Recent Submissions

• Journal Article

The Economy of Canopy Space Occupation and Shade Production in Early- to Late-Successional Temperate Tree Species and Their Relation to Productivity ﻿

Forests 2020; 11(3) p.1-18: Art. 317
Light capture is linked to occupation of canopy space by tree crowns, which requires investment of carbon and nutrients. We hypothesize that (i) late-successional trees invest more in casting shade than in occupying space than early-successional trees, and (ii) shade production and crown volume expansion are generally greater in more productive species. For six Central European early-successional (Betula pendula, Pinus sylvestris), mid/late-successional (Quercus petraea, Carpinus betulus), and late-successional tree species (Tilia cordata, Fagus sylvatica), we measured through full-tree harvests (1) crown volume, (2) the costs of canopy space exploration (carbon (C) and nutrients invested to fill crown volume), of space occupation (annual foliage production per volume), and of shade production (foliage needed to reduce light transmittance), and (3) related the costs to aboveground productivity (ANPP). The C and nutrient costs of canopy volume exploration and occupation were independent of the species’ seral stage, but increased with ANPP. In contrast, the cost of shade production decreased from early-to late-successional species, suggesting that the economy of shade production is more decisive for the competitive superiority of late-successional species than the economy of canopy space exploration and occupation.
• Journal Article

Biomass, Morphology, and Dynamics of the Fine Root System Across a 3,000-M Elevation Gradient on Mt. Kilimanjaro ﻿

Frontiers in Plant Science 2020; 11 p.1-16: Art. 13
Fine roots (≤2 mm) consume a large proportion of photosynthates and thus play a key role in the global carbon cycle, but our knowledge about fine root biomass, production, and turnover across environmental gradients is insufficient, especially in tropical ecosystems. Root system studies along elevation transects can produce valuable insights into root trait-environment relationships and may help to explore the evidence for a root economics spectrum (RES) that should represent a trait syndrome with a trade-off between resource acquisitive and conservative root traits. We studied fine root biomass, necromass, production, and mean fine root lifespan (the inverse of fine root turnover) of woody plants in six natural tropical ecosystems (savanna, four tropical mountain forest types, tropical alpine heathland) on the southern slope of Mt. Kilimanjaro (Tanzania) between 900 and 4,500 m a.s.l. Fine root biomass and necromass showed a unimodal pattern along the slope with a peak in the moist upper montane forest (~2,800 m), while fine root production varied little between savanna and upper montane forest to decrease toward the alpine zone. Root:shoot ratio (fine root biomass and production related to aboveground biomass) in the tropical montane forest increased exponentially with elevation, while it decreased with precipitation and soil nitrogen availability (decreasing soil C:N ratio). Mean fine root lifespan was lowest in the ecosystems with pronounced resource limitation (savanna at low elevation, alpine heathland at high elevation) and higher in the moist and cool forest belt (~1,800–3,700 m). The variation in root traits across the elevation gradient fits better with the concept of a multi-dimensional RES, as root tissue density and specific root length showed variable relations to each other, which does not agree with a simple trade-off between acquisitive and conservative root traits. In conclusion, despite large variation in fine root biomass, production, and morphology among the different plant species and ecosystems, a general belowground shift in carbohydrate partitioning is evident from 900 to 4,500 m a.s.l., suggesting that plant growth is increasingly limited by nutrient (probably N) shortage toward higher elevations.
• Journal Article

Notes on the leaf insects of the genus Phyllium of Sumatra and Java, Indonesia, including the description of two new species with purple coxae (Phasmatodea, Phylliidae) ﻿

ZooKeys 2020; 913 p.89-126
Within the last two years, the leaf insects of the genus Phyllium of both the islands of Java and Sumatra have been reviewed extensively based on morphological observations. However, cryptic species which cannot be differentiated morphologically may be present among the various populations. Since it has frequently been demonstrated that analyses based on molecular data can bring clarity in such cases, we conducted a phylogenetic analysis based on three genes (nuclear gene 28S and mitochondrial genes COI and 16S) from the Phyllium species of these islands. The results show distinct molecular divergence for several populations and suggest the presence of two new cryptic species, morphologically inseparable from Phyllium hausleithneri Brock, 1999. From Sumatra, the population originally thought to be a range expansion for Phyllium hausleithneri, is now here described as Phyllium nisus sp. nov., with the only consistent morphological difference being the color of the eggs between the two populations (dark brown in P. hausleithneri and tan in P. nisus sp. nov.). Further, an additional population with purple coxae from Java was morphologically examined and found to have no consistent features to separate it morphologically from the other purple coxae species. This cryptic species from Java was however shown to be molecularly distinct from the other purple coxae populations from Sumatra and Peninsular Malaysia and is here described as Phyllium gardabagusi sp. nov. In addition, Phyllium giganteum is here officially reported from Java for the first time based on both historic and modern records of male specimens.
• Journal Article

