Find research datasets worth reusing

opencc-by-4.0Apr 2024View details →

Gene family expansions underpin context-dependency of the oldest mycorrhizal symbiosis

This Zenodo archive is associated with the manuscript: Hernandez, D.J., Pohlmann, G.B., Afkhami, M.E. (2025) Gene family expansions provide molecular flexibility required for context-dependent species interactions. Ecology Letters. Abstract: As environments worldwide change at unprecedented rates during the Anthropocene, understanding context-dependency – how species regulate interactions to match changing environments – is crucial. However, generalizable molecular mechanisms underpinning context-dependency remain elusive. Combining comparative genomics across 42 angiosperms with transcriptomics, genome-wide association mapping, and gene duplication origin analyses, we show for the first time that gene family expansions undergird context-dependent regulation of species interactions. Gene families expanded in mycorrhizal fungi-associating plants display up to 200% more context-dependent gene expression and double the genetic variation associated with mycorrhizal benefits to plant fitness. Moreover, we discover these gene family expansions arise primarily from tandem duplications with >2-times more tandem duplications genome-wide, indicating gene family expansions continuously supply genetic variation throughout plant evolution allowing fine-tuning of context-dependency in species interactions.

opencc-by-4.0Nov 2022View details →

Gene family data from the PhyloGenes (release version 5.0, phylogenes.org)

The data files were generated from the PhyloGenes 5.0release (see release notes <a href="https://conf.arabidopsis.org/display/PHGSUP/About+PhyloGenes">here</a>). About the two zip files:  1. phyloXML.zip PhyloGenes gene family trees in PhyloXML format, one file per family (e.g. <family_ID>.xml). The following information is provided for each node of a tree: 1) leaf node: branch length name <gene_id> taxonomy scientific_name sequence accession <UniProt ID> 2) non-leaf node: branch length events <duplication or speciation> 2. panther_csv.zip Functional information of family members in CSV format, one file per family (e.g. <family_ID>.csv).  A CSV file includes the following columns: Uniprot ID Gene <Gene name. If none then Gene ID> Gene ID Gene name Organism Subfamily name The columns displayed after 'Subfamily name', if any, are GO annotations. Each column is a GO molecular function or biological process term that is annotated to at least one member of the gene family AND the annotation is supported by an experimental evidence (indicated by 'EXP') or phylogenetic inference (indicated by 'IBA'). A '0' indicates absence of either annotations.

opencc-by-4.0Oct 2023View details →

Most bacterial gene families are biased toward specific chromosomal positions

The arrangement of genes along bacterial chromosomes influences their expression through growth rate-dependent gene copy number changes during DNA replication. While translation and transcription genes often cluster near the origin of replication, the extent of positional biases across gene families remains unclear. We hypothesized that natural selection broadly favors specific chromosomal positions to optimize growth rate-dependent expression. Analyzing 910 bacterial species and proteomics data from Escherichia coli and Bacillus subtilis, we find that about two-thirds of bacterial gene families are positionally biased, mainly near the origin or terminus of replication, with the strongest natural selection in fast-growing species. Our findings reveal chromosomal positioning as a fundamental mechanism for coordinating gene expression with growth rate, highlighting evolutionary constraints on bacterial genome architecture.

opencc-by-4.0Nov 2021View details →

Metagenomes: gene function and family annotations

Functional annotations of genes for all contigs in 1,782 metagenomes. Genes were annotated to three sources: (1) COGs, (2) Pfams, and (3) de novo families from reference sequences. These gene annotations are used to train and run PlasX.

opencc-by-4.0May 2019View details →

Dataset for genes and gene variants from familial gastroschisis

The dataset consists of records from whole exome sequecing and bioinformatic analysis which includes genes and gene variants from a Mexican family with recurrence for gastroschisis (two affected half-sisters with gastroschisis, mother, and father of the proband). Release of this dataset was based on the Human Genome annotation, GRCh37/hg19. The full list of tables is described in the file READ ME and remain available in csv files.

