Cascading effects of herbivore protective symbionts on hyperparasitoids

1. Microbial symbionts can play an important role in defending their insect hosts against natural enemies. However, we have little idea how the presence of such protective symbionts impacts food web interactions and species diversity. 2. We investigated the effects of a protective symbiont (Hamiltonella defensa) in pea aphids (Acyrthosiphon pisum) on hyperparasitoids, which are a trophic level above the natural enemy target of the symbiont (primary parasitoids). 3. Pea aphids, with and without their natural infections of H. defensa, were exposed first to a primary parasitoid against which the symbiont provides partial protection (either Aphidius ervi or Aphelinus abdominalis), and second to a hyperparasitoid known to attack the primary parasitoid species. 4. We found that hyperparasitoid hatch rate was substantially affected by the presence of the symbiont. This effect appears to be entirely due to the removal of potential hosts by the action of the symbiont: there was no additional benefit or cost experienced by the hyperparasitoids in response to symbiont presence. The results were similar across the two different aphid-parasitoid-hyperparasitoid interactions we studied. 5. We conclude that protective symbionts can have an important cascading effect on multiple trophic levels by altering the success of natural enemies, but that there is no evidence for more complex interactions. Our findings demonstrate that the potential influence of protective symbionts on the wider community should be considered in future food web studies

Wolbachia and DNA barcoding insects: patterns, potential and problems

Wolbachia is a genus of bacterial endosymbionts that impacts the breeding systems of their hosts. Wolbachia can confuse the patterns of mitochondrial variation, including DNA barcodes, because it influences the pathways through which mitochondria are inherited. We examined the extent to which these endosymbionts are detected in routine DNA barcoding, assessed their impact upon the insect sequence divergence and identification accuracy, and considered the variation present in Wolbachia COI. Using both standard PCR assays (Wolbachia surface coding protein – wsp), and bacterial COI fragments we found evidence of Wolbachia in insect total genomic extracts created for DNA barcoding library construction. When >2 million insect COI trace files were examined on the Barcode of Life Datasystem (BOLD) Wolbachia COI was present in 0.16% of the cases. It is possible to generate Wolbachia COI using standard insect primers; however, that amplicon was never confused with the COI of the host. Wolbachia alleles recovered were predominantly Supergroup A and were broadly distributed geographically and phylogenetically. We conclude that the presence of the Wolbachia DNA in total genomic extracts made from insects is unlikely to compromise the accuracy of the DNA barcode library; in fact, the ability to query this DNA library (the database and the extracts) for endosymbionts is one of the ancillary benefits of such a large scale endeavor – for which we provide several examples. It is our conclusion that regular assays for Wolbachia presence and type can, and should, be adopted by large scale insect barcoding initiatives. While COI is one of the five multi-locus sequence typing (MLST) genes used for categorizing Wolbachia, there is limited overlap with the eukaryotic DNA barcode region

Molecular analyses reveal consistent food web structure with elevation in rainforest Drosophila – parasitoid communities

The analysis of interaction networks across spatial environmental gradients is a powerful approach to investigate the responses of communities to global change. Using a combination of DNA metabarcoding and traditional molecular methods we built bipartite Drosophila-parasitoid food webs from six Australian rainforest sites across gradients spanning 850 m in elevation and 5° Celsius in mean temperature. Our cost-effective hierarchical approach to network reconstruction separated the determination of host frequencies from the detection and quantification of interactions. The food webs comprised 5-9 host and 5-11 parasitoid species at each site, and showed a lower incidence of parasitism at high elevation. Despite considerable turnover in the relative abundance of host Drosophila species, and contrary to some previous results, we did not detect significant changes to fundamental metrics of network structure including nestedness and specialisation with elevation. Advances in community ecology depend on data from a combination of methodological approaches. It is therefore especially valuable to develop model study systems for sets of closely-interacting species that are diverse enough to be representative, yet still amenable to field and laboratory experiments

