bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomics and introgression: Discovery and mapping of thousands of species-diagnostic SNPs using RAD sequencing
Authors: Hand Brian K. , Hether Tyler D. , Kovach Ryan P. , Muhlfeld Clint C. , Amish Stephen J. , Boyer Matthew C. , O’rourke Sean M. , Miller Michael R. , Lowe Winsor H. , Hohenlohe Paul A. , Luikart Gordon 
Published: February 2016

Abstract
Invasive hybridization and introgression pose a serious threat to the persistence of many native species. Understanding the effects of hybridization on native populations (e.g., fitness consequences) requires numerous species-diagnostic loci distributed genome-wide. Here we used RAD sequencing to discover thousands of single-nucleotide polymorphisms (SNPs) that are diagnostic between rainbow trout (RBT, Oncorhynchus mykiss), the world’s most widely introduced fish, and native westslope cutthroat trout (WCT, O. clarkii lewisi) in the northern Rocky Mountains, USA. We advanced previous work that identified 4,914 species-diagnostic loci by using longer sequence reads (100 bp vs. 60 bp) and a larger set of individuals (n = 84). We sequenced RAD libraries for individuals from diverse sampling sources, including native populations of WCT and hatchery broodstocks of WCT and RBT. We also took advantage of a newly released reference genome assembly for RBT to align our RAD loci. In total, we discovered 16,788 putatively diagnostic SNPs, 10,267 of which we mapped to anchored chromosome locations on the RBT genome. A small portion of previously discovered putative diagnostic loci (325 of 4,914) were no longer diagnostic (i.e., fixed between species) based on our wider survey of non-hybridized RBT and WCT individuals. Our study suggests that RAD loci mapped to a draft genome assembly could provide the marker density required to identify genes and chromosomal regions influencing selection in admixed populations of conservation concern and evolutionary interest.
Hybridization and the species problem in conservation
Authors: Fitzpatrick Benjamin M. , Ryan Maureen E. , Johnson Jarrett R. , Corush Joel , Carter Evin T. 
Published: February 2016

Abstract
Most biologists recognize the “species phenomenon” as a real pattern in nature: Biodiversity is characterized by discontinuities between recognizable groups classified as species. Many conservation laws focus on preventing species extinction. However, species are not fixed. Discontinuities evolve gradually and sometimes disappear. Exactly how to define particular species is not always obvious. Hybridization between taxonomic species reminds us that species classification is not a perfect representation of nature. Classification is a model that is very useful, but not adequate in all cases. Conservationists often confront questions about how to apply species-based laws when hybridization confounds classification. Development of sophisticated techniques and nuanced interpretation of data in the basic study of species and speciation has exposed the need for deeper education in genetics and evolution for applied conservationists and decision makers. Here we offer a brief perspective on hybridization and the species problem in conservation. Our intended audience is conservation practitioners and decision-makers more than geneticists and evolutionary biologists. We wish to emphasize that the goals and premises of legislative classification are not identical to those of scientific classification. Sometimes legal classification is required when the best available science indicates that discrete classification is not an adequate model for the case. Establishing legal status and level of protection for hybrids and hybrid populations means choosing from a range of scientifically valid alternatives. Although we should not abandon species-based approaches to conservation, we must recognize their limitations and work to clarify the roles of science and values in ethical and legal decisions.
I smell a rat: Can New Zealand birds recognize the odor of an invasive mammalian predator?
Authors: Stanbury Mailee , Briskie James V. 
Published: February 2016

