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Horseshoe crabs are famous for their blood lysate that is extensively used for the detection of bacterial endotoxin contamination in injectable drugs and medical equipment. However, their existence is now threatened because of overexploitation for bleeding. Synthetic antimicrobial peptides or proteins created by bioengineering may be effective in solving the present predicament. Factor D (FD) is a bioactive substance that shows significant sensitivity to gram-negative bacteria. However, little is known about the expansion information of FD orthologs. In the present study, a total of nine FD orthologs were detected in horseshoe crabs according to the reference genomes. The composition of the FD orthologs in different species was highly conserved, although the common ancestor of the extant horseshoe crabs dates back to the Silurian period. These data suggested that the composition of FD orthologs in horseshoe crabs was formed before the speciation of these species. Considering that three rounds of whole-genome duplication (WGD) events may expanded the homologs in horseshoe crabs, while only one pair of FD orthologs showed significant collinearity according to the intraspecies comparative analysis. Unexpectedly, tandem duplication events that occurred before speciation also expanded the FD orthologs. In addition, several separately distributed FD orthologs also showed high conservation with each other. These data revealed that transposon-mediated duplication may have expanded the FD orthologs in horseshoe crabs. Intriguingly, the C-terminus of the FD orthologs is extremely conserved, although the expansion occurred more than 400 million years ago. In summary, our research provides evidence for the duplication of FD orthologs in horseshoe crabs. Additionally, by demonstrating the conservation of the segments in the C-terminus of these duplicated orthologs, our results also contributed to understanding the functional differentiation mechanism of the diversified FD orthologs. [ABSTRACT FROM AUTHOR]

Vernal pool clam shrimp (Eulimnadia texana) are a promising model system due to their ease of lab culture, short generation time, modest sized genome, a somewhat rare stable androdioecious sex determination system, and a requirement to reproduce via desiccated diapaused eggs. We generated a highly contiguous genome assembly using 46× of PacBio long read data and 216× of Illumina short reads, and annotated using Illumina RNAseq obtained from adult males or hermaphrodites. Of the 120 Mb genome 85% is contained in the largest eight contigs, the smallest of which is 4.6 Mb. The assembly contains 98% of transcripts predicted via RNAseq. This assembly is qualitatively different from scaffolded Illumina assemblies: It is produced from long reads that contain sequence data along their entire length, and is thus gap free. The contiguity of the assembly allows us to order the HOX genes within the genome, identifying two loci that contain HOX gene orthologs, and which approximately maintain the order observed in other arthropods. We identified a partial duplication of the Antennapedia complex adjacent to the few genes homologous to the Bithorax locus. Because the sex chromosome of an androdioecious species is of special interest, we used existing allozyme and microsatellite markers to identify the E. texana sex chromosome, and find that it comprises nearly half of the genome of this species. Linkage patterns indicate that recombination is extremely rare and perhaps absent in hermaphrodites, and as a result the location of the sex determining locus will be difficult to refine using recombination mapping.

Penelope -like elements (PLEs) are an enigmatic clade of retrotransposons whose reverse transcriptases (RTs) share a most recent common ancestor with telomerase RTs. The single ORF of canonical endonuclease (EN)+ PLEs encodes RT and a C-terminal GIY–YIG EN that enables intrachromosomal integration, whereas EN− PLEs lack EN and are generally restricted to chromosome termini. EN+ PLEs have only been found in animals, except for one case of horizontal transfer to conifers, whereas EN− PLEs occur in several kingdoms. Here, we report a new, deep-branching PLE clade with a permuted domain order, whereby an N-terminal GIY–YIG EN is linked to a C-terminal RT by a short domain with a characteristic CxC motif. These N-terminal EN+ PLEs share a structural organization, including pseudo-LTRs and complex tandem/inverted insertions, with canonical EN+ PLEs from Penelope / Poseidon , Neptune , and Nematis clades, and show insertion bias for microsatellites, but lack canonical hammerhead ribozyme motifs. However, their phylogenetic distribution is much broader. The Naiads , found in numerous invertebrate phyla, can reach tens of thousands of copies per genome. In spiders and clams, Naiads independently evolved to encode selenoproteins containing multiple selenocysteines. Chlamys , which lack the CCHH motif universal to PLE ENs, occur in green algae, spike mosses (targeting ribosomal DNA), and slime molds. Unlike canonical PLEs, RTs of N-terminal EN+ PLEs contain the insertion-in-fingers domain (IFD), strengthening the link between PLEs and telomerases. Additionally, we describe Hydra , a novel metazoan C-terminal EN+ clade. Overall, we conclude that PLE diversity, taxonomic distribution, and abundance are comparable with non-LTR and LTR-retrotransposons. [ABSTRACT FROM AUTHOR]

In genetic control programmes, including the sterile insect technique (SIT), it is crucial to release insects of the highest quality with maximum survival. It is likely that male mosquitoes will follow the trend of other insects in SIT programmes and be stored, transported and eventually released under chilled conditions. The aim of our study was to investigate the impact of different chilling temperatures on male Aedes aegypti and Ae. albopictus survival by exposing them to a range of temperatures for different durations. Ae. aegypti were found to be less sensitive to the impact of chilling, with only 6°C causing a marginal decrease in survival in comparison to non-chilled controls. Conversely, Ae. albopictus displayed a significantly reduced survival at all chilling temperatures even when exposed for a short time. In both species, longer exposure to low temperatures reduced survival. Our results uncovered that Ae. albopictus are more sensitive to chilling, regardless of the temperature, when compared to Ae. aegypti. Such results indicate differences in thermal tolerances between species and the necessity of conducting experiments on a species by species basis when determining temperature limits for any insect destined for release as part of a genetic control programme. [ABSTRACT FROM AUTHOR]

Abstract Complete mitochondrial genome (mitogenome) provides important information for better understanding of gene rearrangement, molecular evolution and phylogenetic analysis. Currently, only a few Paguridae mitogenomes have been reported. Herein, we described the complete mitogenome of hermit crab Pagurus nigrofascia. The total length was 15,423 bp, containing 13 protein-coding genes (PCGs), two ribosomal RNA, 22 transfer RNA genes, as well as an AT-rich region. The genome composition was highly A + T biased (71.4%), and exhibited a negative AT-skew (−0.006) and GC-skew (−0.138). Eight tRNA genes, two PCGs and an AT-rich region found to be rearranged with respect to the pancrustacean ground pattern gene order. Duplication-random loss and recombination model were adopted to explain the large-scale gene rearrangement events. Two phylogenetic trees of Anomura involving 12 families were constructed. The results showed that all Paguridae species were clustered into one clade except Pagurus longicarpus , which for the first time imposed raises doubt about the morphological taxonomy of this species. Furthermore, the present study found that higher- level phylogenetic relationships within Anomura were controversial, compared with the previous studies. Our results help to better understand gene rearrangements and the evolutionary status of P. nigrofascia and lay foundation for further phylogenetic study of Anomura. Highlights • Complete mitogenome of P. nigrofascia was described. • Large-scale gene rearrangements were identified. • Possible rearrangement mechanisms were discussed. • Phylogenetic trees showed controversial results. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • Alpine scorpions are highly diverse both at the chromosomal and genetic level. • Ten deeply divergent lineages with discrete geographical distributions were found. • The diversification events took place during the Plio-Pleistocene. • Macrostructural chromosomal changes accompanied the diversification process. Abstract Over time, mountain biota has undergone complex evolutionary histories that have left imprints on its genomic arrangement, geographical distribution and diversity of contemporary lineages. Knowledge on these biogeographical aspects still lags behind for invertebrates inhabiting the Alpine region. In the present study, we examined three scorpion species of the subgenus Euscorpius (Alpiscorpius) from the European Alps using cytogenetic and molecular phylogenetic approaches to determine the variation and population structure of extant lineages at both chromosome and genetic level, and to provide an insight into the species diversification histories. We detected considerable intraspecific variability in chromosome complements and localization of the 18S rDNA loci in all studied species. Such chromosome differences were noticeable as the existence of three [in E. (A.) alpha and E. (A.) germanus ] or four [in E. (A.) gamma ] range-restricted karyotypic races. These races differed from one another either by 2n [in E. (A.) alpha 2n = 54, 60, 90; in E. (A.) gamma 2n = 58, 60, 88, 86–92], or by the karyotypic formula [in E. (A.) germanus 2n = 34m + 12sm; 36m + 10sm; 42m + 4sm]. Using mitochondrial (16S rRNA, COI) and nuclear (28S rDNA) genetic markers, we examined genetic variation and reconstructed phylogenetic relationships among the karyotypic races. Both approaches provided evidence for the existence of ten deeply divergent lineages exhibiting the features of local endemics and indicating the presence of cryptic species. Molecular dating analyses suggest that these lineages diversified during the Plio-Pleistocene and this process was presumably accompanied by dynamic structural changes in the genome organization. [ABSTRACT FROM AUTHOR]

