randtip, a generalized framework to expand incomplete phylogenies using non-molecular phylogenetic information

The increasing availability of molecular information has lifted our understanding of species evolutionary relationships to unprecedent levels. However, current estimates of the world's biodiversity suggest that about a fifth of all extant species are yet to be described, and we still lack molecular information for many of the known species. Hence, evolutionary biologists will have to tackle phylogenetic uncertainty for a long time to come. This prospect has urged the development of software to expand phylogenies based on non-molecular phylogenetic information, and while the available tools provide some valuable features, major drawbacks persist and some of the proposed solutions are hardly generalizable to any group of organisms. Here, we present a completely generalized and flexible framework to expand incomplete molecular phylogenies. The framework is implemented in the R package "randtip", a toolkit of functions that was designed to randomly bind phylogenetically uncertain taxa in backbone phylogenies through a fully customizable and automatic procedure that uses taxonomic ranks as a major source of phylogenetic information. Although randtip is capable of automatically generating fully operative phylogenies for any group of organisms using just a list of species and a backbone tree, we stress that the "blind" expansion of phylogenies (using randtip or any other available software) often leads to suboptimal solutions. Thus, we discuss a variety of circumstances that may require customizing simulation parameters beyond default settings to optimally expand the trees, including a detailed step-by-step workflow. Phylogenetic uncertainty should be tackled with caution, assessing potential pitfalls and opportunities to optimize parameter space prior to launch any simulation. Used judiciously, our framework will help evolutionary biologists to efficiently expand incomplete molecular phylogenies and thereby account for phylogenetic uncertainty in quantitative analyses.

New and interesting species of Agaricomycetes from Panama

Panama forms part of the Central American biodiversity hotspot, one of the most important biodiversity hotspots in the world. While plants are relatively well studied in Panama, the documentation of fungal diversity is still in a pioneer phase. In this publication, four species of Agaricomycetes recently collected in Panama are described as new to science, two in Agaricales, namely Gliophorus roseus and Humidicutis roseorubra, a lichenised species in Cantharellales, called Multiclavula caput-serpentis, and a species in Gomphales, called Gloeocantharellus salmonicolor. These species are described and illustrated. Their phylogenetic affinities are discussed based on morphological characters and molecular phylogenies. Further six species of Agaricales, which have not been reported from Panama before, are presented as new records for the country, along with data on their morphology, ecology and taxonomy.

Identification of the Oligocene to early Miocene loricariid catfish †Taubateia paraiba as a member of the Rhinelepinae

Correct identification of fossil taxa is immensely important for dating molecular phylogenies and understanding when and how quickly modern biodiversity evolved. Fossils that are available for a clade of interest and can be directly incorporated in the phylogenetic analysis are considered primary sources of time calibration, whereas calibrations inferred from other studies are secondary (Arroyave et al., 2013). Studies of taxonomic groups that lack fossils must either expand their analyses to include fossilized outgroup lineages, use secondary calibrations, or use more problematic primary calibrations, e.g., vicariant geologic events. The use of vicariant geologic events to calibrate phylogenies poses the risk of circular reasoning, because the goal of many such studies is to determine how geologic events have affected diversification. Near et al. (2012) argued that fossil calibrations external to clades of interest, but still within the broader Actinopterygian (ray-finned fishes) tree, could be used as means of calibrating a generalized molecular clock, but internal calibrations are still valuable for refining such inferences (Arroyave et al., 2013).

Twenty Years after De Ley and Blaxter—How Far Did We Progress in Understanding the Phylogeny of the Phylum Nematoda?

Molecular phylogenetics brought radical changes to our understanding of nematode evolution, resulting in substantial modifications to nematode classification implemented by De Ley and Blaxter and widely accepted now. Numerous phylogenetic studies were subsequently published that both improved and challenged this classification. Here we present a summary of these changes. We created cladograms that summarise phylogenetic relationships within Nematoda using phylum-wide to superfamily-wide molecular phylogenies published in since 2005, and supplemented with the phylogenetic analyses for Enoplia and Chromadoria with the aim of clarifying the position of several taxa. The results show which parts of the Nematode tree are well resolved and understood, and which parts require more research, either by adding taxa that have not been included yet (increasing taxon coverage), or by changing the phylogenetic approach (improving data quality, using different types of data or different methods of analysis). The currently used classification of the phylum Nematoda in many cases does not reflect the phylogeny and in itself requires numerous improvements and rearrangements.

Hidden diversity within a polytypic species: The enigmatic Sceloporus torquatus Wiegmann, 1828 (Reptilia, Squamata, Phrynosomatidae)

The spiny lizard genus Sceloporus was described by Wiegmann in 1828, with S. torquatus posteriorly designated as the type species. The taxonomic history of S. torquatus is complicated, as it has been confused with other taxa by numerous authors. Many modern systematics works have been published on Sceloporus, but none have included all five recognized S. torquatus subspecies: S. t. torquatus, S. t. melanogaster, S. t. binocularis, S. t. mikeprestoni, and S. t. madrensis. Additionally, there is previous evidence for at least one unnamed taxon. The present study is the first taxonomic revision of the enigmatic S. torquatus based on molecular phylogenies using combined molecular data from 12S, ND4 and RAG1 genes, and Maximum Likelihood and Bayesian inference phylogenetic methods. This work includes the most extensive sampling across the entire distribution, as well as divergence time estimates and environmental niche modelling, which combined offer a spatio-temporal framework for understanding the evolution of the species. Additionally, a series of morphological characters are analyzed to identify significant differences between lineages consistently recovered in the molecular phylogenies. Using this integrative approach, evidence is presented for eight lineages within the S. torquatus complex, five of which correspond to previously recognized subspecies and three represent unnamed taxa masked by morphological conservatism. Finally, to maintain taxonomic stability a lectotype and paralectoype are designated for S. torquatus, and certain taxonomic changes are suggested in order to reflect the phylogenetic relationships within the S. torquatus complex.