Dbp5/DDX19 between Translational Readthrough and Nonsense Mediated Decay ﻿

International Journal of Molecular Sciences 2020; 21(3) p.1-13: Art. 1085
The DEAD-box protein Dbp5 (human DDX19) remodels RNA-protein complexes. Dbp5 functions in ribonucleoprotein export and translation termination. Termination occurs, when the ribosome has reached a stop codon through the Dbp5 mediated delivery of the eukaryotic termination factor eRF1. eRF1 contacts eRF3 upon dissociation of Dbp5, resulting in polypeptide chain release and subsequent ribosomal subunit splitting. Mutations in DBP5 lead to stop codon readthrough, because the eRF1 and eRF3 interaction is not controlled and occurs prematurely. This identifies Dbp5/DDX19 as a possible potent drug target for nonsense suppression therapy. Neurodegenerative diseases and cancer are caused in many cases by the loss of a gene product, because its mRNA contained a premature termination codon (PTC) and is thus eliminated through the nonsense mediated decay (NMD) pathway, which is described in the second half of this review. We discuss translation termination andNMDin the light of Dbp5/DDX19 and subsequently speculate on reducing Dbp5/DDX19 activity to allow readthrough of the PTC and production of a full-length protein to detract the RNA from NMD as a possible treatment for diseases.
• Journal Article

A Collection of 13 Archaeal and 46 Bacterial Genomes Reconstructed from Marine Metagenomes Derived from the North Sea ﻿

Data 2020; 5(1) p.1-5: Art. 15
Marine bacteria are key drivers of ocean biogeochemistry. Despite the increasing number of studies, the complex interaction of marine bacterioplankton communities with their environment is still not fully understood. Additionally, our knowledge about prominent marine lineages is mostly based on genomic information retrieved from single isolates, which do not necessarily represent these groups. Consequently, deciphering the ecological contributions of single bacterioplankton community members is one major challenge in marine microbiology. In the present study, we reconstructed 13 archaeal and 46 bacterial metagenome-assembled genomes (MAGs) from four metagenomic data sets derived from the North Sea. Archaeal MAGs were a liated to Marine Group II within the Euryarchaeota. Bacterial MAGs mainly belonged to marine groups within the Bacteroidetes as well as alpha- and gammaproteobacteria. In addition, two bacterial MAGs were classified as members of the Actinobacteria and Verrucomicrobiota, respectively. The reconstructed genomes contribute to our understanding of important marine lineages and may serve as a basis for further research on functional traits of these groups.
• Journal Article

Stochastic and Arbitrarily Generated Input Patterns to the Mushroom Bodies Can Serve as Conditioned Stimuli in Drosophila ﻿

Frontiers in Physiology 2020; 11 p.1-15: Art. 53
Single neurons in the brains of insects often have individual genetic identities and can be unambiguously identified between animals. The overall neuronal connectivity is also genetically determined and hard-wired to a large degree. Experience-dependent structural and functional plasticity is believed to be superimposed onto this more-or-less fixed connectome. However, in Drosophila melanogaster, it has been shown that the connectivity between the olfactory projection neurons (OPNs) and Kenyon cells, the intrinsic neurons of the mushroom body, is highly stochastic and idiosyncratic between individuals. Ensembles of distinctly and sparsely activated Kenyon cells represent information about the identity of the olfactory input, and behavioral relevance can be assigned to this representation in the course of associative olfactory learning. Previously, we showed that in the absence of any direct sensory input, artificially and stochastically activated groups of Kenyon cells could be trained to encode aversive cues when their activation coincided with aversive stimuli. Here, we have tested the hypothesis that the mushroom body can learn any stochastic neuronal input pattern as behaviorally relevant, independent of its exact origin. We show that fruit flies can learn thermogenetically generated, stochastic activity patterns of OPNs as conditioned stimuli, irrespective of glomerular identity, the innate valence that the projection neurons carry, or inter-hemispheric symmetry.
• Journal Article

