Landscape genetics of the nonnative red fox of California

Invasive mammalian carnivores contribute disproportionately to declines in global biodiversity. In California, nonnative red foxes (Vulpes vulpes) have significantly impacted endangered ground‐nesting birds and native canids. These foxes derive primarily from captive‐reared animals associated with the fur‐farming industry. Over the past five decades, the cumulative area occupied by nonnative red fox increased to cover much of central and southern California. We used a landscape‐genetic approach involving mitochondrial DNA (mtDNA) sequences and 13 microsatellites of 402 nonnative red foxes removed in predator control programs to investigate source populations, contemporary connectivity, and metapopulation dynamics. Both markers indicated high population structuring consistent with origins from multiple introductions and low subsequent gene flow. Landscape‐genetic modeling indicated that population connectivity was especially low among coastal sampling sites surrounded by mountainous wildlands but somewhat higher through topographically flat, urban and agricultural landscapes. The genetic composition of populations tended to be stable for multiple generations, indicating a degree of demographic resilience to predator removal programs. However, in two sites where intensive predator control reduced fox abundance, we observed increases in immigration, suggesting potential for recolonization to counter eradication attempts. These findings, along with continued genetic monitoring, can help guide localized management of foxes by identifying points of introductions and routes of spread and evaluating the relative importance of reproduction and immigration in maintaining populations. More generally, the study illustrates the utility of a landscape‐genetic approach for understanding invasion dynamics and metapopulation structure of one of the world's most destructive invasive mammals, the red fox.     

Capture efficiency and trophic adaptations of a specialist and generalist predator: A comparison

Specialist true predators are expected to exhibit higher capture efficiencies for the capture of larger and dangerous prey than generalist predators due to their possession of specialized morphological and behavioral adaptations. We used an araneophagous spider (Lampona murina) and a generalist spider (Drassodes lapidosus) as phylogenetically related model species and investigated their realized and fundamental trophic niches and their efficacy with respect to prey capture and prey handling. The trophic niche of both species confirmed that Lampona had a narrow trophic niche with a predominance of spider prey (including conspecifics), while the niche of Drassodes was wide, without any preference. DNA analysis of the gut contents of Lampona spiders collected in the field revealed that spiders form a significant part of its natural diet. Lampona captured significantly larger prey than itself and the prey captured by Drassodes. As concerns hunting strategy, Lampona grasped the prey with two pairs of legs possessing scopulae, whereas Drassodes immobilized prey with silk. Lampona possess forelegs equipped with scopulae and a thicker cuticle similar to other nonrelated araneophagous spiders. Lampona fed for a longer time and extracted more nutrients than Drassodes. We show that specialized behavioral and morphological adaptations altogether increase the hunting efficiency of specialists when compared to generalists.     

Using the dog genome to find single nucleotide polymorphisms in red foxes and other distantly related members of the Canidae

Single nucleotide polymorphisms (SNP) are the ideal marker for characterizing genomic variation but can be difficult to find in nonmodel species. We explored the usefulness of the dog genome for finding SNPs in distantly related nonmodel canids and evaluated so-ascertained SNPs. Using 40 primer pairs designed from randomly selected bacterial artificial chromosome clones from the dog genome, we successfully sequenced 80-88% of loci in a coyote (Canis latrans), grey fox (Urocyon cinereoargenteus), and red fox (Vulpes vulpes), which compared favourably to a 60% success rate for each species using 10 primer pairs conserved across mammals. Loci were minimally heterogeneous with respect to SNP density, which was similar, overall, in a discovery panel of nine red foxes to that previously reported for a panel of eight wolves (Canis lupus). Additionally, individual heterozygosity was similar across the three canids in this study. However, the proportion of SNP sites shared with the dog decreased with phylogenetic divergence, with no SNPs shared between red foxes and dogs. Density of interspecific SNPs increased approximately linearly with divergence time between species. Using red foxes from three populations, we estimated F(ST) based on each of 42 SNPs and 14 microsatellites and simulated null distributions conditioned on each marker type. Relative to SNPs, microsatellites systematically underestimated F(ST) and produced biased null distributions, indicating that SNPs are superior markers for these functions. By reconstituting the frequency spectrum of SNPs discovered in nine red foxes, we discovered an estimated 77-89% of all SNPs (within the region screened) present in North American red foxes. In sum, these findings indicate that information from the dog genome enables easy ascertainment of random and gene-linked SNPs throughout the Canidae and illustrate the value of SNPs in ecological and evolutionary genetics.     

