Genetic insight into a polygenic trait using a novel genome-wide association approach in a wild amphibian population

Body size variation is central in the evolution of life-history traits in amphibians, but the underlying genetic architecture of this complex trait is still largely unknown. Herein, we studied the genetic basis of body size and fecundity of the alternative morphotypes in a wild population of the Greek smooth newt (Lissotriton graecus). By combining a genome-wide association approach with linkage disequilibrium network analysis, we were able to identify clusters of highly correlated loci thus maximizing sequence data for downstream analysis. The putatively associated variants explained 12.8% to 44.5% of the total phenotypic variation in body size and were mapped to genes with functional roles in the regulation of gene expression and cell cycle processes. Our study is the first to provide insights into the genetic basis of complex traits in newts and provides a useful tool to identify loci potentially involved in fitness-related traits in small data sets from natural populations in non-model species.

Viability, behavior, and color expression in the offspring of matings between common wall lizard Podarcis muralis color morphs

Color polymorphisms are widely studied to identify the mechanisms responsible for the origin and maintenance of phenotypic variability in nature. Two of the mechanisms of balancing selection currently thought to explain the long-term persistence of polymorphisms are the evolution of alternative phenotypic optima through correlational selection on suites of traits including color and heterosis. Both of these mechanisms can generate differences in offspring viability and fitness arising from different morph combinations. Here, we examined the effect of parental morph combination on fertilization success, embryonic viability, newborn quality, antipredator, and foraging behavior, as well as inter-annual survival by conducting controlled matings in a polymorphic lacertid Podarcis muralis, where color morphs are frequently assumed to reflect alternative phenotypic optima (e.g., alternative reproductive strategies). Juveniles were kept in outdoor tubs for a year in order to study inter-annual growth, survival, and morph inheritance. In agreement with a previous genome-wide association analysis, morph frequencies in the year-old juveniles matched the frequencies expected if orange and yellow expressions depended on recessive homozygosity at 2 separate loci. Our findings also agree with previous literature reporting higher reproductive output of heavy females and the higher overall viability of heavy newborn lizards, but we found no evidence for the existence of alternative breeding investment strategies in female morphs, or morph-combination effects on offspring viability and behavior. We conclude that inter-morph breeding remains entirely viable and genetic incompatibilities are of little significance for the maintenance of discrete color morphs in P. muralis from the Pyrenees.

Pheromone Gene Diversification and the Evolution of Courtship Glands in Plethodontid Salamanders

Proteinaceous pheromones that diversify through gene duplication can result in shifts in courtship cocktails that may serve as a mechanism for reproductive isolation. The molecular evolution of pheromones has been extensively studied in salamanders, but how these genes and associated novel courtship glands have codiversified has not been evaluated. In this study we used transcriptional analyses to examine the relationship between pheromone diversification and gland type in three divergent lineages of plethodontid salamanders. Our results revealed that plethodontid salamanders express up to eight divergent Sodefrin Precursor-like Factor genes (spf, representing both alpha and beta subfamilies) along with Plethodontid Modulating Factor (pmf) and Plethodontid Receptivity Factor (prf). Expression of pheromone genes is tissue specific with pmf, prf, and some spf genes restricted to the mental gland. In contrast, the caudal gland shows strong expression of the other spf genes. We found evidence for punctuated changes in pheromone cocktail composition related to the loss of metamorphosis, and subsequent extreme reduction of the mental gland, in a paedomorphic lineage. Our study provides insight into how pheromone diversification can be partitioned into unique glands, which may lead to cocktail specificity in behavioral modules during courtship.

Geography is more important than life history in the recent diversification of the tiger salamander complex

The North American tiger salamander species complex, including its best-known species, the Mexican axolotl, has long been a source of biological fascination. The complex exhibits a wide range of variation in developmental life history strategies, including populations and individuals that undergo metamorphosis; those able to forego metamorphosis and retain a larval, aquatic lifestyle (i.e., paedomorphosis); and those that do both. The evolution of a paedomorphic life history state is thought to lead to increased population genetic differentiation and ultimately reproductive isolation and speciation, but the degree to which it has shaped population- and species-level divergence is poorly understood. Using a large multilocus dataset from hundreds of samples across North America, we identified genetic clusters across the geographic range of the tiger salamander complex. These clusters often contain a mixture of paedomorphic and metamorphic taxa, indicating that geographic isolation has played a larger role in lineage divergence than paedomorphosis in this system. This conclusion is bolstered by geography-informed analyses indicating no effect of life history strategy on population genetic differentiation and by model-based population genetic analyses demonstrating gene flow between adjacent metamorphic and paedomorphic populations. This fine-scale genetic perspective on life history variation establishes a framework for understanding how plasticity, local adaptation, and gene flow contribute to lineage divergence. Many members of the tiger salamander complex are endangered, and the Mexican axolotl is an important model system in regenerative and biomedical research. Our results chart a course for more informed use of these taxa in experimental, ecological, and conservation research.

