Florian Leese

Florian Leese
University of Duisburg-Essen | uni-due · Aquatic Ecosystem Research

Prof. Dr. rer. nat.

About

373
Publications
120,085
Reads
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6,683
Citations
Introduction
Interested in molecular ecology, ecological genomics, phylogeography and evolution of aquatic organisms from the poles to the tropical regions. Developing tools for molecular bioassessment of aquatic ecosystems. http://udue.de/leeselab, http://GeneStream.de, http://www.cost.eu/COST_Actions/ca/CA15219, http://www.DNAqua.Net
Additional affiliations
July 2015 - present
University of Duisburg-Essen
Position
  • Professor (Full)
January 2013 - July 2015
Ruhr-Universität Bochum
Position
  • Junior Research Group Leader
Description
  • http://GeneStream.de
January 2008 - December 2012
Ruhr-Universität Bochum
Position
  • PostDoc Position

Publications

Publications (373)
Article
Full-text available
The protection, preservation and restoration of aquatic ecosystems and their functions are of global importance. For European states it became legally binding mainly through the EU-Water Framework Directive (WFD). In order to assess the ecological status of a given water body, aquatic biodiversity data are obtained and compared to a reference water...
Article
Full-text available
Metabarcoding is an emerging genetic tool to rapidly assess biodiversity in ecosystems. It involves high-throughput sequencing of a standard gene from an environmental sample and comparison to a reference database. However, no consensus has emerged regarding laboratory pipelines to screen species diversity and infer species abundances from environm...
Article
Full-text available
Background: The actual connectivity between populations of freshwater organisms is largely determined by species biology, but is also influenced by many area- and site-specific factors, such as water pollution and habitat fragmentation. Therefore, the prediction of effective gene flow, even for well-studied organisms, is difficult. The amphipod cr...
Article
Full-text available
Restriction-site associated DNA sequencing (RAD) has emerged as a powerful marker system for study-ing genome-wide DNA polymorphisms using next-genera-tion sequencing. A recent technical facilitation of RAD is double-digest RAD (ddRAD), which utilizes two restriction enzymes for library preparation. The more flexible and balanced ddRAD allows analy...
Poster
Full-text available
Gelatinous zooplankton (GZP; including salps and cnidarians) are reputed to be climate change winners. This so-called “jellification” is affecting several marine ecosystems worldwide, including the Southern Ocean (SO) in particular which has undergone a significant shift from a krill-based to a salp-based ecosystem over the last decades. A better k...
Article
Full-text available
Recent advances in molecular biomonitoring open new horizons for aquatic ecosystem assessment. Rapid and cost-effective methods based on organismal DNA or environmental DNA (eDNA) now offer the opportunity to produce inventories of indicator taxa that can subsequently be used to assess biodiversity and ecological quality. However, the integration o...
Article
Full-text available
Water flow in river networks is frequently regulated by man‐made in‐stream barriers. These obstacles can hinder dispersal of aquatic organisms and isolate populations leading to the loss of genetic diversity. Although millions of small in‐stream barriers exist worldwide, their impact on dispersal of macroinvertebrates remains unclear. Therefore, we...
Preprint
Full-text available
Background The emergence of DNA taxonomy sparked a paradigm shift in biodiversity assessments and revealed the existence of many morphologically cryptic species in all ecosystems worldwide. For animals, DNA-based assessments of species diversity usually rely on the mitochondrial cytochrome c oxidase subunit I (COI) gene. However, an increasing numb...
Preprint
Full-text available
Background The emergence of DNA taxonomy sparked a paradigm shift in biodiversity assessments and revealed the existence of many morphologically cryptic species in all ecosystems worldwide. For animals, DNA-based assessments of species diversity usually rely on the mitochondrial cytochrome c oxidase subunit I (COI) gene. However, an increasing numb...
Preprint
Full-text available
1. Forest canopies are a highly diverse ecosystem, but despite several decades of intense research, there remain substantial gaps in our knowledge of their biodiversity and ecological interactions. One fundamental challenge in canopy research is the limited accessibility of the ecosystem. Consequently, previous studies have relied on the applicatio...
Article
Full-text available
Global freshwater biodiversity is declining dramatically, and meeting the challenges of this crisis requires bold goals and the mobilisation of substantial resources. While the reasons are varied, investments in both research and conservation of freshwater biodiversity lag far behind those in the terrestrial and marine realms. Inspired by a global...
Article
Full-text available
The cover image is based on the Viewpoint A global agenda for advancing freshwater biodiversity research by Alain Maasri et al., https://doi.org/10.1111/ele.13931. Image Credit: Solvin Zankl. image
Article
Full-text available
The Mediterranean region with its islands is among the top biodiversity hotspots. It houses numerous freshwater taxa with a high rate of endemism, but is heavily impacted by anthropogenic pressures and global climate change. To conserve biodiversity, reliable data on species and genetic diversity are needed especially for the scarcely known insular...
