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Fig. 2 Coalescent tree reconstruction for all concatenated genes. Only posterior probabilities higher than 0.95 in A multigene phylogeny demonstrates that Tuber aestivum and Tuber uncinatum are conspecific
Fig. 2 Coalescent tree reconstruction for all concatenated genes. Only posterior probabilities higher than 0.95 are indicated. The tree is rooted with MAC (T. macrosporum) and MAG (T. magnatum)
Figure 11 in Fantastic beasts and how to delimit them: an integrative approach using multispecies coalescent methods reveals two new, endemic Dugesia species (Platyhelminthes: Tricladida) from Corsica and Sardinia
Figure 11. Dugesia hoidi: A, holotype RMNH.VER.21056.1, photomicrograph showing the penial fold (pf) in sagiưal section; B, paratype RMNH.VER.21056.2, photomicrograph showing the penis papilla (pp) and the penial fold (pf) in transverse section.
Figure 10. Dugesia hoidi. Holotype RMNH.VER.21056.1 in Fantastic beasts and how to delimit them: an integrative approach using multispecies coalescent methods reveals two new, endemic Dugesia species (Platyhelminthes: Tricladida) from Corsica and Sardinia
Figure 10. Dugesia hoidi. Holotype RMNH.VER.21056.1: A, sagiưal reconstruction of the male copulatory apparatus (anterior to the right); B, sagiưal reconstruction of the penial fold and female copulatory apparatus; C, photomicrograph of sagiưal section, showing penis bulb (pb) with the seminal vesicle (sv), right (rvd) and the less (lvd) vas deferens, penis papilla (pp) with the pointed diaphragm (d), and the ejaculatory duct (ed).
Figure 7. Dugesia benazzii s.s., CGAS Pla 25.1 in Fantastic beasts and how to delimit them: an integrative approach using multispecies coalescent methods reveals two new, endemic Dugesia species (Platyhelminthes: Tricladida) from Corsica and Sardinia
Figure 7. Dugesia benazzii s.s., CGAS Pla 25.1: A, sagiưal reconstruction of the male copulatory apparatus (anterior to the right); B, sagiưal reconstruction of the fold and female copulatory apparatus; C, photomicrograph of sagiưal section, showing the penis bulb (pb), penis papilla (pp) with conical, pointed diaphragm (d), ejaculatory duct (ed), penial fold (pf), and 'angled' bursal canal (abc).
Figure 6 in Fantastic beasts and how to delimit them: an integrative approach using multispecies coalescent methods reveals two new, endemic Dugesia species (Platyhelminthes: Tricladida) from Corsica and Sardinia
Figure 6. Karyogram of (A) Dugesia benazzii s.s. from Su Rizzolu River (Oưi, loc. 13) and (B) Dugesia hoidi.
Figure 1. A in Fantastic beasts and how to delimit them: an integrative approach using multispecies coalescent methods reveals two new, endemic Dugesia species (Platyhelminthes: Tricladida) from Corsica and Sardinia
Figure 1. A, sampling localities of the present study. Numbers correspond to population codes listed in Appendix, Table A1 and coincide with those in Dols-Serrate et al. (2020). Red circles indicate populations used for morphological analyses. B, rectangular inset: enlargement of the Bunnari–Mascari confluence area. Ŋe map was created using Q-GIS v.3.2.2 (hưps://qgis.org/es/site/ last accessed September 2023) and edited in ILLUSTÞTOR CC v.22.0.1 (hưps://www.adobe.com/products/illustrator.html last accessed September 2023).
Figure 14 in Fantastic beasts and how to delimit them: an integrative approach using multispecies coalescent methods reveals two new, endemic Dugesia species (Platyhelminthes: Tricladida) from Corsica and Sardinia
Figure 14. Dugesia mariae: A, CGAS Pla 27. 1, photomicrograph showing the penis bulb with the seminal vesicle (sv), less (lvd) and right (rvd) vas deferens, the penial papilla (pp) and the two atrial folds (af) in horizontal section; B, CGAS Pla 27. 4, photomicrograph showing the penis papilla (pp) and the penial fold (pf) in transverse section.
Figure 9. Dugesia benazzii s.s in Fantastic beasts and how to delimit them: an integrative approach using multispecies coalescent methods reveals two new, endemic Dugesia species (Platyhelminthes: Tricladida) from Corsica and Sardinia
Figure 9. Dugesia benazzii s.s.: A, CGAS Pla 25. 6, photomicrograph showing the penial fold (pf) and the two atrial folds (af) in sagiưal section; B, CGAS Pla 25. 4, photomicrograph showing the penis papilla (pp) and the penial fold (pf) in transverse section.
