Journal articles on the topic 'Partitioned Bremer Support'

Partitioned Bremer support examination of combined cladistic analyses indicates nodes at which the support from the partitions differs, and also identifies the location of character disagreement generated by the combination of data matrices. Significant character incongruence was found between mtDNA sequence data and adult morphological characters from three tribes of bee flies (Diptera : Bombyliidae : Anthracinae : Villini, Anthracini, Exoprosopini). Partitioned Bremer support quantitatively reveals the location of significant conflict between characters from the different partitions. Examination of several partitioned support measures show which characters contributed to the disagreement at that node. A very high value of increased support at another node occurred upon combination of the data partitions and was also examined using these support measures.

AbstractScarabaeus (Pachysoma) comprises 13 flightless dung beetle species endemic to the west coast of southern Africa that are biologically unique and have a variable taxonomic history at the generic level. Initially considered a valid genus Pachysoma was subsequently synonymised with the genus Scarabaeus and later assigned sub-generic status within this genus. In an attempt to resolve past taxonomic inconsistencies, morphological and molecular data partitions, and combinations thereof, were analysed and compared across different phylogenetic inference methods. Trees obtained from the individual datasets which comprised 64 morphological characters and 1197 nucleotide sites of the mitochondrial Cytochrome Oxidase I (COI) gene, were less well-resolved than those obtained from analyses in which the data partitions were combined whilst Bayesian inference generally out-performed parsimony. However, both the individual and combined data partitions, irrespective of the method of analysis, confirmed the monophyly of the Pachysoma lineage. The relative contribution of each data partition to individual nodes as assessed by positive partitioned Bremer support values was 6:5:4 for the molecular:combined:morphological data partitions. However, in terms of contribution to the resolution of terminal versus internal nodes, the morphological dataset made proportionally the greatest contribution and was crucial for recovering a sister relationship of Pachysoma to Scarabaeus, i.e. a generic level, rather than a sub-generic one. This together with the monophyly of the Pachysoma lineage across all methods of analysis and data partitions as well as the unique morphology and biology of its constituent species warrants reinstatement of Pachysoma to its former full generic status.

Phylogenetic analyses using 28S rDNA, elongation factor (EF)-1α, and mt 16S rDNA sequences were performed to test the monophyly of Thereva Latreille. Two of the three Afrotropical Thereva species groups lack the genitalia characters that unambiguously diagnose Thereva in the Holarctic Region, but phylogenetic relationships among Thereva species groups and therevine genera are poorly understood. Using an extensive taxonomic sample (39 of the 62 therevine genera) and Thereva, sensu lato (15 spp.), simultaneous analyses of all three gene partitions recovered Nearctic and Palaearctic Thereva species in a well supported clade that includes the Afrotropical seminitida-group but excludes the Afrotropical analis- and turneri-groups. Stronger phylogenetic signal from the EF-1α partition, measured by the skewness statistic and proportion of total parsimony informative characters, dominated conflicting signal from the 16S partition and weaker, but more congruent, signal from 28S. Reducing the taxonomic sample in analyses of Therevinae reduced homoplasy, increased phylogenetic structure and partitioned Bremer support values and reduced incongruence with 28S for the 16S partition. Although molecular analyses yielded partial recovery of informal therevine genus-groups, morphological diagnoses of higher-level groups are poorly supported with the exception of Cyclotelini. The ‘Holarctic radiation’ refers to a diverse clade of genera closely related to Pandivirilia Irwin & Lyneborg and Acrosathe Irwin & Lyneborg widely distributed throughout the Holarctic Region that is the sister-group to Thereva, sensu stricto. Results from these analyses underscore the importance of male and female genitalia characters in recognising monophyletic groups and regional endemism in therevine diversification.

