Automatic selection of partitioning schemes for phylogenetic analyses using iterative k-means clustering of site rates.

Background: Model selection is a vital part of most phylogenetic analyses, and accounting for the heterogeneity in evolutionary patterns across sites is particularly important. Mixture models and partitioning are commonly used to account for this variation, and partitioning is the most popular approach. Most current partitioning methods require some a priori partitioning scheme to be defined, typically guided by known structural features of the sequences, such as gene boundaries or codon positions.

Infectious disease and group size: more than just a numbers game.

Increased risk of infectious disease is assumed to be a major cost of group living, yet empirical evidence for this effect is mixed. We studied whether larger social groups are more subdivided structurally. If so, the social subdivisions that form in larger groups may act as barriers to the spread of infection, weakening the association between group size and infectious disease.

Evolution of the indoor biome.

Few biologists have studied the evolutionary processes at work in indoor environments. Yet indoor environments comprise approximately 0.5% of ice-free land area--an area as large as the subtropical coniferous forest biome.

Baby on board: olfactory cues indicate pregnancy and fetal sex in a non-human primate.

Olfactory cues play an integral, albeit underappreciated, role in mediating vertebrate social and reproductive behaviour. These cues fluctuate with the signaller's hormonal condition, coincident with and informative about relevant aspects of its reproductive state, such as pubertal onset, change in season and, in females, timing of ovulation. Although pregnancy dramatically alters a female's endocrine profiles, which can be further influenced by fetal sex, the relationship between gestation and olfactory cues is poorly understood.

No evidence of inhibition of horizontal gene transfer by CRISPR-Cas on evolutionary timescales.

The CRISPR (clustered, regularly, interspaced, short, palindromic repeats)-Cas (CRISPR-associated genes) systems of archaea and bacteria provide adaptive immunity against viruses and other selfish elements and are believed to curtail horizontal gene transfer (HGT). Limiting acquisition of new genetic material could be one of the sources of the fitness cost of CRISPR-Cas maintenance and one of the causes of the patchy distribution of CRISPR-Cas among bacteria, and across environments. We sought to test the hypothesis that the activity of CRISPR-Cas in microbes is negatively correlated with the extent of recent HGT.

Vocal traits and diet explain avian sensitivities to anthropogenic noise.

Global population growth has caused extensive human-induced environmental change, including a near-ubiquitous transformation of the acoustical environment due to the propagation of anthropogenic noise. Because the acoustical environment is a critical ecological dimension for countless species to obtain, interpret and respond to environmental cues, highly novel environmental acoustics have the potential to negatively impact organisms that use acoustics for a variety of functions, such as communication and predator/prey detection. Using a comparative approach with 308 populations of 183 bird species from 14 locations in Europe, North American and the Caribbean, I sought to reveal the intrinsic and extrinsic factors responsible for avian sensitivities to anthropogenic noise as measured by their habitat use in noisy versus adjacent quiet locations.

The effects of partitioning on phylogenetic inference.

Partitioning is a commonly used method in phylogenetics that aims to accommodate variation in substitution patterns among sites. Despite its popularity, there have been few systematic studies of its effects on phylogenetic inference, and there have been no studies that compare the effects of different approaches to partitioning across many empirical data sets. In this study, we applied four commonly used approaches to partitioning to each of 34 empirical data sets, and then compared the resulting tree topologies, branch-lengths, and bootstrap support estimated using each approach.

Finding our way through phenotypes.

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes.

Once upon a time the cell membranes: 175 years of cell boundary research.

All modern cells are bounded by cell membranes best described by the fluid mosaic model. This statement is so widely accepted by biologists that little attention is generally given to the theoretical importance of cell membranes in describing the cell. This has not always been the case.

Not just a theory--the utility of mathematical models in evolutionary biology.

Progress in science often begins with verbal hypotheses meant to explain why certain biological phenomena exist. An important purpose of mathematical models in evolutionary research, as in many other fields, is to act as “proof-of-concept” tests of the logic in verbal explanations, paralleling the way in which empirical data are used to test hypotheses. Because not all subfields of biology use mathematics for this purpose, misunderstandings of the function of proof-of-concept modeling are common.

Calibration uncertainty in molecular dating analyses: there is no substitute for the prior evaluation of time priors.

