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Comparative methods used to study patterns of evolutionary change in a continuous trait on a phylogeny range from Brownian motion processes to models where the trait is assumed to evolve according to an Ornstein—Uhlenbeck (OU) process. Although these models have proved useful in a variety of contexts, they still do not cover all the scenarios biologists want to examine. For models based on the OU process, model complexity is restricted in current implementations by assuming that the rate of stochastic motion and the strength of selection do not vary among selective regimes. Here, we expand the OU model of adaptive evolution to include models that variously relax the assumption of a constant rate and strength of selection. In its most general form, the methods described here can assign each selective regime a separate trait optimum, a rate of stochastic motion parameter, and a parameter for the strength of selection. We use simulations to show that our models can detect meaningful differences in the evolutionary process, especially with larger sample sizes. We also illustrate our method using an empirical example of genome size evolution within a large flowering plant clade.

First appearing in the latest Cretaceous, Crocodylia is a clade of semi-aquatic, predatory reptiles, defined by the last common ancestor of extant alligators, caimans, crocodiles, and gharials. Despite large strides in resolving crocodylian interrelationships over the last three decades, several outstanding problems persist in crocodylian systematics. Most notably, there has been persistent discordance between morphological and molecular datasets surrounding the affinities of the extant gharials, Gavialis gangeticus and Tomistoma schlegelii . Whereas molecular data consistently support a sister taxon relationship, in which they are more closely related to crocodylids than to alligatorids, morphological data indicate that Gavialis is the sister taxon to all other extant crocodylians. Here we present a new morphological dataset for Crocodylia based on a critical reappraisal of published crocodylian character data matrices and extensive firsthand observations of a global sample of crocodylians. This comprises the most taxonomically comprehensive crocodylian dataset to date (144 OTUs scored for 330 characters) and includes a new, illustrated character list with modifications to the construction and scoring of characters, and 46 novel characters. Under a maximum parsimony framework, our analyses robustly recover Gavialis as more closely related to Tomistoma than to other extant crocodylians for the first time based on morphology alone. This result is recovered regardless of the weighting strategy and treatment of quantitative characters. However, analyses using continuous characters and extended implied weighting (with high k -values) produced the most resolved, well-supported, and stratigraphically congruent topologies overall. Resolution of the gharial problem reveals that: (1) several gavialoids lack plesiomorphic features that formerly drew them towards the stem of Crocodylia; and (2) more widespread similarities occur between species traditionally divided into tomistomines and gavialoids, with these interpreted here as homology rather than homoplasy. There remains significant temporal incongruence regarding the inferred divergence timing of the extant gharials, indicating that several putative gavialids (‘thoracosaurs’) are incorrectly placed and require future re-appraisal. New alligatoroid interrelationships include: (1) support for a North American origin of Caimaninae in the latest Cretaceous; (2) the recovery of the early Paleogene South American taxon Eocaiman as a ‘basal’ alligatoroid; and (3) the paraphyly of the Cenozoic European taxon Diplocynodon . Among crocodyloids, notable results include modifications to the taxonomic content of Mekosuchinae, including biogeographic affinities of this clade with latest Cretaceous–early Paleogene Asian crocodyloids. In light of our new results, we provide a comprehensive review of the evolutionary and biogeographic history of Crocodylia, which included multiple instances of transoceanic and continental dispersal.

A large proportion of genomic information, particularly repetitive elements, is usually ignored when researchers are using next-generation sequencing. Here we demonstrate the usefulness of this repetitive fraction in phylogenetic analyses, utilizing comparative graph-based clustering of next-generation sequence reads, which results in abundance estimates of different classes of genomic repeats. Phylogenetic trees are then inferred based on the genome-wide abundance of different repeat types treated as continuously varying characters; such repeats are scattered across chromosomes and in angiosperme can constitute a majority of nuclear genomic DNA. In six diverse examples, five angiosperms and one insect, this method provides generally well-supported relationships at interspecific and intergeneric levels that agree with results from more standard phylogenetic analyses of commonly used markers. We propose that this methodology may prove especially useful in groups where there is little genetic differentiation in standard phylogenetic markers. At the same time as providing data for phylogenetic inference, this method additionally yields a wealth of data for comparative studies of genome evolution.

