Browsing by Subject "1181 Ecology, evolutionary biology"

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  • Fondi, Marco; Karkman, Antti; Tamminen, Manu V.; Bosi, Emanuele; Virta, Marko; Fani, Renato; Alm, Eric; McInerney, James O. (2016)
    The spatial distribution of microbes on our planet is famously formulated in the Baas Becking hypothesis as everything is everywhere but the environment selects." While this hypothesis does not strictly rule out patterns caused by geographical effects on ecology and historical founder effects, it does propose that the remarkable dispersal potential of microbes leads to distributions generally shaped by environmental factors rather than geographical distance. By constructing sequence similarity networks from uncultured environmental samples, we show that microbial gene pool distributions are not influenced nearly as much by geography as ecology, thus extending the Bass Becking hypothesis from whole organisms to microbial genes. We find that gene pools are shaped by their broad ecological niche (such as sea water, fresh water, host, and airborne). We find that freshwater habitats act as a gene exchange bridge between otherwise disconnected habitats. Finally, certain antibiotic resistance genes deviate from the general trend of habitat specificity by exhibiting a high degree of cross-habitat mobility. The strong cross-habitat mobility of antibiotic resistance genes is a cause for concern and provides a paradigmatic example of the rate by which genes colonize new habitats when new selective forces emerge.
  • Sahlin, Ullrika; Helle, Inari; Perepolkin, Dmytro (2021)
    Failing to communicate current knowledge limitations, that is, epistemic uncertainty, in environmental risk assessment (ERA) may have severe consequences for decision making. Bayesian networks (BNs) have gained popularity in ERA, primarily because they can combine variables from different models and integrate data and expert judgment. This paper highlights potential gaps in the treatment of uncertainty when using BNs for ERA and proposes a consistent framework (and a set of methods) for treating epistemic uncertainty to help close these gaps. The proposed framework describes the treatment of epistemic uncertainty about the model structure, parameters, expert judgment, data, management scenarios, and the assessment's output. We identify issues related to the differentiation between aleatory and epistemic uncertainty and the importance of communicating both uncertainties associated with the assessment predictions (direct uncertainty) and the strength of knowledge supporting the assessment (indirect uncertainty). Probabilities, intervals, or scenarios are expressions of direct epistemic uncertainty. The type of BN determines the treatment of parameter uncertainty: epistemic, aleatory, or predictive. Epistemic BNs are useful for probabilistic reasoning about states of the world in light of evidence. Aleatory BNs are the most relevant for ERA, but they are not sufficient to treat epistemic uncertainty alone because they do not explicitly express parameter uncertainty. For uncertainty analysis, we recommend embedding an aleatory BN into a model for parameter uncertainty. Bayesian networks do not contain information about uncertainty in the model structure, which requires several models. Statistical models (e.g., hierarchical modeling outside the BNs) are required to consider uncertainties and variability associated with data. We highlight the importance of being open about things one does not know and carefully choosing a method to precisely communicate both direct and indirect uncertainty in ERA. Integr Environ Assess Manag 2020;00:1-12. (c) 2020 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC)
  • Sennikov, Alexander N.; Sukhorukov, Alexander P. (2021)
  • Salonen, Iines S.; Chronopoulou, Panagiota-Myrsini; Nomaki, Hidetaka; Langlet, Dewi; Tsuchiya, Masashi; Koho, Karoliina A. (2021)
    Foraminifera are unicellular eukaryotes that are an integral part of benthic fauna in many marine ecosystems, including the deep sea, with direct impacts on benthic biogeochemical cycles. In these systems, different foraminiferal species are known to have a distinct vertical distribution, i.e., microhabitat preference, which is tightly linked to the physico-chemical zonation of the sediment. Hence, foraminifera are well-adapted to thrive in various conditions, even under anoxia. However, despite the ecological and biogeochemical significance of foraminifera, their ecology remains poorly understood. This is especially true in terms of the composition and diversity of their microbiome, although foraminifera are known to harbor diverse endobionts, which may have a significant meaning to each species' survival strategy. In this study, we used 16S rRNA gene metabarcoding to investigate the microbiomes of five different deep-sea benthic foraminiferal species representing differing microhabitat preferences. The microbiomes of these species were compared intra- and inter-specifically, as well as with the surrounding sediment bacterial community. Our analysis indicated that each species was characterized with a distinct, statistically different microbiome that also differed from the surrounding sediment community in terms of diversity and dominant bacterial groups. We were also able to distinguish specific bacterial groups that seemed to be strongly associated with particular foraminiferal species, such as the family Marinilabiliaceae for Chilostomella ovoidea and the family Hyphomicrobiaceae for Bulimina subornata and Bulimina striata. The presence of bacterial groups that are tightly associated to a certain foraminiferal species implies that there may exist unique, potentially symbiotic relationships between foraminifera and bacteria that have been previously overlooked. Furthermore, the foraminifera contained chloroplast reads originating from different sources, likely reflecting trophic preferences and ecological characteristics of the different species. This study demonstrates the potential of 16S rRNA gene metabarcoding in resolving the microbiome composition and diversity of eukaryotic unicellular organisms, providing unique in situ insights into enigmatic deep-sea ecosystems.
