title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1778 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Sexual reproduction in the Caribbean coral genus Isophyllia (Scleractinia: Mussidae) link: https://peerj.com/articles/2665 last-modified: 2016-11-10 description: The sexual pattern, reproductive mode, and timing of reproduction of Isophyllia sinuosa and Isophyllia rigida, two Caribbean Mussids, were assessed by histological analysis of specimens collected monthly during 2000–2001. Both species are simultaneous hermaphroditic brooders characterized by a single annual gametogenetic cycle. Spermatocytes and oocytes of different stages were found to develop within the same mesentery indicating sequential maturation for extended planulation. Oogenesis took place during May through April in I. sinuosa and from August through June in I. rigida. Oocytes began development 7–8 months prior to spermaries but both sexes matured simultaneously. Zooxanthellate planulae were observed in I. sinuosa during April and in I. rigida from June through September. Higher polyp and mesenterial fecundity were found in I. rigida compared to I. sinuosa. Larger oocyte sizes were found in I. sinuosa than in I. rigida, however larger planula sizes were found in I. rigida. Hermaphroditism is the exclusive sexual pattern within the Mussidae while brooding has been documented within the related genera Mussa, Scolymia and Mycetophyllia. This study represents the first description of the sexual characteristics of I. rigida and provides an updated description of I. sinuosa. creator: Derek Soto creator: Ernesto Weil uri: https://doi.org/10.7717/peerj.2665 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Soto and Weil title: Hyainailourine and teratodontine cranial material from the late Eocene of Egypt and the application of parsimony and Bayesian methods to the phylogeny and biogeography of Hyaenodonta (Placentalia, Mammalia) link: https://peerj.com/articles/2639 last-modified: 2016-11-10 description: Hyaenodonta is a diverse, extinct group of carnivorous mammals that included weasel- to rhinoceros-sized species. The oldest-known hyaenodont fossils are from the middle Paleocene of North Africa and the antiquity of the group in Afro-Arabia led to the hypothesis that it originated there and dispersed to Asia, Europe, and North America. Here we describe two new hyaenodont species based on the oldest hyaenodont cranial specimens known from Afro-Arabia. The material was collected from the latest Eocene Locality 41 (L-41, ∼34 Ma) in the Fayum Depression, Egypt. Akhnatenavus nefertiticyon sp. nov. has specialized, hypercarnivorous molars and an elongate cranial vault. In A. nefertiticyon the tallest, piercing cusp on M1–M2 is the paracone. Brychotherium ephalmos gen. et sp. nov. has more generalized molars that retain the metacone and complex talonids. In B. ephalmos the tallest, piercing cusp on M1–M2 is the metacone. We incorporate this new material into a series of phylogenetic analyses using a character-taxon matrix that includes novel dental, cranial, and postcranial characters, and samples extensively from the global record of the group. The phylogenetic analysis includes the first application of Bayesian methods to hyaenodont relationships. B. ephalmos is consistently placed within Teratodontinae, an Afro-Arabian clade with several generalist and hypercarnivorous forms, and Akhnatenavus is consistently recovered in Hyainailourinae as part of an Afro-Arabian radiation. The phylogenetic results suggest that hypercarnivory evolved independently three times within Hyaenodonta: in Teratodontinae, in Hyainailourinae, and in Hyaenodontinae. Teratodontines are consistently placed in a close relationship with Hyainailouridae (Hyainailourinae + Apterodontinae) to the exclusion of “proviverrines,” hyaenodontines, and several North American clades, and we propose that the superfamily Hyainailouroidea be used to describe this relationship. Using the topologies recovered from each phylogenetic method, we reconstructed the biogeographic history of Hyaenodonta using parsimony optimization (PO), likelihood optimization (LO), and Bayesian Binary Markov chain Monte Carlo (MCMC) to examine support for the Afro-Arabian origin of Hyaenodonta. Across all analyses, we found that Hyaenodonta most likely originated in Europe, rather than Afro-Arabia. The clade is estimated by tip-dating analysis to have undergone