On the identification of paedomorphic and overwintering larval newts based on cloacal shape: review and guidelines

Paedomorphosis is an alternative process to metamorphosis in which adults retain larval traits at the adult stage. It is frequent in newts and salamanders, where larvae reach sexual maturity without losing their gills. However, in some populations, larvae overwinter in water, while remaining immature. These alternative ontogenetic processes are of particular interest in various research fields, but have different causes and consequences, as only paedomorphosis allows metamorphosis to be bypassed before maturity. It is thus relevant to efficiently identify paedomorphs versus overwintering larvae. In this context, the aim of this article was 3-fold: firstly, to perform a meta-analysis of the identification procedures carried out in the literature; secondly, to determine the effectiveness of body size to make inferences about adulthood by surveying natural newt populations of Lissotriton helveticus and Ichthyosaura alpestris, and thirdly, to propose easy guidelines for an accurate distinction between large larvae and paedomorphs based on an external sexual trait, which is essential for reproduction-the cloaca. More than half of the studies in the literature do not mention the diagnostic criteria used for determining adulthood. The criteria mentioned were the presence of mature gonads (10%), eggs laid (4%), courtship behavior (10%), and external morphological sexual traits (39%) including the cloaca (24%). Body-size thresholds should not be used as a proxy for paedomorphosis, because overwintering larvae can reach a larger size than paedomorphs within the same populations. In contrast, diagnosis based on cloacal external morphology is recommended, as it can be processed by the rapid visual assessment of all caught specimens, thus providing straightforward data at the individual level for both sexes.

High gene flow between alternative morphs and the evolutionary persistence of facultative paedomorphosis

Paedomorphosis and metamorphosis are two major developmental processes that characterize the evolution of complex life cycles in many lineages. Whereas these processes were fixed in some taxa, they remained facultative in others, with alternative phenotypes expressed in the same populations. From a genetic perspective, it is still unknown whether such phenotypes form a single population or whether they show some patterns of isolation in syntopy. This has deep implications for understanding the evolution of the phenotypes, i.e. towards their persistence or their fixation and speciation. Newts and salamanders are excellent models to test this hypothesis because they exhibit both developmental processes in their populations: the aquatic paedomorphs retain gills, whereas the metamorphs are able to colonize land. Using microsatellite data of coexisting paedomorphic and metamorphic palmate newts (Lissotriton helveticus), we found that they formed a panmictic population, which evidences sexual compatibility between the two phenotypes. The high gene flow could be understood as an adaptation to unstable habitats in which phenotypic plasticity is favored over the fixation of developmental alternatives. This makes then possible the persistence of a polyphenism: only metamorphosis could be maintained in case of occasional drying whereas paedomorphosis could offer specific advantages in organisms remaining in water.

Expression of sexual ornaments in a polymorphic species: phenotypic variation in response to environmental risk

Secondary sexual traits may evolve under the antagonistic context of sexual and natural selection. In some polymorphic species, these traits are only expressed during the breeding period and are differently expressed in alternative phenotypes. However, it is unknown whether such phenotypes exhibit phenotypic plasticity of seasonal ornamentations in response to environmental pressures such as in the presence of fish (predation risk). This is an important question to understand the evolution of polyphenisms. We used facultative paedomorphosis in newts as a model system because it involves the coexistence of paedomorphs that retain gills in the adult stage with metamorphs that have undergone metamorphosis, but also because newts exhibit seasonal sexual traits. Our aim was therefore to determine the influence of fish on the development of seasonal ornamentation in the two phenotypes of the palmate newt (Lissotriton helveticus). During the entire newt breeding period, we assessed the importance of phenotype and fish presence with an information-theoretic approach. Our results showed that paedomorphs presented much less developed ornamentation than metamorphs and those ornamentations varied over time. Fish inhibited the development of sexual traits but differently between phenotypes: in contrast to metamorphs, paedomorphs lack the phenotypic plasticity of sexual traits to environmental risk. This study points out that internal and external parameters act in complex ways in the expression of seasonal sexual ornamentations and that similar environmental pressure can induce a contrasted evolution in alternative phenotypes.