Abstract
Although it is well known that birds can assess predation risk through visual and auditory cues, there has been little research into whether similar processes occur with olfactory cues. We examined the role of odor cues in assessing nest predation risk in four species of passerine birds in New Zealand. We compared the ability of two introduced European species (common starling Sturnus vulgaris and song thrush Turdus philomelos) and two native New Zealand species (rifleman Acanthisitta chloris and South Island robin Petroica australis) to respond to the scent of rat urine placed in the nest. Rats are an introduced predator in New Zealand and we expected the native birds, which did not co-evolve with any mammalian predators, to lack behavioral adaptations to the scent of rats at their nest. As expected, both riflemen and robins failed to show any change in their behavior at their nest when rat urine was present compared to a control period in which no scent was present. However, a similar lack of response was observed in the introduced song thrush; only the common starling changed its behavior in the presence of the rat urine. Starlings with rat urine at the nest box were more likely to hesitate before entering and they also approached the nest, but refused to enter more often in the presence of rat scent. Both responses suggest they detected the presence of a predator and changed their behavior to minimize risk to themselves. Although based on a small number of species, our results suggest that responses to predator scent may be less common in New Zealand species, and may be a factor contributing to the vulnerability of native birds to introduced mammalian predators.
Dominance network structure across reproductive contexts in the cooperatively breeding cichlid fish Neolamprologus pulcher
Authors: Dey Cody J. , Tan Q.Y. Joanne , O’Connor Constance M. , Reddon Adam R. , Caldwell J. Ryan 
Published: February 2016

Abstract
While a large number of studies have described animal social networks, we have a poor understanding of how these networks vary with ecological and social conditions. For example, reproductive periods are an important life-history stage that may involve changes in dominance relationships among individuals, yet no study to date has compared social networks of dominance interactions (i.e. dominance networks) across reproductive contexts. We first analyzed a long-term dataset on captive social groups of the cooperatively breeding cichlid Neolamprologus pulcher, and found that eviction events were significantly more common around reproduction than expected by chance. Next, we compared the structure of dominance networks during early parental care and non-reproductive periods, using one of the first applications of exponential random graph models in behavioral biology. Contrary to our predictions, we found that dominance networks showed few changes between early parental care and non-reproductive periods. We found no evidence that dominance interactions became more skewed towards larger individuals, became more frequent between similar-sized individuals, or became more biased towards a particular sex during parental care. However, we did find that there were relatively more dominance interactions between opposite-sex dyads in the early parental care period, which may be a by-product of increased sexual interactions during this time. This is the first study in behavioral ecology to compare social networks using exponential random graph modeling, and demonstrates a powerful analytical framework for future studies in the field.
Self-deception can evolve under appropriate costs
Authors: Ramírez Juan Camilo , Marshall James A. R. 
Published: February 2016

Abstract
Apparent biases in decision making by animals, including humans, seem to present an evolutionary puzzle, since one would expect decisions based on biased (unrealistic) information to be suboptimal. Although cognitive biases are hard to diagnose in real animals (Marshall et al., 2013b), we investigate Trivers’ proposal that individuals should self-deceive first in order to better deceive others (Trivers, 2011). Although this proposal has been scrutinized extensively (Bandura et al., 2011) it has not been formally modelled. We present the first model designed to investigate Trivers’ proposal. We introduce an extension to a recent model of the evolution of self-deception (Johnson and Fowler, 2011). In the extended model individuals make decisions by taking directly into account the benefits and costs of each outcome and by choosing the course of action that can be estimated as the best with the information available. It is shown that in certain circumstances self-deceiving decision-makers are the most evolutionarily successful, even when there is no deception between these. In a further extension of this model individuals additionally exhibit deception biases and Trivers’ premise (that effective deception is less physiologically costly with the aid of self-deception) is incorporated. It is shown that under Trivers’ hypothesis natural selection favors individuals that self-deceive as they deceive others.
An elevational trend of body size variation in a cold-climate agamid lizard, Phrynocephalus theobaldi
Authors: Jin Yuanting , Liao Pinghu 
Published: February 2016

