Y-Chromosome variation in hominids: intraspecific variation is limited to the polygamous chimpanzee

Background

We have previously demonstrated that the Y-specific ampliconic fertility genes DAZ (deleted in azoospermia) and CDY (chromodomain protein Y) varied with respect to copy number and position among chimpanzees (Pan troglodytes). In comparison, seven Y-chromosomal lineages of the bonobo (Pan paniscus), the chimpanzee''s closest living relative, showed no variation. We extend our earlier comparative investigation to include an analysis of the intraspecific variation of these genes in gorillas (Gorilla gorilla) and orangutans (Pongo pygmaeus), and examine the resulting patterns in the light of the species'' markedly different social and mating behaviors.

Methodology/Principal Findings

Fluorescence in situ hybridization analysis (FISH) of DAZ and CDY in 12 Y-chromosomal lineages of western lowland gorilla (G. gorilla gorilla) and a single lineage of the eastern lowland gorilla (G. beringei graueri) showed no variation among lineages. Similar findings were noted for the 10 Y-chromosomal lineages examined in the Bornean orangutan (Pongo pygmaeus), and 11 Y-chromosomal lineages of the Sumatran orangutan (P. abelii). We validated the contrasting DAZ and CDY patterns using quantitative real-time polymerase chain reaction (qPCR) in chimpanzee and bonobo.

Conclusion/Significance

High intraspecific variation in copy number and position of the DAZ and CDY genes is seen only in the chimpanzee. We hypothesize that this is best explained by sperm competition that results in the variant DAZ and CDY haplotypes detected in this species. In contrast, bonobos, gorillas and orangutans—species that are not subject to sperm competition—showed no intraspecific variation in DAZ and CDY suggesting that monoandry in gorillas, and preferential female mate choice in bonobos and orangutans, probably permitted the fixation of a single Y variant in each taxon. These data support the notion that the evolutionary history of a primate Y chromosome is not simply encrypted in its DNA sequences, but is also shaped by the social and behavioral circumstances under which the specific species has evolved.     

Predicting variation in sperm precedence

Sperm competition theory predicts that males are adapted for success in sperm competition by the production of large numbers of sperm. This is supported by both inter- and intraspecific studies showing that males mating under high sperm competition risk increase investment in sperm production. Such an increase in sperm production is an advantage if sperm mix randomly or if sperm displacement occurs. When two males mate with the same female, the measurement of the proportion of eggs fertilized by the second male to mate (termed P₂) has been used to help elucidate sperm competition mechanisms. P₂ is usually quoted as a mean value, with little attention being paid to its variance, although P₂ estimates are notoriously variable. By predicting an expected variance for P₂, additional information on sperm competition mechanisms may be obtained. Here we present a technique for analysing the variance in P₂ when a given mechanism of P₂ is assumed. We apply this technique to P₂ data collected from Plodia interpunctella (Lepidoptera, Pyralidae), assuming a ''fair raffle'' mechanism of sperm competition. We compare observed distributions of P₂ with theoretical distributions generated assuming random mixing of two ejaculates drawn randomly from a population of known mean and variance in sperm numbers. Ejaculates of known size were obtained by counting the number of sperm ejaculated by males mating for the first (large ejaculate) or second (small ejaculate) time. Females either received two small or one small and one large ejaculate, and the distribution of P₂ (estimated using the sterile male technique) was compared with our theoretical predictions. The observed variance in P₂ was greater than our model prediction, thus we conclude that sperm from P. interpunctella do not mix randomly before fertilization. <br>     

Wolbachia mediate variation of host immunocompetence

Background

After decades during which endosymbionts were considered as silent in their hosts, in particular concerning the immune system, recent studies have revealed the contrary. In the present paper, we addressed the effect of Wolbachia, the most prevalent endosymbiont in arthropods, on host immunocompetence. To this end, we chose the A. vulgare-Wolbachia symbiosis as a model system because it leads to compare consequences of two Wolbachia strains (wVulC and wVulM) on hosts from the same population. Moreover, A. vulgare is the only host-species in which Wolbachia have been directly observed within haemocytes which are responsible for both humoral and cellular immune responses.

