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333 results for “Convergent evolution”
Fig. 2 in New data on the Paleocene monotreme Monotrematum sudamericanum, and the convergent evolution of triangulate molars
Fig. 2. Schematic occlusal view of the advanced ornithorhynchid Obdurodon dicksoni; RM2 (A), Rm1 (B). The only know m1 of Monotrematum sudamericanum is incomplete (Fig. 1D). As both genera show similar crown pattern, we figure here the homologous teeth of O. dicksoni. Not to scale.
Fig. 1 in New data on the Paleocene monotreme Monotrematum sudamericanum, and the convergent evolution of triangulate molars
Fig. 1. Monotrematum sudamericanum RM2 (MPEF−PV 1634) in occlusal (A) and posterior (B) views. C. Base of crown showing fragment of roots. Rm1(MPEF−PV 1635); occlusal view (D), posterior view (E). F. Base of crown showing fragmentary roots. Not to scale.
Fig. 4. Monotrematum sudamericanum. A in New data on the Paleocene monotreme Monotrematum sudamericanum, and the convergent evolution of triangulate molars
Fig. 4. Monotrematum sudamericanum. A. Stereopair of RM2, occlusal view. B. Stereopair of Rm1, occlusal view. Anterior is up in A and B.
Linked collectors and determiners for: Impatiens smetsiana, another example of convergent evolution of flower morphology in Impatiens.
Natural history specimen data linked to collectors and determiners held within, "Impatiens smetsiana, another example of convergent evolution of flower morphology in Impatiens". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/12519b86-b0a3-4b15-b713-f447c1eae8ab">https://bionomia.net/dataset/12519b86-b0a3-4b15-b713-f447c1eae8ab</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/12519b86-b0a3-4b15-b713-f447c1eae8ab">https://gbif.org/dataset/12519b86-b0a3-4b15-b713-f447c1eae8ab</a>. Formatted as a Frictionless Data package.
Transcriptomic data reveal divergent paths of chitinase evolution underlying dietary convergence in anteaters and pangolins
<p><strong>Transcriptomic data reveal divergent paths of chitinase evolution underlying dietary convergence in anteaters and pangolins</strong><br> </p> <p>Rémi Allio<sup>1,2,§,</sup>*, Sophie Teullet<sup>1,§</sup>, Dave Lutgen<sup>1,3,4,§</sup>, Amandine Magdeleine<sup>1</sup>, Rachid Koual<sup>1</sup>, Marie-Ka Tilak<sup>1</sup>, Benoit de Thoisy<sup>5,6</sup>, Christopher A. Emerling<sup>1,7</sup>, Tristan Lefébure<sup>8</sup>, and Frédéric Delsuc<sup>1,</sup>*</p> <p><br><sup>1</sup>ISEM, Univ. Montpellier, CNRS, IRD, Montpellier, France</p> <p><sup>2</sup>CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier, Montpellier, France </p> <p><sup>3</sup>Institute of Ecology and Evolution, University of Bern, Bern, Switzerland</p> <p><sup>4</sup>Swiss ornithological Institute, Sempach, Switzerland</p> <p><sup>5</sup>Institut Pasteur de la Guyane, Cayenne, French Guiana, France</p> <p><sup>6</sup>Kwata NGO, Cayenne, French Guiana, France</p> <p><sup>7</sup>Biology Department, Reedley College, Reedley, CA, USA</p> <p><sup>8</sup>Univ. Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622, Villeurbanne, France</p> <p><sup>§</sup>Equal contribution</p> <p> </p> <p>*Correspondence</p> <p>Rémi Allio: remi.allio@inrae.fr</p> <p>Frédéric Delsuc: frederic.delsuc@umontpellier.fr</p> <p> </p> <p><strong>Abstract</strong></p> <p>Ant-eating mammals represent a textbook example of convergent evolution. Among them, anteaters and pangolins exhibit the most extreme convergent phenotypes with complete tooth loss, elongated skulls, protruding tongues, hypertrophied salivary glands producing large amounts of saliva, and powerful claws for ripping open ant and termite nests. However, comparative genomic analyses have shown that anteaters and pangolins differ in their chitinase acidic gene (CHIA) repertoires, which potentially degrade the chitinous exoskeletons of ingested ants and termites. While the southern tamandua (Tamandua tetradactyla) harbors four functional CHIA paralogs (CHIA1-4), Asian pangolins (Manis spp.) have only one