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
The distribution shifts of Pinus armandii and its response to temperature and precipitation in China
Background The 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. Methods We 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. Results We 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. Conclusion The 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.
Zheng et al. (2017) The distribution shifts of Pinus armandii and its response to temperature and precipitation in China. PeerJ 5:e3807 https://doi.org/10.7717/peerj.3807
Effects of long-term preservation on amphibian body conditions: implications for historical morphological research
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.
Shu et al. (2017) Effects of long-term preservation on amphibian body conditions: implications for historical morphological research. PeerJ 5:e3805 https://doi.org/10.7717/peerj.3805
Inferring ‘weak spots’ in phylogenetic trees: application to mosasauroid nomenclature
Mosasauroid squamates represented the apex predators within the Late Cretaceous marine and occasionally also freshwater ecosystems. Proper understanding of the origin of their ecological adaptations or paleobiogeographic dispersals requires adequate knowledge of their phylogeny. The studies assessing the position of mosasauroids on the squamate evolutionary tree and their origins have long given conflicting results. The phylogenetic relationships within Mosasauroidea, however, have experienced only little changes throughout the last decades. Considering the substantial improvements in the development of phylogenetic methodology that have undergone in recent years, resulting, among others, in numerous alterations in the phylogenetic hypotheses of other fossil amniotes, we test the robustness in our understanding of mosasauroid beginnings and their evolutionary history. We re-examined a data set that results from modifications assembled in the course of the last 20 years and performed multiple parsimony analyses and Bayesian tip-dating analysis. Following the inferred topologies and the ‘weak spots’ in the phylogeny of mosasauroids, we revise the nomenclature of the ‘traditionally’ recognized mosasauroid clades, to acknowledge the overall weakness among branches and the alternative topologies suggested previously, and discuss several factors that might have an impact on the differing phylogenetic hypotheses and their statistical support.
Madzia et al. (2017) Inferring ‘weak spots’ in phylogenetic trees: application to mosasauroid nomenclature. PeerJ 5:e3782 https://doi.org/10.7717/peerj.3782
Impacts of land use and invasive species on native avifauna of Mo’orea, French Polynesia
Oceanic islands are among the most endemically biodiverse ecosystems in the world. They have been adversely impacted by human expansion, which affects regional biodiversity by altering the natural habitats of vulnerable, indigenous species. Birds represent a valuable indicator species of environmental change due to their ability to adapt quickly. Investigating the relationship between environmental change, abundance, and behaviors of birds can help us better anticipate potential impacts to island ecosystems. In addition, we can understand the population trends and restricted ranges of native avifauna, identify the regions needing protection, and assess habitat vulnerability linked to anthropogenic activities. In Mo’orea, French Polynesia, we studied nine passerine bird species using automated acoustic recording devices placed in agricultural, forested, and mixed habitats. Based on call counts per unit time and occupancy modeling, we found evidence that three non-native species preferred agricultural areas and low-canopy cover over dense forested areas. Furthermore, native bird detectability and possibly abundance was significantly lower than non-native birds. Using hierarchical cluster analysis to support inferences regarding behavioral differences, we found that native bird calling activity was negatively associated with non-native bird calling activity. Altogether, these results suggest native bird populations are at risk in all of the habitats studied, but forests serve as a potential refuge.
ZoBell et al. (2017) Impacts of land use and invasive species on native avifauna of Mo’orea, French Polynesia. PeerJ 5:e3761 https://doi.org/10.7717/peerj.3761