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296 results for “evolution pattern”
Data from: Rapid evolution in native plants cultivated for ecological restoration: not a general pattern
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Data from: Clinically relevant cranio-caudal patterns of cervical cord atrophy evolution in MS
Objectives. To characterize the distribution and regional evolution of cervical cord atrophy in multiple sclerosis (MS) patients in a multicentre dataset. Methods. MRI and clinical evaluations were acquired from 179 controls and 435 patients (35 clinically isolated syndromes [CIS], 259 relapsing-remitting [RR], 99 secondary-progressive [SP] and 42 primary-progressive [PP]MS). Sixty-nine controls and 178 patients underwent a one-year MRI and clinical follow-up. Patients were classified as clinically stable/worsened according to their disability change. Longitudinal changes of cord atrophy were investigated with linear mixed-effect models. Sample size calculations were performed using age-, sex- and site-adjusted annualized percentage normalized cord cross-sectional area (CSAn) changes..Results. Baseline CSAn was lower in MS patients vs controls (p<0.001), but not different between controls and CIS or between early RRMS (disease duration<5 years) and CIS patients. Late RRMS (disease duration>5 years) showed significant cord atrophy vs early RRMS (p=0.02). Progressive MS patients had decreased CSAn (p<0.001) vs RRMS. Atrophy was located between C1/C2 and C5 in RRMS vs CIS, and widespread along the cord in progressive MS vs RRMS, with an additional C5/C6 involvement in SPMS vs PPMS. At follow-up, CSAn decreased in all phenotypes (p<0.001), except CIS. Cord atrophy rates were highest in early RRMS and clinically worsened patients, who had a more widespread cord involvement than stable patients. The sample size per arm required to detect a 50% treatment effect was 118 for early RRMS patients. Conclusions. Cord atrophy increased in MS during one year, except for CIS. A faster atrophy contributed to explain clinical worsening.
Female and male song exhibit both parallel and divergent patterns of cultural evolution: a long-term study of song structure and diversity in tropical wrens
<p>Animal culture changes over time through processes that include drift, immigration, selection, and innovation. Cultural change has been particularly well-studied for animal vocalizations, especially for the vocalizations of male animals in the temperate zone. Here we examine cultural change in the vocalizations of tropical Rufous-and-white Wrens (<i>Thryophilus rufalbus</i>), quantifying temporal variation in song structure, song type diversity, and population-level distribution of song types in both males and females. We use data from 10 microsatellite loci to quantify patterns of immigration and neutral genetic differentiation over time, to investigate whether cultural diversity changes with rates of immigration. Based on 11 years of data, we show that the spectro-temporal features of several widely-used persistent song types maintain a relatively high level of consistency for both males and females, whereas the distribution and frequency of particular song types change over time for both sexes. Males and females exhibit comparable levels of cultural diversity (i.e. the diversity of song types across the population), although females exhibit greater rates of cultural change over time. We found that female changes in cultural diversity increased when immigration is high, whereas male cultural diversity did not change with immigration. Our study is the first long-term study to explore cultural evolution for both male and female birds and suggests that cultural patterns exhibit notable differences between the sexes.</p>
Macroevolution of flower color patterning: biased transition rates and correlated evolution with flower size
<p>Floral pigmentation patterns can both mediate plant-pollinator interactions and modify the abiotic environment of reproductive structures. To date there have been no inquiries into the rate and directionality of macroevolutionary transitions between patterned and non-patterned petals despite their ecological importance and ubiquity across angiosperms. Petals in the Potentilleae tribe (Rosaceae) display color patterns in the ultraviolet (UV) and human-visible spectrum, or can be uniform in color (i.e., patternless). Using a phylogeny of Potentilleae, I test whether evolutionary transition rates between patterned and non-patterned petals are biased in either direction. I then examine whether UV and human-visible patterns are phylogenetically correlated and test the prediction that color patterns will evolve in concert with larger flowers if they function as guides to orient pollinators to floral rewards. I found that transition rates were biased toward petals that were uniform in color. Transition rates from patterned to uniformly-colored petals were two and six times higher than the reverse for UV and human-visible pattern, respectively. The presence of UV and human-visible pattern evolved independently from one another. However, the evolution of human-visible pattern was associated with the evolution of larger flowers but the evolution of UV pattern was correlated with the evolution of smaller flowers. I posit that the transition bias towards non-patterned flowers may reflect developmental constraints on spatial regulation of pigments required to produce floral color patterning. The correlated evolution of larger flowers and human-visible pigmentation patterns support the hypothesis that nectar or pollen guides are more likely to evolve in larger-flowered species. This work provides insight into how transition rate bias and trait correlations can shape phylogenetic patterns of floral color pattern diversity.</p>
