Heterochrony repolarized: a phylogenetic analysis of developmental timing in plethodontid salamanders

Stage-Specific Demographic Effects of Hydrologic Variation in a Stream Salamander

AbstractWe lack a strong understanding of how organisms with complex life histories respond to climate variation. Many stream-associated species have multistage life histories that are likely to influence the demographic consequences of floods and droughts. However, tracking stage-specific demographic responses requires high-resolution, long-term data that are rare. We used 8 years of capture-recapture data for the headwater stream salamander Gyrinophilus porphyriticus to quantify the effects of flooding and drying magnitude on stage-specific vital rates and population growth. Drying reduced larval recruitment but increased the probability of metamorphosis (i.e., adult recruitment). Flooding reduced adult recruitment but had no effect on larval recruitment. Larval and adult survival declined with flooding but were unaffected by drying. Annual population growth rates (λ) declined with flooding and drying. Lambda also declined over the study period (2012-2021), although mean λ was 1.0 over this period. Our results indicate that G. porphyriticus populations are resilient to hydrologic variation because of compensatory effects on recruitment of larvae versus adults (i.e., reproduction vs. metamorphosis). Complex life cycles may enable this resilience to climate variation by creating opportunities for compensatory demographic responses across stages. However, more frequent and intense hydrologic variation in the latter half of this study contributed to a decline in λ over time, suggesting that increasing environmental variability poses a threat even when demographic compensation occurs.

Individual growth rates and size at metamorphosis increase with watershed area in a stream salamander

A fundamental goal of ecology is to understand how the physical environment influences intraspecific variability in life history and, consequently, fitness. In streams, discharge and associated habitat conditions change along a continuum from intermittency to permanence: Headwater streams typically have smaller watersheds and are thus more prone to drying than higher-order streams with larger watersheds and more consistent discharge. However, few empirical studies have assessed life history and associated population responses to this continuum in aquatic organisms. We tested the prediction that individual growth, rate of development, and population growth increase with watershed area in the long-lived stream salamander Gyrinophilus porphyriticus, where we use watershed area as a proxy for hydrologic intermittence. To address this hypothesis, we used 8 years of mark-recapture data from 53 reaches across 10 headwater streams in New Hampshire, USA. Individual growth rates and mean size at metamorphosis increased with watershed area for watersheds from 0.12 to 1.66 km2 . Population growth rates increased with watershed area; however, this result was not statistically significant at our sample size. Mean age of metamorphosis did not vary across watershed areas. Lower individual growth rates and smaller sizes at metamorphosis likely contributed to reduced lifetime fecundity and population growth in reaches with the smallest watershed areas and highest vulnerability to drought. These responses suggest that as droughts increase due to climate change, headwater specialists in hydrologically intermittent environments will experience a reduction in fitness due to smaller body sizes or other growth-related mechanisms.

Using salamanders as model taxa to understand vertebrate feeding constraints during the late Devonian water-to-land transition

The vertebrate water-to-land transition and the rise of tetrapods brought about fundamental changes for the groups undergoing these evolutionary changes (i.e. stem and early tetrapods). These groups were forced to adapt to new conditions, including the distinct physical properties of water and air, requiring fundamental changes in anatomy. Nutrition (or feeding) was one of the prime physiological processes these vertebrates had to successfully adjust to change from aquatic to terrestrial life. The basal gnathostome feeding mode involves either jaw prehension or using water flows to aid in ingestion, transportation and food orientation. Meanwhile, processing was limited primarily to simple chewing bites. However, given their comparatively massive and relatively inflexible hyobranchial system (compared to the more muscular tongue of many tetrapods), it remains fraught with speculation how stem and early tetrapods managed to feed in both media. Here, we explore ontogenetic water-to-land transitions of salamanders as functional analogues to model potential changes in the feeding behaviour of stem and early tetrapods. Our data suggest two scenarios for terrestrial feeding in stem and early tetrapods as well as the presence of complex chewing behaviours, including excursions of the jaw in more than one dimension during early developmental stages. Our results demonstrate that terrestrial feeding may have been possible before flexible tongues evolved. This article is part of the theme issue 'Food processing and nutritional assimilation in animals'.

