Rapid Evolution of Plethodontid Modulating Factor, a Hypervariable Salamander Courtship Pheromone, is Driven by Positive Selection

Sexual communication in plethodontid salamanders is mediated by a proteinaceous pheromone that a male delivers to a female during courtship, boosting her receptivity. The pheromone consists of three proteins from three unrelated protein families. These proteins are among a small group of pheromones known to affect female receptivity in vertebrates. Previously, we showed that the genes of two of these proteins (PRF and SPF) are prone to incessant evolution driven by positive selection, presumably as a consequence of coevolution with female receptors. In this report, we focus on the evolution of the third pheromone protein gene family, plethodontid modulating factor (PMF), to determine whether it shows the same pattern of diversification. We used RT-PCR in mental gland cDNA to survey PMF sequences from three genera of plethodontid salamanders (27 spp.) to measure rates of evolution, level of gene diversification, modes of selection, and types of amino acid substitution. Like PRF and SPF, PMF is produced by a multigene family characterized by gene duplication and high levels of polymorphism. PMF evolution is rapid, incessant, and driven by positive selection. PMF is more extreme in these dimensions than both PRF and SPF. Nestled within this extraordinary variation, however, is a signature of purifying selection, acting to preserve important structural and biochemical features of the PMF protein (i.e., secretion signal, cysteine residues, and pI). Although a pattern of persistent diversification exists at the molecular level, the morphological and behavioral aspects of the pheromone delivery system show evolutionary stasis over millions of years.     

Stabilizing selection on behavior and morphology masks positive selection on the signal in a salamander pheromone signaling complex

Natural selection maintains the integration and coordination of sets of phenotypic characters that collectively perform a task. In functional complexes in which characters span molecular to behavioral levels of organization, we might then expect similar modes of selection to produce similar patterns in evolutionary divergence at each level. To test this expectation, we diagnosed selection at behavioral, morphological, and molecular levels for courtship pheromone signaling by plethodontid salamanders. At the levels of morphology and behavior tens of millions of years of stasis (stabilizing selection) occur on each side of a transition from vaccination to olfactory delivery modes. As a proxy for the molecular level, we used plethodontid receptivity factor (PRF), a protein that is an active component of the pheromone. We cloned PRF from 12 Plethodon spp. spanning the delivery transition and obtained multiple alleles from each individual surveyed. Analyses of 61 alleles for PRF identified elevated nonsynonymous over synonymous substitution rates along lineages in a molecular phylogeny, and at 8% of sites in the protein, indicating that positive (directional) selection has acted on this vertebrate pheromone gene. Structural models showed PRF is in a family of cytokines characterized by a four-alpha-helix bundle. Positive selection in PRF was associated with receptor binding sites that are under purifying selection in other cytokines of that family. The evolutionary dynamics of the plethodontid pheromone delivery complex consists of stabilizing selection on morphological and behavioral aspects of signal delivery but positive selection on the signal mediated by receptors. Thus, different selection modes prevail at different levels in this reproductive functional complex. Evolutionary studies of integrated sets of characters therefore require separate analyses of selective action at each level.     

Digits lost or gained? Evidence for pedal evolution in the dwarf salamander complex (Eurycea, Plethodontidae)

Change in digit number, particularly digit loss, has occurred repeatedly over the evolutionary history of tetrapods. Although digit loss has been documented among distantly related species of salamanders, it is relatively uncommon in this amphibian order. For example, reduction from five to four toes appears to have evolved just three times in the morphologically and ecologically diverse family Plethodontidae. Here we report a molecular phylogenetic analysis for one of these four-toed lineages--the Eurycea quadridigitata complex (dwarf salamanders)--emphasizing relationships to other species in the genus. A multilocus phylogeny reveals that dwarf salamanders are paraphyletic with respect to a complex of five-toed, paedomorphic Eurycea from the Edwards Plateau in Texas. We use this phylogeny to examine evolution of digit number within the dwarf-Edwards Plateau clade, testing contrasting hypotheses of digit loss (parallelism among dwarf salamanders) versus digit gain (re-evolution in the Edwards Plateau complex). Bayes factors analysis provides statistical support for a five-toed common ancestor at the dwarf-Edwards node, favoring, slightly, the parallelism hypothesis for digit loss. More importantly, our phylogenetic results pinpoint a rare event in the pedal evolution of plethodontid salamanders.     