Patterns of genetic divergence and demographic history shed light on island-mainland population dynamics and melanic plumage evolution in the white-winged fairywren
<p>The existence of distinct traits in island versus mainland populations offers opportunities to gain insights into how eco-evolutionary processes operate under natural conditions. We used two island colonization events in the white-winged fairywren (<i>Malurus </i><i>leucopterus</i>) to investigate the genomic and demographic origin of melanic plumage. This avian species is distributed across most of Australia, and males of the mainland subspecies (<i>M. l. leuconotus</i>) exhibit a blue nuptial plumage in contrast to males of two island subspecies – <i>M. l. leucopterus </i>on Dirk Hartog Island<i> </i>and <i>M. l. edouardi</i>on Barrow Island – that exhibit a black nuptial plumage. We used reduced-representation sequencing to explore differentiation and demographic history in this species and found clear patterns of divergence between mainland and island populations, with additional substructuring on the mainland. Divergence between the mainland and Dirk Hartog was approximately 10 times more recent than the split between the mainland and Barrow Island, supporting two independent colonizations. In both cases, estimated gene flow between the mainland and the islands was low, contributing to signals of divergence among subspecies. Our results present demographic reconstructions of mainland-island dynamics and associated plumage variation in white-winged fairywrens, with broader implications regarding our understanding of convergent evolution in insular populations.</p>
Data from: Multi-locus phylogenetic analysis reveals the pattern and tempo of bony fish evolution
Over half of all vertebrates are "fishes", which exhibit enormous diversity in morphology, physiology, behavior, reproductive biology, and ecology. Investigation of fundamental areas of vertebrate biology depend critically on a robust phylogeny of fishes, yet evolutionary relationships among the major actinopterygian and sarcopterygian lineages have not been conclusively resolved. Although a consensus phylogeny of teleosts has been emerging recently, it has been based on analyses of various subsets of actinopterygian taxa, but not on a full sample of all bony fishes. Here we conducted a comprehensive phylogenetic study on an unprecedented combination of broad taxonomic sampling of actinopterygian and sarcopterygian lineages (with a chondrichthyan outgroup) using a molecular data set of 21 independent loci. These data yielded a resolved phylogenetic hypothesis for extant Osteichthyes, including 1) reciprocally monophyletic Sarcopterygii and Actinopterygii, as currently understood, with polypteriforms as the first diverging lineage within Actinopterygii; 2) a monophyletic group containing gars and bowfin (= Holostei) as sister group to Teleostei; and 3) the earliest diverging lineage among teleosts being Elopomorpha, rather than Osteoglossomorpha. Relaxed-clock dating analysis employing a set of 24 newly applied fossil calibrations reveals divergence times that are more consistent with paleontological estimates than previous studies. Establishing a new phylogenetic pattern with accurate divergence dates for bony fishes illustrates several areas where the fossil record is incomplete and provides critical new insights on diversification of this important vertebrate group.
Data from: Phylogenomics resolves the timing and pattern of insect evolution
Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight to the Early Devonian (~406 Ma), of major extant lineages to the Mississippian (~345 Ma), and the major diversification of holometabolous insects to the Early Cretaceous. Our phylogenomic study provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects.
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: Evolution of patterned plumage as a sexual signal in estrildid finches
Colour patterns, such as bars or dots, that cover the body surface of animals are generally thought to play roles in signalling and camouflage. In birds, however, the macroscopic aspects of plumage colouration are less well understood, as past studies typically described plumage colourations by using spectrophotometric analyses. To provide insight into the evolution of plumage patterns as sexual signals, we characterised interspecific and intersexual variations in the plumage patterns of estrildid finches and tested their associations with other courtship signals and life-history traits using a comparative phylogenetic approach. Our results support the idea that plumage patterns in estrildids are favoured by sexual selection because large-sized conspicuous plumage patterns are possessed by species with an elaborate courtship dance. These plumage patterns may also play roles in social signalling because patterns are more conspicuous in species with intraspecific brood parasitism. We predict that pattern traits can be favoured by mate choice or intra-sexual competition when they can serve as honest indicators of individual condition. As our results are consistent between the sexes, we suggest that the same selective force is acting on the evolution of plumage patterns in males and females in parallel. Finally, we also found a trade-off between large size and vivid colour patterns, suggesting that too conspicuous patterns are costly, presumably because of the risk of catching the eyes of potential predators. Therefore, plumage patterns are also shaped by natural selection.
