Coupled mutation finder: A new entropy-based method quantifying phylogenetic noise for the detection of compensatory mutations

Background: The detection of significant compensatory mutation signals in multiple sequence alignments (MSAs) is often complicated by noise. A challenging problem in bioinformatics is remains the separation of significant signals between two or more non-conserved residue sites from the phylogenetic noise and unrelated pair signals. Determination of these non-conserved residue sites is as important as the recognition of strictly conserved positions for understanding of the structural basis of protein functions and identification of functionally important residue regions. In this study, we developed a new method, the Coupled Mutation Finder (CMF) quantifying the phylogenetic noise for the detection of compensatory mutations.Results: To demonstrate the effectiveness of this method, we analyzed essential sites of two human proteins: epidermal growth factor receptor (EGFR) and glucokinase (GCK). Our results suggest that the CMF is able to separate significant compensatory mutation signals from the phylogenetic noise and unrelated pair signals. The vast majority of compensatory mutation sites found by the CMF are related to essential sites of both proteins and they are likely to affect protein stability or functionality.Conclusions: The CMF is a new method, which includes an MSA-specific statistical model based on multiple testing procedures that quantify the error made in terms of the false discovery rate and a novel entropy-based metric to upscale BLOSUM62 dissimilar compensatory mutations. Therefore, it is a helpful tool to predict and investigate compensatory mutation sites of structural or functional importance in proteins. We suggest that the CMF could be used as a novel automated function prediction tool that is required for a better understanding of the structural basis of proteins. The CMF server is freely accessible at http://cmf.bioinf.med.uni-goettingen.de

Benefits do not balance costs of biological invasions

Acknowledgments LC was supported by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior—Brasil (Capes)—(001). RNC is funded by the Leverhulme Trust (grant no. ECF-2021-001). CJAB is supported by the Australian Research Council (grant no. CE170100015). SB was supported by the Swiss National Science Foundation through grants no. 31003A_179491 and no. 31BD30_184114. FC is supported by the Biological Invasion Chair of the AXA Research Fund of University Paris Saclay and a salary from the French CNRS.Peer reviewe

A Biodiverse Rich Environment Does Not Contribute to a Better Diet: A Case Study from DR Congo

The potential of biodiversity to increase and sustain nutrition security is increasingly recognized by the international research community. To date however, dietary assessment studies that have assessed how biodiversity actually contributes to human diets are virtually absent. This study measured the contribution of wild edible plants (WEP) to the dietary quality in the high biodiverse context of DR Congo. The habitual dietary intake was estimated from 2 multiple-pass 24 h dietary recalls for 363 urban and 129 rural women. All WEP were collected during previous ethnobotanical investigations and identified and deposited in the National Botanical Garden of Belgium (BR). Results showed that in a high biodiverse region with precarious food security, WEP are insufficiently consumed to increase nutrition security or dietary adequacy. The highest contribution came from Dacryodes edulis in the village sample contributing 4.8% of total energy intake. Considering the nutrient composition of the many WEP available in the region and known by the indigenous populations, the potential to increase nutrition security is vast. Additional research regarding the dietary contribution of agricultural biodiversity and the nutrient composition of WEP would allow to integrate them into appropriate dietary guidelines for the region and pave the way to domesticate the most interesting WEP

A global-scale screening of non-native aquatic organisms to identify potentially invasive species under current and future climate conditions

The threat posed by invasive non-native species worldwide requires a global approach to identify which introduced species are likely to pose an elevated risk of impact to native species and ecosystems. To inform policy, stakeholders and management decisions on global threats to aquatic ecosystems, 195 assessors representing 120 risk assessment areas across all six inhabited continents screened 819 non-native species from 15 groups of aquatic organisms (freshwater, brackish, marine plants and animals) using the Aquatic Species Invasiveness Screening Kit. This multi-lingual decision-support tool for the risk screening of aquatic organisms provides assessors with risk scores for a species under current and future climate change conditions that, following a statistically based calibration, permits the accurate classification of species into high-, medium-and low-risk categories under current and predicted climate conditions. The 1730 screenings undertaken encompassed wide geographical areas (regions, political entities, parts thereof, water bodies, river basins, lake drainage basins, and marine regions), which permitted thresholds to be identified for almost all aquatic organismal groups screened as well as for tropical, temperate and continental climate classes, and for tropical and temperate marine ecoregions. In total, 33 species were identified as posing a 'very high risk' of being or becoming invasive, and the scores of several of these species under current climate increased under future climate conditions, primarily due to their wide thermal tolerances. The risk thresholds determined for taxonomic groups and climate zones provide a basis against which area-specific or climate-based calibrated thresholds may be interpreted. In turn, the risk rankings help decision-makers identify which species require an immediate 'rapid' management action (e.g. eradication, control) to avoid or mitigate adverse impacts, which require a full risk assessment, and which are to be restricted or banned with regard to importation and/or sale as ornamental or aquarium/fishery enhancement. Decision support tools AS-ISK Hazard identification Non-native species Risk analysis Climate changepublishedVersio

A global-scale screening of non-native aquatic organisms to identify potentially invasive species under current and future climate conditions

