Showing papers by "Karen W. Hughes published in 2015"
19 Jun 2015
TL;DR: Chimeric sequences are likely an artifact of the PCR-cloning process and not a consequence of natural recombination events found in nature, nor are they due to hidden existing variation within the ribosomal repeat.
Abstract: Gymnopus dichrous exists in the southern Appalachians (USA) as two distinct entities with essentially identical nuclear ribosomal ITS1 sequences but differing ITS2 and LSU sequences (for convenience, called G. dichrous I and II). F1 ITS heterozygotes between the two are routinely collected from nature. Cloning of ITS PCR products from F1 heterozygotes produced sequences of both parental haplotypes but also numerous chimeric sequences (21.9%). The location of template switching was non-random leading to recovery of the same chimera several times and the chimeric region varied from 45bp to 300bp. By comparison, single-basidiospore isolates from heterozygote F1 fruitbodies showed no recombinant haplotypes within the ITS + LSU span and clones derived from P1 homozygotes were identical to the P1 parent. Thus, chimeric sequences are likely an artifact of the PCR-cloning process and not a consequence of natural recombination events found in nature, nor are they due to hidden existing variation within the ribosomal repeat. Chimeras and PCR-induced mutations are common in cloned PCR products and may result in incorrect sequence information in public databases.
14 citations
TL;DR: Phylogenetic and geographical evidence suggests that X. enigmatica may have given rise to the eastern North American endemic, Xeromphalina kauffmanii, which also is reproductively isolated and is characterized by a hardwood substrate and a difference in basidiospore shape.
Abstract: European, North American and northeastern Asian collections of Xeromphalina section Xeromphalina were studied by sequencing the nuc rDNA ITS1-5.8SITS2 and 28S 5' regions and partial RNA polymerase II second largest subunit gene (RPB2). Previously designated Xeromphalina campanella I is designated X. campanella s. str. and a neotype for this species from the topotype region is established. This species is shown to be a discrete, cold-tolerant organism that is distributed across North America and Eurasia and does not exhibit significant geographical partitioning. A second closely related phylogenetic species previously designated X. campanella II, proposed as X. enigmatica, cannot be distinguished from X. campanella morphologically but is reproductively isolated and is sympatric with X. campanella across much of Eurasia and North America. Unlike X. campanella it shows geographical partitioning and some of the geographical populations likely have become reproductively isolated. Phylogenetic and geographical evidence suggests that X. enigmatica may have given rise to the eastern North American endemic, Xeromphalina kauffmanii, which also is reproductively isolated and is characterized by a hardwood substrate and a difference in basidiospore shape. Two putatively interbreeding haplotypes are evident for both eastern North American X. kauffmanii and eastern North American X. enigmatica and might be contributions from different glacial refugia. Cryptic taxa related to X. enigmatica are identified but not named due to small sample sizes including Asian taxa 1-5 and an apparent endemic from Idaho and British Columbia. Several species-delineation procedures were attempted and compared with this complex molecular dataset. Rosenberg's PAB statistic and PID (liberal) were the most liberal, assigning species status to haplotypes or interbreeding clades within species. PID (strict) and PRD (randomly distinct) were more stringent. Ability to intercross was the most stringent criterion for species delineation and did not correlate well with PAB, PID and PRD delineations.
14 citations
TL;DR: Investigation of collections of a pleurotoid fungus from dead aspen in eastern Russia showed that the Russian fungus was the same as Pleurotus vetlinianus described from Poland, and a new genus, Lignomyces, is described and characterized.
Abstract: Collections of a pleurotoid fungus from dead aspen in eastern Russia were initially identified as Lentinus sp., then as Phyllotopsis nidulans. DNA sequencing of cultures derived from these specimens using the nuclear ribosomal 28S (nrLSU) and nuclear ribosomal ITS1-5.8S-ITS2 regions (nrITS) showed that they were neither Lentinus nor Phyllotopsis and were not related to other pleurotoid genera Hohen- buehelia and Pleurotus. Subsequent investigation showed that the Russian fungus was the same as Pleurotus vetlinianus described from Poland. A new genus, Lignomyces, is described and characterized and L. vetlinianus comb. nov. is proposed.
8 citations
04 Mar 2015
TL;DR: Phylogeographic data indicate that DNA differences consistently exist between the North American and European allopatric populations of Gymnopus confluens and pairing experiments show that collections from both populations were sexually compatible in vitro and detailed morphological examinations of numerous fresh and dried basidiomata do not produce qualitative differences.
Abstract: Phylogeographic data indicate that DNA differences consistently exist between the North American and European allopatric populations of Gymnopus confluens. Conversely, pairing experiments show that collections from both populations were sexually compatible in vitro and detailed morphological examinations of numerous fresh and dried basidiomata do not produce qualitative differences. Percent ITS sequence divergence between Europe and North American collections of G. confluens was 3.25%. Species delineation metrics including Rosenberg’s PAB statistic, PID metrics, RRD (randomly distributed) and PTP (Poisson Tree Processes) gave mixed indications that North American and European populations were distinct at species rank. The North American populations are described as Gymnopus confluens subsp. campanulatus (Peck) R.H. Petersen.
6 citations
TL;DR: Phylogenetic placement shows that European and North American entities differ and that different names are appropriate, and it is shown that S. nemecii is a morphological variant of S. brevipes and S. herbstii likewise appears to be a morphologically variant ofS.
Abstract: Taxo-nomenclaturally, transatlantic disjunctions among fleshy fungi take two forms: 1) the same name is used on both continents, but the phylotaxonomic congruity of the organisms is questionable; and 2) different names are used, but whether they refer to the same or different organisms is questionable. This paper takes up an example of the latter case, where the European representative is known as Sparassis brevipes (or S. nemecii) and the American as S. spathulata (or S. herbstii). Phylogenetic placement shows that European and North American entities differ and that different names are appropriate. The study further shows that S. nemecii is a morphological variant of S. brevipes and that S. herbstii likewise appears to be a morphological variant of S. spathulata. In order to bring taxonomic stability to this taxonomic complex, S. brevipes is typified, epitypes are designated for S. nemecii and S. spathulata, and all taxa are redescribed. Two new combinations are proposed: S. brevipes f. nemecii and S. spathulata f. herbstii.
4 citations