Browsing by Subject "diversity"

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  • Repetti, Sonja I. (Helsingin yliopisto, 2022)
    My master’s thesis aims to determine the effect of salinity on phytoplankton traits related to nutrient acquisition, and particularly how this interacts with resource availability. Salinity is an important driver structuring phytoplankton communities in the Baltic Sea. Salinity can also influence nutrient uptake by increasing metabolic rates required for osmotic adjustment. Thus, interaction between salinity and nutrient availability is expected to change community structure by altering phytoplankton traits determining resource competition. This is a particularly relevant area of study for the Baltic Sea due to predicted future freshening of the sea’s upper layer. We performed a microcosm experiment using artificial communities of 10 diverse phytoplankton species grown under different combinations of salinity (0, 5, 12 and 24), Nitrogen to Phosphorus molar ratio (N:P ratio = 2, 10, 16 and 80) and light (10 and 130 µmol photon m-2 s-1) conditions. A three-way interaction among these environmental parameters influenced phytoplankton traits associated with resource competition, as well as the presence and proportions of phytoplankton taxa. Light limitation inhibited community growth under all salinity conditions, but allowed diatom Phaeodactylum tricornutum to dominate. Community growth rate was higher under high light, but also more variable between salinity conditions. The strongest negative effects of nutrient limitation (N, P, and both nutrients together), both on growth rate and taxonomic diversity, were observed in the highest salinity treatment. In the freshwater treatment with the highest proportion of green algae Monoraphidium sp., N-limitation did not inhibit phytoplankton community growth and P-limitation had a more profound negative effect on community performance. Decreasing salinity appeared to decrease community C:N and C:P ratios. This shift is in opposition to the increasing C:N and C:P predicted as a consequence of other climate change-related drivers. Our results emphasise the importance of a trade-off between salinity and resource limitation in functioning of phytoplankton communities and suggest that future freshening of the Baltic Sea is likely to modify phytoplankton community composition and performance.
  • Gonçalves, Paula; Vierikko, Kati; Elands, Birgit; Haase, Dagmar; Catarina Luz, Ana; Santos-Reis, Margarida (Elsevier BV, 2021)
    Environmental and Sustainability Indicators 11: 100131
    Cities face growing challenges and urban greenspaces (UGS) play a key role in improving cities liveability. UGS are complex socio-ecological systems and evidence-based and context-sensitive tools are needed to assist planning and manage environmentally sound and socially inclusive UGS. In this paper, we propose an innovative indicator-based tool to operationalize the biocultural diversity (BCD) framework in urban contexts, deriving from its three conceptual layers – materialized, lived and stewardship. Indicators proposed are bundled in themes representing essential components when assessing and analyzing urban BCD from a contextual and sensitizing perspective. The set of indicators highlight key features of socio-cultural and ecological systems, theirs links and interactions, both material and non-material, to capture the essence of biocultural diversity at site-level. By offering a uniform scoring system with the possibility to set site-specific benchmarks, these can be used in any type of greenspace of any city, while allowing different communities/neighborhoods/city councils to embrace different approaches to meet their objectives towards larger scale goals. Twelve urban parks in Lisbon were used as a test-bed for the indicator-based tool and proved its feasibility to gather an overall snapshot of all parks and to demonstrate the possibility to deepen the study to only two parks uncovering self-exclusion processes that otherwise would have remained hidden. The BCD tool brings together essential information scattered over several quality and good practices assessment tools and protocols and, by including indicators specifically addressing governance and stewardship, offers a policy-driven instrument able to capture trade-offs and/or synergies between ecological, social and political domains.
