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377 results for “evolution of complexity”
Data from: Reticulate evolution within a spruce (Picea) species complex revealed by population genomic analysis
The role of reticulation in the rapid diversification of organisms is attracting greater attention in evolutionary biology. Here, we report a population genomics approach to test the role of hybridization and introgression in the evolution of the Picea likiangensis species complex. Based on 84,793 SNPs detected in transcriptomes of 82 trees collected from 35 localities, we identified 18 hybrids (including backcrosses) distributed within the range boundaries of the four taxa. Coalescent simulations, for each pair of taxa and for all taxa taken together, rejected several tree-like divergence models and supported instead a reticulate evolution model with secondary contacts occurring during Pleistocene glacial cycles after initial divergence in the late Pliocene. Significant gene flow occurred among some taxa after secondary contact according to an analysis based on modified ABBA-BABA statistics that accommodated a rapid diversification scenario. A novel finding was that introgression between certain taxa can contribute to increasing divergence (and possibly reproductive isolation) between those taxa and other taxa within a complex at some loci. These results illuminate the reticulate nature of evolution within the P. likiangensis complex and highlight the value of population genomic data in detecting the effects of introgression in the rapid diversification of related taxa.
GENOMIC INSIGHTS INTO THE GLOBAL EVOLUTION AND ANTIBIOTIC RESISTANCE OF THE MYCOBACTERIUM TUBERCULOSIS COMPLEX
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Evolution towards increasing complexity through functional diversification in a protocell model of the RNA world
<p>The encapsulation of genetic material inside compartments together with the creation and sustenance of functionally diverse internal components are likely to have been key steps in the formation of 'live', replicating protocells in an RNA world. Several experiments have shown that RNA encapsulated inside lipid vesicles can lead to vesicular growth and division through physical processes alone. Replication of RNA inside such vesicles can produce a large number of RNA strands. Yet, the impact of such replication processes on the emergence of the first ribozymes inside such protocells and on the subsequent evolution of the protocell population remains an open question. In this paper, we present a model for the evolution of protocells with functionally diverse ribozymes. Distinct ribozymes can be created with small probabilities during the error-prone RNA replication process via the rolling circle mechanism. We identify the conditions that can synergistically enhance the number of different ribozymes inside a protocell and allow functionally diverse protocells containing multiple ribozymes to dominate the population. Our work demonstrates the existence of an effective pathway towards increasing complexity of protocells that might have eventually led to the origin of life in an RNA world.</p>
Polyploidy promotes divergent evolution across the leaf economics spectrum and plant edaphic niche in the Dianthus broteri complex
<ol> <li>The evolution of the leaf economics spectrum (LES) is known to be constrained by genetic relatedness but also promoted at small geographic and phylogenetic scales. In those cases, we hypothesised that polyploidy would play a prominent role as an outstanding source of functional divergence and adaptive potential.</li> <li>We registered leaf-level nutrient, water and light economy related traits from the LES as well as edaphic properties in the four cytotypes of the autopolyploid <i>Dianthus broteri</i> complex (2×, 4×, 6× and 12×). We analysed the effect of ploidy level on the integration of the LES network, checked if concerted evolution occurred between LES and soil niche and tested the influence of phylogeny on the variables. Alternative evolutionary models for both sets of traits were compared.</li> <li> <span>We found higher divergence of polyploids (especially 6</span>×<span> and 12</span>×<span>) compared to diploids</span> in the LES and soil niche, but these traits are not coevolving. <span>6</span>×<span> and 12</span>× showed opposite ecological strategies regarding resource use and higher uncoupling of the LES network. Early divergence of traits prevailed in both LES and edaphic niche (supported by better fitted evolutionary models with one optimum per cytotype), but post-polyploidization processes played an important role for the photochemical behaviour.</li> <li> <i>Synthesis.</i><b> </b><span>Our results indicated shifts in ecological strategies across <i>D. broteri</i> cytotypes and suggested a powerful role of polyploidy in overcoming constraints for the evolution of plant functional traits.</span> </li> </ol>
