Zoological Research Museum Alexander Koenig

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 to the Early Devonian (~406 Ma), of major extant lineages to the Mississippian (~345 Ma), and the major diversification of holometabolous insects to the Early Cretaceous. Our phylogenomic study provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects.

Although research on human-mediated exchanges of species has substantially intensified during the last centuries, we know surprisingly little about temporal dynamics of alien species accumulations across regions and taxa. Using a novel database of 45,813 first records of 16,926 established alien species, we show that the annual rate of first records worldwide has increased during the last 200 years, with 37% of all first records reported most recently (1970-2014). Inter-continental and inter-taxonomic variation can be largely attributed to the diaspora of European settlers in the nineteenth century and to the acceleration in trade in the twentieth century. For all taxonomic groups, the increase in numbers of alien species does not show any sign of saturation and most taxa even show increases in the rate of first records over time. This highlights that past efforts to mitigate invasions have not been effective enough to keep up with increasing globalization.

Functional traits offer a rich quantitative framework for developing and testing theories in evolutionary biology, ecology and ecosystem science. However, the potential of functional traits to drive theoretical advances and refine models of global change can only be fully realised when species-level information is complete. Here we present the AVONET dataset containing comprehensive functional trait data for all birds, including six ecological variables, 11 continuous morphological traits, and information on range size and location. Raw morphological measurements are presented from 90,020 individuals of 11,009 extant bird species sampled from 181 countries. These data are also summarised as species averages in three taxonomic formats, allowing integration with a global phylogeny, geographical range maps, IUCN Red List data and the eBird citizen science database. The AVONET dataset provides the most detailed picture of continuous trait variation for any major radiation of organisms, offering a global template for testing hypotheses and exploring the evolutionary origins, structure and functioning of biodiversity.

MAXENT is now a common species distribution modeling (SDM) tool used by conservation practitioners for predicting the distribution of a species from a set of records and environmental predictors. However, datasets of species occurrence used to train the model are often biased in the geographical space because of unequal sampling effort across the study area. This bias may be a source of strong inaccuracy in the resulting model and could lead to incorrect predictions. Although a number of sampling bias correction methods have been proposed, there is no consensual guideline to account for it. We compared here the performance of five methods of bias correction on three datasets of species occurrence: one "virtual" derived from a land cover map, and two actual datasets for a turtle (Chrysemys picta) and a salamander (Plethodon cylindraceus). We subjected these datasets to four types of sampling biases corresponding to potential types of empirical biases. We applied five correction methods to the biased samples and compared the outputs of distribution models to unbiased datasets to assess the overall correction performance of each method. The results revealed that the ability of methods to correct the initial sampling bias varied greatly depending on bias type, bias intensity and species. However, the simple systematic sampling of records consistently ranked among the best performing across the range of conditions tested, whereas other methods performed more poorly in most cases. The strong effect of initial conditions on correction performance highlights the need for further research to develop a step-by-step guideline to account for sampling bias. However, this method seems to be the most efficient in correcting sampling bias and should be advised in most cases.

With the rapid increase of sequenced metazoan mitochondrial genomes, a detailed manual annotation is becoming more and more infeasible. While it is easy to identify the approximate location of protein-coding genes within mitogenomes, the peculiar processing of mitochondrial transcripts, however, makes the determination of precise gene boundaries a surprisingly difficult problem. We have analyzed the properties of annotated start and stop codon positions in detail, and use the inferred patterns to devise a new method for predicting gene boundaries in de novo annotations. Our method benefits from empirically observed prevalances of start/stop codons and gene lengths, and considers the dependence of these features on variations of genetic codes. Albeit not being perfect, our new approach yields a drastic improvement in the accuracy of gene boundaries and upgrades the mitochondrial genome annotation server MITOS to an even more sophisticated tool for fully automatic annotation of metazoan mitochondrial genomes.

BACKGROUND: Partitioning involves estimating independent models of molecular evolution for different subsets of sites in a sequence alignment, and has been shown to improve phylogenetic inference. Current methods for estimating best-fit partitioning schemes, however, are only computationally feasible with datasets of fewer than 100 loci. This is a problem because datasets with thousands of loci are increasingly common in phylogenetics. METHODS: We develop two novel methods for estimating best-fit partitioning schemes on large phylogenomic datasets: strict and relaxed hierarchical clustering. These methods use information from the underlying data to cluster together similar subsets of sites in an alignment, and build on clustering approaches that have been proposed elsewhere. RESULTS: We compare the performance of our methods to each other, and to existing methods for selecting partitioning schemes. We demonstrate that while strict hierarchical clustering has the best computational efficiency on very large datasets, relaxed hierarchical clustering provides scalable efficiency and returns dramatically better partitioning schemes as assessed by common criteria such as AICc and BIC scores. CONCLUSIONS: These two methods provide the best current approaches to inferring partitioning schemes for very large datasets. We provide free open-source implementations of the methods in the PartitionFinder software. We hope that the use of these methods will help to improve the inferences made from large phylogenomic datasets.

