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238 results for “Evolutionary relationships”
Figure 1 in Evolutionary relationships of euthyneuran gastropods (Mollusca): a cladistic re-evaluation of morphological characters
Figure 1. Phylogeny of Euthyneura proposed by Salvini-Plawen & Steiner (1996) according to anatomical characters.
Data from: Whole genomes reveal evolutionary relationships and mechanisms underlying gene-tree discordance in Neodiprion sawflies
<p>Rapidly evolving taxa are excellent models for understanding the mechanisms that give rise to biodiversity. However, developing an accurate historical framework for comparative analysis of such lineages remains a challenge due to ubiquitous incomplete lineage sorting and introgression. Here, we use a whole-genome alignment, multiple locus-sampling strategies, and locus-based and SNP-based species-tree methods to infer a species tree for eastern North American <em>Neodiprion</em> species, a clade of pine-feeding sawflies (Order: Hymenopteran; Family: Diprionidae). We recovered a well-supported species tree that—except for three uncertain relationships—is robust to different strategies for analyzing whole-genome data. Despite this consistency, underlying gene-tree discordance is high. To understand this discordance, we use multiple regression to model topological discordance as a function of several genomic features. We find that gene-tree discordance tends to be higher in regions of the genome that may be more prone to gene-tree estimation error, as indicated by a lower density of parsimony-informative sites, a higher density of genes, a higher average pairwise genetic distance, and gene trees with lower average bootstrap support. Also, contrary to the expectation that discordance via incomplete lineage sorting is reduced in low-recombination regions of the genome, we find a <em>negative</em> correlation between recombination rate and topological discordance. We offer potential explanations for this pattern and hypothesize that it may be unique to lineages that have diverged with gene flow. Our analysis also reveals an unexpected discordance hotspot on Chromosome 1, which contains several genes potentially involved in mitochondrial-nuclear interactions and produces a gene-tree that resembles a highly discordant mitochondrial tree. Based on these observations, we hypothesize that our genome-wide scan for topological discordance has identified a nuclear locus involved in a mito-nuclear incompatibility. Together, these results demonstrate how phylogenomic analysis coupled with high-quality, annotated genomes can generate novel hypotheses about the mechanisms that drive divergence and produce variable genealogical histories across genomes.</p>
Data from: Phylogenomic insights into the relationship and the evolutionary history of planthoppers (Insecta: Hemiptera: Fulgoromorpha)
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Data from: Evolutionary relationships among bullhead sharks (Chondrichthyes: Heterodontiformes)
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A Bayesian extension of phylogenetic generalized least squares (PGLS): incorporating uncertainty in the comparative study of trait relationships and evolutionary rates
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Data from: Whole genomes reveal evolutionary relationships and mechanisms underlying gene-tree discordance in Neodiprion sawflies
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Data from: A multilocus analysis of Epicopeiidae (Lepidoptera, Geometroidea) provides new insights into their relationships and the evolutionary history of mimicry
<p>The family Epicopeiidae is a small group of day-flying moths, known for mimicking many different groups of butterflies and moths. So far, there still lacks a reliable phylogenetic framework of Epicopeiidae that is necessary to our understanding of the evolutionary process of their mimicry. In this study, we sequenced 94 nuclear protein-coding markers for 56 epicopeiid samples and 11 outgroups, covering all ten genera of Epicopeiidae. We used homemade PCR-generated baits to capture target sequences, which allowed us to utilize old and dried specimens that were difficult to handle by conventional PCR + Sanger sequencing. Maximum likelihood and Bayesian analyses of the newly obtained dataset (86,388 bp) at both DNA and protein levels produced identical phylogenies with strong support. The non-mimicry genus <em>Deuveia</em> is the sister group of other epicopeiid genera. <em>Epicopeia</em> and <em>Nossa</em> are not monophyletic, and these two genera nest together to form a clade. We also estimated divergence times of Epicopeiidae and found that their initial diversification happened in Eocene about 41 million years ago. The ancestral state reconstruction of mimicry type for this family suggested that the last common ancestor of epicopeiid moths is non-mimetic, and the Riodinidae-mimicry type evolved first. In summary, our work provides a comprehensive and robust time-calibrated phylogeny of Epicopeiidae that provides a sound framework for revising their classification and interpreting character evolution.</p>
Data from: Divergent trait and environment relationships among parallel radiations in Pelargonium (Geraniaceae): a role for evolutionary legacy?
Functional traits in closely related lineages are expected to vary similarly along common environmental gradients due to shared evolutionary and biogeographic history, or legacy effects, and due to biophysical tradeoffs in construction. We test these predictions in Pelargonium, a relatively recent evolutionary radiation. Bayesian phylogenetic mixed effects models assessed, at the subclade level, associations between plant height, leaf area, leaf nitrogen content and leaf mass per area (LMA), and five environmental variables capturing temperature and rainfall gradients across the Greater Cape Floristic Region of South Africa. Trait-trait integration was assessed via pairwise-correlations within subclades. Of 20 trait-environment associations, 17 differed among subclades. Signs of regression coefficients diverged for height, leaf area and leaf nitrogen content, but not for LMA. Subclades also differed in trait-trait relationships and these differences were modulated by rainfall seasonality. Leave-one-out cross-validation revealed that whether trait variation was better predicted by environmental predictors or trait-trait integration depended on the clade and trait in question. Legacy signals in trait-environment and trait-trait relationships were apparently lost during the earliest diversification of Pelargonium, but then retained during subsequent subclade evolution. Overall, we demonstrate that global-scale patterns are poor predictors of patterns of trait variation at finer geographic and taxonomic scales.
