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120 results for “evolutionary rate”
Data from: Human face-off: a new method for mapping evolutionary rates on three-dimensional digital models
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The role of evolutionary time, diversification rates and dispersal in determining the global diversity of a large radiation of passerine birds
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Influence of Quaternary environmental changes on mole populations inferred from mitochondrial sequences and evolutionary rate estimation
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Evolutionary rates and shape variation along the anuran vertebral column with attention to phylogeny, body size, and ecology
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The Jurassic rise of squamates as supported by lepidosaur disparity and evolutionary rates
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Growing in the city: urban evolutionary ecology of avian growth rates.
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Phylogenomic dataset used for evolutionary rate covariation analyses in Forsythe et al.
<p>Nuclear and plastid (chloroplast) genomes experience different mutation rates, levels of selection, and transmission modes, yet key cellular functions depend on coordinated interactions between proteins encoded in both genomes. Functionally related proteins often show correlated changes in rates of sequence evolution across a phylogeny (evolutionary rate covariation or ERC), offering a means to detect previously unidentified suites of coevolving and cofunctional genes. We performed phylogenomic analyses across angiosperm diversity, scanning the nuclear genome for genes that exhibit ERC with plastid genes. As expected, the strongest hits are highly enriched for plastid-targeted proteins, providing evidence that cytonuclear interactions affect rates of molecular evolution at genome-wide scales. Many identified nuclear genes function in post-transcriptional regulation and the maintenance of protein homeostasis (proteostasis), including protein translation (in both the plastid and cytosol), import, quality control and turnover. We also identified nuclear genes that exhibit strong signatures of coevolution with the plastid genome but lack organellar-targeting annotations, making them candidates for having previously underibed roles in plastids. In sum, our genome-wide analyses reveal that plastid-nuclear coevolution extends beyond the intimate molecular interactions within chloroplast enzyme complexes and may be driven by frequent rewiring of the machinery responsible for maintenance of plastid proteostasis in angiosperms.</p>
Data from: A test for rate-coupling of trophic and cranial evolutionary dynamics in New World bats
<p>Data supporting article Shi et al. 2021, Evolution: <a href="https://doi.org/10.1111/evo.14188">https://doi.org/10.1111/evo.14188</a></p> <p>Morphological evolution is often assumed to be causally related to underlying patterns of ecological trait evolution. However, few studies have directly tested whether evolutionary dynamics of and major shifts in ecological resource use are coupled with morphological shifts that may facilitate trophic innovation. Using diet and multivariate cranial (microCT) data, we tested whether rates of trophic and cranial evolution are coupled in the radiation of New World bats. <span>We developed a generalizable information-theoretic method for describing evolutionary rate heterogeneity across large candidate sets of multi-rate models of evolution, without relying on a single best-fitting model</span>. We found considerable variation in trophic evolutionary dynamics, in sharp contrast to a largely homogeneous cranial evolutionary process. This dichotomy is surprising given documented functional associations between overall skull morphology and trophic ecology. We suggest that assigning discrete trophic states may underestimate trophic generalism, and that this radiation could be characterized by generally labile crania that result in a homogeneous dynamic of overall high morphological rates. Overall, we discuss how trophic classification could substantively impact our interpretation of how these dynamics covary in adaptive radiations.</p>
Data from: Estimating the molecular evolutionary rates of mitochondrial genes referring to Quaternary Ice Age events with inferred population expansions and dispersals in Japanese Apodemus
Background: Determining reliable evolutionary rates of molecular markers is essential in illustrating historical episodes with phylogenetic inferences. Although emerging evidence has suggested a high evolutionary rate for intraspecific genetic variation, it is unclear how long such high evolutionary rates persist because a recent calibration point is rarely available. Other than using fossil evidence, it is possible to estimate evolutionary rates by relying on the well-established temporal framework of the Quaternary glacial cycles that would likely have promoted both rapid expansion events and interisland dispersal events. Results: We examined mitochondrial cytochrome b (Cytb) and control region (CR) gene sequences in two Japanese wood mouse species, Apodemus argenteus and A. speciosus, of temperate origin and found signs of rapid expansion in the population from Hokkaido, the northern island of Japan. Assuming that global warming after the last glacial period 7–10 thousand years before present (kyr BP) was associated with the expansion, the evolutionary rates (sites per million years, myr) of Cytb and CR were estimated as 11–16% and 22–32%, respectively, for A. argenteus, and 12–17% and 17–24%, respectively, for A. speciosus. Additionally, the significant signature of rapid expansion detected in the mtDNA sequences of A. speciosus from the remaining southern main islands, Honshu, Shikoku, and Kyushu, provided an estimated Cytb evolutionary rate of 3.1%/site/myr under the assumption of a postglacial population expansion event long ago, most probably at 130 kyr BP. Bayesian analyses using the higher evolutionary rate of 11–17%/site/myr for Cytb supported the recent demographic or divergence events associated with the Last Glacial Maximum. However, the slower evolutionary rate of 3.1%/site/myr would be reasonable for several divergence events that were associated with glacial periods older than 130 kyr BP. Conclusions: The faster and slower evolutionary rates of Cytb can account for divergences associated with the last and earlier glacial maxima, respectively, in the phylogenetic inference of murine rodents. The elevated evolutionary rate seemed to decline within 100,000 years.
