title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1742 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Making inference from wildlife collision data: inferring predator absence from prey strikes link: https://peerj.com/articles/3014 last-modified: 2017-02-22 description: Wildlife collision data are ubiquitous, though challenging for making ecological inference due to typically irreducible uncertainty relating to the sampling process. We illustrate a new approach that is useful for generating inference from predator data arising from wildlife collisions. By simply conditioning on a second prey species sampled via the same collision process, and by using a biologically realistic numerical response functions, we can produce a coherent numerical response relationship between predator and prey. This relationship can then be used to make inference on the population size of the predator species, including the probability of extinction. The statistical conditioning enables us to account for unmeasured variation in factors influencing the runway strike incidence for individual airports and to enable valid comparisons. A practical application of the approach for testing hypotheses about the distribution and abundance of a predator species is illustrated using the hypothesized red fox incursion into Tasmania, Australia. We estimate that conditional on the numerical response between fox and lagomorph runway strikes on mainland Australia, the predictive probability of observing no runway strikes of foxes in Tasmania after observing 15 lagomorph strikes is 0.001. We conclude there is enough evidence to safely reject the null hypothesis that there is a widespread red fox population in Tasmania at a population density consistent with prey availability. The method is novel and has potential wider application. creator: Peter Caley creator: Geoffrey R. Hosack creator: Simon C. Barry uri: https://doi.org/10.7717/peerj.3014 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Caley et al. title: Gait changes in a line of mice artificially selected for longer limbs link: https://peerj.com/articles/3008 last-modified: 2017-02-22 description: In legged terrestrial locomotion, the duration of stance phase, i.e., when limbs are in contact with the substrate, is positively correlated with limb length, and negatively correlated with the metabolic cost of transport. These relationships are well documented at the interspecific level, across a broad range of body sizes and travel speeds. However, such relationships are harder to evaluate within species (i.e., where natural selection operates), largely for practical reasons, including low population variance in limb length, and the presence of confounding factors such as body mass, or training. Here, we compared spatiotemporal kinematics of gait in Longshanks, a long-legged mouse line created through artificial selection, and in random-bred, mass-matched Control mice raised under identical conditions. We used a gait treadmill to test the hypothesis that Longshanks have longer stance phases and stride lengths, and decreased stride frequencies in both fore- and hind limbs, compared with Controls. Our results indicate that gait differs significantly between the two groups. Specifically, and as hypothesized, stance duration and stride length are 8–10% greater in Longshanks, while stride frequency is 8% lower than in Controls. However, there was no difference in the touch-down timing and sequence of the paws between the two lines. Taken together, these data suggest that, for a given speed, Longshanks mice take significantly fewer, longer steps to cover the same distance or running time compared to Controls, with important implications for other measures of variation among individuals in whole-organism performance, such as the metabolic cost of transport. creator: Leah M. Sparrow creator: Emily Pellatt creator: Sabrina S. Yu creator: David A. Raichlen creator: Herman Pontzer creator: Campbell Rolian uri: https://doi.org/10.7717/peerj.3008 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Sparrow et al. title: Seven new species of Night Frogs (Anura, Nyctibatrachidae) from the Western Ghats Biodiversity Hotspot of India, with remarkably high diversity of diminutive forms link: https://peerj.com/articles/3007 last-modified: 2017-02-21 description: The Night Frog genus Nyctibatrachus (Family Nyctibatrachidae) represents an endemic anuran lineage of the Western Ghats Biodiversity Hotspot, India. Until now, it included 28 recognised species, of which more than half were described recently over the last five years. Our amphibian explorations have further revealed the presence of undescribed species of Nights Frogs in the southern Western Ghats. Based on integrated molecular, morphological and bioacoustic evidence, seven new species are formally described here as Nyctibatrachus athirappillyensis sp. nov., Nyctibatrachus manalari sp. nov., Nyctibatrachus pulivijayani sp. nov., Nyctibatrachus radcliffei sp. nov., Nyctibatrachus robinmoorei sp. nov., Nyctibatrachus sabarimalai sp. nov. and Nyctibatrachus webilla sp. nov., thereby bringing the total number of valid Nyctibatrachus species