Methodology/Principal Findings

We sampled gravid females from the same population that were either asymbiotic, infected with wVulC, or infected with wVulM. The offspring from these females were tested and it was revealed that individuals harbouring wVulC exhibited: (i) lower haemocyte densities, (ii) more intense septicaemia in their haemolymph and (iii) a reduced lifespan as compared to individuals habouring wVulM or asymbiotic ones. Therefore, individuals in this population of A. vulgare appeared to suffer more from wVulC than from wVulM. Symbiotic titer and location in the haemocytes did not differ for the two Wolbachia strains showing that these two parameters were not responsible for differences observed in their extended phenotypes in A. vulgare.

Conclusion/Significance

The two Wolbachia strains infecting A. vulgare in the same population induced variation in immunocompetence and survival of their hosts. Such variation should highly influence the dynamics of this host-symbiont system. We propose in accordance with previous population genetic works, that wVulM is a local strain that has attenuated its virulence through a long term adaptation process towards local A. vulgare genotypes whereas wVulC, which is a widespread and invasive strain, is not locally adapted.     

Morphological variation ofStromatella monostromatica

Thirty two isolates ofStromatella monostromatica (Dangeard) Kornmann were studied in unialgal culture; extensive morphological variation was documented. The shape of bicellular germlings and development of young plants were similar for all isolates which had globular sporangia. These features are, therefore, the most important diagnostic characteristics of the species. The widespread distribution ofS. monostromatica suggests that this is a cosmopolitan species.     

Genotypic variation in carboxylation of tomatoes

The gas exchange characteristics of 24 genotypes of Lycopersicon esculentum Mill. and one of L. minutum were measured with an infrared gas analyzer and dew point hygrometer in an open system. Net carbon exchange (NCE) and transpiration rate were measured at 50, 100, 150, and 300 μ1 1⁻¹ CO₂, and a regression of NCE versus internal lead [CO₂] estimates was calculated. The slope of the regression curve at the CO₂ compensation point was used as the measure of carboxylation efficiency (CE). Significant genotypic differences for CE were obtained. Differences in CE did not appear to be due to differences in diffusive resistance defined as the sum of the boundary layer resistance (r_a) and the stomatal plus cuticular resistance (r₁). There was no correlation (r = -0.07) between (r_a + r₁) and CE. Within groups with nonsignificantly different means for (r_a + r₁) there were genotypes with extremes for CE.     

Anthocyanidin variation in Clarkia

Previous reports of anthocyanin variation in Clarkia indicated intersectional differentiation, suggesting an additional marker for evaluating infrageneric relationships. Therefore, an investigation of anthocyanidin content of 19 species representing seven of the 10 sections was conducted. The anthocyanidins malvidin, cyanidin and delphinidin were detected. Interspecific variation in anthocyanidin profile was observed: some taxa possessed only malvidin, whereas others exhibited all three anthocyanidins. However, this variation does not coincide with proposed sectional boundaries based on evidence from morphology and enzyme electrophoresis. This suggests that anthocyanidins are homoplasious characters in Clarkia.     

Molecular genetics of antigenic variation

Antigenic variation is one of the most effective strategies developed by parasites to escape immune destruction. It requires a large wardrobe of surface coats and mechanisms to exchange one coat for an unrelated one. The molecular principles of antigenic variation are now largely known in the bacterial species Borrelia and Neisseria and in the protozoa of the African trypanosome group and these three examples are discussed here by Piet Borst.     

Isozyme variation in Desmodium nudiflorum

Five populations of Desmodium nudiflorum were assayed for genetic variability in eight enzyme systems encoding thirteen genetic loci. The proportion of polymorphic loci for the species as a whole is 46.2% while the proportion of polymorphic loci within populations averages 13.5%. Average individual heterozygosity is 2.3%. D. nudiflorum shows significant differences in gene frequencies between populations, and genotypic frequencies within populations conform to Hardy-Weinberg expectations.     