  • Neefjes, Ivo; Laapas, Mikko; Liu, Yang; Medus, Erika; Miettunen, Elina; Ahonen, Lauri; Quelever, Lauriane; Aalto, Juho; Bäck, Jaana; Kerminen, Veli-Matti; Lampilahti, Janne; Luoma, Krista; Mäki, Mari; Mammarella, Ivan; Petäjä, Tuukka; Räty, Meri; Sarnela, Nina; Ylivinkka, Ilona; Hakala, Simo; Kulmala, Markku; Nieminen, Tuomo; Lintunen, Anna (2022)
    Boreal forests are an important source of trace gases and atmospheric aerosols, as well as a crucial carbon sink. As such, they form a strongly interconnected coupled system with the atmosphere. The SMEAR II station is located in a boreal Scots pine forest in Hyytiala, Finland, and has over 25 years of continuous measurements of atmospheric and ecosystem variables. In this study, we analyse the seasonal variations of trace gases, atmospheric aerosols, greenhouse gases, and meteorological variables, measured at the SMEAR II sta-tion during the past two and a half decades. Several ecosystem and atmospheric variables show seasonal correlations with each other, which suggests seasonal interactions within the climate system that links together ecosystem processes, greenhouse gases, trace gases and atmospheric aerosols. For instance, increased global radiation in summer increases air temperature and consequently affects the plant phenology, which promotes the ecosystem carbon exchange and biogenic volatile organic compound (biogenic VOC) release. This further affects the ambient concentrations of highly oxygenated organic molecules (HOMs) as well as the formation and growth of atmospheric organic aerosols. Organic aerosols subsequently influence aerosol optical properties and, through increased scattering, have the potential to cool the climate. We also discuss the impacts of the warm and dry summers of 2010 and 2018 on the studied variables. For these years, we find a higher-than-average ecosystem primary production especially in June, leading to an increased VOC flux from the forest. The increased VOC flux in turn leads to higher HOM and secondary aerosol concentration in the atmosphere. The latter increases light scattering by atmospheric aero-sol particles and thus leads to climate cooling. The results obtained in this study improve our understanding of how boreal forests respond to climate change.
  • Tian, Xiaoqing; Pan, Huachen; Köngäs, Riia Margit Petrina; Horppila, Jukka Antero (2017)
    A 3D-model was developed to study the effects of hypolimnetic aeration on the temperature profile of a thermally stratified Lake Vesijärvi (southern Finland). Aeration was conducted by pumping epilimnetic water through the thermocline to the hypolimnion without breaking the thermal stratification. The model used time transient equation based on Navier–Stokes equation. The model was fitted to the vertical temperature distribution and environmental parameters (wind, air temperature, and solar radiation) before the onset of aeration, and the model was used to predict the vertical temperature distribution 3 and 15 days after the onset of aeration (1 August and 22 August). The difference between the modelled and observed temperature was on average 0.6 °C. The average percentage model error was 4.0% on 1 August and 3.7% on 22 August. In the epilimnion, model accuracy depended on the difference between the observed temperature and boundary conditions. In the hypolimnion, the model residual decreased with increasing depth. On 1 August, the model predicted a homogenous temperature profile in the hypolimnion, while the observed temperature decreased moderately from the thermocline to the bottom. This was because the effect of sediment was not included in the model. On 22 August, the modelled and observed temperatures near the bottom were identical demonstrating that the heat transfer by the aerator masked the effect of sediment and that exclusion of sediment heat from the model does not cause considerable error unless very short-term effects of aeration are studied. In all, the model successfully described the effects of the aerator on the lake’s temperature profile. The results confirmed the validity of the applied computational fluid dynamic in artificial aeration; based on the simulated results, the effect of aeration can be predicted.
