Brian R Moore's research while affiliated with University of California, Davis and other places

Publications (23)

Preprint
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Phylodynamic methods are central to studies of the geographic and demographic history of disease outbreaks. Inference under discrete-geographic phylodynamic models---which involve many parameters that must be inferred from minimal information---is inherently sensitive to our prior beliefs about the model parameters. We present an interactive utilit...
Preprint
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Epidemiology has been transformed by the advent of Bayesian phylodynamic models that allow researchers to infer the geographic history of pathogen dispersal over a set of discrete geographic areas (1, 2). These models provide powerful tools for understanding the spatial dynamics of disease outbreaks, but contain many parameters that are inferred fr...
Article
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Phylodynamic methods reveal the spatial and temporal dynamics of viral geographic spread, and have featured prominently in studies of the COVID-19 pandemic. Virtually all such studies are based on phylodynamic models that assume-despite direct and compelling evidence to the contrary-that rates of viral geographic dispersal are constant through time...
Preprint
Full-text available
Phylodynamic methods reveal the spatial and temporal dynamics of viral geographic spread, and have featured prominently in studies of the COVID-19 pandemic. Virtually all previous studies are based on phylodynamic models that assume---despite direct and compelling evidence to the contrary---that rates of viral geographic dispersal are constant thro...
Preprint
We performed phylodynamic analyses of all available SARS-CoV-2 genomes from the early phase of the COVID-19 pandemic—combined with a novel dataset on contemporary global air-travel volume—to assess the efficacy of public-health measures on viral geographic spread. Globally, viral dispersal rates are significantly correlated with air-travel volume,...
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Significance How do the cells of an organism—each with an identical genome—give rise to tissues of incredible phenotypic diversity? Key to answering this question is the transcriptome: the set of genes expressed in a given tissue. We would clearly benefit from the ability to identify qualitative differences in expression (whether a gene is active o...
Article
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Understanding how and why rates of character evolution vary across the Tree of Life is central to many evolutionary questions; e.g., does the trophic apparatus (a set of continuous characters) evolve at a higher rate in fish lineages that dwell in reef versus non-reef habitats (a discrete character)? Existing approaches for inferring the relationsh...
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Transcriptomes are key to understanding the relationship between genotype and phenotype. The ability to infer the expression state (active or inactive) of genes in the transcriptome offers unique benefits for addressing this issue. For example, qualitative changes in gene expression may underly the origin of novel phenotypes, and expression states...
Preprint
Full-text available
Understanding how and why rates of character evolution vary across the Tree of Life is central to many evolutionary questions; e.g., does the trophic apparatus (a set of continuous characters) evolve at a higher rate in fish lineages that dwell in reef versus non-reef habitats (a discrete character)? Existing approaches for inferring the relationsh...
Preprint
Full-text available
Species richness varies considerably among the tree of life which can only be explained by heterogeneous rates of diversification (speciation and extinction). Previous approaches use phylogenetic trees to estimate branch-specific diversification rates. However, all previous approaches disregard diversification-rate shifts on extinct lineages althou...
Article
Maternally transmitted Wolbachia, Spiroplasma, and Cardinium bacteria are common in insects [1], but their interspecific spread is poorly understood. Endosymbionts can spread rapidly within host species by manipulating host reproduction, as typified by the global spread of wRi Wolbachia observed in Drosophila simulans [2, 3]. However, because Wolba...
Article
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Bayesian analysis of macroevolutionary mixtures (BAMM) has recently taken the study of lineage diversification by storm. BAMM estimates the diversification-rate parameters (speciation and extinction) for every branch of a study phylogeny and infers the number and location of diversification-rate shifts across branches of a tree. Our evaluation of B...
Article
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Programs for Bayesian inference of phylogeny currently implement a unique and fixed suite of models. Consequently, users of these software packages are simultaneously forced to use a number of programs for a given study, while also lacking the freedom to explore models that have not been implemented by the developers of those programs. We developed...
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Evolutionary biologists have long been fascinated by the extreme differences in species numbers across branches of the Tree of Life. This has motivated the development of statistical methods for detecting shifts in the rate of lineage diversification across the branches of phylogenic trees. One of the most frequently used methods, MEDUSA, explores...
Article
The paleontological record chronicles numerous episodes of mass extinction that severely culled the Tree of Life. Biologists have long sought to assess the extent to which these events may have impacted particular groups. We present a novel method for detecting the impact of mass-extinction events on molecular phylogenies, even in the presence of t...
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Many fundamental questions in evolutionary biology entail estimating rates of lineage diversification (speciation–extinction) that are modeled using birth–death branching processes. We leverage recent advances in branching-process theory to develop a flexible Bayesian framework for specifying diversification models—where rates are constant, vary co...
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Previous Bayesian phylogeographic studies of H5N1 highly pathogenic avian influenza viruses (HPAIVs) explored the origin and spread of the epidemic from China into Russia, indicating that HPAIV circulated in Russia prior to its detection there in 2005. In this study, we extend this research to explore the evolution and spread of HPAIV within Europe...
Preprint
Full-text available
Evolutionary biologists have long been fascinated by the extreme differences in species numbers across branches of the Tree of Life. This has motivated the development of statistical phylogenetic methods for detecting shifts in the rate of lineage diversification (speciation – extinction). One of the most frequently used methods—implemented in the...
Article
Full-text available
Variation in the evolutionary process across the sites of nucleotide sequence alignments is well established, and is an increasingly pervasive feature of datasets composed of gene regions sampled from multiple loci and/or different genomes. Inference of phylogeny from these data demands that we adequately model the underlying process heterogeneity;...
Article
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Recent progress in resolving the tree of life continues to expose relationships that resist resolution, which drives the search for novel sources of information to solve these difficult phylogenetic problems. A recent example, the presence and absence of microRNA families, has been vigorously promoted as an ideal source of phylogenetic data and has...
Article
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The scientific enterprise depends critically on the preservation of and open access to published data. This basic tenet applies acutely to phylogenies (estimates of evolutionary relationships among species). Increasingly, phylogenies are estimated from increasingly large, genome-scale datasets using increasingly complex statistical methods that req...
Article
The exceptional species diversity of flowering plants, exceeding that of their sister group more than 250-fold, is especially evident in floral innovations, interactions with pollinators and sexual systems. Multiple theories, emphasizing flower-pollinator interactions, genetic effects of mating systems or high evolvability, predict that floral evol...
Article
Full-text available
Historical biogeography is increasingly studied from an explicitly statistical perspective, using stochastic models to describe the evolution of species range as a continuous-time Markov process of dispersal between and extinction within a set of discrete geographic areas. The main constraint of these methods is the computational limit on the numbe...

