Andean and California condors possess dissimilar genetic composition but exhibit similar demographic histories

While genetic diversity of threatened species is a major concern of conservation biologists, historic patterns of genetic variation are often unknown. A powerful approach to assess patterns and processes of genetic erosion is via ancient DNA techniques. Herein, we analyzed mtDNA from historical samples (1800s to present) of Andean Condors (Vultur gryphus) to investigate whether contemporary low genetic variability is the result of recent human expansion and persecution, and compared this genetic history to that of California condors (Gymnogyps californianus).We then explored historic demographies for both species via coalescent simulations. We found that Andean condors have lost at least 17% of their genetic variation in the early 20th century. Unlike California condors, however, low mtDNA diversity in the Andean condor was mostly ancient, before European arrival. However, we found that both condor species shared similar demographies in that population bottlenecks were recent and co-occurred with the introduction of livestock to the Americas and the global collapse of marine mammals. Given the combined information on genetic and demographic processes, we suggest that the protection of key habitats should be targeted for conserving extant genetic diversity and facilitate the natural recolonization of lost territories, while nuclear genomic data should be used to inform translocation plans.Fil: Padró, Julian. Universidad Nacional del Comahue. Centro Regional Universitario Bariloche; Argentina. University of Wisconsin; Estados UnidosFil: Lambertucci, Sergio Agustin. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Conicet - Patagonia Norte. Instituto de Investigaciones En Biodiversidad y Medioambiente. Subsede San Martín de Los Andes-inibioma | Universidad Nacional del Comahue. Centro Regional Universitario Bariloche. Instituto de Investigaciones En Biodiversidad y Medioambiente. Subsede San Martín de Los Andes-inibioma.; ArgentinaFil: Perrig, Paula Leticia. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Conicet - Patagonia Norte. Instituto de Investigaciones En Biodiversidad y Medioambiente. Subsede San Martín de Los Andes-inibioma | Universidad Nacional del Comahue. Centro Regional Universitario Bariloche. Instituto de Investigaciones En Biodiversidad y Medioambiente. Subsede San Martín de Los Andes-inibioma.; Argentina. University of Wisconsin; Estados UnidosFil: Pauli, Jonathan Nicholas. University of Wisconsin; Estados Unido

Monitoring vultures in the 21st century: The need for standardized protocols

This article calls on scientists, managers and organizations focused on vulture conservation to promote and use standardized monitoring programs based on sampling of molted feathers.Fil: Perrig, Paula Leticia. University of Wisconsin; Estados UnidosFil: Lambertucci, Sergio Agustin. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto de Investigaciones en Biodiversidad y Medioambiente. Universidad Nacional del Comahue. Centro Regional Universidad Bariloche. Instituto de Investigaciones en Biodiversidad y Medioambiente; ArgentinaFil: Donadio, Emiliano. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto de Investigaciones en Biodiversidad y Medioambiente. Universidad Nacional del Comahue. Centro Regional Universidad Bariloche. Instituto de Investigaciones en Biodiversidad y Medioambiente; ArgentinaFil: Padro, Julian. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto de Investigaciones en Biodiversidad y Medioambiente. Universidad Nacional del Comahue. Centro Regional Universidad Bariloche. Instituto de Investigaciones en Biodiversidad y Medioambiente; Argentina. University of Wisconsin; Estados UnidosFil: Pauli, Jonathan Nicholas. University of Wisconsin; Estados Unido

Multiply Recurrent Episodes of Gastric Emphysema

Introduction. Gastric emphysema can present both a diagnostic challenge and a life-threatening condition for patients and has only once been reported as being recurrent. Background. A 64-year-old male presented with chronic abdominal pain and was found to have gastric pneumatosis on CT scan. The patient was successfully managed conservatively. The cause was attributed to aberrant arterial anatomy and atherosclerosis along with hypotension. The patient has since had 3 episodes of recurrent gastric emphysema, all managed nonoperatively. Discussion. To our knowledge, this is the first case of both serial episodes of gastric pneumatosis and gastric mucosal ischemia as a precipitating factor for the development of gastric emphysema

Finding the right coverage:The impact of coverage and sequence quality on single nucleotide polymorphism genotyping error rates

