Effective population size is strongly correlated with breeding pond size in the endangered California tiger salamander, <Emphasis Type="Italic">Ambystoma californiense</Emphasis>

Maintaining genetic diversity and population viability in endangered and threatened species is a primary concern of conservation biology. Genetic diversity depends on population connectivity and effective population size (N_e), both of which are often compromised in endangered taxa. While the importance of population connectivity and gene flow has been well studied, investigating effective population sizes in natural systems has received far less attention. However, N_e plays a prominent role in the maintenance of genetic diversity, the prevention of inbreeding depression, and in determining the probability of population persistence. In this study, we examined the relationship between breeding pond characteristics and N_e in the endangered California tiger salamander, Ambystoma californiense. We sampled 203 individuals from 10 breeding ponds on a local landscape, and used 11 polymorphic microsatellite loci to quantify genetic structure, gene flow, and effective population sizes. We also measured the areas of each pond using satellite imagery and classified ponds as either hydrologically-modified perennial ponds or naturally occurring vernal pools, the latter of which constitute the natural breeding habitat for A. californiense. We found no correlation between pond area and heterozygosity or allelic diversity, but we identified a strong positive relationship between breeding pond area and N_e, particularly for vernal pools. Our results provide some of the first empirical evidence that variation in breeding habitat can be associated with differences in N_e and suggest that a more complete understanding of the environmental features that influence N_e is an important component of conservation genetics and management.     

Livestock grazing affects vernal pool specialists more than habitat generalists in montane vernal pools

Questions

Do livestock grazing and seasonal precipitation structure species composition in montane vernal pools? Which grazing and precipitation variables best predict cover of vernal pool specialists and species with broader habitat requirements? Is vernal pool species diversity correlated with livestock exclosure, and at what spatial scales?

Location

Montane vernal pools, northeast California, USA.

Methods

Vegetation was sampled in 20 vernal pools, including pools where livestock had been excluded for up to 20 years We compared plant species composition, functional group composition and species diversity among sites that varied in grazing history and seasonal precipitation using CCA and LMM.

Results

Although vernal pool specialists were dominant in montane vernal pools, over a third of plant cover was comprised of species that occur over a broad range of wetland or upland environments. The species composition of vernal pool plant communities was influenced by both livestock grazing and precipitation patterns, however the relative effects of these environmental variables differed by functional group. Livestock exclosures favoured perennial vernal pool specialists over annual vernal pool specialists. In contrast, the cover of habitat generalists was more strongly influenced by seasonal precipitation than livestock grazing. At small spatial scales, species richness and diversity decreased as the number of years a pool had been fenced increased, but this relationship was not significant at a larger spatial scale.

Conclusions

Both livestock grazing and seasonal precipitation structure the montane vernal pool plant community. We found that livestock grazing promotes the cover of annual vernal pool specialists, but at the expense of perennial vernal pool specialists. Wetter vernal pools, however, support higher cover of wetland generalist species regardless of whether pools are grazed.     

Effects of Timber Management on Pond-Breeding Salamanders

Abstract: Pond-breeding salamanders spend most of their lives in forested habitat surrounding the vernal pools where they breed. Timber harvesting has been demonstrated to have negative impacts on salamander populations due to changes in soil temperature, soil compaction, and general degradation of habitat. However, little is known about how long it takes for harvested forest habitat to once again become suitable for salamanders. Questions also remain as to whether salamanders will use an area that has been harvested in recent years if an older intact forest area is available. We used drift fences and pitfall traps to capture adult spotted salamanders (Ambystoma maculatum) and marbled salamanders (A. opacum) migrating to 3 vernal ponds during their breeding seasons. The study area contained tracts of forest that were clear-cut 11–12 years prior to the study. All 3 ponds were surrounded by areas of clear-cut and intact forest and drift fences were placed in both habitat types. Similar numbers of spotted salamanders entered the ponds from clear-cut and intact forest areas. The number of marbled salamanders migrating to the ponds did not differ between areas of clear-cut and intact forest. These results suggest that clear-cut habitats may become suitable for adult pond-breeding salamanders after a relatively short regeneration period.     

