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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. We show that plotting a noisy numerator divided by time versus time leads to the observed hyperbolic pattern; in fact, randomizing the amount of change over time generates patterns functionally identical to observed patterns. Ignoring errors can not only obscure true patterns but create novel patterns that have long misled scientists. Author summary: For decades, evolutionary biologists have observed that rates of evolution seem to accelerate over short time periods, a pattern seen across diverse data sources, from genomes to the fossil record. This observation has sparked debates about its implications for understanding the link between microevolution and macroevolution. Our research challenges this widely accepted notion, revealing that these apparent patterns are actually statistical artifacts resulting from time-independent "noise". By employing a novel statistical approach, we found that this time-independent noise, often overlooked as inconsequential, create a misleading hyperbolic pattern, making it seem like evolutionary rates increase over shorter time frames when, in fact, they do not. In other words, our findings suggest that smaller, younger clades appear to evolve faster not due to intrinsic properties but because of statistical noise. Ultimately, our study underscores the critical importance of accounting for inherent biases and errors in interpreting biodiversity patterns across both shallow and deep time scales. [ABSTRACT FROM AUTHOR] more...

It is standard statistical practice to provide measures of uncertainty around parameter estimates. Unfortunately, this very basic and necessary enterprise is often absent in macroevolutionary studies using maximum likelihood estimates (MLEs).dentist is an R package that allows an approximation of confidence intervals (CI) around parameter estimates without an analytic solution to likelihood equations. This package works by 'denting' the likelihood surface by sampling points a specified distance around the MLE following what is essentially a Metropolis‐Hastings walk.We describe the importance of estimating uncertainty around parameter estimates, as well as demonstrate the ability of dentist to accurately approximate CI.We introduce several plotting tools to visualize the results of a dentist analysis. dentist is freely available from https://github.com/bomeara/dentist, written in the R language, and can be used for any given likelihood function. [ABSTRACT FROM AUTHOR] more...

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. We then employ an improved framework with a coalescent simulation approach to test and confirm previous hybridization hypotheses and identify one new intergeneric hybridization event. Focusing on the North American distribution of Heuchereae, we introduce and implement a newly developed approach to reconstruct potential past distributions for ancestral lineages across all species in the clade and across a paleoclimatic record extending from the late Pliocene. Time calibration based on both nuclear and chloroplast trees recovers a mid- to late-Pleistocene date for most inferred hybridization events, a timeframe concomitant with repeated geographic range restriction into overlapping refugia. Our results indicate an important role for past episodes of climate change, and the contrasting responses of species with differing ecological strategies, in generating novel patterns of range contact among plant communities and therefore new opportunities for hybridization. The new ancestral niche method flexibly models the shape of niche while incorporating diverse sources of uncertainty and will be an important addition to the current comparative methods toolkit. [Ancestral niche reconstruction; hybridization; paleoclimate; pleistocene.] [ABSTRACT FROM AUTHOR] more...

Flowering plants (angiosperms) today grow in a vast range of environmental conditions, with this breadth probably related to their diverse morphology and physiology (7). However, early angiosperms are generally thought [...], Early flowering plants are thought to have been woody species restricted to warm habitats (1-3). This lineage has since radiated into almost every climate, with manifold growth forms (4). As angiosperms spread and climate changed, they evolved mechanisms to cope with episodic freezing. To explore the evolution of traits underpinning the ability to persist in freezing conditions, we assembled a large species-level database of growth habit (woody or herbaceous; 49,064 species), as well as leaf phenology (evergreen or deciduous), diameter of hydraulic conduits (that is, xylem vessels and tracheids) and climate occupancies (exposure to freezing). To model the evolution of species' traits and climate occupancies, we combined these data with an unparalleled dated molecular phylogeny (32,223 species) for land plants. Here we show that woody clades successfully moved into freezing-prone environments by either possessing transport networks of small safe conduits (5) and/or shutting down hydraulic function by dropping leaves during freezing. Herbaceous species largely avoided freezing periods by senescing cheaply constructed aboveground tissue. Growth habit has long been considered labile (6), but we find that growth habit was less labile than climate occupancy. Additionally, freezing environments were largely filled by lineages that had already become herbs or, when remaining woody, already had small conduits (that is, the trait evolved before the climate occupancy). By contrast, most deciduous woody lineages had an evolutionary shift to seasonally shedding their leaves only after exposure to freezing (that is, the climate occupancy evolved before the trait). For angiosperms to inhabit novel cold environments they had to gain new structural and functional trait solutions; our results suggest that many of these solutions were probably acquired before their foray into the cold. more...