The threshold model developed by Sewall Wright in 1934 can be used to model the evolution of two-state discrete characters along a phylogeny. The model assumes that there is a quantitative character, called liability, that is unobserved and that determines the discrete character according to whether the liability exceeds a threshold value. A Markov chain Monte Carlo algorithm is used to infer the evolutionary covariances of the liabilities for discrete characters, sampling liability values consistent with the phylogeny and with the observed data. The same approach can also be used for continuous characters by assuming that the tip species have values that have been observed. In this way, one can make a comparative-methods analysis that combines both discrete and continuous characters. Simulations are presented showing that the covariances of the liabilities are successfully estimated, although precision can be achieved only by using a large number of species, and we must always worry whether the covariances and the model apply throughout the group. An advantage of the threshold model is that the model can be straightforwardly extended to accommodate within-species phenotypic variation and allows an interface with quantitative-genetics models.

Background Isolating phylogenetic signal from morphological data is crucial for accurately merging fossils into the tree of life and for calibrating molecular dating. However, subjective character definition is a major limitation which can introduce biases that mislead phylogenetic inferences and divergence time estimation. The use of quantitative data, e.g., geometric morphometric (GMM; shape) data can allow for more objective integration of morphological data into phylogenetic inference. This systematic review describes the current state of the field in using continuous morphometric data (e.g., GMM data) for phylogenetic reconstruction and assesses the efficacy of these data compared to discrete characters using the PRISMA-EcoEvo v1.0. reporting guideline, and offers some pathways for approaching this task with GMM data. A comprehensive search string yielded 11,123 phylogenetic studies published in English up to Oct 2023 in the Web of Science database. Title and abstract screening removed 10,975 articles, and full-text screening was performed for 132 articles. Of these, a total of twelve articles met final inclusion criteria and were used for downstream analyses. Results Phylogenetic performance was compared between approaches that employed continuous morphometric and discrete morphological data. Overall, the reconstructed phylogenies did not show increased resolution or accuracy (i.e., benchmarked against molecular phylogenies) as continuous data alone or combined with discrete morphological datasets. Conclusions An exhaustive search of the literature for existing empirical continuous data resulted in a total of twelve articles for final inclusion following title/abstract, and full-text screening. Our study was performed under a rigorous framework for systematic reviews, which showed that the lack of available comparisons between discrete and continuous data hinders our understanding of the performance of continuous data. Our study demonstrates the problem surrounding the efficacy of continuous data as remaining relatively intractable despite an exhaustive search, due in part to the difficulty in obtaining relevant comparisons from the literature. Thus, we implore researchers to address this issue with studies that collect discrete and continuous data sets with directly comparable properties (i.e., describing shape, or size).

Despite being the objects of numerous macroevolutionary studies, many of the best represented constituents of the fossil record—including diverse examples such as foraminifera, brachiopods, and mollusks—have mineralized skeletons with limited discrete characteristics, making morphological phylogenies difficult to construct. In contrast to their paucity of phylogenetic characters, the mineralized structures (tests and shells) of these fossil groups frequently have distinctive shapes that have long proved useful for their classification. The recent introduction of methodologies for including continuous data directly in a phylogenetic analysis has increased the number of available characters, making it possible to produce phylogenies based, in whole or part, on continuous character data collected from such taxa. Geometric morphometric methods provide tools for accurately characterizing shape variation and can produce quantitative data that can therefore now be included in a phylogenetic matrix in a nonarbitrary manner. Here, the marine gastropod genus Conus is used to evaluate the ability of continuous characters—generated from a geometric morphometric analysis of shell shape—to contribute to a total evidence phylogenetic hypothesis constructed using molecular and morphological data. Furthermore, the ability of continuous characters derived from geometric morphometric analyses to place fossil taxa with limited discrete characters into a phylogeny with their extant relatives was tested by simulating the inclusion of fossil taxa. This was done by removing the molecular partition of individual extant species to produce a \"cladistic pseudofossil\" with only the geometric morphometric derived characters coded. The phylogenetic position of each cladistic pseudofossil taxon was then compared with its placement in the total evidence tree and a symmetric resampling tree to evaluate the degree to which morphometric characters alone can correctly place simulated fossil species. In 33–45% of the test cases (depending upon the approach used for measuring success), it was possible to place the pseudofossil taxon into the correct regions of the phylogeny using only the morphometric characters. This suggests that the incorporation of extinct Conus taxa into phylogenetic hypotheses will be possible, permitting a wide range of macroevolutionary questions to be addressed within this genus. This methodology also has potential to contribute to phylogenetic reconstructions for other major components of the fossil record that lack numerous discrete characters.

