Evolution Of Salamanders Research Articles

The Effect of Thermally Robust Ballistic Mechanisms on Climatic Niche in Salamanders.

SynopsisMany organismal functions are temperature-dependent due to the contractile properties of muscle. Spring-based mechanisms offer a thermally robust alternative to temperature-sensitive muscular movements and may correspondingly expand a species’ climatic niche by partially decoupling the relationship between temperature and performance. Using the ballistic tongues of salamanders as a case study, we explore whether the thermal robustness of elastic feeding mechanisms increases climatic niche breadth, expands geographic range size, and alters the dynamics of niche evolution. Combining phylogenetic comparative methods with global climate data, we find that the feeding mechanism imparts no discernable signal on either climatic niche properties or the evolutionary dynamics of most climatic niche parameters. Although biomechanical innovation in feeding influences many features of whole-organism performance, it does not appear to drive macro-climatic niche evolution in salamanders. We recommend that future work incorporate micro-scale environmental data to better capture the conditions that salamanders experience, and we discuss a few outstanding questions in this regard. Overall, this study lays the groundwork for an investigation into the evolutionary relationships between climatic niche and biomechanical traits in ectotherms.

Middle Jurassic fossils document an early stage in salamander evolution

Salamanders are an important group of living amphibians and model organisms for understanding locomotion, development, regeneration, feeding, and toxicity in tetrapods. However, their origin and early radiation remain poorly understood, with early fossil stem-salamanders so far represented by larval or incompletely known taxa. This poor record also limits understanding of the origin of Lissamphibia (i.e., frogs, salamanders, and caecilians). We report fossils from the Middle Jurassic of Scotland representing almost the entire skeleton of the enigmatic stem-salamander Marmorerpeton. We use computed tomography to visualize high-resolution three-dimensional anatomy, describing morphologies that were poorly characterized in early salamanders, including the braincase, scapulocoracoid, and lower jaw. We use these data in the context of a phylogenetic analysis intended to resolve the relationships of early and stem-salamanders, including representation of important outgroups alongside data from high-resolution imaging of extant species. Marmorerpeton is united with Karaurus, Kokartus, and others from the Middle Jurassic-Lower Cretaceous of Asia, providing evidence for an early radiation of robustly built neotenous stem-salamanders. These taxa display morphological specializations similar to the extant cryptobranchid "giant" salamanders. Our analysis also demonstrates stem-group affinities for a larger sample of Jurassic species than previously recognized, highlighting an unappreciated diversity of stem-salamanders and cautioning against the use of single species (e.g., Karaurus) as exemplars for stem-salamander anatomy. These phylogenetic findings, combined with knowledge of the near-complete skeletal anatomy of Mamorerpeton, advance our understanding of evolutionary changes on the salamander stem-lineage and provide important data on early salamanders and the origins of Batrachia and Lissamphibia.

Recurrent Co-Option and Recombination of Cytokine and Three Finger Proteins in Multiple Reproductive Tissues Throughout Salamander Evolution.

Reproductive proteins evolve at unparalleled rates, resulting in tremendous diversity of both molecular composition and biochemical function between gametes of different taxonomic clades. To date, the proteomic composition of amphibian gametes is largely a molecular mystery, particularly for Urodeles (salamanders and newts) for which few genomic-scale resources exist. In this study, we provide the first detailed molecular characterization of gametes from two salamander species (Plethodon shermani and Desmognathus ocoee) that are models of reproductive behavior. Long-read PacBio transcriptome sequencing of testis and ovary of both species revealed sex-specific expression of many genes common to vertebrate gametes, including a similar expression profile to the egg coat genes of Xenopus oocytes. In contrast to broad conservation of oocyte genes, major testis transcripts included paralogs of salamander-specific courtship pheromones (PRF, PMF, and SPF) that were confirmed as major sperm proteins by mass spectrometry proteomics. Sperm-specific paralogs of PMF and SPF are likely the most abundant secreted proteins in P. shermani and D. ocoee, respectively. In contrast, sperm PRF lacks a signal peptide and may be expressed in cytoplasm. PRF pheromone genes evolved independently multiple times by repeated gene duplication of sperm PRF genes with signal peptides recovered through recombination with PMF genes. Phylogenetic analysis of courtship pheromones and their sperm paralogs support that each protein family evolved for these two reproductive contexts at distinct evolutionary time points between 17 and 360 million years ago. Our combined phylogenetic, transcriptomic and proteomic analyses of plethodontid reproductive tissues support that the recurrent co-option and recombination of TFPs and cytokine-like proteins have been a novel driving force throughout salamander evolution and reproduction.

