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332 results for “Ecological niches”
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.
Supplementary material 2 from: Vázquez-López M, Morrone JJ, Ramírez-Barrera SM, López-López A, Robles-Bello SM, Hernández-Baños BE (2020) Multilocus, phenotypic, behavioral, and ecological niche analyses provide evidence for two species within Euphonia affinis (Aves, Fringillidae). ZooKeys 952: 129-157. https://doi.org/10.3897/zookeys.952.51785
Raw morphometric data and collection information
Supplementary material 1 from: Vázquez-López M, Morrone JJ, Ramírez-Barrera SM, López-López A, Robles-Bello SM, Hernández-Baños BE (2020) Multilocus, phenotypic, behavioral, and ecological niche analyses provide evidence for two species within Euphonia affinis (Aves, Fringillidae). ZooKeys 952: 129-157. https://doi.org/10.3897/zookeys.952.51785
Tables S1, S2, S3. Sampling, genbank sequences and sequences of primers
Figure 1 from: Vázquez-López M, Morrone JJ, Ramírez-Barrera SM, López-López A, Robles-Bello SM, Hernández-Baños BE (2020) Multilocus, phenotypic, behavioral, and ecological niche analyses provide evidence for two species within Euphonia affinis (Aves, Fringillidae). ZooKeys 952: 129-157. https://doi.org/10.3897/zookeys.952.51785
Figure 1 Geographic distribution and morphotypes of Euphonia affinis, sampling, phylogeny, and haplotype networks. A geographic distribution of E. affinis: in blue E. a. godmani, in yellow E. a. affinis, and in red E. a. olmecorum (Geographic distribution modified from NatureServe shapefile in ArcGIS, ArcMAP 10.2.2; Esri, Redlands, CA, USA). Tissue sampling locations are indicated by circles in the map. Plumage morphotypes of E. a. godmani (female and male) with white undertail coverts, and E. a. affinis (female and male) with yellow undertail coverts. The previously proposed subspecies E. a. olmecorum (not shown) is similar to E. a. affinis, but paler plumage in females and a purple-blue back in males have been reported. B haplotype networks obtained for the mitochondrial gene ND2 and the nuclear genes ODC, MUSK, GAPDH intron 11, and BRM intron 15. Samples from the western distribution, assigned as E. a. godmani, are shown in blue and from the eastern distribution, assigned as E. a. affinis are indicated in yellow, E. a. olmecorum in red. C bayesian Inference concatenated phylogeny of E. a. godmani (west) and E. a. affinis-E. a. olmecorum (eastern Mexico, Central America).
Figure 4 from: Vázquez-López M, Morrone JJ, Ramírez-Barrera SM, López-López A, Robles-Bello SM, Hernández-Baños BE (2020) Multilocus, phenotypic, behavioral, and ecological niche analyses provide evidence for two species within Euphonia affinis (Aves, Fringillidae). ZooKeys 952: 129-157. https://doi.org/10.3897/zookeys.952.51785
Figure 4 Vocalization analysis. Boxplot of note emission rate A and PCA of measured vocal characters B Calls differ between the two groups in temporal structure, but not in frequency or number of notes.
Figure 6 from: Vázquez-López M, Morrone JJ, Ramírez-Barrera SM, López-López A, Robles-Bello SM, Hernández-Baños BE (2020) Multilocus, phenotypic, behavioral, and ecological niche analyses provide evidence for two species within Euphonia affinis (Aves, Fringillidae). ZooKeys 952: 129-157. https://doi.org/10.3897/zookeys.952.51785
Figure 6 Equivalence and similarity tests in environmental space for E. a. affinis and E. a. godmani. A PCA of Ecological niche for of E. affinis lineages and the variables contribution to the analyses. The gray gradient indicates the density of the occurrences of the lineages, and the dashed and solid line indicates the 50% and 100% of the environmental background B graphical results of the equivalency tests comparing the two lineages. For both tests (equivalence and similarity) we only presented values for the D metrics. For all graphs the D observed values of the overlap niche analyses are present with the black diamond. The p value is showing in each graphic, all of them not significant for these analyses C graphical results of the similarity test comparing the two lineages in both directions (E. a. affinis vs. E. a. godmani and vice versa), ns = Not significant, p > 0.05.
Figure 5 from: Vázquez-López M, Morrone JJ, Ramírez-Barrera SM, López-López A, Robles-Bello SM, Hernández-Baños BE (2020) Multilocus, phenotypic, behavioral, and ecological niche analyses provide evidence for two species within Euphonia affinis (Aves, Fringillidae). ZooKeys 952: 129-157. https://doi.org/10.3897/zookeys.952.51785
Figure 5 Ecological niche modelling and its projection in the geographic areas for E. a. affinis (yellow) and E. a. godmani (blue). In all four panels (a-d), the contribution values of each environmental variable of ENM's is illustrated in the left and the projection of the Ecological niche conditions in the geographic distribution area is shown in the maps. a Ecological Niche projected in the current geographic distribution area of E. affinis and E. a. godmani. b ENM's projected into the geography for each lineage. c ENM of E. a. affinis and E. a. godmani projected in the Last Maximum Glacial ecological conditions. d ENM of E. a. affinis and E. a. godmani projected in the Last Inter Glacial ecological conditions.
