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377 results for “evolution of complexity”
Figure 4 from: Gąsiorek P, Vončina K, Michalczyk Ł (2020) An overview of the sexual dimorphism in Echiniscus (Heterotardigrada, Echiniscoidea), with the description of Echiniscus masculinus sp. nov. (the virginicus complex) from Borneo. Zoosystematics and Evolution 96(1): 103-113. https://doi.org/10.3897/zse.96.49989
Figure 4 Bayesian phylogenetic trees showing the relationships between members of the E. virginicus complex; E. succineus was used as an outgroup, and branches within species-specific clades were collapsed. Bayesian posterior probability values are given above tree branches. Phylogenetic analyses were run on the subsequent DNA markers to assure that the tree topology was congruent: COI, ITS-1, and ITS-2.
Figure 1 from: Gąsiorek P, Vončina K, Michalczyk Ł (2020) An overview of the sexual dimorphism in Echiniscus (Heterotardigrada, Echiniscoidea), with the description of Echiniscus masculinus sp. nov. (the virginicus complex) from Borneo. Zoosystematics and Evolution 96(1): 103-113. https://doi.org/10.3897/zse.96.49989
Figure 1 Morphology of Echiniscus masculinus sp. nov. (PCM). A. Adult female (holotype, dorsolateral view); B. Juvenile (paratype, dorsolateral view); C. Subcephalic plates; D. Genital plates enclosing male gonopore; E. First leg pair with claws and spine I. All scale bars in µm.
Supplementary material 1 from: Gąsiorek P, Vončina K, Michalczyk Ł (2020) An overview of the sexual dimorphism in Echiniscus (Heterotardigrada, Echiniscoidea), with the description of Echiniscus masculinus sp. nov. (the virginicus complex) from Borneo. Zoosystematics and Evolution 96(1): 103-113. https://doi.org/10.3897/zse.96.49989
: Data type: morphometric data
Figs 69a-69b in ClassiIication, Natural History, and Evolution oI the SubIamily Peloniinae OPITZ (Coleoptera, Cleroidea, Cleridae). Part XIII. The New World genera oI checkered beetles of the Labasiella complex
Figs 69a-69b: (69a) Proposed phylogeny of Labasiella species group and related genera. (69b) Bootstrap consensus tree of Labasiella species group and related genera.
Figs 72-80 in ClassiIication, Natural History, and Evolution oI the SubIamily Peloniinae OPITZ (Coleoptera, Cleroidea, Cleridae). Part XIII. The New World genera oI checkered beetles of the Labasiella complex
Figs 72-80: Habitus. (72) Amphelissus goniodus. (73) A. meieri. (74) Inconnexus lunarus. (75) Labasiella bimaculatus. (76) L. boyaca. (77) L. cochabamba. (78) L. mcclarini. (79) L. eugeniae. (80) L. robles.
Figs 61-62 in ClassiIication, Natural History, and Evolution oI the SubIamily Peloniinae OPITZ (Coleoptera, Cleroidea, Cleridae). Part XIII. The New World genera oI checkered beetles of the Labasiella complex
Figs 61-62: Pronotum and prothoracic venter of Amphelissus meieri. (61) Pronotum. (62) Prothoracic venter.
Figs 1-27 in ClassiIication, Natural History, and Evolution oI the SubIamily Peloniinae OPITZ (Coleoptera, Cleroidea, Cleridae). Part XIII. The New World genera oI checkered beetles of the Labasiella complex
Figs 1-27: Antennae. (1) Amphelissus goniodus, female. (2) A. meieri, female. (3) Inconnexus lunarus, male. (4) Labasiella lata, female. (5) L. labaticollis, female. (6) L. machupicchu, male. 7. L. santa, female. (8) L. stangei, male. (9) L. tucumanensis, male. (10) L. varipennis, male. (11) Pelmatus barri, male. (12) P. barri, female. (13) P. bicolor, female. (14) Macilentus micidus, female. (15) Oncochelyna barrigai, female. (16) O. tuberculata, female. (17) Silvanoclerus dilatus, female. (18) S. beechi, male. (19) Labasiela bimaculata, female. (20) L. boyaca, male. (21) L. cochabamba, male. (22) L. eugeniae, male. (23) L. mcclarini, female. (24) L. solervicensi, female. (25) L. robles, female. (26) L. transversalis, male. (27) L. transversalis, female.