to 35 and increasing the former diversity estimates by a quarter. Detailed morphological descriptions, comparisons with other members of the genus, natural history notes, and genetic relationships inferred from phylogenetic analyses of a mitochondrial dataset are presented for all the new species. Additionally, characteristics of male advertisement calls are described for four new and three previously known species. Among the new species, six are currently known to be geographically restricted to low and mid elevation regions south of Palghat gap in the states of Kerala and Tamil Nadu, and one is probably endemic to high-elevation mountain streams slightly northward of the gap in Tamil Nadu. Interestingly, four new species are also among the smallest known Indian frogs. Hence, our discovery of several new species, particularly of easily overlooked miniaturized forms, reiterates that the known amphibian diversity of the Western Ghats of India still remains underestimated. creator: Sonali Garg creator: Robin Suyesh creator: Sandeep Sukesan creator: SD Biju uri: https://doi.org/10.7717/peerj.3007 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Garg et al. title: On Prophoca and Leptophoca (Pinnipedia, Phocidae) from the Miocene of the North Atlantic realm: redescription, phylogenetic affinities and paleobiogeographic implications link: https://peerj.com/articles/3024 last-modified: 2017-02-21 description: BackgroundProphoca and Leptophoca represent the oldest known genera of phocine seals, dating from the latest early to middle Miocene. Originally, Prophoca rousseaui and Prophoca proxima were described based on fragmentary remains from the Miocene of Belgium. However, several researchers contested the union of Prophoca rousseaui and Prophoca proxima into one genus, without providing evidence. The stratigraphic context of Prophoca remained poorly constrained due to the lack of precise data associated with the original specimens collected in the area of Antwerp (north of Belgium).MethodsProphoca and Leptophoca are redescribed and their phylogenetic position among Phocidae is reassessed using PAUP. Dinoflagellate biostratigraphy has been carried out on sediment samples associated with specimens from Prophoca and Leptophoca to elucidate their approximate ages.ResultsWhereas the species Prophoca rousseaui is redescribed, Prophoca proxima is considered synonymous to Leptophoca lenis, with the proposal of a new combination Leptophoca proxima (Van Beneden, 1877). Sediment samples from specimens of both taxa have been dated to the late Langhian–early Serravallian (middle Miocene). Following a reinvestigation of Leptophoca amphiatlantica, characters from the original diagnosis are questioned and the specimens of Leptophoca amphiatlantica are considered Leptophoca cf. L. proxima. In a phylogenetic analysis, Prophoca rousseaui and Leptophoca proxima constitute early branching stem-phocines.DiscussionLeptophoca proxima from the North Sea Basin is younger than the oldest known find of Leptophoca proxima from North America, which does not contradict the hypothesis that Phocinae originated along the east coast of North America during the late early Miocene, followed by dispersal to Europe shortly after. Morphological features of the appendicular skeleton indicate that Prophoca rousseaui and Leptophoca proxima have archaic locomotory modes, retaining a more prominent use of the fore flipper for aquatic propulsion than extant Phocidae. creator: Leonard Dewaele creator: Olivier Lambert creator: Stephen Louwye uri: https://doi.org/10.7717/peerj.3024 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Dewaele et al. title: Modeling using clinical examination indicators predicts interstitial lung disease among patients with rheumatoid arthritis link: https://peerj.com/articles/3021 last-modified: 2017-02-21 description: Interstitial lung disease (ILD) is a severe extra-articular manifestation of rheumatoid arthritis (RA) that is well-defined as a chronic systemic autoimmune disease. A proportion of patients with RA-associated ILD (RA-ILD) develop pulmonary fibrosis (PF), resulting in poor prognosis and increased lifetime risk. We investigated whether routine clinical examination indicators (CEIs) could be used to identify RA patients with high PF risk. A total of 533 patients with established RA were recruited in this study for model building and 32 CEIs were measured for each of them. To identify PF risk, a new artificial neural network (ANN) was built, in which inputs were generated by calculating Euclidean distance of CEIs between patients. Receiver operating characteristic curve analysis indicated that the ANN performed well in predicting the PF risk (Youden index = 0.436) by only incorporating four CEIs including age, eosinophil count, platelet count, and white blood cell count. A set of 218 RA patients with healthy lungs or suffering from ILD and a set of 87 RA patients suffering from PF were used for independent validation. Results showed that the model successfully identified ILD and PF with a true positive rate of 84.9% and 82.8%, respectively. The present study suggests that model integration of multiple routine CEIs