Browsing by Subject "DIVERSITY"

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  • Saarinen, Minna; Mattila, Satu (2018)
    The article examines issues related to peer interactions and group joining in upper secondary schools in Finland. The study elaborates on how young people describe students who are left out/excluded or who remain outside the social networks. The study also elucidates on how a student can join the group. The research is motivated by the current educational ethos, which emphasizes inclusion and tolerance. The data were collected from an upper secondary school and vocational and technical institute. The students were asked to recall the prior high school year and write an essay on the topic. A total of 49 students wrote about their memories. The data were analyzed using inductive content analysis, and the study found that students are either excluded or included due to the social skills they possess. Those who do not exhibit the same approach to being in a group will stay on the sidelines. The essays also described factors that connect students, such as hobbies and leisure activities. Similarity in many external factors (e.g., the family’s economic situation) unites students. Contrary to expectations, young people described themselves, and not just others, as outsiders.
  • Harrison, Jesse P.; Chronopoulou, Panagiota-Myrsini; Salonen, Iines S.; Jilbert, Tom; Koho, Karoliina A. (2021)
    Metabarcoding analyses of bacterial and eukaryotic communities have been proposed as efficient tools for environmental impact assessment. It has been unclear, however, to which extent these analyses can provide similar or differing information on the ecological status of the environment. Here, we used 16S and 18S rRNA gene metabarcoding to compare eutrophication-induced shifts in sediment bacterial and eukaryotic community structure in relation to a range of porewater, sediment and bottom-water geochemical variables, using data obtained from six stations near a former rainbow trout farm in the Archipelago Sea (Baltic Sea). Shifts in the structure of both community types were correlated with a shared set of variables, including porewater ammonium concentrations and the sediment depth-integrated oxygen consumption rate. Distance-based redundancy analyses showed that variables typically employed in impact assessments, such as bottom water nutrient concentrations, explained less of the variance in community structure than alternative variables (e.g., porewater NH4+ inventories and sediment depth-integrated O2 consumption rates) selected due to their low collinearity (up to 40 vs. 58% of the variance explained, respectively). In monitoring surveys where analyses of both bacterial and eukaryotic communities may be impossible, either 16S or 18S rRNA gene metabarcoding can serve as reliable indicators of wider ecological impacts of eutrophication.
  • 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.
  • Murillo-Ramos, Leidys; Sihvonen, Pasi; Brehm, Gunnar; Rios-Malaver, Indiana C.; Wahlberg, Niklas (2021)
    Background Molecular DNA sequence data allow unprecedented advances in biodiversity assessments, monitoring schemes and taxonomic works, particularly in poorly-explored areas. They allow, for instance, the sorting of material rapidly into operational taxonomic units (such as BINs -Barcode Index Numbers), sequences can be subject to diverse analyses and, with linked metadata and physical vouchers, they can be examined further by experts. However, a prerequisite for their exploitation is the construction of reference libraries of DNA sequences that represent the existing biodiversity. To achieve these goals for Geometridae (Lepidoptera) moths in Colombia, expeditions were carried out to 26 localities in the northern part of the country in 2015-2019. The aim was to collect specimens and sequence their DNA barcodes and to record a fraction of the species richness and occurrences in one of the most biodiversity-rich countries. These data are the beginning of an identification guide to Colombian geometrid moths, whose identities are currently often provisional only, being morpho species or operational taxonomic units (OTUs). Prior to the current dataset, 99 Geometridae sequences forming 44 BINs from Colombia were publicly available on the Barcode of Life Data System (BOLD), covering 20 species only. New information We enrich the Colombian Geometridae database significantly by including DNA barcodes, two nuclear markers, photos of vouchers and georeferenced occurrences of 281 specimens of geometrid moths from different localities. These specimens are classified into 80 genera. Analytical tools on BOLD clustered 157 of the mentioned sequences to existing BINs identified to species level, identified earlier by experts. Another 115 were assigned to BINs that were identified to genus or tribe level only. Eleven specimens did not match any existing BIN on BOLD and are, therefore, new additions to the database. It is likely that many BINs represent undescribed species. Nine short sequences (< 500bp) were not assigned to BINs, but identified to the lowest taxonomic category by expert taxonomists and with comparisons of type material photos. The released new genetic information will help to further progress the systematics of Geometridae. An illustrated catalogue of all new records allows validation of our identifications; it is also the first document of this kind for Colombian Geometridae. All specimens are deposited at the Museo de Zoologia of Universidad de Sucre (MZUS), North Colombia. DNA BINs are reported in this study through dx.doi.org/10.5883/DS-GEOCO, the species occurrences are available on SIB Colombia https://sibcolombia.net/ and the Global Biodiversity Information Facility (GBIF) https://www.gbif.org/ through https://doi.org/10.15472/ucfmkh.
