title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1660 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: The complete chloroplast genome of Cinnamomum camphora and its comparison with related Lauraceae species link: https://peerj.com/articles/3820 last-modified: 2017-09-18 description: Cinnamomum camphora, a member of the Lauraceae family, is a valuable aromatic and timber tree that is indigenous to the south of China and Japan. All parts of Cinnamomum camphora have secretory cells containing different volatile chemical compounds that are utilized as herbal medicines and essential oils. Here, we reported the complete sequencing of the chloroplast genome of Cinnamomum camphora using illumina technology. The chloroplast genome of Cinnamomum camphora is 152,570 bp in length and characterized by a relatively conserved quadripartite structure containing a large single copy region of 93,705 bp, a small single copy region of 19,093 bp and two inverted repeat (IR) regions of 19,886 bp. Overall, the genome contained 123 coding regions, of which 15 were repeated in the IR regions. An analysis of chloroplast sequence divergence revealed that the small single copy region was highly variable among the different genera in the Lauraceae family. A total of 40 repeat structures and 83 simple sequence repeats were detected in both the coding and non-coding regions. A phylogenetic analysis indicated that Calycanthus is most closely related to Lauraceae, both being members of Laurales, which forms a sister group to Magnoliids. The complete sequence of the chloroplast of Cinnamomum camphora will aid in in-depth taxonomical studies of the Lauraceae family in the future. The genetic sequence information will also have valuable applications for chloroplast genetic engineering. creator: Caihui Chen creator: Yongjie Zheng creator: Sian Liu creator: Yongda Zhong creator: Yanfang Wu creator: Jiang Li creator: Li-An Xu creator: Meng Xu uri: https://doi.org/10.7717/peerj.3820 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Chen et al. title: Can squirrel monkeys learn an ABnA grammar? A re-evaluation of Ravignani et al. (2013) link: https://peerj.com/articles/3806 last-modified: 2017-09-18 description: Ravignani et al. (2013) habituated squirrel monkeys to sound sequences conforming to an ABnA grammar (n = 1, 2, 3), then tested them for their reactions to novel grammatical and non-grammatical sequences. Although they conclude that the monkeys “consistently recognized and generalized the sequence ABnA,” I remark that this conclusion is not robust. The statistical significance of results depends on specific choices of data analysis, namely dichotomization of the response variable and omission of specific data points. Additionally, there is little evidence of generalization to novel patterns (n = 4, 5), which is important to conclude that the monkeys recognized the ABnA grammar beyond the habituation patterns. Lastly, many test sequences were perceptually similar to habituation sequences, raising the possibility that the monkeys may have generalized based on perceptual similarity rather than based on grammaticality. creator: Stefano Ghirlanda uri: https://doi.org/10.7717/peerj.3806 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Ghirlanda title: Integrative taxonomy of the ornamental ‘peppermint’ shrimp public market and population genetics of Lysmata boggessi, the most heavily traded species worldwide link: https://peerj.com/articles/3786 last-modified: 2017-09-18 description: The ornamental trade is a worldwide industry worth >15 billion USD with a problem of rampant product misidentification. Minimizing misidentification is critical in the face of overexploitation of species in the trade. We surveyed the peppermint shrimp ornamental marketplace in the southeastern USA, the most intense market for peppermint shrimps worldwide, to characterize the composition of species in the trade, reveal the extent of misidentification, and describe the population genetics of the true target species. Shrimps were bought from aquarium shops in FL, GA, SC, and NC. We demonstrated, contrary to popular belief (information from dealers), that the most heavily traded species in the market was Lysmata boggessi, an endemic species to the eastern Gulf of Mexico, and not Lysmata wurdemanni. Importantly, only when color pattern or genetic markers in conjunction with morphological traits were employed, was it was possible to unequivocally identify L. boggessi as the only species in the trade. The intensity of the market for peppermint shrimps in the USA has led to L. boggessi being the most traded species worldwide. Misidentification in the shrimp aquarium trade is accidental and involuntary, and is explained by remarkable similarity among congeneric species. Using sequences of the 16S-mt-DNA marker, we found no indication of population genetic structure in the endemic L. boggessi across  550 km of linear coast. Therefore, this species can be considered genetically homogeneous and a single fished stock. Still, we argue in favor of additional studies using more powerful markers (e.g., SNPs) capable of