Daniel W. A. Noble

Unisexual salamanders (genus Ambystoma) present a new reproductive mode for eukaryotes.

To persist, unisexual and asexual eukaryotes must have reproductive modes that circumvent normal bisexual reproduction. Parthenogenesis, gynogenesis, and hybridogenesis are the modes that have generally been ascribed to various unisexuals. Unisexual Ambystoma are abundant around the Great Lakes region of North America, and have variously been described as having all 3 reproductive modes. Diploid and polyploid unisexuals have nuclear genomes that combine the haploid genomes of 2 to 4 distinct sexual species, but the mtDNA is unlike any of those 4 species and is similar to another species, Ambystoma barbouri. To obtain better resolution of the reproductive mode used by unisexual Ambystoma and to explore the relationship of A. barbouri to the unisexuals, we sequenced the mitochondrial control and highly variable intergenic spacer region of 48 ambystomatids, which included 28 unisexuals, representatives of the 4 sexual species and A. barbouri. The unisexuals have similar sequences over most of their range, and form a close sister group to A. barbouri, with an estimated time of divergence of 2.4-3.9 million years ago. Individuals from the Lake Erie Islands (Kelleys, Pelee, North Bass) have a haplotype that demonstrates an isolation event. We examined highly variable microsatellite loci, and found that the genetic makeup of the unisexuals is highly variable and that unisexual individuals share microsatellite alleles with sexual individuals within populations. Although many progeny from the same female had the same genotype for 5 microsatellite DNA loci, there was no indication that any particular genome is consistently inherited in a clonal fashion in a population. The reproductive mode used by unisexual Ambystoma appears to be unique; we suggest kleptogenesis as a new unisexual reproductive mode that is used by these salamanders.

Sex and boldness explain individual differences in spatial learning in a lizard

Understanding individual differences in cognitive performance is a major challenge to animal behaviour and cognition studies. We used the Eastern water skink (Eulamprus quoyii) to examine associations between exploration, boldness and individual variability in spatial learning, a dimension of lizard cognition with important bearing on fitness. We show that males perform better than females in a biologically relevant spatial learning task. This is the first evidence for sex differences in learning in a reptile, and we argue that it is probably owing to sex-specific selective pressures that may be widespread in lizards. Across the sexes, we found a clear association between boldness after a simulated predatory attack and the probability of learning the spatial task. In contrast to previous studies, we found a nonlinear association between boldness and learning: both ‘bold’ and ‘shy’ behavioural types were more successful learners than intermediate males. Our results do not fit with recent predictions suggesting that individual differences in learning may be linked with behavioural types via high–low-risk/reward trade-offs. We suggest the possibility that differences in spatial cognitive performance may arise in lizards as a consequence of the distinct environmental variability and complexity experienced by individuals as a result of their sex and social tactics.

Meta-evaluation of meta-analysis: ten appraisal questions for biologists

Meta-analysis is a statistical procedure for analyzing the combined data from different studies, and can be a major source of concise up-to-date information. The overall conclusions of a meta-analysis, however, depend heavily on the quality of the meta-analytic process, and an appropriate evaluation of the quality of meta-analysis (meta-evaluation) can be challenging. We outline ten questions biologists can ask to critically appraise a meta-analysis. These questions could also act as simple and accessible guidelines for the authors of meta-analyses. We focus on meta-analyses using non-human species, which we term ‘biological’ meta-analysis. Our ten questions are aimed at enabling a biologist to evaluate whether a biological meta-analysis embodies ‘mega-enlightenment’, a ‘mega-mistake’, or something in between.

Colour discrimination and associative learning in hatchling lizards incubated at ‘hot’ and ‘cold’ temperatures

The ability of an animal to acquire, process and learn from information in their environment is thought to be fundamental to fitness. We currently have a poor understanding of the learning ability of young animals within the first few months of their life, the types of learning they use and the extent of their learning ability. Furthermore, an animal’s developmental environment, such as nest incubation temperature, may profoundly influence motor and cognitive skills. We first tested the ability of hatchling three-lined skinks (Bassiana duperreyi) incubated at ‘hot’ and ‘cold’ temperatures to solve an instrumental (motor) task before assessing their ability to learn colour associations in a multi-stage instrumental task, with a choice reversal. While 53 (88.3xa0%) lizards successfully completed the training phase, 14 (46.7xa0%) of the ‘hot’ incubated and none of the ‘cold’ incubated lizards successfully completed the instrumental task. Thirteen of these lizards rapidly learnt to discriminate colours, and this culminated in eight individuals successfully completing a choice reversal. Hatchling B. duperreyi demonstrated surprisingly rapid learning, and these results highlight the potentially important role of cognition during development and ultimately, in fitness.

