title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1813 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Ancient phylogenetic divergence of the enigmatic African rodent Zenkerella and the origin of anomalurid gliding link: https://peerj.com/articles/2320 last-modified: 2016-08-16 description: The “scaly-tailed squirrels” of the rodent family Anomaluridae have a long evolutionary history in Africa, and are now represented by two gliding genera (Anomalurus and Idiurus) and a rare and obscure genus (Zenkerella) that has never been observed alive by mammalogists. Zenkerella shows no anatomical adaptations for gliding, but has traditionally been grouped with the glider Idiurus on the basis of craniodental similarities, implying that either the Zenkerella lineage lost its gliding adaptations, or that Anomalurus and Idiurus evolved theirs independently. Here we present the first nuclear and mitochondrial DNA sequences of Zenkerella, based on recently recovered whole-body specimens from Bioko Island (Equatorial Guinea), which show unambiguously that Zenkerella is the sister taxon of Anomalurus and Idiurus. These data indicate that gliding likely evolved only once within Anomaluridae, and that there were no subsequent evolutionary reversals. We combine this new molecular evidence with morphological data from living and extinct anomaluromorph rodents and estimate that the lineage leading to Zenkerella has been evolving independently in Africa since the early Eocene, approximately 49 million years ago. Recently discovered fossils further attest to the antiquity of the lineage leading to Zenkerella, which can now be recognized as a classic example of a “living fossil,” about which we know remarkably little. The osteological markers of gliding are estimated to have evolved along the stem lineage of the Anomalurus–Idiurus clade by the early Oligocene, potentially indicating that this adaptation evolved in response to climatic perturbations at the Eocene–Oligocene boundary (∼34 million years ago). creator: Steven Heritage creator: David Fernández creator: Hesham M. Sallam creator: Drew T. Cronin creator: José Manuel Esara Echube creator: Erik R. Seiffert uri: https://doi.org/10.7717/peerj.2320 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Heritage et al. title: The adder (Vipera berus) in Southern Altay Mountains: population characteristics, distribution, morphology and phylogenetic position link: https://peerj.com/articles/2342 last-modified: 2016-08-16 description: As the most widely distributed snake in Eurasia, the adder (Vipera berus) has been extensively investigated in Europe but poorly understood in Asia. The Southern Altay Mountains represent the adder’s southern distribution limit in Central Asia, whereas its population status has never been assessed. We conducted, for the first time, field surveys for the adder at two areas of Southern Altay Mountains using a combination of line transects and random searches. We also described the morphological characteristics of the collected specimens and conducted analyses of external morphology and molecular phylogeny. The results showed that the adder distributed in both survey sites and we recorded a total of 34 sightings. In Kanas river valley, the estimated encounter rate over a total of 137 km transects was 0.15 ± 0.05 sightings/km. The occurrence of melanism was only 17%. The small size was typical for the adders in Southern Altay Mountains in contrast to other geographic populations of the nominate subspecies. A phylogenetic tree obtained by Bayesian Inference based on DNA sequences of the mitochondrial cytochrome b (1,023 bp) grouped them within the Northern clade of the species but failed to separate them from the subspecies V. b. sachalinensis. Our discovery extends the distribution range of V. berus and provides a basis for further researches. We discuss the hypothesis that the adder expands its distribution border to the southwest along the mountains’ elevation gradient, but the population abundance declines gradually due to a drying climate. creator: Shaopeng Cui creator: Xiao Luo creator: Daiqiang Chen creator: Jizhou Sun creator: Hongjun Chu creator: Chunwang Li creator: Zhigang Jiang uri: https://doi.org/10.7717/peerj.2342 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Cui et al. title: Evolution of morphological and climatic adaptations in Veronica L. (Plantaginaceae) link: https://peerj.com/articles/2333 last-modified: 2016-08-16 description: Perennials and annuals apply different strategies to adapt to the adverse environment, based on ‘tolerance’ and ‘avoidance’, respectively. To understand lifespan evolution and its impact on plant adaptability, we carried out a comparative study of perennials and annuals in the genus Veronica from a phylogenetic perspective. The results showed that ancestors of the genus Veronicawere likely to be perennial plants. Annual life history of Veronica has evolved multiple times and subtrees with more annual species have a higher substitution rate. Annuals can adapt to more xeric habitats than perennials. This indicates that annuals are more drought-resistant than their perennial relatives. Due to adaptation to similar selective pressures, parallel