Biogeography, phylogeny, and morphological evolution of central Texas cave and spring salamanders

Extensive Admixture Among Karst-Obligate Salamanders Reveals Evidence of Recent Divergence and Gene Exchange Through Aquifers

Karst ecosystems often contain extraordinary biodiversity, but the complex underground aquifers of karst regions present challenges for assessing and conserving stygobiont diversity and investigating their evolutionary history. We examined the karst-obligate salamanders of the Eurycea neotenes species complex in the Edwards Plateau region of central Texas using population genomics data to address questions about population connectivity and the potential for gene exchange within the underlying aquifer system. The E. neotenes species complex has historically been divided into three nominal species, but their status, and spatial extent of species ranges, have remained uncertain. We discovered evidence of extensive admixture among species within the complex and with adjacent lineages. We observed relatively low levels of differentiation among all sampling localities which supports the hypothesis of recent divergence. Nominal taxonomy, aquifer region and geography each accounted for a modest amount of the overall population genomic variation; however, these predictors were largely confounded and difficult to disentangle. Importantly, current taxonomy of the three nominal species does not reflect the admixture apparent in clustering analyses. Inference of migration events revealed a complex pattern of gene exchange, suggesting that Eurycea salamanders have a dynamic history of dispersal through the aquifer system. These results highlight the need for greater understanding of how stygobiont populations are connected via dispersal and gene exchange through karst aquifers. These results also highlight the applicability of population genomics data as a powerful lever for investigating connectivity among populations in systems where direct detection of dispersal paths is difficult, as in underground, aquatic systems.

From Cave Dragons to Genomics: Advancements in the Study of Subterranean Tetrapods

Throughout most of the kingdom Animalia, evolutionary transitions from surface life to a life permanently bound to caves and other subterranean habitats have occurred innumerous times. Not so in tetrapods, where a mere 14 cave-obligate species-all plethodontid and proteid salamanders-are known. We discuss why cave tetrapods are so exceptional and why only salamanders have made the transition. Their evolution follows predictable and convergent, albeit independent pathways. Among the many known changes associated with transitions to subterranean life, eye degeneration, starvation resistance, and longevity are especially relevant to human biomedical research. Recently, sequences of salamander genomes have become available opening up genomic research for cave tetrapods. We discuss new genomic methods that can spur our understanding of the evolutionary mechanisms behind convergent phenotypic change, the relative roles of selective and neutral evolution, cryptic species diversity, and data relevant for conservation such as effective population size and demography.

Comparative development and ocular histology between epigean and subterranean salamanders (Eurycea) from central Texas

The salamander clade Eurycea from the karst regions of central Texas provides an ideal platform for comparing divergent nervous and sensory systems since some species exhibit extreme phenotypes thought to be associated with inhabiting a subterranean environment, including highly reduced eyes, while others retain an ancestral ocular phenotype appropriate for life above ground. We describe ocular morphology, comparing three salamander species representing two phenotypes-the surface-dwelling Barton Springs salamander (E. sosorum) and San Marcos salamander (E. nana) and the obligate subterranean Texas blind salamander (E. rathbuni) - in terms of structure and size of their eyes. Eyes were examined using confocal microscopy and measurements were made using ImageJ. Statistical analysis of data was carried out using R. We also provide a developmental series and track eye development and immunolocalization of Pax6 in E. sosorum and E. rathbuni. Adult histology of the surface-dwelling San Marcos salamander (E. nana) shows similarities to E. sosorum. The eyes of adults of the epigean species E. nana and E. sosorum appear fully developed with all the histological features of a fully functional eye. In contrast, the eyes of E. rathbuni adults have fewer layers, lack lenses and other features associated with vision as has been reported previously. However, in early developmental stages eye morphology did not differ significantly between E. rathbuni and E. sosorum. Parallel development is observed between the two phenotypes in terms of morphology; however, Pax6 labeling seems to decrease in the latter stages of development in E.rathbuni. We test for immunolabeling of the visual pigment proteins opsin and rhodopsin and observe immunolocalization around photoreceptor disks in E. nana and E. sosorum, but not in the subterranean E. rathbuni. Our results from examining developing salamanders suggest a combination of underdevelopment and degeneration contribute to the reduced eyes of adult E. rathbuni.