Lineage-specific differences in evolutionary mode in a salamander courtship pheromone

Functionally equivalent genes may evolve heterogeneously across closely related taxa as a consequence of lineage-specific selective pressures. Such disparate evolutionary modes are especially prevalent in genes that encode postcopulatory reproductive proteins, presumably as a result of sexual selection. We might therefore expect genes that mediate reproduction prior to insemination to evolve in a similar manner. Plethodontid receptivity factor (PRF), a proteinaceous salamander pheromone produced by the male, increases female receptivity during courtship interactions. To test for lineage-specific differences in PRF's evolution, we intensively sampled PRF genes across the eastern Plethodon phylogeny (27 spp.; 34 populations) to compare gene diversification, rates of evolution, modes of selection, and types of amino acid substitution. Our analyses indicate that PRF evolutionary dynamics vary considerably from lineage to lineage. Underlying this heterogeneity, however, are two well-defined transitions in evolutionary mode. The first mode is representative of a typical protein profile, wherein neutral divergence and purifying selection are the dominant features. The second mode is characterized by incessant, cyclical evolution driven by positive selection. In this mode, the positively selected sites are bound by a limited assortment of acceptable amino acids that appear to evolve independently of other sites, resulting in a tremendous number of unique PRF alleles. Several of these selected sites are implicated in receptor binding. These sites are apparently involved in a molecular tango in which the male signal and female receptors coevolve within a confined molecular space. PRF's lineage-specific evolutionary dynamics, in combination with evidence of a molecular tango, highlight the molecular action of sexual selection on a chemical signal that is used during courtship.     

Ecological radiation with limited morphological diversification in salamanders

A major goal of evolutionary biology is to explain morphological diversity among species. Many studies suggest that much morphological variation is explained by adaptation to different microhabitats. Here, we test whether morphology and microhabitat use are related in plethodontid salamanders, which contain the majority of salamander species, and have radiated into a striking diversity of microhabitats. We obtained microhabitat data for 189 species that also had both morphometric and phylogenetic data. We then tested for associations between morphology and microhabitat categories using phylogenetic comparative methods. Associations between morphology and ecology in plethodontids are largely confined to a single clade within one subfamily (Bolitoglossinae), whereas variation in morphology across other plethodontids is unrelated to microhabitat categories. These results demonstrate that ecological radiation and morphological evolution can be largely decoupled in a major clade. The results also offer a striking contrast to lizards, which typically show close relationships between morphology and microhabitat.     

Are rates of species diversification correlated with rates of morphological evolution?

Some major evolutionary theories predict a relationship between rates of proliferation of new species (species diversification) and rates of morphological divergence between them. However, this relationship has not been rigorously tested using phylogeny-based approaches. Here, we test this relationship with morphological and phylogenetic data from 190 species of plethodontid salamanders. Surprisingly, we find that rates of species diversification and morphological evolution are not significantly correlated, such that rapid diversification can occur with little morphological change, and vice versa. We also find that most clades have undergone remarkably similar patterns of morphological evolution (despite extensive sympatry) and that those relatively novel phenotypes are not associated with rapid diversification. Finally, we find a strong relationship between rates of size and shape evolution, which has not been previously tested.     

Phylogenetic evidence for a major reversal of life-history evolution in plethodontid salamanders

The transition from aquatic to terrestrial eggs is a key evolutionary change that has allowed vertebrates to successfully colonize and exploit the land. Although most amphibians retain the primitive biphasic life cycle (eggs deposited in water that hatch into free-living aquatic larvae), direct development of terrestrial eggs has evolved repeatedly and may have been critical to the evolutionary success of several amphibian groups. We provide the first conclusive evidence for evolutionary reversal of direct development in vertebrates. The family Plethodontidae (lungless salamanders) contains the majority of salamander species, including major radiations of direct developers. We reconstruct the higher level phylogenetic relationships of plethodontid salamanders using molecular and morphological data and use this phylogeny to examine the evolution of direct development. We show that the predominantly biphasic desmognathines, previously considered the sister group of other plethodontids, are nested inside a group of direct-developing species (Plethodontini) and have re-evolved the aquatic larval stage. Rather than being an evolutionary dead end, the reversal from direct developing to biphasic life history may have helped communities in eastern North America to achieve the highest local diversity of salamander species in the world.     