  • Hammerl, Jens Andre; Barac, Andrea; Bienert, Anja; Demir, Aslihan; Drueke, Niklas; Jaeckel, Claudia; Matthies, Nina; Jun, Jin Woo; Skurnik, Mikael; Ulrich, Juliane; Hertwig, Stefan (2022)
    Yersinia pseudotuberculosis is an important animal pathogen, particularly for birds, rodents, and monkeys, which is also able to infect humans. Indeed, an increasing number of reports have been published on zoo animals that were killed by this species. One option to treat diseased animals is the application of strictly lytic (virulent) phages. However, thus far relatively few phages infecting Y. pseudotuberculosis have been isolated and characterized. To determine the prevalence of Y. pseudotuberculosis phages in zoo animals, fecal samples of birds and some primates, maras, and peccaries kept in the Tierpark Berlin were analyzed. Seventeen out of 74 samples taken in 2013 and 2017 contained virulent phages. The isolated phages were analyzed in detail and could be allocated to three groups. The first group is composed of 10 T4-like phages (PYps2T taxon group: Myoviridae; Tevenvirinae; Tequatrovirus), the second group (PYps23T taxon group: Chaseviridae; Carltongylesvirus; Escherichia virus ST32) consists of five phages encoding a podovirus-like RNA polymerase that is related to an uncommon genus of myoviruses (e.g., Escherichia coli phage phiEcoM-GJ1), while the third group is comprised of two podoviruses (PYps50T taxon group: Autographiviridae; Studiervirinae; Berlinvirus) which are closely related to T7. The host range of the isolated phages differed significantly. Between 5.5 and 86.7% of 128 Y. pseudotuberculosis strains belonging to 20 serotypes were lysed by each phage. All phages were additionally able to lyse Y. enterocolitica B4/O:3 strains, when incubated at 37 degrees C. Some phages also infected Y. pestis strains and even strains belonging to other genera of Enterobacteriaceae. A cocktail containing two of these phages would be able to lyse almost 93% of the tested Y. pseudotuberculosis strains. The study indicates that Y. pseudotuberculosis phages exhibiting a broad-host range can be isolated quite easily from zoo animals, particularly birds.
  • Kozlov, Mikhail V.; Zverev, Vitali; Gusarov, Vladimir I.; Korobushkin, Daniil I.; Krivosheina, Nina P.; Mattila, Jaakko; Mutanen, Marko; Popova, Anna; Prosvirov, Alexander S; Punttila, Pekka; Söderman, Guy; Stanska, Marzena; Taylor, Astrid; Vahtera, Varpu; Zubrii, Natalia; Zvereva, Elena L. (MDPI AG, 2022)
    Insects
    Simple Summary We used a 1000 km long latitudinal gradient in north-western Russia to study the potential impacts of a changing climate on soil invertebrates visible by a naked eye (insects, spiders, earthworms etc.). We extracted these animals from soil, weighed them and identified them to the species level. We found that the diversity of soil invertebrates decreased towards the north, whereas the latitudinal pattern in biomass depended on the animal’s feeding habit. The biomass of species feeding on live plant roots and fungal mycelia decreased towards the north, whereas the biomass of species feeding on dead plant tissues and live invertebrates showed no significant latitudinal changes. The discovery of this variation in latitudinal biomass patterns suggests that soil invertebrates from different feeding guilds may respond differently to climate change. As a result, the biomass ratio between consumers and their food resources (e.g., herbivores and plants, predators and prey) may change. We poorly understood how this change will affect the future structure and functions of boreal forest ecosystems. Abstract Latitudinal gradients allow insights into the factors that shape ecosystem structure and delimit ecosystem processes, particularly climate. We asked whether the biomass and diversity of soil macrofauna in boreal forests change systematically along a latitudinal gradient spanning from 60° N to 69° N. Invertebrates (3697 individuals) were extracted from 400 soil samples (20 × 20 cm, 30 cm depth) collected at ten sites in 2015–2016 and then weighed and identified. We discovered 265 species living in soil and on the soil surface; their average density was 0.486 g d·w·m−2. The species-level diversity decreased from low to high latitudes. The biomass of soil macrofauna showed no latitudinal changes in early summer but decreased towards the north in late summer. This variation among study sites was associated with the decrease in mean annual temperature by ca 5 °C and with variation in fine root biomass. The biomass of herbivores and fungivores decreased towards the north, whereas the biomass of detritivores and predators showed no significant latitudinal changes. This variation in latitudinal biomass patterns among the soil macrofauna feeding guilds suggests that these guilds may respond differently to climate change, with poorly understood consequences for ecosystem structure and functions.