contributes to identification of potential PF risk among patients with RA. creator: Yao Wang creator: Wuqi Song creator: Jing Wu creator: Zhangming Li creator: Fengyun Mu creator: Yang Li creator: He Huang creator: Wenliang Zhu creator: Fengmin Zhang uri: https://doi.org/10.7717/peerj.3021 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Wang et al. title: Molecular and morphological data reveal three new cryptic species of Chiasmocleis (Mehely 1904) (Anura, Microhylidae) endemic to the Atlantic Forest, Brazil link: https://peerj.com/articles/3005 last-modified: 2017-02-21 description: Three new cryptic species of Chiasmocleis from the Atlantic Forest of Brazil are described. Two of these species occur in the northeastern states of Sergipe and Bahia, whereas the third species is found in the southeastern state of São Paulo. The new species can be distinguished from other congeneric species by the molecular data, as evidenced in the phylogeny, and by a combination of morphological characters including: size, foot webbing, dermal spines, and coloration patterns. Chiasmocleis species differ in osteological traits, therefore we also provide an osteological description of each new species and comparsions with data reported for other species in the genus. creator: Mauricio C. Forlani creator: João F.R. Tonini creator: Carlos A.G. Cruz creator: Hussam Zaher creator: Rafael O. de Sá uri: https://doi.org/10.7717/peerj.3005 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Forlani et al. title: A detailed observation of the ejection and retraction of defense tissue acontia in sea anemone (Exaiptasia pallida) link: https://peerj.com/articles/2996 last-modified: 2017-02-21 description: Acontia, located in the gastrovascular cavity of anemone, are thread-like tissue containing numerous stinging cells which serve as a unique defense tissue against predators of the immobile acontiarian sea anemone. Although its morphology and biological functions, such as defense and digestion, have been studied, the defense behavior and the specific events of acontia ejection and retraction are unclear. The aim of this study is to observe and record the detailed process of acontia control in anemones. Observations reveal that the anemone, Exaiptasia pallida, possibly controls a network of body muscles and manipulates water pressure in the gastrovascular cavity to eject and retract acontia. Instead of resynthesizing acontia after each ejection, the retraction and reuse of acontia enables the anemone to respond quickly at any given time, thus increasing its overall survivability. Since the Exaiptasia anemone is an emerging model for coral biology, this study provides a foundation to further investigate the biophysics, neuroscience, and defense biology of this marine model organism. creator: Julie Lam creator: Ya-Wen Cheng creator: Wan-Nan U. Chen creator: Hsing-Hui Li creator: Chii-Shiarng Chen creator: Shao-En Peng uri: https://doi.org/10.7717/peerj.2996 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Lam et al. title: How patch size and refuge availability change interaction strength and population dynamics: a combined individual- and population-based modeling experiment link: https://peerj.com/articles/2993 last-modified: 2017-02-21 description: Knowledge on how functional responses (a measurement of feeding interaction strength) are affected by patch size and habitat complexity (represented by refuge availability) is crucial for understanding food-web stability and subsequently biodiversity. Due to their laborious character, it is almost impossible to carry out systematic empirical experiments on functional responses across wide gradients of patch sizes and refuge availabilities. Here we overcame this issue by using an individual-based model (IBM) to simulate feeding experiments. The model is based on empirically measured traits such as body-mass dependent speed and capture success. We simulated these experiments in patches ranging from sizes of petri dishes to natural patches in the field. Moreover, we varied the refuge availability within the patch independently of patch size, allowing for independent analyses of both variables. The maximum feeding rate (the maximum number of prey a predator can consume in a given time frame) is independent of patch size and refuge availability, as it is the physiological upper limit of feeding rates. Moreover, the results of these simulations revealed that a type III functional response, which is known to have a stabilizing effect on population dynamics, fitted the data best. The half saturation density (the prey density where a predator consumes half of its maximum feeding rate) increased with refuge availability but was only marginally influenced by patch size. Subsequently, we investigated how patch size and refuge availability influenced stability and coexistence of predator-prey systems. Following common practice, we used an allometric scaled Rosenzweig–MacArthur predator-prey model based on results from our in silico IBM experiments. The results suggested that densities of both populations are nearly constant across the range of patch sizes simulated, resulting from the constant