Publications by authors named "O'Meara B"

Key innovations, traits that provide species access to novel niches, are thought to be a major generator of biodiversity. One commonly cited example of key innovation is pharyngognathy, a set of modifications to the pharyngeal jaws found in some highly species-rich fish clades such as cichlids and wrasses. Here, using comparative phylogenomics and phylogenetic comparative methods, we investigate the genomic basis of pharyngognathy and the impact of this innovation on diversification.

View Article and Find Full Text PDF

The selection of appropriate defensive behaviors in the face of potential threat is fundamental to survival. However, after repeated exposures to threatening stimuli that did not signal real danger, an animal must learn to adjust and optimize defensive behaviors. Despite extensive research on innate threat processing, little is known how individuals change their defensive behaviors when presented with recurrent threat exposures without evidence of a real risk.

View Article and Find Full Text PDF

Across a variety of biological datasets, from genomes to conservation to the fossil record, evolutionary rates appear to increase toward the present or over short time scales. This has long been seen as an indication of processes operating differently at different time scales, even potentially as an indicator of a need for new theory connecting macroevolution and microevolution. Here we introduce a set of models that assess the relationship between rate and time and demonstrate that these patterns are statistical artifacts of time-independent errors present across ecological and evolutionary datasets, which produce hyperbolic patterns of rates through time.

View Article and Find Full Text PDF

Root nodule symbiosis (RNS) is a complex trait that enables plants to access atmospheric nitrogen converted into usable forms through a mutualistic relationship with soil bacteria. Pinpointing the evolutionary origins of RNS is critical for understanding its genetic basis, but building this evolutionary context is complicated by data limitations and the intermittent presence of RNS in a single clade of ca. 30,000 species of flowering plants, i.

View Article and Find Full Text PDF

Chronograms-phylogenies with branch lengths proportional to time-represent key data on timing of evolutionary events, allowing us to study natural processes in many areas of biological research. Chronograms also provide valuable information that can be used for education, science communication, and conservation policy decisions. Yet, achieving a high-quality reconstruction of a chronogram is a difficult and resource-consuming task.

View Article and Find Full Text PDF

Applications of molecular phylogenetic approaches have uncovered evidence of hybridization across numerous clades of life, yet the environmental factors responsible for driving opportunities for hybridization remain obscure. Verbal models implicating geographic range shifts that brought species together during the Pleistocene have often been invoked, but quantitative tests using paleoclimatic data are needed to validate these models. Here, we produce a phylogeny for Heuchereae, a clade of 15 genera and 83 species in Saxifragaceae, with complete sampling of recognized species, using 277 nuclear loci and nearly complete chloroplast genomes.

View Article and Find Full Text PDF

The correlated evolution of multiple characters is a crucial aspect of evolutionary change. If change in a particular character influences the evolution of a separate trait, then modeling these features independently can mislead our understanding of the evolutionary process. Progress toward jointly modeling several characters has involved modeling multivariate evolution of the same class of character, but there are far fewer options when jointly modeling traits when one character is discrete and the other is continuous.

View Article and Find Full Text PDF

The fossilized birth-death (FBD) model is a naturally appealing way of directly incorporating fossil information when estimating diversification rates. However, an important yet often overlooked property of the original FBD derivation is that it distinguishes between two types of sampled lineages. Here, we first discuss and demonstrate the impact of severely undersampling, and even not including fossils that represent samples of lineages that also had sampled descendants.

View Article and Find Full Text PDF

Estimates of diversification rates at the tips of a phylogeny provide a flexible approach for correlation analyses with multiple traits and to map diversification rates in space while also avoiding the uncertainty of deep time rate reconstructions. Available methods for tip rate estimation make different assumptions, and thus their accuracy usually depends on the characteristics of the underlying model generating the tree. Here, we introduce MiSSE, a trait-free, state-dependent speciation and extinction approach that can be used to estimate varying speciation, extinction, net diversification, turnover, and extinction fractions at the tips of the tree.

View Article and Find Full Text PDF

In 1974, G. Ledyard Stebbins provided a metaphor illustrating how spatial gradients of biodiversity observed today are by-products of the way environment-population interactions drive species diversification through time. We revisit the narrative behind Stebbins's "cradles" and "museums" of biodiversity to debate two points.

View Article and Find Full Text PDF

Ultraconserved elements (UCEs) are stretches of hundreds of nucleotides with highly conserved cores flanked by variable regions. Although the selective forces responsible for the preservation of UCEs are unknown, they are nonetheless believed to contain phylogenetically meaningful information from deep to shallow divergence events. Phylogenetic applications of UCEs assume the same degree of rate heterogeneity applies across the entire locus, including variable flanking regions.

