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FIGURE 39 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 39. Audiospectrogram and corresponding oscillogram of a 1000 ms section of one advertisement call (call duration 1545 ms) of Mantidactylus tripunctatus, recorded February 1991 near Tolagnaro. Recording bandpass-filtered at 1200–4100 Hz.
FIGURE 34 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 34. Mantidactylus betsileanus in life, in anterior, dorsolateral, and ventral view. (a,b,c) Adult male from Andasibe, photographed in 1991. (d) Adult male from Andasibe, photographed in situ in a small cavity next to a swamp where it was emitting its call, photographed in 1991. (e,f) Adult male from Mahasoa, photographed in 2008. (g,h) Adult male from Andasibe, photographed in 1995. Note in the ventral views the relatively small femoral glands, with the distal ulcerous macroglands placed at considerable distances from each other, which constitutes a typical character state of this species; and in the frontal view (a), the white dot on the snout tip which is typical for this and several allied species.
FIGURE 10 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 10. Mantidactylus curtus in life, in dorsolateral and ventral view. (a,b) Female specimen (ZSM 768/2001 = FGMV 2001.489) from Itremo, photographed in 2001 (note the almost complete absence of femoral glands). (c,d) Probable female (note small femoral glands) from Antoetra, photographed in 2003. (e,f), Probable female (ZSM 758/2001 = FGMV 2001.423; note rather small femoral glands) from Mount Ibity/Col des Tapias, photographed in 2001.
FIGURE 8 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 8. Heat map of Brygoomantis species distribution overlap (plotted as minimum convex polygons). This map is only based on species that are recorded from more than two localities (i.e. those for which a polygon could be plotted).
FIGURE 4 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 4. Network based on sequences of the nuclear-encoded Rag-1 gene (alignment length 351 bp) from 265 specimens of Brygoomantis. The network was built from phased alleles, i.e. each sample is represented twice. The size of circles is proportional to the number of sequences with the same allele. Small black dots represent hypothetical haplotypes (not sampled or extinct) separating sampled haplotypes, when they differ by more than one mutational step.
FIGURE 7 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 7. Mantidactylus subgenus Brygoomantis species distribution based on verified records, divided by clade (Mantidactylus stelliger sp. nov. is presented alongside the inaudax clade for practicality). Colours for species correspond to those in Figs 2 and 4. Inset map shows the geographic regions of Madagascar identified by Boumans et al. (2007), referred to throughout the text.
FIGURE 6 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 6. Overview of morphometrics of Mantidactylus (Brygoomantis) species. Points and boxplots are coloured by sex (purple = female, blue = male), with sample size per sex given beside the taxon names. Species are arranged according to the main clades to which they belong according to our phylogenomic analysis. SVL is repeated in the upper and lower panels to enable the reader to access relevant information quickly.
FIGURE 5 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 5. Maximum-Likelihood tree based on a partitioned analysis of 12,818 nuclear-encoded markers obtained via the FrogCap strategy, calculated with IQ-tree, for 58 representative individuals of species-level lineages in the subgenus Mantidactylus (Brygoomantis). Note that three species are missing from this analysis (M. bletzae sp. nov., M. marintsoai sp. nov., and M. riparius sp. nov.) and the identity of the two samples of M. katae sp. nov. in this tree is uncertain. For those lineages that previously (Perl et al. 2014; Vieites et al. 2009) had candidate species numbers assigned, these are reported in parenthesis after the name used in the classification proposed herein. All branches were fully supported by SH-like approximate likelihood ratio tests with 1000 pseudoreplicates (100% support, symbolized by black dots at nodes). The tree was rooted with Mantidactylus grandidieri (subgenus Mantidactylus) as outgroup (removed from graphical representation for better visualization of ingroup relationships), with the inclusion of M. melanopleura (subgenus Chonomantis) as hierarchical outgroup. Red arrows in the M. curtus clade indicate the two reticulation events detected by a Phylonetworks analysis performed separately for this clade (note that the topology recovered by this analysis in the Phylonetworks analysis differs in the position of M. bourgati; see original results of the Phylonetworks analysis in Zenodo repository, DOI 10.5281/zenodo.668741
FIGURE 2 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 2. Maximum Likelihood tree of 1305 sequences of a fragment of the 16S rRNA gene (alignment length 519 bp) from a RAxML analysis. Numbers at nodes are bootstrap proportions in percent (100 ML fast bootstrap replicates); not shown if <50%. A sequence of Mantidactylus melanopleura was used as the outgroup (removed from the tree after analysis for better graphical representation). Note that some of the 'Museomics' sequences (obtained by targeted capture from historical type specimens) are represented twice, after assembly with different reference sequences. Some sequences in the analysis (several 'Museomics' sequences as well as others obtained from Illumina sequencing) only partially covered the fragment analysed (226 sequences <300 bp). We emphasize that this tree is based on a single short mitochondrial marker and therefore is unlikely to represent the deep relationships among lineages correctly; for such relationships, refer to the phylogenomic tree (Fig. 5).
