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Dominant contribution of Asgard archaea to eukaryogenesis (2024) Tobiasson, V., Koonin, E. PROCESSED DATA AND METADATA
<h1>Main data deposit for "Dominant contribution of Asgard archaea to eukaryogenesis". </h1> <p>Victor Tobiasson, Jacob Luo, Yuri I Wolf, Eugene V Koonin</p> <p>Computational Biology Branch, Division of Intramural Research, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA</p> <p><strong>The Origin of eukaryotes is one of the key problems in evolutionary biology. The demonstration that the Last Eukaryotic Common Ancestor (LECA) already contained the mitochondrion, an endosymbiotic organelle derived from an alphaproteobacterium, and the discovery of Asgard archaea, the closest archaeal relatives of eukaryotes inform and constrain evolutionary scenarios of eukaryogenesis. We undertook a comprehensive analysis of the origins of the core eukaryotic genes tracing to the LECA within a rigorous statistical framework centered around evolutionary hypotheses testing using constrained phylogenetic trees. The results reveal dominant contributions of Asgard archaea to the origin of most of the conserved eukaryotic functional systems and pathways. A limited contribution from Alphaproteobacteria was identified, primarily relating to the energy transformation systems and Fe-S cluster biogenesis, whereas ancestry from other bacterial phyla was scattered across the eukaryotic functional landscape, without consistent trends. These findings suggest a model of eukaryogenesis in which key features of eukaryotic cell organization evolved in the Asgard ancestor, followed by the capture of the Alphaproteobacterial endosymbiont, and augmented by numerous but sporadic horizontal acquisition of genes from other bacteria both before and after endosymbiosis. </strong></p> <div> <div> <div>Version 0.3, updated 180325</div> <div> </div> <div> </div> <div>Main data repository for:</div> <div>Dominant contribution of Asgard archaea to eukaryogenesis (2024) </div> <div>Tobiasson, V., Koonin, E.</div> <div> </div> <div>Contains all final parsed data from the main Eukaryogenesis project </div> <div>investigating the evolutionary ancetries of eukaryotic protein families. </div> <div> </div> <div>Currently (non-static) available at: </div> <div>https://www.biorxiv.org/content/10.1101/2024.10.14.618318v2</div> <div>https://assets-eu.researchsquare.com/files/rs-5352492/v1/2f9c68ae-cf3e-420a-8d29-867b6fb1a878.pdf</div> <div> </div> <div>All code used to generate the data present within this repository available at: </div> <div>https://github.com/VictorTobiasson/eukgen </div> <div> </div> <div> </div> <div>### General information</div> <div> </div> <div>To identify associations between prokaryotic and eukaryotic protein families, separate</div> <div>hidden Markov model (HMM) databases for prokaryotes and eukaryotes were constructed </div> <div>using a custom, cascaded, sequence-to-profile clustering pipeline, implemented using </div> <div>mmseqs2, followed by a multistep data-reduction and multiple sequence alignment (MSA) </div> <div>procedure to generate HMM profiles using hhsuite. </div> <div> </div> <div>A prokaryotic database of 37 million protein sequences was curated from prokaryotic </div> <div>genomes obtained from the NCBI GenBank in November 2023 and supplemented with proteins </div> <div>extracted from 146 Asgard genome assemblies. To avoid inclusion of genes present only </div> <div>within a narrow subset of species, possibly resulting from horizontal transfer from </div> <div>eukaryotes post LECA, we reconstructed the “soft-core” pangenome for each of the 26 </div> <div>curated prokaryotic taxonomic classes. These pangenomes include only those genes that </div> <div>are present in at least 67% of the families within each class of Bacteria and Archaea. </div> <div>The initial eukaryotic database consisted of 30 million protein sequences from 993 </div> <div>species taken from EukprotV3 and cleaned using mmseqs2 to remove likely prokaryotic </div> <div>contaminants. </div> <div> </div> <div>Both