Metamorphosis shapes cranial diversity and rate of evolution in salamanders.

Metamorphosis is widespread across the animal kingdom and induces fundamental changes in the morphology, habitat and resources used by an organism during its lifetime. Metamorphic species are likely to experience more dynamic selective pressures through ontogeny compared with species with single-phase life cycles, which may drive divergent evolutionary dynamics. Here, we reconstruct the cranial evolution of the salamander using geometric morphometric data from 148 species spanning the order's full phylogenetic, developmental and ecological diversity. We demonstrate that life cycle influences cranial shape diversity and rate of evolution. Shifts in the rate of cranial evolution are consistently associated with transitions from biphasic to either direct-developing or paedomorphic life cycle strategies. Direct-developers exhibit the slowest rates of evolution and the lowest disparity, and paedomorphic species the highest. Species undergoing complete metamorphosis (biphasic and direct-developing) exhibit greater cranial modularity (evolutionary independence among regions) than do paedomorphic species, which undergo differential metamorphosis. Biphasic and direct-developing species also display elevated disparity relative to the evolutionary rate for bones associated with feeding, whereas this is not the case for paedomorphic species. Metamorphosis has profoundly influenced salamander cranial evolution, requiring greater autonomy of cranial elements and facilitating the rapid evolution of regions that are remodelled through ontogeny. Rather than compounding functional constraints on variation, metamorphosis seems to have promoted the morphological evolution of salamanders over 180 million years, which may explain the ubiquity of this complex life cycle strategy across disparate organisms.

Sixty-Five Million Years of Change in Temperature and Topography Explain Evolutionary History in Eastern North American Plethodontid Salamanders.

For many taxa and systems, species richness peaks at midelevations. One potential explanation for this pattern is that large-scale changes in climate and geography have, over evolutionary time, selected for traits that are favored under conditions found in contemporary midelevation regions. To test this hypothesis, we use records of historical temperature and topographic changes over the past 65 Myr to construct a general simulation model of plethodontid salamander evolution in eastern North America. We then explore possible mechanisms constraining species to midelevation bands by using the model to predict plethodontid evolutionary history and contemporary geographic distributions. Our results show that models that incorporate both temperature and topographic changes are better able to predict these patterns, suggesting that both processes may have played an important role in driving plethodontid evolution in the region. Additionally, our model (whose annotated source code is included as a supplement) represents a proof of concept to encourage future work that takes advantage of recent advances in computing power to combine models of ecology, evolution, and earth history to better explain the abundance and distribution of species over time.

Courtship Pheromone Use in a Model Urodele, the Mexican Axolotl (Ambystoma mexicanum).

Sex pheromones have been shown to constitute a crucial aspect of salamander reproduction. Until now, courtship pheromones of Salamandridae and Plethodontidae have been intensively studied, but information on chemical communication in other urodelan families is essentially lacking. The axolotl (Ambystoma mexicanum, Ambystomatidae) has a courtship display that suggests a key role for chemical communication in the orchestration of its sexual behavior, but no sex pheromones have yet been characterized from this species. Here we combined whole transcriptome analyses of the male cloaca with proteomic analyses of water in which axolotls were allowed to court to show that male axolotls secrete multiple ca. 20 kDa glycosylated sodefrin precursor-like factor (SPF) proteins during courtship. In combination with phylogenetic analyses, our data show that the male cloaca essentially secretes a courtship-specific clade of SPF proteins that is orthologous to salamandrid courtship pheromones. In addition, we identified an SPF protein for which no orthologs have been described from other salamanders so far. Overall, our study advocates a central role for SPF proteins during the courtship display of axolotls and adds knowledge on pheromone use in a previously unexplored deep evolutionary branch of salamander evolution.