Genetic variation in cultivated Rheum tanguticum populations

To examine whether cultivation reduced genetic variation in the important Chinese medicinal plant Rheum tanguticum, the levels and distribution of genetic variation were investigated using ISSR markers. Fifty-eight R. tanguticum individuals from five cultivated populations were studied. Thirteen primers were used and a total of 320 DNA bands were scored. High levels of genetic diversity were detected in cultivated R. tanguticum (PPB = 82.19, H = 0.2498, H_B = 0.3231, I = 0.3812) and could be explained by the outcrossing system, as well as long-lived and human-mediated seed exchanges. Analysis of molecular variance (AMOVA) showed that more genetic variation was found within populations (76.1%) than among them (23.9%). This was supported by the coefficient of gene differentiation (G_st = 0.2742) and Bayesian analysis (θ_B = 0.1963). The Mantel test revealed no significant correlation between genetic and geographic distances among populations (r = 0.1176, p = 0.3686). UPGMA showed that the five cultivated populations were separated into three clusters, which was in good accordance with the results provided by the Bayesian software STRUCTURE (K = 3). A short domestication history and no artificial selection may be an effective way of maintaining and conserving the gene pools of wild R. tanguticum.     

The genome and variation of Bacillus anthracis

The Bacillus anthracis genome reflects its close genetic ties to Bacillus cereus and Bacillus thuringiensis but has been shaped by its own unique biology and evolutionary forces. The genome is comprised of a chromosome and two large virulence plasmids, pXO1 and pXO2. The chromosome is mostly co-linear among B. anthracis strains and even with the closest near neighbor strains. An exception to this pattern has been observed in a large inversion in an attenuated strain suggesting that chromosome co-linearity is important to the natural biology of this pathogen. In general, there are few polymorphic nucleotides among B. anthracis strains reflecting the short evolutionary time since its derivation from a B. cereus-like ancestor. The exceptions to this lack of diversity are the variable number tandem repeat (VNTR) loci that exist in genic and non genic regions of the chromosome and both plasmids. Their variation is associated with high mutability that is driven by rapid insertion and deletion of the repeats within an array. A notable example is found in the vrrC locus which is homologous to known DNA translocase genes from other bacteria.     

Flavonoid variation in some North Americna Saxifraga species

Eight species of Saxifraga representing sections Micranthes, Hirculus, Dactyloides and Xanthizoon were studied for their flavonoids (S. california, S. integrifolia, S. michauxii, S. ferruginea, S. eschscholtzii, S. hirculus, S. caespitosa and S. aizoides). The major compounds present in most species were kaempferol and quercetin monogluocosides and galactosides. Glucosides of kaempferol and quercetin predominate in the first four species listed, while galactosides of quercetin and myricetin are dominant in the lastthree. 3-O-Methyl- and 3,3′-di-O-methylquercetin were identified from S. californica and S. integrifolia. Saxifraga caespitosa synthesizes a complex mixture of O-methylated flavonols as well as a novel O-methylated dihydrokaempferol.Species pairs S. michauxii/S. ferruginea and S. californica/S.integrifolia exhibit close flavonoid similarity which may reflect their morphological similarities.     

Intraspecific variation in Triassic Ophthalmidiid Foraminifera from Timor

Four ophthalmidiid species are described as free specimens extracted from mudstones and wackestones of Triassic age: Atsabella bandeiraensis nov. gen. nov. sp., Karaburunia atsabensis nov. sp., Ophthalmidium sp. cf. O. primitivum Ho and Spirophthalmidium grunaui nov. sp. Analysis of morphological variation found in large suites of specimens suggests that, as in modern miliolids, apertural characteristics, chamber shape and adult test size are features that vary within narrow limits and may be used to define species. In genera with milioline coiling in the post-embryonic stage, chamber arrangement may be highly variable. Post-embryonic coiling in K. atsabensis varies from quinqueloculine to almost spiroloculine and encompasses morphotypes that, in thin-section studies, have been attributed to a number of other genera. In Timor Leste, A. bandeiraensis, K. atsabensis and S. grunaui have been found with conodonts indicative of the Carnian, but the full local stratigraphic range of these species is uncertain. K. atsabensis occurs at another locality with conodonts suggestive of the Middle Triassic or less likely Carnian. Ophthalmidium sp. cf. O. primitivum has been found at one locality associated with A. bandeiraensis and K. atsabensis in a stratigraphic succession that suggests a correlation to the Carnian or Norian. The ophthalmidiids are found commonly associated with organic-cemented agglutinated and hyaline foraminifera and at some localities common to abundant ostracods and mollusc debris. They were most common in organic-rich carbonate mud of shallow-marine environments.     

