New fossil of Gaoloufangchaeta advances the origin of Errantia (Annelida) to the early Cambrian.

Molecular clock estimates suggest the origin of Annelida dates back to the Ediacaran period, which is in discordance with the first appearance of this taxon in the early Cambrian, as evidenced by the fossil records of stem-group and basally branching crown-group annelids. Using new material from the early Cambrian Guanshan biota (Cambrian Series 2, Stage 4), we re-interpret Gaoloufangchaeta bifurcus Zhao, Li & Selden, 2023, as the earliest known errantian annelid. Gaoloufangchaeta has a prominent anterior end bearing three pairs of putatively sensory appendages and a pair of anterior eyes; a muscular eversible pharynx with papillae is identified. The presence of enlarged parapodia with acicula-like structures and long capillary chaetae suggests a pelagic lifestyle for this taxon. Our phylogenetic analyses recover Gaoloufangchaeta within the Phyllodocida (Pleistoannelida, Errantia), extending the origin of Errantia back to the early Cambrian. Our data are in line with the hypothesis that Annelida diverged before the Cambrian and indicate both morphological and ecological diversification of annelids in the early Cambrian.

Impact of environmental factors on spider silk properties.

Spider orb webs have evolved to stop flying prey, fast and slow alike. One of the main web elements dissipating impact energy is the radial fibers, or major ampullate silks, which possess a toughness surpassing most man-made materials. Orb webs are extended phenotypes, and as such their architectural elements, including major ampullate silks, have been selected to optimize prey capture under the respective environmental conditions. In this study, we investigated the correlation of three landscape scales and three microhabitat characteristics with intrinsic silk properties (elastic modulus, yield stress, tensile strength, extensibility, and toughness) to understand underlying ecological patterns. For this purpose, we collected and mechanically tested major ampullate silks from 50 spider species inhabiting large altitudinal and climatic gradients in Colombia. Using regression analysis and model selection, we investigated the environmental drivers of inter- and intra-specific patterns of major ampullate silk properties, taking into account phylogenetic relatedness based on newly sequenced mitochondrial genomes. We found that the total amount of energy absorbed, i.e., toughness and tensile strength, is higher for fibers from species inhabiting regions where heavy rainfall is common. Interestingly, we observe the same general trend between individuals of the same species, stressing the importance of this environmental driver. We also observe a phylogenetic conservation in the relation of environmental variables with silk tensile strength and yield stress. In conclusion, the increase in major ampullate silk tensile strength and toughness may reflect an adaptation to prevent frequent rain damage to orb webs and the associated energetic loss.

Patchwork: Alignment-Based Retrieval and Concatenation of Phylogenetic Markers from Genomic Data.

Low-coverage whole-genome sequencing (also known as "genome skimming") is becoming an increasingly affordable approach to large-scale phylogenetic analyses. While already routinely used to recover organellar genomes, genome skimming is rather rarely utilized for recovering single-copy nuclear markers. One reason might be that only few tools exist to work with this data type within a phylogenomic context, especially to deal with fragmented genome assemblies. We here present a new software tool called Patchwork for mining phylogenetic markers from highly fragmented short-read assemblies as well as directly from sequence reads. Patchwork is an alignment-based tool that utilizes the sequence aligner DIAMOND and is written in the programming language Julia. Homologous regions are obtained via a sequence similarity search, followed by a "hit stitching" phase, in which adjacent or overlapping regions are merged into a single unit. The novel sliding window algorithm trims away any noncoding regions from the resulting sequence. We demonstrate the utility of Patchwork by recovering near-universal single-copy orthologs within a benchmarking study, and we additionally assess the performance of Patchwork in comparison with other programs. We find that Patchwork allows for accurate retrieval of (putatively) single-copy genes from genome skimming data sets at different sequencing depths with high computational speed, outperforming existing software targeting similar tasks. Patchwork is released under the GNU General Public License version 3. Installation instructions, additional documentation, and the source code itself are all available via GitHub at https://github.com/fethalen/Patchwork.

Evolutionary dynamics of whole-body regeneration across planarian flatworms.

