Factors shaping arthropod and plant community structure at fine spatial scales are poorly underst... more Factors shaping arthropod and plant community structure at fine spatial scales are poorly understood. This includes microclimate, which likely plays a large role in shaping local community patterns, especially in heterogeneous landscapes characterised by high microclimatic variability in space and in time. We explored differences in local microclimatic conditions and regional species pools in two subarctic regions: Kilpisjärvi in north‐west Finland and Varanger in north‐east Norway. We then investigated the relationship between fine‐scale climatic variation and local community characteristics (species richness and abundance) among plants and arthropods, differentiating the latter into two groups: flying and ground‐dwelling arthropods collected by Malaise and pitfall traps, respectively. Arthropod taxa were identified through DNA metabarcoding. Finally, we examined if plant richness can be used to predict patterns in arthropod communities. Variation in soil temperature, moisture and ...
Honeybees are major pollinators for our food crops, but at the same time they face many stressors... more Honeybees are major pollinators for our food crops, but at the same time they face many stressors all over the world. One of the major threats to honeybee health are bacterial diseases, the most severe of which is the American Foulbrood (AFB). Recently a trans-generational vaccination approach against AFB has been proposed, showing strong potential in protecting the colonies from AFB outbreaks. Yet, what remains unstudied is whether the priming of the colony has any undesired side-effects. It is widely accepted that immune function is often a trade-off against other life-history traits, hence immune priming could have an effect on the colony performance. In this experiment we set up 48 hives, half of them with primed queens and half of them as controls. The hives were placed in six apiaries, located as pair of apiaries in three regions. Through a 2-year study we monitored the hives and measured their health and performance. We measured hive weight and frame contents such as brood am...
To assess a species’ impact on its environment–and the environment’s impact upon a species–we nee... more To assess a species’ impact on its environment–and the environment’s impact upon a species–we need to pinpoint its links to surrounding taxa. The honeybee (Apis mellifera) provides a promising model system for such an exercise. While pollination is an important ecosystem service, recent studies suggest that honeybees can also provide disservices. Developing a comprehensive understanding of the full suite of services and disservices that honeybees provide is a key priority for such a ubiquitous species. In this perspective paper, we propose that the DNA contents of honey can be used to establish the honeybee’s functional niche, as reflected by ecosystem services and disservices. Drawing upon previously published genomic data, we analysed the DNA found within 43 honey samples from Northern Europe. Based on metagenomic analysis, we find that the taxonomic composition of DNA is dominated by a low pathogenicity bee virus with 40.2% of the reads, followed by bacteria (16.7%), plants (9.4%...
A crucial step in the use of DNA markers for biodiversity surveys is the assignment of Linnaean t... more A crucial step in the use of DNA markers for biodiversity surveys is the assignment of Linnaean taxonomies (species, genus, etc.) to sequence reads. This allows the use of all the information known based on the taxonomic names. Taxonomic placement of DNA barcoding sequences is inherently probabilistic because DNA sequences contain errors, because there is natural variation among sequences within a species, and because reference data bases are incomplete and can have false annotations. However, most existing bioinformatics methods for taxonomic placement either exclude uncertainty, or quantify it using metrics other than probability. In this paper we evaluate the performance of the recently proposed probabilistic taxonomic placement method PROTAX by applying it to both annotated reference sequence data as well as to unknown environmental data. Our four case studies include contrasting taxonomic groups (fungi, bacteria, mammals and insects), variation in the length and quality of the barcoding sequences (from individually Sanger-sequenced sequences to short Illumina reads), variation in the structures and sizes of the taxonomies (800–130 000 species) and variation in the completeness of the reference data bases (representing 15–100% of known species). Our results demonstrate that PROTAX yields essentially unbiased probabilities of taxonomic placement, which means its quantification of species identification uncertainty is reliable. As expected, the accuracy of taxonomic placement increases with increasing coverage of taxonomic and reference sequence data bases, and with increasing ratio of genetic variation among taxonomic levels over within taxonomic levels. We conclude that reliable species-level identification from environmental samples is still challenging and that neglecting identification uncertainty can lead to spurious inference. A key aim for future research is the completion of taxonomic and reference sequence data bases and making these two types of data compatible