Subterranean movement inferred by temporary emigration in Barton Springs salamanders (Eurycea sosorum)

Movement behavior is an important aspect of animal ecology but is challenging to study in species that are unobservable for some portion of their lives, such as those inhabiting subterranean environments. Using four years of robust-design capture-recapture data, we examined the probability of movement into subterranean habitat by a population of endangered Barton Springs salamanders (Eurycea sosorum), a species that inhabits both surface and subterranean groundwater habitats. We tested the effects of environmental variables and body size on survival and temporary emigration, using the latter as a measure of subterranean habitat use. Based on 2,046 observations of 1,578 individuals, we found that temporary emigration was higher for larger salamanders, 79% of which temporarily emigrated into subterranean habitat between primary sampling intervals, on average. Body size was a better predictor of temporary emigration and survival compared to environmental covariates, although coefficients from lower ranked models suggested turbidity and dissolved oxygen may influence salamander movement between the surface and subsurface. Surface population dynamics are partly driven by movement below ground and therefore surface abundance estimates represent a fraction of the superpopulation. As such, while surface habitat management remains an important conservation strategy for this species, periodic declines in apparent surface abundance do not necessarily indicate declines of the superpopulation associated with the spring habitat.

Tracking parallel adaptation of shell morphology through geological times in the land snail genus Pupilla (Gastropoda: Stylommatophora: Pupillidae)

Changing environmental conditions force species either to disperse or to adapt locally either genetically or via phenotypic plasticity. Although limits of plasticity can be experimentally tested, the predictability of genetic adaptation is restricted due to its stochastic nature. Nevertheless, our understanding of evolutionary adaptation has been improving in particular through studies of parallel adaptation. Based on molecular phylogenetic inferences and morphological investigations of both recent and fossil shells we tracked the morphological changes in three land snails, Pupilla alpicola, Pupilla loessica and Pupilla muscorum. These species differ in habitat requirements as well as historical and extant distributions with P. alpicola and P. loessica being more similar to each other than to P. muscorum. Therefore, we hypothesized, that the three species reacted independently and individually to the conditions changing throughout the Pleistocene, but expected that changes within P. alpicola and P. loessica would be more similar compared to P. muscorum. Indeed, intraspecific shell shape differences across time were similar in P. alpicola and P. loessica, suggesting that similar niche shifts have led to similar transformations in parallel. In contrast, extant P. muscorum populations were practically identical in shape to their ancestors. They have probably tracked their ecological niches through time.

Subterranean life: Behavior, metabolic, and some other adaptations of Astyanax cavefish

The ability of fishes to adapt to any aquatic environment seems limitless. It is enthralling how new species keep appearing at the deep sea or in subterranean environments. There are close to 230 known species of cavefishes, still today the best-known cavefish is Astyanax mexicanus, a Characid that has become a model organism, and has been studied and scrutinized since 1936. There are two morphotypes for A. mexicanus, a surface fish and a cavefish. The surface fish lives in central and northeastern Mexico and south of the United States, while the cavefish is endemic to the "Sierra del Abra-Tanchipa region" in northeast Mexico. The extensive genetic and genomic analysis depicts a complex origin for Astyanax cavefish, with multiple cave invasions and persistent gene flow among cave populations. The surface founder population prevails in the same region where the caves are. In this review, we focus on both morphotype's main morphological and physiological differences, but mainly in recent discoveries about behavioral and metabolic adaptations for subterranean life. These traits may not be as obvious as the troglomorphic characteristics, but are key to understand how Astyanax cavefish thrives in this environment of perpetual darkness.

Ecological contributions to body shape evolution in salamanders of the genus Eurycea (Plethodontidae)

BACKGROUND

Body shape can be both a consequence and cause of a species' evolution and ecology. There are many examples of phenotypes associated with specific ecological niches, likely as a result of specific selective regimes. A classic example of this is the phenotypic change associated with colonization of caves, including body and limb elongation. However, studies explicitly testing for differences in body shape between cave-dwelling and non-cave-dwelling lineages have been limited and so the role of the cave environment in determining morphological characteristics is still not completely understood. Here we examine variation in body shape among 405 individuals representing 20 species in the salamander genus Eurycea (Plethodontidae) and select outgroups exhibiting great diversity in morphology, ecological niche, and life history.