Paedomorphic salamanders are larval in form and patterns of limb emergence inform life cycle evolution

Amphibians undergo a variety of post-embryonic transitions (PETr) that are partly governed by thyroid hormone (TH). Transformation into a terrestrial form follows an aquatic larval stage (biphasic) or precedes hatching (direct development). Some salamanders maintain larval characteristics and an aquatic lifestyle into adulthood (paedomorphosis), which obscures the conclusion of their larval period. Paedomorphic axolotls exhibit elevated TH during early development that is concomitant with transcriptional reprogramming and limb emergence. A recent perspective suggested this cryptic TH-based PETr is uncoupled from metamorphosis in paedomorphs and concludes the larval period. This led to their question: "Are paedomorphs actual larvae?". To clarify, paedomorphs are only considered larval in form, even though they possess some actual larval characteristics. However, we strongly agree that events during larval development inform amphibian life cycle evolution. We build upon their perspective by considering the evolution of limb emergence and metamorphosis. Limbless hatchling larval salamanders are generally associated with ponds, while limbed larvae are common to streams and preceded the evolution of direct development. Permian amphibians had limbed larvae, so their PETr was likely uncoupled from metamorphosis, equivalent to most extant biphasic and paedomorphic salamanders. Coupling of these events was likely derived in frogs and direct developing salamanders. This article is protected by copyright. All rights reserved.

Repeated ecological and life cycle transitions make salamanders an ideal model for evolution and development

Observations on the ontogeny and diversity of salamanders provided some of the earliest evidence that shifts in developmental trajectories have made a substantial contribution to the evolution of animal forms. Since the dawn of evo-devo there have been major advances in understanding developmental mechanisms, phylogenetic relationships, evolutionary models, and an appreciation for the impact of ecology on patterns of development (eco-evo-devo). Molecular phylogenetic analyses have converged on strong support for the majority of branches in the Salamander Tree of Life, which includes 764 described species. Ancestral reconstructions reveal repeated transitions between life cycle modes and ecologies. The salamander fossil record is scant, but key Mesozoic species support the antiquity of life cycle transitions in some families. Colonization of diverse habitats has promoted phenotypic diversification and sometimes convergence when similar environments have been independently invaded. However, unrelated lineages may follow different developmental pathways to arrive at convergent phenotypes. This article summarizes ecological and endocrine-based causes of life cycle transitions in salamanders, as well as consequences to body size, genome size, and skeletal structure. Salamanders offer a rich source of comparisons for understanding how the evolution of developmental patterns has led to phenotypic diversification following shifts to new adaptive zones.

Patterns of Natural Selection on Mitochondrial Protein-Coding Genes in Lungless Salamanders: Relaxed Purifying Selection and Presence of Positively Selected Codon Sites in the Family Plethodontidae

There are two distinct lungless groups in caudate amphibians (salamanders and newts) (the family Plethodontidae and the genus Onychodactylus, from the family Hynobiidae). Lunglessness is considered to have evolved in response to environmental and/or ecological adaptation with respect to oxygen requirements. We performed selection analyses on lungless salamanders to elucidate the selective patterns of mitochondrial protein-coding genes associated with lunglessness. The branch model and RELAX analyses revealed the occurrence of relaxed selection (an increase of the dN/dS ratio = ω value) in most mitochondrial protein-coding genes of plethodontid salamander branches but not in those of Onychodactylus. Additional branch model and RELAX analyses indicated that direct-developing plethodontids showed the relaxed pattern for most mitochondrial genes, although metamorphosing plethodontids had fewer relaxed genes. Furthermore, aBSREL analysis detected positively selected codons in three plethodontid branches but not in Onychodactylus. One of these three branches corresponded to the most recent common ancestor, and the others corresponded with the most recent common ancestors of direct-developing branches within Hemidactyliinae. The positive selection of mitochondrial protein-coding genes in Plethodontidae is probably associated with the evolution of direct development.