Poster
Full-text available
Many studies in different ecosystems have shown that stressors co-occur and interact with each other to influence organisms. In river networks, local stressors change the quantity and quality of the material that subsidizes downstream sections. However, most of the multiple stressor research has focused on the effects of stressors at the place of t...
Book
Full-text available
This publication is an output from EU COST Action DNAqua-Net (CA 15219 - Developing new genetic tools for bioassessment of aquatic ecosystems in Europe) and would not have been possible without the opportunities for international collaboration provided by the network, supported by COST (European Cooperation in Science and Technology). Therefore, ou...
Article
Full-text available
Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for identification of whole communities within a targeted group) is revolutionizing the field of aquatic biomonitoring. To date, most metabarcoding studies aiming to assess the ecological status of aquatic ecosystems have focused on water eDNA and macroinvertebrate bulk samples....
Article
Full-text available
Metabarcoding of DNA extracted from environmental or bulk specimen samples is increasingly used to profile biota in basic and applied biodiversity research because of its targeted nature that allows sequencing of genetic markers from many samples in parallel. To achieve this PCR amplification is carried out with primers designed to target a taxonom...
Article
Full-text available
Intermittent rivers and ephemeral streams (IRES) – waterways in which flow ceases periodically or that dry completely – are found worldwide, and their frequency and extent are expected to increase in the future in response to global climate change and growing anthropogenic demand for fresh water. Repeated wet–dry cycles generate highly dynamic sett...
Article
Full-text available
Reliable and comprehensive monitoring data are required to trace and counteract biodiversity loss. High-throughput metabarcoding of DNA extracted from community samples (bulk) or from water or sediment (environmental DNA) has revolutionized biomonitoring, given the capability to assess biodiversity across the tree of life rapidly with feasible effo...
Article
Full-text available
Most metabarcoding protocols for invertebrate bulk samples start with sample homogenisation, followed by DNA extraction, amplification of a specific marker region, and sequencing. Many of the above-mentioned laboratory steps have been verified thoroughly and best practice strategies exist, yet, no clear recommendation for the basis of almost all me...
Article
Full-text available
Fast, reliable, and comprehensive biodiversity monitoring data are needed for environmental decision making and management. Recent work on fish environmental DNA (eDNA) metabarcoding shows that aquatic diversity can be captured fast, reliably, and non-invasively at moderate costs. Because water in a catchment flows to the lowest point in the landsc...
Chapter
Ziel der biologischen Systematik ist es, die Vielfalt der Organismen zu ordnen und zu benennen. Die Systematik beschäftigt sich mit der Einteilung (Taxonomie), Benennung (Nomenklatur) und Bestimmung von Lebewesen. Die Rekonstruktion der Stammesgeschichte (Phylogenie) und die Aufklärung der Prozesse und Mechanismen, die zur heutigen Vielfalt der Leb...
Chapter
Die Gesamtheit des Erbmaterials eines Organismus wird als Genom bezeichnet, die Gesamtheit der transkribierten, also abgelesenen und in RNA übersetzten Sequenzen als Transkriptom. Werden Organismengesellschaften mit vielen Individuen und verschiedenen Arten betrachtet spricht man von Metagenomen und Metatranskriptomen. Die genetische Information in...
Chapter
Zu den wichtigsten Voraussetzungen in der Populationsgenetik zählen sogenannte Nullmodelle, die Erwartungswerte unter neutralen Bedingungen, also ohne den Einfluss von Evolutionsfaktoren, formulieren. Mit diesen Erwartungswerten kann man beobachtete Werte vergleichen und die Abweichungen statistisch quantifizieren. Die Hardy-Weinberg-Regel, auch al...
Article
Full-text available
DNA metabarcoding is a powerful tool to assess arthropod diversity in environmental bulk samples such as Malaise trap, pitfall trap, or hand net samples. While comparative performance tests for different extraction protocols, primers, and Taq polymerases have been made, the effect of different PCR volumes on bulk sample metabarcoding performance is...
Preprint
Full-text available
The Mediterranean region with its islands is among top biodiversity hotspots. It houses numerous freshwater taxa with a high rate of endemism, but is heavily impacted by anthropogenic pressures and global climate change. To conserve biodiversity, reliable data on species and genetic diversity are needed especially for the scarcely known insular fre...
Preprint
Full-text available
Metabarcoding of DNA extracted from environmental or bulk specimen samples is increasingly used to detect plant and animal taxa in basic and applied biodiversity research because of its targeted nature that allows sequencing of genetic markers from many samples in parallel. To achieve this, PCR amplification is carried out with primers designed to...
