Persistence and extirpation in invaded landscapes: patch characteristics and connectivity determine effects of non-native predatory fish on native salamanders

Studies have demonstrated negative effects of non-native, predatory fishes on native amphibians, yet it is still unclear why some amphibian populations persist, while others are extirpated, following fish invasion. We examined this question by developing habitat-based occupancy models for the long-toed salamander (Ambystoma macrodactylum) and non-native fish using survey data from 1,749 water bodies across 470 catchments in the Northern Rocky Mountains, USA. We first modeled the habitat associations of salamanders at 468 fishless water bodies in 154 catchments where non-native fish were historically, and are currently, absent from the entire catchment. We then applied this habitat model to the complete data set to predict the probability of salamander occupancy in each water body, removing any effect of fish presence. Finally, we compared field-observed occurrences of salamanders and fish to modeled probability of salamander occupancy. Suitability models indicated that fish and salamanders had similar habitat preferences, possibly resulting in extirpations of salamander populations from entire catchments where suitable habitats were limiting. Salamanders coexisted with non-native fish in some catchments by using marginal quality, isolated (no inlet or outlet) habitats that remained fishless. They rarely coexisted with fish within individual water bodies and only where habitat quality was highest. Connectivity of water bodies via streams resulted in increased probability of fish invasion and consequently reduced probability of salamander occupancy. These results could be used to identify and prioritize catchments and water bodies where control measures would be most effective at restoring amphibian populations. Our approach could be useful as a framework for improved investigations into questions of persistence and extirpation of native species when non-native species have already become established.     

Spatial extent of analysis influences observed patterns of population genetic structure in a widespread darter species (Percidae)

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Impact of introduced brown trout on native fish communities in the Pilica River catchment (Poland)

We compared post- and pre-introduction data for the upper Pilica River and its tributaries to investigate the impact of introduced non-native brown trout on native fish communities. Extirpations of species were recorded. More changes concerned differences in abundance and distribution in the investigated rivers rather than extirpations. Human stressors (pollution, regulation) obviously helped the invasion of trout. Repeated introduction to one tributary of the Pilica enabled brown trout to survive for 10 years, despite the presence of pike and the recent appearance of domestic pollution.     

Effects of forest-dune ecotone management on the endangered heath grasshopper, Chorthippus vagans (Orthoptera: Acrididae)

Dry, oligotrophic ecosystems are highly threatened in Europe due to massive changes in land use and eutrophication. The conservation of these xeric habitats has received much attention, whereas the ecotones between xeric habitats and other habitat types are often disregarded. One species which mainly inhabits the transition zone between pine forests and adjacent xeric habitats is the heath grasshopper, Chorthippus vagans. This species is endangered in large parts of Europe. One of the largest populations in northern Germany is found on a degraded inland dune near Hanover. This population is threatened by dense growth of deciduous trees and litter accumulation. We analyzed changes in the distribution of this population after the implementation of conservation measures (thinning out the forest and removal of leaf litter). Moreover, we examined dispersal distances of the species in order to assess its colonization potential. We also studied the microhabitat preferences of C. vagans to assess key factors influencing its local distribution. Our data show a substantial growth in population size, which might be a consequence of the conservation measures. New patches on the dune were colonized, promoting dispersal between the subpopulations. We propose that restoration of forest-dune ecotones should be considered more often in landscape planning and conservation management.     

Do pathogens reduce genetic diversity of their hosts? Variable effects of sylvatic plague in black‐tailed prairie dogs