Predictive context biases binocular rivalry in children and adults with no positive relation to two measures of social cognition ﻿

Scientific Reports 2020; 10 p.1-12: Art. 2059
Integration of prior experience and contextual information can help to resolve perceptually ambiguous situations and might support the ability to understand other peoples’ thoughts and intentions, called Theory of Mind. We studied whether the readiness to incorporate contextual information for resolving binocular rivalry is positively associated with Theory-of-Mind-related social cognitive abilities. In children (12 to 13 years) and adults (18 to 25 years), a predictive temporal context reliably modulated the onset of binocular rivalry to a similar degree. In contrast, adult participants scored better on measures of Theory of Mind compared to children. We observed considerable interindividual differences regarding the influence of a predictive context on binocular rivalry, which were associated with differences in sensory eye dominance. The absence of a positive association between predictive effects on perception and Theory of Mind performance suggests that predictive effects on binocular rivalry and higher-level Theory-of-Mind-related abilities stem from different neurocognitive mechanisms. We conclude that the influence of predictive contextual information on basic visual processes is fully developed at an earlier age, whereas social cognitive skills continue to evolve from adolescence to adulthood.
• Journal Article

Parenchyma Abundance in Wood of Evergreen Trees Varies Independently of Nutrients ﻿

Frontiers in Plant Science 2020; 11 p.1-15: Art. 86
The abundance of living cells in wood—mainly as interconnected axial and ray parenchyma networks—varies widely between species. However, the functional significance of this variation and its role in plant ecological strategies is poorly understood, as is the extent to which different parenchyma fractions are favored in relation to soil nutrients and hydraulic functions. We analyzed wood tissue fractions of 16 Australian angiosperm species sampled from two nearby areas with similar climate but very different soil nutrient profiles and investigated structure-function links with soil and tissue nutrient concentrations and other plant traits. We expected the variation in parenchyma fractions to influence nutrient concentrations in wood xylem, and to find species with lower parenchyma fractions and accordingly lower nutrient requirements on lower-nutrient soils. Surprisingly, both axial and ray parenchyma fractions were mostly unrelated to tissue and soil nutrient concentrations, except for nitrogen concentration in stem sapwood. Species from low nutrient soils showed higher fractional P translocation from both leaves and sapwood, but little patterning with respect to tissue nitrogen. While species from high and low nutrient soils clearly clustered along the soil-fertility axis, their tissue composition varied independently from plant functional traits related to construction costs and hydraulic anatomy. Our findings imply that there is considerable variation among species in the nutrient concentrations within different parenchyma tissues. The anatomical composition of wood tissue seems unrelated to plant nutrient requirements. Even though xylem parenchyma is involved in metabolic functions such as nutrient translocation and storage, parenchyma abundance on its own does not directly explain variation in these functions, even in co-occurring species. While parenchyma is highly abundant in wood of angiosperm trees, we are still lacking a convincing ecological interpretation of its variability and role in whole-tree nutrient budgets.
• Journal Article

The number of k-mer matches between two DNA sequences as a function of k and applications to estimate phylogenetic distances ﻿

PLOS ONE 2020; 15(2) p.1-18: Art. e0228070
We study the number $N_k$ of length-k word matches between pairs of evolutionarily related DNA sequences, as a function of k. We show that the Jukes-Cantor distance between two genome sequences—i.e. the number of substitutions per site that occurred since they evolved from their last common ancestor—can be estimated from the slope of a function $F$ that depends on $N_k$ and that is affine-linear within a certain range of $k$. Integers kmin and $k_{max}$ can be calculated depending on the length of the input sequences, such that the slope of $F$ in the relevant range can be estimated from the values $F(k_{min})$ and $F(k_{max})$. This approach can be generalized to so-called $Spaced-word$ $Matches$ $(SpaM)$, where mismatches are allowed at positions specified by a user-defined binary pattern. Based on these theoretical results, we implemented a prototype software program for alignment-free sequence comparison called $Slope-SpaM$. Test runs on real and simulated sequence data show that $Slope-SpaM$ can accurately estimate phylogenetic distances for distances up to around 0.5 substitutions per position. The statistical stability of our results is improved if spaced words are used instead of contiguous words. Unlike previous alignment-free methods that are based on the number of (spaced) word matches, $Slope-SpaM$ produces accurate results, even if sequences share only local homologies.
• Journal Article