Clustered to OTUs using USEARCH algorithm with default (97%) similarity. This way there is a litt... more Clustered to OTUs using USEARCH algorithm with default (97%) similarity. This way there is a little bit of oversplitting, and OTUs belonging to same biological species are clustered subsequently
This readmap contains the final read counts for each sample. The difference to raw readmap is tha... more This readmap contains the final read counts for each sample. The difference to raw readmap is that some OTU's in this version have been clumped together. The information in this sheet was used as presense/absence data in the study
The file contains all the commandds used in this study to generate the final data. The bioinforma... more The file contains all the commandds used in this study to generate the final data. The bioinformatics was carried out at servers on CSC - IT Center for SCience in Finland
Clustered to OTUs using USEARCH algorithm with default (97%) similarity. This way there is a litt... more Clustered to OTUs using USEARCH algorithm with default (97%) similarity. This way there is a little bit of oversplitting, and OTUs belonging to same biological species are clustered subsequently
The file contains all the commands used in this study to generate the final data. The bioinformat... more The file contains all the commands used in this study to generate the final data. The bioinformatics was carried out at servers on CSC - IT Center for SCience in Finland
Collected while handling the birds or from the field while observing the birds. DNA extracted fro... more Collected while handling the birds or from the field while observing the birds. DNA extracted from individual pellets using Zymo Research Faecal Mini Kit. Sequenced using Ion Torrent PGM. FASTQ file header stands for: @READNUMBER;barcodelabel=SAMPLEID_COLLECTIONLOCALITY_DAY-MONTH-YEAR_BIRDSPECIES_BIRDAGE
How food webs are structured has major implications for their stability and dynamics. While poorl... more How food webs are structured has major implications for their stability and dynamics. While poorly studied to date, arctic food webs are commonly assumed to be simple in structure, with few links per species. If this is the case, then different parts of the web may be weakly connected to each other, with populations and species united by only a low number of links. We provide the first highly resolved description of trophic link structure for a large part of a high-arctic food web. For this purpose, we apply a combination of recent techniques to describing the links between three predator guilds (insectivorous birds, spiders, and lepidopteran parasitoids) and their two dominant prey orders (Diptera and Lepidoptera). The resultant web shows a dense link structure and no compartmentalization or modularity across the three predator guilds. Thus, both individual predators and predator guilds tap heavily into the prey community of each other, offering versatile scope for indirect interactions across different parts of the web. The current description of a first but single arctic web may serve as a benchmark toward which to gauge future webs resolved by similar techniques. Targeting an unusual breadth of predator guilds, and relying on techniques with a high resolution, it suggests that species in this web are closely connected. Thus, our findings call for similar explorations of link structure across multiple guilds in both arctic and other webs. From an applied perspective, our description of an arctic web suggests new avenues for understanding how arctic food webs are built and function and of how they respond to current climate change. It suggests that to comprehend the community-level consequences of rapid arctic warming, we should turn from analyses of populations, population pairs, and isolated predator–prey interactions to considering the full set of interacting species
How species interact modulate their dynamics, their response to environmental change, and ultimat... more How species interact modulate their dynamics, their response to environmental change, and ultimately the functioning and stability of entire communities. Work conducted at Zackenberg, Northeast Greenland, has changed our view on how networks of arctic biotic interactions are structured, how they vary in time, and how they are changing with current environmental change: firstly, the high arctic interaction webs are much more complex than previously envisaged, and with a structure mainly dictated by its arthropod component. Secondly, the dynamics of species within these webs reflect changes in environmental conditions. Thirdly, biotic interactions within a trophic level may affect other trophic levels, in some cases ultimately affecting land-atmosphere feedbacks. Finally, differential responses to environmental change may decouple interacting species. These insights form Zackenberg emphasize that the combination of long-term, ecosystem-based monitoring, and targeted research projects ...
