Modeling the Evolution of Rates of Continuous Trait Evolution

The emergence and demise of giant sloths

The emergence of multi-tonne herbivores is a recurrent aspect of the Cenozoic mammalian radiation. Several of these giants have vanished within the past 130,000 years, but the timing and macroevolutionary drivers behind this pattern of rise and collapse remain unclear for some megaherbivore lineages. Using trait modeling that combines total-evidence evolutionary trees and a comprehensive size dataset, we show that sloth body mass evolved with major lifestyle shifts and that most terrestrial lineages reached their largest sizes through slower evolutionary rates compared with extant arboreal forms. Size disparity increased during the late Cenozoic climatic cooling, but paleoclimatic changes do not explain the rapid extinction of ground sloths that started approximately 15,000 years ago. Their abrupt demise suggests human-driven factors in the decline and extinction of ground sloths.

The diffused evolutionary dynamics of morphological novelty

Rates of evolution are fundamental to understand the processes that shaped the history of life. The predominant view holds that high rates of phenotypic evolution result from lineage transitions across peaks in an adaptive landscape, with subsequent slow-downs, but evidence remains debated. I developed a phylogenetic "diffused Brownian motion" model that characterizes nuanced variations in evolutionary rates and use it to comprehensively assess body size evolution and its underlying rates for 2,950 extinct and 792 extant species that span over 450 Mys of evolution. I find that evolutionary rates do not conform to expectations from adaptive landscape theory, but rather have been stable, unaffected by the accumulation of phenotypic disparity. Long-term evolutionary trends, such as several net increases in clade-average body size, result both from sustained evolution at the lineage level and the sorting of species phenotypes and their underlying evolutionary rates at the clade level, sometimes acting in opposite directions. These findings substantiate an active role of species in shaping their environment that generate continuous novelty of life forms.

Evolution of accessory bones in cetacean skull coupled with decreasing rate of ossification of cranial sutures

The skulls of cetaceans (whales, dolphins and porpoises) are distinguished by incomplete ossification of cranial sutures during their lifetime. We suggested suture ossification may correlate with the evolution of rarely reported accessory bones and examine the evolutionary patterns of cranial suture ossification and the presence of accessory elements in the skulls of 47 cetacean species and, for comparison, 15 terrestrial artiodactyls (even-hoofed mammals). A strong phylogenetic signal was found for both suture ossification rate and accessory bone presence. Cetaceans were shown to have a lower ossification rate than most terrestrial artiodactyls, except deer (Cervidae) and mouse deer (Tragulidae), which showed somewhat similar patterns. There were also several types of accessory bony elements, some of them first reported in the skulls of cetaceans and in one case, a muntjac deer. These elements (bones and clefts) evolved in the crania with the least number of ossified sutures. They can be identified as novel elements or, some of them, as plesiomorphies rarely seen in mammals but existing in reptiles and other ancestral groups. This leads to breaking a general trend of mammalian evolution: a reversal of Williston's law (reduction in bone number) and the development of new accessory cranial bones. Slowing cranial development rates explain these trends, and feeding mechanics may be a driver of decreasing suture ossification in cetaceans.

TraitTrainR: accelerating large-scale simulation under models of continuous trait evolution

Motivation

The scale and scope of comparative trait data are expanding at unprecedented rates, and recent advances in evolutionary modeling and simulation sometimes struggle to match this pace. Well-organized and flexible applications for conducting large-scale simulations of evolution hold promise in this context for understanding models and more so our ability to confidently estimate them with real trait data sampled from nature.

Results

We introduce TraitTrainR, an R package designed to facilitate efficient, large-scale simulations under complex models of continuous trait evolution. TraitTrainR employs several output formats, supports popular trait data transformations, accommodates multi-trait evolution, and exhibits flexibility in defining input parameter space and model stacking. Moreover, TraitTrainR permits measurement error, allowing for investigation of its potential impacts on evolutionary inference. We envision a wealth of applications of TraitTrainR, and we demonstrate one such example by examining the problem of evolutionary model selection in three empirical phylogenetic case studies. Collectively, these demonstrations of applying TraitTrainR to explore problems in model selection underscores its utility and broader promise for addressing key questions, including those related to experimental design and statistical power, in comparative biology.

