title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=1680
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Late Pleistocene songbirds of Liang Bua (Flores, Indonesia); the first fossil passerine fauna described from Wallacea
link: https://peerj.com/articles/3676
last-modified: 2017-08-17
description: BackgroundPasserines (Aves: Passeriformes) dominate modern terrestrial bird communities yet their fossil record is limited. Liang Bua is a large cave on the Indonesian island of Flores that preserves Late Pleistocene–Holocene deposits (∼190 ka to present day). Birds are the most diverse faunal group at Liang Bua and are present throughout the stratigraphic sequence.MethodsWe examined avian remains from the Late Pleistocene deposits of Sector XII, a 2 × 2 m area excavated to about 8.5 m depth. Although postcranial passerine remains are typically challenging to identify, we found several humeral characters particularly useful in discriminating between groups, and identified 89 skeletal elements of passerines.ResultsAt least eight species from eight families are represented, including the Large-billed Crow (Corvus cf. macrorhynchos), the Australasian Bushlark (Mirafra javanica), a friarbird (Philemon sp.), and the Pechora Pipit (Anthus cf. gustavi).DiscussionThese remains constitute the first sample of fossil passerines described in Wallacea. Two of the taxa no longer occur on Flores today; a large sturnid (cf. Acridotheres) and a grassbird (Megalurus sp.). Palaeoecologically, the songbird assemblage suggests open grassland and tall forests, which is consistent with conditions inferred from the non-passerine fauna at the site. Corvus cf. macrorhynchos, found in the Homo floresiensis-bearing layers, was likely part of a scavenging guild that fed on carcasses of Stegodon florensis insularis alongside vultures (Trigonoceps sp.), giant storks (Leptoptilos robustus), komodo dragons (Varanus komodoensis), and probably H. floresiensis as well.
creator: Hanneke J.M. Meijer
creator: Rokus Awe Due
creator: Thomas Sutikna
creator: Wahyu Saptomo
creator:  Jatmiko
creator: Sri Wasisto
creator: Matthew W. Tocheri
creator: Gerald Mayr
uri: https://doi.org/10.7717/peerj.3676
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Meijer et al.

title: Mesoscale spatiotemporal variability in a complex host-parasite system influenced by intermediate host body size
link: https://peerj.com/articles/3675
last-modified: 2017-08-17
description: BackgroundParasites are essential components of natural communities, but the factors that generate skewed distributions of parasite occurrences and abundances across host populations are not well understood.MethodsHere, we analyse at a seascape scale the spatiotemporal relationships of parasite exposure and host body-size with the proportion of infected hosts (i.e., prevalence) and aggregation of parasite burden across ca. 150 km of the coast and over 22 months. We predicted that the effects of parasite exposure on prevalence and aggregation are dependent on host body-sizes. We used an indirect host-parasite interaction in which migratory seagulls, sandy-shore molecrabs, and an acanthocephalan worm constitute the definitive hosts, intermediate hosts, and endoparasite, respectively. In such complex systems, increments in the abundance of definitive hosts imply increments in intermediate hosts’ exposure to the parasite’s dispersive stages.ResultsLinear mixed-effects models showed a significant, albeit highly variable, positive relationship between seagull density and prevalence. This relationship was stronger for small (cephalothorax length >15 mm) than large molecrabs (<15 mm). Independently of seagull density, large molecrabs carried significantly more parasites than small molecrabs. The analysis of the variance-to-mean ratio of per capita parasite burden showed no relationship between seagull density and mean parasite aggregation across host populations. However, the amount of unexplained variability in aggregation was strikingly higher in larger than smaller intermediate hosts. This unexplained variability was driven by a decrease in the mean-variance scaling in heavily infected large molecrabs.ConclusionsThese results show complex interdependencies between extrinsic and intrinsic population attributes on the structure of host-parasite interactions. We suggest that parasite accumulation—a characteristic of indirect host-parasite interactions—and subsequent increasing mortality rates over ontogeny underpin size-dependent host-parasite dynamics.
creator: Sara M. Rodríguez
creator: Nelson Valdivia
uri: https://doi.org/10.7717/peerj.3675
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Rodríguez and Valdivia