RESULTS

After analyzing morphometric data in a phylogenetic context using phylogenetic MANOVA and examination of the phylomorphospace, we found significant differences in body shape among cave-dwelling and non-cave-dwelling species and between aquatic and terrestrial species. Notably, limb elongation and reduced body and tail size characterized cave-dwelling species. Terrestrial species also exhibited elongation of the limbs and digits. We also observed differences in shape variance among paedomorphic and biphasic species. Our results suggest that the functional limitations imposed by habitat and life history played a key role in the evolution of body shape in this group in the context of their phylogenetic history.

A Vavraia-like microsporidium as the cause of deadly infection in threatened and endangered Eurycea salamanders in the United States

Background

Eurycea sosorum (Barton Springs salamander) and Eurycea nana (San Macros salamander) are listed as endangered and threatened species, respectively, by the U.S. Fish and Wildlife Service (USFWS) with habitats restricted to small regions near Austin, Texas, USA. The conservation efforts with the Eurycea salamanders at the captive breeding program in San Marcos Aquatic Resources Center (SMARC), a USFWS facility, have seen an unexpected and increased mortality rate over the past few years. The clinical signs of sick or dead salamanders included erythema, tail loss, asymmetric gills or brachial loss, rhabdomyolysis, kyphosis, and behavior changes, suggesting that an infectious disease might be the culprit. This study aimed to identify the cause of the infection, determine the taxonomic position of the pathogen, and investigate the potential reservoirs of the pathogen in the environment.

Results

Histopathological examination indicated microsporidian infection (microsporidiosis) in the sick and dead Eurycea salamanders that was later confirmed by PCR detection. We also determined the near full-length small subunit ribosomal RNA (SSU rRNA) gene from the microsporidian pathogen, which allowed us to determine its phylogenetic position, and to design primers for specific and sensitive detection of the pathogen. Phylogenetic analysis indicated that this pathogen was closely related to the insect parasites Vavraia spp. and the human opportunistic pathogen, Trachipleistophora hominis. This Vavraia-like microsporidium was present in dead salamanders at SMARC archived between 2011 and 2015 (positive rates ranging between 52.0–88.9% by PCR detection), as well as in some aquatic invertebrates at the facility (e.g. snails and small crustaceans).

Conclusions

A Vavraia-like microsporidian was at least one of the major pathogens, if not solely, responsible for the sickness and mortality in the SMARC salamanders, and the pathogen had been present in the center for years. Environmental invertebrates likely served as a source and reservoir of the microsporidian pathogen. These observations provide new knowledge and a foundation for future conservation efforts for Eurycea salamanders including molecular surveys, monitoring of the pathogen, and discovery of effective treatments.

Electronic supplementary material

The online version of this article (10.1186/s13071-019-3369-z) contains supplementary material, which is available to authorized users.

Species delimitation in endangered groundwater salamanders: Implications for aquifer management and biodiversity conservation

Groundwater-dependent species are among the least-known components of global biodiversity, as well as some of the most vulnerable because of rapid groundwater depletion at regional and global scales. The karstic Edwards-Trinity aquifer system of west-central Texas is one of the most species-rich groundwater systems in the world, represented by dozens of endemic groundwater-obligate species with narrow, naturally fragmented distributions. Here, we examine how geomorphological and hydrogeological processes have driven population divergence and speciation in a radiation of salamanders (Eurycea) endemic to the Edwards-Trinity system using phylogenetic and population genetic analysis of genome-wide DNA sequence data. Results revealed complex patterns of isolation and reconnection driven by surface and subsurface hydrology, resulting in both adaptive and nonadaptive population divergence and speciation. Our results uncover cryptic species diversity and refine the borders of several threatened and endangered species. The US Endangered Species Act has been used to bring state regulation to unrestricted groundwater withdrawals in the Edwards (Balcones Fault Zone) Aquifer, where listed species are found. However, the Trinity and Edwards-Trinity (Plateau) aquifers harbor additional species with similarly small ranges that currently receive no protection from regulatory programs designed to prevent groundwater depletion. Based on regional climate models that predict increased air temperature, together with hydrologic models that project decreased springflow, we conclude that Edwards-Trinity salamanders and other codistributed groundwater-dependent organisms are highly vulnerable to extinction within the next century.