Preprint
Full-text available
Fast, reliable, and comprehensive biodiversity monitoring data are needed for environmental decision making and management. Recent work on fish environmental DNA (eDNA) metabarcoding shows that aquatic diversity can be captured fast, reliably, and non-invasively at moderate costs. Because water in a catchment flows to the lowest point in the landsc...
Preprint
Full-text available
Freshwater biodiversity is declining dramatically, and the current biodiversity crisis requires defining bold goals and mobilizing substantial resources to meet the challenges. While the reasons are varied, both research and conservation of freshwater biodiversity lag far behind efforts in the terrestrial and marine realms. We identify fifteen pres...
Poster
Full-text available
Abstract Fast, reliable, and comprehensive biodiversity monitoring data are needed for environmental decision making and management. Recent work on fish environmental DNA (eDNA) metabarcoding shows that aquatic diversity can be captured fast, reliably, and non-invasively at moderate costs. Because freshwater ecosystems act as sinks in the landscap...
Article
Full-text available
Dear participants of DNAQUA2021 International Conference, Undoubtedly, DNAQUA2021 is a major highlight of the EU COST Action DNAqua-Net (CA15219). Even though we cannot claim that the organisation of DNAQUA2021 was a piece of cake, it is simply wonderful to see the great interest in this event. With 1,498 registered participants from 79 nations, 20...
Article
Full-text available
Bioindication has become an indispensable part of water quality monitoring in most countries of the world, with the presence and abundance of bioindicator taxa, mostly multicellular eukaryotes, used for biotic indices. In contrast, microbes (bacteria, archaea and protists) are seldom used as bioindicators in routine assessments, although they have...
Article
Full-text available
DNA barcoding and metabarcoding is increasingly used to effectively and precisely assess and monitor biodiversity in aquatic ecosystems. As these methods rely on data availability and quality of barcode reference libraries, it is important to develop and follow best practices to ensure optimal quality and traceability of the metadata associated wit...
Preprint
Full-text available
Freshwater biodiversity is declining dramatically, and the current biodiversity crisis requires defining bold goals and mobilizing substantial resources to meet the challenges. While the reasons are varied, both research and conservation of freshwater biodiversity lag far behind efforts in the terrestrial and marine realms. We identify fifteen pres...
Article
Full-text available
Ecological stability under environmental change is determined by both interspecific and intraspecific processes. Particularly for planktonic microorganisms it is challenging to follow intraspecific dynamics over space and time. We propose a new method, Microsatellite PoolSeq Barcoding (MPB), for tracing allele frequency changes in protist populatio...
Article
Full-text available
A recent global meta‐analysis reported a decrease in terrestrial but increase in freshwater insect abundance and biomass (van Klink et al., Science 368, p. 417). The authors suggested that water quality has been improving, thereby challenging recent reports documenting drastic global declines in freshwater biodiversity. We raise two major concerns...
Article
Full-text available
DNA metabarcoding is increasingly used as a tool to assess biodiversity in research and environmental management. Powerful analysis software exists to process raw data. However, the translation of sequence read data into biological information and downstream analyses may be difficult for end users with limited expertise in bioinformatics. Thus, the...
Article
Most animal species on Earth are insects, and recent reports suggest that their abundance is in drastic decline. Although these reports come from a wide range of insect taxa and regions, the evidence to assess the extent of the phenomenon is sparse. Insect populations are challenging to study, and most monitoring methods are labor intensive and ine...
Article
Full-text available
High‐throughput sequencing (HTS) is increasingly being used for the characterisation and monitoring of biodiversity. If applied in a structured way, across broad geographic scales, it offers the potential for a much deeper understanding of global biodiversity through the integration of massive quantities of molecular inventory data generated indepe...
Article
Water is essential to human societies and a prerequisite for flourishing nature, especially in arid regions. Yet, climate change and socio-economic developments are expected to exacerbate current and future stresses on water resources, demanding innovative approaches to balance water needs for society and nature conservation. In this study, we use...
Article
Full-text available
DNA metabarcoding of freshwater communities typically relies on PCR amplification of a fragment of the mitochondrial cytochrome c oxidase I (COI) gene with degenerate primers. The advantage of COI is its taxonomic resolution and the availability of an extensive reference database. However, when universal primers are used on environmental DNA (eDNA)...
Article
Full-text available
Chironomids have been proposed as important indicators for monitoring freshwater ecosystems, however, morphological determination is very challenging. In this study, we investigated the effectiveness of metabarcoding for chironomid diversity assessment and tested the retrieved chironomid operational taxonomic units (OTUs) for possible changes in re...
