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42 results for “evolutionary transition”
Data from: Demography and adaptation promoting evolutionary transitions in a mammalian genus that diversified during the Pleistocene
<p>Species that evolved in temperate regions during the Pleistocene experienced periods of extreme climatic transitions. Consequent population fragmentation and dynamics had the potential to generate small, isolated populations where the influence of genetic drift would be expected to be strong. We use comparative genomics to assess the evolutionary influence of historical demographics and natural selection through a series of transitions associated with the formation of the genus <i>Capreolus</i>, speciation within this genus during the Quaternary and during divergence among European roe deer (<i>C. capreolus</i>) populations. Our analyses were facilitated by the generation of a new high-coverage reference genome for the Siberian roe deer (<i>Capreolus pygargus</i>). We find progressive reductions in effective population size (<i>Ne</i>), despite very large census sizes in modern <i>C. capreolus</i> populations and show that low <i>Ne</i> has impacted the <i>C. capreolus</i> genome, reducing diversity and increasing linkage disequilibrium. Even so, we find evidence for natural selection shared among <i>C. capreolus</i> populations, including a population that has been through a severe bottleneck. During each period of transition there is evidence for selection, including at loci associated with diapause (delayed embryonic development), a phenotype restricted to this genus among the even-toed ungulates. Together these data allow us to assess expectations for the origin and diversification of a mammalian genus during a period of extreme environmental change.</p>
Evolutionary changes of non-coding elements associated with transition of sexual mode in Caenorhabditis nematodes
<p>The transition of the sexual mode occurs widely in animal evolution. In Caenorhabditis nematodes, androdioecy, a sexual polymorphism composed of males and hermaphrodites having the ability to self-fertilize, has evolved independently multiple times. Although regulatory elements in non-coding regions are likely involved in the evolution of hermaphroditism, their contribution to the transition of sexual mode is ambiguous. Here, we conducted a genome-wide analysis of conserved non-coding elements (CNEs) focusing on the evolution of hermaphroditism in Caenorhabditis nematodes. We found that, in androdioecious nematodes, mutations rapidly accumulated in CNEs neighboring genes associated with sexual traits. Expression analysis indicate that the identified CNEs are involved in spermatogenesis in hermaphrodites and associated with the transition of gene expression from dioecious to androdioecious nematodes. Finally, genome editing of a CNE neighboring laf-1 resulted in a change in its expression in the gonadal region undergoing spermatogenesis. Our bioinformatic and experimental analyses highlight the importance of CNEs to the transition of sexual mode.</p>
Engineering DszC Mutants from Transition State Macrodipole Considerations and Evolutionary Sequence Analysis
<p>Gaussian input and output files required to reproduce the results and analyses in the work.</p> <p>Code required to conduct analysis and representation.</p>
Dataset for "Ancient whale rhodopsin reconstructs dim-light vision over a major evolutionary transition: Implications for ancestral diving behaviour"
<p>Dataset files include:</p> <p>- Alignment of rhodopsin (Rh1) sequences formatted for PAML</p> <p>- Corresponding species tree in Newick format for PAML</p> <p>- Ancestral Rh1 amino acid sequences (for Cetacean and Whippomorpha nodes) estimated with PAML (random sites, clade, and amino acid models), Datamonkey, and ProtASR</p>
Global distribution and evolutionary transitions of floral symmetry in angiosperms
<p><span>Floral symmetry plays a crucial role in plant-pollinator interactions and has remarkable impacts on angiosperm evolution. However, the spatiotemporal patterns in floral symmetry and drivers of these patterns </span><span>remain poorly known</span><span>. Here, using global distributions and </span><span>floral symmetry data </span><span>of 280,140 angiosperm species, we presented the global geographic and evolutionary patterns of floral symmetry </span><span>composition and demonstrated the climatic drivers of these patterns</span><span>. We found that the frequency of actinomorphic (radial) species increased with latitude, while that of </span><span>zygomorphic</span><span> (</span><span>bilateral</span><span>) species decreased</span><span>.</span><span> Solar radiation, present-day temperature and Quaternary temperature change explained the geographic variation in floral symmetry. Evolutionary transitions from actinomorphy to</span><span> zygomorphy dominated floral symmetry evolution, although the rate of this transition decreased through the Cenozoic associated with decreasing </span><span>paleo-temperature</span><span>. </span><span>Our study </span><span>provides novel insights into the ecology and evolution of angiosperm floral symmetry and suggests that climate change may influence species distributions via its effect on floral symmetry.</span></p>