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: Population size changes and selection drive patterns of parallel evolution in a host-virus system
Predicting the repeatability of evolution remains elusive. Theory and empirical studies suggest that strong selection and large population sizes increase the probability for parallel evolution at the phenotypic and genotypic levels. However, selection and population sizes are not constant, but rather change continuously and directly affect each other even on short time scales. Here, we examine the degree of parallel evolution shaped through eco-evolutionary dynamics in an algal host population coevolving with a virus. We find high degrees of parallelism at the level of population size changes (ecology) and at the phenotypic level between replicated populations. At the genomic level, we find evidence for parallelism, as the same large genomic region was duplicated in all replicated populations, but also substantial novel sequence divergence between replicates. These patterns of genome evolution can be explained by considering population size changes as an important driver of rapid evolution.
Data from: Patterns and evolution of nucleotide landscapes in seed plants
Nucleotide landscapes, which is the way base composition is distributed along a genome, strongly vary among species. The underlying causes of these variations have been much debated. Though mutational bias and selection were initially invoked, GC-biased gene conversion (gBGC), a recombination-associated process favoring the G and C over A and T bases, is increasingly recognized as a major factor. As opposed to vertebrates, evolution of GC content is less well known in plants. Most studies have focused on the GC-poor and homogeneous Arabidopsis genome and the much more GC-rich and heterogeneous rice (Oryza sativa) genome and has often been generalized as a dicot/monocot dichotomy. This vision is clearly phylogenetically biased and does not allow understanding the mechanisms involved in GC-content evolution in plants. To tackle these issues, we used EST data from more than 200 species and provided the most comprehensive description of gene GC content across the seed plant phylogeny so far available. As opposed to the classically assumed dicot/monocot dichotomy, we found continuous variations in GC content from the probably ancestral GC-poor and homogeneous genomes to the more derived GC-rich and highly heterogeneous ones, with several independent enrichment episodes. Our results suggest that gBGC could play a significant role in the evolution of GC content in plant genomes.
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: Using historical biogeography models to study color pattern evolution
Color is among the most striking features of organisms, varying not only in spectral properties like hue and brightness, but also in where and how it is produced on the body. Different combinations of colors on a bird's body are important in both environmental and social contexts. Previous comparative studies have treated plumage patches individually or derived plumage complexity scores from color measurements across a bird's body. However, these approaches do not consider the multivariate nature of plumages (allowing for plumage to evolve as a whole) or account for interpatch distances. Here, we leverage a rich toolkit used in historical biogeography to assess color pattern evolution in a cosmopolitan radiation of birds, kingfishers (Aves: Alcedinidae). We demonstrate the utility of this approach and test hypotheses about the tempo and mode of color evolution in kingfishers. Our results highlight the importance of considering interpatch distances in understanding macroevolutionary trends in color diversity and demonstrate how historical biogeography models are a useful way to model plumage color pattern evolution. Furthermore, they show that distinct color mechanisms (pigments or structural colors) spread across the body in different ways and at different rates. Specifically, net rates are higher for structural colors than pigment-based colors. Together, our study suggests a role for both development and selection in driving extraordinary color pattern diversity in kingfishers. We anticipate this approach will be useful for modeling other complex phenotypes besides color, such as parasite evolution across the body.
Data from: Agouti-related peptide 2 facilitates convergent evolution of stripe patterns across cichlid fish radiations
The color patterns of African cichlid fishes provide notable examples of phenotypic convergence. Across the more than 1200 East African rift lake species, melanic horizontal stripes have evolved numerous times. We discovered that regulatory changes of the gene agouti-related peptide 2 (agrp2) act as molecular switches controlling this evolutionarily labile phenotype. Reduced agrp2 expression is convergently associated with the presence of stripe patterns across species flocks. However, cis-regulatory mutations are not predictive of stripes across radiations, suggesting independent regulatory mechanisms. Genetic mapping confirms the link between the agrp2 locus and stripe patterns. The crucial role of agrp2 is further supported by a CRISPR-Cas9 knockout that reconstitutes stripes in a nonstriped cichlid. Thus, we unveil how a single gene affects the convergent evolution of a complex color pattern.