Calibration is the rate-determining step in every molecular clock analysis and, hence, considerable effort has been expended in the development of approaches to distinguish good from bad calibrations. These can be categorized into a priori evaluation of the intrinsic fossil evidence, and a posteriori evaluation of congruence through cross-validation. We contrasted these competing approaches and explored the impact of different interpretations of the fossil evidence upon Bayesian divergence time estimation.

Generation time, life history and the substitution rate of neutral mutations.

Our understanding of molecular evolution is hampered by a lack of quantitative predictions about how life-history (LH) traits should correlate with substitution rates. Comparative studies have shown that neutral substitution rates vary substantially between species, and evidence shows that much of this diversity is associated with variation in LH traits. However, while these studies often agree, some unexplained and contradictory results have emerged.

Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex.

Background: Phenex (http://phenex.phenoscape.org/) is a desktop application for semantically annotating the phenotypic character matrix datasets common in evolutionary biology.

Phylogenomics resolves the timing and pattern of insect evolution.

Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips.

The colorful language of Australian flowers.

The enormous increase in phylogenetic information in recent years has allowed many old questions to be reexamined from a macroevolutionary perspective. We have recently considered evolutionary convergence in floral colors within pollination syndromes, using bird-pollinated species in Australia. We combined quantitative measurements of floral reflectance spectra, models of avian color vision, and a phylogenetic tree of 234 Australian species to show that bird-pollinated flowers as a group do not have colors that are significantly different from the colors of insect-pollinated flowers.

Aposematism increases acoustic diversification and speciation in poison frogs.

Multimodal signals facilitate communication with conspecifics during courtship, but they can also alert eavesdropper predators. Hence, signallers face two pressures: enticing partners to mate and avoiding detection by enemies. Undefended organisms with limited escape abilities are expected to minimize predator recognition over mate attraction by limiting or modifying their signalling.

Opportunity for selection in human health.

Natural selection defined by differential survival and reproduction of individuals in populations is influenced by genetic, developmental, and environmental factors operating at every age and stage in human life history: generation of gametes, conception, birth, maturation, reproduction, senescence, and death. Biological systems are built upon a hierarchical organization nesting subcellular organelles, cells, tissues, and organs within individuals, individuals within families, and families within populations, and the latter among other populations. Natural selection often acts simultaneously at more than one level of biological organization and on specific traits, which we define as multilevel selection.

Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology.

Background: Spatial terminology is used in anatomy to indicate precise, relative positions of structures in an organism. While these terms are often standardized within specific fields of biology, they can differ dramatically across taxa. Such differences in usage can impair our ability to unambiguously refer to anatomical position when comparing anatomy or phenotypes across species.

Sources of variance in a female fertility signal: exaggerated estrous swellings in a natural population of baboons.

Signals of fertility in female animals are of increasing interest to evolutionary biologists, a development that coincides with increasing interest in male mate choice and the potential for female traits to evolve under sexual selection. We characterized variation in size of an exaggerated female fertility signal in baboons and investigated the sources of that variance. The number of sexual cycles that a female had experienced after her most recent pregnancy ("cycles since resumption") was the strongest predictor of swelling size.

The Bioinformatics Open Source Conference (BOSC) 2013.

nlharris@lbl.gov

Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon.

Background: Elucidating disease and developmental dysfunction requires understanding variation in phenotype. Single-species model organism anatomy ontologies (ssAOs) have been established to represent this variation. Multi-species anatomy ontologies (msAOs; vertebrate skeletal, vertebrate homologous, teleost, amphibian AOs) have been developed to represent 'natural' phenotypic variation across species.

Does energy availability predict gastropod reproductive strategies?

The diversity of reproductive strategies in nature is shaped by a plethora of factors including energy availability. For example, both low temperatures and limited food availability could increase larval exposure to predation by slowing development, selecting against pelagic and/or feeding larvae. The frequency of hermaphroditism could increase under low food availability as population density (and hence mate availability) decreases.

Flight performance of the largest volant bird.

Pelagornithidae is an extinct clade of birds characterized by bizarre tooth-like bony projections of the jaws. Here, the flight capabilities of pelagornithids are explored based on data from a species with the largest reported wingspan among birds. Pelagornis sandersi sp.