  • Castel, Guillaume; Couteaudier, Mathilde; Sauvage, Frank; Pons, Jean-Baptiste; Murri, Severine; Plyusnina, Angelina; Pontier, Dominique; Cosson, Jean-Francois; Plyusnin, Alexander; Marianneau, Philippe; Tordo, Noel (2015)
    Puumala virus (PUUV) is the agent of nephropathia epidemica (NE), a mild form of hemorrhagic fever with renal syndrome (HFRS) in Europe. NE incidence presents a high spatial variation throughout France, while the geographical distribution of the wild reservoir of PUUV, the bank vole, is rather continuous. A missing piece of the puzzle is the current distribution and the genetic variation of PUUV in France, which has been overlooked until now and remains poorly understood. During a population survey, from 2008 to 2011, bank voles were trapped in eight different forests of France located in areas known to be endemic for NE or in area from where no NE case has been reported until now. Bank voles were tested for immunoglobulin (Ig)G ELISA serology and two seropositive animals for each of three different areas (Ardennes, Jura and Orleans) were then subjected to laboratory analyses in order to sequence the whole S, M and L segments of PUUV. Phylogenetic analyses revealed that French PUUV isolates globally belong to the central European (CE) lineage although isolates from Ardennes are clearly distinct from those in Jura and Orleans, suggesting a different evolutionary history and origin of PUUV introduction in France. Sequence analyses revealed specific amino acid signatures along the N protein, including in PUUV from the Orleans region from where NE in humans has never been reported. The relevance of these mutations in term of pathophysiology is discussed.
  • Bairoh, Susanna (Svenska handelshögskolan, 2008)
    Working Papers
    This paper discusses various theoretical approaches to diversity management, analysing their similarities and differences. I start with a review of certain previously presented classifications, and then proceed to describing the different approaches in more detail. In this paper, I propose that the various viewpoints can be categorized into three groups: 1) practitioner/consultant approach, 2) mainstream approach, and 3) critical approaches. Although there are differences within these groups, in particular regarding the critical approaches, these differences appear less significant than those between the groups. Those representing the first group are mainly interested in how to get most out of a diverse workforce, while those in the second group focus on the effects of diversity on performance or work group functioning. While some of the mainstream writers can be rather critical towards earlier research, they hardly ever discuss or even recognize the wide ranging criticism put forward by critical scholars. The critical researchers, then, remain a rather scattered group who do not always share much more than a conviction that the mainstream research keeps missing highly significant issues. Nonetheless, in order to increase our understanding of how different persons can and do work together, more dialogue is required between the varying standpoints.
  • Niittynen, Pekka; Heikkinen, Risto K.; Luoto, Miska (2020)
    Proceedings of the National Academy of Sciences of the United States of America 117: 35, 21480-21487
    The Arctic is one of the least human-impacted parts of the world, but, in turn, tundra biome is facing the most rapid climate change on Earth. These perturbations may cause major reshuffling of Arctic species compositions and functional trait profiles and diversity, thereby affecting ecosystem processes of the whole tundra region. Earlier research has detected important drivers of the change in plant functional traits under warming climate, but studies on one key factor, snow cover, are almost totally lacking. Here we integrate plot-scale vegetation data with detailed climate and snow information using machine learning methods to model the responsiveness of tundra communities to different scenarios of warming and snow cover duration. Our results show that decreasing snow cover, together with warming temperatures, can substantially modify biotic communities and their trait compositions, with future plant communities projected to be occupied by taller plants with larger leaves and faster resource acquisition strategies. As another finding, we show that, while the local functional diversity may increase, simultaneous biotic homogenization across tundra communities is likely to occur. The manifestation of climate warming on tundra vegetation is highly dependent on the evolution of snow conditions. Given this, realistic assessments of future ecosystem functioning require acknowledging the role of snow in tundra vegetation models.