  • Laurila-Pant, Mirka; Mäntyniemi, Samu; Östman, Örjan; Olsson , Jens; Uusitalo, Laura; Lehikoinen, Annukka (2021)
    Ecological indicator approaches typically compare the prevailing state of an ecosystem component to a reference state reflecting good environmental conditions, i.e. the desirable state. However, defining the reference state is challenging due to a wide range of uncertainties related to natural variability and measurement error in data, as well as ecological understanding. This study propose a novel probabilistic approach combining historical monitoring data and ecological understanding to estimate the uncertainty associated with the boundary value of an ecological indicator between good and poor environmental states. Bayesian inference is used to estimate the epistemic uncertainty about the true state of an indicator variable during an historical reference period. This approach replaces the traditional boundary value with probability distribution, indicating the uncertainty about the boundary between environmental states providing a transparent safety margin associated with the risk of misclassification of the indicator's state. The approach is demonstrated by applying it to a time-series of an ecological status indicator, 'Abundance of coastal key fish species', included in HELCOM's Baltic Sea regional status assessment. We suggest that acknowledgement of the uncertainty behind the final classification leads to more transparent and better-informed decision-making processes.
  • Azevedo, Anna Karoline; Vieira, Felipe A. S.; Guedes-Santos, Jhonatan; Gaia, Joao Arthur; Pinheiro, Barbara R.; Bragagnolo, Chiara; Correia, Ricardo A.; Ladle, Richard J.; Malhado, Ana C. M. (2022)
    In August 2019, the Northeast coast of Brazil was impacted by an extensive oil spill, with immediate effects on marine and coastal ecosystems and significant impacts on tourism and food security. The human dimension of those impacts also includes the loss of cultural ecosystem services (CES); the non-material benefits stemming from strongly rooted cultural practices and relationships with nature. CES are of great importance for local residents and visitors that flock to Brazilian iconic beaches, however, they are difficult to measure using traditional assessment methods due to their subjective and non-tangible nature. Here, we use a big data approach to assess and map the loss of CES in the Northeast coast of Brazil caused by the recent oil spill. We analysed 2,880 digital images (published on the image sharing platform Flickr) taken before and during the disaster in affected locations, using a combination of automated techniques. Results showed a sharp decline in the number of users posting photos of locations affected by oil spill, and a decline in photos representing landscape and cultural appreciation. Our big data approach provides a fast and automated way to assess CES at large spatial scales that can be used to monitor the social impacts of environmental disasters.
  • Silvonen, Soila; Niemistö, Juha; Csibrán, Adrián; Jilbert, Tom; Torma, Péter; Krámer, Tamás; Nurminen, Leena; Horppila, Jukka (2021)
    Hypolimnetic withdrawal (HW) is a lake restoration method that is based on the removal of phosphorus (P) along with near-bottom water. While it has often proven to be effective, the method also sets challenges: it is about balancing between effective P removal and maintenance of the thermal stratification of the lake. The success of different HW projects has been reviewed in some studies retrospectively, but scientific literature still lacks studies that use detailed data on the lake biogeochemistry to scale and optimize the method in advance, and to predict the outcomes of the restoration measure. In the current study, we investigated the seasonal biogeochemistry, P stocks and thermal stratification of a eutrophic lake (Lake Kymijarvi/Myllypohja basin, southern Finland) to determine an optimal withdrawal rate, to assess its effects on stratification, and to evaluate the expected success of HW. We found that by adjusting HW with P diffusive fluxes from the sediment (diffusion-adjusted HW), it is possible to remove a notable part of the cycling P without causing major disturbances to the thermal stratification even in a relatively shallow lake. Our results show that HW can have great potential in lake restoration: diffusion-adjusted HW in our study lake could increase the annual P output by 35-46%, shifting the P budget of the lake to negative. We thus propose a novel approach to optimize HW on the basis of the diffusive flux of P from the sediment, with the goal of extracting P continuously at an equivalent rate to the diffusive flux. We finally discuss how this can be achieved more effectively with HW based on a closed-circuit system. (c) 2020 The Authors. Published by Elsevier B.V.
