Personality traits, rank attainment, and siring success throughout the lives of male chimpanzees of Gombe National Park.

Personality traits in many taxa correlate with fitness. Several models have been developed to try to explain how variation in these traits is maintained. One model proposes that variation persists because it is linked to trade-offs between current and future adaptive benefits.

Correlates of individual participation in boundary patrols by male chimpanzees.

Group territory defence poses a collective action problem: individuals can free-ride, benefiting without paying the costs. Individual heterogeneity has been proposed to solve such problems, as individuals high in reproductive success, rank, fighting ability or motivation may benefit from defending territories even if others free-ride. To test this hypothesis, we analysed 30 years of data from chimpanzees () in the Kasekela community, Gombe National Park, Tanzania (1978-2007).

The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata.

Background: Lichens, encompassing 20,000 known species, are symbioses between specialized fungi (mycobionts), mostly ascomycetes, and unicellular green algae or cyanobacteria (photobionts). Here we describe the first parallel genomic analysis of the mycobiont Cladonia grayi and of its green algal photobiont Asterochloris glomerata. We focus on genes/predicted proteins of potential symbiotic significance, sought by surveying proteins differentially activated during early stages of mycobiont and photobiont interaction in coculture, expanded or contracted protein families, and proteins with differential rates of evolution.

Personality in the chimpanzees of Gombe National Park.

Researchers increasingly view animal personality traits as products of natural selection. We present data that describe the personalities of 128 eastern chimpanzees (Pan troglodytes schweinfurthii) currently living in or who lived their lives in the Kasekela and Mitumba communities of Gombe National Park, Tanzania. We obtained ratings on 24 items from an established, reliable, well-validated questionnaire used to study personality in captive chimpanzee populations.

Early evolution of polyisoprenol biosynthesis and the origin of cell walls.

After being a matter of hot debate for years, the presence of lipid membranes in the last common ancestor of extant organisms (i.e., the cenancestor) now begins to be generally accepted.

Male mate choice, male quality, and the potential for sexual selection on female traits under polygyny.

Observations of male mate choice are increasingly common, even in species with traditional sex roles. In addition, female traits that bear the hallmarks of secondary sexual characters are increasingly reported. These concurrent empirical trends have led to the repeated inference that, even under polygyny, male mate choice is a mechanism of sexual selection on female traits.

Computational Evaluation of the Strict Master and Random Template Models of Endogenous Retrovirus Evolution.

Transposable elements (TEs) are DNA sequences that are able to replicate and move within and between host genomes. Their mechanism of replication is also shared with endogenous retroviruses (ERVs), which are also a type of TE that represent an ancient retroviral infection within animal genomes. Two models have been proposed to explain TE proliferation in host genomes: the strict master model (SMM), and the random template (or transposon) model (TM).

The multiple evolutionary origins of the eukaryotic N-glycosylation pathway.

Background: The N-glycosylation is an essential protein modification taking place in the membranes of the endoplasmic reticulum (ER) in eukaryotes and the plasma membranes in archaea. It shares mechanistic similarities based on the use of polyisoprenol lipid carriers with other glycosylation pathways involved in the synthesis of bacterial cell wall components (e.g.

The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.

Background: The Cell Ontology (CL) is an OBO Foundry candidate ontology covering the domain of canonical, natural biological cell types. Since its inception in 2005, the CL has undergone multiple rounds of revision and expansion, most notably in its representation of hematopoietic cells. For in vivo cells, the CL focuses on vertebrates but provides general classes that can be used for other metazoans, which can be subtyped in species-specific ontologies.

A morphological supermatrix-based phylogeny for the Neotropical fish superfamily Anostomoidea (Ostariophysi: Characiformes): phylogeny, missing data and homoplasy.

Although 11 studies have addressed the systematics of the four families and 281 fish species of the ecomorphologically diverse Anostomoidea, none has proposed a global hypothesis of relationships. We synthesized these studies to yield a supermatrix with 463 morphological characters among 174 ingroup species, and inferred phylogeny with parsimony and Bayesian optimization. We evaluated the applicability of the supermatrix approach to morphological datasets, tested its sensitivity to missing data, determined the impact of homoplastic characters on phylogenetic resolution, and determined the distribution of homologies and homoplasies on the topology.

Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals.

Background: In recent years large bibliographic databases have made much of the published literature of biology available for searches. However, the capabilities of the search engines integrated into these databases for text-based bibliographic searches are limited. To enable searches that deliver the results expected by comparative anatomists, an underlying logical structure known as an ontology is required.

Estimation of evolutionary parameters using short, random and partial sequences from mixed samples of anonymous individuals.

Background: Over the last decade, next generation sequencing (NGS) has become widely available, and is now the sequencing technology of choice for most researchers. Nonetheless, NGS presents a challenge for the evolutionary biologists who wish to estimate evolutionary genetic parameters from a mixed sample of unlabelled or untagged individuals, especially when the reconstruction of full length haplotypes can be unreliable. We propose two novel approaches, least squares estimation (LS) and Approximate Bayesian Computation Markov chain Monte Carlo estimation (ABC-MCMC), to infer evolutionary genetic parameters from a collection of short-read sequences obtained from a mixed sample of anonymous DNA using the frequencies of nucleotides at each site only without reconstructing the full-length alignment nor the phylogeny.

Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes.