Single-fly genome assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life

AU Long-read: Pleaseconfirmthatallheadinglevelsarerepresentedcorrectly sequencing is driving rapid progress in genome assembly : across all major groups of life, including species of the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. We previously developed a cost-effective hybrid Oxford Nanopore (ONT) long-read and Illumina short-read sequencing approach and used it to assemble 101 drosophilid genomes from laboratory cultures, greatly increasing the number of genome assemblies for this taxonomic group. The next major challenge is to address the laboratory culture bias in taxon sampling by sequencing genomes of species that cannot easily be reared in the lab. Here, we build upon our previous methods to perform amplification-free ONT sequencing of single wild flies obtained either directly from the field or from ethanol-preserved specimens in museum collections, greatly improving the representation of lesser studied drosophilid taxa in whole-genome data. Using Illumina Novaseq X Plus and ONT P2 sequencers with R10.4.1 chemistry, we set a new benchmark for inexpensive hybrid genome assembly at US $150 per genome while assembling genomes from as little as 35 ng of genomic DNA from a single fly. We present 183 new genome assemblies for 179 species as a resource for drosophilid systematics, phylogenetics, and comparative genomics. Of these genomes, 62 are from pooled lab strains and 121 from single adult flies. Despite the sample limitations of working with small insects, most single-fly diploid assemblies are comparable in contiguity (\u3e1 Mb contig N50), completeness (\u3e98% complete dipteran BUSCOs), and accuracy (\u3eQV40 genome-wide with ONT R10.4.1) to assemblies from inbred lines. We present a well-resolved multi-locus phylogeny for 360 drosophilid and 4 outgroup species encompassing all publicly available (as of August 2023) genomes for this group. Finally, we present a Progressive Cactus whole-genome, reference-free alignment built from a subset of 298 suitably high-quality drosophilid genomes. The new assemblies and alignment, along with updated laboratory protocols and computational pipelines, are released as an open resource and as a tool for studying evolution at the scale of an entire insect family

Continent-wide differentiation of fitness traits and patterns of climate adaptation among European populations of Drosophila melanogaster

Funding: This research was supported by a Special Topics Network (STN) grant from the European Society of Evolutionary Biology (ESEB) to the DrosEU consortium as well as by individual grants and fellowships (grantees in alphabetical order): J.A.: Swedish Research Council (VR) grants 2015-04680 and 2020-05412; A.J.B.: European Research Council (ERC CoG TE_INVASION); S.D.: Ministry of Science, Technological Development and Innovation of the Republic of Serbia (NITRA) grant 451-03-66/2024-03/200007; K.E.: Ministry of Science, Technological Development and Innovation of the Republic of Serbia (NITRA) grant 451-03-66/2024-03/200007; P.E.: Ministry of Science, Technological Development and Innovation of the Republic of Serbia (NITRA) grant 451-03-66/2024-03/200007; P.E.: Jane Coffin Childs Memorial Fund for Medical Research 61-1673: T.F.: Swiss National Science Foundation (SNSF) grants 31003A-182262, 310030_219283, FZEB-0-214654; C.F.: Deutsche Forschungsgemeinschaft (DFG) grants 2973/5-1 and 2973/11; J.G.: Ministerio de Ciencia, Innovación y Universidades/Agencia Estatal de Investigación (MICIU/AEI/10.13039/501100011033/) grant PID2020-115874GB-I00; Ministerio de Ciencia, Innovación y Universidades/Agencia Estatal de Investigación (MICIU/AEI/10.13039/501100011033 and FEDER, UE) grant PID2023-148838NB-I00; Departament de Recerca i Universitats Generalitat de Catalunya grant 2021 SGR 00417; S.G.: Deutsche Forschungsgemeinschaft (DFG) grants 271330745 and 514085304; K.M.H.: Marie Skłodowska-Curie Individual Fellowship (H2020-MSCA-IF-2015) 701949; J.H.: Czech Ministry of Education, grant; European Research Council (ERC CZ LL2001); M.J.: Ministry of Science, Technological Development and Innovation of the Republic of Serbia (NITRA) grant 451-03-65/2024-03/200178; M.K.: Academy of Finland grant 322980; E.K.: European Molecular Biology Organization (EMBO) ALTF 248-2018; M.S.M.: ALW Open Programme grant 101185; J.P.: Deutsche Forschungsgemeinschaft (DFG) grants 255619725 (GR 4495/2-2) and 503272152 (GR 4495/4-1); E.G.P.: Russian state budget, assignment NRC “KI”; A.P.: Ministry of Science, Technological Development and Innovation of the Republic of Serbia (NITRA) grant 451-03-66/2024-03/200007; N.P.: Deutsche Forschungsgemeinschaft (DFG) grants PO 1648/7-1, PO 1648/3-1, PO 1648/3-2; M.S.V.: Ministry of Science, Technological Development and Innovation of the Republic of Serbia (NITRA) grant 451-03-65/2024-03/200178; C.S.: Austrian Science Fund (FWF) grants 10.55776/P32935, 10.55776/W1225, 10.55776/P33734; P.S.: National Institutes of Health (NIH) R01GM137430; M.S.-R.: Ministry of Science, Technological Development and Innovation of the Republic of Serbia (NITRA) grant 451-03-47/2023-01/200178; M.T.: Ministry of Science, Technological Development and Innovation of the Republic of Serbia (NITRA) grant 451-03-66/2024-03/200007; E.T.: Israel Science Foundation (ISF) 2121/23; C.V.: Agence Nationale de la Recherche (ANR) grant Longevity ANR-20-CE02-0015, J.V.: Fundação para a Ciência e a Tecnologia (FCT) UIDB/04293/2020; C.W.: Deutsche Forschungsgemeinschaft (DFG) grant WE 2652/7-1.A particularly well-studied evolutionary model is the vinegar fly Drosophila melanogaster, a cosmopolitan insect of ancestral southern-central African origin. Recent work suggests that it expanded out of Africa ∼9,000 years ago, and spread from the Middle East into Europe ∼1,800 years ago. During its global expansion, this human commensal adapted to novel climate zones and habitats. Despite much work on phenotypic differentiation and adaptation on several continents (especially North America and Australia), typically in the context of latitudinal clines, little is known about phenotypic divergence among European populations. Here, we sought to provide a continent-wide study of phenotypic differentiation among European populations of D. melanogaster. In a consortium-wide phenomics effort, we assayed 16 fitness-related traits on a panel of 173 isofemale lines from 9 European populations, with the majority of traits measured by several groups using semi-standardized protocols. For most fitness-related traits, we found significant differentiation among populations on a continental scale. Despite inevitable differences in assay conditions among labs, the reproducibility and hence robustness of our measurements were overall remarkably good. Several fitness components (e.g., viability, development time) exhibited significant latitudinal or longitudinal clines, and populations differed markedly in multivariate trait structure. Notably, populations experiencing higher humidity/rainfall and lower maximum temperature showed higher viability, fertility, starvation resistance, and lifespan at the expense of lower heat-shock survival, suggesting a pattern of local adaptation. Our results indicate that derived populations of this tropical fly have been shaped by pervasive spatially varying multivariate selection and adaptation to different climates on the European continent.Peer reviewe