Data from: The cryptic origins of evolutionary novelty: 1,000-fold-faster trophic diversification rates without increased ecological opportunity or hybrid swarm
Ecological opportunity is frequently proposed as the sole ingredient for adaptive radiation into novel niches. An additional trigger may be genome-wide hybridization resulting from 'hybrid swarm'. However, these hypotheses have been difficult to test due to the rarity of comparable control environments lacking adaptive radiations. Here I exploit such a pattern in microendemic radiations of Caribbean pupfishes. I show that a sympatric three-species radiation on San Salvador Island, Bahamas diversified 1,445 times faster than neighboring islands in jaw length due to evolution of a novel scale-eating adaptive zone from a generalist ancestral niche. I then sampled 22 generalist populations on seven neighboring islands and measured morphological diversity, stomach content diversity, dietary isotopic diversity, genetic diversity, lake/island areas, macroalgae richness, and Caribbean-wide patterns of gene flow. None of these standard metrics of ecological opportunity or gene flow were associated with adaptive radiation, except for slight increases in macroalgae richness. Thus, exceptional trophic diversification is highly localized despite myriad generalist populations in comparable environmental and genetic backgrounds. This study provides a strong counterexample to the ecological/hybrid-swarm theories of adaptive radiation and suggests that diversification of novel specialists on a sparse fitness landscape is constrained by more than ecological opportunity and gene flow.
Data from: Accelerated evolutionary rate of housekeeping genes in tunicates
Phylogenomics has recently revealed that tunicates represent the sister-group of vertebrates in the newly defined clade Olfactores. However, phylogenomic and comparative genomic studies have also suggested that tunicates are characterized by an elevated rate of molecular evolution and a high degree of genomic divergence. Despite the recurrent interest in the group, the picture of tunicate peculiar evolutionary dynamics is still fragmentary, as it mainly lies in studies focusing on only a few model species. In order to expand the available genomic data for the group, we used the high-throughput 454 technology to sequence the partial transcriptome of a previously unsampled tunicate, Microcosmus squamiger. This allowed us to get further insights into tunicate-accelerated evolution through a comparative analysis based on pertinent phylogenetic markers, i.e., a core of 35 housekeeping genes conserved across bilaterians. Our results showed that tunicates evolved on average about two times faster than the other chordates, yet the degree of this acceleration varied extensively upon genes and upon lineages. Appendicularia and Aplousobranchia were detected as the most divergent groups which were also characterized by highly heterogeneous substitution rates across genes. Finally, an estimation of the d (N)/d (S) ratio in three pairs of closely related taxa within Olfactores did not reveal strong differences between the tunicate and vertebrate lineages suggesting that for this set of housekeeping genes, the accelerated evolution of tunicates is plausibly due to an elevated mutation rate rather than to particular selective effects.