The present investigation reports the occurrence and prevalence of the parasitic cymothoid, Norileca indica infesting bigeyescad, Selar crumenophthalmus from the Andaman Islands. Damage in the form of erosion of gill filament and necrosis in the gill chamber of the host fish, with a prevalence of 26.08% and a mean intensity of 1.5 is recorded. Molecular characterization of the mitochondrial COI and 28S rDNA genes is done to establish its phylogenetic status with its known congener. The present report is the first record of N. indica infesting S. crumenophthalmus from the Andaman Islands. [ABSTRACT FROM AUTHOR]

Comparative endocrinology has traditionally focused on studies of the evolution of endocrine systems, regulation of hormone actions in animals, development of model systems, and the role of the environment in controlling hormone functions related to major life-history events. Comparative endocrinology also has made important contributions to basic research and clinical endocrinology. In recent years there has been a shift to a focus on anthropogenic chemical factors and their alteration of major life history events through endocrine disruption. During the 21st century, environmental comparative endocrinologists must play an important role in the identification and assessment of endocrine disruption on vertebrate and invertebrate animals and their environment as well as in monitoring remediation. All comparative biologists are encouraged to communicate their understanding of threats to biological systems to non-scientists to facilitate their understanding of the human impacts of various kinds of pollution and habitat destruction on wildlife and ecosystems as well as their long-term consequences. [ABSTRACT FROM AUTHOR]

Amblypygi and Schizomida were collected at the private protected area ACP Panguana, located in the primary evergreen lowland rainforest of Amazonian Peru. Through integrative taxonomy, using COI barcoding and morphological determination, all amblypygids could be identified as Heterophrynus elaphus Pocock, 1903, and the schizomids as Surazomus chavin Pinto-da-Rocha, 1996. COI p-distances are provided and DNA sequences were uploaded to BOLD. [ABSTRACT FROM AUTHOR]

Microorganisms, including rotifers, are thought to be capable of long distance dispersal. Therefore, they should show little population genetic structure due to high gene flow. Nevertheless, substantial genetic structure has been reported among populations of many taxa. In rotifers, genetic studies have focused on planktonic taxa leaving sessile groups largely unexplored. Here, we used COI gene and ITS region sequences to study genetic structure and delimit cryptic species in two sessile species (Limnias melicerta [32 populations]; L. ceratophylli [21 populations]). Among populations, ITS region sequences were less variable as compared to those of the COI gene (ITS; L. melicerta: 0–3.1% and L. ceratophylli: 0–4.4%; COI; L. melicerta: 0–22.7% and L. ceratophylli: 0–21.7%). Moreover, L. melicerta and L. ceratophylli were not resolved in phylogenetic analyses based on ITS sequences. Thus, we used COI sequences for species delimitation. Bayesian Species Delimitation detected nine putative cryptic species within L. melicerta and four putative cryptic species for L. ceratophylli. The genetic distance in the COI gene was 0–15.4% within cryptic species of L. melicerta and 0.5–0.6% within cryptic species of L. ceratophylli. Among cryptic species, COI genetic distance ranged 8.1–21.9% for L. melicerta and 15.1–21.2% for L. ceratophylli. The correlation between geographic and genetic distance was weak or lacking; thus geographic isolation cannot be considered a strong driver of genetic variation. In addition, geometric morphometric analyses of trophi did not show significant variation among cryptic species. In this study we used a conservative approach for species delimitation, yet we were able to show that species diversity in these sessile rotifers is underestimated. [ABSTRACT FROM AUTHOR]

More than 70 species of the Superfamily Paramphistomoidea, have been identified in ruminants in different parts of the world. Most are pathogenic, causing amphistomosis. Adult flukes within this family have a predilection for the forestomach (rumen) or bile duct of the liver, where they may cause epithelial damage. Identification of adult Paramphistomum , Calicophoron , Gastrothylax and Fischoederius at the species level based on morphology requires specialised expertise, whereas molecular genetic marker analysis is more precise and transferable. In the present study, we performed molecular characterisation of twenty seven adult flukes collected from the forestomachs of buffalo, cattle and goats in the Punjab province of Pakistan. PCR and sequencing of the ITS-2 rDNA region revealed a single haplotype in all cases. Phylogenetic comparison of P. epiclitum ITS2-rDNA sequences with those from other Paramphistomum , Calicophoron , Gastrothylax and Fischoederius species was performed to assess within and between species variation and validate the use of ITS-2 rDNA as a robust species-specific marker for P. epiclitum identification . This work provides a validated species-specific marker of P. epiclitum and the first report of this parasite species from Pakistan. The results of this study also have implications for the diagnosis and control of rumen flukes in the region and the need for accurate species identification to understand parasite distribution and population genetics. [ABSTRACT FROM AUTHOR]

RNA interference (RNAi) is the major antiviral defense mechanism of plants and invertebrates, rendering the capacity to evade it a defining factor in shaping the viral landscape. Here we sought to determine whether different virus replication strategies provided any inherent capacity to evade RNAi in the absence of an antagonist. Through the exploitation of host microRNAs, we recreated an RNAi-like environment in vertebrates and directly compared the capacity of positive- and negative-stranded RNA viruses to cope with this selective pressure. Applying this defense against four distinct viral families revealed that the capacity to undergo homologous recombination was the defining attribute that enabled evasion of this defense. Independent of gene expression strategy, positive-stranded RNA viruses that could undergo strand switching rapidly excised genomic material, while negative-stranded viruses were effectively targeted and cleared upon RNAi-based selection. These data suggest a dynamic relationship between host antiviral defenses and the biology of virus replication in shaping pathogen prevalence. [ABSTRACT FROM AUTHOR]

Abstract: Mammals are mainly exposed to trace metals (TMs) via consuming contaminated food. Several studies have demonstrated relationships between metal concentrations in food and in animal tissues. However, potential effects of TMs on feeding behaviour of wildlife have been poorly documented under field conditions, despite experimental evidence showing that food selection is impacted by resource contamination. Here, we test the hypothesis that the diet of a generalist rodent, the wood mouse (Apodemus sylvaticus), is altered by soil TM contamination in the field. Wood mice were sampled in spring and in autumn along a gradient of soil contamination in the surroundings of a former smelter located in northern France. Available resources in the field were inventoried, and the diet of the animals was analysed using DNA “metabarcoding.” We demonstrated that (a) relationship between the resource richness in the diet and their richness in the field was altered by soil metal contamination. Wood mice specialized their diet along the gradient of soil metal contamination for both plant and invertebrate resources in spring. We also showed that (b) preference for Salicaceae, a plant family accumulating metals, decreased when soil contamination increased. These results suggest that environmental TM pollution could act as a force modulating trophic interactions in terrestrial food webs, thereby affecting wildlife exposure to contaminants by trophic route. [ABSTRACT FROM AUTHOR]