Figure 3 in Fantastic beasts and how to delimit them: an integrative approach using multispecies coalescent methods reveals two new, endemic Dugesia species (Platyhelminthes: Tricladida) from Corsica and Sardinia
Figure 3. mtDNA (dataset I) phylogenetic tree and species discovery delimitation schemes for ABGD, GMYC, and mPTP, as well as PSHs and PSCs. Ultrametric tree from BEAST is shown only for visual purposes; posterior probabilities (pp) and bootstrap support values (bs) relate to MrBayes and ÞxML analyses, respectively; pp and bs node support values represented by squares and circles, filled with white (unsupported), grey (supported), and black (maximum support), respectively.
Figure 8. Dugesia benazzii s.s., CGAS Pla 25.1 in Fantastic beasts and how to delimit them: an integrative approach using multispecies coalescent methods reveals two new, endemic Dugesia species (Platyhelminthes: Tricladida) from Corsica and Sardinia
Figure 8. Dugesia benazzii s.s., CGAS Pla 25.1. Photomicrograph of the copulatory bursa with a ciliate parasite (cp) and a spermatophore (sp) in a sagiưal section.
Figure 5 in Fantastic beasts and how to delimit them: an integrative approach using multispecies coalescent methods reveals two new, endemic Dugesia species (Platyhelminthes: Tricladida) from Corsica and Sardinia
Figure 5. BFD results for the array of models tested (1–6), with different a priori species-delimitation hypotheses tested on three datasets (I, IV, and V). Each column represents a model with a unique combination of lineages (rows). Star symbol indicates reassignment of PSC4. Marginal-likelihood estimates (MLE) and Bayes' factors comparison results (2lnBf) from the combined analyses of five independent runs with PS (path-sampling) and SS (stepping stone) are represented with circles and a grey-scale scheme. 2lnBf comparison support indicates differences from the best model: non-significant indicates no difference in support for the two models; positively supported and decisively-supported indicate clear support in favour of the best-fiưing model over its alternative.
Figure 4 in Fantastic beasts and how to delimit them: an integrative approach using multispecies coalescent methods reveals two new, endemic Dugesia species (Platyhelminthes: Tricladida) from Corsica and Sardinia
Figure 4. Schematic representation of BPP results on multi-locus data for two topologies. Colour scheme and squares represent posterior probability (pp) for each node under four different prior combinations, using two algorithms (A0 and A1) and three datasets (I, IV, and V). *Unsupported node with a pp of 0.94.
Figure 2 in Fantastic beasts and how to delimit them: an integrative approach using multispecies coalescent methods reveals two new, endemic Dugesia species (Platyhelminthes: Tricladida) from Corsica and Sardinia
Figure 2. Simplified Bayesian (A–E1) and ML dendrograms (E2). A, dataset I: COI–NADH4–tRNAW–COII; B, dataset II: Dunuc10; C, dataset III: Dunuc12; D, dataset IV: Dunuc10 * 12; E, dataset V: mtDNA * nDNA. Posterior probabilities (pp) are indicated by filled squares and bootstrap support values (bs) with filled circles. Full trees are represented in Figure 3 (dataset I) and Supporting Information, Figure S1 (datasets I–V).
Figure 13. Dugesia mariae. Holotype RMNH.VER.21056.1 in Fantastic beasts and how to delimit them: an integrative approach using multispecies coalescent methods reveals two new, endemic Dugesia species (Platyhelminthes: Tricladida) from Corsica and Sardinia
Figure 13. Dugesia mariae. Holotype RMNH.VER.21056.1: A, sagiưal reconstruction of the copulatory apparatus (anterior to the right); B, photomicrograph showing, in a sagiưal section, the penis bulb (pb) with seminal vesicle (sv), penis papilla (pp) with the pointed diaphragm (d), pleated ejaculatory duct (ed), and the penial fold (pf).
Figure 12 in Fantastic beasts and how to delimit them: an integrative approach using multispecies coalescent methods reveals two new, endemic Dugesia species (Platyhelminthes: Tricladida) from Corsica and Sardinia
Figure 12. Dugesia mariae. Photomicrograph of a preserved sexual specimen from the Golo River (Barcheưa, loc. 24).