  • Opedal, Oystein H.; Martins, Adriana A.; Marjakangas, Emma-Liina (2020)
    Euglossine bees are an ecologically important group, which due to their diverse resource needs act as pollinators of many neotropical plants. Male euglossines collect fragrant compounds used in mating displays from diverse sources, including the flowers of orchids and other plants. This aspect of euglossine biology has proven exceptionally useful for studies of euglossine bee populations, because male bees can be readily attracted to fragrance baits deployed in natural habitats. We synthesise the data accumulated over the 50 years since the introduction of euglossine bee baiting inventories and make these data openly available in the EUGCOMM database. By fitting hierarchical joint species distribution models to presence-absence and abundance data, we reveal that the assemblages of bees attracted depend on the baits used in interaction with species-specific fragrance preferences and that bee assemblages are most diverse at sites in landscapes characterised by partial but not complete forest cover. We suggest that these results reflect the diverse resource needs of euglossine bees and are consistent with the hypothesis that male euglossines establish home ranges incorporating multiple habitat types. These results may have important consequences for the design of nature reserves in the tropics, if these iconic pollinators are to be conserved for the future.
  • Crespo, L.C.; Domenech, M; Enguídanos, A.; Malumbres-Olarte, Jagoba; Cardoso, Pedro; Moya-Larano, J; Frias-Lopez, Cristina; Macias Hernandez, Nuria Esther; de Mas, Eva; Mazzuca, Paola; Mora, E.; Opatova, Vera; Planas, Enric; Ribera, Carles; Roca-Cusachs, M.; Ruiz, D.; Sousa, Pedro; Tonzo, V.; Arnedo, M.A. (2018)
    Background A large scale semi-quantitative biodiversity assessment was conducted in white oak woodlands in areas included in the Spanish Network of National Parks, as part of a project aimed at revealing biogeographic patterns and identify biodiversity drivers. The semi-quantitative COBRA sampling protocol was conducted in sixteen 1-ha plots across six national parks using a nested design. All adult specimens were identified to species level based on morphology. Uncertain delimitations and identifications due to either limited information of diagnostic characters or conflicting taxonomy were further investigated using DNA barcode information. New information We identified 376 species belonging to 190 genera in 39 families, from the 8,521 adults found amongst the 20,539 collected specimens. Faunistic results include the discovery of 7 new species to the Iberian Peninsula, 3 new species to Spain and 11 putative new species to science. As largely expected by environmental features, the southern parks showed a higher proportion of Iberian and Mediterranean species than the northern parks, where the Palearctic elements were largely dominant. The analysis of approximately 3,200 DNA barcodes generated in the present study, corroborated and provided finer resolution to the morphologically based delimitation and identification of specimens in some taxonomically challenging families. Specifically, molecular data confirmed putative new species with diagnosable morphology, identified overlooked lineages that may constitute new species, confirmed assignment of specimens of unknown sexes to species and identified cases of misidentifications and phenotypic polymorphisms.