Phenotypes resulting from mutations in genetic model organisms can help reveal candidate genes for evolutionarily important phenotypic changes in related taxa. Although testing candidate gene hypotheses experimentally in nonmodel organisms is typically difficult, ontology-driven information systems can help generate testable hypotheses about developmental processes in experimentally tractable organisms. Here, we tested candidate gene hypotheses suggested by expert use of the Phenoscape Knowledgebase, specifically looking for genes that are candidates responsible for evolutionarily interesting phenotypes in the ostariophysan fishes that bear resemblance to mutant phenotypes in zebrafish.

Synthesis of phylogeny and taxonomy into a comprehensive tree of life.

Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny.

Using the phenoscape knowledgebase to relate genetic perturbations to phenotypic evolution.

The abundance of phenotypic diversity among species can enrich our knowledge of development and genetics beyond the limits of variation that can be observed in model organisms. The Phenoscape Knowledgebase (KB) is designed to enable exploration and discovery of phenotypic variation among species. Because phenotypes in the KB are annotated using standard ontologies, evolutionary phenotypes can be compared with phenotypes from genetic perturbations in model organisms.

Marine extinction risk shaped by trait-environment interactions over 500 million years.

Perhaps the most pressing issue in predicting biotic responses to present and future global change is understanding how environmental factors shape the relationship between ecological traits and extinction risk. The fossil record provides millions of years of insight into how extinction selectivity (i.e.

Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream.

Quest for Orthologs (QfO) is a community effort with the goal to improve and benchmark orthology predictions. As quality assessment assumes prior knowledge on species phylogenies, we investigated the congruency between existing species trees by comparing the relationships of 147 QfO reference organisms from six Tree of Life (ToL)/species tree projects: The National Center for Biotechnology Information (NCBI) taxonomy, Opentree of Life, the sequenced species/species ToL, the 16S ribosomal RNA (rRNA) database, and trees published by Ciccarelli et al. (Ciccarelli FD, et al.

Potential for bias and low precision in molecular divergence time estimation of the Canopy of Life: an example from aquatic bird families.

Uncertainty in divergence time estimation is frequently studied from many angles but rarely from the perspective of phylogenetic node age. If appropriate molecular models and fossil priors are used, a multi-locus, partitioned analysis is expected to equally minimize error in accuracy and precision across all nodes of a given phylogeny. In contrast, if available models fail to completely account for rate heterogeneity, substitution saturation and incompleteness of the fossil record, uncertainty in divergence time estimation may increase with node age.

Toward Synthesizing Our Knowledge of Morphology: Using Ontologies and Machine Reasoning to Extract Presence/Absence Evolutionary Phenotypes across Studies.

The reality of larger and larger molecular databases and the need to integrate data scalably have presented a major challenge for the use of phenotypic data. Morphology is currently primarily described in discrete publications, entrenched in noncomputer readable text, and requires enormous investments of time and resources to integrate across large numbers of taxa and studies. Here we present a new methodology, using ontology-based reasoning systems working with the Phenoscape Knowledgebase (KB; kb.

Embracing multiple definitions of learning.

Definitions of learning vary widely across disciplines, driven largely by different approaches used to assess its occurrence. These definitions can be better reconciled with each other if each is recognized as coherent with a common conceptualization of learning, while appreciating the practical utility of different learning definitions in different contexts.

Moving the mountain: analysis of the effort required to transform comparative anatomy into computable anatomy.

The diverse phenotypes of living organisms have been described for centuries, and though they may be digitized, they are not readily available in a computable form. Using over 100 morphological studies, the Phenoscape project has demonstrated that by annotating characters with community ontology terms, links between novel species anatomy and the genes that may underlie them can be made. But given the enormity of the legacy literature, how can this largely unexploited wealth of descriptive data be rendered amenable to large-scale computation? To identify the bottlenecks, we quantified the time involved in the major aspects of phenotype curation as we annotated characters from the vertebrate phylogenetic systematics literature.

Patterns of gut bacterial colonization in three primate species.

Host fitness is impacted by trillions of bacteria in the gastrointestinal tract that facilitate development and are inextricably tied to life history. During development, microbial colonization primes the gut metabolism and physiology, thereby setting the stage for adult nutrition and health. However, the ecological rules governing microbial succession are poorly understood.

Phylesystem: a git-based data store for community-curated phylogenetic estimates.

Motivation: Phylogenetic estimates from published studies can be archived using general platforms like Dryad (Vision, 2010) or TreeBASE (Sanderson et al., 1994). Such services fulfill a crucial role in ensuring transparency and reproducibility in phylogenetic research.

Extinctions. Paleontological baselines for evaluating extinction risk in the modern oceans.

Marine taxa are threatened by anthropogenic impacts, but knowledge of their extinction vulnerabilities is limited. The fossil record provides rich information on past extinctions that can help predict biotic responses. We show that over 23 million years, taxonomic membership and geographic range size consistently explain a large proportion of extinction risk variation in six major taxonomic groups.

The Fossil Calibration Database-A New Resource for Divergence Dating.

Fossils provide the principal basis for temporal calibrations, which are critical to the accuracy of divergence dating analyses. Translating fossil data into minimum and maximum bounds for calibrations is the most important-often least appreciated-step of divergence dating. Properly justified calibrations require the synthesis of phylogenetic, paleontological, and geological evidence and can be difficult for nonspecialists to formulate.