Data from: Analysis of evolutionary relationships provides new clues to the origins of weedy rice
<p>Weedy rice (Oryza sativa f. spontanea) is considered to be a pest in modern rice production systems because it competes for resources, has poor yield characteristics, and subsequently has a negative effect on rice grain yield. The evolutionary relationships among weedy rice, landrace rice, improved rice cultivars, and wild rice are largely unknown. In this study, we conducted a population genetic analysis based on neutral markers and gene haplotypes in 524 rice accessions and a comparative transcriptomic analysis using 15 representative samples. The results showed that weedy rice populations have the highest level of genetic diversity (He=0.8386), and can be divided into two groups (japonica-type and indica-type). The japonica-type weedy rice accessions from HLJ, JL, LN, and NX provinces clustered with the landraces grown in these same provinces. The indica-types from JS province also clustered with the indica-type landraces from JS province. Comparative transcriptome analysis of weedy rice populations, improved rice populations. and landrace rice from HLJ, JL and LN provinces showed that the weedy rice still clustered with the landrace rice, and that the improved rice lines comprise a single population. Thirty-two differentially expressed genes were shared by the improved rice and landrace rice groups as well as between the improved rice and weedy rice groups. Using GO analysis, we identified 19 shared GO terms in the improved rice and landrace rice groups as well as between the improved rice and weedy rice groups. Our results suggest that weedy rice populations in China have diverse origins, and comparative transcriptome analysis of different types of rice from HLJ, JL, and LN suggests that improved rice populations have become a medium or end point in the evolution of weedy rice, which provides a new perspective for the study of weedy rice origins and lays a solid foundation for rice breeding.</p>
A quantitative assessment of the patterns of integration in the mandible of bovids and their relationships with trophic ecology, phylogeny, and evolutionary rates
<p>Dataset and R script supporting the findings of the study "A quantitative assessment of the patterns of integration in the mandible of bovids and their relationships with trophic ecology, phylogeny, and evolutionary rates". </p>
The Community Coevolution Model with application to the study of evolutionary relationships between genes based on phylogenetic profiles
<p>Organismal traits can evolve in a coordinated way, with correlated patterns of gains and losses reflecting important evolutionary associations. Discovering these associations can reveal important information about the functional and ecological linkages among traits. Phylogenetic profiles treat individual genes as traits distributed across sets of genomes and can provide a fine-grained view of the genetic underpinnings of evolutionary processes in a set of genomes. Phylogenetic profiling has been used to identify genes that are functionally linked, and to identify common patterns of lateral gene transfer in microorganisms. However, comparative analysis of phylogenetic profiles and other trait distributions should take into account the phylogenetic relationships among the organisms under consideration.</p> <p>Here we propose the Community Coevolution Model (CCM), a new coevolutionary model to analyze the evolutionary associations among traits, with a focus on phylogenetic profiles. In the CCM, traits are considered to evolve as a community with interactions, and the transition rate for each trait depends on the current states of other traits. Surpassing other comparative methods for pairwise trait analysis, CCM has the additional advantage of being able to examine multiple traits as a community to reveal more dependency relationships. We also develop a simulation procedure to generate phylogenetic profiles with correlated evolutionary patterns that can be used as benchmark data for evaluation purposes.</p> <p>A simulation study demonstrates that CCM is more accurate than other methods including the Jaccard Index and three tree-aware methods. The parameterization of CCM makes the interpretation of the relations between genes more direct, which leads to Darwin's scenario being identified easily based on the estimated parameters. We show that CCM is more efficient and fits real data better than other methods resulting in higher likelihood scores with fewer parameters. An examination of 3786 phylogenetic profiles across a set of 659 bacterial genomes highlights linkages between genes with common functions, including many patterns that would not have been identified under a non-phylogenetic model of common distribution. We also applied the CCM to 44 proteins in the well-studied Mitochondrial Respiratory Complex I and recovered associations that mapped well onto the structural associations that exist in the complex.</p>
Figure 1 in Evolutionary relationships among several species from the genus Cricotopus (Diptera: Chironomidae): What about Turkish representatives of this genus?
Figure 1. Sampling localities of the collected Cricotopus specimens in this study.
