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Figure 6 from: Ossowska E, Guzow-Krzemińska B, Kolanowska M, Szczepańska K, Kukwa M (2019) Morphology and secondary chemistry in species recognition of Parmelia omphalodes group – evidence from molecular data with notes on the ecological niche modelling and genetic variability of photobionts. MycoKeys 61: 39-74. https://doi.org/10.3897/mycokeys.61.38175
Figure 6 Association network between lichen mycobionts of P. omphalodes group (i.e. Parmelia discordans, P. omphalodes and P. pinnatifida) and photobiont OTUs. The line width is proportional to the number of specimens forming the association with the particular OTU. SUn1 and SUn2 represent unnamed lineages of Trebouxia belonging to clade S.
Figure 3 from: Ossowska E, Guzow-Krzemińska B, Kolanowska M, Szczepańska K, Kukwa M (2019) Morphology and secondary chemistry in species recognition of Parmelia omphalodes group – evidence from molecular data with notes on the ecological niche modelling and genetic variability of photobionts. MycoKeys 61: 39-74. https://doi.org/10.3897/mycokeys.61.38175
Figure 3 Haplotype network showing relationships between ITS rDNA sequences from Parmelia discordans and P. omphalodes. The names of species are followed with herbarium numbers of specimens or GenBank Accession Numbers. Mutational changes are presented as numbers in brackets near lines between haplotypes.
Supplementary material 2 from: Ossowska E, Guzow-Krzemińska B, Kolanowska M, Szczepańska K, Kukwa M (2019) Morphology and secondary chemistry in species recognition of Parmelia omphalodes group – evidence from molecular data with notes on the ecological niche modelling and genetic variability of photobionts. MycoKeys 61: 39-74. https://doi.org/10.3897/mycokeys.61.38175
: Data type: multimedia
Figure 2 from: Ossowska E, Guzow-Krzemińska B, Kolanowska M, Szczepańska K, Kukwa M (2019) Morphology and secondary chemistry in species recognition of Parmelia omphalodes group – evidence from molecular data with notes on the ecological niche modelling and genetic variability of photobionts. MycoKeys 61: 39-74. https://doi.org/10.3897/mycokeys.61.38175
Figure 2 Phylogenetic placement of Trebouxia photobionts from selected Parmelia spp., based on Bayesian analysis of the ITS rDNA dataset. Posterior probabilities and maximum likelihood bootstrap values are shown near the internal branches. Newly generated sequences are in bold, with collecting numbers preceding the species names. Representative Trebouxia OTUs, as described in Leavitt et al. (2015), were downloaded from Dryad database (Dryad Digital Repository, Leavitt et al. 2015). Clades with photobionts from Parmelia discordans, P. omphalodes and P. pinnatifida are highlighted.
Figure 5 from: Ossowska E, Guzow-Krzemińska B, Kolanowska M, Szczepańska K, Kukwa M (2019) Morphology and secondary chemistry in species recognition of Parmelia omphalodes group – evidence from molecular data with notes on the ecological niche modelling and genetic variability of photobionts. MycoKeys 61: 39-74. https://doi.org/10.3897/mycokeys.61.38175
Figure 5 AParmelia discordans, with marginal and laminal pseudocyphellae, laminal pseudocyphellae mostly not connected with marginal ones (S F-252494) BP. omphalodes, with marginal and laminal pseudocyphellae, laminal pseudocyphellae mostly not connected with marginal ones (S F-252845) CP. pinnatifida, with marginal pseudocyphellae (UGDA L-24298) DP. pinnatifida, with marginal and laminal pseudocyphellae, laminal pseudocyphellae starting predominantly from pseudocyphellae formed at the edge of lobes (S F-239397). Scale bars: 200 μm (A, B, D), 150 μm (C).
Figure 7 from: Ossowska E, Guzow-Krzemińska B, Kolanowska M, Szczepańska K, Kukwa M (2019) Morphology and secondary chemistry in species recognition of Parmelia omphalodes group – evidence from molecular data with notes on the ecological niche modelling and genetic variability of photobionts. MycoKeys 61: 39-74. https://doi.org/10.3897/mycokeys.61.38175
Figure 7 Distribution of suitable niches of P. discordans (A), P. omphalodes (B) and P. pinnatifida (C) in the Northern Hemisphere.