AbstractThe results of a cladistic analysis based on a combined character matrix consisting of the morphological data set of Meier & Hilger (2000) and the molecular data set of Baker & al. (2001) is presented. The data set is subjected to an extensive sensitivity analysis and equal character weighting is found to perform best according to character incongruence and tree support. The sensitivity analysis also reveals a remarkable stability of the preferred tree with 25 of the 36 tree nodes supported under 16 different analysis conditions. Cyrtodiopsis is synonymized with Teleopsis and Shillito's (1971) synonymization of Trichodiopsis and Chaetodiopsis with Diasemopsis is confirmed. Morphological and DNA sequence data agree on all major clades and conflict is restricted to the placement of two species within their respective genera. Only in one case can the conflict be confidently resolved. Partitioned Bremer Support values reveal that 90% of the tree support is generated by the DNA sequence characters, although the average morphological character contributes twice the support of an average molecular character. The evolution of eye-stalk morphology and of a meiotic drive chromosome system in Teleopsis is briefly discussed in the light of the phylogenetic tree.

AbstractThe cactus-feeding Phycitinae are a New World group of moth genera that has long been the focus of ecological and biological control related studies, but the group's evolutionary and phylogenetic relationships have remained largely unknown. Here phylogenetic relationships of 15 cactus-associated and 12 allegedly related but non cactus-associated genera of Phycitinae are established based on 64 characters from adult morphology. The resulting phylogeny is the first cladistic higher-level phylogenetic analysis for any group of Phycitinae genera. It is well resolved, albeit weakly supported, and supports the monophyly of a previously suggested group comprised by the true cactus-feeders and the genera Baphala, Zophodia and Rhagea. A clade comprising all cactus feeders with the non-cactus feeder genus Rhagea nested within is retrieved, indicating a single origin of cactus feeding within Phycitinae; however, this clade is poorly supported. Larvae that are predacious on scale insects appear to have evolved at least twice. Evaluations of the different character systems in adult skeletal morphology demonstrate that although some systems contribute little to overall partitioned Bremer support, they might provide critical support at individual nodes. This is supporting earlier workers who suggested that as many characters as possible are needed to establish phylogenetic relationships within Phycitinae. The hitherto scarcely explored region of the pregenitalic abdomen promises to be of considerable importance in phycitine phylogenetics.

Sequence data from 658 base pairs of mitochondrial cytochrome c oxidase I (cox1) were analysed for 28 described species of Pipunculidae (Diptera) in an effort to test the concept of DNA Barcoding on this family. Two recently revised but distantly related pipunculid lineages with presumed different evolutionary histories were used for the test (Clistoabdominalis Skevington, 2001 and Nephrocerus Zetterstedt, 1838). An effort was made to test the concept using sister taxa and morphologically similar sibling species swarms in these two genera. Morphological species concepts for Clistoabdominalis taxa were either supported by cox1 data or found to be too broad. Most of the discordance could be accounted for after reassessing morphological characters. In these cases, the molecular data were invaluable in assisting taxonomic decision-making. The radiation of Nearctic species of Nephrocerus could not be diagnosed using cox1. The ability of cox1 to recover phylogenetic signal was also tested on Clistoabdominalis. Morphological data for Clistoabdominalis were combined with the molecular data set. The pipunculid phylogeny from molecular data closely resembles the published phylogeny based on morphology. Partitioned Bremer support is used to localize areas of conflict between the datasets.

Aetosauria is an early-diverging clade of pseudosuchians (crocodile-line archosaurs) that had a global distribution and high species diversity as a key component of various Late Triassic terrestrial faunas. It is one of only two Late Triassic clades of large herbivorous archosaurs, and thus served a critical ecological role. Nonetheless, aetosaur phylogenetic relationships are still poorly understood, owing to an overreliance on osteoderm characters, which are often poorly constructed and suspected to be highly homoplastic. A new phylogenetic analysis of the Aetosauria, comprising 27 taxa and 83 characters, includes more than 40 new characters that focus on better sampling the cranial and endoskeletal regions, and represents the most comprenhensive phylogeny of the clade to date. Parsimony analysis recovered three most parsimonious trees; the strict consensus of these trees finds an Aetosauria that is divided into two main clades: Desmatosuchia, which includes the Desmatosuchinae and the Stagonolepidinae, and Aetosaurinae, which includes the Typothoracinae. As defined Desmatosuchinae now containsNeoaetosauroides engaeusand several taxa that were previously referred to the genusStagonolepis, and a new clade, Desmatosuchini, is erected for taxa more closely related toDesmatosuchus. Overall support for some clades is still weak, and Partitioned Bremer Support (PBS) is applied for the first time to a strictly morphological dataset demonstrating that this weak support is in part because of conflict in the phylogenetic signals of cranial versus postcranial characters. PBS helps identify homoplasy among characters from various body regions, presumably the result of convergent evolution within discrete anatomical modules. It is likely that at least some of this character conflict results from different body regions evolving at different rates, which may have been under different selective pressures.

