Unimodal head-width distribution of the European eel (Anguilla anguilla L.) from the Zeeschelde does not support disruptive selection
Since the early 20th century, European eels (Anguilla anguilla L.) have been dichotomously classified into ‘narrow’ and ‘broad’ heads. These morphs are mainly considered the result of a differential food choice, with narrow heads feeding primarily on small/soft prey and broad heads on large/hard prey. Yet, such a classification implies that head-width variation follows a bimodal distribution, leading to the assumption of disruptive selection. We investigated the head morphology of 272 eels, caught over three consecutive years (2015–2017) at a single location in the Zeeschelde (Belgium). Based on our results, BIC favored a unimodal distribution, while AIC provided equal support for a unimodal and a bimodal distribution. Notably, visualization of the distributions revealed a strong overlap between the two normal distributions under the bimodal model, likely explaining the ambiguity under AIC. Consequently, it is more likely that head-width variation followed a unimodal distribution, indicating there are no disruptive selection pressures for bimodality in the Zeeschelde. As such, eels could not be divided in two distinct head-width groups. Instead, their head widths showed a continuum of narrow to broad with a normal distribution. This pattern was consistent across all maturation stages studied here.
Verhelst et al. (2018) Unimodal head-width distribution of the European eel (Anguilla anguilla L.) from the Zeeschelde does not support disruptive selection. PeerJ 6:e5773 https://doi.org/10.7717/peerj.5773
Sexual dimorphism in the Arachnid orders
Sexual differences in size and shape are common across the animal kingdom. The study of sexual dimorphism (SD) can provide insight into the sexual- and natural-selection pressures experienced by males and females in different species. Arachnids are diverse, comprising over 100,000 species, and exhibit some of the more extreme forms of SD in the animal kingdom, with the males and females of some species differing dramatically in body shape and/or size. Despite this, research on arachnid SD has primarily focused on specific clades as opposed to observing traits across arachnid orders, the smallest of which have received comparatively little attention. This review provides an overview of the research to date on the trends and potential evolutionary drivers for SD and sexual size dimorphism (SSD) in individual arachnid orders, and across arachnids as a whole. The most common trends across Arachnida are female-biased SSD in total body size, male-biased SSD in relative leg length and SD in pedipalp length and shape. However, the evolution of sexually dimorphic traits within the group is difficult to elucidate due to uncertainty in arachnid phylogenetic relationships. Based on the dataset we have gathered here, we highlight gaps in our current understanding and suggest areas for future research.
McLean et al. (2018) Sexual dimorphism in the Arachnid orders. PeerJ 6:e5751 https://doi.org/10.7717/peerj.5751
Genetic population structure of the pelagic mollusk Limacina helicina in the Kara Sea
Background Pelagic pteropods Limacina helicina are widespread and can play an important role in the food webs and in biosedimentation in Arctic and Subarctic ecosystems. Previous publications have shown differences in the genetic structure of populations of L. helicina from populations found in the Pacific Ocean and Svalbard area. Currently, there are no data on the genetic structure of L. helicina populations in the seas of the Siberian Arctic. We assessed the genetic structure of L. helicina from the Kara Sea populations and compared them with samples from around Svalbard and the North Pacific. Methods We examined genetic differences in L. helicina from three different locations in the Kara Sea via analysis of a fragment of the mitochondrial gene COI. We also compared a subset of samples with L. helicina from previous studies to find connections between populations from the Atlantic and Pacific Oceans. Results 65 individual L. helinica from the Kara Sea were sequenced to produce 19 different haplotypes. This is comparable with numbers of haplotypes found in Svalbard and Pacific samples (24 and 25, respectively). Haplotypes from different locations sampled around the Arctic and Subarctic were combined into two different groups: H1 and H2. The H2 includes sequences from the Kara Sea and Svalbard, was present only in the Atlantic sector of the Arctic. The other genetic group, H1, is widespread and found throughout all L. helicina populations. ϕ ST analyses also indicated significant genetic difference between the Atlantic and Pacific regions, but no differences between Svalbard and the Kara Sea. Discussion The obtained results support our hypothesis about genetic similarity of L. helicina populations from the Kara Sea and Svalbard: the majority of haplotypes belongs to the haplotype group H2, with the H1 group representing a minority of the haplotypes present. In contrast, in the Canadian Arctic and the Pacific Ocean only haplogroup H1 is found. The negative values of Fu’s Fs indicate directed selection or expansion of the population. The reason for this pattern could be an isolation of the Limacina helicina population during the Pleistocene glaciation and a subsequent rapid expansion of this species after the last glacial maximum.