The effectiveness of short‐term fox control in protecting a seasonally vulnerable species,the Eastern Long‐necked Turtle (Chelodina longicollis)

Reducing predation by introduced predators on seasonally vulnerable prey is of interest to biodiversity and game managers around the world. In Australia, the Red Fox (Vulpes vulpes) is a significant predator of freshwater turtle nests, destroying up to 93% of nests. We used a nonrandomized intervention study to assess the effectiveness of a short‐term (3‐week) but broad‐scale baiting operation in reducing the level of nest predation on artificial turtle nests around a complex lake system during a major flooding event in north‐western Victoria. Estimates of fox occupancy declined from 0.58 (0.44–0.70 95% CI) to 0.34 (0.21–0.46 95% CI) following fox control. Modelling of nest‐survival rates indicated there was no significant change in survival rates. Effective short‐term predator control to protect seasonally vulnerable prey is desirable and achievable. Knowledge of underlying predator density, predator–bait encounter and consumption rates, and the optimal duration of short‐term control is needed to reduce the risk to prey.     

Stable isotope analysis as a tool to monitor dietary trends in little penguins Eudyptula minor

Long‐term dietary monitoring of seabirds can be used to relate population fluctuations to at‐sea events. Stomach flushing is a conventional dietary monitoring technique, but has a number of disadvantages. Stable isotope analysis (SIA) is a less invasive method that provides unbiased dietary information over a longer period. We evaluated stable isotope analysis as a potential tool for monitoring long‐term little penguin Eudyptula minor diet. We determined diet composition during the chick feeding stage using stomach flushing and SIA at three separate colonies, using spatial variation in diet as a surrogate for potential temporal variation. Bayesian isotopic mixing models were generated for blood and feathers to evaluate their ability to discriminate broad‐scale (fish, squid, crustaceans) and fine‐scale (individual prey species) diet composition. Differences in stable carbon and nitrogen isotope ratios were found between colonies: broad‐scale isotopic mixing models predicted different proportional contributions of broad taxa (fish, cephalopod, crustacean) to diet than was indicated by stomach samples, reflecting the bias incurred by one‐off stomach contents analysis. Fine‐scale isotopic mixing models predicted proportional contributions of prey items with less certainty. Blood isotopic mixing models had narrower confidence intervals than models for feathers, but trends in δ¹⁵N for feathers mirrored those for blood. Our results suggest that relying on stomach contents analysis to detect shifts in prey consumption in little penguins could be very misleading, resulting in a less‐than‐complete idea of total prey consumption. SIA of little penguin tissues could be used to monitor dietary shifts across dissimilar taxa that may affect population numbers, but would fail to detect shifts between fish species.     

Individual specialization and trophic adaptability of northern pike (Esox lucius): an isotope and dietary analysis

Northern pike (Esox lucius) are often considered to be specialist piscivores, but under some circumstances will continue to eat invertebrates as adults. To examine effects of fish assemblage composition on the trophic ecology of pike, we combined stable isotope analysis (SIA) of carbon and nitrogen and stomach content analysis (SCA) on pike from five lakes in northern Alberta, three of which contain only pike (“pike-only”) and two that also contain yellow perch (Perca flavescens) or white sucker (Catostomus commersoni) (“pike-other”). Fish were more important as prey and empty stomachs, which often characterize piscivores, were significantly more frequent in pike-other than in pike-only lakes. However, even though invertebrates were more important for pike in pike-only lakes, SIA and SCA indicated that invertebrates were also an important component of pike diets in pike-other lakes. SIA and SCA also revealed considerable intrapopulation variation in trophic ecology, with individuals in some populations differing by as much as two trophic levels. Comparisons of stomach contents and isotope signatures of the same fish suggested that within these variable populations, specialization on invertebrates or fish was a long-term trait of some individuals. SIA indicated that trophic position increased and diets shifted to a greater importance of littoral prey as pike grew in pike-only lakes, but not in lakes with other fish present. Trophic adaptability in northern pike is expressed at both the population level, where the trophic ecology is sensitive to differences in prey regimes, and at the organismal level, in the form of intrapopulation variation and individual specialization. Received: 1 July 1998 / Accepted: 3 February 1999     

The time scale of isotope signals in spiders: molting the remains of a previous diet