opencc-by-4.0Jan 2023View details →

Dataset for 53 gene families from 16 eukaryotes

NEXUS file representing Guigo et al.'s (1996) dataset for 53 gene families from 16 eukaryotes, used in a number of gene tree reconciliation studies. Original data from Guigo et al., this NEXUS encoding by Roderic Page.

opencc-by-4.0Jan 2023View details →

Vertebrate gene family trees

This is a dataset of phylogenies for 118 vertebrate gene families, used in two papers published by James Cotton and Roderic Page in 2002. The folder named "genes.zip" contains FASTA and NEXUS sequence files, and Newick-format tree files for each gene family. There is a PDF file "suppl.pdf" listing the names of each family. The file "final_dataset.gml" contains a graph of the taxonomic overlap in the gene trees. All 118 gene trees have been combined into the file "final_dataset.gtr" which is a NEXUS file with custom blocks recognised by GeneTree. <table> <tbody> <tr> <th>HOVERGEN FAMILY CODE</th> <th>GENE FAMILY NAME</th> </tr> <tr> <td>FAM000030A</td> <td>wnt 5</td> </tr> <tr> <td>FAM000030B</td> <td>wnt 7</td> </tr> <tr> <td>FAM000030C</td> <td>wnt 11</td> </tr> <tr> <td>FAM000030D</td> <td>wnt/int 1</td> </tr> <tr> <td>FAM000030E</td> <td>wnt 4</td> </tr> <tr> <td>FAM000030F</td> <td>wnt 10/12</td> </tr> <tr> <td>FAM000030G</td> <td>wnt 3</td> </tr> <tr> <td>FAM000030H</td> <td>wnt 2</td> </tr> <tr> <td>FAM000030I</td> <td>wnt 8</td> </tr> <tr> <td>FAM000105</td> <td>rhodopsin</td> </tr> <tr> <td>FAM000214</td> <td>beta-B globin</td> </tr> <tr> <td>FAM000033</td> <td>protamine 1</td> </tr> <tr> <td>FAM000370</td> <td>PrP a prion-protein</td> </tr> <tr> <td>FAM000014</td> <td>growth hormone</td> </tr> <tr> <td>FAM000556</td> <td>Rag-1 recombination activation gene</td> </tr> <tr> <td>FAM001493</td> <td>c-mos proto-oncogene</td> </tr> <tr> <td>FAM001462</td> <td>tyrosine kinase / yes / fyn / src / lck</td> </tr> <tr> <td>FAM001041</td> <td>metallothionein</td> </tr> <tr> <td>FAM000364</td> <td>Ldh-2 lactate dehydrogenase-B (EC</td> </tr> <tr> <td>FAM000215</td> <td>alpha globin</td> </tr> <tr> <td>FAM000016</td> <td>placental lactogen - prolactin</td> </tr> <tr> <td>FAM000008</td> <td>insulin</td> </tr> <tr> <td>FAM000824</td> <td>phosphoglycerate kinase</td> </tr> <tr> <td>FAM000550</td> <td>neurotrophin-4 (NT-4)</td> </tr> <tr> <td>FAM001478</td> <td>tyrosine kinase receptor, c-fms oncogene</td> </tr> <tr> <td>FAM000173A</td> <td>guanine nucleotide-binding protein</td> </tr> <tr> <td>FAM000173B</td> <td>transducin alpha</td> </tr> <tr> <td>FAM000502</td> <td>cytochrome P-450 aromatase</td> </tr> <tr> <td>FAM000192</td> <td>alpha-fetoprotein / serum albumin</td> </tr> <tr> <td>FAM000627</td> <td>neurone-specific enolase</td> </tr> <tr> <td>FAM001232</td> <td>preprotrypsin (ta)</td> </tr> <tr> <td>FAM000664</td> <td>complement component 3 (C3)</td> </tr> <tr> <td>FAM000175</td> <td>Ras</td> </tr> <tr> <td>FAM000248</td> <td>alpha B-crystallin</td> </tr> <tr> <td>FAM000006</td> <td>insulin-like growth factor II</td> </tr> <tr> <td>FAM000639</td> <td>transthyretin (prealbumin)</td> </tr> <tr> <td>FAM001303</td> <td>butylcholinesterase (BCHE)</td> </tr> <tr> <td>FAM000242</td> <td>connexin / gap junction protein</td> </tr> <tr> <td>FAM000058</td> <td>dopamine D1 receptor</td> </tr> <tr> <td>FAM000055</td> <td>beta-3-adrenergic receptor .</td> </tr> <tr> <td>FAM000131</td> <td>ATPase (Na+K+, H+K+)</td> </tr> <tr> <td>FAM003983</td> <td>preprogastrin</td> </tr> <tr> <td>FAM000353</td> <td>vasopressin</td> </tr> <tr> <td>FAM000152</td> <td>acetylcholine receptor</td> </tr> <tr> <td>FAM001327</td> <td>peripherin, desmin, vimentin, GFAP</td> </tr> <tr> <td>FAM003199</td> <td>(C57BL/6J)</td> </tr> <tr> <td>FAM002881</td> <td>cytochrome P-450, 17a-hydroxylase (CYP17)</td> </tr> <tr> <td>FAM002789</td> <td>(MUAHRB-1) Ah-receptor (Ah)</td> </tr> <tr> <td>FAM001461</td> <td>tropomyosin</td> </tr> <tr> <td>FAM000385</td> <td>Y3 peptide supply factor</td> </tr> <tr> <td>FAM000378</td> <td>pancreatic polypeptide, neuropeptide Y</td> </tr> <tr> <td>FAM001329</td> <td>cytokeratin</td> </tr> <tr> <td>FAM001619</td> <td>amelogenin (enamel-specific protein)</td> </tr> <tr> <td>FAM000286</td> <td>glucagon</td> </tr> <tr> <td>FAM000330</td> <td>tissue inhibitor of</td> </tr> <tr> <td>FAM000475</td> <td>lipophilin</td> </tr> <tr> <td>FAM001060</td> <td>ornithine carbamoyltransferase</td> </tr> <tr> <td>FAM001328</td> <td>neurofilament</td> </tr> <tr> <td>FAM001370</td> <td>peroxisome proliferator</td> </tr> <tr> <td>FAM000371</td> <td>somatostatin</td> </tr> <tr> <td>FAM001607</td> <td>Wilms tumor assocated protein (WT1)</td> </tr> <tr> <td>FAM000495</td> <td>aldolase A, B, C</td> </tr> <tr> <td>FAM001365</td> <td>liver receptor homologous protein (LRH-1)</td> </tr> <tr> <td>FAM000672</td> <td>ribosomal protein S4,</td> </tr> <tr> <td>FAM000135</td> <td>Na, K-ATPase beta-1 subunit</td> </tr> <tr> <td>FAM000271</td> <td>enkephalin : 1 2.</td> </tr> <tr> <td>FAM000799</td> <td>RING10</td> </tr> <tr> <td>FAM001664</td> <td>glutamate decarboxylase</td> </tr> <tr> <td>FAM000617</td> <td>creatine kinase</td> </tr> <tr> <td>FAM001337</td> <td>amyloid beta protein precursor</td> </tr> <tr> <td>FAM000274</td> <td>basic fibroblast growth factor (bFGF)</td> </tr> <tr> <td>FAM001108</td> <td>Sl-d mutant allele kit ligand (KL)</td> </tr> <tr> <td>FAM000504</td> <td>anion exchange protein 3</td> </tr> <tr> <td>FAM001239</td> <td>prothrombin</td> </tr> <tr> <td>FAM001360</td> <td>high mobility group proteins HMG1 and HMG2</td> </tr> <tr> <td>FAM000534</td> <td>glutamine