Reducing the Biases in False Correlations Between Discrete Characters.

The correlation between two characters is often interpreted as evidence that there exists a significant and biologically important relationship between them. However, Maddison and FitzJohn (in The unsolved challenge to phylogenetic correlation tests for categorical characters. Syst. Biol. 2015;64:127-136) recently pointed out that evidence of correlated evolution between two categorical characters is often spurious, particularly, when the dependent relationship stems from a single replicate deep in time. Here we will show that there may, in fact, be a statistical solution to the problem posed by Maddison and FitzJohn naturally embedded within the expanded model space afforded by the hidden Markov model (HMM) framework. We demonstrate that the problem of single unreplicated evolutionary events manifests itself as rate heterogeneity within our models and that this is the source of the false correlation. Therefore, we argue that this problem is better understood as model misspecification rather than a failure of comparative methods to account for phylogenetic pseudoreplication. We utilize HMMs to develop a multirate independent model which, when implemented, drastically reduces support for correlation. The problem itself extends beyond categorical character evolution, but we believe that the practical solution presented here may lend itself to future extensions in other areas of comparative biology. [Macroevolution; model adequacy; phylogenetic comparative methods; rate heterogeneity].

Fossils Do Not Substantially Improve, and May Even Harm, Estimates of Diversification Rate Heterogeneity.

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.].

Investigating historical drivers of latitudinal gradients in polyploid plant biogeography: A multiclade perspective.

PREMISE: The proportion of polyploid plants in a community increases with latitude, and different hypotheses have been proposed about which factors drive this pattern. Here, we aimed to understand the historical causes of the latitudinal polyploidy gradient using a combination of ancestral state reconstruction methods. Specifically, we assessed whether (1) polyploidization enables movement to higher latitudes (i.e., polyploidization precedes occurrences in higher latitudes) or (2) higher latitudes facilitate polyploidization (i.e., occurrence in higher latitudes precedes polyploidization). METHODS: We reconstructed the ploidy states and ancestral niches of 1032 angiosperm species at four paleoclimatic time slices ranging from 3.3 million years ago to the present, comprising taxa from four well-represented clades: Onagraceae, Primulaceae, Solanum (Solanaceae), and Pooideae (Poaceae). We used ancestral niche reconstruction models alongside a customized discrete character evolution model to allow reconstruction of states at specific time slices. Patterns of latitudinal movement were reconstructed and compared in relation to inferred ploidy shifts. RESULTS: No single hypothesis applied equally well across all analyzed clades. While significant differences in median latitudinal occurrence were detected in the largest clade, Poaceae, no significant differences were detected in latitudinal movement in any clade. CONCLUSIONS: Our preliminary study is the first to attempt to connect ploidy changes to continuous latitudinal movement, but we cannot favor one hypothesis over another. Given that patterns seem to be clade-specific, more clades must be analyzed in future studies for generalities to be drawn.

The evolutionary responses of life-history strategies to climatic variability in flowering plants.

The evolution of annual or perennial strategies in flowering plants likely depends on a broad array of temperature and precipitation variables. Previous documented climate life-history correlations in explicit phylogenetic frameworks have been limited to certain clades and geographic regions. To gain insights which generalize to multiple lineages we employ a multi-clade approach analyzing 32 groups of angiosperms across eight climatic variables. We utilize a recently developed method that accounts for the joint evolution of continuous and discrete traits to evaluate two hypotheses: annuals tend to evolve in highly seasonal regions prone to extreme heat and drought; and annuals tend to have faster rates of climatic niche evolution than perennials. We find that temperature, particularly highest temperature of the warmest month, is the most consistent climatic factor influencing the evolution of annual strategy in flowering plants. Unexpectedly, we do not find significant differences in rates of climatic niche evolution between perennial and annual lineages. We propose that annuals are consistently favored in areas prone to extreme heat due to their ability to escape heat stress as seeds, but they tend to be outcompeted by perennials in regions where extreme heat is uncommon or nonexistent.

A Spatially Explicit Model of Stabilizing Selection for Improving Phylogenetic Inference.

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.