Sex in unisexual salamanders: discovery of a new sperm donor with ancient affinities.

Although bisexual reproduction has considerable evolutionary benefits, several all-female vertebrates exist. Unisexual salamanders in the genus Ambystoma are common around the Great Lakes region in eastern North America. They originated from a hybridization event that involved a female that shared a common ancestor with Ambystoma barbouri 2.4 to 3.9 million years ago but, unexpectedly, A. barbouri nuclear genomes were unknown in unisexuals. Unisexual salamanders steal sperm from donors of normally bisexual species, so their reproductive mode is described as kleptogenesis. Most known unisexuals are polyploid and they all possess at least one A. laterale genome. One or more other genomes are taken from sperm donors that may include A. jeffersonianum, A. laterale, A. texanum and A. tigrinum. We examined unisexual adults and larvae in a southern Ohio pond where unisexual individuals coexist with male A. barbouri. This population provided an opportunity to test hypotheses pertaining to the role of A. barbouri in the evolution of the disparate cytoplasmic and nuclear genomes in unisexual salamanders. Microsatellite DNA loci, mitochondrial DNA sequences and genomic in situ hybridization were used to identify the genomic constitution of individuals. A. barbouri was found to be an acceptable sperm donor for unisexuals but only contributed genomes in ploidy-elevated individuals. In the absence of A. jeffersonianum, this Ohio population is likely experiencing a recent switch in sperm donors from A. jeffersonianum to A. barbouri and demonstrates the evolutionary flexibility and dynamics of kleptogenesis.

Species delineation using Bayesian model-based assignment tests: a case study using Chinese toad-headed agamas (genus Phrynocephalus)

BackgroundSpecies are fundamental units in biology, yet much debate exists surrounding how we should delineate species in nature. Species discovery now requires the use of separate, corroborating datasets to quantify independently evolving lineages and test species criteria. However, the complexity of the speciation process has ushered in a need to infuse studies with new tools capable of aiding in species delineation. We suggest that model-based assignment tests are one such tool. This method circumvents constraints with traditional population genetic analyses and provides a novel means of describing cryptic and complex diversity in natural systems. Using toad-headed agamas of the Phrynocephalus vlangalii complex as a case study, we apply model-based assignment tests to microsatellite DNA data to test whether P. putjatia, a controversial species that closely resembles P. vlangalii morphologically, represents a valid species. Mitochondrial DNA and geographic data are also included to corroborate the assignment test results.ResultsAssignment tests revealed two distinct nuclear DNA clusters with 95% (230/243) of the individuals being assigned to one of the clusters with > 90% probability. The nuclear genomes of the two clusters remained distinct in sympatry, particularly at three syntopic sites, suggesting the existence of reproductive isolation between the identified clusters. In addition, a mitochondrial ND2 gene tree revealed two deeply diverged clades, which were largely congruent with the two nuclear DNA clusters, with a few exceptions. Historical mitochondrial introgression events between the two groups might explain the disagreement between the mitochondrial and nuclear DNA data. The nuclear DNA clusters and mitochondrial clades corresponded nicely to the hypothesized distributions of P. vlangalii and P. putjatia.ConclusionsThese results demonstrate that assignment tests based on microsatellite DNA data can be powerful tools for distinguishing closely related species and support the validity of P. putjatia. Assignment tests have the potential to play a significant role in elucidating biodiversity in the era of DNA data. Nonetheless, important limitations do exist and multiple independent datasets should be used to corroborate results from assignment programs.

Nonindependence and sensitivity analyses in ecological and evolutionary meta‐analyses

Meta‐analysis is an important tool for synthesizing research on a variety of topics in ecology and evolution, including molecular ecology, but can be susceptible to nonindependence. Nonindependence can affect two major interrelated components of a meta‐analysis: (i) the calculation of effect size statistics and (ii) the estimation of overall meta‐analytic estimates and their uncertainty. While some solutions to nonindependence exist at the statistical analysis stages, there is little advice on what to do when complex analyses are not possible, or when studies with nonindependent experimental designs exist in the data. Here we argue that exploring the effects of procedural decisions in a meta‐analysis (e.g. inclusion of different quality data, choice of effect size) and statistical assumptions (e.g. assuming no phylogenetic covariance) using sensitivity analyses are extremely important in assessing the impact of nonindependence. Sensitivity analyses can provide greater confidence in results and highlight important limitations of empirical work (e.g. impact of study design on overall effects). Despite their importance, sensitivity analyses are seldom applied to problems of nonindependence. To encourage better practice for dealing with nonindependence in meta‐analytic studies, we present accessible examples demonstrating the impact that ignoring nonindependence can have on meta‐analytic estimates. We also provide pragmatic solutions for dealing with nonindependent study designs, and for analysing dependent effect sizes. Additionally, we offer reporting guidelines that will facilitate disclosure of the sources of nonindependence in meta‐analyses, leading to greater transparency and more robust conclusions.

