Whatever one's definition of species, it is generally expected that individuals of the same species should be genetically more similar to each other than they are to individuals of another species. Here, we show that in the presence of cross-species gene flow, this expectation may be incorrect. We use the multispecies coalescent model with continuous-time migration or episodic introgression to study the impact of gene flow on genetic differences within and between species and highlight a surprising but plausible scenario in which different population sizes and asymmetrical migration rates cause a genetic sequence to be on average more closely related to a sequence from another species than to a sequence from the same species. Our results highlight the extraordinary impact that even a small amount of gene flow may have on the genetic history of the species. We suggest that contrasting long-term migration rate and short-term hybridization rate, both of which can be estimated using genetic data, may be a powerful approach to detecting the presence of reproductive barriers and to define species boundaries.[Gene flow; introgression; migration; multispecies coalescent; species concept; species delimitation.].

Researchers commonly present results of comparative studies of taxonomic groups. In this review, we criticize the focus on named clades, usually, comparably ranked groups such as families or orders, for comparative evolutionary analyses and question the general practice of using clades as units of analysis. The practice of analyzing sets of named groups persists despite widespread appreciation that the groups we have chosen to name are based on subjective human concerns rather than objective properties of nature. We demonstrate an effect of clade selection on results in one study and present some potential alternatives to selecting named clades for analysis that are relatively objective in clade choice. However, we note that these alternatives are only partial solutions for clade-based studies. The practice of analyzing named clades obviously is biased and problematic, but its issues portend broader problems with the general approach of employing clades as units of analysis. Most clade-based studies do not account for the nonindependence of clades, and the biological insight gained from demonstrating some pattern among a particular arbitrary sample of groups is arguable. [Clades; comparative biology; taxonomic groups.].

We describe a new and computationally efficient Bayesian methodology for inferring species trees and demographics from unlinked binary markers. Likelihood calculations are carried out using diffusion models of allele frequency dynamics combined with novel numerical algorithms. The diffusion approach allows for analysis of data sets containing hundreds or thousands of individuals. The method, which we call Snapper, has been implemented as part of the BEAST2 package. We conducted simulation experiments to assess numerical error, computational requirements, and accuracy recovering known model parameters. A reanalysis of soybean SNP data demonstrates that the models implemented in Snapp and Snapper can be difficult to distinguish in practice, a characteristic which we tested with further simulations. We demonstrate the scale of analysis possible using a SNP data set sampled from 399 fresh water turtles in 41 populations. [Bayesian inference; diffusion models; multi-species coalescent; SNP data; species trees; spectral methods.].

Mitochondrial genetic material (mtDNA) is widely used for phylogenetic reconstruction and as a barcode for species identification. The utility of mtDNA in these contexts derives from its particular molecular properties, including its high evolutionary rate, uniparental inheritance, and small size. But mtDNA may also play a fundamental role in speciation-as suggested by recent observations of coevolution with the nuclear DNA, along with the fact that respiration depends on coordination of genes from both sources. Here, we study how mito-nuclear interactions affect the accuracy of species identification by mtDNA, as well as the speciation process itself. We simulate the evolution of a population of individuals who carry a recombining nuclear genome and a mitochondrial genome inherited maternally. We compare a null model fitness landscape that lacks any mito-nuclear interaction against a scenario in which interactions influence fitness. Fitness is assigned to individuals according to their mito-nuclear compatibility, which drives the coevolution of the nuclear and mitochondrial genomes. Depending on the model parameters, the population breaks into distinct species and the model output then allows us to analyze the accuracy of mtDNA barcode for species identification. Remarkably, we find that species identification by mtDNA is equally accurate in the presence or absence of mito-nuclear coupling and that the success of the DNA barcode derives mainly from population geographical isolation during speciation. Nevertheless, selection imposed by mito-nuclear compatibility influences the diversification process and leaves signatures in the genetic content and spatial distribution of the populations, in three ways. First, speciation is delayed and the resulting phylogenetic trees are more balanced. Second, clades in the resulting phylogenetic tree correlate more strongly with the spatial distribution of species and clusters of more similar mtDNA's. Third, there is a substantial increase in the intraspecies mtDNA similarity, decreasing the number of alleles substitutions per locus and promoting the conservation of genetic information. We compare the evolutionary patterns observed in our model to empirical data from copepods (Tigriopus californicus). We find good qualitative agreement in the geographic patterns and the topology of the phylogenetic tree, provided the model includes selection based on mito-nuclear interactions. These results highlight the role of mito-nuclear compatibility in the speciation process and its reconstruction from genetic data.[Mito-nuclear coevolution; mtDNA barcode; parapatry; phylogeny.].