Data from: Head-turning morphologies: evolution of shape diversity in the mammalian atlas-axis complex
Mammals flex, extend, and rotate their spines as they perform behaviors critical for survival, such as foraging, consuming prey, locomoting, and interacting with conspecifics or predators. The atlas-axis complex is a mammalian innovation that allows precise head movements during these behaviors. While morphological variation in other vertebral regions has been linked to ecological differences in mammals, less is known about morphological specialization in the cervical vertebrae, which are developmentally constrained in number but highly variable in size and shape. Here, we present the first phylogenetic comparative study of the atlas-axis complex across mammals. We used spherical harmonics to quantify 3D shape variation of the atlas and axis across a diverse sample of species, and performed phylogenetic analyses to investigate if vertebral shape is associated with body size, locomotion, and diet. We found that differences in atlas and axis shape are partly explained by phylogeny, and that mammalian subclades differ in morphological disparity. Atlas and axis shape diversity is associated with differences in body size and locomotion; large terrestrial mammals have craniocaudally elongated vertebrae, while smaller mammals and aquatic mammals have more compressed vertebrae. These results provide a foundation for investigating functional hypotheses underlying the evolution of neck morphologies across mammals.
Data from: The evolution of colour pattern complexity: selection for conspicuousness favours contrasting within-body colour combinations in lizards
Many animals display complex colour patterns that comprise several adjacent, often contrasting colour patches. Combining patches of complementary colours increases the overall conspicuousness of the complex pattern, enhancing signal detection. Therefore, selection for conspicuousness may act not only on the design of single colour patches, but also on their combination. Contrasting long- and short-wavelength colour patches are located on the ventral and lateral surfaces of many lacertid lizards. As the combination of long- and short-wavelength-based colours generates local chromatic contrast, we hypothesized that selection may favour the co-occurrence of lateral and ventral contrasting patches, resulting in complex colour patterns that maximize the overall conspicuousness of the signal. To test this hypothesis, we performed a comparative phylogenetic study using a categorical colour classification based on spectral data and descriptive information on lacertid coloration collected from the literature. Our results demonstrate that conspicuous ventral (long-wavelength-based) and lateral (short-wavelength-based) colour patches co-occur throughout the lacertid phylogeny more often than expected by chance, especially in the subfamily Lacertini. These results suggest that selection promotes the evolution of the complex pattern rather than the acquisition of a single conspicuous colour patch, possibly due to the increased conspicuousness caused by the combination of colours with contrasting spectral properties.
Data from: Is sociality required for the evolution of communicative complexity? Evidence weighed against alternative hypotheses in diverse taxonomic groups
Complex social communication is expected to evolve whenever animals engage in many and varied social interactions; that is, sociality should promote communicative complexity. Yet informal comparisons among phylogenetically independent taxonomic groups seem to cast doubt on the putative role of social factors in the evolution of complex communication. Here, we provide a formal test of the sociality hypothesis along side alternative explanations for the evolution of communicative complexity. We compiled data documenting variation in signal complexity among closely related species for several case study groups – ants, frogs, lizards and birds – and used new phylogenetic methods to investigate the factors underlying communication evolution. Social factors were only implicated in the evolution of complex visual signals in lizards. Ecology, and to some degree allometry, were most likely explanations for complexity in the vocal signals of frogs (ecology) and birds (ecology and allometry). There was some evidence for adaptive evolution in the pheromone complexity of ants, although no compelling selection pressure was identified. For most taxa, phylogenetic null models were consistently ranked above adaptive models and, for some taxa, signal complexity seems to have accumulated in species via incremental or random changes over long periods of evolutionary time. Becoming social presumably lead to the origin of social communication in animals, but its subsequent influence on the trajectory of signal evolution has been neither clear-cut nor general among taxonomic groups.
Data from: Genomic evidence for the parallel evolution of coastal forms in the Senecio lautus complex
Instances of parallel ecotypic divergence where adaptation to similar conditions repeatedly cause similar phenotypic changes in closely related organisms are useful for studying the role of ecological selection in speciation. Here we used a combination of traditional and next generation genotyping techniques to test for the parallel divergence of plants from the Senecio lautus complex, a phenotypically variable groundsel that has adapted to disparate environments in the South Pacific. Phylogenetic analysis of a broad selection of Senecio species showed that members of the S. lautus complex form a distinct lineage that has diversified recently in Australasia. An inspection of thousands of polymorphisms in the genome of 27 natural populations from the S. lautus complex in Australia revealed a signal of strong genetic structure independent of habitat and phenotype. Additionally, genetic differentiation between populations was correlated with the geographical distance separating them, and the genetic diversity of populations strongly depended on geographical location. Importantly, coastal forms appeared in several independent phylogenetic clades, a pattern that is consistent with the parallel evolution of these forms. Analyses of the patterns of genomic differentiation between populations further revealed that adjacent populations displayed greater genomic heterogeneity than allopatric populations and are differentiated according to variation in soil composition. These results are consistent with a process of parallel ecotypic divergence in face of gene flow.
