Using a Handful of Transcriptomes to Detect Sex-Linked Markers and Develop Molecular Sexing Assays in a Species with Homomorphic Sex Chromosomes.

To understand the biology of a species, it is often crucial to be able to differentiate males and females. However, many species lack easily identifiable sexually dimorphic traits. In those that possess sex chromosomes, molecular sexing offers a good alternative, and molecular sexing assays can be developed through the comparison of male and female genomic sequences. However, in many nonmodel species, sex chromosomes are poorly differentiated, and identifying sex-linked sequences and developing sexing assays can be challenging. In this study, we highlight a simple transcriptome-based procedure for the detection of sex-linked markers suitable for the development of sexing assays that circumvents limitations of more commonly used approaches. We apply it to the spotted snow skink Carinascincus ocellatus, a viviparous lizard with homomorphic XY chromosomes that has environmentally induced sex reversal. With transcriptomes from three males and three females alone, we identify thousands of putative Y-linked sequences. We confirm linkage through alignment of assembled transcripts to a distantly related lizard genome and readily design multiple single locus polymerase chain reaction primers to sex C. ocellatus and related species. Our approach also facilitates valuable comparisons of sex determining systems on a broad taxonomic scale.

Episodic population fragmentation and gene flow reveal a trade-off between heterozygosity and allelic richness.

In episodic environments like deserts, populations of some animal species exhibit irregular fluctuations such that populations are alternately large and connected or small and isolated. Such dynamics are typically driven by periodic resource pulses due, for example, to large but infrequent rainfall events. The repeated population bottlenecks resulting from fragmentation should lower genetic diversity over time, yet species undergoing these fluctuations appear to maintain high levels of genetic diversity. To resolve this apparent paradox, we simulated a metapopulation of constant size undergoing repeat episodes of fragmentation and change in gene flow to mimic outcomes experienced by mammals in an Australian desert. We show that episodic fragmentation and gene flow have contrasting effects on two measures of genetic diversity: heterozygosity and allelic richness. Specifically, fragmentation into many, small subpopulations, coupled with periods of infrequent gene flow, preserves allelic richness at the expense of heterozygosity. In contrast, fragmentation into a few, large subpopulations maintains heterozygosity at the expense of allelic richness. The strength of the trade-off between heterozygosity and allelic richness depends on the amount of gene flow and the frequency of gene flow events. Our results imply that the type of genetic diversity maintained among species living in strongly fluctuating environments will depend on the way populations fragment, with our results highlighting different mechanisms for maintaining allelic richness and heterozygosity in small, fragmented populations.

Sex reversal explains some, but not all, climate-mediated sex ratio variation within a viviparous reptile.

Evolutionary transitions in sex-determining systems have occurred frequently yet understanding how they occur remains a major challenge. In reptiles, transitions from genetic to temperature-dependent sex determination can occur if the gene products that determine sex evolve thermal sensitivity, resulting in sex-reversed individuals. However, evidence of sex reversal is limited to oviparous reptiles. Here we used thermal experiments to test whether sex reversal is responsible for differences in sex determination in a viviparous reptile, Carinascincus ocellatus, a species with XY sex chromosomes and population-specific sex ratio response to temperature. We show that sex reversal is occurring and that its frequency is related to temperature. Sex reversal was unidirectional (phenotypic males with XX genotype) and observed in both high- and low-elevation populations. We propose that XX-biased genotypic sex ratios could produce either male- or female-biased phenotypic sex ratios as observed in low-elevation C. ocellatus under variable rates of XX sex reversal. We discuss reasons why sex reversal may not influence sex ratios at high elevation. Our results suggest that the mechanism responsible for evolutionary transitions from genotypic to temperature-dependent sex determination is more complex than can be explained by a single process such as sex reversal.

Pleistocene divergence in the absence of gene flow among populations of a viviparous reptile with intraspecific variation in sex determination.

Polymorphisms can lead to genetic isolation if there is differential mating success among conspecifics divergent for a trait. Polymorphism for sex-determining system may fall into this category, given strong selection for the production of viable males and females and the low success of heterogametic hybrids when sex chromosomes differ (Haldane's rule). Here we investigated whether populations exhibiting polymorphism for sex determination are genetically isolated, using the viviparous snow skink Carinascincus ocellatus. While a comparatively high elevation population has genotypic sex determination, in a lower elevation population there is an additional temperature component to sex determination. Based on 11,107 SNP markers, these populations appear genetically isolated. "Isolation with Migration" analysis also suggests these populations diverged in the absence of gene flow, across a period encompassing multiple Pleistocene glaciations and likely greater geographic proximity of populations. However, further experiments are required to establish whether genetic isolation may be a cause or consequence of differences in sex determination. Given the influence of temperature on sex in one lineage, we also discuss the implications for the persistence of this polymorphism under climate change.

Differences in Homomorphic Sex Chromosomes Are Associated with Population Divergence in Sex Determination in Carinascincus ocellatus (Scincidae: Lygosominae).