Avifauna associated with ephemeral ponds on the Cumberland Plateau, Tennessee

ABSTRACT.   Although ephemeral ponds act as small hotspots of plant, invertebrate, and salamander diversity, the importance of such ponds for birds has been little studied. We hypothesized that ephemeral ponds on the Cumberland Plateau in Tennessee would support a greater abundance, richness, and diversity of birds than the surrounding hardwood forests. In 2004, we recorded all birds seen or heard in 10 min within 50-m radius circles at 25 ephemeral ponds. We repeated the counts at control sites located 150 m from each pond in the surrounding forest. To quantify potential food availability, we captured aerial invertebrates using sweep nets at four points around a subsample of eight ephemeral ponds and at an equal number of control sites. We found significantly greater bird abundance, richness, and species diversity at ephemeral ponds than at control sites, and that pond area was not associated with either bird abundance or richness. Bird community composition at pond and control sites was similar. Aerial invertebrates were significantly more abundant at ephemeral ponds than at adjacent forest sites, providing one possible explanation for greater bird abundance at ephemeral ponds.     

Dobzhansky-Muller model of hybrid dysfunction supported by poor burst-speed performance in hybrid tiger salamanders

Speciation may result from 'complementary' genetic differences that cause dysfunction when brought together in hybrids despite having no deleterious effects within pure species genomes. The theory of complementary genes, independently proposed by Dobzhansky and Muller, yields specific predictions about the genetics of hybrid fitness. Here, I show how alternative models of hybrid dysfunction can be compared using a simple multivariate analysis of hybrid indices calculated from molecular markers. I use the approach to fit models of hybrid dysfunction to swimming performance in hybrid tiger salamander larvae. Poor burst-speed performance is a dysfunction suggesting low vigour and could translate directly into low survival. My analyses show that the Dobzhansky-Muller model fits these data better than heterozygote disadvantage. The approach demonstrated here can be applied to a broad array of nonmodel species, potentially leading to important generalizations about the genetics of hybrid dysfunction.     

Landscape epidemiology of Batrachochytrium dendrobatidis in central California

Amphibian chytridiomycosis (caused by Batrachochytrium dendrobatis; Bd) was first identified in 1998 and has since been implicated in numerous amphibian declines worldwide. Most researchers have since investigated broad‐scale geographic and taxonomic occurrences of the pathogen in tropical lotic or cool montane systems. In this study, we analyzed how environmental factors, land use practices, and landscape structure may affect the dynamics of the pathogen's distribution in a landscape dominated by lentic systems within a region of Mediterranean climate. We quantified the occurrence of Bd testing the six resident amphibian species that occur in 54 isolated perennial and ephemeral ponds in central California between May and June annually from 2004 to 2007. The geographic distribution of Bd within the landscape varied markedly between years. Inter‐annual variation in climate affected the pond landscape structure indicating that climate conditions indirectly influence the distribution of the pathogen. Fourteen ponds, 12 perennial and 2 ephemeral, were positive for Bd≥3 yr of the study and were treated as Bd hotpots for comparative purposes. Occurrences of Bd within the landscape were spatially autocorrelated and ponds within ~1000–1500 m of Bd hotspots were more likely to test positive. Local land use, (presence/absence of grazing or recreational activity and developed lands), did not influence Bd status of a pond, indicating that the most likely means of Bd transmission between ponds may be waterfowl and/or amphibians.     

