DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work

Effective identification of species using short DNA fragments (DNA barcoding and DNA metabarcoding) requires reliable sequence reference libraries of known taxa. Both taxonomically comprehensive coverage and content quality are important for sufficient accuracy. For aquatic ecosystems in Europe, reliable barcode reference libraries are particularly important if molecular identification tools are to be implemented in biomonitoring and reports in the context of the EU Water Framework Directive (WFD) and the Marine Strategy Framework Directive (MSFD). We analysed gaps in the two most important reference databases, Barcode of Life Data Systems (BOLD) and NCBI GenBank, with a focus on the taxa most frequently used in WFD and MSFD. Our analyses show that coverage varies strongly among taxonomic groups, and among geographic regions. In general, groups that were actively targeted in barcode projects (e.g. fish, true bugs, caddisflies and vascular plants) are well represented in the barcode libraries, while others have fewer records (e.g. marine molluscs, ascidians, and freshwater diatoms). We also found that species monitored in several countries often are represented by barcodes in reference libraries, while species monitored in a single country frequently lack sequence records. A large proportion of species (up to 50%) in several taxonomic groups are only represented by private data in BOLD. Our results have implications for the future strategy to fill existing gaps in barcode libraries, especially if DNA metabarcoding is to be used in the monitoring of European aquatic biota under the WFD and MSFD. For example, missing species relevant to monitoring in multiple countries should be prioritized for future collaborative programs. We also discuss why a strategy for quality control and quality assurance of barcode reference libraries is needed and recommend future steps to ensure full utilisation of metabarcoding in aquatic biomonitoring.This paper is a deliverable of the European Cooperation in Science and Technology (COST) Action DNAqua-Net (CA15219) Working Group 1, led by Torbjørn Ekrem and Fedor Čiampor. Thanks to the University of Minho and University of Pécs for hosting workshops and working group meetings. We also thank staff at National Environment Agencies and others that provided national checklists of taxa used in biomonitoring, and otherwise assisted with checklist proof-reading: Jarmila Makovinská and Emília Mišíková Elexová (Slovakia); Steinar Sandøy and Dag Rosland (Norway); Mišel Jelič (Croatia); Marlen Vasquez (Cyprus); Adam Petrusek (Czech Republic); Kristel Panksep (Estonia); Panagiotis Kaspiditis (Greece); Matteo Montagna (Italy); Marija Katarzyte (Lithuania); Ana Rotter (Slovenia); Rosa Trabajo (Spain); Florian Altermatt (Switzerland); Kristian Meissner (Finland), Rigers Bakiu (Albania), Valentina Stamenkovic and Jelena Hinic (Macedonia); Patricia Mergen (Belgium); Gael Denys & the French Biodiversity Agency (France); Mary Kelly-Quinn (Ireland); Piotr Panek and Andrzej Zawal (Poland); Cesare Mario Puzzi (Italy); Carole Fitzpatrick (United Kingdom); Simon Vitecek (Austria); Ana Filipa Filipe (Portugal); Peter Anton Stæhr & Anne Winding (Denmark); Michael Monaghan (Germany); Alain Dohet, Lionel L'Hoste, Nora Welschbillig & Luc Ector (Luxembourg), Lujza Keresztes, (Romania). The authors also want to thank Dirk Steinke for providing the original European ERMS list for marine taxa and Florian Malard for comments on the manuscript. The preparation of the AMBI checklist was carried out in the scope of a Short-term Scientific Mission (ECOST-STSM-CA15219-150217- 082111) granted to SD visiting AZTI, Spain. ZC was supported by grants EFOP-3.6.1.-16-2016-00004 and 20765-3/2018/FEKUTSTRAT. TE was supported by the NorBOL-grant (226134/F50) from the Research Coun cil of Norway. BR, FL and MFG contributed through support from the GBOL project, which is generously funded by the German Federal Min istry of Education and Research (FKZ 01LI1101 and 01LI1501). MG contributed through support of the Polish National Science Centre, grants N N303 5794 39 and 2014/15/B/NZ8/00266. SF was funded by the project PORBIOTA - Portuguese E-Infrastructure for Information and Research on Biodiversity (POCI-01-0145-FEDER-022127), supported by Operational Thematic Program for Competitiveness and Internationalization (POCI), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (FEDER)

