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79 results for “Macroevolution”
Online Appendix and Cetacean Datasets for: The Occurrence Birth-Death Process for combined-evidence analysis in macroevolution and epidemiology
<p>Phylodynamic models generally aim at jointly inferring phylogenetic relationships, model parameters, and more recently, the number of lineages through time, based on molecular sequence data. In the fields of epidemiology and macroevolution these models can be used to estimate, respectively, the past number of infected individuals (prevalence) or the past number of species (paleodiversity) through time. Recent years have seen the development of "total-evidence" analyses, which combine molecular and morphological data from extant and past sampled individuals in a unified Bayesian inference framework. Even sampled individuals characterized only by their sampling time, i.e. lacking morphological and molecular data, which we call occurrences, provide invaluable information to reconstruct the past number of lineages.</p> <p>Here, we present new methodological developments around the Fossilized Birth-Death Process enabling us to (i) incorporate occurrence data in the likelihood function; (ii) consider piecewise-constant birth, death and sampling rates; and (iii) reconstruct the past number of lineages, with or without knowledge of the underlying tree. We implement our method in the RevBayes software environment, enabling its use along with a large set of models of molecular and morphological evolution, and validate the inference workflow using simulations under a wide range of conditions.</p> <p>We finally illustrate our new implementation using two empirical datasets stemming from the fields of epidemiology and macroevolution. In epidemiology, we infer the prevalence of the COVID-19 outbreak on the Diamond Princess ship, by taking into account jointly the case count record (occurrences) along with viral sequences for a fraction of infected individuals. In macroevolution, we infer the diversity trajectory of cetaceans using molecular and morphological data from extant taxa, morphological data from fossils, as well as numerous fossil occurrences. The joint modeling of occurrences and trees holds the promise to further bridge the gap between between traditional epidemiology and pathogen genomics, as well as paleontology and molecular phylogenetics.</p>
Bridging macroecology and macroevolution in the radiation of sigmodontine rodents
<p>Investigations of phenotypic disparity across geography often ignore macroevolutionary processes. As a corollary, the random null expectations to which disparity is compared and interpreted may be unrealistic. We tackle this issue by representing, in geographical space, distinct processes of phenotypic evolution underlying ecological disparity. Under divergent natural selection, assemblages in a given region should have empirical disparity higher than expected under an evolutionarily-oriented null model, while the opposite may indicate constraints on phenotypic evolution. We gathered phylogenies, biogeographic distributions, and data on the skull morphology of sigmodontine rodents to discover which regions of the Neotropics were more influenced by divergent, neutral, or constrained phenotypic evolution. We found that regions with higher disparity than expected by the evolutionary-oriented null model, in terms of both size and shape, were concentrated in the Atlantic Forest, suggesting a larger role for divergent natural selection there. Phenotypic disparity in the rest of South America, mainly the Amazon basin, northeastern Brazil and Southern Andes, was constrained — lower than predicted by the evolutionary model. We also demonstrated equivalence between the disparity produced by randomization-based null models and constrained-evolution null models. Therefore, including evolutionary simulations into the null modeling framework used in ecophylogenetics can strengthen inferences on the processes underlying phenotypic evolution.</p>
Linking micro and macroevolution of head shape in an island radiation
<p>Phenotypic traits have been shown to evolve in response to variation in the environment. However, the evolutionary processes underlying the emergence of phenotypic diversity can typically only be understood at the population level. Consequently, how subtle phenotypic differences at the intraspecific level can give rise to larger-scale changes in performance and ecology remains poorly understood. We here tested for the covariation between ecology, bite force, jaw muscle architecture, and the three-dimensional shape of the cranium and mandible in 16 insular populations of the lizards <i>Podarcis melisellensis</i> and <i>P. sicula</i>. We then compared the patterns observed at the among-population level with those observed at the interspecific level. We found that three-dimensional head shape as well as jaw musculature evolve similarly under similar ecological circumstances. Depending on the type of food consumed or on the level of sexual competition, different muscle groups were more developed and appeared to underlie changes in cranium and mandible shape. Our findings show that the local selective regimes are primary drivers of phenotypic variation resulting in predictable patterns of form and function. Moreover, intraspecific patterns of variation were generally consistent with those at the interspecific level, suggesting that microevolutionary variation may translate into macroevolutionary patterns of ecomorphological diversity.</p>