Abstract Complexity in physical habitats may modify predation pressure by allowing differential access of predators to prey. Rocky subtidal environments are inherently complex with many cryptic micro habitats, such as overhangs and crevices. Here, we examine the influence of habitat complexity in mediating predation on sessile assemblage structure by experimentally manipulating fish access to a range of crevice orientations and sizes. Nine fish species/families were recorded actively feeding within crevices, but australian mado, eastern stripey, wrasses and sawtail surgeon accounted for almost 70% of all entries. Sessile assemblages were influenced by crevice width, fish predation and surface orientation, with more predation activity in larger crevices. Assemblage similarity on upward facing surfaces decreased as crevice width increased. While assemblage structure on downward and vertical surfaces was influenced by crevice width and caging separately. Thus, crevice size and orientation are important habitat complexity features that act to partition predation pressure. This may allow distinct sessile assemblages to persist, even when predation can be intense. Graphical abstract Image 1 Highlights • Fish predation affects sessile hard-substrate assemblages. • We used video observation and experimental predator exclusion. • Predation pressure is mediated by crevice size and orientation. • Habitat complexity partitions sessile invertebrate community diversity. • Crevice size and orientation are important features of rocky-reef habitat. [ABSTRACT FROM AUTHOR]

Extracellular traps (ETs), web-like structures composed of DNA and histones, are released by innate immune cells in a wide range of organisms. ETs capture microorganisms, thereby avoiding their spread, and also concentrate antimicrobial molecules, which helps to kill microbes. Although vertebrate innate immune systems share homology with the insect immune system, ETosis have yet to be characterized in insects. Here, we report that the hemocytes of the hemimetabolous insect Periplaneta americana release ETs upon in vitro stimulation. We further discuss the relationship between ETs and nodulation and in controlling bacterial spread in vivo . [ABSTRACT FROM AUTHOR]

The marine isopod genus Limnoria contains algae-eating species. Previous phylogeographic studies have suggested that Limnoria species feeding on buoyant kelp underwent low genetic differentiation on a large spatial scale because rafting on floating host kelps promotes high levels of gene flow. In this paper, we survey the genetic structure of Limnoria nagatai, which bores into the non-buoyant kelps Eisenia bicyclis and E. arborea. We analyze the mitochondrial DNA (cytochrome oxidase subunit I [COI] gene) and morphological traits of L. nagatai, and the host kelps E. bicyclis and E. arborea from 14 populations along the Japanese archipelago of the Pacific Ocean and the Sea of Japan. Four major lineages are recognized within L. nagatai: three lineages in the Pacific Ocean, and one lineage in the Sea of Japan which might be a cryptic species. For L. nagatai, we show high genetic differentiation between geographically separated habitats in the Pacific Ocean, while low differentiation is found among continuous host kelps habitats in the Pacific Ocean as well as the Sea of Japan. L. nagatai in E. bicyclis in the Pacific Ocean has experienced large population expansion after the Last Glacial Maximum (LGM), whereas the lineage in E. bicyclis in the Sea of Japan has not. We suggest that Limnoria feeding on non-buoyant kelps, may attain low genetic differentiation because they might be able to disperse long distance if the habitat of host kelps is continuous. The historical events affecting Limnoria after the LGM may differ between the coasts of the Pacific Ocean and the Sea of Japan. [ABSTRACT FROM AUTHOR]

Abstract: A number of horizontal gene transfers (HGTs) have been identified in the spider mite Tetranychus urticae, a chelicerate herbivore. However, the genome of this mite species has at present not been thoroughly mined for the presence of HGT genes. Here, we performed a systematic screen for HGT genes in the T. urticae genome using the h‐index metric. Our results not only validated previously identified HGT genes but also uncovered 25 novel HGT genes. In addition to HGT genes with a predicted biochemical function in carbohydrate, lipid and folate metabolism, we also identified the horizontal transfer of a ketopantoate hydroxymethyltransferase and a pantoate β‐alanine ligase gene. In plants and bacteria, both genes are essential for vitamin B5 biosynthesis and their presence in the mite genome strongly suggests that spider mites, similar to Bemisia tabaci and nematodes, can synthesize their own vitamin B5. We further show that HGT genes were physically embedded within the mite genome and were expressed in different life stages. By screening chelicerate genomes and transcriptomes, we were able to estimate the evolutionary histories of these HGTs during chelicerate evolution. Our study suggests that HGT has made a significant and underestimated impact on the metabolic repertoire of plant‐feeding spider mites. [ABSTRACT FROM AUTHOR]

Abstract: Biologists frequently sort specimen‐rich samples to species. This process is daunting when based on morphology, and disadvantageous if performed using molecular methods that destroy vouchers (e.g., metabarcoding). An alternative is barcoding every specimen in a bulk sample and then presorting the specimens using DNA barcodes, thus mitigating downstream morphological work on presorted units. Such a “reverse workflow” is too expensive using Sanger sequencing, but we here demonstrate that is feasible with an next‐generation sequencing (NGS) barcoding pipeline that allows for cost‐effective high‐throughput generation of short specimen‐specific barcodes (313 bp of COI; laboratory cost <$0.50 per specimen) through next‐generation sequencing of tagged amplicons. We applied our approach to a large sample of tropical ants, obtaining barcodes for 3,290 of 4,032 specimens (82%). NGS barcodes and their corresponding specimens were then sorted into molecular operational taxonomic units (mOTUs) based on objective clustering and Automated Barcode Gap Discovery (ABGD). High diversity of 88–90 mOTUs (4% clustering) was found and morphologically validated based on preserved vouchers. The mOTUs were overwhelmingly in agreement with morphospecies (match ratio 0.95 at 4% clustering). Because of lack of coverage in existing barcode databases, only 18 could be accurately identified to named species, but our study yielded new barcodes for 48 species, including 28 that are potentially new to science. With its low cost and technical simplicity, the NGS barcoding pipeline can be implemented by a large range of laboratories. It accelerates invertebrate species discovery, facilitates downstream taxonomic work, helps with building comprehensive barcode databases and yields precise abundance information. [ABSTRACT FROM AUTHOR]

Abstract: Wildlife detection in urban areas is very challenging. Conventional monitoring techniques such as direct observation are faced with the limitation that urban wildlife is extremely elusive. It was recently shown that invertebrate‐derived DNA (iDNA) can be used to assess wildlife diversity in tropical rainforests. Flies, which are ubiquitous and very abundant in most cities, may also be used to detect wildlife in urban areas. In urban ecosystems, however, overwhelming quantities of domestic mammal DNA could completely mask the presence of wild mammal DNA. To test whether urban wild mammals can be detected using fly iDNA, we performed DNA metabarcoding of pools of flies captured in Berlin, Germany, using three combinations of blocking primers. Our results show that domestic animal sequences are, as expected, very dominant in urban environments. Nevertheless, wild mammal sequences can often be retrieved, although they usually only represent a minor fraction of the sequence reads. Fly iDNA metabarcoding is therefore a viable approach for quick scans of urban wildlife diversity. Interestingly, our study also shows that blocking primers can interact with each other in ways that affect the outcome of metabarcoding. We conclude that the use of complex combinations of blocking primers, although potentially powerful, should be carefully planned when designing experiments. [ABSTRACT FROM AUTHOR]