Nitzschia anatoliensis sp. nov., a cryptic diatom species from the highly alkaline Van Lake (Turkey)

In this article we describe Nitzschia anatoliensis Górecka, Gastineau & Solak sp. nov., an example of a diatom species inhabiting extreme habitats. The new species has been isolated and successfully grown from the highly alkaline Van Lake in East Turkey. The description is based on morphology (light and scanning electron microscopy), the sequencing of its organellar genomes and several molecular phylogenies. This species could easily be overlooked because of its extreme similarity to Nitzschia aurariae but molecular phylogenies indicate that they are only distantly related. Furthermore, molecular data suggest that N. anatoliensis may occur in several alkaline lakes of Asia Minor and Siberia, but was previously misidentified as Nitzschia communis. It also revealed the very close genetic proximity between N. anatoliensis and the endosymbiont of the dinotom Kryptoperidinium foliaceum, providing additional clues on what might have been the original species of diatoms to enter symbiosis.

New species of Crella (Pytheas) Topsent, 1890 and Crellomima Rezvoi, 1925 (Crellidae, Poecilosclerida, Demospongiae) from Chilean shallow and Argentinean deep waters, with a synthesis on the known phylogenetic relationships of crellid sponges

Here, we describe four new species of Crellidae Dendy, 1922 and discuss characters and relationships from published molecular phylogenies including crellid sponges. New species proposed are Crella (Pytheas) chiloensis Fernandez, Gastaldi, Pardo & Hajdu, sp. nov., from southern Chile (15 m depth), C. (P.) desventuradae Fernandez, Gastaldi, Zapata-Hernández & Hajdu, sp. nov., from Desventuradas Archipelago (10–20 m depth), Crella (P.) santacruzae Fernandez, Gastaldi, Thompson & Hajdu, sp. nov., from deep waters off Argentina (750 m depth) and Crellomima sigmatifera Fernandez, Gastaldi & Hajdu, sp. nov., from the Chilean fjords region (ca. 20 m depth). These new species are set apart from each other and from known species mainly due to aspects of their spiculation. Chelae microscleres and acanthostyles supply characters that might be used to infer phylogenetic relationships and to verify the monophyly of Crella Gray, 1867 and Crellidae, which has seemingly been contradicted by preliminary molecular data available in the systematics’ literature. Our own interpretation of phylogenetic affinities, in the light of morphological characters from previous taxonomic studies, argues for a classification reassessment of materials (vouchers) included in these molecular phylogenies, especially in the case of Crella incrustans (Carter, 1885). We argue that currently available molecular phylogenetic outcomes for crellid sponges are not supportive of the polyphyly of Crella and Crellidae.

Molecular Phylogenies Map to Biogeography Better than Morphological Ones

Phylogenetic relationships are inferred principally from two classes of data: morphological and molecular. Most current phylogenies of extant taxa are inferred from molecules, and when morphological and molecular trees conflict the latter are often preferred. Although supported by simulations, the superiority of molecular trees has never been assessed empirically. Here we test phylogenetic accuracy using two independent data sources: biogeographical distributions and fossil first occurrences. For 48 pairs of morphological and molecular trees, we show that molecular trees are, on average, significantly more biogeographically congruent than their morphological counterparts. We also report an increase in the biogeographical congruence of phylogenies over research time. We find no significant differences in stratigraphical congruence between morphological and molecular trees. These findings have implications for understanding homoplasy in morphological data sets, the utility of morphology as a test of molecular hypotheses, and the difficulty of analysing fossil groups for which molecular data are unavailable.

Carinicateres merkli gen. et sp. nov. from Thailand, with notes on identification of two lophocateride beetles used in recent molecular phylogenies (Cleroidea, Lophocateridae)

Carinicateres merkli gen. et sp. nov. of Lophocateridae from eastern Thailand is described. The monotypic genus is distinct in its unique synapomorphies, namely the tarsal formula 4-4-4, elytron with 2 complete and 3 incomplete carinae, antenna 10-segmented with 2-segmented club. The emarginate frontoclypeal suture, mandible with mola, prementum divided into two parts, cranium dorsally with large impressions, each with seta in centre, crenulate lateral margins of pronotum, and distinct dorsal vestiture are shared with lophocateride genera Indopeltis Crowson and Trichocateres Kolibáč. Two specimens affiliated to Lophocateres Olliff and recently used in three molecular phylogenetic analyses are unambiguously identified as members of the clade Ancyrona + Neaspis and associated with Neaspis Pascoe.