Using Spatial Capture–Recapture to Elucidate Population Processes and Space-Use in Herpetological Studies

Range-wide salamander densities reveal a key component of terrestrial vertebrate biomass in eastern North American forests

Characterizing the population density of species is a central interest in ecology. Eastern North America is the global hotspot for biodiversity of plethodontid salamanders, an inconspicuous component of terrestrial vertebrate communities, and among the most widespread is the eastern red-backed salamander, Plethodon cinereus. Previous work suggests population densities are high with significant geographic variation, but comparisons among locations are challenged by lack of standardization of methods and failure to accommodate imperfect detection. We present results from a large-scale research network that accounts for detection uncertainty using systematic survey protocols and robust statistical models. We analysed mark-recapture data from 18 study areas across much of the species range. Estimated salamander densities ranged from 1950 to 34 300 salamanders ha-1, with a median of 9965 salamanders ha-1. We compared these results to previous estimates for P. cinereus and other abundant terrestrial vertebrates. We demonstrate that overall the biomass of P. cinereus, a secondary consumer, is of similar or greater magnitude to widespread primary consumers such as white-tailed deer (Odocoileus virginianus) and Peromyscus mice, and two to three orders of magnitude greater than common secondary consumer species. Our results add empirical evidence that P. cinereus, and amphibians in general, are an outsized component of terrestrial vertebrate communities in temperate ecosystems.

Population densities and home range of the vulnerable Pyrenean brook newt in its core aquatic habitat

Accurate estimations of population size and space-use are critical issues, for assessing population trends and extinction risk. In this study, we applied spatially explicit capture-recapture (SECR) modelling customized for linear habitats to a three-year Capture-Mark-Recapture (CMR) monitoring of three populations of stream-dwelling Pyrenean brook newt (Calotriton asper), an endemic species of the Pyrenean mountain range. Our aim was to explore (1) spatial and temporal variation in population densities, home range size and individual detection probability during breeding season between populations and years, and (2) the influence of water temperature and flow on activity of newts. Estimates of population density range from 3044 to 4641 individuals/km of stream across the three years of the study. Linear home range along the stream was estimated to be 13.31 m from the home range centre on average over the three years. All detection probability estimates were similar, both between years and between sites, with a mean probability of 0.09, except in Fougax in 2020 where detection probability was 0.03. Activity of the Pyrenean brook newt was influenced by water temperature and flow, but these factors acted at different time scales. Overall, population densities are locally high in both populations but home range of the Pyrenean brook newt during breeding season is very small indicating a strong site attachment. The importance of water temperature and flow on activity emphasizes the sensitivity of the species to these factors that are forecasted to change in coming decades.

Experimental evaluation of spatial capture-recapture study design

A principal challenge impeding strong inference in analyses of wild populations is the lack of robust and long-term data sets. Recent advancements in analytical tools used in wildlife science may increase our ability to integrate smaller data sets and enhance the statistical power of population estimates. One such advancement, the development of spatial capture-recapture (SCR) methods, explicitly accounts for differences in spatial study designs, making it possible to equate multiple study designs in one analysis. SCR has been shown to be robust to variation in design as long as minimal sampling guidance is adhered to. However, these expectations are based on simulation and have yet to be evaluated in wild populations. Here we conduct a rigorously designed field experiment by manipulating the arrangement of artificial cover objects (ACOs) used to collect data on red-backed salamanders (Plethodon cinereus) to empirically evaluate the effects of design configuration on inference made using SCR. Our results suggest that, using SCR, estimates of space use and detectability are sensitive to study design configuration, namely the spacing and extent of the array, and that caution is warranted when assigning biological interpretation to these parameters. However, estimates of population density remain robust to design except when the configuration of detectors grossly violates existing recommendations.

Genetic variation in Plethodon cinereus and Plethodon hubrichti from in and around a contact zone

Climate change poses several challenges to biological communities including changes in the frequency of encounters between closely related congeners as a result of range shifts. When climate change leads to increased hybridization, hybrid dysfunction or genetic swamping may increase extinction risk-particularly in range-restricted species with low vagility. The Peaks of Otter Salamander, Plethodon hubrichti, is a fully terrestrial woodland salamander that is restricted to ~18 km of ridgeline in the mountains of southwestern Virginia, and its range is surrounded by the abundant and widespread Eastern Red-backed Salamander, Plethodon cinereus. In order to determine whether these two species are hybridizing and how their range limits may be shifting, we assessed variation at eight microsatellite loci and a 1,008 bp region of Cytochrome B in both species at allopatric reference sites and within a contact zone. Our results show that hybridization between P. hubrichti and P. cinereus either does not occur or is very rare. However, we find that diversity and differentiation are substantially higher in the mountaintop endemic P. hubrichti than in the widespread P. cinereus, despite similar movement ability for the two species as assessed by a homing experiment. Furthermore, estimation of divergence times between reference and contact zone populations via approximate Bayesian computation is consistent with the idea that P. cinereus has expanded into the range of P. hubrichti. Given the apparent recent colonization of the contact zone by P. cinereus, future monitoring of P. cinereus range limits should be a priority for the management of P. hubrichti populations.