databases were clustered and MSAs constructed for all non, singleton clusters </div> <div>and HMM profiles created. The resulting eukaryotic HMM dataset was queried against </div> <div>the prokaryotic dataset using hhblits to identify sets of homologous protein sequences. </div> <div>Each eukaryotic cluster and all its significant prokaryotic hits constituted an individual</div> <div> sequence set, hereinafter referred to as an Eukaryotic/Prokaryotic Orthologous Cluster </div> <div>(EPOC). The EPOCs constitute groups of homologous proteins from eukaryotes and prokaryotes </div> <div>(each EPOC contains a unique set of eukaryotic proteins, but some clusters of prokaryotic </div> <div>proteins can be present in multiple EPOCs) that were used for phylogenetic tree </div> <div>construction, annotation, and evolutionary hypothesis testing. </div> <div> </div> <div>To infer the most likely prokaryotic ancestry of the eukaryotic proteins in each EPOC, </div> <div>rather than relying on the tree topology directly, we employed a probabilistic approach </div> <div>for evolutionary hypothesis testing using constraint trees. We exhaustively sampled all </div> <div>arrangements of likely sister clades and obtained Expected Likelihood Weights (ELW) for </div> <div>the set of possible sister clade models. As the ELW metric is analogous to model selection </div> <div>confidence, here we take it to be proportional to the probability of a sampled prokaryotic </div> <div>clade to be the true sister group of the given eukaryotic clade among a set of competing </div> <div>sister clades. For each EPOC, our analysis dynamically accounts for long branch outliers </div> <div>and is robust to phylogenetically non-homogenous clades. This analysis is further capable </div> <div>of resolving eukaryotic paraphyly, treating each eukaryotic clade within a EPOC as a </div> <div>single datapoint for downstream analysis. Our resulting data contains EPOCs annotated </div> <div>using profiles generated from KEGG Orthology Groups (KOGs), each with an MSA generated </div> <div>using muscle5, a maximum likelihood tree inferred using IQtree2 and associated ELW values </div> <div>for all candidate prokaryotic sister phyla. The analysis of prokaryotic ancestry was </div> <div>performed only for those eukaryotic clades that included more than 5 distinct taxonomic </div> <div>labels, with at least one coming from Amorphea and one from Diaphoretickes, the two </div> <div>expansive eukaryotic clades considered to represent either the first or the second </div> <div>bifurcation in the evolution of eukaryotes. Thus, these clades likely represent genes </div> <div>mapping back to the LECA.</div> <div> </div> <div>For further details please see main publication or contact</div> <div>victor.tobiasson@nih.gov</div> <div>eugene.koonin@nih.gov</div> <div> </div> <div> </div> <div>### Included files</div> <div> </div> <div>Unless otherwise stated all files contained are tab separated and utf-8 encoded </div> <div>with the first row containing header information. </div> <div>All data entries encoding lists are “|” (pipe) separated. </div> <div>Fields without data values are filled with string entries of “none”.</div> <div> </div> <div>--- Databases ---</div> <div>euk72_ep.tar.gz</div> <div>prok2311_as.tar.gz</div> <div>Prok2311As_final_clusters.tsv</div> <div>Euk72Ep_final_clusters.tsv</div> <div>prok2311_as.hmmDB.tar.gz</div> <div>euk72_ep.hmmDB.tar.gz</div> <div> </div> <div>--- Annotation and Curation ---</div> <div>NCBI_taxonomy_species_addendum.tsv</div> <div>NCBI_taxonomy_class_addendum.tsv</div> <div>Euk72Ep_Prok2311As_final_classes.tsv</div> <div>Euk72Ep_Prok2311As_final_classes.GTDB.tsv</div> <div>KEGG_category_mapping.tsv</div> <div>KEGG_metadata.tsv</div> <div> </div> <div>--- EPOC data ---</div> <div>EPOC_data.tar.gz</div> <div>EPOC_annotation_KEGG.tsv</div> <div>EPOC_data.tsv</div> <div>EPOC_data.pangenomes_s10.tsv</div> <div>EPOC_data.pangenomes_s25.tsv</div> <div>EPOC_data.pangenomes_s67.tsv</div> <div>EPOC_data.GTDB.tsv</div> <div> </div> <div># euk72_ep.tar.gz</div> <div>Gunzip-ed .tar archive containing a single directory with 10 files </div> <div>constituting the initial eukaryotic mmseqs2 database with taxonomy annotation. </div> <div>Constructed from a pre-selected list of 72 eukaryotic proteomes downloaded from </div> <div>NCBI as well as a “clean” version of Eukprot, lacking highly prokaryotic-like </div> <div>contaminant sequences. </div> <div> </div> <div># prok2311_as.tar.gz</div> <div>Gunzip-ed .tar archive containing a single directory with 10 files constituting the </div> <div>initial prokaryotic mmseqs2 database with taxonomy annotation. Constructed from </div> <div>47545 complete genomes retrieved from NCBI in November 2023. </div> <div> </div> <div># prok2311_as.hmmDB.tar.gz</div> <div>Gunzip-ed .tar archive containing 6 files. Comprises an HHSuite Databse formatted </div> <div>from prok2311_as non--singleton clusters, contains 26286 profiles.</div> <div> </div> <div># euk72_ep.hmmDB.tar.gz</div> <div>Gunzip-ed .tar archive containing 6 files. Comprises an HHSuite Databse formatted </div> <div>from euk72_ep non-singleton clusters, contains 1631704 profiles.</div> <div> </div> <div># NCBI_taxonomy_species_addendum.tsv</div> <div>Taxonomy mapping file with manually curated ‘class’ level annotation for poorly </div> <div>annotated species. </div> <div> </div> <div>taxid: NCBI taxid</div> <div>proposed_class_id: Manually assigned NCBI taxid</div> <div>proposed_class_label: NCBI class name</div> <div>org_name: NCBI organism name</div> <div> </div> <div># NCBI_taxonomy_class_addendum.tsv</div> <div>Class revision file mapping poorly populated class level entries to higher order </div> <div>manually curated labels. Also includes information for small classes with shallow </div> <div>taxonomy which are deleted from the EPOC analysis at the level of tree construction.</div> <div> </div> <div>taxid: NCBI taxid</div> <div>ncbi_class: NCBI taxid of rank corresponding to ‘class’ following manual </div> <div>amendment as per NCBI_taxonomy_species_addendum.tsv</div> <div>revised_class_id: Manually assigned NCBI taxid of rank corresponding to ‘class’</div> <div>revised_class_label: Proposed cleartext name of manually revised revised_class_id </div> <div> </div> <div># Euk72Ep_Prok2311As_final_classes.tsv</div> <div>Final taxonomy at NCBI rank ‘class’ following revisions for all sequences in Euk72Ep or </div> <div>Prok2311As. These taxonomic labels are used for EPOC tree annotation. </div> <div> </div> <div>acc: mmseqs database header in either prok2311_as or euk72_ep databases</div> <div>taxid: NCBI taxid for organism</div> <div>superkingdom: Top level NCBI taxonomy classification Bacteria, Archaea or Eukarya, </div> <div>used to define Eukaryotic outgroups in EPOC analysis</div> <div>class: Cleartext name of manually revised NCBI rank ‘class’ identifier for annotation</div> <div> </div> <div># Euk72Ep_Prok2311As_final_classes.GTDB.tsv</div> <div>Final taxonomy at GTDB rank ‘phylum’ transferred using marker genes from GTDB release 220</div> <div> </div> <div>acc: mmseqs database header in either prok2311_as or euk72_ep databases</div> <div>taxid: NCBI taxid for organism</div> <div>superkingdom: Top level NCBI taxonomy classification Bacteria, Archaea or Eukarya, </div> <div>used to define Eukaryotic outgroups in EPOC analysis</div> <div>class: Cleartext name of assigne GTDB phylum</div> <div> </div> <div># Prok2311As_final_clusters.tsv</div> <div>Cluster mapping file for accessions within the initial Prok2311A database to the </div> <div>final clusters used for HMM creation </div> <div> </div> <div>cluster_acc: cluster representative</div> <div>acc: cluster member</div> <div> </div> <div># Euk72Ep_final_clusters.tsv</div> <div>Cluster mapping file for accessions within the initial Prok2311A database to the </div> <div>final clusters used for HMM creation</div> <div> </div> <div>cluster_acc: cluster representative</div> <div>acc: cluster member</div> <div> </div> <div># EPOC_data.tar.gz</div> <div>Gunzip-ed directory containing 16035 EPOC