Well-Behaved Variants Seldom Make the Apparatus: Stemmata and Apparatus in Digital Research

This article describes computer-assisted methods for the analysis of textual variation within large textual traditions. It focuses on the conversion of the XML apparatus into NEXUS, a file type commonly used in bioinformatics. Phylogenetics methods are described with particular emphasis on maximum parsimony, the preferred approach for our research. The article provides details on the reasons for favouring maximum parsimony, as well as explaining our choice of settings for PAUP. It gives examples of how to use VBase, our variant database, to query the data and gain a better understanding of the phylogenetic trees. The relationship between the apparatus and the stemma explained. After demonstrating the vast number of decisions taken during the analysis, the article concludes that as much as computers facilitate our work and help us expand our understanding, the role of the editor continues to be fundamental in the making of editions.

Morphological and Phylogenetic Evidence for Recognition of Two New Species of Phanerochaete from East Asia

Two new corticioid fungal species, Phanerochaete pruinosa and P. rhizomorpha spp. nov. are proposed based on a combination of morphological features and molecular evidence. Phanerochaete pruinosa is characterized by the resupinate basidiomata with the pruinose hymenial surface, a monomitic hyphal system with simple-septate generative hyphae and subcylindrical basidiospores measuring as 3.5–6.7 × 1.5–2.7 µm. Phanerochaete rhizomorpha is characterized by having a smooth hymenophore covered by orange hymenial surface, the presence of rhizomorphs, subulate cystidia, and narrower ellipsoid to ellipsoid basidiospores. Sequences of ITS+nLSU nrRNA gene regions of the studied specimens were generated and phylogenetic analyses were performed with maximum likelihood, maximum parsimony, and Bayesian inference methods. These phylogenetic analyses showed that two new species clustered into genus Phanerochaete, in which P. pruinosa was sister to P. yunnanensis with high supports (100% BS, 100% BT, 1.00 BPP); morphologically differing by a pale orange to greyish orange and densely cracked hymenial surface. Another species P. rhizomorpha was closely grouped with P. citrinosanguinea with lower supports; morphologically having yellow to reddish yellow hymenial surface, and smaller cystidia measuring as 31–48 × 2.3–4.8 µm.

Calcatedessa gen.n. a new genus sister to Grammedessa Correia & Fernandes (Heteroptera, Pentatomidae, Edessinae) based on a cladistic analysis

Grammedessa Correia & Fernandes, 2016 is a genus raised to include some species of Edessa Fabricius, 1803 that is a very common group of stink bugs inhabiting only the Neotropical region. Grammedessa was proposed excluding a few species that were morphologically similar but not completely fitting in the diagnostic requirements of the genus. Grammedessa was also proposed without considering a phylogenetic context. In this work, the monophyly of Grammedessa was tested using a cladistic analysis, including all species that were originally excluded, under both Maximum Parsimony and Bayesian methods. As a result, six new species are now included in Grammedessa, which will be described in a forthcoming paper; Edessa botocudo Kirkaldy, 1909 was considered an unnecessary new name for Edessa hamata Walker, 1868 that was transferred to Grammedessa, resulting in G. hamata (Walker, 1868) comb.n. Calcatedessa gen.n., a new genus sister to Grammedessa, is here proposed to include four new species: C. anthomorpha sp.n., C. clarimarginata sp.n., C. germana sp.n. and C. temnomarginata sp.n. The Calcatedessa–Grammedessa clade and both genera were recovered as monophyletic by Maximum Parsimony and Bayesian methods. An identification key to the species of Calcatedessa gen.n. is provided. The new genus is distributed in Guyana, Suriname, French Guyana, and Brazil.

Five Independent Lineages Revealed by Integrative Taxonomy in the Dendropsophus nanus–Dendropsophus walfordi Species Complex

One of the many taxonomic challenges found in the Dendropsophus microcephalus species group is the Dendropsophus walfordi distinction from D. nanus. Recent phylogenetic inferences have indicated the paraphyly of these species, although they were not designed to assess this issue. To contribute to the delimitation of these species, we analyzed the 12S, 16S and COI mitochondrial genes, the morphological traits, and the advertisement calls of specimens from northern Amazonia to Argentina, including the type localities of D. nanus and D. walfordi. Paraphyly of D. nanus with respect to D. walfordi was inferred by maximum-parsimony and Bayesian analyses, and five major clades exhibiting nonoverlapping geographic distributions were recognized. The bPTP and ABGD analyses supported the existence of five independently evolving lineages in this complex. Acoustic and morphological data clearly distinguished the clade that included the topotypes of D. walfordi from the others, corroborating the validity of this species. To avoid the paraphyly of D. nanus with respect to D. walfordi, we recognize the clade distributed from central-southern Brazil to Argentina as D. nanus, the clade distributed in Amazonia as D. walfordi, and discuss the existence of unnamed cryptic species closely related to D. nanus and D. walfordi.