title: Quercivorol as a lure for the polyphagous and Kuroshio shot hole borers, Euwallacea spp. nr. fornicatus (Coleoptera: Scolytinae), vectors of Fusarium dieback
link: https://peerj.com/articles/3656
last-modified: 2017-08-17
description: The polyphagous shot hole borer and Kuroshio shot hole borer, two members of the Euwallacea fornicatus species complex (Coleoptera: Curculionidae: Scolytinae), are invasive ambrosia beetles that harbor distinct species of Fusarium fungal symbionts. Together with the damage caused by gallery construction, these two phytopathogenic Fusarium species are responsible for the emerging tree disease Fusarium dieback, which affects over 50 common tree species in Southern California. Host trees suffer branch dieback as the xylem is blocked by invading beetles and fungi, forcing the costly removal of dead and dying trees in urban areas. The beetles are also threatening natural riparian habitats, and avocado is susceptible to Fusarium dieback as well, resulting in damage to the avocado industries in California and Israel. Currently there are no adequate control mechanisms for shot hole borers. This paper summarizes efforts to find a suitable lure to monitor shot hole borer invasions and dispersal. Field trials were conducted in two counties in Southern California over a span of two years. We find that the chemical quercivorol is highly attractive to these beetles, and perform subsequent field experiments attempting to optimize this lure. We also explore other methods of increasing trap catch and effects of other potential attractants, as well as the deterrents verbenone and piperitone.
creator: Christine Dodge
creator: Jessica Coolidge
creator: Miriam Cooperband
creator: Allard Cossé
creator: Daniel Carrillo
creator: Richard Stouthamer
uri: https://doi.org/10.7717/peerj.3656
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2017 Dodge et al.

title: Genome-wide association study identifies novel type II diabetes risk loci in Jordan subpopulations
link: https://peerj.com/articles/3618
last-modified: 2017-08-17
description: The prevalence of Type II Diabetes (T2D) has been increasing and has become a disease of significant public health burden in Jordan. None of the previous genome-wide association studies (GWAS) have specifically investigated the Middle East populations. The Circassian and Chechen communities in Jordan represent unique populations that are genetically distinct from the Arab population and other populations in the Caucasus. Prevalence of T2D is very high in both the Circassian and Chechen communities in Jordan despite low obesity prevalence. We conducted GWAS on T2D in these two populations and further performed meta-analysis of the results. We identified a novel T2D locus at chr20p12.2 at genome-wide significance (rs6134031, P = 1.12 × 10−8) and we replicated the results in the Wellcome Trust Case Control Consortium (WTCCC) dataset. Another locus at chr12q24.31 is associated with T2D at suggestive significance level (top SNP rs4758690, P = 4.20 × 10−5) and it is a robust eQTL for the gene, MLXIP (P = 1.10 × 10−14), and is significantly associated with methylation level in MLXIP, the functions of which involves cellular glucose response. Therefore, in this first GWAS of T2D in Jordan subpopulations, we identified novel and unique susceptibility loci which may help inform the genetic underpinnings of T2D in other populations.
creator: Rana Dajani
creator: Jin Li
creator: Zhi Wei
creator: Michael E. March
creator: Qianghua Xia
creator: Yousef Khader
creator: Nancy Hakooz
creator: Raja Fatahallah
creator: Mohammed El-Khateeb
creator: Ala Arafat
creator: Tareq Saleh
creator: Abdel Rahman Dajani
creator: Zaid Al-Abbadi
creator: Mohamed Abdul Qader
creator: Abdel Halim Shiyab
creator: Anwar Bateiha
creator: Kamel Ajlouni
creator: Hakon Hakonarson
uri: https://doi.org/10.7717/peerj.3618
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Dajani et al.

