Fixed Allele Differences Associated With the Centromere Reveal Chromosome Morphology and Rearrangements in a Reptile (Varanus acanthurus BOULENGER).

Chromosome rearrangements are often implicated with genomic divergence and are proposed to be associated with species evolution. Rearrangements alter the genomic structure and interfere with homologous recombination by isolating a portion of the genome. Integration of multiplatform next-generation DNA sequencing technologies has enabled putative identification of chromosome rearrangements in many taxa; however, integrating these data sets with cytogenetics is still uncommon beyond model genetic organisms. Therefore, to achieve the ultimate goal for the genomic classification of eukaryotic organisms, physical chromosome mapping remains critical. The ridge-tailed goannas (Varanus acanthurus BOULENGER) are a group of dwarf monitor lizards comprised of several species found throughout northern Australia. These lizards exhibit extreme divergence at both the genic and chromosomal levels. The chromosome polymorphisms are widespread extending across much of their distribution, raising the question if these polymorphisms are homologous within the V. acanthurus complex. We used a combined genomic and cytogenetic approach to test for homology across divergent populations with morphologically similar chromosome rearrangements. We showed that more than one chromosome pair was involved with the widespread rearrangements. This finding provides evidence to support de novo chromosome rearrangements have occurred within populations. These chromosome rearrangements are characterized by fixed allele differences originating in the vicinity of the centromeric region. We then compared this region with several other assembled genomes of reptiles, chicken, and the platypus. We demonstrated that the synteny of genes in Reptilia remains conserved despite centromere repositioning across these taxa.

Sex and early-life conditions shape telomere dynamics in an ectotherm.

Telomeres, the repetitive DNA regions that protect the ends of chromosomes, and their shortening have been linked to key life history trade-offs among growth, reproduction and lifespan. In contrast to most endotherms, many ectotherms can compensate for telomere shortening throughout life by upregulation of telomerase in somatic tissues. However, during development, marked by rapid growth and an increased sensitivity to extrinsic factors, the upregulation of telomerase may be overwhelmed, resulting in long-term impacts on telomere dynamics. In ectotherms, one extrinsic factor that may play a particularly important role in development is temperature. Here, we investigated the influence of developmental temperature and sex on early-life telomere dynamics in an oviparous ectotherm, Lacerta agilis. While there was no effect of developmental temperature on telomere length at hatching, there were subsequent effects on telomere maintenance capacity, with individuals incubated at warm temperatures exhibiting less telomere maintenance compared with cool-incubated individuals. Telomere dynamics were also sexually dimorphic, with females having longer telomeres and greater telomere maintenance compared with males. We suggest that selection drives this sexual dimorphism in telomere maintenance, in which females maximise their lifetime reproductive success by investing in traits promoting longevity such as maintenance, while males invest in short-term reproductive gains through a polygynous mating behaviour. These early-life effects, therefore, have the potential to mediate life-long changes to life histories.

Widespread chromosomal rearrangements preceded genetic divergence in a monitor lizard, Varanus acanthurus (Varanidae).

Chromosomal rearrangements are often associated with local adaptation and speciation because they suppress recombination, and as a result, rearrangements have been implicated in disrupting gene flow. Although there is strong evidence to suggest that chromosome rearrangements are a factor in genetic isolation of divergent populations, the underlying mechanism remains elusive. Here, we applied an integrative cytogenetics and genomics approach testing whether chromosomal rearrangements are the initial process, or a consequence, of population divergence in the dwarf goanna, Varanus acanthurus. Specifically, we tested whether chromosome rearrangements are indicators of genetic barriers that can be used to identify divergent populations by looking at gene flow within and between populations with rearrangements. We found that gene flow was present between individuals with chromosome rearrangements within populations, but there was no gene flow between populations that had similar chromosome rearrangements. Moreover, we identified a correlation between reduced genetic variation in populations with a higher frequency of homozygous submetacentric individuals. These findings suggest that chromosomal rearrangements were widespread prior to divergence, and because we found populations with higher frequencies of submetacentric chromosomes were associated with lower genetic diversity, this could indicate that polymorphisms within populations are early indicators of genetic drift.

Thermal Plasticity in Behavioral Traits Mediates Mating and Reproductive Dynamics in an Ectotherm.