AbstractThe phylogeny of semi-aquatic bugs (Hemiptera-Heteroptera: Gerromorpha) was tested in parsimony analyses of 64 morphological characters and approximately 2.5 kb of DNA sequence data from the mitochondrial genes encoding COI+II and 16SrRNA and the nuclear gene encoding 28SrRNA. The taxon sample included representatives of all families and most subfamilies of Gerromorpha and a selection of outgroup taxa representing the two basal infraorders of Heteroptera, Enicocephalomorpha and Dipsocoromorpha, and two families of Nepomorpha. A simultaneous analysis (SA) of all data, and with gaps scored as fifth state characters, gave a single most parsimonious tree with all families resolved as monophyletic, except the Veliidae, where Microveliinae + Haloveliinae, Veliinae, Rhagoveliinae, Perittopinae, and Ocelloveliinae were resolved as successive sister groups to the Gerridae, thus confirming earlier statements about paraphyly of this family. The Gerridae + Veliidae clade was strongly supported, but otherwise only the Gerridae + Veliidae less Ocelloveliinae and the Gerridae itself had support. These three clades could all be diagnosed on apomorphic morphological characters, although no characters diagnosing the Gerridae were without convergences or present in all included taxa. While the Ocelloveliinae, Veliinae and Haloveliinae could not be diagnosed on convincing apomorphies, the Microveliinae + Haloveliinae, and their sister group relationship with the Gerridae, could be diagnosed on rather strong morphological synapomorphies, suggesting that Gerridae could be expanded to include these two veliid subfamilies, while Ocelloveliinae, and perhaps the remaining veliid subfamilies, could be elevated to new families. In Gerridae, the Ptilomerinae + Halobatinae was sister group to all other subfamilies, while the Rhagadotarsinae + Trepobatinae was sister group to a clade comprising the Gerrinae, Eotrechinae, Cylindrostethinae and Charmatometrinae. Most relationships in this clade were poorly supported and diagnosed, and Cylindrostethinae was surprisingly found to be paraphyletic. The sister group to the Gerridae + Veliidae clade was a strongly supported clade comprising the Paraphrynoveliidae and Macroveliidae, and this, and the lack of convincing synapomorphies for Paraphrynoveliidae, suggest that these two small families could be synonymized. For the basal relationships of Gerromorpha, the Mesoveliidae was strongly supported sister group to all other families, while the Hebridae, Hermatobatidae and Hydrometridae formed a poorly supported and poorly diagnosed sister group to the Gerridae + Veliidae + Paraphrynoveliidae + Macroveliidae clade. The unexpected sister group relationship between Hermatobatidae and Hydrometridae was moderately supported, and could be diagnosed on two synapomorphies, thus giving a new hypothesis about the relationships of these very divergent families. Phylogenetic analyses of individual character partitions gave less resolved and less supported relationships, and the mitochondrial genes COI+II and 16SrRNA contributed negative hidden partitioned Bremer support (HPBS) to the simultaneous analysis tree, probably due to homoplasy caused by saturation effects.

External and internal features of the head of adult Nevrorthus apatelios are described in detail. The results are compared with data from literature. The mouthpart muscle M. stipitalis transversalis and a hypopharyngeal transverse ligament are newly described for Neuroptera and herewith reported for the first time in Endopterygota. A submental gland with multiporous opening is described for Nevrorthidae and Osmylidae and is apparently unique among insects. The parsimony analysis indicates that Sisyridae is the sister group to all remaining Neuroptera. This placement is supported by the development of 1) a transverse division of the galea in two parts in all Neuroptera excluding Sisyridae, 2) the above mentioned submental gland in Nevrorthidae and Osmylidae, and 3) a poison system in all neuropteran larvae except Sisyridae. Implications for the phylogenetic relationships from the interpretation of larval character evolution, specifically the poison system, cryptonephry and formation of the head capsule are discussed.