synthetase</td> </tr> <tr> <td>FAM001053</td> <td>nucleoside diphosphate kinase</td> </tr> <tr> <td>FAM001390</td> <td>low density lipoprotein receptor LDLR</td> </tr> <tr> <td>FAM001464</td> <td>Cek6 receptor tyrosine kinase</td> </tr> <tr> <td>FAM000801</td> <td>manganese-containing superoxide</td> </tr> <tr> <td>FAM003946</td> <td>Six2 / Six1 mRNA</td> </tr> <tr> <td>FAM001606</td> <td>Ikaros binding protein (Ikaros)</td> </tr> <tr> <td>FAM000350</td> <td>SPARC protein</td> </tr> <tr> <td>FAM001339</td> <td>calcium-binding protein</td> </tr> <tr> <td>FAM000553</td> <td>pyruvate kinase</td> </tr> <tr> <td>FAM000604</td> <td>t complex polypeptide 1 (Tcp-1-a)</td> </tr> <tr> <td>FAM002988</td> <td>mSlo</td> </tr> <tr> <td>FAM001266</td> <td>transcription factor / hepatocyte nuclear factor</td> </tr> <tr> <td>FAM000453</td> <td>terminal deoxynucleotidyltransferase</td> </tr> <tr> <td>FAM001642</td> <td>transformation associated protein p53</td> </tr> <tr> <td>FAM000300A</td> <td>glucose-regulated protein 78 / HSP70 PART A</td> </tr> <tr> <td>FAM000300B</td> <td>glucose-regulated protein 78 / HSP70 PART B</td> </tr> <tr> <td>FAM000492A</td> <td>alpha actin etc</td> </tr> <tr> <td>FAM000492B</td> <td>beta actin etc</td> </tr> <tr> <td>FAM000649</td> <td>Myelin Basic Protein</td> </tr> <tr> <td>FAM000843</td> <td>ribosomal protein S4</td> </tr> <tr> <td>FAM000170</td> <td>atrial natriuretic protein</td> </tr> <tr> <td>FAM000871A</td> <td>tyrosinase</td> </tr> <tr> <td>FAM000871B</td> <td>tyrosinase related protein 1</td> </tr> <tr> <td>FAM001605</td> <td>ZFX put. transcription activator</td> </tr> <tr> <td>FAM001479</td> <td>fibroblast growth factor</td> </tr> <tr> <td>FAM000160</td> <td>pro-opiomelanocortin (POMC)</td> </tr> <tr> <td>FAM001644</td> <td>fibrinogen alpha subunit</td> </tr> <tr> <td>FAM000564</td> <td>SNAP-25</td> </tr> <tr> <td>FAM000266</td> <td>nitric oxide synthase</td> </tr> <tr> <td>FAM004159</td> <td>chondroitin-6 sulfotransferase</td> </tr> <tr> <td>FAM000800</td> <td>Lmp-2 (LMPq) proteasome subunit</td> </tr> <tr> <td>FAM001595</td> <td>factor B</td> </tr> <tr> <td>FAM001134</td> <td>zona pellucida (ZP)</td> </tr> <tr> <td>FAM001632</td> <td>stromelysin-3</td> </tr> <tr> <td>FAM001366</td> <td>steroid receptor (TR2-9)</td> </tr> <tr> <td>FAM000526</td> <td>c-ski protein</td> </tr> <tr> <td>FAM002463</td> <td>thymosin beta 4 peptide</td> </tr> <tr> <td>FAM000904</td> <td>sequence-specific DNA-binding protein (AP-2)</td> </tr> <tr> <td>FAM001465</td> <td>T-cell specific tyrosine kinase (ltk)</td> </tr> <tr> <td>FAM000567</td> <td>triosephosphate isomerase</td> </tr> <tr> <td>FAM006113</td> <td>DNA-dependent RNA polymerase III, large subunit</td> </tr> <tr> <td>FAM001733</td> <td>DNA-dependent RNA polymerase II</td> </tr> </tbody> </table>

