Time to a single hybridization event in a group of species with unknown ancestral history

We consider a stochastic process for the generation of species which combines a Yule process with a simple model for hybridization between pairs of co-existent species. We assume that the origin of the process, when there was one species, occurred at an unknown time in the past, and we condition the process on producing n species via the Yule process and a single hybridization event. We prove results about the distribution of the time of the hybridization event. In particular we calculate a formula for all moments, and show that under various conditions, the distribution tends to an exponential with rate twice that of the birth rate for the Yule process

Evolution of plant RNA polymerase IV/V genes: evidence of subneofunctionalization of duplicated NRPD2/NRPE2-like paralogs in Viola (Violaceae)

<p>Abstract</p> <p>Background</p> <p>DNA-dependent RNA polymerase IV and V (Pol IV and V) are multi-subunit enzymes occurring in plants. The origin of Pol V, specific to angiosperms, from Pol IV, which is present in all land plants, is linked to the duplication of the gene encoding the largest subunit and the subsequent subneofunctionalization of the two paralogs (<it>NRPD1 </it>and <it>NRPE1</it>). Additional duplication of the second-largest subunit, <it>NRPD2/NRPE2</it>, has happened independently in at least some eudicot lineages, but its paralogs are often subject to concerted evolution and gene death and little is known about their evolution nor their affinity with Pol IV and Pol V.</p> <p>Results</p> <p>We sequenced a ~1500 bp <it>NRPD2/E2</it>-like fragment from 18 <it>Viola </it>species, mostly paleopolyploids, and 6 non-<it>Viola </it>Violaceae species. Incongruence between the <it>NRPD2/E2</it>-like gene phylogeny and species phylogeny indicates a first duplication of <it>NRPD2 </it>relatively basally in Violaceae, with subsequent sorting of paralogs in the descendants, followed by a second duplication in the common ancestor of <it>Viola </it>and <it>Allexis</it>. In <it>Viola</it>, the mutation pattern suggested (sub-) neofunctionalization of the two <it>NRPD2/E2</it>-like paralogs, <it>NRPD2/E2-a </it>and <it>NRPD2/E2-b</it>. The <it>d</it>_<it>N</it>/<it>d</it>_{<it>S </it>}ratios indicated that a 54 bp region exerted strong positive selection for both paralogs immediately following duplication. This 54 bp region encodes a domain that is involved in the binding of the Nrpd2 subunit with other Pol IV/V subunits, and may be important for correct recognition of subunits specific to Pol IV and Pol V. Across all <it>Viola </it>taxa 73 <it>NRPD2/E2</it>-like sequences were obtained, of which 23 (32%) were putative pseudogenes - all occurring in polyploids. The <it>NRPD2 </it>duplication was conserved in all lineages except the diploid MELVIO clade, in which <it>NRPD2/E2-b </it>was lost, and its allopolyploid derivates from hybridization with the CHAM clade, section <it>Viola </it>and section <it>Melanium</it>, in which <it>NRPD2/E2-a </it>occurred in multiple copies while <it>NRPD2/E2-b </it>paralogs were either absent or pseudogenized.</p> <p>Conclusions</p> <p>Following the relatively recent split of Pol IV and Pol V, our data indicate that these two multi-subunit enzymes are still in the process of specialization and each acquiring fully subfunctionalized copies of their subunit genes. Even after specialization, the <it>NRPD2/E2</it>-like paralogs are prone to pseudogenization and gene conversion and <it>NRPD2 </it>and <it>NRPE2 </it>copy number is a highly dynamic process modulated by allopolyploidy and gene death.</p