Multiple paedomorphic lineages of soft-substrate burrowing invertebrates: parallels in the origin of Xenocratena and Xenoturbella

Paedomorphosis is an important evolutionary force. It has previously been suggested that a soft-substrate sediment-dwelling (infaunal) environment facilitates paedomorphic evolution in marine invertebrates. However, until recently this proposal was never rigorously tested with robust phylogeny and broad taxon selection. Here, for the first time, we present a molecular phylogeny for a majority of the 21 families of one of the largest nudibranch subgroups (Aeolidacea) and show that the externally highly simplified vermiform nudibranch family, Pseudovermidae, with clearly defined paedomorphic traits and inhabiting a soft-substrata environment, is a sister group to the complex nudibranch family, Cumanotidae. We also report the rediscovery of one of the most enigmatic nudibranchs-Xenocratena suecica-on the Swedish and Norwegian coasts 70 years after it was first found. Xenocratena was described from the same location and environment in the Swedish Gullmar fjord as one of the most enigmatic vermiform organisms, Xenoturbella bocki, which represents either an original simple bilaterian body plan or secondary simplification of a more complex organisation. Our results show that Xenocratena suecica reveals an onset of parallel paedomorphic evolution so we have proposed the new family, Xenocratenidae fam. n., to accommodate the molecular and morphological disparities we discovered. The paedomorphic origin of another aeolidacean family, Embletoniidae, is also demonstrated for the first time. Thus, by presenting three independent lineages from non-closely related aeolidacean families, Xenocratenidae fam. n., Cumanotidae and Embletoniidae, we confirm with phylogenetic data that a soft-substrata burrowing-related environment strongly favours paedomorphic evolution. We suggest criteria to distinguish ancestral and derived characters in the context of modifications of ontogenetic cycles. Applying an evolutionary model of the soft substrate-driven multiple paedomorphic origin of several families of nudibranch molluscs we propose that it is plausible to extend this model to other marine invertebrates and suggest that the ancestral organisation of the enigmatic metazoan, Xenoturbella, might correspond to the larval part of a complex ancestral bilaterian ontogenetic cycle with sedentary/semi-sedentary adult stages and planula-like larval stages.

Sexual selection and male-biased size dimorphism in a lineage of lungless salamander (Ampibia: Plethodontidae)

Evolutionary biologists have long focused on the patterns and causes of sexual size dimorphism (SSD). While female-biased SSD is common among ectotherms, a few lineages predominately exhibit male-biased SSD. One example is the clade of desmognathans, a monophyletic group of two genera within the Plethodontinae of the lungless salamander family Plethodontidae. Members of these two genera have a unique pattern of SSD: males mature earlier and at smaller sizes than females but reach greater maximum sizes. We used comparative phylogenetic methods to test whether SSD in these salamanders is the result of sexual selection on males. Spatial evolutionary and ecological vicariance analysis indicated a significant divergence in SSD associated with the phylogenetic origin of the desmognathans. Phylogenetic least-squares regression across the two most speciose genera of the subfamily determined a significant relationship between SSD and adult sex ratio. While male desmognathans are not sexually dimorphic in head size, they have a unique head morphology that causes their heads to grow more rapidly as their body size increases as compared with the heads of other salamanders. This pattern of allometric growth combines with a powerful bite force and enlarged premaxillary teeth to create formidable weaponry that probably is more responsive to sexual selection.

Rapid phenotypic evolution following shifts in life cycle complexity

Life cycle strategies have evolved extensively throughout the history of metazoans. The expression of disparate life stages within a single ontogeny can present conflicts to trait evolution, and therefore may have played a major role in shaping metazoan forms. However, few studies have examined the consequences of adding or subtracting life stages on patterns of trait evolution. By analysing trait evolution in a clade of closely related salamander lineages we show that shifts in the number of life cycle stages are associated with rapid phenotypic evolution. Specifically, salamanders with an aquatic-only (paedomorphic) life cycle have frequently added vertebrae to their trunk skeleton compared with closely related lineages with a complex aquatic-to-terrestrial (biphasic) life cycle. The rate of vertebral column evolution is also substantially lower in biphasic lineages, which may reflect the functional compromise of a complex cycle. This study demonstrates that the consequences of life cycle evolution can be detected at very fine scales of divergence. Rapid evolutionary responses can result from shifts in selective regimes following changes in life cycle complexity.