Data from: Chloroplast phylogenomic data from the green algal order Sphaeropleales (Chlorophyceae, Chlorophyta) reveal complex patterns of sequence evolution
Chloroplast sequence data are widely used to infer phylogenies of plants and algae. With the increasing availability of complete chloroplast genome sequences, the opportunity arises to resolve ancient divergences that were heretofore problematic. On the flip side, properly analyzing large multi-gene data sets can be a major challenge, as these data may be riddled with systematic biases and conflicting signals. Our study contributes new data from nine complete and four fragmentary chloroplast genome sequences across the green algal order Sphaeropleales. Our phylogenetic analyses of a 56-gene data set show that analyzing these data on a nucleotide level yields a well-supported phylogeny – yet one that is quite different from a corresponding amino acid analysis. We offer some possible explanations for this conflict through a range of analyses of modified data sets. In addition, we characterize the newly sequenced genomes in terms of their structure and content, thereby further contributing to the knowledge of chloroplast genome evolution.
Data from: Turning one into five: integrative taxonomy uncovers complex evolution of cryptic species in the harvester ant Messor "structor"
Seed harvesting ants are ecosystem engineers that shape vegetation, nutrient cycles, and microclimate. Progress in ecological research is, however, slowed down by poor species delimitation. For example, it has not been resolved to date, how many species the European harvester ant Messor "structor" (Latreille, 1798) represents. Since its first description, splitting into additional taxa was often proposed but not accepted later on due to inconsistent support from morphology and ecology. Here, we took an iterative integrative-taxonomy approach – comparing multiple, independent data sets on the same sample – and used traditional morphometrics, Wolbachia symbionts, mitochondrial DNA, amplified fragment length polymorphism, and ecological niche modelling. Using the complementarity of the data sets applied, we resolved multiple, strong disagreements over the number of species, ranging from four to ten, and the allocation of individuals to species. We consider most plausible a five-species hypothesis and conclude the taxonomic odyssey by redescribing Messor structor, M. ibericus Santschi, 1925, and M. muticus (Nylander, 1849) stat.rev., and by describing two new species, M. ponticus sp.n. and M. mcarthuri sp.n. The evolutionary explanations invoked in resolving the various data conflicts include pronounced morphological crypsis, incomplete lineage-sorting or ongoing cospeciation of endosymbionts, and peripatric speciation – these ants' significance to evolutionary biology parallels that to ecology. The successful solution of this particular problem illustrates the usefulness of the integrative approach to other systematic problems of comparable complexity and the importance of understanding evolution to drawing correct conclusions on species' attributes, including their ecology and biogeography.
Data from: Multiple sexual selection pressures drive the rapid evolution of complex morphology in a male secondary genital structure
The genitalia of internally fertilizing taxa represent a striking example of rapid morphological evolution. Although sexual selection can shape variation in genital morphology, it has been difficult to test whether multiple sexual selection pressures combine to drive the rapid evolution of individual genital structures. Here, we test the hypothesis that both pre- and postcopulatory sexual selection can act in concert to shape complex structural variation in secondary genital morphology. We genetically modified the size and shape of the posterior lobes of Drosophila melanogaster males and tested the consequences of morphological variation on several reproductive measures. We found that the posterior lobes are necessary for genital coupling and that they are also the targets of multiple postcopulatory processes that shape quantitative variation in morphology, even though these structures make no direct contact with the external female genitalia or internal reproductive organs during mating. We also found that males with smaller and less structurally complex posterior lobes suffer substantial fitness costs in competitive fertilization experiments. Our results show that sexual selection mechanisms can combine to shape the morphology of a single genital structure and that the posterior lobes of D. melanogaster are the targets of multiple postcopulatory selection pressures.