  • Schmidt, Alexander; Sadowski, Eva-Maria; Kaasalainen, Ulla; Rikkinen, Jouko Kalevi (The Gdańsk International Fair Co. (MTG SA), Gdańsk SA, 2019)
    Baltic amber forms the largest amber deposit on earth and it is particularly well-known for the plethora of arthropod inclusions. The floristic composition, habitat types and climate of its Eocene source area, however, are still controversial. The differing suggestions range from early Eocene tropical to late Eocene temperate environments, and from lowland to montane forests. We screened a large number of inclusions from historic collections and from recently discovered amber pieces and found many inclusions of seed plants, lichens and microfungi that provide important insights into habitat structure and climate.
  • Peris Tamayo, Ana-Maria; Devineau, Olivier; Praebel, Kim; Kahilainen, Kimmo K.; ostbye, Kjartan (2020)
    Adaptive radiation is the diversification of species to different ecological niches and has repeatedly occurred in different salmonid fish of postglacial lakes. In Lake Tinnsjoen, one of the largest and deepest lakes in Norway, the salmonid fish, Arctic charr (Salvelinus alpinus(L.)), has likely radiated within 9,700 years after deglaciation into ecologically and genetically segregated Piscivore, Planktivore, Dwarf, and Abyssal morphs in the pelagial, littoral, shallow-moderate profundal, and deep-profundal habitats. We compared trait variation in the size of the head, the eye and olfactory organs, as well as the volumes of five brain regions of these four Arctic charr morphs. We hypothesised that specific habitat characteristics have promoted divergent body, head, and brain sizes related to utilized depth differing in environmental constraints (e.g., light, oxygen, pressure, temperature, and food quality). The most important ecomorphological variables differentiating morphs were eye area, habitat, and number of lamellae. The Abyssal morph living in the deepest areas of the lake had the smallest brain region volumes, head, and eye size. Comparing the olfactory bulb with the optic tectum in size, it was larger in the Abyssal morph than in the Piscivore morph. The Piscivore and Planktivore morphs that use more illuminated habitats have the largest optic tectum volume, followed by the Dwarf. The observed differences in body size and sensory capacities in terms of vision and olfaction in shallow and deepwater morphs likely relates to foraging and mating habitats in Lake Tinnsjoen. Further seasonal and experimental studies of brain volume in polymorphic species are needed to test the role of plasticity and adaptive evolution behind the observed differences.
  • Kaasalainen, Ulla Susanna; Heinrichs, Jochen; Renner, Matthew; Hedenäs, Lars; Schäfer-Verwimp, Alfons; Lee, Gaik; Ignatov, Michael; Rikkinen, Jouko; Schmidt, Alexander (2018)
    Fossil tree resins preserve a wide range of animals, plants, fungi and microorganisms in microscopic fidelity. Fossil organisms preserved in an individual piece of amber lived at the same time in Earth history and mostly even in the same habitat, but they were not necessarily parts of the same interacting community. Here, we report on an in situ preserved corticolous community from a piece of Miocene Dominican amber which is composed of a lichen, a moss and three species of leafy liverworts. The lichen is assigned to the extant genus Phyllopsora (Ramalinaceae, Lecanoromycetes) and is described as P. magna Kaasalainen, Rikkinen & A. R. Schmidt sp. nov. The moss, Aptychellites fossilis Schaf.-Verw., Hedenas, Ignatov & Heinrichs gen. & sp. nov., closely resembles the extant genus Aptychella of the family Pylaisiadelphaceae. The three leafy liverworts comprise the extinct Lejeuneaceae species Cheilolejeunea antiqua (Grolle) Ye & Zhu, 2010 and Lejeunea miocenica Heinrichs, Schaf.-Verw., M. A. M. Renner & G. E. Lee sp. nov. and the extinct Radulaceae species Radula intecta M. A. M. Renner, Schaf.-Verw. & Heinrichs sp. nov. The presence of five associated extinct cryptogam species, four of which belong to extant genera, further substantiates the notion of a stasis in morphotype diversity, but a certain turnover of species, in the Caribbean since the early Miocene.