Ototyphlonemertes is a cosmopolitan genus of meiofaunal nemerteans. Their morphological characters are insufficient to reliably identify and delimit species. Consequently, some of the species are considered cosmopolitan despite anticipated low dispersion capability of the adults and a short planktonic larval phase. Indeed, recent studies show that some species actually comprise cryptic species, and populations are connected by stochastic events of long-distance dispersion. Based solely on morphological traits, a Lactea and a Pallida morph of Ototyphlonemertes are recognized here from collections at eight and five locations respectively along the Chilean coast. To assess the phylogeographic patterns of their populations, two mitochondrial markers (COI and COX3) of 162 specimens of Lactea and 25 of Pallida were sequenced. Final sequences are 605bp and 362bp for COI and COX3, respectively. Results from phylogenetic and haplotype network analyses suggest that the Lactea morph comprises up to three independent evolutionary units (one with only COX3 sequences). A COI gene tree including other previously published Ototyphlonemertes sequences groups the Chilean Lactea with other Lactea, while the Chilean Pallida is grouped with other Pallida. Different structuring and gene flow patterns found for the four groups support the hypothesis that these are four independent evolutionary entities with different ecological, dispersal and demographical characteristics. [ABSTRACT FROM AUTHOR]

The banded coral shrimp, Stenopus hispidus (Crustacea: Decapoda: Stenopodidea) is a popular marine ornamental species with a circumtropical distribution. The planktonic larval stage lasts ~120-253 days, indicating considerable dispersal potential, but few studies have investigated genetic connectivity on a global scale in marine invertebrates. To resolve patterns of divergence and phylogeography of S. hispidus, we surveyed 525 bp of mitochondrial cytochrome c oxidase subunit I (COI) from 198 individuals sampled at 10 locations across ~27,000 km of the species range. Phylogenetic analyses reveal that S. hispidus has a Western Atlantic lineage and a widely distributed Indo-Pacific lineage, separated by sequence divergence of 2.1%. Genetic diversity is much higher in the Western Atlantic (h = 0.929; π =0.004) relative to the Indo-Pacific (h = 0.105; π <0.001), and coalescent analyses indicate that the Indo-Pacific population expanded more recently (95% HPD (highest posterior density) = 60,000-400,000 yr) than the Western Atlantic population (95% HPD = 300,000-760,000 yr). Divergence of the Western Atlantic and Pacific lineages is estimated at 710,000-1.8 million years ago, which does not readily align with commonly implicated colonization events between the ocean basins. The estimated age of populations contradicts the prevailing dispersal route for tropical marine biodiversity (Indo-Pacific to Atlantic) with the oldest and most diverse population in the Atlantic, and a recent population expansion with a single common haplotype shared throughout the vast Indian and Pacific oceans. In contrast to the circumtropical fishes, this diminutive reef shrimp challenges our understanding of conventional dispersal capabilities of marine species. [ABSTRACT FROM AUTHOR]

The relative roles of ecological niche conservatism versus niche divergence in promoting montane speciation remains an important topic in biogeography. Here, our aim was to test whether lineage diversification in a species complex of trapdoor spiders corresponds with riverine barriers or with an ecological gradient associated with elevational tiering. Aliatypus janus was sampled from throughout its range, with emphasis on populations in the southern Sierra Nevada Mountains of California. We collected multi-locus genetic data to generate a species tree for A. janus and its close relatives. Coalescent based hypothesis tests were conducted to determine if genetic breaks within A . janus conform to riverine barriers. Ecological niche models (ENM) under current and Last Glacial Maximum (LGM) conditions were generated and hypothesis tests of niche conservatism and divergence were performed. Coalescent analyses reveal deeply divergent genetic lineages within A . janus , likely corresponding to cryptic species. Two primary lineages meet along an elevational gradient on the western slopes of the southern Sierra Nevada Mountains. ENMs under both current and LGM conditions indicate that these groups occupy largely non-overlapping niches. ENM hypothesis testing rejected niche identity between the two groups, and supported a sharp ecological gradient occurring where the groups meet. However, the niche similarity test indicated that the two groups may not inhabit different background niches. The Sierra Nevada Mountains provide a natural laboratory for simultaneously testing ecological niche divergence and conservatism and their role in speciation across a diverse range of taxa. Aliatypus janus represents a species complex with cryptic lineages that may have diverged due to parapatric speciation along an ecological gradient, or been maintained by the evolution of ecological niche differences following allopatric speciation. [ABSTRACT FROM AUTHOR]

Epigenetic mechanisms can stably maintain gene expression states even after the initiating conditions have changed. Often epigenetic information is transmitted only to daughter cells, but evidence is emerging, in both vertebrate and invertebrate systems, for transgenerational epigenetic inheritance (TEI), the transmission of epigenetic gene regulatory information across generations. Each new description of TEI helps uncover the properties, molecular mechanisms and biological roles for TEI. The nematode Caenorhabditis elegans has been particularly instrumental in the effort to understand TEI, as multiple environmental and genetic triggers can initiate an epigenetic signal that can alter the expression of both transgenes and endogenous loci. Here, we review recent studies of TEI in C. elegans . [ABSTRACT FROM AUTHOR]

Apoptosis is orchestrated by a family of cysteine proteases known as the caspases, and caspase3 is the primary executioner caspase in the apoptosis. In the present study, the potential role of caspase3 was investigated under the exposure to high temperature and elevated ammonium in stony coral Pocillopora damicornis . The cDNA of a caspase3 (PdCaspase3) was identified to encode a polypeptide of 344 amino acids, and the encoded protein contained one CASc domain (Caspase, interleukin-1 beta converting enzyme homologues, from Val76 to Asn333). The recombinant protein of the mature PdCaspase3 was expressed in Escherichia coli BL21 (DE3)-Transetta, and it displayed caspase3-like activity which catalyzed the reaction of DEVD-p-nitroanilide cleavage. The expression level of PdCaspase3 mRNA increased significantly at 24 h after acute heat stress and 12 h after acute ammonium stress, reached 2.28-fold ( P < 0.05) and 1.76-fold ( P < 0.05) of that in the blank group, respectively. The activation level of caspase3 began to increase at 12 h (1.41-fold, P < 0.05), and reached the peak at 24 h (1.54-fold, P < 0.05) after acute heat stress. Furthermore, the activation level of caspase3 increased significantly during 6–24 h, with the highest level at 24 h (1.44-fold, P < 0.05) after acute ammonium stress. These results collectively suggested that PdCaspase3, as a homologue of caspase3, was involved in the response to high temperature and elevated ammonium, which might further regulate the symbiosis between the host and zooxanthellae in the stony coral P. damicornis . [ABSTRACT FROM AUTHOR]

A phylogenetic analysis of Polycladida based on two partial mitochondrial genes ( cox1 and 16S) is provided. The analysis includes 30 polyclad terminals that represent species from the two taxa which traditionally divide the groups Cotylea and Acotylea. Our phylogenetic analyses produced a well-supported hypothesis that confirms the monophyly of Polycladida, as well as Acotylea and Cotylea. Within Acotylea, there are two lineages not highly supported: on one hand, Leptoplanoidea (excluding Hoploplana elisabelloi) and one Stylochoidea member ( Pseudostylochus intermedius) (classification sensu Faubel, 1983, 1984), and on the other hand, Stylochoidea members together with Discocelis tigrina and H. elisabelloi. The genera Stylochus and Imogine are not monophyletic. Within Cotylea, Pseudocerotidae and Euryleptidae are monophyletic, though not highly supported, while Prosthiostomidae is not. Euryleptoidea is paraphyletic. The genera Pseudobiceros and Pseudoceros are monophyletic and highly supported. Our results suggest that, within Acotylea, the prostatoid organs of Discocelis may have been derived from a prostatic vesicle. The genus Hoploplana could be included in Stylochoidea. Within Cotylea, the common ancestor of Euryleptidae and Pseudocerotidae might have been an aposematic animal with tentacles. [ABSTRACT FROM AUTHOR]

