Hanna Susi

Host-parasite coevolution describes the continuous reciprocal selection driving host defense and parasite infectivity, with direct consequences for disease dynamics. While abundant evidence exists for coevolution shaping host-parasite dynamics within the ‘one host-one parasite’ framework, hosts are typically infected by multiple parasites and the extent to which coevolutionary processes shape within-host parasite communities remains poorly understood. Investigating these interactions is essential for understanding how coevolution drives parasite diversity, competition, and coexistence within hosts. Here, we conducted a local adaptation experiment to investigate the effects of coevolution on within-host viral community assembly in Plantago lanceolata. Greenhouse-grown individuals were reciprocally transplanted into wild populations during natural viral epidemics. We combined small-RNA sequencing to identify the viral communities and joint species distribution modelling to quantify the effects of local adaptation, population and host characteristics on viral community assembly. Our results show that host populations vary in the extent to which local adaptation influences within-host viral diversity. Across all populations, host maternal line and origin population were the main determinants of viral community composition and infection status. The effects varied across virus families, suggesting virus-specific assembly processes and variation in the potential for coevolution to shape these interactions.

• While viruses are predicted to be the most diverse group of parasites wild plant hosts encounter, the extent and mechanisms maintaining viral resistance diversity remains poorly understood. Here, we test the hypothesis that allocation trade-offs maintain genetic variation in viral resistance and assess whether phenotypic resistance variation may may arise from altered expression under multiple viral attack. • We inoculated clones from 24 Plantago lanceolata genotypes with two viruses to quantify intraspecific variation among host genotypes and test possible trade-offs in resistance to either of the viruses. Furthermore, we performed subsequent viral inoculations to investigate if prior viral infection changes host resistance phenotype. • We found striking intraspecific variation in resistance among the 24 host genotypes against the two studied viruses, with limited evidence for trade-offs maintaining this variation. We also found that prior infection by Plantago lanceolata enamovirus altered the host resistance phenotype, rendering the host more vulnerable to subsequent infection. • Jointly, our results show that intraspecific variation in resistance may have a substantial role in mitigating viral infections in wild hosts. Furthermore, our results highlight the importance of arrival order for the resistance phenotype and for shaping viral coinfections.

Temperature plays a pivotal role in defining the distribution of species and the fitness of individuals within species' ranges. Phenotypic plasticity can allow individuals to cope with varying environmental conditions, including rapid climate change. Populations at range edges experience more variable conditions than core populations and thus are hypothesized to exhibit higher thermal plasticity. However, as the strength of plasticity often varies between individuals, it can also differ among local populations at range edges. We studied the extent of and variation in thermal plasticity for several traits within and between populations of the perennial herb Plantago lanceolata L. (Plantaginaceae) at its northern range edge. We sampled seeds from nine sites within a 50 × 50 km region and grew them under three temperature regimes in a greenhouse. We measured traits related to size, flowering, pathogen responses, and inflorescence pigmentation. We expected to find higher plasticity in traits less strongly connected to fitness and that differences between individuals would outweigh differences between populations in underpinning this variation in plasticity. Our results show thermal plasticity in leaf size and abundance, flowering probability and abundance, and pigmentation. Notably, we also found increased pathogen symptoms and higher infection rates of one of two viruses screened, highlighting the potential for changes in pathogen sensitivity and exposure under climate change. Importantly, in all traits but flower abundance, more variation in plasticity was attributable to differences within populations than between populations. Although this contribution was small in magnitude compared to thermal effects on traits, the higher intra‐ versus interpopulation variation in plasticity suggests that differences between individuals provide most of the variation in thermal plasticity, which may be driven by small‐scale variations in habitat conditions, highlighting the need for conservation strategies that consider microhabitat variation to support short‐term adaptive responses to thermal variability.

The Siberian flying squirrel Pteromys volans is an arboreal rodent with a distribution range that covers large parts of the Eurasian taiga forest zone. However, extensive forestry has resulted in widespread local population declines and extinctions in recent decades. Even though it is widely distributed in Eurasia, almost nothing is known about its phylogeography. Here we used genome‐wide single nucleotide polymorphisms (SNPs) and mitochondrial DNA (mtDNA) to investigate population structure, connectivity and genetic diversity in different sites throughout its distribution. Overall, the species shows low nucleotide diversity and heterozygosity. Locations in Finland, on the western edge of the distribution, had the lowest diversities in genomic SNPs and mtDNA, while individuals in the Far East (Sikhote‐Alin, Russia) show the highest diversity. These findings fit with a rapid range expansion from the Far East to the west. We found a strong genetic differentiation between Sikhote‐Alin and all other populations investigated, which might warrant a revision of their taxonomic classification. The inferred low genetic diversities at the western edge of their distribution are especially worrisome as they are currently experiencing strong population declines and major habitat changes, which can be especially detrimental when standing variation is low. Thus, there is a pressing need to revise the species' conservation status.