Data from: Elevated evolutionary rates of biting biomechanics reveal patterns of extraordinary cranio-dental adaptations in some herbivorous dinosaurs
<p>Adaptation to specialist ecologies is a key innovation that has contributed to the evolutionary success of many vertebrate clades, underpinning the acquisition of diverse skull morphologies. Dinosaurs, which dominated Mesozoic terrestrial faunas, acquired herbivory multiple times, including in clades historically regarded as predominantly carnivorous. The evolution of herbivory in theropod dinosaurs is linked to drastic changes in dental and craniomandibular functional morphology, yet whether such changes occurred more rapidly in herbivorous lineages compared to in carnivorous lineages remains untested in a phylogenetic framework. Here, we infer rates of phenotypic evolution in relative biting edge lengths to test the hypothesis that the acquisition of herbivory is associated with rapid changes in jaw biomechanics. We find elevated rates of biomechanical evolution in theropods with foreshortened and beaked skulls (Oviraptorosauria, <em>Limusaurus</em>), as well as in ceratopsians and <em>Diplodocus</em>. A reduced biting edge length and increased jaw efficiency unites these high-rate lineages, indicating selection for greater efficiency in biting biomechanics. Additionally, we hypothesise that extreme ontogenetic changes within species' lifetimes may be behind some instances of branch-wise elevated rates. Thus, we show how exceptional rates of biomechanical evolution can reveal signatures of adaptations within dinosaur lineages and potentially along ontogenetic sequences.</p>
Supplementary data and codes for ammonoids morphological complexity and evolutionary rates
<p>The "code" folder contains the code for calculating evolutionary rates and analysing the data, and the input and output data. We used the Bayesian framework implemented within the program PyRate, the per capita boundary-crosser rate, per-taxon rate, and Van Valen metric to calculate extinction and origination rates for early Pliensbachian species and Cretaceous genera datasets. The Pyrate method is implemented in python, all other methods use R code.</p> <p>The "obj" folder includes 292 three-dimensional models of 146 specimens.</p> <p>The "Expanded Data" file containing supplementary tables, original data, processed data and specimen tables.</p>
Phenotypic rates of change evolutionary and ecological dataset (PROCEED) version 5.0
<p>Wild populations must continuously respond to environmental changes or they risk extinction. Those responses can be measured as phenotypic rates of change which can allow us to predict contemporary adaptive responses, some of which are evolutionary. About two decades ago, a database of phenotypic rates of change in wild populations was compiled. Since then, researchers have used (and expanded) this database to examine phenotypic responses to specific types of human disturbance. Here, we updatedthe database adding 5675 new estimates of phenotypic changes. Using this newer version of the database, now containing 7338 estimates of phenotypic change, we revisit the conclusions of four published articles. We then synthesize the expanded dataset to compare rates of change across different types of human disturbance. Analyses of this expanded database suggests that: I. a small absolute difference in rates of change exists between human disturbed and natural populations, II. harvesting by humans results in higher rates of change than other types of disturbances, III. introduced populations have increased rates of change, and IV. body size does not increase through time. Thus, findings from earlier analyses have largely held-up in analyses of our new database that encompass a much larger breadth of species, traits, and human disturbances. Lastly, we use new analyses to explore how various types of human disturbances affect rates of phenotypic change, and we call for this database to serve as a stepping stone for further analyses to understand patterns of contemporary phenotypic change.</p>
Evolutionary change in metabolic rate of Daphnia pulicaria following invasion by the predator Bythotrephes longimanus
<p><span>Metabolic rate is a trait that may evolve in response to the direct and indirect effects of predator-induced mortality. Predators may indirectly alter selection by lowering prey densities and increasing resource availability or by intensifying resource limitation through changes in prey behaviour (e.g. use of less productive areas). In the current study </span><span>we quantify evolution of metabolic rate in the zooplankton </span><em><span>Daphnia pulicaria</span></em><span> following an invasive event by the predator </span><em><span>Bythotrephes longimanus</span></em><span> in Lake Mendota, Wisconsin, US. This invasion has been shown to dramatically impact </span><em><span>D. pulicaria</span></em><span>, </span><span>causing a ~60% decline in their biomass. </span><span>Using a resurrection ecology approach, we compared the metabolic rate of D. pulicaria clones originating from prior to the <em>Bythotrephes</em> invasion with that of clones having evolved in the presence of <em>Bythotrephes</em>. </span><span>We observed</span><span> a 7.4% reduction in metabolic rate among post-invasive clones compared to pre-invasive clones, and discuss the potential roles of direct and indirect selection in driving this change. </span></p>
Progenitors of Type IIb Supernovae: I. Evolutionary Pathways and Rates
<p>Mesa templates and data associated with <a href="https://ui.adsabs.harvard.edu/abs/2018arXiv180807580S/abstract">Sravan et al. (2018)</a>. MESA version 9575.</p> <p>Each tar.xz contains one set of simulations, with files marked as binaries_* and singles_* corresponding to binary star, and single star simulations. Files ending in *high_Z.tar.xz and *low_Z.tar.xz correspond to the high and low metallicity simulations in the paper. for binary runs, the three digits indicate the mass transfer efficiency with 001, 010, 050 and 100 corresponding to efficiencies of 0.01, 0.10, 0.50 and 1.00.</p> <p>Within the files, simulation results are contained in individual folders, that also include all necessary MESA files to recreate the simulation. For single star simulations, the folder name indicates the value of log10(M_ZAMS/Msun), so for example, the folder named "1.6000" represents a star with ZAMS mass of 39.81 Msun. For binary systems, data is arranged such that, for example, the folder "1.400/0.825_3.000" represents a binary system with a primary mass at ZAMS of log10(M_1,ZAMS/Msun)=1.4, mass ratio q=M_2,ZAMS/M_1,ZAMS=0.825 and initial orbital period log P_i/days=3.</p> <p>All MESA output files have been post-processed to reduce their size. within each folder, the files named "last_prof*.data.s" contain the structure of the models at the end of a simulation. Files "LOGS/history.data.s", "LOGS1/history.data.s" and "LOGS2/history.data.s" contain information that can be represented by a single number at each timestep, such as the age, luminosity and effective temperature of the star. "LOGS/history.data.s" is used in single star simulations, while "LOGS1/history.data.s" and "LOGS2/history.data.s" correspond to each star in a binary run.</p> <p>MESA templates are available in the file IIb_progenitors_MESA_templates.zip.</p>