The spatial distribution of biomes has changed considerably over deep time, so the geographical opportunity for an evolutionary lineage to shift into a new biome may depend on how the availability and connectivity of biomes has varied temporally. To better understand how lineages shift between biomes in space and time, we developed a phylogenetic biome shift model in which each lineage shifts between biomes and disperses between regions at rates that depend on the lineage's biome affinity and location relative to the spatial distribution of biomes at any given time. To study the behavior of the biome shift model in an empirical setting, we developed a literature-based representation of paleobiome structure for three mesic forest biomes, six regions, and eight time strata, ranging from the Late Cretaceous (100 Ma) through the present. We then fitted the model to a time-calibrated phylogeny of 119 Viburnum species to compare how the results responded to various realistic or unrealistic assumptions about paleobiome structure. Ancestral biome estimates that account for paleobiome dynamics reconstructed a warm temperate (or tropical) origin of Viburnum, which is consistent with previous fossil-based estimates of ancestral biomes. Imposing unrealistic paleobiome distributions led to ancestral biome estimates that eliminated support for tropical origins, and instead inflated support for cold temperate ancestry throughout the warmer Paleocene and Eocene. The biome shift model we describe is applicable to the study of evolutionary systems beyond Viburnum, and the core mechanisms of our model are extensible to the design of richer phylogenetic models of historical biogeography and/or lineage diversification. We conclude that biome shift models that account for dynamic geographical opportunities are important for inferring ancestral biomes that are compatible with our understanding of Earth history.[Ancestral states; biome shifts; historical biogeography; niche conservatism; phylogenetics].

The common ancestor of spiders likely used silk to line burrows or make simple webs, with specialized spinning organs and aerial webs originating with the evolution of the megadiverse "true spiders" (Araneomorphae). The base of the araneomorph tree also concentrates the greatest number of changes in respiratory structures, a character system whose evolution is still poorly understood, and that might be related to the evolution of silk glands. Emphasizing a dense sampling of multiple araneomorph lineages where tracheal systems likely originated, we gathered genomic-scale data and reconstructed a phylogeny of true spiders. This robust phylogenomic framework was used to conduct maximum likelihood and Bayesian character evolution analyses for respiratory systems, silk glands, and aerial webs, based on a combination of original and published data. Our results indicate that in true spiders, posterior book lungs were transformed into morphologically similar tracheal systems six times independently, after the evolution of novel silk gland systems and the origin of aerial webs. From these comparative data, we put forth a novel hypothesis that early-diverging web-building spiders were faced with new energetic demands for spinning, which prompted the evolution of similar tracheal systems via convergence; we also propose tests of predictions derived from this hypothesis.[Book lungs; discrete character evolution; respiratory systems; silk; spider web evolution; ultraconserved elements.].

Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrichment protocol targeting hundreds of conserved exons which are effective across the class. After obtaining data from 220 loci for 286 species (representing 94% of the families and 44% of the genera), we estimate a phylogeny for extant amphibians and identify gene tree-species tree conflict across the deepest branches of the amphibian phylogeny. We perform locus-by-locus genealogical interrogation of alternative topological hypotheses for amphibian monophyly, focusing on interordinal relationships. We find that phylogenetic signal deep in the amphibian phylogeny varies greatly across loci in a manner that is consistent with incomplete lineage sorting in the ancestral lineage of extant amphibians. Our results overwhelmingly support amphibian monophyly and a sister relationship between frogs and salamanders, consistent with the Batrachia hypothesis. Species tree analyses converge on a small set of topological hypotheses for the relationships among extant amphibian families. These results clarify several contentious portions of the amphibian Tree of Life, which in conjunction with a set of vetted fossil calibrations, support a surprisingly younger timescale for crown and ordinal amphibian diversification than previously reported. More broadly, our study provides insight into the sources, magnitudes, and heterogeneity of support across loci in phylogenomic data sets.[AIC; Amphibia; Batrachia; Phylogeny; gene tree-species tree discordance; genomics; information theory.].