Macroevolution of sexually selected weapons: weapon evolution in chameleons
Abstract The evolution of sexually selected traits is a major topic in evolutionary biology. However, large-scale evolutionary patterns in these traits remain understudied, especially those traits used in male–male competition (weapons sensu lato). Here, we analyze weapon evolution in chamaeleonid lizards, both within and between the sexes. Chameleons are an outstanding model system because of their morphological diversity (including 11 weapon types among ~220 species) and a large-scale time-calibrated phylogeny. We analyze these 11 traits among 165 species using phylogenetic methods, addressing many questions for the first time in any group. We find that all 11 weapons have each evolved multiple times and that weapon origins are generally more frequent than their losses. We find that almost all weapons have each persisted for &gt;30 million years (and some for &gt;65 million years). Across chameleon phylogeny, we identify both hotspots for weapon evolution (up to 10 types present per species) and coldspots (all weapons absent, many through loss). These hotspots are significantly associated with larger male body size, but are only weakly related to sexual-size dimorphism. We also find that weapon evolution is strongly correlated between males and females. Overall, these results provide a baseline for understanding large-scale patterns of weapon evolution within clades.
Data from: Evolutionary lability of sexual selection and its implications for speciation and macroevolution
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Data from: Evolvability predicts macroevolution under fluctuating selection
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Phylogenomics and macroevolution of a florally diverse Neotropical plant clade
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Linking micro and macroevolution of head shape in an island radiation
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Macroevolution of sexually selected weapons: weapon evolution in chameleons
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Bridging macroecology and macroevolution in the radiation of sigmodontine rodents
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Online Appendix and Cetacean Datasets for: The Occurrence Birth-Death Process for combined-evidence analysis in macroevolution and epidemiology
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Interspecific allometry for sexual shape dimorphism: macroevolution of multivariate sexual phenotypes with application to Rensch's rule
<p>Allometric trends in the degree of sexual dimorphism with body size have long fascinated evolutionary biologists. Many male-biased clades display more prominent sexual dimorphism in larger taxa (Rensch's rule), with most examples documenting this pattern for body size dimorphism. While sexual dimorphism in traits other than body size is equally functionally relevant, characterizing allometric patterns of sexual dimorphism in such traits is hampered by lack of an analytical framework that can accommodate multivariate phenotypes. In this paper we derive a multivariate equivalency for investigating trends in sexual dimorphism – relative to overall body size – across taxa and provide a generalized test to determine whether such allometric patterns correspond with Rensch's rule. For univariate linear traits like body size, our approach yields equivalent results to those from standard procedures, but our test is also capable of detecting trends in multivariate datasets like shape. Computer simulations reveal the method displays appropriate statistical properties, and an empirical example in Mediterranean lizards provides the first demonstration of Rensch's rule in a multivariate phenotype (head shape). Our generalized procedure substantially extends the analytical toolkit for investigating macroevolutionary patterns of sexual dimorphism and seeking a better understanding of the processes that underlie them.</p>
Data from: The neck as a keystone structure in avian macroevolution and mosaicism
<p><strong>Background</strong><br>The origin of birds from non-avian theropod dinosaur ancestors required a comprehensive restructuring of the body plan to enable the evolution of powered flight. One of the proposed key mechanisms that allowed birds to acquire flight and modify the associated anatomical structures into diverse forms is mosaic evolution, which describes the parcelization of phenotypic traits into separate modules that evolve with heterogeneous tempo and mode. Avian mosaicism has been investigated with a focus on the cranial and appendicular skeleton, and as such we don't understand the role of the axial column in avian macroevolution. The long, flexible neck of extant birds lies between the cranial and pectoral modules and represents an opportunity to study the contribution of the axial skeleton to avian mosaicism. <br><strong><br>Results</strong><br>Here we use 3D geometric morphometrics in tandem with phylogenetic