Abstract Background: Prostate cancer (PCa) frequently presents as multifocal lesions with histologic and molecular heterogeneity. A comprehensive understanding of tumor immune responses within the context of the complex PCa microenvironment remains elusive. Through the use of Digital Pathology and innovative Pathomics image analysis tools, tumor infiltrating lymphocytes (TILs) can be mapped, visualized, and quantified in whole slide images (WSIs) of H&E stained PCa slides. We have developed a novel workflow to map and quantify TILs by Gleason histologic grade (Gleason-TIL maps) in whole radical prostatectomy specimens. Approach: WSIs from 211 H&E tissue sections from eight whole radical prostatectomy specimens containing Gleason histologic patterns 3 and 4 were used in the development of the PCa Pathomics workflow. Pathomics tools generated PCa Tumor-TIL and Gleason-TIL maps for each corresponding H&E WSI for all eight prostatectomy specimens. To support tissue sampling for correlative biomarker studies and genomic testing in PCa clinical trials, each Tumor-TIL and Gleason-TIL map was partitioned to quantify total PCa content, Gleason grade (3 vs 4/5) content, and intratumoral and peritumoral TILs per 0.5 x 0.5 cm area tile of tissue in the WSI. Results: Both Tumor-TIL and Gleason-TIL maps reveal complex and heterogeneous tumor immune interactions across multifocal lesions within each radical prostatectomy specimen. Our novel workflow added the ability to quantify PCa, Gleason grade, and TILs to specific 0.5 x 0.5 cm tissue tiles to quantify TILs relative to Gleason grade that varies within and across each case of multifocal PCa. Quantification of the TIL tile maps showed that in 6 of the 8 prostatectomies the “hot spot” tile with the most intratumoral TILs had more TILs in the Gleason 4/5 patches than in the adjacent Gleason 3 patches. Conclusionsand Future Studies: This novel workflow was developed to generate Tumor-TIL and Gleason-TIL maps for every PCa H&E WSI to serve as powerful visual tools for real world laboratory tissue sampling for downstream genomics, immunohistochemistry, and other correlative studies for PCa clinical trials. Adding a 0.5 x 0.5 cm tile partitioning function increases the efficiency of identifying and quantitatively mapping TILs in the complex and heterogeneous PCa microenvironment. The preliminary association of TILs with higher grade Gleason 4/5 PCa appears provocative as potential actionable information as an immune biomarker in PCa. Citation Format: Yuwei Zhang, Rajarsi Gupta, Joel Saltz, Tahsin Kurc, Jakub Kaczmarzyk, Erich Bremer, Veronica Wallaengen, Amanda Galvez, Abigail Bartley, Leonard Salcedo, Alan Pollack, Sanoj Punnen, Oleksandr Kryvenko, Radka Stoyanova, Sandra M. Gaston. Mapping tumor infiltrating lymphocytes in whole prostatectomy specimens to visualize and quantify the immune microenvironment of prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 5315.

AbstractIn this paper we examine the relative contribution of information to nodes in a phylogenomic analysis combined with morphological datasets. We examine the behaviour of branch support metrics using the partitioned Bremer support (PBS) and its likelihood counterpart partitioned likelihood support (PLS). These metrics measure the contribution of a data partition to a node in question, and can be easily computed for likelihood and parsimony. Specifically, we assess the ratios of support values for morphological data to molecular data at this recalcitrant node. We find that there is a strong linear correlation between this ratio with the weight of the weaker partition where a flip (the flip weight) in topology ensues. This linear relationship allows us to estimate the amount of morphological data it will take to flip a phylogenomic hypothesis. For the datasets we use in this study flip weights are surprisingly small.