Facultative sexual species employ a dual reproductive strategy (heterogony) comprising primarily asexual reproduction with intermittent sexual reproduction. Given the higher relative costs of sexual reproduction, elucidating the triggers underlying these transitions might help our understanding of the evolution of (obligate) sex in general. Existing hypotheses into how and when facultative sexuals invest into sex focus largely either on environmental (habitat-deterioration and resource-demanding hypotheses) or genetic factors (condition-dependent hypothesis), but tend to lack experimental evidence, especially with respect to within-population variation. To address this deficit, we examined the influence of several variables that potentially affect fitness (food quality, water temperature, physiological acclimation, and all combinations thereof) on both the lifetime reproduction (total number of offspring) and investment into sexual offspring per female in a clonal population of the monogonont rotifer Brachionus rubens. Investment into sex, both absolutely and relative to lifetime reproduction, was tied most closely to and positively correlated with individual fitness (i.e., lifetime reproduction): individuals with higher fitness invested more into sexual reproduction. These results run contra to the condition-dependent hypothesis and indicate an energy-budget analogue of the resource-demanding hypothesis. Furthermore, investment into sex increased after a period of physiological acclimation to the new conditions, probably because of the amelioration of short-term stress effects or clonal selection. Our results underscore that life history and general phenotypic considerations-here, energetic provisioning of offspring, the presence of a sexual resting stage, and the relative timing of sexual versus asexual reproduction-can modify existing hypotheses based either on environmental or genetic factors alone. [ABSTRACT FROM AUTHOR]

Genetic and morphological analysis of endemic sponges of the Lubomirskiidae family from Lake Baikal and the upper reaches of the Angara River was performed. Various sponge species acquired a number of similar morphological traits after the transition from the lake into the river. These traits enabled an increase of sponge skeleton strength under the conditions of elevated hydrodynamic activity. The changes significantly impeded morphology-based species identification of Angara sponges. Phylogenetic analysis of ITS regions and noncoding mitochondrial DNA fragments confirmed that the Angara sponges belonged to the Baikalian Lubomirskiidae family and demonstrated the polyphyletic origin of the sponges. The use of combined molecular and morphological data allowed for the clustering of some sponge samples into groups that corresponded to individual species. The absence of genetic isolation between the Baikalospongia intermedia and Lubomirskia baicalensis species was demonstrated, whereas the B. intermedia profundalis subspecies was well separated from B. intermedia. This finding pointed to the necessity of further studies for the clarification of the taxonomic status of this subspecies. [ABSTRACT FROM AUTHOR]

Ticks endure stressful off-host periods and perform as vectors of a diversity of infectious agents, thus engaging pathways that expectedly demand for autophagy. Little is known of ticks' autophagy, a conserved eukaryotic machinery assisting in homeostasis processes that also participates in tissue-dependent metabolic functions. Here, the autophagy-related ATG4 (autophagin-1), ATG6 (beclin-1) and ATG8 (LC3) mRNAs from the human diseases vector Amblyomma sculptum and the cattle-tick Rhipicephalus microplus were identified. Comparative qPCR quantifications evidenced different transcriptional status for the ATG genes in the salivary glands (SG), ovaries and intestines of actively feeding ticks. These ATGs had increased relative transcription under nutrient-deprivation, as determined by validation tests with R. microplus embryo-derivative cells BME26 and A. sculptum SG explants incubations in HBSS. Starvation lead to 4-31.8× and ~ 60-500× increments on the ATGs mRNA loads in BME26 and A. sculptum SG explants, respectively. PI3K inhibitor 3MA treatment also affected ATGs expression in BME26. Some ATGs were more transcribed in the SGs than in the ovaries of cattle-ticks. Amblyomma sculptum/ R. microplus interspecific comparisons showed that ATG4 and ATG6 were 0.18× less expressed in A. sculptum SGs, but ~ 10-100× more expressed in their ovaries when compared to R. microplus organs. ATG4 and ATG8a transcript loads were ~ 120× and ~ 40× higher, respectively, in A. sculptum intestines when compared to cattle-ticks of similar weight category. ATGs expression in A. sculptum intestines increased with tick weight, indicating Atgs contribution to intracellular blood digestion. Possible roles of the autophagy machinery and their organ-specific expression profile on vector biology are discussed. [ABSTRACT FROM AUTHOR]

“Filariasis free India” is National Health Policy’s vision. Currently, India has undertaken Mass Drug Administration drive (MDA) to eliminate the filariasis infection. Taking this into account, the emergence of new Wuchereria bancrofti resistant strains against the current choice of drugs cannot be ruled out. In this study, we report the genetic diversity of Wuchereria bancrofti from four districts (Amravati, Nagpur, Chandrapur and Wardha) of Vidarbha, a region in the eastern part of Maharashtra state of India and considered a hot spot of filariasis infections. The RAPD profiles were generated for 21 populations using nine random RAPD primers. The RAPD- PCR based distance matrix shows maximum genetic distance of 0.425 between the parasites from Nagpur and Amravati region and minimum genetic distance of 0.210 between the parasites of Wardha and Nagpur. The tree inferred by Neighbour-Joining (NJ) method shows four distinct clusters. With the single exception of isolates from Amravati, all other clusters show the intermingling of isolates with other districts. Further, the representation of isolates from Chandrapur in three out of four clusters revealed to be a founder and indicates towards the entry of the filarial worm into the Maharashtra state through southern route. [ABSTRACT FROM AUTHOR]

Sampling in the deep sea is a technical challenge, which has hindered the acquisition of robust datasets that are necessary to determine the fine-grained biological patterns and processes that may shape genetic diversity. Estimates of the extent of clonality in deep-sea species, despite the importance of clonality in shaping the local dynamics and evolutionary trajectories, have been largely obscured by such limitations. Cold-water coral reefs along European margins are formed mainly by two reef-building species, Lophelia pertusa and Madrepora oculata . Here we present a fine-grained analysis of the genotypic and genetic composition of reefs occurring in the Bay of Biscay, based on an innovative deep-sea sampling protocol. This strategy was designed to be standardized, random, and allowed the georeferencing of all sampled colonies. Clonal lineages discriminated through their Multi-Locus Genotypes (MLG) at 6–7 microsatellite markers could thus be mapped to assess the level of clonality and the spatial spread of clonal lineages. High values of clonal richness were observed for both species across all sites suggesting a limited occurrence of clonality, which likely originated through fragmentation. Additionally, spatial autocorrelation analysis underlined the possible occurrence of fine-grained genetic structure in several populations of both L. pertusa and M. oculata . The two cold-water coral species examined had contrasting patterns of connectivity among canyons, with among-canyon genetic structuring detected in M. oculata , whereas L. pertusa was panmictic at the canyon scale. This study exemplifies that a standardized, random and georeferenced sampling strategy, while challenging, can be applied in the deep sea, and associated benefits outlined here include improved estimates of fine grained patterns of clonality and dispersal that are comparable across sites and among species. [ABSTRACT FROM AUTHOR]