revealing genetic structure at a finer spatial-scale. Our results will help advance management and conservation policies in this lucrative yet understudied fishery. Future studies of other ornamental fisheries will benefit from using an integrative taxonomic approach, as we demonstrate here. creator: J. Antonio Baeza creator: Donald C. Behringer uri: https://doi.org/10.7717/peerj.3786 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Baeza et al. title: Asymmetric responses to simulated global warming by populations of Colobanthus quitensis along a latitudinal gradient link: https://peerj.com/articles/3718 last-modified: 2017-09-18 description: The increase in temperature as consequence of the recent global warming has been reported to generate new ice-free areas in the Antarctic continent, facilitating the colonization and spread of plant populations. Consequently, Antarctic vascular plants have been observed extending their southern distribution. But as the environmental conditions toward southern localities become progressively more departed from the species’ physiological optimum, the ecophysiological responses and survival to the expected global warming could be reduced. However, if processes of local adaptation are the main cause of the observed southern expansion, those populations could appear constrained to respond positively to the expected global warming. Using individuals from the southern tip of South America, the South Shetland Islands and the Antarctic Peninsula, we assess with a long term experiment (three years) under controlled conditions if the responsiveness of Colobanthus quitensis populations to the expected global warming, is related with their different foliar traits and photoprotective mechanisms along the latitudinal gradient. In addition, we tested if the release of the stress condition by the global warming in these cold environments increases the ecophysiological performance. For this, we describe the latitudinal pattern of net photosynthetic capacity, biomass accumulation, and number of flowers under current and future temperatures respective to each site of origin after three growing seasons. Overall, was found a clinal trend was found in the foliar traits and photoprotective mechanisms in the evaluated C. quitensis populations. On the other hand, an asymmetric response to warming was observed for southern populations in all ecophysiological traits evaluated, suggesting that low temperature is limiting the performance of C. quitensis populations. Our results suggest that under a global warming scenario, plant populations that inhabiting cold zones at high latitudes could increase in their ecophysiological performance, enhancing the size of populations or their spread. creator: Ian S. Acuña-Rodríguez creator: Cristian Torres-Díaz creator: Rasme Hereme creator: Marco A. Molina-Montenegro uri: https://doi.org/10.7717/peerj.3718 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Acuña-Rodríguez et al. title: Candidate genes for shell colour polymorphism in Cepaea nemoralis link: https://peerj.com/articles/3715 last-modified: 2017-09-18 description: The characteristic ground colour and banding patterns on shells of the land snail Cepaea nemoralis form a classic study system for genetics and adaptation as it varies widely between individuals. We use RNAseq analysis to identify candidate genes underlying this polymorphism. We sequenced cDNA from the foot and the mantle (the shell-producing tissue) of four individuals of two phenotypes and produced a de novo transcriptome of 147,397 contigs. Differential expression analysis identified a set of 1,961 transcripts that were upregulated in mantle tissue. Sequence variant analysis resulted in a set of 2,592 transcripts with single nucleotide polymorphisms (SNPs) that differed consistently between the phenotypes. Inspection of the overlap between the differential expression analysis and SNP analysis yielded a set of 197 candidate transcripts, of which 38 were annotated. Four of these transcripts are thought to be involved in production of the shell’s nacreous layer. Comparison with morph-associated Restriction-site Associated DNA (RAD)-tags from a published study yielded eight transcripts that were annotated as metallothionein, a protein that is thought to inhibit the production of melanin in melanocytes. These results thus provide an excellent starting point for the elucidation of the genetic regulation of the Cepaea nemoralis shell colour polymorphism. creator: Jesse Kerkvliet creator: Tjalf de Boer creator: Menno Schilthuizen creator: Ken Kraaijeveld uri: https://doi.org/10.7717/peerj.3715 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Kerkvliet et al. title: Genomic analysis of P elements in natural populations of Drosophila melanogaster link: https://peerj.com/articles/3824 last-modified: 2017-09-15 description: The Drosophila melanogaster P transposable element provides one of the best cases of horizontal transfer of a mobile DNA sequence in eukaryotes. Invasion of natural populations by the P element has led to a syndrome of phenotypes known as P-M hybrid dysgenesis that emerges