Conflicting phylogenetic signals in the SlX1/Y1 gene in Silene

<p>Abstract</p> <p>Background</p> <p>Increasing evidence from DNA sequence data has revealed that phylogenies based on different genes may drastically differ from each other. This may be due to either inter- or intralineage processes, or to methodological or stochastic errors. Here we investigate a spectacular case where two parts of the same gene (<it>SlX1</it>/<it>Y1</it>) show conflicting phylogenies within <it>Silene (Caryophyllaceae)</it>. <it>SlX1 </it>and <it>SlY1 </it>are sex-linked genes on the sex chromosomes of dioecious members of <it>Silene </it>sect. <it>Elisanthe</it>.</p> <p>Results</p> <p>We sequenced the homologues of the <it>SlX1</it>/<it>Y1 </it>genes in several <it>Sileneae </it>species. We demonstrate that different parts of the <it>SlX1/Y1 </it>region give different phylogenetic signals. The major discrepancy is that <it>Silene vulgaris </it>and <it>S</it>. sect. <it>Conoimorpha </it>(<it>S. conica </it>and relatives) exchange positions. To determine whether gene duplication followed by recombination (an intralineage process) may explain the phylogenetic conflict in the <it>Silene SlX1/Y1 </it>gene, we use a novel probabilistic, multiple primer-pair PCR approach. We did not find any evidence supporting gene duplication/loss as explanation to the phylogenetic conflict.</p> <p>Conclusion</p> <p>The phylogenetic conflict in the <it>Silene SlX1/Y1 </it>gene cannot be explained by paralogy or artefacts, such as <it>in vitro </it>recombination during PCR. The support for the conflict is strong enough to exclude methodological or stochastic errors as likely sources. Instead, the phylogenetic incongruence may have been caused by recombination of two divergent alleles following ancient interspecific hybridization or incomplete lineage sorting. These events probably took place several million years ago. This example clearly demonstrates that different parts of the genome may have different evolutionary histories and stresses the importance of using multiple genes in reconstruction of taxonomic relationships.</p

Untangling phylogenetic patterns and taxonomic confusion in tribe Caryophylleae (Caryophyllaceae) with special focus on generic boundaries

Assigning correct names to taxa is a challenging goal in the taxonomy of many groups within the Caryophyllaceae. This challenge is most serious in tribe Caryophylleae since the supposed genera seem to be highly artificial, and the available morphological evidence cannot effectively be used for delimitation and exact determination of taxa. The main goal of the present study was to re–assess the monophyly of the genera currently recognized in this tribe using molecular phylogenetic data. We used the sequences of nuclear ribosomal internal transcribed spacer (ITS) and the chloroplast gene rps16 for 135 and 94 accessions, respectively, representing all 16 genera currently recognized in the tribe Caryophylleae, with a rich sampling of Gypsophila as one of the most heterogeneous groups in the tribe. Phylogenetic trees were reconstructed using maximum parsimony and Bayesian inference methods. The results show that most of the large genera of Caryophylleae are not monophyletic. As a result, we propose a new classification system matching both molecular phylogenetic and morphological evidence. The main taxonomic conclusions include: (1) the description of three new genera, (2) treating five small genera as synonyms, (3) resurrecting the genus Heterochroa with six species, and (4) proposing 23 new combinations plus 2 replacement names at the specific level. As a result, we recognize 14 genera in Caryophylleae. A diagnostic key to all genera of Caryophylleae is provided.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/146908/1/tax6716.pd

A new taxonomic backbone for the infrageneric classification of the species‐rich genus Silene (Caryophyllaceae)

