Matthew W. Pennell's research while affiliated with University of British Columbia - Vancouver and other places

Publications (85)

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Across vertebrates, live-bearing has evolved at least 150 times from the ancestral state of egg-laying into a diverse array of forms and degrees of prepartum maternal investment. A key question is how this diversity of reproductive modes arose and whether reproductive diversification underlies species diversification? To test these questions, we ev...
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Evolutionary rates play a central role in connecting micro- and macroevolution. All evolutionary rate estimates, including rates of molecular evolution, trait evolution, and lineage diversification, share a similar scaling pattern with time: The highest rates are those measured over the shortest time interval. This creates a disconnect between micr...
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Birth-death stochastic processes are the foundation of many phylogenetic models and are widely used to make inferences about epidemiological and macroevolutionary dynamics. There are a large number of birth-death model variants that have been developed; these impose different assumptions about the temporal dynamics of the parameters and about the s...
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While the fundamental biophysics of C 3 photosynthesis is highly conserved across plants, substantial leaf structural and enzymatic variation translates into variability in rates of carbon assimilation. Although this variation is well documented, it remains poorly understood how photosynthetic rates evolve, and whether macroevolutionary changes are...
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Viral phylogenies provide crucial information on the spread of infectious diseases, and many studies fit mathematical models to phylogenetic data to estimate epidemiological parameters such as the effective reproduction ratio (Re) over time. Such phylodynamic inferences often complement or even substitute for conventional surveillance data, particu...
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Premise: Long-term observations show that flowering phenology has shifted in many lineages in response to climate change. However, it remains unclear whether these results can be generalized to predict the presence, direction, or magnitude of responses in lineages for which we lack long time-series data. If phenological responses are phylogenetica...
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Emerging large-scale datasets coupled with statistical advances have provided new insights into the processes that generate the latitudinal diversity gradient (LDG). But many of these studies run into an old, if often underappreciated, problem: The interpretation of the data critically depends on the consistent application of criteria to define wha...
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Time-calibrated phylogenies of extant species (“extant timetrees”) are widely used to estimate historical speciation and extinction rates by fitting stochastic birth-death models.¹ These approaches have long been controversial, as many phylogenetic studies report zero extinction in many taxa, contradicting the high extinction rates seen in the foss...
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Phylogenetic comparative methods are often used to test functional relationships between traits. However, million‐year macroevolutionary observational datasets cannot definitively prove causal links between traits — correlation does not equal causation and experimental manipulation over such timescales is impossible. While this caveat is widely und...
Preprint
Full-text available
Viral phylogenies provide crucial information on the spread of infectious diseases, and many studies fit mathematical models to phylogenetic data to estimate epidemiological parameters such as the effective reproduction ratio (Re) over time. Such phylodynamic inferences often complement or even substitute for conventional surveillance data, particu...
Preprint
Full-text available
Time-calibrated phylogenies comprising only extant lineages are widely used to estimate historical speciation and extinction rates. Such extinction rate estimates have long been controversial as many phylogenetic studies report zero extinction in many taxa, a finding in conflict with the fossil record. To date, the causes of this widely observed di...
Preprint
Full-text available
Birth-death stochastic processes are the foundation of many phylogenetic models and are widely used to make inferences about epidemiological and macroevolutionary dynamics. There are a large number of birth-death model variants that have been developed; these impose different assumptions about the temporal dynamics of the parameters and about the s...
Article
Full-text available
It is widely recognized that different regions of a genome often have different evolutionary histories and that ignoring this variation when estimating phylogenies can be misleading. However, the extent to which this is also true for morphological data is still largely unknown. Discordance among morphological traits might plausibly arise due to eit...
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Time-calibrated phylogenies of extant species (referred to here as ‘extant timetrees’) are widely used for estimating diversification dynamics¹. However, there has been considerable debate surrounding the reliability of these inferences2–5 and, to date, this critical question remains unresolved. Here we clarify the precise information that can be e...
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Despite substantial progress in understanding the genetic basis for differences in morphology, physiology, and behavior, many phenotypes of interest are difficult to study with traditional genetic approaches because their origin traces to deep nodes in the tree of life. Moreover, many species are not amenable to either large-scale sampling or labor...
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Biostatistics courses are integral to many undergraduate biology programs. Such courses have often been taught using point-and-click software, but these programs are now seldom used by researchers or professional biologists. Instead, biology professionals typically use programming languages, such as R, which are better suited to analyzing complex d...
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Figs and their pollinating fig wasps are a classic example of long‐term obligate associations between different species. Satler et al. (2019) use a process‐based model adopted from molecular evolution to identify the major processes that affect cophylogenetic matching between figs and fig wasps. They find that host‐switching is one of the most impo...
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As the size of phylogenetic trees and comparative data continue to grow and more complex models are developed to investigate the processes that gave rise to them, macroevolutionary analyses are becoming increasingly limited by computational requirements. Here we introduce a novel algorithm, based on the "flow" of the differential equations that des...