Multiscale resistant kernel surfaces derived from inferred gene flow: An application with vernal pool breeding salamanders

The importance of assessing spatial data at multiple scales when modelling species–environment relationships has been highlighted by several empirical studies. However, no landscape genetics studies have optimized landscape resistance surfaces by evaluating relevant spatial predictors at multiple spatial scales. Here, we model multiscale/layer landscape resistance surfaces to estimate resistance to inferred gene flow for two vernal pool breeding salamander species, spotted (Ambystoma maculatum) and marbled (A. opacum) salamanders. Multiscale resistance surface models outperformed spatial layers modelled at their original spatial scale. A resistance surface with forest land cover at a 500‐m Gaussian kernel bandwidth and normalized vegetation index at a 100‐m Gaussian kernel bandwidth was the top optimized resistance surface for A. maculatum, while a resistance surface with traffic rate and topographic curvature, both at a 500‐m Gaussian kernel bandwidth, was the top optimized resistance surface for A. opacum. Species‐specific resistant kernels were fit at all vernal pools in our study area with the optimized multiscale/layer resistance surface controlling kernel spread. Vernal pools were then evaluated and scored based on surrounding upland habitat (local score) and connectivity with other vernal pools on the landscape, with resistant kernels driving vernal pool connectivity scores. As expected, vernal pools that scored highest were in areas within forested habitats and with high vernal pool densities and low species‐specific landscape resistance. Our findings highlight the success of using a novel analytical approach in a multiscale framework with applications beyond vernal pool amphibian conservation.     

Landscape genetics and least-cost path analysis reveal unexpected dispersal routes in the California tiger salamander (Ambystoma californiense)

A major goal of landscape genetics is to understand how landscapes structure genetic variation in natural populations. However, landscape genetics still lacks a framework for quantifying the effects of landscape features, such as habitat type, on realized gene flow. Here, we present a methodology for identifying the costs of dispersal through different habitats for the California tiger salamander ( Ambystoma californiense ), an endangered species restricted to grassland/vernal pool habitat mosaics. We sampled larvae from all 16 breeding ponds in a geographically restricted area of vernal pool habitat at the Fort Ord Natural Reserve, Monterey County, California. We estimated between-pond gene flow using 13 polymorphic microsatellite loci and constructed GIS data layers of habitat types in our study area. We then used least-cost path analysis to determine the relative costs of movement through each habitat that best match rates of gene flow measured by our genetic data. We identified four measurable rates of gene flow between pairs of ponds, with between 10.5% and 19.9% of larvae having immigrant ancestry. Although A. californiense is typically associated with breeding ponds in grassland habitat, we found that dispersal through grassland is nearly twice as costly as dispersal through chaparral and that oak woodland is by far the most costly habitat to traverse. With the increasing availability of molecular resources and GIS data, we anticipate that these methods could be applied to a broad range of study systems, particularly those with cryptic life histories that make direct observation of movement challenging.     

Plant communities as a tool in temporary ponds conservation in SW Portugal

Temporary ponds are seasonal wetlands annually subjected to extreme and unstable ecological conditions, neither truly aquatic nor truly terrestrial. This habitat and its flora have been poorly studied and documented because of the ephemeral character of the flora, the changeable annual weather that has a great effect on the small, herbaceous taxa and the declining abundance of temporary ponds. The objectives of this study are: (a) to define plant community diversity in terms of floristic composition of ephemeral wetlands in SW Portugal, (b) to identify temporary pond types according to their vegetation composition and (c) to identify those ponds that configure the European community priority habitat (3170* – Mediterranean temporary ponds). Vegetation sampling was conducted in 29 ponds, identifying 168 species grouped among 15 plant communities. Soil texture, pH, organic C and N content were measured, but only N and percent of clay appear to be related with the distribution of each community type. The results showed that ephemeral wetlands could be classified into four type: vernal pools, marshlands, deep ponds and disturbed wetlands. Vernal pools correspond to the Mediterranean temporary ponds (3170*), protected as priority habitat under the EU Habitats Directive. Submersed Isoetes species (Isoetes setaceum and Isoetes velatum) represents, together with Eryngium corniculatum, the indicator species for vernal pools. We identify also indicator plant communities of this priority habitat, namely I. setaceum and E. corniculatum–Baldellia ranunculoides plant communities. In this region, the conservation of temporary ponds has so far been compatible with traditional agricultural activities, but today these ponds are endangered by the intensification of agriculture and the loss of traditional land use practices and by the development of tourism. Guest editors: B. Oertli, R. Cereghino, A. Hull & R. Miracle Pond Conservation: From Science to Practice. 3rd Conference of the European Pond Conservation Network, Valencia, Spain, 14–16 May 2008     