Numerous methods for inferring species-level phylogenies under the coalescent model have been proposed within the last 20 years, and debates continue about the relative strengths and weaknesses of these methods. One desirable property of a phylogenetic estimator is that of statistical consistency, which means intuitively that as more data are collected, the probability that the estimated tree has the same topology as the true tree goes to 1. To date, consistency results for species tree inference under the multispecies coalescent (MSC) have been derived only for summary statistics methods, such as ASTRAL and MP-EST. These methods have been found to be consistent given true gene trees but may be inconsistent when gene trees are estimated from data for loci of finite length. Here, we consider the question of statistical consistency for four taxa for SVDQuartets for general data types, as well as for the maximum likelihood (ML) method in the case in which the data are a collection of sites generated under the MSC model such that the sites are conditionally independent given the species tree (we call these data coalescent independent sites [CIS] data). We show that SVDQuartets is statistically consistent for all data types (i.e., for both CIS data and for multilocus data), and we derive its rate of convergence. We additionally show that ML is consistent for CIS data under the JC69 model and discuss why a proof for the more general multilocus case is difficult. Finally, we compare the performance of ML and SDVQuartets using simulation for both data types. [Consistency; gene tree; maximum likelihood; multilocus data; hylogenetic inference; species tree; SVDQuartets.].

Markov models of character substitution on phylogenies form the foundation of phylogenetic inference frameworks. Early models made the simplifying assumption that the substitution process is homogeneous over time and across sites in the molecular sequence alignment. While standard practice adopts extensions that accommodate heterogeneity of substitution rates across sites, heterogeneity in the process over time in a site-specific manner remains frequently overlooked. This is problematic, as evolutionary processes that act at the molecular level are highly variable, subjecting different sites to different selective constraints over time, impacting their substitution behavior. We propose incorporating time variability through Markov-modulated models (MMMs), which extend covarion-like models and allow the substitution process (including relative character exchange rates as well as the overall substitution rate) at individual sites to vary across lineages. We implement a general MMM framework in BEAST, a popular Bayesian phylogenetic inference software package, allowing researchers to compose a wide range of MMMs through flexible XML specification. Using examples from bacterial, viral, and plastid genome evolution, we show that MMMs impact phylogenetic tree estimation and can substantially improve model fit compared to standard substitution models. Through simulations, we show that marginal likelihood estimation accurately identifies the generative model and does not systematically prefer the more parameter-rich MMMs. To mitigate the increased computational demands associated with MMMs, our implementation exploits recent developments in BEAGLE, a high-performance computational library for phylogenetic inference. [Bayesian inference; BEAGLE; BEAST; covarion, heterotachy; Markov-modulated models; phylogenetics.].

Organismal interactions drive the accumulation of diversity by influencing species ranges, morphology, and behavior. Interactions vary from agonistic to cooperative and should result in predictable patterns in trait and range evolution. However, despite a conceptual understanding of these processes, they have been difficult to model, particularly on macroevolutionary timescales and across broad geographic spaces. Here, we investigate the influence of biotic interactions on trait evolution and community assembly in monitor lizards (Varanus). Monitors are an iconic radiation with a cosmopolitan distribution and the greatest size disparity of any living terrestrial vertebrate genus. Between the colossal Komodo dragon Varanus komodoensis and the smallest Australian dwarf goannas, Varanus length and mass vary by multiple orders of magnitude. To test the hypothesis that size variation in this genus was driven by character displacement, we extended existing phylogenetic comparative methods which consider lineage interactions to account for dynamic biogeographic history and apply these methods to Australian monitors and marsupial predators. Incorporating both exon-capture molecular and morphological data sets we use a combined evidence approach to estimate the relationships among living and extinct varaniform lizards. Our results suggest that communities of Australian Varanus show high functional diversity as a result of continent-wide interspecific competition among monitors but not with faunivorous marsupials. We demonstrate that patterns of trait evolution resulting from character displacement on continental scales are recoverable from comparative data and highlight that these macroevolutionary patterns may develop in parallel across widely distributed sympatric groups.[Character displacement; comparative methods; phylogenetics; trait evolution; Varanus.].