BACKGROUND: Phylogenetic and population genetic studies often deal with multiple sequence alignments that require manipulation or processing steps such as sequence concatenation, sequence renaming, sequence translation or consensus sequence generation. In recent years phylogenetic data sets have expanded from single genes to genome wide markers comprising hundreds to thousands of loci. Processing of these large phylogenomic data sets is impracticable without using automated process pipelines. Currently no stand-alone or pipeline compatible program exists that offers a broad range of manipulation and processing steps for multiple sequence alignments in a single process run. RESULTS: Here we present FASconCAT-G, a system independent editor, which offers various processing options for multiple sequence alignments. The software provides a wide range of possibilities to edit and concatenate multiple nucleotide, amino acid, and structure sequence alignment files for phylogenetic and population genetic purposes. The main options include sequence renaming, file format conversion, sequence translation between nucleotide and amino acid states, consensus generation of specific sequence blocks, sequence concatenation, model selection of amino acid replacement with ProtTest, two types of RY coding as well as site exclusions and extraction of parsimony informative sites. Convieniently, most options can be invoked in combination and performed during a single process run. Additionally, FASconCAT-G prints useful information regarding alignment characteristics and editing processes such as base compositions of single in- and outfiles, sequence areas in a concatenated supermatrix, as well as paired stem and loop regions in secondary structure sequence strings. CONCLUSIONS: FASconCAT-G is a command-line driven Perl program that delivers computationally fast and user-friendly processing of multiple sequence alignments for phylogenetic and population genetic applications and is well suited for incorporation into analysis pipelines.

The order Coleoptera (beetles) is arguably the most speciose group of animals, but the evolutionary history of beetles, including the impacts of plant feeding (herbivory) on beetle diversification, remain poorly understood. We inferred the phylogeny of beetles using 4,818 genes for 146 species, estimated timing and rates of beetle diversification using 89 genes for 521 species representing all major lineages and traced the evolution of beetle genes enabling symbiont-independent digestion of lignocellulose using 154 genomes or transcriptomes. Phylogenomic analyses of these uniquely comprehensive datasets resolved previously controversial beetle relationships, dated the origin of Coleoptera to the Carboniferous, and supported the codiversification of beetles and angiosperms. Moreover, plant cell wall-degrading enzymes (PCWDEs) obtained from bacteria and fungi via horizontal gene transfers may have been key to the Mesozoic diversification of herbivorous beetles-remarkably, both major independent origins of specialized herbivory in beetles coincide with the first appearances of an arsenal of PCWDEs encoded in their genomes. Furthermore, corresponding (Jurassic) diversification rate increases suggest that these novel genes triggered adaptive radiations that resulted in nearly half of all living beetle species. We propose that PCWDEs enabled efficient digestion of plant tissues, including lignocellulose in cell walls, facilitating the evolution of uniquely specialized plant-feeding habits, such as leaf mining and stem and wood boring. Beetle diversity thus appears to have resulted from multiple factors, including low extinction rates over a long evolutionary history, codiversification with angiosperms, and adaptive radiations of specialized herbivorous beetles following convergent horizontal transfers of microbial genes encoding PCWDEs.

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.