Activity predicts male reproductive success in a polygynous lizard

Activity patterns and social interactions play a key role in determining reproductive success, although this is poorly understood for species that lack overt social behaviour. We used genetic paternity analysis to quantify both multiple paternity and the relative roles of activity and social behaviour in determining reproductive success in a nondescript Australian lizard. During the breeding season we intensively followed and recorded the behaviour of a group of seven males and 13 females in a naturalistic outdoor enclosure to examine the relative roles of body size, activity and social interactions in determining male fertilization success. We found multiple paternity in 42% of clutches. No single behaviour was a significant predictor of male fertilization success in isolation, but male-female association, interactions and courtship explained 41% of the variation in male fertilization success. Males with the highest number of offspring sired invested heavily in interacting with females but spent very little time in interactions with males. These same males also sired offspring from more clutches. When taken collectively, an index of overall male activity, including locomotion and all social interactions, significantly explained 81% of the variation in the total number of offspring sired and 90% of the variation in the number of clutches in which males sired offspring. We suggest that the most successful male strategy is a form of endurance rivalry in which active mate searching and interactions with females have the greatest fitness benefits.

Learning outdoors: male lizards show flexible spatial learning under semi-natural conditions

Spatial cognition is predicted to be a fundamental component of fitness in many lizard species, and yet some studies suggest that it is relatively slow and inflexible. However, such claims are based on work conducted using experimental designs or in artificial contexts that may underestimate their cognitive abilities. We used a biologically realistic experimental procedure (using simulated predatory attacks) to study spatial learning and its flexibility in the lizard Eulamprus quoyii in semi-natural outdoor enclosures under similar conditions to those experienced by lizards in the wild. To evaluate the flexibility of spatial learning, we conducted a reversal spatial-learning task in which positive and negative reinforcements of learnt spatial stimuli were switched. Nineteen (32%) male lizards learnt both tasks within 10 days (spatial task mean: 8.16 ± 0.69 (s.e.) and reversal spatial task mean: 10.74 ± 0.98 (s.e.) trials). We demonstrate that E. quoyii are capable of flexible spatial learning and suggest that future studies focus on a range of lizard species which differ in phylogeny and/or ecology, using biologically relevant cognitive tasks, in an effort to bridge the cognitive divide between ecto- and endotherms.

Developmental temperatures and phenotypic plasticity in reptiles: a systematic review and meta-analysis: Incubation temperature and plasticity

Early environments can profoundly influence an organism in ways that persist over its life. In reptiles, early thermal environments (nest temperatures) can impact offspring phenotype and survival in important ways, yet we still lack an understanding of whether general trends exist and the magnitude of impact. Understanding these patterns is important in predicting how climate change will affect reptile populations and the role of phenotypic plasticity in buffering populations. We compiled data from 175 reptile studies to examine, and quantify, the effect of incubation temperature on phenotype and survival. Using meta‐analytic approaches (standardized mean difference between incubation treatments, Hedges g), we show that across all trait types examined there is, on average, a moderate to large magnitude of effect of incubation temperatures (absolute effect: |g| = 0.75). Unsurprisingly, this influence was extremely large for incubation duration, as predicted, with warmer temperatures decreasing incubation time overall (g = −8.42). Other trait types, including behaviour, physiology, morphology, performance, and survival experienced reduced, but still mostly moderate to large effects, with particularly strong effects on survival. Moreover, the impact of incubation temperature persisted at least one‐year post‐hatching, suggesting that these effects have the potential to impact fitness in the long term. The magnitude of effect increased as the change in temperature increased (e.g. 6°C versus 2°C) in almost all cases, and tended to decrease when temperatures of the treatments fluctuated around a mean temperature compared to when they were constant. The effect also depended on the mid‐temperature of the comparison, but not in consistent ways, with some traits experiencing the greatest effects at extreme temperatures, while others did not. The highly heterogeneous nature of the effects we observe, along with a large amount of unexplained variability, indicates that the shape of reaction norms between phenotype and temperature, along with ecological and/or experimental factors, are important when considering general patterns. Our analyses provide new insights into the effects of incubation environments on reptile phenotype and survival and allow general, albeit coarse, predictions for taxa experiencing warming nest temperatures under climatic change.