63 Works

Data from: Species distribution models contribute to determine the effect of climate and interspecific interactions in moving hybrid zones

Jan O. Engler, Dennis Rödder, Ortwin Elle, Axel Hochkirch & Jean Secondi
Climate is a major factor delimiting species’ distributions. However, biotic interactions may also be prominent in shaping geographical ranges, especially for parapatric species forming hybrid zones. Determining the relative effect of each factor and their interaction of the contact zone location has been difficult due to the lack of broad scale environmental data. Recent developments in species distribution modelling (SDM) now allow disentangling the relative contributions of climate and species’ interactions in hybrid zones and...

Data from: Decisive datasets in phylogenomics: lessons from studies on the phylogenetic relationships of primarily wingless insects

Emiliano Dell'Ampio, Karen Meusemann, Nikolaus U. Szucsich, Ralph S. Peters, Benjamin Meyer, Janus Borner, Malte Petersen, Andre J. Aberer, Alexandros Stamatakis, Manfred G. Walzl, Bui Quang Minh, Arndt Von Haeseler, Ingo Ebersberger, Günther Pass & Bernhard Misof
Phylogenetic relationships of the primarily wingless insects are still considered unresolved. Even the most comprehensive phylogenomic studies that addressed this question did not yield congruent results. In order to get a grip on these problems, we here analyzed the sources of incongruence in these phylogenomic studies using an extended transcriptome dataset.Our analyses showed that unevenly distributed missing data can be severely misleading by inflating node support despite the absence of phylogenetic signal. In consequence, only...

Data from: Mitochondrial capture enriches mito-DNA 100 folds enabling PCR-free mitogenomics biodiversity analysis

Shanlin Liu, Xin Wang, Lin Xie, Meihua Tan, Zhenyu Li, Xu Su, Hao Zhang, Bernhard Misof, Karl M. Kjer, Min Tang, Oliver Niehuis, Hui Jiang & Xin Zhou
Biodiversity analyses based on Next Generation Sequencing (NGS) platforms have developed by leaps and bounds in recent years. A PCR-free strategy, which can alleviate taxonomic bias, was considered as a promising approach to delivering reliable species compositions of targeted environments. The major impediment of such a method is the lack of appropriate mitochondrial DNA enrichment ways. Because mitochondrial genomes (mitogenomes) make up only a small proportion of total DNA, PCR-free methods will inevitably result in...

Data from: Phylogenomics resolves the timing and pattern of insect evolution

Bernhard Misof, Shanlin Liu, Karen Meusemann, Ralph S. Peters, Alexander Donath, Christoph Mayer, Paul B. Frandsen, Jessica Ware, Tomas Flouri, Rolf G. Beutel, Oliver Niehuis, Malte Petersen, Fernando Izquierdo-Carrasco, Torsten Wappler, Jes Rust, Andre J. Aberer, Ulrike Aspöck, Horst Aspöck, Daniela Bartel, Alexander Blanke, Simon Berger, Alexander Böhm, Thomas Buckley, Brett Calcott, Junqing Chen … & Xin Zhou
Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight...

Data from: Exploiting gene families for phylogenomic analysis of myzostomid transcriptome data

Stefanie Hartmann, Conrad Helm, Birgit Nickel, Matthias Meyer, Torsten H. Struck, Ralph Tiedemann, Joachim Selbig & Christoph Bleidorn
BACKGROUND: In trying to understand the evolutionary relationships of organisms, the current flood of sequence data offers great opportunities, but also reveals new challenges with regard to data quality, the selection of data for subsequent analysis, and the automation of steps that were once done manually for single-gene analyses. Even though genome or transcriptome data is available for representatives of most bilaterian phyla, some enigmatic taxa still have an uncertain position in the animal tree...

Data from: Transcriptomic data from panarthropods shed new light on the evolution of insulator binding proteins in insects

Thomas Pauli, Lucia Vedder, Daniel Dowling, Malte Petersen, Karen Meusemann, Alexander Donath, Ralph S. Peters, Lars Podsiadlowski, Christoph Mayer, Shanlin Liu, Xin Zhou, Peter Heger, Thomas Wiehe, Lars Hering, Georg Mayer, Bernhard Misof & Oliver Niehuis
Background Body plan development in multi-cellular organisms is largely determined by homeotic genes. Expression of homeotic genes, in turn, is partially regulated by insulator binding proteins (IBPs). While only a few enhancer blocking IBPs have been identified in vertebrates, the common fruit fly Drosophila melanogaster harbors at least twelve different enhancer blocking IBPs. We screened recently compiled insect transcriptomes from the 1KITE project and genomic and transcriptomic data from public databases, aiming to trace the...