opencc-by-4.0Dec 2019View details →

Gene family data from the PhyloGenes (release version 1.2, phylogenes.org)

The compressed file contains:  1. PhyloXML_files  This folder has family trees in PhyloXML format, one file per family (e.g. <family_ID>.xml). The following information is provided for each node of a tree: 1) leaf node: branch length name <gene_id> taxonomy scientific_name sequence accession <UniProt ID> 2) non-leaf node: branch length events <duplication or speciation> 2. phylogenes_csv.tar.xz This tar file has gene information of family members in CSV format, one file per family (e.g. <family_ID>.csv).  A CSV file includes the following columns: Uniprot ID Gene <Gene name. If none then Gene ID> Gene ID Gene name Organism Subfamily name Any columns displayed after 'Subfamily name' are 'Known functions'. Each 'Known function' is a GO molecular function term that is annotated to at least one member of the gene family AND that the annotation is supported by an experimental evidence. Number 1 or 0 indicates the presence or absence of a particular function in a gene.

opencc-by-nd-3.0Dec 2020View details →

Worldwide Fraxinus Genome Assemblies, Annotations, and Gene Families v0.2

The worldwide Fraxinus genome project was conducted to assess the pathogenic resistance of 34 Ash tree species to Ash Dieback and Emerald Ash Borer. The project is led by Dr. Richard Buggs. v0.1 genomes are available at ashgenome.org and on ENA. As part of Josiah Seaman's PhD thesis, he improved the assembly of 13 genomes included here as v0.2. New de novo annotations, gene families, and all associated files are included for future studies and reproducibility.  Annotations are done with GeMoMa using F. excelsior as a reference (Keilwagen et al. 2016). Gene families are defined as genes originating from a single copy at the last common ancestor with Solanum. Orthofinder outputs reconciled gene trees, aligned CDS, and gene families (Emms and Kelly 2015; Tekaia 2016). Species tree was calibrated based on fossil evidence using r8s, RAxML across 25,182,399 sites (SpeciesTreeAlignment.fa). More methods details can be found in the full Chapter two of Josiah Seaman's PhD thesis (2021). I'd be happy to talk with you if you'd like any additional information or help visualizing your genomic data. You can find the tools used to browse this data at https://fluentdna.com/ and http://graphgenome.org/ Contact me at josiah@newline.us

opencc-by-4.0Jan 2021View details →

New genetic markers for Sapotaceae phylogenomics: more than 600 nuclear genes applicable from family to population levels

Some tropical plant families, such as the Sapotaceae, have a complex taxonomy, which can be resolved using Next Generation Sequencing (NGS). For most groups however, methodological protocols are still missing. Here we identified 531 monocopy genes and 227 Short tandem repeats (STR) markers and tested them on Sapotaceae using target capture and NGS. The probes were designed using two genome skimming samples fromCapurodendron delphinense and Bemangidia lowryi, both from the Tseboneae tribe, as well as the published Manilkara zapota transcriptome from the Sapotoideae tribe. We combined our probes with 261 additional ones previously published and designed for the entire angiosperm group. On a total of 792 low-copy genes, 638 showed no signs of paralogy and were used to build a phylogeny of the family with 231 individuals from all main lineages. A highly supported topology was obtained at high taxonomic ranks but also at the species level. This phylogeny revealed the existence of more than 20 putative new species. Single nucleotide polymorphisms (SNPs) extracted from the 638 genes were able to distinguish lineages within a species complex and to highlight geographical structuration. STR were recovered efficiently for the species used as reference (C. delphinense) but the recovery rate decreased dramatically with the phylogenetic distance to the focal species. All together, the new loci will help reaching a sound taxonomic understanding of the family Sapotaceae for which many circumscriptions and relationships are still debated, at the species, genus and tribe levels.