Figure 4 from: Ossowska E, Guzow-Krzemińska B, Kolanowska M, Szczepańska K, Kukwa M (2019) Morphology and secondary chemistry in species recognition of Parmelia omphalodes group – evidence from molecular data with notes on the ecological niche modelling and genetic variability of photobionts. MycoKeys 61: 39-74. https://doi.org/10.3897/mycokeys.61.38175
Figure 4 Localities of Parmelia discordans (red), P. omphalodes (blue) and P. pinnatifida (green) used in ENM analysis.
Figure 10 from: Ossowska E, Guzow-Krzemińska B, Kolanowska M, Szczepańska K, Kukwa M (2019) Morphology and secondary chemistry in species recognition of Parmelia omphalodes group – evidence from molecular data with notes on the ecological niche modelling and genetic variability of photobionts. MycoKeys 61: 39-74. https://doi.org/10.3897/mycokeys.61.38175
Figure 10 Principal components analysis (PCA) of P. discordans (red), P. omphalodes (blue) and P. pinnatifida (green), based on the bioclimatic factors from individuals.
Figure 1 from: Ossowska E, Guzow-Krzemińska B, Kolanowska M, Szczepańska K, Kukwa M (2019) Morphology and secondary chemistry in species recognition of Parmelia omphalodes group – evidence from molecular data with notes on the ecological niche modelling and genetic variability of photobionts. MycoKeys 61: 39-74. https://doi.org/10.3897/mycokeys.61.38175
Figure 1 Phylogenetic relationships of Parmelia discordans, P. omphalodes and P. pinnatifida, based on Bayesian analysis of the ITS rDNA dataset. Posterior probabilities and maximum likelihood bootstrap values are shown near the internal branches. Newly generated sequences are described with herbarium numbers following the species names. GenBank Accession numbers of sequences downloaded from GenBank follow the species names. Clades with Parmelia discordans, P. omphalodes and P. pinnatifida are highlighted.
Supplementary material 4 from: Ossowska E, Guzow-Krzemińska B, Kolanowska M, Szczepańska K, Kukwa M (2019) Morphology and secondary chemistry in species recognition of Parmelia omphalodes group – evidence from molecular data with notes on the ecological niche modelling and genetic variability of photobionts. MycoKeys 61: 39-74. https://doi.org/10.3897/mycokeys.61.38175
: Data type: multimedia
Figure 9 from: Ossowska E, Guzow-Krzemińska B, Kolanowska M, Szczepańska K, Kukwa M (2019) Morphology and secondary chemistry in species recognition of Parmelia omphalodes group – evidence from molecular data with notes on the ecological niche modelling and genetic variability of photobionts. MycoKeys 61: 39-74. https://doi.org/10.3897/mycokeys.61.38175
Figure 9 Distribution of suitable niches of P. discordans (A), P. omphalodes (B) and P. pinnatifida (C) in Eurasia.
