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.     

Sources of Lipids in Anoxic Lacustrine Sediments Using Stable Carbon Isotopes

The origin of organic matter in recent anoxic sediments of the alpine Lake Bled (NW Slovenia) was determined by analyzing the carbon isotope composition of lipid biomarkers, i.e. alkanes, alcohols, sterols and fatty acids, busing compound specific, carbon isotope analysis. The results indicate that, although biomarker analysis indicated mostly plankton and terrestrial sources for lipids, an important part of sedimentary lipids, especially sterols, are autochthonous, of anaerobic microbial (methanotrophic) origin. Marked differences were observed in δ¹³C values of lipid biomarkers in settling particles collected 2 m above the bottom, and in δ¹³C values determined in surface sediment. These results indicate that even some compounds found in both particulate organic matter and sediments are the same in terms of chemical structures, their sources can be different and thus, isotopic composition should be used as a complementary tool for source identification.     

Natal Dispersal and Philopatry of Red Foxes in Urban and Agricultural Areas of Illinois

Abstract: Dispersal and philopatry may be influenced by habitat, intraspecific and interspecific interactions, and resource quality. Dispersal may vary substantially between urban and rural wildlife populations due to differences in urban-rural habitat and trophic relationships. We examined effects of environmental, body condition, and social influences on dispersal and philopatry of urban and rural red foxes (Vulpes vulpes) in east-central Illinois and western Indiana, USA. We recorded 96 dispersal events and 66 cases of philopatry in juvenile foxes. We used Akaike's Information Criterion to evaluate regression models of dispersal probability, initiation date, distance, and days spent dispersing. Habitat (i.e., urban-rural), sex, row-crop percentage in natal home ranges, family home-range overlap, and social interactions with family members all influenced dispersal probability. Juvenile foxes with fewer row crops in their home ranges, individuals with high intra-familial overlap of summer range, females, and urban foxes were associated with philopatry. Dispersals began mid-September and ended in March. Rural juveniles dispersed 23 days earlier than did urban conspecifics. Heavier foxes (capture wt) and those with heavily row-cropped home ranges dispersed earlier. Littermates dispersed at similar times, although in different directions. Dispersal distances averaged 44.8 km for all foxes (range = 1–478 km). Male and urban foxes dispersed farther than female and rural foxes, respectively. Time between dispersal and settlement averaged 41.2 days (range = 2–114 days), with urban foxes dispersing over longer time periods. Dispersal direction between the sexes had different directional distributions, though mean vectors for both were oriented north. Dispersing foxes selected cropland in proportion to availability, whereas grassland was selected preferentially. We demonstrate influences of habitat, resource availability, familial social interactions, and interspecific interactions on dispersal and philopatry of juvenile red foxes in an intensively row-cropped region of the Midwest. Our findings demonstrate red fox dispersal ecology differences in urban and rural environments. In intensively row-cropped regions of the Midwest where landscape crop harvest alters dispersal timing, minimizing seasonal habitat changes with permanent vegetative structure (e.g., crop food plots, native grass fields) would likely delay dispersal activity, and increase survival.     

Diet and trophic position of two mackerel species in the archipelago of Madeira,Portugal

The Atlantic chub mackerel Scomber colias and the blue jack mackerel Trachurus picturatus are two abundant species in the Macaronesia region which includes the archipelago of Madeira, Portugal. Both are key species in the trophic web, being important prey for several local top predators, such as seabirds and marine mammals. Nonetheless, little is known about their feeding ecology in oceanic environments. In this study, the authors describe the seasonal variation in the diet of S. colias and T. picturatus in the oceanic region of Madeira throughout a year. Visual inspection of stomach contents revealed that S. colias fed on a broader range of prey groups than T. picturatus, but for both species, zooplankton (particularly calanoid copepods) and fish were the most important food items. The diet of S. colias included a higher proportion of fish, namely Atlantic saury Scomberesox saurus and S. colias, than that of T. picturatus, that included mostly the longspine snipefish Macroramphosus scolopax. T. picturatus consumed a higher proportion of decapods and other copepods. Seasonal variation was found in the diet of both species, with zooplanktonic species being more important in colder months (February to April) for S. colias and during warm months (May to October) for T. picturatus. Their diet in other seasons was dominated by fish. Although they consume similar prey, carbon and nitrogen stable isotope analysis of muscle of S. colias and T. picturatus showed little overlap in their diets, and T. picturatus showed higher δ¹⁵N and a narrower isotopic niche.     