Evidence for complex life cycle constraints on salamander body form diversification

Metazoans display a tremendous diversity of developmental patterns, including complex life cycles composed of morphologically disparate stages. In this regard, the evolution of life cycle complexity promotes phenotypic diversity. However, correlations between life cycle stages can constrain the evolution of some structures and functions. Despite the potential macroevolutionary consequences, few studies have tested the impacts of life cycle evolution on broad-scale patterns of trait diversification. Here we show that larval and adult salamanders with a simple, aquatic-only (paedomorphic) life cycle had an increased rate of vertebral column and body form diversification compared to lineages with a complex, aquatic-terrestrial (biphasic) life cycle. These differences in life cycle complexity explain the variations in vertebral number and adult body form better than larval ecology. In addition, we found that lineages with a simple terrestrial-only (direct developing) life cycle also had a higher rate of adult body form evolution than biphasic lineages, but still 10-fold lower than aquatic-only lineages. Our analyses demonstrate that prominent shifts in phenotypic evolution can follow long-term transitions in life cycle complexity, which may reflect underlying stage-dependent constraints.

How Metamorphosis Is Different in Plethodontids: Larval Life History Perspectives on Life-Cycle Evolution

Plethodontid salamanders exhibit biphasic, larval form paedomorphic, and direct developing life cycles. This diversity of developmental strategies exceeds that of any other family of terrestrial vertebrate. Here we compare patterns of larval development among the three divergent lineages of biphasic plethodontids and other salamanders. We discuss how patterns of life-cycle evolution and larval ecology might have produced a wide array of larval life histories. Compared with many other salamanders, most larval plethodontids have relatively slow growth rates and sometimes exceptionally long larval periods (up to 60 mo). Recent phylogenetic analyses of life-cycle evolution indicate that ancestral plethodontids were likely direct developers. If true, then biphasic and paedomorphic lineages might have been independently derived through different developmental mechanisms. Furthermore, biphasic plethodontids largely colonized stream habitats, which tend to have lower productivity than seasonally ephemeral ponds. Consistent with this, plethodontid larvae grow very slowly, and metamorphic timing does not appear to be strongly affected by growth history. On the basis of this, we speculate that feeding schedules and stress hormones might play a comparatively reduced role in governing the timing of metamorphosis of stream-dwelling salamanders, particularly plethodontids.

Paedomorphosis as an Evolutionary Driving Force: Insights from Deep-Sea Brittle Stars

Heterochronic development has been proposed to have played an important role in the evolution of echinoderms. In the class Ophiuroidea, paedomorphosis (retention of juvenile characters into adulthood) has been documented in the families Ophiuridae and Ophiolepididae but not been investigated on a broader taxonomic scale. Historical errors, confusing juvenile stages with paedomorphic species, show the difficulties in correctly identifying the effects of heterochrony on development and evolution. This study presents a detailed analysis of 40 species with morphologies showing various degrees of juvenile appearance in late ontogeny. They are compared to a range of early ontogenetic stages from paedomorphic and non-paedomorphic species. Both quantitative and qualitative measurements are taken and analysed. The results suggest that strongly paedomorphic species are usually larger than other species at comparable developmental stage. The findings support recent notions of polyphyletic origin of the families Ophiuridae and Ophiolepididae. The importance of paedomorphosis and its correct recognition for the practice of taxonomy and phylogeny are emphasized.

