82 Works

Data from: A single-nucleotide polymorphism-based approach for rapid and cost-effective genetic wolf monitoring in Europe based on noninvasively collected samples

Robert H. S. Kraus, Bridgett VonHoldt, Berardino Cocchiararo, Verena Harms, Helmut Bayerl, Ralph Kühn, Daniel W. Förster, Jörns Fickel, Christian Roos & Carsten Nowak
Noninvasive genetics based on microsatellite markers has become an indispensable tool for wildlife monitoring and conservation research over the past decades. However, microsatellites have several drawbacks, such as the lack of standardisation between laboratories and high error rates. Here, we propose an alternative single-nucleotide polymorphism (SNP)-based marker system for noninvasively collected samples, which promises to solve these problems. Using nanofluidic SNP genotyping technology (Fluidigm), we genotyped 158 wolf samples (tissue, scats, hairs, urine) for 192...

Beyond the landscape: resistance modelling infers physical and behavioural gene flow barriers to a mobile carnivore across a metropolitan area

Sophia Kimmig, Joscha Beninde, Myriam Brandt, Anna Schleimer, Stephanie Kramer-Schadt, Heribert Hofer, Konstantin Börner, Christoph Schulze, Ulrich Wittstatt, Mike Heddergott, Tania Halczok, Christoph Staubach & Alain Frantz
Urbanization affects key aspects of wildlife ecology. Dispersal in urban wildlife species may be impacted by geographical barriers but also by a species’ inherent behavioural variability. There are no functional connectivity analyses using continuous individual-based sampling across an urban-rural continuum that would allow a thorough assessment of the relative importance of physical and behavioural dispersal barriers. We used 16 microsatellite loci to genotype 374 red foxes (Vulpes vulpes) from the city of Berlin and surrounding...

Data from: Transcriptome profiling of ontogeny in the acridid grasshopper Chorthippus biguttulus

Emma L. Berdan, Jonas Finck, Paul R. Johnston, Isabelle Waurick, Camila J. Mazzoni & Frieder Mayer
Acridid grasshoppers (Orthoptera:Acrididae) are widely used model organisms for developmental, evolutionary, and neurobiological research. Although there has been recent influx of orthopteran transcriptomic resources, many use pooled ontogenetic stages obscuring information about changes in gene expression during development. Here we developed a de novo transcriptome spanning 7 stages in the life cycle of the acridid grasshopper Chorthippus biguttulus. Samples from different stages encompassing embryonic development through adults were used for transcriptomic profiling, revealing patterns of...

Data from: Predictors and immunological correlates of sublethal mercury exposure in vampire bats

Daniel J. Becker, Matthew M. Chumchal, Alexandra B. Bentz, Steven G. Platt, Gábor A. Czirják, Thomas R. Rainwater, Sonia Altizer & Daniel G. Streicker
Mercury (Hg) is a pervasive heavy metal that often enters the environment from anthropogenic sources such as gold mining and agriculture. Chronic exposure to Hg can impair immune function, reducing the ability of animals to resist or recover from infections. How Hg influences immunity and susceptibility remains unknown for bats, which appear immunologically distinct from other mammals and are reservoir hosts of many pathogens of importance to human and animal health. We here quantify total...

Measurements of fecal cortisol metabolites (fGMC) and activity budget of male spotted hyenas in the Ngorongoro Crater (Tanzania)

Eve Davidian, Bettina Wachter, Ilja Heckmann, Martin Dehnhard, Heribert Hofer & Oliver P Höner
This excel table contains 3 sheets:
(1) fGMC, with the fecal cortisol metabolite concentrations and associated activity of male spotted hyenas,
(2) Activity Budget, with the proportion of sightings where males engaged in each of 4 categories of activities
(3) Quality of courted females, with the mean social rank of the females that were courted by males.

These data were used for the original publication: "The interplay between social rank, physiological constraints and investment...

