A genome-wide investigation of the worldwide invader Sargassum muticum shows high success albeit (almost) no genetic diversity

Twenty years of genetic studies of marine invaders have shown that successful invaders are often characterized by native and introduced populations displaying similar levels of genetic diversity. This pattern is presumably due to high propagule pressure and repeated introductions. The opposite pattern is reported in this study of the brown seaweed, Sargassum muticum, an emblematic species for circumglobal invasions. Albeit demonstrating polymorphism in the native range, microsatellites failed to detect any genetic variation over 1,269 individuals sampled from 46 locations over the Pacific-Atlantic introduction range. Single-nucleotide polymorphisms (SNPs) obtained from ddRAD sequencing revealed some genetic variation, but confirmed severe founder events in both the Pacific and Atlantic introduction ranges. Our study thus exemplifies the need for extreme caution in interpreting neutral genetic diversity as a proxy for invasive potential. Our results confirm a previously hypothesized transoceanic secondary introduction from NE Pacific to Europe. However, the SNP panel unexpectedly revealed two additional distinct genetic origins of introductions. Also, conversely to scenarios based on historical records, southern rather than northern NE Pacific populations could have seeded most of the European populations. Finally, the most recently introduced populations showed the lowest selfing rates, suggesting higher levels of recombination might be beneficial at the early stage of the introduction process (i.e., facilitating evolutionary novelties), whereas uniparental reproduction might be favored later in sustainably established populations (i.e., sustaining local adaptation).Agence Nationale de la Recherche - ANR-10-BTBR-04; European Regional Development Fund; Fundacao para a Ciencia e a Tecnologia - SFRH/BPD/107878/2015, UID/Multi/04326/2016, UID/Multi/04326/2019; Brittany Region;info:eu-repo/semantics/publishedVersio

Characterization and comparison of bacterial communities of an invasive and two native Caribbean seagrass species sheds light on the possible influence of the microbiome on invasive mechanisms

Invasive plants, including marine macrophytes, are one of the most important threats to biodiversity by displacing native species and organisms depending on them. Invasion success is dependent on interactions among living organisms, but their study has been mostly limited to negative interactions while positive interactions are mostly underlooked. Recent studies suggested that microorganisms associated with eukaryotic hosts may play a determinant role in the invasion process. Along with the knowledge of their structure, taxonomic composition, and potential functional profile, understanding how bacterial communities are associated with the invasive species and the threatened natives (species-specific/environmentally shaped/tissue-specific) can give us a holistic insight into the invasion mechanisms. Here, we aimed to compare the bacterial communities associated with leaves and roots of two native Caribbean seagrasses (Halodule wrightii and Thalassia testudinum) with those of the successful invader Halophila stipulacea, in the Caribbean island Curaçao, using 16S rRNA gene amplicon sequencing and functional prediction. Invasive seagrass microbiomes were more diverse and included three times more species-specific core OTUs than the natives. Associated bacterial communities were seagrass-specific, with higher similarities between natives than between invasive and native seagrasses for both communities associated with leaves and roots, despite their strong tissue differentiation. However, with a higher number of OTUs in common, the core community (i.e., OTUs occurring in at least 80% of the samples) of the native H. wrightii was more similar to that of the invader H. stipulacea than T. testudinum, which could reflect more similar essential needs (e.g., nutritional, adaptive, and physiological) between native and invasive, in contrast to the two natives that might share more environment-related OTUs. Relative to native seagrass species, the invasive H. stipulacea was enriched in halotolerant bacterial genera with plant growth-promoting properties (like Halomonas sp. and Lysinibacillus sp.) and other potential beneficial effects for hosts (e.g., heavy metal detoxifiers and quorum sensing inhibitors). Predicted functional profiles also revealed some advantageous traits on the invasive species such as detoxification pathways, protection against pathogens, and stress tolerance. Despite the predictive nature of our findings concerning the functional potential of the bacteria, this investigation provides novel and important insights into native vs. invasive seagrasses microbiome. We demonstrated that the bacterial community associated with the invasive seagrass H. stipulacea is different from native seagrasses, including some potentially beneficial bacteria, suggesting the importance of considering the microbiome dynamics as a possible and important influencing factor in the colonization of non-indigenous species. We suggest further comparison of H. stipulacea microbiome from its native range with that from both the Mediterranean and Caribbean habitats where this species has a contrasting invasion success. Also, our new findings open doors to a more in-depth investigation combining meta-omics with bacterial manipulation experiments in order to confirm any functional advantage in the microbiome of this invasive seagrass.CEECINST/00114/2018info:eu-repo/semantics/publishedVersio