Data from "Disk Evolution Study Through Imaging of Nearby Young Stars (DESTINYS): A Panchromatic View of DO Tau's Complex Kilo-au Environment'
<p>Reduced data from Huang et al., 2022, "Disk Evolution Study Through Imaging of Nearby Young Stars (DESTINYS): A Panchromatic View of DO Tau's Complex Kilo-astronomical-unit Environment,' ApJ, 930, 171 (arXiv:2204.01758). </p> <p>See Table 1 of the article for the corresponding observing program codes and attributions for archival data (if applicable). </p> <p><strong>Images:</strong></p> <p>DOTau_12CO_automask.image.pbcor.fits: 12CO J=2-1 image cube<br> DOTau_12CO_automask.mom1.fits: 12CO J=2-1 moment 1 map<br> DOTau_12CO_automask.pbcor.2sigcut.mom0.fits: 12CO J=2-1 moment 0 map<br> DOTau_13CO_automask.image.pbcor.fits: 13CO J=2-1 image cube<br> DOTau_13CO_automask.mom1.fits: 13CO J=2-1 moment 1 map<br> DOTau_13CO_automask.pbcor.2sigcut.mom0.fits: 13CO J=2-1 moment 0 map<br> DOTau_C18O_automask.image.pbcor.fits: C18O J=2-1 image cube<br> DOTau_C18O_automask.pbcor.2sigcut.mom0.fits: C18O J=2-1 moment 0 map<br> DOTau_C18O_automask.pbcor.mom1.fits: C18O J=2-1 moment 1 map<br> DOTau_cADI_average.fits: SPHERE H-band cADI image (pixel scale: 0.01225 arcseconds)<br> DOTau_CS_automask.image.pbcor.fits: DO Tau CS J=5-4 image cube<br> DOTau_CS_automask.mom1.fits: DO Tau CS J=5-4 moment 1 map<br> DOTau_CS_automask.pbcor.2sigcut.mom0.fits: DO Tau CS J=5-4 moment 0 map<br> DOTau_DoLP.fits: DO Tau degree of linear polarization map (pixel scale: .0245 arcseconds)<br> DOTau_IDF-RDI.fits: SPHERE total intensity image produced with IDF-RDI (pixel scale: 0.01225 arcseconds)<br> DO-TAU_NICMOS_F110W_MRDILib-18_KL-2_Pixel.fits: HST NICMOS F110W image (pixel scale: 0.075 arcseconds)<br> DO-TAU_NICMOS_F160W_MRDILib-100_KL-1_Pixel.fits: HST NICMOS F160W image (pixel scale: 0.075 arcseconds)<br> DOTau_Qphi_average.fits: SPHERE H-band Qphi image (pixel scale: 0.01225 arcseconds)<br> DO_Tau_STIS_KlipWithin160pixel_counts_s_pixel.fits: HST STIS image (pixel scale: 0.0507 arcseconds)</p> <p><strong>Measurement sets:</strong></p> <p>DOTau_12CO.ms.contsub.tar: Self-calibrated, continuum-subtracted 12CO J=2-1 visibilities<br> DOTau_13CO.ms.contsub.tar: Self-calibrated, continuum-subtracted 13CO J=2-1 visibilities<br> DOTau_C18O.ms.contsub.tar: Self-calibrated, continuum-subtracted C18O J=2-1 visibilities<br> DOTau_CS.ms.contsub.tar: Self-calibrated, continuum-subtracted CS J=5-4 visibilities</p> <p><strong>Scripts:</strong></p> <p>DOTau_1.1mmreduction.py: CASA self-cal and imaging script for CS data <br> DOTau_1.3mmreduction.py: CASA self-cal and imaging script for CO data </p>
The evolution of C4 photosynthesis in Flaveria (Asteraceae): Insights from the Flaveria linearis complex
<p>Flaveria is a leading model for C4 plant evolution due to the presence of a dozen C3-C4 intermediate species, many of which are associated with a phylogenetic complex centered around F. linearis. To investigate C4 evolution in Flaveria, we updated the Flaveria phylogeny and evaluated gas exchange, starch δ13C, and activity of C4 cycle enzymes in 19 Flaveria species and 28 populations within the F. linearis complex. A principal component analysis identified six functional clusters: i) C3, ii) sub-C2, iii) full C2, iv) enriched C2, v) sub-C4, and vi) fully C4 species. The sub-C2 species lacked a functional C4 cycle, while a gradient was present in the C2 clusters from little to modest C4 cycle activity as indicated by δ13C and enzyme activities. Three Yucatan populations of F. linearis had photosynthetic CO2 compensation points equivalent to C4 plants but showed little evidence for an enhanced C4 cycle, indicating they have an optimized C2 pathway that recaptures all photorespired CO2 in the bundle sheath (BS) tissue. All C2 species had enhanced aspartate aminotransferase activity relative to C3 species and most had enhanced alanine aminotransferase activity. These aminotransferases form aspartate and alanine from glutamate and in doing so help return photorespiratory nitrogen (N) from BS to mesophyll cells, preventing glutamate feedback onto photorespiratory N assimilation. Their use requires upregulation of parts of the C4 metabolic cycle to generate carbon skeletons to sustain N return to the mesophyll, and thus could facilitate the evolution of the full C4 photosynthetic pathway.</p>