Data from: Shifting up a gear with iDNA: from mammal detection events to standardized surveys

Jesse F. Abrams, Lisa Hörig, Robert Brozovic, Jan Axtner, Alex Crampton-Platt, Azlan Mohamed, Seth T. Wong, Rahel Sollmann, Douglas W. Yu & Andreas Wilting
1.Invertebrate‐derived DNA (iDNA), in combination with high throughput sequencing, has been proposed as a cost‐efficient and powerful tool to survey vertebrate species. Previous studies, however, have only provided evidence that vertebrates can be detected using iDNA, but have not taken the next step of placing these detection events within a statistical framework that allows for robust biodiversity assessments. 2.Here, we compare concurrent iDNA and camera‐trap surveys. Leeches were repeatedly collected in close vicinity to 64...

Spatiotemporal interactions of a novel mesocarnivore community in an urban environment before and during SARS‐CoV‐2 lockdown

Julie Louvrier, Aimara Planillo, Milena Stillfried, Robert Hagen, Konstantin Boerner, Sophia Kimmig, Sylvia Ortmann, Anke Schumann, Miriam Brandt & Stephanie Kramer-Schadt
1. Studying species interactions and niche segregation under human pressure provides important insights into species adaptation, community functioning and ecosystem stability. Due to their high plasticity in behaviour and diet, urban mesocarnivores are ideal species for studying community assembly in novel communities. 2. We analysed the spatial and temporal species interactions of an urban mesocarnivore community composed of the red fox (Vulpes vulpes) and the marten (Martes sp.) as native species, the raccoon (Procyon lotor)...

A hierarchical N-mixture model to estimate behavioral variation and a case study of Neotropical birds

Alison Ke, Rahel Sollmann, Luke Frishkoff & Daniel Karp
Understanding how and why animals use the environments where they occur is both foundational to behavioral ecology and essential to identify critical habitats for species conservation. However, some behaviors are more difficult to observe than others, which can bias analyses of raw observational data. To our knowledge, no method currently exists to model how animals use different environments while accounting for imperfect behavior-specific detection probability. We developed an extension of a binomial N-mixture model (hereafter...

Data from: Multiple types of genomic variation contribute to adaptive traits in the mustelid subfamily Guloninae

Lorena Derežanin
Species of the mustelid subfamily Guloninae inhabit diverse habitats on multiple continents, and occupy a variety of ecological niches. They differ in feeding ecologies, reproductive strategies and morphological adaptations. To identify candidate loci associated with adaptations to their respective environments, we generated a de novo assembly of the tayra (Eira barbara), the earliest diverging species in the subfamily, and compared this with the genomes available for the wolverine (Gulo gulo) and the sable (Martes zibellina)....

Data from: Weak population structure in European roe deer (Capreolus capreolus) and evidence of introgressive hybridization with Siberian roe deer (C. pygargus) in northeastern Poland

Juanita Olano-Marin, Kamila Plis, Leif Sönnichsen, Tomasz Borowik, Magdalena Niedziałkowska & Bogumiła Jędrzejewska
We investigated contemporary and historical influences on the pattern of genetic diversity of European roe deer (Capreolus capreolus). The study was conducted in northeastern Poland, a zone where vast areas of primeval forests are conserved and where the European roe deer was never driven to extinction. A total of 319 unique samples collected in three sampling areas were genotyped at 16 microsatellites and one fragment (610 bp) of mitochondrial DNA (mtDNA) control region. Genetic diversity...

Data from: The evolutionary legacy of size-selective harvesting extends from genes to populations

Silva Uusi-Heikkilä, Andrew R. Whiteley, Anna Kuparinen, Shuichi Matsumura, Paul A. Venturelli, Christian Wolter, Jon Slate, Craig R. Primmer, Thomas Meinelt, Shaun S. Killen, David Bierbach, Giovanni Polverino, Arne Ludwig & Robert Arlinghaus
Size-selective harvesting is assumed to alter life histories of exploited fish populations, thereby negatively affecting population productivity, recovery, and yield. However, demonstrating that fisheries-induced phenotypic changes in the wild are at least partly genetically determined has proved notoriously difficult. Moreover, the population-level consequences of fisheries-induced evolution are still being controversially discussed. Using an experimental approach, we found that five generations of size-selective harvesting altered the life histories and behavior, but not the metabolic rate, of...