Collembola are an important group of indigenous terrestrial invertebrates in the sub-Antarctic region and, compared to the most continental regions, their limited diversity is well known. Several invasive species, introduced by humans, have also established in the region, with some of these widespread while others are more restricted to disturbed areas. In this study, we report the spread of two non-indigenous Collembola species on Macquarie Island. Protaphorura fimata (Gisin, 1952) (Collembola:Poduromorpha:Onychiuridae) and Proisotoma minuta (Tullberg, 1871) (Entomobryomorpha:Isotomidae) are both cosmopolitan species that have been present on the island for several decades, but restricted to the area around the research station. Here, we report their spread up to 3 and 11 km, respectively, from the research station. We discuss the implications of this finding for biosecurity across the Antarctic region. We also document the presence of a new non-indigenous species, Parisotoma notabilis (Schäffer, 1896) (Entomobryomorpha:Isotomidae). [ABSTRACT FROM AUTHOR]

miR-92a, a well-documented oncogene, was previously found to be differentially expressed in diseased sea cucumber Apostichopus japonicus by high-throughput sequencing. In this study, we identified Aj14-3-3ζ as a novel target of miR-92a in this species and investigated their regulatory roles in vivo . The negative expression profiles between miR-92a and Aj14-3-3ζ protein were detected in both LPS-exposed primary coelomocytes and Vibrio splendidus -challenged sea cucumbers. Over-expression of miR-92a by injection of miR-92a agomir significantly depressed the mRNA and protein expression of Aj14-3-3ζ and promoted coelomocytes apoptosis with 5.04-fold increase in vivo , which was consistent with those from siRNA-mediated Aj14-3-3ζ knockdown assay. In contrast, miR-92a antagomir significantly elevated the mRNA and protein expression of Aj14-3-3ζ and decreased coelomocytes apoptosis. Taken together, our result confirmed that miR-92a is involved in apoptotic signaling pathway regulation perhaps via targeting Aj14-3-3ζ in sea cucumbers, which will enhance our understanding of miR-92a regulatory roles in sea cucumber pathogenesis. [ABSTRACT FROM AUTHOR]

Tumor necrosis factor (TNF)-α-induced protein 8 (TNFAIP8) family is a newly identified protein with vital roles in maintaining immune homeostasis. In the current study, we first cloned and characterized a TNFAIP8 gene from the invertebrate sea cucumber Apostichopus japonicus . The gene was designated as AjTNFAIP8 . The full-length cDNA of AjTNFAIP8 was 1455 bp long and encoded a matured protein of 201 amino acid residues. Structural analysis indicated that AjTNFAIP8 had a death effector domain (DED)-like domain and composed of six α-helices. Multiple sequence alignment and phylogenetic analysis supported that AjTNFAIP8 is a new member of the TNFAIP8 family. Analysis of basal transcription in five tissues revealed the constitutive expression of AjTNFAIP8 in the detected tissues with highest expression in the respiratory tree and minimum expression in the tentacle. Vibrio splendidus infection and LPS stimulation could significantly downregulate the mRNA expression of AjTNFAIP8 . More importantly, the transcription of pro-inflammatory molecule NOS and its production of NO content were significantly increased after AjTNFAIP8 silencing, with the suppression of agmatinase transcript and arginase activity. These results clearly indicated that AjTNFAIP8 is an essential negative regulator in innate immunity. Basic information for further exploration of the functional mechanisms of TNFAIP8 family in other marine invertebrate is provided. [ABSTRACT FROM AUTHOR]

Despite the deep sea being the largest habitat on Earth, there are just 77 population genetic studies of invertebrates (115 species) inhabiting non-chemosynthetic ecosystems on the deep-sea floor (below 200 m depth). We review and synthesize the results of these papers. Studies reveal levels of genetic diversity comparable to shallow-water species. Generally, populations at similar depths were well connected over 100s-1,000s km, but studies that sampled across depth ranges reveal population structure at much smaller scales (100s-1,000s m) consistent with isolation by adaptation across environmental gradients, or the existence of physical barriers to connectivity with depth. Few studies were ocean-wide (under 4%), and 48% were Atlantic-focused. There is strong emphasis on megafauna and commercial species with research into meiofauna, 'ecosystem engineers' and other ecologically important species lacking. Only nine papers account for ~50% of the planet's surface (depths below 3,500 m). Just two species were studied below 5,000 m, a quarter of Earth's seafloor. Most studies used single-locus mitochondrial genes revealing a common pattern of non-neutrality, consistent with demographic instability or selective sweeps; similar to deep-sea hydrothermal vent fauna. The absence of a clear difference between vent and non-vent could signify that demographic instability is common in the deep sea, or that selective sweeps render single-locus mitochondrial studies demographically uninformative. The number of population genetics studies to date is miniscule in relation to the size of the deep sea. The paucity of studies constrains meta-analyses where broad inferences about deep-sea ecology could be made. [ABSTRACT FROM AUTHOR]

Molecular analyses of the ecologically important gorgonian octocoral genus Leptogorgia are scant and mostly deal with few species from restricted geographical regions. Here we explore the phylogenetic relationships and the evolutionary history of Leptogorgia using the complete mitochondrial genomes of six Leptogorgia species from different localities in the Atlantic, Mediterranean and eastern Pacific as well as four other genera of Gorgoniidae and Plexauridae. Our mitogenomic analyses showed high inter-specific diversity, variable nucleotide substitution rates and, for some species, novel genomic features such as ORFs of unknown function. The phylogenetic analyses using complete mitogenomes and an extended mtMutS dataset recovered Leptogorgia as polyphyletic, and the species considered in the analyses were split into two defined groups corresponding to different geographic regions, namely the eastern Pacific and the Atlantic-Mediterranean. Our phylogenetic analysis based on mtMutS also showed a clear separation between the eastern Atlantic and South African Leptogorgia , suggesting the need of a taxonomic revision for these forms. A time-calibrated phylogeny showed that the separation of eastern Pacific and western Atlantic species started ca. 20 Mya and suggested a recent divergence for eastern Pacific species and for L. sarmentosa-L. capverdensis . Our results also revealed high inter-specific diversity among eastern Atlantic and South African species, highlighting a potential role of the geographical diversification processes and geological events occurring during the last 30 Ma in the Atlantic on the evolutionary history of these organisms. [ABSTRACT FROM AUTHOR]

Inflammatory/defensive response after pathogen invasion is considered a local defense reaction in vertebrates. Inflammation response in Apostichopus japonicus was hardly determined due to scarce information available for nucleotide binding domain-like receptor family, pyrin domain-containing (NLRP) family. In the present study, invertebrate NLRP homologue was identified from A. japonicus (designated as AjNLRP3-like ) by rapid amplification of cDNA ends. Full-length cDNA of AjNLRP3-like measured 2970 bp with 2265 bp open reading frame encoding a 754-amino acid (aa) residue protein. Structural analysis revealed that AjNLRP3-like processed characteristic domains of pyrin (32–102aa) and NACHT (183–339aa). Multiple sequence alignment and phylogenetic analysis supported that AjNLRP3-like belongs to a new member of NLRP3 protein subfamily. Spatial expression analysis revealed that AjNLRP3-like was ubiquitously expressed in all examined tissues with larger magnitude in coelomocytes. Both Vibrio splendidus challenge in vivo and lipopolysaccharide stimulation in vitro significantly upregulated mRNA expression of AjNLRP3-like when compared with the control group. NLRP3-mediated inflammation response depended on release of lysosomal cathepsin B (CTSB) and subsequent activation of high-mobility group box (HMGB) in vertebrates. We investigated expression profiles of AjNLRP3-like and AjHMGB after AjCTSB knock-down and discovered that AjNLRP3-like was depressed by 0.66-fold and 0.47-fold, whereas AjHMGB was depressed by 0.70-fold and 0.50-fold at 24 and 48 h in AjCTSB -silenced group, respectively. Similarly, down-regulation of AjHMGB was also observed after AjNLRP3-like knock-down. This study therefore suggests that A. japonicus feature similar inflammatory events as those in vertebrates, and activation of AjNLRP3-like depends on AjCTSB expression and release of AjHMGB . [ABSTRACT FROM AUTHOR]

The large American liver fluke, Fascioloides magna , is an economically relevant parasite of both domestic and wild ungulates. F. magna was repeatedly introduced into Europe, for the first time already in the 19th century. In Austria, a stable population of F. magna has established in the Danube floodplain forests southeast of Vienna. The aim of this study was to determine the genetic diversity of F. magna in Austria. A total of 26 individuals from various regions within the known area of distribution were investigated for their cytochrome oxidase subunit 1 ( cox1 ) and nicotinamide dehydrogenase subunit 1 ( nad1 ) gene haplotypes. Interestingly, all 26 individuals revealed one and the same haplotype, namely concatenated haplotype Ha5. This indicates a homogenous population of F. magna in Austria and may argue for a single introduction. Alternatively, genetic homogeneity might also be explained by a bottleneck effect and/or genetic drift. [ABSTRACT FROM AUTHOR]