Data from: Diversity and evolution of the transposable element repertoire in arthropods with particular reference to insects

Malte Petersen, David Armisén, Richard Gibbs, Lars Hering, Abderrahman Khila, Georg Mayer, Stephen Richards, Oliver Niehuis & Bernhard Misof
Background: Transposable elements (TEs) are a major component of metazoan genomes and are associated with a variety of mechanisms that shape genome architecture and evolution. Despite the ever-growing number of insect genomes sequenced to date, our understanding of the diversity and evolution of insect TEs remains poor. Results: Here, we present a standardized characterization and an order-level comparison of arthropod TE repertoires, encompassing 62 insect and 11 outgroup species. The insect TE repertoire contains TEs...

Conflicting signal in transcriptomic markers leads to a poorly resolved backbone phylogeny of Chalcidoid wasps

Junxia Zhang, Amelia R.I. Lindsey, Ralph S. Peters, John M. Heraty, Keith R. Hopper, John H. Werren, Ellen O. Martinson, James B. Woolley, Matt J. Yoder & Lars Krogmann
Chalcidoidea (Hymenoptera) are a megadiverse superfamily of wasps with astounding variation in both morphology and biology. Most species are parasitoids and important natural enemies of insects in terrestrial ecosystems. In this study, we explored a transcriptome-based phylogeny of Chalcidoidea and found that poorly resolved relationships could only be marginally improved by adding more genes (a total of 5,591) and taxa (a total of 65), proof-checking for errors of homology and contamination, and decreasing missing data....

Drivers and dynamics of a massive adaptive radiation in cichlid fishes

Fabrizia Ronco, Michael Matschiner, Astrid Böhne, Anna Boila, Heinz H. Büscher, Athimed El Taher, Adrian Indermaur, Milan Malinsky, Virginie Ricci, Ansgar Kahmen, Sissel Jentoft & Walter Salzburger
Adaptive radiation is the likely source of much of the ecological and morphological diversity of life. How adaptive radiations proceed and what determines their extent remains elusive in most cases. Here we report the in-depth examination of the spectacular adaptive radiation of cichlid fishes in African Lake Tanganyika. Based on whole-genome phylogenetic analyses, multivariate morphological measurements of three ecologically relevant trait complexes (body shape, upper oral jaw morphology, and lower pharyngeal jaw shape), scoring of...

Transcriptomic signatures of ageing vary in solitary and social forms of an orchid bee

Alice Séguret, Eckart Stolle, Fernando Fleites-Ayil, Javier Quezada-Euán, Klaus Hartfelder, Karen Meusemann, Mark Harrison, Antonella Soro & Robert Paxton
Eusocial insect queens are remarkable in their ability to maximise both fecundity and longevity, thus escaping the typical trade-off between these two traits. Several mechanisms have been proposed to underlie the remoulding of the trade-off, such as reshaping of the juvenile hormone pathway, or caste-specific susceptibility to oxidative stress. However, it remains a challenge to disentangle the molecular mechanisms underlying the remoulding of the trade-off in eusocial insects from caste-specific physiological attributes that have subsequently...

Data from: Eco-genomic analysis of the poleward range expansion of the wasp spider Argiope bruennichi shows rapid adaptation and genomic admixture

Henrik Krehenwinkel, Dennis Rödder & Diethard Tautz
Poleward range expansions are commonly attributed to global change, but could alternatively be driven by rapid evolutionary adaptation. A well-documented example of a range expansion during the past decades is provided by the European wasp spider Argiope bruennichi. Using ecological niche modeling, thermal tolerance experiments and a genome-wide analysis of gene expression divergence, we show that invasive populations have adapted to novel climatic conditions in the course of their expansion. Their climatic niche shift is...

Data from: Molecular diversity of Germany’s freshwater fishes and lampreys assessed by DNA barcoding

Thomas Knebelsberger, Andreas R. Dunz, Dirk Neumann & Matthias F. Geiger
This study represents the first comprehensive molecular assessment of freshwater fishes and lampreys from Germany. We analysed COI sequences for almost 80% of the species mentioned in the current German Red List. In total, 1056 DNA barcodes belonging to 92 species from all major drainages were used to (i) build a reliable DNA barcode reference library, (ii) test for phylogeographic patterns, (iii) check for the presence of barcode gaps between species and (iv) evaluate the...

