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Dataset for: Combined Ca, Sr isotope and trace element analyses of Late Cretaceous dinosaur teeth: assessing diet versus diagenesis
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FIGURE. Phylogenetic tree based on RAxML analyses of a combined LSU, ITS and SSU dataset. Bootstrap support values for ML and MP equal to or greater than 75% and PP value greater than 0.95 are in thickened. Ex-type isolates are in bold, and new taxa are indicated in red. The tree is rooted with Atractospora aquatica (S-1297) and A. aquatica (MFLU 18–2322). in Conlarium sichuanense sp. nov., on Ficus virens from Sichuan Province, China
FIGURE. Phylogenetic tree based on RAxML analyses of a combined LSU, ITS and SSU dataset. Bootstrap support values for ML and MP equal to or greater than 75% and PP value greater than 0.95 are in thickened. Ex-type isolates are in bold, and new taxa are indicated in red. The tree is rooted with Atractospora aquatica (S-1297) and A. aquatica (MFLU 18–2322).
FIGURE. Dendrogram of P. charlesworthii var. lannaense and 10 other Paphiopedilum species in section Paphiopedilum by 7 AFLP primer combinations, 1= first main group, 2= second main group, 2.1= subgroup 2.1 and 2.2 = subgroup 2.2. in Paphiopedilum charlesworthii var. lannaense, a new slipper orchid from Northern Thailand identified by morphological and AFLP analyses
FIGURE. Dendrogram of P. charlesworthii var. lannaense and 10 other Paphiopedilum species in section Paphiopedilum by 7 AFLP primer combinations, 1= first main group, 2= second main group, 2.1= subgroup 2.1 and 2.2 = subgroup 2.2.
FIGURE. Dendrogram of P. charlesworthii var. lannaense and 49 other Paphiopedilum species by 6 AFLP primer combinations, 1= Brachypetalum, 2= Cochlopetalum, 3= Parvisepalum, 4= Polyantha, 5= Sigmatopetalum, 6= Paphiopedilum, 7= Laosianum, and 8= Megastaminodium. in Paphiopedilum charlesworthii var. lannaense, a new slipper orchid from Northern Thailand identified by morphological and AFLP analyses
FIGURE. Dendrogram of P. charlesworthii var. lannaense and 49 other Paphiopedilum species by 6 AFLP primer combinations, 1= Brachypetalum, 2= Cochlopetalum, 3= Parvisepalum, 4= Polyantha, 5= Sigmatopetalum, 6= Paphiopedilum, 7= Laosianum, and 8= Megastaminodium.
Combining population genomics with demographic analyses highlights habitat patchiness and larval dispersal as determinants of connectivity in coastal fish species
<p>Gene flow shapes spatial genetic structure as well as the potential for local adaptation of populations. Among marine animals with non-migratory adults, the presence or absence of a pelagic larval stage is thought to be a key determinant in shaping gene flow and the genetic structure of populations. In addition, the spatial distribution of suitable habitats will influence the distribution of biological populations and their pattern of gene flow. We used whole genome sequencing to study demographic history and reduced representation (ddRAD) sequencing data to analyze spatial genetic structure in the broadnosed pipefish (<em>Syngnathus typhle</em>). Its main habitat are seagrass meadows, which along the study coast (SW Norway) have a patchy distribution. Combining the results from several analyses including scans for selection, suggests that stochastic genetic drift has shaped the observed population structure largely due to its patchy habitat distribution. The restricted gene flow is further driven by life history traits such as the presence of parental care combined with no pelagic life stages, resulting in a clear isolation-by-distance pattern spanning 100s of kilometers.</p> <p>The spatial scale of demographic connectivity was inferred from long-term (~30 year) census population counts that uncovered a sharp decline in spatial correlations in abundance with distance (37% decorrelation over 2 km). These findings were contrasted with data from two other fish species sampled along the same coastline, both having pelagic larval stages lasting ~20 days (corkwing wrasse, <em>Symphodus melops</em>, and black goby, <em>Gobus niger</em>) where the population structure is not that evident. For these species, we found a wider spatial scale of demographic connectivity (decorrelation distances of 14 and 28 km, respectively), and weaker isolation-by-distance except at one point along the coast where both species revealed a strong barrier to gene flow, seemingly due to a lack of suitable habitat. Combined, these findings suggest that habitat fragmentation and absence of a pelagic larval stage in pipefish strongly increases geographic structuring, while the pelagic larvae of wrasse and goby increase genetic and demographic connectivity, except over extensive habitat shifts.</p>
Figure 3 in The evolution of tinamous (Palaeognathae: Tinamidae) in light of molecular and combined analyses
Figure 3. Divergence-date estimates obtained with the two alternative molecular matrices (black lines, complete; grey lines, RAG2 only). In both cases, the fossil-based calibration scheme used the Diogenornis age constraint (see Table 1). Nodes used in fossil calibration are marked with diamonds.
Figure 2 in The evolution of tinamous (Palaeognathae: Tinamidae) in light of molecular and combined analyses
Figure 2. Relationships of the tinamous using a combined matrix of molecular and morphological data as inferred by Bayesian inference (BI) (Supporting Information, Fig. S7). The subtree topology in the inset was recovered under maximum parsimony (MP). Well-supported nodes having support values> 90% under MP and> 0.95 under BI are marked by dots on the cladogram. Differences among the BI topology and the topologies obtained with the MP (Supporting Information, Fig. S6) and maximum likelihood (ML) searches (Supporting Information, Fig. S8) are marked in grey and with an X, respectively.