title: RNA sequencing (RNA-Seq) of lymph node, spleen, and thymus transcriptome from wild Peninsular Malaysian cynomolgus macaque (Macaca fascicularis)
link: https://peerj.com/articles/3566
last-modified: 2017-08-17
description: The cynomolgus macaque (Macaca fascicularis) is an extensively utilised nonhuman primate model for biomedical research due to its biological, behavioural, and genetic similarities to humans. Genomic information of cynomolgus macaque is vital for research in various fields; however, there is presently a shortage of genomic information on the Malaysian cynomolgus macaque. This study aimed to sequence, assemble, annotate, and profile the Peninsular Malaysian cynomolgus macaque transcriptome derived from three tissues (lymph node, spleen, and thymus) using RNA sequencing (RNA-Seq) technology. A total of 174,208,078 paired end 70 base pair sequencing reads were obtained from the Illumina Hi-Seq 2500 sequencer. The overall mapping percentage of the sequencing reads to the M. fascicularis reference genome ranged from 53–63%. Categorisation of expressed genes to Gene Ontology (GO) and KEGG pathway categories revealed that GO terms with the highest number of associated expressed genes include Cellular process, Catalytic activity, and Cell part, while for pathway categorisation, the majority of expressed genes in lymph node, spleen, and thymus fall under the Global overview and maps pathway category, while 266, 221, and 138 genes from lymph node, spleen, and thymus were respectively enriched in the Immune system category. Enriched Immune system pathways include Platelet activation pathway, Antigen processing and presentation, B cell receptor signalling pathway, and Intestinal immune network for IgA production. Differential gene expression analysis among the three tissues revealed 574 differentially expressed genes (DEG) between lymph and spleen, 5402 DEGs between lymph and thymus, and 7008 DEGs between spleen and thymus. Venn diagram analysis of expressed genes revealed a total of 2,630, 253, and 279 tissue-specific genes respectively for lymph node, spleen, and thymus tissues. This is the first time the lymph node, spleen, and thymus transcriptome of the Peninsular Malaysian cynomolgus macaque have been sequenced via RNA-Seq. Novel transcriptomic data will further enrich the present M. fascicularis genomic database and provide future research potentials, including novel transcript discovery, comparative studies, and molecular markers development.
creator: Joey Ee Uli
creator: Christina Seok Yien Yong
creator: Swee Keong Yeap
creator: Jeffrine J. Rovie-Ryan
creator: Nurulfiza Mat Isa
creator: Soon Guan Tan
creator: Noorjahan Banu Alitheen
uri: https://doi.org/10.7717/peerj.3566
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Ee Uli et al.

title: Shoreline oiling effects and recovery of salt marsh macroinvertebrates from the Deepwater Horizon Oil Spill
link: https://peerj.com/articles/3680
last-modified: 2017-08-16
description: Salt marshes in northern Barataria Bay, Louisiana, USA were oiled, sometimes heavily, in the aftermath of the Deepwater Horizon oil spill. Previous studies indicate that fiddler crabs (in the genus Uca) and the salt marsh periwinkle (Littoraria irrorata) were negatively impacted in the short term by the spill. Here, we detail longer-term effects and recovery from moderate and heavy oiling over a 3-year span, beginning 30 months after the spill. Although neither fiddler crab burrow density nor diameter differed between oiled and reference sites when combined across all sampling events, these traits differed among some individual sampling periods consistent with a pattern of lingering oiling impacts. Periwinkle density, however, increased in all oiling categories and shell-length groups during our sampling period, and periwinkle densities were consistently highest at moderately oiled sites where Spartina alterniflora aboveground biomass was highest. Periwinkle shell length linearly increased from a mean of 16.5 to 19.2 mm over the study period at reference sites. In contrast, shell lengths at moderately oiled and heavily oiled sites increased through month 48 after the spill, but then decreased. This decrease was associated with a decline in the relative abundance of large adults (shell length 21–26 mm) at oiled sites which was likely caused by chronic hydrocarbon toxicity or oil-induced effects on habitat quality or food resources. Overall, the recovery of S. alterniflora facilitated the recovery of fiddler crabs and periwinkles. However, our long-term record not only indicates that variation in periwinkle mean shell length and length-frequency distributions are sensitive indicators of the health and recovery of the marsh, but agrees with synoptic studies of vegetation and infaunal communities that full recovery of heavily oiled sites will take longer than 66 months.
creator: Donald R. Deis
creator: John W. Fleeger
creator: Stefan M. Bourgoin
creator: Irving A. Mendelssohn
creator: Qianxin Lin
creator: Aixin Hou
uri: https://doi.org/10.7717/peerj.3680
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Deis et al.