functional paralog (CHIA5). Here, we performed a comparative transcriptomic analysis of salivary glands in 33 placental species, including 16 novel transcriptomes from ant-eating species and close relatives. Our results suggest that salivary glands play an important role in adaptation to an insect-based diet, as expression of different CHIA paralogs is observed in insectivorous species. Furthermore, convergently-evolved pangolins and anteaters express different chitinases in their digestive tracts. In the Malayan pangolin, CHIA5 is overexpressed in all major digestive organs, whereas in the southern tamandua, all four functional paralogs are expressed, at very high levels for CHIA1 and CHIA2 in the pancreas, and for CHIA3 and CHIA4 in the salivary glands, stomach, liver, and pancreas. Overall, our results demonstrate that divergent molecular mechanisms within the chitinase acidic gene family underlie convergent adaptation to the ant-eating diet in pangolins and anteaters. This study highlights the role of historical contingency and molecular tinkering of the chitin-digestive enzyme toolkit in this classic example of convergent evolution.</p> <p> </p> <p><strong><em>Figures & Tables</em></strong></p> <p><strong>Figure 1</strong>: Dated placental mammal phylogeny including representative species of the four major clades (Afrotheria, Xenarthra, Euarchontoglires, and Laurasiatheria) for which CHIA gene repertoires have been previously characterized. Numbers between brackets represent percentages of invertebrates included in the diet with myrmecophagous species indicated by an ant silhouette. Ψ symbols indicate CHIA pseudogenes as determined in previous studies (Emerling et al. 2018; Janiak et al. 2018; Wang et al. 2020<a href="https://www.zotero.org/google-docs/?IVkGtZ">)</a>. Ancestral CHIA gene repertoires for Placentalia and Ferae (Pholidota + Carnivora) as inferred by Emerling et al. (2018) are presented. The chronogram was extracted from <a href="http://www.timetree.org">www.timetree.org</a> <a href="https://www.zotero.org/google-docs/?Vr0bO1">(Kumar et al. 2022)</a>. Silhouettes were obtained from <a href="http://www.phylopic.org">www.phylopic.org</a>.</p> <p><strong>Figure 2</strong>: A. Mammalian chitinase-like gene family tree reconstructed using a maximum likelihood gene-tree/species-tree reconciliation approach on protein sequences. The nine chitinase paralogs are indicated on the outer circle. Scale bar represents the mean number of amino acid substitutions per site. B. Synteny analysis of the nine chitinase paralogs in humans (Homo sapiens), tarsier (Carlito syrichta), nine-banded armadillo (Dasypus novemcinctus) and the two main focal convergent ant-eating species: the southern tamandua (Tamandua tetradactyla) and the Malayan pangolin (Manis javanica). Assembly names and accession numbers are indicated below species names. Boxes represent different contigs with their most upstream and downstream BLAST hit positions to chitinase genes (colored arrows). Genes PIFO and DENND2D (grey arrows) are not chitinase paralogs but were used in the synteny analysis. Arrow direction indicates gene transcription direction as inferred in Genomicus v100.01 <a href="https://www.zotero.org/google-docs/?qjXWzo">(Nguyen et al. 2022)</a> for genes located on short contigs. Ψ symbols indicate pseudogenes as determined in <a href="https://www.zotero.org/google-docs/?IVkGtZ">Emerling et al. (2018)</a>. Genes with non significant BLAST hits were not represented and are probably not functional or absent. Silhouettes were obtained from <a href="http://www.phylopic.org">www.phylopic.org</a>.</p> <p><strong>Figure 3</strong>: Comparison of predicted ancestral protein sequences of the nine mammalian chitinase paralogs. A. Conserved amino acid residues of the canonical chitinolytic domain active site (DXXDXDXE). Arrows indicate paralogs in which changes occurred in the active site. B. Summary of the evolution of chitinase paralogs functionality. C. Conserved cysteine residues of the chitin-binding domain. The arrow indicates OVGP1 in which the last four cysteines have been replaced.