opencc-by-4.0Nov 2024View details →

Data for phylogenomic analysis of chelicerate gene family evolution

We used phylogenomics to investigate patterns of gene family evolution across ticks and other chelicerates, which include a diverse array of parasites. We used phylogenetic profiling and trait-association tests to predict gene families that may enable parasitic species to feed on hosts undetected for prolonged periods (>1 day). This release accompanies the pub, “<a href="https://doi.org/10.57844/arcadia-4e3b-bbea">Comparative phylogenomic analysis of Chelicerates points to gene families associated with long-term suppression of host detection</a>." Please see the pub for more information. <ul> <li>chelicerata-v1-10062023.zip contains the outputs from NovelTree that are needed as inputs for phylogenetic profiling.</li> <li>annotated.zip contains gene annotations used to do orthogroup filtering.</li> <li>tx2gene.tsv has presence/absence of expression for each Amblyomma americanum transcript. </li> <li>chelicerate_proteome_preprocessing_outputs.zip contains the outputs of chelicerate protein data curation.</li> <li>chelicerata-v1-parameterfile.json & chelicerata-v1-samplesheet.csv were inputs for setting up the initial NovelTree run.</li> <li>2024-06-24-all-chelicerate-noveltree-proteins.fasta has the full set of chelicerate protein sequences.</li> <li>summary_of_noveltree_results.zip contains summary figures from the outputs of the NovelTree run.</li> <li>chelicerate-samples.tsv is the sample sheet used in proteome curation upstream of NovelTree.</li> </ul>

opencc-by-4.0Feb 2011View details →

Fig. 2 in Karyotype characterization of Mugil incilis Hancock, 1830 (Mugiliformes: Mugilidae), including a description of an unusual co-localization of major and minor ribosomal genes in the family

Fig. 2. Metaphase plates of Mugil incilis after (a) C-banding and (b) AgNO -staining. Arrows indicate chromosome pair number 1.

opencc-by-4.0Feb 2021View details →

Fig. 4 in Phylogenomics of the tropical plant family Ochnaceae using targeted enrichment of nuclear genes and 250+ taxa

Fig. 4. Distribution of specimen ages and the number of loci recovered in the phylogenomic study of Ochnaceae. A, Histogram of the collection years of all Ochnaceae specimens; B & C, Relationship between the year of collection of the specimens and the number of loci recovered for tissue obtained from herbarium material (excluding specimens with silica-dried leaf material), analysed for Ochneae and all the remaining Ochnaceae separately, either using the consensus-alignment (B) or the sample-specific (C) reference-based assembly approach. Pearson correlation coefficients and confidence intervals are given for each group.

opencc-by-4.0Feb 2021View details →

Fig. 2 in Phylogenomics of the tropical plant family Ochnaceae using targeted enrichment of nuclear genes and 250+ taxa

Fig. 2. RAxML trees based on the concatenated nuclear loci of Ochnaceae. A, Early-diverging branches of Ochnaceae and relationships within Quiinoideae based on the FAM dataset; B, Phylogenetic relationships of Sauvagesieae, Luxemburgieae and Testuleeae based on the SLT dataset. Numbers on the branches are bootstrap values>50%. Numbers in parentheses after species names correspond to the specimen IDs (only for species with multiple accessions). The indicated classification of subfamilies and tribes follows Schneider & al. (2014).

opencc-by-4.0Feb 2021View details →

Fig. 1 in Phylogenomics of the tropical plant family Ochnaceae using targeted enrichment of nuclear genes and 250+ taxa