  • Wuori, Naomi Mathilda (Helsingin yliopisto, 2021)
    Avhandlingen består av en diskursanalys av intervjuer med kvinnoidentifierade personer verksamma inom startupekosystemet i Finland. Syftet med avhandlingen är att utforska kvinnornas tolkningar av startupekosystemets kultur från ett jämställdhets- och mångfaldsperspektiv. Avhandlingen bidrar med ett kritiskt perspektiv på startupkulturer och ämnar inspirera till nya synvinklar på sociologisk forskning om startupekosystem. De huvudsakliga forskningsfrågorna lyder: ”Hur förstår och tolkar kvinnor verksamma inom det finska startupekosystemet startupkulturen?”, ”Hur tolkar kvinnorna entreprenörsfiguren i rollen av det ideala startupsubjektet?” och ”Hur upplever kvinnorna jämställdhets- och mångfaldsdiskurser inom kontexten av det finska startupekosystemet?”. Det empiriska materialet består av kvalitativa semistrukturerade intervjuer med fyra kvinnor som på ett eller annat sätt är verksamma inom det finska startupekosystemet. Intervjuerna analyseras genom diskursanalys. Det teoretiska ramverket för avhandlingen består av synen på startupekosystem som performativa diskurser – diskurser som konstruerar de verkligheter de beskriver – och entreprenören som en performativ figur och det ideala startupsubjektet. Det teoretiska ramverket betonar vikten av att inkludera ekosystemet som en forskningsparameter i kulturell forskning om startupkulturer. Avhandlingen hämtar inspiration från akademiska diskussioner om den diskursiva konstruktionen av startup, entreprenörskap och teknologifältet. I avhandlingen framhävs i enlighet med forskning tre diskursiva teman som beskriver startupkulturen: öppenhet och hierarkilöshet; passion och heroism; samt rationalitet och hårt arbete. Samtliga diskursiva teman bidrar till en hegemonisk förståelse om startupkulturen som inkluderande, jämlik och rättvis. Avhandlingen ifrågasätter dessa premisser och argumenterar för att startupdiskurser bidrar till att reproducera en förgivettagen sanning om inkludering och jämlikhet som osynliggör maktstrukturer och förhindrar att status quo ifrågasätts. Dessa diskursiva formationer konstruerar entreprenörsfiguren, som representerar ett demokratiserat och jämlikt ideal inom en objektiv marknadsekonomi. Analysen påvisar att entreprenören, trots sina neutrala premisser, är könad och rasifierad, och lättare fäster sig vid maskulint kodade kroppar. Slutligen påvisar avhandlingen att respondenterna blivit marginaliserade som kunskapsinnehavare när det gäller frågor om jämställdhet och likabehandling. Avhandlingen föreslår att startupdiskurser och konstruktionen av entreprenörsfiguren påverkar hur jämställdhet och mångfald förstås inom fältet och skapar en förutsättning för icke-performativa diskurser och tystnader gällande jämställdhet och mångfald.
  • Hoekman, David; LeVan, Katherine E.; Ball, George E.; Browne, Robert A.; Davidson, Robert L.; Erwin, Terry L.; Knisley, C. Barry; LaBonte, James R.; Lundgren, Jonathan; Maddison, David R.; Moore, Wendy; Niemelä, Jari; Ober, Karen A.; Pearson, David L.; Spence, John R.; Will, Kipling; Work, Timothy (2017)
    The National Ecological Observatory Network (NEON) will monitor ground beetle populations across a network of broadly distributed sites because beetles are prevalent in food webs, are sensitive to abiotic factors, and have an established role as indicator species of habitat and climatic shifts. We describe the design of ground beetle population sampling in the context of NEON's long-term, continentalscale monitoring program, emphasizing the sampling design, priorities, and collection methods. Freely available NEON ground beetle data and associated field and laboratory samples will increase scientific understanding of how biological communities are responding to land-use and climate change.
  • Sgarabotto, Elena (Helsingin yliopisto, 2022)
    In the past 20 years, three known disease emergence events of highly pathogenic coronaviruses have highlighted the importance of monitoring wildlife for the presence of these viruses. Their peculiar characteristics, like high mutation and recombination rate, have increased their potential for species adaptation and interspecies transmission. Understanding the diversity of these viruses in wildlife and increased surveillance might be key to predicting and preventing future spillovers and pandemics. Studies on wildlife coronaviruses commonly focus on the order Chiroptera, mainly in temperate and tropical regions of the Asian continent. Even though animals belonging to this order are considered the main reservoir, the importance of other small terrestrial mammals should not be overlooked. Rodents, for instance, are animals of great interest for many zoonoses, as they often host parasites, bacteria and other groups of viruses that cause diseases in humans. A recent description of several lineages of coronaviruses recovered from rodents from China highlighted and suggested the presence of these viruses in small terrestrial rodents. In this project, we aimed to investigate the presence of coronaviruses in small mammals from France. Samples were collected during spring 2021 in twelve different locations, within two regions of eastern France, Auvergne Rhône-Alpes and Franche Comté. A total of 448 rodents, 13 shrews and 416 bat samples were collected. The samples were screened and coronaviruses sequences were recovered in 20 different samples. Nine Betacoronavirus genus sequences were recovered from rodent colon samples, and one Alpha- and ten Betacoronavirus sequences from bat guano. These results confirmed previous evidence of these viruses’ presence in small mammals from France and provide the first evidence of betacoronaviruses circulating in wild French bats. The study covers two eastern regions that have not been surveilled in previously released studies therefore this highlights the need to increase the efforts in monitoring these viruses and their wildlife host