Phylogeny of Mental Glands, Revisited

Mental glands and their associated delivery behaviors during courtship are unique to the plethodontid salamanders. Because previous interpretations of the evolution of these features were conducted using older phylogenetic hypotheses, we reanalyzed these traits with newer courtship descriptions and contemporary phylogenetic methods. Using Bayesian ancestral state reconstruction methods that have been developed since the first phylogenetic analyses were conducted in the mid-1990s, we reconstructed mental gland and courtship behavior evolution on a Bayesian phylogeny of the nuclear gene Rag1. The most probable ancestral condition for plethodontids was resolved as presence of a mental gland. Loss of a mental gland occurred in each subfamily and was recovered as the most probable ancestral condition for the Spelerpinae. In contrast, parsimony reconstruction recovered the presence of a mental gland in the ancestor to Spelerpinae with multiple secondary losses. We hypothesize that that absence of a mental gland is possibly ancestral in some clades (i.e., Spelerpinae) and secondary in others (e.g., paedomorphic Eurycea). The most probable ancestral form of the mental gland is likely to be the large pad-type distributed extensively in Plethodontinae and Bolitoglossinae. Desmognathans have the most unique mental glands, occurring in an anterior protrusion or bifurcated form (in Desmognathus wrighti). Fan-shaped mental glands evolved independently in Eurycea and Oedipina. Small pads arose independently in Bolitoglossinae, Plethodontinae, and Spelerpinae. Head-rubbing behavior for mental gland delivery mode was recovered as the most probable and parsimonious ancestral state for the Plethodontidae, with independent losses of this behavior in Plethodontinae and Spelerpinae. Because head-rubbing was observed in outgroups, we hypothesize that head-rubbing behavior predated mental gland evolution. Pulling, snapping, slapping, and biting behaviors evolved independently in the Plethodontinae and Spelerpinae and are not homologous with head-rubbing. All hypotheses of mental gland and courtship evolution invoke homoplasy.

Transposons, Genome Size, and Evolutionary Insights in Animals

The relationship between genome size and the percentage of transposons in 161 animal species evidenced that variations in genome size are linked to the amplification or the contraction of transposable elements. The activity of transposable elements could represent a response to environmental stressors. Indeed, although with different trends in protostomes and deuterostomes, comprehensive changes in genome size were recorded in concomitance with particular periods of evolutionary history or adaptations to specific environments. During evolution, genome size and the presence of transposable elements have influenced structural and functional parameters of genomes and cells. Changes of these parameters have had an impact on morphological and functional characteristics of the organism on which natural selection directly acts. Therefore, the current situation represents a balance between insertion and amplification of transposons and the mechanisms responsible for their deletion or for decreasing their activity. Among the latter, methylation and the silencing action of small RNAs likely represent the most frequent mechanisms.

Enlarged Multilocus Data set Provides Surprisingly Younger Time of Origin for the Plethodontidae, the Largest Family of Salamanders

Deep phylogenetic relationships of the largest salamander family Plethodontidae have been difficult to resolve, probably reflecting a rapid diversification early in their evolutionary history. Here, data from 50 independent nuclear markers (total 48,582 bp) are used to reconstruct the phylogeny and divergence times for plethodontid salamanders, using both concatenation and coalescence-based species tree analyses. Our results robustly resolve the position of the enigmatic eastern North American four-toed salamander (Hemidactylium) as the sister taxon of Batrachoseps + Tribe Bolitoglossini, thus settling a long-standing question. Furthermore, we statistically reject sister taxon status of Karsenia and Hydromantes, the only plethodontids to occur outside the Americas, leading us to new biogeographic hypotheses. Contrary to previous long-standing arguments that plethodontid salamanders are an old lineage originating in the Cretaceous (more than 90 Ma), our analyses lead to the hypothesis that these salamanders are much younger, arising close to the K-T boundary (~66 Ma). These time estimates are highly stable using alternative calibration schemes and dating methods. Our data simulation highlights the potential risk of making strong arguments about phylogenetic timing based on inferences from a handful of nuclear genes, a common practice. Based on the newly obtained timetree and ancestral area reconstruction results, we argue that (i) the classic "Out of Appalachia" hypothesis of plethodontid origins is problematic; (ii) the common ancestor of extant plethodontids may have originated in northwestern North America in the early Paleocene; (iii) origins of Eurasian plethodontids likely result from two separate dispersal events from western North America via Beringia in the late Eocene (~42 Ma) and the early Miocene (~23 Ma), respectively.