Phenotyping in the era of genomics: MaTrics—a digital character matrix to document mammalian phenotypic traits

A new and uniquely structured matrix of mammalian phenotypes, MaTrics (Mammalian Traits for Comparative Genomics) in a digital form is presented. By focussing on mammalian species for which genome assemblies are available, MaTrics provides an interface between mammalogy and comparative genomics.MaTrics was developed within a project aimed to find genetic causes of phenotypic traits of mammals using Forward Genomics. This approach requires genomes and comprehensive and recorded information on homologous phenotypes that are coded as discrete categories in a matrix. MaTrics is an evolving online resource providing information on phenotypic traits in numeric code; traits are coded either as absent/present or with several states as multistate. The state record for each species is linked to at least one reference (e.g., literature, photographs, histological sections, CT scans, or museum specimens) and so MaTrics contributes to digitalization of museum collections. Currently, MaTrics covers 147 mammalian species and includes 231 characters related to structure, morphology, physiology, ecology, and ethology and available in a machine actionable NEXUS-format*. Filling MaTrics revealed substantial knowledge gaps, highlighting the need for phenotyping efforts. Studies based on selected data from MaTrics and using Forward Genomics identified associations between genes and certain phenotypes ranging from lifestyles (e.g., aquatic) to dietary specializations (e.g., herbivory, carnivory). These findings motivate the expansion of phenotyping in MaTrics by filling research gaps and by adding taxa and traits. Only databases like MaTrics will provide machine actionable information on phenotypic traits, an important limitation to genomics. MaTrics is available within the data repository Morph·D·Base (www.morphdbase.de).

Physcraper: a Python package for continually updated phylogenetic trees using the Open Tree of Life

Background Phylogenies are a key part of research in many areas of biology. Tools that automate some parts of the process of phylogenetic reconstruction, mainly molecular character matrix assembly, have been developed for the advantage of both specialists in the field of phylogenetics and non-specialists. However, interpretation of results, comparison with previously available phylogenetic hypotheses, and selection of one phylogeny for downstream analyses and discussion still impose difficulties to one that is not a specialist either on phylogenetic methods or on a particular group of study. Results Physcraper is a command-line Python program that automates the update of published phylogenies by adding public DNA sequences to underlying alignments of previously published phylogenies. It also provides a framework for straightforward comparison of published phylogenies with their updated versions, by leveraging upon tools from the Open Tree of Life project to link taxonomic information across databases. The program can be used by the nonspecialist, as a tool to generate phylogenetic hypotheses based on publicly available expert phylogenetic knowledge. Phylogeneticists and taxonomic group specialists will find it useful as a tool to facilitate molecular dataset gathering and comparison of alternative phylogenetic hypotheses (topologies). Conclusion The Physcraper workflow showcases the benefits of doing open science for phylogenetics, encouraging researchers to strive for better scientific sharing practices. Physcraper can be used with any OS and is released under an open-source license. Detailed instructions for installation and usage are available at https://physcraper.readthedocs.io.

Diversification through sexual selection on gustatorial courtship traits in dwarf spiders

Sexual dimorphism can evolve under sexual selection or ecological factors. Sexually dimorphic male prosomal modifications are associated with gustatorial courtship in erigonines. The modifications vary from moderate elevations to bizarre shapes. Males transfer substances from these structures to females, which affect mate acceptance and fecundity. Here, we explore lability of these traits by investigating if modified prosomata are inherently linked to secretory glands, if glands evolved prior to prosomal modifications, and the possibility of convergent evolution and cryptic differentiation, aiming at assessing the possible role of this trait complex in speciation. We reconstructed the positions of glands and the musculature in the anterior part of prosomata of 76 erigonines and three outgroups using micro-CT. We incorporated these characters into an existing morphological character matrix and reanalyzed the phylogeny. Our results support the possession of glands as the ancestral state. The manifold modifications of the prosomal shape have evolved convergently. Differences in glandular positions between species with modified/unmodified prosomata suggest high lability of these traits. Cases of gland loss suggest considerable costs of gustatorial courtship. Our findings demonstrate divergent evolutionary patterns of these traits, and a likely facilitating effect of this type of sexual selection on speciation.

Evidence for a billion-years arms race between viruses, virophages and eukaryotes

The PRD1-adenovirus lineage is one of the oldest and most diverse lineages of viruses. In eukaryotes, they have diversified to an unprecedented extent giving rise to adenoviruses, virophages, Mavericks, Polinton-like viruses and Nucleocytoplasmic Large DNA viruses (NCLDVs) which include the poxviruses, asfarviruses and iridoviruses, among others. Two major hypotheses for their origins have been proposed: the 'virophage first' and 'nuclear escape' hypotheses, but their plausibility until now has remained unexplored. Here, we use maximum-likelihood and Bayesian hypothesis-testing to compare the two scenarios based on the shared proteins forming the virus particle and a comprehensive genomic character matrix. We also compare the phylogenetic origin of the transcriptional proteins shared by NCLDVs and cytoplasmic linear plasmids. Our analyses overwhelmingly favour the virophage first model. These findings shed light on one of the earliest diversifications seen in the virosphere, supporting a billion-years arms race between viruses, virophages and eukaryotes.

An escape from the Espinhaço Range: a new species of Paepalanthus subg. Xeractis (Eriocaulaceae) from the campos rupestres of Serra do Padre Ângelo, Minas Gerais, Brazil

Background and aims – Recent botanical discoveries have highlighted the occurrence of campos rupestres in the Serra do Padre Ângelo (SPA), eastern Minas Gerais, Brazil. Here, we introduce the first new species of Paepalanthus subg. Xeractis to be described in the last three decades. Discovered in the SPA, it belongs to an emblematic lineage endemic to the campos rupestres of Minas Gerais.Material and methods – The new species is described based on herbarium material and in situ observations. A morphological phylogenetic analysis was carried out by including the new species in a previously published character matrix. Its spatial distribution is discussed based on the obtained topology.Key results – The new species is endemic to the SPA, but its closest related taxa are endemic to the Espinhaço Range (ER), ca 200 km distant. Its placement in the phylogeny supports the inclusion in P. ser. Fuscati, representing an escape from the ER. We present a clear morphological differentiation between the new species and its closest related taxa. Other similar cases of disjunct distribution among these areas of campos rupestres (SPA vs ER) are reviewed and discussed.Conclusion – Based on the restricted distribution, allied with threats to the habitat, the new species is inserted in the IUCN category of Critically Endangered (CR). This new discovery reinforces the singularity of the SPA and the relevance of biodiversity inventories and conservation studies in the easternmost campos rupestres, and their classification as a priority area for conservation.