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230 results for “biogeographic patterns”
Data from: Biogeographic patterns of soil microbial biomass in alpine ecosystems depend on local rather than regional drivers
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Data for: Biogeographic pattern of living vegetation carbon turnover time in mature forests across continents
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Richness and resilience in the Pacific: DNA metabarcoding enables parallelized evaluation of biogeographic patterns
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Data from: The biogeographical patterns of species richness and abundance distribution in stream diatoms are driven by climate and water chemistry
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Holocene plant diversity dynamics shows a distinct biogeographical pattern in temperate Europe
<p>Data for manuscript "<strong>Holocene plant diversity dynamics shows a distinct biogeographical pattern in temperate Europe</strong>" by Roleček J., Abraham V., Vild O., Svitavská Svobodová H., Jamrichová E., Plesková Z., Pokorný P. & Kuneš P. </p> <p>Data originate from 18 sites in Czech and Slovak Republic. Original data and further metadata are stored in <a href="https://botany.natur.cuni.cz/palycz/">Czech Quaternary Palynological Database</a>. Data presented here were adjusted by following procedure:</p> <p>Pollen counts of trees were adjusted (divided) by <a href="https://doi.pangaea.de/10.1594/PANGAEA.908862">mean pollen productivity for North Hemisphere</a> :</p> <p>Abies 6.88<br> Alnus 7.46<br> Betula 4.4<br> Carpinus betulus 4.52<br> Corylus 1.97<br> Fagus 1.96<br> Fraxinus excelsior-Typ 1.25<br> Juniperus 9.8<br> Picea 2.29<br> Pinus 10.47<br> Quercus 3.33<br> Tilia 1.17<br> Ulmus 7.32</p> <p>and subsequently whole spectra were resampled for the same pollen sum (100 grains) in all depths and time windows (300 years).</p> <p>Resampling was done by function "spectra_to_target_sum" at <a href="https://github.com/vojtechabraham/pollen">https://github.com/vojtechabraham/pollen</a>.</p> <p>See repository <a href="https://github.com/vojtechabraham/HolDivTempEur">https://github.com/vojtechabraham/HolDivTempEur</a> for the analysis presented in the paper.</p>
Supplementary material 1 from: Martínez-Domínguez L, Nicolalde-Morejón F, Lorea-Hernández FG, Vergara-Silva F, Stevenson DWm (2020) A novelty in Ceratozamia (Zamiaceae, Cycadales) from the Sierra Madre del Sur, Mexico: biogeographic and morphological patterns, DNA barcoding and phenology. PhytoKeys 156: 1-25. https://doi.org/10.3897/phytokeys.156.53502
File S1. GenBank accession numbers of sequences used in the analyses for ITS and matK, respectively. Sequences were generated by this study are in bold.
Data from: Exploring patterns of beta-diversity to test the consistency of biogeographical boundaries: a case study across forest plant communities of Italy
Aim. To date, despite their great potential biogeographical regionalization models have been mostly developed on descriptive and empirical bases. This paper aims at applying the beta-diversity framework on a statistically representative data set to analytically test the consistency of the biogeographical regionalization of Italian forests. Location. Italy Taxon. Vascular plants Methods. Forest plant communities were surveyed in 804 plots made in a statistically representative sample of forest communities, made by 201 sites of Italian forests across the three biogeographical regions of the country: Alpine, Continental, and Mediterranean. We conducted an ordination analysis and an analysis of beta diversity, decomposing it into its turnover and nestedness components. Results. Our results provide only partial support to the consistency of the biogeographical regionalization of Italy. While the differences in forest plant communities support the distinction between the Alpine and the other two regions, differences between Continental and Mediterranean regions had lower statistical support. Pairwise beta-diversity and its turnover component are higher between- than within biogeographical regions. This suggests that different regional species pools contribute to assembly of local communities and that spatial distance between-regions has a stronger effect than that within-regions. Main conclusions. Our findings confirm a biogeographical structure of the species pools that is captured by the biogeographical regionalization. However, non-significant differences between the Mediterranean and Continental biogeographical regions suggest that this biogeographical regionalization is not consistent for forest plant communities. Our results demonstrate that an analytical evaluation of species composition differences among regions using beta-diversity analysis is a promising approach for testing the consistency of biogeographical regionalization models. This approach is recommended to provide support to the biogeographic regionalization used in some environmental conservation polices adopted by EU.