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Full-text available
Time-calibrated molecular phylogenies of extant species ("extant timetrees") are widely used for estimating the dynamics of speciation and extinction rates and reconstructing macroevolutionary events such as mass extinctions. However, there has been considerable debate surrounding the reliability of these inferences in the absence of fossil data, a...
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The persistence of ecological systems in changing environments requires energy, materials, and information. Although the importance of information to ecological function has been widely recognized, the fundamental principles of ecological science as commonly expressed do not reflect this central role of information processing. We articulate five fu...
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It is often claimed that conserving evolutionary history is more efficient than species‐based approaches for capturing the attributes of biodiversity that benefit people. This claim underpins academic analyses and recommendations about the distribution and prioritization of species and areas for conservation, but evolutionary history is rarely cons...
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Alternative prioritization strategies have been proposed to safeguard biodiversity over macro-evolutionary timescales. The first prioritizes the most distantly related species (maximizing phylogenetic diversity) in the hopes of capturing at least some lineages that will successfully diversify into the future. The second prioritizes lineages that ar...
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The sharing and re-use of data has become a cornerstone of modern science. Multiple platforms now allow easy publication of datasets. So far, however, platforms for data sharing offer limited functions for distributing and interacting with evolving datasets— those that continue to grow with time as more records are added, errors fixed, and new data...
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Species interactions lie at the heart of many theories of macroevolution, from adaptive radiation to the Red Queen. Although some theories describe the imprint that interactions will have over long time scales, we are still missing a comprehensive understanding of the effects of interactions on macroevolution. Current research shows strong evidence...
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For centuries, biologists have been captivated by the vast disparity in species richness between different groups of organisms. Variation in diversity is widely attributed to differences between groups in how fast they speciate or go extinct. Such macroevolutionary rates have been estimated for thousands of groups and have been correlated with an i...
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Comparative methods allow researchers to make inferences about evolutionary processes and patterns from phylogenetic trees. In Bayesian phylogenetics, estimating a phylogeny requires specifying priors on parameters characterizing the branching process and rates of substitution among lineages, in addition to others. Accordingly, characterizing the e...
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The original version of this Article contained a plotting error in Fig. 3g. The Serranidae and Siganidae families were misplaced in the plotted phylogeny. This error has now been corrected in the PDF and HTML versions of the Article. For comparison, the original, incorrect version of Fig. 3g is presented below as Fig. 1. The authors thank P. Cowman...
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Numerous studies have estimated plant and animal diversification dynamics; however, no comparable rigorous estimates exist for bacteria-the most ancient and widespread form of life on Earth. Here, we analyse phylogenies comprising up to 448,112 bacterial lineages to reconstruct global bacterial diversification dynamics. To handle such large phyloge...
Preprint
Full-text available
For centuries, biologists have been captivated by the vast disparity in species richness between different groups of organisms. Variation in diversity is widely attributed to differences between groups in how fast they speciate or go extinct. Such macroevolutionary rates have been estimated for thousands of groups and have been correlated with an i...
Article
Full-text available
In the face of the biodiversity crisis, it is argued that we should prioritize species in order to capture high functional diversity (FD). Because species traits often reflect shared evolutionary history, many researchers have assumed that maximizing phylogenetic diversity (PD) should indirectly capture FD, a hypothesis that we name the "phylogenet...
Preprint
Full-text available
Comparative methods allow researchers to make inferences about evolutionary processes and patterns from phylogenetic trees. In Bayesian phylogenetics, estimating a phylogeny requires specifying priors on parameters characterizing the branching process and rates of substitution among lineages, in addition to others. However, the effect that the sele...
Preprint
Full-text available
In the face of the biodiversity crisis, it is argued that we should prioritize species in order to capture high functional diversity (FD). Because species traits often reflect shared evolutionary history, many researchers have advocated for a “phylogenetic gambit”: maximizing phylogenetic diversity (PD) should indirectly capture FD. For the first t...
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As a result of the process of descent with modification, closely related species tend to be similar to one another in a myriad different ways. In statistical terms, this means that traits measured on one species will not be independent of traits measured on others. Since their introduction in the 1980s, phylogenetic comparative methods (PCMs) have...
Preprint
Full-text available
As a result of the process of descent with modification, closely related species tend to be similar to one another in a myriad different ways. In statistical terms, this means that traits measured on one species will not be independent of traits measured on others. Since their introduction in the 1980s, phylogenetic comparative methods (PCMs) have...
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Full-text available
Despite the prevalence of sexual reproduction across eukaryotes, there is a remarkable diversity of sex determination mechanisms. The underlying causes of this diversity remain unclear, and it is unknown if there are convergent trends in the directionality of turnover in sex determination mechanisms. We used the recently assembled Tree of Sex datab...
Preprint
Full-text available
The sharing and re-use of data has become a cornerstone of modern science. Multiple platforms now allow quick and easy data sharing. So far, however, data publishing models have not accommodated on-going scientific improvements in data: for many problems, datasets continue to grow with time -- more records are added, errors fixed, and new data stru...