Restriction-enzyme-based sequencing methods enable the genotyping of thousands of single nucleotide polymorphism (SNP) loci in nonmodel organisms. However, in contrast to traditional genetic markers, genotyping error rates in SNPs derived from restriction-enzyme-based methods remain largely unknown. Here, we estimated genotyping error rates in SNPs genotyped with double digest RAD sequencing from Mendelian incompatibilities in known mother-offspring dyads of Hoffman's two-toed sloth (Choloepus hoffmanni) across a range of coverage and sequence quality criteria, for both reference-aligned and de novo-assembled data sets. Genotyping error rates were more sensitive to coverage than sequence quality and low coverage yielded high error rates, particularly in de novo-assembled data sets. For example, coverage &gt;= 5 yielded median genotyping error rates of &gt;= 0.03 and &gt;= 0.11 in reference-aligned and de novo-assembled data sets, respectively. Genotyping error rates declined to = 30, but remained &gt;= 0.04 in the de novo-assembled data sets. We observed approximately 10- and 13-fold declines in the number of loci sampled in the reference-aligned and de novo-assembled data sets when coverage was increased from &gt;= 5 to &gt;= 30 at quality score &gt;= 30, respectively. Finally, we assessed the effects of genotyping coverage on a common population genetic application, parentage assignments, and showed that the proportion of incorrectly assigned maternities was relatively high at low coverage. Overall, our results suggest that the trade-off between sample size and genotyping error rates be considered prior to building sequencing libraries, reporting genotyping error rates become standard practice, and that effects of genotyping errors on inference be evaluated in restriction-enzyme-based SNP studies.</p

More than just meat: Carcass decomposition shapes trophic identities in a terrestrial vertebrate

Most food web models fail to account for the full complexity of interactions within a community, particularly where microbes are involved. Carcasses are microbe-rich resources and may represent a common nexus for the macrobiome and microbiome, effectively uniting autotrophs, consumers, predators and microbiota. We evaluated the role of carcasses as multitrophic resources and explored dietary partitioning for a sexually dimorphic obligate scavenger known for its hierarchical social system. This study was set in a well-studied community of camelids Vicugna, Lama guanicoe, pumas Puma concolor and Andean condors Vultur gryphus in the Andes. We hypothesized that condors, by feeding on trophically distinct dietary substrates within any given carcass, would have highly variable trophic position (TP) values. Furthermore, we expected that the microbial consumers within the carcass would inflate TP values in both, the carrion and the condors. Thus, we expected that the trophic heterogeneity within a carcass could facilitate sex-based dietary partitioning in condors. We used a multifaceted approach to assess the foraging of Andean condors, using regurgitated pellet and bulk isotopic analyses, and also quantified the TP of the entire community of graminoids, camelids, camelid carrion, pumas, and female and male condors employing compound-specific stable isotopes analysis of amino acids. Our analysis of condor pellets and bulk isotopes revealed non-trivial plant consumption, close to 10% of condor diet. Isotope analysis of amino acids revealed that condors had highly variable TPs (2.9 ± 0.3) compared to pumas (3.0 ± 0.0) and camelids (2.0 ± 0.1), likely representing ‘trophic omnivory’, wherein the condors consume plants (TP = 1.0 ± 0.1) and microbe-colonized carrion (2.3 ± 0.1). Female condors exhibited a TP (2.8 ± 0.2) lower than strict carnivory, suggesting that they consume more plant biomass in a carcass, while males (TP = 3.1 ± 0.3) are likely consuming more of the microbe-rich animal tissue. Our study highlights that carcasses represent a trophically heterogeneous resource and that vertebrate scavengers can feed across trophic groups within the carcass, from autotrophs to secondary consumers, and from both the macrobiome and microbiome. Thus, integration of microbes in macroecological contexts can help to resolve trophic identity, and better characterize the importance of microbes in detritivorous and omnivorous species. Read the free Plain Language Summary for this article on the Journal blog.Fil: Barceló, Gonzalo. University of Wisconsin; Estados UnidosFil: Perrig, Paula Leticia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto de Investigaciones en Biodiversidad y Medioambiente. Universidad Nacional del Comahue. Centro Regional Universidad Bariloche. Instituto de Investigaciones en Biodiversidad y Medioambiente; Argentina. University of Wisconsin; Estados UnidosFil: Dharampal, Prarthana. University of Wisconsin; Estados UnidosFil: Donadio, Emiliano. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto de Investigaciones en Biodiversidad y Medioambiente. Universidad Nacional del Comahue. Centro Regional Universidad Bariloche. Instituto de Investigaciones en Biodiversidad y Medioambiente; Argentina. Fundación Rewilding Argentina; ArgentinaFil: Steffan, Shawn A.. United States Department of Agriculture. Agriculture Research Service; Estados Unidos. University of Wisconsin; Estados UnidosFil: Pauli, Jonathan Nicholas. University of Wisconsin; Estados Unido

