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Supplementary material 2 from: Virgilio M, Delatte H, Nzogela YB, Simiand C, Quilici S, De Meyer M, Mwatawala M (2015) Population structure and cryptic genetic variation in the mango fruit fly, Ceratitis cosyra (Diptera, Tephritidae). In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 525-538. https://doi.org/10.3897/zookeys.540.9618
Genotype accumulation curve:
Supplementary material 1 from: Virgilio M, Delatte H, Nzogela YB, Simiand C, Quilici S, De Meyer M, Mwatawala M (2015) Population structure and cryptic genetic variation in the mango fruit fly, Ceratitis cosyra (Diptera, Tephritidae). In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 525-538. https://doi.org/10.3897/zookeys.540.9618
Map of sampling locations:
Figure 1 in Genetic characterization of sharpsnout seabream (Diplodus puntazzo) populations along the Tunisian coasts
Figure 1. – Sampling localities of Diplodus puntazzo. STS: Siculo-Tunisian Strait; 1: Bizerta Bay; 2: Ghar El Melh lagoon; 3: Gulf of Tunis; 4: Monastir; 5: Chebba; 6: Kerkennah Island; 7: Zarzis; 8: El Biban lagoon.
Figure 1 in Strong genetic difference of Eurasian perch Perca fluviatilis from two Alpine lakes used as founder populations for farming
Figure 1. – Maps of the studied lakes depicting sampling localities of Eurasian perch (Perca fluviatilis).
Figure 2 in Strong genetic difference of Eurasian perch Perca fluviatilis from two Alpine lakes used as founder populations for farming
Figure 2. – Bayesian clustering analysis of Eurasian perch population in Lake Geneva (LP1, LP2) and Lake Neuchâtel (NP1, NP2), during June 2012 (P1) and September 2012 (P2).
FIGURE 2 in Development of microsatellite loci and population genetics in the bumblebee catfish species Pseudopimelodus atricaudus and Pseudopimelodus magnus (Siluriformes: Pseudopimelodidae)
FIGURE 2 | Population structure suggested by STRUCTURE (A-C) and the Discriminant Analysis of the Principal Components (D, E) for Pseudopimelodus magnus (A, B, D), and Pseudopimelodus atricaudus (A, C, E). S1: sector 1 of the middle Cauca River; S4, S5, and S8: sectors 4, 5 and 8 of the lower Cauca River, respectively.
FIGURE 2 in Genetic evidence supports polygamous mating system in a wild population of Prochilodus lineatus (Characiformes: Prochilodontidae), a Neotropical shoal spawner fish
FIGURE 2 | Alternative schematic representations of spawning in Prochilodus lineatus. A. Schematic drawing of spawning moment of Prochilodus lineatus (=Prochilodus scrofa), according to Godoy (1975), whom described that males, positioned in the center of the river channel, performed distinctive sounds, possibly attracting females (figure drawn by Josiane Ribolli and Dennis Fernando Moreno, inspired from the original by Godoy, M. P, 1975, fig. 153, p.684); B. Hypothetical schematic representation of reproduction and spawning of P. lineatus in the wild according to direct observations made by Evoy Zaniboni-Filho (personal communication). The exhausted mature female is marked with an asterisk. Figure drawn by Josiane Ribolli and Dennis Fernando Moreno.
FIGURE 1 in Genetic evidence supports polygamous mating system in a wild population of Prochilodus lineatus (Characiformes: Prochilodontidae), a Neotropical shoal spawner fish
FIGURE 1 | Inferred parentage and mating patterns derived from analysis of 87 Prochilodus lineatus larvae sampled at the Middle Uruguay River in Brazil. A. Number of adults identified as parents of the sampled larvae; B. Number of different mates inferred for males and females.
Fig. 1 in Morphological and genetic variation in Mexican wild populations of Tamarixia radiata (Hymenoptera: Eulophidae)
Fig. 1. Neighbor-joining tree showing the genetic distance between Tamarixia radiata haplotypes. The tree was inferred according to the Tamura-3-parameter model. Next to each branch appear the bootstrap values as percentage of 1,000 replications. Next to each sequence are between brackets the gene bank accession numbers; the asterisks (*) indicate the report where the sequences were obtained, i.e., *Barr et al. 2009, **De León & Sétamou (2010), and ***González-Hernández et al. (2010).
Fig. 1 in Genetic diversity and population structure of endangered Neofinetia falcata (Orchidaceae) in South Korea based on microsatellite analysis
Fig. 1. Geographic distribution of N. falcata populations. Abbreviations are shown in Table 1. Pie charts represent assignment probability of belonging to each K = 2 clusters identified by STRUCTURE based on microsatellite allele frequencies, with probability values normalized using CLUMPP.