  • Virkkala, Raimo; Leikola, Niko; Kujala, Heini; Kivinen, Sonja; Hurskainen, Pekka; Kuusela, Saija; Valkama, Jari; Heikkinen, Risto K. (Wiley, 2022)
    Ecological Applications
    The use of indicator species in forest conservation and management planning can facilitate enhanced preservation of biodiversity from the negative effects of forestry and other uses of land. However, this requires detailed and spatially comprehensive knowledge of the habitat preferences and distributions of selected focal indicator species. Unfortunately, due to limited resources for field surveys, only a small proportion of the occurrences of focal species is usually known. This shortcoming can be circumvented by using modeling techniques to predict the spatial distribution of suitable sites for the target species. Airborne laser scanning (ALS) and other remote sensing (RS) techniques have the potential to provide useful environmental data covering systematically large areas for these purposes. Here, we focused on six bird of prey and woodpecker species known to be good indicators of boreal forest biodiversity values. We used known nest sites of the six indicator species based on nestling ringing records. Thus, the most suitable nesting sites of these species provide important information for biodiversity-friendly forest management and conservation planning. We developed fine-grained, that is, 96 × 96 m grid cell resolution, predictive maps across the whole of Finland of the suitable nesting habitats based on ALS and other RS data and spatial information on the distribution of important forest stands for the six studied biodiversity indicator bird species based on nesting-habitat suitability modeling, that is, the MaxEnt model. Habitat preferences of the study species, as determined by MaxEnt, were in line with the previous knowledge of species-habitat relations. The proportion of suitable habitats of these species in protected areas (PAs) was considerable, but our analysis also revealed many potentially high-quality forest stands outside PAs. However, many of these sites are increasingly threatened by logging because of increased pressures for using forests for bioeconomy and forest industry based on National Forest Strategy. Predicting habitat suitability based on information on the nest sites of indicator species provides a new tool for systematic conservation planning over large areas in boreal forests in Europe, and a corresponding approach would also be feasible and recommendable elsewhere where similar data are available.
  • Virta, Leena; Soininen, Janne; Norkko, Alf (2020)
    Aim Global biodiversity loss has raised interest in understanding variation in diversity at different scales. In particular, studies conducted across large spatial gradients are crucial, because they can increase perspectives on how ecological patterns change relative to environmental factors and facilitate predictions of possible responses to environmental change. We explored the full extent of a brackish sea to test the hypotheses that: (a) benthic communities are defined by the limited ranges of species, controlled by varying drivers along a large environmental gradient; (b) the responses of taxonomic and functional community composition and turnover to the environmental gradient are different, thus highlighting the need to include both measures in ecological studies; and (c) diversity reaches the minimum at intermediate salinities (Remane curve) owing to the low adaptation of freshwater and marine species. Location A large environmental and spatial gradient spanning the entire Swedish coastline (c. 2,300 km; salinity 1.2-27.6), the Baltic Sea. Time period August 2018. Major taxa studied Benthic diatoms. Methods We assessed environmental drivers for the communities and calculated the taxonomic and functional alpha and beta diversity along the gradient. We also compared the taxonomic and functional composition and diversity of communities among areas with different salinity. Results We found support for the hypothesis of limited species ranges, because taxonomic beta diversity, mainly induced by changes in salinity and climate, was high, whereas functional beta diversity remained considerably lower, and the composition and diversity of communities, in addition to environmental drivers controlling the communities, differed between regions with different salinity. The lowest taxonomic diversity was found at intermediate salinities of 5-6. Main conclusions These findings advance understanding of large-scale patterns of benthic diversity, emphasize the importance of large gradient studies for a better understanding of general ecological patterns and highlight the vulnerability of brackish water ecosystems as ecologically important tipping-point realms.