Molecular ecological network analyses: An effective conservation tool for the assessment of biodiversity, trophic interactions, and community structure
<p>Global biodiversity is threatened by the anthropogenic restructuring of animal communities, which rewires species interaction networks in real-time as individuals are extirpated or introduced. Conservation science and adaptive ecosystem management demands more rapid, quantitative, and non-invasive technologies for robustly capturing changing biodiversity and quantifying species interactions. Here we develop molecular ecological network analyses (MENA) as an ecosystem assessment tool to address these needs. To construct the ecological network, we used environmental DNA from feces to identify the plant and mammal diet of two carnivores: puma (<i>Puma concolor</i>) and bobcat (<i>Lynx rufus</i>); two omnivores: coyote (<i>Canis latrans</i>) and gray fox (<i>Urocyon cinereoargenteus</i>); and two herbivores: black-tailed deer (<i>Odocoileus hemionus</i>) and black-tailed jackrabbit (<i>Lepus californicus)</i> in a well-studied Californian reserve<i>. </i>To evaluate MENA as a comprehensive biodiversity tool, we applied our framework to identify the structure of the network, patterns of trophic interactions, key species, and to assess its utility in capturing the biodiversity of the area. The high dietary taxonomic resolution enabled the assessment of species diversity, niche breadth and overlap. The network analysis revealed a dense ecological network with a high diversity of weakly connected species and a community that is highly modular and non-nested. The significant prevalence of tri-trophic chain and exploitative competition patterns indicates (i) the removal or reintroduction of a top predator would trigger a trophic cascade within this community, directly affecting their prey and indirectly the plant communities, and (ii) the potential impact of indirect effects between two predators that consume the same prey. These results suggest that the recent resurgence of puma in the study area may impact the herbaceous and woody vegetation and the population size of other predators. This effect of fluctuating predator populations and plant communities could be predicted through MENA's fine-scale assessment of the diet selection and the identified keystone species. Although just using a subset of species, MENA more rapidly, accurately, and effectively captured the broader biodiversity of the area in comparison to other methodologies. MENA reconstructed and unveiled the hidden complexity in trophic structure and interaction networks within the community, providing a promising toolkit for biodiversity and ecosystem management.</p>
Figure 9 from: Spiridonov VA, Simakova UV, Anosov SE, Zalota AK, Timofeev VA (2020) Review of Macropodia in the Black Sea supported by molecular barcoding data; with the redescription of the type material, observations on ecology and epibiosis of Macropodia czernjawskii (Brandt, 1880) and notes on other Atlanto-Mediterranean species of Macropodia Leach, 1814 (Crustacea, Decapoda, Inachidae). Zoosystematics and Evolution 96(2): 609-635. https://doi.org/10.3897/zse.96.48342
Figure 9 Morphometric relationships and fecundity characteristics of Macropodia czernjawskii. a. Relationships between carapace width (CW) and the geometric mean of chela length, height and thickness (ChGM). b. Relationships between CW and decimal logarithm of the number of developing eggs (I or II stage of development) on pleopods (F). For statistical data see Table 2.
Figure 7 from: Spiridonov VA, Simakova UV, Anosov SE, Zalota AK, Timofeev VA (2020) Review of Macropodia in the Black Sea supported by molecular barcoding data; with the redescription of the type material, observations on ecology and epibiosis of Macropodia czernjawskii (Brandt, 1880) and notes on other Atlanto-Mediterranean species of Macropodia Leach, 1814 (Crustacea, Decapoda, Inachidae). Zoosystematics and Evolution 96(2): 609-635. https://doi.org/10.3897/zse.96.48342
Figure 7 Macropodia czernjawskii. a. Right chela, male, CW 11.0 (ZMMU Ma 3547); b. Right chela, male. CW 6.0 mm (ZMMU Ma 3544) c. Malformed right chela, male, CW 8.0 mm (ZMMU Ma 3543); d, e. Same specimen as c. dactylus and propodus of P 5. Scale bars: 1 mm (a–c, e), 0.5 mm (d).
Figure 6 from: Spiridonov VA, Simakova UV, Anosov SE, Zalota AK, Timofeev VA (2020) Review of Macropodia in the Black Sea supported by molecular barcoding data; with the redescription of the type material, observations on ecology and epibiosis of Macropodia czernjawskii (Brandt, 1880) and notes on other Atlanto-Mediterranean species of Macropodia Leach, 1814 (Crustacea, Decapoda, Inachidae). Zoosystematics and Evolution 96(2): 609-635. https://doi.org/10.3897/zse.96.48342
Figure 6 Macropodia czernjawskii. a. Anterior part of the body with basal antennal segment (ZMMU Ma 3543); b. Anterior part of the body with basal antennal segments, male (ZMMU Ma 3547). c. Male pleon (ZMMU Ma 3547); d. Female sterno-pleonal cavity with exposed genital segment (ZMMU Ma 3538). Scale bar: 1 mm.