comparative methods to provide, to our knowledge, the first integrative analysis of avian neck evolution in context with the head and wing and to interrogate how the interactions between these anatomical systems have influenced macroevolutionary trends across a broad sample of extant birds. We find that the neck is integrated with both the head and the forelimb. These patterns of integration are variable across clades and only specific ecological groups exhibit either head-neck or neck-forelimb integration. Finally, we find that ecological groups that display head-neck and neck-forelimb integration tend to display significant shifts in the rate of neck morphological evolution. <br><br><strong>Conclusions</strong><br>Combined, these results suggest that the interaction between trophic ecology and head-neck-forelimb mosaicism influences the evolutionary variance of the avian neck. By linking together the biomechanical functions of these distinct anatomical systems, the cervical vertebral column serves as a keystone structure in avian mosaicism and macroevolution.</p>
Considering decoupled phenotypic diversification between ontogenetic phases in macroevolution: An example using Triggerfishes (Balistidae)
<p>Across the Tree of Life, most studies of phenotypic disparity and diversification have been restricted to adult organisms. However, many lineages have distinct ontogenetic phases that differ from their adult forms in morphology and ecology. Focusing disproportionately on the evolution of adult forms unnecessarily hinders our understanding of the pressures shaping evolution over time. Non-adult disparity patterns are particularly important to consider for coastal ray-finned fishes, which often have juvenile phases with distinct phenotypes. These juvenile forms are often associated with sheltered nursery environments, with phenotypic shifts between adults and juvenile stages that are readily apparent in locomotor morphology. Whether this ontogenetic variation in locomotor morphology reflects a decoupling of diversification dynamics between life stages remains unknown. Here we investigate the evolutionary dynamics of locomotor morphology between adult and juvenile triggerfishes. We integrate a time-calibrated phylogenetic framework with geometric morphometric approaches and measurement data of fin aspect ratio and incidence and reveal a mismatch between morphospace occupancy, the evolution of morphological disparity, and the tempo of trait evolution between life stages. Collectively, our results illuminate how the heterogeneity of morpho-functional adaptations can decouple the mode and tempo of morphological diversification between ontogenetic stages.</p>
Data from: Natural history constrains the macroevolution of foot morphology in European plethodontid salamanders
The natural history of organisms can have major effects on the tempo and mode of evolution, but few examples show how unique natural histories affect rates of evolution at macroevolutionary scales. European plethodontid salamanders (Plethodontidae: Hydromantes) display a particular natural history relative to other members of the family. Hydromantes commonly occupy caves and small crevices, where they cling to the walls and ceilings. On the basis of this unique and strongly selected behavior, we test the prediction that rates of phenotypic evolution will be lower in traits associated with climbing. We find that, within Hydromantes, foot morphological traits evolve at significantly lower rates than do other phenotypic traits. Additionally, Hydromantes displays a lower rate of foot morphology evolution than does a nonclimbing genus, Plethodon. Our findings suggest that macroevolutionary trends of phenotypic diversification can be mediated by the unique behavioral responses in taxa related to particular attributes of their natural history.
Data from: Fifty shades of brown: Macroevolution of plumage brightness in the Furnariida, a large clade of drab Neotropical passerines
Both natural and sexual selection are thought to affect the evolution of bird color. Most studies of the topic have focused on sexually dichromatic taxa and showy plumages, which are expected to be more influenced by social selection and usually result in increased conspicuousness. However, many bird clades display dull brown or grey plumages that vary greatly in brightness (lightness), but little in hue (shade). Here, we examine the macroevolution of brightness in one such clade, the Furnariida. We make comparisons across light environments, body parts, and across monochromatic lineages and each sex of dichromatic lineages. We found that support for models including light environments is greater for the dorsum than for the venter, and that brightness evolution is more constrained in the latter than in the former. Plumages in this clade have evolved to be darker in darker habitats, consistent with natural selection for increased crypsis. Finally, the features of brightness macroevolution are broadly similar across the sexes of the dichromatic clade, challenging the view that sexual dichromatism is driven by different evolutionary processes acting in each sex. We conclude that, in the Furnariida, light environments and dorsal-ventral variation are more important than sex as axes of color evolution.