  • Hakola, Outi (2021)
    Background: The 21st century has seen a proliferation of end-of-life documentary films and television documentaries that contribute to building a public image of hospice and palliative care. The way in which terminally ill patients are represented in these documentaries creates impressions of who is welcomed to receive end-of-life care. These documentary representations have not been previously mapped. Methods: Using quantitative content analysis, I analyzed 35 contemporary Western documentaries and studied their diversity in the representations. I focused on terminally ill patients who are given time and space in the narration to voice their views about the end-of-life process. I paid attention to such elements as gender, race and ethnicity, age, class, religion and sexuality. Results: The documentaries welcomed the representations and voices of terminally ill people. Class, religion and sexuality often had a marginal role in narration. The gender diversity of the representations was quite balanced. Regarding age, the documentaries preferred stories about working age patients for dramatic purposes, yet all age groups were represented. However, the documentaries had an identifiable racial and ethnic bias. With a few exceptions, terminally ill who had a personal voice in the narrations were white. In comparison, racial and ethnic minorities were either absent from most of the documentaries, or their role was limited to illustrations of the general story. Conclusions: End-of-life documentaries provide identifiable access to the patients’ experiences and as such they provide emotionally and personally engaging knowledge about hospice and palliative care. While these representations are people-oriented, they include racial disparities and they focus mostly on the experiences of white terminally ill patients. This bias reinforces the misleading image of hospice and palliative care as a racialized healthcare service.
  • Rowlett, J.; Karlsson, C. J.; Nursultanov, M. (2022)
    How does the composition of a collection of individuals affect its outcome in competition with other collections of individuals? Assuming that individuals can be different, we develop a model to interpolate between individual-level interactions and collective-level consequences. Rooted in theoretical mathematics, the model is not constrained to any specific context. Potential applications include research, education, sports, politics, ecology, agriculture, algorithms and finance. Our first main contribution is a game theoretic model that interpolates between the internal composition of an ensemble of individuals and the repercussions for the ensemble as a whole in competition with others. The second main contribution is the rigorous identification of all equilibrium points and strategies. These equilibria suggest a mechanistic underpinning for biological and physical systems to tend towards increasing diversity due to the strength it imparts to the system in competition with others.
  • Louvrier, Jonna (Hanken School of Economics, 2013)
    Economics and Society – 259
    In many countries diversity management has become an increasingly common way of treating differences between people in the world of work. Companies may sign diversity charters to show their engagement in promoting diversity, design and implement diversity management programmes, and communicate about their diversity initiatives to internal and external stakeholders. But what does diversity in the workplace mean? Who is defined as being different? And what do those defined as being different think about diversity and difference in work? By addressing these questions this book sheds light on the complex meanings of diversity management. The meanings of diversity management have long been developed and discussed in relation to equality and anti-discrimination policy and practice. A key question has been whether diversity management is a better way to enhance equality between organisational members or, on the contrary, is it diluting the results of equality approaches. The scope of this study is broader and shows that meanings of diversity management are constructed by drawing on not only knowledge about equality and anti-discrimination, but also understandings of society, the organisation, the individual, and the nature of differences. The study is informed by poststructuralist theory and based on interview data produced with 23 diversity managers and 52 ethnic minority employees in diversity promoting organisations in Finland and France. The findings contribute to the field of diversity management in several ways. First of all, the results show that there is no unitary meaning of diversity, difference and diversity management, but a number of discourses together forming the complexity and variety of what diversity management can come to mean in a given context and at a given point of time. Secondly, the findings challenge the idea that diversity management initiatives would be based solely on essentialist views of difference. However, the findings also show that even when differences are seen to be socially constructed, the organisation is not seen as participating in the construction of differences and in the production of related inequalities. Thirdly, the findings show that ethnic minority employees rarely draw on their differences as positive resources in work, and that they often are left alone to manage challenging situations related to difference, even in organisations promoting diversity. Lastly, the study highlights the importance of being attentive to national societal context, as discursively constructed, throughout the research process.
