Sarah Bourlat

Research Museum Alexander Koenig | ZFMK · Centre for Biodiversity Monitoring (ZBM)

Deuterostomes comprise vertebrates, the related invertebrate chordates (tunicates and cephalochordates) and three other invertebrate taxa: hemichordates, echinoderms and Xenoturbella. The relationships between invertebrate and vertebrate deuterostomes are clearly important for understanding our own distant origins. Recent phylogenetic studies of ch...

This viewpoint paper explores the potential of genomics technology to provide accurate, rapid, and cost efficient observations of the marine environment. The use of such approaches in next generation marine monitoring programs will help achieve the goals of marine legislation implemented world-wide. Genomic methods can yield faster results from mon...

This volume presents the latest protocols for both laboratory and bioinformatics based analyses in the field of marine genomics. The chapters presented in the book cover a wide range of topics, including the sampling and genomics of bacterial communities, DNA extraction in marine organisms, high-throughput sequencing of whole mitochondrial genomes,...

Forest habitats host enormous diversity, but little is known about the seasonal turnover of arthropod species between the above- and below ground forest layers. In this study, we used metabarcoding approaches to uncover arthropod diversity in different forest types and seasons. Our study shows that metabarcoding soil eDNA and Malaise trap bulk samp...

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...

Insects are crucial for ecosystem health but climate change and pesticide use are driving massive insect decline. To mitigate this loss, we need new and effective monitoring techniques. Over the past decade there has been a shift to DNA-based techniques. We describe key emerging techniques for sample collection. We suggest that the selection of too...

Biodiversity monitoring is an important tool to document rapid ecosystem changes and on-going species loss by collecting high-resolution biodiversity data over long periods of time. Large-scale monitoring provides long-range information on species occurrence, interactions, and migrations. In the German project "Automated Multisensor Stations for Mo...

Abstract DNA metabarcoding is routinely used for biodiversity assessment, especially targeting highly diverse groups for which limited taxonomic expertise is available. Various protocols are currently in use, although standardization is key to its application in large‐scale monitoring. DNA metabarcoding of arthropod bulk samples can be either condu...

DNA metabarcoding is routinely used for biodiversity assessment, especially targeting highly diverse groups for which limited taxonomic expertise is available. Various protocols are currently in use, although standardization is key to its application in large-scale monitoring. DNA metabarcoding of arthropod bulk samples can be either conducted dest...

Rapid changes of the biosphere observed in recent years are caused by both small and large scale drivers, like shifts in temperature, transformations in land-use, or changes in the energy budget of systems. While the latter processes are easily quantifiable, documentation of the loss of biodiversity and community structure is more difficult. Change...

Background Small and rare specimens can remain undetected when metabarcoding is applied on bulk samples with a high specimen size heterogeneity. This is especially critical for Malaise trap samples, where most of the biodiversity is contributed by small taxa with low biomass. The separation of samples in different size fractions for downstream anal...

Insect declines and biodiversity loss have attracted much attention in recent years, but lack of comprehensive data, conflicting interests among stakeholders and insufficient policy guidance hinder progress in preserving biodiversity. The project DINA (Diversity of Insects in Nature protected Areas) investigates insect communities in 21 nature rese...

Declines of large predatory fish due to overexploitation are restructuring food webs across the globe. It is now becoming evident that restoring these altered food webs requires addressing not only ecological processes, but evolutionary ones as well, because human‐induced rapid evolution may in turn affect ecological dynamics. We studied the potent...

Metabarcoding has proven to be a powerful tool to assess ecological patterns and diversity from different habitats. Terrestrial invertebrate diversity is frequently based on bulk samples, which require comparatively high sampling effort. With environmental DNA (eDNA) metabarcoding, field sampling effort can be reduced while increasing the number of...

Fishing and translocation of marine species for use in aquaculture is widespread. Corkwing, goldsinny, and ballan wrasse (Symphodus melops, Ctenolabrus rupestris, and Labrus bergylta) are fished on the Swedish west coast for use as cleaner-fish in Norwegian salmon farms. Here, we aim to provide knowledge and recommendations to support ecosystem-bas...

To stop biodiversity loss, new methods are needed to measure extinction risk, especially for aquatic invertebrates. Today extinction risk is measured by the Red List of Threatened Species. We want to improve the evaluation status for marine crustaceans and freshwater mollusks that today are missing a red-listing process in most Northern European co...

Small and rare specimens can remain undetected when metabarcoding bulk samples with a high size heterogeneity of specimens. This is especially critical for malaise trap samples, where most of the biodiversity is often contributed by small specimens. How to size sort and in which proportions to pool these samples has not been widely explored. We set...