Sex differences in ventral side colouration of Alpine newts

Sexual selection based on visual stimuli was recently studied in several amphibian species with permanent or temporary dichromatism. The Alpine newt (Ichthyosaura alpestris) is a Caudate species with prominent sexual dichromatism during the breeding period. We focused on the intersexual differences in the orange, carotenoid-base ventral colouration of this widespread European species. We used an image analysis approach to compare the content of the red colour and saturation of the belly in 80 male and 62 female aquatic adult newts captured during spring migration in two localities in the Czech Republic. Both studied colour parameters of the ventral side of the Alpine newt are connected with sex. Males have significantly higher values of saturation on both localities, but the relationship with red content was not so clear. Individual characteristics (body condition, body length) affect colour variables of males and females similarly. Effect of body condition on colour variables was not demonstrated. Therefore we presume that the pronounced colouration of males is a cue facilitating detection, localisation or interspecies identification, rather than a direct component of male quality as assessed by females.

Introduced goldfish affect amphibians through inhibition of sexual behaviour in risky habitats: an experimental approach

The introduction of alien species is one of the major causes of current and global biodiversity loss. The introduction of fish can be a particular threat to native amphibian populations, which are declining worldwide. One way for amphibians to persist in such altered environments is to adopt anti-predator strategies especially at the behavioural level. However, although it has been shown that avoidance behaviour may decrease the probability of being detected by a potential predator, little is known on the consequences on sexual behaviour. In this study, we tested the hypothesis that adult Alpine newts (Ichthyosaura alpestris) use shelters more often and exhibit less sexual activity in the presence of goldfish (Carassius auratus) and that they reduce sexual activity more in risky micro-habitats than in safe environments. To this end, we assessed behavioural patterns of adult newts in a replicated laboratory design. Goldfish were present in direct contact with newts in half of the tanks. Consistently throughout the study period, significantly more newts used shelter in the presence of fish than in their absence. Newts also significantly decreased their sexual activity level overall, but specially outside the shelter when they were in direct contact with fish. These results show that fish presence can affect newts in complex ways, such as through inhibition of their reproduction. Our work highlights that integrating behaviour in conservation studies is essential to understanding the patterns of coexistence and exclusion between introduced fish and amphibians.

Habitat adaptation rather than genetic distance correlates with female preference in fire salamanders (Salamandra salamandra)

BACKGROUND

Although some mechanisms of habitat adaptation of conspecific populations have been recently elucidated, the evolution of female preference has rarely been addressed as a force driving habitat adaptation in natural settings. Habitat adaptation of fire salamanders (Salamandra salamandra), as found in Middle Europe (Germany), can be framed in an explicit phylogeographic framework that allows for the evolution of habitat adaptation between distinct populations to be traced. Typically, females of S. salamandra only deposit their larvae in small permanent streams. However, some populations of the western post-glacial recolonization lineage use small temporary ponds as larval habitats. Pond larvae display several habitat-specific adaptations that are absent in stream-adapted larvae. We conducted mate preference tests with females from three distinct German populations in order to determine the influence of habitat adaptation versus neutral genetic distance on female mate choice. Two populations that we tested belong to the western post-glacial recolonization group, but are adapted to either stream or pond habitats. The third population is adapted to streams but represents the eastern recolonization lineage.

RESULTS

Despite large genetic distances with FST values around 0.5, the stream-adapted females preferred males from the same habitat type regardless of genetic distance. Conversely, pond-adapted females did not prefer males from their own population when compared to stream-adapted individuals of either lineage.

CONCLUSION

A comparative analysis of our data showed that habitat adaptation rather than neutral genetic distance correlates with female preference in these salamanders, and that habitat-dependent female preference of a specific pond-reproducing population may have been lost during adaptation to the novel environmental conditions of ponds.

Recent divergence with gene flow in Tennessee cave salamanders (Plethodontidae: Gyrinophilus) inferred from gene genealogies

Cave organisms occupy a special place in evolutionary biology because convergent morphologies of many species demonstrate repeatability in evolution even as they obscure phylogenetic relationships. The origin of specialized cave-dwelling species also raises the issue of the relative importance of isolation vs. natural selection in speciation. Two alternative hypotheses describe the origin of subterranean species. The 'climate-relict' model proposes allopatric speciation after populations of cold-adapted species become stranded in caves due to climate change. The 'adaptive-shift' model proposes parapatric speciation driven by divergent selection between subterranean and surface habitats. Our study of the Tennessee cave salamander complex shows that the three nominal forms (Gyrinophilus palleucus palleucus, G. p. necturoides, and G. gulolineatus) arose recently and are genealogically nested within the epigean (surface-dwelling) species, G. porphyriticus. Short branch lengths and discordant gene trees were consistent with a complex history involving gene flow between diverging forms. Results of coalescent-based analysis of the distribution of haplotypes among groups reject the allopatric speciation model and support continuous or recurrent genetic exchange during divergence. These results strongly favour the hypothesis that Tennessee cave salamanders originated from spring salamanders via divergence with gene flow.

