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296 results for “evolution pattern”
Phylogenetic patterns of trait and trait plasticity evolution: Insights from tadpoles
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Data from: How geographic productivity patterns affect food-web evolution
<p>This dataset contains the generated data analyzed in the manuscript, as well as the code for analyzing the generated data. It also contains the code used to generate the data.</p>
Data from: Surf and Turf Vision: Patterns and predictors of visual acuity in compound eye evolution
<p><span><span>Eyes have the flexibility to evolve to meet the ecological demands of their users.</span><b><span> </span></b><span>Relative to camera-type eyes, the fundamental limits of optical diffraction in arthropod compound eyes restricts the ability to resolve fine detail (visual acuity) to much lower degrees. We tested the capacity of several ecological factors to predict arthropod visual acuity, while simultaneously controlling for shared phylogenetic history. In this study, we have generated the most comprehensive review of compound eye visual acuity measurements to date, containing </span></span><span><span>375 </span></span><span><span>species that span six of the major arthropod classes. An arthropod phylogeny, made custom to this database, was used to develop a phylogenetically-corrected generalized least squares (PGLS) linear model to evaluate four ecological factors predicted to underlie compound eye visual acuity: environmental light intensity, foraging strategy (predator vs. non-predator), horizontal structure of the visual scene, and environmental medium (air vs. water). To account for optical constraints on acuity related to animal size, body length was also included, though this did not show a significant effect in any of our models. Rather, the PGLS revealed that the strongest predictors of compound eye acuity are described by a combination of environmental medium, foraging strategy, and environmental light intensity.</span></span></p>
Data and script for: The patterns and modes of the evolution of disparity in Mesozoic Birds
<p>The origin of birds from non-avian theropod dinosaurs is one of the greatest transitions in evolution. Shortly after diverging from other theropods in the Late Jurassic, Mesozoic birds diversified into two major clades—the Enantiornithes and Ornithuromorpha—acquiring many features previously considered unique to the crown groups along the way. Here we present a comparative phylogenetic study of the patterns and modes of Mesozoic bird skeletal morphology and limb proportions. Our results show that the major Mesozoic avian groups are distinctive in discrete character space, but constrained in morphospace defined by limb proportions. The Enantiornithines, despite being the dominant group of Mesozoic birds, are much less morphologically disparate than their sister clade, the Ornithuromorpha—the clade that gave rise to living birds, showing decoupled disparity and diversity in early avian history. This relatively low disparity suggests that diversification of enantiornithines was characterized in exhausting fine morphologies, whereas ornithuromorphs continuously explored a broader array of morphologies and ecological opportunities. We suggest this clade-specific evolutionary versatility contribute to their contrasting survivorship of the end-Cretaceous mass extinction.</p>
Data from: What makes a leaf tough? Patterns of correlated evolution between leaf toughness traits and demographic rates among 197 shade-tolerant woody species in a neotropical forest
Slow-growing juveniles of shade-tolerant plant species are predicted to have tough leaves because of the high cost of leaf replacement in shade relative to potential carbon gain. We assessed the degree of correlated evolution among eight traits associated with leaf toughness and their relationships with growth and mortality rates of 197 tree and shrub species from the understory of the 50-hectare forest dynamics plot on Barro Colorado Island, Panama. Path analysis with phylogenetically independent contrasts revealed that leaves attained material toughness (resistance to fracture per unit fracture area) through increases in tissue density, percent cellulose per unit dry mass, and vein fracture toughness. Lamina density and cellulose content evolved independently, and thus represent different paths to material toughness. Structural toughness (resistance to fracture per unit fracture length) depended on material toughness and lamina thickness. Mortality rates of individuals 1-10 cm in stem diameter were negatively correlated with material toughness and lamina density, but were independent of structural toughness and cell wall fiber contents. Leaf toughness traits were uncorrelated with relative growth rates. These results imply that material toughness enhances resistance to natural enemies, which increases survival and offsets the biomass allocation cost of producing tough leaves in the shaded understory.
Data from: Evaluating patterns of convergent evolution and trans-species polymorphism at MHC immunogenes in two sympatric stickleback species
The immunologically important major histocompatibility complex (MHC) harbors some of the most polymorphic genes in vertebrates. These genes presumably evolve under parasite-mediated selection and frequently show inconsistent allelic genealogies, where some alleles are more similar between species than within species. This phenomenon is thought to arise either from convergent evolution under parallel selection or from the preservation of ancient allelic lineages beyond speciation events (trans-species polymorphism, TSP). Here we examine natural populations of two sympatric stickleback species (Gasterosteus aculeatus and Pungitius pungitius) to investigate the contribution of these two mechanisms to the evolution of inconsistent allelic genealogies at the MHC. Overlapping parasite taxa between the two host species in three different habitats suggest contemporary parallel selection on the MHC genes. Accordingly, we detected a lack of species-specific phylogenetic clustering in the immunologically relevant antigen-binding residues of the MHC IIB genes which contrasted with the rest of the coding and non-coding sequence. However, clustering was not habitat-specific and a codon-usage analysis revealed patterns of similarity by descent. In this light, common descent via TSP, in combination with intra-species gene conversion, rather than convergent evolution is the more strongly supported scenario for the inconsistent genealogy at the MHC.