Environmental DNA studies targeting multiple taxa using metabarcoding provide remarkable insights into levels of species diversity in any habitat. The main drawbacks are presence of primer bias and difficulty in identifying rare species. We tested a DNA sequence‐capture method in parallel with the metabarcoding approach to reveal possible advantage...

Declines of large predatory fish due to overexploitation are restructuring food webs across the globe. It is now becoming evident that restoring these altered food webs requires addressing not only ecological processes, but evolutionary ones as well, because human-induced rapid evolution may in turn affect ecological dynamics. In the central Baltic...

Background: Fungi are heterotrophic, unicellular or filamentous organisms that exhibit a wide range of different lifestyles as, e.g., symbionts, parasites, and saprotrophs. Mycologists have traditionally considered fungi to be a nearly exclusively terrestrial group of organisms, but it is now known that fungi have a significant presence in aquatic...

Background:In today’s biodiversity crisis, there is an urgent need tomonitor aquatic species in their natural habitats, especially those that may be endangered or elusive. Traditional species observation methods, based on acoustic or observational surveys, are inefficient, costly, and time consuming. Environmental DNA (eDNA) allows us to detectspec...

The rainforests of Amazonia comprise some of the most biologically diverse ecosystems on Earth. Despite this high biodiversity, little is known about how landscape changes that took place in deep history have affected the assembly of its species, and whether the impact of such changes on biodiversity can still be observed. Here, we present a hypoth...

The three-spined stickleback (Gasterosteus aculeatus L., hereafter ‘stickleback’) is a common mesopredatory fish in marine, coastal and freshwater areas. In large parts of the Baltic Sea, stickleback densities have increased >10-fold during the last decades, and it is now one of the dominating fish species both in terms of biomass and effects on lo...

Summary of some studies on three-spined stickleback diet. (DOCX)

Taxa found in three-spined stickleback stomachs as revealed by DNA metabarcoding (Primates and Aves excluded). Items in italics were considered as secondary/ accidental prey %Fbar- frequency of occurrence (percentage of stomachs in which a prey was present). (DOCX)

Diet of three-spined stickleback as revealed by visual stomach content analysis. %Fvis—the percentage of stomachs in which a prey was present. (DOCX)

Stickleback size (total length, mm) distribution in a sample. (TIF)

Gammaridae size distribution in the bays studied. (TIF)

Comparison of quantification from OTU reads and results of visual stomach content analysis. (DOCX)

Precision and reliability of barcode-based biodiversity assessment can be affected at several steps during acquisition and analysis of data. Identification of operational taxonomic units (OTUs) is one of the crucial steps in the process and can be accomplished using several different approaches, namely, alignment-based, probabilistic, tree-based an...

Aim: The aim of this study was to assess the biodiversity and community structure of Swedish meiofaunal eukaryotes using metabarcoding. To validate the reliability of the metabarcoding approach, we compare the taxonomic resolution obtained using the mitochondrial cytochrome oxidase 1 (COI) 'mini-barcode' and nuclear 18S small ribosomal subunit (18S...

OTUs identified to species level in the samples using 97% sequence similarity, all organism groups

OTU table for 18S

OTU table for COI

Background Making forecasts about biodiversity and giving support to policy relies increasingly on large collections of data held electronically, and on substantial computational capability and capacity to analyse, model, simulate and predict using such data. However, the physically distributed nature of data resources and of expertise in advanced...

This protocol details the preparation of multiplexed amplicon libraries for metabarcoding (amplicon-based) studies of microscopic marine eukaryotes. Metabarcoding studies, based on the amplification of a taxonomically informative marker from a collection of organisms or an environmental sample, can be performed to analyze biodiversity patterns or p...

Amplicon-based studies of marine microscopic eukaryotes, also referred to as metabarcoding studies, can be performed to analyze patterns of biodiversity or predator–prey interactions targeting the mitochondrial cytochrome oxidase 1 (CO1) or the small ribosomal subunit (SSU) markers. Because high-throughput sequencing (HTS) Illumina platforms provid...

Marine biological invasions have increased with the development of global trading, causing the homogenization of communities and the decline of biodiversity. A main vector is ballast water exchange from shipping. This study evaluates the use of ecological niche modelling (ENM) to predict the spread of 18 non-indigenous species (NIS) along shipping...

Aim: The Baltic Sea is one of the world's largest semi-enclosed brackish water bodies characterized by many special features, including endemic species that may be particularly threatened by climate change. We mapped potential distribution patterns under present and future conditions for a community with three trophic levels. We analysed climate-i...