In phylogenetic studies of extinct species, researchers often exclude postcranial data because postcranial elements are missing, underrepresented, or difficult to assign to particular species. However, in some cases these decisions revolve around the idea that postcranial data are inappropriate for phylogenetic analyses because they are functionally or developmentally integrated or otherwise “prone to homoplasy.” In this study, we used a character congruence approach to test the hypothesis that postcranial data cannot be used to reconstruct phylogenies instead of the taxonomic congruence approaches most often employed in paleoanthropological studies. We identified 98 published mammalian phylogenetic datasets that included sufficient numbers of characters from the skull, dentition, and postcranium to be included in the analysis. We calculated partitioned Bremer support (PBS) values for each data partition on each strict consensus cladogram using the programs Phylogenetic Analysis Using Parsimony (PAUP) v. 4.0b10 and TreeRot.v3, calculated partition congruence indices (PCI), and assessed significant differences between data partitions using Fischer's least significant difference test. Averaged across each cladogram, postcranial PBS values are greater than, or not significantly different from, 69.4% of skull PBS values (68 studies) and 64.3% of dental PBS values (63 studies). Postcranial data provided primary support (“winning sites”) at 301/1448 nodes (20.8%), exhibited positive values at 710/1483 nodes (47.9%), and “do no harm” at 1196/1483 nodes (80.6%). There is no correlation between PBS values and data partition size as long as there are at least ten characters in each data partition. These results highlight the potential for using postcranial data to construct hominin phylogenies and argue against their exclusion from phylogenetic analyses for a priori reasons.Support or Funding InformationUndergraduate student research in this study was supported by the Benedictine University Natural Science Summer Research Program.

AbstractAfter a confused taxonomic history, Prosthechea (Laeliinae, Orchidaceae) has been circumscribed in a broad sense to include species previously placed in Encyclia subg. Osmophytum. However, recent alternative classifications resurrecting old names such as Anacheilium and Hormidium, and proposing new genera such as Euchile, Panarica, Pollardia, and Pseudencyclia were presented, splitting Prosthechea into narrower genera. In this study, we provide a molecular phylogeny of Prosthechea to reassess alternative generic classifications and shed light on evolutionary aspects of this highly diverse Neotropical lineage. Eighty species of Prosthechea s.l. and 12 species of related genera were sampled. Bayesian and maximum parsimony analyses of sequences from three plastid regions (rpl32‐trnL, trnD‐trnT, ycf1) and nrITS were included. Possible conflicts between nuclear and plastid data were assessed with partitioned Bremer support. Ancestral state reconstructions of morphological characters relevant to the genus taxonomy are provided. Our results reinforce the monophyly of the lineage corresponding to a broad circumscription of Prosthechea. The small lineages corresponding to Euchile, Panarica, and Hormidium are monophyletic, whereas the larger Anacheilium, Pollardia, and Pseudencyclia are not monophyletic. Splitting Prosthechea into smaller genera is not supported by our phylogeny, and nonmonophyly also hinders the proposal of a comprehensive infrageneric classification. The phylogenetic relationships recovered reflect better the biogeographic patterns than the previously proposed morphological affinities, pointing to the existence of homoplastic floral traits within the genus. Conflicts between nuclear and plastid partitions were detected, suggesting a possible scenario of reticulate evolution.

Abstract The present study offers a broad comparative analysis of the dorsolateral head musculature in the Gymnotiformes, with detailed descriptions and illustrations of the dorsolateral head muscles of 83 species representing combined all valid genera. Results permit a detailed assessment of primary homologies and taxonomically-relevant variation across the order. This provides the basis for a myological synonymy, which organizes 33 previously proposed names for 15 recognized muscles. Morphological variation derived from dorsolateral head musculature was coded into 56 characters. When analyzed in isolation, that set of characters results in Gymnotidae as the sister group of remaining gymnotiforms, and all other currently recognized families as monophyletic groups. In a second analysis, myological characters were concatenated with other previously proposed characters into a phenotypic matrix. Results of that analysis reveal new myological synapomorphies for nearly all taxonomic categories within Gymnotiformes. A Partitioned Bremer Support (PBS) was used to asses the significance of comparative myology in elucidating phylogenetic relationships. PBS values show strongly non-uniform distributions on the tree, with positive scores skewed towards more inclusive taxa, and negative PBS values concentrated on less inclusive clades. Our results provide background for future studies on biomechanical constraints evolved in the early stages of gymnotiform evolution.