Stable isotope analysis (SIA) has emerged as an important tool for understanding consumer diets and diet shifts. However, although the general idea behind SIA is clear, the interpretation of data is often fraught with problems because tissue turnover and fractionations are not known. We investigated shifts in stable isotope composition of spiders following a diet shift, using mealworms fed either maize (C4) or wheat (C3) flour. Mealworms had different carbon isotope composition depending on their diet and this difference was reflected in spider body parts. In the experiment, we first fed the spiders on a diet of either maize‐fed or wheat‐fed mealworms and then switched diet at the time of the second molt. Spiders were then sampled repeatedly until the next molt. We sampled both legs and abdomens, as these are presumed to have different turnover of tissue, and also molt remains were sampled when this was relevant. The data indicated that the spider legs had a turnover of about 20 days, whereas the spider abdomens had a turnover of about 8 days. Molt remains had the slowest turnover and reflected the diet at the previous molt, when the exoskeleton was formed. Both these observations indicate that SIA may be successfully used for elucidating diet shifts. More problematic was the fact that fractionation of carbon isotope ratios varied with body parts and diets. When spiders were fed maize‐mealworms then the fractionation was larger for abdomens, but when the spiders were fed wheat‐mealworms then the fractionation was larger for legs. The mechanisms underlying this pattern are unclear and deserve further attention.     

Using stable isotope analysis to obtain dietary profiles from old hair: a case study from Plains Indians

Stable isotope composition of human tissue reflects that of foods consumed, and can provide information about diet independent of artifactual remains. Here we refine and test this method by analyzing nitrogen (delta(15)N) and carbon (delta(13)C) isotope ratios in historic North American Plains Indians hair. Gas-source isotope-ratio mass spectrometry provides high-precision data for both delta(15)N and delta(13)C (+/-0.2 per thousand, 1 sigma) in single hair strands as short as 2 cm (100-150 mug). Because hair contains more carbon than nitrogen, if only delta(13)C data are needed, shorter strands (<1 cm) can be analyzed. This reduction in sample size opens new opportunities for analysis of small hair fragments found in archaeological excavations, as well as for analysis of seasonal variations in long hair strands. We find distinct isotope profiles (delta(15)N vs. delta(13)C) for two cultural groups, the Lower Brule reservation Sioux of 1892 and the reservation Blackfoot of 1892 and 1935. The resultant dietary profiles indicate a higher consumption of meat by the Blackfoot and a higher consumption of maize (or of animals that had fed on maize or other C(4) plants) by the Lower Brule. The two groups of Blackfoot yield similar isotopic profiles despite the passage of four decades, suggesting a strong role for cultural preference even as food sources change. Such stable isotope profiles can be used to link samples from the same cultural tradition based on their similar diets.     

Determination of zooplankton dietary shift following a zebra mussel invasion, as indicated by stable isotope analysis

1. Freshwaters with established zebra mussel populations typically exhibit reduced chlorophyll a concentrations, but the subsequent impacts upon zooplankton are varied. We hypothesised that in an invaded system with less phytoplankton but available allochthonous subsidy, zooplankton may utilise greater proportions of allochthonous matter and that this could be traced by analysis of stable carbon and nitrogen isotopes. 2. We used archived zooplankton samples which had been consistently preserved and which spanned the invasion period of an Irish lake, Lough Erne. Increasing reliance upon allochthonous resources would be reflected in an increase in zooplankton δ¹³C away from phytoplankton which is relatively ¹³C‐depleted in humic‐stained L. Erne. 3. Analysis of a series of monthly samples (1992–96, 1999–2003) revealed significant ¹³C‐enrichment of mixed zooplankton, Eudiaptomus gracilis and Mysis relicta post‐zebra mussel invasion; δ¹³C values approached ?27‰ typical of terrestrial organic matter during spring and autumn. Changes in zooplankton elemental composition also suggested a switch to a lower quality diet. However, analysis of zooplankton δ¹³C from an annual, single‐point (June) time series spanning 28 years (1977–2004) suggested that when phytoplankton was sufficiently abundant, zooplankton used this resource and their δ¹³C remained relatively constant around ?32‰. Post‐invasion enrichment of mysid δ¹⁵N may reflect a shift towards carnivory, but planktonic prey abundance was reduced and a subsequent loss of body condition could result in the same isotopic changes. 4. Our results indicate that in L. Erne, when phytoplankton was reduced by zebra mussel filtering, zooplankton assimilated more from allochthonous matter, and potentially sustained a higher population than would otherwise be possible. Thus, zebra mussel impact on foodweb structure and function is likely to be different in lakes subject to varying subsidy levels.     