Data provider names for occurrence records downloaded from GBIF. Appendix S2 Data references from a literature survey for all study species (a) and occurrence records manually geo-referenced by species (b–e). Appendix S3 Occurrence records from museum material (a) and material collected by S. Leidenberger (b).

This report summarizes the proceedings of the 14 th workshop of the Genomic Standards Con-sortium (GSC) held at the University of Oxford in September 2012. The primary goal of the workshop was to work towards the launch of the Genomic Observatories (GOs) Network un-der the GSC. For the first time, it brought together potential GOs sites, GSC member...

This report describes the work that has been performed in the Ballast Water Option in the framework of the ESA GSE project Marcoast-2. The Option was dedicated to provide an assessment of the combination of Earth Observation data with modelling and biological data for questions arising with the ballast water topic.

Xenoturbella bocki, a marine animal with a simple body plan, has recently been suggested to be sister group to the Acoelomorpha, together forming the new phylum Xenacoelomorpha. The phylogenetic position of the phylum is still under debate, either as an early branching bilaterian or as a sister group to the Ambulacraria (hemichordates and echinoder...

An unhatched embryo rotating counter-clockwise within the fertilization envelope. An outer extracellular layer is present outside the thicker fertilization envelope. Moving cilia are visible on the surface of the embryo.

An embryo five days after hatching, the same individual as shown in Figure 2f. It is held in place with a cover slip with the anterior to the left. It can contract and change shape using internal musculature.

Newly hatched stage swimming with a clockwise rotation when seen from the posterior.

An embryo three days after hatching, swimming near the water surface at the edge of the culture dish. It abruptly changes direction when the apical tuft touches the wall.

Obst, M., Nakano, H., Bourlat, S.J., Thorndyke, M.C., Telford, M.J., Nyengaard, J.R. and Funch, P. 2011. Spermatozoon ultrastructure of Xenoturbella bocki (Westblad 1949). —Acta Zoologica (Stockholm) 92: 109–115. Here, we report on the sperm ultrastructure of Xenoturbella bocki (Westblad 1949), which we studied for the first time in detail using li...

Supplemental Figs. S1-3. Gene order comparison with CREX (number of common intervals, breakpoint distances); phylogenetic analysis under exclusion of Acoela and Nemertodermatida; phylogenetic analysis under exclusion of Xenoturbella.

Acoels are simply organized unsegmented worms, lacking hindgut and anus. Several publications over recent years challenge the long-held view that acoels are early offshoots of the flatworms. Instead a basal position as sister group to all other bilaterian animals was suggested, mainly based on molecular evidence. This led to the view that features...

Ecdysozoa is a clade composed of eight phyla, three of which - arthropods, tardigrades, and onychophorans - share segmentation and have appendages, and the remaining five - nematodes, nematomorphs, priapulids, kinorhynchs, and loriciferans - are worms with an anterior proboscis or introvert. Ecdysozoa contains the vast majority of animal species an...

Background Mitochondrial genome comparisons contribute in multiple ways when inferring animal relationships. As well as primary sequence data, rare genomic changes such as gene order, shared gene boundaries and genetic code changes, which are unlikely to have arisen through convergent evolution, are useful tools in resolving deep phylogenies. Xenot...

Assumed phylogeny of Bilateria. Assumed phylogeny of Bilateria (12 echinoderms, 2 hemichordates, 6 urochordates, 3 ecdysozoans and 17 lophotrochozoans for which mitochondrial genomes are available), used in the breakpoint and inversion analyses. The phylogeny was constructed from a number of different sources (see main text).

Primer pairs and fragment sizes obtained in mitochondrial genome amplification.

Genetic code and codon usage of all protein coding genes from the mitochondrial genome of Xenoturbella bocki.

Hypotheses tested for the phylogenetic position of Xenoturbella bocki. Different hypotheses were tested by using breakpoint and inversion scores for the phylogenetic affiliation of Xenoturbella: X1 – basal vertebrate; X2 – basal cephalochordate; X3 – basal chordate; X4 – basal ambulacrarian; X5 – basal echinoderm; X6 – basal hemichordate; X7 – basa...

Annotation of the Xenoturbella bocki mitochondrial genome. Position, orientation, size, start and stop codons of protein coding and tRNA genes as well as gaps along the circular mitochondrial genome of Xenoturbella bocki.

Species used in the breakpoint and inversion analyses. Genbank accession numbers of the mitochondrial genomes used in breakpoint and inversion analyses.