a rapid radiation in the Late Cretaceous and Paleocene; a radiation currently not documented by fossil evidence. During the Paleocene, lineages are reconstructed as dispersing to Asia, Afro-Arabia, and North America. The place of origin of Hyainailouroidea is likely Afro-Arabia according to the Bayesian topologies but it is ambiguous using parsimony. All topologies support the constituent clades–Hyainailourinae, Apterodontinae, and Teratodontinae–as Afro-Arabian and tip-dating estimates that each clade is established in Afro-Arabia by the middle Eocene. creator: Matthew R. Borths creator: Patricia A. Holroyd creator: Erik R. Seiffert uri: https://doi.org/10.7717/peerj.2639 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Borths et al. title: Pico and nanoplankton abundance and carbon stocks along the Brazilian Bight link: https://peerj.com/articles/2587 last-modified: 2016-11-10 description: Pico and nanoplankton communities from the Southwest Atlantic Ocean along the Brazilian Bight are poorly described. The hydrography in this region is dominated by a complex system of layered water masses, which includes the warm and oligotrophic Tropical Water (TW), the cold and nutrient rich South Atlantic Central Water (SACW) and the Coastal Water (CW), which have highly variable properties. In order to assess how pico- and nanoplankton communities are distributed in these different water masses, we determined by flow cytometry the abundance of heterotrophic bacteria, Prochlorococcus, Synechococcus and autotrophic pico and nanoeukaryotes along three transects, extending from 23°S to 31°S and 39°W to 49°W. Heterotrophic bacteria (including archaea, maximum of 1.5 × 106 cells mL−1) were most abundant in Coastal and Tropical Water whereas Prochlorococcus was most abundant in open-ocean oligotrophic waters (maximum of 300 × 103 cells mL−1). Synechococcus(up to 81 × 103 cells mL−1), as well as autotrophic pico and nanoeukaryotes seemed to benefit from the influx of nutrient-rich waters near the continental slope. Autotrophic pico and nanoeukaryotes were also abundant in deep chlorophyll maximum (DCM) layers from offshore waters, and their highest abundances were 20 × 103 cells mL−1 and 5 × 103 cells mL−1, respectively. These data are consistent with previous observations in other marine areas where Synechococcus and autotrophic eukaryotes dominate mesotrophic waters, whereas Prochlorococcus dominate in more oligotrophic areas. Regardless of the microbial community structure near the surface, the carbon stock dominance by autotrophic picoeukaryotes near the DCM is possibly linked to vertical mixing of oligotrophic surface waters with the nutrient-rich SACW and their tolerance to lower light levels. creator: Catherine Gérikas Ribeiro creator: Adriana Lopes dos Santos creator: Dominique Marie creator: Vivian Helena Pellizari creator: Frederico Pereira Brandini creator: Daniel Vaulot uri: https://doi.org/10.7717/peerj.2587 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Gérikas Ribeiro et al. title: Factors influencing infection and transmission of Anopheles gambiae densovirus (AgDNV) in mosquitoes link: https://peerj.com/articles/2691 last-modified: 2016-11-09 description: Anopheles gambiae densovirus (AgDNV) is a potential microbial agent for paratransgenesis and gene transduction in An. gambiae, the major vector of human malaria in sub-Saharan Africa. Understanding the interaction between AgDNV and An. gambiae is critical for using AgDNV in a basic and applied manner for Anopheles gene manipulation. Here, we tested the effects of mosquito age, sex, blood feeding status, and potential for horizontal transmission using an enhanced green fluorescent protein (EGFP) reporter AgDNV system. Neither mosquito age at infection nor feeding regime affected viral titers. Female mosquitoes were more permissive to viral infection than males. Despite low viral titers, infected males were able to venereally transmit virus to females during mating, where the virus was localized with the transferred sperm in the spermathecae. These findings will be useful for designing AgDNV-based strategies to manipulate Anopheles gambiae. creator: Tapan K. Barik creator: Yasutsugu Suzuki creator: Jason L. Rasgon uri: https://doi.org/10.7717/peerj.2691 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Barik et al. title: Charge neutralization as the major factor for the assembly of nucleocapsid-like