The Genetic Structure of American Black Bear Populations in the Southern Rocky Mountains

Large and wide-ranging carnivores typically display genetic connectivity across their distributional range. American black bears (Ursus americanus) are vagile carnivores and habitat generalists. However, they are strongly associated with forested habitats; consequently, habitat patchiness and fragmentation have the potential to drive connectivity and the resultant structure between black bear subpopulations. Our analysis of genetic structure of black bears in the southern Rocky Mountains of Wyoming and Colorado (n = 296) revealed two discrete populations: bears in northern Wyoming were distinct (FST = 0.217) from bears in southern Wyoming and Colorado, despite higher densities of anthropogenic development within Colorado. The differentiation we observed indicates that bears in Wyoming originated from two different clades with structure driven by the pattern of contiguous forest, rather than the simple distance between populations. We posit that forested habitat and competitive interactions with brown bears reinforced patterns of genetic structure resulting from historic colonization. Our work suggests that forested habitat is an important force structuring populations in the southern Rocky Mountains, even for populations of highly vagile carnivores

SEARCH: Spatially Explicit Animal Response to Composition of Habitat.

Complex decisions dramatically affect animal dispersal and space use. Dispersing individuals respond to a combination of fine-scale environmental stimuli and internal attributes. Individual-based modeling offers a valuable approach for the investigation of such interactions because it combines the heterogeneity of animal behaviors with spatial detail. Most individual-based models (IBMs), however, vastly oversimplify animal behavior and such behavioral minimalism diminishes the value of these models. We present program SEARCH (Spatially Explicit Animal Response to Composition of Habitat), a spatially explicit, individual-based, population model of animal dispersal through realistic landscapes. SEARCH uses values in Geographic Information System (GIS) maps to apply rules that animals follow during dispersal, thus allowing virtual animals to respond to fine-scale features of the landscape and maintain a detailed memory of areas sensed during movement. SEARCH also incorporates temporally dynamic landscapes so that the environment to which virtual animals respond can change during the course of a simulation. Animals in SEARCH are behaviorally dynamic and able to respond to stimuli based upon their individual experiences. Therefore, SEARCH is able to model behavioral traits of dispersing animals at fine scales and with many dynamic aspects. Such added complexity allows investigation of unique ecological questions. To illustrate SEARCH\u27s capabilities, we simulated case studies using three mammals. We examined the impact of seasonally variable food resources on the weight distribution of dispersing raccoons (Procyon lotor), the effect of temporally dynamic mortality pressure in combination with various levels of behavioral responsiveness in eastern chipmunks (Tamias striatus), and the impact of behavioral plasticity and home range selection on disperser mortality and weight change in virtual American martens (Martes americana). These simulations highlight the relevance of SEARCH for a variety of applications and illustrate benefits it can provide for conservation planning

Prey of reintroduced fishers and their habitat relationships in the Cascades T Range, Washington