  • Tolonen, Kimmo T.; Karjalainen, Juha; Hämäläinen, Heikki; Nyholm, Kristiina; Rahkola-Sorsa, Minna; Cai, Yongjiu; Heino, Jani (Springer Link, 2020)
    Aquatic Ecology 54 3 (2020)
    Lake littoral environments are heterogeneous, and different organisms typically show specific responses to this environmental variation. We examined local environmental and spatial factors affecting lake littoral biodiversity and the structuring of assemblages of phytoplankton, zooplankton and macroinvertebrates within and among three basins of a large lake system. We explored congruence of species composition and species richness among the studied organism groups to evaluate their general indicator potential to represent spatial variation in other groups. We expected that effects of water chemistry on plankton assemblages were stronger than effects of habitat characteristics. In contrast, we anticipated stronger effects of habitat on macroinvertebrates due to their mainly benthic mode of life. We also expected that within-basin spatial effects would be strongest on macroinvertebrates and weakest on phytoplankton. We predicted weak congruence in assemblage composition and species richness among the organism groups. Phytoplankton assemblages were mainly structured by the shared effects of water chemistry and large-scale spatial factors. In contrast to our expectations, habitat effects were stronger than water chemistry effects on zooplankton assemblages. However, as expected, macroinvertebrate species composition and richness were mainly affected by habitat conditions. Among-group congruence was weak for assemblage composition and insignificant for richness. Albeit weak, congruence was strongest between phytoplankton and zooplankton assemblages, as we expected. In summary, our analyses do not support the idea of using a single organism group as a wholesale biodiversity indicator.
  • BEEHIVE Collaboration; Wymant, Chris; Blanquart, Francois; Golubchik, Tanya; Gall, Astrid; Bakker, Margreet; Bezemer, Daniela; Croucher, Nicholas J.; Hall, Matthew; Hillebregt, Mariska; Ong, Swee Hoe; Ratmann, Oliver; Albert, Jan; Bannert, Norbert; Fellay, Jacques; Fransen, Katrien; Gourlay, Annabelle; Grabowski, M. Kate; Gunsenheimer-Bartmeyer, Barbara; Gunthard, Huldrych F.; Kivelä, Pia; Kouyos, Roger; Laeyendecker, Oliver; Liitsola, Kirsi; Meyer, Laurence; Porter, Kholoud; Ristola, Matti; van Sighem, Ard; Berkhout, Ben; Cornelissen, Marion; Kellam, Paul; Reiss, Peter; Fraser, Christophe (2018)
    Studying the evolution of viruses and their molecular epidemiology relies on accurate viral sequence data, so that small differences between similar viruses can be meaningfully interpreted. Despite its higher throughput and more detailed minority variant data, next-generation sequencing has yet to be widely adopted for HIV. The difficulty of accurately reconstructing the consensus sequence of a quasispecies from reads (short fragments of DNA) in the presence of large between-and within-host diversity, including frequent indels, may have presented a barrier. In particular, mapping (aligning) reads to a reference sequence leads to biased loss of information; this bias can distort epidemiological and evolutionary conclusions. De novo assembly avoids this bias by aligning the reads to themselves, producing a set of sequences called contigs. However contigs provide only a partial summary of the reads, misassembly may result in their having an incorrect structure, and no information is available at parts of the genome where contigs could not be assembled. To address these problems we developed the tool shiver to pre-process reads for quality and contamination, then map them to a reference tailored to the sample using corrected contigs supplemented with the user's choice of existing reference sequences. Run with two commands per sample, it can easily be used for large heterogeneous data sets. We used shiver to reconstruct the consensus sequence and minority variant information from paired-end short-read whole-genome data produced with the Illumina platform, for sixty-five existing publicly available samples and fifty new samples. We show the systematic superiority of mapping to shiver's constructed reference compared with mapping the same reads to the closest of 3,249 real references: median values of 13 bases called differently and more accurately, 0 bases called differently and less accurately, and 205 bases of missing sequence recovered. We also successfully applied shiver to whole-genome samples of Hepatitis C Virus and Respiratory Syncytial Virus. shiver is publicly available from https://github.com/ChrisHIV/shiver.