Foraging habits in a generalist predator: Sex and age influence habitat selection and resource use among bottlenose dolphins (Tursiops truncatus)

This study examines resource use (diet, habitat use, and trophic level) within and among demographic groups (males, females, and juveniles) of bottlenose dolphins (Tursiops truncatus). We analyzed the δ¹³C and δ¹⁵N values of 15 prey species constituting 84% of the species found in stomach contents. We used these data to establish a trophic enrichment factor (TEF) to inform dietary analysis using a Bayesian isotope mixing model. We document a TEF of 0‰ and 2.0‰ for δ¹³C and δ¹⁵N, respectively. The dietary results showed that all demographic groups relied heavily on low trophic level seagrass‐associated prey. Bayesian standard ellipse areas (SEA_b) were calculated to assess diversity in resource use. The SEA_b of females was nearly four times larger than that of males indicating varied resource use, likely a consequence of small home ranges and habitat specialization. Juveniles possessed an intermediate SEA_b, generally feeding at a lower trophic level compared to females, potentially an effect of natal philopatry and immature foraging skills. The small SEA_b of males reflects a high degree of specialization on seagrass associated prey. Patterns in resource use by the demographic groups are likely linked to differences in the relative importance of social and ecological factors.     

TDFCAM: A method for estimating stable isotope trophic discrimination in wild populations

1. Stable isotope mixing models (SIMMs) are widely used for characterizing wild animal diets. Such models rely upon using accurate trophic discrimination factors (TDFs) to account for the digestion, incorporation, and assimilation of food. Existing methods to calculate TDFs rely on controlled feeding trials that are time-consuming, often impractical for the study taxon, and may not reflect natural variability of TDFs present in wild populations.
2. We present TDF_CAM as an alternative approach to estimating TDFs in wild populations, by using high-precision diet estimates from a secondary methodological source—in this case nest cameras—in lieu of controlled feeding trials, and provide a framework for how and when it should be applied.
3. In this study, we evaluate the TDF_CAM approach in three datasets gathered on wild raptor nestlings (gyrfalcons Falco rusticolus; peregrine falcons Falco perigrinus; common buzzards Buteo buteo) comprising contemporaneous δ¹³C & δ¹⁵N stable isotope data and high-quality nest camera dietary data. We formulate Bayesian SIMMs (BSIMMs) incorporating TDFs from TDF_CAM and analyze their agreement with nest camera data, comparing model performance with those based on other relevant TDFs. Additionally, we perform sensitivity analyses to characterize TDF_CAM variability, and identify ecological and physiological factors contributing to that variability in wild populations.
4. Across species and tissue types, BSIMMs incorporating a TDF_CAM outperformed any other TDF tested, producing reliable population-level estimates of diet composition. We demonstrate that applying this approach even with a relatively low sample size (n < 10 individuals) produced more accurate estimates of trophic discrimination than a controlled feeding study conducted on the same species. Between-individual variability in TDF_CAM estimates for ∆¹³C & ∆¹⁵ N increased with analytical imprecision in the source dietary data (nest cameras) but was also explained by natural variables in the study population (e.g., nestling nutritional/growth status and dietary composition).
5. TDF_CAM is an effective method of estimating trophic discrimination in wild animal populations. Here, we use nest cameras as source dietary data, but this approach is applicable to any high-accuracy method of measuring diet, so long as diet can be monitored over an interval contemporaneous with a tissue's isotopic turnover rate.

     

Diet of harbor porpoises along the Dutch coast: A combined stable isotope and stomach contents approach

High stranding frequency of porpoises, Phocoena phocoena, along the Dutch coast since 2006 has led to increased interest in the ecology of porpoises in the North Sea. Stranded porpoises were collected along the Dutch coast (2006–2008) and their diet was assessed through stomach content and stable isotope analysis (δ¹³C and δ¹⁵N) of porpoise muscle and prey. Stable isotope analysis (SIAR) was used to estimate the contribution of prey species to the porpoises' diet. This was compared to prey composition from stomach contents, to analyze differences between long‐ and short‐term diet. According to stomach contents, 90.5% of the diet consisted of gobies, whiting, lesser sandeel, herring, cod, and sprat. Stable isotope analysis revealed that 70‐83% of the diet consisted of poor cod, mackerel, greater sandeel, lesser sandeel, sprat, and gobies, highlighting a higher importance of pelagic, schooling species in the porpoises' diet compared to stomach contents. This could be due to prey distribution as well as differences in behavior of porpoises and prey between the coastal zone and offshore waters. This study supports the need for multi‐method approaches. Future ecological and fishery impact assessment studies and management decisions for porpoise conservation should acknowledge this difference between the long‐ and short‐term diet.     