folders. Each folder is named corresponding </div> <div>to the eukaryotic cluster representative which generated its profile as an ID </div> <div>Matches the tree_name field in EPOC_data_prok2311As.tsv</div> <div>contains the following files:</div> <div> </div> <div><EPOC_ID>.merged.fasta: sequences for all members of the EPOC</div> <div><EPOC_ID>.merged.fasta.leaf_mapping: tsv separated file containing taxonomy and tree reduction data</div> <div><EPOC_ID>.merged.fasta.muscle: main cropped MSA for tree generation </div> <div><EPOC_ID>.merged.fasta.muscle.iqtree: IQtree2 output from tree generation</div> <div><EPOC_ID>.merged.fasta.muscle.treefile.annot: annotated newick tree file with final tree</div> <div><EPOC_ID>.merged.tree_data.tsv: final parsed tree data with columns matching EPOC_data_prok2311As.tsv</div> <div> </div> <div>EPOCs with more than one possible eukaryotic sister phyla also contains </div> <div>a folder "constraint_analysis" with constraint tree information used for </div> <div>ELW value calculation. </div> <div> </div> <div># EPOC_data.tsv</div> <div>Main resulting data from all Eukaryotic/Prokaryotic Orthologous Clusters (EPOCs) </div> <div>based on pangenomes defined as including 10% of species per class. This is the main</div> <div>data to be used for genereting the core dataset and for data visualistation</div> <div>Contains information regarding tree breakdown, LCA membership and phylogenetic </div> <div>distances between all detected LCAs. Equivalent to the stacked dataframes from all </div> <div>EPOC directories in EPOC_data </div> <div> </div> <div>tree_name: unique index for each EPOC </div> <div>euk_clade_rep: unique index for each annotated eukaryotic clade within each tree_name</div> <div>euk_clade_size: number of original sequences represented by euk_clade_rep</div> <div>euk_clade_weight: metric for taxonomic purity for each euk_clade_rep</div> <div>euk_leaf_clade: boolean indicating whether euk_clade_rep contains a single leaf</div> <div>euk_LCA: lowest taxa spanning all members in euk_clade_rep</div> <div>euk_scope: list of all taxonomic classes in euk_clade_rep</div> <div>euk_scope_len: length of euk_scope list</div> <div>prok_clade_rep: unique index for each annotated prokaryotic clade for each euk_clade_rep</div> <div>prok_clade_size: number of original sequences represented by prok_clade_rep</div> <div>prok_clade_weight: metric for taxonomic purity for each prok_clade_rep</div> <div>prok_leaf_clade: boolean indicating whether prok_clade_rep contains a single leaf</div> <div>prok_taxa: lowest taxa spanning all members in prok_clade_rep</div> <div>dist: tree-distance from lowest tree node containing all members of prok_clade_rep to lowest tree node containing all members of euk_clade_rep</div> <div>top_dist: graph-distance (node-distance) from lowest tree node containing all members of prok_clade_rep to lowest tree node containing all members of euk_clade_rep</div> <div>raw_stem_length: tree-distance from lowest tree node containing the union of all members of prok_clade_rep and euk_clade_rep to the tree node containing all members of euk_clade_rep</div> <div>median_euk_leaf_dist: median value for all tree distances from the tree node containing all members of euk_clade_rep to the individual leaves</div> <div>stem_length: raw_stem_length/median_euk_leaf_dist</div> <div>logL: log likelihood of best constraint tree constructed</div> <div>deltaL: log likelihood difference between constraint tree for prok_clade_rep and best constraint tree constructed</div> <div>bp-RELL: validation metric from IQtree -trees, see iqtree.org</div> <div>bp-RELL_accept: as above</div> <div>p-KH: as above</div> <div>p-KH_accept: as above</div> <div>p-SH: as above</div> <div>p-SH_accept: as above</div> <div>c-ELW: as above</div> <div>c-ELW_accept: as above</div> <div>p-AU: as above</div> <div>p-AU_accept: as above</div> <div> </div> <div># EPOC_data.pangenomes_s10.tsv</div> <div>Resulting data from all Eukaryotic/Prokaryotic Orthologous Clusters (EPOCs) calculated </div> <div>based on pangenomes defined as including 10% of species per class.