Sublethal Effects of Nitrite on Eastern Tiger Salamander (<Emphasis Type="Italic">Ambystoma tigrinum tigrinum</Emphasis>) and Wood Frog (<Emphasis Type="Italic">Rana sylvatica</Emphasis>) Embryos and Larvae: Implications for Field Populations

Ephemeral pools, which can have high animal biomass and low dissolved oxygen, may be prone to nitrite accumulation. As such, it is important to understand how exposure to nitrite might affect development and growth of amphibians that breed in these ephemeral pools. Wood frog (Rana sylvatica) and eastern tiger salamander (Ambystoma tigrinum tigrinum) embryos and tadpoles and young larvae were exposed to elevated concentrations of nitrite derived from sodium nitrite: 0, 0.3, 0.6, 1.2, 2.1, 4.6, and 6.1 mg l⁻¹ NO₂–N. Increasing nitrite exposure slowed embryonic and larval development in both the eastern tiger salamander and the wood frog, reduced growth in tiger salamander embryos and larvae, and delayed metamorphosis in the wood frog. At concentrations less than 2 mg l⁻¹ NO₂–N nitrite delayed hatching, and at concentrations above 2 mg l⁻¹ time to hatching decreased causing more individuals to hatch at less developed stages. Nitrite also increased asynchrony in tiger salamander hatching. The sublethal effects of nitrite on amphibian development, growth and hatching could have serious repercussions on amphibian fitness in ephemeral environments. Potential increases in mortality on field populations caused by sublethal effects of nitrite are discussed.     

The molecular phylogenetics of endangerment: cryptic variation and historical phylogeography of the California tiger salamander, Ambystoma californiense

A primary goal of conservation genetics is the discovery, delimitation and protection of phylogenetic lineages within sensitive or endangered taxa. Given the importance of lineage protection, a combination of phylogeography, historical geology and molecular clock analyses can provide an important historical context for overall species conservation. We present the results of a range-wide survey of genetic variation in the California tiger salamander, Ambystoma californiense, as well as a summary of the past several million years of inundation and isolation of the Great Central Valley and surrounding uplands that constitute its limited range. A combination of population genetic and phylogenetic analyses of mitochondrial DNA variation among 696 samples from 84 populations revealed six well-supported genetic units that are geographically discrete and characterized by nonoverlapping haplotype distributions. Populations from Santa Barbara and Sonoma Counties are particularly well differentiated and geographically isolated from all others. The remaining units in the Southern San Joaquin Valley, Central Coast Range, Central Valley and Bay Area are separated by geological features, ecological zone boundaries, or both. The geological history of the California landscape is consistent with molecular clock evidence suggesting that the Santa Barbara unit has been isolated for at least 0.74-0.92 Myr, and the Sonoma clade is equally ancient. Our work places patterns of genetic differentiation into both temporal- and landscape-level contexts, providing important insights into the conservation genetics of the California tiger salamander.     

Macroinvertebrate community composition and diversity in ephemeral and perennial ponds on unregulated floodplain meadows in the UK

Ponds are common and abundant landscape features in temperate environments, particularly on floodplains where lateral connectivity with riverine systems persists. Despite their widespread occurrence and importance to regional diversity, research on the ecology and hydrology of temperate ephemeral and perennial floodplain ponds lags behind that of other shallow waterbodies. This study examines the aquatic macroinvertebrate diversity of 34 ponds (20 perennial and 14 ephemeral) on two unregulated riverine floodplain meadows in Leicestershire, UK. Perennial ponds supported nearly twice the diversity of ephemeral ponds. Despite frequent inundation of floodwater and connectivity with other floodplain waterbodies, ephemeral ponds supported distinct invertebrate communities when compared to perennial ponds. When the relative importance of physical, chemical, biological and spatial characteristics was examined, physical and chemical characteristics were found to account for more variation in community composition than biological or spatial variables. The results suggest that niche characteristics rather than neutral colonisation processes dominate the structure of invertebrate communities of floodplain ponds. The maintenance of pond networks with varying hydroperiod lengths and environmental characteristics should be encouraged as part of conservation management strategies to provide heterogeneous environmental conditions to support and enhance aquatic biodiversity at a landscape scale.     

