GRMT: Generative Reconstruction of Mutation Tree From Scratch Using Single-Cell Sequencing Data

Single-cell sequencing (SCS) now promises the landscape of genetic diversity at single cell level, and is particularly useful to reconstruct the evolutionary history of tumor. There are multiple types of noise that make the SCS data notoriously error-prone, and significantly complicate tumor tree reconstruction. Existing methods for tumor phylogeny estimation suffer from either high computational intensity or low-resolution indication of clonal architecture, giving a necessity of developing new methods for efficient and accurate reconstruction of tumor trees. We introduce GRMT (Generative Reconstruction of Mutation Tree from scratch), a method for inferring tumor mutation tree from SCS data. GRMT exploits the k-Dollo parsimony model to allow each mutation to be gained once and lost at most k times. Under this constraint on mutation evolution, GRMT searches for mutation tree structures from a perspective of tree generation from scratch, and implements it to an iterative process that gradually increases the tree size by introducing a new mutation per time until a complete tree structure that contains all mutations is obtained. This enables GRMT to efficiently recover the chronological order of mutations and scale well to large datasets. Extensive evaluations on simulated and real datasets suggest GRMT outperforms the state-of-the-arts in multiple performance metrics. The GRMT software is freely available at https://github.com/qasimyu/grmt.

Exaggeration and suppression of iridescence: the evolution of two-dimensional butterfly structural colours

Many butterfly species possess ‘structural’ colour, where colour is due to optical microstructures found in the wing scales. A number of such structures have been identified in butterfly scales, including three variations on a simple multi-layer structure. In this study, we optically characterize examples of all three types of multi-layer structure, as found in 10 species. The optical mechanism of the suppression and exaggeration of the angle-dependent optical properties (iridescence) of these structures is described. In addition, we consider the phylogeny of the butterflies, and are thus able to relate the optical properties of the structures to their evolutionary development. By applying two different types of analysis, the mechanism of adaptation is addressed. A simple parsimony analysis, in which all evolutionary changes are given an equal weighting, suggests convergent evolution of one structure. A Dollo parsimony analysis, in which the evolutionary ‘cost’ of losing a structure is less than that of gaining it, implies that ‘latent’ structures can be reused.

PCR-RFLP ANALYSIS OF THE CHLOROPLAST GENE trn K IN THE PINACEAE, WITH SPECIAL REFERENCE TO THE SYSTEMATIC POSITION OF CATHAYA

The molecular phylogeny of the Pinaceae represented by 13 species of 10 genera was constructed from PCR-RFLP analysis of the chloroplast gene trn K, which was approximately 2557 bp long. Ninety-two restriction sites, of which 68 were variable, were identified by 16 restriction enzymes. Thirty-five of the 68 polymorphic sites were phylogenetically informative. The restriction site data were analyzed by PAUP (version 3.1.1) with both the Wagner parsimony method and the Dollo parsimony method. As a result, Dollo and Wagner parsimonious trees have similar topologies except for the position of Cedrus. The Abies-Keteleeria-Tsuga-Pseudolarix clade was well resolved in all trees. Pseudotsuga is closely related to Larix, while Abies is relatively closely related to Keteleeria. As an isolated genus, Cathaya is distantly related to the Abies-Keteleeria-Tsuga-Pseudolarix clade, and is not very closely related to any other genus of the Pinaceae.

Evaluation of the subtribes Moricandiinae, Savignyinae, Vellinae, and Zillinae (Brassicaceae, tribe Brassiceae) using chloroplast DNA restriction site variation

Chloroplast DNA restriction site data was used to assess relationships among 21 taxa of the subtribes Moricandiinae, Savignyinae, Vellinae, and Zillinae (tribe Brassiceae, Brassicaceae). A total of 301 restriction site mutations was observed, with 154 (51.2%) phylogenetically informative. Cladistic analyses, based on Wagner and Dollo parsimony, indicated two major clades. One of these, the Vellinae–Zillinae clade, included members of the Vellinae and Zillinae, with a clarification of the positions of certain genera. The second, the Brassicinae : Rapa–Oleracea clade included Brassica rapa, Moricandia, Pseuderucaria, and Rytidocarpus. The position of Henophyton (Savignyinae) was not clearly resolved. Within the Vellinae–Zillinae clade, two main lineages were evident: (i) Vellinae-core clade, which includes Boleum, Carrichtera, and Vella (all members of the Vellinae) and Euzomodendron (Savignyinae); (ii) Zillinae clade, which includes Fortuynia, Physorrhynchus, Zilla (all Zillinae), and Foleyola and Schouwia (assigned to Moricandiinae and Vellinae, respectively). The positions of Psychine and Succowia (both assigned to Vellinae) were not clearly resolved in the strict consensus but were aligned with the Vellinae-core clade in almost all of the most-parsimonious Wagner trees. The cpDNA data did not support the current separate subtribal ranking for the Moricandiinae but instead revealed the genetic similarity of Moricandia, Pseuderucaria, and Rytidocarpus to subtribe Brassicinae. Key words: Brassicinae, Moricandiinae, Savignyinae, Vellinae, Zillinae, molecular systematics.