Data from: Trade-offs in lactation and milk intake by competing siblings in a fluctuating environment

Heribert Hofer, Sarah Benhaiem, Waltraud Golla & Marion L. East
Income breeders which forage without their offspring in attendance should adjust nursing frequency and the quantity and composition of milk to prevailing ecological conditions, and increase the quantity or quality of milk transferred if the frequency of nursing visits declines. When milk delivery to a litter is insufficient, sibling competition should skew milk consumption in favor of dominant litter members. We quantified milk nutritional composition and gross energy density, nursing bout durations, per capita milk...

Data from: Transition from conventional to light-emitting diode street lighting changes activity of urban bats

Daniel Lewanzik & Christian C. Voigt
Light pollution is rapidly increasing and can have deleterious effects on biodiversity, yet light types differ in their effect on wildlife. Among the light types used for street lamps, light-emitting diodes (LEDs) are expected to become globally predominant within the next few years. In a large-scale field experiment, we recorded bat activity at 46 street lights for 12 nights each and investigated how the widespread replacement of conventional illuminants by LEDs affects urban bats: we...

Data from: The summary-likelihood method and its implementation in the Infusion package

Francois Rousset, Alexandre Gouy, Camille Martinez-Almoyna & Alexandre Courtiol
In recent years, simulation methods such as approximate Bayesian computation have extensively been used to infer parameters of population genetic models where the likelihood is intractable. We describe an alternative approach, summary likelihood, that provides a likelihood-based analysis of the information retained in the summary statistics whose distribution is simulated. We provide an automated implementation as a standard R package, Infusion, and we test the method, in particular for a scenario of inference of population-size...

Reproduction affects immune defenses in the guinea pig even under ad libitum food

Fritz Trillmich, Anja Guenther, Manuela Jäckel & Gábor Czirják
Reproduction is one of the most costly processes in the life of an animal. Life history theory assumes that when resources are limiting allocation to reproduction will reduce allocation to other essential processes thereby inducing costs of reproduction. The immune system is vital for survival. If reproduction reduces investment in immune function, this could increase the risk of disease, morbidity and mortality. We here test in the guinea pig, if even under ad libitum food...

Data (D2H values) from: Generational shift in the migratory common noctule bat: first-year males lead the way to hibernacula at higher latitudes

Kseniia Kravchenko
Supplementary_Table_3_D2H values noctules_Kravchenko et al The dataset contains stable hydrogen values (D2H) (column "sample_value") in fur keratin of 413 common noctule bats (Nyctalus noctula) from Kharkiv (Ukraine). Samples were collected in winter colonies over 12 years (2004-2015). Each row is one individual. Column "sample_ID" is an ID of an individual. Columns "lat" and "long" are coordinates of Kharkiv city (sampling site). Column "sex" is sex of individuals. Column "age1" shows the age of individuals: ad...

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

Carolin Scholz
Some carnivores are known to survive well in urban habitats, yet the underlying behavioural 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...

Measurements of fecal cortisol metabolites (fGMC) and activity budget of male spotted hyenas in the Ngorongoro Crater (Tanzania)

Eve Davidian, Bettina Wachter, Ilja Heckmann, Martin Dehnhard, Heribert Hofer & Oliver P Höner
This excel table contains 3 sheets:
(1) fGMC, with the fecal cortisol metabolite concentrations and associated activity of male spotted hyenas,
(2) Activity Budget, with the proportion of sightings where males engaged in each of 4 categories of activities
(3) Quality of courted females, with the mean social rank of the females that were courted by males.

These data were used for the original publication: "The interplay between social rank, physiological constraints and investment...

Increased immune marker variance in a population of invasive birds

Hanna Prüter, Mathias Franz, Sönke Twietmeyer, Niklas Böhm, Gudrun Middendorff, Ruben Portas, Jörg Melzheimer, Holger Kolberg, Georg Von Samson‐Himmelstjerna, Alex D. Greenwood, Dörte Lüchow, Kristin Mühldorfer & Gábor Árpád Czirják
Immunity and parasites have been linked to the success of invasive species. Especially lower parasite burden in invasive populations has been suggested to enable a general downregulation of immune investment (Enemy Release and Evolution of Increased Competitive Ability Hypotheses). Simultaneously, keeping high immune competence towards potentially newly acquired parasites in the invasive range is essential to allow population growth. To investigate the variation of immune effectors of invasive species, we compared the mean and variance...