Coca is the natural source of cocaine as well as a sacred and medicinal plant farmed by South American Amerindians and mestizos. The coca crop comprises four closely related varieties classified into two species (Amazonian and Huánuco varieties within Erythroxylum coca Lam., and Colombian and Trujillo varieties within Erythroxylum novogranatense (D. Morris) Hieron.) but our understanding of the domestication and evolutionary history of these taxa is nominal. In this study, we use genomic data from natural history collections to estimate the geographic origins and genetic diversity of this economically and culturally important crop in the context of its wild relatives. Our phylogeographic analyses clearly demonstrate the four varieties of coca comprise two or three exclusive groups nested within the diverse lineages of the widespread, wild species Erythroxylum gracilipes; establishing a new and robust hypothesis of domestication wherein coca originated two or three times from this wild progenitor. The Colombian and Trujillo coca varieties are descended from a single, ancient domestication event in northwestern South America. Huánuco coca was domesticated more recently, possibly in southeastern Peru. Amazonian coca either shares a common domesticated ancestor with Huánuco coca, or it was the product of a third and most recent independent domestication event in the western Amazon basin. This chronology of coca domestication reveals different Holocene peoples in South America were able to independently transform the same natural resource to serve their needs; in this case, a workaday stimulant. [Erythroxylum; Erythroxylaceae; Holocene; Museomics; Neotropics; phylogeography; plant domestication; target-sequence capture.].

In a recent paper, Poe et al. assert that scientists should abandon clade-based approaches, particularly those using named taxonomic ranks. Poe et al. attempt to demonstrate that clade selection can have effects on the results of evolutionary analyses but unfortunately fall short of making any robust conclusions. Here, we demonstrate that the assertions made by Poe et al. have two important flaws: (i) an erroneous view of modern phylogenetic comparative methods; and (ii) a lack of statistical rigor in their analyses. We repeat Poe et al.'s analysis but using appropriate phylogenetic comparative approaches. We demonstrate that results remain consistent regardless of the clade definition. We go on to discuss the value of taxonomic groupings and how they can provide meaningful units of comparison in evolutionary study. Unlike the disheartening suggestion to abandon the use of clades, scientists can instead continue to use phylogenetic " corrections" that are already the standard for most comparative evolutionary analyses. [Comparative methods; evolution; phylogeny; taxonomy.].

How can we best learn the history of a protein's evolution? Ideally, a model of sequence evolution should capture both the process that generates genetic variation and the functional constraints determining which changes are fixed. However, in practical terms the most suitable approach may simply be the one that combines the convenience of easily available input data with the ability to return useful parameter estimates. For example, we might be interested in a measure of the strength of selection (typically obtained using a codon model) or an ancestral structure (obtained using structural modeling based on inferred amino acid sequence and side chain configuration). But what if data in the relevant state-space are not readily available? We show that it is possible to obtain accurate estimates of the outputs of interest using an established method for handling missing data. Encoding observed characters in an alignment as ambiguous representations of characters in a larger state-space allows the application of models with the desired features to data that lack the resolution that is normally required. This strategy is viable because the evolutionary path taken through the observed space contains information about states that were likely visited in the "unseen" state-space. To illustrate this, we consider two examples with amino acid sequences as input. We show that $$\omega$$, a parameter describing the relative strength of selection on nonsynonymous and synonymous changes, can be estimated in an unbiased manner using an adapted version of a standard 61-state codon model. Using simulated and empirical data, we find that ancestral amino acid side chain configuration can be inferred by applying a 55-state empirical model to 20-state amino acid data. Where feasible, combining inputs from both ambiguity-coded and fully resolved data improves accuracy. Adding structural information to as few as 12.5% of the sequences in an amino acid alignment results in remarkable ancestral reconstruction performance compared to a benchmark that considers the full rotamer state information. These examples show that our methods permit the recovery of evolutionary information from sequences where it has previously been inaccessible. [Ancestral reconstruction; natural selection; protein structure; state-spaces; substitution models.].