CMB power spectrum parameter degeneracies in the era of precision cosmology

Cosmological parameter constraints from the CMB power spectra alone suffer several well-known degeneracies. These degeneracies can be broken by numerical artefacts and also a variety of physical effects that become quantitatively important with high-accuracy data e.g. from the Planck satellite. We study degeneracies in models with flat and non-flat spatial sections, non-trivial dark energy and massive neutrinos, and investigate the importance of various physical degeneracy-breaking effects. We test the CAMB power spectrum code for numerical accuracy, and demonstrate that the numerical calculations are accurate enough for degeneracies to be broken mainly by true physical effects (the integrated Sachs-Wolfe effect, CMB lensing and geometrical and other effects through recombination) rather than numerical artefacts. We quantify the impact of CMB lensing on the power spectra, which inevitably provides degeneracy-breaking information even without using information in the non-Gaussianity. Finally we check the numerical accuracy of sample-based parameter constraints using CAMB and CosmoMC. In an appendix we document recent changes to CAMB's numerical treatment of massive neutrino perturbations, which are tested along with other recent improvements by our degeneracy exploration results.Comment: 27 pages, 28 figures. Latest CAMB version available from http://camb.info/. Reduced number of figures, plot legend corrected and minor edits to match published versio

Marine forests of the Mediterranean-Atlantic Cystoseira tamariscifolia complex show a southern Iberian genetic hotspot and no reproductive isolation in parapatry

Climate-driven range-shifts create evolutionary opportunities for allopatric divergence and subsequent contact, leading to genetic structuration and hybrid zones. We investigate how these processes influenced the evolution of a complex of three closely related Cystoseira spp., which are a key component of the Mediterranean-Atlantic seaweed forests that are undergoing population declines. The C. tamariscifolia complex, composed of C. tamariscifolia s.s., C. amentacea and C. mediterranea, have indistinct boundaries and natural hybridization is suspected. Our aims are to (1) infer the genetic structure and diversity of these species throughout their distribution ranges using microsatellite markers to identify ancient versus recent geographical populations, contact zones and reproductive barriers, and (2) hindcast past distributions using niche models to investigate the influence of past range shifts on genetic divergence at multiple spatial scales. Results supported a single, morphologically plastic species the genetic structure of which was incongruent with a priori species assignments. The low diversity and low singularity in northern European populations suggest recent colonization after the LGM. The southern Iberian genetic hotspot most likely results from the role of this area as a climatic refugium or a secondary contact zone between differentiated populations or both. We hypothesize that life-history traits (selfing, low dispersal) and prior colonization effects, rather than reproductive barriers, might explain the observed genetic discontinuities.Pew Charitable Trusts (USA); MARINERA, Spain [CTM2008-04183-E/MAR]; FCT (Portugal) [FCT-BIODIVERSA/004/2015, CCMAR/Multi/04326/2013, SFRH/BPD/107878/2015, SFRH/BPD/85040/2012]; FPU fellowship of the Spanish Ministry of Education; European Community ASSEMBLE visiting grant [00399/2012]; University of Cadi

An evaluation of clone detection techniques for identifying crosscutting concerns

Code implementing a crosscutting concern is often spread over many different parts of an application. Identifying such code automatically greatly improves both the maintainability and the evolvability of the application. First of all, it allows a developer to more easily find the places in the code that must be changed when the concern changes, and thus makes such changes less time consuming and less prone to errors. Second, it allows a developer to refactor the code, so that it uses modern and more advanced abstraction mechanisms, thereby restoring its modularity. In this paper, we evaluate the suitability of clone detection as a technique for the identification of crosscutting concerns. To that end, we manually identify four specific concerns in an industrial C application, and analyze to what extent clone detection is capable of finding these concerns. We consider our results as a stepping stone toward an automated 'concern miner' based on clone detection