Preprint
Full-text available
The sharing and re-use of data has become a cornerstone of modern science. Multiple platforms now allow quick and easy data sharing. So far, however, data publishing models have not accommodated on-going scientific improvements in data: for many problems, datasets continue to grow with time -- more records are added, errors fixed, and new data stru...
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For decades, academic biologists have advocated for making conservation decisions in light of evolutionary history. Specifically, they suggest that policymakers should prioritize conserving phylogenetically diverse assemblages. The most prominent argument is that conserving phylogenetic diversity (PD) will also conserve diversity in traits and feat...
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Global patterns of biodiversity are influenced by spatial and environmental variations in the rate at which new species form. We relate variations in speciation rates to six key patterns of biodiversity worldwide, including the species-area relationship, latitudinal gradients in species and genetic diversity, and between-habitat differences in spec...
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Metabolism is the link between ecology and physiology—it dictates the flow of energy through individuals and across trophic levels. Much of the predictive power of metabolic theories of ecology derives from the scaling relationship between organismal size and metabolic rate. There is growing evidence that this scaling relationship is not universal,...
Preprint
Full-text available
For decades, academic biologists have advocated for making conservation decisions in light of evolutionary history. Specifically, they suggest that policymakers should prioritize conserving phylogenetically diverse assemblages. The most prominent argument is that conserving phylogenetic diversity (PD) will also conserve diversity in traits and feat...
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Species selection - variation in diversification rates associated with variation in species traits - was once a fringe idea, at least among population biologists. But following the development of a novel suite of phylogenetic comparative methods (e.g, BiSSE; Maddison et al. 2007), comparative biologists went looking for evidence of species selectio...
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Both body size and temperature directly influence consumer-resource dynamics. There is also widespread empirical evidence for the temperature-size rule (TSR), which creates a negative relationship between temperature and body size. However, it is not known how the TSR affects community dynamics. Here we integrate temperature- and size-dependent mod...
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Biologists are increasingly using curated, public data sets to conduct phylogenetic comparative analyses. Unfortunately, there is often a mismatch between species for which there is phylogenetic data and those for which other data are available. As a result, researchers are commonly forced to either drop species from analyses entirely or else imput...
Preprint
Full-text available
Biologists are increasingly using curated, public data sets to conduct phylogenetic comparative analyses. Unfortunately, there is often a mismatch between species for which there is phylogenetic data and those for which other data is available. As a result, researchers are commonly forced to either drop species from analyses entirely or else impute...
Article
Making meaningful inferences from phylogenetic comparative data requires a meaningful model of trait evolution. It is thus important to determine whether the model is appropriate for the data and the question being addressed. One way to assess this is to ask whether the model provides a good statistical explanation for the variation in the data. To...
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Full-text available
Our growing understanding of the plant tree of life provides a novel opportunity to uncover the major drivers of angiosperm diversity. Using a time-calibrated phylogeny, we characterized hot and cold spots of lineage diversification across the angiosperm tree of life by modeling evolutionary diversification using stepwise AIC (MEDUSA). We also test...
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Chromosomal fusion plays a recurring role in the evolution of adaptations and reproductive isolation among species, yet little is known of the evolutionary drivers of chromosomal fusions. Because sex chromosomes (X and Y in male heterogametic systems, Z and W in female heterogametic systems) differ in their selective, mutational, and demographic en...
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Most existing methods for modeling trait evolution are univariate, while researchers are often interested in investigating evolutionary patterns and processes across multiple traits. Principal components analysis (PCA) is commonly used to reduce the dimensionality of multivariate data as univariate trait models can be fit to the individual principa...
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Quantitative geneticists long ago recognized the value of studying evolution in a multivariate framework (Pearson, 1903). Due to linkage, pleiotropy, coordinated selection and mutational covariance, the evolutionary response in any phenotypic trait can only be properly understood in the context of other traits (Lande, 1979; Lynch and Walsh, 1998)....
Preprint
Full-text available
Making meaningful inferences from phylogenetic comparative data requires a meaningful model of trait evolution. It is thus important to determine whether the model is appropriate for the data and the question being addressed. One way to assess this is to ask whether the model provides a good statistical explanation for the variation in the data. To...
Article
Various monitoring methods have been developed for large carnivores, but not all are practical or sufficiently accurate for long-term monitoring over large spatial scales. From 2009 to 2010, we used a predictive habitat model to locate gray wolf rendezvous sites in 4 study areas in Idaho, USA and conducted noninvasive genetic sampling (NGS) of scat...
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The vast majority of eukaryotic organisms reproduce sexually, yet the nature of the sexual system and the mechanism of sex determination often vary remarkably, even among closely related species. Some species of animals and plants change sex across their lifespan, some contain hermaphrodites as well as males and females, some determine sex with hig...
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Phylogenetic comparative methods are essential for addressing evolutionary hypotheses with interspecific data. The scale and scope of such data has increased dramatically in the last few years. Many existing approaches are either computationally infeasible or inappropriate for data of this size. To address both of these problems, we present geiger...