Biogeography and evolution of Central American cloud forest salamanders (Caudata: Plethodontidae: Cryptotriton), with the description of a new species

The cloud forests of Mesoamerica are notable for their high endemism, and plethodontid salamanders provide a striking example of divergence and microendemism across cloud forest blocks at a regional level. Salamanders that make use of arboreal bromeliad microhabitats in the cloud forest appear to be especially prone to divergence driven by natural habitat fragmentation, and are expected to show high endemism at small spatial scales. We use a multilocus dataset to investigate the biogeographic history and relationships among species of a small genus of salamander, Cryptotriton, restricted to the cloud forests of Nuclear Central America. We use a morphological data set along with a coalescent species delimitation method to reveal the presence of at least one undescribed species from an isolated cloud forest in eastern Guatemala. Biogeographic analyses show that Cryptotriton has a different biogeographic history than another clade of cloud forest‐restricted salamanders in the same region, perhaps indicating that each genus restricted the spatial expansion and diversification of the other through preemptive occupancy. Our results suggest that isolation across relatively short geographic distances has led to range fragmentation and deep divergence between species. Exploration of remaining patches of cloud forest likely will continue to reveal undetected diversity. © 2015 The Linnean Society of London     

What explains patterns of species richness? The relative importance of climatic‐niche evolution,morphological evolution,and ecological limits in salamanders

A major goal of evolutionary biology and ecology is to understand why species richness varies among clades. Previous studies have suggested that variation in richness among clades might be related to variation in rates of morphological evolution among clades (e.g., body size and shape). Other studies have suggested that richness patterns might be related to variation in rates of climatic‐niche evolution. However, few studies, if any, have tested the relative importance of these variables in explaining patterns of richness among clades. Here, we test their relative importance among major clades of Plethodontidae, the most species‐rich family of salamanders. Earlier studies have suggested that climatic‐niche evolution explains patterns of diversification among plethodontid clades, whereas rates of morphological evolution do not. A subsequent study stated that rates of morphological evolution instead explained patterns of species richness among plethodontid clades (along with “ecological limits” on richness of clades, leading to saturation of clades with species, given limited resources). However, they did not consider climatic‐niche evolution. Using phylogenetic multiple regression, we show that rates of climatic‐niche evolution explain most variation in richness among plethodontid clades, whereas rates of morphological evolution do not. We find little evidence that ecological limits explain patterns of richness among plethodontid clades. We also test whether rates of morphological and climatic‐niche evolution are correlated, and find that they are not. Overall, our results help explain richness patterns in a major amphibian group and provide possibly the first test of the relative importance of climatic niches and morphological evolution in explaining diversity patterns.     

Pheromonal communication in amphibians

Pheromonal communication is widespread in salamanders and newts and may also be important in some frogs and toads. Several amphibian pheromones have been behaviorally, biochemically and molecularly identified. These pheromones are typically peptides or proteins. Study of pheromone evolution in plethodontid salamanders has revealed that courtship pheromones have been subject to continual evolutionary change, perhaps as a result of co-evolution between the pheromonal ligand and its receptor. Pheromones are detected by the vomeronasal organ and main olfactory epithelium. Chemosensory neurons express vomeronasal receptors or olfactory receptors. Frogs have relatively large numbers of vomeronasal receptors that are transcribed in both the vomeronasal organ and the main olfactory epithelium. Salamander vomeronasal receptors apparently are restricted to the vomeronasal organ. To date, no chemosensory ligands have been matched to vomeronasal receptors or olfactory receptors so it is unknown whether particular receptor types are (1) specialized for detection of pheromones versus other chemosignals, or (2) specialized for detection of volatile, nonvolatile, or water-borne chemosignals. Despite progress in understanding amphibian pheromonal communication, only a small fraction of amphibian species have been examined. Study of additional species of amphibians will indicate which traits related to pheromonal communication are evolutionarily conserved and which traits have diverged over time.     

