Browsing by Subject "MULTILOCUS GENOTYPE DATA"

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  • Monzon-Argueello, Catalina; Consuegra, Sofia; Gajardo, Gonzalo; Marco-Rius, Francisco; Fowler, Daniel M.; De Faveri, Jacquelin; de Leaniz, Carlos Garcia (2014)
  • Radenkovic, Snezana; Zoric, Ljiljana Sasic; Djan, Mihajla; Vidakovic, Dragana Obreht; Acanski, Jelena; Ståhls, Gunilla; Velickovic, Nevena; Markov, Zlata; Petanidou, Theodora; Tubic, Natasa Kocis; Vujic, Ante (2018)
    The Merodon aureus group is characterized by high endemism and the presence of morphologically cryptic species. Within one of its subgroups, M.bessarabicus, seven species and four more species complexes have been described to date. One of these complexes, the M.luteomaculatus, comprises new taxa that are the subject of the present study. Its members have allopatric ranges restricted to the Balkan Peninsula and Aegean islands. This complex exhibits morphological variability that could not be characterized using a traditional morphological approach. Thus, we used integrative taxonomy with independent character sets (molecular, geometric morphometric, distributional) to delimit species boundaries. Data on three molecular markers (COI, 28S rRNA, and ISSR) and geometric morphometry of the wing and male genitalia, together with distributional data, enabled recognition of six cryptic species within the complex: M.andriotes sp. n., M.euri sp. n., M.erymanthius sp. n., M.luteomaculatus sp. n., M.naxius sp. n., and M.peloponnesius sp. n. We discuss the possible influence of Aegean paleogeographical history on the speciation of this complex.
  • Pohjanmies, Tähti; Elshibli, Sakina; Pulkkinen, Pertti; Rusanen, Mari; Vakkari, Pekka; Korpelainen, Helena; Roslin, Tomas (2016)
    Populations at species' range margins are expected to show lower genetic diversity than populations at the core of the range. Yet, long-lived, widespread tree species are expected to be resistant to genetic impoverishment, thus showing comparatively high genetic diversity within populations and low differentiation among populations. Here, we study the distribution of genetic variation in the pedunculate oak (Quercus robur L.) at its range margin in Finland at two hierarchical scales using 15 microsatellite loci. At a regional scale, we compared variation within versus among three oak populations. At a landscape scale, we examined genetic structuring within one of these populations, growing on an island of ca 5 km(2). As expected, we found the majority of genetic variation in Q. robur to occur within populations. Nonetheless, differentiation among populations was markedly high (F-ST = 0.12) compared with values reported for populations of Q. robur closer to the core of its range. At the landscape level, some spatial and temporal sub-structuring was observed, likely explained by the history of land-use on the island. Overall, Q. robur fulfils the expectation of the central-marginal hypothesis of high differentiation among marginal populations, but the notable population differentiation has most likely been influenced also by the long, ongoing fragmentation of populations. Finnish oak populations may still be adjusting to the drastic habitat changes of the past centuries. Preservation of genetic variation within the remaining stands is thus an important factor in the conservation of Q. robur at its range margin.
  • Petersen, Jessica L.; Mickelson, James R.; Cothran, E. Gus; Andersson, Lisa S.; Axelsson, Jeanette; Bailey, Ernie; Bannasch, Danika; Binns, Matthew M.; Borges, Alexandre S.; Brama, Pieter; Machado, Artur da Camara; Distl, Ottmar; Felicetti, Michela; Fox-Clipsham, Laura; Graves, Kathryn T.; Guerin, Gerard; Haase, Bianca; Hasegawa, Telhisa; Hemmann, Karin; Hill, Emmeline W.; Leeb, Tosso; Lindgren, Gabriella; Lohi, Hannes; Lopes, Maria Susana; McGivney, Beatrice A.; Mikko, Sofia; Orr, Nicholas; Penedo, M. Cecilia T.; Piercy, Richard J.; Raekallio, Marja; Rieder, Stefan; Roed, Knut H.; Silvestrelli, Maurizio; Swinburne, June; Tozaki, Teruaki; Vaudin, Mark; Wade, Claire M.; McCue, Molly E. (2013)
  • Pino-Bodas, Raquel; Laakso, Into; Stenroos, Soili (2017)
    Heterocephalacria bachmannii is a lichenicolous fungus that takes as hosts numerous lichen species of the genus Cladonia. In the present study we analyze whether the geographical distance, the host species or the host secondary metabolites determine the genetic structure of this parasite. To address the question, populations mainly from the Southern Europe, Southern Finland and the Azores were sampled. The specimens were collected from 20 different host species representing ten chemotypes. Three loci, ITS rDNA, LSU rDNA and mtSSU, were sequenced. The genetic structure was assessed by AMOVA, redundance analyses and Bayesian clustering methods. The results indicated that the host species and the host secondary metabolites are the most influential factors over the genetic structure of this lichenicolous fungus. In addition, the genetic structure of H. bachmannii was compared with that of one of its hosts, Cladonia rangiformis. The population structure of parasite and host were discordant. The contents in phenolic compounds and fatty acids of C. rangiformis were quantified in order to test whether it had some influence on the genetic structure of the species. But no correlation was found with the genetic clusters of H. bachmannii.