Retiring "Cradles" and "Museums" of Biodiversity.

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.

Population Genetics Based Phylogenetics Under Stabilizing Selection for an Optimal Amino Acid Sequence: A Nested Modeling Approach.

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.

Comparative Analyses of Phenotypic Sequences Using Phylogenetic Trees.

Phenotypic sequences are a type of multivariate trait organized structurally, such as teeth distributed along the dental arch, or temporally, such as the stages of an ontogenetic series. Unlike other multivariate traits, the elements of a phenotypic sequence are distributed along an ordered set, which allows for distinct evolutionary patterns between neighboring and distant positions. In fact, sequence traits share many characteristics with molecular sequences, although important distinctions pose challenges to current comparative methods. We implement an approach to estimate rates of trait evolution that explicitly incorporates the sequence organization of traits. We apply models to study the temporal pattern evolution of cricket calling songs. We test whether neighboring positions along a phenotypic sequence have correlated rates of evolution or whether rate variation is independent of sequence position. Our results show that cricket song evolution is strongly autocorrelated and that models perform well when used with sequence phenotypes even under small sample sizes. Our approach is flexible and can be applied to any multivariate trait with discrete units organized in a sequence-like structure.

Geophytism in monocots leads to higher rates of diversification.

Geophytes, plants with buds on underground structures, are found throughout the plant tree of life. These below ground structures allow plants to inhabit highly seasonal and disturbance-prone environments across ecosystems. Past researchers have hypothesised that the bulbous, cormous and tuberous habits promote diversification, but this had yet to be tested. Using a comprehensive monocot data set of almost 13 000 taxa, we investigated the effects of the geophytic habit on diversification using both state-dependent and state-independent models. We found that geophytes exhibit increased rates of diversification relative to nongeophytes. State-dependent analyses recovered higher yet similar rates of diversification for bulbous, cormous and tuberous taxa compared with rhizomatous and nongeophytic taxa. However, the state-independent model returned no difference in rates among the different traits. Geophytism shows higher rates of diversification relative to nongeophytes but we found little support for the hypothesis that the evolution of the bulb, corm or tuber appears to provide a diversification increase relative to rhizomatous and nongeophytic taxa. Our broad-scale analysis highlights the overall evolutionary importance of the geophytic habit (i.e. belowground bud placement). However, our results also suggest that belowground morphological diversity alone cannot explain this rate increase. In order to further test the evolutionary significance of these underground structures, future studies should consider these in combination with other biotic and abiotic factors.

Three keys to the radiation of angiosperms into freezing environments.

Early flowering plants are thought to have been woody species restricted to warm habitats. This lineage has since radiated into almost every climate, with manifold growth forms. 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 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, 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.

The monocotyledonous underground: global climatic and phylogenetic patterns of geophyte diversity.

PREMISE: Geophytes-plants that typically possess a bulb, corm, tuber, and/or rhizome-have long captured the attention of hobbyists and researchers. However, despite the economic and evolutionary importance of these traits, the potential drivers of their morphological diversity remain unknown. Using a comprehensive phylogeny of monocots, we test for correlations between climate and geophyte growth form to better understand why we observe such a diversity of underground traits in geophytes. Understanding the evolutionary factors promoting independent origins of these potentially adaptive organs will lend insights into how plants adapt to environmental hardships. METHODS: Using a comprehensive phylogeny incorporated with global occurrence and climate data for the monocots, we investigated whether climatic patterns could explain differences between geophytes and non-geophytes, as well as differences among bulbous, cormous, tuberous, rhizomatous, and non-geophytic taxa. We used phylogenetically-informed ANOVAs, MANOVAs, and PCAs to test differences in climatic variables between the different growth forms. RESULTS: Geophytes inhabit cooler, drier, and more thermally variable climates compared to non-geophytes. Although some underground traits (i.e., bulb, corm, and tuber) appear to inhabit particular niches, a result supported by strong phylogenetic signal, our data has limited evidence for an overall role of climate in the evolution of these traits. However, temperature may be a driving force in rhizome evolution, as well as the evolution of taxa which we considered here as non-geophytic (e.g., trees, epiphytes, etc.). CONCLUSIONS: While precipitation patterns have played a role in the evolution of geophytism, our results suggest that temperature should be more strongly considered as a contributing factor promoting the evolution of belowground bud placement, specifically in rhizomatous and non-geophytic taxa. Bulbous, cormous, and tuberous taxa need closer examination of other mechanisms, such as anatomical constraints or genetic controls, in order to begin to understand the causes behind the evolution of their underground morphology.