Figure 3 from: Vázquez-López M, Morrone JJ, Ramírez-Barrera SM, López-López A, Robles-Bello SM, Hernández-Baños BE (2020) Multilocus, phenotypic, behavioral, and ecological niche analyses provide evidence for two species within Euphonia affinis (Aves, Fringillidae). ZooKeys 952: 129-157. https://doi.org/10.3897/zookeys.952.51785
Figure 3 Morphometric analyses results. A) Females boxplots and PCA for WC, TLE, and BD morphometric characters. B) Males boxplot and PCA for WC, TLE, and BD morphometric characters. C) Boxplot and PCA for TL, BL, and BW. WC, TLE, and BD characters were analyzed by separated sex, because the analyses indicated sexual dimorphism (see results and Table 3). Bill length (BL, from the upper base of the bill to the tip of the upper mandible), bill width (BW), bill depth (BD, from the upper mandible to the base of the bill at the distal edge of the nostrils), wing chord (WC, distance from the carpal joint the tip of the longest primary), tarsus length (TL), and tail length (TLE, distance from the uropygial gland to the tip of the longest rectrix).
Figure 2 from: Vázquez-López M, Morrone JJ, Ramírez-Barrera SM, López-López A, Robles-Bello SM, Hernández-Baños BE (2020) Multilocus, phenotypic, behavioral, and ecological niche analyses provide evidence for two species within Euphonia affinis (Aves, Fringillidae). ZooKeys 952: 129-157. https://doi.org/10.3897/zookeys.952.51785
Figure 2 Ultrametric phylogenetic tree obtained by BEAST using ND2, ODC, and GAPDH concatenated matrix. The rhombus node represents the calibration point 17.1104 My with a 95% HPD of (14.7743, 19.6278) (see methods), dark gray circle node represents the E. affinis origin and light gray circle node represents the break between E. a. godmani and E. a. affinis. Above the branch the diversification dates (My) and in brackets the 95% HPD. Below branch the number indicated the posterior probability. The green area corresponds to the period when lowland dry forests had a greater expansion in Western Mexico.
Ecological specialization and niche overlap of subterranean rodents inferred from DNA metabarcoding diet analysis
<p>Knowledge of how animal species use food resources available in the environment increases our understanding of ecological processes. However, obtaining this information using traditional methods is a hard task for species feeding on a large variety of food items in highly diverse environments. We amplified the DNA of plants for 306 scat and 40 soil samples, and applied an eDNA metabarcoding approach to investigate food preferences, degree of diet specialization and diet overlap of seven herbivore rodent species of the <i>Ctenomys</i> genus distributed in southern and midwestern Brazil.<b> </b>The metabarcoding approach revealed that species consume more than 60% of the plant families recovered in soil samples, indicating generalist feeding habits of ctenomyids. The Poaceae family was the most common food resource retrieved in scats of all species as well in soil samples. Niche overlap analysis indicated high overlap in the plant families and Molecular Operational Taxonomic Units consumed, mainly among the southern species.<b> </b>Interspecific difference in diet composition was influenced, among other factors, by the availability of resources in the environment. In addition, our results provide support for the hypothesis that the allopatric distributions of ctenomyids allow them to exploit the same range of resources when available, possibly because of the absence of interspecific competition.</p>
Intraspecific dietary variation in niche partitioning within a community of ecologically similar snakes
<p><span>Niche partitioning is an important mechanism for allowing ecologically similar species to coexist, contributing to biodiversity and the functioning of ecological communities. Species partition niches by taking advantage of environmental heterogeneity. However, niche partitioning and species coexistence investigations often do not include intraspecific variation or individual differences like sex and body size even though these factors can have important ecological consequences. Such intrapopulation factors can reduce the number of individuals among species that overlap in resource use and potentially facilitate coexistence. Using stable isotopes (δ<sup>13</sup>C and δ<sup>15</sup>N), we quantified dietary differences among three ecologically similar, sympatric watersnake species: <i>Nerodia erythrogaster</i>, <i>N. rhombifer </i>and <i>N. sipedon</i>. Additionally for each species, we determined intraspecific dietary patterns and determined how those within-species patterns may contribute to dietary niche partitioning among species. <i>Nerodia erythrogaster </i>fed more on terrestrial prey, while <i>N. rhombifer </i>fed at higher trophic levels. Females across species fed at higher trophic levels than did males, and isotopic variance differed between the sexes in <i>N. sipedon</i>. Larger watersnakes foraged at higher trophic levels and fed more on terrestrial prey. Each watersnake species had a distinct diet that overlapped to some degree with the other species' diets, but these diets varied both between sexes and among size groups within species. This inter- and intraspecific dietary variation can facilitate species coexistence by reducing the number of individuals from all species that use the same resources. Intraspecific variation can add important and nuanced layers to the evolution of species coexistence, and research on interspecific niche relationships needs to increasingly consider the effects of these intraspecific variations.</span></p>