Arid Recovery – A comparison of reptile and small mammal populations inside and outside a large rabbit,cat and fox‐proof exclosure in arid South Australia

Australian arid zone mammal species within the Critical Weight Range (CWR) of 35 g–5.5 kg have suffered disproportionately in the global epidemic of contemporary faunal extinctions. CWR extinctions have been attributed largely to the effects of introduced or invasive mammals; however, the impact of these threatening processes on smaller mammals and reptiles is less clear. The change in small mammal and reptile assemblages after the removal of rabbits, cats and foxes was studied over a 6‐year period in a landscape‐scale exclosure in the Australian arid zone. Rodents, particularly Notomys alexis and Pseudomys bolami, increased to 15 times higher inside the feral‐proof Arid Recovery Reserve compared with outside sites, where rabbits, cats and foxes were still present. Predation by cats was thought to exert the greatest influence on rodent numbers owing to the maintenance of the disparity in rodent responses through dry years and the differences in dietary preferences between rabbits and P. bolami. The presence of introduced Mus domesticus or medium‐sized re‐introduced mammal species did not significantly affect resident small mammal or reptile abundance. Abundance of most dasyurids and small lizards did not change significantly after the removal of feral animals although reductions in gecko populations inside the reserve may be attributable to second order trophic interactions or subtle changes in vegetation structure and cover. This study suggests that populations of rodent species in northern South Australia below the CWR may also be significantly affected by introduced cats, foxes and/or rabbits and that a taxa specific model of Australian mammal decline may be more accurate than one based on body weight.     

Stable carbon and nitrogen isotopes in multiple tissues of wild and captive harbor seals (Phoca vitulina) off the California coast

Stable carbon and nitrogen isotope ratios (δ¹³C and δ¹⁵N) of serum, red blood cells (RBC), muscle, and blubber were measured in captive and wild northeast Pacific harbor seals (Phoca vitulina richardii) at three coastal California sites (San Francisco Bay, Tomales Bay, and Channel Islands). Trophic discrimination factors (Δ_{Tissue‐Diet}) were calculated for captive seals and then applied in wild counterparts in each habitat to estimate trophic position and feeding behavior. Trophic discrimination factors for δ¹⁵N of serum (+3.8‰), lipid‐extracted muscle (+1.6‰), and lipid‐blubber (+6.5‰) are proposed to determine trophic position. An offset between RBC and serum of +0.3‰ for δ¹³C and ?0.6‰ for δ¹⁵N was observed, which is consistent with previous research. Specifically, weaner seals (<1 yr) had large offsets, suggesting strong trophic position shifts during this life stage. Isotopic values indicated an average trophic position of 3.6 at both San Francisco Bay and Tomales Bay and 4.2 at Channel Islands. Isotopic means were strongly dependent on age class and also suggested that mean diet composition varies considerably between all locations. Together, these data indicate that isotopic composition of blood fractions can be an effective approach to estimate trophic position and dietary behavior in wild pinnipeds.     

Survival and Cause-Specific Mortality of Red Foxes in Agricultural and Urban Areas of Illinois

Abstract: Range expansion and population increase by coyotes (Canis latrans), reduced hunting and trapping, and intensified agricultural practices in the Midwest have altered red fox (Vulpes vulpes) mortality, although relative impacts of these factors are unknown. We examined mortality causes and survival of red foxes in urban and rural agricultural areas of Illinois, using radio telemetry data from 335 foxes (Nov 1996 to May 2002). We used Akaike's Information Criterion to evaluate six survival models for foxes reflecting 1) environmental effects, 2) intrinsic effects, 3) temporal effects, 4) behavioral effects, 5) social effects, and 6) a global model. Environmental and intrinsic models of survival were optimal for adult foxes. Adult foxes with low (0-20%) and high (80-100%) percentages of row crops in their home ranges had higher survival than adults with moderate percentages (40-70%). Heavier adults at capture also survived better. A global model (all covariates) was optimal for juvenile foxes. Higher juvenile survival associated with larger litters, lower body fat, and reduced dispersal time. Yearly survival ranged from 0.18 for rural male juveniles to 0.44 for rural female adults. Adult survival rates (0.35) were 11% higher than juvenile survival rates (0.24). Yearly survival varied for urban foxes due to cyclic outbreaks of sarcoptic mange (Sarcoptes scabei). Thus, summer survival (May-Sep) of urban juveniles ranged from 0.10 (mange present) to 0.83 (no mange recorded). Mange was the most common (45% of all fatalities) source of mortality for urban foxes, followed by road kill (31%). We recorded only 4 mange fatalities (2%) for rural foxes. Rural foxes experienced low hunting mortality (7%) and equivalent road kill and coyote predation fatalities (40% each). Sources of mortality for midwestern foxes have dramatically changed since the 1970s when hunting was the major cause of mortality. Coyote predation has effectively replaced hunting mortality, and cyclic patterns of mange outbreaks in urban fox populations might indicate a dynamic source or sink relationship to surrounding rural fox populations. Absent mange, urban areas might provide refugia for red foxes where coyote populations persist at high densities in rural areas. Managers of sympatric urban and rural wildlife populations must understand survival dynamics influencing the population at the landscape level.     