  • Hayes, A.; Nguyen, D.; Andersson, M.; Anton, A.; Bailly, J-L; Beard, S.; Benschop, K. S. M.; Berginc, N.; Blomqvist, S.; Cunningham, E.; Davis, D.; Dembinski, J. L.; Diedrich, S.; Dudman, S. G.; Dyrdak, R.; Eltringham, G. J. A.; Gonzales-Goggia, S.; Gunson, R.; Howson-Wells, H. C.; Jääskeläinen, A. J.; Lopez-Labrador, F. X.; Maier, M.; Majumdar, M.; Midgley, S.; Mirand, A.; Morley, U.; Nordbo, S. A.; Oikarinen, S.; Osman, H.; Papa, A.; Pellegrinelli, L.; Piralla, A.; Rabella, N.; Richter, J.; Smith, M.; Strand, A. Söderlund; Templeton, K.; Vipond, B.; Vuorinen, T.; Williams, C.; Wollants, E.; Zakikhany, K.; Fischer, T. K.; Harvala, H.; Simmonds, P. (2020)
    Polymerase chain reaction (PCR) detection has become the gold standard for diagnosis and typing of enterovirus (EV) and human parechovirus (HPeV) infections. Its effectiveness depends critically on using the appropriate sample types and high assay sensitivity as viral loads in cerebrospinal fluid samples from meningitis and sepsis clinical presentation can be extremely low. This study evaluated the sensitivity and specificity of currently used commercial and in-house diagnostic and typing assays. Accurately quantified RNA transcript controls were distributed to 27 diagnostic and 12 reference laboratories in 17 European countries for blinded testing. Transcripts represented the four human EV species (EV-A71, echovirus 30, coxsackie A virus 21, and EV-D68), HPeV3, and specificity controls. Reported results from 48 in-house and 15 commercial assays showed 98% detection frequencies of high copy (1000 RNA copies/5 mu L) transcripts. In-house assays showed significantly greater detection frequencies of the low copy (10 copies/5 mu L) EV and HPeV transcripts (81% and 86%, respectively) compared with commercial assays (56%, 50%; P = 7 x 10(-5)). EV-specific PCRs showed low cross-reactivity with human rhinovirus C (3 of 42 tests) and infrequent positivity in the negative control (2 of 63 tests). Most or all high copy EV and HPeV controls were successfully typed (88%, 100%) by reference laboratories, but showed reduced effectiveness for low copy controls (41%, 67%). Stabilized RNA transcripts provide an effective, logistically simple and inexpensive reagent for evaluation of diagnostic assay performance. The study provides reassurance of the performance of the many in-house assay formats used across Europe. However, it identified often substantially reduced sensitivities of commercial assays often used as point-of-care tests.
  • Vesterinen, Eero J.; Kaunisto, Kari M.; Lilley, Thomas M. (2020)
    We report a detection of a surprising similarity in the diet of predators across distant phyla. Though just a first glimpse into the subject, our discovery contradicts traditional aspects of biology, as the earliest notions in ecology have linked the most severe competition of resources with evolutionary relatedness. We argue that our finding deserves more research, and propose a plan to reveal more information on the current biodiversity loss around the world. While doing so, we expand the recently proposed conservation roadmaps into a parallel study of global interaction networks.
  • Tollenaere, C.; Pernechele, B.; Mäkinen, H. S.; Parratt, S. R.; Nemeth, M. Z.; Kovacs, G. M.; Kiss, L.; Tack, A. J. M.; Laine, A. -L. (2014)
  • Lumby, Casper K.; Zhao, Lei; Breuer, Judith; Illingworth, Christopher J. R. (2020)
    Strains of the influenza virus form coherent global populations, yet exist at the level of single infections in individual hosts. The relationship between these scales is a critical topic for understanding viral evolution. Here we investigate the within-host relationship between selection and the stochastic effects of genetic drift, estimating an effective population size of infection N-e for influenza infection. Examining whole-genome sequence data describing a chronic case of influenza B in a severely immunocompromised child we infer an N-e of 2.5 x 10(7) (95% confidence range 1.0 x 10(7) to 9.0 x 10(7)) suggesting that genetic drift is of minimal importance during an established influenza infection. Our result, supported by data from influenza A infection, suggests that positive selection during within-host infection is primarily limited by the typically short period of infection. Atypically long infections may have a disproportionate influence upon global patterns of viral evolution.
  • Valori, Miko; Jansson, Lilja; Kiviharju, Anna; Ellonen, Pekka; Rajala, Hanna; Awad, Shady; Mustjoki, Satu; Tienari, Pentti J. l (2017)
    Somatic mutations have a central role in cancer but their role in other diseases such as autoimmune disorders is poorly understood. Earlier work has provided indirect evidence of rare somatic mutations in autoreactive T-lymphocytes in multiple sclerosis (MS) patients but such mutations have not been identified thus far. We analysed somatic mutations in blood in 16 patients with relapsing MS and 4 with other neurological autoimmune disease. To facilitate the detection of somatic mutations CD4 +, CD8 +, CD19 + and CD4-/CD8-/CD19- cell subpopulations were separated. We performed next-generation DNA sequencing targeting 986 immune related genes. Somatic mutations were called by comparing the sequence data of each cell subpopulation to other subpopulations of the same patient and validated by amplicon sequencing. We found non-synonymous somatic mutations in 12 (60%) patients (10 MS, 1 myasthenia gravis, 1 narcolepsy). There were 27 mutations, all different and mostly novel (67%). They were discovered at subpopulation-wise allelic fractions of 0.2%-4.6% (median 0.95%). Multiple mutations were found in 8 patients. The mutations were enriched in CD8 + cells (85% of mutations). In follow-up after a median time of 2.3 years, 96% of the mutations were still detectable. These results unravel a novel class of persistent somatic mutations, many of which were in genes that may play a role in autoimmunity (ATM, BTK, CD46, CD180, CLIP2, HMMR, IKEF3, ITGB3, KIR3DL2, MAPK10, CD56/NCAM1, RBM6, RORA, RPM and STAT3). Whether some of this class of mutations plays a role in disease is currently unclear, but these results define an interesting hitherto unknown research target for future studies. (C) 2016 The Authors. Published by Elsevier Inc.