Origin and diversification of a salamander sex pheromone system.

Sex pheromones form an important facet of reproductive strategies in many organisms throughout the Animal Kingdom. One of the oldest known sex pheromones in vertebrates are proteins of the Sodefrin Precursor-like Factor (SPF) system, which already had a courtship function in early salamanders. The subsequent evolution of salamanders is characterized by a diversification in courtship and reproduction, but little is known on how the SPF pheromone system diversified in relation to changing courtship strategies. Here, we combined transcriptomic, genomic, and phylogenetic analyses to investigate the evolution of the SPF pheromone system in nine salamandrid species with distinct courtship displays. First, we show that SPF originated from vertebrate three-finger proteins and diversified through multiple gene duplications in salamanders, while remaining a single copy in frogs. Next, we demonstrate that tail-fanning newts have retained a high phylogenetic diversity of SPFs, whereas loss of tail-fanning has been associated with a reduced importance or loss of SPF expression in the cloacal region. Finally, we show that the attractant decapeptide sodefrin is cleaved from larger SPF precursors that originated by a 62 bp insertion and consequent frameshift in an ancestral Cynops lineage. This led to the birth of a new decapeptide that rapidly evolved a pheromone function independently from uncleaved proteins.

A relict stem salamander: evidence from the Early Cretaceous of Siberia

The early evolution of salamanders, which are one of the three living groups of lissamphibians, is not well known. Both stem- and crown-group salamanders first appeared in the Middle Jurassic (Bathonian), but subsequently had different evolutionary histories: stem salamanders were thought to have gone extinct in the Late Jurassic, while crown salamanders persist to the present day. Here, I report the discovery of an indeterminate stem salamander in the Lower Cretaceous (Aptian—Albian) Ilek Formation of Western Siberia. This is new evidence that the most basal salamanders survived beyond the Jurassic—Cretaceous boundary and co-existed with crown-group salamanders during approximately the first 40 million years of the known history of salamanders. The recognition of stem salamanders in the Early Cretaceous of Western Siberia adds to the inventory of taxa that suggest this area was a refugium for various groups of vertebrates with Jurassic affinities.

LOW METABOLIC RATES IN SALAMANDERS ARE CORRELATED WITH WEAK SELECTIVE CONSTRAINTS ON MITOCHONDRIAL GENES

Mitochondria are the site for the citric acid cycle and oxidative phosphorylation (OXPHOS), the final steps of ATP synthesis via cellular respiration. Each mitochondrion contains its own genome; in vertebrates, this is a small, circular DNA molecule that encodes 13 subunits of the multiprotein OXPHOS electron transport complexes. Vertebrate lineages vary dramatically in metabolic rates; thus, functional constraints on mitochondrial-encoded proteins likely differ, potentially impacting mitochondrial genome evolution. Here, we examine mitochondrial genome evolution in salamanders, which have the lowest metabolic requirements among tetrapods. We show that salamanders experience weaker purifying selection on protein-coding sequences than do frogs, a comparable amphibian clade with higher metabolic rates. In contrast, we find no evidence for weaker selection against mitochondrial genome expansion in salamanders. Together, these results suggest that different aspects of mitochondrial genome evolution (i.e., nucleotide substitution, accumulation of noncoding sequences) are differently affected by metabolic variation across tetrapod lineages.

LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders.

Among vertebrates, most of the largest genomes are found within the salamanders, a clade of amphibians that includes 613 species. Salamander genome sizes range from ∼14 to ∼120 Gb. Because genome size is correlated with nucleus and cell sizes, as well as other traits, morphological evolution in salamanders has been profoundly affected by genomic gigantism. However, the molecular mechanisms driving genomic expansion in this clade remain largely unknown. Here, we present the first comparative analysis of transposable element (TE) content in salamanders. Using high-throughput sequencing, we generated genomic shotgun data for six species from the Plethodontidae, the largest family of salamanders. We then developed a pipeline to mine TE sequences from shotgun data in taxa with limited genomic resources, such as salamanders. Our summaries of overall TE abundance and diversity for each species demonstrate that TEs make up a substantial portion of salamander genomes, and that all of the major known types of TEs are represented in salamanders. The most abundant TE superfamilies found in the genomes of our six focal species are similar, despite substantial variation in genome size. However, our results demonstrate a major difference between salamanders and other vertebrates: salamander genomes contain much larger amounts of long terminal repeat (LTR) retrotransposons, primarily Ty3/gypsy elements. Thus, the extreme increase in genome size that occurred in salamanders was likely accompanied by a shift in TE landscape. These results suggest that increased proliferation of LTR retrotransposons was a major molecular mechanism contributing to genomic expansion in salamanders.