Data from: Re-assessing the diversity of negative strand RNA viruses in insects

Simon Käfer, Sofia Paraskevopoulou, Florian Zirkel, Nicolas Wieseke, Alexander Donath, Malte Petersen, Terry C. Jones, Shanlin Liu, Xin Zhou, Martin Middendorf, Sandra Junglen, Bernhard Misof & Christian Drosten
The spectrum of viruses in insects is important for subjects as diverse as public health, veterinary medicine, food production, and biodiversity conservation. The traditional interest in vector-borne diseases of humans and livestock has drawn the attention of virus studies to hematophagous insect species. However, these represent only a tiny fraction of the broad diversity of Hexapoda, the most speciose group of animals. Here, we systematically probed the diversity of negative strand RNA viruses in the...

Data from: Sex-biased dispersal obscures species boundaries in integrative species delimitation approaches

Jonas Eberle, Erika Bazzato, Silvia Fabrizi, Michele Rossini, Mariastella Colomba, Davide Cillo, Marco Uliana, Ignazio Sparacio, Guido Sabatinelli, Rachel Warnock, Giuseppe Carpaneto & Dirk Ahrens
Accurate delimitation of species is crucial for a stable taxonomy, which provides the foundation for the study of evolutionary biology, ecology and essentially all biological disciplines. Several approaches towards impartial and repeatable taxonomic practices are available but all existing methods have potentially unacceptable shortcomings. In particular, problems can arise when the underlying model assumptions are violated, for instance in the presence of reduced gene flow. This is observed in the context of sex-biased dispersal, which...

Niches and radiations: A case study on the Andean Sapphire-vented Puffleg (Eriocnemis luciani) and Coppery-naped Puffleg (E. sapphiropygia) (Aves, Trochilidae)

Paolo Ramoni-Perazzi, Karl-L. Schuchmann, André Weller, Irma Alejandra Soto-Werschitz & Marcelo Passamani
The interaction between ecology and evolution, particularly with regard to speciation processes, remains a main topic of scientific research. Andean hummingbirds have undergone a remarkable radiation, with many species exhibiting patchy distributions and, in some cases, taxonomic controversy. An example is the Sapphire-vented Puffleg (Eriocnemis luciani; ssp. baptistae, luciani, and meridae), which some authors merge with the Coppery-naped Puffleg (E. sapphiropygia; ssp. catharina and sapphiropygia). Each group is distributed either north or south from the...

ZFMK Diptera collection

The dipteran collection at the Zoological Research Museum Alexander Koenig contains some 300,000 specimens of more than 6000 species. The majority of specimens are pinned, but also includes of large alcohol collection of Tipulidae s.lat. In addition to 327 primary types (excluding the Phoridae), 32 are represented by syntypes and 295 species represented by secondary types. The holdings include the following important specialist collections: Phoridae (H. Schmitz, E. Beyer, E. Baumann), Tipuloidea (B. Mannheims, H....

ZFMK Opiliones collection

The collections of basal arthropods including Opiliones at the Zoological Research Museum Alexander Koenig Bonn

Midgut transcriptome assessment of the cockroach-hunting wasp Ampulex compressa (Apoidea: Ampulicidae)

Manuela Sann, Jovana M. Jasso-Martínez, Alexander Donath, Dieter Schulten & Alejandro Zaldívar-Riverón
The emerald jewel wasp Ampulex compressa (Hymenoptera: Ampulicidae) is a solitary wasp that is widely known for its specialized hunting of cockroaches as larvae provision. Adult wasps mainly feed on pollen and nectar, while their larvae feed on the cockroachs’ body, first as ecto- and later as endoparsitoids. Little is known about the expression of digestive, detoxification and stress-response-related genes in the midgut of A. compressa, or about its transcriptional versatility between life stages. To...

ZFMK Ichthyology collection

The ichthyological collection at the Zoological Research Museum Alexander Koenig contains mainly freshwater fishes, with emphasis on South American and later on European, African and Asian species.

Ecological variation drives morphological differentiation in a highly social vertebrate

Annika Freudiger, Dario Josi, Timo Thünken, Fabian Herder, Jana Flury, David Marques, Michael Taborsky & Joachim Frommen
1. Animals may respond to ecological heterogeneity by genetic differentiation or phenotypic plasticity. Responses of organisms to their ecology can include adaptation at various levels of organization, including morphology, behaviour and social structure. Adaptations at one level might con-strain or enhance adaptations on other levels, which highlights the importance of understanding their interactions. 2. In highly social animals, understanding the influence of ecology on the evolution and maintenance of complex social organization poses an intriguing...