  • Moilanen, Atte; Kujala, Heini; Mikkonen, Ninni (2020)
    Biodiversity offsetting is a tool to balance ecological damage caused by human activity with new benefits created elsewhere. Offsetting is implemented by protecting, restoring or managing sufficiently large areas of habitat. While there are concerns about the true feasibility of offsetting, they are becoming a common policy tool world-wide. Operationally uncomplicated, quantitative approaches to spatial analysis of offsets are rare and their use is often restricted by the availability of suitable spatial data. We describe a practical method for offsets that builds upon two layers of relatively easily sourced spatial data, a balanced spatial priority ranking and a weighted range size rarity map. Together with (a) spatial information about impact and offset areas, and (b) extra parameters for the effectiveness of avoided loss and the amount of leakage expected, we can evaluate whether the proposed offset exchange represents a credible no net loss or net positive impact with an upward trade. The priority ranking and range size rarity maps can be produced in various ways, most notably using existing conservation planning tools. Here we used the standard outputs of the Zonation spatial prioritization software. We illustrate the method and associated visualization in the context of offsetting of boreal forests in Finland, where forests experience high and increasing pressures from forestry and bioenergy sectors. The example is timely as there is political demand for the uptake of biodiversity offset policies in Finland, and boreal forests are the most common biotope. The methods described here are applicable to biomes around the world. The described tools are made available as r scripts that utilize standard Zonation outputs, thus providing direct linkage to any past or future Zonation applications. As a limitation, the present methods only apply to avoided loss offsets.
  • Webb, Anne; Cottage, Amanda; Wood, Thomas; Khamassi, Khalil; Hobbs, Douglas; Gostkiewicz, Krystyna; White, Mark; Khazaei, Hamid; Ali, Mohamed; Street, Daniel; Duc, Gerard; Stoddard, Fred L.; Maalouf, Fouad; Ogbonnaya, Francis C.; Link, Wolfgang; Thomas, Jane; O'Sullivan, Donal M. (2016)
    Faba bean (Vicia faba L.) is a globally important nitrogen-fixing legume, which is widely grown in a diverse range of environments. In this work, we mine and validate a set of 845 SNPs from the aligned transcriptomes of two contrasting inbred lines. Each V. faba SNP is assigned by BLAST analysis to a single Medicago orthologue. This set of syntenically anchored polymorphisms were then validated as individual KASP assays, classified according to their informativeness and performance on a panel of 37 inbred lines, and the best performing 757 markers used to genotype six mapping populations. The six resulting linkage maps were merged into a single consensus map on which 687 SNPs were placed on six linkage groups, each presumed to correspond to one of the six V. faba chromosomes. This sequence-based consensus map was used to explore synteny with the most closely related crop species, lentil and the most closely related fully sequenced genome, Medicago. Large tracts of uninterrupted colinearity were found between faba bean and Medicago, making it relatively straightforward to predict gene content and order in mapped genetic interval. As a demonstration of this, we mapped a flower colour gene to a 2-cM interval of Vf chromosome 2 which was highly colinear with Mt3. The obvious candidate gene from 78 gene models in the collinear Medicago chromosome segment was the previously characterized MtWD40-1 gene controlling anthocyanin production in Medicago and resequencing of the Vf orthologue showed a putative causative deletion of the entire 50 end of the gene.