The systematization of species in plant taxonomy based on the phylogenetic relationships among them are of utmost importance and also very challenging in large genera. In those, phylogenetic results often may suggest substantially different relationships than previous classifications, and call for large‐scale taxonomic revisions. Delimitation of the genus Silene has been and is still somewhat controversial, and recent molecular phylogenetic studies have settled several monophyletic groups that differ substantially from previous taxonomies. The infrageneric taxonomy of Silene s.str. has not been updated as a whole taking the phylogenetic information into account. In this study, we review previous phylogenetic results based on multiple loci, and conducted comprehensive gene tree analyses based on the nrDNA ITS and cpDNA rps16 regions for 1586 and 944 samples representing 415 and 397 species, respectively, including Silene and its allies, as well as a species tree analysis including 262 samples representing 243 species. We sampled representatives from all 44 sections recognized in the most recent global revision of the genus. The results support the recognition of three subgenera, i.e., S. subg. Behenantha, S. subg. Lychnis and S. subg. Silene, which is partly in agreement with previous molecular phylogenetic findings and contradicts all previous traditional classifications. Silene sect. Atocion, with a few annual species showing a narrow distribution range in the eastern Mediterranean, is treated as incertae sedis because of its uncertain phylogenetic position, possibly due to exceptionally high substitution rates. Silene subg. Lychnis, weakly supported as sister to the other subgenera, splits into three main clades and includes four sections. Silene subg. Behenantha, which forms a possible sister group in relation to S. subg. Silene, is poorly resolved basally and includes a large number of mostly small clades recognized as 18 sections. In S. subg. Silene, 11 sections are recognized, among which four are broadly circumscribed: S. sect. Auriculatae, S. sect. Sclerocalycinae, S. sect. Silene and S. sect. Siphonomorpha. Silene sect. Acutifoliae and S. sect. Portenses are described here as new taxa, whereas new status or new combinations are proposed for S. sect. Anotites, S. sect. Muscipula, S. sect. Petrocoma, S. sect. Pulvinatae, S. sect. Sclerophyllae and S. sect. Uebelinia. Five new combinations and two new names are proposed for taxa in Silene formerly assigned to Lychnis and Uebelinia. The correct infrageneric nomenclature compatible with the new infrageneric system is provided along with synonymy and type citations. Shortcomings of this study, such as the lack of a morphological diagnostic key and sparse sampling of some large sections, are listed and discussed.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/156144/5/tax12230.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156144/4/tax12230-sup-0006-Supinfo06.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156144/3/tax12230-sup-0001-Supinfo01.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156144/2/tax12230-sup-0007-FigureS1.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156144/1/tax12230_am.pd

Origin and Diversification of South American Polyploid Silene Sect. Physolychnis (Caryophyllaceae) in the Andes and Patagonia

The Andes are an important biogeographic region in South America extending for about 8000 km from Venezuela to Argentina. They are – along with the Patagonian steppes – the main distribution area of ca. 18 polyploid species of Silene sect. Physolychnis. Using nuclear ITS and plastid psbE-petG and matK sequences, flow cytometric ploidy level estimations and chromosome counts, and including 13 South American species, we explored the origin and diversification of this group. Our data suggest a single, late Pliocene or early Pleistocene migration of the North American S. verecunda lineage to South America, which was followed by dispersal and diversification of this tetraploid lineage in the Andes, other Argentinian mountain ranges and the Patagonian steppes. Later in the Pleistocene South American populations hybridized with the S. uralensis lineage, which led to allopolyploidisation and origin of decaploid S. chilensis and S. echegarayi occurring at high elevations. Additionally, we show that the morphological differentiation in leaf shape correlated with divergent habitats (high elevation Andes vs. lower elevation Patagonian steppes) is also supported phylogenetically, especially in the ITS tree. Lastly, the species boundaries among the narrow-leaved Patagonian steppe species are poorly resolved and need more thorough taxonomic revision

Incorporating molecular data in fungal systematics: a guide for aspiring researchers

The last twenty years have witnessed molecular data emerge as a primary research instrument in most branches of mycology. Fungal systematics, taxonomy, and ecology have all seen tremendous progress and have undergone rapid, far-reaching changes as disciplines in the wake of continual improvement in DNA sequencing technology. A taxonomic study that draws from molecular data involves a long series of steps, ranging from taxon sampling through the various laboratory procedures and data analysis to the publication process. All steps are important and influence the results and the way they are perceived by the scientific community. The present paper provides a reflective overview of all major steps in such a project with the purpose to assist research students about to begin their first study using DNA-based methods. We also take the opportunity to discuss the role of taxonomy in biology and the life sciences in general in the light of molecular data. While the best way to learn molecular methods is to work side by side with someone experienced, we hope that the present paper will serve to lower the learning threshold for the reader.Comment: Submitted to Current Research in Environmental and Applied Mycology - comments most welcom

Research Notes : United States : Superoxide dismutase (SOD) in soybean

We are using vertical polyacrylamide gel electrophoresis (Davis, 1964) and a staining system modified after Beauchamp and Fridovich (1971) to study superoxide dismutase polymorphisms in the subgenus soja. This staining system generates superoxide radical; hence, it is specific for SOD activity. We re-solve up to 9 SOD bands in dry or germinating soybean cotyledons, and in leaves

BookMark Vol.105 2017ネン9・10ガツゴウ

巻頭言 経営学部 教授 図書館運営委員 塚本成