Footprints of worldwide adaptation in structured populations of Drosophila melanogaster through the expanded DEST 2.0 genomic resource

Funding: M.Kap. was supported by the Horizon Europe project FAIRiCUBE (grant #101059238). S.S. was supported by the Horizon Europe project FAIRiCUBE (grant #101059238). D.O. was supported by the UK Biotechnology and Biological Sciences Research Council (BBSRC) grant BB/T007516/1. M.G.R. was supported by Natural Environment Research Council (NERC), UK award NE/V001566/1.Large-scale genomic resources can place genetic variation into an ecologically informed context. To advance our understanding of the population genetics of the fruit fly Drosophila melanogaster, we present an expanded release of the community-generated population genomics resource Drosophila Evolution over Space and Time (DEST 2.0; https://dest.bio/). This release includes 530 high-quality pooled libraries from flies collected across six continents over more than a decade (2009 to 2021), most at multiple time points per year; 211 of these libraries are sequenced and shared here for the first time. We used this enhanced resource to elucidate several aspects of the species' demographic history and identify novel signs of adaptation across spatial and temporal dimensions. For example, we showed that the spatial genetic structure of populations is stable over time, but that drift due to seasonal contractions of population size causes populations to diverge over time. We identified signals of adaptation that vary between continents in genomic regions associated with xenobiotic resistance, consistent with independent adaptation to common pesticides. Moreover, by analyzing samples collected during spring and fall across Europe, we provide new evidence for seasonal adaptation related to loci associated with pathogen response. Furthermore, we have also released an updated version of the DEST genome browser. This is a useful tool for studying spatiotemporal patterns of genetic variation in this classic model system.Peer reviewe

The global change of species interactions

A recommendation of the preprint: Mennerat A, Charmantier A, Hurtrez-Bousses S, Perret P, and Lambrechts MM. 2019. Parasite intensity is driven by temperature in a wild bird. bioRxiv 323311, ver 4 peer-reviewed and recommended by Peer Community in Ecology. doi: 10.1101/32331

Individual-based eco-evolutionary framework: towards unifying ecology and evolution

Evolution is increasingly found to be rapid and entangled with ecological processes in complex eco-evolutionary dynamics, calling for a common conceptual framework. Yet, ecological and evolutionary theory remain largely separated, which constrains the development of integrative research. To overcome this separation, I suggest treating the entangled dynamics as a single eco-evolutionary process rather than as separate ecological and evolutionary processes connected by feedbacks. I propose a unified conceptual framework that integrates ecological and evolutionary processes at population and community levels by considering which of them result from the same individual-based process. The resulting framework is a means to understand the entangled dynamics through the interaction of five basic eco-evolutionary processes: natural selection, drift, dispersal, gene transfer, and mutation. The framework reveals relationships between existing theories and models, provides simple means to discuss complex dynamics, and outlines a holistic approach to major topics including diversity, stability, and stochasticity. The framework thus presents a step towards conceptually uniting ecology and evolutionary biology