Data from: Evolutionary rates of mid-Permian tetrapods from South Africa and the role of temporal resolution in turnover reconstruction
The Main Karoo Basin of South Africa contains a near-continuous sequence of continental deposition spanning 45 million years from the middle Permian to the Early Jurassic. The terrestrial vertebrates of this sequence provide a high-resolution stratigraphic record of regional origination and extinction, especially for the middle–late Permian. Until now, data have only been surveyed at coarse stratigraphic resolution using methods that are biased by non-uniform sampling rates, limiting our understanding of the dynamics of diversification through this important time period. High-resolution data now cross the mid-to-late Permian transition; to these we apply robust methods (gap-filler and modified gap-filler rates) for the inference of patterns of species richness, origination rates and extinction rates to a subset of 1321 securely-identified fossil occurrences resolved to approximately 50 metre stratigraphic intervals. This dataset provides an approximate time resolution of 0.3-0.6 million years and shows that extinction rates increased considerably in the upper 100 metres of the middle Permian Abrahamskraal Formation, corresponding to the latest part of the Tapinocephalus Assemblage Zone (AZ). Origination rates were weakly elevated in the same interval, and were not sufficient to compensate for these extinctions. Subsampled species richness estimates for the lower part of the overlying Teekloof Formation (corresponding to the Pristerognathus and Tropidostoma AZs) are low, and show that species richness remained low for at least 1.5–3 million years after the main extinction pulse. A high unevenness of the taxon abundance-frequency distribution, which is classically associated with trophically unstable post-extinction faunas, in fact developed shortly before the acme of elevated extinction rates due to the appearance and proliferation of the dicynodont Diictodon. Our findings provide strong support for a Capitanian ('end-Guadalupian') extinction event among terrestrial vertebrates and suggest that further high-resolution quantitative studies may help resolve the lack of consensus among palaeobiologists regarding this event.
Data from: Increased evolutionary rates and conserved transcriptional response following allopolyploidisation in brown algae
Genome mergers between independently evolving lineages, via allopolyploidy, can potentially lead to instantaneous sympatric speciation. However, little is known about the consequences of allopolyploidy and the resultant "genome shock" on genome evolution and expression beyond the plant and fungal branches of the Tree of Life. The aim of this study was to compare substitution rates and gene expression patterns in two allopolyploid brown algae (Phaeophyceae, Heterokonta) and their progenitors in the genus Pelvetiopsis N.L. Gardner in the north-east Pacific, and to date their relationships. We used RNA-seq data and putative single-copy loci for phylogenomic, divergence and gene expression analyses. The multispecies coalescent placed the origin of allopolyploids in the late Pleistocene (0.35 – 0.05 Ma). Homoeologues displayed increased non-synonymous divergence compared with parental orthologues, consistent with relaxed selective constraint following allopolyploidization, including for genes with no evidence of pseudogenization or neo-functionalization. Patterns of homeologue-orthologue expression conservation and expression-level dominance were shared with both natural plant and fungal allopolyploids. Interestingly, gene expression also appeared partially linked to the gender of origin of homoeologues. Our results provide further support for common cross-Kingdom patterns of allopolyploid genome evolution and transcriptional responses, here in the evolutionarily distinct marine heterokont brown algae.
Data from: Slow and fast evolutionary rates in the history of lepidosaurs
<p>Biodiversity today is uneven, with equally ancient sister groups containing few or many species. It has often been assumed that high biodiversity indicates fast evolution, and yet in a classic work in 1944 George Simpson suggested that fast evolution might generate instability and extinction, and that slow evolution led to high biodiversity. Here we show that evolutionary rates can vary substantially through the history of a clade and find evidence for Simpson's claim. In a comparative phylogenetic study deploying Bayesian methods, we find that Squamata, comprising today over 10,000 species of lizards and snakes, showed slow rates of evolution in the first two-thirds of their history, whereas their sister clade, Rhynchocephalia, comprising just one living species, showed high rates of evolution in the past. Slow and steady won the race for the Mesozoic squamates, and the high-rate boom and bust existence of rhynchocephalians at that time leaves them with a single survivor. We need to explore other cases where fast evolution can lead to short-term high diversification, but in the end long-term low biodiversity.</p>
Data from: The influence of climatic variability on morphological integration, evolutionary rates, and disparity in the Carnivora
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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)
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DANDI Archive for NWB datasets
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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.
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