The mitochondrial genome structure of Xenoturbella bocki (phylum Xenoturbellida) is ancestral within the deuterostomes

Mitochondrial genome comparisons contribute in multiple ways when inferring animal relationships. As well as primary sequence data, rare genomic changes such as gene order, shared gene boundaries and genetic code changes, which are unlikely to have arisen through convergent evolution, are useful tools in resolving deep phylogenies. Xenoturbella bocki is a morphologically simple benthic marine worm recently found to belong among the deuterostomes. Here we present analyses comparing the Xenoturbella bocki mitochondrial gene order, genetic code and control region to those of other metazoan groups

The phylogenetic position of Acoela as revealed by the complete mitochondrial genome of Symsagittifera roscoffensis

<p>Abstract</p> <p>Background</p> <p>Acoels are simply organized unsegmented worms, lacking hindgut and anus. Several publications over recent years challenge the long-held view that acoels are early offshoots of the flatworms. Instead a basal position as sister group to all other bilaterian animals was suggested, mainly based on molecular evidence. This led to the view that features of acoels might reflect those of the last common ancestor of Bilateria, and resulted in several evo-devo studies trying to interpret bilaterian evolution using acoels as a proxy model for the "Urbilateria".</p> <p>Results</p> <p>We describe the first complete mitochondrial genome sequence of a member of the Acoela, <it>Symsagittifera roscoffensis</it>. Gene content and circular organization of the mitochondrial genome does not significantly differ from other bilaterian animals. However, gene order shows no similarity to any other mitochondrial genome within the Metazoa. Phylogenetic analyses of concatenated alignments of amino acid sequences from protein coding genes support a position of Acoela and Nemertodermatida as the sister group to all other Bilateria. Our data provided no support for a sister group relationship between Xenoturbellida and Acoela or Acoelomorpha. The phylogenetic position of <it>Xenoturbella bocki </it>as sister group to or part of the deuterostomes was also unstable.</p> <p>Conclusions</p> <p>Our phylogenetic analysis supports the view that acoels and nemertodermatids are the earliest divergent extant lineage of Bilateria. As such they remain a valid source for seeking primitive characters present in the last common ancestor of Bilateria. Gene order of mitochondrial genomes seems to be very variable among Acoela and Nemertodermatida and the groundplan for the metazoan mitochondrial genome remains elusive. More data are needed to interpret mitochondrial genome evolution at the base of Bilateria.</p

Wrasse fishery on the Swedish West Coast: towards ecosystem-based management

Fishing and translocation of marine species for use in aquaculture is widespread. Corkwing, goldsinny, and ballan wrasse (Symphodus melops, Ctenolabrus rupestris, and Labrus bergylta) are fished on the Swedish west coast for use as cleaner-fish in Norwegian salmon farms. Here, we aim to provide knowledge and recommendations to support ecosystem-based management for wrasse fisheries in Sweden. We compared fished and non-fished areas to test if current fishery levels have led to stock depletion. To gain insight on the role of wrasse in the algal belt trophic chain, we analysed the gut contents of goldsinny and corkwing using metabarcoding. Finally, we analysed the trophic interactions of wrasse and potential prey in a mesocosm study. We could not detect any signs of stock depletion or altered size structure in fished areas compared to the protected control area. Gut analyses confirmed both goldsinny and corkwing as non-specialized, omnivorous opportunists and revealed, with 189 prey taxa detected, a broader spectrum of prey than previously known. Common prey items included mesoherbivores such as small gastropods and crustaceans, but also insects and algae. We conclude that there are no visible signs of stock depletion at the current removal level of wrasses by the fishery. However, this emerging fishery should be closely monitored for potential cascading effects on the algal belt ecosystem, and our study could provide a baseline for future monitoring

Ecdysozoan mitogenomics: evidence for a common origin of the legged invertebrates, the Panarthropoda

Ecdysozoa is the recently recognized clade of molting animals that comprises the vast majority of extant animal species and the most important invertebrate model organisms—the fruit fly and the nematode worm. Evolutionary relationships within the ecdysozoans remain, however, unresolved, impairing the correct interpretation of comparative genomic studies. In particular, the affinities of the three Panarthropoda phyla (Arthropoda, Onychophora, and Tardigrada) and the position of Myriapoda within Arthropoda (Mandibulata vs. Myriochelata hypothesis) are among the most contentious issues in animal phylogenetics. To elucidate these relationships, we have determined and analyzed complete or nearly complete mitochondrial genome sequences of two Tardigrada, Hypsibius dujardini and Thulinia sp. (the first genomes to date for this phylum); one Priapulida, Halicryptus spinulosus; and two Onychophora, Peripatoides sp. and Epiperipatus biolleyi; and a partial mitochondrial genome sequence of the Onychophora Euperipatoides kanagrensis. Tardigrada mitochondrial genomes resemble those of the arthropods in term of the gene order and strand asymmetry, whereas Onychophora genomes are characterized by numerous gene order rearrangements and strand asymmetry variations. In addition, Onychophora genomes are extremely enriched in A and T nucleotides, whereas Priapulida and Tardigrada are more balanced. Phylogenetic analyses based on concatenated amino acid coding sequences support a monophyletic origin of the Ecdysozoa and the position of Priapulida as the sister group of a monophyletic Panarthropoda (Tardigrada plus Onychophora plus Arthropoda). The position of Tardigrada is more problematic, most likely because of long branch attraction (LBA). However, experiments designed to reduce LBA suggest that the most likely placement of Tardigrada is as a sister group of Onychophora. The same analyses also recover monophyly of traditionally recognized arthropod lineages such as Arachnida and of the highly debated clade Mandibulata

