Browsing by Subject "SELECTION"

Sort by: Order: Results:

Now showing items 1-20 of 166
  • Murillo-Ramos, Leidys; Brehm, Gunnar; Sihvonen, Pasi; Hausmann, Axel; Holm, Sille; Reza Ghanavi, Hamid; Õunap, Erki; Truuverk, Andro; Staude, Hermann; Friedrich, Egbert; Tammaru, Toomas; Wahlberg, Niklas (2019)
    Our study aims to investigate the relationships of the major lineages within the moth family Geometridae, with a focus on the poorly studied Oenochrominae-Desmobathrinae complex, and to translate some of the results into a coherent subfamilial and tribal level classification for the family. We analyzed a molecular dataset of 1,206 Geometroidea terminal taxa from all biogeographical regions comprising up to 11 molecular markers that includes one mitochondria) (COI) and 10 protein-coding nuclear gene regions (wingless, ArgK, MDH, RpS5, GAPDH, IDH, Ca-ATPase, Nex9, EF-1 alpha, CAD). The molecular data set was analyzed using maximum likelihood as implemented in IQ-TREE and RAxML. We found high support for the subfamilies Larentiinae, Geometrinae and Ennominae in their traditional scopes. Sterrhinae becomes monophyletic only if Ergavia Walker, Ametris Hubner and Macrotes Westwood, which are currently placed in Oenochrominae, are formally transferred to Sterrhinae. Desmobathrinae and Oenochrominae are found to be polyphyletic. The concepts of Oenochrominae and Desmobathrinae required major revision and, after appropriate rearrangements, these groups also form monophyletic subfamily-level entities. Oenochrominae s.str. as originally conceived by Guenee is phylogenetically distant from Epidesmia and its close relatives. The latter is hereby described as the subfamily Epidesmiinae Murillo-Ramos, Sihvonen & Brehm, subfam. nov. Epidesmiinae are a lineage of "slender-bodied Oenochrominae" that include the genera Ecphyas Turner, Systatica Turner, Adeixis Warren, Dichromodes Guenee, Phrixocomes Turner, Abraxaphantes Warren, Epidesmia Duncan & Westwood and Phrataria Walker. Archiearinae are monophyletic when Dirce and Acalyphes are formally transferred to Ennominae. We also found that many tribes were para- or polyphyletic and therefore propose tens of taxonomic changes at the tribe and subfamily levels. Archaeobalbini stat. rev. Viidalepp (Geometrinae) is raised from synonymy with Pseudoterpnini Warren to tribal rank. Chlorodontoperini Murillo-Ramos, Sihvonen & Brehm, trib. nov. and Drepanogynini Murillo-Ramos, Sihvonen & Brehm, trib. nov. are described as new tribes in Geometrinae and Ennominae, respectively.
  • Cornetti, Luca; Fields, Peter D.; Van Damme, Kay; Ebert, Dieter (2019)
    In the post-genomic era, much of phylogenetic analyses still relies on mitochondrial DNA, either alone or in combination with few nuclear genes. Although this approach often makes it possible to construct well-supported trees, it is limited because mtDNA describes the history of a single locus, and nuclear phylogenies based on a few loci may be biased, leading to inaccurate tree topologies and biased estimations of species divergence time. In this study, we perform a phylogenomic analysis of the Daphniidae family (Crustacea: Branchiopoda: Anomopoda) including some of the most frequently studied model organisms (Daphnia magna and D. pulex) whose phylogenetic relationships have been based primarily on an assessment of a few mtDNA genes. Using high-throughput sequencing, we were able to assemble 38 whole mitochondrial genomes and draft nuclear genomes for 18 species, including at least one species for each known genus of the family Daphniidae. Here we present phylogenies based on 636 nuclear single-copy genes shared among all sampled taxa and based on whole mtDNA genomes. The phylogenies we obtained were highly supported and showed some discrepancies between nuclear and mtDNA based trees at deeper nodes. We also identified a new candidate sister lineage of Daphnia magna. Our time-calibrated genomic trees, which we constructed using both fossil records and substitution rates, yielded very different estimates of branching event times compared to those based on mtDNA. By providing multi-locus, fossil-calibrated trees of the Daphniidae, our study contributes to an improved phylogenetic framework for ecological and evolutionary studies that use water fleas as a model system.