Regenerative abilities vary dramatically across animals. Even amongst planarian flatworms, well-known for complete regeneration from tiny body fragments, some species have restricted regeneration abilities while others are almost entirely regeneration incompetent. Here, we assemble a diverse live collection of 40 planarian species to probe the evolution of head regeneration in the group. Combining quantification of species-specific head-regeneration abilities with a comprehensive transcriptome-based phylogeny reconstruction, we show multiple independent transitions between robust whole-body regeneration and restricted regeneration in freshwater species. RNA-mediated genetic interference inhibition of canonical Wnt signalling in RNA-mediated genetic interference-sensitive species bypassed all head-regeneration defects, suggesting that the Wnt pathway is linked to the emergence of planarian regeneration defects. Our finding that Wnt signalling has multiple roles in the reproductive system of the model species Schmidtea mediterranea raises the possibility that a trade-off between egg-laying, asexual reproduction by fission/regeneration and Wnt signalling drives regenerative trait evolution. Although quantitative comparisons of Wnt signalling levels, yolk content and reproductive strategy across our species collection remained inconclusive, they revealed divergent Wnt signalling roles in the reproductive system of planarians. Altogether, our study establishes planarians as a model taxon for comparative regeneration research and presents a framework for the mechanistic evolution of regenerative abilities.

How genomics can help biodiversity conservation.

The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.

Effect of high temperature on Wolbachia density and impact on cytoplasmic incompatibility in confused flour beetle, Tribolium confusum (Coleoptera: Tenebrionidae).

OBJECTIVES: Environmental constraints, especially temperature, have been identified as a key in understanding host-symbiont relationships, as they can directly impact the fitness of the symbiont population and the host development. Here we investigated the effect of temperature during the host development on the density of intracellular bacteria of the Wolbachia, wTcon strain within the confused flour beetle, Tribolium confusum. The wTcon can induce a complete cytoplasmic incompatibility (CI) in T. confusum beetles; therefore, we observed the effect of heat stress on the symbiont-mediated CI. RESULTS: The density of CI inducing Wolbachia in the Tribolium confusum is temperature-specific. Our observation of the beetles reared in five different temperatures (30-34 °C) measured the highest Wolbachia density at 30-31 °C and lowest at 34 °C within a single insect generation. In this species, changes in the density of Wolbachia related to higher temperature did not influence CI. However, the fertility of beetles reared in higher temperatures showed a substantial decrease in the number of laid and hatched eggs. Thus, we can confirm the effect of high temperature on lowering the wTcon density and no impact on induction of cytoplasmic incompatibility (CI) in T. confusum beetles.

Whole-Genome Sequence of the Wolbachia Strain wTcon, an Endosymbiont of the Confused Flour Beetle, Tribolium confusum.

Up to 60% of insects are infected with symbiont intracellular alphaproteobacteria of the genus Wolbachia, which are often able to manipulate their host's reproduction. Here, we report the annotated draft genome sequence of strain wTcon from the confused flour beetle, Tribolium confusum, based on long- and short-read sequence data. The assembled genome is located on 12 contigs with a total size of 1,418,452 bp.

The era of reference genomes in conservation genomics.

Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics.

Wolbachia Infection in Native Populations of the Invasive Tawny Crazy Ant Nylanderia fulva.

Antagonistic interactions can affect population growth and dispersal of an invasive species. Wolbachia are intracellular endosymbiont bacteria that infect arthropod and nematode hosts and are able to manipulate reproduction, which in some cases leads to cocladogenesis. Moreover, the presence of the strictly maternally transferred Wolbachia in a population can indirectly induce selective sweeps on the hosts' mitochondria. Ants have a Wolbachia infection rate of about 34%, which makes phylogenetic studies using mitochondrial markers vulnerable of being confounded by the effect of the endosymbiont. Nylanderia fulva is an invasive ant native to South America, considered a pest in the United States. Its distribution and biology are poorly known in its native range, and the taxonomic identity of this and its closely related species, Nylanderia pubens, has only recently been understood with the aid of molecular phylogenies. Aiming at estimating robust phylogenetic relationships of N. fulva in its native range, we investigated the presence and pattern of Wolbachia infection in populations of N. fulva from Argentina, part of its native range, to account for its possible effect on the host population structure. Using the ftsZ gene, 30 nests of N. fulva and four from sympatric Nylanderia species were screened for the presence of Wolbachia. We sequenced the MLST genes, the highly variable gene wsp, as well as glyQ, a novel target gene for which new primers were designed. Phylogeny of the ants was estimated using mtDNA (COI). We found supergroup A Wolbachia strains infecting 73% of N. fulva nests and two nests of Nylanderia sp. 1. Wolbachia phylogenetic tree inferred with MLST genes is partially congruent with the host phylogeny topology, with the exception of a lineage of strains shared by ants from different N. fulva clades. Furthermore, by comparing with Wolbachia sequences infecting other ants, we found that the strains infecting different N. fulva clades are not monophyletic. Our findings suggest there are three recent independent horizontally transmitted Wolbachia infections in N. fulva, and we found no evidence of influence of Wolbachia in the host mtDNA based phylogeny.