AbstractEnvironmental temperatures potentially influence reproductive performance and sexual selection by restricting opportunities for activity. However, explicit tests of the behavioral mechanisms linking thermal variation to mating and reproductive performance are rare. We address this gap in a temperate lizard by combining social network analysis with molecular pedigree reconstruction in a large-scale thermal manipulation experiment. Populations exposed to cool thermal regimes presented fewer high-activity days compared with populations exposed to a warmer regime. While plasticity in thermal activity responses in males masked overall differences in activity levels, prolonged restriction nevertheless affected the timing and consistency of male-female interactions. Females were less capable than males of compensating for lost activity time under cold stress, and less active females in this group were significantly less likely to reproduce. While sex-biased activity suppression appeared to limit male mating rates, this did not correspond to a heightened intensity of sexual selection or shifts in the targets of sexual selection. In many populations facing thermal activity restriction, sexual selection on males may play a limited role relative to other thermal performance traits in facilitating adaptation.

Quantitative genetics of breeding coloration in sand lizards; genic capture unlikely to maintain additive genetic variance.

Sexual selection on fitness-determining traits should theoretically erode genetic variance and lead to low heritability. However, many sexually selected traits maintain significant phenotypic and additive genetic variance, with explanations for this "lek paradox" including genic capture due to condition-dependence, and breaks on directional selection due to environmental sources of variance including maternal effects. Here we investigate genetic and environmental sources of variance in the intrasexually selected green badge of the sand lizard (Lacerta agilis). The badge functions as a cue to male fighting ability in this species, and male-male interactions determine mate acquisition. Using animal models on a pedigree including three generations of males measured over an extensive 9-year field study, we partition phenotypic variance in both badge size and body condition into additive genetic, maternal, and permanent environmental effects experienced by an individual over its lifespan. Heritability of badge size was 0.33 with a significant estimate of underlying additive genetic variance. Body condition was strongly environmentally determined in this species and did not show either significant additive genetic variance or heritability. Neither badge size nor body condition was responsive to maternal effects. We propose that the lack of additive genetic variance and heritability of body condition makes it unlikely that genic capture mechanisms maintain additive genetic variance for badge size. That said, genic capture was originally proposed for male traits under female choice, not agonistic selection. If developmental pathways generating variance in body condition, and/or the covarying secondary sex trait, differ between inter- and intrasexual selection, or the rate at which their additive genetic variance or covariance is depleted, future work may show whether genic capture is largely restricted to intersexual selection processes.

Limited effects of inbreeding on breeding coloration.

Animal color signals may function as indicators of fighting ability when males compete for access to females. This allows opponents to settle aggressive interactions before they escalate into physical combat and injury. Thus, there may be strong directional selection on these traits, toward enhanced signal quality. This renders sexually selected traits particularly susceptible to inbreeding depression, due to relatively low ratios of additive genetic variance to dominance variance. We measured the effects of inbreeding on an intrasexually selected color signal (the badge) in a population of Swedish sand lizards (Lacerta agilis) using the Rhh software based on 17 to 21 microsatellites. Males of this sexually dichromatic species use the badge during aggressive interactions to display, and assess, fighting ability. We found negative effects of homozygosity on badge size, saturation, and brightness. However, no such effects were observed on color hue. Pairwise correlations between badge size, hue, and saturation were all statistically significant. Thus, the sand lizard "badge" is a multicomponent signal with variation explained by covariation in badge size, saturation, and color hue. Body mass corrected for skeletal size (body condition) positively predicted badge size and saturation, encouraging future research on the extent that sexual signals may convey information on multigene targets (i.e. "genic capture").

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.

Of telomeres and temperature: Measuring thermal effects on telomeres in ectothermic animals.

Ectotherms are classic models for understanding life-history tradeoffs, including the reproduction-somatic maintenance tradeoffs that may be reflected in telomere length and their dynamics. Importantly, life-history traits of ectotherms are tightly linked to their thermal environment, with diverse or synergistic mechanistic explanations underpinning the variation. Telomere dynamics potentially provide a mechanistic link that can be used to monitor thermal effects on individuals in response to climatic perturbations. Growth rate, age and developmental stage are all affected by temperature, which interacts with telomere dynamics in complex and intriguing ways. The physiological processes underpinning telomere dynamics can be visualized and understood using thermal performance curves (TPCs). TPCs reflect the evolutionary history and the thermal environment during an individual's ontogeny. Telomere maintenance should be enhanced at or near the thermal performance optimum of a species, population and individual. The thermal sensitivity of telomere dynamics should reflect the interacting TPCs of the processes underlying them. The key processes directly underpinning telomere dynamics are mitochondrial function (reactive oxygen production), antioxidant activity, telomerase activity and telomere endcap protein status. We argue that identifying TPCs for these processes will significantly help design robust, repeatable experiments and field studies of telomere dynamics in ectotherms. Conceptually, TPCs are a valuable framework to predict and interpret taxon- and population-specific telomere dynamics across thermal regimes. The literature of thermal effects on telomeres in ectotherms is sparse and mostly limited to vertebrates, but our conclusions and recommendations are relevant across ectothermic animals.