Size related dietary shifts of Epinephelus marginatus in a western Mediterranean littoral ecosystem: an isotope and stomach content analysis

The diet of the dusky grouper Epinephelus marginatus , from the Balearic Islands, western Mediterranean, consisted primarily of crustaceans, molluscs and fishes, but diet composition varied with body size. The smaller dusky groupers (<300 mm L _T) fed primarily on crustaceans, and particularly on brachyurans, which accounted for 46% of the prey identified. As dusky groupers grew, cephalopods became increasingly important and constituted 10 to 40% of the prey identified in subadult and adult specimens. The largest dusky groupers fed primarily on fishes that represented 40·9% of prey identified. These shifts in diet were accompanied by a positive selection of increasingly large prey and by an expansion of trophic niche. δ ¹⁵N values of dusky grouper white muscle ranged from 8·8 to 13·1% and 71% of the variation in δ ¹⁵N was explained by differences in dusky grouper size. δ ¹³C values ranged from – 17·9 to – 15·9%, and no significant body size effect on δ ¹³C was detected. Stomach content and ¹³C values indicated that from 1 year old, the diet of E. marginatus was based on the benthic food web. The enrichment in δ ¹⁵N registered from juvenile to large males was c . 3·8%. Overall, there was good agreement between gut content and stable isotope data indicating that the latter may be useful as a tool in trophic studies in marine protected areas where sampling for fishes is not allowed.     

Trophic ecology of three stingrays (Myliobatoidei: Dasyatidae) off the Brazilian north-eastern coast: Habitat use and resource partitioning

Understanding the ecological role of species with overlapping distributions is central to inform ecosystem management. Here we describe the diet, trophic level and habitat use of three sympatric stingrays, Hypanus guttatus, H. marianae and H. berthalutzae, through combined stomach content and stable isotope (δ¹³C and δ¹⁵N) analyses. Our integrated approach revealed that H. guttatus is a mesopredator that feeds on a diverse diet of benthic and epibenthic marine and estuarine organisms, principally bivalve molluscs, Alpheus shrimp and teleost fishes. Isotopic data supported movement of this species between marine and estuarine environments. H. berthalutzae is also a marine generalist feeder, but feeds primarily on teleost fishes and cephalopods, and consequently occupies a higher trophic level. In contrast, H. marianae is a mesopredator specialized on shrimps and polychaetas occurring only in the marine environment and occupying a low niche breadth. While niche overlap occurred, the three stingrays utilized the same prey resources at different rates and occupied distinct trophic niches, potentially limiting competition for resources and promoting coexistence. These combined data demonstrate that these three mesopredators perform different ecological roles in the ecosystems they occupy, limiting functional redundancy.     

Individual dietary specialization in a generalist predator: A stable isotope analysis of urban and rural red foxes

Some carnivores are known to survive well in urban habitats, yet the underlying behavioral tactics are poorly understood. One likely explanation for the success in urban habitats might be that carnivores are generalist consumers. However, urban populations of carnivores could as well consist of specialist feeders. Here, we compared the isotopic specialization of red foxes in urban and rural environments, using both a population and an individual level perspective. We measured stable isotope ratios in increments of red fox whiskers and potential food sources. Our results reveal that red foxes have a broad isotopic dietary niche and a large variation in resource use. Despite this large variation, we found significant differences between the variance of the urban and rural population for δ¹³C as well as δ¹⁵N values, suggesting a habitat‐specific foraging behavior. Although urban regions are more heterogeneous regarding land cover (based on the Shannon index) than rural regions, the dietary range of urban foxes was smaller compared with that of rural conspecifics. Moreover, the higher δ¹³C values and lower δ¹⁵N values of urban foxes suggest a relatively high input of anthropogenic food sources. The diet of most individuals remained largely constant over a longer period. The low intraindividual variability of urban and rural red foxes suggests a relatively constant proportion of food items consumed by individuals. Urban and rural foxes utilized a small proportion of the potentially available isotopic dietary niche as indicated by the low within‐individual variation compared to the between‐individual variation. We conclude that generalist fox populations consist of individual food specialists in urban and rural populations at least over those periods covered by our study.     

Prey composition and ontogenetic shift in coastal populations of longnose gar Lepisosteus osseus

Longnose gar Lepisosteus osseus were collected from May 2012 to July 2013 in the Charleston Harbor and Winyah Bay estuaries (SC, U.S.A.). This study examined trends in stomach fullness, described major prey components and their importance in the diet of L. osseus, compared stomach content‐based trophic level estimates with the stable‐isotope‐based proxy: δ¹⁵N and tested for the occurrence of an ontogenetic diet shift using stomach content analysis and stable C and N isotopes (δ¹³C and δ¹⁵N). Dominant prey families were Clupeidae, Sciaenidae, Penaeidae, Fundulidae and Mugilidae, with the highest consumption rates in autumn. Trophic levels calculated using stomach contents did not correspond to δ¹⁵N (P > 0·05). Stomach contents and stable‐isotope signatures indicate ontogenetic prey composition shifts from low trophic level benthic prey (fundulids) to higher trophic level pelagic prey (clupeids) as the fish grow between 400 and 600 mm in standard length. Due to their biomass, abundance and top predator status, L. osseus play a significant ecological role in the estuarine community composition, although this effect has often been overlooked by past researchers and should be considered in future estuarine community studies.     