Citations

... They identified increases in diversification rates in ancestors of the current plant groups and reported that these increases were preferentially clustered after paleopolyploidization. Nevertheless, the estimations of diversification rates were based on family richness, which has been shown to yield a very high rate of false positives [26]. Moreover, it does not model explicitly the changes in diversification rates as a function of time, but rather the global rate at which descendants of a particular internal node of the phylogenetic tree diversify. ...
... To determine whether a gene was likely to be transcribed based on the count data, we ran Zigzag [48] on our data. A full description of how this program was utilized, see Supplemental File 3. ...
... In that case, we would recommend considering an approach that allows the explicit incorporation of uncertainty, such as integrating over a set of character histories sampled in proportion to their probability under a model (Huelsenbeck, Nielsen & Bollback, 2003;e.g., Price, Friedman & Wainwright, 2015), as illustrated in the Appendix of this article for our rock-and non-rock-dwelling lizard empirical example. As shown in Revell (2013a), however, this common practice can also result in certain biases, such as causing estimated evolutionary rates to resemble each other more closely than the generating rates (Revell, 2013a; also see May & Moore, 2019). An interesting approach that was suggested by Caetano & Harmon (2019) involves first generating a posterior sample of discrete character histories using stochastic mapping, and then sampling from this set during Bayesian MCMC. ...
... We also conducted a lineage-specific birth-death-shift (LSBDS) analysis in RevBayes (94) with an MCMC chain of 10,000 steps; following the parameters employed in Höhna et al. (95). Rate variables were set to lognormal distributions for both mean speciation and extinction rates, the rate of rate-shift events was set to uniform, and six rate categories were set as a global parameter. ...
... In addition to the widely used SIT, some insect population control approaches utilize the Incompatible Insect Technique (IIT) that is based on the infection of the insect reproductive tissues with the Alphaproteobacteria Wolbachia pipientis. Wolbachia are maternally inherited endosymbiotic bacteria that can infect insects, isopods, spiders, and filarial nematodes [64][65][66][67]. The most pronounced Wolbachia effect on their hosts is the ability to manipulate host reproduction using several strategies, such as parthenogenesis [68,69], feminization [70,71], male killing [72][73][74][75], and cytoplasmic incompatibility (CI), to promote its transmission and increase its occurrence in the population [64,76,77]. ...
... Convergence between runs was assessed through visual inspection of the log-likelihoods and effective sampling of the target posterior distribution of parameter values was assessed through quantification of ESS values (ESS >200). We assessed the sensitivity of our diversification rate analysis to the prior in BAMM (Moore et al. 2016;Rabosky et al. 2017) with replicate analyses favoring 0, 1, and 2 rate shifts. ...
... Taxa that were not endemic to bare rock grew on decomposed substrates, which were defined as various weathered soils that fracture on contact and are composed of gravel, sand, silt, or clay. We estimated rates of transitions and inferred ancestral states for life history and edaphic specialization using Bayesian model testing with rjMCMC and stochastic character mapping in RevBayes (48). To test for associations between life history and endemism on rocky outcrops we used BayesTraits to compare the fit (log-likelihood) of two continuous-time Markov models of life history and edaphic evolution, a dependent and independent model (49). ...
... Apioideae are also an interesting target for investigation of diversification patterns associated with pseudanthia because the distribution of species within this group is highly uneven among the major clades-often formally recognized as tribes-with some small (e.g., Coriandreae) or monospecific (e.g., Erigenieae) and others (particularly, Selineae and Scandiceae) comprising a few hundred species each (Plunkett et al., 2018). This variation, coupled with a comprehensively sampled molecular phylogeny and multiple independent origins of pseudanthia allow to address the limitations of existing trait-dependent diversification models (Maddison and FitzJohn, 2015;Gamisch, 2016;Rabosky and Goldberg, 2015;May and Moore, 2016;Kodandaramaiah and Murali, 2018;Simpson et al., 2018). ...
... • Episodic BD models allow for instantaneous tree-wide shifts of speciation and extinction rates at specific time points (see the methods of Stadler, 2011, implemented in TreePar, and the CoMET method by May et al., 2016). Both these methods further model mass extinction events, and differ principally by the fact that CoMET models speciation rate shifts, extinction rate shifts, and mass extinction events as independent compound Poisson processes, while TreePar assigns no prior distribution on shifts. ...
... To evaluate the robustness of the diversification pattern inferred by BAMM, we also performed an analysis using CoMET within the TESS R package [114]. Before running CoMET, we specified the prior distribution of model parameters following Höhna et al. [115], and we used the same sampling probability and input tree as in the BAMM analysis. ...