  • 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.
  • Darragh, Kathy; Orteu, Anna; Black, Daniella; Byers, Kelsey J. R. P.; Szczerbowski, Daiane; Warren, Ian A.; Rastas, Pasi; Pinharanda, Ana; Davey, John W.; Fernanda Garza, Sylvia; Abondano Almeida, Diana; Merrill, Richard M.; McMillan, W. Owen; Schulz, Stefan; Jiggins, Chris D. (2021)
    Plants and insects often use the same compounds for chemical communication, but not much is known about the genetics of convergent evolution of chemical signals. The terpene (E)-beta-ocimene is a common component of floral scent and is also used by the butterfly Heliconius melpomene as an anti-aphrodisiac pheromone. While the biosynthesis of terpenes has been described in plants and microorganisms, few terpene synthases (TPSs) have been identified in insects. Here, we study the recent divergence of 2 species, H. melpomene and Heliconius cydno, which differ in the presence of (E)-beta-ocimene; combining linkage mapping, gene expression, and functional analyses, we identify 2 novel TPSs. Furthermore, we demonstrate that one, HmelOS, is able to synthesise (E)-beta-ocimene in vitro. We find no evidence for TPS activity in HcydOS (HmelOS ortholog of H. cydno), suggesting that the loss of (E)-beta-ocimene in this species is the result of coding, not regulatory, differences. The TPS enzymes we discovered are unrelated to previously described plant and insect TPSs, demonstrating that chemical convergence has independent evolutionary origins.
  • Kangas, Johanna; Ollikainen, Markku (2022)
    Forests can play a significant role both in halting biodiversity loss and in mitigating climate change. A variety of payments for ecosystem services (PES) schemes exists to promote biodiversity conservation in forests. These schemes could be used to strengthen the role of forests as carbon sinks as well. This paper analyzes the implications of supplementing a PES scheme that targets boreal forest biodiversity with a carbon index. We use a site selection framework to examine how the proposed scheme impacts the promotion of both targets. We compare a case where the selection is done solely based on biodiversity values to a case where the selection is done based on both biodiversity and carbon benefits. The carbon index is formulated as current carbon storage or as future carbon sink. Correspondingly, biodiversity is maximized based on either current ecological values or potential ones. We compare equal or differing weights for biodiversity and carbon indexes, and examine trade-offs between biodiversity and CO2 in current and future values. Combined index values increase with the carbon index, but there is a trade-off between biodiversity and CO2 values if the conservation budget is not increased when the carbon index is introduced. There is a temporal trade-off in biodiversity and carbon values between selecting sites based on current or future values. Younger stands are preferred at the expense of old-growth stands with the carbon index. Weights can be used to balance the trade-off between biodiversity and carbon benefits. Overall, risks to losing significant ecological value from the conservation network are negligible, but the limited number of sites decreases the generalizability of the results.
  • Karges, Kathleen; Bellingrath-Kimura, Sonoko D.; Watson, Christine A.; Stoddard, Frederick L.; Halwani, Mosab; Reckling, Moritz (2022)
    Soybean is one of the five crops that dominate global agriculture, along with maize, wheat, cotton and rice. In Europe, soybean still plays a minor role and is cultivated mainly in the South and East. Very little is known about the potential for soybean in higher latitudes with relatively cool conditions. To investigate the agronomic potential and limitations of soybean for feed (high grain yield) and food (high protein content, e.g., for tofu production) in higher latitudes, an organic soybean cropping system experiment was carried out from 2015 to 2017 in northeastern Germany. The objectives were: (1) to identify food- and feed-grade soybean cultivars that are adapted to a central European climate in terms of protein, grain yield, and yield stability, (2) to explore the effect of irrigation on soybean protein and grain yield under relatively dry growing conditions, and (3) to determine the agro-economic potential of soybean cultivation for both feed and food markets. Three soybean cultivars were tested with and without irrigation. The soybean feed-grade cultivars 'Sultana' and 'Merlin' were better adapted to the growing cycle and temperature, providing higher and more stable yields (average 2700 kg ha(-1)) than the food-grade cultivar 'Protibus' (average 1300 kg ha(-1)). Irrigation increased soybean grain yields by 41% on average. In the year with sufficient precipitation, no additional irrigation was necessary. Gross margins of organic soybean ranged between 750 (sic) ha(-1) for the rainfed food-grade soybean and 2000 (sic) ha(-1) for the irrigated feed-grade soybean and were higher than other crops. We demonstrated a large agro-economic potential for soybean as a novel grain legume crop to diversify cropping systems and increase the production of protein crops in central Europe.