Abyzova et al. (2018) Genetic population structure of the pelagic mollusk Limacina helicina in the Kara Sea. PeerJ 6:e5709 https://doi.org/10.7717/peerj.5709
All you can eat: the functional response of the cold-water coral Desmophyllum dianthus feeding on krill and copepods
The feeding behavior of the cosmopolitan cold-water coral (CWC) Desmophyllum dianthus (Cnidaria: Scleractinia) is still poorly known. Its usual deep distribution restricts direct observations, and manipulative experiments are so far limited to prey that do not occur in CWC natural habitat. During a series of replicated incubations, we assessed the functional response of this coral feeding on a medium-sized copepod (Calanoides patagoniensis) and a large euphausiid (Euphausia vallentini). Corals showed a Type I functional response, where feeding rate increased linearly with prey abundance, as predicted for a tentaculate passive suspension feeder. No significant differences in feeding were found between prey items, and corals were able to attain a maximum feeding rate of 10.99 mg C h−1, which represents an ingestion of the 11.4% of the coral carbon biomass per hour. These findings suggest that D. dianthus is a generalist zooplankton predator capable of exploiting dense aggregations of zooplankton over a wide prey size-range.
Höfer et al. (2018) All you can eat: the functional response of the cold-water coral Desmophyllum dianthus feeding on krill and copepods. PeerJ 6:e5872 https://doi.org/10.7717/peerj.5872
Optimization of the cytogenetic protocol for Pangasianodon hypophthalmus (Sauvage, 1878) and Clarias gariepinus (Burchell, 1822)
To obtain well spread chromosomes, the cytogenetic protocol for Pangasianodon hypophthalmus and Clarias gariepinus were optimized. This includes, the colchicine concentration (0.01%, 0.025%, 0.05%)/exposure duration (1, 3, and 5 h), hypotonic solution (distilled water or 0.075M KCl solution)/exposure duration (30 min, 1, and 2 h), the time of cell suspension preparation (at hypotonic treatment or before slide preparation) and chromosome aging period (0, 3, and 7 days in Carnoy’s fixative). In addition, the type (i.e., fin, gill or kidney) and the amount of tissue (10, 50, 100 or 150 mg) were also investigated. Regardless of the species, the result obtained showed that well-spread chromosomes could be obtained using the following optimized protocol: Juveniles are injected with 0.05% colchicine (at one ml kg−1) and allowed to swim for 3 h. Then, 50 mg of gill tissue is made into cell suspension in 0.075M KCl for 1 h. The cell suspension is treated in Carnoy’s fixative (changed three times at 20 min interval) and then aged for 3 days. Finally, chromosome slides are made and stained with 10% Giemsa for 1 h.
Okomoda et al. (2018) Optimization of the cytogenetic protocol for Pangasianodon hypophthalmus (Sauvage, 1878) and Clarias gariepinus (Burchell, 1822). PeerJ 6:e5712 https://doi.org/10.7717/peerj.5712
A trait-based ecology to assess the acclimation of a sperm-dependent clonal fish compared to its sexual host
Background Survival in temporally or spatially changing environments is a prerequisite for the perpetuation of a given species. In addition to genetic variation, the role of epigenetic processes is crucial in the persistence of organisms. For instance, mechanisms such as developmental flexibility enable the adjustment of the phenotype of a given individual to changing conditions throughout its development. However, the extent of factors other than genetic variability, like epigenetic processes, in the production of alternative phenotype and the consequences in realized ecological niches is still unclear. Methods In this study, we compared the extent of realized niches between asexual and sexual individuals from different environments. We used a trait-based ecology approach exploiting trophic and locomotive structures to infer the environment that each biotype actually used. More specifically, we compared the morphology of the all-female clonal and sperm-dependent fish Chrosomus eos-neogaeus to that of their sexual host species C. eos in common garden and natural conditions. Results Transfer from natural to controlled conditions resulted in a similar shift in measured morphology for clonal and sexual individuals suggesting comparable level of flexibility in both kinds of organisms. However, clonal, but not sexual, individuals displayed a consistent phenotype when reared in uniform conditions indicating that in absence of genetic variation, one phenotype corresponds to one niche. This contrasted with results from natural conditions where clones were morphologically as variable as sexual individuals within a sampled site. In addition, similar phenotypic changes for both clonal and sexual individuals were observed among the majority of sampled sites, indicating that they responded similarly to the same environments. Discussion Our results indicated that clones can efficiently use different niches and may evolve in a range of environmental conditions comparable to that of a sexual species, thus underlying the importance of factors other than genetic variability, like epigenetic processes, for coping with environmental heterogeneity.
Leung et al. (2018) A trait-based ecology to assess the acclimation of a sperm-dependent clonal fish compared to its sexual host. PeerJ 6:e5896 https://doi.org/10.7717/peerj.5896
imGLAD: accurate detection and quantification of target organisms in metagenomes
Accurate detection of target microbial species in metagenomic datasets from environmental samples remains limited because the limit of detection of current methods is typically inaccessible and the frequency of false-positives, resulting from inadequate identification of regions of the genome that are either too highly conserved to be diagnostic (e.g., rRNA genes) or prone to frequent horizontal genetic exchange (e.g., mobile elements) remains unknown. To overcome these limitations, we introduce imGLAD, which aims to detect (target) genomic sequences in metagenomic datasets. imGLAD achieves high accuracy because it uses the sequence-discrete population concept for discriminating between metagenomic reads originating from the target organism compared to reads from co-occurring close relatives, masks regions of the genome that are not informative using the MyTaxa engine, and models both the sequencing breadth and depth to determine relative abundance and limit of detection. We validated imGLAD by analyzing metagenomic datasets derived from spinach leaves inoculated with the enteric pathogen Escherichia coli O157:H7 and showed that its limit of detection can be comparable to that of PCR-based approaches for these samples (∼1 cell/gram).