</p> <p><strong>Figure 4</strong>: Expression of the nine chitinase paralogs in 40 mammalian salivary gland transcriptomes. The 33 species are presented in their phylogenetic context covering the four major placental clades: Afrotheria (AFR), Xenarthra (XEN), Euarchontoglires (EUA), and Laurasiatheria (LAU). The chronogram was extracted from <a href="http://www.timetree.org">www.timetree.org</a> <a href="https://www.zotero.org/google-docs/?Vr0bO1">(Kumar et al. 2022)</a>. Non-functional pseudogenes are only indicated for the three focal species (in bold) using a Ψ symbol: nine-banded armadillo (Dasypus novemcinctus), southern tamandua (Tamandua tetradactyla) and Malayan pangolin (Manis javanica). Expression level is represented as log10 (Normalized Counts + 1). Asterisks indicate the 16 new transcriptomes produced in this study. Myrmecophagous and insectivorous species are indicated by ant and beetle silhouettes, respectively. Silhouettes were obtained from <a href="http://www.phylopic.org">www.phylopic.org</a>.</p> <p><strong>Figure 5</strong>: Expression of the nine chitinase paralogs in 72 transcriptomes from different organs of the three focal species: the nine-banded armadillo (Dasypus novemcinctus), the Malayan pangolin (Manis javanica), and the southern tamandua (Tamandua tetradactyla). Non-functional pseudogenes are represented by a Ψ symbol and hatched background. Boxes indicate organs of the digestive tract. Expression level is represented as log10 (Normalized Counts + 1). Silhouettes were obtained from <a href="http://www.phylopic.org">www.phylopic.org</a>.</p> <p><strong>Figure 6</strong>: Summary figure presenting the evolution and expression of chitinase acidic (CHIA) paralogous genes in the convergently evolved Malayan pangolin (Manis javanica) and southern tamandua (Tamandua tetradactyla) in their phylogenetic context. Reconstructed CHIA gene repertoires are indicated for the two myrmecophagous species and for the most recent common ancestor (MRCA) of placentals, pangolins+carnivores (Ferae) and anteaters+sloths (Pilosa). Non-functional pseudogenes are represented by the Ψ symbol and dashed line contour. Organ icons indicate expression of the corresponding gene in different digestive organs. SG: Salivary glands; S: Stomach; T: Tongue; P: Pancreas; L: Liver; I: Intestine. Silhouettes were obtained from <a href="http://www.phylopic.org">www.phylopic.org</a> and <a href="https://www.vecteezy.com/">www.vecteezy.com</a>.</p> <p> </p> <p><em><strong>Supplementary Materials</strong></em></p> <p><strong>Table S1: </strong>Detailed information on the tissues sequenced or retrieved from public databases for the project.</p> <p><strong>Table S2</strong>: BUSCO v5 scores of all transcriptomes based on a dataset of 9,226 single-copy orthologs conserved in over 90% of mammalian species <a href="https://www.zotero.org/google-docs/?lrFE5h">(Manni et al. 2021)</a>. </p> <p> </p> <p><strong><em>Zenodo supplementary files</em></strong></p> <p><strong>CHIAs_OG_tree-RAxML_EPA</strong><strong>.zip </strong>contains CHIA sequences (obtained from the OrthoFinder orthogroups and the sequences used to infer the chitinase genes evolution) and the corresponding ML tree. </p> <p><strong>Chitinases_ancestral_sequences.zip </strong>contains the ancestral chitinase sequence reconstructions, the associated posterior probabilities, and the alignment of the ancestral sequences inferred by RAxML-NG. </p> <p><strong>Chitinases_gene_tree.zip</strong> contains input and output files corresponding to the chitinase gene tree presented in Figure 2: </p> <p>- mammalina_species_tree_input_Generax.newick = species tree used for the reconciliation with Generax</p> <p>- chitinase_gene_alignment_renamed_input_Generax.fasta = chitinase gene alignment with the sequence names renamed for Generax</p> <p>- chitinase_gene_alignment_not_renamed.fasta = chitinase gene alignment with the original sequence names (for information)</p> <p>- chitinases_gene_tree_sequences_renamed_input_Generax.newick = chitinase gene tree inferred with RAxML-NG and reconciled using the TreeRecs algorithm to find the optimal rooting scheme; this tree was used for Generax</p> <p>- reconciled_chitinase_genes_tree_output_Generax.newick = reconciled chitinase gene tree inferred by Generax and presented in Figure 2</p> <p><strong>Chitinases_expression.zip </strong>contains all orthogroup gene expressions plus chitinase gene expressions.