title: Microbiome succession during ammonification in eelgrass bed sediments
link: https://peerj.com/articles/3674
last-modified: 2017-08-16
description: BackgroundEelgrass (Zostera marina) is a marine angiosperm and foundation species that plays an important ecological role in primary production, food web support, and elemental cycling in coastal ecosystems. As with other plants, the microbial communities living in, on, and near eelgrass are thought to be intimately connected to the ecology and biology of eelgrass. Here we characterized the microbial communities in eelgrass sediments throughout an experiment to quantify the rate of ammonification, the first step in early remineralization of organic matter, also known as diagenesis, from plots at a field site in Bodega Bay, CA.MethodsSediment was collected from 72 plots from a 15 month long field experiment in which eelgrass genotypic richness and relatedness were manipulated. In the laboratory, we placed sediment samples (n = 4 per plot) under a N2 atmosphere, incubated them at in situ temperatures (15 °C) and sampled them initially and after 4, 7, 13, and 19 days to determine the ammonification rate. Comparative microbiome analysis using high throughput sequencing of 16S rRNA genes was performed on sediment samples taken initially and at seven, 13 and 19 days to characterize changes in the relative abundances of microbial taxa throughout ammonification.ResultsWithin-sample diversity of the sediment microbial communities across all plots decreased after the initial timepoint using both richness based (observed number of OTUs, Chao1) and richness and evenness based diversity metrics (Shannon, Inverse Simpson). Additionally, microbial community composition changed across the different timepoints. Many of the observed changes in relative abundance of taxonomic groups between timepoints appeared driven by sulfur cycling with observed decreases in predicted sulfur reducers (Desulfobacterales) and corresponding increases in predicted sulfide oxidizers (Thiotrichales). None of these changes in composition or richness were associated with variation in ammonification rates.DiscussionOur results showed that the microbiome of sediment from different plots followed similar successional patterns, which we infer to be due to changes related to sulfur metabolism. These large changes likely overwhelmed any potential changes in sediment microbiome related to ammonification rate. We found no relationship between eelgrass presence or genetic composition and the microbiome. This was likely due to our sampling of bulk sediments to measure ammonification rates rather than sampling microbes in sediment directly in contact with the plants and suggests that eelgrass influence on the sediment microbiome may be limited in spatial extent. More in-depth functional studies associated with eelgrass microbiome will be required in order to fully understand the implications of these microbial communities in broader host-plant and ecosystem functions (e.g., elemental cycling and eelgrass-microbe interactions).
creator: Cassandra L. Ettinger
creator: Susan L. Williams
creator: Jessica M. Abbott
creator: John J. Stachowicz
creator: Jonathan A. Eisen
uri: https://doi.org/10.7717/peerj.3674
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Ettinger et al.