particles from C-terminal truncated hepatitis C virus core protein link: https://peerj.com/articles/2670 last-modified: 2016-11-09 description: BackgroundHepatitis C virus (HCV) core protein, in addition to its structural role to form the nucleocapsid assembly, plays a critical role in HCV pathogenesis by interfering in several cellular processes, including microRNA and mRNA homeostasis. The C-terminal truncated HCV core protein (C124) is intrinsically unstructured in solution and is able to interact with unspecific nucleic acids, in the micromolar range, and to assemble into nucleocapsid-like particles (NLPs) in vitro. The specificity and propensity of C124 to the assembly and its implications on HCV pathogenesis are not well understood.MethodsSpectroscopic techniques, transmission electron microscopy and calorimetry were used to better understand the propensity of C124 to fold or to multimerize into NLPs when subjected to different conditions or in the presence of unspecific nucleic acids of equivalent size to cellular microRNAs.ResultsThe structural analysis indicated that C124 has low propensity to self-folding. On the other hand, for the first time, we show that C124, in the absence of nucleic acids, multimerizes into empty NLPs when subjected to a pH close to its isoelectric point (pH ≈ 12), indicating that assembly is mainly driven by charge neutralization. Isothermal calorimetry data showed that the assembly of NLPs promoted by nucleic acids is enthalpy driven. Additionally, data obtained from fluorescence correlation spectroscopy show that C124, in nanomolar range, was able to interact and to sequester a large number of short unspecific nucleic acids into NLPs.DiscussionTogether, our data showed that the charge neutralization is the major factor for the nucleocapsid-like particles assembly from C-terminal truncated HCV core protein. This finding suggests that HCV core protein may physically interact with unspecific cellular polyanions, which may correspond to microRNAs and mRNAs in a host cell infected by HCV, triggering their confinement into infectious particles. creator: Theo Luiz Ferraz de Souza creator: Sheila Maria Barbosa de Lima creator: Vanessa L. de Azevedo Braga creator: David S. Peabody creator: Davis Fernandes Ferreira creator: M. Lucia Bianconi creator: Andre Marco de Oliveira Gomes creator: Jerson Lima Silva creator: Andréa Cheble de Oliveira uri: https://doi.org/10.7717/peerj.2670 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 De Souza et al. title: Low self-concept in poor readers: prevalence, heterogeneity, and risk link: https://peerj.com/articles/2669 last-modified: 2016-11-09 description: There is evidence that poor readers are at increased risk for various types of low self-concept—particularly academic self-concept. However, this evidence ignores the heterogeneous nature of poor readers, and hence the likelihood that not all poor readers have low self-concept. The aim of this study was to better understand which types of poor readers have low self-concept. We tested 77 children with poor reading for their age for four types of self-concept, four types of reading, three types of spoken language, and two types of attention. We found that poor readers with poor attention had low academic self-concept, while poor readers with poor spoken language had low general self-concept in addition to low academic self-concept. In contrast, poor readers with typical spoken language and attention did not have low self-concept of any type. We also discovered that academic self-concept was reliably associated with reading and receptive spoken vocabulary, and that general self-concept was reliably associated with spoken vocabulary. These outcomes suggest that poor readers with multiple impairments in reading, language, and attention are at higher risk for low academic and general self-concept, and hence need to be assessed for self-concept in clinical practice. Our results also highlight the need for further investigation into the heterogeneous nature of self-concept in poor readers. creator: Genevieve McArthur creator: Anne Castles creator: Saskia Kohnen creator: Erin Banales uri: https://doi.org/10.7717/peerj.2669 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 McArthur et al. title: A global analysis of bird plumage patterns reveals no association between habitat and camouflage link: https://peerj.com/articles/2658 last-modified: 2016-11-09 