evolution occurs in morphological characters among annual species of Veronica. creator: Jian-Cheng Wang creator: Bo-Rong Pan creator: Dirk C. Albach uri: https://doi.org/10.7717/peerj.2333 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Wang et al. title: The health care and life sciences community profile for dataset descriptions link: https://peerj.com/articles/2331 last-modified: 2016-08-16 description: Access to consistent, high-quality metadata is critical to finding, understanding, and reusing scientific data. However, while there are many relevant vocabularies for the annotation of a dataset, none sufficiently captures all the necessary metadata. This prevents uniform indexing and querying of dataset repositories. Towards providing a practical guide for producing a high quality description of biomedical datasets, the W3C Semantic Web for Health Care and the Life Sciences Interest Group (HCLSIG) identified Resource Description Framework (RDF) vocabularies that could be used to specify common metadata elements and their value sets. The resulting guideline covers elements of description, identification, attribution, versioning, provenance, and content summarization. This guideline reuses existing vocabularies, and is intended to meet key functional requirements including indexing, discovery, exchange, query, and retrieval of datasets, thereby enabling the publication of FAIR data. The resulting metadata profile is generic and could be used by other domains with an interest in providing machine readable descriptions of versioned datasets. creator: Michel Dumontier creator: Alasdair J.G. Gray creator: M. Scott Marshall creator: Vladimir Alexiev creator: Peter Ansell creator: Gary Bader creator: Joachim Baran creator: Jerven T. Bolleman creator: Alison Callahan creator: José Cruz-Toledo creator: Pascale Gaudet creator: Erich A. Gombocz creator: Alejandra N. Gonzalez-Beltran creator: Paul Groth creator: Melissa Haendel creator: Maori Ito creator: Simon Jupp creator: Nick Juty creator: Toshiaki Katayama creator: Norio Kobayashi creator: Kalpana Krishnaswami creator: Camille Laibe creator: Nicolas Le Novère creator: Simon Lin creator: James Malone creator: Michael Miller creator: Christopher J. Mungall creator: Laurens Rietveld creator: Sarala M. Wimalaratne creator: Atsuko Yamaguchi uri: https://doi.org/10.7717/peerj.2331 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Dumontier et al. title: Moderate evidence for a Lombard effect in a phylogenetically basal primate link: https://peerj.com/articles/2328 last-modified: 2016-08-16 description: When exposed to enhanced background noise, humans avoid signal masking by increasing the amplitude of the voice, a phenomenon termed the Lombard effect. This auditory feedback-mediated voice control has also been found in monkeys, bats, cetaceans, fish and some frogs and birds. We studied the Lombard effect for the first time in a phylogenetically basal primate, the grey mouse lemur, Microcebus murinus. When background noise was increased, mouse lemurs were able to raise the amplitude of the voice, comparable to monkeys, but they did not show this effect consistently across context/individuals. The Lombard effect, even if representing a generic vocal communication system property of mammals, may thus be affected by more complex mechanisms. The present findings emphasize an effect of context, and individual, and the need for further standardized approaches to disentangle the multiple system properties of mammalian vocal communication, important for understanding the evolution of the unique human faculty of speech and language. creator: Christian Schopf creator: Sabine Schmidt creator: Elke Zimmermann uri: https://doi.org/10.7717/peerj.2328 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Schopf et al. title: On the diversity of the SE Indo-Pacific species of Terebellides (Annelida; Trichobranchidae), with the description of a new species link: https://peerj.com/articles/2313 last-modified: 2016-08-16 description: The study of material collected during routine monitoring surveys dealing with oil extraction and aquaculture in waters off Myanmar (North Andaman Sea) and in the Gulf of Thailand, respectively, allowed us to analyse the taxonomy and diversity of the polychaete genus Terebellides (Annelida). Three species were found, namely Terebellides cf. woolawa, Terebellides hutchingsaespec. nov. (a new species fully described and illustrated), and Terebellides sp. (likely a new species, but with only one available specimen). The new species is characterised by the combination of some branchial (number, fusion and relative length of lobes and papillation of lamellae), and thoracic (lateral lobes and relative length of notopodia) characters and is compared with all species described or reported in the SW Indo-Pacific area, as well as with those sharing similar morphological characteristics all around the world. The taxonomic relevance of the relative length of branchial lobes and different types of ciliature in branchial lamellae for species discrimination in the genus is discussed. A key to all Terebellides species described in SE Indo-Pacific waters is presented. creator: Julio Parapar creator: Juan Moreira creator: Daniel Martin uri: https://doi.org/10.7717/peerj.2313 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Parapar et al. title: An energetics-based honeybee nectar-foraging model used to assess the potential for landscape-level pesticide exposure dilution link: https://peerj.com/articles/2293 last-modified: 2016-08-16 description: Estimating the exposure of honeybees to pesticides on a landscape scale requires models of their spatial foraging behaviour. For this purpose, we developed a mechanistic, energetics-based model for a single day of nectar foraging in complex landscape mosaics. Net energetic efficiency determined resource patch choice. In one version of the model a single optimal patch was selected each hour. In another version, recruitment of foragers was simulated and several patches could be exploited simultaneously. Resource availability changed during the day due to depletion and/or intrinsic properties of the resource (anthesis). The model accounted for the impact of patch distance and size, resource depletion and replenishment, competition with other nectar foragers, and seasonal and diurnal patterns in availability of nectar-providing crops and wild flowers. From the model we derived simple rules for resource patch selection, e.g., for landscapes with mass-flowering crops only, net energetic efficiency would be proportional to the ratio of the energetic content of the nectar divided by distance to the hive. We also determined maximum distances at which resources like oilseed rape and clover were still energetically attractive. We used the model to assess the potential for pesticide exposure dilution in landscapes of different composition and complexity. Dilution means a lower concentration in nectar arriving at the hive compared to the concentration in nectar at a treated field and can result from foraging effort being diverted away from treated fields. Applying the model for all possible hive locations over a large area, distributions of dilution factors were obtained that were characterised by their 90-percentile value. For an area for which detailed spatial data on crops and off-field semi-natural habitats were available, we tested three landscape management scenarios that were expected to lead to exposure dilution: providing alternative resources than the target crop (oilseed rape) in the form of (i) other untreated crop fields, (ii) flower strips of different widths at field edges (off-crop in-field resources), and (iii) resources on off-field (semi-natural) habitats. For both model versions, significant dilution occurred only when alternative resource patches were equal or more attractive than oilseed rape, nearby and numerous and only in case of flower strips and off-field habitats. On an area-base, flower strips were more than one order of magnitude more effective than off-field habitats, the main reason being that flower strips had an optimal location. The two model versions differed in the predicted number of resource patches exploited over the day, but mainly in landscapes with numerous small resource patches. In landscapes consisting of few large resource patches (crop fields) both versions predicted the use of a small number of patches. creator: Johannes M. Baveco creator: Andreas Focks creator: Dick Belgers creator: Jozef J.M. van der Steen creator: Jos J.T.I. Boesten creator: Ivo Roessink uri: https://doi.org/10.7717/peerj.2293 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Baveco et al. title: Experimental exposure to urban and pink noise affects brain development and song learning in zebra finches (Taenopygia guttata) link: https://peerj.com/articles/2287 last-modified: 2016-08-16 description: Recently, numerous studies have observed changes in bird vocalizations—especially song—in urban habitats. These changes are often interpreted as adaptive, since they increase the active space of the signal in its environment. However, the proximate mechanisms driving cross-generational changes in song are still unknown. We performed a captive experiment to identify whether noise experienced during development affects song learning and the development of song-control brain regions. Zebra finches (Taeniopygia guttata) were bred while exposed, or not exposed, to recorded traffic urban noise (Study 1) or pink noise (Study 2). We recorded the songs of male offspring and compared these to fathers’ songs. We also measured baseline corticosterone and measured the size of song-control brain regions when the males reached adulthood (Study 1 only). While male zebra finches tended to copy syllables accurately from tutors regardless of noise environment, syntax (the ordering of syllables within songs) was incorrectly copied affected by juveniles exposed to noise. Noise did not affect baseline corticosterone, but did affect the size of brain regions associated with song learning: these regions were smaller in males that had been had been exposed to recorded traffic urban noise in early development. These findings provide a possible mechanism by which noise affects behaviour, leading to potential population differences between wild animals occupying noisier urban environments compared with those in quieter habitats. creator: Dominique A. Potvin