Sterol composition of three marine sponge species from the genus Cinachyrella

• 1.1. The hitherto undescribed sterol compositions of three marine sponge species belonging to the genus Cinachyrella are reported: C. alloclada and C. kükenthali from the Senegalese coast, at two different depths, and C. aff. schulzei from the lagoon of Nouméa, New Caledonia.
• 2.2. Fourteen free sterols have been identified by GC and GC/MS studies, including the 23,24ξ-dimethylcholesta-5,22-dien-3β-ol (10) and the rare 24-norcholesta-5,22-dien-3β-ol (1).
• 3.3. The first compound (10) is reported for the second time in a marine sponge and it was found only in Senegalese sponges collected in shallow waters.
• 4.4. Sterol (10) has been isolated by HPLC and identified by NMR techniques.
• 5.5. Significant amounts of cholest-7-en-3β-ol (7) were also found in the Senegalese sponge species.
• 6.6. Apart from these two compounds, the three sponge sterol compositions are found to be very similar.

     

Body‐size distribution and biogeographical patterns in non‐marine ostracods (Crustacea: Ostracoda)

The idea that free‐living minute organisms have ubiquitous distributions has been recently revitalized, causing significant controversy. The ubiquitous model predicts that a threshold where ubiquity leaves room to biogeography might exist somewhere along the animal body‐size range. In the present study, such a prediction is tested by analysing body‐size frequency distribution, species distribution, and local‐to‐global species ratio at the scale of biogeographical realms in cypridoidean non‐marine ostracods, a group with a body‐size range in the ubiquity–biogeography (U‐B) boundary. Data were gathered for all described extant cypridoidean ostracod species (N = 1761), with body‐size recorded for 1134 of them. Although local‐to‐global species ratios show significant over‐dispersal of small‐body ostracods for the Palaearctic and the Australasian regions, there are explanations alternative to the ‘Everything is Everywhere’ model that can account for such a result. Indicators of taxonomic structure do not support the hypothesis of a random distribution of cypridoidean species among realms. Nevertheless, the strong biogeography signal occurring at a large scale vanishes at the local scale (country‐level within the Palaearctic), and suggests wide dispersion within biogeographical realms. Additional factors, including inconsistent taxonomic criteria for species recognition, uneven sampling effort, and an excess of ‘single‐report’ occurrences, have been identified too as potential distorters of the observed patterns. Taxonomic harmonization, open databases of biogeographical data, and better ecological information are suggested as critical goals that need to be achieved for further understanding of ostracod global distribution patterns. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 409–423.     

The sterol composition of the marine sponge Aplysina (= Verongia) archeri: a comparative study of the Verongidae

1. The sterol composition of the marine sponge Aplysina archeri was studied revealing the presence, besides other common sterols, of considerable amounts (75%) of aplysterol (1), verongulasterol (3), and 25-dehydroaplysterol (4). 2. 24,28-Didehydroaplysterol (2) was not present in the sterol mixture as it was previously reported for the Verongidae. 3. A comparison between the characteristic sterols of the Verongidae was carried out.     

Early Cretaceous non‐marine Ostracoda from the North Falkland Basin,South Atlantic

Twenty‐seven species of well‐preserved and abundant Early Cretaceous non‐marine ostracod crustaceans were recovered from the North Falkland Basin. The assemblage is unusually diverse for a non‐marine palaeoenvironment and is sourced from cuttings samples collected during 2011 drilling of wells by Desire and Rockhopper Exploration, in the northern and southern areas of the basin. Ostracoda are entirely undocumented in published accounts from this basin, and all but one species appear to be new to science. For the new taxa, one new family (Alloiocyprideidae; type genus Hourcqia) is proposed and includes Hourcqia woodi sp. nov. Four new genera are erected: Falklandicypris gen. nov.; type species F. petrasaltata sp. nov., Gangamoncythere gen. nov.; type species G. colini sp. nov., Paraplesiocypridea gen. nov.; type species P. alloios sp. nov., and Musacchiocythere gen nov.; type species M. sarunata (Musacchio, 1978 ). Nine other species are described as new and are Falklandicypris desiderata, Clinocypris epacrus, Cypria poietes, Ilhasina? leiodermatus, Looneyellopsis tuberculatus, Theriosynoecum petasmathylacus, Theriosynoecum ballentae, Timiriasevia fluitans, and Vecticypris samesi. The remainder are left in open nomenclature due to paucity of material. The ostracod assemblage is largely restricted to the southern part of the basin (wells 25/5‐1 and 26/6‐1). In the northern part of the basin only four species, dominated by Vecticypris samesi, are present and with one possible exception are restricted there. There appears to have been little or no interchange of species suggesting that a barrier probably existed between the northern and southern regions. The more diverse southern assemblage indicates that more favourable conditions existed to the south. Stratigraphically, a distinct change in faunal composition recorded in both southern wells is likely to be an isochronous event correlatable across the southern area, and of an age no younger than Hauterivian.     

