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.     

Miniaturization and its effects on cranial morphology in plethodontid salamanders, genus Thorius (Amphibia: Plethodontidae). I. Osteological variation

Cranial skeletal morphology, ontogeny and variation are examined in five species of Thorius , a genus of diminutive plethodontid salamanders that are among the smallest, extant, tailed tetrapods. The skull of adull Thorius is characterized by: (1) limited development or absence of several ossified elements and dentition; (2) increased inter-and intraspecific variability; (3) novel morphological configurations of the braincase and jaw suspensorium. Posthatching cranial mineralization in all species of Thorius is truncated precociously with respect to that typical of larger and more generalized plethodontid genera, such as Pseudoeurycea. These features implicate paedomorphosis as a predominant mechanism responsible for the evolution of decreased size in Thorius from larger plethodontid ancestors. Interspecific differences in cranial morphology are evident; species may be characterized by greater or lesser degrees of truncated development. However, there is no consistent relationship between degree of paedomorphosis and mean adult body size in interspecific comparisons. Adult morphology of several individual elements represent potentially useful taxonomic characters for distinguishing species.
Reduction, increased variability, and morphological novelty are common to many lineages of dwarfed taxa. They represent a null hypothesis for examination of the developmental mechanisms and morphological consequences of miniaturization in other groups.     

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.     

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

Background

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

Results

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

Conclusion

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

Modification of genital kidney nephrons for sperm transport in a plethodontid salamander,Eurycea longicauda

Salamanders possess kidneys with two distinct regions: a caudal pelvic portion and cranial genital portion. Nephrons of the pelvic region are responsible for urine formation and transport. Nephrons of the genital region transport sperm from testes to Wolffian ducts; however, nephrons of the genital region possess all the same functional regions found in pelvic kidney nephrons that are involved with urine formation and transport (renal corpuscles, proximal tubules, distal tubules, and collecting ducts). Morphological similarities between pelvic and genital regions stimulated past researchers to hypothesize that nephrons of genital kidneys possess dual function; that is, sperm transport and urine formation/transport. Considering size of glomeruli is directly related to the total amount of blood plasma filtered into the Bowman's space, we tested the hypothesis that nephrons of genital kidneys have reduced urine formation function by comparing glomerular size between nephrons of pelvic and genital kidney regions in Eurycea longicauda with general histological techniques. Light microscopy analysis revealed that glomeruli of pelvic kidneys were significantly larger than those measured from genital kidneys. Transmission electron microscopy analysis also revealed modifications in genital kidney nephrons when compared to pelvic kidney nephrons that suggested a decrease in urine formation function in genital kidneys. Such modifications included a decrease in basal and lateral plasma membrane folding in genital kidney proximal and distal tubules compared to that of pelvic kidney proximal and distal tubules. Genital kidney proximal tubules were also ciliated, which was not observed in pelvic kidney proximal tubules. In conclusion, although structurally similar at the histological level, it appears that nephrons of genital kidneys have decreased urine formation function based on glomerular size comparison and nephron ultrastructure.     

Demographics,reproduction, growth,and abundance of Jollyville Plateau salamanders (Eurycea tonkawae)

Insights into the ecology and natural history of the neotenic salamander, Eurycea tonkawae, are provided from eight years of capture‐recapture data from 10,041 captures of 7,315 individuals at 16 sites. Eurycea tonkawae exhibits seasonal reproduction, with peak gravidity occurring in the fall and winter. Size frequency data indicated recruitment occurred in the spring and summer. Open‐population capture‐recapture models revealed a similar seasonal pattern at two of three sites, while recruitment was dependent on flow at the third site. Females can reach sexual maturity within one year, and oviposition likely takes place below ground. The asymptotic body length of 1,290 individuals was estimated as 31.73 mm (at ca. two years of age), although there was substantial heterogeneity among growth trajectories. Longevity was approximately eight years, and the median age for a recaptured adult was 2.3 years. Abundance estimated from closed‐population and robust‐design capture‐recapture models varied widely within and among sites (range 41–834), although, surprisingly, dramatic changes in abundance were not observed following prolonged dry periods. Seasonal migration patterns of second‐year and older adults may help explain lower ratios of large individuals and higher temporary emigration during the latter half of the year, but further study is required. Low numbers of captures and recaptures precluded the use of open‐population models to estimate demographic parameters at several sites; therefore, closed‐population (or robust‐design) methods are generally recommended. Based on observations of their life history and population demographics, E. tonkawae seems well adapted to conditions where spring flow is variable and surface habitat periodically goes dry.     