Abstract
The pattern that many ectotherms have smaller body sizes in cold environments follows the converse to Bergmann’s rule and is most frequently found in lizards. Allen’s rule predicts animals from warm climates usually have longer tails and limbs, while these traits tend to be shorter in individuals from cold climates. We examined body size variation in an endemic Chinese lizard Phrynocephalus theobaldi along a broad elevational gradient (3,600–5,000 m on the Qinghai-Tibetan Plateau). Female body size showed a U-shaped cline, decreasing with increased elevation within the range 3,600–4,200 m, but increasing at elevations &gt; 4200 m. Male body size continued to increase with increasing elevations. Both sexes showed an increased pattern of extremity length with elevation that does not conform to Allen’s rule. Limb length and tail length increased along the elevational gradients. In terms of color pattern, an abdominal black speckled area appears at elevations &gt;4,200 m. This trait increases in size with increased elevation. Unlike most studies, our results indicated that annual sunshine hours corresponding to the activity period of the lizards could play an important role on the positive body size cline in environments at very high elevations &gt; 4200 m.
A review of ecological impacts of global climate change on persistent organic pollutant and mercury pathways and exposures in arctic marine ecosystems
Authors: Mckinney Melissa A. , Pedro Sara , Dietz Rune , Sonne Christian , Fisk Aaron T. , Roy Denis , Jenssen Bjørn M. , Letcher Robert J. 
Published: February 2016

Abstract
Bioaccumulative and biomagnifying contaminants, such as persistent organic pollutants (POPs) and mercury (Hg), have for decades been recognized as a health concern in arctic marine biota. In recent years, global climate change (GCC) and related loss of arctic sea ice have been observed to be driving substantial change in arctic ecosystems. This review summarizes findings documenting empirical links between GCC-induced ecological changes and alterations in POP and Hg exposures and pathways in arctic marine ecosystems. Most of the studies have reported changes in POP or Hg concentrations in tissue in relation to GCC-induced changes in species trophic interactions. These studies have typically focused on the role of changes in abundance, habitat range or accessibility of prey species, particularly in relation to sea ice changes. Yet, the ecological change that resulted in contaminant trend changes has often been unclear or assumed. Other studies have successfully used chemical tracers, such as stable nitrogen and carbon isotope ratios and fatty acid signatures to link such ecological changes to contaminant level variations or trends. Lower sea ice linked-diet changes/variation were associated with higher contaminant levels in some populations of polar bears, ringed seals, and thick-billed murres, but the influence of changing trophic interactions on POP levels and trends varied widely in both magnitude and direction. We suggest that future research in this new area of GCC-linked ecotoxicology should focus on routine analysis of ancillary ecological metrics with POP and Hg studies, simultaneous consideration of the multiple mechanisms by which GCC and contaminant interactions can occur, and targeted research on changing exposures and toxicological effects in species known to be sensitive to both GCC and contaminants.
Interactive effects of metal pollution and ocean acidification on physiology of marine organisms
Authors: Ivanina Anna V. , Sokolova Inna M. 
Published: February 2016

Abstract
Changes in the global environment such as ocean acidification (OA) may interact with anthropogenic pollutants including trace metals threatening the integrity of marine ecosystems. We analyze recent studies on the interactive effects of OA and trace metals on marine organisms with a focus on the physiological basis of these interactions. Our analysis shows that the responses to elevated CO2 and metals are strongly dependent on the species, developmental stage, metal biochemistry and the degree of environmental hypercapnia, and cannot be directly predicted from the CO2-induced changes in metal solubility and speciation. The key physiological functions affected by both the OA and trace metal exposures involve acid-base regulation, protein turnover and mitochondrial bioenergetics, reflecting the sensitivity of the underlying molecular and cellular pathways to CO2and metals. Physiological interactions between elevated CO2 and metals may impact the organisms’ capacity to maintain acid-base homeostasis and reduce the amount of energy available for fitness-related functions such as growth, development and reproduction thereby affecting survival and performance of estuarine populations. Environmental hypercapnia may also affect the marine food webs by altering predator-prey interactions and the trophic transfer of metals in the food chain. However, our understanding of the degree to which these effects can impact the function and integrity of marine ecosystems is limited due the scarcity of the published research and its bias towards certain taxonomic groups. Future research priorities should include studies of metal x PCO2 interactions focusing on critical physiological functions (including acid-base, protein and energy homeostasis) in a greater range of ecologically and economically important marine species, as well as including the field populations naturally exposed (and potentially adapted) to different levels of metals and CO2 in their environments.
The art and science of species delimitation
Authors: Rannala Bruce 
Published: February 2016