Life history trait divergence among populations of a non‐palatable species reveals strong non‐trophic indirect effects of an abundant herbivore

When large herbivores exert selection on their prey plant species, co‐occurring, non‐prey species may experience selection through non‐trophic indirect effects. Such selection is likely common where herbivores are overabundant. Yet, empirical studies of non‐trophic indirect effects as drivers of non‐prey trait evolution are lacking. Here we test for adaptive shifts in life history traits in an unpalatable species, Arisaema triphyllum, a common forest perennial that is unique because it exhibits size‐dependent sex switching. We collected A. triphyllum from six sites that experience a gradient in abiotic stress caused by deer browse pressure on prey plant species that generate indirect effects. We grew A. triphyllum from these sites in a common garden for five years to evaluate life history predictions linking strong indirect effects and abiotic stress to changes in life history traits: flowering onset size threshold, female flowering size threshold, relative growth rate (RGR), biomass allocation, and asexual reproduction. Despite observed differences among phenotypes in the field, expression of flowering onset size threshold, biomass allocation, and asexual reproduction did not differ among the six populations in the garden, indicating common plastic responses. In contrast, A. triphyllum collected from sites experiencing the two highest deer impacts exhibited smaller female flowering size thresholds and the highest RGR. Responses in these traits support the predictions of adaptive divergence in response to indirect effects. Our results reinforce the idea that non‐trophic indirect effects of large herbivores can elicit evolutionary responses in some traits of non‐prey species. In general, life history traits of unpalatable species may be cryptically adapting to stressful indirect effects where large herbivores are overabundant.     

Callyspongiamides A and B,sterol O-acyltransferase inhibitors,from the Indonesian marine sponge Callyspongia sp.

Callyspongiamides A (1) and B (2), two new sterol O-acyltransferase (SOAT) inhibitors, were isolated from the Indonesian marine sponge Callyspongia sp. together with a known congener, dysamide A (3). The structures of 1 and 2 were elucidated to be polychlorine-containing modified dipeptides based on their spectroscopic data. Compounds 1–3 inhibited both of the SOAT isozymes, SOAT1 and SOAT2, in cell-based and enzyme-based assays.     

Silybum marianum: non‐medical exploitation of the species

Silybum marianum (milk thistle) is currently utilised as a medicinal plant which provides raw material for the production of silymarin. Silymarin is composed of a group of flavonolignans that are well known and studied for their medicinal properties. However, the biomass yield potential and the chemical composition of its biomass suggest opportunities for much broader utilisation of S. marianum. This paper reviews the available literature about S. marianum biomass productivity and composition and about properties of products and byproducts of silymarin extraction. Alternative uses of whole plant biomass include fodder, bioenergy production and phytoremediation. Byproducts of silymarin extraction such as oil and flour have possible applications in food, feed and cosmetics. Moreover, the review explores potential alternative applications of silymarin. We conclude that a pivotal issue for further utilisation of S. marianum is the development of improved cultivars suited for the different possible utilisations.     

Pathologies of non‐marine bivalve shells from the Late Triassic of Poland

Gorzelak, P., Nied?wiedzki, G. & Skawina, A. 2010: Pathologies of non‐marine bivalve shells from the Late Triassic of Poland. Lethaia, Vol. 43, pp. 285–289. Shells of Late Triassic non‐marine bivalves from Lisowice (Lipie ?l?skie clay pit, southern Poland), which co‐occur with remains of several vertebrate taxa (mammal‐like reptiles, carnivorous dinosaurs, pterosaurs, temnospondyl amphibians, hybodont sharks, dipnoan and ganoid fish), bear evidence of pathologies. Distribution, dimension and shape of some of these injuries (radiate tooth marks) closely match the dental morphology of lungfish (here probably represented by the genus Ceratodus). Thus, we interpret these pathologies as evidence of unsuccessful predatory attack on bivalves by this fish. This interpretation is also consistent with modern examples of such behaviour among lungfish. The feasibility that other culprits caused other pathologies (shell scarring and wedges) on the bivalves analysed is also discussed. Discovery of these traces constitutes important evidence of predator–prey interaction, which provides ‘fingerprints’ of trophic structure within this Late Triassic freshwater ecosystem. □Freshwater bivalves, lungfish, pathologies, predation, Triassic.     