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. Here, we develop such a framework to explicitly estimate the joint likelihood for discrete and continuous characters. Specifically, our model combines the probability of observing the continuous character under a generalized OU process with the probability of the discrete character under a hidden Markov model, linked by a shared underlying regime. We use simulation studies to demonstrate that this approach, hOUwie , can accurately evaluate parameter values across a broad set of models. We then apply our model to test whether fleshy and dry fruits of Ericaceae lineages are correlated with their climatic niche evolution as represented by the aridity index. Consistent with expectations, we find that the climatic niche of lineages with fleshy fruits is more conserved while lineages with dry fruits have higher rates of climatic niche evolution and a more humid climatic optimum. [ABSTRACT FROM AUTHOR] more...

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. We then explore the benefits of including fossils, generally, by implementing and then testing two types of FBD models, including one that converts a fossil set into stratigraphic ranges, in more complex likelihood-based models that assume multiple rate classes across the tree. Under various simulation scenarios, including a scenario that exists far outside the set of models we evaluated, including fossils rarely outperform analyses that exclude them altogether. At best, the inclusion of fossils improves precision but does not influence bias. Similarly, we found that converting the fossil set to stratigraphic ranges, which is one way to remedy the effects of undercounting the number of k -type fossils, results in turnover rates and extinction fraction estimates that are generally underestimated. Although fossils remain essential for understanding diversification through time, in the specific case of understanding diversification given an existing, largely modern tree, they are not especially beneficial. [Fossilized birth–death; fossils; MiSSE; state speciation extinction; stratigraphic ranges; turnover rate.] [ABSTRACT FROM AUTHOR] more...

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. First, the usual high-speciation versus low-extinction and tropical versus temperate dichotomies are oversimplifications of the original metaphor and may obscure how gradients of diversity are formed. Second, the way in which we use modern gradients of biodiversity to interpret the potential historical processes that generated them are often still biased by the reasons that motivated Stebbins to propose his original metaphor. Specifically, the field has not yet abandoned the idea that species-rich areas and "basal lineages" indicate centers of origin, nor has it fully appreciated the role of traits as regulators of environment-population dynamics. We acknowledge that the terms "cradles" and "museums" are popular in the literature and that terminologies can evolve with the requirements of the field. However, we also argue that the concepts of cradles and museums have outlived their utility in studies of biogeography and macroevolution and should be replaced by discussions of actual processes at play. [ABSTRACT FROM AUTHOR] more...

Abstract Background A number of innovations underlie the origin of rapid reproductive cycles in angiosperms. A critical early step involved the modification of an ancestrally short and slow-growing pollen tube for faster and longer distance transport of sperm to egg. Associated with this shift are the predominantly callose (1,3-β-glucan) walls and septae (callose plugs) of angiosperm pollen tubes. Callose synthesis is mediated by callose synthase (CalS). Of 12 CalS gene family members in Arabidopsis, only one (CalS5) has been directly linked to pollen tube callose. CalS5 orthologues are present in several monocot and eudicot genomes, but little is known about the evolutionary origin of CalS5 or what its ancestral function may have been. Results We investigated expression of CalS in pollen and pollen tubes of selected non-flowering seed plants (gymnosperms) and angiosperms within lineages that diverged below the monocot/eudicot node. First, we determined the nearly full length coding sequence of a CalS5 orthologue from Cabomba caroliniana (CcCalS5) (Nymphaeales). Semi-quantitative RT-PCR demonstrated low CcCalS5 expression within several vegetative tissues, but strong expression in mature pollen. CalS transcripts were detected in pollen tubes of several species within Nymphaeales and Austrobaileyales, and comparative analyses with a phylogenetically diverse group of sequenced genomes indicated homology to CalS5. We also report in silico evidence of a putative CalS5 orthologue from Amborella. Among gymnosperms, CalS5 transcripts were recovered from germinating pollen of Gnetum and Ginkgo, but a novel CalS paralog was instead amplified from germinating pollen of Pinus taeda. Conclusion The finding that CalS5 is the predominant callose synthase in pollen tubes of both early-diverging and model system angiosperms is an indicator of the homology of their novel callosic pollen tube walls and callose plugs. The data suggest that CalS5 had transient expression and pollen-specific functions in early seed plants and was then recruited to novel expression patterns and functions within pollen tube walls in an ancestor of extant angiosperms. more...