  • Hochkirch, Axel; Samways, Michael J.; Gerlach, Justin; Bohm, Monika; Williams, Paul; Cardoso, Pedro; Cumberlidge, Neil; Stephenson, P. J.; Seddon, Mary B.; Clausnitzer, Viola; Borges, Paulo A.; Mueller, Gregory M.; Pearce-Kelly, Paul; Raimondo, Domitilla C.; Danielczak, Anja; Dijkstra, Klaas-Douwe B. (2021)
    Measuring progress toward international biodiversity targets requires robust information on the conservation status of species, which the International Union for Conservation of Nature (IUCN) Red List of Threatened Species provides. However, data and capacity are lacking for most hyperdiverse groups, such as invertebrates, plants, and fungi, particularly in megadiverse or high-endemism regions. Conservation policies and biodiversity strategies aimed at halting biodiversity loss by 2020 need to be adapted to tackle these information shortfalls after 2020. We devised an 8-point strategy to close existing data gaps by reviving explorative field research on the distribution, abundance, and ecology of species; linking taxonomic research more closely with conservation; improving global biodiversity databases by making the submission of spatially explicit data mandatory for scientific publications; developing a global spatial database on threats to biodiversity to facilitate IUCN Red List assessments; automating preassessments by integrating distribution data and spatial threat data; building capacity in taxonomy, ecology, and biodiversity monitoring in countries with high species richness or endemism; creating species monitoring programs for lesser-known taxa; and developing sufficient funding mechanisms to reduce reliance on voluntary efforts. Implementing these strategies in the post-2020 biodiversity framework will help to overcome the lack of capacity and data regarding the conservation status of biodiversity. This will require a collaborative effort among scientists, policy makers, and conservation practitioners.
  • Brown, Hugh C. A.; Berninger, Frank A.; Larjavaara, Markku; Appiah, Mark (2020)
    High deforestation rates, especially in the tropics, currently result in the annual emission of large amounts of carbon, contributing to global climate change. There is therefore an urgent need to take actions to mitigate climate change both by slowing down deforestation and by initiating new sinks. Tropical forest plantations are generally thought to sequester carbon rapidly during the initial years but there is limited knowledge on their long-term potential. In this study, we assessed the carbon sequestration in old (42-47 years) timber plantations of Aucoumea klaineana, Cedrela odorata, Tarrietia utilis, and Terminalia ivorensis, and secondary forests of similar ages, by comparing their basal areas and above-ground carbon stocks (AGC) to that of nearby primary forests. Additionally, we estimated and compared timber volume and stumpage value in the three forest types. Systematic random sampling of ninety-three 20 m x 20 m plots in eleven forest sites (2 secondary forests, 2 primary forests, and 7 timber plantations) was undertaken to determine the effect of forest type on AGC, basal area, timber volume, and stumpage value. After 42 years of growth, mean AGC of the timber plantations (159.7 +/- 14.3 Mg ha(-1)) was similar to that of primary forests (173.0 +/- 25.1 Mg ha(-1)) and both were significantly higher than the mean AGC of the secondary forests (103.6 +/- 12.3 Mg ha(-1)). Mean basal area and timber volume of the timber plantations and secondary forests were similar to that of the primary forests, though in each case the timber plantations had significantly higher values compared to the secondary forests. Mean timber value of the plantations ($8577 ha(-1)) was significantly higher than both secondary ($1870 ha(-1)) and primary forests ($3112 ha(-1)). Contrary to our expectations, naturally regenerated trees (woody recruits) within the timber plantations had similar AGC levels, basal area, timber volume, and value compared to the secondary forests. Long-rotation tropical forest plantations under low-intensity management could achieve higher AGC levels and thus have higher climate change mitigation potential and timber values compared to naturally regenerated secondary forests, and are able to reach values similar to primary forests. Monoculture timber plantations could facilitate the successful colonization of their understoreys by native woody recruits that contribute considerably to stand AGC and timber values. Long-rotation forest plantations in the tropics therefore have a critical role to play in forest rehabilitation and climate change mitigation while having the potential to provide modest financial returns to landowners through selective harvesting of timber and/or payments for carbon sequestration.