Conservation and recovery of forest carnivores requires an understanding of their habitat requirements, as well as requirements of their prey. In much of the western United States, trapping and habitat loss led to extirpations of fishers (Pekania pennanti) by the mid-20th century, and reintroductions are ongoing to restore fishers to portions of their former range. Fisher recovery in Washington State has been limited by isolation from other populations, but other potentially important factors, such as diet of fishers in this region and prey availability, have not been thoroughly investigated. We collected hair samples from potential prey and fishers for stable isotope analysis to identify important prey items for fishers within a reintroduction area in southern Washington. We then estimated the abundance of prey species at 21 sites across a gradient of forest structural classes within the fisher reintroduction area, and assessed the effects of forest age and vegetation on the prey community using permutational multivariate analysis of variance and non-metric multidimensional scaling. Stable isotopes revealed that larger prey items, including snowshoe hares (Lepus americanus) and/or mountain beavers (Aplodontia rufa), were the most important prey item(s) for fishers in the southern Cascades. We found distinct but equally diverse prey communities in old-growth (unmanaged) and young (heavily managed) forest stands, with snowshoe hares and mountain beavers most common in young forests, while chipmunks (Neotamius spp.) and small mammals were more common in older forests. Our results suggest a discrepancy between the habitats where important fisher prey are most abundant and habitat requirements of fishers. Snowshoe hares and mountain beavers were most abundant in young forests, whereas fishers are associated with landscapes dominated by older forest stands or those that provide large woody structures, which fishers use for denning and resting. Our results add to growing evidence that forest landscape mosaics provide valuable habitat for fishers in the Pacific Northwest, suggesting that both mature and younger forest stands are important for fishers and fisher recovery

Estimating the atmospheric concentration of Criegee intermediates and their possible interference in a FAGE-LIF instrument

We analysed the extensive dataset from the HUMPPA-COPEC 2010 and the HOPE 2012 field campaigns in the boreal forest and rural environments of Finland and Germany, respectively, and estimated the abundance of stabilised Criegee intermediates (SCIs) in the lower troposphere. Based on laboratory tests, we propose that the background OH signal observed in our IPI-LIF-FAGE instrument during the aforementioned campaigns is caused at least partially by SCIs. This hypothesis is based on observed correlations with temperature and with concentrations of unsaturated volatile organic compounds and ozone. Just like SCIs, the background OH concentration can be removed through the addition of sulfur dioxide. SCIs also add to the previously underestimated production rate of sulfuric acid. An average estimate of the SCI concentration of similar to 5.0 x 10(4) molecules cm(-3) (with an order of magnitude uncertainty) is calculated for the two environments. This implies a very low ambient concentration of SCIs, though, over the boreal forest, significant for the conversion of SO2 into H2SO4. The large uncertainties in these calculations, owing to the many unknowns in the chemistry of Criegee intermediates, emphasise the need to better understand these processes and their potential effect on the self-cleaning capacity of the atmosphere.Peer reviewe

Identifying Criegee intermediates as potential oxidants in the troposphere

Abstract and poster presented at the AGU Fall meeting, San Francisco 2015.Criegee intermediates (CI) are formed during the ozonolysis of unsaturated compounds and have been intensively studied in the last few years due to their possible role as oxidants in the troposphere. Stabilised CI (SCI) are now known to react very rapidly, k(298 K) = 10-12 to 10-10 cm3 molecule-1 s-1, with a large number of trace gases (SO2, NO2, organic acids, water dimers). Still, it remains challenging to assess their effective oxidative capacity, as CI chemistry is complex, spans a large range of rate coefficients for different SCI conformers reacting with water dimers and trace gases, and in addition no reliable measurement technique able to detect ambient SCI concentrations is currently available. In this study, we examine the extensive dataset from the HUMPPA-COPEC 2010 and the HOPE 2012 field campaigns, aided by literature data, to estimate the abundance of SCI in the lower troposphere. The budget of SCI is analyzed using four different approaches: 1) based on an observed yet unexplained H2SO4 production; 2) from the measured concentrations of unsaturated volatile organic compounds (VOC); 3) from OH reactivity measurements; 4) from the unexplained production rate of OH. A SCI concentration range between 5 x 103 and 2 x 106 molecule cm-3 is calculated for the two environments. The central weighted estimate of the SCI concentration over the boreal forest of ~ 5 x 104 molecules cm-3 implies a significant impact on the conversion of SO2 into H2SO4. In addition, we present measurements obtained using our inlet pre-injector laser-induced fluorescence assay by gas expansion technique (IPI-LIF-FAGE) for the above-mentioned campaigns. A recent laboratory study performed with the same instrumental setup showed that the IPI-LIF-FAGE system is sensitive to the detection of the OH formed from unimolecular decomposition of SCI. Building on these measurements, the background OH (OHbg) measured during the two field campaigns is investigated in comparison with many other trace gases to assess if the observations in controlled conditions are transferable to ambient conditions