Phylogeny, molecular sequences, fossils, biogeography, and biome occupancy are all lines of evidence that reflect the singular evolutionary history of a clade, but they are most often studied separately, by first inferring a fossil-dated molecular phylogeny, then mapping on ancestral ranges and biomes inferred from extant species. Here we jointly model the evolution of biogeographic ranges, biome affinities, and molecular sequences, while incorporating fossils to estimate a dated phylogeny for all of the 163 extant species of the woody plant clade Viburnum (Adoxaceae) that we currently recognize in our ongoing worldwide monographic treatment of the group. Our analyses indicate that while the major Viburnum lineages evolved in the Eocene, the majority of extant species originated since the Miocene. Viburnum radiated first in Asia, in warm, broad-leaved evergreen (lucidophyllous) forests. Within Asia, we infer several early shifts into more tropical forests, and multiple shifts into forests that experience prolonged freezing. From Asia, we infer two early movements into the New World. These two lineages probably first occupied warm temperate forests and adapted later to spreading cold climates. One of these lineages (Porphyrotinus) occupied cloud forests and moved south through the mountains of the Neotropics. Several other movements into North America took place more recently, facilitated by prior adaptations to freezing in the Old World. We also infer four disjunctions between Asia and Europe: the Tinus lineage is the oldest and probably occupied warm forests when it spread, whereas the other three were more recent and in cold-adapted lineages. These results variously contradict published accounts, especially the view that Viburnum radiated initially in cold forests and, accordingly, maintained vessel elements with scalariform perforations. We explored how the location and biome assignments of fossils affected our inference of ancestral areas and biome states. Our results are sensitive to, but not entirely dependent upon, the inclusion of fossil biome data. It will be critical to take advantage of all available lines of evidence to decipher events in the distant past. The joint estimation approach developed here provides cautious hope even when fossil evidence is limited. [Biogeography; biome; combined evidence; fossil pollen; phylogeny; Viburnum.].

Phylogenomic data from a rapidly increasing number of studies provide new evidence for resolving relationships in recently radiated clades, but they also pose new challenges for inferring evolutionary histories. Most existing methods for reconstructing phylogenetic hypotheses rely solely on algorithms that only consider incomplete lineage sorting (ILS) as a cause of intra- or intergenomic discordance. Here, we utilize a variety of methods, including those to infer phylogenetic networks, to account for both ILS and introgression as a cause for nuclear and cytoplasmic-nuclear discordance using phylogenomic data from the recently radiated flowering plant genus Polemonium (Polemoniaceae), an ecologically diverse genus in Western North America with known and suspected gene flow between species. We find evidence for widespread discordance among nuclear loci that can be explained by both ILS and reticulate evolution in the evolutionary history of Polemonium. Furthermore, the histories of organellar genomes show strong discordance with the inferred species tree from the nuclear genome. Discordance between the nuclear and plastid genome is not completely explained by ILS, and only one case of discordance is explained by detected introgression events. Our results suggest that multiple processes have been involved in the evolutionary history of Polemonium and that the plastid genome does not accurately reflect species relationships. We discuss several potential causes for this cytoplasmic-nuclear discordance, which emerging evidence suggests is more widespread across the Tree of Life than previously thought. [Cyto-nuclear discordance, genomic discordance, phylogenetic networks, plastid capture, Polemoniaceae, Polemonium, reticulations.].