Data from: Whole genome shotgun phylogenomics resolves the pattern and timing of swallowtail butterfly evolution
Evolutionary relationships have remained unresolved in many well-studied groups, even though advances in next-generation sequencing and analysis, using approaches such as transcriptomics, anchored hybrid enrichment, or ultraconserved elements, have brought systematics to the brink of whole genome phylogenomics. Recently, it has become possible to sequence the entire genomes of numerous non-biological models in parallel at reasonable cost, particularly with shotgun sequencing. Here we identify orthologous coding sequences from whole-genome shotgun sequences, which we then use to investigate the relevance and power of phylogenomic relationship inference and time-calibrated tree estimation. We study an iconic group of butterflies - swallowtails of the family Papilionidae - that has remained phylogenetically unresolved, with continued debate about the timing of their diversification. Low-coverage whole genomes were obtained using Illumina shotgun sequencing for all genera. Genome assembly coupled to BLAST-based orthology searches allowed extraction of 6,621 orthologous protein-coding genes for 45 Papilionidae species and 16 outgroup species (with 32% missing data after cleaning phases). Supermatrix phylogenomic analyses were performed with both maximum-likelihood (IQ-TREE) and Bayesian mixture models (PhyloBayes) for amino acid sequences, which produced a fully resolved phylogeny providing new insights into controversial relationships. Species tree reconstruction from gene trees was performed with ASTRAL and SuperTriplets and recovered the same phylogeny. We estimated gene site concordant factors to complement traditional node-support measures, which strengthens the robustness of inferred phylogenies. Bayesian estimates of divergence times based on a reduced dataset (760 orthologs and 12% missing data) indicate a mid-Cretaceous origin of Papilionoidea around 99.2 million years ago (Ma) (95% credibility interval: 68.6-142.7 Ma) and Papilionidae around 71.4 Ma (49.8-103.6 Ma), with subsequent diversification of modern lineages well after the Cretaceous-Paleogene event. These results show that shotgun sequencing of whole genomes, even when highly fragmented, represents a powerful approach to phylogenomics and molecular dating in a group that has previously been refractory to resolution.
Data from: Conflicting phylogenomic signals reveal a pattern of reticulate evolution in a recent high-Andean diversification (Asteraceae: Astereae: Diplostephium)
High-throughput sequencing is helping biologists to overcome the difficulties of inferring the phylogenies of recently diverged taxa. The present study analyzes the phylogenetic signal of genomic regions with different inheritance patterns using genome skimming and ddRAD-seq in a species-rich Andean genus (Diplostephium) and its allies. We analyzed the complete nuclear ribosomal cistron, the complete chloroplast genome, a partial mitochondrial genome, and a nuclear-ddRAD matrix separately with phylogenetic methods. We applied several approaches to understand the causes of incongruence among datasets, including simulations and the detection of introgression using the D-statistic (ABBA-BABA test). We found significant incongruence among the nuclear, chloroplast, and mitochondrial phylogenies. The strong signal of hybridization found by simulations and the D-statistic among genera and inside the main clades of Diplostephium indicate reticulate evolution as a main cause of phylogenetic incongruence. Our results add evidence for a major role of reticulate evolution in events of rapid diversification. Hybridization and introgression confound chloroplast and mitochondrial phylogenies in relation to the species tree as a result of the uniparental inheritance of these genomic regions. Practical implications regarding the prevalence of hybridization are discussed in relation to the phylogenetic method.