</p> <p><strong>Kallisto_abundances.zip</strong> contains the abundances estimated with kallisto for each organ of each species<em>.</em></p> <p><strong>Supplementary table figure 2B - BLAST</strong> <strong>results.xlsx</strong> contains BLAST results supporting sequence inferences. </p> <p><strong>Transcriptome_assemblies.tar.gz</strong> contains the transcriptome assemblies obtained for each organ and species with Trinity.</p>
Deep-time convergent evolution in animal communication presented by shared adaptations for coping with noise in lizards and other animals
<p>Convergence in communication appears rare compared to other forms of adaptation. This is puzzling, given communication is acutely dependent on the environment and expected to converge in form when animals communicate in similar habitats. We uncover deep-time convergence in territorial communication between two groups of tropical lizards separated by over 140 million years of evolution: the Southeast Asian Draco and Caribbean Anolis. These groups have repeatedly converged in multiple aspects of display along common environmental gradients. Robot playbacks to free-ranging lizards confirmed the most prominent convergence in display is adaptive, as it improves signal detection. We then provide evidence from a sample of the literature to further show convergent adaptation among highly divergent animal groups is almost certainly widespread in nature. Signal evolution is therefore curbed towards the same set of adaptive solutions, especially when animals are challenged with the problem of communicating effectively in noisy environments.</p>
Figure 1 in Convergent evolution of shell shape in freshwater limpets: the African genus Burnupia
Figure 1. General shell shape, size and chirality of the taxa studied. Shells are derived from the populations utilized here, but not necessarily from the specimen used for DNA work. The representative for the genus Burnupia is B. stenochorias. Scale bars = 2 mm.
Figure 2 in Convergent evolution of shell shape in freshwater limpets: the African genus Burnupia
Figure 2. Bayesian phylogram for basommatophoran taxa based on 2423 nucleotide positions of combined COI and 18S rRNA sequences showing the 50% majority-rule consensuses of topologies sampled during the Bayesian search. The tree was rooted with the outgroup Acroloxus lacustris. The scale bar indicates the expected number of substitutions per site according to the model of sequence evolution applied. Posterior probabilities are provided above the branches. Note that the topology of a maximum likelihood phylogram (not presented here) is identical with the Bayesian phylogram. Maximum likelihood bootstrap support (1000 replicates) is indicated below the branches. Family assignments follow Boss (1982). Ambiguous assignments are indicated by hatchings.
Fig. 5 in Disporella guada sp. nov., an erect-ramose rectangulate cyclostome (Bryozoa, Stenolaemata) from the Caribbean Sea: convergent evolution in bryozoan colony morphology
Fig. 5. Brood chambers in Disporella guada Harmelin, Taylor & Waeschenbach sp. nov. A. Paratype (NHMUK 2021.2.25.1). B–D. Holotype (MNHN-IB-2017-696). A. Brood chamber with 8 lateral branches, thinly covered by secondary calcification. B. Thicker mesh of secondary calcification over a brood chamber. C. Transverse section of branch intersecting six lobes of ramifying brood chambers. D. Two ooeciopores (open arrowheads) at the end of a lateral branch of a brood chamber.