Salamander evolution across a latitudinal cline in gape‐limited predation risk

General predictions of community dynamics require that insights derived from local habitats can be scaled up to explain phenomena across geographic scales. Across these larger spatial extents, adaptation can play an increasing role in determining the outcome of species interactions. If local adaptation is common, then our ability to generalize measures of species interaction strength across communities will be limited without an additional understanding of the genetic variation underlying interaction traits. In the context of predator–prey interactions, prey individuals commonly are expected to reduce risky foraging behaviors and subsequent growth under predation threat. However, rapid growth into a large body size can defend against gape‐limited predators, creating a tradeoff between increased predation risk due to elevated foraging activity and decreased predation risk due to large size. Here I combine field observations, natural selection experiments, and common garden assays to understand potential adaptations of spotted salamander Ambystoma maculatum larvae to gape‐limited and gape‐unconstrained predators. Field observations and natural selection trials suggested antagonistic selection on prey body size among ponds dominated by gape‐limited predator salamanders A. opacum and gape‐unconstrained beetle larvae Dytiscus. In common garden experiments, prey from sites with high gape‐limited predation risk grew larger than those from other sites, suggesting the evolution of rapid growth into a prey size refuge. Larvae from all sites grew to a large size when exposed to the gape‐limited N. viridescens predator's kairomones. Hence, induced rapid growth into a size refuge may be an adaptive response to gape‐limited predation risk. Results point to an important role for cross‐community generalizations based on functional classifications of predators by their gape constraints and inter‐site genetic variation in prey growth rates and behaviors.

Evolutionary cytogenetics in salamanders

Salamanders (Amphibia: Caudata/Urodela) have been the subject of numerous cytogenetic studies, and data on karyotypes and genome sizes are available for most groups. Salamanders show a more-or-less distinct dichotomy between families with large chromosome numbers and interspecific variation in chromosome number, relative size, and shape (i.e. position of the centromere), and those that exhibit very little variation in these karyological features. This dichotomy is the basis of a major model of karyotype evolution in salamanders involving a kind of 'karyotypic orthoselection'. Salamanders are also characterized by extremely large genomes (in terms of absolute mass of nuclear DNA) and extensive variation in genome size (and overall size of the chromosomes), which transcends variation in chromosome number and shape. The biological significance and evolution of chromosome number and shape within the karyotype is not yet understood, but genome size variation has been found to have strong phenotypic, biogeographic, and phylogenetic correlates that reveal information about the biological significance of this cytogenetic variable. Urodeles also present the advantage of only 10 families and less than 600 species, which facilitates the analysis of patterns within the entire order. The purpose of this review is to present a summary of what is currently known about overall patterns of variation in karyology and genome size in salamanders. These patterns are discussed within an evolutionary context.

A Late Jurassic salamander (Amphibia: Caudata) from the Morrison Formation of North America

Despite some remarkable recent discoveries, the Mesozoic fossil record of salamanders remains limited, particularly for the Jurassic. Here we describe the first articulated salamander skeleton from the Jurassic of Euramerica, recovered from Upper Jurassic deposits of the Morrison Formation, Dinosaur National Monument, USA. The specimen was studied using both conventional methods and high-resolution computed tomography. It shows a combination of primitive and derived character states that distinguish it from all known Mesozoic salamanders and which permit the erection of a new genus and species, Iridotriton hechti. The derived states (including the presence of spinal nerve foramina in the tail) suggest a position on the stem of the Salamandroidea. Together with microvertebrate material from Britain, Portugal, and North America, this specimen confirms the presence of both stem- and crown-group salamanders in Euramerica from the Middle Jurassic (Bathonian) onwards, paralleling their evolution in Central and eastern Asia. This, in turn, provides qualified support for the current vicariance model of salamander evolution whereby basal caudates on an undivided Laurasian plate became separated into two populations by the incursion of the Turgai Sea in the Middle Jurassic, yielding Cryptobranchoidea in Asia and Salamandroidea in Euramerica. (c) 2005 The Linnean Society of London.