Figure 5 from: Spiridonov VA, Simakova UV, Anosov SE, Zalota AK, Timofeev VA (2020) Review of Macropodia in the Black Sea supported by molecular barcoding data; with the redescription of the type material, observations on ecology and epibiosis of Macropodia czernjawskii (Brandt, 1880) and notes on other Atlanto-Mediterranean species of Macropodia Leach, 1814 (Crustacea, Decapoda, Inachidae). Zoosystematics and Evolution 96(2): 609-635. https://doi.org/10.3897/zse.96.48342
Figure 5 Macropodia czernjawskii, photographs in natural coloration. a. male (ZMMU Ma 3547), dorsal view. b. Same specimen as a. ventral view. c. female ov (ZMMU Ma 3542), dorsal view. d. Same specimen as c. ventral view. Scale bar: 10 mm. Photographs by SE Anosov.
Figure 4 from: Spiridonov VA, Simakova UV, Anosov SE, Zalota AK, Timofeev VA (2020) Review of Macropodia in the Black Sea supported by molecular barcoding data; with the redescription of the type material, observations on ecology and epibiosis of Macropodia czernjawskii (Brandt, 1880) and notes on other Atlanto-Mediterranean species of Macropodia Leach, 1814 (Crustacea, Decapoda, Inachidae). Zoosystematics and Evolution 96(2): 609-635. https://doi.org/10.3897/zse.96.48342
Figure 4 Macropodia czernjawskii (a, b. possible paralectotype ZIN-RAS 1609; c, d.ZIN-RAS 35102) and Macropodia longirostris (JC Fabricius, 1775) (e.SMF 3752). a. Right cheliped, ventral view. b. Right cheliped, dorsal view. c. Cphalothorax, dorsal view. d. Cephalothorax, ventral view. e. Cephalothorax, dorsal view. Scale bar: 10 mm.
Figure 3 from: Spiridonov VA, Simakova UV, Anosov SE, Zalota AK, Timofeev VA (2020) Review of Macropodia in the Black Sea supported by molecular barcoding data; with the redescription of the type material, observations on ecology and epibiosis of Macropodia czernjawskii (Brandt, 1880) and notes on other Atlanto-Mediterranean species of Macropodia Leach, 1814 (Crustacea, Decapoda, Inachidae). Zoosystematics and Evolution 96(2): 609-635. https://doi.org/10.3897/zse.96.48342
Figure 3 Comparison of Macropodia czernjawskii (a–d. possible paralectotype, male, ZIN-RAS 88750) to Macropodia tenuirostris (Leach, 1814) (a'–d'. male, SMF 3749) and Macropodia rostrata (Linnaeus, 1761) (a''–d''.SMF 40660). a. Dorsal view. b. Lateral view. c. Anterior part of the body, with antennules, basal antennal segments, and epistome, ventral view. d. Dactylus of pereopod 5. Scale bars: 10 mm (a–a''–b–b''), 1 mm (c–c''–d–d'').
Figure 2 from: Spiridonov VA, Simakova UV, Anosov SE, Zalota AK, Timofeev VA (2020) Review of Macropodia in the Black Sea supported by molecular barcoding data; with the redescription of the type material, observations on ecology and epibiosis of Macropodia czernjawskii (Brandt, 1880) and notes on other Atlanto-Mediterranean species of Macropodia Leach, 1814 (Crustacea, Decapoda, Inachidae). Zoosystematics and Evolution 96(2): 609-635. https://doi.org/10.3897/zse.96.48342
Figure 2 Macropodia czernjawskii (Brandt, 1880), female lectotype (ZIN-RAS 88751). a. Dorsal view. b. Ventral view. c. Lateral view. Scale bar: 5 mm.
Figure 8 from: Spiridonov VA, Simakova UV, Anosov SE, Zalota AK, Timofeev VA (2020) Review of Macropodia in the Black Sea supported by molecular barcoding data; with the redescription of the type material, observations on ecology and epibiosis of Macropodia czernjawskii (Brandt, 1880) and notes on other Atlanto-Mediterranean species of Macropodia Leach, 1814 (Crustacea, Decapoda, Inachidae). Zoosystematics and Evolution 96(2): 609-635. https://doi.org/10.3897/zse.96.48342
Figure 8 Macropodia czernjawskii. Male (ZMMU Ma 3543), right gonopod . a. Pleonal view. b. Sternal view. Scale bar: 1 mm.
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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.