  • Nováková, Eliška; Zablatzká , Lenka; Brus , Jan; Nesrstová , Viktorie; Hanáček, Pavel; Kalendar, Ruslan; Cvrčková , Fatima; Majeský , Ľuboš; Smýkal, Petr (2019)
    Reproductive isolation is an important component of species differentiation. The plastid accD gene coding for the acetyl-CoA carboxylase subunit and the nuclear bccp gene coding for the biotin carboxyl carrier protein were identified as candidate genes governing nuclear-cytoplasmic incompatibility in peas. We examined the allelic diversity in a set of 195 geographically diverse samples of both cultivated (Pisum sativum, P. abyssinicum) and wild (P. fulvum and P. elatius) peas. Based on deduced protein sequences, we identified 34 accD and 31 bccp alleles that are partially geographically and genetically structured. The accD is highly variable due to insertions of tandem repeats. P. fulvum and P. abyssinicum have unique alleles and combinations of both genes. On the other hand, partial overlap was observed between P. sativum and P. elatius. Mapping of protein sequence polymorphisms to 3D structures revealed that most of the repeat and indel polymorphisms map to sequence regions that could not be modeled, consistent with this part of the protein being less constrained by requirements for precise folding than the enzymatically active domains. The results of this study are important not only from an evolutionary point of view but are also relevant for pea breeding when using more distant wild relatives.
  • Zöttl, Markus; Vullioud, Philippe; Goddard, Katy; Torrents-Ticó, Miquel; Gaynor, David; Bennett, Nigel C.; Clutton-Brock, Tim (2018)
    Abstract In Damaraland mole-rats (Fukomys damarensis), non-breeding subordinates contribute to the care of offspring born to the breeding pair in their group by carrying and retrieving young to the nest. In social mole-rats and some cooperative breeders, dominant females show unusually high testosterone levels and it has been suggested that high testosterone levels may increase reproductive and aggressive behavior and reduce investment in allo-parental and parental care, generating age and state-dependent variation in behavior. Here we show that, in Damaraland mole-rats, allo-parental care in males and females is unaffected by experimental increases in testosterone levels. Pup carrying decreases with age of the non-breeding helper while the change in social status from non-breeder to breeder has contrasting effects in the two sexes. Female breeders were more likely than female non-breeders to carry pups but male breeders were less likely to carry pups than male non-breeders, increasing the sex bias in parental care compared to allo-parental care. Our results indicate that testosterone is unlikely to be an important regulator of allo-parental care in mole-rats.
  • Day-Williams, Aaron G.; McLay, Kirsten; Drury, Eleanor; Edkins, Sarah; Coffey, Alison J.; Palotie, Aarno; Zeggini, Eleftheria (2011)
  • Serra, Angela; Önlü, Serli; Coretto, Pietro; Greco, Dario (2019)
    Traditional quantitative structure-activity relationship models usually neglect the molecular alterations happening in the exposed systems (the mechanism of action, MOA), that mediate between structural properties of compounds and phenotypic effects of an exposure.