Butterflies and moths (Lepidoptera) are one of the major superradiations of insects, comprising nearly 160,000 described extant species. As herbivores, pollinators, and prey, Lepidoptera play a fundamental role in almost every terrestrial ecosystem. Lepidoptera are also indicators of environmental change and serve as models for research on mimicry and genetics. They have been central to the development of coevolutionary hypotheses, such as butterflies with flowering plants and moths’ evolutionary arms race with echolocating bats. However, these hypotheses have not been rigorously tested, because a robust lepidopteran phylogeny and timing of evolutionary novelties are lacking. To address these issues, we inferred a comprehensive phylogeny of Lepidoptera, using the largest dataset assembled for the order (2,098 orthologous protein-coding genes from transcriptomes of 186 species, representing nearly all superfamilies), and dated it with carefully evaluated synapomorphy-based fossils. The oldest members of the Lepidoptera crown group appeared in the Late Carboniferous (∼300 Ma) and fed on nonvascular land plants. Lepidoptera evolved the tube-like proboscis in the Middle Triassic (∼241 Ma), which allowed them to acquire nectar from flowering plants. This morphological innovation, along with other traits, likely promoted the extraordinary diversification of superfamily-level lepidopteran crown groups. The ancestor of butterflies was likely nocturnal, and our results indicate that butterflies became day-flying in the Late Cretaceous (∼98 Ma). Moth hearing organs arose multiple times before the evolutionary arms race between moths and bats, perhaps initially detecting a wide range of sound frequencies before being co-opted to specifically detect bat sonar. Our study provides an essential framework for future comparative studies on butterfly and moth evolution.

Abstract The wing surfaces of 97 insect species from virtually all relevant major groups were examined by high resolution scanning‐electron‐microscopy, in order to identify the relationships between the wing microstructures, their wettability with water and their behaviour under the influence of contamination. Isolated wings with contact angles between 31.6° and 155.5° were artificially contaminated with silicate dusts and subsequently fogged until drops of water (“dew”) formed and rolled off. The remaining particles were counted via a digital image analysis system. Remaining particle values between 0.41% and 103% were determined in comparison with unfogged controls. Some insects with very unwettable wings show a highly significant “self‐cleaning” effect under the influence of rain or dew. Detailed analysis revealed that there is a correlation between the wettability and the “SM Index” (quotient of wing surface/(body mass) 0.67 ) with values ranging from 2.42 to 57.0. Furthermore, there is a correlation between the “self‐cleaning” effect and the SM Index, meaning that taxa with a high SM Index, e.g. “large‐winged” Ephemeroptera, Odonata, Planipennia, and many Lepidoptera, have very unwettable wings and show high particle removal due to dripping water drops. The “small‐winged” insects, such as Diptera and Hymenoptera, and insects with elytra, such as Blattariae, Saltatoria, Heteroptera and Coleoptera, show completely opposite effects. This is clearly a result of the fact that species with a high SM Index are, in principle, more restricted in flight by contamination than species with a low SM Index which can also actively clean their own wings. The wings primarily serve a protection function in insects with elytra, so that the effects of contamination are probably of minor importance in these insects. Copyright © 1996 The Royal Swedish Academy of Sciences. Published by Elsevier Science Ltd.

It has been argued that globalization in human-mediated dispersal of species breaks down biogeographic boundaries, yet empirical tests are still missing. We used data on native and alien ranges of terrestrial gastropods to analyze dissimilarities in species composition among 56 globally distributed regions. We found that native ranges confirm the traditional biogeographic realms, reflecting natural dispersal limitations. However, the distributions of gastropods after human transport are primarily explained by the prevailing climate and, to a smaller extent, by distance and trade relationships. Our findings show that human-mediated dispersal is causing a breakdown of biogeographic barriers, and that climate and to some extent socioeconomic relationships will define biogeography in an era of global change.

Hemipteroid insects (Paraneoptera), with over 10% of all known insect diversity, are a major component of terrestrial and aquatic ecosystems. Previous phylogenetic analyses have not consistently resolved the relationships among major hemipteroid lineages. We provide maximum likelihood-based phylogenomic analyses of a taxonomically comprehensive dataset comprising sequences of 2,395 single-copy, protein-coding genes for 193 samples of hemipteroid insects and outgroups. These analyses yield a well-supported phylogeny for hemipteroid insects. Monophyly of each of the three hemipteroid orders (Psocodea, Thysanoptera, and Hemiptera) is strongly supported, as are most relationships among suborders and families. Thysanoptera (thrips) is strongly supported as sister to Hemiptera. However, as in a recent large-scale analysis sampling all insect orders, trees from our data matrices support Psocodea (bark lice and parasitic lice) as the sister group to the holometabolous insects (those with complete metamorphosis). In contrast, four-cluster likelihood mapping of these data does not support this result. A molecular dating analysis using 23 fossil calibration points suggests hemipteroid insects began diversifying before the Carboniferous, over 365 million years ago. We also explore implications for understanding the timing of diversification, the evolution of morphological traits, and the evolution of mitochondrial genome organization. These results provide a phylogenetic framework for future studies of the group.