A new primer pair for barcoding of bees (Hymenoptera: Anthophila) without amplifying the orthologous coxA gene of Wolbachia bacteria.

OBJECTIVES: DNA barcoding became an effective method for the identification and monitoring of bees. However, standard primer pairs used for barcoding often result in (co-) amplification of bacterial endosymbionts of the genus Wolbachia, which are widespread among bee species. Here we designed a new primer pair and compared it with the performance of the standard Folmer-primers for a small sample set of bees representing the main taxonomic groups of bees. RESULTS: The newly designed primer pair (BeeCox1F1/BeeCox1R2) outperformed the standard barcoding primer (LCO1490/HCO2198). By generating barcodes for a small test set of bees we found that the new primer pair produced high-quality sequences in all cases for unambiguous species identification using BOLD. Conversely, the standard barcoding primers often co-amplified the homologous Wolbachia gene and resulted in mixed chromatogram signals. These sequences showed high similarity with the bacterial endosymbiont instead of the host.

Infection Patterns and Fitness Effects of Rickettsia and Sodalis Symbionts in the Green Lacewing Chrysoperla carnea.

Endosymbionts are widely distributed in insects and can strongly affect their host ecology. The common green lacewing (Chrysoperla carnea) is a neuropteran insect which is widely used in biological pest control. However, their endosymbionts and their interactions with their hosts have not been very well studied. Therefore, we screened for endosymbionts in natural and laboratory populations of Ch. carnea using diagnostic PCR amplicons. We found the endosymbiont Rickettsia to be very common in all screened natural and laboratory populations, while a hitherto uncharacterized Sodalis strain was found only in laboratory populations. By establishing lacewing lines with no, single or co-infections of Sodalis and Rickettsia, we found a high vertical transmission rate for both endosymbionts (>89%). However, we were only able to estimate these numbers for co-infected lacewings. Sodalis negatively affected the reproductive success in single and co-infected Ch. carnea, while Rickettsia showed no effect. We hypothesize that the fitness costs accrued by Sodalis infections might be more tolerable in the laboratory than in natural populations, as the latter are also prone to fluctuating environmental conditions and natural enemies. The economic and ecological importance of lacewings in biological pest control warrants a more profound understanding of its biology, which might be influenced by symbionts.

Sex-specific gene expression differences in reproducing Syllis prolifera and Nudisyllis pulligera (Annelida, Syllidae).

Syllidae is an annelid family characterized by its complex life cycles involving some of the most outstanding annelid reproductive strategies. Syllid reproductive modes sometimes imply the modification of the posterior body to form independent reproductive units (schizogamy) or the development of swimming adults (epigamy). These modes of sexual reproduction have been studied for more than 150 years, and yet, little is known regarding their molecular background. Notably, while several studies during the last three decades have revealed details about molecular mechanisms involved in the reproduction of some few model annelids, studies focusing on syllids remain limited. Thus, we performed differential gene expression analyses of female, male, and non-reproducing individuals of Syllis prolifera (schizogamic) and Nudisyllis pulligera (epigamic), as representatives of two different reproductive strategies. For that, transcriptomes from specimens of three conditions (non-reproducing, male, female) were de novo assembled and annotated for S. prolifera and N. pulligera. We found rather similar gene expression profiles for female and non-reproducing individuals, while male gene expression is clearly different. Although previous studies have suggested that femininity in syllids might require additional signalling, our analyses support a scenario, where masculinity may also involve several specific genetic processes.

Urban areas as hotspots for bees and pollination but not a panacea for all insects.

Urbanisation is an important global driver of biodiversity change, negatively impacting some species groups whilst providing opportunities for others. Yet its impact on ecosystem services is poorly investigated. Here, using a replicated experimental design, we test how Central European cities impact flying insects and the ecosystem service of pollination. City sites have lower insect species richness, particularly of Diptera and Lepidoptera, than neighbouring rural sites. In contrast, Hymenoptera, especially bees, show higher species richness and flower visitation rates in cities, where our experimentally derived measure of pollination is correspondingly higher. As well as revealing facets of biodiversity (e.g. phylogenetic diversity) that correlate well with pollination, we also find that ecotones in insect-friendly green cover surrounding both urban and rural sites boost pollination. Appropriately managed cities could enhance the conservation of Hymenoptera and thereby act as hotspots for pollination services that bees provide to wild flowers and crops grown in urban settings.