Ecological plant epigenetics: Evidence from model and non‐model species,and the way forward

Growing evidence shows that epigenetic mechanisms contribute to complex traits, with implications across many fields of biology. In plant ecology, recent studies have attempted to merge ecological experiments with epigenetic analyses to elucidate the contribution of epigenetics to plant phenotypes, stress responses, adaptation to habitat, and range distributions. While there has been some progress in revealing the role of epigenetics in ecological processes, studies with non‐model species have so far been limited to describing broad patterns based on anonymous markers of DNA methylation. In contrast, studies with model species have benefited from powerful genomic resources, which contribute to a more mechanistic understanding but have limited ecological realism. Understanding the significance of epigenetics for plant ecology requires increased transfer of knowledge and methods from model species research to genomes of evolutionarily divergent species, and examination of responses to complex natural environments at a more mechanistic level. This requires transforming genomics tools specifically for studying non‐model species, which is challenging given the large and often polyploid genomes of plants. Collaboration among molecular geneticists, ecologists and bioinformaticians promises to enhance our understanding of the mutual links between genome function and ecological processes.     

The first non‐marine ostracod fauna from the Lower Barremian dysodiles of Lebanon

Dysodiles are finely laminated sedimentary rocks rich in organic matter and in exceptionally well‐preserved fossils, hence their petroleum and palaeontological interest. However, few studies focused on the dysodiles of Lebanon, leaving their palaeontological content and their depositional environment largely unknown. Our previous investigations show a variety of well‐preserved lacustrine fossils including ichthyofauna, chelonians, insects, plant debris, gastropods, palynomorphs and ostracods. The present study focuses on the ostracods of five sampling localities from the Lower Barremian of Lebanon. Being the most abundant fossils, ostracods raise some taphonomic and palaeoecological questions that may help us understand the depositional environment and enrich the story of these Early Barremian lakes. Faunal differences between the sampled sections provide clues to the specific characteristics of each lake. The abundance of ‘butterfly’ preservation of carapaces, together with the association of adults and juveniles, indicates calm depositional environments without post‐mortem transport. The assemblages comprise ostracods with known swimming ability (Cyprois and Zonocypris) or that are thought to have been swimmers (Cypridea), while non‐swimmers are absent, suggesting that nektobenthonic ostracods must have lived only in the shallow margins of the lakes or among floating vegetation because hypolimnion conditions were hostile to benthos. This study provides different scenarios on how this fauna ended up preserved in the laminated lake sediments.     

EstimateS turns 20: statistical estimation of species richness and shared species from samples,with non‐parametric extrapolation

EstimateS offers statistical tools for analyzing and comparing the diversity and composition of species assemblages, based on sampling data. The latest version computes a wide range of biodiversity statistics for both sample‐based and individual‐based data, including analytical rarefaction and non‐parametric extrapolation, estimators of asymptotic species richness, diversity indices, Hill numbers, and (for sample‐based data) measures of compositional similarity among assemblages. In the first 20 yr of its existence, EstimateS has been downloaded more than 70 000 times by users in 140 countries, who have cited it in 5000 publications in studies of taxa from microbes to mammals in every biome.     

More species, fewer specialists: 100 years of changes in community composition in an island biogeographical study

Aim  We measured the changes in an island avifauna over more than 100 years (1898–2006), using community indices accounting for difference in expected species sensitivity to land-use and climate changes.
Location  Ouessant Island, France, Great Britain.
Methods  We assessed the temporal trend of the relative proportion of generalist species breeding on Ouessant island and whether high-temperature tolerant species have replaced less tolerant species over this time period. We further tested the relationship between the observed change in the avifauna composition, and long-term population species' trends measured independently in potential source regions of colonist species (France and Great Britain).
Results  During the whole study period, Ouessant island has experienced a strong increase in species richness (+41%), but a severe decline in specialist species. In contrast, we found no change in species composition in terms of their temperature-tolerance. The observed trend was highly correlated with species trends measured in the Great Britain.
Main conclusions  Our results revealed an ongoing biotic homogenization process towards more generalist species, coupled with a strong local increase in species richness. The observed trend was most likely driven by a strong habitat change in the island occurring during the period considered, favouring the colonization of generalist species. Our results show that an increase in species richness can be misinterpreted as a sign of conservation improvement and that assessing change in community composition using species-specific ecological traits provides more accurate insights for conservation planning purposes.     