Availability and implementation

TraitTrainR is developed in R 4.4.0 and is freely available at https://github.com/radamsRHA/TraitTrainR/, which includes detailed documentation, quick-start guides, and a step-by-step tutorial.

Testing for heterogeneous rates of discrete character evolution on phylogenies

Many hypotheses in the field of phylogenetic comparative biology involve specific changes in the rate or process of trait evolution. This is particularly true of approaches designed to connect macroevolutionary pattern to microevolutionary process. We present a method to test whether the rate of evolution of a discrete character has changed in one or more clades, lineages, or time periods. This method differs from other related approaches (such as the "covarion" model) in that the "regimes" in which the rate or process is postulated to have changed are specified a priori by the user, rather than inferred from the data. Similarly, it differs from methods designed to model a correlation between two binary traits in that the regimes mapped onto the tree are fixed. We apply our method to investigate the rate of dewlap colour and/or caudal vertebra number evolution in Caribbean and mainland clades of the diverse lizard genus Anolis. We find little evidence to support any difference in the evolutionary process between mainland and island evolution for either character. We also examine the statistical properties of the method more generally and show that it has acceptable type I error, parameter estimation, and power. Finally, we discuss some general issues of frequentist hypothesis testing and model adequacy, as well as the relationship of our method to existing models of heterogeneity in the rate of discrete character evolution on phylogenies.

Differential Conservation and Loss of Chicken Repeat 1 (CR1) Retrotransposons in Squamates Reveal Lineage-Specific Genome Dynamics Across Reptiles

Transposable elements (TEs) are repetitive DNA sequences which create mutations and generate genetic diversity across the tree of life. In amniote vertebrates, TEs have been mainly studied in mammals and birds, whose genomes generally display low TE diversity. Squamates (Order Squamata; including ∼11,000 extant species of lizards and snakes) show as much variation in TE abundance and activity as they do in species and phenotypes. Despite this high TE activity, squamate genomes are remarkably uniform in size. We hypothesize that novel, lineage-specific genome dynamics have evolved over the course of squamate evolution. To understand the interplay between TEs and host genomes, we analyzed the evolutionary history of the chicken repeat 1 (CR1) retrotransposon, a TE family found in most tetrapod genomes which is the dominant TE in most reptiles. We compared 113 squamate genomes to the genomes of turtles, crocodilians, and birds and used ancestral state reconstruction to identify shifts in the rate of CR1 copy number evolution across reptiles. We analyzed the repeat landscapes of CR1 in squamate genomes and determined that shifts in the rate of CR1 copy number evolution are associated with lineage-specific variation in CR1 activity. We then used phylogenetic reconstruction of CR1 subfamilies across amniotes to reveal both recent and ancient CR1 subclades across the squamate tree of life. The patterns of CR1 evolution in squamates contrast other amniotes, suggesting key differences in how TEs interact with different host genomes and at different points across evolutionary history.

Phylogenomic analyses of all species of swordtail fishes (genus Xiphophorus) show that hybridization preceded speciation

Hybridization has been recognized to play important roles in evolution, however studies of the genetic consequence are still lagging behind in vertebrates due to the lack of appropriate experimental systems. Fish of the genus Xiphophorus are proposed to have evolved with multiple ancient and ongoing hybridization events. They have served as an informative research model in evolutionary biology and in biomedical research on human disease for more than a century. Here, we provide the complete genomic resource including annotations for all described 26 Xiphophorus species and three undescribed taxa and resolve all uncertain phylogenetic relationships. We investigate the molecular evolution of genes related to cancers such as melanoma and for the genetic control of puberty timing, focusing on genes that are predicted to be involved in pre-and postzygotic isolation and thus affect hybridization. We discovered dramatic size-variation of some gene families. These persisted despite reticulate evolution, rapid speciation and short divergence time. Finally, we clarify the hybridization history in the entire genus settling disputed hybridization history of two Southern swordtails. Our comparative genomic analyses revealed hybridization ancestries that are manifested in the mosaic fused genomes and show that hybridization often preceded speciation.