Fig. 2 in Disporella guada sp. nov., an erect-ramose rectangulate cyclostome (Bryozoa, Stenolaemata) from the Caribbean Sea: convergent evolution in bryozoan colony morphology
Fig. 2. Photographs (A–B) and scanning electron micrographs of Disporella guada Harmelin, Taylor & Waeschenbach sp. nov. A. Holotype, specimen kept dry (MNHN-IB-2017-696). B. Seven variously shaped colonies (top row, left to right: NHMUK 2021.2.25.1, 2021.3.19.2, 2018.1.15.63, 2021.3.19.1; bottom row, left to right: NHMUK 2021.6.14.1, 2021.6.14.2, 2021.6.14.3). C. Longitudinal section of a specimen (NHMUK 2021.3.19.1) with two branches; 1: endozone, 2: exozone, 3: basal part with central primary attachment zone (3a) and secondary peripheral attachment zone (3b). D–E. NHMUK 2021.3.19.2. D. Growing tip. E. Interzooecial walls at growing tip.
Fig. 3 in Disporella guada sp. nov., an erect-ramose rectangulate cyclostome (Bryozoa, Stenolaemata) from the Caribbean Sea: convergent evolution in bryozoan colony morphology
Fig. 3. Disporella guada Harmelin, Taylor & Waeschenbach sp. nov.A. Non-type (MNHN-IB-2017-700). B–C, E. Holotype (MNHN-IB-2017-696). D. Paratype (NHMUK 2021.2.25.1). A. Elongated maculae. B. Mixture of peristomate autozooids and kenozooids. C. Part of a transverse section of a terminal branch showing the endozone, exozone and intersecting ramifications of several gonozooids (larger white cavities). D. Kenozooids and autozooids with small peristomes bearing pointed processes. E. Kenozooids and autozooidal peristomes of various sizes and shapes.
Fig. 1 in Disporella guada sp. nov., an erect-ramose rectangulate cyclostome (Bryozoa, Stenolaemata) from the Caribbean Sea: convergent evolution in bryozoan colony morphology
Fig. 1. Underwater photos of specimens of Disporella guada Harmelin, Taylor & Waeschenbach sp. nov.; Guadeloupe, Islet Tête-à-l'Anglais, 5 m. A. Holotype (MNHN-IB-2017-696); photo Y. Bouchon- Navaro, 10 Oct. 2014. B. Another large specimen; photo C. Bouchon, 7 Nov. 2016.
Supplementary Data for "Convergent evolution as an indicator for selection during acute HIV-1 infection"
<p><strong>Supplementary Data 1. Position of all identified mutations in the <em>env</em> gene. </strong>This file contains detailed information about the identity of the observed mutations. It provides the position in the HXB2 genome, the amino acid change they cause in the different genetic backgrounds and the number of HIV-1 subtypes (out of a total of 170) the mutations occurs in.</p> <p><strong>Supplementary Data 2. Position of all identified mutations in the <em>rev</em> exon part of the <em>env </em>gene. </strong>Same as Supplementary Data 1, except that only mutations and amino acid substitutions in the <em>rev</em> exon 2 are shown.</p> <p><strong>Supplementary Program.</strong> With this program one can redo the analyses and simulations of the manuscript.</p>
Diadromy drives elevated rates of trait evolution and ecomorphological convergence in Clupeiformes (herring, shad, and anchovies)
<p>Migration can have a profound influence on rates and patterns of phenotypic evolution. Diadromy is the migration between marine and freshwater habitats for feeding and reproduction that can require individuals to travel tens to thousands of kilometers. The high energetic demands of diadromy are predicted to select for ecomorphological traits that maximize swimming and locomotor efficiency. Intraspecific studies have shown repeated instances of divergence among diadromous and non-diadromous populations in locomotor and foraging traits, which suggests that at a macroevolutionary scale, diadromous lineages may experience convergent evolution onto one or multiple adaptive optima. We tested for differences in rates and patterns of phenotypic evolution among diadromous and non-diadromous lineages in Clupeiformes, a clade that has evolved diadromy more than 10 times. Our results show that diadromous clupeiforms show convergent evolution for some locomotor traits, and faster rates of evolution, which we propose are adaptive responses to the locomotor demands of migration. We also find evidence that diadromous lineages show convergence into multiple regions of multivariate traitspace and suggest these respective traitspaces are associated with differences in migration and trophic ecology. However, not all locomotor traits and no trophic traits show evidence of convergence or elevated rates of evolution associated with diadromy. Our results show that long-distance migration influences the tempo and patterns of phenotypic evolution at macroevolutionary scales, but there is not a single diadromous syndrome. </p>