Fig. 1. Overview of the phylogenetic relationships of the major clades of Ochnaceae based on the FAM dataset together with images of representative species. The classification follows Schneider & al. (2014). Ochninae is by far the most species-rich clade comprising about two-thirds of the family's species and six genera (Brack. = Brackenridgea; Cmp. = Campylospermum, clades A and B; I. = Idertia; Ochna; Ouratea; Rh. = Rhabdophyllum). Letters around the tree refer to the photos (mostly flowers except where indicated) and the relative position of the displayed taxa on the tree. A, Medusagyne oppositifolia (Medusagynoideae); B, Froesia venezuelensis (Quiinoideae); C, Luxemburgia schwackeana (Luxemburgieae); D, Rhytidanthera sulcata; E, Cespedesia spathulata; F, Poecilandra retusa; G, Godoya antioquiensis; H, Wallacea insignis; I, Sauvagesia semicylindrifolia; J, Sauvagesia erecta (Sauvagesieae); K, Infructescence of Lophira lanceolata with accrescent sepals (Lophirinae); L, Flower of Elvasia kollmannii (Elvasiinae); M, Perissocarpa umbellifera; N, Fruiting Rhabdophyllum arnoldianum; O, Brackenridgea nitida; P, Campylospermum glaberrimum; Q, Ochna serrulata; R, Fruit of Ochna integerrima with drupelets sitting on enlarged receptacle; S, Fruit of Ouratea sp. with enlarged red receptable; T, Ouratea sp. — Photos: A, K & N from www.africanplants.senckenberg.de (Dressler & al., 2014–); B by Julio Schneider; C by William Milliken/ Royal Botanic Gardens, Kew; D by Sandra Reinales; E by Reinaldo Aguilar; F, H & M by Francisco Farroñay; G by John Clark; I, J, S & T by Domingos Cardoso; L by Claudio Nicoletti de Fraga; O by John Elliott; P by Warran McCleland; Q by Marja Broersma; R by Pierre Grard.

Figure 1 in Phylogenetic analyses suggest that Psammomitra (Ciliophora, Urostylida) should represent an urostylid family, based on small subunit rRNA and alpha-tubulin gene sequence information

Figure 1. Morphology and infraciliature of Psammomitra retractilis (F–J, from Song & Warren, 1996). A, B, F, individuals in extended states to show the typical body shapes. Arrowheads in (A) mark the long, dominant membranelles. C, lateral view of a contracted specimen. D, posterior part, to demonstrate the long dorsal cilia. E, anterior part. Arrowheads indicate the long membranelles, whereas arrows mark the dorsal cilia. G, H, dorsal and lateral views of contracted cells. I, J, ventral and dorsal views to show the infraciliature and macronuclear nodules. Scale bars: A, C, D, F = 40 Mm; E = 30 Mm.

Figure 3 in Phylogenetic analyses suggest that Psammomitra (Ciliophora, Urostylida) should represent an urostylid family, based on small subunit rRNA and alpha-tubulin gene sequence information

Figure 3. Maximum parsimony phylogeny of small subunit rRNA genes. Psammomitra is highlighted in black, and holostichids are enclosed in rectangles. Thick branches and arrows denote position of investigated species. Numbers on branches are values generated from 1000 bootstrap replicates.

Figure 2 in Phylogenetic analyses suggest that Psammomitra (Ciliophora, Urostylida) should represent an urostylid family, based on small subunit rRNA and alpha-tubulin gene sequence information

Figure 2. Phylogenetic tree based on small subunit rRNA sequences showing the position of Psammomitra retractilis, by Bayesian inferences applying the GTR + G + I model. '-' reflects disagreement between a method and the reference Bayesian tree at a given node. The fully supported (1.00/100%/100%) branches are marked with solid circles. Psammomitra is shaded black, and holostichids are enclosed in rectangles. Thick branches and arrows denote position of investigated species. The scale bar corresponds to five substitutions per 100 nucleotide positions. Infraciliature of Oxytricha and Uroleptus (from Foissner et al., 2004), Amphisiella (from Li et al., 2007), Trachelostyla (from Gong et al., 2006), and Holosticha (from Hu & Song, 2001) are also shown.

Figure 4 in Phylogenetic analyses suggest that Psammomitra (Ciliophora, Urostylida) should represent an urostylid family, based on small subunit rRNA and alpha-tubulin gene sequence information

Figure 4. Bayesian trees based on different data sets showing phylogenetic relationships amongst Spirotrichea. '-' reflects disagreement between the maximum likelihood/ maximum parsimony method and the reference Bayesian tree at a given node. The fully supported (1.00/100%/100%) branches are marked with solid circles. Species sequenced in the present study are shown in bold type. The scale bar corresponds to 10/2 substitutions per 100 nucleotide positions. A, phylogenetic analyses inferred from alpha-tubulin gene sequences data set. B, phylogenetic analyses inferred from alpha-tubulin amino acids data set.