gene expression. Our results to date suggest that the three most proximal genes in 3L heterochromatin have key roles in development, and indicate strong effects of combinations of genetic modifiers of PEV on het gene expression. This revised version was published online in July 2006 with corrections to the Cover Date.     

Molecular phylogeny of caprines (Bovidae, Antilopinae): the question of their origin and diversification during the Miocene

Caprines include all bovids related to sheep and goat. The composition of the group is controversial and inter-generic relationships have been widely debated. Here, we analysed 2469 characters draw from three distinct molecular markers, i.e. two mitochondrial genes (cytochrome b and 12S rRNA) and one nuclear fragment (exon 4 of the κ -casein gene). The taxonomic sampling includes all genera putatively described as caprines, as well as several other bovid genera in order to elucidate the position of caprines within the family Bovidae, and to determine the exact composition of the group. Phylogenetic analyses confirm firstly that Pseudoryx and Saiga do not belong to caprines, and secondly, that all tribes classically defined in the literature are not monophyletic, supporting the inclusion of all caprine species into a unique enlarged tribe Caprini sensu lato . Our results are in contradiction with previous investigations suggesting a sister-group relationship between Ovis (sheep and mouflons) and Budorcas (takins). By using a molecular calibration point at 18.5 Mya for the first appearance of bovids, we estimated divergence times with our molecular data. We also performed biogeographic inferences to better understand the origin and diversification of caprines during the Neogene. Our analyses suggest that caprines shared a common ancestor with Alcelaphini and Hippotragini in the middle-late Miocene (13.37 ± 0.70 Mya). Our results also indicate that the extant generic diversity of caprines resulted from a rapid adaptive radiation during the late Miocene, at 10.96 ± 0.73 Mya. We propose that this adaptive radiation resulted from the acquisition of reduced metacarpals, a key innovation which occurred during the late Miocene as a consequence of insularity isolation in the mountainous mega-archipelago between Mediterranean and Paratethys Seas.     

Heterochromatin variation in Cryptobothrus chrysophorus

The endemic grasshopper Cryptobothrus chrysophorus is widely distributed throughout S.E. Australia and its populations display an extensive and spectacular pattern of autosomal variation. While the standard telocentric complement of three long (L1–3), six medium (M4–9) and two short (S10–11) autosome pairs is present throughout most of its range, two quite distinct chromosome races can be defined within this species. Populations in the northern part of its distribution (northern N.S.W. and southern Queensland-northern race) are differentiated from the remainder (southern race) by fixed blocks of distal heterochromatin on autosomes M4, 5, 6, 8 and 9 and by differences in the character of the megameric M7 chromosome. Additionally, while many populations in both races show a polymorphic system of supernumerary segments on the two smallest autosomes (S10–11), that found in the northern race is both more variable and more complex. On the other hand all the populations of the southern race we have examined are polymorphic for a series of centric shifts which convert telocentrics into acro- or meta-centrics. These occur more commonly in the megameric M7 and the two smallest autosomes (S10–11) although in one population (Forbes Creek, N.S.W.) at least 12 different shifts involving 8 of the autosomes (L3, M4, 5, 6, 7, 8, 9 and S10) are known. By contrast, in the northern erace only the small autosomes (S10–11) show centric shifts. These several floating and fixed variants thus involve all chromosomes of the standard set other than the two largest autosomes (L1–2) and the X-chromosome, which appear to be invariate. Finally, morphologically distinct supernumerary (B) chromosomes, intermediate in size between the standard S10 and the M9 elements, are found in both races but are especially common in Tasmania, the most southerly point of the species range. These B-chromosomes are partly heterochromatic and partly euchromatic so that they too add to the considerable heterochromatin variation in this species.     

Heterochromatin recognition with fluorochromes

Some types of acridine derivative and especially Quinacrine dihydrochloride and its mustard may be successfully used as chromosome marker and to investigate the chemical differentiation of euchromatin and heterochromatin. — There are at least four main types of heterochromatin, showing all possible combinations of positive and negative cold effect starvation (St. + or St. -) and enhanced or reduced fluorescence (Fl. + or Fl. -). —The relationship between the four different classes of heterochromatin is not yet clear.     

Regional and temporal changes in the pattern of X-chromosome replication during the early post-implantation development of the female mouse

We have made a detailed study of the X-chromosome replication pattern during the period when X-inactivation is occurring in the mouse embryo. Our observations show unequivocal regionalization of the embryo with respect to the temporal appearance, parental origin and DNA replication pattern of the allocyclic X-chromosome. The switch from isocyclic to allocyclic replication occurs in the embryonic ectoderm at approximately 6 days of development and is random with respect to parental origin of the X-chromosome. In the extra-embryonic tissues, however, the switch to allocyclic replication has apparently occurred prior to 5.3 days of development and almost exclusively involves the paternally-derived X-chromosome. Since these findings are consistent with results obtained in biochemical studies of X-chromosome activity in female embryos, we conclude that there is a close temporal relationship between the cytogenetic and biochemical manifestations of the X-inactivation process. In addition, we have observed a pattern of early paternal X-chromosome replication, transitory in some cases, that is unique to extra-embryonic tissues. These results suggest that there may be some differences in the mechanism by which X-inactivation occurs in the extra-embryonic tissues as compared with the embryonic ectoderm.