FIGURE 1 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 1. Graphic scheme indicating (a) regions of the body and (b) morphometrics measurements of Mantidactylus specimens of the subgenus Brygoomantis (exemplified by a specimen of M. ulcerosus), as referred to in the descriptions of morphology and tables throughout the manuscript. Labels in (a) refer to regions of the body and not necessarily to anatomical features. Femoral gland terminology as explained in the text. Measurement abbreviations in (b) are explained in the text; FORL (stretched forelimb length), HIL (stretched hindlimb length), and FOTL (foot length including tarsus) are not shown.
FIGURE 3 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 3. Distribution of uncorrected pairwise genetic distances for a fragment of the mitochondrial 16S rRNA gene, in an alignment of 976 sequences, complete or almost complete for 488 bp.
Data for manuscript "Synteny identifies reliable orthologs for phylogenomics and comparative genomics of the Brassicaceae"
<p>Data and code for manuscript "Synteny identifies reliable orthologs for phylogenomics and comparative genomics of the Brassicaceae". Preprint available at bioRxiv: https://doi.org/10.1101/2022.09.07.506897.</p>
Fig. 4. A. Dorsal, B in Ultraconserved elements-based phylogenomic systematics of the snake superfamily Elapoidea, with the description of a new Afro-Asian family
Fig. 4. A. Dorsal, B, lateral and C. ventral view of the skull of Micrelaps muelleri (SMNH.R 17777). D. Ectopterygoid of the same specimen in ventral view. E. Ventral and F. lateral views of the palatomaxillary arch.
Fig. 1. A. ASTRAL and B. wASTRAL-hybrid species trees for the superfamily Elapoidea from the 50 in Ultraconserved elements-based phylogenomic systematics of the snake superfamily Elapoidea, with the description of a new Afro-Asian family
Fig. 1. A. ASTRAL and B. wASTRAL-hybrid species trees for the superfamily Elapoidea from the 50 % complete dataset, consisting of 4561 loci. Circles on the branch represent a local posterior probability support of 0.95 to 1.0. Abbreviations – AT – Atractaspidinae, CL – Cyclocoridae, EL – Elapidae, LM – Lamprophiinae, MC – Micrelapidae fam. nov., OG – outgroup, PD – Pseudaspidinae, PR – Prosymninae, PS – Psammophiinae, PX – Pseudoxyrhophiinae.
Fig. 3 in Ultraconserved elements-based phylogenomic systematics of the snake superfamily Elapoidea, with the description of a new Afro-Asian family
Fig. 3. Time calibrated phylogeny (50 % complete dataset) of elapoid snakes, estimated with the Maximum Likelihood implementation of the RelTime method (with lognormal node calibration densities). Values on the branches indicate the estimated divergence times. The blue bar represents the 95 % confidence intervals around the estimated divergence times.
Fig. 2. Maximum Likelihood species tree from the concatenated 50 in Ultraconserved elements-based phylogenomic systematics of the snake superfamily Elapoidea, with the description of a new Afro-Asian family
Fig. 2. Maximum Likelihood species tree from the concatenated 50 % complete dataset consisting of 4561 loci. Values on the branch indicate Shimodaira Hasegawalike approximate likelihood ratio test and ultrafast bootstrap. Abbreviations as in Fig. 1.