Use of Deep Learning for structural analysis of CT-images of soil samples

Ralf Wieland, Chinatsu Ukawa, Monika Joschko, Adrian Krolczyk, Guido Fritsch, Thomas Hildebrandt, Juliane Filser, Olaf Schmidt & Juan J. Jimenez
Soil samples from several European countries were scanned using medical computer tomography (CT) device and are now available as CT images. The analysis of these samples was carried out using deep learning methods. For this purpose, a VGG16 network was trained with the CT-images (X). For the annotation (y) a new method for automated annotation, "surrogate'' learning, was introduced. The generated neural networks (NN) were subjected to a detailed analysis. Among other things, transfer learning...

Comparison of mosquitoes and fly derived DNA as a tool for sampling vertebrate biodiversity in suburban forests in Berlin, Germany

Aimara Planillo, Renita Danabalan, Susanne Butschkau, Sita Deeg, Pierre Gras, Cincia Thion, Sébastien Calvignac-Spencer, Stephanie Kramer-Schadt & Camila Mazzoni
The use of invertebrate-derived DNA (iDNA) is a promising non-invasive tool to monitor wildlife. While most studies have been carried out in dense tropical and sub-tropical forests and have focused on the use of a single category of invertebrates, this study compares the use of flies and mosquitoes derived DNA to assess vertebrate diversity in semi-urban environments. We conducted our sampling in four different forest plots in Berlin, Germany. Pools of flies and non-bloodfed mosquitoes...

Data from: Invasion genetics of a human commensal rodent: the black rat Rattus rattus in Madagascar

Carine Brouat, Charlotte Tollenaere, Arnaud Estoup, Anne Loiseau, Simone Sommer, Rahelinirina Soanandrasana, Lila Rahalison, Minoarisoa Rajerison, Sylvain Piry, S. M. Goodman, Jean-Marc Duplantier & J.-M. Duplantier
Studies focusing on geographical genetic patterns of commensal species and on human history complement each other, and provide proxies to trace common colonisation events. On Madagascar, the unintentional introduction and spread of the commensal species Rattus rattus by people may have left a living clue of human colonization patterns and history. In this study, we addressed this question by characterising the genetic structure of natural populations of R. rattus using both microsatellites and mitochondrial sequences,...

Data from: Lysozyme-associated bactericidal activity in the ejaculate of a wild passerine

Melissah Rowe, Gábor Árpád Czirják, Jan Lifjeld, Mathieu T. Giraudeau, Jan T. Lifjeld & Mathieu Giraudeau
Numerous antibacterial substances have been identified in the ejaculates of animals and are suggested to protect sperm from bacterial-induced damage in both the male and female reproductive tracts. Lysozymes, enzymes that exhibit bactericidal activity through their ability to break down bacterial cell walls, are likely to be particularly important for sperm defence as they are part of the constitutive innate immune system and are thus immediately available to protect sperm from bacterial attack. Birds are...

Data from: Evidence for an association between post-fledging dispersal and microsatellite multilocus heterozygosity in a large population of greater flamingos

Mark A. F. Gillingham, Frank Cézilly, Rémi Wattier & Arnaud Béchet
Dispersal can be divided into three stages: departure, transience and settlement. Despite the fact that theoretical studies have emphasized the importance of heterozygosity on dispersal strategies, empirical evidence of its effect on different stages of dispersal is lacking. Here, using multi-event capture-mark-recapture models, we show a negative association between microsatellite multilocus heterozygosity (MLH; 10 loci; n = 1023) and post-fledging dispersal propensity for greater flamingos, Phoenicopterus roseus, born in southern France. We propose that the...

Data from: Impact of enrichment conditions on cross-species capture of fresh and degraded DNA

Johanna L. A. Paijmans, Joerns Fickel, Alexandre Courtiol, Michael Hofreiter & Daniel W. Förster
By combining high-throughput sequencing with target-enrichment (“hybridization capture”), researchers are able to obtain molecular data from genomic regions of interest for projects that are otherwise constrained by sample quality (e.g. degraded and contamination-rich samples) or a lack of a priori sequence information (e.g. studies on non-model species). Despite the use of hybridization capture in various fields of research for many years, the impact of enrichment conditions on capture success are not yet thoroughly understood. We...

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