Data to reproduce analysis in Convergent evolution of extrachromosomal DNA in mCRPC paper
<p>Targeted cancer therapies can prolong the lives of men with metastatic castration resistant prostate cancer (mCRPC). However, these treatments also selectively favor the growth of tumor cells that harbor therapy resistance, and mCRPC is currently lethal. It has been challenging to study factors influencing how therapy resistance develops in this setting because few autopsy studies of have been performed in the settings of DNA-repair deficient mCRPC. Here, we assessed how resistance to targeted cancer therapies evolved in an autopsy cohort of 53 mCRPC tumors from six such men using deep whole genome and transcriptome analysis, validating our observations in an independent cohort of 135 mCRPC tumors. We identified intra-patient heterogeneity in clinically actionable DNA repair deficiencies and transcriptionally-defined tumor subtypes. Identical polygenic DNA repair resistance mutations were present in physically distinct tumors within the same individual, suggesting that these mutations pre-exist selection by later targeted therapy. Extra-chromosomal DNA (ecDNA) was present in more than half of mCRPC biopsies and frequently amplified the androgen receptor (<em>AR</em>) and enhancers of <em>AR</em> and <em>MYC</em>. Individual ecDNA amplicons included multiple driver genes on different chromosomes, and arose multiple times within distinct tumors in a single patient. The presence of ecDNA was significantly associated with whole genome doubling, chromothripsis, and with inactivating <em>TP53</em> alterations. We conclude that ecDNA amplification is a major contributor to therapy resistance in mCRPC and that late-stage mCRPC develops intra-patient heterogeneity in response to targeted therapy.</p>
Episodic evolution of a protracted convergent margin revealed by detrital zircon geochronology in the Greater Caucasus
<p class="MsoNormal">Convergent margins play a fundamental role in the construction and modification of Earth's lithosphere and are characterized by poorly understood episodic processes that occur during the progression from subduction to terminal collision. On the northern margin of the active Arabia-Eurasia collision zone, the Greater Caucasus Mountains provide an opportunity to study a protracted convergent margin that spanned most of the Phanerozoic and culminated in Cenozoic continental collision. However, the main episodes of lithosphere formation and deformation along this margin remain enigmatic. Here, we use detrital zircon U-Pb geochronology from Paleozoic and Mesozoic (meta)sedimentary rocks in the Greater Caucasus, along with select zircon U-Pb and Hf isotopic data from coeval igneous rocks, to link key magmatic and depositional episodes along the Caucasus convergent margin. Devonian to Early Carboniferous rocks were deposited prior to Late Carboniferous accretion of the Greater Caucasus crystalline core onto the Laurussian margin. Permian to Triassic rocks document a period of northward subduction and forearc deposition south of a continental margin volcanic arc in the Northern Caucasus and Scythian Platform. Jurassic rocks record the opening of the Caucasus Basin as a back-arc rift during southward migration of the arc front into the Lesser Caucasus. Cretaceous rocks have few Jurassic-Cretaceous zircons, indicating a period of relative magmatic quiescence and minimal exhumation within this basin. Late Cenozoic closure of the Caucasus Basin juxtaposed the Lesser Caucasus arc to the south against the crystalline core of the Greater Caucasus to the north and led to the formation of a hypothesized terminal suture. We expect this suture to be within ~20 kilometers of the southern range front of the Greater Caucasus because all analyzed rocks to the north exhibit a provenance affinity with the crystalline core of the Greater Caucasus.</p>
Data from: Convergence and constraint in the cranial evolution of mosasaurid reptiles and early cetaceans
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Data from: Diversification rates have no effect on the convergent evolution of foraging strategies in the most speciose genus of bats, Myotis
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Convergent evolution of artemisinin and chloroquine resistance in Ethiopian Plasmodium falciparum parasites
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Data from: The role of mutation bias in adaptive molecular evolution: insights from convergent changes in protein function
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