Marine ectotherms inhabiting intertidal and shallow subtidal environments are continuously exposed to diurnal tidal cycles and seasonal variability in temperature. These organisms have adaptive mechanisms to maintain cellular homeostasis, irrespective of thermal environmental variation. In this study, we describe the molecular responses to thermal stress in the edible sea urchin Loxechinus albus . In particular, we determined the differential expression of a set of molecular markers that have been identified as targets of stress-related responses. These include the heat shock proteins ( hsp70 and hsp90 ), cell detoxification proteins ( cytochrome P450 ), and osmorregulatory proteins ( α and ß - Na + /K + ATPase ). We exposed individuals to different temperatures; a warm treatment (18±1.0 °C), a cold treatment (10±1.0 °C), and a control treatment (average local temperature of 14±1.0 °C) and differential expression was quantified after 2, 6, 12 and 48 h of exposure. Levels of mRNA were quantified by reverse transcription-quantitative polymerase chain reaction, and the relative expression of each gene was calculated using the 18S rRNA gene as a reference, and the control treatment as a calibrator. We found that the expression levels of all studied genes increased during exposure to warmth. The largest increase in expression was observed in cytochrome p450 genes (ca. sixteen-fold); this was followed by increases in the expression of the Na + /K + ATPase (ca. eight-fold) and by the hsp (ca. six fold) genes. These results indicate that sea urchin thermal stress responses depend on differential gene-regulation, involving heat-shock, membrane potential, and detoxification genes that generate an integrated adaptive response to acute environmental changes. [ABSTRACT FROM AUTHOR]

Recent studies have highlighted that the accidental acquisition of DNA from other species by invertebrate genomes is much more common than originally thought. The transferred DNAs are of bacterial or eukaryote origin and in both cases the receiver species may end up utilising the transferred genes for its own benefit. Frequent contact with prokaryotic DNA from symbiotic endocellular bacteria may predispose invertebrates to incorporate this genetic material into their genomes. Increasing evidence also points to viruses as major players in transferring genes and mobile elements between the species they infect. Unexpectedly a gene flux between Hymenoptera and Lepidoptera mediated by endogenous viruses of parasitic wasps has been recently unravelled, suggesting we are probably just seeing the tip of the iceberg concerning horizontal gene transfers in invertebrates. In the context of insect for feed and food, if the new technology of insect genome editing (such as Crisper/Cas9) were used to modify the genome of reared insects it is important to take into account the risk that an introduced gene can be transferred. More generally, although insects are traditionally consumed in Asia and Africa, knowledge on insect viruses is still limited rendering it difficult to predict the impact they might have in the context of insect rearing at an industrial scale. [ABSTRACT FROM AUTHOR]

Arachnida is an ancient, diverse and ecologically important animal group that contains a number of species of interest for medical, agricultural and engineering applications. Despite their importance, many aspects of the arachnid tree of life remain unresolved, hindering comparative approaches to arachnid biology. Biologists have made considerable efforts to resolve the arachnid phylogeny; yet, limited and challenging morphological characters, as well as a dearth of genetic resources, have hindered progress. Here, we present a genomic toolkit for arachnids featuring hundreds of conserved DNA regions (ultraconserved elements or UCEs) that allow targeted sequencing of any species in the arachnid tree of life. We used recently developed capture probes designed from conserved regions of available arachnid genomes to enrich a sample of loci from 32 diverse arachnids. Sequence capture returned an average of 487 UCE loci for all species, with a range from 170 to 722. Phylogenetic analysis of these UCEs produced a highly resolved arachnid tree with relationships largely consistent with recent transcriptome-based phylogenies. We also tested the phylogenetic informativeness of UCE probes within the spider, scorpion and harvestman orders, demonstrating the utility of these markers at shallower taxonomic scales and suggesting that these loci will be useful for species-level differences. This probe set will open the door to phylogenomic and population genomic studies across the arachnid tree of life, enabling systematics, species delimitation, species discovery and conservation of these diverse arthropods. [ABSTRACT FROM AUTHOR]

Major gaps remain in our understanding of the ecology, evolution, biodiversity, biogeography, extinction risk, and adaptive potential of reef building corals. One of the central challenges remains that there are few informative genetic markers for studying boundaries between species, and variation within species. Reduced representation sequencing approaches, such as RADseq (Restriction site Associated DNA sequencing) have great potential for resolving such relationships. However, it is necessary to identify loci in order to make inferences for endosymbiotic organisms such as corals. Here, we examined twenty-one coral holobiont ezRAD libraries from Hawaiʻi, focusing on P. lobata and P. compressa , two species with contrasting morphology and habitat preference that previous studies have not resolved. We used a combination of de novo assembly and reference mapping approaches to identify and compare loci: we used reference mapping to extract and compare nearly complete mitochondrial genomes, ribosomal arrays, and histone genes. We used de novo clustering and phylogenomic methods to compare the complete holobiont data set with coral and symbiont subsets that map to transcriptomic data. In addition, we used reference assemblies to examine genetic structure from SNPs (Single Nucleotide Polymorphisms). All approaches resolved outgroup taxa but failed to resolve P. lobata and P. compressa as distinct, with mito-nuclear discordance and shared mitochondrial haplotypes within the species complex. The holobiont and ‘coral transcriptomic’ datasets were highly concordant, revealing stronger genetic structure between sites than between coral morphospecies. These results suggest that either branching morphology is a polymorphic trait, or that these species frequently hybridize. This study provides examples of several approaches to acquire, identify, and compare loci across metagenomic samples such as the coral holobiont while providing insights into the nature of coral variability. [ABSTRACT FROM AUTHOR]

The description and delimitation of species in an evolutionary framework is essential for understanding patterns of biodiversity and distribution, and in the assessment of conservation strategies for natural resources. This study seeks to clarify the evolutionary history and genetic variation within and between closely related octocoral species that are fundamental to benthic marine ecosystems for harbouring a high diversity of associated fauna. For our study system, we focused on members of the Gorgoniidae family in the Eastern Pacific, particularly of the Ecuadorian littoral, a less studied marine ecosystem. According to our results, the diagnosis of the genus Pacifigorgia is here amended to include species previously considered in the genus Leptogorgia. The genera Leptogorgia and Eugorgia are included within a single clade, and neither are recovered as monophyletic. In this case, according to the priority rule of the International Code of Zoological Nomenclature (ICZN), our proposal is to include the species considered in these two genera in Leptogorgia. In addition, we found evidence of interesting speciation patterns: morphological differentiation with no apparent genetic differentiation (in Pacifigorgia ), and inconsistencies between mitochondrial and nuclear data that suggest a hybridisation phenomenon (in Leptogorgia ). In the first case, recent radiation, ancient hybridisation, sympatric speciation, and in the second, reticulate evolution may have contributed to the evolutionary history of the studied taxa. Therefore, incongruences observed between morphological and molecular evidences in these octocorals, and in corals in general, may reveal the types of events/patterns that have influenced their evolution. [ABSTRACT FROM AUTHOR]

Scabies is a parasitic disease, caused by the mite Sarcoptes scabiei, and is considered one of the top 50 epidemic diseases and one the most common human skin disease, worldwide. Allergic dermatitis, including an intense itch, is a common symptom, however diagnosis is difficult and there is currently no effective vaccine. The goal of this study was to examine the immune interaction mechanism of both S. scabiei and infected hosts. mRNA-seq and microRNA-seq were conducted on the S. scabiei mite and on infected and uninfected hosts. We focused on differential expression of unigenes and microRNAs, as well as the real targets of unigenes in enriched immune signaling pathways. S. scabiei enhanced host immune function and decreased metabolism after infection, while the immune response of the host inhibited S. scabiei proliferation and metabolism signaling pathways. Differentially expressed unigenes of S. scabiei were enriched in the JAK-STAT signaling pathway and the Toll-like receptor signaling pathway. The differential expression analysis indicated that microRNAs of S. scabiei and hosts have major roles in regulating immune interactions between parasites and hosts. [ABSTRACT FROM AUTHOR]