Accelerated diversification is related to life history and locomotion in a hyperdiverse lineage of microbial eukaryotes (Diatoms, Bacillariophyta).

Patterns of species richness are commonly linked to life history strategies. In diatoms, an exceptionally diverse lineage of photosynthetic heterokonts important for global photosynthesis and burial of atmospheric carbon, lineages with different locomotory and reproductive traits differ dramatically in species richness, but any potential association between life history strategy and diversification has not been tested in a phylogenetic framework. We constructed a time-calibrated, 11-gene, 1151-taxon phylogeny of diatoms - the most inclusive diatom species tree to date. We used this phylogeny, together with a comprehensive inventory of first-last occurrences of Cenozoic fossil diatoms, to estimate ranges of expected species richness, diversification and its variation through time and across lineages. Diversification rates varied with life history traits. Although anisogamous lineages diversified faster than oogamous ones, this increase was restricted to a nested clade with active motility in the vegetative cells. We propose that the evolution of motility in vegetative cells, following an earlier transition from oogamy to anisogamy, facilitated outcrossing and improved utilization of habitat complexity, ultimately leading to enhanced opportunity for adaptive divergence across a variety of novel habitats. Together, these contributed to a species radiation that gave rise to the majority of present-day diatom diversity.

Can we build it? Yes we can, but should we use it? Assessing the quality and value of a very large phylogeny of campanulid angiosperms.

PREMISE OF THE STUDY: The study of very large and very old clades holds the promise of greater insights into evolution across the tree of life. However, there has been a fair amount of criticism regarding the interpretations and quality of studies to date, with some suggesting that detailed studies carried out on smaller, tractable scales should be preferred over the increasingly grand syntheses of these data. METHODS: We provided in detail our trials and tribulations of compiling a large, sparsely sampled matrix from GenBank data and inferring a well-supported, time-calibrated phylogeny of Campanulidae. We also used a simulation approach to assess tree quality and to study the value of using very large, comprehensive phylogenies in a comparative context. KEY RESULTS: A robust and well-supported phylogeny can be produced as long as automated procedures are supplemented with some human intervention. In the case of campanulids, the overall topology may be driven not only by particular genes, but also particular sequences for a gene. We also determined that estimates of divergence times should be fairly robust to issues related to clade-specific heterogeneity. Finally, we demonstrated how relying on results from smaller, younger clades are prone to produce biased interpretations of tropical to temperate evolution across campanulids as a whole. CONCLUSIONS: While we were both surprised and encouraged by the robust and fairly well-resolved, comprehensive phylogeny of campanulids, challenges still remain. Nevertheless, large phylogenies are inherently valuable in a comparative context if only to attenuate the issue of ascertainment bias.

Variation in seed size is structured by dispersal syndrome and cone morphology in conifers and other nonflowering seed plants.

Seed size varies tremendously in plants and its evolution is influenced by multiple ecological and biological factors that are difficult to disentangle. In this study, we focus on understanding the role of seed dispersal by animals in the evolution of seed size in conifers, the most diverse extant nonflowering seed plant group. Relationships among seed size, dispersal syndrome, climate and cone morphology were analyzed across conifers using quantitative models of character evolution and phylogenetic regression techniques. Dispersal syndrome is a more consistent predictor of seed size within major extant conifer clades than climate. Seeds are generally larger in animal-dispersed than wind-dispersed species, and particular cone morphologies are consistently associated with specific ranges in seed size. Seed size and cone morphology evolve in a correlated manner in many animal-dispersed conifers, following a trade-off that minimizes the total size of the dispersal unit. These relationships are also present in other nonflowering seed plant groups, and have been important in the evolution of seeds and cones at least over the Cenozoic and perhaps over much of the later Mesozoic.