Supplementary material 4 from: Davoli F, Cozzo M, Angeli F, Groff C, Randi E (2018) Infanticide in brown bear: a case-study in the Italian Alps – Genetic identification of perpetrator and implications in small populations. Nature Conservation 25: 55-75. https://doi.org/10.3897/natureconservation.25.23776
Table S1. Detailed results of the biological model (consensus and composite) :
Supplementary material 1 from: Davoli F, Cozzo M, Angeli F, Groff C, Randi E (2018) Infanticide in brown bear: a case-study in the Italian Alps – Genetic identification of perpetrator and implications in small populations. Nature Conservation 25: 55-75. https://doi.org/10.3897/natureconservation.25.23776
Text S1. Parameters used for parentage analysis :
Supplementary material 3 from: Davoli F, Cozzo M, Angeli F, Groff C, Randi E (2018) Infanticide in brown bear: a case-study in the Italian Alps – Genetic identification of perpetrator and implications in small populations. Nature Conservation 25: 55-75. https://doi.org/10.3897/natureconservation.25.23776
Text S3. Detailed results of LRmix STUDIO for each suspected male: Global Composite (ADO 0.55) :
Supplementary material 2 from: Davoli F, Cozzo M, Angeli F, Groff C, Randi E (2018) Infanticide in brown bear: a case-study in the Italian Alps – Genetic identification of perpetrator and implications in small populations. Nature Conservation 25: 55-75. https://doi.org/10.3897/natureconservation.25.23776
Text S2. Detailed results of LRmix STUDIO for each suspected male: Global Consensus (ADO 0.65) :
Figure 3 from: Rocha-Méndez A, Sánchez-González LA, Arbeláez-Cortés E, Navarro-Sigüenza AG (2018) Phylogeography indicates incomplete genetic divergence among phenotypically differentiated montane forest populations of Atlapetes albinucha (Aves, Passerellidae). ZooKeys 809: 125-148. https://doi.org/10.3897/zookeys.809.28743
Figure 3 Bayesian skyline plot derived from the concatenated gene dataset of Atlapetesalbinucha species. Time in millions of years. Population size change (Ne*generation time) in the Y axis. Mean estimate is shown as a thick solid line, and the 95% HDP limits are shown in solid purple color area surrounding the mean estimate.
Figure 4 from: Rocha-Méndez A, Sánchez-González LA, Arbeláez-Cortés E, Navarro-Sigüenza AG (2018) Phylogeography indicates incomplete genetic divergence among phenotypically differentiated montane forest populations of Atlapetes albinucha (Aves, Passerellidae). ZooKeys 809: 125-148. https://doi.org/10.3897/zookeys.809.28743
Figure 4 Maxent ENMs for A.albinucha species projected into present and past scenarios. Darker blue areas depict higher logistic prediction values. ENM projected in the a present b the Mid-Holocene Climatic Optimum (MH) c the Last Glacial Maximum (LGM) and d the Last Interglacial (LIG).
Figure 1 from: Rocha-Méndez A, Sánchez-González LA, Arbeláez-Cortés E, Navarro-Sigüenza AG (2018) Phylogeography indicates incomplete genetic divergence among phenotypically differentiated montane forest populations of Atlapetes albinucha (Aves, Passerellidae). ZooKeys 809: 125-148. https://doi.org/10.3897/zookeys.809.28743
Figure 1 Atlapetesalbinucha distribution shown in green stapled lines, based on Sánchez-González et al. (2015) and Natureserve (http://natureserve.org). Blue dots depict tissue samples used in the present study. Red dots depict records of the species used to construct the distribution model. Bird pictures depict the geographic regions where color morphs are found. Blue line depicts the location of the putative distribution barrier of the morphs in Chiapas.
Figure 2 from: Rocha-Méndez A, Sánchez-González LA, Arbeláez-Cortés E, Navarro-Sigüenza AG (2018) Phylogeography indicates incomplete genetic divergence among phenotypically differentiated montane forest populations of Atlapetes albinucha (Aves, Passerellidae). ZooKeys 809: 125-148. https://doi.org/10.3897/zookeys.809.28743
Figure 2 A Dated Bayesian maximum clade credibility tree showing phylogenetic relationships among members of Atlapetesalbinucha species. Node bars depict 95% HDP interval, scale bar represents millions of years. Nodal values above branches indicate posterior probabilities/ bootstrap supports of BI/ML. Capital letters depict haplotypes. An asterisk (*) indicate birds representing yellow morphs B Median-joining haplotype network for the concatenated dataset. Each color depicts the geographic provenance of samples: green-northern Chiapas (subspecies albinucha), red-southern Chiapas (subspeciesgriseipectus), blue-El Salvador (subspecies griseipectus), yellow-Honduras (subspecies fuscipygius) and light blue-Colombia (subspecies gutturalis). Each branch represents a single nucleotide change, transversal black lines along branches depict the occurrence of three mutations. Gray dots indicate median vectors inferred for the data.
Figure 6 from: Liu L, Zhang X, Li C, Zhang H, Yanagimoto T, Song N, Gao T (2019) Population genetic structure of Marbled Rockfish, Sebastiscus marmoratus (Cuvier, 1829), in the northwestern Pacific Ocean. ZooKeys 830: 127-144. https://doi.org/10.3897/zookeys.830.30586
Figure 6 Bayesian skyline plot showing the effective female S.marmoratus population size through time. Black solid lines are median estimates of NeT (Ne=effective female population size; T=generation time); blue shading represents the 95% confidence interval of NeT. The y-axis was plotted on a logarithmic scale.
Figure 2 from: Liu L, Zhang X, Li C, Zhang H, Yanagimoto T, Song N, Gao T (2019) Population genetic structure of Marbled Rockfish, Sebastiscus marmoratus (Cuvier, 1829), in the northwestern Pacific Ocean. ZooKeys 830: 127-144. https://doi.org/10.3897/zookeys.830.30586
Figure 2 Phylogenetic tree of control region haplotypes constructed using neighbor-joining algorithms of S.marmoratus with S.schlegelii as outgroup.
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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.