Introduced diseases can cause dramatic declines in—and even the loss of—natural populations. Extirpations may be followed by low recolonization rates, leading to inbreeding and a loss of genetic variation, with consequences on population viability. Conversely, extirpations may create vacant habitat patches that individuals from multiple source populations can colonize, potentially leading to an influx of variation. We tested these alternative hypotheses by sampling 15 colonies in a prairie dog metapopulation during 7 years that encompassed an outbreak of sylvatic plague, providing the opportunity to monitor genetic diversity before, during and after the outbreak. Analysis of nine microsatellite loci revealed that within the metapopulation, there was no change in diversity. However, within extirpated colonies, patterns varied: In half of the colonies, allelic richness after recovery was less than the preplague conditions, and in the other half, richness was greater than the preplague conditions. Finally, analysis of variation within individuals revealed that prairie dogs present in recolonized colonies had higher heterozygosity than those present before plague. We confirmed plague survivorship in six founders; these individuals had significantly higher heterozygosity than expected by chance. Collectively, our results suggest that high immigration rates can maintain genetic variation at a regional scale despite simultaneous extirpations in spatially proximate populations. Thus, virulent diseases may increase genetic diversity of host populations by creating vacant habitats that allow an influx of genetic diversity. Furthermore, even highly virulent diseases may not eliminate individuals randomly; rather, they may selectively remove the most inbred individuals.     

The significance of meandering channel to habitat diversity and fish assemblage: a case study in the Shibetsu River,northern Japan

This study examined the structure and function of habitats for fish, the contribution to fish populations, and the effects of channel modification on habitats and fish populations in the lowland meandering Shibetsu River, northern Japan. Electrofishing and environmental measurements were conducted in bank areas of habitats constituting natural meandering and modified reaches. All types of habitats in a meandering reach highly contributed to the fish population(s). In particular, the contributions of lateral and wood habitats to fish populations were generally high, despite the low spatial extent of these habitats. The modified reach was simplified and had fewer types of habitats with uniform currents, and there was a low abundance of most fish within these habitats. Abundance of each fish group (taxa) was negatively affected by the changes in the habitats and/or channel shortening (i.e., decrease in the absolute abundance of habitat) due to river modification, which was implemented during 1950–1978. This study suggests that the recovery of all the habitat types is important in meander restoration and that the changes in habitat types and abundance should be examined in monitoring meander restoration and channel shortening.     

Habitat size, recruitment, and longevity as factors limiting population size in stage-structured species

Surprisingly little research has evaluated how habitat size may limit the population size of species that use different habitats at different stages of their lives. Here we develop simple discrete-time models to describe the population dynamics of species that use separate juvenile and adult habitats. Analytic solutions, model simulations, and elasticity and sensitivity analyses show that adult abundance is only limited by the size of the juvenile habitat when both adult habitat size and recruitment are much larger than juvenile habitat size. Juvenile habitat plays a marginally greater role in limiting population size for species with closed populations, where recruitment is proportional to adult abundance, versus open populations. Because adult populations often accumulate pulses of juveniles, adult habitat size can strongly limit population size over a broad range of parameter values, an effect that increases as the longevity of a species increases. Limited empirical research from a range of taxa supports these model predictions, although few studies were designed to actually test the limiting role of juvenile versus adult habitat. Future research must carefully evaluate whether and how processes at the juvenile stage affect adult abundance, and conservation efforts may be able to use this model to evaluate the cost-effectiveness, vis-a-vis increasing adult abundance, of time and money allocated to protecting juvenile habitats.     

Phylogeographic structure and gene flow in the scale-eating cichlid Perissodus microlepis (Teleostei, Perciformes, Cichlidae) in southern Lake Tanganyika

One of the most fragmented habitats in freshwater lakes is the rocky littoral zone, where the already richly structured habitat is frequently interspersed with more pronounced barriers such as sandy bays, river estuaries and deep slopes. Although habitat fragmentation generally constrains the dispersal of specialized rock-dwelling species, patterns of population structure vary in sympatric taxa due to species-specific traits. In the present study, we examine the phylogeographic and population genetic structure of Perissodus microlepis , a presumptively highly mobile scale-eating cichlid fish endemic to Lake Tanganyika with a lake-wide distribution in the rocky littoral zone and no obvious geographical colour variation. Analysis of the mitochondrial DNA of six populations in the southern end of the lake suggests isolation by distance along rocky shoreline. Across a large muddy bay, a phylogeographic break indicates that environmental barriers restrict gene flow even in this highly mobile species. Restricted dispersal across the bay is not necessarily a consequence of an intrinsic propensity to avoid sand, but may be connected with the association between P. microlepis and other rock-dwelling fish, which the scale-eaters mimic and intermingle in order to be able to approach other fish to rip off scales from their bodies.     