  • Cardós, J.L.H.; Prieto, M.; Jylhä, Maarit Johanna; Aragón, G.; Molina, M.C.; Martínez, I.; Rikkinen, Jouko (2019)
    BACKGROUND AND AIMS: In order to re-establish lichen symbiosis, fungal spores must first germinate and then associate with a compatible photobiont. To detect possible establishment limitations in a sexually reproducing cyanolichen species, we studied ascospore germination, photobiont growth and photobiont association patterns in Pectenia plumbea. METHODS: Germination tests were made with ascospores from 500 apothecia under different treatments, and photobiont growth was analysed in 192 isolates obtained from 24 thalli. We determined the genotype identity [tRNALeu (UAA) intron] of the Nostoc cyanobionts from 30 P. plumbea thalli from one population. We also sequenced cyanobionts of 41 specimens of other cyanolichen species and 58 Nostoc free-living colonies cultured from the bark substrate. KEY RESULTS: Not a single fungal ascospore germinated and none of the photobiont isolates produced motile hormogonia. Genetic analyses revealed that P. plumbea shares Nostoc genotypes with two other cyanolichen species of the same habitat, but these photobionts were hardly present in the bark substrate. CONCLUSIONS: Due to the inability of both symbionts to thrive independently, the establishment of P. plumbea seems to depend on Dendriscocaulon umhausense, the only cyanolichen species in the same habitat that reproduces asexually and acts as a source of appropriate cyanobionts. This provides support to the hypothesis about facilitation among lichens.
  • Enroth, Johannes; Olsson, Sanna; Long, David G.; Quandt, Dietmar (2012)
    Pinnatella gollanii Broth., previously known only from north Indian collections dating back to 1903, was rediscovered in Nepal in 2001.
  • Sætre, Camilla Lo Cascio; Eroukhmanoff, Fabrice; Rönkä, Katja; Kluen, Edward; Thorogood, Rose; Torrance, James; Tracey, Alan; Chow, William; Pelan, Sarah; Howe, Kerstin; Jakobsen, Kjetill S.; Tørresen, Ole K. (2021)
    The reed warbler (Acrocephalus scirpaceus) is a long-distance migrant passerine with a wide distribution across Eurasia. This species has fascinated researchers for decades, especially its role as host of a brood parasite, and its capacity for rapid phenotypic change in the face of climate change. Currently, it is expanding its range northwards in Europe, and is altering its migratory behavior in certain areas. Thus, there is great potential to discover signs of recent evolution and its impact on the genomic composition of the reed warbler. Here, we present a high-quality reference genome for the reed warbler, based on PacBio, 10×, and Hi-C sequencing. The genome has an assembly size of 1,075,083,815 bp with a scaffold N50 of 74,438,198 bp and a contig N50 of 12,742,779 bp. BUSCO analysis using aves_odb10 as a model showed that 95.7% of BUSCO genes were complete. We found unequivocal evidence of two separate macrochromosomal fusions in the reed warbler genome, in addition to the previously identified fusion between chromosome Z and a part of chromosome 4A in the Sylvioidea superfamily. We annotated 14,645 protein-coding genes, and a BUSCO analysis of the protein sequences indicated 97.5% completeness. This reference genome will serve as an important resource, and will provide new insights into the genomic effects of evolutionary drivers such as coevolution, range expansion, and adaptations to climate change, as well as chromosomal rearrangements in birds.