Temperature plays a pivotal role in defining the distribution of species and the fitness of individuals within species’ ranges. Phenotypic plasticity can allow individuals to cope with varying environmental conditions, including rapid climate change. Populations at range edges experience more variable conditions than core populations and thus are hypothesized to exhibit higher thermal plasticity. However, as the strength of plasticity often varies between individuals, it can also differ among local populations at range edges. We studied the extent of and variation in thermal plasticity for several traits within and between populations of the perennial herb Plantago lanceolata L. (Plantaginaceae) at its northern range edge. We sampled seeds from nine sites within a 50 x 50 km region and grew them under three temperature regimes in a greenhouse. We measured traits related to size, flowering, pathogen responses, and inflorescence pigmentation. We expected to find higher plasticity in traits less strongly connected to fitness and that differences between individuals would outweigh differences between populations in underpinning this variation in plasticity. Our results show thermal plasticity in leaf size and abundance, flowering probability and abundance, and pigmentation. Notably, we also found increased pathogen symptoms and higher infection rates of one of two viruses screened, highlighting the potential for changes in pathogen sensitivity and exposure under climate change. Importantly, in all traits but flower abundance, more variation in plasticity was attributable to differences within populations than between populations. Although this contribution was small in magnitude compared to thermal effects on traits, the higher intra- versus interpopulation variation in plasticity suggests that differences between individuals provide most of the variation in thermal plasticity, which may be driven by small-scale variations in habitat conditions; highlighting the need for conservation strategies that consider microhabitat variation to support short-term adaptive responses to thermal variability.

1. Biodiversity loss from intensive agriculture poses a major threat to the long-term sustainability and resilience of food production systems. Sustainable land management practices, such as carbon farming, offer promising alternatives, but their biodiversity impacts and the most effective methods for detecting these impacts remain poorly understood. 2. We surveyed 19 farms in boreal Finland to assess the effects of four carbon farming practices—cover crops, all-in mixes, adaptive grazing and ley mixtures—on plants, arthropods, nematodes and birds. We evaluated biodiversity responses using four alpha diversity metrics (abundance, species richness, Shannon diversity and Pielou’s evenness) and two beta diversity metrics (Bray–Curtis and Chi-square dissimilarity). 3. Biodiversity responses were strongly context-dependent, varying by farming practice, taxonomic group and diversity metric. Abundance emerged as the most sensitive alpha metric across taxa, often detecting changes not reflected in community composition metrics. These findings suggest that abundance may serve as a useful early indicator of ecological change in managed landscapes. 4. Arthropods were particularly responsive to adaptive grazing, while ley mix and adaptive grazing supported higher nematode abundances. All diversity metrics except species richness detected changes in at least one species group, practice or field status, but abundance consistently captured the broadest responses. 5. Synthesis and applications. Carbon farming practices can support biodiversity when tailored to species group and context. Monitoring approaches that incorporate multiple metrics—and prioritise abundance as a sensitive and early indicator—can improve the detection of ecological responses to sustainable farming interventions.

The Siberian flying squirrel ( Pteromys volans ) is an arboreal rodent with a distribution range that covers large parts of the Eurasian taiga forest zone. However, extensive forestry has resulted in widespread local population declines and extinctions in recent decades. Even though it is widely distributed in Eurasia, almost nothing is known about its phylogeography. Here we used genome-wide single nucleotide polymorphisms (SNPs) and mitochondrial DNA (mtDNA) to investigate population structure, connectivity and genetic diversity in different sites throughout its distribution. Overall, the species shows low nucleotide diversity and heterozygosity. Locations in Finland, on the western edge of the distribution, had the lowest diversities in genomic SNPs and mtDNA, while individuals in the Far East (Sikhote-Alin, Russia) show the highest diversity. These findings fit with a rapid range expansion from the Far East to the west. We found a strong genetic differentiation between Sikhote-Alin and all other populations investigated, which might warrant a revision of their taxonomic classification. The inferred low genetic diversities at the western edge of their distribution are especially worrisome as they are currently experiencing strong population declines and major habitat changes, which can be especially detrimental when standing variation is low. Thus, stressing the need for the revision of the species conservation status.

Most pathogens are generalists capable of infecting multiple host species or strains. Trade‐offs in performance among different hosts are expected to limit the evolution of generalism. Despite the commonness of generalism, the variation in infectivity, transmission, and trade‐offs in performance among host species have rarely been studied in the wild. To understand the ecological and evolutionary drivers of multi‐host pathogen infectivity and transmission potential, I studied disease severity, transmission dynamics, and infectivity variation of downy mildew pathogen Peronospora sparsa on its three host plants Rubus arcticus, R. chamaemorus, and R. saxatilis. In a survey of 20 wild and cultivated sites of the three host species, disease severity varied by host species and by host population size but not among wild and cultivated sites. To understand how alternative host presence and plant diversity affect transmission of the pathogen, I conducted a transmission experiment. In this experiment, alternative host abundance and plant diversity together modified P. sparsa transmission to trap plants. To understand how resistance to P. sparsa varies among host species and genotypes, I conducted an inoculation experiment using 10 P. sparsa strains from different locations and 20 genotypes of the three host species. Significant variation in infectivity was found among host genotypes but not among host species. When trade‐offs for infectivity were tested, high infectivity in one host species correlated with high infectivity in another host species. However, when pathogen transmission‐related life‐history correlations were tested, a positive correlation was found in R. arcticus but not in R. saxatilis. The results suggest that host resistance may shape pathogen life‐history evolution with epidemiological consequences in a multi‐host pathogen.

Integration of community ecology with disease biology is viewed as a promising avenue for uncovering determinants of pathogen diversity, and for predicting disease risks. Plant-infecting viruses represent a vastly underestimated component of biodiversity with potentially important ecological and evolutionary roles. We performed hierarchal spatial analysis of wild plant populations to characterise the diversity and coexistence structure of within-host virus communities, and their predictors. Our results show that these virus communities are characterised by single infections of few, dominating virus taxa as well as diverse, non-random coinfections. Using a novel graphical modelling framework we demonstrate that after accounting for environmental heterogeneity at the level of both individual host plants and populations, most virus co-occurrence patterns can be attributed to virus-virus associations. Moreover, we show that conditioning variables changed virus association networks especially through their indirect effects. This highlights a previously underestimated mechanism of how human-driven environmental change can influence disease risks.