FIGURE 10 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 10. Dorsal pattern and color variation of six living specimens of Boophis boppa.
Figure 2 from: Ito T, Fukuda T, Morimune T, Hosoya K (2017) Evolution of the connection patterns of the cephalic lateral line canal system and its use to diagnose opsariichthyin cyprinid fishes (Teleostei, Cyprinidae). ZooKeys 718: 115-131. https://doi.org/10.3897/zookeys.718.13574
Figure 2 - Diagram of the cephalic lateral line canal systems in the opsariichthyin fishes. A Candidia barbata, FKUN 34180, 94.8 mm SL B C. pingtungensis, FKUN 35215, 72.9 mm SL C Nipponocypris koreanus, FKUN 40587, 94.1 mm SL. Scale bar 5 mm. D N. sieboldii, FKUN 40571, 90.5 mm SL E N. temminckii, FKUN 40575, 94.5 mm SL F Opsariichthys bidens, LBM 8852, 94.8 mm SL. Scale bar 5 mm. G O. evolans, FKUN 35199, 81.1 mm SL H O. kaopingensis, KUN-P40545, 80.0 mm SL I O. pachycephalus, FKUN 35181, 69.4 mm SL. Scale bar 5 mm. J O. uncirostris, FKUN 16487, 219.0 mm SL K Parazacco spilurus, KUN-P45852, 57.5 mm SL L Zacco platypus, FKUN 40558, 93.0 mm SL. Scale bar 5 mm.
Figure 3 from: Ito T, Fukuda T, Morimune T, Hosoya K (2017) Evolution of the connection patterns of the cephalic lateral line canal system and its use to diagnose opsariichthyin cyprinid fishes (Teleostei, Cyprinidae). ZooKeys 718: 115-131. https://doi.org/10.3897/zookeys.718.13574
Figure 3 - Parsimonious ancestral state reconstruction of the connecting states of the cephalic lateral line canal systems of the opsariichthyin fishes and their out-groups from the maximum likelihood tree inferred from cytochrome b sequences (InL = 12054.39). A The connecting states between the supraorbital (SO) and infraorbital (IO) canals B the connecting states between the temporal (TC) and preoperculomandibular (POM) canals C the connecting states between the left and right sides of the supratemporal canals (ST). The color of each node indicates the connecting states of the cephalic lateral line canal system: black, continuity; white, discontinuity; gray, both sides of the ST connected and extending anteriorly.
Figure 1 from: Ito T, Fukuda T, Morimune T, Hosoya K (2017) Evolution of the connection patterns of the cephalic lateral line canal system and its use to diagnose opsariichthyin cyprinid fishes (Teleostei, Cyprinidae). ZooKeys 718: 115-131. https://doi.org/10.3897/zookeys.718.13574
Figure 1 - Terminology used for cephalic lateral line canal systems: SO supraorbital canal IO infraorbital canal TC temporal canal POM preoperculomandibular canal ST supratemporal canal frb frontal bridge cpb centroparietal bridge itb infratemporal bridge apj anteropteroitic joint.
Figure 9 from: Sroka P, Godunko RJ, Rutschmann S, Angeli KB, Salles FF, Gattolliat J-L (2019) A new species of Bungona in Turkey (Ephemeroptera, Baetidae): an unexpected biogeographic pattern within a pantropical complex of mayflies. Zoosystematics and Evolution 95(1): 1-13. https://doi.org/10.3897/zse.95.29487
Figure 9 Molecular reconstruction including representative set of taxa of the Cloeodes-complex (comprising Bungona (Chopralla) pontica sp. n.) and additional taxa of other lineages. Bayesian inference was used to reconstruct the tree based on the mitochondrial DNA barcoding gene cytochrome c oxidase subunit 1. Bayesian posterior probabilities > 0.8 are indicated. Scale bar represents substitutions per site. Geographic origins of the specimens are indicated. Colours: green = Bungona (Bungona); blue = Bungona (Chopralla); purple = Bungona (Centroptella); yellow = Cloeodes; white = other genera.
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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.