Beyond Refugia: New insights on Quaternary climate variation and the evolution of biotic diversity in tropical South America

Haffer’s (Science 165: 131–137, 1969) Pleistocene refuge theory has provided motivation for 50 years of investigation into the connections between climate, biome dynamics, and neotropical speciation, although aspects of the orig- inal theory are not supported by subsequent studies. Recent advances in paleocli- matology suggest the need for reevaluating the role of Quaternary climate on evolutionary history in tropical South America. In addition to the many repeated large-amplitude climate changes associated with Pleistocene glacial-interglacial stages (~40 kyr and 100 kyr cyclicity), we highlight two aspects of Quaternary climate change in tropical South America: (1) an east-west precipitation dipole, induced by solar radiation changes associated with Earth’s precessional variations (~20 kyr cyclicity); and (2) periods of anomalously high precipitation that persisted for centuries-to-millennia (return frequencies ~1500 years) congruent with cold “Heinrich events” and cold Dansgaard-Oeschger “stadials” of the North Atlantic region. The spatial footprint of precipitation increase due to this North Atlantic forcing extended across almost all of tropical South America south of the equator. Combined, these three climate modes present a picture of climate change with different spatial and temporal patterns than envisioned in the original Pleistocene refuge theory. Responding to these climate changes, biomes expanded and contracted and became respectively connected and disjunct. Biome change undoubtedly influenced biotic diversification, but the nature of diversification likely was more complex than envisioned by the original Pleistocene refuge theory. In the lowlands, intermittent forest expansion and contraction led to species dispersal and subsequent isolation, promoting lineage diversification. These pulses of climate-driven biotic interchange profoundly altered the composition of regional species pools and triggered new evolutionary radiations. In the special case of the tropical Andean forests adjacent to the Amazon lowlands, new phylogenetic data provide abundant evidence for rapid biotic diversification during the Pleistocene. During warm interglacials and intersta- dials, lowland taxa dispersed upslope. Isolation in these disjunct climate refugia led to extinction for some taxa and speciation for others.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/155561/1/Baker2020.pdfDescription of Baker2020.pdf : Main articl

Functional traits explain crayfish invasive success in the Netherlands

Biological invasions by nonindigenous species can have negative effects on economies and ecosystems. To limit this impact, current research on biological invasions uses functional traits to facilitate a mechanistic understanding of theoretical and applied questions. Here we aimed to assess the role of functional traits in the progression of crayfish species through different stages of invasion and determine the traits associated with invasive success. A dataset of thirteen functional traits of 15 species currently occurring or available for sale in the Netherlands was evaluated. Six of these crayfish appeared invasive. Important traits distinguishing successful from unsuccessful invaders were a temperate climate in the native range, a medium to high egg count and producing more than one egg clutch per year. The most successful invaders had different functional trait combinations: Procambarus clarkii has a higher reproductive output, can migrate over longer distances and possesses a higher aggression level; Faxonius limosus is adapted to a colder climate, can reproduce parthenogetically and has broader environmental tolerances. Using a suit of functional traits to analyse invasive potential can help risk management and prevention. For example, based on our data Procambarus virginalis is predicted to become the next successful invasive crayfish in the Netherlands.</p

Increased performance of DNA metabarcoding of macroinvertebrates by taxonomic sorting.