AbstractMating between species occurs within many insect orders. The result of heterospecific mating depends upon the effectiveness of pre‐ and post‐reproductive barriers. Incomplete reproductive barriers lead to introgression of DNA into one species or both. Intricate genital morphology among dragonflies provides little assurance of species specificity given that heterospecific mating or mating attempts have been observed among many species. The genetic consequence is unknown for many heterospecific matings. For example, Somatochlora species mating and genetic exchange have been hypothesized based on observational records and individuals with hybrid morphology. We investigate the potential of heterospecific mating between North American Somatochlora species as inferred from multi‐gene phylogenies. We used mitochondrial genes (COI and ND3) and nuclear genes (EF1‐α and ITS2) to construct phylogenies using maximum parsimony. Observation of non‐monophyletic mtDNA lineages but monophyletic nDNA lineages between Somatochlora sister‐species would indicate mtDNA introgression and suggest heterospecific matings. Our results highlighted three instances of non‐monophyly of mtDNA clades in the following groups: (i) S. hineana + S. tenebrosa; (ii) S. kennedyi + S. forcipata + S. franklini; and (iii) S. calverti + S. provocans + S. filosa. Analysis of partitioned Bremer support indicates that mtDNA COI largely contributed to the non‐monophyly of these species, thus suggesting mtDNA introgression resulting from heterospecific matings. Additionally, the topology resulting from the combined data analysis was concordant with previous taxonomic understanding of Somatochlora species groups. These multi‐gene phylogenies of North American Somatochlora are the first, providing a foundation for future ecological and evolution studies and knowledge for effective decision‐making and public policy, which is especially important for the endangered species, S. hineana.