interaction strength across the patch sizes. However, constant densities with decreasing patch sizes mean a decrease of absolute number of individuals, consequently leading to extinction of predators in the smallest patches. Moreover, increasing refuge availabilities also allowed predator and prey to coexist by decreased interaction strengths. Our results underline the need for protecting large patches with high habitat complexity to sustain biodiversity. creator: Yuanheng Li creator: Ulrich Brose creator: Katrin Meyer creator: Björn C. Rall uri: https://doi.org/10.7717/peerj.2993 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Li et al. title: Counting complete? Finalising the plant inventory of a global biodiversity hotspot link: https://peerj.com/articles/2984 last-modified: 2017-02-21 description: The Cape Floristic Region—the world’s smallest and third richest botanical hotspot—has benefited from sustained levels of taxonomic effort and exploration for almost three centuries, but how close is this to resulting in a near-complete plant species inventory? We analyse a core component of this flora over a 250-year period for trends in taxonomic effort and species discovery linked to ecological and conservation attributes. We show that >40% of the current total of species was described within the first 100 years of exploration, followed by a continued steady rate of description. We propose that <1% of the flora is still to be described. We document a relatively constant cohort of taxonomists, working over 250 years at what we interpret to be their ‘taxonomic maximum.’ Rates of description of new species were independent of plant growth-form but narrow-range taxa have constituted a significantly greater proportion of species discoveries since 1950. This suggests that the fraction of undiscovered species predominantly comprises localised endemics that are thus of high conservation concern. Our analysis provides important real-world insights for other hotspots in the context of global strategic plans for biodiversity in informing considerations of the likely effort required in attaining set targets of comprehensive plant inventories. In a time of unprecedented biodiversity loss, we argue for a focused research agenda across disciplines to increase the rate of species descriptions in global biodiversity hotspots. creator: Martina Treurnicht creator: Jonathan F. Colville creator: Lucas N. Joppa creator: Onno Huyser creator: John Manning uri: https://doi.org/10.7717/peerj.2984 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Treurnicht et al. title: Patient satisfaction with doctor-patient interaction and its association with modifiable cardiovascular risk factors among moderately-high risk patients in primary healthcare link: https://peerj.com/articles/2983 last-modified: 2017-02-21 description: BackgroundThe outcomes of the physician-patient discussion intervene in the satisfaction of cardiovascular disease risk patients. Adherence to treatment, provision of continuous care, clinical management of the illness and patients’ adjustment are influenced by satisfaction with physician-patient interaction. This study aims to determine patient satisfaction with doctor-patient interactions and, over six months after following prevention counselling, its associations with modifiable cardiovascular risk factors amongst moderately-high risk patients in a primary healthcare clinic in Kelantan, Malaysia.MethodsA prospective survey was conducted amongst patients with moderately-high cardiovascular risk. A total of 104 moderately-high risk patients were recruited and underwent structured prevention counselling based on the World Health Organization guideline, and their satisfaction with the doctor-patient interaction was assessed using ‘Skala Kepuasan Interaksi Perubatan-11,’ the Malay version of the Medical Interview Satisfaction Scale-21. Systolic blood pressure, total cholesterol and high-density lipoprotein cholesterol were measured at baseline and at a follow-up visit at six months. Descriptive analysis, paired t test and linear regression analyses were performed.ResultsA total of 102 patients responded, giving a response rate of 98.1%. At baseline, 76.5% of the respondents were satisfied with the relation with their doctor, with the favourable domain of distress relief (85.3%) and rapport/confidence (91.2%). The unfavourable domain was interaction outcome, with satisfaction in only 67.6% of the respondents. Between the two visits, changes had occurred in total cholesterol (P = 0.022) and in systolic blood pressure (P < 0.001). Six months after the initial visits, no relationship existed between patient satisfaction scores and changes in modifiable cardiovascular risks.DiscussionThe ‘Skala Kepuasan Interaksi Perubatan-11’ which represents a component of the interpersonal doctor-patient relationship can be used to assess improvements of the medical skills and in medical training to enhance the quality of therapeutic communication. creator: Mohd Noor Norhayati creator: Abd Aziz Masseni creator: Ishak Azlina uri: https://doi.org/10.7717/peerj.2983 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Norhayati et al.