Genetic structure of a native cyprinid in a reservoir‐altered stream network

1. Reservoirs modify riverine ecosystems worldwide, and often with deleterious impacts on native biota. The immediate effects of reservoirs on native fish species below dams and in impounded reaches have received considerable attention, but it is unclear how reservoirs may affect fish species at larger spatial and temporal scales. Documented declines of stream fish populations in direct tributaries of reservoirs suggest reservoir pools may reduce gene flow among historically connected populations. 2. Because of increased predator densities in reservoirs and the extent of habitat alteration in impounded reaches, I predicted reservoir habitats would reduce gene flow among small‐bodied fish populations separated by reservoir habitat. I used microsatellite markers to assess the spatial genetic structure of populations of the red shiner (Cyprinella lutrensis), in a reservoir‐fragmented stream network (Lake Texoma, U.S.A.). I also tested the prediction that populations in two direct tributaries that have experienced population declines would have low genetic diversity. Individuals were collected from six sites upstream of the reservoir, three sites in the reservoir and three sites in direct tributaries of the reservoir during 2008 and 2009. 3. Results indicate that most populations were isolated by distance with little divergence among populations. In one direct tributary population, however, there was substantial genetic divergence, and genetic diversity was significantly lower than in other populations. Gene flow also seemed to be lower in reservoir habitats than in intact stream habitats, suggesting reservoir habitats may be reducing gene flow among the reservoir‐separated populations. These results indicate that reservoirs may reduce gene flow among reservoir‐fragmented stream fish populations, altering the evolutionary trajectories of fragmented populations.     

Genetic structure in remnant populations of an endangered cyprinodontid fish, <Emphasis Type="Italic">Orestias ascotanensis</Emphasis>, endemic to the Ascotán salt pan of the Altiplano

The impact of recent habitat fragmentation on population genetic diversity and structure has often been studied, mainly related to anthropogenic causes; however its long-term effect has been much less evaluated. In this study we analyzed the genetic variability of Orestias ascotanensis, a fish endemic to the Ascotán salt pan of Chile. This species, which formed a single and large population during the last wet period that ended 10,000 years ago, is currently represented by small populations inhabiting freshwater springs on the eastern border of the salt pan. Therefore, this species represents a unique model to evaluate the consequences of a drastic habitat fragmentation process that initiated thousands of years ago. Analysis of the control region of the mitochondrial DNA revealed high genetic diversity (haplotipic diversity ranged between 0.78 and 0.94) and marked differences among populations (Φ_ST = 0.46). Estimated effective population sizes greatly surpassed the real sizes, particularly among springs that remained connected. These results reflect the long-term consequences of habitat fragmentation on natural populations: structuring of the populations and loss of genetic diversity of the isolated fragments.     

Simple predictions of instream habitat model outputs for fish habitat guilds in large streams

1. In the context of a generalised modification of hydraulic conditions in medium to large streams, modelling the impacts of stream regulation on fish communities in multiple streams is an important challenge for basic and applied freshwater ecology. Conventional instream habitat models such as PHABSIM link a hydraulic model with preference curves for various species to estimate habitat value changes with discharge in stream reaches. Despite world‐wide applications, they have been scarcely used in multiple sites with multiple species. 2. We assigned 21 size classes of European fish species to four habitat guilds (cluster analysis grouping size classes with comparable microhabitat preference curves). Then, we ran a conventional instream habitat model on 28 French stream reaches belonging to the `barbel zone', to estimate habitat values versus discharge curves for the 21 size classes. We summarised the outputs as mean habitat values for guilds, and tested if they were predictable from average characteristics of reaches (discharge, depth, width, particle size). 3. As was obtained elsewhere for populations, habitat values for guilds were strongly related to average, dimensionless characteristics of reaches. The Reynolds number of reaches, equivalent to a discharge per width unit, reflected most of the discharge‐dependent changes in habitat values (within reaches). In particular, habitat values of species preferring bank (respectively midstream) microhabitats decreased (respectively increased) with increasing Reynolds number. The Froude number at median discharge was the major predictor of reach‐dependent but discharge‐independent variations in habitat values. Habitat values of species preferring riffle versus pool or bank microhabitats were higher in reaches with high Froude numbers. These relationships were consistent with existing knowledge on the different species. 4. Such results suggest that the input variables required to estimate habitat values for fish communities can be greatly simplified, as illustrated by a general estimation of the sensitivity of species preferring midstream habitats to discharge changes in any reach. Cost‐efficient alternatives to conventional instream habitat models should facilitate their validation in multiple sites, a point that remains critical in instream habitat modelling of fish communities.     