The article &quot;Fundamental evolution of all <em>Orthocoronavirinae</em>&nbsp;including three deadly lineages descendent from Chiroptera-hosted coronaviruses: SARS-CoV, MERS-CoV, and SARS-CoV-2&quot; was written by Denis Jacob Machado,&nbsp;Rachel Scott, Sayal Guirales, and Daniel A. Janies. The article was published online on April 26, 2021 (<strong>Cladistics</strong>,&nbsp;DOI: 10.1111/cla.12454). &nbsp; <strong>I. SUPPLEMENTARY DIGITAL MATERIAL</strong> &nbsp; The supplementary digital material is available at Zenodo, DOI: 10.5281/zenodo.3740770. In all files containing molecular information from GISAID&#39;s EpiCoV database, we masked GISAID&#39;s data, viz. each nucleotide was replaced by missing data (&quot;?&quot; or &quot;N&quot;), in compliance with that database&#39;s policies. &nbsp; <em>Selected terminals</em> &nbsp; The accession numbers of the 2,006 terminals (76 COVID-2019 from GISAID and 1,930 sequences from NCBI&#39;s RefSeq and GenBank databases) used in this study are listed in &quot;<strong>terminals.csv</strong>.&quot; Sequence metadata (with different tabs that contain notes on terminal names and host information) is in &quot;<strong>metadata.xlsx</strong>.&quot; All sequences here are unique, and no sequence is a substring of another complete genome on the database. Also, selected sequences are longer than 26 Kbp and have less than 0.1% of character states that are different from A, C, T, or G (e.g., missing data and gaps). Finally, we were able to predict the partitions ORF1ab, M, S, and N for all sequences herein. &nbsp; <em>Data matrix</em> &nbsp; The final DNA matrix in &quot;<strong>matrix.ss</strong>&quot; comprises 38,274 characters divided into four partitions, representing the genes ORF1ab (translated by ribosomal frameshifting), S (spike glycoprotein trimer), M (membrane protein), and N (nucleoprotein). The same matrix is also available in NEXUS format (&quot;<strong>matrix.nex</strong>&quot;), and the partitions and selected models are descriped in the NEXUS file &quot;<strong>partitions.nex</strong>.&quot; &nbsp; <em>Tree search</em> &nbsp; The template for the script used to perform different tree search replicates on TNT is named &quot;<strong>treeSearch.RUN</strong>.&quot; This script was executed ten times, changing the replicate number accordingly. A total of 100 rounds of tree fusing were executed using all trees found this way (see &quot;<strong>fuse.RUN</strong>&quot;). Consensus trees were produced with &quot;<strong>consensus.RUN</strong>.&quot; Trees with branch lengths were produced with &quot;<strong>branchLength.RUN</strong>.&quot; Bootstrap calculations were performed with &quot;<strong>bootstrap.RUN</strong>.&quot; The calculation of Goodman-Bremer support values was based on the macro &quot;<strong>Bremer.RUN</strong>&quot;. &nbsp; <em>Recombination analyses</em> &nbsp; The parameters used for whole-genome alignment and recombination detection among the complete genomes of the SARS-CoV-2 reference sequence (RefSeq accession number NC_045512.2), a bat-hosted COV RaTG13 (GISAID accession number EPI_ISL_41402131), a representative of the Pan_SL-CoV_GD clade (GISAID accession number EPI_ISL_410721), and two other bat-hosted SARS-like viruses (GenBank accession numbers MG772933.1 and MG772934.1), as well as the main results, are provided in a single PDF file (&quot;<strong>recombination.pdf</strong>&quot;). &nbsp; <em>Graphical abstract</em> &nbsp; The graphical abstract below summarizes our main results. See full image in file &quot;<strong>graphicalAbstract.pdf</strong>&quot;. &nbsp; <em>Phylogenetic trees from parsimony analyses</em> &nbsp; The NEXUS file &quot;<strong>parsimony.nex</strong>&quot; contains the best heuristic results from the parsimony analyses (six trees), the tree with branch lengths, the tree with bootstrap values, the tree with Goodman-Bremer support values, the tree with REP values, and the strict consensus tree. The file also contains a tree with merged data (e.g., node numbers, clade frequencies, branch lengths). &nbsp; <em>Bootstrap values and clade sizes from parsimony analysis</em> &nbsp; Boostrap values among all nodes varied from 0 to 100% (mean = 65.74%, median = 80%, and mode = 100%). Boostrap values on the consensus tree varied from 1 to 100% (mean = 75.17%, median = 90%, and mode = 100%). For scatter plots and histograms showing the variation of boostrap values in relation to clade size, see file &quot;<strong>bootstrap.png</strong>.&quot; &nbsp; <em>Complete consensus tree from parsimony analyses</em> &nbsp; A high-resolution version of the consensus tree from the best six heuristic results from tree search performed under the parsimony criterion is in file &quot;<strong>parsimony.pdf</strong>&quot; Branch lengths are proportional to the number of transformations and branch colors correspond to bootstrap values (see legend in the figure). &nbsp; <em>Host shifts</em> &nbsp; The spreadsheet in &quot;<strong>hosts.csv</strong>&quot; contains the minimum and the maximum number of each type of host transformations. The complete consensus tree with the YBYR&Aacute;&#39;s categorization of host transformations is available in &quot;<strong>hosts.pdf</strong>.