Inbreeding effects on telomeres in hatchling sand lizards (Lacerta agilis): An optimal family affair?

Telomeres are nucleotide-protein caps, predominantly at the ends of Metazoan linear chromosomes, showing complex dynamics with regard to their lengthening and shortening through life. Their complexity has entertained the idea that net telomere length and attrition could be valuable biomarkers of phenotypic and genetic quality of their bearer. Intuitively, those individuals could be more heterozygous and, hence, less inbred. However, some inbred taxa have longer, not shorter, telomeres. To understand the role of inbreeding in this complex scenario we need large samples across a range of genotypes with known maternity and paternity in telomere-screened organisms under natural conditions. We assessed the effects of parental and hatchling inbreeding on telomere length in >1300 offspring from >500 sires and dams in a population of sand lizards (Lacerta agilis). Maternal and paternal ID and their interactions predict hatchling telomere length at substantial effect sizes (R2  > .50). Deviation from mean maternal heterozygosity statistically predicts shorter offspring telomeres but this only when sibship is controlled for by paternal ID, and then is still limited (R2  = .06). Raw maternal heterozygosity scores, ignoring absolute deviation from the mean, explained 0.07% of the variance in hatchling telomere length. In conclusion, inbreeding is not a driver of telomere dynamics in the sand lizard (Lacerta agilis) study system.

The diversity of population responses to environmental change.

The current extinction and climate change crises pressure us to predict population dynamics with ever-greater accuracy. Although predictions rest on the well-advanced theory of age-structured populations, two key issues remain poorly explored. Specifically, how the age-dependency in demographic rates and the year-to-year interactions between survival and fecundity affect stochastic population growth rates. We use inference, simulations and mathematical derivations to explore how environmental perturbations determine population growth rates for populations with different age-specific demographic rates and when ages are reduced to stages. We find that stage- vs. age-based models can produce markedly divergent stochastic population growth rates. The differences are most pronounced when there are survival-fecundity-trade-offs, which reduce the variance in the population growth rate. Finally, the expected value and variance of the stochastic growth rates of populations with different age-specific demographic rates can diverge to the extent that, while some populations may thrive, others will inevitably go extinct.

How accurately do behavioural observations predict reproductive success in free-ranging lizards?

Behavioural ecologists often use data on patterns of male-female association to infer reproductive success of free-ranging animals. For example, a male seen with several females during the mating season is predicted to father more offspring than a male not seen with any females. We explored the putative correlation between this behaviour and actual paternity (as revealed by microsatellite data) from a long-term study on sand lizards ( Lacerta agilis), including behavioural observations of 574 adult males and 289 adult females, and paternity assignment of more than 2500 offspring during 1998-2007. The number of males that contributed paternity to a female's clutch was correlated with the number of males seen accompanying her in the field, but not with the number of copulation scars on her body. The number of females that a male accompanied in the field predicted the number of females with whom he fathered offspring, and his annual reproductive success (number of progeny). Although behavioural data explained less than one-third of total variance in reproductive success, our analysis supports the utility of behavioural-ecology studies for predicting paternity in free-ranging reptiles.

Low food availability during gestation enhances offspring post-natal growth, but reduces survival, in a viviparous lizard.

The environment experienced by a mother can have profound effects on the fitness of her offspring (i.e., maternal effects). Maternal effects can be adaptive when the developmental environments experienced by offspring promote phenotypes that provide fitness benefits either via matching offspring phenotype to the post-developmental environment (also known as anticipatory maternal effects) or through direct effects on offspring growth and survival. We tested these hypotheses in a viviparous lizard using a factorial experimental design in which mothers received either high or low amounts of food during gestation, and resultant offspring were raised on either high or low amounts of food post-birth. We found no effect of food availability during gestation on reproductive traits of mothers or offspring traits at birth. However, offspring from mothers who received low food during gestation exhibited a greater increase in condition in the post-birth period, suggesting some form of priming of offspring by mothers to cope with an anticipated poor environment after birth. Offspring that received low food during gestation were also more likely to die, suggesting a trade-off for this accelerated growth. There were also significant effects of post-birth food availability on offspring snout-vent length and body condition growth, with offspring with high food availability post birth doing better. However, the effects of the pre- and post-natal resource evnironment on offspring growth were independent on one another, therefore, providing no support for the presence of anticipatory maternal effects in the traditional sense.