Chemical variation and defense of Encelia farinosa

Chemical analysis of leaves from 12 different localities of Encelia farinosa (including var. phenicodonta and var. radians) collected on the peninsula of Baja California (Mexico) revealed the presence of various chemotypes that differed with regard to the concentrations of chromenes and sesquiterpene lactones. Localities of E. farinosa collected in the northern part of Baja California were characterized by high concentrations of the chromene encecalin (up to 252 μmol g⁻¹ dry wt.), whereas the sesquiterpene lactone farinosin was not detected. Localities of E. farinosa collected at the southern tip of the peninsula lacked encecalin, but were shown to accumulate farinosin (up to 85 μmol g⁻¹ dry wt.) instead. On the mainland of Mexico, as well as in Arizona (U.S.A.), farinosin concentrations varied from 18 to 44 μmol g⁻¹ dry wt. for 10 different localities analyzed. Chromenes were not detected or present only in minor amounts (up to 13 μmol g⁻¹ dry wt.), when compared to the samples from northern Baja California. Chemical variation within localities was small when compared to variation between different localities. Accumulation of encecalin and aridity seem to coincide at least on the peninsula of Baja California, as localities of E. farinosa that receive the least amount of rainfall contained the largest amounts of encecalin in their leaves. Leaves of E. farinosa that contained sufficiently large amounts of either encecalin or farinosin were both detrimental to neonate larvae of the polyphagous pest insect Spodoptera littoralis as shown by addition of the respective crude leaf extracts to artificial diet. Possible advantages of the observed intraspecific chemical variability of E. farinosa with regard to adaptation by generalist insect herbivores are discussed.     

Geographical variation in Fennoscandian and Estonian Schoenus wetlands

Using TABORD five Schoenus ferrugineus associations have been distinguished from the literature. They are well distinguished by differential-species combinations and most of them are described earlier under identical names, e.g., the Primula-, Oxycoccus-, Myrica-, and Trichophorum-Schoenus ferrugineus ass. The Thalictrum-Schoenus ferrugineus ass. is a new syntaxon. They are further characterized by different floristic elements according to their geographical distribution. The Primula-Schoenus ferrugineus ass. is related to Central Europe, the Primulo-Schoenetum ferruginei from Oberd. (1957) 1962. All other associations discussed have no counterparts elsewhere in Europe. The shortcoming of this classification and the impossibility of a syntaxonomical ranking are emphasized. The variation in species composition and site conditions is elucidated by RA ordination. A complex soil moisture gradient is related to the differences in species composition between the Primula-, Oxycoccus-, and Myrica-Schoenus ferrugineus ass. Wet topogenous mire sites with peat formation and a rather low pH is typical of the Myrica-Schoenus ferrugineus ass., while the Primula-Schoenus ferrugineus ass. occurs either in moist soligenous mire sites or in to pogenous sites with strongly shifting water tables and with muck (Anmoor) instead of peat. The site conditions of the Oxycoccus-Schoenus ferrugineus ass. are most similar to those of the Myrica-Schoenus ferrugineus ass. The Trichophorum- and Thalictrum-Schoenus ferrugineus ass. occur on soligenous mire sites.     