View Article and Find Full Text PDF

The tropics are the source of most biodiversity yet inadequate sampling obscures answers to fundamental questions about how this diversity evolves. We leveraged samples assembled over decades of fieldwork to study diversification of the largest tropical bird radiation, the suboscine passerines. Our phylogeny, estimated using data from 2389 genomic regions in 1940 individuals of 1283 species, reveals that peak suboscine species diversity in the Neotropics is not associated with high recent speciation rates but rather with the gradual accumulation of species over time.

View Article and Find Full Text PDF

Speciation rates vary considerably among lineages, and our understanding of what drives the rapid succession of speciation events within young adaptive radiations remains incomplete. The cichlid fish family provides a notable example of such variation, with many slowly speciating lineages as well as several exceptionally large and rapid radiations. Here, by reconstructing a large phylogeny of all currently described cichlid species, we show that explosive speciation is solely concentrated in species flocks of several large young lakes.

View Article and Find Full Text PDF

Background: For decades, codon usage has been used as a measure of adaptation for translational efficiency and translation accuracy of a gene's coding sequence. These patterns of codon usage reflect both the selective and mutational environment in which the coding sequences evolved. Over this same period, gene transfer between lineages has become widely recognized as an important biological phenomenon.

View Article and Find Full Text PDF

Leaf reflectance spectra have been increasingly used to assess plant diversity. However, we do not yet understand how spectra vary across the tree of life or how the evolution of leaf traits affects the differentiation of spectra among species and lineages. Here we describe a framework that integrates spectra with phylogenies and apply it to a global dataset of over 16 000 leaf-level spectra (400-2400 nm) for 544 seed plant species.

View Article and Find Full Text PDF

Background: Researchers often measure changes in gene expression across conditions to better understand the shared functional roles and regulatory mechanisms of different genes. Analogous to this is comparing gene expression across species, which can improve our understanding of the evolutionary processes shaping the evolution of both individual genes and functional pathways. One area of interest is determining genes showing signals of coevolution, which can also indicate potential functional similarity, analogous to co-expression analysis often performed across conditions for a single species.

View Article and Find Full Text PDF

A comprehensive phylogeny of species, i.e., a tree of life, has potential uses in a variety of contexts, including research, education, and public policy.

View Article and Find Full Text PDF

Nervous systems are comprised of diverse cell types that differ functionally and morphologically. During development, extrinsic signals, e.g.

View Article and Find Full Text PDF

Phylogenetic comparative analyses use trees of evolutionary relationships between species to understand their evolution and ecology. A phylogenetic tree of taxa can be algebraically transformed into an by squared symmetric phylogenetic covariance matrix where each element in represents the affinity between extant species and extant species . This matrix is used internally in several comparative methods: for example, it is often inverted to compute the likelihood of the data under a model.

View Article and Find Full Text PDF

We present a new phylogenetic approach, selection on amino acids and codons (SelAC), whose substitution rates are based on a nested model linking protein expression to population genetics. Unlike simpler codon models that assume a single substitution matrix for all sites, our model more realistically represents the evolution of protein-coding DNA under the assumption of consistent, stabilizing selection using a cost-benefit approach. This cost-benefit approach allows us to generate a set of 20 optimal amino acid-specific matrix families using just a handful of parameters and naturally links the strength of stabilizing selection to protein synthesis levels, which we can estimate.

View Article and Find Full Text PDF

Trophic ecology is thought to exert a profound influence on biodiversity, but the specifics of the process are rarely examined at large spatial and evolutionary scales. We investigate how trophic position and diet breadth influence functional trait evolution in one of the most species-rich and complex vertebrate assemblages, coral reef fishes, within a large-scale phylogenetic framework. We show that, in contrast with established theory, functional traits evolve fastest in trophic specialists with narrow diet breadths at both very low and high trophic positions.

View Article and Find Full Text PDF

The state-dependent speciation and extinction (SSE) models have recently been criticized due to their high rates of "false positive" results. Many researchers have advocated avoiding SSE models in favor of other "nonparametric" or "semiparametric" approaches. The hidden Markov modeling (HMM) approach provides a partial solution to the issues of model adequacy detected with SSE models.

View Article and Find Full Text PDF

Background: DNA sequences are pivotal for a wide array of research in biology. Large sequence databases, like GenBank, provide an amazing resource to utilize DNA sequences for large scale analyses. However, many sequence records on GenBank contain more than one gene or are portions of genomes.

View Article and Find Full Text PDF