Genomes record past climatic impact on species’ range shifts, admixture, refugial isolation, and adaptative evolution. However, these processes are poorly understood in perennial herbaceous species forming a dominant group of temperate flora. We present a demographic history of the perennial herb woodland strawberry (Fragaria vesca L.) reconstructed from 200 genomes spanning most of its European range. Temporal population structure reveals a strong division into western and eastern genetic clusters along a longitudinal climatic gradient, with eastern core populations showing greater resilience during glaciations. Divergence patterns indicate that postglacial recolonization of western and eastern Europe occurred from distinct refugia in multiple waves. The current largest, admixed populations from the Mediterranean to northern Europe form a continuous chain maintained by east–west gene flow through Central Europe, with historical migration patterns indicating comparable connections during earlier interglacials. Our reconstruction of woodland strawberry’s climatic history with high temporal resolution reveals how the late Pleistocene core-periphery dynamics shaped its survival and genome evolution under climate change. The data points to populations that are essential for maintaining the long term genetic diversity of the species and opens new avenues to understand climatic adaptation of temperate flora. Population genomics of European woodland strawberry reveal distinct western and eastern genetic clusters with contrasting demographic histories across multiple glacial-interglacial cycles.
Invasive plant species present a growing ecological and economic challenge, and often adapt rapidly to their novel environments through complex demographic and evolutionary processes. Invasion genomics offers powerful tools to disentangle these processes, but most studies rely on geographically narrow sampling across native and non-native ranges. Erigeron canadensis is a cosmopolitan weed native to North America that has successfully invaded diverse climates worldwide. We used double-digest restriction site-associated DNA sequencing (ddRADseq) to investigate the genetic diversity and structure of 280 E. canadensis populations across the Northern Hemisphere. We found that native and non-native populations maintained comparable genetic diversity. Population structure analyses revealed four genetic clusters that were mainly differentiated along latitudinal and aridity gradients. However, one cluster was strongly overrepresented in the non-native compared to the native range. In the native range, genetic differentiation was shaped by spatial and environmental gradients, while in non-native regions human-mediated dispersal and repeated introductions disrupted environmentally driven genetic structure. Migration network analyses revealed limited intercontinental connectivity and a possible role of long-distance dispersal in within-range expansions. Genomic offset analyses showed that genotype-environment mismatches in non-native populations associated with reduced growth and reproduction. Together, our results indicate that the invasion dynamics of E. canadensis were driven by multiple introductions, population admixture, and lineage sorting, while some genotypes contributed disproportionately to the spread of this invader. The presence of apparent maladaptation suggests that even long-established invaders may still be evolving in response to their novel environment, raising concerns about potential future expansions.
Fungi have been used by humans since prehistoric times. Informal structures or groups for knowledge exchange regarding mushrooms and lichens probably existed for ages. Only recently, mycological activities have been structured in formal organizations. And where until a few centuries ago there were only learned societies and naturalists’ clubs, nowadays also mycological societies and citizen scientists have joined the landscape. However, the history of mycological organizations and activities in Europe is difficult to track. Here, we initiated two surveys to characterize the current landscape of mycological organizations focused on fungal diversity across Europe and to collate citizen science activities mapping fungi. The surveys were shared on social media and sent to mycologists in 49 countries in Europe. Responses of the surveys allowed us to present the history, geographical distribution, and structure of mycological organizations in Europe as well as their types of activities, including the publication of journals and magazines, the organization of meetings and educational initiatives, and citizen science projects. In addition to the surveys, local mycologists presented expert knowledge for a more comprehensive overview. Our data show that the mycological landscape in Europe is diverse and heterogeneous. We discuss ways to overcome economic, cultural, and linguistic barriers towards better integration of mycological communities, activities, and data in Europe. Mycological societies focused on studying fungal diversity can be leveraged towards common goals that include raising public awareness, data integration, uniting academics and non-academics, and developing common standards for research and communication.
Mutant-based research is a cornerstone for elucidating gene function in barley (Hordeum vulgare) and other cereals. In this study, we exploited a unique collection of barley tweaky spike (tw) mutants to identify the locus controlling floret and spike development. We combined genetic mapping with structural variant and gene-expression analyses across a tw allelic series, supported by functional validation, and quantified endogenous auxin levels alongside auxin-application assays to test phytohormone involvement. Analysis of independent tw allelic mutants revealed that the phenotype results from loss of function of HvAP2L5, most often due to complete open reading frame (ORF) deletions, and, in one allele, due to transcriptional silencing. tw mutants showed a reproducible endogenous indole-3-acetic acid deficit, and exogenous auxin could partially phenocopy and/or rescue core tw-associated traits, indicating compromised auxin homeostasis. We conclude that HvAP2L5 is essential for normal spike/floret development and that its loss disrupts auxin balance. Auxin imbalance is a compelling working model that can account for most of the pleiotropic features of tw mutants.
Parasites are ubiquitous and exert varied ecological and evolutionary pressures on their hosts. Yet, characterising parasite diversity and distributions can be challenging and costly. Leveraging existing data to identify parasites is thus an attractive alternative. High-throughput sequencing (HTS) can generate whole genome sequence (WGS) data which are increasingly freely available in public repositories and represent an untapped resource for characterising parasites affiliated with hosts. In this study, we examine WGS data generated for the silvereye (Zosterops lateralis), to identify endogenous eukaryotic parasites that were inadvertently captured during host sequencing. We compared detection of parasite genera by this approach with detection via 18S metabarcoding. Mining WGS data for parasite DNA revealed the broadest range of genera. Results were verified by traditional microscopy of blood slides and conducting a targeted multiplex Polymerase Chain Reaction (PCR) for haemosporidian parasites. Detection of haemosporidians was largely consistent across microscopy, multiplex PCR and WGS data while 18S metabarcoding entirely failed to detect this group of parasites. Our results demonstrate that existing WGS datasets can be used to estimate endoparasite diversity and provide greater insights on diversity than metabarcoding whilst also avoiding the costs and challenges of direct sampling. We provide a framework outlining opportunities and constraints to consider when mining WGS data to identify parasite sequences. The framework particularly stresses the influences of sequencing depth, database completeness, and methodological biases. Our findings demonstrate how repurposing existing WGS data can provide a cost-effective and informative means of unravelling complex host-parasite interactions in future disease ecology studies.