Data from: Predators and patterns of within-host growth can mediate both among-host competition and the evolution of transmission potential of parasites
Parasite prevalence shows tremendous spatiotemporal variation. Theory indicates this variation might stem from life history characteristics of parasites and key ecological factors. Here, we illustrate how the interaction of an important predator and the schedule of 'transmission potential' of two parasites can explain parasite abundance. A field survey showed that a non-castrating fungus (Metschnikowia bicuspidata) commonly infected a dominant zooplankton host (Daphnia dentifera), while a castrating bacterial parasite (Pasteuria ramosa) was rare. This result seemed surprising given that the bacterium produces many more infectious propagules (spores) than the fungus upon host death. The fungus's dominance can be explained by the schedule of within host growth of parasites (i.e., how transmission potential changes over the course of infection) and spore release from 'sloppy predators' (Chaoborus spp., who consume Daphnia prey whole, then later regurgitate the carapace and parasite spores). In essence, sloppy predators create a niche that the faster-schedule fungus currently occupies. However, a selection experiment showed the slower-schedule bacterium can evolve into this faster-schedule, predator-mediated niche (but pays a cost in maximal spore yield to do so). Hence, our study shows how parasite life history can interact with predation to strongly influence the ecology, epidemiology, and evolution of infectious disease. 18 pages, 1 table, 5 figures; Appendix
Data from: Integrating phylogenomic and population genomic patterns in avian lice provides a more complete picture of parasite evolution
Parasite diversity accounts for most of the biodiversity on earth, and is shaped by many processes (e.g. cospeciation, host-switching). To identify the effects of the processes that shape parasite diversity, it is ideal to incorporate both deep (phylogenetic) and shallow (population) perspectives. To this end, we developed a novel workflow to obtain phylogenetic and population genetic data from whole genome sequences of body lice parasitizing New World ground-doves. Phylogenies from these data showed consistent, highly resolved species-level relationships for the lice. By comparing the louse and ground-dove phylogenies, we found that over long-term evolutionary scales their phylogenies were largely congruent. Many louse lineages (both species and populations) also demonstrated high host-specificity, suggesting ground-dove divergence is a primary driver of their parasites' diversity. However, the few louse taxa that are generalists are structured according to biogeography at the population level. This suggests dispersal among sympatric hosts has some effect on body louse diversity, but over deeper time scales the parasites eventually sort according to host species. Overall, our results demonstrate that multiple factors explain the patterns of diversity in this group of parasites, and that the effects of these factors can vary over different evolutionary scales. The integrative approach we employed was crucial for uncovering these patterns, and should be broadly applicable to other studies.
Data from: Megaphylogeny resolves global patterns of mushroom evolution
Mushroom-forming fungi (Agaricomycetes) have the greatest morphological diversity and complexity of any group of fungi. They have radiated into most niches and fulfill diverse roles in the ecosystem, including wood decomposers, pathogens or mycorrhizal mutualists. Despite the importance of mushroom-forming fungi, large-scale patterns of their evolutionary history are poorly known, in part due to the lack of a comprehensive and dated molecular phylogeny. Here, using multigene and genome-based data, we assemble a 5,284-species phylogenetic tree and infer molecular clock ages and broad patterns of speciation/extinction and morphological innovation in mushroom-forming fungi. Agaricomycetes started a rapid class-wide radiation in the Jurassic, coinciding with the spread of (sub)tropical coniferous forests and a warming climate. A possible mass extinction, several clade-specific adaptive radiations, and morphological diversification of fruiting bodies followed during the Cretaceous and the Paleogene, convergently giving rise to the classic toadstool morphology, with a cap, stalk, and gills. This morphology is associated with increased rates of lineage diversification, suggesting it represents a key innovation in the evolution of mushroom-forming fungi. The accumulation of mushroom diversity started during the Mesozoic-Cenozoic radiation event, an era of humid climate when terrestrial communities dominated by gymnosperms and reptiles were also expanding.
Data from: Adaptive evolution and environmental durability jointly structure phylodynamic patterns in avian influenza viruses
Avian influenza viruses (AIVs) have been pivotal to the origination of human pandemic strains. Despite their scientific and public health significance, however, there remains much to be understood about the ecology and evolution of AIVs in wild birds, where major pools of genetic diversity are generated and maintained. Here, we present comparative phylodynamic analyses of human and AIVs in North America, demonstrating (i) significantly higher standing genetic diversity and (ii) phylogenetic trees with a weaker signature of immune escape in AIVs than in human viruses. To explain these differences, we performed statistical analyses to quantify the relative contribution of several potential explanations. We found that HA genetic diversity in avian viruses is determined by a combination of factors, predominantly subtype-specific differences in host immune selective pressure and the ecology of transmission (in particular, the durability of subtypes in aquatic environments). Extending this analysis using a computational model demonstrated that virus durability may lead to long-term, indirect chains of transmission that, when coupled with a short host lifespan, can generate and maintain the observed high levels of genetic diversity. Further evidence in support of this novel finding was found by demonstrating an association between subtype-specific environmental durability and predicted phylogenetic signatures: genetic diversity, variation in phylogenetic tree branch lengths, and tree height. The conclusion that environmental transmission plays an important role in the evolutionary biology of avian influenza viruses—a manifestation of the "storage effect"—highlights the potentially unpredictable impact of wildlife reservoirs for future human pandemics and the need for improved understanding of the natural ecology of these viruses.