Standardized nuclear markers improve and homogenize species delimitation in Metazoa

Lars Dietz, Jonas Eberle, Christoph Mayer, Sandra Kukowka, Claudia Bohacz, Hannes Baur, Marianne Espeland, Bernhard A. Huber, Carl Hutter, Ximo Mengual, Ralph S. Peters, Miguel Vences, Thomas Wesener, Keith Willmott, Bernhard Misof, Oliver Niehuis & Dirk Ahrens
Species are the fundamental units of life and evolution. Their recognition is essential for science and society. Molecular methods have been increasingly employed for the identification of animal species, despite several challenges. Here, we explore with genomic data from nine animal lineages a set of nuclear markers, namely metazoan-level universal single-copy orthologs (metazoan USCOs), for their use in species delimitation. Our data sets include arthropods and vertebrates. We use various data assembly strategies and employ...

Data from: Phylogeographic analysis of Ligia oceanica (Crustacea: Isopoda) reveals two deep divergent mitochondrial lineages

Michael Raupach, Olaf Bininda-Emonds, Thomas Knebelsberger, Silke Laakmann, Jobst Pfaender & Florian Leese
Isopods of the species Ligia oceanica are typical inhabitants of the rocky intertidal of the northern European coastline. The aim of this study was to assess the genetic structure of this species using mitochondrial and nuclear sequence data. We analysed partial mitochondrial cytochrome c oxidase subunit I (CO1) and 16S rRNA gene sequence data of 161 specimens collected from ten sites ranging from Spain to Norway. For selected specimens, we also sequenced the hypervariable V7...

Data from: Isolation and characterization of nine polymorphic microsatellite markers for the deep-sea shrimp Nematocarcinus lanceopes (Crustacea: Decapoda: Caridea)

Johannes Dambach, Michael J. Raupach, Christoph Mayer, Julia Schwarzer & Florian Leese
BACKGROUND: The shrimp Nematocarcinus lanceopes Bate, 1888 is found in the deep sea around Antarctica and sub-Antarctic islands. Previous studies on mitochondrial data and species distribution models provided evidence for a homogenous circum-Antarctic population of N. lanceopes. However, to analyze the fine-scale population genetic structure and to examine influences of abiotic environmental conditions on population composition and genetic diversity, a set of fast evolving nuclear microsatellite markers is required. FINDINGS: We report the isolation and...

Data from: Age estimates for an adaptive lake fish radiation, its mitochondrial introgression, and an unexpected sister group: Sailfin silversides of the Malili Lakes system in Sulawesi

Björn Stelbrink, Isabella Stöger, Renny K. Hadiaty, Ulrich K. Schliewen & Fabian Herder
Background: The Malili Lakes system in central Sulawesi (Indonesia) is a hotspot of freshwater biodiversity in the Wallacea, characterized by endemic species flocks like the sailfin silversides (Teleostei: Atherinomorpha: Telmatherinidae) radiation. Phylogenetic reconstructions of these freshwater fishes have previously revealed two Lake Matano Telmatherina lineages (sharpfins and roundfins) forming an ancient monophyletic group, which is however masked by introgressive hybridization of sharpfins with riverine populations. The present study uses mitochondrial data, newly included taxa, and...

Data from: Reconstructing Asian faunal introductions to eastern Africa from multi-proxy biomolecular and archaeological datasets

Mary E. Prendergast, Michael Buckley, Alison Crowther, Heidi Eager, Laurent Frantz, Ophélie Lebrasseur, Rainer Hutterer, Ardern Hulme-Beaman, Wim Van Neer, Katerina Douka, Margaret-Ashley Veall, Eréndira M. Quintana Morales, Verena J. Schuenemann, Ella Reiter, Richard Allen, Evangelos A. Dimopoulos, Richard M. Helm, Ceri Shipton, Ogeto Mwebi, Christiane Denys, Mark C. Horton, Stephanie Wynne-Jones, Jeffrey Fleisher, Chantal Radimilahy, Henry Wright … & Mark Horton
Human-mediated biological exchange has had global social and ecological impacts. In sub-Saharan Africa, several domestic and commensal animals were introduced from Asia in the pre-modern period; however, the timing and nature of these introductions remain contentious. One model supports introduction to the eastern African coast after the mid-first millennium CE, while another posits introduction dating back to 3000 BCE. These distinct scenarios have implications for understanding the emergence of long-distance maritime connectivity, and the ecological...

Registration Year

  • 2022
  • 2021
  • 2020
  • 2019
  • 2018
  • 2017
  • 2016
  • 2015
  • 2014
  • 2013

Resource Types

  • Dataset


  • Zoological Research Museum Alexander Koenig
  • China Agricultural University
  • University of Freiburg
  • University of Bonn
  • Beijing Genomics Institute
  • University of Hamburg
  • University of Tsukuba
  • University of Vienna
  • Sam Ratulangi University
  • Heidelberg Institute for Theoretical Studies