Two transects reveal remarkable variation in gene flow on opposite ends of a European toad hybrid zone.

Speciation entails a reduction in gene flow between lineages. The rates at which genomic regions become isolated varies across space and time. Barrier markers are linked to putative genes involved in (processes of) reproductive isolation, and, when observed over two transects, indicate species-wide processes. In contrast, transect-specific putative barrier markers suggest local processes. We studied two widely separated transects along the 900 km hybrid zone between Bufo bufo and B. spinosus, in northern and southern France, for ~1200 RADseq markers. We used genomic and geographic cline analyses to identify barrier markers based on their restricted introgression, and found that some markers are transect-specific, while others are shared between transects. Twenty-six barrier markers were shared across both transects, of which some are clustered in the same chromosomal region, suggesting that their associated genes are involved in reduced gene flow across the entire hybrid zone. Transect-specific barrier markers were twice as numerous in the southern than in the northern transect, suggesting that the overall barrier effect is weaker in northern France. We hypothesize that this is consistent with a longer period of secondary contact in southern France. The smaller number of introgressed genes in the northern transect shows considerably more gene flow towards the southern (B. spinosus) than the northern species (B. bufo). We hypothesize that hybrid zone movement in northern France and hybrid zone stability in southern France explain this pattern. The Bufo hybrid zone provides an excellent opportunity to separate a general barrier effect from localized gene flow-reducing conditions.

Toxic Relationships and Arms-Race Coevolution Revisited.

Toxin evolution in animals is one of the most fascinating and complex subjects of scientific inquiry today. Gaining an understanding of toxins poses a multifaceted challenge given the diverse modes of acquisition, evolutionary adaptations, and abiotic components that affect toxin phenotypes. Here, we highlight some of the main genetic and ecological factors that influence toxin evolution and discuss the role of antagonistic interactions and coevolutionary dynamics in shaping the direction and extent of toxicity and resistance in animals. We focus on toxic Pacific newts (family Salamandridae, genus Taricha) as a system to investigate and better evaluate the widely distributed toxin they possess, tetrodotoxin (TTX), and the hypothesized model of arms-race coevolution with snake predators that is used to explain phenotypic patterns of newt toxicity. Finally, we propose an alternative coevolutionary model that incorporates TTX-producing bacteria and draws from an elicitor-receptor concept to explain TTX evolution and ecology.

Phylogenomics of the adaptive radiation of Triturus newts supports gradual ecological niche expansion towards an incrementally aquatic lifestyle.

Newts of the genus Triturus (marbled and crested newts) exhibit substantial variation in the number of trunk vertebrae (NTV) and a higher NTV corresponds to a longer annual aquatic period. Because the Triturus phylogeny has thwarted resolution to date, the evolutionary history of NTV, annual aquatic period, and their potential coevolution has remained unclear. To resolve the phylogeny of Triturus, we generated a c. 6000 transcriptome-derived marker data set using a custom target enrichment probe set, and conducted phylogenetic analyses using: (1) data concatenation with RAxML, (2) gene-tree summary with ASTRAL, and (3) species-tree estimation with SNAPP. All analyses produce the same, highly supported topology, despite cladogenesis having occurred over a short timeframe, resulting in short internal branch lengths. Our new phylogenetic hypothesis is consistent with the minimal number of inferred changes in NTV count necessary to explain the diversity in NTV observed today. Although a causal relationship between NTV, body form, and aquatic ecology has yet to be experimentally established, our phylogeny indicates that these features have evolved together, and suggest that they may underlie the adaptive radiation that characterizes Triturus.

Thyroid hormone responsive QTL and the evolution of paedomorphic salamanders.

The transformation of ancestral phenotypes into novel traits is poorly understood for many examples of evolutionary novelty. Ancestrally, salamanders have a biphasic life cycle with an aquatic larval stage, a brief and pronounced metamorphosis, followed by a terrestrial adult stage. Repeatedly during evolution, metamorphic timing has been delayed to exploit growth-permissive environments, resulting in paedomorphic salamanders that retain larval traits as adults. We used thyroid hormone (TH) to rescue metamorphic phenotypes in paedomorphic salamanders and then identified quantitative trait loci (QTL) for life history traits that are associated with amphibian life cycle evolution: metamorphic timing and adult body size. We demonstrate that paedomorphic tiger salamanders (Ambystoma tigrinum complex) carry alleles at three moderate effect QTL (met1-3) that vary in responsiveness to TH and additively affect metamorphic timing. Salamanders that delay metamorphosis attain significantly larger body sizes as adults and met2 explains a significant portion of this variation. Thus, substitution of alleles at TH-responsive loci suggests an adaptive pleiotropic basis for two key life-history traits in amphibians: body size and metamorphic timing. Our study demonstrates a likely pathway for the evolution of novel paedomorphic species from metamorphic ancestors via selection of TH-response alleles that delay metamorphic timing and increase adult body size.