The threat posed by invasive non-native species worldwide requires a global approach to identify which introduced species are likely to pose an elevated risk of impact to native species and ecosystems. To inform policy, stakeholders and management decisions on global threats to aquatic ecosystems, 195 assessors representing 120 risk assessment areas across all six inhabited continents screened 819 non-native species from 15 groups of aquatic organisms (freshwater, brackish, marine plants and animals) using the Aquatic Species Invasiveness Screening Kit. This multi-lingual decision-support tool for the risk screening of aquatic organisms provides assessors with risk scores for a species under current and future climate change conditions that, following a statistically based calibration, permits the accurate classification of species into high-, medium- and low-risk categories under current and predicted climate conditions. The 1730 screenings undertaken encompassed wide geographical areas (regions, political entities, parts thereof, water bodies, river basins, lake drainage basins, and marine regions), which permitted thresholds to be identified for almost all aquatic organismal groups screened as well as for tropical, temperate and continental climate classes, and for tropical and temperate marine ecoregions. In total, 33 species were identified as posing a ‘very high risk’ of being or becoming invasive, and the scores of several of these species under current climate increased under future climate conditions, primarily due to their wide thermal tolerances. The risk thresholds determined for taxonomic groups and climate zones provide a basis against which area-specific or climate-based calibrated thresholds may be interpreted. In turn, the risk rankings help decision-makers identify which species require an immediate ‘rapid’ management action (e.g. eradication, control) to avoid or mitigate adverse impacts, which require a full risk assessment, and which are to be restricted or banned with regard to importation and/or sale as ornamental or aquarium/fishery enhancement.publishedVersio

Biological invasions are a population-level rather than a species-level phenomenon.

Biological invasions pose a rapidly expanding threat to the persistence, functioning and service provisioning of ecosystems globally, and to socio-economic interests. The stages of successful invasions are driven by the same mechanism that underlies adaptive changes across species in general-via natural selection on intraspecific variation in traits that influence survival and reproductive performance (i.e., fitness). Surprisingly, however, the rapid progress in the field of invasion science has resulted in a predominance of species-level approaches (such as deny lists), often irrespective of natural selection theory, local adaptation and other population-level processes that govern successful invasions. To address these issues, we analyse non-native species dynamics at the population level by employing a database of European freshwater macroinvertebrate time series, to investigate spreading speed, abundance dynamics and impact assessments among populations. Our findings reveal substantial variability in spreading speed and abundance trends within and between macroinvertebrate species across biogeographic regions, indicating that levels of invasiveness and impact differ markedly. Discrepancies and inconsistencies among species-level risk screenings and real population-level data were also identified, highlighting the inherent challenges in accurately assessing population-level effects through species-level assessments. In recognition of the importance of population-level assessments, we urge a shift in invasive species management frameworks, which should account for the dynamics of different populations and their environmental context. Adopting an adaptive, region-specific and population-focused approach is imperative, considering the diverse ecological contexts and varying degrees of susceptibility. Such an approach could improve and refine risk assessments while promoting mechanistic understandings of risks and impacts, thereby enabling the development of more effective conservation and management strategies

Taming the terminological tempest in invasion science

Standardized terminology in science is important for clarity of interpretation and communication. In invasion science — a dynamic and quickly evolving discipline — the rapid proliferation of technical terminology has lacked a standardized framework for its language development. The result is a convoluted and inconsistent usage of terminology, with various discrepancies in descriptions of damages and interventions. A standardized framework is therefore needed for a clear, universally applicable, and consistent terminology to promote more effective communication across researchers, stakeholders, and policymakers. Inconsistencies in terminology stem from the exponential increase in scientific publications on the patterns and processes of biological invasions authored by experts from various disciplines and countries since the 1990s, as well as publications by legislators and policymakers focusing on practical applications, regulations, and management of resources. Aligning and standardizing terminology across stakeholders remains a prevailing challenge in invasion science. Here, we review and evaluate the multiple terms used in invasion science (e.g. 'non-native', 'alien', 'invasive' or 'invader', 'exotic', 'non-indigenous', 'naturalized, 'pest') to propose a more simplified and standardized terminology. The streamlined framework we propose and translate into 28 other languages is based on the terms (i) 'non-native', denoting species transported beyond their natural biogeographic range, (ii) 'established non-native', i.e. those non-native species that have established self-sustaining populations in their new location(s) in the wild, and (iii) 'invasive non-native' — populations of established non-native species that have recently spread or are spreading rapidly in their invaded range actively or passively with or without human mediation. We also highlight the importance of conceptualizing 'spread' for classifying invasiveness and 'impact' for management. Finally, we propose a protocol for classifying populations based on (1) dispersal mechanism, (2) species origin, (3) population status, and (4) impact. Collectively and without introducing new terminology, the framework that we present aims to facilitate effective communication and collaboration in invasion science and management of non-native species

Knowledge needs in economic costs of invasive species facilitated by canalisation

Canals provide wide-ranging economic benefits, while also serving as corridors for the introduction and spread of aquatic alien species, potentially leading to negative ecological and economic impacts. However, to date, no comprehensive quantifications of the reported economic costs of these species have been done. Here, we used the InvaCost database on the monetary impact of invasive alien species to identify the costs of those facilitated by three major canal systems: the European Inland Canals, Suez Canal, and Panama Canal. While we identified a staggering number of species having spread via these systems, monetary costs have been reported only for a few. A total of $33.6 million in costs have been reported from species linked to European Inland Canals (the fishhook waterflea Cercopagis pengoi and the zebra mussel Dreissena polymorpha) and$8.6 million linked to the Suez Canal (the silver-cheeked toadfish Lagocephalus sceleratus, the lionfish Pterois miles, and the nomad jellyfish Rhopilema nomadica), but no recorded costs were found for species facilitated by the Panama Canal. We thus identified a pervasive lack of information on the monetary costs of invasions facilitated by canals and highlighted the uneven distribution of costs