Data from: Biophysical modeling of the temporal niche: from first principles to the evolution of activity patterns
Most mammals can be characterized as nocturnal or diurnal. However infrequently, species may overcome evolutionary constraints and alter their activity patterns. We modeled the fundamental temporal niche of a diurnal desert rodent, the golden spiny mouse, Acomys russatus. This species can shift into nocturnal activity in the absence of its congener, the common spiny mouse, A. cahirinus, suggesting that it was competitively driven into diurnality, and that this shift in a small desert rodent may involve physiological costs. Therefore, we compared metabolic costs of diurnal vs. nocturnal activity using a biophysical model to evaluate the preferred temporal niche of this species. The model predicted that energy expenditure during foraging is almost always lower during the day except during mid-day in summer at the less sheltered microhabitat. We also found that a shift in summer to foraging in less sheltered microhabitats in response to predation pressure and food availability involves a significant physiological cost moderated by midday reduction in activity. Thus adaptation to diurnality may reflect the 'ghost of competition past'; Climate-driven diurnality is an alternative but less likely hypothesis. While climate is considered to play a major role in the physiology and evolution of mammals, this is the first study to model its effect on the evolution of activity patterns of mammals.
FIGURE 6 in A new species of bright-eyed treefrog (Mantellidae) from Madagascar, with comments on call evolution and patterns of syntopy in the Boophis ankaratra complex
FIGURE 6. Comparative oscillograms (top) and corresponding spectrograms (bottom) of single notes of the advertisement calls on the same time scale in the Boophis ankaratra complex. Species shown are: (A) B. boppa (Maharira); (B) B. miadana (Andohahela); (C) B. ankaratra (Maharira); (D) B. schuboeae (Ambatolahy); and (E) B. haingana (Andohahela). Spectrogram was produced in SEEWAVE using a Hanning window length of 512.
FIGURE 12 in A new species of bright-eyed treefrog (Mantellidae) from Madagascar, with comments on call evolution and patterns of syntopy in the Boophis ankaratra complex
FIGURE 12. Reproductive behavior of species of the B. ankaratra complex. (A) A typical perch of a male B. boppa preparing to call; (B) a male B. boppa during emission of advertisement call; and (C) amplexus, male not collected, female KU 336829 of B. boppa.
FIGURE 9 in A new species of bright-eyed treefrog (Mantellidae) from Madagascar, with comments on call evolution and patterns of syntopy in the Boophis ankaratra complex
FIGURE 9. Minimum-spanning haplotype network for the nuclear exon DNAH-3 in the B. albipunctatus group. Ticks on branches represent single nucleotide changes. Branch lengths are not meaningful.
FIGURE 1 in A new species of bright-eyed treefrog (Mantellidae) from Madagascar, with comments on call evolution and patterns of syntopy in the Boophis ankaratra complex
FIGURE 1. The distribution of species in the Boophis albipunctatus group in southeastern Madagascar. The black dotted line shows the boundaries of Ranomafana National Park (RNP), and partially colored circles indicate syntopy of their corresponding species. The numbered localities are as follows (species occurring at each locality abbreviated as BA, B. ankaratra; BB, B. boppa, BL, B. luciae; BS, B. schuboeae): Within RNP: (1) Maharira (BA, BB; type locality of BB); (2) Valohoaka (BL); (3) Vohiparara (BS); (4) Andranoroa river (BA, BB); (5) Sakaroa (BB); (6) Ambatolahy (BL, BS); (7–8) Imaloka (BB, BL); and (9) Andemaka (BB, BL). Outside RNP: (10) Ambohitsara-Ranomafana (BL); (11) Farihimazava (BA, BB); (12) Soamazaka (BA, BB); and (13) Vohisokina (BA, BB). Note that at Ambohitsara, records also exist for another species of the group (B. albipunctatus) that is not discussed herein.
FIGURE 5 in A new species of bright-eyed treefrog (Mantellidae) from Madagascar, with comments on call evolution and patterns of syntopy in the Boophis ankaratra complex
FIGURE 5. Comparative photographs of members of the Boophis ankaratra complex. (A) Boophis ankaratra; (B) Boophis haingana; (C) Boophis miadana; and (D) Boophis schuboeae.
FIGURE 8 in A new species of bright-eyed treefrog (Mantellidae) from Madagascar, with comments on call evolution and patterns of syntopy in the Boophis ankaratra complex
FIGURE 8. Results of phylogenetic analysis of the concatenated 16S alignment for maximum likelihood (ML) and Bayesian (BA) analyses. Topology is a consensus tree from MrBayes. Significant support for ML and BA analyses are indicated by the black circles at the nodes (analyses were completely consistent). Note that Boophis boppa is strongly supported as reciprocally monophyletic with respect to all other species of the B. ankaratra complex.
FIGURE 11 in A new species of bright-eyed treefrog (Mantellidae) from Madagascar, with comments on call evolution and patterns of syntopy in the Boophis ankaratra complex
FIGURE 11. Close-up photographs of different living specimens of Boophis boppa showing variation in eye color.
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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.