Three sex phenotypes in a haploid algal species give insights into the evolutionary transition to a self-compatible mating system
<p>Mating systems of haploid species such as fungi, algae, and bryophytes are either heterothallic (self-incompatible) with two sex phenotypes (male and female, or mating type <i>minus</i> and <i>plus</i> in isogamous species) or homothallic (self-compatible) with only a bisexual phenotype producing zygotes within a clone. The anisogamous volvocine green alga <i>Pleodorina starrii</i> is a haploid species previously reported to have a heterothallic mating system. Here, we found that two additional culture strains originating from the same water system of <i>P. starrii</i> were taxonomically identified as <i>P. starrii</i> and produced male and female gametes and zygotes within a clone (bisexual). Sequences of rapidly evolving plastid genome regions were identical between the bisexual and unisexual (male or female) <i>P. starrii</i> strains. Intercrossings between the bisexual and unisexual strains demonstrated normal thick-walled zygotes and high survivability of F1 strains. Thus, these strains belong to the same biological species. <i>P. starrii</i> has a new haploid mating system that is unique in having three sex phenotypes; namely, male, female, and bisexual. Genetic analyses suggested the existence of autosomal "bisexual factor" locus independent of volvocine male and female determining regions. The present findings increase our understanding of the initial evolutionary step of transition from heterothallism to homothallism.</p>
Supporting data for: Evolutionary drivers, morphological evolution and diversity dynamics of a surviving mammal clade: cainotherioids at the Eocene-Oligocene transition
<p><span><span><span><span><span><span><span><span><span><span><span>The Eocene-Oligocene transition (EOT) represents a period of global environmental changes particularly marked in Europe and coincides with a dramatic biotic turnover. Here, using an exceptional fossil preservation, we document and analyse the diversity dynamics of a mammal clade, Cainotherioidea (Artiodactyla), that survived the EOT and radiated rapidly immediately after. We infer their diversification history from Quercy Konzentrat-Lagerstätte (South-West France) at the species level using Bayesian birth-death models. We show that cainotherioid diversity fluctuated through time, with extinction events at the EOT and in the late Oligocene, and a major speciation burst in the early Oligocene. The latter is in line with our finding that cainotherioids had a high morphological adaptability following environmental changes throughout the EOT, which likely played a key role in the survival and evolutionary success of this clade in the aftermath. Speciation is positively associated with temperature and continental fragmentation in a time-continuous way, while extinction seems to synchronize with environmental change in a punctuated way. Within-clade interactions negatively affected the cainotherioid diversification, while inter-clade competition might explain their final decline during the late Oligocene. Our results provide a detailed dynamic picture of the evolutionary history of a mammal clade in a context of global change.</span></span></span></span></span></span></span></span></span></span></span></p>
Multiple evolutionary transitions of reproductive strategies in a phylum of aquatic colonial invertebrates
<p><strong>PHYLOGENIES</strong></p> <p><strong>All_genes_alignment.nex</strong></p> <p>The concatenated mixed alignment consisting of, 13 mitochondrial protein-coding genes as amino acids, mitochondrial ribosomal RNA genes 12S+16S, and nuclear 18S+28S rRNA genes. Gene boundaries and excludes sites are indicated.</p> <p><strong>Fig_2.nex</strong></p> <p>Topology of the Bayesian phylogenetic analysis of the mixed concatenated alignment consisting of three partitions: (i) 13 mitochondrial protein-coding genes as amino acids, (ii) mitochondrial ribosomal RNA genes 12S+16S, (iii) nuclear 18S+28S rRNA genes. The analysis was performed in MrBayes5D v. 3.2.6 under the GTR+G model of nucleotide evolution (nucleotides) and the MTZOA+G model (amino acids). The analysis was run for 2.4 million generations; 1.5 million generations were discarded as burn-in.</p> <p><strong>Fig_S3</strong></p> <p>Topology of the Bayesian phylogenetic analysis of the mixed concatenated alignment consisting of three partitions: (i) 13 mitochondrial protein-coding genes (PCGs) as amino acids, (ii) mitochondrial ribosomal RNA genes 12S+16S, (iii) nuclear 18S+28S rRNA genes. The analysis was performed in p4 under the GTR+G model of nucleotide evolution (nucleotides) and the MTZOA+G+F model (amino acids). The +F model component accommodates empirical composition in the amino acid model. The analysis used three separate runs for 300,000 generations; 200,000 generations were discarded as burn-in.