Phylogeographical structure and demographic expansion in the endemic alpine stream salamander (Hynobiidae: Batrachuperus) of the Qinling Mountains

The Qinling Mountains of China provide an excellent study area for assessing the effect of Pleistocene climatic oscillations and paleogeological events on intraspecific diversification. To assess genetic diversity of an endemic stream salamander, Batrachuperus tibetanus, for its conservation, a phylogeographical survey was performed based on mitochondrial DNA and morphological data. The mitochondrial data revealed three lineages of B. tibetanus in the Qinling Mountains. A lineage present in the northwestern Qinling Mountains groups with the Tibet lineage of B. tibetanus, and the remaining Qinling populations are eastern and western lineages that separated ~3–4 million years ago (Ma). The eastern and western Qinling lineage delineation is supported by three morphological variables (snout length, eye diameter and axilla-groin length). The divergence of the two major lineages was likely caused by orogenesis of the Qinling Mountains during the late Cenozoic, and the two lineages were subsequently affected at different levels by Pleistocene climatic oscillations showing different signals of demographic expansion. A large suitable area of B. tibetanus through the Qinling Mountains since the last glacial maximum (LGM) indicated the adaptation of this species to the climatic changes. However, low genetic diversity within populations indicate the urgency of preserving the vulnerable populations and endemic lineages.

Surveying Europe's Only Cave-Dwelling Chordate Species (Proteus anguinus) Using Environmental DNA

In surveillance of subterranean fauna, especially in the case of rare or elusive aquatic species, traditional techniques used for epigean species are often not feasible. We developed a non-invasive survey method based on environmental DNA (eDNA) to detect the presence of the red-listed cave-dwelling amphibian, Proteus anguinus, in the caves of the Dinaric Karst. We tested the method in fifteen caves in Croatia, from which the species was previously recorded or expected to occur. We successfully confirmed the presence of P. anguinus from ten caves and detected the species for the first time in five others. Using a hierarchical occupancy model we compared the availability and detection probability of eDNA of two water sampling methods, filtration and precipitation. The statistical analysis showed that both availability and detection probability depended on the method and estimates for both probabilities were higher using filter samples than for precipitation samples. Combining reliable field and laboratory methods with robust statistical modeling will give the best estimates of species occurrence.

Movement, demographics, and occupancy dynamics of a federally-threatened salamander: evaluating the adequacy of critical habitat

Critical habitat for many species is often limited to occupied localities. For rare and cryptic species, or those lacking sufficient data, occupied habitats may go unrecognized, potentially hindering species recovery. Proposed critical habitat for the aquatic Jollyville Plateau salamander (Eurycea tonkawae) and two sister species were delineated based on the assumption that surface habitat is restricted to springs and excludes intervening stream reaches. To test this assumption, we performed two studies to understand aspects of individual, population, and metapopulation ecology of E. tonkawae. First, we examined movement and population demographics using capture-recapture along a spring-influenced stream reach. We then extended our investigation of stream habitat use with a study of occupancy and habitat dynamics in multiple headwater streams. Indications of extensive stream channel use based on capture-recapture results included frequent movements of >15 m, and high juvenile abundance downstream of the spring. Initial occupancy of E. tonkawae was associated with shallow depths, maidenhair fern presence and low temperature variation (indicative of groundwater influence), although many occupied sites were far from known springs. Additionally, previously dry sites were three times more likely to be colonized than wet sites. Our results indicate extensive use of stream habitats, including intermittent ones, by E. tonkawae. These areas may be important for maintaining population connectivity or even as primary habitat patches. Restricting critical habitat to occupied sites will result in a mismatch with actual habitat use, particularly when assumptions of habitat use are untested, thus limiting the potential for recovery.

Semi-permeable species boundaries in Iberian barbels (Barbus and Luciobarbus, Cyprinidae)

BACKGROUND

The evolution of species boundaries and the relative impact of selection and gene flow on genomic divergence are best studied in populations and species pairs exhibiting various levels of divergence along the speciation continuum. We studied species boundaries in Iberian barbels, Barbus and Luciobarbus, a system of populations and species spanning a wide degree of genetic relatedness, as well as geographic distribution and range overlap. We jointly analyze multiple types of molecular markers and morphological traits to gain a comprehensive perspective on the nature of species boundaries in these cyprinid fishes.

