Population density affects sex ratio variation in red deer.

Many mammal populations show significant deviations from an equal sex ratio at birth, but these effects are notoriously inconsistent. This may be because more than one mechanism affects the sex ratio and the action of these mechanisms depends on environmental conditions. Here we show that the adaptive relationship between maternal dominance and offspring sex ratio previously demonstrated in red deer (Cervus elaphus), where dominant females produced more males, disappeared at high population density. The proportion of males born each year declined with increasing population density and with winter rainfall, both of which are environmental variables associated with nutritional stress during pregnancy. These changes in the sex ratio corresponded to reductions in fecundity, suggesting that they were caused by differential fetal loss. In contrast, the earlier association with maternal dominance is presumed to have been generated pre-implantation. The effects of one source of variation superseded the other within about two generations. Comparison with other ungulate studies indicates that positive associations between maternal quality and the proportion of male offspring born have only been documented in populations below carrying capacity.     

Rapid dwarfing of red deer on Jersey in the last interglacial

The dwarfing of large mammals on islands occurred repeatedly in the Pleistocene. Elephants, deer, hippopotami and other species became dwarfed on islands in Indonesia, the Mediterranean, the east Pacific and elsewhere. In most cases, the full-sized ancestral form can be recognized among the adjacent mainland fauna, but evolutionary rates cannot be estimated because the entry of the ancestor onto the island, and appearance of the dwarf form, are poorly dated. Here I give the first example in which the island dwarf is well dated, the full-sized ancestor is found in demonstrably older deposits on the island, and a good estimate can be made for the duration of the isolation leading to dwarfing. In the Last Interglacial, red deer on Jersey, Channel Islands, became reduced to one sixth of their body weight in less than six thousand years.     

Roaring by red deer stags advances the date of oestrus in hinds

Some male mammals call loudly and repeatedly during the breeding season. Although the song of male birds is known to have effects on male-male competition, mate selection and ovulation, until now the loud calls of male mammals have been shown to affect only competition between males. Although it has been suggested that loud calling could also serve to attract females, the possibility that it has a direct effect on reproduction in females has not previously been investigated for any mammal. Here I report that roaring in red deer (Cervus elaphus) advances ovulation and that harem-holding males can improve their mating success by regular calling.     

Polymorphism in red photopigment underlies variation in colour matching.

Genetic variation of human senses within the normal range probably exists but usually cannot be investigated in detail for lack of appropriate methods. The study of subtle perceptual differences in red-green colour vision is feasible since both photopigment genotypes and psychophysical phenotypes can be assessed by sophisticated techniques. Red-green colour vision in humans is mediated by two different visual pigments: red (long-wavelength sensitive) and green (middle-wavelength sensitive). The apoproteins of these highly homologous photopigments are encoded by genes on the X chromosome. Colour matches of males with normal colour vision fall into two main groups that appear to be transmitted by X-linked inheritance. This difference in colour matching is likely to reflect small variations in the absorption maxima of visual pigments, suggesting the presence of two common variants of the red and/or green visual pigments that differ in spectral positioning. We report that a common single amino-acid polymorphism (62% Ser, 38% Ala) at residue 180 of the X-linked red visual pigment explains the finding of two major groups in the distribution of colour matching among males with normal colour vision.     

Condition-dependent signalling of genetic variation in stalk-eyed flies

Handicap models of sexual selection predict that male sexual ornaments have strong condition-dependent expression and this allows females to evaluate male genetic quality. A number of previous experiments have demonstrated heightened condition-dependence of sexual ornaments in response to environmental stress. Here we show that genetic variation underlies the response to environmental stress (variable food quality) of a sexual ornament (male eye span) in the stalk-eyed fly Cyrtodiopsis dalmanni. Some male genotypes develop large eye span under all conditions, whereas other genotypes progressively reduce eye span as conditions deteriorate. Several non-sexual traits (female eye span, male and female wing length) also show genetic variation in condition-dependent expression, but their genetic response is entirely explained by scaling with body size. In contrast, the male sexual ornament still reveals genetic variation in the response to environmental stress after accounting for differences in body size. These results strongly support the hypothesis that female mate choice yields genetic benefits for offspring.     