Paedomorphosis in Ambystoma talpoideum: effects of initial body size variation and density

Facultative paedomorphosis is the ability of a salamander to either metamorphose into a terrestrial, metamorphic adult or retain a larval morphology to become a sexually mature paedomorphic adult. It has been hypothesized that density and initial body size variation within populations are instrumental in cueing metamorphosis or paedomorphosis in salamanders, yet few studies have adequately tested these hypotheses in long-term experiments. Beginning in the spring of 2004, 36 experimental ponds were used to manipulate three body size variation levels (low, medium, high) and two density levels (low, high) of Ambystoma talpoideum larvae. Larvae were individually marked using visible implant elastomers and collected every 2 weeks in order to measure snout-vent length and mass. Bi-nightly sampling was used to collect new metamorphs as they appeared. Analysis revealed significant effects of density, size variation and morph on body size of individuals during the summer. Individuals that metamorphosed during the fall and following spring were significantly larger as larvae than those becoming paedomorphic across all treatments. These results support the Best-of-a-Bad-Lot hypothesis, which proposes that the largest larvae metamorphose in order to escape unfavorable aquatic habitats. Large larvae may metamorphose to leave aquatic habitats, regardless of treatment, due to the colder climate and lower productivity found in Kentucky, which is in the northern-most part of A. talpoideum's range. By maintaining a long-term experiment, we have provided evidence for the transition of both larvae and paedomorphs into metamorphs during fall and spring metamorphosis events. Furthermore, the production of similar morphs under different environmental conditions observed in this research suggests that the ecological mechanisms maintaining polyphenisms may be more diverse that first suspected.

Streambed microstructure predicts evolution of development and life history mode in the plethodontid salamander Eurycea tynerensis

Background

Habitat variation strongly influences the evolution of developmentally flexible traits, and may drive speciation and diversification. The plethodontid salamander Eurycea tynerensis is endemic to the geologically diverse Ozark Plateau of south-central North America, and comprises both strictly aquatic paedomorphic populations (achieving reproductive maturity while remaining in the larval form) and more terrestrial metamorphic populations. The switch between developmental modes has occurred many times, but populations typically exhibit a single life history mode. This unique system offers an opportunity to study the specific ecological circumstances under which alternate developmental and life history modes evolve. We use phylogenetic independent contrasts to test for relationships between a key microhabitat feature (streambed sediment) and this major life history polymorphism.

Results

We find streambed microstructure (sediment particle size, type and degree of sorting) to be highly correlated with life-history mode. Eurycea tynerensis is paedomorphic in streams containing large chert gravel, but metamorphoses in nearby streams containing poorly sorted, clastic material such as sandstone or siltstone.

Conclusion

Deposits of large chert gravel create loosely associated streambeds, which provide access to subsurface water during dry summer months. Conversely, streambeds composed of more densely packed sandstone and siltstone sediments leave no subterranean refuge when surface water dries, presumably necessitating metamorphosis and use of terrestrial habitats. This represents a clear example of the relationship between microhabitat structure and evolution of a major developmental and life history trait, and has broad implications for the role of localized ecological conditions on larger-scale evolutionary processes.

Evolutionary ecology of facultative paedomorphosis in newts and salamanders

Facultative paedomorphosis is an environmentally induced polymorphism that results in the coexistence of mature, gilled, and fully aquatic paedomorphic adults and transformed, terrestrial, metamorphic adults in the same population. This polymorphism has been of interest to scientists for decades because it occurs in a large number of caudate amphibian taxa as well as in a large diversity of habitats. Numerous experimental and observational studies have been conducted to explain the proximate and ultimate factors affecting these heterochronic variants in natural populations. The production of each alternative phenotype is based on a genotypexenvironment interaction and research suggests that differences in the environment can produce paedomorphs through several ontogenetic pathways. No single advantage accounts for the maintenance of this polymorphism. Rather, the interplay of different costs and benefits explains the success of the polyphenism across variable environments. Facultative paedomorphosis allows individuals to cope with habitat variation, to take advantage of environmental heterogeneity in the presence of open niches, and to increase their fitness. This process is expected to constitute a first step towards speciation events, and is also an example of biodiversity at the intraspecific level. The facultative paedomorphosis system is thus ripe for future studies encompassing ecology, evolution, behaviour, endocrinology, physiology, and conservation biology. Few other systems have been broad enough to provide varied research opportunities on topics as diverse as phenotypic plasticity, speciation, mating behaviour, and hormonal regulation of morphology. Further research on facultative paedomorphosis will provide needed insight into these and other important questions facing biologists.