title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1741 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Eotaria citrica, sp. nov., a new stem otariid from the “Topanga” formation of Southern California link: https://peerj.com/articles/3022 last-modified: 2017-02-23 description: A new taxon of stem otariid, Eotaria citrica sp. nov., is described from the upper Burdigalian to lower Langhian “Topanga” formation of Orange County, California. The new species is described from mandibular and dental remains that show a unique combination of plesiomorphic and derived characters. Specifically, it is characterized by having trenchant and prominent paraconid cusps in p3–m1, lingual cingula of p2–4 with faint crenulations, premolars and molars with vestigial metaconid, bilobed root of m2 and a genial tuberosity located under p3. Furthermore, additional material of the contemporaneous Eotaria crypta is described, providing new information on the morphology of this taxon. Both species of Eotaria represent the earliest stem otariids, reinforcing the hypothesis that the group originated in the north Eastern Pacific Region. At present, the “Topanga” Fm. pinniped fauna includes Eotaria citrica, Eotaria crypta, the desmatophocid Allodesmus sp., the odobenids Neotherium sp., Pelagiarctos sp. and includes the oldest records of crown pinnipeds in California. Overall this pinniped fauna is similar to the nearly contemporaneous Sharktooth Hill bonebed. However, unambiguous records of Eotaria are still missing from Sharktooth Hill. This absence may be due to taphonomic or paleoenvironmental factors. The new “Topanga” record presented here was integrated into an overview of the late Oligocene through early Pleistocene pinniped faunas of Southern California. The results show an overall increase in body size over time until the Pleistocene. Furthermore, desmatophocids were the largest pinnipeds during the middle Miocene, but were extinct by the beginning of the late Miocene. Odobenids diversified and became the dominant pinnipeds in late Miocene through Pleistocene assemblages, usually approaching or exceeding 3 m in body length, while otariids remained as the smallest taxa. This pattern contrasts with modern assemblages, in which the phocid Mirounga angustirostris is the largest pinniped taxon in the region, odobenids are extinct and medium and small size ranges are occupied by otariids or other phocids. creator: Jorge Velez-Juarbe uri: https://doi.org/10.7717/peerj.3022 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Velez-Juarbe title: Genetic diversity and differentiation in reef-building Millepora species, as revealed by cross-species amplification of fifteen novel microsatellite loci link: https://peerj.com/articles/2936 last-modified: 2017-02-23 description: Quantifying the genetic diversity in natural populations is crucial to address ecological and evolutionary questions. Despite recent advances in whole-genome sequencing, microsatellite markers have remained one of the most powerful tools for a myriad of population genetic approaches. Here, we used the 454 sequencing technique to develop microsatellite loci in the fire coral Millepora platyphylla, an important reef-builder of Indo-Pacific reefs. We tested the cross-species amplification of these loci in five other species of the genus Millepora and analysed its success in correlation with the genetic distances between species using mitochondrial 16S sequences. We succeeded in discovering fifteen microsatellite loci in our target species M. platyphylla, among which twelve were polymorphic with 2–13 alleles and a mean observed heterozygosity of 0.411. Cross-species amplification in the five other Millepora species revealed a high probability of amplification success (71%) and polymorphism (59%) of the loci. Our results show no evidence of decreased heterozygosity with increasing genetic distance. However, only one locus enabled measures of genetic diversity in the Caribbean species M. complanata due to high proportions of null alleles for most of the microsatellites. This result indicates that our novel markers may only be useful for the Indo-Pacific species of Millepora. Measures of genetic diversity revealed significant linkage disequilibrium, moderate levels of observed heterozygosity (0.323–0.496) and heterozygote deficiencies for the Indo-Pacific species. The accessibility to new polymorphic microsatellite markers for hydrozoan Millepora species creates new opportunities for future research on processes driving the complexity of their colonisation success on many Indo-Pacific reefs. creator: Caroline E. Dubé creator: Serge Planes creator: Yuxiang Zhou creator: Véronique Berteaux-Lecellier creator: Emilie Boissin uri: https://doi.org/10.7717/peerj.2936 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Dubé et al. title: Using visuo-kinetic virtual reality to induce illusory spinal movement: the MoOVi Illusion link: https://peerj.com/articles/3023 last-modified: 2017-02-22 description: BackgroundIllusions that alter perception of the body provide novel opportunities to target brain-based contributions to problems such as persistent pain. One example of this, mirror therapy, uses vision to augment perceived movement of a painful limb to treat pain. Since mirrors can’t be used to induce augmented neck or other spinal movement, we aimed to test whether such an illusion could be achieved using virtual reality, in advance of testing its potential therapeutic benefit. We hypothesised that perceived head rotation would depend on visually suggested movement.MethodIn a within-subjects repeated measures experiment, 24 healthy volunteers performed neck movements to 50o of rotation, while a virtual reality system delivered corresponding visual feedback that was offset by a factor of 50%–200%—the Motor Offset Visual Illusion (MoOVi)—thus simulating more or less movement than that actually occurring. At 50o of real-world head rotation, participants pointed in the direction that they perceived they were facing. The discrepancy between actual and perceived direction was measured and compared between conditions. The impact of including multisensory (auditory and visual) feedback, the presence of a virtual body reference, and the use of 360o immersive virtual reality with and without three-dimensional properties, was also investigated.ResultsPerception of head movement was dependent on visual-kinaesthetic feedback (p = 0.001, partial eta squared = 0.17). That is, altered visual feedback caused a kinaesthetic drift in the direction of the visually suggested movement. The magnitude of the drift was not moderated by secondary variables such as the addition of illusory auditory feedback, the presence of a virtual body reference, or three-dimensionality of the scene.DiscussionVirtual reality can be used to augment perceived movement and body position, such that one can perform a small movement, yet perceive a large one. The MoOVi technique tested here has clear potential for assessment and therapy of people with spinal pain. creator: Daniel S. Harvie creator: Ross T. Smith creator: Estin V. Hunter creator: Miles G. Davis creator: Michele Sterling creator: G. Lorimer Moseley uri: https://doi.org/10.7717/peerj.3023 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Harvie et al. 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.