Abstract
DNA-based approaches to systematics have changed dramatically during the last two decades with the rise of DNA barcoding methods and newer multi-locus methods for species delimitation. During the last half-decade, partly driven by the new sequencing technologies, the focus has shifted to multi-locus sequence data and the identification of species within the framework of the multi-species coalescent (MSC). In this paper, I discuss model-based Bayesian methods for species delimitation that have been developed in recent years using the MSC. Several approximate methods for species delimitation (and their limitations) are also discussed. Explicit species delimitation models have the advantage of clarifying more precisely what is being delimited and what assumptions we are making in doing so. Moreover, the methods can be very powerful when applied to large multi-locus datasets and thus take full advantage of data generated using today’s technologies.
Novel insights into the historical biogeography of the streak-breasted scimitar babbler complex (Aves: Timaliidae: Pomatorhinus ruficollis complex)
Authors: Reddy Sushma , Nyári Árpád S. 
Published: February 2016

Abstract
The Streak-breasted Scimitar Babblers of the Pomatorhinus ruficollis species complex are found in most of the forested habitats across southern and eastern Asia. The diversification history of this group is obscured by high plumage variation across populations and conflicting genetic signal across loci. We combined genetic and geographic data from several recent studies to investigate how these species diversified across China using both phylogenetic and ecological niche modeling analyses. These two lines of evidence are consistent in showing that two well-sampled species, P. reconditus and P. nigrostellatus, in central and southern China respectively, likely experienced a history of isolation and expansion as suitable habitat contracted during the last interglacial and expanded in patchy extent during the glacial maximum. The genetic analysis showed that populations of P. nigrostellatus on Hainan Island are very similar to the ones in nearby mainland southern China. We recovered two well-supported clades within P. reconditus that were not geographically structured with both containing individuals from the same localities across central China. This phylogenetic result corresponded to the ecological niche models that showed expansion from refugia since the last interglacial. This study illustrates the value of using an integrative approach and detailed geographic sampling to help understand the recent diversification of birds in China.
Passive and active, predator and prey: using acoustics to study interactions between cetaceans and forage fish
Authors: Lawrence Joshua M. , Armstrong Eric , Gordon Jonathan , Lusseau Susan Mærsk , Fernandes Paul G. 
Published: February 2016

AbstractFisheries acoustics surveys provide platforms for deploying passive acoustic equipment to detect cetacean vocalizations. Passive acoustic methods are developing as viable alternatives to visual surveys, particularly for small, inconspicuous species such as the harbour porpoise (Phocoena phocoena). Passive acoustic monitoring using a towed hydrophone array was carried out during an acoustic survey of clupeids in the Clyde Sea and surrounding sea lochs to identify spatial relationships between porpoises and their prey. Methods were developed to process passive acoustic data, successfully identifying porpoise echolocation clicks while discriminating them from the transmitted 120-kHz echosounder pulse and its reflections. To date, this has been a confounding factor which has made these survey techniques potentially incompatible. The highest biomass of pelagic fish was detected in the northernmost parts of the survey region, as were the largest number of porpoises. A moving average was used to examine the scale of the relationships identified, and it was found that while porpoises show no significant preferences for pelagic prey numbers at the smallest scales, they do show significant avoidance of larger areas (5+ km) with very low pelagic fish biomass. This study demonstrates that high-frequency passive acoustic monitoring can be used effectively alongside multifrequency fisheries echosounder surveys to provide novel insights into the trophic interactions between these species, and that further work will hopefully prove useful in improving the efficacy of management strategies for harbour porpoises.
Clinical Features of Spontaneous Partial Healing During Mycobacterium ulcerans Infection
Authors: Marion Estelle , Chauty Annick , Kempf Marie , Le Corre Yannick , Delneste Yves , Croue Anne , Marsollier Laurent ,   for the Franco-Beninese Buruli Research Group, Vincent Quentin B. , Abel Laurent , Johnson Christian , Alcaïs Alexandre , Marion Estelle , Marsollier Laurent , Kempf Marie , Saint-André Jean-Paul , Adeye Ambroise , Chauty Annick , Agossadou Didier 
Published: February 2016