A New Model and Dating for the Evolution of Complex Plastids of Red Alga Origin
<p>The zip files includes alignments of protein sequences in fasta format (SequenceAlignments.zip) and their concatenated sets used in our research project (ConcatenatedAlignments.zip). Additionally, we included raw (unaligned) protein sequences in fasta format (RawSequences.zip). In total, we employed 97 amino acid sequences of conserved plastid-encoded proteins, carefully selected from the NCBI reference sequence database (<a href="https://www.ncbi.nlm.nih.gov/refseq/">https://www.ncbi.nlm.nih.gov/refseq/</a>), and GenBank (<a href="https://www.ncbi.nlm.nih.gov/genbank/">https://www.ncbi.nlm.nih.gov/genbank/</a>), representing 112 organisms. Our dataset included 111 eukaryotes carrying red-alga derived plastids and the closest plastid cyanobacterial relative <i>Gloeomargarita lithophora</i> Alchichica D10. We performed independent alignments of each homologous protein group using a slow and accurate L-INS-i algorithm implemented in MAFFT v7.429 (<a href="https://doi.org/10.1093/molbev/mst010">https://doi.org/10.1093/molbev/mst010</a>). The resulting multiple sequence alignments were carefully assessed using AliView (<a href="http://dx.doi.org/10.1093/bioinformatics/btu531">http://dx.doi.org/10.1093/bioinformatics/btu531</a>), and phylogenetically informative sites were selected through trimAl <a href="https://doi.org/10.1093/bioinformatics/btp348">https://doi.org/10.1093/bioinformatics/btp348</a>and ClipKIT (<a href="https://doi.org/10.1371/journal.pbio.3001007">https://doi.org/10.1371/journal.pbio.3001007</a>). The trimmed alignments were concatenated into supermatrices using SequenceMatrix 1.8 (<a href="https://doi.org/10.1111/j.1096-0031.2010.00329.x">https://doi.org/10.1111/j.1096-0031.2010.00329.x</a>)to generate comprehensive datasets for phylogenetic and molecular clock analyses. We also generated a supermatrix composed of untrimmed alignments.</p>
An efficient CRISPR-mediated genome editing system in diploid and polyploid Tragopogon (Asteraceae) enables functional studies of complex phenotypes and polyploid genome evolution
<p>Polyploidy or whole-genome duplication (WGD) is a significant evolutionary force, especially in angiosperms. However, the underlying mechanisms governing polyploid genome evolution remain unclear, limited largely by a lack of functional analysis tools in organisms that best exemplify the earliest stages of WGD. <em>Tragopogon</em> (Asteraceae) includes an evolutionary model system for studying the immediate consequences of polyploidy. In this study, we significantly improved the genetic transformation of <em>Tragopogon</em> and obtained genome-edited <em>T. porrifolius</em> (2<em>x</em>) and <em>T. mirus</em> (4<em>x</em>) primary generation (T<sub>0</sub>) individuals. Using CRISPR/Cas9, we knocked out the dihydroflavonol 4-reductase (<em>DFR</em>) gene, which controls anthocyanin synthesis, in both <em>T. porrifolius</em> and <em>T. mirus</em>. All transgenic allotetraploid <em>T. mirus</em> individuals had at least one mutant <em>DFR</em> allele and 71.4% of the plants had all four <em>DFR</em> alleles (from both homeologs) edited, indicating a high efficiency of the CRISPR system in polyploid <em>Tragopogon</em>. The anticipated absence of the anthocyanin was observed in both leaf and floral tissues from <em>T. porrifolius</em> and <em>T. mirus</em> mutants. In addition, the mutations were inherited in the T<sub>1</sub> generation. This study demonstrates a highly efficient CRISPR platform producing genome-edited <em>Tragopogon</em> individuals that have successfully completed their life cycle. The approaches used and challenges faced in building the CRISPR system in <em>Tragopogon</em> provide a framework for building similar systems in other nongenetic models. Genome editing in <em>Tragopogon</em> paves the way for novel functional biology studies of polyploid genome evolution and the consequences of WGD on complex traits, which holds enormous potential for both basic and applied research.</p>
GeoTIFF Dataset for: Land-to-sea mapping of the glacial erosion unconformity reveals evolution of the Jasmund Glacitectonic Complex East of Rügen Island (SW Baltic Sea)