title: RNA helicase domains of viral origin in proteins of insect retrotransposons: possible source for evolutionary advantages
link: https://peerj.com/articles/3673
last-modified: 2017-08-16
description: Recently, a novel phenomenon of horizontal gene transfer of helicase-encoding sequence from positive-stranded RNA viruses to LINE transposons in insect genomes was described. TRAS family transposons encoding an ORF2 protein, which comprised all typical functional domains and an additional helicase domain, were found to be preserved in many families during the evolution of the order Lepidoptera. In the present paper, in species of orders Hemiptera and Orthoptera, we found helicase domain-encoding sequences integrated into ORF1 of retrotransposons of the Jockey family. RNA helicases encoded by transposons of TRAS and Jockey families represented separate brunches in a phylogenetic tree of helicase domains and thus could be considered as independently originated in the evolution of insect transposons. Transcriptome database analyses revealed that both TRAS and Jockey transposons encoding the helicase domain represented transcribed genome sequences. Moreover, the transposon-encoded helicases were found to contain the full set of conserved motifs essential for their enzymatic activities. Taking into account the previously reported ability of RNA helicase encoded by TRAS ORF2 to suppress post-transcriptional RNA silencing, we propose possible scenarios of evolutionary fixation of actively expressed functional helicases of viral origin in insect retrotransposons as genetic elements advantageous for both transposons and their insect hosts.
creator: Sergey Y. Morozov
creator: Ekaterina A. Lazareva
creator: Andrey G. Solovyev
uri: https://doi.org/10.7717/peerj.3673
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Morozov et al.

title: Changes in zooplankton community, and seston and zooplankton fatty acid profiles at the freshwater/saltwater interface of the Chowan River, North Carolina
link: https://peerj.com/articles/3667
last-modified: 2017-08-16
description: The variability in zooplankton fatty acid composition may be an indicator of larval fish habitat quality as fatty acids are linked to fish larval growth and survival. We sampled an anadromous fish nursery, the Chowan River, during spring of 2013 in order to determine how the seston fatty acid composition varied in comparison with the zooplankton community composition and fatty acid composition during the period of anadromous larval fish residency. The seston fatty acid profiles showed no distinct pattern in relation to sampling time or location. The mesozooplankton community composition varied spatially and the fatty acid profiles were typical of freshwater species in April. The Chowan River experienced a saltwater intrusion event during May, which resulted in brackish water species dominating the zooplankton community and the fatty acid profile showed an increase in polyunsaturated fatty acids (PUFA), in particular eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). The saltwater intrusion event was followed by an influx of freshwater due to high precipitation levels in June. The zooplankton community composition once again became dominated by freshwater species and the fatty acid profiles shifted to reflect this change; however, EPA levels remained high, particularly in the lower river. We found correlations between the seston, microzooplankton and mesozooplankton fatty acid compositions. Salinity was the main factor correlated to the observed pattern in species composition, and fatty acid changes in the mesozooplankton. These data suggest that anadromous fish nursery habitat likely experiences considerable spatial variability in fatty acid profiles of zooplankton prey and that are correlated to seston community composition and hydrodynamic changes. Our results also suggest that sufficient prey density as well as a diverse fatty acid composition is present in the Chowan River to support larval fish production.
creator: Deborah A. Lichti
creator: Jacques Rinchard
creator: David G. Kimmel
uri: https://doi.org/10.7717/peerj.3667
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Lichti et al.

title: RNA expression and disease tolerance are associated with a “keystone mutation” in the ochre sea star Pisaster ochraceus
link: https://peerj.com/articles/3696
last-modified: 2017-08-15
description: An overdominant mutation in an intron of the elongation factor 1-α (EF1A) gene in the sea star Pisaster ochraceus has shown itself to mediate tolerance to “sea star wasting disease”, a pandemic that has significantly reduced sea star populations on the Pacific coast of North America. Here we use RNA sequencing of healthy individuals to identify differences in constitutive expression of gene regions that may help explain this tolerance phenotype. Our results show that individuals carrying this mutation have lower expression at a large contingent of gene regions. Individuals without this mutation also appear to have a greater cellular response to temperature stress, which has been implicated in the outbreak of sea star wasting disease. Given the ecological significance of P. ochraceus, these results may be useful in predicting the evolutionary and demographic future for Pacific intertidal communities.
creator: V. Katelyn Chandler
creator: John P. Wares
uri: https://doi.org/10.7717/peerj.3696
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Chandler and Wares