Phylogeny and Rates of Character Evolution Among Ringtail Possums (Pseudocheiridae, Marsupialia)

A total of 47 craniodental characters seen in fossil and extant ringtail possums (Pseudocheiridae: Marsupialia) were examined using Wagner, Camin-Sokal, and Dollo parsimony. All extant species form a clade to the exclusion of Miocene genera. Hemibelideus and Petauroides are sister taxa, as are Petropseudes and Pseudochirops. All species of Pseudocheirus are united together, except Pseudocheirus peregrinus, the phylogenetic position of which is uncertain on the basis of craniodental information. Overall, the agreement between cladistic analyses of craniodental characters and biochemical analysis is excellent, although the latter provide much stronger evidence that P. peregrinus is a sister taxon to other Pseudocheirus species. Rates of evolution of craniodental characters are highest in the Pseudochirops-Petropseudes lineage, where widening of the molars, elaboration of cusps and conules, accentuation of cristae and cristids, and the development of highly crenulated enamel create a dental battery that is better equipped to process plant material. Pseudocheirus displays the least modification of the presumed primitive dental condition.

Analyses of heliozoan interrelationships: an example of the potentials and limitations of ultrastructural approaches to the study of protistan phylogeny

Concepts about specific relationships among various groups of protists are diverse and protist taxonomy is consequently unstable. In order to investigate the causes of this variety, data (mainly ultrastructural) relating to 198 characters of 25 species of heliozoa and other protozoa are analysed. Procedures are used which are compatible with numerical taxonomy (single linkage, complete linkage and group average cluster analyses), cladistic procedures (Camin–Sokal, Dollo and Wagner parsimony analyses) and evolutionary taxonomy (an intuitive tree). The results are presented as branching diagrams. There is no complete congruence among any of the techniques, but all give similar results in some important aspects. The Wagner and Dollo parsimony analyses give those results which are most credible. The results corroborate the view that several major traditional taxa of protozoa (the heliozoa, flagellates, amoebae and filose amoebae) are polyphyletic and require revision. All of the analyses identify the following clusters: actinophryid heliozoa, centrohelid heliozoa, chrysophyte flagellates, actinomonad and pedinellid flagellates and nucleariid filose amoebae. As there is no disagreement, these are confirmed as monophyletic taxa. There is a strong suggestion for a close relationship between dimorphid flagellates and desmothoracid heliozoa. There is some support for the suggestion that the actinophryid heliozoa are more closely related to actinomonad helioflagellates than to other heliozoa. The results are summarized as an unrooted ‘true tree'. The lack of agreement among the analyses appears not to be due to a lack of rigour in analytical procedures, but to an inadequate supply of data. The paucity of data cannot be compensated for by the application of repeatable techniques. Most relationships among high level protist taxa are likely to be (currently) obscured by similar limitations. Ultrastructural data are well suited to mapping out the diversity of protozoa. Electron microscopy currently appears to be the most valuable technique for investigating problems of evolutionary relationships of protists. Various hurdles to the development of a natural (phylogenetic) classification of protists are discussed.

A phylogenetic analysis of the tribe Triticeae (Poaceae) based on morphological characters of the genera

A phylogenetic analysis of Triticeae was performed by means of numerical methods. Five methods, each based on extreme assumptions of parameters so interpreted under Felsenstein's (1979) evolutionary model, were used: Camin–Sokal parsimony, Wagner parsimony, Dollo parsimony, polymorphism parsimony, and character-compatibility analysis. Although a considerable amount of parallelism was, for some time, suspected to have occurred in Triticeae (by Stebbins for instance) so that for this reason perhaps the assumptions of polymorphism parsimony might be most suitable for phylogenetic analysis, the five methods were used because the evolutionary assumptions for each investigated character are, and probably will long remain, unknown.Data input consisted of sets of hypothesized transformation series, each set subjected to analyses using the five methods. Results of an analysis provided the basis for altering the set of hypothesized transformation series for subsequent analysis. Analyses were carried out repeatedly until stabilization; that is until, in the author's judgment, the most parsimonious solution was arrived at and further trials were of diminishing return. The most parsimonious tree obtained served as a base for subsequent elaboration of the final tree, taking into consideration genetic information primarily, and for the erection of the proposed phylogenetic classification of Triticeae. A key is provided for identification of the groupings in the tribe. The proposed classification is discussed in the light of previous classifications, even though none of them were phylogenetic in the sense of Hennig.