The Rise of Apomixis in Natural Plant Populations ﻿

Frontiers in Plant Science 2019; 10: Art. 358
Apomixis, the asexual reproduction via seed, has many potential applications for plant breeding by maintaining desirable genotypes over generations. Since most major crops do not express natural apomixis, it is useful to understand the origin and maintenance of apomixis in natural plant systems. Here, we review the state of knowledge on origin, establishment and maintenance of natural apomixis. Many studies suggest that hybridization, either on diploid or polyploid cytotypes, is a major trigger for the formation of unreduced female gametophytes, which represents the ﬁrst step toward apomixis, and must be combined to parthenogenesis, the development of an unfertilized egg cell. Nevertheless, fertilization of endosperm is still needed for most apomictic plants. Coupling of these three steps appears to be a major constraint for shifts to natural apomixis. Adventitious embryony is another developmental pathway toward apomixis. Establishment of a newly arisen apomictic lineage is often fostered by side- effects of polyploidy. Polyploidy creates an immediate reproductive barrier against the diploid parental and progenitor populations; it can cause a breakdown of genetic self- incompatibility (SI) systems which is needed to establish self-fertility of pseudogamous apomictic lineages; and ﬁnally, polyploidy could indirectly help to establish an apomictic cytotype in a novel ecological niche by increasing adaptive potentials of the plants. This step may be followed by a phase of diversiﬁcation and range expansion, mostly described as geographical parthenogenesis. The utilization of apomixis in crops must consider the potential risks of pollen transfer and introgression into sexual crop ﬁelds, which might be overcome by using pollen-sterile or cleistogamous variants. Another risk is the escape into natural vegetation and potential invasiveness of apomictic plants which needs careful management and consideration of ecological conditions.
• Journal Article

Remotely releasable collar mechanism for medium-sized mammals: an affordable technology to avoid multiple captures ﻿

Wildlife Biology 2019; 2019(1)
Collar-mounted monitoring devices for collecting behavioural or positional data (e.g. sound recorders, accelerometers, GPS, VHF) are increasingly used in wildlife research. Although these tools represent an improvement in terms of data quality, they require capturing animals. Using remotely releasable collars allows for reducing the number of captures by half; however, currently this technology is primarily available for large mammals. Here, we present a locking mechanism design that is remotely releasable and light enough (22 g) for medium-sized mammals (>1 kg), can run in low-power mode for years, is reusable directly after recharge, and has a material cost of less than €50. An Android application operates this mechanism over a Bluetooth connection. We developed custom-purpose software for both the locking mechanism and the Android application. We tested two collars equipped with this locking mechanism in field-like conditions on two ring-tailed lemurs Lemur catta. The release mechanism has an operational range of 10–50 m and can run in active mode (allowing remote release) for several hours. Implementation of the presented release mechanism for collars on medium-sized mammals provides a low-cost solution to reduce the number of captures. We demonstrate that some low-cost technical improvements of tools used for studying wildlife can have significant effects on reducing the stress experienced by animals during capture. Detailed description of this new mechanism design provides a starting-block for potential adaptations for a broader range of species.
• Journal Article

Combining cognitive bias modification training (CBM) and transcranial direct current stimulation (tDCS) to treat binge eating disorder: study protocol of a randomised controlled feasibility trial ﻿