Target enrichment of long open reading frames and ultraconserved elements to link microevolution and macroevolution in non-model organisms
<p>Despite the increasing accessibility of high-throughput sequencing, obtaining high-quality genomic data on non-model organisms without proximate well-assembled and annotated genomes remains challenging. Here we describe a workflow that takes advantage of distant genomic resources and ingroup transcriptomes to select and jointly enrich long open reading frames (ORFs) and ultraconserved elements (UCEs) from genomic samples for integrative studies of microevolutionary and macroevolutionary dynamics. This workflow is applied to samples of the African unionid bivalve tribe Coelaturini (Parreysiinae) at basin and continent-wide scales. Our results indicate that ORFs are efficiently captured without prior identification of intron-exon boundaries. The enrichment of UCEs was less successful but nevertheless produced substantial datasets. Exploratory continent-wide phylogenetic analyses with ORF supercontigs (> 515,000 parsimony informative sites) resulted in a fully resolved phylogeny, the backbone of which was also retrieved with UCEs (> 11,000 informative sites). Variant calling on ORFs and UCEs of Coelaturini from the Malawi Basin produced ~2,000 SNPs per population pair. Estimates of nucleotide diversity and population differentiation were similar for ORFs and UCEs. They were low compared to previous estimates in mollusks, but comparable to those in recently diversifying Malawi cichlids and other taxa at an early stage of speciation. Skimming off-target sequence data from the same enriched libraries of Coelaturini from the Malawi Basin, we reconstructed the maternally-inherited mitogenome, which displays the gene order inferred for the most recent common ancestor of Unionidae. Overall, our workflow and results provide exciting perspectives for integrative genomic studies of microevolutionary and macroevolutionary dynamics in non-model organisms.</p>
Data for: Macroevolution in axial morphospace: Innovations accompanying the transition to marine environments in elapid snakes
<p><span>Sea snakes in the <em>Hydrophis</em>-<em>Microcephalophis</em> clade (Elapidae) show exceptional body shape variation along a continuum from similar forebody and hindbody girths, to dramatically reduced girths of the forebody relative to hindbody. The latter is associated with specialisations on burrowing prey. This variation underpins high sympatric diversity and species richness and is not shared by other marine (or terrestrial) snakes. Here, we examined a hypothesis that macroevolutionary changes in axial development contribute to the propensity, at clade level, for body shape change. We quantified variation in the number and size of vertebrae in two body regions (pre- and post-apex of the heart) for ~94 terrestrial and marine elapids. We found <em>Hydrophis</em>-<em>Microcephalophis</em> exhibit increased rates of vertebral evolution in the pre- versus post-apex regions compared to all other Australasian elapids. Unlike other marine and terrestrial elapids, axial elongation in <em>Hydrophis</em>-<em>Microcephalophis</em> occurs via the preferential addition of vertebrae pre heart apex, which is the region that undergoes concomitant shifts in vertebral number and size during transitions along the relative fore- to hindbody girth axis. We suggest that this macroevolutionary developmental change has potentially acted as a key innovation in <em>Hydrophis</em>-<em>Microcephalophis</em> by facilitating novel (especially burrowing) prey specialisations that are not shared with other marine snakes.</span></p>
Data from: Macroevolution of floral scent chemistry across radiations of male euglossine bee-pollinated plants
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Data from: Rapid divergence of a gamete recognition gene promoted macroevolution of Eutheria
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.