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. We present a Wright–Fisher model of selection on nucleotides (SelON) which includes the effects of mutation, drift, and spatially varying, stabilizing selection for an optimal nucleotide sequence. The SelON model assumes the strength of stabilizing selection follows a position-dependent Gaussian function whose exact shape can vary between UCEs. We evaluate SelON by comparing its performance to a simpler and spatially invariant GTR+ Γ model using an empirical data set of 400 vertebrate UCEs used to determine the phylogenetic position of turtles. We observe much improvement in model fit of SelON over the GTR+ Γ model, and support for turtles as sister to lepidosaurs. Overall, the UCE-specific parameters SelON estimates provide a compact way of quantifying the strength and variation in selection within and across UCEs. SelON can also be extended to include more realistic mapping functions between sequence and stabilizing selection as well as allow for greater levels of rate heterogeneity. By more explicitly modeling the nature of selection on UCEs, SelON and similar approaches can be used to better understand the biological mechanisms responsible for their preservation across highly divergent taxa and long evolutionary time scales. [ABSTRACT FROM AUTHOR] more...

Phylogenetic comparative analyses use trees of evolutionary relationships between species to understand their evolution and ecology. A phylogenetic tree of n taxa can be algebraically transformed into an n by n squared symmetric phylogenetic covariance matrix C where each element c ij in C represents the affinity between extant species i and extant species j. This matrix C is used internally in several comparative methods: for example, it is often inverted to compute the likelihood of the data under a model. However, if the matrix is ill-conditioned (ie, if κ , defined by the ratio of the maximum eigenvalue of C to the minimum eigenvalue of C , is too high), this inversion may not be stable, and thus neither will be the calculation of the likelihood or parameter estimates that are based on optimizing the likelihood. We investigate this potential issue and propose several methods to attempt to remedy this issue. [ABSTRACT FROM AUTHOR] more...

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. Using a yeast data set of 100 orthologs for 6 taxa, we find SelAC fits the data much better than popular models by 104–105 Akike information criterion units adjusted for small sample bias. Our results also indicated that nested, mechanistic models better predict observed data patterns highlighting the improvement in biological realism in amino acid sequence evolution that our model provides. Additional parameters estimated by SelAC indicate that a large amount of nonphylogenetic, but biologically meaningful, information can be inferred from existing data. For example, SelAC prediction of gene-specific protein synthesis rates correlates well with both empirical (r =0.33–0.48) and other theoretical predictions (r =0.45–0.64) for multiple yeast species. SelAC also provides estimates of the optimal amino acid at each site. Finally, because SelAC is a nested approach based on clearly stated biological assumptions, future modifications, such as including shifts in the optimal amino acid sequence within or across lineages, are possible. [ABSTRACT FROM AUTHOR] more...

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. Inconsistencies in the way genes are annotated and the numerous synonyms a single gene may be listed under provide major challenges for extracting large numbers of subsequences for comparative analysis across taxa. At present, there is no easy way to extract portions from many GenBank accessions based on annotations where gene names may vary extensively. Results: The R package AnnotationBustR allows users to extract sequences based on GenBank annotations through the ACNUC retrieval system given search terms of gene synonyms and accession numbers. AnnotationBustR extracts subsequences of interest and then writes them to a FASTA file for users to employ in their research endeavors. Conclusion: FASTA files of extracted subsequences and accession tables generated by AnnotationBustR allow users to quickly find and extract subsequences from GenBank accessions. These sequences can then be incorporated in various analyses, like the construction of phylogenies to test a wide range of ecological and evolutionary hypotheses. [ABSTRACT FROM AUTHOR] more...