'Multi-SpaM': a maximum-likelihood approach to phylogeny reconstruction using multiple spaced-word matches and quartet trees.

Word-based or 'alignment-free' methods for phylogeny inference have become popular in recent years. These methods are much faster than traditional, alignment-based approaches, but they are generally less accurate. Most alignment-free methods calculate 'pairwise' distances between nucleic-acid or protein sequences; these distance values can then be used as input for tree-reconstruction programs such as neighbor-joining. In this paper, we propose the first word-based phylogeny approach that is based on 'multiple' sequence comparison and 'maximum likelihood'. Our algorithm first samples small, gap-free alignments involving four taxa each. For each of these alignments, it then calculates a quartet tree and, finally, the program 'Quartet MaxCut' is used to infer a super tree for the full set of input taxa from the calculated quartet trees. Experimental results show that trees produced with our approach are of high quality.

Read-SpaM: assembly-free and alignment-free comparison of bacterial genomes with low sequencing coverage.

BACKGROUND: In many fields of biomedical research, it is important to estimate phylogenetic distances between taxa based on low-coverage sequencing reads. Major applications are, for example, phylogeny reconstruction, species identification from small sequencing samples, or bacterial strain typing in medical diagnostics. RESULTS: We adapted our previously developed software program Filtered Spaced-Word Matches (FSWM) for alignment-free phylogeny reconstruction to take unassembled reads as input; we call this implementation Read-SpaM. CONCLUSIONS: Test runs on simulated reads from semi-artificial and real-world bacterial genomes show that our approach can estimate phylogenetic distances with high accuracy, even for large evolutionary distances and for very low sequencing coverage.

Comparative transcriptomics in Syllidae (Annelida) indicates that posterior regeneration and regular growth are comparable, while anterior regeneration is a distinct process.

BACKGROUND: Annelids exhibit remarkable postembryonic developmental abilities. Most annelids grow during their whole life by adding segments through the action of a segment addition zone (SAZ) located in front of the pygidium. In addition, they show an outstanding ability to regenerate their bodies. Experimental evidence and field observations show that many annelids are able to regenerate their posterior bodies, while anterior regeneration is often limited or absent. Syllidae, for instance, usually show high abilities of posterior regeneration, although anterior regeneration varies across species. Some syllids are able to partially restore the anterior end, while others regenerate all lost anterior body after bisection. Here, we used comparative transcriptomics to detect changes in the gene expression profiles during anterior regeneration, posterior regeneration and regular growth of two syllid species: Sphaerosyllis hystrix and Syllis gracilis; which exhibit limited and complete anterior regeneration, respectively. RESULTS: We detected a high number of genes with differential expression: 4771 genes in S. hystrix (limited anterior regeneration) and 1997 genes in S. gracilis (complete anterior regeneration). For both species, the comparative transcriptomic analysis showed that gene expression during posterior regeneration and regular growth was very similar, whereas anterior regeneration was characterized by up-regulation of several genes. Among the up-regulated genes, we identified putative homologs of regeneration-related genes associated to cellular proliferation, nervous system development, establishment of body axis, and stem-cellness; such as rup and JNK (in S. hystrix); and glutamine synthetase, elav, slit, Hox genes, ß-catenin and PL10 (in S. gracilis). CONCLUSIONS: Posterior regeneration and regular growth show no significant differences in gene expression in the herein investigated syllids. However, anterior regeneration is associated with a clear change in terms of gene expression in both species. Our comparative transcriptomic analysis was able to detect differential expression of some regeneration-related genes, suggesting that syllids share some features of the regenerative mechanisms already known for other annelids and invertebrates.

Divergent evolution in the genomes of closely related lacertids, Lacerta viridis and L. bilineata, and implications for speciation.