A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms

We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms (SNPs). This map is based on a comparison of the sequences of three domestic chicken breeds (a broiler, a layer and a Chinese silkie) with that of their wild ancestor, red jungle fowl. Subsequent experiments indicate that at least 90% of the variant sites are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about five SNPs per kilobase for almost every possible comparison between red jungle fowl and domestic lines, between two different domestic lines, and within domestic lines--in contrast to the notion that domestic animals are highly inbred relative to their wild ancestors. In fact, most of the SNPs originated before domestication, and there is little evidence of selective sweeps for adaptive alleles on length scales greater than 100 kilobases.     

A yeast prion provides a mechanism for genetic variation and phenotypic diversity

A major enigma in evolutionary biology is that new forms or functions often require the concerted effects of several independent genetic changes. It is unclear how such changes might accumulate when they are likely to be deleterious individually and be lost by selective pressure. The Saccharomyces cerevisiae prion [PSI+] is an epigenetic modifier of the fidelity of translation termination, but its impact on yeast biology has been unclear. Here we show that [PSI+] provides the means to uncover hidden genetic variation and produce new heritable phenotypes. Moreover, in each of the seven genetic backgrounds tested, the constellation of phenotypes produced was unique. We propose that the epigenetic and metastable nature of [PSI+] inheritance allows yeast cells to exploit pre-existing genetic variation to thrive in fluctuating environments. Further, the capacity of [PSI+] to convert previously neutral genetic variation to a non-neutral state may facilitate the evolution of new traits.     

Organization of genetic variation in individuals of arbuscular mycorrhizal fungi

Arbuscular mycorrhizal (AM) fungi (Glomeromycota) are thought to be the oldest group of asexual multicellular organisms. They colonize the roots of most land plants, where they facilitate mineral uptake from the soil in exchange for plant-assimilated carbon. Cells of AM fungi contain hundreds of nuclei. Unusual polymorphism of ribosomal DNA observed in individual spores of AM fungi inspired a hypothesis that heterokaryosis--that is, the coexistence of many dissimilar nuclei in cells--occurs throughout the AM fungal life history. Here we report a genetic approach to test the hypothesis of heterokaryosis in AM fungi. Our study of the transmission of polymorphic genetic markers in natural isolates of Glomus etunicatum, coupled with direct amplification of rDNA from microdissected nuclei by polymerase chain reaction, supports the alternative hypothesis of homokaryosis, in which nuclei populating AM fungal individuals are genetically uniform. Intrasporal rDNA polymorphism contained in each nucleus signals a relaxation of concerted evolution, a recombination-driven process that is responsible for homogenizing rDNA repeats. Polyploid organization of glomeromycotan genomes could accommodate intranuclear rDNA polymorphism and buffer these apparently asexual organisms against the effects of accumulating mutations.     

Adaptive variation in environmental and genetic sex determination in a fish

Two general mechanisms of sex determination have been identified among gonochoristic vertebrates: environmental sex determination where offspring become male or female in response to an environmental factor(s) during development (for example, some fishes and reptiles); and genetic sex determination where sex is determined by genotype at conception (as in birds and mammals). How do these sex-determining systems evolve? Direct evidence is virtually non-existent because the sex-determining systems of most species appear to have little genetic variation. Here we provide the first evidence of adaptive variation in environmental and genetic sex determination within a species. We show that in a fish with temperature-dependent sex determination, populations at different latitudes compensate for differences in thermal environment and seasonality by adjusting the response of sex ratio to temperature, and by altering the level of environmental as opposed to genetic control. The adjustments observed are precisely those predicted by adaptive sex ratio theory.     

Proportionally more deleterious genetic variation in European than in African populations