Abstract
Background.  Buruli ulcer, caused by Mycobacterium ulcerans, is a necrotizing skin disease leading to extensive cutaneous and subcutaneous destruction and functional limitations. Spontaneous healing in the absence of medical treatment occurs in rare cases, but this has not been well described in the literature.
Methods.  In a retrospective case study in an area of Benin where this disease is highly endemic, we selected 26 Buruli ulcer patients presenting features of spontaneous healing from a cohort of 545 Buruli ulcer patients treated between 2010 and 2013.
Results.  The 26 patients studied had a median age of 13.5 years and were predominantly male (1.4:1). Three groups of patients were defined on the basis of their spontaneous healing characteristics. The first group (12 patients) consisted of patients with an ulcer of more than 1 year′s duration showing signs of healing. The second (13 patients) group contained patients with an active Buruli ulcer lesion some distance away from a first lesion that had healed spontaneously. Finally, the third group contained a single patient displaying complete healing of lesions from a nodule, without treatment and with no relapse.
Conclusions.  We defined several features of spontaneous healing in Buruli ulcer patients and highlighted the difficulties associated with diagnosis and medical management. Delays in consultation contributed to the high proportion of patients with permanent sequelae and a risk of squamous cell carcinoma. Early detection and antibiotic treatment are the best ways to reduce impairments.
Unnecessary Antibiotics for Acute Respiratory Tract Infections: Association With Care Setting and Patient Demographics
Authors: Barlam Tamar F. , Soria-Saucedo Rene , Cabral Howard J. , Kazis Lewis E. 
Published: February 2016

Abstract
Background.  Up to 40% of antibiotics are prescribed unnecessarily for acute respiratory tract infections (ARTIs). We sought to define factors associated with antibiotic overprescribing of ARTIs to inform efforts to improve practice.
Methods.  We conducted a retrospective analysis of ARTI visits between 2006 and 2010 from the National Ambulatory Medical Care Survey and the National Hospital Ambulatory Medical Care Survey. Those surveys provide a representative sample of US visits to community-based physicians and to hospital-based emergency departments (EDs) and outpatient practices. Patient factors (age, sex, race, underlying lung disease, tobacco use, insurance), physician specialty, practice demographics (percentage poverty, median household income, percentage with a Bachelor's Degree, urban-rural status, geographic region), and care setting (ED, hospital, or community-based practice) were evaluated as predictors of antibiotic overprescribing for ARTIs.
Results.  Hospital and community-practice visits had more antibiotic overprescribing than ED visits (odds ratio [OR] = 1.64 and 95% confidence interval [CI], 1.27–2.12 and OR = 1.59 and 95% CI, 1.26–2.01, respectively). Care setting had significant interactions with geographic region and urban and rural location. The quartile with the lowest percentage of college-educated residents had significantly greater overprescribing (adjusted OR = 1.41; 95% CI, 1.07–1.86) than the highest quartile. Current tobacco users were overprescribed more often than nonsmokers (OR = 1.71; 95% CI, 1.38–2.12). Patient age, insurance, and provider specialty were other significant predictors.
Conclusions.  Tobacco use and a lower grouped rate of college education were associated with overprescribing and may reflect poor health literacy. A focus on educating the patient may be an effective approach to stewardship.