RESULTS

Intraspecific molecular and morphological differentiation is visible among many populations. Genomes of all sympatric species studied are porous to gene flow, even if they are not sister species. Compared to their allopatric counterparts, sympatric representatives of different species share alleles and show an increase in all measures of nucleotide polymorphism (S, Hd, K, π and θ). High molecular diversity is particularly striking in L. steindachneri from the Tejo and Guadiana rivers, which co-varies with other sympatric species. Interestingly, different nuclear markers introgress across species boundaries at various levels, with distinct impacts on population trees. As such, some loci exhibit limited introgression and population trees resemble the presumed species tree, while alleles at other loci introgress more freely and population trees reflect geographic affinities and interspecific gene flow. Additionally, extent of introgression decreases with increasing genetic divergence in hybridizing species pairs.

CONCLUSIONS

We show that reproductive isolation in Iberian Barbus and Luciobarbus is not complete and species boundaries are semi-permeable to (some) gene flow, as different species (including non-sister) are exchanging genes in areas of sympatry. Our results support a speciation-with-gene-flow scenario with heterogeneous barriers to gene flow across the genome, strengthening with genetic divergence. This is consistent with observations coming from other systems and supports the notion that speciation is not instantaneous but a gradual process, during which different species are still able to exchange some genes, while selection prevents gene flow at other loci. We also provide evidence for a hybrid origin of a barbel ecotype, L. steindachneri, suggesting that ecology plays a key role in species coexistence and hybridization in Iberian barbels. This ecotype with intermediate, yet variable, molecular, morphological, trophic and ecological characteristics is the local product of introgressive hybridization of L. comizo with up to three different species (with L. bocagei in the Tejo, with L. microcephalus and L. sclateri in the Guadiana). In spite of the homogenizing effects of ongoing gene flow, species can still be discriminated using a combination of morphological and molecular markers. Iberian barbels are thus an ideal system for the study of species boundaries, since they span a wide range of genetic divergences, with diverse ecologies and degrees of sympatry.

High-stakes species delimitation in eyeless cave spiders (Cicurina, Dictynidae, Araneae) from central Texas

A remarkable radiation of completely eyeless, cave-obligate spider species (Cicurina) has been described from limestone caves of Texas. This radiation includes over 50 described species, with a large number of hypothesized single-cave endemics, and four species listed as US Federally Endangered. Because of this conservation importance, species delimitation in the group is 'high-stakes'- it is imperative that species hypotheses are data rich, objective, and robust. This study focuses on a complex of four cave-dwelling Cicurina distributed on the northwestern edge of Austin, Texas. Several of the existing species hypotheses in this complex are weak, based on morphological comparisons of small samples of adult female specimens; one species description (for C. wartoni) is based on a single adult specimen. Species limits in this group were newly assessed using morphological, mitochondrial and nuclear DNA sequence data evidence, analysed using a variety of approaches. All data support a clear lineage separation between C. buwata versus the C. travisae complex (including C. travisae, C. wartoni and C. reddelli). Observed congruence across multiple analyses indicate that the C. travisae complex represents a single species, and the formal species synonymy presented here has important conservation implications. The integrative framework utilized in this study serves as a potential model for other Texas cave Cicurina, including US Federally Endangered species. More generally, this study illustrates how and why taxon-focused conservation efforts must prioritize modern species delimitation research (if the existing taxonomy is weak), before devoting precious downstream resources to conservation efforts. The study also highlights the issue of taxonomic type II error that diversity biologists increasingly face as species delimitation moves into the genomics era.

Evolution of paedomorphosis in plethodontid salamanders: ecological correlates and re-evolution of metamorphosis

Life-history modes can profoundly impact the biology of a species, and a classic example is the dichotomy between metamorphic (biphasic) and paedomorphic (permanently aquatic) life-history strategies in salamanders. However, despite centuries of research on this system, several basic questions about the evolution of paedomorphosis in salamanders have not been addressed. Here, we use a nearly comprehensive, time-calibrated phylogeny of spelerpine plethodontids to reconstruct the evolution of paedomorphosis and to test if paedomorphosis is (1) reversible; (2) associated with living in caves; (3) associated with relatively dry climatic conditions on the surface; and (4) correlated with limited range size and geographic dispersal. We find that paedomorphosis arose multiple times in spelerpines. We also find evidence for re-evolution of metamorphosis after several million years of paedomorphosis in a lineage of Eurycea from the Edwards Plateau region of Texas. We also show for the first time using phylogenetic comparative methods that paedomorphosis is highly correlated with cave-dwelling, arid surface environments, and small geographic range sizes, providing insights into both the causes and consequences of this major life history transition.