Late Jurassic salamanders from northern China.

With ten extant families, salamanders (urodeles) are one of the three major groups of modern amphibians (lissamphibians). Extant salamanders are often used as a model system to assess fundamental issues of developmental, morphological and biogeographical evolution. Unfortunately, our understanding of these issues has been hampered by the paucity of fossil evidence available to assess the early history of the group. Here we report the discovery of an extraordinary sample of salamander fossils, some with rare soft-tissue impressions, from the Upper Jurassic of China. With over 500 articulated specimens, this assemblage documents the morphological diversity of early urodeles and includes larvae and adults of both neotenic and metamorphosed taxa. Phylogenetic analysis confirms that these salamanders are primitive, and reveals that all basal salamander clades have Asian distributions. This is compelling evidence for an Asian origin of Recent salamanders, as well as for an extensive and early radiation of several major lineages. These discoveries show that the evolution of salamanders has involved phylogenetic and ecological diversification around a body plan that has remained fundamentally stable for over 150 million years.

EVOLUTION IN A PAEDOMORPHIC LINEAGE. I. AN ELECTROPHORETIC ANALYSIS OF THE MEXICAN AMBYSTOMATID SALAMANDERS.

Paedomorphosis, or the retention of ancestral juvenile features in descendant adults (Gould, 1977), is one of a general class of heterochronic events which has recently been invoked as a possible mode of evolutionary change. Gould (1977) and Alberch et al. (1979) among others have reiterated the arguments of Goldschmidt (1940) that it is simpler to change morphology through shifts in the timing of established developmental events than by incorporating mutations that may disrupt the developmental status quo. Although a much more thorough understanding of the genetics of such developmental shifts is necessary before arguments on their evolutionary flexibility can be evaluated, paedomorphosis does seem to be an important mode of morphological evolution (see Gould, 1977, for many zoological examples, and Guerrant, 1982, for a botanical case study). The importance of paedomorphosis in salamander evolution has long been recognized (Noble, 1931; Tihen, 1958; Wake, 1966), and represents one of the major ways in which new morphological characters are acquired in these amphibians. Paedomorphosis has been invoked to explain the evolution of single elements (e.g., the nasal bone in Rhyacotriton olympicus, Wake, 1980a), as well as the simultaneous change of many aspects of salamander morphology (e.g., Wake, 1966; Alberch and Alberch, 1981). The most striking example of the complete reorganization of the adult morphology attributable to paedomorphosis occurs when salamanders fail to metamorphose to the terrestrial condition and mature while retaining virtually the entire larval morphology throughout life. I term this phenomenon larval reproduction. (Pierce and Smith, 1979; Sullivan, 1980; and Wake, 1980b discuss this terminological point.) Operationally, reproductive larvae retain external gills and an enlarged tail fin, lack movable eyelids, and are obligatorily aquatic as sexually mature adults. Although larval reproduction is found, at least occasionally, in most families of salamanders, it reaches its greatest variability of expression in the Ambystoma tigrinum-mexicanum-dumerilii-Rhyacosiredon complex of the family Ambystomatidae (Tihen, 1958). This complex includes about 17 currently recognized species, distributed across North America from southern Canada to the southern rim of the Mexican plateau (Gehlbach, 1967). The group reaches its greatest taxonomic and metamorphic diversity at its southern extreme, in the Mesa Central of central Mexico. Fifteen of the 17 species are endemic to this region (Smith and Taylor, 1948), and individuals exhibiting larval reproduction are known from well over half of these taxa. Of these, the axolotl, A. mexicanum, has been widely cited as a prime example of paedomorphosis in vertebrate evolution (deBeer, 1958; Gould, 1977). Before the importance of metamorphic failure in ambystomatid evolution can be addressed, a phylogeny of the group must be established as a framework for examining the evolution of metamorphosis. Here, I use starch-gel electrophoresis to evaluate the phylogenetic history of the Mexican ambystomatid salaman-

COMPARATIVE ALBUMIN AND BIOCHEMICAL EVOLUTION IN PLETHODONTID SALAMANDERS.