Field Sedation of Coyotes,Red Foxes,and Raccoons With Medetomidine and Atipamezole

Abstract: We chemically restrained free-ranging coyotes (Canis latrans), red foxes (Vulpes vulpes), and raccoons (Procyon lotor) using medetomidine antagonized by atipamezole. All coyotes and 80% of red foxes were sedated with mean ± standard deviation doses of 0.12 ± 0.02 mg/kg and 0.14 ± 0.02 mg/kg medetomidine, respectively. Seventy-seven percent of raccoons were sedated with 0.21 ± 0.05 mg/kg medetomidine. In all species we observed occasional movement, muscle rigidity, and partial-arousal during sedation. Animals were alert within 4.3–8.6 ± 3.5–8.4 min following atipamezole at 0.4 mg/kg. Medetomidine and atipamezole provided safe handling in most animals and rapid recovery without use of a controlled substance. At these doses, biologists in the field should be prepared to administer a supplementary dose of medetomidine to some animals depending on ambient conditions and the objectives of the restraint event.     

Stable isotope evidence for the consumption of millet and other plants in Bronze Age Italy

Stable carbon and nitrogen isotope analysis was carried out on human and animal bones from four inland Early and Middle Bronze Age sites in Northern and Southern Italy. The main aims of the investigation were to explore the contribution of plant foods to the human diet and to examine any dietary differences between and within each of the sites. At two of the sites in Northern Italy, human and animal bones were significantly enriched in ¹³C. This finding was attributed to the consumption of domestic millets (Panicum miliaceum and/or Setaria italica), which are C₄ pathway plants. Conversely, individuals from the two Bronze Age sites in Southern Italy were significantly depleted in ¹³C compared to those from the north. Here, millet was absent from the diet, and protein from C₃ plants made a much greater dietary contribution than animal protein. This finding highlights the importance of cereal cultivation, most likely of wheat and barley, in the south of Italy during the Bronze Age. Overall, our results support the idea that the widespread cultivation of millet first occurred in Northern Italy, following its introduction from across the Alps in Central Europe. Finally, we found no significant differences in the stable isotope values between individuals at each site, when grouped by their sex or presence of grave goods. This leads to the conclusion that any status difference that may have existed is not reflected in the long‐term dietary record, or at least not as measurable by stable isotope analysis. Am J Phys Anthropol, 2009. © 2008 Wiley‐Liss, Inc.     

Feeding strategy and cannibalism of the Argentine hake Merluccius hubbsi

The diet composition and feeding strategy of the Argentine hake Merluccius hubbsi in the San Matías Gulf were analysed in order to use this information for the sustainable management of the fishery. Merluccius hubbsi behaved as an opportunistic predator. Small M. hubbsi consumed planktonic crustaceans, whereas medium and large fish ate numerous prey taxa with low frequency of occurrence and variable specific abundance. Intra- and intercohort cannibalism were detected in all size groups and were particularly significant in large M. hubbsi. Medium-sized M. hubbsi consumed small conspecifics and large-sized M. hubbsi consumed both small and medium M. hubbsi. These results indicate that the removal of large M. hubbsi by fishing may increase the risk of overfishing by two combined effects: a direct effect of recruitment-overfishing and an indirect effect of growth-overfishing through an enhanced cannibalism of medium M. hubbsi on small M. hubbsi. Intra- and intercohort cannibalism and other trophic relationships in the M. hubbsi should therefore be considered explicitly in stock assessment models.     

俄罗斯远东地区特罗伊茨基靺鞨墓地人骨的稳定同位素分析

稳定同位素分析技术近年来发展为复原古代民族饮食结构、社会经济模式的有效手段。本文应用该技术首次对俄罗斯远东地区特罗伊茨基靺鞨墓地出土人骨中的C、N同位素比值进行了测定。结果显示,特罗伊茨基墓地古代靺鞨居民日常饮食习惯中保持着较高比例的动物性食物摄入,植物类食物的摄入中C3类植物的比重较高。结合其他相关资料,初步推测该组靺鞨居民已经有一定农业,渔猎业和饲养业在经济生活中占据重要地位,黑水靺鞨和粟末靺鞨的经济类型有所差别。本文的研究结果可以为复原古代民族的经济模式研究提供有益的线索。