DNA-based identification through the use of metabarcoding has been proposed as the next step in the monitoring of biological communities, such as those assessed under the Water Framework Directive (WFD). Advances have been made in the field of metabarcoding, but challenges remain when using complex samples. Uneven biomass distributions, preferential amplification and reference database deficiencies can all lead to discrepancies between morphological and DNA-based taxa lists. The effects of different taxonomic groups on these issues remain understudied. By metabarcoding WFD monitoring samples, we analyzed six different taxonomic groups of freshwater organisms, both separately and combined. Identifications based on metabarcoding data were compared directly to morphological assessments performed under the WFD. The diversity of taxa for both morphological and DNA-based assessments was similar, although large differences were observed in some samples. The overlap between the two taxon lists was 56.8% on average across all taxa, and was highest for Crustacea, Heteroptera, and Coleoptera, and lowest for Annelida and Mollusca. Taxonomic sorting in six basic groups before DNA extraction and amplification improved taxon recovery by 46.5%. The impact on ecological quality ratio (EQR) scoring was considerable when replacing morphology with DNA-based identifications, but there was a high correlation when only replacing a single taxonomic group with molecular data. Different taxonomic groups provide their own challenges and benefits. Some groups might benefit from a more consistent and robust method of identification. Others present difficulties in molecular processing, due to uneven biomass distributions, large genetic diversity or shortcomings of the reference database. Sorting samples into basic taxonomic groups that require little taxonomic knowledge greatly improves the recovery of taxa with metabarcoding. Current standards for EQR monitoring may not be easily replaced completely with molecular strategies, but the effectiveness of molecular methods opens up the way for a paradigm shift in biomonitoring

Questions clés pour la prochaine génération de biosurveillance

International audienceClassical biomonitoring techniques have focused primarily on measures linked tovarious biodiversity metrics and indicator species. Next-generation biomonitoring (NGB)describes a suite of tools and approaches that allow the examination of a broaderspectrum of organizational levels—from genes to entire ecosystems. Here, we frame10 key questions that we envisage will drive the field of NGB over the next decade. Whilenot exhaustive, this list covers most of the key challenges facing NGB, and provides thebasis of the next steps for research and implementation in this field. These questionshave been grouped into current- and outlook-related categories, corresponding to theorganization of this paper

The evolutionary history of Senna ser. Aphyllae (Leguminosae–Caesalpinioideae), an endemic clade of southern South America

In the legume genus Senna, series Aphyllae includes seven species of leafless shrubs and subshrubs from arid, semiarid and xerophilous areas of three different biogeographic subregions in southern South America. In this study, we investigated the evolutionary history of Aphyllae in a molecular phylogenetic framework. We reconstructed phylogenetic relationships among Aphyllae species based on DNA sequence data of four plastid (rpS16, rpL16, matK, trnL-F) and one nuclear (ITS) region from 23 accessions, analyzed with parsimony, Bayesian and maximum likelihood methods. We inferred the evolutionary and biogeographic history estimating divergence times and reconstructing ancestral character states and ancestral areas of distribution. Series Aphyllae was found to be monophyletic, and the taxa formed two main clades: Clade A gathering S. aphylla var. aphylla, S. crassiramea, S. rigidicaulis and S. spiniflora; and Clade B grouping S. acanthoclada, S. aphylla var. divaricata, S. aphylla var. pendula and S. pachyrrhiza. The morphologically complex S. aphylla appears thus polyphyletic. Molecular dating and ancestral area reconstructions suggest that the Aphyllae clade started to diversify in the South American Transition Zone in the Late Pliocene. Based on these results, we hypothesize that this diversification occurred during the last period of Andean uplift with the aridification in South America. The ancestral character state reconstructions suggest that, in addition to the loss of leaves in adult plants, series Aphyllae evolved various morphological features, such as fastigiate, thickened or decumbent–subdecumbent branches during the colonization and establishment in different arid and semiarid lands in South America.EEA SaltaFil: Robbiati, Federico Omar. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Salta; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Anton, Ana Maria Ramona. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Marazzi, Brigitte. Natural History Museum of Cantone Ticino; SuizaFil: Vásquez-Cruz, Marilyn. Instituto de Ecología. Biología Evolutiva; MéxicoFil: Fortunato, Renee Hersilia. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; Argentina. Universidad de Morón. Facultad de Agronomía y Ciencias Agroalimentarias; Argentin