  • Heino, Jani; Soininen, Janne; Alahuhta, Janne; Lappalainen, Jyrki; Virtanen, Risto (2015)
    Most metacommunity studies have taken a direct mechanistic approach, aiming to model the effects of local and regional processes on local communities within a metacommunity. An alternative approach is to focus on emergent patterns at the metacommunity level through applying the elements of metacommunity structure (EMS; Oikos, 97, 2002, 237) analysis. The EMS approach has very rarely been applied in the context of a comparative analysis of metacommunity types of main microbial, plant, and animal groups. Furthermore, to our knowledge, no study has associated metacommunity types with their potential ecological correlates in the freshwater realm. We assembled data for 45 freshwater metacommunities, incorporating biologically highly disparate organismal groups (i.e., bacteria, algae, macrophytes, invertebrates, and fish). We first examined ecological correlates (e.g., matrix properties, beta diversity, and average characteristics of a metacommunity, including body size, trophic group, ecosystem type, life form, and dispersal mode) of the three elements of metacommunity structure (i.e., coherence, turnover, and boundary clumping). Second, based on those three elements, we determined which metacommunity types prevailed in freshwater systems and which ecological correlates best discriminated among the observed metacommunity types. We found that the three elements of metacommunity structure were not strongly related to the ecological correlates, except that turnover was positively related to beta diversity. We observed six metacommunity types. The most common were Clementsian and quasi-nested metacommunity types, whereas Random, quasi-Clementsian, Gleasonian, and quasi-Gleasonian types were less common. These six metacommunity types were best discriminated by beta diversity and the first axis of metacommunity ecological traits, ranging from metacommunities of producer organisms occurring in streams to those of large predatory organisms occurring in lakes. Our results showed that focusing on the emergent properties of multiple metacommunities provides information additional to that obtained in studies examining variation in local community structure within a metacommunity.
  • Boieiro, Mario; Matthews, Thomas J.; Rego, Carla; Crespo, Luis; Aguiar, Carlos A. S.; Cardoso, Pedro; Rigal, Francois; Silva, Isamberto; Pereira, Fernando; Borges, Paulo A. V.; Serrano, Artur R. M. (2018)
    During the last few centuries oceanic island biodiversity has been drastically modified by human-mediated activities. These changes have led to the increased homogenization of island biota and to a high number of extinctions lending support to the recognition of oceanic islands as major threatspots worldwide. Here, we investigate the impact of habitat changes on the spider and ground beetle assemblages of the native forests of Madeira (Madeira archipelago) and Terceira (Azores archipelago) and evaluate its effects on the relative contribution of rare endemics and introduced species to island biodiversity patterns. We found that the native laurel forest of Madeira supported higher species richness of spiders and ground beetles compared with Terceira, including a much larger proportion of indigenous species, particularly endemics. In Terceira, introduced species are well-represented in both terrestrial arthropod taxa and seem to thrive in native forests as shown by the analysis of species abundance distributions (SAD) and occupancy frequency distributions (OFD). Low abundance range-restricted species in Terceira are mostly introduced species dispersing from neighbouring man-made habitats while in Madeira a large number of true rare endemic species can still be found in the native laurel forest. Further, our comparative analysis shows striking differences in species richness and composition that are due to the geographical and geological particularities of the two islands, but also seem to reflect the differences in the severity of human-mediated impacts between them. The high proportion of introduced species, the virtual absence of rare native species and the finding that the SADs and OFDs of introduced species match the pattern of native species in Terceira suggest the role of man as an important driver of species diversity in oceanic islands and add evidence for an extensive and severe human-induced species loss in the native forests of Terceira.
  • Vrezec, Al; Saurola, Pertti Lauri; Kocijancic, Stiven; Seppo, Sulkava (2018)
    ABSTRACT Capsule: Voles are the main prey of the Ural Owl Strix uralensis in Europe, with larger prey and higher prey diversity being positively associated with owl breeding performance. Aims: To assess the breeding diet and its influence on the breeding performance of the Ural Owl across a north–south gradient of its European range using nest box monitoring data. Methods: Comparable monitoring of nest boxes in different biogeographical regions of Europe (Finland, Latvia, Slovenia) and diet analysis from nest samples to assess the taxonomic and trait influence of prey on owl breeding performance in different environments. Results: High plasticity in the Ural Owl hunting behaviour under different prey availability conditions resulted in significant differences between regions and years. Voles formed the highest proportion of the diet in all studied regions. Owl brood size was positively associated by higher proportions of voles and mice in the diet, and with increasing proportions of seasonally available larger prey and consequently prey diversity. Brood size was negatively associated with the proportion of non-mammalian and predominantly forest-living prey. Conclusions: The study highlighted the importance of comparative studies of raptor ecology across their geographical ranges in different environmental conditions to reveal undiscovered patterns, which may go undetected when conducting studies at the regional scale only.