Report of the 14th Genomic Standards Consortium Meeting, Oxford, UK, September 17-21, 2012

© The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Standards in Genomic Sciences 9 (2014): 1236-1250, doi:10.4056/sigs.4319681.This report summarizes the proceedings of the 14th workshop of the Genomic Standards Consortium (GSC) held at the University of Oxford in September 2012. The workshop’s primary goal was to work towards the launch of the Genomic Observatories (GOs) Network under the GSC. For the first time, it brought together potential GOs sites, GSC members, and a range of interested partner organizations. It thus represented the first meeting of the GOs Network (GOs1). Key outcomes include the formation of a core group of “champions” ready to take the GOs Network forward, as well as the formation of working groups. The workshop also served as the first meeting of a wide range of participants in the Ocean Sampling Day (OSD) initiative, a first GOs action. Three projects with complementary interests – COST Action ES1103, MG4U and Micro B3 – organized joint sessions at the workshop. A two-day GSC Hackathon followed the main three days of meetings.This work was supported in part by the US Na-tional Science Foundation through the research coordination network award RCN4GSC, DBI-0840989 and in part by a grant from the Gordon and Betty Moore Foundation, and travel grants of COST Action ES1103. The stakeholder session was supported by the European Union’s Seventh Framework Programme (FP7 /2007-2013) under grant agreement no 266055, and the Marine Ge-nomics for Users EU FP7 project (Coordination and support action, call FP7-KBBE-2010-4) grant no. 266055. We thank Eppendorf and Biomatters Ltd. for their sponsorship of the meeting

Habitat segregation of plate phenotypes in a rapidly expanding population of three-spined stickleback

Declines of large predatory fish due to overexploitation are restructuring food webs across the globe. It is now becoming evident that restoring these altered food webs requires addressing not only ecological processes, but evolutionary ones as well, because human-induced rapid evolution may in turn affect ecological dynamics. We studied the potential for niche differentiation between different plate armor phenotypes in a rapidly expanding population of a small prey fish, the three-spined stickleback (Gasterosteus aculeatus). In the central Baltic Sea, three-spined stickleback abundance has increased dramatically during the past decades. The increase in this typical mesopredator has restructured near-shore food webs, increased filamentous algal blooms, and threatens coastal biodiversity. Time-series data covering 22 years show that the increase coincides with a decline in the number of juvenile perch (Perca fluviatilis), the most abundant predator of stickleback along the coast. We investigated the distribution of different stickleback plate armor phenotypes depending on latitude, environmental conditions, predator and prey abundances, nutrients, and benthic production; and described the stomach content of the stickleback phenotypes using metabarcoding. We found two distinct lateral armor plate phenotypes of stickleback, incompletely and completely plated. The proportion of incompletely plated individuals increased with increasing benthic production and decreasing abundances of adult perch. Metabarcoding showed that the stomach content of the completely plated individuals more often contained invertebrate herbivores (amphipods) than the incompletely plated ones. Since armor plates are defense structures favored by natural selection in the presence of fish predators, the phenotype distribution suggests that a novel low-predation regime favors stickleback with less armor. Our results suggest that morphological differentiation of the three-spined stickleback has the potential to affect food web dynamics and influence the persistence and resilience of the stickleback take-over in the Baltic Sea.Peer reviewe

The rise of the three-spined stickleback – eco-evolutionary consequences of a mesopredator release

Declines of large predatory fish due to overexploitation are restructuring food webs across the globe. It is now becoming evident that restoring these altered food webs requires addressing not only ecological processes, but evolutionary ones as well, because human-induced rapid evolution may in turn affect ecological dynamics. In the central Baltic Sea, abundances of the mesopredatory fish, the three-spined stickleback (Gasterosteus aculeatus), have increased dramatically during the past decades. Time-series data covering 22 years show that this increase coincides with a decline in the number of juvenile perch (Perca fluviatilis), the most abundant predator of stickleback along the coast. We studied the interaction between evolutionary and ecological effects of this mesopredator take-over, by surveying the armour plate morphology of stickleback and the structure of the associated food web. First, we investigated the distribution of different stickleback phenotypes depending on predator abundances and benthic production; and described the stomach content of the stickleback phenotypes using metabarcoding. Second, we explored differences in the relation between different trophic levels and benthic production, between bays where the relative abundance of fish was dominated by stickleback or not; and compared this to previous cage-experiments to support causality of detected correlations. We found two distinct lateral armour plate phenotypes of stickleback, incompletely and completely plated. The proportion of incompletely plated individuals increased with increasing benthic production and decreasing abundances of adult perch. Stomach content analyses showed that the completely plated individuals had a stronger preference for invertebrate herbivores (amphipods) than the incompletely plated ones. In addition, predator dominance interacted with ecosystem production to determine food web structure and the propagation of a trophic cascade: with increasing production, biomass accumulated on the first (macroalgae) and third (stickleback) trophic levels in stickleback-dominated bays, but on the second trophic level (invertebrate herbivores) in perch-dominated bays. Since armour plates are defence structures favoured by natural selection in the presence of fish predators, the phenotype distribution suggest that a novel low-predation regime favours sticklebacks with less armour. Our results indicate that an interaction between evolutionary and ecological effects of the stickleback take-over has the potential to affect food web dynamics