Range‐wide patterns of greater sage‐grouse persistence

Aim Greater sage‐grouse (Centrocercus urophasianus), a shrub‐steppe obligate species of western North America, currently occupies only half its historical range. Here we examine how broad‐scale, long‐term trends in landscape condition have affected range contraction. Location Sagebrush biome of the western USA. Methods Logistic regression was used to assess persistence and extirpation of greater sage‐grouse range based on landscape conditions measured by human population (density and population change), vegetation (percentage of sagebrush habitat), roads (density of and distance to roads), agriculture (cropland, farmland and cattle density), climate (number of severe and extreme droughts) and range periphery. Model predictions were used to identify areas where future extirpations can be expected, while also explaining possible causes of past extirpations. Results Greater sage‐grouse persistence and extirpation were significantly related to sagebrush habitat, cultivated cropland, human population density in 1950, prevalence of severe droughts and historical range periphery. Extirpation of sage‐grouse was most likely in areas having at least four persons per square kilometre in 1950, 25% cultivated cropland in 2002 or the presence of three or more severe droughts per decade. In contrast, persistence of sage‐grouse was expected when at least 30 km from historical range edge and in habitats containing at least 25% sagebrush cover within 30 km. Extirpation was most often explained (35%) by the combined effects of peripherality (within 30 km of range edge) and lack of sagebrush cover (less than 25% within 30 km). Based on patterns of prior extirpation and model predictions, we predict that 29% of remaining range may be at risk. Main Conclusions Spatial patterns in greater sage‐grouse range contraction can be explained by widely available landscape variables that describe patterns of remaining sagebrush habitat and loss due to cultivation, climatic trends, human population growth and peripherality of populations. However, future range loss may relate less to historical mechanisms and more to recent changes in land use and habitat condition, including energy developments and invasions by non‐native species such as cheatgrass (Bromus tectorum) and West Nile virus. In conjunction with local measures of population performance, landscape‐scale predictions of future range loss may be useful for prioritizing management and protection. Our results suggest that initial conservation efforts should focus on maintaining large expanses of sagebrush habitat, enhancing quality of existing habitats, and increasing habitat connectivity.     

Effects of an introduced crayfish, Procambarus clarkii, on the distribution of south-western Iberian amphibians in their breeding habitats

The introduction of exotic species in aquatic habitats is one of the causes for the amphibian declines observed worldwide. In the 1970s, the red swamp crayfish Procambarus clarkii was introduced in the southwest Iberian Peninsula, where no native crayfish occur. In this study we assess the effect of P. clarkii presence in the breeding site distribution of each of the 13 southwest Iberian amphibians, while simultaneously accounting for the effects of potentially confounding habitat variables, as well as for the effects of the other large aquatic predators in the study area – predatory fish. Amphibian species richness was lower in places where P. clarkii was present than in places without P. clarkii , regardless of fish presence. After accounting for habitat variables and fish, crayfish presence was a negative predictor of the breeding probability for all urodeles ( Pleurodeles waltl , Salamandra salamandra , Triturus boscai and T. marmoratus ) and for two anurans ( Pelobates cultripes and Bufo bufo ). The majority of the species affected usually breed in temporary ponds without fish, but that may be colonized by the crayfish. The ongoing expansion of P. clarkii may eventually lead to a growing isolation of amphibian populations and ultimately to local extinctions and a permanent alteration of the amphibian communities in southwest Iberian Peninsula.     

