TREEasy: An automated workflow to infer gene trees,species trees,and phylogenetic networks from multilocus data

Multilocus genomic data sets can be used to infer a rich set of information about the evolutionary history of a lineage, including gene trees, species trees, and phylogenetic networks. However, user‐friendly tools to run such integrated analyses are lacking, and workflows often require tedious reformatting and handling time to shepherd data through a series of individual programs. Here, we present a tool written in Python—TREEasy—that performs automated sequence alignment (with MAFFT), gene tree inference (with IQ‐Tree), species inference from concatenated data (with IQ‐Tree and RaxML‐NG), species tree inference from gene trees (with ASTRAL, MP‐EST, and STELLS2), and phylogenetic network inference (with SNaQ and PhyloNet). The tool only requires FASTA files and nine parameters as inputs. The tool can be run as command line or through a Graphical User Interface (GUI). As examples, we reproduced a recent analysis of staghorn coral evolution, and performed a new analysis on the evolution of the “WGD clade” of yeast. The latter revealed novel patterns that were not identified by previous analyses. TREEasy represents a reliable and simple tool to accelerate research in systematic biology ( https://github.com/MaoYafei/TREEasy ).     

Genomic blot hybridization as a tool of phylogenetic analysis: Evolutionary divergence in the genusDrosophila

Summary Comparative, quantitative Southern analysis of genomic DNA, using single-copy sequence probes, potentially is valuable for phylogenetic analysis. We have examined 27Drosophila species, belonging to two subgenera, seven species groups, and ten subgroups, using a variety of cloned and characterized probes: twelve cloned sequences fromD. melanogaster, two fromD. pseudoobscura, and two fromD. grimshawi. The data are generally congruent with accepted phylogenetic relationships inDrosophila, and confirm or clarify some previously uncertain relationships. The potential and limitations of the method are discussed.Presented at the FEBS Symposium on Genome Organization and Evolution, held in Crete, Greece, September 1–5, 1986     

A general approach to proving the minimality of phylogenetic trees illustrated by an example with a set of 23 vertebrates

Summary We have recently described a method of building phylogenetic trees and have outlined an approach for proving whether a particular tree is optimal for the data used. In this paper we describe in detail the method of establishing lower bounds on the length of a minimal tree by partitioning the data set into subsets. All characters that could be involved in duplications in the data are paired with all other such characters. A matching algorithm is then used to obtain the pairing of characters that reveals the most duplications in the data. This matching may still not account for all nucleotide substitutions on the tree. The structure of the tree is then used to help select subsets of three or more. characters until the lower bound found by partitioning is equal to the length of the tree. The tree must then be a minimal tree since no tree can exist with a length less than that of the lower bound.The method is demonstrated using a set of 23 vertebrate cytochrome c sequences with the criterion of minimizing the total number of nucleotide substitutions. There are 131130 7045768798 9603440625 topologically distinct trees that can be constructed from this data set. The method described in this paper does identify 144 minimal tree variants. The method is general in the sense that it can be used for other data and other criteria of length. It need not however always be possible to prove a tree minimal but the method will give an upper and lower bound on the length of minimal trees.     

Reproductive isolation and phylogenetic divergence in Neurospora: comparing methods of species recognition in a model eukaryote

We critically examined methods for recognizing species in the model filamentous fungal genus Neurospora by comparing traditional biological species recognition (BSR) with more comprehensive applications of both BSR and phylogenetic species recognition (PSR). Comprehensive BSR was applied to a set of 73 individuals by performing extensive crossing experiments and delineating biological species based on patterns of reproductive success. Within what were originally considered two species, N. crassa and N. intermedia, we recognized four reproductively isolated biological species. In a concurrent study (Dettman et al. 2003), we used genealogical concordance of four independent nuclear loci to recognize phylogenetic species in Neurospora. Overall, the groups of individuals identified as species were similar whether recognized by reproductive success or by phylogenetic criteria, and increased genetic distance between parents was associated with decreased reproductive success of crosses, suggesting that PSR using genealogical concordance can be used to reliably recognize species in organisms that are not candidates for BSR. In one case, two phylogenetic species were recognized as a single biological species, indicating that significant phylogenetic divergence preceded the development of reproductive isolation. However, multiple biological species were never recognized as a single phylogenetic species. Each of the putative N. crassa x N. intermedia hybrids included in this study was confidently assigned to a single species, using both PSR and BSR. As such, no evidence for a history of hybridization in nature among Neurospora species was observed. By performing reciprocal mating tests, we found that mating type, parental role, and species identity of parental individuals could all influence the reproductive success of matings. We also observed sympatry-associated sexual dysfunction in interspecific crosses, which was consistent with the existence of reinforcement mechanisms.     

FASMA: a service to format and analyze sequences in multiple alignments

Multiple sequence alignments are successfully applied in many studies for under- standing the structural and functional relations among single nucleic acids and protein sequences as well as whole families. Because of the rapid growth of sequence databases, multiple sequence alignments can often be very large and difficult to visualize and analyze. We offer a new service aimed to visualize and analyze the multiple alignments obtained with different external algorithms, with new features useful for the comparison of the aligned sequences as well as for the creation of a final image of the alignment. The service is named FASMA and is available at http://bioinformatica.isa.cnr.it/FASMA/.     