BACKGROUND: Identification of species via DNA sequences is the basis for DNA taxonomy and DNA barcoding. Currently there is a strong focus on using a mitochondrial marker for this purpose, in particular a fragment from the cytochrome oxidase I gene (COI). While there is ample evidence that this marker is indeed suitable across a broad taxonomic range to delineate species, it has also become clear that a complementation by a nuclear marker system could be advantageous. Ribosomal RNA genes could be suitable for this purpose, because of their global occurrence and the possibility to design universal primers. However, it has so far been assumed that these genes are too highly conserved to allow resolution at, or even beyond the species level. On the other hand, it is known that ribosomal gene regions harbour also highly divergent parts. We explore here the information content of two adjacent divergence regions of the large subunit ribosomal gene, the D1-D2 region. RESULTS: Universal primers were designed to amplify the D1-D2 region from all metazoa. We show that amplification products in the size between 800-1300 bp can be obtained across a broad range of animal taxa, provided some optimizations of the PCR procedure are implemented. Although the ribosomal genes occur in multiple copies in the genomes, we find generally very little intra-individual polymorphism (<< 0.1% on average) indicating that concerted evolution is very effective in most cases. Studies in two fish taxa (genus Cottus and genus Aphyosemion) show that the D1-D2 LSU sequence can resolve even very closely related species with the same fidelity as COI sequences. In one case we can even show that a mitochondrial transfer must have occurred, since the nuclear sequence confirms the taxonomic assignment, while the mitochondrial sequence would have led to the wrong classification. We have further explored whether hybrids between species can be detected with the nuclear sequence and we show for a test case of natural hybrids among cyprinid fish species (Alburnus alburnus and Rutilus rutilus) that this is indeed possible. CONCLUSION: The D1-D2 LSU region is a suitable marker region for applications in DNA based species identification and should be considered to be routinely used as a marker complementing broad scale studies based on mitochondrial markers.

Abstract Comprehensive assessments of species’ extinction risks have documented the extinction crisis 1 and underpinned strategies for reducing those risks 2 . Global assessments reveal that, among tetrapods, 40.7% of amphibians, 25.4% of mammals and 13.6% of birds are threatened with extinction 3 . Because global assessments have been lacking, reptiles have been omitted from conservation-prioritization analyses that encompass other tetrapods 4–7 . Reptiles are unusually diverse in arid regions, suggesting that they may have different conservation needs 6 . Here we provide a comprehensive extinction-risk assessment of reptiles and show that at least 1,829 out of 10,196 species (21.1%) are threatened—confirming a previous extrapolation 8 and representing 15.6 billion years of phylogenetic diversity. Reptiles are threatened by the same major factors that threaten other tetrapods—agriculture, logging, urban development and invasive species—although the threat posed by climate change remains uncertain. Reptiles inhabiting forests, where these threats are strongest, are more threatened than those in arid habitats, contrary to our prediction. Birds, mammals and amphibians are unexpectedly good surrogates for the conservation of reptiles, although threatened reptiles with the smallest ranges tend to be isolated from other threatened tetrapods. Although some reptiles—including most species of crocodiles and turtles—require urgent, targeted action to prevent extinctions, efforts to protect other tetrapods, such as habitat preservation and control of trade and invasive species, will probably also benefit many reptiles.

The Southern Ocean houses a diverse and productive community of organisms 1,2 . Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-adapted diatom from the Southern Ocean, Fragilariopsis cylindrus 8,9 , based on a comparison with temperate diatoms. We find that approximately 24.7 per cent of the diploid F. cylindrus genome consists of genetic loci with alleles that are highly divergent (15.1 megabases of the total genome size of 61.1 megabases). These divergent alleles were differentially expressed across environmental conditions, including darkness, low iron, freezing, elevated temperature and increased CO 2 . Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most pronounced condition-dependent expression, suggesting a correlation between diversifying selection and allelic differentiation. Divergent alleles may be involved in adaptation to environmental fluctuations in the Southern Ocean.