BACKGROUND: Lacerta viridis and Lacerta bilineata are sister species of European green lizards (eastern and western clades, respectively) that, until recently, were grouped together as the L. viridis complex. Genetic incompatibilities were observed between lacertid populations through crossing experiments, which led to the delineation of two separate species within the L. viridis complex. The population history of these sister species and processes driving divergence are unknown. We constructed the first high-quality de novo genome assemblies for both L. viridis and L. bilineata through Illumina and PacBio sequencing, with annotation support provided from transcriptome sequencing of several tissues. To estimate gene flow between the two species and identify factors involved in reproductive isolation, we studied their evolutionary history, identified genomic rearrangements, detected signatures of selection on non-coding RNA, and on protein-coding genes. FINDINGS: Here we show that gene flow was primarily unidirectional from L. bilineata to L. viridis after their split at least 1.15 million years ago. We detected positive selection of the non-coding repertoire; mutations in transcription factors; accumulation of divergence through inversions; selection on genes involved in neural development, reproduction, and behavior, as well as in ultraviolet-response, possibly driven by sexual selection, whose contribution to reproductive isolation between these lacertid species needs to be further evaluated. CONCLUSION: The combination of short and long sequence reads resulted in one of the most complete lizard genome assemblies. The characterization of a diverse array of genomic features provided valuable insights into the demographic history of divergence among European green lizards, as well as key species differences, some of which are candidates that could have played a role in speciation. In addition, our study generated valuable genomic resources that can be used to address conservation-related issues in lacertids.

Prot-SpaM: fast alignment-free phylogeny reconstruction based on whole-proteome sequences.

Word-based or 'alignment-free' sequence comparison has become an active research area in bioinformatics. While previous word-frequency approaches calculated rough measures of sequence similarity or dissimilarity, some new alignment-free methods are able to accurately estimate phylogenetic distances between genomic sequences. One of these approaches is Filtered Spaced Word Matches. Here, we extend this approach to estimate evolutionary distances between complete or incomplete proteomes; our implementation of this approach is called Prot-SpaM. We compare the performance of Prot-SpaM to other alignment-free methods on simulated sequences and on various groups of eukaryotic and prokaryotic taxa. Prot-SpaM can be used to calculate high-quality phylogenetic trees for dozens of whole-proteome sequences in a matter of seconds or minutes and often outperforms other alignment-free approaches. The source code of our software is available through Github: https://github.com/jschellh/ProtSpaM.

Convergent evolution of the ladder-like ventral nerve cord in Annelida.

BACKGROUND: A median, segmented, annelid nerve cord has repeatedly been compared to the arthropod and vertebrate nerve cords and became the most used textbook representation of the annelid nervous system. Recent phylogenomic analyses, however, challenge the hypothesis that a subepidermal rope-ladder-like ventral nerve cord (VNC) composed of a paired serial chain of ganglia and somata-free connectives represents either a plesiomorphic or a typical condition in annelids. RESULTS: Using a comparative approach by combining phylogenomic analyses with morphological methods (immunohistochemistry and CLSM, histology and TEM), we compiled a comprehensive dataset to reconstruct the evolution of the annelid VNC. Our phylogenomic analyses generally support previous topologies. However, the so far hard-to-place Apistobranchidae and Psammodrilidae are now incorporated among the basally branching annelids with high support. Based on this topology we reconstruct an intraepidermal VNC as the ancestral state in Annelida. Thus, a subepidermal ladder-like nerve cord clearly represents a derived condition. CONCLUSIONS: Based on the presented data, a ladder-like appearance of the ventral nerve cord evolved repeatedly, and independently of the transition from an intraepidermal to a subepidermal cord during annelid evolution. Our investigations thereby propose an alternative set of neuroanatomical characteristics for the last common ancestor of Annelida or perhaps even Spiralia.

Expression of vasa, piwi, and nanos during gametogenesis in Typosyllis antoni (Annelida, Syllidae).

Although model species have proven to be crucial for developmental biology, the evo-devo approach requires a broader picture across phylogeny. Herein, we try to expand the range of studied annelids by presenting a transcriptome of Typosyllis antoni as a tool for the study of developmental and evolutionary processes in Syllidae. Moreover, we provide homologs of the stem-cell markers vasa, piwi, and nanos, and investigate their expression patterns in gamete-producing individuals for the first time in this group. We found no expression in females, while there is a distinct expression pattern in males. Based on this data, we argue that spermatogenesis starts in the gonads and finishes in the coelomic cavity, and it occurs simultaneously in a large number of segments. Surprisingly, no expression of the stem-cell markers was found in the segment addition zone of these reproducing animals (stolonizing). Preliminary explanations like a lack of growth during stolonization, or the absence of a common genetic program between germ and somatic stem cells, are discussed. Finally, no reservoir of primordial cells has been detected, suggesting a possible epigenic origin of the Primordial Germ Cells of this species, though this hypothesis needs to be further investigated.