Breeding system ofDaphniopsis ephemeralis: adaptations to a transient environment

Populations of the vernal cladoceranDaphniopsis ephemeralis are found in woodland ponds throughout southern Ontario. The species reproduces by cyclic parthenogenesis, and genotype frequencies at allozyme loci are ordinarily in good agreement with Hardy-Weinberg expectations. Occasional heterozygote deficiencies are apparently the consequence of admixture of ephippial hatchlings produced in temporally separated bouts of sexual reproduction. Considerable heterogeneity in genotypic frequencies exists among local populations in southwestern Ontario, indicating that gene flow among populations is restricted. Inbreeding coefficients suggest that populations receive an average of 0.3 migrants per generation. The completion of a sexual life cycle is made possible despite the brief persistence of populations by the emergence of males from ephippial eggs and by the production of equal numbers of male and female progeny in the first parthenogenetic brood.     

A comparative study of phenotypic traits related to resource utilization in anuran communities

Larval anuran communities vary along a gradient of pond permanency. The families Hylidae, Ranidae, and Bufonidae have each diversified into multiple pond types. Species using ponds that dry seasonally (vernal ponds) must compete well to metamorphose before pond drying, while permanent ponds, which contain more predators, produce weaker selection for competitive ability. Quantifying phenotypic traits related to resource acquisition in 14 anuran species provides insight into the mechanistic underpinnings of adaptive radiation in anuran lineages. Under controlled laboratory conditions and at both early and late developmental stages, relative growth rate, relative consumption rate, assimilation efficiency and production efficiency varied significantly among species. As predicted, vernal pond species had high growth rates relative to species using more than one pond type. However, within a pond type, families frequently differed in phenotype. In species using permanent ponds with fish predators, hylids had high growth rates while ranids had low growth rates, and in species using vernal ponds, bufonids had higher assimilation efficiencies than hylids. Differences also occurred between stages; hylids and ranids in permanent, but fishless, ponds were similar at an early stage, but late stage hylids in the same pond type had lower growth and consumption rates, and higher assimilation efficiencies than ranids. Functional relationships between phenotypic traits also differed among species and developmental stage. Negative correlations between evolutionary change (independent contrast values) in both mass and growth rate (both stages), and mass and consumption rate (late stage), suggest the presence of trade-offs. These results indicate that different lineages have diversified in different ways into the same pond types.     

Exotic plant invasions in an endemic‐rich habitat: The spread of an introduced Australian grass,Agrostis avenacea J. F. Gmel., in California vernal pools

Abstract The present abundance and historical spread of an exotic grass, Agrostis avenacea, is documented for California, USA, and for the vernal pools of San Diego County in particular. Agrostis avenacea is native to Australia where it is a common grass of ephemeral and fluctuating wetlands. California vernal pools, by reason of their extreme variability and high endemism, have been thought to be relatively resistant to invasion. The recent expansion of A. avenacea in San Diego County demonstrates, however, that the alleged resistance is probably a function of a relatively small pool of invaders and a low probability of targeted dispersal. Although A. avenacea is now abundant in pools with little current disturbance, human disturbance appears to have been a major factor that facilitated its initial establishment. This specific instance adds to the mounting evidence that there are probably few, if any, habitats immune to invasion.     

Tandem repeat markers for population genetic studies of the protected California tiger salamander (<Emphasis Type="Italic">Ambystoma californiense</Emphasis>)

Habitat loss is the single greatest threat to persistence of the critically threatened California tiger salamander (Ambystoma californiense). To aid management plans that designate critical habitat for this species, I developed and characterized 21 tetranucleotide microsatellite markers using two native populations in Santa Barbara and Alameda Counties. Allelic variation and average heterozygosities were lower in the endangered Santa Barbara population (allele range 1–4, mean 2.4; H _O = 0.308 H _E = 0.288) compared with the threatened Alameda population (allele range 2–10, mean 6.7; H _O = 0.712, H _E = 0.722). In-depth population studies using these markers will provide vital information for plans to assign critical habitat that optimize gene flow among breeding populations, as well as for identifying non-native hybrid genotypes that threaten native A. californiense stocks. Beyond the conservation goals for A. californiense, the close phylogenetic relationships within the tiger salamander complex also suggest a broad utility for population studies using these markers.     