Data for: Ancient rapid radiation explains most conflicts among gene trees and well-supported phylogenomic trees of nostocalean cyanobacteria
<p>Prokaryotic genomes are often considered to be mosaics of genes that do not necessarily share the same evolutionary history due to widespread Horizontal Gene Transfers (HGTs). Consequently, representing evolutionary relationships of prokaryotes as bifurcating trees has long been controversial. However, studies reporting conflicts among gene trees derived from phylogenomic datasets have shown that these conflicts can be the result of artifacts or evolutionary processes other than HGT, such as incomplete lineage sorting, low phylogenetic signal, and systematic errors due to substitution model misspecification. Here, we present the results of an extensive exploration of phylogenetic conflicts in the cyanobacterial order Nostocales, for which previous studies have inferred strongly supported conflicting relationships when using different concatenated phylogenomic datasets. We found that most of these conflicts are concentrated in deep clusters of short internodes of the Nostocales phylogeny, where the great majority of individual genes have low resolving power. We then inferred phylogenetic networks to detect HGT events while also accounting for incomplete lineage sorting. Our results indicate that most conflicts among gene trees are likely due to incomplete lineage sorting linked to an ancient rapid radiation, rather than to HGTs. Moreover, the short internodes of this radiation fit the expectations of the anomaly zone, i.e., a region of the tree parameter space where a species tree is discordant with its most likely gene tree. We demonstrated that concatenation of different sets of loci can recover up to 17 distinct and well-supported relationships within the putative anomaly zone of Nostocales, corresponding to the observed conflicts among well-supported trees based on concatenated datasets from previous studies. Our findings highlight the important role of rapid radiations as a potential cause of strongly conflicting phylogenetic relationships when using phylogenomic datasets of bacteria. We propose that polytomies may be the most appropriate phylogenetic representation of these rapid radiations that are part of anomaly zones, especially when all possible genomic markers have been considered to infer these phylogenies.</p>
Phylogenomics illuminates the phylogeny of flower weevils (Curculioninae) and reveals ten independent origins of brood-site pollination mutualism in true weevils
<p><strong>Phylogenomics illuminates the phylogeny of flower weevils (Curculioninae) and reveals ten independent origins of brood-site pollination mutualism in true weevils (142 /150 characters)</strong></p> <p>Haran J.<sup>1*</sup>, Li X.<sup>2,3,4*</sup>, Allio R.<sup>5*</sup>, Shin S.<sup>3,4,6</sup>, Benoit L.<sup>1</sup>, Oberprieler R.G.<sup>7</sup>, Farrell B.D.<sup>8</sup>, Brown S.D.J.<sup>9</sup>, Leschen R.A.B.<sup>10</sup>, Kergoat G.J.<sup>5</sup> & McKenna D.D.<sup>3,4</sup></p> <p>* Equal contribution</p> <p> </p> <p><strong>Affiliations</strong></p> <p><sup>1</sup> CBGP, CIRAD, INRAE, IRD, Institut Agro, Univ. Montpellier, Montpellier, France. ORCID: 0000-0001-9458-3785 (JH); 0000-0003-3740-5346 (LB)</p> <p><sup>2</sup> Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China. ORCID: 0000-0002-0622-2064 (XL)</p> <p><sup>3</sup> Department of Biological Sciences, University of Memphis, Memphis, TN 38152 ORCID: 0000-0002-7823-8727 (DDM)</p> <p><sup>4</sup> Center for Biodiversity Research, University of Memphis, Memphis, TN 38152</p> <p><sup>5</sup> CBGP, INRAE, IRD, CIRAD, Institut Agro, Univ. Montpellier, Montpellier, France. ORCID: 000-0003-3885-5410 (RA); 0000-0002-8284-6215 (GJK)</p> <p><sup>6</sup> School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea.</p> <p>ORCID: 0000-0002-4258-8661 (SS)</p> <p><sup>7</sup> CSIRO, Australian National Insect Collection, GPO Box 1700, Canberra, ACT 2601, Australia. ORCID: 0000-0002-1837-580X (RGO)</p> <p><sup>8</sup> Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA. ORCID: 0000-0002-6843-0539 (BDF)</p> <p><sup>9</sup> Bio-Protection Research Centre, P.O. Box 85084, Lincoln University, Lincoln 7647, New Zealand. Current address: The New Zealand Institute for Plant and Food Research, Mount Albert Research Centre, Private Bag 92169, Auckland 1142, New Zealand. ORCID: 0000-0001-7112-421X (SDJB)</p> <p><sup>10</sup> Manaaki Whenua - Landcare Research, PB 92170, Auckland, New Zealand. ORCID: 0000-0001-8549-8933 (RABL)</p> <p> </p> <p><strong>Abstract</strong></p> <p>Weevils are an unusually species-rich group of phytophagous insects, for which there is increasing evidence of frequent involvement in brood-site pollination. This study examines phylogenetic patterns in the emergence of brood-site pollination mutualism among one of the most speciose beetle groups, the flower weevils (subfamily Curculioninae). We analyzed a novel phylogenomic dataset consisting of 214 nuclear loci for 202 weevil species, with a sampling that mainly includes flower weevils as well as representatives of all major lineages of true weevils (Curculionidae). Our phylogenomic analyses establish a uniquely comprehensive phylogenetic framework for Curculioninae and provide new insights into the relationships among lineages of true weevils. Based on this phylogeny, statistical reconstruction of ancestral character states revealed at least ten independent origins of brood-site pollination in higher weevils through transitions from ancestral associations with reproductive structures in the larval stage. Broadly, our results illuminate the unexpected frequency with which true weevils — typically specialized phytophages and hence antagonists of plants — have evolved mutualistic interactions of ecological significance that are key to both weevil and plant evolutionary fitness and thus a component of their deeply intertwined macroevolutionary success.</p> <p> </p> <p><strong><em>Figures </em></strong></p> <p><strong>Figure 1 (part I).</strong> Maximum-likelihood tree resulting from analyses of 214 nuclear protein-coding genes (focus on the CEGH clade and outgroups). Support at node refers to SH-aLRT values ≥ 80% and uBV ≥ 95% (**). Single * refer to SH-aLRT values ≥ 80% only. Clades with black branches and highlighted in blue are classified in Curculioninae sensu Caldara et al. (2014). Taxa displayed on the left: 1 - Hypsomus sp. (Styphlini); 2 - Myllorhinus sp. (Storeini s. lat.); 3 - Encosmia sp. (Storeini s. lat.).</p> <p><strong>Figure 1 (part II).</strong> Maximum-likelihood tree resulting from analyses of 214 nuclear protein-coding genes (focus on the CCCMS clade). Node support values refer to SH-aLRT values ≥ 80% and uBV ≥ 95% (**). Single * refer to SH-aLRT values ≥ 80% only. Clades with black branches and highlighted in blue are classified in Curculioninae sensu Caldara et al., (2014). Clades highlighted in darker blue contain genera engaged in brood-site pollination mutualism and the corresponding genera are highlighted in orange (higher taxonomic rank when specific genera are not included in the tree). Other lineages of the CCCMS clade are in bold font. Taxa displayed on the right: 1 - Tychius sp. (Tychiini); 2 - Anthonomus sp. (Athonomini); 3 - Tachyerges sp. (Rhamphini); 4 - Derelomus sp. (Derelomini); 5 - Cionus sp. (Cionini); 6 - Daeneus sp. (Ochyromerini); 7 - Meriphus sp. (Eugnomini); 8 - Archarius sp. (Curculionini); 9 - Dorytomus sp. (Ellescini); 10 - Cleopomiarus sp. (Mecinini).</p> <p><strong>Figure 2.</strong> Results of the ASE analysis of larval tissue specialization carried out on the CCCMS clade, with an ER model and using a continuous-time reversible Markov model with 1000 simulations. In addition, red arrows are used to underline the independent origins of brood-site mutualism inferred in another ASE analysis (see Fig. S4). Two clades including brood-site pollinator genera that were not sampled in our study are also highlighted using red rectangles.</p> <p> </p> <p><strong><em>Additional files</em></strong></p> <p><strong>Figure S1</strong>. Full ML tree with support values.</p> <p><strong>Figure S2</strong>. Support for ML analyses.</p> <p><strong>Figure S3</strong>. Results of the ASE analysis of the evolution of the tissue specialization by weevil larvae in the CCCMS clade, with an ER model and using a continuous time-reversible Markov model with 1000 simulations. </p> <p><strong>Figure S4</strong>. Results of the ASE analysis on the evolution of brood-site pollination in the CCCMS clade, with an ER model and using a continuous time-reversible Markov model with 1000 simulations.