Palaeoecology of a billion‐year‐old non‐marine cyanobacterium from the Torridon Group and Nonesuch Formation

A new chroococcalean cyanobacterium is described from approximately 1‐billion‐year‐old non‐marine deposits of the Torridonian Group of Scotland and the Nonesuch Formation of Michigan, USA. Individual cells of the new microfossil, Eohalothece lacustrina gen. et sp. nov., are associated with benthic microbial biofilms, but the majority of samples are recovered in palynological preparations in the form of large, apparently planktonic colonies, similar to extant species of Microcystis. In the Torridonian, Eohalothece is associated with phosphatic nodules, and we have developed a novel hypothesis linking Eohalothece to phosphate deposition in ancient freshwater settings. Extant cyanobacteria can be prolific producers of extracellular microcystins, which are non‐ribosomal polypeptide phosphatase inhibitors. Microcystins may have promoted the retention and concentration of sedimentary organic phosphate prior to mineralization of francolite and nodule formation. This has a further implication that the Torridonian lakes were nitrogen limited as the release of microcystins is enhanced under such conditions today. The abundance and wide distribution of Eohalothece lacustrina attests to the importance of cyanobacteria as oxygen‐producing photoautotrophs in lacustrine ecosystems at the time of the Mesoproterozoic–Neoproterozoic transition.     

Pelagic cephalopods from eastern Australia: species composition, horizontal and vertical distribution determined from the diets of pelagic fishes

The distribution and relative biomass of cephalopods from pelagic waters off eastern Australia was examined between 1997 and 2004 from stomach contents of swordfish, yellowfin tuna and dolphinfish taken in the domestic longline fishery. A total of 38 taxa from 19 families were identified. Comparison of the species composition of the three predators indicated pronounced differences in cephalopod species composition. In swordfish, species of the family Ommastrephidae, particularly Ommastrephes bartramii (Lesueur 1821) and Nototodarus gouldi (McCoy 1888) dominated, whereas a more diverse mix of species was identified from yellowfin-sampled cephalopods. Todaropsis eblanae (Ball 1841) was the main cephalopod sampled from the surface-dwelling dolphinfish. For swordfish-sampled cephalopods, significant relationships were found between biomass and season, fluorescence and year. In yellowfin tuna, cephalopod biomass was significantly correlated with season, area and sea surface temperature. Significant factors differed between predator-sampler, possibly reflecting the limits of the predator, but could also give insights into individual cephalopod species distributions. However, the increase in cephalopod biomass over summer in both swordfish and yellowfin tuna suggested cephalopod biomass was higher over summer in the region.     

Sequence capture phylogenomics of historical ethanol‐preserved museum specimens: Unlocking the rest of the vault

Natural history collections play a crucial role in biodiversity research, and museum specimens are increasingly being incorporated into modern genetics‐based studies. Sequence capture methods have proven incredibly useful for phylogenomics, providing the additional ability to sequence historical museum specimens with highly degraded DNA, which until recently have been deemed less valuable for genetic work. The successful sequencing of ultraconserved elements (UCEs) from historical museum specimens has been demonstrated on multiple tissue types including dried bird skins, formalin‐fixed squamates and pinned insects. However, no study has thoroughly demonstrated this approach for historical ethanol‐preserved museum specimens. Alongside sequencing of “fresh” specimens preserved in >95% ethanol and stored at ?80°C, we used extraction techniques specifically designed for degraded DNA coupled with sequence capture protocols to sequence UCEs from historical museum specimens preserved in 70%–80% ethanol and stored at room temperature, the standard for such ethanol‐preserved museum collections. Across 35 fresh and 15 historical museum samples of the arachnid order Opiliones, an average of 345 UCE loci were included in phylogenomic matrices, with museum samples ranging from six to 495 loci. We successfully demonstrate the inclusion of historical ethanol‐preserved museum specimens in modern sequence capture phylogenomic studies, show a high frequency of variant bases at the species and population levels, and from off‐target reads successfully recover multiple loci traditionally sequenced in multilocus studies including mitochondrial loci and nuclear rRNA loci. The methods detailed in this study will allow researchers to potentially acquire genetic data from millions of ethanol‐preserved museum specimens held in collections worldwide.     