when strains differing in their P element composition mate and produce offspring. Despite extensive research on many aspects of P element biology, many questions remain about the genomic basis of variation in P-M dysgenesis phenotypes across populations. Here we compare estimates of genomic P element content with gonadal dysgenesis phenotypes for isofemale strains obtained from three worldwide populations of D. melanogaster to illuminate the molecular basis of natural variation in cytotype status. We show that P element abundance estimated from genome sequences of isofemale strains is highly correlated across different bioinformatics approaches, but that abundance estimates are sensitive to method and filtering strategies as well as incomplete inbreeding of isofemale strains. We find that P element content varies significantly across populations, with strains from a North American population having fewer P elements but a higher proportion of full-length elements than strains from populations sampled in Europe or Africa. Despite these geographic differences in P element abundance and structure, neither the number of P elements nor the ratio of full-length to internally-truncated copies is strongly correlated with the degree of gonadal dysgenesis exhibited by an isofemale strain. Thus, variation in P element abundance and structure across different populations does not necessarily lead to corresponding geographic differences in gonadal dysgenesis phenotypes. Finally, we confirm that population differences in the abundance and structure of P elements that are observed from isofemale lines can also be observed in pool-seq samples from the same populations. Our work supports the view that genomic P element content alone is not sufficient to explain variation in gonadal dysgenesis across strains of D. melanogaster, and informs future efforts to decode the genomic basis of geographic and temporal differences in P element induced phenotypes. creator: Casey M. Bergman creator: Shunhua Han creator: Michael G. Nelson creator: Vladyslav Bondarenko creator: Iryna Kozeretska uri: https://doi.org/10.7717/peerj.3824 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Bergman et al. title: Association of rs1801157 single nucleotide polymorphism of CXCL12 gene in breast cancer in Pakistan and in-silico expression analysis of CXCL12–CXCR4 associated biological regulatory network link: https://peerj.com/articles/3822 last-modified: 2017-09-15 description: BackgroundC-X-C chemokine ligand 12 (CXCL12) has important implications in breast cancer (BC) pathogenesis. It is selectively expressed on B and T lymphocytes and is involved in hematopoiesis, thymocyte trafficking, stem cell motility, neovascularization, and tumorigenesis. The single nucleotide polymorphism (SNP) rs1801157 of CXCL12 gene has been found to be associated with higher risk of BC.MethodsOur study focuses on the genotypic and allelic distribution of SNP (rs1801157; G/A) in Pakistani population as well as its association with the clinico-pathological features. The association between rs1801157 genotypes (G/A) and BC risks was assessed by a multivariate logistic regression (MLR) analysis. Genotyping was performed in both healthy individuals and patients of BC using PCR-restriction fragment length polymorphism (PCR-RFLP) method. Furthermore, in-silico approaches were adapted to investigate the association of CXCL12 and its receptor CXCR4 with genes/proteins involved in BC signalling.ResultsSignificant differences in allelic and genotypic distribution between BC patients and healthy individuals of genotype (G/G) and (A/G) (p < 0.05) were observed. The frequency of the allele G in the BC group (77%) was significantly higher as compared to control group (61%) (p = 0.01). The association of genotype GG with clinico-pathological features including age, stages of cancer and organ (lung, liver, bones and brain) metastasis (p > 0.05) was assessed. In a MLR analysis, a number of variables including age, weight of an individual, affected lymph nodes, hormonal status (estrogen and progesterone receptor), alcohol consumption and family history associated with the GG genotype (GG:AA, odds ratio (OR) = 1.30, 95% CI [1.06–1.60]) were found to be independent risk factors for BC. Our in-vitro results suggest that genotype GG is possibly increasing the risk of BC in Pakistani cohorts. in-silico analysis finds that CXCL12–CXCR4 is associated with an increased expression of PDZK1, PI3k and Akt which lead the breast tumor towards metastasis.ConclusionMultiple targets such as CXCL12, CXCR4, PDZK1, PI3k and Akt can be inhibited in combined strategies to treat BC metastasis. creator: Samra Khalid creator: Rumeza Hanif uri: https://doi.org/10.7717/peerj.3822 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Khalid and Hanif title: Fish Ontology framework for taxonomy-based fish recognition link: https://peerj.com/articles/3811 last-modified: 2017-09-15 description: Life science ontologies play an important role in Semantic Web. Given the diversity in fish species and the associated wealth of information, it is imperative to develop an ontology