Allee effects and extinction in a lattice model

In the interest of conservation, the importance of having a large habitat available for a species is widely known. Here, we introduce a lattice-based model for a population and look at the importance of fluctuations as well as that of the population density, particularly with respect to Allee effects. We examine the model analytically and by Monte Carlo simulations and find that, while the size of the habitat is important, there exists a critical population density below which the probability of extinction is greatly increased. This has large consequences with respect to conservation, especially in the design of habitats and for populations whose density has become small. In particular, we find that the probability of survival for small populations can be increased by a reduction in the size of the habitat and show that there exists an optimal size reduction.     

Discerning invasion history in an ephemerally connected system: landscape genetics of Procambarus clarkii in Ash Meadows,Nevada

The delimitation of dispersal routes used by individuals moving between populations has the potential to direct management efforts aimed at limiting the spread of invasive species. Red swamp crayfish (Procambarus clarkii) have successfully invaded aquatic ecosystems across much of the globe, causing loss of biodiversity and habitat destruction. Our research focuses on a Mojave Desert spring system in Ash Meadows National Wildlife Refuge, where a combination of anthropogenic habitat degradation and the establishment of invasive species have caused extinctions, extirpations, and severe population declines of endangered fishes. To infer the invasion history of hydrologically isolated springs, we tested alternative hypotheses of P. clarkii dispersal routes and colonization events throughout Ash Meadows using a landscape genetics approach that combined analysis of microsatellite and mitochondrial DNA genotypes with geographic information system (GIS) mapping. Modeled historic outflows, in conjunction with waterway mapping based on aerial imagery and LiDAR data, show variable drainage routes across the flat topography of Ash Meadows. Estimates of gene flow between P. clarkii populations revealed the drainages utilized by crayfish to move from central to peripheral springs. Additionally, analyses of mtDNA haplotype diversity and distribution suggest isolated springs were colonized by few individuals, and subsequent emigration has been rare. These results will inform ecological restoration in Ash Meadows by directing the placement of barriers to prevent reinvasion of distal springs after eradication of P. clarkii populations. Finally, this research provides a case study for elucidating the functional connectivity of ephemerally connected landscapes, using the integration of genetic and GIS techniques.     

Allee effects and extinction in a lattice model

In the interest of conservation, the importance of having a large habitat available for a species is widely known. Here, we introduce a lattice-based model for a population and look at the importance of fluctuations as well as that of the population density, particularly with respect to Allee effects. We examine the model analytically and by Monte Carlo simulations and find that, while the size of the habitat is important, there exists a critical population density below which the probability of extinction is greatly increased. This has large consequences with respect to conservation, especially in the design of habitats and for populations whose density has become small. In particular, we find that the probability of survival for small populations can be increased by a reduction in the size of the habitat and show that there exists an optimal size reduction.     

Avian population consequences of climate change are most severe for long-distance migrants in seasonal habitats

One consequence of climate change is an increasing mismatch between timing of food requirements and food availability. Such a mismatch is primarily expected in avian long-distance migrants because of their complex annual cycle, and in habitats with a seasonal food peak. Here we show that insectivorous long-distance migrant species in The Netherlands declined strongly (1984–2004) in forests, a habitat characterized by a short spring food peak, but that they did not decline in less seasonal marshes. Also, within generalist long-distance migrant species, populations declined more strongly in forests than in marshes. Forest-inhabiting migrant species arriving latest in spring declined most sharply, probably because their mismatch with the peak in food supply is greatest. Residents and short-distance migrants had non-declining populations in both habitats, suggesting that habitat quality did not deteriorate. Habitat-related differences in trends were most probably caused by climate change because at a European scale, long-distance migrants in forests declined more severely in western Europe, where springs have become considerably warmer, when compared with northern Europe, where temperatures during spring arrival and breeding have increased less. Our results suggest that trophic mismatches may have become a major cause for population declines in long-distance migrants in highly seasonal habitats.     