Article
Macroinvertebrate assemblages are the most common bioindicators used for stream biomonitoring, yet the standard approach exhibits several time‐consuming steps, including the sorting and identification of organisms based on morphological criteria. In this study, we examined if DNA metabarcoding could be used as an efficient molecular‐based alternati...
Article
Full-text available
A multitude of anthropogenic pressures deteriorate the Baltic Sea, resulting in the need to protect and restore its marine ecosystem. For an efficient conservation, comprehensive monitoring and assessment of all ecosystem elements is of fundamental importance. The Baltic Marine Environment Protection Commission HELCOM coordinates conservation measu...
Preprint
River networks are frequently fragmented by in-stream barriers. These man-made obstacles can act as dispersal barriers for aquatic organisms and can isolate populations, thereby increasing the effects of genetic drift and inbreeding, and leading to the loss of genetic diversity. Although millions of small in-stream barriers exist worldwide, such as...
Article
Full-text available
Phylogenetic hypotheses for the peracarid order Cumacea are scarce and have not provided solution to the full extent. In the present study a fragment of the mitochondrial 16S rDNA was used to erect a phylogenetic hypothesis for three cumacean families, Diastylidae, Bodotriidae, and Leuconidae, along with intra-family relationships of the latter. Th...
Article
Full-text available
Taxonomic sufficiency represents the level of taxonomic detail needed to detect ecological patterns to a level that match the requirement of a study. Most bioassessments apply the taxonomic sufficiency concept and assign specimens to the family or genus level given time constraints and the difficulty to correctly identify species. This holds partic...
Preprint
Full-text available
DNA metabarcoding is increasingly used in research and application to assess biodiversity. Powerful analysis software exists to process raw data. However, when it comes to the translation of sequence read data into biological information many end users with limited bioinformatic expertise struggle with the downstream analysis and explore data only...
Preprint
Full-text available
Operational taxonomic units (OTUs) are usually treated as if they are internally uniform in environmental metabarcoding studies of microbial and macrobial eukaryotes, even when the OTUs are being used to infer biogeographic patterns. The OTUs constructed by the program Swarm have underlying network topologies in which nodes represent amplicons and...
Article
DNA metabarcoding of macroinvertebrates is increasingly used for aquatic bioassessment and -monitoring. A major strength of metabarcoding is the high taxonomic resolution provided while the inability to deliver reliable abundance data is regarded a main drawback. Data on the potential of metabarcoding to disentangle site-specific and seasonal varia...
Article
Worldwide, multiple stressors that often lead to complex and non-linear biological responses affect stream ecosystems. Combined stressor effects on ecologically diverse and functionally important macroinvertebrate communities are often difficult to assess (such as species-specific responses of many species, effects of different stressors and stress...
Article
Full-text available
Genetic diversity is the most basal level of biodiversity and determines the evolutionary capacity of species to adapt to changing environments, yet it is typically neglected in routine biomonitoring and stressor impact assessment. For a comprehensive analysis of stressor impacts on genetic diversity, it is necessary to assess genetic variants simu...
Preprint
Full-text available
Most animal species on Earth are insects, and recent reports suggest that their abundance is in drastic decline. Although these reports come from a wide range of insect taxa and regions, the evidence to assess the extent of the phenomenon is still sparse. Insect populations are challenging to study and most monitoring methods are labour intensive a...
Article
Full-text available
DNA metabarcoding workflows produce hundreds to ten-thousands of Operational Taxonomic Units (OTUs) or Exact Sequence Variants (ESVs) per analysis. In most workflows, a taxonomic assignment to these generated sequences is needed. This is typically done using publicly available databases. Especially, yet not exclusively, for Eumetazoan metabarcoding...
Article
Full-text available
A decade after environmental scientists integrated high‐throughput sequencing technologies in their toolbox, the genomics‐based monitoring of anthropogenic impacts on the biodiversity and functioning of ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental genomics to this end, tec...
Preprint
Full-text available
DNA metabarcoding of freshwater communities typically relies on PCR amplification of a fragment of the mitochondrial cytochrome c oxidase (COI) gene with degenerate primers. The advantage of COI is its taxonomic resolution and the availability of an extensive reference database. However, when universal primers are used on environmental DNA (eDNA) i...
Article
Full-text available
Colossendeis megalonyx Hoek, 1881 has the broadest distribution of all sea spiders in the Southern Ocean. Previous studies have detected several evolutionarily young lineages within this taxon and interpreted them as a result of allopatric speciation in a few shelf refuges during glacial maxima. However, alternative scenarios such as ecological spe...
Article
Full-text available
Freshwaters face some of the highest rates of species loss, caused by strong human impact. To decrease or even revert this strong impact, ecological restorations are increasingly applied to restore and maintain the natural ecological status of freshwaters. Their ecological status can be determined by assessing the presence of indicator species (e.g...