  • Sampaio, Larissa; Ferraz, Dnilson Oliveira; Moreira da Costa, Ana Carolina; Aleixo, Alexandre; Cerqueira, Pablo Vieira; Araripe, Juliana; do Rego, Pericles Sena (2020)
    The present study aimed to confirm the occurrence of a hybridization event between the band-tailed manakin (Pipra fasciicauda) and the crimson-hooded manakin (Pipra aureola), based on the existence of a specimen that presents morphological traits of both taxa. We analyzed 297 taxidermized skins of adult males of the two species, including the potential hybrid. We also analyzed the mitochondrial (ND2, ND3 e COI) and nuclear (FGB-I5, MB-I2 e GAPDH-I3) genes of 12 adult specimens of the two taxa, diagnosed phenotypically, in addition to the potential hybrid. The analyses of the plumage indicated that the potential hybrid has an intermediate pattern of white banding on the tail that is less extensive than that found in Pipra fasciicauda, but that its other phenotypic traits are characteristic of Pipra aureola. The molecular topologies revealed two clades, one that groups P. aureola together with the potential hybrid, and the other that corresponds to P. fasciicauda. These findings allowed us to confirm the occurrence of a process of hybridization and potential introgression through secondary events in the P. aureola lineage.
  • Salmela, Heli; Stark, Taina; Stucki, Dimitri; Fuchs, Siiri; Freitak, Dalial; Dey, Alivia; Kent, Clement F.; Zayed, Amro; Dhaygude, Kishor; Hokkanen, Heikki; Sundstrom, Liselotte (2016)
    Protection against inflammation and oxidative stress is key in slowing down aging processes. The honey bee (Apis mellifera) shows flexible aging patterns linked to the social role of individual bees. One molecular factor associated with honey bee aging regulation is vitellogenin, a lipoglycophosphoprotein with anti-inflammatory and antioxidant properties. Recently, we identified three genes in Hymenopteran genomes arisen from ancient insect vitellogenin duplications, named vg-like-A, -B, and -C. The function of these vitellogenin homologs is unclear. We hypothesize that some of them might share gene-and protein-level similarities and a longevity-supporting role with vitellogenin. Here, we show how the structure and modifications of the vg-like genes and proteins have diverged from vitellogenin. Furthermore, all three vg-like genes show signs of positive selection, but the spatial location of the selected protein sites differ from those found in vitellogenin. We show that all these genes are expressed in both long-lived winter worker bees and in summer nurse bees with intermediate life expectancy, yet only vg-like-A shows elevated expression in winter bees as found in vitellogenin. Finally, we show that vg-like-A responds more strongly than vitellogenin to inflammatory and oxidative conditions in summer nurse bees, and that also vg-like-B responds to oxidative stress. We associate vg-like-A and, to lesser extent, vg-like-B to the antiaging roles of vitellogenin, but that vg-like-C probably is involved in some other function. Our analysis indicates that an ancient duplication event facilitated the adaptive and functional divergence of vitellogenin and its paralogs in the honey bee.
  • Hiltunen, Teppo; Virta, Marko; Laine, Anna-Liisa (2017)
    The legacy of the use and misuse of antibiotics in recent decades has left us with a global public health crisis: antibiotic-resistant bacteria are on the rise, making it harder to treat infections. At the same time, evolution of antibiotic resistance is probably the best-documented case of contemporary evolution. To date, research on antibiotic resistance has largely ignored the complexity of interactions that bacteria engage in. However, in natural populations, bacteria interact with other species; for example, competition and grazing are import interactions influencing bacterial population dynamics. Furthermore, antibiotic leakage to natural environments can radically alter bacterial communities. Overall, we argue that eco-evolutionary feedback loops in microbial communities can be modified by residual antibiotics and evolution of antibiotic resistance. The aim of this review is to connect some of the well-established key concepts in evolutionary biology and recent advances in the study of eco-evolutionary dynamics to research on antibiotic resistance. We also identify some key knowledge gaps related to eco-evolutionary dynamics of antibiotic resistance, and review some of the recent technical advantages in molecular microbiology that offer new opportunities for tackling these questions. Finally, we argue that using the full potential of evolutionary theory and active communication across the different fields is needed for solving this global crisis more efficiently. This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'.