Detecting Hidden Diversification Shifts in Models of Trait-Dependent Speciation and Extinction.

The distribution of diversity can vary considerably from clade to clade. Attempts to understand these patterns often employ state-dependent speciation and extinction models to determine whether the evolution of a particular novel trait has increased speciation rates and/or decreased extinction rates. It is still unclear, however, whether these models are uncovering important drivers of diversification, or whether they are simply pointing to more complex patterns involving many unmeasured and co-distributed factors. Here we describe an extension to the popular state-dependent speciation and extinction models that specifically accounts for the presence of unmeasured factors that could impact diversification rates estimated for the states of any observed trait, addressing at least one major criticism of BiSSE (Binary State Speciation and Extinction) methods. Specifically, our model, which we refer to as HiSSE (Hidden State Speciation and Extinction), assumes that related to each observed state in the model are "hidden" states that exhibit potentially distinct diversification dynamics and transition rates than the observed states in isolation. We also demonstrate how our model can be used as character-independent diversification models that allow for a complex diversification process that is independent of the evolution of a character. Under rigorous simulation tests and when applied to empirical data, we find that HiSSE performs reasonably well, and can at least detect net diversification rate differences between observed and hidden states and detect when diversification rate differences do not correlate with the observed states. We discuss the remaining issues with state-dependent speciation and extinction models in general, and the important ways in which HiSSE provides a more nuanced understanding of trait-dependent diversification.

Heterogeneous Rates of Molecular Evolution and Diversification Could Explain the Triassic Age Estimate for Angiosperms.

Dating analyses based on molecular data imply that crown angiosperms existed in the Triassic, long before their undisputed appearance in the fossil record in the Early Cretaceous. Following a re-analysis of the age of angiosperms using updated sequences and fossil calibrations, we use a series of simulations to explore the possibility that the older age estimates are a consequence of (i) major shifts in the rate of sequence evolution near the base of the angiosperms and/or (ii) the representative taxon sampling strategy employed in such studies. We show that both of these factors do tend to yield substantially older age estimates. These analyses do not prove that younger age estimates based on the fossil record are correct, but they do suggest caution in accepting the older age estimates obtained using current relaxed-clock methods. Although we have focused here on the angiosperms, we suspect that these results will shed light on dating discrepancies in other major clades.

Identification of the notothenioid sister lineage illuminates the biogeographic history of an Antarctic adaptive radiation.

BACKGROUND: Antarctic notothenioids are an impressive adaptive radiation. While they share recent common ancestry with several species-depauperate lineages that exhibit a relictual distribution in areas peripheral to the Southern Ocean, an understanding of their evolutionary origins and biogeographic history is limited as the sister lineage of notothenioids remains unidentified. The phylogenetic placement of notothenioids among major lineages of perciform fishes, which include sculpins, rockfishes, sticklebacks, eelpouts, scorpionfishes, perches, groupers and soapfishes, remains unresolved. We investigate the phylogenetic position of notothenioids using DNA sequences of 10 protein coding nuclear genes sampled from more than 650 percomorph species. The biogeographic history of notothenioids is reconstructed using a maximum likelihood method that integrates phylogenetic relationships, estimated divergence times, geographic distributions and paleogeographic history. RESULTS: Percophis brasiliensis is resolved, with strong node support, as the notothenioid sister lineage. The species is endemic to the subtropical and temperate Atlantic coast of southern South America. Biogeographic reconstructions imply the initial diversification of notothenioids involved the western portion of the East Gondwanan Weddellian Province. The geographic disjunctions among the major lineages of notothenioids show biogeographic and temporal correspondence with the fragmentation of East Gondwana. CONCLUSIONS: The phylogenetic resolution of Percophis requires a change in the classification of percomorph fishes and provides evidence for a western Weddellian origin of notothenioids. The biogeographic reconstruction highlights the importance of the geographic and climatic isolation of Antarctica in driving the radiation of cold-adapted notothenioids.