Linking movement behaviour to dispersal and divergence in plethodontid salamanders

To better understand the evolutionary and ecological effects of dispersal, there is growing emphasis on the need to integrate direct data on movement behaviour into landscape-scale analyses. However, little is known about the general link between movement behaviour and large-scale patterns of dispersal and gene flow. Likewise, although recent studies suggest that nonrandom, directionally biased movement and dispersal can promote evolutionary divergence, the generality of this mechanism is unknown. We test the hypothesis that directionally biased movement and dispersal by plethodontid salamanders interact with the topography of headwater areas to affect genetic and phenotypic divergence. Movements by Gyrinophilus porphyriticus and Eurycea bislineata show contrasting directional biases: upstream bias in G. porphyriticus and downstream bias in E. bislineata. Consistent with predictions of how these biases interact with slope to affect dispersal and gene flow, genetic distance increased with slope in G. porphyriticus and decreased with slope in E. bislineata over a standardized distance of 1 km along six headwater streams. In both species, phenotypic divergence in relative trunk length was positively related to genetic divergence. These results indicate that landscape-scale patterns of dispersal and gene flow are closely related to movement behaviour in G. porphyriticus and E. bislineata, and underscore the value of information on movement behaviour for predicting and interpreting patterns of dispersal and gene flow in complex landscapes. This study also provides new evidence that directionally biased movement and dispersal can be important sources of intra- and interspecific variation in population divergence, and highlights the value of explicit, a priori predictions in landscape genetic studies.     

Cyto‐nuclear discordance suggests complex evolutionary history in the cave‐dwelling salamander,Eurycea lucifuga

Our understanding of the evolutionary history and ecology of cave‐associated species has been driven historically by studies of morphologically adapted cave‐restricted species. Our understanding of the evolutionary history and ecology of nonrestricted cave species, troglophiles, is limited to a few studies, which present differing accounts of troglophiles’ relationship with the cave habitat, and its impact on population dynamics. Here, we used phylogenetics, demographic statistics, and population genetic methods to study lineage divergence, dates of divergence, and population structure in the Cave Salamander, Eurycea lucifuga, across its range. In order to perform these analyses, we sampled 233 individuals from 49 populations, using sequence data from three gene loci as well as genotyping data from 19 newly designed microsatellite markers. We find, as in many other species studied in a phylogeographic context, discordance between patterns inferred from mitochondrial relationships and those inferred by nuclear markers indicating a complicated evolutionary history in this species. Our results suggest Pleistocene‐based divergence among three main lineages within E. lucifuga corresponding to the western, central, and eastern regions of the range, similar to patterns seen in species separated in multiple refugia during climatic shifts. The conflict between mitochondrial and nuclear patterns is consistent with what we would expect from secondary contact between regional populations following expansion from multiple refugia.     

Diversification and biogeographical history of Neotropical plethodontid salamanders

The Neotropical bolitoglossine salamanders represent an impressive adaptive radiation, comprising roughly 40% of global salamander species diversity. Despite decades of morphological studies and molecular work, a robust multilocus phylogenetic hypothesis based on DNA sequence data is lacking for the group. We estimated species trees based on multilocus nuclear and mitochondrial data for all major lineages within the bolitoglossines, and used our new phylogenetic hypothesis to test traditional biogeographical scenarios and hypotheses of morphological evolution in the group. In contrast to previous phylogenies, our results place all Central American endemic genera in a single clade and suggest that Central America played a critical role in the early biogeographical history of the group. The large, predominantly Mexican genus Pseudoeurycea is paraphyletic, and analyses of the nuclear data place two lineages of Pseudoeurycea as the sister group of Bolitoglossa. Our phylogeny reveals extensive homoplasy in morphological characters, which may be the result of truncation or alteration of a shared developmental trajectory. We used our phylogenetic results to revise the taxonomy of the genus Pseudoeurycea. © 2015 The Linnean Society of London     

Genome size, cell size, and the evolution of enucleated erythrocytes in attenuate salamanders