Candidate gene analysis of metamorphic timing in ambystomatid salamanders.

Although much is known about the ecological significance of metamorphosis and metamorphic timing, few studies have examined the underlying genetic architecture of these traits, and no study has attempted to associate phenotypic variation to molecular variation in specific genes. Here we report on a candidate gene approach (CGA) to test specific loci for a statistical contribution to variation in metamorphic timing. Three segregating populations (SP1, SP2 and SP3) were constructed utilizing three species of paedomorphic Mexican ambystomatid salamander, including the axolotl, Ambystoma mexicanum. We used these replicated species to test the hypothesis that inheritance of alternate genotypes at two thyroid hormone receptor loci (TRalpha, TRbeta) affects metamorphic timing in ambystomatid salamanders. A significant TRalpha*SP effect indicated that variation in metamorphic timing may be influenced by TRalpha genotype, however, the effect was not a simple one, as both the magnitude and direction of the phenotypic effect depended upon the genetic background. These are the first data to implicate a specific gene in contributing to variation in metamorphic timing. In general, candidate gene approaches can be extended to any number of loci and to any organism where simple genetic crosses can be performed to create segregating populations. The approach is thus of particular value in ecological studies where target genes have been identified but the study organism is not one of the few well-characterized model systems that dominate genetic research.

Evolutionary genetics of metamorphic failure using wild-caught vs. laboratory axolotls (Ambystoma mexicanum).

In many organisms metamorphosis allows for an ecologically important habitat-shift from water to land. However, in some salamanders an adaptive life cycle mode has evolved that is characterized by metamorphic failure (paedomorphosis); these species remain in the aquatic habitat throughout the life cycle. Perhaps the most famous example of metamorphic failure is the Mexican axolotl (Ambystoma mexicanum), which has become a focal species for developmental biology since it was introduced into laboratory culture in the 1800s. Our previous genetic linkage mapping analysis, using an interspecific crossing design, demonstrated that a major gene effect underlies the expression of metamorphic failure in laboratory stocks of the Mexican axolotl. Here, we repeated this experiment using A. mexicanum that were sampled directly from their natural habitat at Lake Xochimilco, Mexico. We found no significant association between the major gene and metamorphic failure when wild-caught axolotls were used in the experimental design, although there is evidence of a smaller genetic effect. Thus, there appears to be genetic variation among Mexican axolotls (and possibly A. tigrinum tigrinum) at loci that contribute to metamorphic failure. This result suggests a role for more than one mutation and possibly artificial selection in the evolution of the major gene effect in the laboratory Mexican axolotl.

Candidate gene analysis of thyroid hormone receptors in metamorphosing vs. nonmetamorphosing salamanders.

We used two different experimental approaches to test the hypothesis that thyroid hormone receptor (TR) variation is associated with alternate life cycles modes in ambystomatid salamanders. In the first experiment, the inheritance of TRalpha and TRbeta genotypes was determined for metamorphic and non metamorphic offspring from backcrosses between Ambystoma mexicanum (an obligate metamorphic-failure species) and metamorphic F1 hybrids (A. mexicanum x A. tigrinum tigrinum). The segregation of TR genotype was independent of the expression of life cycle mode phenotype, and neither TR locus was linked to DNA markers that flank a major-effect locus for life cycle mode. In the second experiment, a portion of the ligand-binding domain of TRalpha and TRbeta was cloned and sequenced for DNA samples from 14 different ambystomatid salamander populations, including obligate metamorphic, facultative metamorphic, and obligate metamorphic-failure taxa. Nucleotide sequence variation was found for both TRalpha and TRbeta, with several nonsynonomous substitutions that presumably code for nonconservative amino acid replacements. However, no general relationship was found between TR allelic variation and life cycle mode among populations or species. These data do not implicate TRs as candidate loci involved in the current maintenance or past evolution of alternate life cycle modes in members of the tiger salamander complex.

The genetics of amphibian declines: population substructure and molecular differentiation in the yosemite toad, Bufo canorus (Anura, bufonidae) based on single-strand conformation polymorphism analysis (SSCP) and mitochondrial DNA sequence data.

