Browsing by Subject "molecular systematics"

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  • Spirin, Viacheslav; Volobuev, Sergey; Malysheva, Vera; Miettinen, Otto; Kotiranta, Heikki; Larsson, Karl-Henrik (2021)
    Background and aims - To date, Megalocystidium leucoxanthum, a corticioid fungus originally described from the Italian Alps, was considered as a widely distributed species inhabiting numerous angiosperm hosts in the northern hemisphere. Its specimens collected in different geographic areas and from various host species revealed a high morphological variability and thus obfuscated differences from the closely related M. luridum. The objective of this study was to re-establish M. leucoxanthum based on newly collected and sequenced specimens and clarify the identity of morphologically deviating collections previously ascribed to this species. Material and methods - In total, 87 specimens of Megalocystidium spp. (including two historical types) were studied by morphological methods. Their phylogenetic relations were investigated based on DNA sequences (nrITS, nrLSU, and tef1) of 29 specimens. Key results - Based on morphological, ecological and DNA data, we showed M. leucoxanthum sensu typi is a rare species restricted to Alnus alnobetula in subalpine and subarctic zones. Consequently, records from other hosts (mostly representatives of Salicaceae) belong to three other species, M. olens, M. perticatum, and M. salicis, described as new to science. The fourth newly introduced species, M. pellitum, occurs on the same host tree as M. leucoxanthum but it can be separated from the latter due to distinctive morphological traits and DNA sequences. Additionally, Aleurodiscus diffissus is combined in Megalocystidium and the identity of M. luridum is clarified.
  • Spirin, Viacheslav; Volobuev, Sergey; Malysheva, Vera; Miettinen, Otto; Kotiranta, Heikki; Larsson, Karl-Henrik (Nationale Plantentuin van België, 2021)
    Plant Ecology and Evolution 154: 2, 231-244
    Background and aims – To date, Megalocystidium leucoxanthum, a corticioid fungus originally described from the Italian Alps, was considered as a widely distributed species inhabiting numerous angiosperm hosts in the northern hemisphere. Its specimens collected in different geographic areas and from various host species revealed a high morphological variability and thus obfuscated differences from the closely related M. luridum. The objective of this study was to re-establish M. leucoxanthum based on newly collected and sequenced specimens and clarify the identity of morphologically deviating collections previously ascribed to this species. Material and methods – In total, 87 specimens of Megalocystidium spp. (including two historical types) were studied by morphological methods. Their phylogenetic relations were investigated based on DNA sequences (nrITS, nrLSU, and tef1) of 29 specimens. Key results – Based on morphological, ecological and DNA data, we showed M. leucoxanthum sensu typi is a rare species restricted to Alnus alnobetula in subalpine and subarctic zones. Consequently, records from other hosts (mostly representatives of Salicaceae) belong to three other species, M. olens, M. perticatum, and M. salicis, described as new to science. The fourth newly introduced species, M. pellitum, occurs on the same host tree as M. leucoxanthum but it can be separated from the latter due to distinctive morphological traits and DNA sequences. Additionally, Aleurodiscus diffissus is combined in Megalocystidium and the identity of M. luridum is clarified.
  • Lee, Kyung Min; Kivelä, Sami M.; Ivanov, Vladislav; Hausmann, Axel; Kaila, Lauri; Wahlberg, Niklas; Mutanen, Marko (2018)
    A rapid shift from traditional Sanger sequencing-based molecular methods to the phylogenomic approach with large numbers of loci is underway. Among phylogenomic methods, restriction site associated DNA (RAD) sequencing approaches have gained much attention as they enable rapid generation of up to thousands of loci randomly scattered across the genome and are suitable for nonmodel species. RAD data sets however suffer from large amounts of missing data and rapid locus dropout along with decreasing relatedness among taxa. The relationship between locus dropout and the amount of phylogenetic information retained in the data has remained largely uninvestigated. Similarly, phylogenetic hypotheses based on RAD have rarely been compared with phylogenetic hypotheses based on multilocus Sanger sequencing, even less so using exactly the same species and specimens. We compared the Sanger-based phylogenetic hypothesis (8 loci; 6172 bp) of 32 species of the diverse moth genus Eupithecia (Lepidoptera, Geometridae) to that based on double-digest RAD sequencing (3256 loci; 726,658 bp). We observed that topologies were largely congruent, with some notable exceptions that we discuss. The locus dropout effect was strong. We demonstrate that number of loci is not a precise measure of phylogenetic information since the number of single-nucleotide polymorphisms (SNPs) may remain low at very shallow phylogenetic levels despite large numbers of loci. As we hypothesize, the number of SNPs and parsimony informative SNPs (PIS) is low at shallow phylogenetic levels, peaks at intermediate levels and, thereafter, declines again at the deepest levels as a result of decay of available loci. Similarly, we demonstrate with empirical data that the locus dropout affects the type of loci retained, the loci found in many species tending to show lower interspecific distances than those shared among fewer species. We also examine the effects of the numbers of loci, SNPs, and PIS on nodal bootstrap support, but could not demonstrate with our data our expectation of a positive correlation between them. We conclude that RAD methods provide a powerful tool for phylogenomics at an intermediate phylogenetic level as indicated by its broad congruence with an eight-gene Sanger data set in a genus of moths. When assessing the quality of the data for phylogenetic inference, the focus should be on the distribution and number of SNPs and PIS rather than on loci.
  • Pino-Bodas, Raquel; Rosa Burgaz, Ana; Ahti, Teuvo; Stenroos, Soili (2018)
    The lichen species Cladonia angustiloba is characterized by a well-developed primary thallus and narrow squamules which show deep incisions, and the presence of usnic and fumarprotocetraric acids. Morphologically it is similar to C. foliacea and C. convoluta, from which it can be distiguished by the squamule size and morphology. Since similar characters were used to distinguish C. foliacea from C. convoluta which do not represent different lineages, it is necessary to examine the taxonomic status of C. angustiloba by means of DNA sequences. In this study, the species delimitation within the C. foliacea complex was studied by sequencing three loci, ITS rDNA, cox1 and RPB2. The data were analyzed by means of phylogenetic and species delimitation methods (GMYC, PTP, ABGD and BPP). Our results show that none of the three species is monophyletic. Most of the species delimitation methods did not support the current species as evolutionary lineages. Only some of the BPP analyses supported C. angustiloba as a species distinct from C. foliacea and C. convoluta. However, the hypothesis that considers the C. foliacea complex as constituted by a unique species obtained the best Bayes Factor value. Therefore, C. angustiloba and C. convoluta are synonymized with C. foliacea. A new, thoroughly checked synonymy with typifications of the whole C. foliacea complex is presented. An updated survey of the world distribution data is compiled.