Within the salamander family Plethodontidae, five different clades have evolved high levels of enucleated red blood cells, which are extremely unusual among non-mammalian vertebrates. In each of these five clades, the salamanders have large genomes and miniaturized or attenuated body forms. Such a correlation suggests that the loss of nuclei in red blood cells may be related, in part, to the interaction between large genome size and small body size, which has been shown to have profound morphological consequences for the nervous and visual systems in plethodontids. Previous work has demonstrated that variation in both the level of enucleated cells and the size of the nuclear genome exists among species of the monophyletic plethodontid genus Batrachoseps. Here, we report extensive intraspecific variation in levels of enucleated red blood cells in 15 species and provide measurements of red blood cell size, nucleus size, and genome size for 13 species of Batrachoseps. We present a new phylogenetic hypothesis for the genus based on 6150 bp of mitochondrial DNA sequence data from nine exemplar taxa and use it to examine the relationship between genome size and enucleated red blood cell morphology in a phylogenetic framework. Our analyses demonstrate positive direct correlations between genome size, nucleus size, and both nucleated and enucleated cell sizes within Batrachoseps, although only the relationship between genome size and nucleus size is significant when phylogenetically independent contrasts are used. In light of our results and broader studies of comparative hematology, we propose that high levels of enucleated, variably sized red blood cells in Batrachoseps may have evolved in response to rheological problems associated with the circulation of large red blood cells containing large, bulky nuclei in an attenuate organism.     

Shaping intraspecific variation: Development,ecology and the evolution of morphology and life history variation in tiger salamanders

The tiger salamander,Ambystoma tigrinum, is a geographically widespread, morphologically variable, polytipic species. It is among the most variable species of salamanders in morphology and life history with two larval morphs (typical and cannibal) and three adult morphs (metamorphosed, typical branchiate, cannibal branchiate) that vary in frequency between subspecies and between populations within subspecies. We report morphometric evidence suggesting that branchiate cannibals arose through intraspecific change in the onset or timing of development resulting in the wider head and hypertrophied tooth-bearing skull bones characteristic of this phenotype. We also quantified bilateral symmetry of gill raker counts and abnormalities, then evaluated fluctuating asymmetry as a measure of the developmental stability of each morph. There was a significant interaction between fluctuating asymmetry of developmental abnormalities in cannibals and typicals and the locality where they were collected, suggesting that relative stability of each phenotype could vary among populations. While altered timing of developmental events appears to have a role in the evolution and maintenance of morphs, novel phenotypes persist only under favorable ecological conditions. Predictability of the aquatic habitat, genetic variation, kinship, body size, intraspecific competition and predation all affect expression and survival of the morphs inA. tigrinum. This taxon provides an excellent model for understanding the diversity and complexity of developmental and ecological variables controlling the evolution and maintenance of novel phenotypes.     

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.     

Evolving possibilities: postembryonic axial elongation in salamanders with biphasic (Eurcyea cirrigera,Eurycea longicauda,Eurycea quadridigitata) and paedomorphic life cycles (Eurycea nana and Ambystoma mexicanum)

Vaglia, JL., White, K, and Case, A. 2012. Evolving possibilities: postembryonic axial elongation in salamanders with biphasic (Eurcyea cirrigera, Eurycea longicauda, Eurycea quadridigitata) and paedomorphic life cycles (Eurycea nana and Ambystoma mexicanum). —Acta Zoologica (Stockholm) 93 : 2–13. Typically, the number of vertebrae an organism will have postembryonically is determined during embryogenesis via the development of paired somites. Our research investigates the phenomenon of postembryonic vertebral addition in salamander tails. We describe body and tail growth and patterns of postsacral vertebral addition and elongation in context with caudal morphology for four plethodontids (Eurycea) and one ambystomatid. Eurycea nana and Ambystoma mexicanum have paedomorphic life cycles; Eurcyea cirrigera, Eurycea longicauda and Eurycea quadridigitata are biphasic. Specimens were collected, borrowed and/or purchased, and cleared and stained for bone and cartilage. Data collected include snout‐vent length (SVL), tail length (TL), vertebral counts and centrum lengths. Eurycea species with biphasic life cycles had TLs that surpassed SVL following metamorphosis. Tails in paedomorphic species elongated but rarely exceeded body length. Larger TLs were associated with more vertebrae and longer vertebrae in all species. We observed that rates of postsacral vertebral addition varied little amongst species. Regional variation along the tail becomes prominent following metamorphosis in biphasic developers. In all species, vertebrae in the posterior one‐half of the tail taper towards the tip. We suggest that a developmental link might exist between the ability to continually add vertebrae and regeneration in salamanders.     