DEVELOPMENTAL CORRELATES OF GENOME SIZE IN PLETHODONTID SALAMANDERS AND THEIR IMPLICATIONS FOR GENOME EVOLUTION

We present an analysis of the evolutionary relationship between genome size (C-value, mass of DNA per haploid nucleus) and developmental rate using observations of limb regeneration in salamanders of the family Plethodontidae. Rates of growth and differentiation of regenerating limbs are reported for 27 plethodontid species whose C-values range from 14 to 76 picograms. A phylogenetic analysis employing Felsenstein's method of independent contrasts indicates that rate of differentiation is inversely proportional to genome size, although we have not identified any statistically significant association between genome size and the growth rate of regenerating tissue. Our results are consistent with an interpretation that genome size may place a limit on the maximum rate of regeneration attainable in plethodontid salamanders. The implications of our findings for the “junk DNA,” “nucleotypic DNA,” “selfish DNA,” and “skeletal DNA” hypotheses of genome evolution are discussed.     

核糖核酸酶基因超家族分子进化

核糖核酸酶基因(Ribonuclease A, RNASE A)超家族是进化生物学中研究新基因起源及新功能演变的重要模式系统之一。RNASE A超家族中的很多成员表现出基因复制的进化模式, 而且在适应性(正)选择的驱动下, 发生了功能分化。文章综述了RNASE A超家族成员在不同动物类群中进化模式的研究进展, 包括近年来越来越多在基因组水平上开展的相关研究, 显示该基因超家族可能具有比人们以往认识的更为复杂的基因进化模式。随着越来越多动物基因组数据的产生, 对更多动物代表类群进行RNASE A超家族研究, 将有望揭示新的进化机制和功能分化, 为系统认识动物适应进化的遗传机制奠定基础。     

Early diversification of sperm size in the evolutionary history of the old world leaf warblers (Phylloscopidae)

Sperm morphological traits are highly variable among species and are commonly thought to evolve by post‐copulatory sexual selection. However, little is known about the evolutionary dynamics of sperm morphology, and whether rates of evolutionary change are variable over time and among taxonomic groups. Here, we examine sperm morphology from 21 species of Old World leaf warblers (Phylloscopidae), a group of generally dull, sexually monochromatic birds, which are known to have high levels of extra‐pair paternity. We found that sperm length differs markedly across species, spanning about 40% of the range observed across a larger selection of passerine birds. Furthermore, we found strong support for an ‘early‐burst’ model of trait evolution, implying that the majority of divergence in sperm length has occurred early in the evolutionary history of this clade with subsequent evolutionary stasis. This large early divergence matches the early divergence reported in ecological traits (i.e. body size and feeding behaviour). Our findings demonstrate that rates of evolution in sperm morphology can change over time in passerine taxa, and that evolutionary stasis in sperm traits can occur even in species exhibiting characteristics consistent with moderate‐to‐high levels of sperm competition. It remains a major challenge to identify the selection mechanisms and possible constraints responsible for these variable rates of sperm evolution.     

Stochastic processes are key determinants of short-term evolution in influenza a virus

Understanding the evolutionary dynamics of influenza A virus is central to its surveillance and control. While immune-driven antigenic drift is a key determinant of viral evolution across epidemic seasons, the evolutionary processes shaping influenza virus diversity within seasons are less clear. Here we show with a phylogenetic analysis of 413 complete genomes of human H3N2 influenza A viruses collected between 1997 and 2005 from New York State, United States, that genetic diversity is both abundant and largely generated through the seasonal importation of multiple divergent clades of the same subtype. These clades cocirculated within New York State, allowing frequent reassortment and generating genome-wide diversity. However, relatively low levels of positive selection and genetic diversity were observed at amino acid sites considered important in antigenic drift. These results indicate that adaptive evolution occurs only sporadically in influenza A virus; rather, the stochastic processes of viral migration and clade reassortment play a vital role in shaping short-term evolutionary dynamics. Thus, predicting future patterns of influenza virus evolution for vaccine strain selection is inherently complex and requires intensive surveillance, whole-genome sequencing, and phenotypic analysis.     