Factors shaping arthropod and plant community structure at fine spatial scales are poorly underst... more Factors shaping arthropod and plant community structure at fine spatial scales are poorly understood. This includes microclimate, which likely plays a large role in shaping local community patterns, especially in heterogeneous landscapes characterised by high microclimatic variability in space and in time. We explored differences in local microclimatic conditions and regional species pools in two subarctic regions: Kilpisjärvi in north‐west Finland and Varanger in north‐east Norway. We then investigated the relationship between fine‐scale climatic variation and local community characteristics (species richness and abundance) among plants and arthropods, differentiating the latter into two groups: flying and ground‐dwelling arthropods collected by Malaise and pitfall traps, respectively. Arthropod taxa were identified through DNA metabarcoding. Finally, we examined if plant richness can be used to predict patterns in arthropod communities. Variation in soil temperature, moisture and ...
Honeybees are major pollinators for our food crops, but at the same time they face many stressors... more Honeybees are major pollinators for our food crops, but at the same time they face many stressors all over the world. One of the major threats to honeybee health are bacterial diseases, the most severe of which is the American Foulbrood (AFB). Recently a trans-generational vaccination approach against AFB has been proposed, showing strong potential in protecting the colonies from AFB outbreaks. Yet, what remains unstudied is whether the priming of the colony has any undesired side-effects. It is widely accepted that immune function is often a trade-off against other life-history traits, hence immune priming could have an effect on the colony performance. In this experiment we set up 48 hives, half of them with primed queens and half of them as controls. The hives were placed in six apiaries, located as pair of apiaries in three regions. Through a 2-year study we monitored the hives and measured their health and performance. We measured hive weight and frame contents such as brood am...
To assess a species’ impact on its environment–and the environment’s impact upon a species–we nee... more To assess a species’ impact on its environment–and the environment’s impact upon a species–we need to pinpoint its links to surrounding taxa. The honeybee (Apis mellifera) provides a promising model system for such an exercise. While pollination is an important ecosystem service, recent studies suggest that honeybees can also provide disservices. Developing a comprehensive understanding of the full suite of services and disservices that honeybees provide is a key priority for such a ubiquitous species. In this perspective paper, we propose that the DNA contents of honey can be used to establish the honeybee’s functional niche, as reflected by ecosystem services and disservices. Drawing upon previously published genomic data, we analysed the DNA found within 43 honey samples from Northern Europe. Based on metagenomic analysis, we find that the taxonomic composition of DNA is dominated by a low pathogenicity bee virus with 40.2% of the reads, followed by bacteria (16.7%), plants (9.4%...
A crucial step in the use of DNA markers for biodiversity surveys is the assignment of Linnaean t... more A crucial step in the use of DNA markers for biodiversity surveys is the assignment of Linnaean taxonomies (species, genus, etc.) to sequence reads. This allows the use of all the information known based on the taxonomic names. Taxonomic placement of DNA barcoding sequences is inherently probabilistic because DNA sequences contain errors, because there is natural variation among sequences within a species, and because reference data bases are incomplete and can have false annotations. However, most existing bioinformatics methods for taxonomic placement either exclude uncertainty, or quantify it using metrics other than probability. In this paper we evaluate the performance of the recently proposed probabilistic taxonomic placement method PROTAX by applying it to both annotated reference sequence data as well as to unknown environmental data. Our four case studies include contrasting taxonomic groups (fungi, bacteria, mammals and insects), variation in the length and quality of the barcoding sequences (from individually Sanger-sequenced sequences to short Illumina reads), variation in the structures and sizes of the taxonomies (800–130 000 species) and variation in the completeness of the reference data bases (representing 15–100% of known species). Our results demonstrate that PROTAX yields essentially unbiased probabilities of taxonomic placement, which means its quantification of species identification uncertainty is reliable. As expected, the accuracy of taxonomic placement increases with increasing coverage of taxonomic and reference sequence data bases, and with increasing ratio of genetic variation among taxonomic levels over within taxonomic levels. We conclude that reliable species-level identification from environmental samples is still challenging and that neglecting identification uncertainty can lead to spurious inference. A key aim for future research is the completion of taxonomic and reference sequence data bases and making these two types of data compatible