Nonconvergence in the evolution of primate life history and socio-ecology

The goal of this study was to investigate the extent of convergence in four basic life history and socio-ecological traits among the primates of Africa, Asia, South America and Madagascar. The convergence hypothesis predicts that similar abiotic conditions should result in similar adaptations in independent taxa. Because primates offer a unique opportunity among mammals to examine adaptations of independent groups to tropical environments, we collected information on body mass, activity pattern, diet and group size from all genera for quantitative tests of this hypothesis. We revealed a number of qualitative and quantitative differences among the four primate groups, indicating a lack of convergence in these basic aspects of life history and socio-ecology. Our analyses demonstrated that New World primates are on average significantly smaller than primates in other regions and characterized by a lack of species larger than about 10 kg. Madagascar harbours significantly more nocturnal species than the other regions and is home to all but one of the primates with irregular bursts of activity. Asia is the only region with strictly faunivorous primates, but lacks primarily gummivorous ones. The Neotropics are characterized by the absence of primarily folivorous primates. Solitary species are not represented in the New World, whereas solitary and pair-living species make up the majority of Malagasy primates. Lemurs live in significantly smaller groups than other primates, even after controlling for differences in body size. The lack of convergence among the major primate groups is neither primarily due to phylogenetic constraints as a result of founder effects, nor can it be sufficiently explained as a passive consequence of body size differences. However, because the role of adaptive forces, such as interspecific competition, predation or phenology in shaping the observed differences is largely unexplored, we conclude that it is premature to discard the convergence hypothesis without further tests.     

Population differentiation in plethodontid salamanders: divergence of allozymes and sexual compatibility among populations of Desmognathus imitator and D. ochrophaeus (Gaudata: Plethodontidae)

Plethodontid salamanders of the genus Desmognathus exhibit varying levels of genetic differentiation among and within both allopatric and sympatric taxa. This provides excellent opportunities to study population differentiation and speciation. Two morphologically similar species in this genus, D. imitator and D. ochrophaeus, are genetically well-differentiated from one another and occur in sympatry with no evidence of hybridization and introgression. We report that the degree of sexual isolation between these two species is very high, regardless of whether the populations under comparison are allopatric or sympatric with one another. Neither reinforcement nor reproductive character displacement are required to explain the evolution of sexual incompatibility in sympatry. Sexual behaviour apparently diverges while populations are allopatric with one another. Preliminary study indicates that D. imitator consists of populations among which there may be significant sexual isolation in the absence of detectable genetic differentiation.     

The evolution of the scalation pattern in temnospondyl amphibians

In most Palaeozoic temnospondyls, thin round-oval scales covering the flanks and the back of the trunk can be distinguished from ventral, elongate gastral scales arranged in a chevron pattern. The extensive growth series of the temnospondyl Sclerocephalus reveals that the morphology of the gastral scales in small larvae corresponds to the round-oval scales of the rest of the body. During subsequent ontogeny, the gastral scales differentiate and attain a spindle-shaped morphology. The tapering end of each gastral scale fits into a dorsal groove on the medial adjacent scale. This arrangement allowed telescoping of the scales and thus provided a high degree of flexibility. In the ontogenetically most advanced specimens of Sclerocephalus the gastral scales attain a rhomboid outline, and the articulation by well-defined facets has reduced the flexibility between them. In most temnospondyls, the gastral scales retain the 'juvenile' spindle-shape or the 'larval' round-oval shape, which can be interpreted as a paedomorphic trait. This suggests that the different types of gastral scales in temnospondyls, as well as the scales of the back and the flanks, can be traced back to the same Anlage of round-oval scales that differentiated early in ontogeny. In the Mesozoic, a complete reduction of dermal scalation occurred independently in distinct dissorophoid, capitosauroid, and trematosauroid temnospondyls. This reduction was probably the result of several factors unique to each group, such as cutaneous respiration, the demand for greater mobility, and the decreased importance of belly protection in fully aquatic temnospondyls.  © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 150 , 815–834.