&quot; &nbsp; <em>TreeTime analyses</em> &nbsp; Analyses with TreeTime v0.7.5 (available at github.com/neherlab/treetime) following instructions from its documentation (revision f1c83c30, available at treetime.readthedocs.io). We included the results of the following analyses: The spreadsheet in &quot;<strong>treetime.csv</strong>&quot; contains the main results from TreeTime analysis, including estimated mutation rates and the minimum and maximum estimated dates for the selected virus clades. It also gives each of the virus&#39; earliest publications and their respective DOIs. Finally, this spreadsheet has the details about the earliest genetic sequences submitted to NCBI&#39;s databases for each of the virus it lists. Host shift calculation using the &quot;mugration&quot; model: the compressed folder &quot;<strong>mugration.zip</strong>&quot; contains the GTR model calculations (&quot;<strong>GTR.txt</strong>&quot;), confidence values per node and state (&quot;<strong>confidence.csv</strong>&quot;), and the annotated tree data showing all host shifts (&quot;<strong>annotated_tree.nex</strong>&quot; and &quot;<strong>annotated_tree.pdf</strong>&quot;). Mutation rates: the compressed folder &quot;<strong>mutation_rates.zip</strong>&quot; contains details about selected clades, including branch lengths (&quot;<strong>clade_data.csv</strong>&quot;). It also contains host and collection dates for terminals (&quot;<strong>terminal_data.csv</strong>&quot;) and root-to-tip regression analyses (&quot;<strong>root-to-tip-regressions.csv</strong>&quot; and &quot;<strong>root-to-tip-regressions.pdf</strong>&quot;) <em>Recombination detection analysis</em> &nbsp; The spreadsheet in &quot;<strong>summaryFromRdp5_505terminals.xlsx</strong>&quot; contains the results of the recombination detection analysis of a 505 terminals dataset. The results in there were used to test the sensitivity of phylogenetic analysis to the removal of putative recombinant sequences. &nbsp; <em>Maximum likelihood trees</em> &nbsp; The maximum likelihood tree (log-likelihood: -2,240,329.5917) is available in &quot;<strong>likelihood.nex</strong>.&quot; Node labels show the support values formatted as SH-aLRT support and bootstrap values. The branch lengths are proportional to the average number of nucleotide substitutions per nucleotide site. Unconstrained maximum likelihood trees for each partition are in &quot;<strong>ml_gene_trees.nex</strong>.&quot; &nbsp; <em>Subsets for sensitivity analysis</em> &nbsp; The matrices, partition schemes, best heuristic solutions, and strict consensus trees from the datasets of 505 and 315 terminals used to test the sensitivity to putative recombinant genomes are in the NEXUS files &quot;<strong>dataset505terminals.nex</strong>&quot; and &quot;<strong>dataset315terminals.nex</strong>&quot;, respectively. &nbsp; <em>Phylogenetic analyses of the SARS-CoV-2 related clade</em> &nbsp; The NEXUS file &quot;<strong>sarscov2.nex</strong>&quot; contains the alignment matrix and partition scheme used in the independent phylogenetic analyses of the SARS-CoV-2 clade. The best heuristic solutions (8,900 steps each) and strict consensus tree from parsimony analyses are available in &quot;<strong>sarscov2_parsimony.nex</strong>.&quot; The maximum likelihood tree (likelihood score equal to -67,779.744) is in &quot;<strong>sarscov2_ml.nex</strong>.&quot; Node labels show the support values formatted as SH-aLRT support and bootstrap values. The branch lengths are proportional to the average number of nucleotide substitutions per nucleotide site. &nbsp; <em>Alignment comparisons in the SARS-CoV-2-related clade</em> &nbsp; The file &quot;<strong>sarscov2_aligns.xlsx</strong>&quot; contain summary stats of the alignment comparisons between the SARS-CoV-2 reference sequence (NCBI&#39;s RefSeq accession number NC_045512.2) and related viruses found in humans, bats, and pangolin hosts. &nbsp; <em>Alignment comparisons of the repeat binding motif of the spike glycoprotein</em> &nbsp; The file &quot;<strong>rbm.xlsx</strong>&quot; contains details on the comparisons between the receptor-binding motif (RBM) of the spike glycoprotein of SARS-CoV-2 (NCBI&#39;s RefSeq accession number NC_045512) and other viruses infecting humans, bats, and pangolins in the SARS-CoV-2-related clade. This Excel spreadsheet has two tabs summarizing data from the amino acid and nucleotide alignments, respectively. &nbsp; <strong>II. SUPPLEMENTARY ACKNOWLEDGEMENT TABLE</strong> &nbsp; The complete GISAID acknowledgement table is provided in file &quot;<strong>acknowledgement.xlsx</strong>&quot; (Zenodo, DOI: 10.5281/zenodo.3740770). &nbsp; <strong>III. GLOSSARY</strong> &nbsp; We compose a glossary, provided in file &quot;<strong>glossary.pdf</strong>&quot; (Zenodo, DOI: 10.5281/zenodo.3740770), with selected terms and concepts that are in our manuscript or that are crucial to understanding the references we cited. &nbsp;