Polygenic selection within a single generation leads to subtle divergence among ecological niches
<p>Selection on standing genetic variation may be effective enough to allow for adaptation to distinct niche environments within a single generation. Minor allele frequency changes at multiple, redundant loci of small effect can produce remarkable phenotypic shifts. Yet, demonstrating rapid adaptation via polygenic selection in the wild remains challenging. Here we harness natural replicate populations that experience similar selection pressures and harbor high within-, yet negligible among-population genetic variation. Such populations can be found among the teleost Fundulus heteroclitus which inhabits marine estuaries characterized by high environmental heterogeneity. We identify 10,861 single nucleotide polymorphisms in F. heteroclitus that belong to a single, panmictic population yet reside in environmentally distinct niches (one coastal basin and three replicate tidal ponds). By sampling at two time-points within a single generation we quantify both allele frequency change within as well as spatial divergence among niche subpopulations. We observe few individually significant allele frequency changes yet find that the number of moderate changes exceeds the neutral expectation by 10-100%. We find allele frequency changes to be significantly concordant in both direction and magnitude among all niche subpopulations, suggestive of parallel selection. In addition, within-generation allele frequency changes generate subtle but significant divergence among niches, indicative of local adaptation. Although we cannot distinguish between selection and genotype-dependent migration as drivers of within-generation allele frequency changes, the trait/s determining fitness and/or migration likelihood appear to be polygenic. In heterogeneous environments, polygenic selection and polygenic, genotype-dependent migration offer conceivable mechanisms for within-generation, local adaptation to distinct niches.</p>
Data from: High invasion potential of Hydrilla verticillata in the Americas predicted using ecological niche modeling combined with genetic data
Ecological niche modeling is an effective tool to characterize the spatial distribution of suitable areas for species, and it is especially useful for predicting the potential distribution of invasive species. The widespread submerged plant Hydrilla verticillata (hydrilla) has an obvious phylogeographical pattern: Four genetic lineages occupy distinct regions in native range, and only one lineage invades the Americas. Here, we aimed to evaluate climatic niche conservatism of hydrilla in North America at the intraspecific level and explore its invasion potential in the Americas by comparing climatic niches in a phylogenetic context. Niche shift was found in the invasion process of hydrilla in North America, which is probably mainly attributed to high levels of somatic mutation. Dramatic changes in range expansion in the Americas were predicted in the situation of all four genetic lineages invading the Americas or future climatic changes, especially in South America; this suggests that there is a high invasion potential of hydrilla in the Americas. Our findings provide useful information for the management of hydrilla in the Americas and give an example of exploring intraspecific climatic niche to better understand species invasion.
Data from: A unique ecological niche fosters hybridization of oak-tree and vineyard isolates of Saccharomyces cerevisiae.
Differential adaptation to distinct niches can restrict gene flow and promote population differentiation within a species. However, in some cases the distinction between niches can collapse, forming a hybrid niche with features of both environments. We previously reported that distinctions between vineyards and oak soil present an ecological barrier that restricts gene flow between lineages of Saccharomyces cerevisiae. Vineyard isolates are tolerant to stresses associated with grapes while North American oak strains are particularly tolerant to freeze-thaw cycles. Here, we report the isolation of Saccharomyces cerevisiae strains from Wisconsin cherry trees, which display features common to vineyards (e.g. high sugar concentrations) and frequent freeze-thaw cycles. Genome sequencing revealed that the isolated strains are highly heterozygous and represent recent hybrids of the oak x vineyard lineages. We found that the hybrid strains are phenotypically similar to vineyard strains for some traits, but are more similar to oak strains for other traits. The cherry strains were exceptionally good at growing in cherry juice, raising the possibility that they have adapted to this niche. We performed transcriptome profiling in cherry, oak, and vineyard strains and show that the cherry-tree hybrids display vineyard-like or oak-like expression, depending on the gene sets, and in some cases the expression patterns linked back to shared stress tolerances. Allele-specific expression in these natural hybrids suggested concerted cis-regulatory evolution at sets of functionally regulated genes. Our results raise the possibility that hybridization of the two lineages provides a genetic solution to the thriving in this unique niche.
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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.
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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.
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