Sex determination directs development as male or female in sexually reproducing organisms. Evolutionary transitions in sex determination have occurred frequently, suggesting simple mechanisms behind the transitions, yet their detail remains elusive. Here we explore the links between mechanisms of transitions in sex determination and sex chromosome evolution at both recent and deeper temporal scales (<1 Myr; ~79 Myr). We studied a rare example of a species with intraspecific variation in sex determination, Carinascincus ocellatus, and a relative, Liopholis whitii, using c-banding and mapping of repeat motifs and a custom Y chromosome probe set to identify the sex chromosomes. We identified both unique and conserved regions of the Y chromosome among C. ocellatus populations differing in sex determination. There was no evidence for homology of sex chromosomes between C. ocellatus and L. whitii, suggesting independent evolutionary origins. We discuss sex chromosome homology between members of the subfamily Lygosominae and propose links between sex chromosome evolution, sex determination transitions, and karyotype evolution.

Conservation of Sex-Linked Markers among Conspecific Populations of a Viviparous Skink, Niveoscincus ocellatus, Exhibiting Genetic and Temperature-Dependent Sex Determination.

Sex determination systems are exceptionally diverse and have undergone multiple and independent evolutionary transitions among species, particularly reptiles. However, the mechanisms underlying these transitions have not been established. Here, we tested for differences in sex-linked markers in the only known reptile that is polymorphic for sex determination system, the spotted snow skink, Niveoscincus ocellatus, to quantify the genomic differences that have accompanied this transition. In a highland population, sex is determined genetically, whereas in a lowland population, offspring sex ratio is influenced by temperature. We found a similar number of sex-linked loci in each population, including shared loci, with genotypes consistent with male heterogamety (XY). However, population-specific linkage disequilibrium suggests greater differentiation of sex chromosomes in the highland population. Our results suggest that transitions between sex determination systems can be facilitated by subtle genetic differences.

Controversies and Recent Developments of the Low-FODMAP Diet.

The low-fermentable oligo-, di-, and monosaccharide and polyol (FODMAP) diet is a 2-phased intervention, with strict reduction of all slowly absorbed or indigestible short-chain carbohydrates (ie, FODMAPs) followed by reintroduction of specific FODMAPs according to tolerance. The efficacy of the elimination phase of the FODMAP diet is well established, but the success of maintaining this diet has been shown in only a few observational studies. How the efficacy of the low-FODMAP diet compares with that of other therapies has received limited attention, but recent studies have shown this diet to be comparable or superior to diets that address eating style and choice of food as well as to gut hypnotherapy. There has been no comparison between the low-FODMAP diet and the gluten-free diet, which moderately reduces FODMAP intake. Mechanistically, dietary FODMAPs have very limited effects on the consistency of bowel actions but seem to suppress the release of histamine. Neither symptom pattern nor breath hydrogen testing for fructose or polyol malabsorption is a useful predictor of efficacy, but analysis of gut microbiota has potential. As a restrictive diet, the low-FODMAP diet carries risks of nutritional inadequacy and of fostering disordered eating, which has received little attention. Strict FODMAP restriction induces a potentially unfavorable gut microbiota, although the impact of this consequence upon health is unknown. This observation puts additional impetus on the reintroduction of FODMAPs according to tolerance during the maintenance phase of the diet. Studies of the low-FODMAP diet in children are few but do suggest benefit. However, such a strategy should be implemented with care due to the psychological and nutritional risks of a restrictive diet. Clinical wisdom is required in utilizing the low-FODMAP diet.

The cost of healthy food in rural Victoria.

INTRODUCTION: The cost of healthy food has been associated previously with the degree of remoteness and socioeconomic status. This study aimed to investigate the factors that influence the cost of food in rural Victoria, Australia. It also aimed to compare the cost of nutritious foods with less healthy foods, and to identify the population sub-groups most vulnerable to economic food insecurity. METHODS: A cross-sectional survey of the cost of food was undertaken in 2007 in a convenience sample of 34 supermarkets in rural areas across Victoria using the Victorian Healthy Food Basket (VHFB). The VHFB was designed to meet the nutritional needs of four different family types for a fortnight. RESULTS: The cost of the VHFB for a 'typical family' (2 adults, 2 children) was (mean [interquartile range]) AU $402.81 ($26.36). No association was evident between food cost and remoteness as indicated by the Accessibility/Remoteness Index for Australia (ARIA) score, socioeconomic status as indicated by the Socio-Economic Indices for Areas (SEIFA), population size or density, or distance of the town from the state capital, Melbourne. It was more expensive to purchase the VHFB at an independent store (median cost $406.66 [$29.39]) than at a supermarket chain (median cost $394.93 [$26.64]), p<0.05. Vegetables and legumes were the most expensive component of the VHFB to purchase and this food group showed significantly greater variation in food price than cereals (p<0.05), non-core foods (p<0.05) and unhealthy foods (p<0.001). The median cost of the VHFB was most expensive for a typical family and 'single parent family' (40% and 37% of welfare income) and least expensive for a single man (29% of income) and elderly pensioner (19% income). CONCLUSIONS: The VHFB is an effective tool for assessing economic food security for different population groups. The cost of food in rural Victoria varies in a manner that appears unrelated to remoteness, population, socioeconomic status or distance from the metropolitan centre. Purchase of healthy food requires a considerable proportion of welfare income and may thus be unaffordable for some groups. Food cost must be monitored at a national level to provide a knowledge base to inform development of food and nutrition policies for improved population health.