Data from: Golden orbweavers ignore biological rules: phylogenomic and comparative analyses unravel a complex evolution of sexual size dimorphism
Instances of sexual size dimorphism (SSD) provide the context for rigorous tests of biological rules of size evolution, such as Cope's Rule (phyletic size increase), Rensch's Rule (allometric patterns of male and female size), as well as male and female body size optima. In certain spider groups, such as the golden orbweavers (Nephilidae), extreme female-biased SSD (eSSD, female:male body length ≥ 2) is the norm. Nephilid genera construct webs of exaggerated proportions, which can be aerial, arboricolous, or intermediate (hybrid). First, we established the backbone phylogeny of Nephilidae using 367 Anchored Hybrid Enrichment (AHE) markers, then combined these data with classical markers for a reference species-level phylogeny. Second, we used the phylogeny to test Cope and Rensch's Rules, sex specific size optima, and the coevolution of web size, type, and features with female and male body size and their ratio, SSD. Male, but not female, size increases significantly over time, and refutes Cope's Rule. Allometric analyses reject the converse, Rensch's Rule. Male and female body sizes are uncorrelated. Female size evolution is random, but males evolve towards an optimum size (3.2-4.9 mm). Overall, female body size correlates positively with absolute web size. However, intermediate sized females build the largest webs (of the hybrid type), giant female Nephila and Trichonephila build smaller webs (of the aerial type), and the smallest females build the smallest webs (of the arboricolous type). We propose taxonomic changes based on the criteria of clade age, monophyly and exclusivity, classification information content, and diagnosability. Spider families, as currently defined, tend to be between 37-98 million years old, and Nephilidae is estimated at 133 Ma (97 - 146), thus deserving family status. We therefore resurrect the family Nephilidae Simon 1894 that contains Clitaetra Simon 1889, the Cretaceous Geratonephila Poinar & Buckley 2012, Herennia Thorell 1877, Indoetra Kuntner 2006, new rank, Nephila Leach 1815, Nephilengys L. Koch 1872, Nephilingis Kuntner 2013, Palaeonephila Wunderlich 2004 from Tertiary Baltic amber, and Trichonephila Dahl 1911, new rank. We propose the new clade Orbipurae to contain Araneidae Clerck 1757, Phonognathidae Simon 1894, new rank, and Nephilidae. Nephilid female gigantism is a phylogenetically-ancient phenotype (over 100 Ma), as is eSSD, though their magnitudes vary by lineage.
Data from: Complex models of sequence evolution require accurate estimators as exemplified with the invariable site plus Gamma model
The invariable site plus Γ model is widely used to model rate heterogeneity among alignment sites in maximum likelihood and Bayesian phylogenetic analyses. The proof that the invariable site plus continuous Γ model is identifiable (model parameters can be inferred correctly given enough data) has increased the creditability of its application to phylogeny reconstruction. However, most phylogenetic software implement the invariable site plus discrete Γ model, whose identifiability is likely but unproven. How well the parameters of the invariable site plus discrete Γ model are estimated is still disputed. Especially the correlation of the fraction of invariable sites with the fractions of sites with a slow evolutionary rate is discussed as being problematic. We show that optimization heuristics as implemented in frequently used phylogenetic software cannot always reliably estimate the shape parameter, the proportion of invariable sites and the tree length. Here, we propose an improved optimization heuristic that accurately estimates the three parameters. While research efforts mainly focus on tree search methods, our results signify the equal importance of verifying and developing effective estimation methods for complex models of sequence evolution.
Data from: Evolution of complex asexual reproductive strategies in jellyfish
Many living organisms in terrestrial and aquatic ecosystems rely on multiple reproductive strategies to reduce the risks of extinction in variable environments. Examples are provided by the polyp stage of several bloom-forming jellyfish species, which can reproduce asexually using different "budding" strategies. These strategies broadly fall into three categories: 1) fast localized reproduction, 2) dormant cysts, or 3) motile and dispersing buds. Similar functional strategies are also present in other groups of species. However, mechanisms leading to the evolution of this rich reproductive diversity are yet to be clarified. Here we propose an evolutionary model for jellyfish polyps and determine how local population extinction and unequal fitness of the three modes can drive the evolution of multiple reproductive strategies. Depending on environmental parameters, we find that evolution leads to a unique evolutionary stable strategy, where in general multiple reproductive modes coexist. As the extinction risk increases, this strategy shifts from a pure budding mode to a dual strategy, and finally to one characterized by allocation into all three modes. We determine the existence of relative fitness-dependent thresholds in extinction risk where these transitions can occur and discuss our predictions in light of observations on polyp reproduction in laboratory and natural systems.