Habitat specialization and adaptive phenotypic divergence of anuran populations

We tested for adaptive population structure in the frog Rana temporaria by rearing tadpoles from 23 populations in a common garden experiment, with and without larval dragonfly predators. The goal was to compare tadpole phenotypes with the habitats of their source ponds. The choice of traits and habitat variables was guided by prior information about phenotypic function. There were large differences among populations in life history, behaviour, morphological shape, and the predator-induced plasticities in most of these. Body size and behaviour were correlated with predation risk in the source pond, in agreement with adaptive population divergence. Tadpoles from large sunny ponds were morphologically distinct from those inhabiting small woodland ponds, although here an adaptive explanation was unclear. There was no evidence that plasticity evolves in populations exposed to more variable environments. Much among-population variation in phenotype and plasticity was not associated with habitat, perhaps reflecting rapid changes in wetland habitats.     

Host-dependent genetic variation in freshwater pearl mussel (Margaritifera margaritifera L.)

Freshwater fishes are vulnerable to changes in water quality, physical habitat and connectivity resulting from drought, particularly in regulated rivers. When adequate river flows return, the recovery of populations might depend on the duration and consequences of drought. Rivers of the highly regulated Murray–Darling Basin in south-eastern Australia terminate at two large, shallow lakes that are separated from the estuary by tidal barrages. Over-abstraction of water and widespread prolonged drought (1997–2010) placed the lakes under severe environmental stress, culminating in critical water level recession from 2007 to 2010. Concurrently, most freshwater fish populations collapsed. We investigate shifts in fish assemblages resulting from habitat inundation in the lakes following the drought. The inundation and re-connection of the lakes and fringing habitats led to a substantial reduction of salinity throughout the region, and aquatic vegetation shifted from salt-tolerant to freshwater species. Fish assemblages became increasingly characterized by common freshwater taxa (ecological generalists), including high proportions of alien species. There were no indications of population recovery for three threatened species. The findings emphasize that short-lived fishes with specialized habitat requirements are vulnerable to severe population declines during prolonged drought in regulated rivers, which might restrict their recovery when adequate flows return.     

Large-scale intraspecific variation in life-history traits of European freshwater fish

Aims To test the magnitude and direction of the effects of large‐scale environmental factors (latitude and habitat type: lotic or lentic) on the intraspecific variations in multiple life‐history traits, across multiple European freshwater fish species. To test the relevance of defining species traits by quantifying the magnitude of interspecific vs. intraspecific variability in traits. Location Europe. Methods We obtained estimates of 11 fish traits from published sources for 1089 populations of 25 European freshwater fish species. Traits were: longevity, maximal length, growth rate, asymptotic length, mortality rate, age and length at maturation, fecundity, egg size, gonadosomatic index, and length of breeding season. We described population habitats by latitude and habitat type (lotic or lentic), when available. For each species we tested the combined effect of latitude and habitat type on the intraspecific variation of each trait using analysis of covariance (ancova ). We compared the intraspecific variation in traits with the variation between species using an analysis of variance (anova ) for each trait, all species pooled. Results We found a consistent effect in direction of latitude on six traits, but we showed that this effect is not always significant across species. Higher‐latitude populations often grew more slowly, matured later, had a longer life span and a higher maximal and asymptotic length, and allocated more energy to reproduction than populations at lower latitudes. By contrast, we noted only a slight effect of habitat type on the intraspecific variation in traits, except for Salmo trutta. All traits varied significantly between species. However, traits such as growth rate, mortality rate and length of breeding season varied more between populations than between species, whereas fecundity and traits associated with body length varied more between species. Main conclusions Latitude, in contrast to habitat type, is an important factor influencing several traits of geographically widely dispersed populations of multiple European freshwater fish species. Species traits that vary more between species than between populations are attractive variables for understanding and predicting the responses of stream fish communities to their environment.