Fig. 2 in Coalescence-based species delimitation using genome-wide data reveals hidden diversity in a cosmopolitan group of lichens
Fig. 2 Maximum likelihood tree reconstructions based on single PKS8 gene (a) and four gene: ITS, GPD, mtLSU, and PKS8 (b) data sets. Nodes in bold indicate those with support values of 95% and higher. Black dots
Data from: Data concatenation, Bayesian concordance and coalescent-based analyses of the species tree for the rapid radiation of Triturus newts
The phylogenetic relationships for rapid species radiations are difficult to disentangle. Here we study one such case, namely the genus Triturus, which is composed of the marbled and crested newts. We analyze data for 38 genetic markers, positioned in 3-prime untranslated regions of protein-coding genes, obtained with 454 sequencing. Our dataset includes twenty Triturus newts and represents all nine species. Bayesian analysis of population structure allocates all individuals to their respective species. The branching patterns obtained by data concatenation, Bayesian concordance analysis and coalescent-based estimations of the species tree differ from one another. The data concatenation based species tree shows high branch support but branching order is considerably affected by allele choice in the case of heterozygotes in the concatenation process. Bayesian concordance analysis expresses the conflict between individual gene trees for part of the Triturus species tree as low concordance factors. The coalescent-based species tree is relatively similar to a previously published species tree based upon morphology and full mtDNA and any conflicting internal branches are not highly supported. Our findings reflect high gene tree discordance due to incomplete lineage sorting (possibly aggravated by hybridization) in combination with low information content of the markers employed (as can be expected for relatively recent species radiations). This case study highlights the complexity of resolving rapid radiations and we acknowledge that to convincingly resolve the Triturus species tree even more genes will have to be consulted.
Data from: Species delimitation with ABC and other coalescent-based methods: a test of accuracy with simulations and an empirical example with lizards of the Liolaemus darwinii complex (Squamata: Liolaemidae)
Species delimitation is a major research focus in evolutionary biology because accurate species boundaries are a prerequisite for the study of speciation. New species delimitation methods (SDMs) can accommodate non-monophyletic species and gene tree discordance as a result of incomplete lineage sorting via the coalescent model, but do not explicitly accommodate gene flow after divergence. Approximate Bayesian Computation (ABC) can incorporate gene flow and estimate other relevant parameters of the speciation process while testing alternative species delimitation hypotheses. We evaluated the accuracy of BPP, SpeDeSTEM, and ABC for delimiting species using simulated data and applied these methods to empirical data from lizards of the Liolaemus darwinii complex. Overall, BPP was the most accurate, ABC showed an intermediate accuracy, and SpeDeSTEM was the least accurate under most simulated conditions. All three SDMs showed lower accuracy when speciation occurred despite gene flow, as found in previous studies, but ABC was the method with the smallest decrease in accuracy. All three SDMs consistently supported the distinctness of southern and northern lineages within L. darwinii. These SDMs based on genetic data should be complemented with novel SDMs based on morphological and ecological data to achieve truly integrative and statistically robust approaches to species discovery.
Data from: Coalescence times, life history traits and conservation concerns: an example from four coastal shark species from the Indo-Pacific
<p><span><span><span><span><span><span><span><span><span><span><span>Dispersal abilities play a crucial role in shaping the extent of population genetic structure, with more mobile species being panmictic over large geographic ranges and less mobile ones organized in meta-populations exchanging migrants to different degrees. In turn, population structure directly influences the coalescence pattern of the sampled lineages, but the consequences on the estimated variation of the effective population size<i> </i>(<i>Ne</i>) over time obtained by means of <i>unstructured</i>demographic models remain poorly understood. However, this knowledge is crucial for biologically interpreting the observed <i>Ne </i>trajectory and further devising conservation strategies in endangered species. Here we investigated the demographic history of four shark species (<i>Carharhinus melanopterus</i>, <i>Carharhinus limbatus</i>, <i>Carharhinus amblyrhynchos</i>, <i>Galeocerdo cuvier</i>) with different degrees of endangered status and life history traits related to dispersal distributed in the Indo-Pacific and sampled off New Caledonia. We compared several evolutionary scenarios representing both <i>structured</i> (meta-population) and<i> unstructured</i> models and then inferred the <i>Ne</i> variation through time. By performing extensive coalescent simulations, we provided a general framework relating the underlying population structure and the observed <i>Ne</i> dynamics. On this basis, we concluded that the recent decline observed in three out of the four considered species when assuming <i>unstructured</i> demographic models can be explained by the presence of population structure. Furthermore, we also demonstrated the limits of the inferences based on the sole site frequency spectrum and warn that statistics based on linkage disequilibrium will be needed to exclude recent demographic events affecting meta-populations.</span></span></span></span></span></span></span></span></span></span></span></p>
Figure 2 in Considering gene flow when using coalescent methods to delimit lineages of North American pitvipers of the genus Agkistrodon
Figure 2. Species tree showing the phylogenetic relationships within the genus Agkistrodon implemented in *BEAST (Heled & Drummond, 2010). Posterior probability support for nodes is indicated above branches. The guide trees used for subsequent species delimitation in BPP (Yang & Rannala, 2010) are shown in the insets.
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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.