<p>This dataset comprises two GeoTIFF files, both with a WGS84 UTM 33 N (EPSG: 32633) projection. The erosional unconformity has a grid size of 100 x 100 metres, while the moraine or raft feature was gridded using a grid size of 20 x 20 metres. The two files were created using marine-multichannel seismic data from the Hübscher et al. (2024) dataset (<a href="https://deref-gmx.net/mail/client/7eMD7NnHVnY/dereferrer/?redirectUrl=https%3A%2F%2Fzenodo.org%2Fdoi%2F10.5281%2Fzenodo.11242567" target="_blank" rel="noopener">10.5281/zenodo.11242567</a>). The dataset was employed in the preparation of Paper by the same authors (<a href="https://doi.org/10.1029/2024GL111603">https://doi.org/10.1029/2024GL111603</a>).</p>
Data from: Complex dynamics underlie the evolution of imperfect wing pattern convergence in butterflies
Adaptive radiation is characterized by rapid diversification that is strongly associated with ecological specialization. However, understanding the evolutionary mechanisms fueling adaptive diversification requires a detailed knowledge of how natural selection acts at multiple life-history stages. Butterflies within the genus Adelpha represent one of the largest and most diverse butterfly lineages in the Neotropics. Although Adelpha species feed on an extraordinary diversity of larval hosts, convergent evolution is widespread in this group suggesting that selection for mimicry may contribute to adaptive divergence among species. To investigate this hypothesis, we conducted predation studies in Costa Rica using artificial butterfly facsimiles. Specifically, we predicted that non-toxic, palatable Adelpha species that do not feed on host plants in the family Rubiaceae would benefit from sharing a locally convergent wing pattern with the presumably toxic Rubiaceae-feeding species via reduced predation. Contrary to expectations, we found that the presumed mimic was attacked significantly more than its locally convergent model, at a frequency paralleling attack rates on both novel and palatable prey. Although these data reveal the first evidence for protection from avian predators by the supposed toxic, Rubiaceae-feeding Adelpha species, we conclude that imprecise mimetic patterns have high costs for Batesian mimics in the tropics.
Fig. 93 in Classification, natural history, and evolution of Tarsosteninae (Coleoptera: Cleroidea: Cleridae). Part IV. Taxonomy of the Tarsostenodes complex of Australia, New Caledonia, New Guinea, and Tasmania
Fig. 93: Geographic distribution of species as noted.
Fig. 92 in Classification, natural history, and evolution of Tarsosteninae (Coleoptera: Cleroidea: Cleridae). Part IV. Taxonomy of the Tarsostenodes complex of Australia, New Caledonia, New Guinea, and Tasmania
Fig. 92: Geographic distribution of Tarsostenodes guttulus.
Fig. 91 in Classification, natural history, and evolution of Tarsosteninae (Coleoptera: Cleroidea: Cleridae). Part IV. Taxonomy of the Tarsostenodes complex of Australia, New Caledonia, New Guinea, and Tasmania
Fig. 91: Geographic distribution of species as noted.
Fig. 90 in Classification, natural history, and evolution of Tarsosteninae (Coleoptera: Cleroidea: Cleridae). Part IV. Taxonomy of the Tarsostenodes complex of Australia, New Caledonia, New Guinea, and Tasmania
Fig. 90: Geographic distribution of Tarsostenodes simulator.
Fig. 50 in Classification, natural history, and evolution of Tarsosteninae (Coleoptera: Cleroidea: Cleridae). Part IV. Taxonomy of the Tarsostenodes complex of Australia, New Caledonia, New Guinea, and Tasmania
Fig. 50: Phylogenetic hypothesis of the species of the Tarsostenodes complex.
Fig. 1 in Classification, natural history, and evolution of Tarsosteninae (Coleoptera: Cleroidea: Cleridae). Part IV. Taxonomy of the Tarsostenodes complex of Australia, New Caledonia, New Guinea, and Tasmania
Fig. 1: Habitus of Tarsostenodes cribripennis.
Phylogenomics and evolution of the synaptonemal complex in Drosophila
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Data from: Robust phylogenomics settles controversies of classification and reveals evolution of male embolic complex of the Laufeia clade (Araneae, Salticidae, Euophryini)
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Data from: An experimental investigation of how intraspecific competition and phenotypic plasticity can promote the evolution of novel, complex phenotypes
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Serial disparity in the carnivoran backbone unveil a complex adaptive role in metameric evolution
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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.