Data from: Upload any object and evolve it: injecting complex geometric patterns into CPPNs for further evolution
Ongoing, rapid advances in three-dimensional (3D) printing technology are making it inexpensive for lay people to manufacture 3D objects. However, the lack of tools to help non-technical users design interesting, complex objects represents a significant barrier preventing the public from benefitting from 3D printers. Previous work has shown that an evolutionary algorithm with a generative encoding based on developmental biology-a compositional pattern-producing network (CPPN)-can automate the design of interesting 3D shapes, but users collectively had to start each act of creation from a random object, making it difficult to evolve preconceived target shapes. In this paper, we describe how to modify that algorithm to allow the further evolution of any uploaded shape. The technical insight is to inject the distance to the surface of the object as an input to the CPPN. We show that this seeded-CPPN technique reproduces the original shape to an arbitrary resolution, yet enables morphing the shape in interesting, complex ways. This technology also raises the possibility of two new, important types of science: (1) It could work equally well for CPPN-encoded neural networks, meaning neural wiring diagrams from nature, such as the mouse or human connectome, could be injected into a neural network and further evolved via the CPPN encoding. (2) The technique could be generalized to recreate any CPPN phenotype, but substituting a flat CPPN representation for the rich, originally evolved one. Any evolvability extant in the original CPPN genome can be assessed by comparing the two, a project we take first steps toward in this paper. Overall, this paper introduces a method that will enable non-technical users to modify complex, existing 3D shapes and opens new types of scientific inquiry that can catalyze research on bio-inspired artificial intelligence and the evolvability benefits of generative encodings.
Data from: Asexual genome evolution in the apomictic Ranunculus auricomus complex: examining the effects of hybridization and mutation accumulation
Asexual lineages are thought to be prone to extinction because of deleterious mutation accumulation (Muller's ratchet). Here we analyze genomic effects of hybridity, polyploidy and allelic divergence in apomictic plants, and identify loci under divergent selection among sexual/apomictic lineages. RNAseq was used to sequence the flower-specific transcriptomes of 5 genotypes of the Ranunculus auricomus complex, representing 3 sexual and 2 apomictic reproductive biotypes. The 5 sequence libraries were pooled and de novo assembly performed, and the resultant assembly was used as a backbone for a subsequent alignment of each separate library. High quality single nucleotide (SNP) and insertion-deletion (indel) polymorphisms were mined from each library. Annotated genes for which open reading frames (ORF) could be determined were analyzed for signatures of divergent versus stabilizing selection. A comparison between all genotypes supports the hypothesis of Pleistocene hybrid origin of both apomictic genotypes from R. carpaticola and R. cassubicifolius, with subsequent allelic divergence of apomictic lineages (Meselson effect). Pairwise comparisons of non-synonymous (dN) to synonymous (dS) substitution rate ratios between apomictic and sexual genotypes for 1231 genes demonstrated similar distributions for all comparisons, although 324 genes demonstrated outlier (i.e. elevated) dN/dS ratios. Gene ontology analyses of these outliers revealed significant enrichment of genes associated with reproduction including meiosis and gametogenesis, following predictions of divergent selection between sexual and apomictic reproduction, although no significant signal of genome-wide mutation accumulation could be identified. The results suggest that gene function should be considered in order to understand effects of mutation accumulation in asexual lineages.
Data from: Modular color evolution facilitated by a complex nanostructure in birds
The way in which a complex trait varies, and thus evolves, is critically affected by the independence, or modularity, of its subunits. How modular designs facilitate phenotypic diversification is well studied in non-ornamental (e.g., cichlid jaws), but not ornamental traits. Diverse feather colors in birds are produced by light absorption by pigments and/or light scattering by nanostructures. Such structural colors are deterministically related to the nanostructures that produce them and are therefore excellent systems to study modularity and diversity of ornamental traits. Elucidating if and how these nanostructures facilitate color diversity relies on understanding how nanostructural traits covary, and how these traits map to color. Both of these remain unknown in an evolutionary context. Most dabbling ducks (Anatidae) have a conspicuous wing patch with iridescent color caused by a two-dimensional photonic crystal of small (100–200 nm) melanosomes. Here, we ask how this complex nanostructure affects modularity of color attributes. Using a combination of electron microscopy, spectrophotometry, and comparative methods, we show that nanostructural complexity causes functional decoupling and enables independent evolution of different color traits. These results demonstrate that color diversity is facilitated by how nanostructures function and may explain why some birds are more color-diverse than others.
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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.