  • Yun, Jinhyeon; Muurinen, Johanna; Nykäsenoja, Suvi; Seppä-Lassila, Leena; Sali, Virpi; Suomi, Johanna; Tuominen, Pirkko; Joutsen, Suvi; Hämäläinen, Merja; Olkkola, Satu; Myllyniemi, Anna-Liisa; Peltoniemi, Olli; Heinonen, Mari (2021)
    We investigated connections between antimicrobial use (AMU), biosecurity, and the numbers of pigs and staff in ten Finnish farrow-to-finish herds. Data on AMU in each herd were collected for 12 months. AMU was quantified as treatment incidences per 1000 days at risk (TI) using the consensus defined daily dose calculation. Biosecurity was scored using the Biocheck.UGent T system. We also examined antimicrobial resistance patterns of indicator E. coli isolated from faeces of selected pigs. In each herd, two groups of five pigs were formed: 1) antimicrobial treatment group (ANT: at least one pig in the litter was identified as sick and treated with antimicrobials) and 2) non-antimicrobial treatment group (NON: the litter was not medicated). Faecal samples were taken from these pigs at 5 and 22 weeks of age, cultured, and indicator E. coli isolates were tested for antimicrobial susceptibilities. The AMU varied considerably between the herds. Altogether, most of the antimicrobial treatment courses were assigned to weaned piglets. When AMU was quantified as TIs, suckling piglets had the highest TI (mean 46.6), which was significantly higher (P < 0.05) than TIs in fatteners and breeders (9.3 and 7.3, respectively). The difference between TI in suckling and TI in weaned piglets (19.1) was not statistically significant. There was a tendency for a negative correlation between the TI in breeders and the number of sows (r = 0.56, P = 0.09). Larger herds had higher external biosecurity scores than smaller herds (LS-means; 72 vs. 66, P < 0.05). The proportions of E. coli isolates resistant to at least one antimicrobial were higher in pigs at 5 weeks than in pigs at 22 weeks of age (Binomial proportion means; 40.5 % vs. 15.5 %, P < 0.05); as well as proportions of isolates resistant to at least three antimicrobial classes (23.0 % vs. 3.7 %, P < 0.01). These proportions did not differ between the ANT and NON groups at either 5 or 22 weeks of age (P> 0.05). We found few connections: enhanced external biosecurity levels found in the large herds co-occurred with lower use of antimicrobials and herds with low biosecurity scores - especially in the internal subcategories - appeared to have higher proportions of resistant isolates. Conclusively, we suggest that enhancing internal biosecurity might contribute to a reduction in the spreading of antimicrobial resistance in pig herds.
  • Terraube, J.; Van Doninck, J.; Helle, P.; Cabeza, M. (2020)
    Protected areas (PAs) are essential to prevent further biodiversity loss yet their effectiveness varies largely with governance and external threats. Although methodological advances have permitted assessments of PA effectiveness in mitigating deforestation, we still lack similar studies for the impact of PAs on wildlife populations. Here we use an innovative combination of matching methods and hurdle-mixed models with a large-scale and long-term dataset for Finland's large carnivore species. We show that the national PA network does not support higher densities than non-protected habitat for 3 of the 4 species investigated. For some species, PA effects interact with region or time, i.e., wolverine densities decreased inside PAs over the study period and lynx densities increased inside eastern PAs. We support the application of matching methods in combination of additional analytical frameworks for deeper understanding of conservation impacts on wildlife populations. These methodological advances are crucial for preparing ambitious PA targets post-2020. Assessing the effectiveness of protected areas for wildlife conservation is challenging. Here, Terraube et al. combine statistical matching and hurdle mixed-effects models to show that PAs have limited impact on population densities of large carnivores across Finland.