Castro et al. (2018) imGLAD: accurate detection and quantification of target organisms in metagenomes. PeerJ 6:e5882 https://doi.org/10.7717/peerj.5882
Evaluation of soil intervention values in mine tailings in northern Chile
The aim of this work is to show a methodological proposal for the analysis of soil intervention values in mine tailings in order to determine the intervention requirements in the commune of Andacollo in northern Chile. The purpose of this analysis is to guide the intervention policies of both private and public organizations. The evaluation method is based on the Dutch legislation. The usability of the proposed methods depends on the available geochemical data from soil samples; in particular, we tackle the case when information regarding clay percentage in the soil is not available. We use the concepts of a threshold factor and an adjusted threshold factor to calculate a weighted intervention ranking. In order to illustrate the utility of this methodological proposal, a case study is carried out with the prescribed approach. In particular, this work presents an analysis of the elements of environmental significance related to the mining activity (Hg, Cd, Pb, As, Cu, Ni, Zn, Cr) in the commune of Andacollo, Coquimbo Region, Chile. The analyzed samples are used to determine where the intervention of tailing deposits is necessary and where a solution to these environmental liabilities is required as soon as possible. Out of the 81 samples evaluated, it was found that 18 require a potential intervention, and of these samples, seven of them are associated with abandoned tailings that, in some cases, are located close to the town center itself, one sample is associated with active tailings and the other 10 with inactive tailings.
Environmental Contamination and Remediation
Lam Esquenazi et al. (2018) Evaluation of soil intervention values in mine tailings in northern Chile. PeerJ 6:e5879 https://doi.org/10.7717/peerj.5879
Dynamic proteomic changes in soft wheat seeds during accelerated ageing
Previous research demonstrated that soft wheat cultivars have better post-harvest storage tolerance than harder cultivars during accelerated ageing. To better understand this phenomenon, a tandem mass tag-based quantitative proteomic analysis of soft wheat seeds was performed at different storage times during accelerated ageing (germination ratios of 97%, 45%, 28%, and 6%). A total of 1,010 proteins were differentially regulated, of which 519 and 491 were up- and downregulated, respectively. Most of the differentially expressed proteins were predicted to be involved in nutrient reservoir, enzyme activity and regulation, energy and metabolism, and response to stimulus functions, consistent with processes occurring in hard wheat during artificial ageing. Notably, defense-associated proteins including wheatwin-2, pathogenesis-related proteins protecting against fungal invasion, and glutathione S-transferase and glutathione synthetase participating in reactive oxygen species (ROS) detoxification, were upregulated compared to levels in hard wheat during accelerated ageing. These upregulated proteins might be responsible for the superior post-harvest storage-tolerance of soft wheat cultivars during accelerated ageing compared with hard wheat. Although accelerated ageing could not fully mimic natural ageing, our findings provided novel dynamic proteomic insight into soft wheat seeds during seed deterioration.
Lv et al. (2018) Dynamic proteomic changes in soft wheat seeds during accelerated ageing. PeerJ 6:e5874 https://doi.org/10.7717/peerj.5874
Ontogenetic changes in swimming speed of silver carp, bighead carp, and grass carp larvae: implications for larval dispersal
Bighead, silver, and grass carps are invasive in the waterways of central North America, and grass carp reproduction in tributaries of the Great Lakes has now been documented. Questions about recruitment potential motivate a need for accurate models of egg and larval dispersal. Quantitative data on swimming behaviors and capabilities during early ontogeny are needed to improve these dispersal models. We measured ontogenetic changes in routine and maximum swimming speeds of bighead, grass, and silver carp larvae. Daily measurements of routine swimming speed were taken for two weeks post-hatch using a still camera and the LARVEL program, a custom image-analysis software. Larval swimming speed was calculated using larval locations in subsequent image frames and time between images. Using an endurance chamber, we determined the maximum swimming speed of larvae (post-gas bladder inflation) for four to eight weeks post-hatch. For all species, larval swimming speeds showed similar trends with respect to ontogeny: increases in maximum speed, and decreases in routine speed. Maximum speeds of bighead and grass carp larvae were similar and generally faster than silver carp larvae. Routine swimming speeds of all larvae were highest before gas bladder inflation, most likely because gas bladder inflation allowed the fish to maintain position without swimming. Downward vertical velocities of pre-gas bladder inflation fish were faster than upward velocities. Among the three species, grass carp larvae had the highest swimming speeds in the pre-gas bladder inflation period, and the lowest speeds in the post-gas bladder inflation period. Knowledge of swimming capability of these species, along with hydraulic characteristics of a river, enables further refinement of models of embryonic and larval drift.
George et al. (2018) Ontogenetic changes in swimming speed of silver carp, bighead carp, and grass carp larvae: implications for larval dispersal. PeerJ 6:e5869 https://doi.org/10.7717/peerj.5869