Susceptibility of the endangered California tiger salamander, Ambystoma californiense, to ranavirus infection

Emerging infectious diseases are implicated in the declines and extinctions of amphibians worldwide. Ranaviruses in the family Iridoviridae are a global concern and have caused amphibian die-offs in wild populations in North America, Europe, South America, and in commercial populations in Asia and South America. The movement of amphibians for bait, food, pets, and research provides a route for the introduction of ranaviruses into naive and potentially endangered species. In this report, we demonstrate that the California tiger salamander, Ambystoma californiense, is susceptible to Ambystoma tigrinum virus (ATV). This virus has not been previously reported in California tiger salamander, but observed mortality in experimentally infected animals suggests that California tiger salamander populations could be adversely affected by an ATV introduction.     

Cattle waste reduces plant diversity in vernal pool mesocosms

In California, much of the remaining vernal pool habitat is used for cattle grazing. Some studies suggest that grazing helps promote native plant diversity on grasslands, but the impact of grazing on plants that reside in pool basins is largely unknown. We investigated how one aspect of cattle grazing, the deposition of waste, affects these plant species by adding dung and urine to mesocosms lined with vernal pool soil. As a result of dung input, orthophosphate, conductivity, and turbidity increased in our mesocosms while dissolved oxygen decreased. Such changes in water quality are consistent with a shift toward a eutrophic state. Algal biomass and percent-cover also increased in dung-treated mesocosms. When the mesocosms dried, vascular plant species richness and percent-cover in dung-treated mesocosms were reduced by up to 54% and 87%, respectively. We attribute this to light attenuation by algal mats that flourished in the nutrient-enriched water. We also found that dung input caused significant, but weak, shifts in the composition of the vascular plant community. We conclude that cattle grazing may be detrimental to plant communities in vernal pools via increased nutrient loading, which promotes algal growth. Any beneficial effects of grazing may thus be limited to the surrounding grassland. Studies that examine the regional-scale impacts of grazing on vernal pool grasslands should separately consider the impacts to local-scale (i.e., within-pool) plant diversity, as most of the threatened and endangered plant species of California vernal pools reside primarily in pool basins.     

Limited influence of local and landscape factors on finescale gene flow in two pond‐breeding amphibians

Dispersal and gene flow within animal populations are influenced by the composition and configuration of the landscape. In this study, we evaluated hypotheses about the impact of natural and anthropogenic factors on genetic differentiation in two amphibian species, the spotted salamander (Ambystoma maculatum) and the wood frog (Lithobates sylvaticus) in a commercial forest in central Maine. We conducted this analysis at two scales: a local level, focused on factors measured at each breeding pond, and a landscape level, focused on factors measured between ponds. We investigated the effects of a number of environmental factors in six categories including Productivity, Physical, Land Composition, Land Configuration, Isolation and Location. Embryos were sampled from 56 spotted salamander breeding ponds and 39 wood frog breeding ponds. We used a hierarchical Bayesian approach in the program GESTE at each breeding pond and a random forest algorithm in conjunction with a network analysis between the ponds. We found overall high genetic connectivity across distances up to 17 km for both species and a limited effect of natural and anthropogenic factors on gene flow. We found the null models best explained patterns of genetic differentiation at a local level and found several factors at the landscape level that weakly influenced gene flow. This research indicates multiscale investigations that incorporate local and landscape factors are valuable for understanding patterns of gene flow. Our findings suggest that dispersal rates in this system are high enough to minimize genetic structuring and that current forestry practices do not significantly impede dispersal.