Stable carbon isotope composition of bone hydroxylapatite: significance in paleodietary analysis

The stable carbon isotope composition of the structural carbonate derived from animal bone hydroxylapatite (δ¹³C_B-HA) could record an animal’s diet. These records provide critical evidence for different paleontological disciplines, e.g., paleodiet analyses, and paleoclimate reconstructions. Compared to those of other body tissues, such as bone collagen or teeth enamel hydroxylapatite, δ¹³C_B-HA values record information on the whole diet of an animal in its last years. δ¹³C_B-HA can be applied to fossil animals of various body sizes. The δ¹³C analytical instruments available only require that prepared bone samples be approximately 2–5 mg for precise measurement, allowing δ¹³C_B-HA analysis to be feasible on most vertebrate fossils without destructive sampling, especially on small mammals or birds whose teeth are not large enough for sampling or are lost. Moreover, δ¹³C_B-HA can be used from different times or under less than ideal burial environments. For fossils dating back to Devonian or buried in hot and humid regions, dietary information has been completely lost in bone collagen during post-depositional processes but still remained in the δ¹³C_B-HA values because hydroxylapatite is less influenced by diagenetic effects after deposition. In addition, systematic methods such as X-ray diffraction and Fourier transform infrared spectroscopy have been developed to qualitatively or semiquantitatively assess the influence of diagenesis on bone hydroxylapatite to ensure the credibility of the δ¹³C_B-HA values. With the above merits, δ¹³C_B-HA analysis is therefore becoming an increasingly important method in paleodiet-related research. Currently, applications of the δ¹³C_B-HA method on fossil animals are primarily focused on two aspects, namely, paleodietary reconstruction of fossil animals with uncertain diets and paleoenvironmental reconstruction based on the δ¹³C_B-HA values of fossil herbivores. The published researches, combined with our new results from early birds, demonstrate the considerable significance of the δ¹³C_B-HA method in paleontological and paleoenvironmental research. Notably, the δ¹³C_B-HA-based paleodietary analysis of early vertebrates, especially the large number of small birds or mammals discovered in the past decades would be an important work in the near future.     

Spatial subsidies in spider diets vary with shoreline structure: Complementary evidence from molecular diet analysis and stable isotopes

Inflow of matter and organisms may strongly affect the local density and diversity of organisms. This effect is particularly evident on shores where organisms with aquatic larval stages enter the terrestrial food web. The identities of such trophic links are not easily estimated as spiders, a dominant group of shoreline predator, have external digestion. We compared trophic links and the prey diversity of spiders on different shore types along the Baltic Sea: on open shores and on shores with a reed belt bordering the water. A priori, we hypothesized that the physical structure of the shoreline reduces the flow between ecosystem and the subsidies across the sea–land interface. To circumvent the lack of morphologically detectable remains of spider prey, we used a combination of stable isotope and molecular gut content analyses. The two tools used for diet analysis revealed complementary information on spider diets. The stable isotope analysis indicated that spiders on open shores had a marine signal of carbon isotopes, while spiders on reedy shores had a terrestrial signal. The molecular analysis revealed a diverse array of dipteran and lepidopteran prey, where spiders on open and reedy shores shared a similar diet with a comparable proportion of chironomids, the larvae of which live in the marine system. Comparing the methods suggests that differences in isotope composition of the two spider groups occurred because of differences in the chironomid diets: as larvae, chironomids of reedy shores likely fed on terrestrial detritus and acquired a terrestrial isotope signature, while chironomids of open shores utilized an algal diet and acquired a marine isotope signature. Our results illustrate how different methods of diet reconstruction may shed light on complementary aspects of nutrient transfer. Overall, they reveal that reed belts can reduce connectivity between habitats, but also function as a source of food for predators.