BMJ Open 2019; 9(10): Art. e030023
NTRODUCTION: Binge eating disorder (BED) is a common mental disorder, closely associated with obesity. Existing treatments are only moderately effective with high relapse rates, necessitating novel interventions. This paper describes the rationale for, and protocol of, a feasibility randomised controlled trial (RCT), evaluating the combination of transcranial direct current stimulation (tDCS) and a computerised cognitive training, namely approach bias modification training (ABM), in patients with BED who are overweight or obese. The aim of this trial is to obtain information that will guide decision-making and protocol development in relation to a future large-scale RCT of combined tDCS+ABM treatment in this group of patients, and also to assess the preliminary efficacy of this intervention. METHODS AND ANALYSIS: 66 participants with Diagnostic and Statistical Manual-5 diagnosis of BED and a body mass index (BMI) of ≥25 kg/m2 will be randomly allocated to one of three groups: ABM+real tDCS; ABM+sham tDCS or a wait-list control group. Participants in both intervention groups will receive six sessions of ABM+real/sham tDCS over 3 weeks; engaging in the ABM task while simultaneously receiving bilateral tDCS to the dorsolateral prefrontal cortex. ABM is based on an implicit learning paradigm in which participants are trained to enact an avoidance behaviour in response to visual food cues. Assessments will be conducted at baseline, post-treatment (3 weeks) and follow-up (7 weeks post-randomisation). Feasibility outcomes assess recruitment and retention rates, acceptability of random allocation, blinding success (allocation concealment), completion of treatment sessions and research assessments. Other outcomes include eating disorder psychopathology and related neurocognitive outcomes (ie, delay of gratification and inhibitory control), BMI, other psychopathology (ie, mood), approach bias towards food and surrogate endpoints (ie, food cue reactivity, trait food craving and food intake). ETHICS AND DISSEMINATION: This study has been approved by the North West-Liverpool East Research Ethics Committee. Results will be published in peer-reviewed journals. TRIAL REGISTRATION NUMBER: ISRCTN35717198.
• Journal Article

Distribution of Medically Relevant Antibiotic Resistance Genes and Mobile Genetic Elements in Soils of Temperate Forests and Grasslands Varying in Land Use ﻿

Genes 2020; 11(2): Art. 150
Antibiotic-resistant pathogens claim the lives of thousands of people each year and are currently considered as one of the most serious threats to public health. Apart from clinical environments, soil ecosystems also represent a major source of antibiotic resistance determinants, which can potentially disseminate across distinct microbial habitats and be acquired by human pathogens via horizontal gene transfer. Therefore, it is of global importance to retrieve comprehensive information on environmental factors, contributing to an accumulation of antibiotic resistance genes and mobile genetic elements in these ecosystems. Here, medically relevant antibiotic resistance genes, class 1 integrons and IncP-1 plasmids were quantified via real time quantitative PCR in soils derived from temperate grasslands and forests, varying in land use over a large spatial scale. The generated dataset allowed an analysis, decoupled from regional influences, and enabled the identification of land use practices and soil characteristics elevating the abundance of antibiotic resistance genes and mobile genetic elements. In grassland soils, the abundance of the macrolide resistance gene mefA as well as the sulfonamide resistance gene sul2 was positively correlated with organic fertilization and the abundance of aac(6')-lb, conferring resistance to different aminoglycosides, increased with mowing frequency. With respect to forest soils, the beta-lactam resistance gene blaIMP-12 was significantly correlated with fungal diversity which might be due to the fact that different fungal species can produce beta-lactams. Furthermore, except blaIMP-5 and blaIMP-12, the analyzed antibiotic resistance genes as well as IncP-1 plasmids and class-1 integrons were detected less frequently in forest soils than in soils derived from grassland that are commonly in closer proximity to human activities.
• Journal Article

Facultative mycorrhizal associations promote plant naturalization worldwide ﻿

Ecosphere 2019; 10(11): Art. e02937
Mycorrhizal symbiosis has received relatively little attention as a mechanism explaining plant naturalizations at a global scale. Here, we combined data on vascular plant species occurrences in over 840 mainland and island regions from the Global Naturalized Alien Flora (GloNAF) database with up-to-date databases of mycorrhizal associations. We tested whether the mycorrhizal type (arbuscular, AM; ectomycorrhizal, ECM; and non-mycorrhizal, NM) and status (facultative and obligate) were associated with two measures of naturalization success, (1) naturalization incidence (reflecting the ability to naturalize, and expressed as whether or not a plant species is recorded as naturalized anywhere in the world) and (2) naturalization extent (expressed as the number of GloNAF regions where the species occurs). In total, we found information on mycorrhizal type and status for 3211 naturalized plant species and 4200 non-naturalized plant species. Mycorrhizal plant species, both AM and ECM, were more likely to be naturalized and naturalized to a greater extent than NM plants. The effect of being an AM species was always stronger, with AM species having a greater naturalization extent than ECM species. Being the same mycorrhizal type or status, annual species were generally more likely to be naturalized than perennials. Species with facultative mycorrhizal associations were more successful than those with obligate mycorrhizal associations, but both groups tended to have a greater chance of being naturalized than NM species. These results indicate that being NM is generally less favorable for naturalization. Overall, our results confirm, at the global scale, those of regional studies that facultative association with AM provides plant species with a naturalization advantage. For the first time, we have shown that being mycorrhizal contributes not only to the size of the naturalized range, reflecting the ability to spread, but also to the ability to become naturalized in the first instance.
• Journal Article