We present a comprehensive survey of genetic variation across the range of the narrowly distributed endemic Yosemite toad Bufo canorus, a declining amphibian restricted to the Sierra Nevada of California. Based on 322 bp of mitochondrial cytochrome b sequence data, we found limited support for the monophyly of B. canorus and its closely related congener B. exsul to the exclusion of the widespread western toad B. boreas. However, B. exsul was always phylogenetically nested within B. canorus, suggesting that the latter may not be monophyletic. SSCP (single-strand conformation polymorphism) analysis of 372 individual B. canorus from 28 localities in Yosemite and Kings Canyon National Parks revealed no shared haplotypes among these two regions and lead us to interpret these two parks as distinct management units for B. canorus. Within Yosemite, we found significant genetic substructure both at the level of major drainages and among breeding ponds. Kings Canyon samples show a different pattern, with substantial variation among breeding sites, but no substructure among drainages. Across the range of B. canorus as well as among Yosemite ponds, we found an isolation-by-distance pattern suggestive of a stepping stone model of migration. However, in Kings Canyon we found no hint of such a pattern, suggesting that movement patterns of toads may be quite different in these nearby parklands. Our data imply that management for B. canorus should focus at the individual pond level, and effective management may necessitate reintroductions if local extirpations occur. A brief review of other pond-breeding anurans suggests that highly structured populations are often the case, and thus that our results for B. canorus may be general for other species of frogs and toads.

The role of natural history collections in documenting species declines.

Efforts to document the decline of extant populations require a historical record of previous occurrences. Natural history museums contain such information for most regions of the world, at least at a coarse spatial scale. Museum collections have been successfully used to analyse declines in a wide range of plants and animals, at spatial scales ranging from single localities to large biotic and political regions. Natural history museum collections, when properly analysed, can be an invaluable tool in documenting changes in biodiversity during the past century.

Adaptive evolution via a major gene effect: paedomorphosis in the Mexican axolotl.

Although adaptive evolution is thought to depend primarily on mutations of small effect, major gene effects may underlie many of the important differences observed among species in nature. The Mexican axolotl (Ambystoma mexicanum) has a derived mode of development that is characterized by metamorphic failure (paedomorphosis), an adaptation for an entirely aquatic life cycle. By using an interspecific crossing design and genetic linkage analysis, a major quantitative trait locus for expression of metamorphosis was identified in a local map of amplified fragment length polymorphisms. These data are consistent with a major gene hypothesis for the evolution of paedomorphosis in A. mexicanum.

Large, rapidly evolving intergenic spacers in the mitochondrial DNA of the salamander family Ambystomatidae (Amphibia: Caudata).

We report the presence, in the mitochondrial DNA (mtDNA) of all of the sexual species of the salamander family Ambystomatidae, of a shared 240-bp intergenic spacer between tRNAThr and tRNAPro. We place the intergenic spacer in context by presenting the sequence of 1,746 bp of mtDNA from Ambystoma tigrinum tigrinum, describe the nucleotide composition of the intergenic spacer in all of the species of Ambystomatidae, and compare it to other coding and noncoding regions of Ambystoma and several other vertebrate mtDNAs. The nucleotide substitution rate of the intergenic spacer is approximately three times faster than the substitution rate of the control region, as shown by comparisons among six Ambystoma macrodactylum sequences and eight members of the Ambystoma tigrinum complex. We also found additional inserts within the intergenic spacers of five species that varied from 87-444 bp in length. The presence of the intergenic spacer in all sexual species of Ambystomatidae suggests that it arose at least 20 MYA and has been a stable component of the ambystomatid mtDNA ever since. As such, it represents one of the few examples of a large and persistent intergenic spacer in the mtDNA of any vertebrate clade.

Tests of turtle phylogeny: molecular, morphological, and paleontological approaches.

We present phylogenetic analyses of both molecular and morphological data for the 23 major lineages of living turtles and seven key fossil taxa. Nearly 1 kilobase of cytochrome b sequence, 325 base pairs of 12S ribosomal DNA, and 115 morphological characters contained similar phylogenetic information, although each provided unique information on different nodes of chelonian history. A character-based combinability test (implemented in PAUP*) and a non-parametric test of taxonomic congruence indicated no strong evidence for heterogeneity among data sets, and we used a combined approach to estimate a final phylogeny of the major lineages of living turtles. This approach resulted in a very well-resolved tree, with only a few of the deep branches within the Cryptodira left as an unresolved polytomy. The addition of six relatively complete fossils chosen to help resolve this basal polytomy provided little added resolution to the tree and resulted in a sharp decline in bootstrap proportions for nodes near the fossils. Branch-length analysis and independent dates from the fossil record suggest that these unresolved nodes may represent a rapid radiation of the major cryptodiran lineages 90-120 million years ago.