Differential Conservation and Loss of CR1 Retrotransposons in Squamates Reveals Lineage-Specific Genome Dynamics across Reptiles

Transposable elements (TEs) are repetitive DNA sequences which create mutations and generate genetic diversity across the tree of life. In amniotic vertebrates, TEs have been mainly studied in mammals and birds, whose genomes generally display low TE diversity. Squamates (Order Squamata; ~11,000 extant species of lizards and snakes) show as much variation in TE abundance and activity as they do in species and phenotypes. Despite this high TE activity, squamate genomes are remarkably uniform in size. We hypothesize that novel, lineage-specific dynamics have evolved over the course of squamate evolution to constrain genome size across the order. Thus, squamates may represent a prime model for investigations into TE diversity and evolution. To understand the interplay between TEs and host genomes, we analyzed the evolutionary history of the CR1 retrotransposon, a TE family found in most tetrapod genomes. We compared 113 squamate genomes to the genomes of turtles, crocodilians, and birds, and used ancestral state reconstruction to identify shifts in the rate of CR1 copy number evolution across reptiles. We analyzed the repeat landscapes of CR1 in squamate genomes and determined that shifts in the rate of CR1 copy number evolution are associated with lineage-specific variation in CR1 activity. We then used phylogenetic reconstruction of CR1 subfamilies across amniotes to reveal both recent and ancient CR1 subclades across the squamate tree of life. The patterns of CR1 evolution in squamates contrast other amniotes, suggesting key differences in how TEs interact with different host genomes and at different points across evolutionary history.

phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things)

Phylogenetic comparative methods comprise the general endeavor of using an estimated phylogenetic tree (or set of trees) to make secondary inferences: about trait evolution, diversification dynamics, biogeography, community ecology, and a wide range of other phenomena or processes. Over the past ten years or so, the phytools R package has grown to become an important research tool for phylogenetic comparative analysis. phytools is a diverse contributed R library now consisting of hundreds of different functions covering a variety of methods and purposes in phylogenetic biology. As of the time of writing, phytools included functionality for fitting models of trait evolution, for reconstructing ancestral states, for studying diversification on trees, and for visualizing phylogenies, comparative data, and fitted models, as well numerous other tasks related to phylogenetic biology. Here, I describe some significant features of and recent updates to phytools, while also illustrating several popular workflows of the phytools computational software.

Phylogenomics analyses of all species of Swordtails (Genus Xiphophorus ) highlights hybridization precedes speciation

Hybridization has been recognized as an important driving force for evolution, however studies of the genetic consequence and its cause are still lagging behind in vertebrates due to the lack of appropriate experimental systems. Fish of the central American genus Xiphophorus were proposed to have evolved with multiple ancient and ongoing hybridization events, and served as a valuable research model in evolutionary biology and in biomedical research on human disease for more than a century. Here, we provide the complete genome resource and its annotation of all 26 Xiphophorus species. On this dataset we resolved the so far conflicting phylogeny. Through comparative genomic analyses we investigated the molecular evolution of genes related to melanoma, for a main sexually selected trait and for the genetic control of puberty timing, which are predicted to be involved in pre-and postzygotic isolation and thus to influence the probability of interspecific hybridization in Xiphophorus . We demonstrate dramatic size-variation of some gene families across species, despite the reticulate evolution and short divergence time. Finally, we clarify the hybridization history in the genus Xiphophorus genus, settle the long dispute on the hybridization origin of two Southern swordtails, highlight hybridizations precedes speciation, and reveal the distribution of hybridization ancestry remaining in the fused genome.