Effects of male telomeres on probability of paternity in sand lizards.

Standardized swim-up trials are used in in vitro fertilization clinics to select particularly motile spermatozoa in order to increase the probability of a successful fertilization. Such trials demonstrate that sperm with longer telomeres have higher motility and lower levels of DNA damage. Regardless of whether sperm motility, and successful swim-up to fertilization sites, is a direct or correlational effect of telomere length or DNA damage, covariation between telomere length and sperm performance predicts a relationship between telomere length and probability of paternity in sperm competition, a prediction that for ethical reasons cannot be tested on humans. Here, we test this prediction in sand lizards (Lacerta agilis) using experimental data from twice-mated females in a laboratory population, and telomere length in blood from the participating lizards. Female identity influenced paternity (while the mechanism was not identified), while relatively longer male telomeres predicted higher probability of paternity. We discuss potential mechanisms underpinning this result.

Maternal effects impact decision-making in a viviparous lizard.

Stressful conditions experienced during early development can have deleterious effects on offspring morphology, physiology and behaviour. However, few studies have examined how developmental stress influences an individual's cognitive phenotype. Using a viviparous lizard, we show that the availability of food resources to a mother during gestation influences a key component of her offspring's cognitive phenotype: their decision-making. Offspring from females who experienced low resource availability during gestation did better in an anti-predatory task that relied on spatial associations to guide their decisions, whereas offspring from females who experienced high resource availability during gestation did better in a foraging task that relied on colour associations to inform their decisions. This shows that the prenatal environment can influence decision-making in animals, a cognitive trait with functional implications later in life.

Mate familiarity and social learning in a monogamous lizard.

Social learning is thought to be advantageous as it allows an animal to gather information quickly without engaging in costly trial-and-error learning. However, animals should be selective about when and whom they learn from. Familiarity is predicted to positively influence an animal's reliance on social learning; yet, few studies have empirically tested this theory. We used a lizard (Liopholis whitii) that forms long-term monogamous pair bonds to examine the effects of partner familiarity on social learning in two novel foraging tasks, an association and a reversal task. We allowed female lizards to observe trained conspecifics that were either familiar (social mate) or unfamiliar execute these tasks and compared these two groups with control females that did not receive social information. Lizards preferentially relied on trial-and-error learning in the association task. In the reversal task, lizards that were demonstrated by familiar partners learnt in fewer trials compared to control lizards and made more correct choices. Our results provide some evidence for context-dependent learning with lizards differentiating between when they utilize social learning, and, to a limited degree, whom they learnt from. Understanding the role of the social context in which learning occurs provides important insights into the benefits of social learning and sociality more generally.

Climate and sex ratio variation in a viviparous lizard.

The extent to which key biological processes, such as sex determination, respond to environmental fluctuations is fundamental for assessing species' susceptibility to ongoing climate change. Few studies, however, address how climate affects offspring sex in the wild. We monitored two climatically distinct populations of the viviparous skink Niveoscincus ocellatus for 16 years, recording environmental temperatures, offspring sex and date of birth. We found strong population-specific effects of temperature on offspring sex, with female offspring more common in warm years at the lowland site but no effect at the highland site. In contrast, date of birth advanced similarly in response to temperature at both sites. These results suggest strong population-specific effects of temperature on offspring sex that are independent of climatic effects on other physiological processes. These results have significant implications for our understanding of the ecological and evolutionary consequences of variation in sex ratios under climate change.

Climate-driven population divergence in sex-determining systems.

Sex determination is a fundamental biological process, yet its mechanisms are remarkably diverse. In vertebrates, sex can be determined by inherited genetic factors or by the temperature experienced during embryonic development. However, the evolutionary causes of this diversity remain unknown. Here we show that live-bearing lizards at different climatic extremes of the species' distribution differ in their sex-determining mechanisms, with temperature-dependent sex determination in lowlands and genotypic sex determination in highlands. A theoretical model parameterized with field data accurately predicts this divergence in sex-determining systems and the consequence thereof for variation in cohort sex ratios among years. Furthermore, we show that divergent natural selection on sex determination across altitudes is caused by climatic effects on lizard life history and variation in the magnitude of between-year temperature fluctuations. Our results establish an adaptive explanation for intra-specific divergence in sex-determining systems driven by phenotypic plasticity and ecological selection, thereby providing a unifying framework for integrating the developmental, ecological and evolutionary basis for variation in vertebrate sex determination.