</div> <div>Identical file structure to EPOC_data.tsv</div> <div> </div> <div># EPOC_data.pangenomes_s25.tsv</div> <div>Resulting data from all Eukaryotic/Prokaryotic Orthologous Clusters (EPOCs) calculated </div> <div>based on pangenomes defined as including 25% of species per class.</div> <div>Identical file structure to EPOC_data.tsv</div> <div> </div> <div># EPOC_data.pangenomes_s67.tsv</div> <div>Resulting data from all Eukaryotic/Prokaryotic Orthologous Clusters (EPOCs) calculated </div> <div>based on pangenomes defined as including 67% of species per class.</div> <div>Identical file structure to EPOC_data.tsv</div> <div> </div> <div># EPOC_data.GTDB.tsv</div> <div>Resulting data from all Eukaryotic/Prokaryotic Orthologous Clusters (EPOCs) calculated </div> <div>under revised taxonomy from GTDB based on data from Euk72Ep_Prok2311As_final_classes.GTDB.tsv</div> <div>Identical file structure to EPOC_data.tsv</div> <div> </div> <div># EPOC_data.alpha_replicates.tsv</div> <div>Resulting data from 20 repetitions of Eukaryotic/Prokaryotic Orthologous Clusters (EPOCs) calculated </div> <div>from a subset of Alphaproteobacterial-derived EPOCs. </div> <div>Identical file structure to EPOC_data.tsv with the addition of:</div> <div> </div> <div>rep: indicating technical replicate number, 0-19</div> <div> </div> <div># EPOC_annotation_KEGG.tsv</div> <div>Parsed HHblits output of HMM profiles generated from KEGG KOGs (KEGG Orthologous Groups) </div> <div>against eukaryotic profiles constituting each EPOC</div> <div> </div> <div>Query: query name equal to tree_name from EPOC_data</div> <div>Target: target name equal to kogid in KEGG_category_mapping and KEGG_metadata</div> <div>Prob: data from HHblits, see https://github.com/soedinglab/hh-suite/wiki</div> <div>E-value : as above</div> <div>P-value : as above</div> <div>Score: as above</div> <div>SS: as above</div> <div>Cols: as above</div> <div>Identities: as above</div> <div>Similarity: as above</div> <div>Sum_probs: as above</div> <div>Query-HMM-start: as above</div> <div>Query-HMM-end: as above</div> <div>Template-HMM-start: as above</div> <div>Template-HMM-end: as above</div> <div>Template_columns: as above</div> <div>Template_Neff : as above</div> <div>Pairwise_cov: calculated pairwise coverage from Query and Target start and end</div> <div>Description: category_name from KEGG_category_mapping</div> <div> </div> <div># KEGG_category_mapping.tsv</div> <div>Mapping of relevant KOG identifiers to their higher order categories as </div> <div>"Maps" "Modules" or "Reactions" as per KEGG see https://www.kegg.jp/kegg/pathway.html</div> <div> </div> <div>kogid: unique KOG identifier</div> <div>category_id: KEGG map, module, or reaction number</div> <div>category_name: cleartext name for KOG identifier</div> <div> </div> <div># KEGG_metadata.tsv</div> <div>File mapping KOGs to BRITE classification and to additional databases of chemical properties.</div> <div> </div> <div>kogid: unique KOG identifier</div> <div>name: cleartext name for KOG identifier</div> <div>brite_A: list of BRITE-A sets including KOG</div> <div>brite_B: list of BRITE-A sets including KOG</div> <div>brite_C: list of BRITE-A sets including KOG</div> <div>EC: list of Enzyme commission numbers associated with KOG, see https://enzyme.expasy.org/</div> <div>TC: list of transporter classification numbers associated with KOG, see https://www.tcdb.org/</div> <div>RN: list of KEGG reaction numbers associated with KOG</div> <div>CA: list of CAZY numbers associated with KOG, see http://www.cazy.org/</div> <div>GO: list of GO terms associated with KOG, see https://geneontology.org/</div> </div> <div> </div> </div>
AMOC reconstruction between 1981 and 2016 from hydrographic data using an empirical linear regression model from Worthington, E. L., Moat, B. I., Smeed, D. A., Mecking, J. V., Marsh, R., and McCarthy, G. D.: A 30-year reconstruction of the Atlantic meridional overturning circulation shows no decline, Ocean Sci., 17, 285–299, https://doi.org/10.5194/os-17-285-2021, 2021.
