Revisiting the mitogenomic phylogeny of Salmoninae: new insights thanks to recent sequencing advances
The phylogeny of the Salmonidae family, the only living one of the Order Salmoniformes, remains still unclear because of several reasons. Such reasons include insufficient taxon sampling and/or DNA information. The use of complete mitochondrial genomes (mitogenomics) could provide some light on it, but despite the high number of mitogenomes of species belonging to this family published during last years, an integrative work containing all this information has not been done. In this work, the phylogeny of 46 Salmonidae species was inferred from their mitogenomic sequences. Results include a Bayesian molecular-dated phylogenetic tree with very high statistical support showing Coregoninae and Salmoninae as sister subfamilies, as well as several new phylogenetic relationships among species and genus of the family. All these findings contribute to improve our understanding of the Salmonidae systematics and could have consequences on related evolutionary studies, as well as highlight the importance of revisiting phylogenies with integrative studies.
Horreo (2017) Revisiting the mitogenomic phylogeny of Salmoninae: new insights thanks to recent sequencing advances. PeerJ 5:e3828 https://doi.org/10.7717/peerj.3828
The Parenting to Reduce Adolescent Depression and Anxiety Scale: Assessing parental concordance with parenting guidelines for the prevention of adolescent depression and anxiety disorders
Background Despite substantial evidence demonstrating numerous parental risk and protective factors for the development of adolescent depression and anxiety disorders, there is currently no single measure that assesses these parenting factors. To address this gap, we developed the Parenting to Reduce Adolescent Depression and Anxiety Scale (PRADAS) as a criterion-referenced measure of parental concordance with a set of evidence-based parenting guidelines for the prevention of adolescent depression and anxiety disorders. In this paper, we used a sample of Australian parents of adolescents to: (1) validate the PRADAS as a criterion-referenced measure; (2) examine parental concordance with the guidelines in the sample; and (3) examine correlates of parental concordance with the guidelines. Methods Seven hundred eleven parents completed the PRADAS, as well as two established parenting measures, and parent-report measures of adolescent depression and anxiety symptoms. Six hundred sixty adolescent participants (aged 12–15) also completed the symptom measures. Concordance with the guidelines was assessed via nine subscale scores and a total score. Reliability of the scores was assessed with an estimate of the agreement coefficient, as well as 1-month test-retest reliability. Convergent validity was examined via correlations between the scale and two established parenting measures. Results One proposed subscale was removed from the final version of the scale, resulting in a total of eight subscales. Reliability was high for the total score, and acceptable to high for seven of the eight subscales. One-month test-retest reliability was acceptable to high for the total score. Convergent validity was supported by moderate to high correlations with two established measures of parenting. Overall, rates of parental concordance with the guidelines were low in our sample. Higher scores were associated with being female and higher levels of parental education. Greater parental concordance with the guidelines was associated with fewer symptoms of depression and anxiety in adolescent participants. Discussion This initial validation study provides preliminary support for the reliability and validity of the PRADAS. The scale has potential for use in both clinical and research settings. It may be used to identify parents’ strengths and potential targets for intervention, and as an outcome measure in studies of preventive parenting interventions.
Cardamone-Breen et al. (2017) The Parenting to Reduce Adolescent Depression and Anxiety Scale: Assessing parental concordance with parenting guidelines for the prevention of adolescent depression and anxiety disorders. PeerJ 5:e3825 https://doi.org/10.7717/peerj.3825
The complete chloroplast genome of Cinnamomum camphora and its comparison with related Lauraceae species
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.
Chen et al. (2017) The complete chloroplast genome of Cinnamomum camphora and its comparison with related Lauraceae species. PeerJ 5:e3820 https://doi.org/10.7717/peerj.3820
Can squirrel monkeys learn an ABnA grammar? A re-evaluation of Ravignani et al. (2013)
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.
Ghirlanda (2017) Can squirrel monkeys learn an ABnA grammar? A re-evaluation of Ravignani et al. (2013). PeerJ 5:e3806 https://doi.org/10.7717/peerj.3806
Integrative taxonomy of the ornamental ‘peppermint’ shrimp public market and population genetics of Lysmata boggessi, the most heavily traded species worldwide
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.
Baeza et al. (2017) Integrative taxonomy of the ornamental ‘peppermint’ shrimp public market and population genetics of Lysmata boggessi, the most heavily traded species worldwide. PeerJ 5:e3786 https://doi.org/10.7717/peerj.3786
Asymmetric responses to simulated global warming by populations of Colobanthus quitensis along a latitudinal gradient
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.
Acuña-Rodríguez et al. (2017) Asymmetric responses to simulated global warming by populations of Colobanthus quitensis along a latitudinal gradient. PeerJ 5:e3718 https://doi.org/10.7717/peerj.3718
Candidate genes for shell colour polymorphism in Cepaea nemoralis
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.
Kerkvliet et al. (2017) Candidate genes for shell colour polymorphism in Cepaea nemoralis. PeerJ 5:e3715 https://doi.org/10.7717/peerj.3715
Genomic analysis of P elements in natural populations of Drosophila melanogaster
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.
Bergman et al. (2017) Genomic analysis of P elements in natural populations of Drosophila melanogaster. PeerJ 5:e3824 https://doi.org/10.7717/peerj.3824
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
Background C-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. Methods Our 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. Results Significant 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. Conclusion Multiple targets such as CXCL12, CXCR4, PDZK1, PI3k and Akt can be inhibited in combined strategies to treat BC metastasis.
Khalid et al. (2017) 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. PeerJ 5:e3822 https://doi.org/10.7717/peerj.3822
Fish Ontology framework for taxonomy-based fish recognition
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.
Ali et al. (2017) Fish Ontology framework for taxonomy-based fish recognition. PeerJ 5:e3811 https://doi.org/10.7717/peerj.3811