</p> <p><strong>Fig_S4</strong></p> <p>Topology of the maximum likelihood phylogenetic analysis of the mixed concatenated alignment consisting of three partitions: (i) 13 mitochondrial protein-coding genes as amino acids, (ii) mitochondrial ribosomal RNA genes 12S+16S, (iii) nuclear 18S+28S rRNA genes. The analysis was performed in RAxML HPC-PTHREADS-SSE3 v. 8.2.12 under the GTR+G (nucleotides) and the MTZOA+G+F models (amino acids).</p> <p><strong>Fig_S5</strong></p> <p>Topology of the Bayesian phylogenetic analysis of the 12S+16S rRNA gene partition constructed using MrBayes v. 3.2.6 under the GTR + G model. The analysis was run for 20 million generations; 10 million generations were discarded as burn-in.</p> <p><strong>Fig_S6</strong></p> <p>Topology of the maximum likelihood phylogenetic analysis of the 12S+16S rRNA gene partition constructed using RAxML HPC-PTHREADS-SSE3 v. 8.2.12 under the GTRCAT model.</p> <p><strong>Fig_S7</strong></p> <p>Topology of the Bayesian phylogenetic analysis of the 18S+28S rRNA gene partition constructed using MrBayes v. 3.2.6 under the GTR + G model. The analysis was run for 20 million generations; 10 million generations were discarded as burn-in.</p> <p><strong>Fig_S8</strong></p> <p>Topology of the maximum likelihood phylogenetic analysis of the 18S+28S rRNA gene partition constructed using RAxML HPC-PTHREADS-SSE3 v. 8.2.12 under the GTRCAT model.</p> <p><strong>Fig_S9</strong></p> <p>Topology of the Bayesian phylogenetic analysis of 13 mitochondrial protein-coding genes as amino acids constructed using MrBayes5D v. 3.2.6 under the MTZOA+G model. The analysis was run for 3.7 million generations; 2.5 million generations were discarded as burn-in.</p> <p><strong>Fig_S10</strong></p> <p>Topology of the maximum likelihood phylogenetic analysis of 13 mitochondrial protein-coding genes as amino acids constructed using RAxML HPC-PTHREADS-SSE3 v. 8.2.12 under the PROTGAMMAMTZOA model.</p> <p><strong>Fig_S11</strong></p> <p>Topology of the Bayesian phylogenetic analysis of the mixed concatenated alignment consisting of three partitions: (i) 13 mitochondrial protein-coding genes (PCGs) as amino acids, (ii) mitochondrial ribosomal RNA genes 12S+16S, (iii) nuclear 18S+28S rRNA genes. The analysis was performed in p4 under the NDCH-C2 model. The analysis used four separate runs for 300,000 generations; 200,000 generations were discarded as burn-in. The NDCH model accommodates compositional tree-heterogeneity and was used because there was a large amount of compositional heterogeneity over the sequences, especially in the PCGs and 12S+16S rRNA data partitions. This is an NDCH model with two composition vectors on each of the three data partitions.</p> <p><strong>Fig_S12</strong></p> <p>Topology of the Bayesian phylogenetic analysis of the mixed concatenated alignment consisting of three partitions: (i) 13 mitochondrial protein-coding genes as amino acids, (ii) mitochondrial ribosomal RNA genes 12S+16S, (iii) nuclear 18S+28S rRNA genes. This analysis excluded all terminals for which less than half of mitogenome genes were available, or which only had one of the two nuclear rRNA genes. The analysis was performed in MrBayes5D v. 3.2.6 under the GTR+G model of nucleotide evolution (nucleotides) and the MTZOA+G model (amino acids). The analysis was run for 350,000 generations; 125,000 generations were discarded as burn-in.</p> <p><strong>Fig_S13</strong></p> <p>Topology of the maximum likelihood phylogenetic analysis of the mixed concatenated alignment consisting of three partitions: (i) 13 mitochondrial protein-coding genes as amino acids, (ii) mitochondrial ribosomal RNA genes 12S+16S, (iii) nuclear 18S+28S rRNA genes. This analysis excluded all terminals for which less than half of mitogenome genes were available, or which only had one of the two nuclear rRNA genes. The analysis was performed in RAxML HPC-PTHREADS-SSE3 v. 8.2.12 under the GTR+G (nucleotides) and the MTZOA+G+F models (amino acids).</p> <p><strong>ANCESTRAL CHARACTER ESTIMATION:</strong></p> <p><strong>ACE.R</strong></p> <p>R script of the ancestral character estimation carried out in phytools.</p> <p><strong>Reproductive_strategy_numbers.csv</strong></p> <p>Data input file for ACE analysis (reproductive strategies coded as numbers)</p> <p><strong>Reproductive_strategies.xlsx</strong></p> <p>List of reproductive strategies per taxon with the corresponding numerical codes used in the file 'Reproductive_stategies_numbers.csv'.</p> <p><strong>Tree.tre</strong></p> <p>Input tree for ACE analysis.</p>
Data from: Coordination of bark and wood traits underlies forest-to-savanna evolutionary transitions
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Supporting data for: Evolutionary drivers, morphological evolution and diversity dynamics of a surviving mammal clade: cainotherioids at the Eocene-Oligocene transition
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Leaving academia: Insights from evolutionary biologists on their career transitions and job satisfaction
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Three sex phenotypes in a haploid algal species give insights into the evolutionary transition to a self-compatible mating system
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Global distribution and evolutionary transitions of floral symmetry in angiosperms