capable of linking and integrating this information in an automated fashion. As such, we introduce the Fish Ontology (FO), an automated classification architecture of existing fish taxa which provides taxonomic information on unknown fish based on metadata restrictions. It is designed to support knowledge discovery, provide semantic annotation of fish and fisheries resources, data integration, and information retrieval. Automated classification for unknown specimens is a unique feature that currently does not appear to exist in other known ontologies. Examples of automated classification for major groups of fish are demonstrated, showing the inferred information by introducing several restrictions at the species or specimen level. The current version of FO has 1,830 classes, includes widely used fisheries terminology, and models major aspects of fish taxonomy, grouping, and character. With more than 30,000 known fish species globally, the FO will be an indispensable tool for fish scientists and other interested users. creator: Najib M. Ali creator: Haris A. Khan creator: Amy Y-Hui Then creator: Chong Ving Ching creator: Manas Gaur creator: Sarinder Kaur Dhillon uri: https://doi.org/10.7717/peerj.3811 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Ali et al. title: The distribution shifts of Pinus armandii and its response to temperature and precipitation in China link: https://peerj.com/articles/3807 last-modified: 2017-09-15 description: BackgroundThe changing climate, particularly in regard to temperature and precipitation, is already affecting tree species’ distributions. Pinus armandii, which dominates on the Yungui Plateau and in the Qinba Mountains in China, is of economic, cultural and ecological value. We wish to test the correlations between the distribution shift of P. armandii and changing climate, and figure out how it tracks future climate change.MethodsWe sampled the surface soil at sites throughout the distribution of P. armandii to compare the relative abundance of pollen to the current percent cover of plant species. This was used to determine possible changes in the distribution P. armandii. Given the hilly terrain, elevation was considered together with temperature and precipitation as variables correlated with distribution shifts of P. armandii.ResultsWe show that P. armandii is undergoing change in its geographic range, including retraction, a shift to more northern areas and from the upper high part of the mountains to a lower-altitude part in hilly areas. Temperature was the strongest correlate of this distribution shift. Elevation and precipitation were also both significantly correlated with distribution change of P. armandii, but to a lesser degree than temperature.ConclusionThe geographic range of P. armandii has been gradually decreasing under the influence of climate change. This provides evidence of the effect of climate change on trees at the species level and suggests that at least some species will have a limited ability to track the changing climate. creator: Xiaofeng Zheng creator: Pengxiang Gao creator: ShuoXin Zhang uri: https://doi.org/10.7717/peerj.3807 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Zheng et al. title: Effects of long-term preservation on amphibian body conditions: implications for historical morphological research link: https://peerj.com/articles/3805 last-modified: 2017-09-15 description: Measurements of historical specimens are widely applied in studies of taxonomy, systematics, and ecology, but biologists often assume that the effects of preservative chemicals on the morphology of amphibian specimens are minimal in their analyses. We compared the body length and body mass of 182 samples of 13 live and preserved (up to 10 years) anuran species and found that the body length and body mass of preserved specimens significantly decreased by 6.1% and 24.8%, respectively, compared to those measurements of their live counterparts. The changes in body length and mass also exhibited highly significant variations between species. Similarly, there were significant differences in shrinkage of body length and body mass between sexes, where males showed greater shrinkage in body length and body mass compared to females. Preservation distorted the magnitude of the interspecific differences in body length observed in the fresh specimens. Overall, the reduction in body length or mass was greater in longer or heavier individuals. Due to the effects of preservation on amphibian morphology, we propose two parsimonious conversion equations to back-calculate the original body length and body mass of studied anurans for researchers working with historical data, since morphological data from preserved specimens may lead to incorrect biological interpretations when comparing to fresh specimens. Therefore, researchers should correct for errors due to preservation effects that may lead to the misinterpretation of results. creator: Guocheng Shu creator: Yuzhou Gong creator: Feng Xie creator: Nicholas C. Wu creator: Cheng Li uri: https://doi.org/10.7717/peerj.3805 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Shu et al.