Morphological phylogenetic analyses and taxonomic revision of the Panorpa davidi group (Mecoptera: Panorpidae)

The Chinese Panorpa species without anal horn are normally assigned to the Panorpa davidi group. Here, we taxonomically revise the P. davidi group, which currently includes 17 known species and four new species: P. gaokaii sp. nov., P. huayuani sp. nov., P. uncinata sp. nov. and P. yaoluopingensis sp. nov. Panorpa shanyangensis Chou & Wang, 1981 and P. sexspinosa zhongnanensis Chou & Ran, 1981 are treated as junior synonyms of P. sexspinosa Cheng, 1949. We describe for the first time the male of P. stigmosa Zhou, 2006, and the females of P. curva Carpenter, 1938, P. davidi Navás, 1908, P. difficilis Carpenter, 1938, P. fructa Cheng, 1949, and P. jinchuana Hua, Sun & Li, 2001. A key to species of the group is provided. Phylogenetic analyses of maximum parsimony and maximum likelihood based on 79 morphological characters show that the newly defined P. davidi group is a well-supported monophyletic group and is sister to the genus Cerapanorpa Gao, Ma & Hua, 2016.

Maximum Parsimony Reconciliation in the DTLOR Model

Background: Analyses of microbial evolution often use reconciliation methods. However, the standard duplication-transfer-loss (DTL) model does not account for the fact that species trees are often not fully sampled and thus, from the perspective of reconciliation, a gene family may enter the species tree from the outside. Moreover, within the species tree, genes are often rearranged, causing them to move to new syntenic "regions." Results: We extend the DTL model to account for two events that commonly arise in the evolution of microbes: evolution occurring outside the sampled species tree and changes in the syntenic regions of genes in the genome due to rearrangement. We describe an efficient algorithm for maximum parsimony reconciliation in this new DTLOR model and then show how it can be extended to account for non-binary gene trees. Finally, we describe preliminary experimental results from the integration of our algorithm into the existing xenoGI tool for reconstructing the histories of genomic islands in closely related bacteria. Conclusions: Reconciliation in the DTLOR model can offer new insights into the evolution of microbes that is not currently possible under the DTL model.

Maximum parsimony reconciliation in the DTLOR model

Background Analyses of microbial evolution often use reconciliation methods. However, the standard duplication-transfer-loss (DTL) model does not account for the fact that species trees are often not fully sampled and thus, from the perspective of reconciliation, a gene family may enter the species tree from the outside. Moreover, within the genome, genes are often rearranged, causing them to move to new syntenic regions. Results We extend the DTL model to account for two events that commonly arise in the evolution of microbes: origin of a gene from outside the sampled species tree and rearrangement of gene syntenic regions. We describe an efficient algorithm for maximum parsimony reconciliation in this new DTLOR model and then show how it can be extended to account for non-binary gene trees to handle uncertainty in gene tree topologies. Finally, we describe preliminary experimental results from the integration of our algorithm into the existing xenoGI tool for reconstructing the histories of genomic islands in closely related bacteria. Conclusions Reconciliation in the DTLOR model can offer new insights into the evolution of microbes that is not currently possible under the DTL model.

The Phylogenetic Relationship Revealed Three New Wood-Inhabiting Fungal Species From Genus Trechispora

Wood-inhabiting fungi play a significant role in wood degradation and the cycle of matter in the ecological system. In the present study, three new wood-inhabiting fungal species, Trechispora bambusicola, Trechispora fimbriata, and Trechispora fissurata spp. nov., are nested in Trechispora, which are proposed based on a combination of morphological features and molecular evidence. Sequences of internal transcribed spacer (ITS) and large subunit (nLSU) regions of the studied samples were generated, and the phylogenetic analyses were performed with maximum likelihood, maximum parsimony, and Bayesian inference methods. The phylogenetic analyses inferred from ITS showed that T. bambusicola was sister to Trechispora stevensonii, T. fimbriata grouped with Trechispora nivea, and T. fissurata grouped with Trechispora echinospora. The phylogenetic tree based on ITS + nLSU sequences demonstrated that T. bambusicola formed a single lineage and then grouped with Trechispora rigida and T. stevensonii. T. fimbriata was sister to T. nivea. T. fissurata grouped with Trechispora thelephora.

The Most Parsimonious Reconciliation Problem in the Presence of Incomplete Lineage Sorting and Hybridization is NP-Hard

The maximum parsimony phylogenetic reconciliation problem seeks to explain incongruity between a gene phylogeny and a species phylogeny with respect to a set of evolutionary events. While the reconciliation problem is well-studied for species and gene trees subject to events such as duplication, transfer, loss, and deep coalescence, recent work has examined species phylogenies that incorporate hybridization and are thus represented by networks rather than trees. In this paper, we show that the problem of computing a maximum parsimony reconciliation for a gene tree and species network is NP-hard even when only considering deep coalescence. This result suggests that future work on maximum parsimony reconciliation for species networks should explore approximation algorithms and heuristics.