  • Fountain, Toby; Husby, Arild; Nonaka, Etsuko; DiLeo, Michelle; Korhonen, Janne H.; Rastas, Pasi; Schulz, Torsti Michael; Saastamoinen, Marjo Anna Kaarina; Hanski, Ilkka Aulis (2018)
    Dispersal is important for determining both species ecological processes, such as population viability, and its evolutionary processes, like gene flow and local adaptation. Yet obtaining accurate estimates in the wild through direct observation can be challenging or even impossible, particularly over large spatial and temporal scales. Genotyping many individuals from wild populations can provide detailed inferences about dispersal. We therefore utilized genomewide marker data to estimate dispersal in the classic metapopulation of the Glanville fritillary butterfly (Melitaea cinxia L.), in the Aland Islands in SW Finland. This is an ideal system to test the effectiveness of this approach due to the wealth of information already available covering dispersal across small spatial and temporal scales, but lack of information at larger spatial and temporal scales. We sampled three larvae per larval family group from 3732 groups over a six-year period and genotyped for 272 SNPs across the genome. We used this empirical data set to reconstruct cases where full-sibs were detected in different local populations to infer female effective dispersal distance, that is, dispersal events directly contributing to gene flow. On average this was one kilometre, closely matching previous dispersal estimates made using direct observation. To evaluate our power to detect full-sib families, we performed forward simulations using an individual-based model constructed and parameterized for the Glanville fritillary metapopulation. Using these simulations, 100% of predicted full-sibs were correct and over 98% of all true full-sib pairs were detected. We therefore demonstrate that even in a highly dynamic system with a relatively small number of markers, we can accurately reconstruct full-sib families and for the first time make inferences on female effective dispersal. This highlights the utility of this approach in systems where it has previously been impossible to obtain accurate estimates of dispersal over both ecological and evolutionary scales.
  • Corander, Jukka; Gyllenberg, Mats; Koski, Timo (2010)
  • Leavitt, Steven D.; Lumbsch, H. Thorsten; Stenroos, Soili; St Clair, Larry L. (2013)
    Pleistocene climatic fluctuations influenced patterns of genetic variation and promoted speciation across a wide range of species groups. Lichens are commonly found in habitats that were directly impacted by glacial cycles; however, the role of Pleistocene climate in driving speciation in most lichen symbionts remains unclear. This uncertainty is due in part to limitations in our ability to accurately recognize independently evolving lichen-forming fungal lineages and a lack of relevant fossil calibrations. Using a coalescent-based species tree approach, we estimated divergence times for two sister clades in the genus Xanthoparmelia (Parmeliaceae) restricted to western North America. We assessed the influence of two different species circumscription scenarios and various locus-specific rates of molecular evolution on divergence estimates. Species circumscriptions were validated using the program BP&P. although speciation was generally supported in both scenarios, divergence times differed between traditional species circumscriptions and those based on genetic data, with more recent estimates resulting from the former. Similarly, rates of evolution for different loci resulted in variable divergence time estimates. However, our results unambiguously indicate that diversification in the sampled Xanthoparmelia clades occurred during the Pleistocene. Our study highlights the potential impact of ambiguous species circumscriptions and uncertain rates of molecular evolution on estimating divergence times within a multilocus species tree framework
  • Hilmarsson, Hrannar Smari; Hytonen, Timo; Isobe, Sachiko; Goransson, Magnus; Toivainen, Tuomas; Hallsson, Jon Hallsteinn (2017)
    The woodland strawberry, Fragaria vesca, holds great promise as a model organism. It not only represents the important Rosaceae family that includes economically important species such as apples, pears, peaches and roses, but it also complements the well-known model organism Arabidopsis thaliana in key areas such as perennial life cycle and the development of fleshy fruit. Analysis of wild populations of A. thaliana has shed light on several important developmental pathways controlling, for example, flowering time and plant growth, suggesting that a similar approach using F. vesca might add to our understanding on the development of rosaceous species and perennials in general. As a first step, 298 F. vesca plants were analyzed using microsatellite markers with the primary aim of analyzing population structure and distribution of genetic diversity. Of the 68 markers tested, 56 were polymorphic, with an average of 4.46 alleles per locus. Our analysis partly confirms previous classification of F. vesca subspecies in North America and suggests two groups within the subsp. bracteata. In addition, F. vesca subsp. vesca forms a single global population with evidence that the Icelandic group is a separate cluster from the main Eurasian population.
  • Zeleznik, Peter; Westergren, Marjana; Bozik, Gregor; Eler, Klemen; Bajc, Marko; Helmisaari, Heljä-Sisko Marketta; Horvath, Aniko; Kraigher, Hojka (2019)
    European beech (Fagus sylvatica L.) is commercially and ecologically important tree species in Central European forests but its intra-specific variability in drought and temperature tolerance might endanger its future distribution in Europe. Beech phenological and growth traits have been studied in large-scale international beech provenance trials, yet the growth and turnover of its fine roots (FR) has not been included among the observations. FR growth dynamics and FR architectural traits of three beech provenances in the international beech provenance trial Straza/Kamenski hrib, established in Slovenia in 1998, and from a natural beech regeneration site growing at its border, were studied from 2007 to 2010. We studied FR biomass using soil cores (SC), root production using ingrowth soil cores (IC), and root longevity using minirhizotrons (MR). Significant differences in FR biomass (live and dead) between the provenance P37 and other provenances were discovered in SC, FR biomass of P37 being significantly higher than FR biomass of latter, which could be connected with overall excellent growth performance of P37 due to favourable environmental conditions at trial. Values of specific root length (SRL) in IC varied significantly among P37 and P54. The turnover rates in IC were at the end of the experiment close to MR results. Median MR-based longevities of FR varied between 625 and 934 days. Survival curve of the slowest growing provenance (considering its aboveground characteristics) was significantly different from the other two, median longevities of the latter being higher. Death of FR, older than two years, occurred most likely in the winter. Our results suggest that there are significant differences in FR longevity among provenances, which might contribute to their adaptation to future environmental conditions. Furthermore, the calculated annual C investment into FR growth per ha differs up to twofold between provenances, contributing to different C dynamics of their future stands.