Unexpected hydrogen isotope variation in oceanic pelagic seabirds

Hydrogen isotopes have significantly enhanced our understanding of the biogeography of migratory animals. The basis for this methodology lies in predictable, continental patterns of precipitation δD values that are often reflected in an organism’s tissues. δD variation is not expected for oceanic pelagic organisms whose dietary hydrogen (water and organic hydrogen in prey) is transferred up the food web from an isotopically homogeneous water source. We report a 142 ‰ range in the δD values of flight feathers from the Hawaiian petrel (Pterodroma sandwichensis), an oceanic pelagic North Pacific species, and inquire about the source of that variation. We show δD variation between and within four other oceanic pelagic species: Newell’s shearwater (Puffinus auricularis newellii), Black-footed albatross (Phoebastria nigripes), Laysan albatross (Phoebastria immutabilis) and Buller’s shearwater (Puffinus bulleri). The similarity between muscle δD values of hatch-year Hawaiian petrels and their prey suggests that trophic fractionation does not influence δD values of muscle. We hypothesize that isotopic discrimination is associated with water loss during salt excretion through salt glands. Salt load differs between seabirds that consume isosmotic squid and crustaceans and those that feed on hyposmotic teleost fish. In support of the salt gland hypothesis, we show an inverse relationship between δD and percent teleost fish in diet for three seabird species. Our results demonstrate the utility of δD in the study of oceanic consumers, while also contributing to a better understanding of δD systematics, the basis for one of the most commonly utilized isotope tools in avian ecology.     

Genetic variation of milk proteins in mice

A survey for qualitative and quantitative variation in milk proteins from 58 inbred strains of mice revealed two electrophoretic variants. One is in a whey acidic protein of milk of YBR mice and the other is in a curd protein of the Asian house mouse, Mus musculus castaneus. The whey acidic protein variant is shown to be under the control of a single Mendelian autosomal gene with alleles expressed in a codominant manner. This gene is designated Wap, is not identical to Eg, is not X linked, and is either unlinked or loosely linked to the coat color genes a and b.     

Nuclear genome size variation in fleshy-fruited Neotropical Myrtaceae

In Myrtaceae, reports regarding the nuclear DNA content are scarce. The aim of this study is to present genome size data for fleshy-fruited Myrteae, and to test their relation with chromosome number and ploidy, the available data for cytoevolutionary studies in Myrtaceae. Thirty species out of ten genera were investigated for chromosome number and genome size using flow cytometry. Twenty-eight species were diploid with 2n = 2x = 22 and two species were tetraploid with 2n = 4x = 44. All genome sizes measured are new. Among the diploid species, a gradual and small variation in 2C-values (0.486 pg in Gomidesia schaueriana to 0.636 pg in Eugenia multicostata) was observed, whereas the tetraploid genomes of Psidium acutangulum and P. cattleianum had about twice as much DNA (1.053 and 1.167 pg, respectively). The total interspecific variation of C-values was 2.45-fold. The fleshy-fruited Myrteae have smaller holoploid genomes than the capsular-fruited Eucalypteae and Melaleuceae.     

Epigenetic natural variation in Arabidopsis thaliana

Cytosine methylation of repetitive sequences is widespread in plant genomes, occurring in both symmetric (CpG and CpNpG) as well as asymmetric sequence contexts. We used the methylation-dependent restriction enzyme McrBC to profile methylated DNA using tiling microarrays of Arabidopsis Chromosome 4 in two distinct ecotypes, Columbia and Landsberg erecta. We also used comparative genome hybridization to profile copy number polymorphisms. Repeated sequences and transposable elements (TEs), especially long terminal repeat retrotransposons, are densely methylated, but one third of genes also have low but detectable methylation in their transcribed regions. While TEs are almost always methylated, genic methylation is highly polymorphic, with half of all methylated genes being methylated in only one of the two ecotypes. A survey of loci in 96 Arabidopsis accessions revealed a similar degree of methylation polymorphism. Within-gene methylation is heritable, but is lost at a high frequency in segregating F₂ families. Promoter methylation is rare, and gene expression is not generally affected by differences in DNA methylation. Small interfering RNA are preferentially associated with methylated TEs, but not with methylated genes, indicating that most genic methylation is not guided by small interfering RNA. This may account for the instability of gene methylation, if occasional failure of maintenance methylation cannot be restored by other means.