Quantifying the number of deleterious mutations per diploid human genome is of crucial concern to both evolutionary and medical geneticists. Here we combine genome-wide polymorphism data from PCR-based exon resequencing, comparative genomic data across mammalian species, and protein structure predictions to estimate the number of functionally consequential single-nucleotide polymorphisms (SNPs) carried by each of 15 African American (AA) and 20 European American (EA) individuals. We find that AAs show significantly higher levels of nucleotide heterozygosity than do EAs for all categories of functional SNPs considered, including synonymous, non-synonymous, predicted 'benign', predicted 'possibly damaging' and predicted 'probably damaging' SNPs. This result is wholly consistent with previous work showing higher overall levels of nucleotide variation in African populations than in Europeans. EA individuals, in contrast, have significantly more genotypes homozygous for the derived allele at synonymous and non-synonymous SNPs and for the damaging allele at 'probably damaging' SNPs than AAs do. For SNPs segregating only in one population or the other, the proportion of non-synonymous SNPs is significantly higher in the EA sample (55.4%) than in the AA sample (47.0%; P < 2.3 x 10(-37)). We observe a similar proportional excess of SNPs that are inferred to be 'probably damaging' (15.9% in EA; 12.1% in AA; P < 3.3 x 10(-11)). Using extensive simulations, we show that this excess proportion of segregating damaging alleles in Europeans is probably a consequence of a bottleneck that Europeans experienced at about the time of the migration out of Africa.     

Natural diet and food habitat use of the Tarim red deer, Cervus elaphus yarkandensis

In order to determine the natural diet and food habitat use of Tarim red deer （Cervus elaphus yarkandensis）, a study was carried out in Qiemo, Xinjiang , China from October 2000 to June 2001. Direct observation combined with faecal analysis method was used to determine the natural diet of red deer. 15 different species of plant were identified as food items. Among them, 13 species of plants were identified in winter diet and 9 species in summer. Red deer consumed a wider range of species in winter because of their nutrient requirement as well as the shortage of food and the scarcity of high-quality forage in the study area. Phragmites communis, Glycyrrhiza inflata and populus diversifolia were frequently present in the deer＇s diet whenever in winter and summer. Among them, Phragmites communis was the most abundant plant in the area and was included in the deer＇s diet. Observation on food selection frequency of captive Tarim red deer showed that Populus diversifolia was the first preferred species. However, this food was limited in the study area. Five food habitat types were found in the study area according to plant association： （1） Phragmites communis-Tamarix ramosissima association, （2） Tamarix ramosissima-Halostachys caspica association, （3） Tamarix ramosissima-Phragmites communis association, （4） Populus diversifoliaPhragmites communis association, （5） Burned area. Among them, Phragmites communis-Tamarix ramosissima association （reed meadow and reed marsh） was preferred to other types within the study area whenever in summer and winter. Dense reed cover could reduce the chance of detection from predator and obstruct attack from predator. Furthermore, under the cover of the reed, Tarim red deer was protected from direct solar radiation during the hours of hot day in summer. The reed meadow and marsh was preferred, presumably because the red deer could minimize their movements while searching for food, water and cover.     

Natural diet and food habitat use of the Tarim red deer,Cervus elaphus yarkandensis

In order to determine the natural diet and food habitat use of Tarim red deer (Cervus elaphus yarkandensis), a study was carried out in Qiemo, Xinjiang , China from October 2000 to June 2001. Direct observation combined with faecal analysis method was used to determine the natural diet of red deer. 15 different species of plant were identified as food items. Among them, 13 species of plants were identified in winter diet and 9 species in summer. Red deer consumed a wider range of species in winter because of their nutrient requirement as well as the shortage of food and the scarcity of high-quality forage in the study area. Phragmites communis, Glycyrrhiza inflata and populus diversifo-lia were frequently present in the deer's diet whenever in winter and summer. Among them, Phragmites communis was the most abundant plant in the area and was included in the deer's diet. Observation on food selection frequency of captive Tarim red deer showed that Populus diversifolia was the first preferred species. However, this food was limited in the study area. Five food habitat types were found in the study area according to plant association: (1) Phragmites communis-Tamarix ramosissima association, (2) Tamarix ramosissima-Halostachys cas-pica association, (3) Tamarix ramosissima-Phragmites communis association, (4) Populus diversifolia-Phragmites communis association, (5) Burned area. Among them, Phragmites communis-Tamarix ramosissima association (reed meadow and reed marsh) was preferred to other types within the study area whenever in summer and winter. Dense reed cover could reduce the chance of detection from predator and obstruct attack from predator. Furthermore, under the cover of the reed, Tarim red deer was protected from direct solar radiation during the hours of hot day in summer. The reed meadow and marsh was preferred, presumably because the red deer could minimize their movements while searching for food, water and cover.     