  • Kivikoski, Mikko; Rastas, Pasi; Löytynoja, Ari; Merila, Juha (2021)
    We describe an integrative approach to improve contiguity and haploidy of a reference genome assembly and demonstrate its impact with practical examples. With two novel features of Lep-Anchor software and a combination of dense linkage maps, overlap detection and bridging long reads, we generated an improved assembly of the nine-spined stickleback (Pungitius pungitius) reference genome. We were able to remove a significant number of haplotypic contigs, detect more genetic variation and improve the contiguity of the genome, especially that of X chromosome. However, improved scaffolding cannot correct for mosaicism of erroneously assembled contigs, demonstrated by a de novo assembly of a 1.6-Mbp inversion. Qualitatively similar gains were obtained with the genome of three-spined stickleback (Gasterosteus aculeatus). Since the utility of genome-wide sequencing data in biological research depends heavily on the quality of the reference genome, the improved and fully automated approach described here should be helpful in refining reference genome assemblies.
  • Hurskainen, Pekka; Adhikari, Hari; Siljander, Mika; Pellikka, Petri; Hemp, Andreas (2019)
    Classifying land use/land cover (LULC) with sufficient accuracy in heterogeneous landscapes is challenging using only satellite imagery. To improve classification accuracy inclusion of features from auxiliary geospatial datasets in classification models is applied since 1980s. However, the method is mostly limited to pixel-based classifications, and the coverage, accuracy and resolution of free and open-access auxiliary datasets have been poor until recent years. We evaluated how recent global coverage open-access geospatial datasets improve object-based LULC classification accuracy compared to using only spectral and texture features from satellite images. We applied feature sets topography, population, soil, canopy cover, distance to watercourses and spectral-temporal metrics from Landsat-8 time series on the southern foothills and savanna of Mt. Kilimanjaro, Tanzania, where the landscape is characterized by heterogeneous and fragmented mosaic of disturbed savanna vegetation, croplands, and settlements. The classification was based on image objects (groups of spectrally similar pixels) derived from segmentation of four Formosat-2 scenes with 8m spatial resolution using 1370 ground reference points for training, validation, and for defining 17 LULC classes. We built six Random Forest classification models with different sets of object features in each. The baseline model having only spectral and texture features was compared with five other models supplemented with auxiliary features. Inclusion of auxiliary features significantly improved classification overall accuracy (OA). The baseline model gave a median OA of 60.7%, but auxiliary features in other models increased median OA between 6.1 and 16.5 percentage points. The best OA was achieved with a model including all features of which elevation was the most important auxiliary feature followed by Enhanced Vegetation Index temporal range and slope degree. Applying object-based classification to geospatial information on topography, soil, settlement patterns and vegetation phenology, the discriminatory potential of challenging LULC classes can be significantly improved. We demonstrated this for the first time, and the technique shows good potential for improving LULC mapping across a multitude of fragmented landscapes worldwide.
  • Partanen, Pasi; Hultman, Jenni; Paulin, Lars; Auvinen, Petri; Romantschuk, Martin (2010)
  • Moen, Gro Kvelprud; Ordiz, Andres; Kindberg, Jonas; Swenson, Jon E.; Sundell, Janne; Stoen, Ole-Gunnar (2019)
    Human disturbance causes behavioral responses in wildlife, including large carnivores. Previous research in Scandinavia has documented that brown bears (Ursus arctos) show a variety of behavioral reactions to different human activities. We investigated how proximity to human settlements and roads, as proxies of human influence, affected brown bears' reactions to encountering humans. We analyzed experimental approaches to GPS collared bears, 18 males and 23 single females, in Sweden (n = 148 approaches) and Finland (n = 33), conducted between 2004 and 2012. The bears in Finland inhabited areas with higher human density compared to Sweden. However, the proportion of bears staying or moving when approached and the flight initiation distances were similar in both countries. In Sweden, the flight responses were not dependent on human densities or roads inside the bears' home ranges or the distances from the bears to roads and settlements. Brown bears in Fennoscandia live in areas with relatively low human population densities, but in many areas with high forestry road densities. Our results show that bears' flight reactions were consistent between areas, which is an important message for management, reinforcing previous studies that have documented human avoidance by bears at different spatial and temporal scales.
  • Broms, Ulla; Koskenvuo, Karoliina; Sillanmaki, Lauri H.; Mattila, Kari J.; Koskenvuo, Markku (2012)