Sand lizard (Lacerta agilis) phenology in a warming world.

BACKGROUND: Present-day climate change has altered the phenology (the timing of periodic life cycle events) of many plant and animal populations worldwide. Some of these changes have been adaptive, leading to an increase in population fitness, whereas others have been associated with fitness decline. Representing short-term responses to an altered weather regime, hitherto observed changes are largely explained by phenotypic plasticity. However, to track climatically induced shifts in optimal phenotype as climate change proceeds, evolutionary capacity in key limiting climate- and fitness-related traits is likely to be crucial. In order to produce realistic predictions about the effects of climate change on species and populations, a main target for conservation biologists is thus to assess the potential of natural populations to respond by these two mechanisms. In this study we use a large 15-year dataset on an ectotherm model, the Swedish sand lizard (Lacerta agilis), to investigate how higher spring temperature is likely to affect oviposition timing in a high latitude population, a trait strongly linked to offspring fitness and survival. RESULTS: With an interest in both the short- and potential long-term effect of rising temperatures, we applied a random regression model, which yields estimates of population-level plasticity and among-individual variation in the average, as well as the plastic, response to temperature. Population plasticity represents capacity for short-term adjustments whereas variation among individuals in a fitness-related trait indicates an opportunity for natural selection and hence for evolutionary adaptation. The analysis revealed both population-level plasticity and individual-level variation in average laying date. In contrast, we found no evidence for variation among females in their plastic responses to spring temperature, which could demonstrate a similarity in responses amongst females, but may also be due to a lack of statistical power to detect such an effect. CONCLUSION: Our findings indicate that climate warming may have positive fitness effects in this lizard population through an advancement of oviposition date. This prediction is consistent over shorter and potentially also longer time scales as the analysis revealed both population-level plasticity and individual-level variation in average laying date. However, the genetic basis for this variation would have to be examined in order to predict an evolutionary response.

In utero exposure to the oestrogen mimic diethylstilbestrol disrupts gonadal development in a viviparous reptile.

The ubiquitous presence of endocrine-disrupting chemicals (EDCs) in the environment is of major concern. Studies on oviparous reptiles have significantly advanced knowledge in this field; however, 30% of reptilian species are viviparous (live-bearing), a parity mode in which both yolk and a placenta support embryonic development, thus exposure to EDCs may occur via multiple routes. In this first study of endocrine disruption in a viviparous lizard (Niveoscincus metallicus), we aimed to identify effects of the oestrogen mimic diethylstilbestrol (DES) on gonadal development. At the initiation of sexual differentiation, pregnant N. metallicus were treated with a single dose of DES at 100 or 10µgkg(--1), a vehicle solvent or received no treatment. There was no dose-response effect, but the testes of male neonates born to DES-exposed mothers showed reduced organisation of seminiferous tubules and a lack of germ cells compared with those from control groups. The ovaries of female neonates born to DES-exposed mothers exhibited phenotypic abnormalities of ovarian structure, oocytes and follicles compared with controls. The results indicate that, in viviparous lizards, maternal exposure to oestrogenic EDCs during gestation may have profound consequences for offspring reproductive fitness.

Energy expenditure of the spotted snow skink, Niveoscincus ocellatus, at two climatic extremes of its distribution range.

The study of energy expenditure between populations of a wide ranging ectothermic species may provide an insight into how organisms respond to variation in environmental conditions. In this study, the energy expenditure of male spotted snow skinks, Niveoscincus ocellatus, living at the two extremes of the species' distribution range (warm lowland versus cold alpine site) was measured using the doubly labelled water method. Males at the cold alpine site expended more energy per gram per hour compared to their counterparts living at the warm lowland site. Lizards living at high altitude were active at lower temperatures compared with those at the low altitude site, which resulted in a longer activity time for the highland population. However, the differences in energy expenditure cannot be explained only by these differences in activity time. We further suggest that at the cold alpine site, lizards compensated for the low temperatures by elevating their metabolism which subsequently increased their energy expenditure. An elevated metabolic rate combined with modified thermoregulatory behaviour is likely an important mechanism allowing N. ocellatus to cope with the cold environments at high altitude sites.