description: Evidence suggests that animal patterns (motifs) function in camouflage. Irregular mottled patterns can facilitate concealment when stationary in cluttered habitats, whereas regular patterns typically prevent capture during movement in open habitats. Bird plumage patterns have predominantly converged on just four types—mottled (irregular), scales, bars and spots (regular)—and habitat could be driving convergent evolution in avian patterning. Based on sensory ecology, we therefore predict that irregular patterns would be associated with visually noisy closed habitats and that regular patterns would be associated with open habitats. Regular patterns have also been shown to function in communication for sexually competing males to stand-out and attract females, so we predict that male breeding plumage patterns evolved in both open and closed habitats. Here, taking phylogenetic relatedness into account, we investigate ecological selection for bird plumage patterns across the class Aves. We surveyed plumage patterns in 80% of all avian species worldwide. Of these, 2,756 bird species have regular and irregular plumage patterns as well as habitat information. In this subset, we tested whether adult breeding/non-breeding plumages in each sex, and juvenile plumages, were associated with the habitat types found within the species’ geographical distributions. We found no evidence for an association between habitat and plumage patterns across the world’s birds and little phylogenetic signal. We also found that species with regular and irregular plumage patterns were distributed randomly across the world’s eco-regions without being affected by habitat type. These results indicate that at the global spatial and taxonomic scale, habitat does not predict convergent evolution in bird plumage patterns, contrary to the camouflage hypothesis. creator: Marius Somveille creator: Kate L.A. Marshall creator: Thanh-Lan Gluckman uri: https://doi.org/10.7717/peerj.2658 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Somveille et al. title: The potential for self-seeding by the coral Pocillopora spp. in Moorea, French Polynesia link: https://peerj.com/articles/2544 last-modified: 2016-11-09 description: Coral reefs in Moorea, French Polynesia, suffered catastrophic coral mortality through predation by Acanthaster planci from 2006 to 2010, and Cyclone Oli in 2010, yet by 2015 some coral populations were approaching pre-disturbance sizes. Using long-term study plots, we quantified population dynamics of spawning Pocillopora spp. along the north shore of Moorea between 2010 and 2014, and considered evidence that population recovery could be supported by self-seeding. Results scaled up from study plots and settlement tiles suggest that the number of Pocillopora spp. colonies on the outer reef increased 1,890-fold between 2010 and 2014/2015, and in the back reef, 8-fold between 2010 and 2014/2015. Assuming that spawning Pocillopora spp. in Moorea release similar numbers of eggs as con-generics in Hawaii, and fertilization success is similar to other spawning corals, the capacity of Pocillopora spp. to produce larvae was estimated. These estimates suggest that Pocillopora spp. in Moorea produced a large excess of larvae in 2010 and 2014 relative to the number required to produce the recruits found in the back reef and outer reef in 2010 and 2014, even assuming that ∼99.9% of the larvae do not recruit in Moorea. Less than a third of the recruits in one year would have to survive to produce the juvenile Pocillopora spp. found in the back and outer reefs in 2010 and 2014/2015. Our first order approximations reveal the potential for Pocillopora spp. on the north shore of Moorea to produce enough larvae to support local recruitment and population recovery following a catastrophic disturbance. creator: Georgios Tsounis creator: Peter J. Edmunds uri: https://doi.org/10.7717/peerj.2544 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Tsounis and Edmunds title: The origin of the lower fourth molar in canids, inferred by individual variation link: https://peerj.com/articles/2689 last-modified: 2016-11-08 description: BackgroundAn increase in tooth number is an exception during mammalian evolution. The acquisition of the lower fourth molar in the bat-eared fox (Otocyon megalotis, Canidae, Carnivora, Mammalia) is one example; however, its developmental origin is not clear. In some canids (Canidae), individual variation exist as supernumerary molar M4. This study focuses on the acquisition of the lower fourth molar in canids and proposes that the inhibitory cascade model can explain its origin.MethodsOcclusal view projected area of lower molars was determined from 740 mandibles obtained from Canis latrans, Nyctereutes procyonoides, and Urocyon cinereoargenteus museum specimens. For each molar, relative sizes of molars (M2/M1 and M3/M1 scores) affected by inhibition/activation dynamics during development, were compared between individuals with and without supernumerary molar (M4).ResultsPossession of a supernumerary molar was associated with significantly larger M2/M1 score in Canis latrans, M3/M1 score in Nyctereutes procyonoides, and M2/M1 and M3/M1 scores in Urocyon cinereoargenteus compared to individuals of these species that lacked supernumerary molars.DiscussionWe propose that, in canids, the supernumerary fourth molar is attributable to reduced inhibition and greater activation during molar development. In the bat-eared fox, altered inhibition and activation dynamics of dental development during omnivorous-insectivorous adaptation may be a contributing factor in the origin of the lower fourth molar. creator: Masakazu Asahara uri: https://doi.org/10.7717/peerj.2689 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Asahara title: Antioxidant nutrition in Atlantic salmon (Salmo salar) parr and post-smolt, fed diets with high inclusion of plant ingredients and graded levels of micronutrients and selected amino acids link: https://peerj.com/articles/2688 last-modified: 2016-11-08 description: The shift from marine to plant-based ingredients in fish feeds affects the dietary concentrations and bioavailability of micronutrients, amino acids and lipids and consequently warrants a re-evaluation of dietary nutrient recommendations. In the present study, an Atlantic salmon diet high in plant ingredients was supplemented with graded levels of nutrient premix (NP), containing selected amino acids, taurine, cholesterol, vitamins and minerals. This article presents the results on the antioxidant nutrients vitamin C, E and selenium (Se), and effects on tissue redox status. The feed ingredients appeared to contain sufficient levels of vitamin E and Se to cover the requirements to prevent clinical deficiency symptoms. The body levels of α-tocopherol (TOH) in parr and that of Se in parr and post-smolt showed a linear relationship with dietary concentration, while α-TOH in post-smolt seemed to be saturable with a breakpoint near 140 mg kg−1. Ascorbic acid (Asc) concentration in the basal feed was below the expected minimum requirement, but the experimental period was probably too short for the fish to develop visible deficiency symptoms. Asc was saturable in both parr and post-smolt whole body at dietary concentrations of 190 and 63–89 mg kg−1, respectively. Maximum whole body Asc concentration was approximately 40 mg kg−1 in parr and 14 mg kg−1 in post-smolt. Retention ranged from 41 to 10% in parr and from −206 to 12% in post-smolt with increasing NP supplementation. This indicates that the post-smolts had an extraordinarily high consumption of Asc. Analyses of glutathione (GSH) and glutathione disulphide (GSSG) concentrations and the calculated GSH based redox potentials in liver and muscle tissue, indicated only minor effects of diets on redox regulation. However, the post-smolt were more oxidized than the parr. This was supported by the high consumption of Asc and high expression of gpx1 and gpx3 in liver. Based on the present trials, the recommendations for supplementation of vitamin C and E in diets for Atlantic salmon are similar to current practices, e.g. 150 mg kg−1 of α-TOH and 190 mg kg−1 Asc which was the saturating concentration in parr. Higher concentrations than what would prevent clinical deficiency symptoms are necessary to protect fish against incidents of oxidative stress and to improve immune and stress responses. There were no indications that the Se requirement exceeded the current recommendation of 0.3 mg kg−1. creator: Kristin Hamre creator: Nini H. Sissener creator: Erik-Jan Lock creator: Pål A. Olsvik creator: Marit Espe creator: Bente E. Torstensen creator: Joana Silva creator: Johan Johansen creator: Rune Waagbø creator: Gro-Ingunn Hemre uri: https://doi.org/10.7717/peerj.2688 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Hamre et al.