Body mass as a supertrait linked to abundance and behavioral dominance in hummingbirds: A phylogenetic approach

Body mass has been considered one of the most critical organismal traits, and its role in many ecological processes has been widely studied. In hummingbirds, body mass has been linked to ecological features such as foraging performance, metabolic rates, and cost of flying, among others. We used an evolutionary approach to test whether body mass is a good predictor of two of the main ecological features of hummingbirds: their abundances and behavioral dominance. To determine whether a species was abundant and/or behaviorally dominant, we used information from the literature on 249 hummingbird species. For abundance, we classified a species as “plentiful” if it was described as the most abundant species in at least part of its geographic distribution, while we deemed a species to be “behaviorally dominant” when it was described as pugnacious (notably aggressive). We found that plentiful hummingbird species had intermediate body masses and were more phylogenetically related to each other than expected by chance. Conversely, behaviorally dominant species tended to have larger body masses and showed a random pattern of distribution in the phylogeny. Additionally, small‐bodied hummingbird species were not considered plentiful by our definition and did not exhibit behavioral dominance. These results suggest a link between body mass, abundance, and behavioral dominance in hummingbirds. Our findings indicate the existence of a body mass range associated with the capacity of hummingbird species to be plentiful, behaviorally dominant, or to show both traits. The mechanisms behind these relationships are still unclear; however, our results provide support for the hypothesis that body mass is a supertrait that explains abundance and behavioral dominance in hummingbirds.     

MotViz: a tool for sequence motif prediction in parallel to structural visualization and analyses

Linking similar proteins structurally is a challenging task that may help in finding the novel members of a protein family. In this respect, identification of conserved sequence can facilitate understanding and classifying the exact role of proteins. However, the exact role of these conserved elements cannot be elucidated without structural and physiochemical information. In this work, we present a novel desktop application MotViz designed for searching and analyzing the conserved sequence segments within protein structure. With MotViz, the user can extract a complete list of sequence motifs from loaded 3D structures, annotate the motifs structurally and analyze their physiochemical properties. The conservation value calculated for an individual motif can be visualized graphically. To check the efficiency, predicted motifs from the data sets of 9 protein families were analyzed and MotViz algorithm was more efficient in comparison to other online motif prediction tools. Furthermore, a database was also integrated for storing, retrieving and performing the detailed functional annotation studies. In summary, MotViz effectively predicts motifs with high sensitivity and simultaneously visualizes them into 3D strucures. Moreover, MotViz is user-friendly with optimized graphical parameters and better processing speed due to the inclusion of a database at the back end. MotViz is available at http://www.fi-pk.com/motviz.html.     

sandflyDST: a dynamic web‐based decision support tool for the morphological identification of sandflies present in Anatolia and mainland Europe,and user study

Species identification of sandflies is mainly performed according to morphological characters using classical written identification keys. This study introduces a new web‐based decision support tool (sandflyDST) for guiding the morphological identification of sandfly species present in Anatolia and mainland Europe and classified in the Phlebotomus and Sergentomyia genera (both: Diptera: Psychodidae). The current version of the tool consists of 111 questions and 36 drawings obtained from classical written keys, and 107 photographs for the quick and easy identification of 26 species of the genus Phlebotomus and four species of the genus Sergentomyia. The tool guides users through a decision tree using yes/no questions about the morphological characters of the specimen. The tool was applied by 30 individuals, who then completed study questionnaires. The results of subsequent analyses indicated that the usability () and users' level of appreciation (86.6%) of the tool were quite high; almost all of the participants considered recommending the tool to others. The tool may also be useful in training new entomologists and maintaining their level of expertise. This is a dynamic tool and can be improved or upgraded according to feedback. The tool is now available online at http://parasitology.ege.edu.tr/sandflyDST/index.php .     

Morphology‐based phylogenetic binning to assess a taxonomic challenge: a case study in Graphidaceae (Ascomycota) requires a new generic name for the widespread Leptotrema wightii

Molecular phylogenetic analysis presents two challenges when it is transformed into formal classifications: the taxonomic challenge (whether and how to distinguish monophyletic sister clades or how to deal with paraphyletic grades) and the nomenclatural challenge (naming clades, i.e. placing name‐giving types accurately on a tree). One approach to the latter is morphology‐based phylogenetic binning, which places specimens based on phenotypic features on a molecular tree and assigns uncertainty values to alternative placement options. Here, we use the example of the lichenized fungal genus Leptotrema to demonstrate how morphology‐based phylogenetic binning can help to clarify taxonomic and nomenclatural issues when naming phylogenetically defined entities. Leptotrema is known for a common and widespread species, L. wightii, and phylogenetic analyses have been based exclusively on this species, including the recognition of a separate tribe, Leptotremateae. However, the genus name Leptotrema and the tribal name Leptotremateae are based on the name L. zollingeri, which was initially considered to be a synonym of L. wightii, but has recently been shown to represent a distinct species. As L. zollingeri differs considerably in phenotypic features from L. wightii, it can be questioned whether the two are at all related or whether L. zollingeri is actually closer to the genera Myriotrema and Ocellularia in tribe Ocellularieae. The solution to this problem is not trivial, as it affects the correct use of the names Leptotrema and Leptotremateae. Morphology‐based phylogenetic binning indeed demonstrated that L. zollingeri clusters with the Myriotrema album group in tribe Ocellularieae with high support. Hence, in contrast with current use, the name Leptotrema becomes available for the M. album group and Leptotremateae becomes a synonym of Ocellularieae. As a consequence, the new names Sanguinotrema and Sanguinotremateae are introduced to accommodate L. wightii and the tribe including this species and the genus Reimnitzia. Although the studied case is specific to lichen fungi, the approach can be used in a much broader context with any kind of taxon or organism. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 436–443.