RAPD Analysis for Genetic Variation within the Endangered Quillwort Isoetes hypsophila （Isoetaceae）

The genetie variation in the critically endangered species Isoetes hypsophila was investigated using Random Amplified Polymorphism DNA (RAPD) markers. Thirteen primers were screened from sixty primers, and a total of 104 DNA fragments were scored, of which, 52 were polymorphic loci. Low-level genetic diversity within populations with PPB values ranging from 7.69% to 25.96% was found. An Analysis of Molecular Variance (AMOVA) indicated that the most of variance (78.30%) occurred between Yunnan and Sichuan. The variances among populations within regions and within populations were only 3.89% and 17.82%, respectively.     

Predicting mutation outcome from early stochastic variation in genetic interaction partners

Many mutations, including those that cause disease, only have a detrimental effect in a subset of individuals. The reasons for this are usually unknown, but may include additional genetic variation and environmental risk factors. However, phenotypic discordance remains even in the absence of genetic variation, for example between monozygotic twins, and incomplete penetrance of mutations is frequent in isogenic model organisms in homogeneous environments. Here we propose a model for incomplete penetrance based on genetic interaction networks. Using Caenorhabditis elegans as a model system, we identify two compensation mechanisms that vary among individuals and influence mutation outcome. First, feedback induction of an ancestral gene duplicate differs across individuals, with high expression masking the effects of a mutation. This supports the hypothesis that redundancy is maintained in genomes to buffer stochastic developmental failure. Second, during normal embryonic development we find that there is substantial variation in the induction of molecular chaperones such as Hsp90 (DAF-21). Chaperones act as promiscuous buffers of genetic variation, and embryos with stronger induction of Hsp90 are less likely to be affected by an inherited mutation. Simultaneously quantifying the variation in these two independent responses allows the phenotypic outcome of a mutation to be more accurately predicted in individuals. Our model and methodology provide a framework for dissecting the causes of incomplete penetrance. Further, the results establish that inter-individual variation in both specific and more general buffering systems combine to determine the outcome inherited mutations in each individual.     

Cryptic simplicity in DNA is a major source of genetic variation

DNA regions which are composed of a single or relatively few short sequence motifs usually in tandem ('pure simple sequences') have been reported in the genomes of diverse species, and have been implicated in a range of functions including gene regulation, signals for gene conversion and recombination, and the replication of telomeres. They are thought to accumulate by DNA slippage and mispairing during replication and recombination or extension of single-strand ends. In order to systematize the range of DNA simplicity and the genetic nature of the regions that are simple, we have undertaken an extensive computer search of the DNA sequence library of the European Molecular Biology Laboratory (EMBL). We show here that nearly all possible simple motifs occur 5-10 times more frequently than equivalent random motifs. Furthermore, a new computer algorithm reveals the widespread occurrence of significantly high levels of a new type of 'cryptic simplicity' in both coding and noncoding DNA. Cryptically simple regions are biased in nucleotide composition and consist of scrambled arrangements of repetitive motifs which differ within and between species. The universal existence of DNA simplicity from monotonous arrays of single motifs to variable permutations of relatively short-lived motifs suggests that ubiquitous slippage-like mechanisms are a major source of genetic variation in all regions of the genome, not predictable by the classical mutation process.     

Cryptic genetic variation promotes rapid evolutionary adaptation in an RNA enzyme

Cryptic variation is caused by the robustness of phenotypes to mutations. Cryptic variation has no effect on phenotypes in a given genetic or environmental background, but it can have effects after mutations or environmental change. Because evolutionary adaptation by natural selection requires phenotypic variation, phenotypically revealed cryptic genetic variation may facilitate evolutionary adaptation. This is possible if the cryptic variation happens to be pre-adapted, or "exapted", to a new environment, and is thus advantageous once revealed. However, this facilitating role for cryptic variation has not been proven, partly because most pertinent work focuses on complex phenotypes of whole organisms whose genetic basis is incompletely understood. Here we show that populations of RNA enzymes with accumulated cryptic variation adapt more rapidly to a new substrate than a population without cryptic variation. A detailed analysis of our evolving RNA populations in genotype space shows that cryptic variation allows a population to explore new genotypes that become adaptive only in a new environment. Our observations show that cryptic variation contains new genotypes pre-adapted to a changed environment. Our results highlight the positive role that robustness and epistasis can have in adaptive evolution.