The quantification of periphyton growth in situ poses numerous difficulties., The RNA/ DNA ratio is widely used as a growth indicator in marine ecology. We tested its applicability as a growth indicator of periphyton in streams of different sizes., Periphyton-covered stones sampled from two different watercourses during two seasons were exposed in laboratory flumes to different light levels to induce different growth rates. The relationship between rate of biomass accrual and RNA/ DNA ratio was analysed by measuring the chlorophyll- a content and the RNA and DNA content of total nucleic acid extract of the periphyton respectively., The RNA/ DNA ratios showed a linear relationship with the biomass accrual at all sampling times. The slopes of these relationships varied significantly between the two watercourses, but not between seasons within the same watercourse., These results indicate that the RNA/ DNA ratio can be used as a growth indicator for the periphyton studied here. We recommend that it be used to detect differences in growth rate of the same periphyton community either over time or between different treatments in ecological or ecotoxicological experiments. However, for long-term monitoring studies, we recommend taxonomic analyses of the assemblages because the observed differences in the relationship between the RNA/ DNA ratio and growth rate might be attributed to community structure differences in the assemblages. [ABSTRACT FROM AUTHOR]

Temporal collinearity is often considered the main force preserving Hox gene clusters in animal genomes. Studies that combine genomic and gene expression data are scarce, however, particularly in invertebrates like the Lophotrochozoa. As a result, the temporal collinearity hypothesis is currently built on poorly supported foundations. Here we characterize the complement, cluster, and expression of Hox genes in two brachiopod species, Terebratalia transversa and Novocrania anomala. T. transversa has a split cluster with 10 genes (lab, pb, Hox3, Dfd, Scr, Lox5, Antp, Lox4, Post2, and Post1), whereas N. anomala has 9 genes (apparently missing Post1). Our in situ hybridization, real-time quantitative PCR, and stage-specific transcriptomic analyses show that brachiopod Hox genes are neither strictly temporally nor spatially collinear; only pb (in T. transversa), Hox3 (in both brachiopods), and Dfd (in both brachiopods) show staggered mesodermal expression. Thus, our findings support the idea that temporal collinearity might contribute to keeping Hox genes clustered. Remarkably, expression of the Hox genes in both brachiopod species demonstrates cooption of Hox genes in the chaetae and shell fields, two major lophotrochozoan morphological novelties. The shared and specific expression of Hox genes, together with Arx, Zic, and Notch pathway components in chaetae and shell fields in brachiopods, mollusks, and annelids provide molecular evidence supporting the conservation of the molecular basis for these lophotrochozoan hallmarks. [ABSTRACT FROM AUTHOR]

Opiliones are iconic arachnids with a Palaeozoic origin and a diversity that reflects ancient biogeographic patterns dating back at least to the times of Pangea. Owing to interest in harvestman diversity, evolution and biogeography, their relationships have been thoroughly studied using morphology and PCR-based Sanger approaches to infer their systematic relationships. More recently, two studies utilized transcriptomics-based phylogenomics to explore their basal relationships and diversification, but sampling was limiting for understanding deep evolutionary patterns, as they lacked good taxon representation at the family level. Here, we analysed a set of the 14 existing transcriptomes with 40 additional ones generated for this study, representing approximately 80% of the extant familial diversity in Opiliones. Our phylogenetic analyses, including a set of data matrices with different gene occupancy and evolutionary rates, and using a multitude of methods correcting for a diversity of factors affecting phylogenomic data matrices, provide a robust and stable Opiliones tree of life, where most families and higher taxa are precisely placed. Our dating analyses using alternative calibration points, methods and analytical parameters provide well-resolved old divergences, consistent with ancient regionalization in Pangea in some groups, and Pangean vicariance in others. The integration of state-of-the-art molecular techniques and analyses, together with the broadest taxonomic sampling to date presented in a phylogenomic study of harvestmen, provide new insights into harvestmen interrelationships, as well as an overview of the general biogeographic patterns of this ancient arthropod group. [ABSTRACT FROM AUTHOR]

Beta_defensin have been solely found in vertebrates until β-defensin-like peptides were described as transcript isoforms in two species of Panulirus genus. They were considered as putative antimicrobials since their biological activity have not been demonstrated. Here we purified and characterized a defensin-like peptide from the hemocytes of spiny lobster P. argus , hereafter named panusin. Structurally, panusin presents a cysteine-stabilized α/β motif, and is prone to form homodimers. Biological activity of panusin showed broad-spectrum antimicrobial activity, characterized for being strikingly salt-resistant. Panusin did not showed hemolytic activity but was demonstrated its binding capacity to different lipid membrane models, indicating amphipathicity of β-sheet core as driving force for its antimicrobial activity. Panusin is considered a new kind of arthropod defensin which share structural and biological features with beta-defensin from vertebrates. The presence of beta-defensin like peptides in crustacean might suggest the emergence of the evolutionary relationship of β-defensins from vertebrates. [ABSTRACT FROM AUTHOR]

The precious octocoral Corallium rubrum has a long history of exploitation in the Mediterranean Sea. Historically, harvesting followed the 'boom and bust' cycles whereby newly discovered beds were overexploited to depletion. In the past, most of the red coral harvesting came form France, Italy, and Spain. Today, landing data show that Tunisia is the third largest supplier of C. rubrum. The aim of this study was to asses whether and how the exploitation effort affects size distribution and genetic diversity of Tunisian commercial populations. Biometric data and microsatellite markers were used to characterize 113 colonies collected on nine commercial banks. Size and branching pattern indicate that collected colonies are up to 100 years old with a high reproductive rate. Nevertheless, 38% of the colonies were undersized according to FAO-GFCM recommendations (basal diameter <7 mm). Tunisian populations showed a weak genetic structuring and significant differentiation between coastal and offshore populations. Harvesting did not alter the structure of red coral populations. However, technological improvement and intensive harvesting of Tunisian banks, if not properly managed, may lead to their rapid depletion, causing long-lasting shifts in population demography and genetic structure, and the loss of this valuable resource. [ABSTRACT FROM AUTHOR]

Although genetic diversity is recognized as an important consideration for coral restoration, genotypes for use in restoration are not typically selected based on an evaluation of phenotype. Systematic documentation of phenotypic variability within coral nurseries could inform restoration efforts. To quantify differences in phenotype, ten known genotypes of Acropora cervicornis in an established coral nursery in the Florida Keys were selected for study. Twelve 5-cm replicate colonies of each genotype were individually tagged for identification and suspended from four identical PVC tree structures within the nursery for grow-out. Total linear extension (TLE) and number of branches were measured at approximately 45-day intervals for a period of 13 months. Buoyant weight was determined for each colony initially and after five and 13 months in order to quantify calcification. Sub-lethal bleaching was observed among experimental colonies following a natural thermal stress event, and significant differences in bleaching prevalence were present among genotypes. At the conclusion of the study, significant differences in all growth parameters were detected among genotypes. Specific growth rate across genotypes decreased following bleaching. The ratio of buoyant weight to TLE varied among genotypes and decreased with increasing TLE, suggesting a potential tradeoff between extension and skeletal density in nursery-reared A. cervicornis . Phenotypic variation documented in this study has implications for nursery management and may be useful in selecting genotypes for A. cervicornis population enhancement. [ABSTRACT FROM AUTHOR]