Random similarity of sequences or sequence sections can impede phylogenetic analyses or the identification of gene homologies. Additionally, randomly similar sequences or ambiguously aligned sequence sections can negatively interfere with the estimation of substitution model parameters. Phylogenomic studies have shown that biases in model estimation and tree reconstructions do not disappear even with large data sets. In fact, these biases can become pronounced with more data. It is therefore important to identify possible random similarity within sequence alignments in advance of model estimation and tree reconstructions. Different approaches have been already suggested to identify and treat problematic alignment sections. We propose an alternative method that can identify random similarity within multiple sequence alignments (MSAs) based on Monte Carlo resampling within a sliding window. The method infers similarity profiles from pairwise sequence comparisons and subsequently calculates a consensus profile. This consensus profile represents a summary of all calculated single similarity profiles. In consequence, consensus profiles identify dominating patterns of nonrandom similarity or randomness within sections of MSAs. We show that the approach clearly identifies randomness in simulated and real data. After the exclusion of putative random sections, node support drastically improves in tree reconstructions of both data. It thus appears to be a powerful tool to identify possible biases of tree reconstructions or gene identification. The method is currently restricted to nucleotide data but will be extended to protein data in the near future.

Engel, Michael S, Ceríaco, Luis M P, Daniel, Gimo M, Dellapé, Pablo M, Löbl, Ivan, Marinov, Milen, Reis, Roberto E, Young, Mark T, Dubois, Alain, Agarwal, Ishan, Lehmann A., Pablo, Alvarado, Mabel, Alvarez, Nadir, Andreone, Franco, Araujo-Vieira, Katyuscia, Ascher, John S, Baêta, Délio, Baldo, Diego, Bandeira, Suzana A, Barden, Phillip, Barrasso, Diego A, Bendifallah, Leila, Bockmann, Flávio A, Böhme, Wolfgang, Borkent, Art, Brandão, Carlos R F, Busack, Stephen D, Bybee, Seth M, Channing, Alan, Chatzimanolis, Stylianos, Christenhusz, Maarten J M, Crisci, Jorge V, D'elía, Guillermo, Da Costa, Luis M, Davis, Steven R, De Lucena, Carlos Alberto S, Deuve, Thierry, Fernandes Elizalde, Sara, Faivovich, Julián, Farooq, Harith, Ferguson, Adam W, Gippoliti, Spartaco, Gonçalves, Francisco M P, Gonzalez, Victor H, Greenbaum, Eli, Hinojosa-Díaz, Ismael A, Ineich, Ivan, Jiang, Jianping, Kahono, Sih, Kury, Adriano B, Lucinda, Paulo H F, Lynch, John D, Malécot, Valéry, Marques, Mariana P, Marris, John W M, Mckellar, Ryan C, Mendes, Luis F, Nihei, Silvio S, Nishikawa, Kanto, Ohler, Annemarie, Orrico, Victor G D, Ota, Hidetoshi, Paiva, Jorge, Parrinha, Diogo, Pauwels, Olivier S G, Pereyra, Martín O, Pestana, Lueji B, Pinheiro, Paulo D P, Prendini, Lorenzo, Prokop, Jakub, Rasmussen, Claus, Rödel, Mark-Oliver, Rodrigues, Miguel Trefaut, Rodríguez, Sara M, Salatnaya, Hearty, Sampaio, Íris, Sánchez-García, Alba, Shebl, Mohamed A, Santos, Bruna S, Solórzano-Kraemer, Mónica M, Sousa, Ana C A, Stoev, Pavel, Teta, Pablo, Trape, Jean-François, Dos Santos, Carmen Van-Dúnem, Vasudevan, Karthikeyan, Vink, Cor J, Vogel, Gernot, Wagner, Philipp, Wappler, Torsten, Ware, Jessica L, Wedmann, Sonja, Zacharie, Chifundera Kusamba (2021): EDITORIAL The taxonomic impediment: a shortage of taxonomists, not the lack of technical approaches. Zoological Journal of the Linnean Society 193 (2): 381-387, DOI: 10.1093/zoolinnean/zlab072, URL: https://academic.oup.com/zoolinnean/article/193/2/381/6374389

ABSTRACT To establish a framework for discussing mammalian vocalizations, relevant terminology and concepts from the theory of nonlinear dynamics are introduced. It is suggested that a variety of nonlinear phenomena including subharmonics, biphonation, and deterministic chaos are normally occurring phonatory events. The whole spectrum of these phenomena can be found in the repertoire of the African wild dog Lycaon pictus. In addition, examples of nonlinear phenomena in a wide range of other mammalian taxa will be presented. Moreover, some artifacts in sound spectrographic analysis are listed which may be misinterpreted as nonlinear phenomena. Within the framework of nonlinear dynamics, a consistent terminology is proposed and our observations are related to laryngeal sound production mechanisms. Finally, some hypotheses concerning the communicative potential of the described phenomena are discussed.

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