<p>Dataset used to create Figure 8 in Worthington et al., 2021 (https://doi.org/10.5194/os-17-285-2021). Details of the data and methods can be found in the journal article.<br> <br> Worthington, E. L., Moat, B. I., Smeed, D. A., Mecking, J. V., Marsh, R., and McCarthy, G. D.: A 30-year reconstruction of the Atlantic meridional overturning circulation shows no decline, Ocean Sci., 17, 285–299, <a href="https://doi.org/10.5194/os-17-285-2021">https://doi.org/10.5194/os-17-285-2021</a>, 2021.</p>
Figure 4. Odontoxenus thailandicus. A elytron B pronotum C male abdominal tergite VIII D male abdominal sternite VIII E male abdominal tergite IV & V F female abdominal tergite VIII G in Two new species of Aleocharinae (Coleoptera, Staphylinidae) found in fungus gardens of Odontotermes termites (Isoptera, Termitidae, Macrotermitinae) in Khao Yai National Park, Thailand
Figure 4. Odontoxenus thailandicus. A elytron B pronotum C male abdominal tergite VIII D male abdominal sternite VIII E male abdominal tergite IV & V F female abdominal tergite VIII G median lobe of aedeagus, and H spermatheca.
Dataset from Pardini, E. A., Parsons, L. S., Ştefan, V., & Knight, T. M. (2018). GLMM BACI environmental impact analysis shows coastal dune restoration reduces seed predation on an endangered plant. Restoration Ecology, 26(6), 1190-1194.
<p>Data and its metadata used in the analysis from the publication: Pardini, E. A., Parsons, L. S., Ştefan, V., & Knight, T. M. (2018). GLMM BACI environmental impact analysis shows coastal dune restoration reduces seed predation on an endangered plant. Restoration Ecology, 26(6), 1190-1194. <a href="https://onlinelibrary.wiley.com/doi/full/10.1111/rec.12678">https://onlinelibrary.wiley.com/doi/full/10.1111/rec.12678</a> </p>
Fig. 31 in Postnatal Ontogeny Of The Skull In Th E Ex Tant North Am Eric An Turtle Sternotherus Odoratus (Crypto Dir A: Kinosterni Dae) G A B E S. B E V Er
Fig. 31. Photographs and line drawings of the basicranial region of M-2984 (A) and M-2967 (B) showing the morphology of the parabasisphenoid-basiocccipital suture. The suture in M-2984 is relatively straight and exhibits a remnant of the fenestra basicranialis (fb). The suture in M-2967 is rostrally curved and marked by two caudolateral processes of the parabasisphenoid. The fenestra basicranialis is obliterated. A rostrally convex ridge marking the insertion of the M. rectus capitis is present and has a rostral position on the parabasisphenoid in both specimens.
Fig. 25 in Postnatal Ontogeny Of The Skull In Th E Ex Tant North Am Eric An Turtle Sternotherus Odoratus (Crypto Dir A: Kinosterni Dae) G A B E S. B E V Er
Fig. 25. Photographs and line drawings of the pterygoid in dorsolateral view showing the ossified dorsal wall that separates the canalis cavernosus (foreground) and the internal carotid canal, which terminates rostrally with the foramen caroticum laterale (fcl). This wall is penetrated by the foramen pro ramo nervi vidiani, which transmits the vidian nerve from the canalis cavernosus to the internal carotid canal. The ossification of the wall around this foramen is variable in the SMRS as seen in M-2992 (A, left), (B, right), and M-2991 (C, right). The prootic, which is not articulated in these photographs, lies above the pterygoid and participates in the foramen caroticum laterale and foramen pro ramo nervi vidiani.