</p> <p> </p> <p><strong><em>Zenodo supplementary files</em></strong></p> <p><strong>AHE_pipeline.txt </strong>shows the detailed step-by-step script used to generate the phylogeny obtained in this study from raw sequencing data.</p> <p><strong>ASE Analyses.zip</strong> contains the script and the associated raw results of the ASE analyses.</p> <p><strong>Cole_tcas_probes.fasta</strong> contains the Coleopteran probes used.</p> <p><strong>IBA results.zip</strong> contains IBA results.</p> <p><strong>IQ-TREE files.zip</strong> contains input and output files of the IQ-TREE analysis.</p> <p><strong>Scripts.zip</strong> contains the scripts associated with the file AHE_pipeline.txt.</p> <p> </p>
Phylogenomic analyses resolve relationships among garter snakes (Thamnophis: Natricinae: Colubridae) and elucidate biogeographic history and morphological evolution
<p>Garter snakes (<i>Thamnophis</i>) are a successful group of natricines endemic to North America. They have become important natural models for ecological and evolutionary research, yet prior efforts to resolve phylogenetic relationships have resulted in conflicting topologies and weak support for certain relationships. Here, we use phylogenomic data generated with a reduced representation double-digest RADseq approach to reassess the evolutionary relationships across <i>Thamnophis</i>. We then use the resulting phylogeny to better understand how biogeography and feeding ecology have influenced lineage diversification and morphological evolution. We recovered highly congruent and strongly supported topologies from maximum likelihood and Bayesian inference analyses, but some discordance with a multispecies coalescent approach. All phylogenomic estimates split <i>Thamnophis</i> into two clades largely defined by northern and southern North American species. Divergence time estimates and biogeographic analyses indicate a mid-Miocene origin of <i>Thamnophis </i>in Mexico. In addition, historical vicariant events thought to explain biogeographic patterns in other lineages (e.g., Isthmus of Tehuantepec, Rocky Mountain Range, and Trans-Mexican Volcanic Belt) appear to have influenced patterns of diversification in <i>Thamnophis</i> as well. Analyses of morphological traits associated with feeding ecology showed degrees of phylogenetic signal, and ancestral state reconstruction suggested some association between head morphology and diet composition. Our new estimate of <i>Thamnophis</i> phylogeny yields an improved understanding of the biogeographic history and morphological evolution of garter snakes, and provides a robust framework for future research on these snakes.</p>
Data for: Phylogenomics and historical biogeography of Hydrangeeae (Hydrangeaceae) elucidate the effects of geologic and climatic dynamics on diversification
<p>Demonstrating the process of transregional biogeography and mechanisms underlying evolutionary radiations is crucial to understanding biological evolution. Here, we use Hydrangeeae (Hydrangeaceae), a tribe with a unique disjunct distribution and complex trait variations, using a solid phylogenetic framework, to investigate how geographical and climatic factors interact with functional traits to trigger plant evolutionary radiations. We constructed the first highly supported and dated phylogenetic framework using 79 protein-coding genes obtained from 81 plastomes, representing 63 species and all major clades, and found that most extant species originated from asynchronous diversification of two lineages undergoing repeated expansion and retraction, at middle and high latitudes of the Northern Hemisphere between East Asia and North America, during the Eocene to Pleistocene (driven by geologic and climatic dynamics). In accordance with these drivers, interactions of flora between central-eastern China and Japan occurred frequently after the Late Tertiary. We found that resource limitation and range fragmentation likely accelerated the diversification of Hydrangeeae, which supports the resource-use hypothesis. Our study sheds light on the evolutionary radiation and assembly of flora within East Asia, and the East Asian-North American disjunction, through integration of phylogenomic and biogeographic data with functional trait and ecological data.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.