Microtiming Deviations and Swing Feel in Jazz ﻿

Scientific Reports 2019; 9(1): Art. 19824
Jazz music that swings has the fascinating power to elicit a pleasant sensation of flow in listeners and the desire to synchronize body movements with the music. Whether microtiming deviations (MTDs), i.e. small timing deviations below the bar or phrase level, enhance the swing feel is highly debated in the current literature. Studies on other groove related genres did not find evidence for a positive impact of MTDs. The present study addresses jazz music and swing in particular, as there is some evidence that microtiming patterns are genre-specific. We recorded twelve piano jazz standards played by a professional pianist and manipulated the natural MTDs of the recordings in systematic ways by quantizing, expanding and inverting them. MTDs were defined with respect to a grid determined by the average swing ratio. The original and manipulated versions were presented in an online survey and evaluated by 160 listeners with various musical skill levels and backgrounds. Across pieces the quantized versions (without MTDs) were rated slightly higher and versions with expanded MTDs were rated lower with regard to swing than the original recordings. Unexpectedly, inversion had no impact on swing ratings except for two pieces. Our results suggest that naturally fluctuating MTDs are not an essential factor for the swing feel.
• Journal Article

Evolutionary transitions toward pair living in nonhuman primates as stepping stones toward more complex societies ﻿

Science Advances 2019; 5(12): Art. eaay1276
Nonhuman primate societies vary tremendously in size and composition, but how and why evolutionary transitions among different states occurred remains highly controversial. In particular, how many times pair living evolved and the social states of the ancestors of pair- and group-living species remains contentious. We examined evolutionary transitions in primate social evolution by using new, independent categorizations of sociality and different phylogenetic hypotheses with a vastly expanded dataset. Using Bayesian phylogenetic comparative methods, we consistently found the strongest support for a model that invokes frequent transitions between solitary ancestors and pair-living descendants, with the latter giving rise to group-living species. This result was robust to systematic variation in social classification, sample size, and phylogeny. Our analyses therefore indicate that pair living was a stepping stone in the evolution of structurally more complex primate societies, a result that bolsters the role of kin selection in social evolution.
• Journal Article

How to Achieve Tax Compliance by the Wealthy: A Review of the Literature and Agenda for Policy ﻿

Social Issues and Policy Review 2019; 14(1) p.108-151
Tax compliance by the wealthy is relevant not only because their contributions are essential to maintain public budgets and social equality, but because their (non)compliance behavior and the perceived (un)fairness of their contributions can fuel social unrest. In this article, after giving a brief history of taxing the wealthy, we review the existing theoretical, empirical, and policy literature on their tax compliance. We discuss how and why the wealthy differ from less affluent taxpayers because of specific interrelated political, social, and psychological conditions. Understanding the psychological mechanisms that determine the tax compliance of the wealthy can provide policy insights on how to better integrate the wealthy in the tax system. Therefore, the present review is also a starting point for new policy approaches to increase tax compliance and tax morale among the wealthy.
• Journal Article

Invasive lumbricid earthworms in North America—Different life histories but common dispersal? ﻿