Fig. 22 in Postnatal Ontogeny Of The Skull In Th E Ex Tant North Am Eric An Turtle Sternotherus Odoratus (Crypto Dir A: Kinosterni Dae) G A B E S. B E V Er
Fig. 22. Photographs and line drawings of the basicranial region of M-2984 (A) and M-2966 (B) in caudoventral view. In M-2984, the chorda tympani nerve passes through a groove in the quadrate rather than through a fully enclosed foramen (canalis chorda tympani quadrati) as seen in M-2966. The path of the chorda tympani external to this opening is preserved in M-2984 and denoted here by an arrow.
Fig. 27 in Postnatal Ontogeny Of The Skull In Th E Ex Tant North Am Eric An Turtle Sternotherus Odoratus (Crypto Dir A: Kinosterni Dae) G A B E S. B E V Er
Fig. 27. Photographs and line drawings of the left opisthotic in rostral (M-2964, A) and medial (M- 2992, B) views. The arrow marks the path of the glossopharyngeal nerve along the caudal wall of the cavum labyrinthicum (cl), which is formed by the processus interfenestralis of the opisthotic (pi). Note the differences in the ossification of the medial wall of the fenestra perilymphatica in the two specimens.
Fig. 19 in Postnatal Ontogeny Of The Skull In Th E Ex Tant North Am Eric An Turtle Sternotherus Odoratus (Crypto Dir A: Kinosterni Dae) G A B E S. B E V Er
Fig. 19. Photographs and line drawings of the palatal surface of M-2985 (A) and M-2999 (B) showing the contacts of the palatine, maxilla, and foramen palatinum posterius. The most common condition in the SMRS is for the maxilla to form the lateral margin of this foramen (A). The palatines sometimes meet lateral to the foramen palatinum posterius on the ventral surface of the palate.
Fig. 18 in Postnatal Ontogeny Of The Skull In Th E Ex Tant North Am Eric An Turtle Sternotherus Odoratus (Crypto Dir A: Kinosterni Dae) G A B E S. B E V Er
Fig. 18. Photographs and line drawings of the palatal surface of M-2979 (A), M-2974 (B), and M-2983 (C). The palatines obscure the vomer-pterygoid contact in M-2974. The shape of the vomer-pterygoid contact can be broadly rounded or obtuse as in M-2974 or the vomer can terminate caudally at a single point as in M-2983. The development of the rostral margin of pterygoid appears to be the major factor controlling the morphology of this character.
Fig. 30 in Postnatal Ontogeny Of The Skull In Th E Ex Tant North Am Eric An Turtle Sternotherus Odoratus (Crypto Dir A: Kinosterni Dae) G A B E S. B E V Er
Fig. 30. Photographs and line drawings of the occipital and basicranial regions in M-2980 (A) and M- 2983 (B) (the least and most mature specimens in the SMRS). Note the relative ossification of the exoccipitals. IX? (B) marks the possible path of the glossopharyngeal nerve out of the recessus scalae tympani, which is delimited by small, processlike ossifications around the rim of the fenestra postotica.
Fig. 17 in Postnatal Ontogeny Of The Skull In Th E Ex Tant North Am Eric An Turtle Sternotherus Odoratus (Crypto Dir A: Kinosterni Dae) G A B E S. B E V Er
Fig. 17. Photographs and line drawings of the palatal surface of M-2989 (A) and M-2958 (B). The paired foramina praepalatinum are exposed ventrally in M-2989, whereas they are concealed by caudal development of the premaxillae on the secondary palate in M-2958. Ventral exposure of these foramina is the most common condition within the SMRS.
Fig. 16 in Postnatal Ontogeny Of The Skull In Th E Ex Tant North Am Eric An Turtle Sternotherus Odoratus (Crypto Dir A: Kinosterni Dae) G A B E S. B E V Er
Fig. 16. Photographs and line drawings of the relationships of the premaxillae, maxillae, and ventral margin of the apertura narium externa. The most common condition within the SMRS is for the maxillae to send small secondary processes over the premaxillae to form the ventral margin of aperture (A, M- 2967). This medial contact can be recessed such that the premaxillae still contribute to the ventral margin of aperture (B, M-2967). Sometimes the maxillae fail to meet medially above the premaxillae (C, M-2956).