creator: Michael T. Curcio creator: John P. Swaddle creator: Scott A. MacDougall-Shackleton uri: https://doi.org/10.7717/peerj.2287 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Potvin et al. title: Effect of wetland management: are lentic wetlands refuges of plant-species diversity in the Andean–Orinoco Piedmont of Colombia? link: https://peerj.com/articles/2267 last-modified: 2016-08-16 description: Accelerated degradation of the wetlands and fragmentation of surrounding vegetation in the Andean–Orinoco Piedmont are the main threats to diversity and ecological integrity of these ecosystems; however, information on this topic is of limited availability. In this region, we evaluated the value of 37 lentic wetlands as reservoirs of woody and aquatic plants and analyzed diversity and changes in species composition within and among groups defined according to management given by: (1) type (swamps, heronries, rice fields, semi-natural lakes, constructed lakes and fish farms) and (2) origins (natural, mixed and artificial). A total of 506 plant species were recorded: 80% woody and 20% aquatic. Of these, 411 species (81%) were considered species typical of the area (Meta Piedmont distribution). Diversity patterns seem to be driven by high landscape heterogeneity and wetland management. The fish farms presented the highest diversity of woody plants, while swamps ranked highest for aquatic plant diversity. Regarding wetland origin, the artificial systems were the most diverse, but natural wetlands presented the highest diversity of typical species and can therefore be considered representative ecosystems at the regional scale. Our results suggest that lentic wetlands act as refuges for native vegetation of Meta Piedmont forest, hosting 55% of the woody of Piedmont species and 29% of the aquatic species of Orinoco basin. The wetlands showed a high species turnover and the results indicated that small wetlands (mean ± SD: size = 11 ± 18.7 ha), with a small area of surrounding forest (10 ± 8.6 ha) supported high local and regional plant diversity. To ensure long-term conservation of lentic wetlands, it is necessary to develop management and conservation strategies that take both natural and created wetlands into account. creator: Johanna I. Murillo-Pacheco creator: Matthias Rös creator: Federico Escobar creator: Francisco Castro-Lima creator: José R. Verdú creator: Germán M. López-Iborra uri: https://doi.org/10.7717/peerj.2267 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Murillo-Pacheco et al. title: Pseudorhabdosynochus sulamericanus (Monogenea, Diplectanidae), a parasite of deep-sea groupers (Serranidae) occurs transatlantically on three congeneric hosts (Hyporthodus spp.), one from the Mediterranean Sea and two from the western Atlantic link: https://peerj.com/articles/2233 last-modified: 2016-08-16 description: Little is known of the diversity of the monogenean parasites infesting deep-sea groupers, and there is even less information available about their geographic distributions within the ranges of their hosts. To improve our understanding of these host-parasite relationships we conducted parasitological evaluations of the deep-water Haifa grouper Hyporthodus haifensis from the southern Mediterranean off Tunisia and Libya. We collected more than one species of diplectanid monogeneans from this host, but among these only one dominant species was abundant. This proved to be morphologically very similar to Pseudorhabdosynochus sulamericanus Santos, Buchmann & Gibson, 2000, a species originally described from the congeneric host H. niveatus off Brazil and also recorded from H. niveatus and H. nigritus off Florida. Here, we conducted a morphological comparison between newly collected specimens and those previously deposited in museum collections by other authors. Further, we used COI barcoding to ascertain the specific identity of the three host species to better elucidate the circumstances that might explain the unexpectedly broad distribution of P. sulamericanus. We assigned our specimens from H. haifensis to P. sulamericanus primarily on the basis of morphological characteristics of the sclerotized vagina. We also noted morphological characteristics of eastern and western Atlantic specimens that are not clearly described or not given in previous descriptions and so prepared a redescription of the species. We confirmed, by COI barcoding, that no sister-species relationships were evident among the three hosts of P. sulamericanus. Our observation that P. sulamericanus infects unrelated host species with putatively allopatric distributions was unexpected given the very limited dispersive capabilities and the high degree of host specificity common to members of Pseudorhabdosynochus. This transatlantic distribution raises questions with regard to phylogeography and assumptions about the allopatry of Atlantic grouper species from the Americas and Afro-Eurasia. Here, we propose some hypothetical explanations for our findings. creator: Amira Chaabane creator: Jean-Lou Justine creator: Delphine Gey creator: Micah D. Bakenhaster creator: Lassad Neifar uri: https://doi.org/10.7717/peerj.2233 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Chaabane et al.