  • Martikainen, Julia; Penttilä, Antti; Gritsevich, M.; Videen, Gorden; Muinonen, Karri Olavi (2019)
    We present a new physics-based approach to model the absolute reflectance spectra of asteroid (4) Vesta. The spectral models are derived by utilizing a ray-optics code that simulates light scattering by particles large compared to the wavelength of the incident light. In the light of the spectral data obtained by the Dawn spacecraft, we use howardite powder to model Vesta's surface regolith and its particle size distribution for 10-200 mu m sized particles. Our results show that the modelled spectrum mimics well the observations. The best match was found using a power-law particle size distribution with an index 3.2. This suggests that Vesta's regolith is dominated by howardite particles
  • Abrego, Nerea; Roslin, Tomas; Huotari, Tea; Tack, Ayco J. M.; Lindahl, Bjorn D.; Tikhonov, Gleb; Somervuo, Panu; Schmidt, Niels Martin; Ovaskainen, Otso (2020)
    Understanding the role of interspecific interactions in shaping ecological communities is one of the central goals in community ecology. In fungal communities, measuring interspecific interactions directly is challenging because these communities are composed of large numbers of species, many of which are unculturable. An indirect way of assessing the role of interspecific interactions in determining community structure is to identify the species co-occurrences that are not constrained by environmental conditions. In this study, we investigated co-occurrences among root-associated fungi, asking whether fungi co-occur more or less strongly than expected based on the environmental conditions and the host plant species examined. We generated molecular data on root-associated fungi of five plant species evenly sampled along an elevational gradient at a high arctic site. We analysed the data using a joint species distribution modelling approach that allowed us to identify those co-occurrences that could be explained by the environmental conditions and the host plant species, as well as those co-occurrences that remained unexplained and thus more probably reflect interactive associations. Our results indicate that not only negative but also positive interactions play an important role in shaping microbial communities in arctic plant roots. In particular, we found that mycorrhizal fungi are especially prone to positively co-occur with other fungal species. Our results bring new understanding to the structure of arctic interaction networks by suggesting that interactions among root-associated fungi are predominantly positive.
  • Lamnidis, Thiseas C.; Majander, Kerttu; Jeong, Choongwon; Salmela, Elina; Wessman, Anna; Moiseyev, Vyacheslav; Khartanovich, Valery; Balanovsky, Oleg; Ongyerth, Matthias; Weihmann, Antje; Sajantila, Antti; Kelso, Janet; Pääbo, Svante; Onkamo, Päivi; Haak, Wolfgang; Krause, Johannes; Schiffels, Stephan (2018)
    European population history has been shaped by migrations of people, and their subsequent admixture. Recently, ancient DNA has brought new insights into European migration events linked to the advent of agriculture, and possibly to the spread of Indo-European languages. However, little is known about the ancient population history of north-eastern Europe, in particular about populations speaking Uralic languages, such as Finns and Saami. Here we analyse ancient genomic data from 11 individuals from Finland and north-western Russia. We show that the genetic makeup of northern Europe was shaped by migrations from Siberia that began at least 3500 years ago. This Siberian ancestry was subsequently admixed into many modern populations in the region, particularly into populations speaking Uralic languages today. Additionally, we show that ancestors of modern Saami inhabited a larger territory during the Iron Age, which adds to the historical and linguistic information about the population history of Finland.
  • Smaragdov, M. G.; Kudinov, A. A. (2020)
    Background Due to the advent of SNP array technology, a genome-wide analysis of genetic differences between populations and breeds has become possible at a previously unattainable level. The Wright's fixation index (F-st) and the principal component analysis (PCA) are widely used methods in animal genetics studies. In paper we compared the power of these methods, their complementing each other and which of them is the most powerful. Results Comparative analysis of the power Principal Components Analysis (PCA) and F-st were carried out to reveal genetic differences between herds of Holsteinized cows. Totally, 803 BovineSNP50 genotypes of cows from 13 herds were used in current study. Obtained F-st values were in the range of 0.002-0.012 (mean 0.0049) while for rare SNPs with MAF 0.0001-0.005 they were even smaller in the range of 0.001-0.01 (mean 0.0027). Genetic relatedness of the cows in the herds was the cause of such small F-st values. The contribution of rare alleles with MAF 0.0001-0.01 to the F-st values was much less than common alleles and this effect depends on linkage disequilibrium (LD). Despite of substantial change in the MAF spectrum and the number of SNPs we observed small effect size of LD - based pruning on F-st data. PCA analysis confirmed the mutual admixture and small genetic difference between herds. Moreover, PCA analysis of the herds based on the visualization the results of a single eigenvector cannot be used to significantly differentiate herds. Only summed eigenvectors should be used to realize full power of PCA to differentiate small between herds genetic difference. Finally, we presented evidences that the significance of F-st data far exceeds the significance of PCA data when these methods are used to reveal genetic differences between herds. Conclusions LD - based pruning had a small effect on findings of F-st and PCA analyzes. Therefore, for weakly structured populations the LD - based pruning is not effective. In addition, our results show that the significance of genetic differences between herds obtained by F-st analysis exceeds the values of PCA. Proposed, to differentiate herds or low structured populations we recommend primarily using the F-st approach and only then PCA.