Courtship in the Zig-Zag Salamander (Plethodon dorsalis): Insights into a Transition in Pheromone-Delivery Behavior

Courtship in plethodontid salamanders includes the delivery of male courtship pheromones by two distinct modes. Within the eastern Plethodon clade of the tribe Plethodontini, members of the Plethodon cinereus species group use an ancestral ‘vaccination’ mode of delivery, while members of the P. glutinosus group use an olfactory delivery mode. In order to shed light on this transition in delivery mode, I observed courtship behavior in P. dorsalis, a species that is phylogenetically intermediate to the P. cinereus and P. glutinosus groups. My observations indicate that P. dorsalis also is intermediate to the P. cinereus and P. glutinosus species groups in terms of courtship behavior. The context of delivery of male courtship pheromones in P. dorsalis is similar to that of the P. cinereus species group; however, the mode of pheromone delivery in P. dorsalis is olfactory. Thus, a transition in the context of pheromone delivery underlies the more obvious change in pheromone delivery mode. I discuss these findings in terms of the evolution of courtship pheromone delivery across the eastern Plethodon clade. I also report the first observations of ‘premature’ spermatophore deposition by male plethodontids.     

Diversification on an ecologically constrained adaptive landscape

We used phylogenetic analysis of body-size ecomorphs in a crustacean species complex to gain insight into how spatial complexity of ecological processes generates and maintains biological diversity. Studies of geographically widespread species of Hyalella amphipods show that phenotypic evolution is tightly constrained in a manner consistent with adaptive responses to alternative predation regimes. A molecular phylogeny indicates that evolution of Hyalella ecomorphs is characterized by parallel evolution and by phenotypic stasis despite substantial levels of underlying molecular change. The phylogeny suggests that species diversification sometimes occurs by niche shifts, and sometimes occurs without a change in niche. Moreover, diversification in the Hyalella ecomorphs has involved the repeated evolution of similar phenotypic forms that exist in similar ecological settings, a hallmark of adaptive evolution. The evolutionary stasis observed in clades separated by substantial genetic divergence, but existing in similar habitats, is also suggestive of stabilizing natural selection acting to constrain phenotypic evolution within narrow bounds. We interpret the observed decoupling of genetic and phenotypic diversification in terms of adaptive radiation on an ecologically constrained adaptive landscape, and suggest that ecological constraints, perhaps acting together with genetic and functional constraints, may explain the parallel evolution and evolutionary stasis inferred by the phylogeny.     

Gene lineages and eastern North American palaeodrainage basins: phylogeography and speciation in salamanders of the Eurycea bislineata species complex

Contemporary North American drainage basins are composites of formerly isolated drainages, suggesting that fragmentation and fusion of palaeodrainage systems may have been an important factor generating current patterns of genetic and species diversity in stream-associated organisms. Here, we combine traditional molecular-phylogenetic, multiple-regression, nested clade, and molecular-demographic analyses to investigate the relationship between phylogeographic variation and the hydrogeological history of eastern North American drainage basins in semiaquatic plethodontid salamanders of the Eurycea bislineata species complex. Four hundred forty-two sequences representing 1108 aligned bases from the mitochondrial genome are reported for the five formally recognized species of the E. bislineata complex and three outgroup taxa. Within the in-group, 270 haplotypes are recovered from 144 sampling locations. Geographic patterns of mtDNA-haplotype coalescence identify 13 putatively independent population-level lineages, suggesting that the current taxonomy of the group underestimates species-level diversity. Spatial and temporal patterns of phylogeographic divergence are strongly associated with historical rather than modern drainage connections, indicating that shifts in major drainage patterns played a pivotal role in the allopatric fragmentation of populations and build-up of lineage diversity in these stream-associated salamanders. More generally, our molecular genetic results corroborate geological and faunistic evidence suggesting that palaeodrainage connections altered by glacial advances and headwater erosion occurring between the mid-Miocene and Pleistocene epochs explain regional patterns of biodiversity in eastern North American streams.