Identifying potentially invasive non‐native marine and brackish water species for the Arabian Gulf and Sea of Oman

Invasive non‐native species (NNS) are internationally recognized as posing a serious threat to global biodiversity, economies and human health. The identification of invasive NNS is already established, those that may arrive in the future, their vectors and pathways of introduction and spread, and hotspots of invasion are important for a targeted approach to managing introductions and impacts at local, regional and global scales. The aim of this study was to identify which marine and brackish NNS are already present in marine systems of the northeastern Arabia area (Arabian Gulf and Sea of Oman) and of these which ones are potentially invasive, and which species have a high likelihood of being introduced in the future and negatively affect biodiversity. Overall, 136 NNS were identified, of which 56 are already present in the region and a further 80 were identified as likely to arrive in the future, including fish, tunicates, invertebrates, plants and protists. The Aquatic Species Invasiveness Screening Kit (AS‐ISK) was used to identify the risk of NNS being (or becoming) invasive within the region. Based on the AS‐ISK basic risk assessment (BRA) thresholds, 36 extant and 37 horizon species (53.7% of all species) were identified as high risk. When the impact of climate change on the overall assessment was considered, the combined risk score (BRA+CCA) increased for 38.2% of all species, suggesting higher risk under warmer conditions, including the highest‐risk horizon NNS the green crab Carcinus maenas, and the extant macro‐alga Hypnea musciformis. This is the first horizon‐scanning exercise for NNS in the region, thus providing a vital baseline for future management. The outcome of this study is the prioritization of NNS to inform decision‐making for the targeted monitoring and management in the region to prevent new bio‐invasions and to control existing species, including their potential for spread.     

A comparative study on the phylogenetic diversity of culturable actinobacteria isolated from five marine sponge species

A cultivation-based approach was employed to compare the culturable actinobacterial diversity associated with five marine sponge species (Craniella australiensis, Halichondria rugosa, Reniochalina sp., Sponge sp., and Stelletta tenuis). The phylogenetic affiliation of the actinobacterial isolates was assessed by 16S rDNA-RFLP analysis. A total of 181 actinobacterial strains were isolated using five different culture media (denoted as M1–M5). The type of medium exhibited significant effects on the number of actinobacteria recovered, with the highest number of isolates on M3 (63 isolates) and the lowest on M1 (12 isolates). The genera isolated were also different, with the recovery of three genera on M2 and M3, and only a single genus on M1. The number of actinobacteria isolated from the five sponge species was significantly different, with a count of 83, 36, 30, 17, and 15 isolates from S. tenuis, H. rugosa, Sponge sp., Reniochalina sp., and C. australiensis, respectively. M3 was the best isolation medium for recovery of actinobacteria from S. tenuis, H. rugosa, and Sponge sp., while no specific medium preference was observed for the recovery of actinobacteria from Reniochalina sp., and C. australiensis. The RFLP fingerprinting of 16S rDNA genes digested with HhaI revealed six different patterns, in which 16 representative 16S rDNAs were fully sequenced. Phylogenetic analysis indicated that 12 strains belong to the group Streptomyces, three strains belong to Pseudonocardia, and one strain belongs to Nocardia. Two strains C14 (from C. australiensis) and N13 (from Sponge sp.) have only 96.26% and 96.27% similarity to earlier published sequences, and are therefore potential candidates for new species. The highest diversity of three actinobacteria genera was obtained from Sponge sp., though the number of isolates was low. Two genera of actinobacteria, Streptomyces, and Pseudonocardia, were isolated from both S. tenuis and C. australiensis. Only the genus of Streptomyces was isolated from H. rugosa and Reniochalina sp. Sponge species have been demonstrated here to vary as sources of culturable actinobacterial diversity, and the methods for sampling such diversity presented may be useful for improved sampling of such diversity.     

Lessons from the fish: a multi‐species analysis reveals common processes underlying similar species‐genetic diversity correlations

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