Author(s): Amy E. Zanne; David C. Tank; William K. Cornwell; Jonathan M. Eastman; Stephen A. Smith; Richard G. FitzJohn; Daniel J. McGlinn; Brian C. O'Meara; Angela T. Moles; Peter B. [...]

Species are commonly thought to be evolutionarily independent in a way that populations within a species are not. In recent years, studies that seek to identify evolutionarily independent lineages (i.e., to delimit species) using genetic data have typically adopted multispecies coalescent approaches that assume that evolutionary independence is formed by the differential sorting of ancestral alleles due to genetic drift. However, gene flow appears to be common among populations and nascent species, and while this process may inhibit lineage divergence (and thus independence), it is usually not explicitly considered when delimiting species. In this article, we apply Phylogeographic Inference using Approximate Likelihoods (PHRAPL), a recently described method for phylogeographic model selection, to species delimitation. We describe an approach to delimiting species using PHRAPL that attempts to account for both genetic drift and gene flow, and we compare the method's performance to that of a popular delimitation approach (BPP) using both simulated and empirical datasets. PHRAPL generally infers the correct demographic-delimitation model when the generating model includes gene flow between taxa, given a sufficient amount of data. When the generating model includes only isolation in the recent past, PHRAPL will in some cases fail to differentiate between gene flow and divergence, leading to model misspecification. Nevertheless, the explicit consideration of gene flow by PHRAPL is an important complement to existing delimitation approaches, particularly in systems where gene flow is likely important. [ABSTRACT FROM AUTHOR] more...

Trait consistency over time is one of the cornerstones of animal personality. Behavioral syndromes are the result of correlations between behaviors. While repeatability in behavior is not a requirement for behavioral syndromes, the two concepts studied together provide a more comprehensive understanding of how behavior can change over ontogeny. The roles of ontogenetic processes in the emergence of personality and behavioral syndromes have received much individual attention. However, the characterization of both individual trait consistency and behavioral syndromes across both sexes, as in our study, has been relatively rare. Ontogeny refers to changes that occur from conception to maturation, and juveniles might be expected to undergo different selection pressures than sexually mature individuals and also will experience profound changes in hormones, morphology, and environment during this period. In this study, we test for behavioral trait consistency and behavioral syndromes across six time points during ontogenetic development in the desert funnel-web spider ( Agelenopsis lisa). Our results indicate behavioral traits generally lack consistency (repeatability) within life stages and across ontogeny. However, penultimate males and mature females do exhibit noticeable mean-level changes, with greater aggressive responses toward prey, shorter latencies to explore their environment and in the exhibition of risk-averse responses to predatory cues. These traits also show high repeatability. Some trait correlations do exist as well. In particular, a strong correlation between aggressiveness toward prey and exploration factors is observed in mature males. However, because correlations among these factors are unstable across ontogeny and vary in strength over time, we conclude that behavioral syndromes do not exist in this species. Nevertheless, our results indicate that increased consistency, increasing average trait values, and varying correlations between traits may coincide with developmentally important changes associated with sexual maturation, albeit at different time points in males and females. This period of the life cycle merits systematic examination across taxa. [ABSTRACT FROM AUTHOR] more...

What factors in animal life history facilitate or reduce the probability that a species will perform play behavior? While some relationships are known within species and across individuals, it is not obvious that such relationships can be used to explain differences and similarities in amount and type of play across large taxonomic groupings of animals, let alone transitions among them. Primates encompass a relatively large assemblage of species that differ in numerous dietary, habitat, reproductive, and physiological processes. While all juvenile primates engage in social play, far fewer primate species engage in social play as adults. Here, derived from theory and more small-scale comparisons, we explore several biological and behavioral phenomena that differ among nonhuman primates and which may explain differences in the occurrence of adult–adult social play. We used phylogenetic logistic regression to assess the correlation of adult play with various life-history, metabolic and socioecological variables. Although the main contribution of our paper is demonstrating use of phylogenetic methods in the context of play evolution, suggestive but not significant evidence was found that adult sexual and nonsexual social play is influenced by diet, habitat, reproductive, and metabolic factors, sometimes in opposite directions, that we discuss along with needed future analyses involving improved data and interactions among traits. [ABSTRACT FROM AUTHOR] more...