Journal of Biogeography p.1-12
Aim: Lumbricid earthworms are invasive across northern North America, caus‐ ing notable changes in forest ecosystems. During their range expansion, they en‐ countered harsher climatic conditions compared to their native ranges in short time (~400 years). This study investigated if (a) dispersal barriers, (b) climatic selection or (c) anthropogenic activities, that is fishing bait disposal, structure the dispersal of free‐living earthworm populations. Location: North America, forest habitats along former Wisconsinan glaciation line. Taxon: Lumbricus terrestris, L. rubellus. Methods: Lumbricus terrestris and L. rubellus co‐occur in the same habitats but dif‐ fer in ecology and use as fishing bait. Both species were sampled in five transects ranging from the east to the west coast of northern North America, including major dispersal barriers, three different climate zones, and bait shops near sampling loca‐ tions. Genetic diversity and structure were compared between the two species, and the presence of free‐living bait shop genotypes was assessed using four markers (COI, 16S rDNA, 12S rDNA, and H3). Results: Populations of both species were genetically diverse with some geographic structure, which was more pronounced in L. terrestris than in L. rubellus. Common haplotypes were present in all regions, but locally restricted haplotypes also oc‐ curred. Furthermore, two distinct genetic clades of L. terrestris co‐occurred only in the two most distant transects (Alberta and Minnesota). Genotypes identical to bait individuals were omnipresent in field populations of L. terrestris. Main Conclusions: Genetic diversity was high in both species, and invasive popula‐ tions represented a genetic subset of European earthworms. Geographic and climatic dispersal barriers affected the less mobile species, L. terrestris, resulting in differ‐ ences in genetic structure between the two species. Our results indicate common long‐distance dispersal vectors and vectors affecting only L. terrestris. The roles of climate and anthropogenic activities are discussed, providing additional explanations of dispersal and new insights into establishment of invasive earthworm populations.
• Journal Article

The number of k-mer matches between two DNA sequences as a function of k and applications to estimate phylogenetic distances ﻿

PLOS ONE 2020; 15(2): Art. e0228070
We study the number Nk of length-k word matches between pairs of evolutionarily related DNA sequences, as a function of k. We show that the Jukes-Cantor distance between two genome sequences—i.e. the number of substitutions per site that occurred since they evolved from their last common ancestor—can be estimated from the slope of a function F that depends on Nk and that is affine-linear within a certain range of k. Integers kmin and kmax can be calculated depending on the length of the input sequences, such that the slope of F in the relevant range can be estimated from the values F(kmin) and F(kmax). This approach can be generalized to so-called Spaced-word Matches (SpaM), where mismatches are allowed at positions specified by a user-defined binary pattern. Based on these theoretical results, we implemented a prototype software program for alignment-free sequence comparison called Slope-SpaM. Test runs on real and simulated sequence data show that Slope-SpaM can accurately estimate phylogenetic distances for distances up to around 0.5 substitutions per position. The statistical stability of our results is improved if spaced words are used instead of contiguous words. Unlike previous alignment-free methods that are based on the number of (spaced) word matches, Slope-SpaM produces accurate results, even if sequences share only local homologies.
• Journal Article

Polyclad phylogeny persists to be problematic ﻿

Organisms Diversity & Evolution 2019; 19(4) p.585-608
Two conflicting morphological approaches to polyclad systematics highlight the relevance of molecular data for resolving the interrelationships of Polycladida. In the present study, phylogenetic trees were reconstructed based on a short alignment of the 28S rDNA marker gene with 118 polyclad terminals (24 new) including 100 different polyclad species from 44 genera and 22 families, as well as on a combined dataset using 18S and 28S rDNA genes with 27 polyclad terminals (19 new) covering 26 different polyclad species. In both approaches, Theamatidae and Cestoplanidae were included, two families that have previously been shown to switch from Acotylea to Cotylea. Three different alignment methods were used, both with and without alignment curation by Gblocks, and all alignments were subjected to Bayesian inference and maximum likelihood tree calculations. Over all trees of the combined dataset, an extended majority-rule consensus tree had weak support for Theamatidae and Cestoplanidae as acotyleans, and also the cotylean genera Boninia, Chromyella and Pericelis appeared as acotyleans. With the most inclusive short 28S dataset, on the other hand, there is good support for the aforementioned taxa as cotyleans. Especially with the short 28S matrix, taxon sampling, outgroup selection, alignment method and curation, as well as model choice were all decisive for tree topology. Well-supported parts of the phylogeny over all trees include Pseudocerotoidea, Prosthiostomoidea, Stylochoidea, Leptoplanoidea and Cryptoceloidea, the latter three with new definitions. Unstable positions in the tree were found not only for Theamatidae, Cestoplanidae, Boninia, Chromyella and Pericelis, but also for Anonymus, Chromoplana and Cycloporus.