An inventory of psychosocial oncological interventions in The Netherlands:identifying availability, gaps, and overlap in care provision

Purpose: While a wide range of psychosocial oncological (PO) interventions has been developed, a systematic overview of interventions to inform patients, care providers, as well as researchers, policy makers and health insurers, is lacking. The aims of this paper were (1) to describe the attainment of this overview, which may be used in other jurisdictions and for other health conditions and (2) to reflect on what determines developments in this field. Methods: Dutch researchers and care providers were invited to describe PO-interventions they apply in research or clinical practice. Selection criteria for what constituted a PO-intervention were determined. The input was organized in 12 predefined categories (e.g. physical functioning, genetics). Findings: Sixty-six PO-interventions were included in the overview. Two major categories were psychosocial functioning (24%) and physical functioning and recovery (24%). Interventions are mostly directed at adults (65%) and not aimed at a specific type of cancer (61%). Nearly 25% of the interventions lacked scientific underpinning. Conclusions: This paper provides an overview of Dutch PO-interventions and input on what drives their development. The categorizing method can be used in other jurisdictions and for other health care conditions. A next step would be to investigate the effectiveness and evidence of PO-interventions. Implications for Psychosocial Providers and Policy: The open access overview of interventions provides referral information for care providers. By identifying possible gaps and overlap, the overview looks at possible drivers behind developments in this field which will be of interest to policy makers

Integrating reproductive phenology in ecological niche models changed the predicted future ranges of a marine invader

Aim Phenology of a wide diversity of organisms has a dependency on climate, usually with reproductive periods beginning earlier in the year and lasting longer at lower latitudes. Temperature and day length are known environmental drivers of the reproductive timing of many species. Hence, reproductive phenology is sensitive to warming and is important to be considered for reliable predictions of species distributions. This is particularly relevant for rapidly spreading non-indigenous species (NIS). In this study, we forecast the future ranges of a NIS, the seaweed Sargassum muticum, including its reproductive phenology. Location Coastal areas of the Northern Hemisphere (Pacific and Atlantic oceans). Methods We used ecological niche modelling to predict the distribution of S. muticum under two scenarios forecasting limited (RCP 2.6) and severe (RCP 8.5) future climate changes. We then refined our predictions with a hybrid model using sea surface temperature constraints on reproductive phenology. Results Under the most severe climate change scenario, we predicted northward expansions which may have significant ecological consequences for subarctic coastal ecosystems. However, in lower latitudes, habitats currently occupied by S. muticum will no longer be suitable, creating opportunities for substantial community changes. The temperature constraints imposed by the reproductive window were shown to restrict the modelled future species expansion strongly. Under the RCP 8.5 scenario, the total range area was expected to increase by 61.75% by 2100, but only by 1.63% when the reproductive temperature window was considered. Main conclusions Altogether these results exemplify the need to integrate phenology better to improve the prediction of future distributional shifts at local and regional scales.Agência financiadora Número do subsídio Fundacao para a Ciencia e a Tecnologia CCMAR/Multi/04326/2019 FCT-BIODIVERSA/004/2015 FCT-SEAS-ERA/0001/2012 SFRH/BPD/107878/2015 SFRH/BPD/85040/2012 Erasmus Mundus Doctoral Programme MARES on Marine Ecosystem Health Conservation MARES_13_08 Pew Marineinfo:eu-repo/semantics/publishedVersio

Program transformations using temporal logic side conditions

This paper describes an approach to program optimisation based on transformations, where temporal logic is used to specify side conditions, and strategies are created which expand the repertoire of transformations and provide a suitable level of abstraction. We demonstrate the power of this approach by developing a set of optimisations using our transformation language and showing how the transformations can be converted into a form which makes it easier to apply them, while maintaining trust in the resulting optimising steps. The approach is illustrated through a transformational case study where we apply several optimisations to a small program