What insights into the developmental traits of urodeles does the study of interspecific hybrids provide?

Natural and artificial hybrids represent an important source of material for developmental and evolutionary studies of urodeles. We review the available literature on hybrid salamanders, emphasizing the unique developmental insights that these organisms provide. Of particular interest is the application of new molecular tools to identify DNA markers for traditional characters in developmental research, and we discuss our own results using Bulk Segregant Analysis to identify RAPD markers for the white phenotype in the axolotl. We pay particular attention to the inferences that can be drawn from the many disparate crosses between ambystomatid salamanders that vary in their metamorphic response. These crossing experiments suggest that 1) metamorphosis is dominant to paedomorphosis, 2) that different ambystomatids use different genetic mechanisms to block metamorphosis and become sexually mature, larval paedomorphs, and 3) metamorphosis may be controlled by a few genetic loci. As increasingly sophisticated molecular approaches are applied to these and other hybrid crossing schemes, it should be possible to understand the mechanistic basis of a wide variety of developmental characters that differentiate urodele species.

Functional morphology of the feeding mechanism in aquatic ambystomatid salamanders.

This study addresses four questions in vertebrate functional morphology through a study of aquatic prey capture in ambystomatid salamanders: How does the feeding mechanism of aquatic salamanders function as a biomechanical system? How similar are the biomechanics of suction feeding in aquatic salamanders and ray-finned fishes? What quantitative relationship does information extracted from electromyograms of striated muscles bear to kinematic patterns and animal performance? and What are the major structural and functional patterns in the evolution of the lower vertebrate skull? During prey capture, larval ambystomatid salamanders display a kinematic pattern similar to that of other lower vertebrates, with peak gape occurring prior to both peak hyoid depression and peak cranial elevation. The depressor mandibulae, rectus cervicis, epaxialis, hypaxialis, and branchiohyoideus muscles are all active for 40-60 msec during the strike and overlap considerably in activity. The two divisions of the adductor mandibulae are active in a continuous burst for 110-130 msec, and the intermandibularis posterior and coracomandibularis are active in a double burst pattern. The antagonistic depressor mandibulae and adductor mandibulae internus become active within 0.2 msec of each other, but the two muscles show very different spike and amplitude patterns during their respective activity periods. Coefficients of variation for kinematic and most electromyographic recordings reach a minimum within a 10 msec time period, just after the mouth starts to open. Pressure within the buccal cavity during the strike reaches a minimum of -25 mmHg, and minimum pressure occurs synchronously with maximum gill bar adduction. The gill bars (bearing gill rakers that interlock with rakers of adjacent arches) clearly function as a resistance within the oral cavity and restrict posterior water influx during mouth opening, creating a unidirectional flow during feeding. Durations of electromyographic activity alone are poor predictors of kinematic patterns. Analyses of spike amplitude explain an additional fraction of the variance in jaw kinematics, whereas the product of spike number and amplitude is the best statistical predictor of kinematic response variables. Larval ambystomatid salamanders retain the two primitive biomechanical systems for opening and closing the mouth present in nontetrapod vertebrates: elevation of the head by the epaxialis and depression of the mandible by the hyoid apparatus.

Aquatic prey capture in ambystomatid salamanders: patterns of variation in muscle activity.

Functional morphologists commonly study feeding behavior in vertebrates by recording electrical activity from head muscles during unrestrained prey capture. Rarely are experiments designed to permit a partitioning variation in muscle electrical activity patterns. Analysis of muscle activity during aquatic prey capture in two morphologically distinct species of salamanders, Ambystoma dumerilii and A. mexicanum, is conducted to assess variation at four levels: between species, among individuals within species, among experiments conducted on different days, and among feedings. The results show that 1) mean correlations among the 11 electromyographic variables measured for each feeding are low and vary considerably among individuals, 2) many of the variables show significant differences among experimental days, 3) only one variable, the difference in timing between the depressor mandibulae and sternohyoideus muscles, showed significant variation between species, and 4) seven of the 11 variables showed significant variation among individuals within species. Overall, the variation between feedings (trials) was high, and there was some variation between days on which the experiments were conducted. Neither electrode position within the muscle nor satiation contributed to the high trial variance. The results suggest that functional analyses of feeding behavior should include an assessment of variation due to individuals, days, and trials, because the amount of variation at these levels may render differences between species nonsignificant.