Premise of the Study The Polytrichaceae are a widespread and morphologically isolated moss lineage. Early attempts to characterize phylogenetic relationships within the family suggested that morphology is not phylogenetically informative. Two well‐characterized fossils similar to basal and derived Polytrichaceae (Meantoinea alophosioides and Eopolytrichum antiquum, respectively), are known from Cretaceous rocks. To assess the phylogenetic positions of these fossils and compare hypotheses of relationships recovered using molecular vs. morphological methods, we conducted a comprehensive morphology‐based phylogenetic study of Polytrichaceae. Methods We evaluated the phylogenetic relationships of Polytrichaceae using a data set of 100 morphological characters (including 11 continuously varying traits codified as continuous characters) scored for 44 species of acrocarpous mosses and parsimony as the optimality criterion. Key Results Continuous characters significantly increased the resolving power of the analyses. The overall ingroup topology was sensitive to rooting as determined by outgroup selection, with some analyses yielding results that were incongruent with those of molecular studies. Both fossils had stable phylogenetic relationships, irrespective of outgroup sampling. Conclusions Our results suggest that morphology is useful in resolving phylogenetic relationships in the Polytrichaceae, if both discrete and continuous characters are used. However, our rooting experiments demonstrate that there is no superior way to root analyses and indicate that relationships within the family are best evaluated using unrooted networks without outgroup taxa. These rooting problems suggest that additional information is needed to understand the phylogenetic relationships of Polytrichaceae. Such additional information could come from fossils of stem group polytrichaceous mosses, which await discovery.

The application of genomic and sub‐genomic data in species delimitation has facilitated the discovery of cryptic species. As the name implies, cryptic species are difficult, if not impossible, to distinguish based on morphology alone. The integrative species delimitation process employed herein comprises three steps: species discovery, species validation, and species description. Phylogenetic analysis of sub‐genomic data revealed three major lineages within the trapdoor spider Aptostichus simus. These lineages identified candidate species that were then tested using further genetic and morphological analyses. The species validation step supported the discovery of a novel cryptic species, A. ramirezae sp. nov., and potential incipient species. Aptostichus simus and A. ramirezae sp. nov., are endemic to coastal dune habitats in California and Baja California, which face many threats such as erosion, human development, habitat fragmentation, coastal squeeze, and sea level rise. Understanding the patterns of genetic diversity in these species is crucial for informing conservation efforts of both the animals and habitat in which they live. The integrative species delimitation process employed herein comprises three steps: species discovery, species validation, and species description. Phylogenetic analysis of sub‐genomic data revealed three major lineages within the trapdoor spider Aptostichus simus. The species validation step supported the discovery of a novel cryptic species, A. ramirezae sp. nov., and potential incipient species.

Rates of phenotypic evolution have changed throughout the history of life, producing variation in levels of morphological, functional, and ecological diversity among groups. Testing for the presence of these rate shifts is a key component of evaluating hypotheses about what causes them. In this paper, general predictions regarding changes in phenotypic diversity as a function of evolutionary history and rates are developed, and tests are derived to evaluate rate changes. Simulations show that these tests are more powerful than existing tests using standardized contrasts. The new approaches are distributed in an application called Brownie and in r8s.

Premise of research. The biogeographic and ecological origins and recruitment of arctic species were analyzed in a text-mining framework of expert knowledge. The newly defined multidimensional habitat spaces of clades and their geographical distribution were used to reveal unique and parallel avenues of a biome assembly. Methodology. Printed and online floristic works were screened for distribution data and habitat information. Distribution data were directly used to infer diversity centers of clades and their arctic members. From the habitat information, a multidimensional habitat matrix was constructed and analyzed via principal component analysis (PCA). The obtained species score matrix was used to infer the size—that is, the length of the habitat space of the clades along the principal component axes, which was subsequently assessed for similarities and differences. Pivotal results. The diversity centers of the clades were widely distributed across the northern hemisphere, mostly in mountains. Some areas may have served multiple times as sources for arctic species. The process of defining the habitat space offers the opportunity to compare this important ecological characteristic of species across the study area and reveals ecological differentiations. The size of the habitat space of the clades is significantly and positively related to their species numbers. The similarity of the occupied habitat space of the clades forms a continuum in pairwise comparisons. Some clades within and between the genera were similar in the size and locations of their habitat spaces, revealing considerable ecological parallelisms occurring partly in distant areas. Conclusions. The recruitment of arctic species in Micranthes and Saxifraga reveals as a complex geographical and ecological pattern that is part of a continuous variation rather than discrete evolutionary events. Considerable redundancy and parallelisms seem to be the rule rather than the exception for the assembly of plants in ecosystems.