  • Brittain, John E.; Heino, Jani; Friberg, Nikolai; Aroviita, Jukka; Kahlert, Maria; Karjalainen, Satu‐Maaria; Keck, François; Lento, Jennifer; Liljaniemi, Petri; Mykrä, Heikki; Schneider, Susanne C.; Ylikörkkö, Jukka (Blackwell Scientific, 2022)
    Freshwater Biology
    1. Arctic freshwaters support biota adapted to the harsh conditions at these latitudes, but the climate is changing rapidly and so are the underlying environmental filters. Currently, we have limited understanding of broad-scale patterns of Arctic riverine biodiversity and the correlates of α- and β-diversity. 2. Using information from a database set up within the scope of the Arctic Council's Conservation of Arctic Flora and Fauna Circumpolar Biodiversity Monitoring Plan, we analysed patterns and correlates of α- and β-diversity in benthic diatom and macroinvertebrate communities across northern Norway, Sweden, and Finland. We analysed variation in total β-diversity and its replacement and richness difference components in relation to location of the river reach and its drainage basin (Baltic Sea in the south, the Barents Sea in the east and the north, and the Norwegian Sea in the west), in addition to climate and environmental variables. 3. In both macroinvertebrates and diatoms, the replacement and richness difference components showed wide variation. For macroinvertebrates, the richness difference component was the more important, whereas for diatoms, the replacement component was the more important in contributing to variation in β-diversity. There was no significant difference in β-diversity between the three main drainage basins, but species composition differed among the drainage basins. 4. Based on the richness difference component of β-diversity, climate variables were most strongly associated with community variation in macroinvertebrates. In diatoms, both environmental and climate variables were strongly correlated with community compositional variation. In both groups, there were also significant differences in α-diversity among the three main drainage basins, and several taxa were significant indicators of one of these drainage basins. Alpha diversity was greater in areas with a continental climate, while the oceanic areas in the west harboured greatly reduced flora and fauna. 5. The correlates of biodiversity were relatively similar in macroinvertebrates and diatoms. Climate variables, in particular temperature, were the most strongly associated with biodiversity patterns in the Arctic rivers of Fennoscandia. Sedimentary geology may be associated with increased productivity and, to a lesser extent, with sensitivity to acidification. There was considerable variation in community composition across Arctic Fennoscandia, indicating the necessity of protecting several stream reaches or even whole catchments within each region to conserve total riverine biodiversity. Furthermore, it is likely that the predicted changes in temperature in Arctic areas will influence riverine diversity patterns across Fennoscandia.
  • Vilmi, A.; Zhao, W.; Picazo, F.; Li, M.; Heino, J.; Soininen, J.; Wang, J. (2019)
    Science of the Total Environment 702: 134974
    Understanding the role of climatic variation on biodiversity is of chief importance due to the ongoing biodiversity loss and climate change. Freshwaters, one of the most threatened ecosystems in the world, offer a valuable context to study biodiversity patterns of distinct organism groups in relation to climatic variation. In the Tibetan Plateau biodiversity hotspot - Hengduan Mountain region, we studied the effects of climate and local physico-chemical factors on stream microorganisms (i.e. bacteria) and macroorganisms (i.e. macroinvertebrates) in two parallel catchments with contrasting precipitation and temperature, that is, the Nujiang and Lancang Rivers. Diversities and community structures were better explained by climatic and local environmental variables in the drier and colder catchment and at higher elevations, than in the warmer and wetter conditions and at lower elevations. This suggests that communities may be more strongly assembled by deterministic processes in the former, comparatively harsher conditions, compared to the latter, more benign conditions. Macroinvertebrates were more strongly affected by climatic and local environmental factors compared to bacteria, but the diversities and community structures of the two groups showed spatially similar responses to overall abiotic variation, being especially evident with their community structures' responses to climate. Furthermore, bacterial and macroinvertebrate diversities were positively correlated in the drier and colder catchment, implying that these biologically and ecologically distinct organism groups are likely to be driven by similar processes in areas with such climatic conditions. We conclude that changes in climatic and local environmental conditions may affect the diversity of macroorganisms more strongly than that of microorganisms, at least in subtropical mountainous stream ecosystems studied here, but simultaneous responses of both groups to environmental changes can also be expected.
  • Valkó, Orsolya; Zmihorski, Michal; Biurrun, Idoia; Loos, Jacqueline; Labadessa, Rocco; Venn, Stephen (2016)
    Palaearctic grasslands encompass a diverse variety of habitats, many of high nature value and vulnerability. The main challenges are climate-change, land-use change, agricultural intensification and abandonment. Many measures are in place to address these challenges, through restoration and appropriate management, though more work is necessary. We present eight studies from China/Germany, Greece, Kazakhstan, Russia and Ukraine. The papers cover a wide range of grassland and steppe habitats and cover vegetation ecology, syntaxonomy and zoology. We also conducted a systematic search on steppe and grassland diversity. The greatest number of studies was from China, followed by Germany and England. We conclude that the amount of research being carried out on Eurasian grasslands is inadequate considering their high levels of biodiversity and vulnerability. We hope to encourage readers to address current major challenges, such as how to manage grasslands for the benefit of diverse taxa, to ensure that conservation initiatives concentrate on sites where there is good potential for success and for the generation of realistic and viable conservation strategies.