Clustered to OTUs using USEARCH algorithm with default (97%) similarity. This way there is a litt... more Clustered to OTUs using USEARCH algorithm with default (97%) similarity. This way there is a little bit of oversplitting, and OTUs belonging to same biological species are clustered subsequently
This readmap contains the final read counts for each sample. The difference to raw readmap is tha... more This readmap contains the final read counts for each sample. The difference to raw readmap is that some OTU's in this version have been clumped together. The information in this sheet was used as presense/absence data in the study
The file contains all the commandds used in this study to generate the final data. The bioinforma... more The file contains all the commandds used in this study to generate the final data. The bioinformatics was carried out at servers on CSC - IT Center for SCience in Finland
Clustered to OTUs using USEARCH algorithm with default (97%) similarity. This way there is a litt... more Clustered to OTUs using USEARCH algorithm with default (97%) similarity. This way there is a little bit of oversplitting, and OTUs belonging to same biological species are clustered subsequently
The file contains all the commands used in this study to generate the final data. The bioinformat... more The file contains all the commands used in this study to generate the final data. The bioinformatics was carried out at servers on CSC - IT Center for SCience in Finland
Collected while handling the birds or from the field while observing the birds. DNA extracted fro... more Collected while handling the birds or from the field while observing the birds. DNA extracted from individual pellets using Zymo Research Faecal Mini Kit. Sequenced using Ion Torrent PGM. FASTQ file header stands for: @READNUMBER;barcodelabel=SAMPLEID_COLLECTIONLOCALITY_DAY-MONTH-YEAR_BIRDSPECIES_BIRDAGE
How food webs are structured has major implications for their stability and dynamics. While poorl... more How food webs are structured has major implications for their stability and dynamics. While poorly studied to date, arctic food webs are commonly assumed to be simple in structure, with few links per species. If this is the case, then different parts of the web may be weakly connected to each other, with populations and species united by only a low number of links. We provide the first highly resolved description of trophic link structure for a large part of a high-arctic food web. For this purpose, we apply a combination of recent techniques to describing the links between three predator guilds (insectivorous birds, spiders, and lepidopteran parasitoids) and their two dominant prey orders (Diptera and Lepidoptera). The resultant web shows a dense link structure and no compartmentalization or modularity across the three predator guilds. Thus, both individual predators and predator guilds tap heavily into the prey community of each other, offering versatile scope for indirect interactions across different parts of the web. The current description of a first but single arctic web may serve as a benchmark toward which to gauge future webs resolved by similar techniques. Targeting an unusual breadth of predator guilds, and relying on techniques with a high resolution, it suggests that species in this web are closely connected. Thus, our findings call for similar explorations of link structure across multiple guilds in both arctic and other webs. From an applied perspective, our description of an arctic web suggests new avenues for understanding how arctic food webs are built and function and of how they respond to current climate change. It suggests that to comprehend the community-level consequences of rapid arctic warming, we should turn from analyses of populations, population pairs, and isolated predator–prey interactions to considering the full set of interacting species
How species interact modulate their dynamics, their response to environmental change, and ultimat... more How species interact modulate their dynamics, their response to environmental change, and ultimately the functioning and stability of entire communities. Work conducted at Zackenberg, Northeast Greenland, has changed our view on how networks of arctic biotic interactions are structured, how they vary in time, and how they are changing with current environmental change: firstly, the high arctic interaction webs are much more complex than previously envisaged, and with a structure mainly dictated by its arthropod component. Secondly, the dynamics of species within these webs reflect changes in environmental conditions. Thirdly, biotic interactions within a trophic level may affect other trophic levels, in some cases ultimately affecting land-atmosphere feedbacks. Finally, differential responses to environmental change may decouple interacting species. These insights form Zackenberg emphasize that the combination of long-term, ecosystem-based monitoring, and targeted research projects ...
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Papers by Helena Wirta