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Evolutionary changes of non-coding elements associated with transition of sexual mode in Caenorhabditis nematodes
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Data from: Demography and adaptation promoting evolutionary transitions in a mammalian genus that diversified during the Pleistocene
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Data from: Evolutionary implications of a new transitional blastozoan echinoderm from the mid Cambrian of Czech Republic
The primitive blastozoan Felbabkacystis luckae n. gen. n. sp. is described from the Drumian Jince Formation, Barrandian area (Czech Republic) based on eleven fairly well-preserved specimens. Its unique body plan organization is composed of a relatively long stalk-like imbricate structure directly connected to the aboral imbricate cup of the test and of an adoral vaulted tessellate test supporting the ambulacral and brachiolar systems. Its bipartite test, called prototheca, highlights the evolution of the body wall among blastozoans. Felbabkacystis n. gen. shows the combination of plesiomorphic (imbricate stalk-like appendage) and derived features (highly domed peristome, elongate epispires). The new genus is interpreted as a transitional form between calyx-bearing and theca-bearing blastozoans, and is attributed to the new Family Felbabkacystidae. The lithology, the associated fauna and the possession of a long stalk suggest that Felbabkacystis was probably a low-level suspension feeder in relatively deep settings.
Are evolutionary transitions in sexual size dimorphism related to sex determination in reptiles? - Electronic supplementary material
<p class="western"><span><span><span><span>Sex determination systems are highly variable in vertebrates, although neither the causes nor the implications of this diversity are fully understood. Theory suggests that sex determination is expected to relate to sexual size dimorphism, because environmental sex determination promotes sex-specific developmental bias in embryonic growth rates. Furthermore, selection for larger size in one sex or the other has been proposed to drive the evolution of different genetic sex determination systems. Here we investigate whether sex determination systems relate to adult sexual size dimorphism, using 250 species of reptiles (Squamata, Testudines, Crocodylia) representing 26 families. Using phylogenetically informed analyses, we find that sexual size dimorphism is associated with sex determination: species with TSDIa sex determination (i.e. in which the proportion of female offspring increases with incubation temperature), have more female-biased size dimorphism than species with TSDII (i.e., species in which males are produced at mid temperatures). We also found a trend that species with TSD ancestors had more male-biased size dimorphism in XY sex-chromosome systems than in ZW sex-chromosome systems. Taken together, our results support the prediction that sexual size dimorphism is linked to sex-dependent developmental variations caused by environmental factors and also by sex chromosomes. Since the extent of size dimorphism is related to various behavioural, ecological and life-history differences between sexes, our results imply profound impacts of sex determination systems for vertebrate diversity.</span></span></span></span></p>
Critical transitions and evolutionary hysteresis in movement: Habitat fragmentation can cause abrupt shifts in dispersal that are difficult to revert
<p>Under habitat fragmentation, plant species' survival hinges on the ability of individuals to disperse from one habitat patch to another. While there is evidence that severe habitat fragmentation leads to evolution of reduced dispersal ability and that such decreased mobility is generally detrimental for species' survival, it is unknown whether species adapt via a gradual loss in dispersal ability or via a sudden shift from frequent to infrequent dispersal between patches (i.e., a critical transition). Using both a spatially explicit deterministic and individual-based stochastic model of hydrochorous seed dispersal, we show that a small increase in inter-patch distance can generate an abrupt shift in plant seed dispersal strategy from long to short distances. Most importantly, we found that a substantial increase in connectivity between habitat fragments is required to reverse this loss of long-distance dispersal, due to an evolutionary hysteresis effect. Our theory prompts for re-consideration of the eco-evolutionary consequences of habitat fragmentation as restoring habitat connectivity may require restoration of much higher connectivity levels than currently assumed.</p>
Data from: New perspectives on transitions between ecological-evolutionary subunits in the "type interval" for Coordinated Stasis
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Critical transitions and evolutionary hysteresis in movement: Habitat fragmentation can cause abrupt shifts in dispersal that are difficult to revert
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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.