Metabarcoding dietary analysis in the insectivorous bat Nyctalus leisleri and implications for conservation

In this study, we aim to uncover diet preferences for the insectivorous bat Nyctalus leisleri (Leisler's bat, the lesser noctule) and to provide recommendations for conservation of the species, based on the analysis of prey source habitats. Using a novel guano trap, we sampled bat faeces at selected roosts in a forest in Germany and tested two mitochondrial markers (COI and 16S) and three primer pairs for the metabarcoding of bat faecal pellets.We found a total of 17 arthropod prey orders comprising 358 species in N. leisleri guano. The most diverse orders were Lepidoptera (126 species), Diptera (86 species) and Coleoptera (48 species), followed by Hemiptera (28 species), Trichoptera (16 species), Neuroptera (15 species) and Ephemeroptera (10 species), with Lepidoptera species dominating in spring and Diptera in summer. Based on the ecological requirements of the most abundant arthropod species found in the bat guano, we propose some recommendations for the conservation of N. leisleri that are relevant for other insectivorous bat species

Could coastal plants in western Amazonia be relicts of past marine incursions?

The rainforests of Amazonia comprise some of the most biologically diverse ecosystems on Earth. Despite this high biodiversity, little is known about how landscape changes that took place in deep history have affected the assembly of its species, and whether the impact of such changes on biodiversity can still be observed. Here, we present a hypothesis to explain our observation that plants typical of Neotropical coastal habitats also occur in western Amazonia, in some cases thousands of kilometres away from the coast. Evidence on their current distribution, dispersal biology and divergence times estimated from molecular phylogenies suggest that these plants may be the legacy of the large marine‐influenced embayment that dominated the area for millions of years in the Neogene. We hypothesize that coastal plants dispersed along the shores of this embayment and persisted as inland relicts after the marine incursion(s) retreated, probably with the aid of changes in soil conditions caused by the deposition of marine sediments. This dispersal corridor may also have facilitated the colonization of coastal environments by Amazonian lineages. These scenarios could imply an unexpected coastal source that has contributed to Amazonia's high floristic diversity and led to disjunct distributions across the Neotropics. We highlight the need for future studies and additional evidence to validate and shed further light on this potentially important pattern.</p

Towards a multisensor station for automated biodiversity monitoring

Rapid changes of the biosphere observed in recent years are caused by both small and large scale drivers, like shifts in temperature, transformations in land-use, or changes in the energy budget of systems. While the latter processes are easily quantifiable, documentation of the loss of biodiversity and community structure is more difficult. Changes in organismal abundance and diversity are barely documented. Censuses of species are usually fragmentary and inferred by often spatially, temporally and ecologically unsatisfactory simple species lists for individual study sites. Thus, detrimental global processes and their drivers often remain unrevealed. A major impediment to monitoring species diversity is the lack of human taxonomic expertise that is implicitly required for large-scale and fine-grained assessments. Another is the large amount of personnel and associated costs needed to cover large scales, or the inaccessibility of remote but nonetheless affected areas. To overcome these limitations we propose a network of Automated Multisensor stations for Monitoring of species Diversity (AMMODs) to pave the way for a new generation of biodiversity assessment centers. This network combines cutting-edge technologies with biodiversity informatics and expert systems that conserve expert knowledge. Each AMMOD station combines autonomous samplers for insects, pollen and spores, audio recorders for vocalizing animals, sensors for volatile organic compounds emitted by plants (pVOCs) and camera traps for mammals and small invertebrates. AMMODs are largely self-containing and have the ability to pre-process data (e.g. for noise filtering) prior to transmission to receiver stations for storage, integration and analyses. Installation on sites that are difficult to access require a sophisticated and challenging system design with optimum balance between power requirements, bandwidth for data transmission, required service, and operation under all environmental conditions for years. An important prerequisite for automated species identification are databases of DNA barcodes, animal sounds, for pVOCs, and images used as training data for automated species identification. AMMOD stations thus become a key component to advance the field of biodiversity monitoring for research and policy by delivering biodiversity data at an unprecedented spatial and temporal resolution. (C) 2022 Published by Elsevier GmbH on behalf of Gesellschaft fur Okologie