Data from: Genomewide variation provides insight into evolutionary relationships in a monkeyflower species complex (Mimulussect.Diplacus)
PREMISE OF THE STUDY: Evolutionary radiations provide excellent opportunities to study the origins of biodiversity, but rapid divergence and ongoing gene flow make inferring evolutionary relationships among taxa difficult. Consequently, multiple tools that combine morphological and genomic analyses may be necessary to provide a clear picture of relationships. We used an integrative approach to shed light on relationships within a diverse radiation of monkeyflowers (Mimulus section Diplacus) with a controversial taxonomic history. METHODS: Using genome-wide SNP data, we performed a combination of phylogenetic and population genomic analyses to infer the evolutionary relationships within the group. Tests for hybridization were performed to reveal sources of shared variation, and multivariate analyses of floral trait data were conducted to examine the relationship between phenotypic and phylogenetic information. KEY RESULTS: We identified four primary clades with evidence for some shared variation among them. We also detected evidence for recent gene flow between closely related subclades and populations. Strong discordance between floral trait and molecular data provides evidence for divergent and convergent phenotypic evolution. CONCLUSIONS: Mimulus section Diplacus exhibits all of the hallmarks of a rapid radiation, including diverse taxa that are at different stages of divergence, extensive shared variation among taxa, and complex patterns of phenotypic evolution. Our findings will direct future evolutionary research and have important taxonomic implications, highlighting the need for a new revision of section Diplacus.
Data from: Evolutionary–phylogenetic pathway of the Cretaceous ammonite genus Aegocrioceras and its relationship to Juddiceras spp. and Crioceratites spp.
<p>The systematics of ammonoids are complicated by their large degree of intra-specific variation, which complicates a stable validation of species. <i>Aegocrioceras</i> is a heteromorph ammonite from the Lower Saxony Basin in the Hauterivian Boreal, and a prime example of a genus with an unstable internal systematic and external relationship to other ammonoids. Here, we use quantitative morphometrics on <i>Aegocrioceras</i> species from an assemblage collected in the clay pit Resse (north-west Germany) to evaluate the systematics and phylogeny of this Cretaceous genus. We simplify the systematic of the genus into the three entities <i>A. bicarinatum</i> [m]/<i>A. semicinctum</i> [M] complex (which potentially contains <i>A. quadratum</i> as well), <i>A. raricostatum</i> and <i>A. spathi</i>. The most likely phylogeny coincides very well with the stratigraphic record of the species and implies anagenetic adaptations in <i>A. raricostatum</i> and <i>A. spathi</i> after the origin of the species. <i>Aegocrioceras</i> most likely derived from warm-water adapted Tethyan <i>Crioceratites</i> species, and Boreal <i>Crioceratites</i> are potentially warm-water adapted descendants of the cold-water adapted <i>Aegocrioceras </i>but may alternatively represent renewed Tethyan invasions. Our data imply that <i>Aegocrioceras</i>' success against incumbent ammonites in the Boreal was rooted in abiotic change (Court Jester) processes due to its high adaptability, while selection within the <i>Aegocrioceras</i> clade was more likely based on biotic interaction (Red Queen) processes.</p>
Fig. 1. A in Cytotaxonomic diagnosis of Trichomycterus diabolus (Teleostei: Trichomycteridae) with comments about its evolutionary relationships with co-generic species
Fig. 1. A specimen of Trichomycterus diabolus with 110 mm in total length. Photo by C. Oliveira.
Plastid phylogenomics shed light on intergeneric relationships and spatiotemporal evolutionary history of Melocanninae (Poaceae: Bambusoideae)
Melocanninae is sister to other subtribes of Paleotropical woody bamboos with some 90 species mainly concentrated in Asia. However, phylogenetic relationships within the subtribe are poorly known. Here, we filled the gaps in complete plastome data of Melocanninae, reconstructed the phylogeny of Melocanninae, and further estimated divergence time and ancestral distribution range. Our results showed that the two major genera, <i>Cephalostachyum </i>and <i>Schizostachyum</i>, were paraphyletic. Species of <i>Cephalostachyum</i> were resolved in two successive basal clades, while <i>Annamocalamus</i> was embedded in the <i>Schizostachyum</i> clade. Different plastid regions provided inconsistent signals for the relationship of <i>Melocanna</i> and <i>Pseudostachyum</i>. Conservative loci supported a successive divergence rather than sister relationship between them and the difference may be caused by long-branch attraction. We infer that Melocanninae originated in the East Himalaya to northern Myanmar in the early Miocene. Three routes were revealed in forming its present biogeographic pattern: <i>in situ</i> diversification on the Asian mainland; dispersing southwest to Sri Lanka and to the Western Ghats in South India; and spreading southeast to Malesia and Oceania via the Indo-China Peninsula. The rapid uplift of the Tibetan Plateau and the intensification of Asian monsoons since the Miocene and the sea-level-fall events since the late Miocene might be potential driving forces for diversification of Melocanninae and, particularly the latter event, for the species radiation of <i>Schizostachyum</i>.
Data from: Divergent trait and environment relationships among parallel radiations in Pelargonium (Geraniaceae): a role for evolutionary legacy?
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Evolutionary relationship between plants and insects: Insights from island communities
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Data from: Genomewide variation provides insight into evolutionary relationships in a monkeyflower species complex (Mimulussect.Diplacus)
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Data from: Evolutionary–phylogenetic pathway of the Cretaceous ammonite genus Aegocrioceras and its relationship to Juddiceras spp. and Crioceratites spp.
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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.