Fig. 21 in Postnatal Ontogeny Of The Skull In Th E Ex Tant North Am Eric An Turtle Sternotherus Odoratus (Crypto Dir A: Kinosterni Dae) G A B E S. B E V Er
Fig. 21. Photographs and line drawings of the incisura columella auris and surrounding basicranial region in M-2975 (A, left), M-2966 (B, right), and M-2983 (C, left). The incisura is open caudally in M- 2975, restricted caudally by a descending secondary process of the quadrate in M-2966, and restricted by an ascending secondary process of the quadrate in M-2983.
Fig. 14 in Postnatal Ontogeny Of The Skull In Th E Ex Tant North Am Eric An Turtle Sternotherus Odoratus (Crypto Dir A: Kinosterni Dae) G A B E S. B E V Er
Fig. 14. Photograph and line drawing of the caudal margin of the right orbital floor in M-2985 as seen through the orbit. A relatively large and distinct foramen is present in the medial process of the jugal in this specimen, which represents a variant condition for the SMRS. The maxillary branch of the trigeminal nerve may pass through this foramen before traveling rostrally along the floor of the orbit to the foramen supramaxillare.
Fig. 12 in Postnatal Ontogeny Of The Skull In Th E Ex Tant North Am Eric An Turtle Sternotherus Odoratus (Crypto Dir A: Kinosterni Dae) G A B E S. B E V Er
Fig. 12. Photographs and line drawings of the foramen nervi trigemini in right lateral (M-2983, A) and left lateral (M-2983, B; M-2988, C) views. Note the small foramen or groove in the dorsal margin of the foramen nervi trigemini that occurs as a variant in the SMRS.
Fig. 24 in Postnatal Ontogeny Of The Skull In Th E Ex Tant North Am Eric An Turtle Sternotherus Odoratus (Crypto Dir A: Kinosterni Dae) G A B E S. B E V Er
Fig. 24. Photographs and line drawings of the dorsal surface of the pterygoid in M-2960 (A, left), the rostral end of the pterygoid in M-2982 (B, left), and lateral view of the rostral half of the pterygoid in M- 2960 (C, left). A fossa lying just rostral to the foramen caroticum laterale houses foramina involved in the transmission of the vidian nerve and vein. The anterior canalis nervi vidiani (acnv) transmits the vidian nerve and vein rostrally through the crista pterygoidea before it eventually bifurcates sending branches of the vidian onto the dorsal and ventral surfaces of the palate. Arrows mark the path of the vidian nerve through the foramen pro ramo nervi vidiani (A) and the anterior canalis nervi vidiani (C).
Fig. 11 in Postnatal Ontogeny Of The Skull In Th E Ex Tant North Am Eric An Turtle Sternotherus Odoratus (Crypto Dir A: Kinosterni Dae) G A B E S. B E V Er
Fig. 11. Photographs and line drawings of the dorsal roof showing the relative development of the prefrontal process of the frontal in M-2985 (A) and M-2965 (B). Also note that the frontal does not participate in the orbit or temporal fenestration.
Fig. 35 in Postnatal Ontogeny Of The Skull In Th E Ex Tant North Am Eric An Turtle Sternotherus Odoratus (Crypto Dir A: Kinosterni Dae) G A B E S. B E V Er
Fig. 35. Examples of allometry trends in Sternotherus odoratus based on least squares regression model showing the best (A) and worst (B) fitted regressions on greatest length of the skull. The data are in millimeters and are log transformed.
Fig. 10 in Postnatal Ontogeny Of The Skull In Th E Ex Tant North Am Eric An Turtle Sternotherus Odoratus (Crypto Dir A: Kinosterni Dae) G A B E S. B E V Er
Fig. 10. Photographs and line drawings of the interorbital region in M-2968 (A) and M-2983 (B). Note differences in the breadth of contact of the prefrontal (PF) and palatine (PAL) above the foramen orbitonasale (fon).
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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)
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DANDI Archive for NWB datasets
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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
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