Figure 1 in The evolution of tinamous (Palaeognathae: Tinamidae) in light of molecular and combined analyses
Figure 1. Bayesian inference (BI) majority consensus tree based on the concatenated molecular data, showing the phylogenetic relationships of tinamous (see also Supporting Information, Figs S6–S8). The maximum likelihood (ML) tree topology was identical to that of the BI tree. Clade-support values are indicated above branches (posterior probability under BI/bootstrap values under ML/bootstrap values under maximum parsimony, respectively).
Figure 4 in The evolution of tinamous (Palaeognathae: Tinamidae) in light of molecular and combined analyses
Figure 4. Taxonomic distribution and optimization of phenotypic characters: eggshell coloration, development of postacetabular pelvis and changes in plumage pattern (characters 9, 101 and 185, described in more detail in the Supporting Information, Appendix S1). For the data matrix, see the Supporting Information (Appendix S2). Further discussion is provided in the main text.
Supplementary material 7 from: Tedersoo L, Anslan S, Bahram M, Põlme S, Riit T, Liiv I, Kõljalg U, Kisand V, Nilsson RH, Hildebrand F, Bork P, Abarenkov K (2015) Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi. MycoKeys 10: 1-43. https://doi.org/10.3897/mycokeys.10.4852
Table S7. Taxonomic classification of the rDNA of fungal.: Explanation note: Taxonomic classification of the rDNA of fungal shotgun metagenome.
Supplementary material 3 from: Tedersoo L, Anslan S, Bahram M, Põlme S, Riit T, Liiv I, Kõljalg U, Kisand V, Nilsson RH, Hildebrand F, Bork P, Abarenkov K (2015) Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi. MycoKeys 10: 1-43. https://doi.org/10.3897/mycokeys.10.4852
Table S3. Data set of the SSU V4 and V5 barcodes.: Explanation note: Data set of the SSU V4 and V5 barcodes.
Supplementary material 1 from: Tedersoo L, Anslan S, Bahram M, Põlme S, Riit T, Liiv I, Kõljalg U, Kisand V, Nilsson RH, Hildebrand F, Bork P, Abarenkov K (2015) Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi. MycoKeys 10: 1-43. https://doi.org/10.3897/mycokeys.10.4852
Table S1. Characteristics of soil samples.: Explanation note: Characteristics of soil samples used in this study.
Supplementary material 6 from: Tedersoo L, Anslan S, Bahram M, Põlme S, Riit T, Liiv I, Kõljalg U, Kisand V, Nilsson RH, Hildebrand F, Bork P, Abarenkov K (2015) Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi. MycoKeys 10: 1-43. https://doi.org/10.3897/mycokeys.10.4852
Table S6. Data set of the LSU D1, D2, and D3 barcodes.: Explanation note: Data set of the LSU D1, D2, and D3 barcodes.
Supplementary material 2 from: Tedersoo L, Anslan S, Bahram M, Põlme S, Riit T, Liiv I, Kõljalg U, Kisand V, Nilsson RH, Hildebrand F, Bork P, Abarenkov K (2015) Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi. MycoKeys 10: 1-43. https://doi.org/10.3897/mycokeys.10.4852
Table S2. Taxonomic composition and clustering of the mock community sample.: Explanation note: Taxonomic composition and clustering of the mock community sample.
Figure 40 in A new classification of the family Ariidae (Osteichthyes: Ostariophysi: Siluriformes) based on combined analyses of morphological and molecular data
Figure 40. Bleekeriella leptaspis, northern Australia and New Guinea, photograph by Ricardo Betancur-R., type species of the genus.
Figure 46 in A new classification of the family Ariidae (Osteichthyes: Ostariophysi: Siluriformes) based on combined analyses of morphological and molecular data
Figure 46. Nedystoma dayi, New Guinea, photograph by Ricardo Betancur-R., type species of the genus.
Figure 41 in A new classification of the family Ariidae (Osteichthyes: Ostariophysi: Siluriformes) based on combined analyses of morphological and molecular data
Figure 41. Brustiarius nox, New Guinea, photograph by Ricardo Betancur-R., type species of the genus.
Figure 37 in A new classification of the family Ariidae (Osteichthyes: Ostariophysi: Siluriformes) based on combined analyses of morphological and molecular data
Figure 37. Pseudosciades sona, Indo-West Pacific, photograph by Ricardo Betancur-R., type species of the genus.
Figure 38 in A new classification of the family Ariidae (Osteichthyes: Ostariophysi: Siluriformes) based on combined analyses of morphological and molecular data
Figure 38. Representative skulls, in dorsal view, and distribution of the subtribe Doiichthyina. A, Brustiarius nox, AUM 47488. B, Paracinetodus carinatus, AUM 47550. C, Cochlefelis spatula, AUM 50296. D, Nedystoma dayi, AUM 47500. E, Aceroichthys dioctes, AUM 47507. F, Pachyula crassilabris, AUM 47509. G, Pararius proximus, AUM 47486. H, Potamosilurus velutinus, AUM 47489. * marine, ** brackish waters, *** freshwater.
Figure 35 in A new classification of the family Ariidae (Osteichthyes: Ostariophysi: Siluriformes) based on combined analyses of morphological and molecular data
Figure 35. Kyataphisa nenga, Indo-West Pacific, photograph by Ricardo Betancur-R., type species of the genus.
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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.