Unexpected spatial population ecology of a widespread terrestrial salamander near its southern range edge

Under the current amphibian biodiversity crisis, common species provide an opportunity to measure population dynamics across a wide range of environmental conditions while examining the processes that determine abundance and structure geographical ranges. Studying species at their range limits also provides a window for understanding the dynamics expected in future environments under increasing climate change and human modification. We quantified patterns of seasonal activity, density and space use in the eastern red-backed salamander (Plethodon cinereus) near its southern range edge and compare the spatial ecology of this population to previous findings from the core of their range. This southern population shows the expected phenology of surface activity based on temperature limitations in warmer climates, yet maintains unexpectedly high densities and large home ranges during the active season. Our study suggests that ecological factors known to strongly affect amphibian populations (e.g. warm temperature and forest fragmentation) do not necessarily constrain this southern population. Our study highlights the utility of studying a common amphibian as a model system for investigating population processes in environments under strong selective pressure.

North-facing slopes and elevation shape asymmetric genetic structure in the range-restricted salamander Plethodon shenandoah

Species with narrow environmental tolerances are often distributed within fragmented patches of suitable habitat, and dispersal among these subpopulations can be difficult to directly observe. Genetic data can help quantify gene flow between localities, which is especially important for vulnerable species with a disjunct range. The Shenandoah salamander (Plethodon shenandoah) is a federally endangered species known only from three mountaintops in Virginia, USA. To reconstruct the evolutionary history and population connectivity of this species, we generated both mitochondrial and nuclear data using sequence capture from individuals collected across all three mountaintops. Applying population and landscape genetic methods, we found strong population structure that was independent of geographic distance. Both the nuclear markers and mitochondrial genomes indicated a deep split between the most southern population and the genetically similar central and northern populations. Although there was some mitochondrial haplotype-splitting between the central and northern populations, there was admixture in nuclear markers. This is indicative of either a recent split or current male-biased dispersal among mountain isolates. Models of landscape resistance found that dispersal across north-facing slopes at mid-elevation levels best explain the observed genetic structure among populations. These unexpected results highlight the importance of incorporating landscape features in understanding and predicting the movement and fragmentation of this range-restricted salamander species across space.

Use of field-portable ultrasonography reveals differences in developmental phenology and maternal egg provisioning in two sympatric viviparous snakes

A thorough understanding of the life cycles underlying the demography of wild species is limited by the difficulty of observing hidden life‐history traits, such as embryonic development. Major aspects of embryonic development, such as the rate and timing of development, and maternal–fetal interactions can be critical features of early‐life fitness and may impact population trends via effects on individual survival. While information on development in wild snakes and lizards is particularly limited, the repeated evolution of viviparity and diversity of reproductive mode in this clade make it a valuable subject of study. We used field‐portable ultrasonography to investigate embryonic development in two sympatric garter snake species, Thamnophis sirtalis and Thamnophis elegans in the Sierra Nevada mountains of California. This approach allowed us to examine previously hidden reproductive traits including the timing and annual variation in development and differences in parental investment in young. Both species are viviparous, occupy similar ecological niches, and experience the same annual environmental conditions. We found that T. sirtalis embryos were more developmentally advanced than T. elegans embryos during June of three consecutive years. We also found that eggs increased in volume more substantially across developmental stages in T. elegans than in T. sirtalis, indicating differences in maternal provisioning of embryos via placental transfer of water. These findings shed light on interspecific differences in parental investment and timing of development within the same environmental context and demonstrate the value of field ultrasonography for pursuing questions relating to the evolution of reproductive modes, and the ecology of development.

Spatial capture-recapture analysis of artificial cover board survey data reveals small scale spatial variation in slow-worm Anguis fragilis density

Vague and/or ad hoc definitions of the area sampled in monitoring efforts are common, and estimates of ecological state variables (e.g. distribution and abundance) can be sensitive to such specifications. The uncertainty in population metrics due to data deficiencies, vague definitions of space and lack of standardized protocols is a major challenge for monitoring, managing and conserving amphibian and reptile populations globally. This is especially true for the slow-worm (Anguis fragilis), a cryptic and fossorial legless lizard; uncertainty about spatial variation in density has hindered conservation efforts (e.g. in translocation projects). Spatial capture-recapture (SCR) methods can be used to estimate density while simultaneously and explicitly accounting for space and individual movement. We use SCR to analyse mark-recapture data of the slow-worm that were collected using artificial cover objects (ACO). Detectability varied among ACO grids and through the season. Estimates of slow-worm density varied across ACO grids (13, 45 and 46 individuals ha^-1, respectively). The estimated 95% home range size of slow-worms was 0.38 ha. Our estimates provide valuable information about slow-worm spatial ecology that can be used to inform future conservation management.