Evidence that the serum protein albumin evolves step with other proteins was presented in 1973 (Sarich et al., 1973). A good correlation was demonstrated between micro-complement fixation (MC'F) measured albumin evolution and multiprotein evolution (as measured by Nei distance calculations from electrophoretic studies) for a few pairs of frog species and several pairs of primate species. This work was extended for frogs (Case et al., 1975) and further substantiated for mammals and reptiles by Sarich (1977). We present additional data on lungless salamanders of the family Plethodontidae, stemming from studies of several plethodontid genera (Wake et al., 1978; Highton and Larson, 1979; Maxson et al., 1979). We also compare albumin evolution in the genus Plethodon with DNA evolution as measured by DNA hybridization studies of Mizuno and Macgregor (1974). A good correlation is observed between albumin evolution and these other independent assessments of molecular evolution in salamanders.

RATES OF MOLECULAR AND CHROMOSOMAL EVOLUTION IN SALAMANDERS.

Changes in karyotype are receiving increasing attention from evolutionary biologists. This is in part because recent observations suggest that evolution at the organismal level is correlated more highly with karyotypic evolution than with structural gene evolution (Wilson et al., 1974b, 1975, 1977b; Prager et al., 1976; Bush et al., 1977). The salamander order Urodela is of interest in this regard because, as has long been recognized by herpetologists (D. B. Wake, pers. comm), this group is karyotypically conservative. To determine how conservative a group is, it is desirable to calculate rates of evolution. Recently, a fossil-based method was used to calculate a mean rate for 11 extant genera of salamanders (Wilson et al., 1975; Bush et al., 1977). As the authors pointed out, this method has several weaknesses, especially when applied to a group whose fossil record is so little known. For this reason, we thought it important to examine chromosomal evolution in salamanders by another method, preferably one that is not so dependent on the fossil record. Biochemical methods of comparing protein sequences can also provide estimates of divergence times among species and thus enable independent calculation of rates of chromosomal evolution (Wilson et al., 1974a,b; Wilson et al., 1977a). In this article we present the results of using a biochemical method to estimate rates of chromosomal evolution in the urodeles. The biochemical method is based on comparing the serum albumins of species whose karyotypes are known. The albumin comparisons provide an approximate estimate of the time elapsed since the species compared last shared a common ancestor. With this time, one can calculate an approximate minimum value for the mean rate at which karyotypic differences have arisen between the species compared. Two methods of analyzing the biochemical data were used and both give results in approximate agreement with those obtained by the fossil-based method, confirming that karyotypic evolution in salamanders has been slower than in frogs and very much slower than in mammals.

Chromosomes, DNA sequences, and evolution in salamanders of the genus Aneides

Chromosomes, DNA sequences, and evolution in salamanders of the genus Aneides

Chromosomes, DNA sequences, and evolution in salamanders of the genus Plethodon.

Chromosomes and DNA sequence homologies have been studied in 15 species of North American salamander belonging to the genus Plethodon. These include 4 Eastern small species, 5 Eastern large species, 5 Western, and 1 New Mexican species. All species have 14 metacentric or sub-metacentric chromosomes. Their karyotypes are closely similar, but their C values range from 18–69 pg. DNA:DNA molecular hybridization studies showed that salamanders belonging to the same species group had between 60 and 90% of the observed repetitive DNA sequences in common, different groups of Eastern species had between 40 and 60% in common, and Eastern and Western groups had less than 10% in common. The slowly reassociating DNA sequences were also diverse among species, but higher levels of homology were observed than in the case of repetitive sequences. The New Mexican species was exceptional in showing little homology with other species with respect to either repetitive or slowly reassociating sequences.