The preservation potential of terrestrial biogeographic patterns
<p>Extinction events in the geological past are similar to the present-day biodiversity crisis in that they have a pronounced biogeography, producing dramatic changes in the spatial distributions of species. Reconstructing paleobiogeographic patterns from fossils therefore allows us to examine the long-term processes governing the formation of regional biotas, and potentially helps build spatially-explicit models for future biodiversity loss in a potential '6<sup>th</sup> mass extinction' event. However, the extent to which biogeographic patterns can be preserved in the fossil record is not well understood. Here, we perform a suite of simulations based on the present-day distribution of North American mammals, aimed at quantifying the preservation potential of beta diversity and spatial richness patterns over extinction events of varying intensities, and after applying a stepped series of taphonomic filters. We show that taphonomic biases related to body size are the biggest barrier to reconstructing biogeographic patterns over extinction events, but that these may be compensated for by both the small-mammal record preserved in bird castings, as well as range-expansion in surviving species. Overall our results suggest that the preservation potential of biogeographic patterns is surprisingly high, and thus that the fossil record represents an invaluable dataset recording the changing spatial distribution of biota over key intervals in Earth History.</p>
FIGURE 5 in Freshwater fishes from Paraná State, Brazil: an annotated list, with comments on biogeographic patterns, threats, and future perspectives
FIGURE 5. Cumulative number of lots of fish collected by state (marine lots included). The dashed line represents the approximate collection year of the first lots deposited in the state's main freshwater fish collections, especially MZUEL and NUP. State abbreviations: PR, Paraná; SP, São Paulo; RS, Rio Grande do Sul; MS, Mato Grosso do Sul.
FIGURE 4 in Freshwater fishes from Paraná State, Brazil: an annotated list, with comments on biogeographic patterns, threats, and future perspectives
FIGURE 4. Cumulative descriptions of the native freshwater fish species from Paraná State (blue line), species occurring naturally in the Paraná State, but originally described from São Paulo State (SP; green line) and species originally described from Paraná State (PR; red line). 1 = early descriptions of species from the upper rio Iguaçu basin (Haseman, 1911); 2 = foundation of main freshwater fish collections from Paraná State, especially MZUEL and NUP.
FIGURE 3 in Freshwater fishes from Paraná State, Brazil: an annotated list, with comments on biogeographic patterns, threats, and future perspectives
FIGURE 3. Number of species in the richest families of each order of the freshwater ichthyofauna from Paraná State, Brazil. Colors indicate orders.
FIGURE 1 in Freshwater fishes from Paraná State, Brazil: an annotated list, with comments on biogeographic patterns, threats, and future perspectives
FIGURE 1. Partial map of South America, with the Brazilian states outlined in black (Paraná State filled with blue). A) Map of Paraná State highlighting the ecoregions and sub-ecoregions. B) Sampling localities used to compile the list of the Paraná State freshwater fish species (red points). Each red point can represent more than one sampling site. Green bar = Sete Quedas waterfalls (currently submerged under the Itaipu Reservoir); black bar = Itaipu dam; blue bar = Iguaçu waterfalls.
Data from: A molecular phylogeny for the genus Coccoloba (Polygonaceae) with an assessment of biogeographic patterns
<p>Species in the genus <i>Coccoloba</i> are trees, shrubs, and lianas present in low elevation tropical and sub-tropical forests. Since 1756, well over 400 taxa have been described for <i>Coccoloba</i>. <i>Coccoloba</i> species are natively distributed throughout the New World in a variety of habitats. Despite being distributed throughout the Neotropics, the concentration of <i>Coccoloba</i> species in a given area varies considerably, with four centers of diversity for the genus: Southern and Coastal Brazil, the West Indies, Mesoamerica, and Amazonia. We here present the first molecular phylogeny of <i>Coccoloba</i> and use this phylogeny to investigate geographic patterns of diversity within the genus. The topology of the phylogeny and the closest related genera to <i>Coccoloba</i> suggest a Mesoamerican origin for the genus. The South American species are recovered as the crown group of the phylogeny with one instance of a separate migration event from Mesoamerica to South America. <i>Coccoloba</i> species in Mesoamerica and the Caribbean show little to no geographic pattern to their diversification. Mesoamerica and the Caribbean are best considered as one phytogeographic region for <i>Coccoloba</i>.</p>
Data from: Contrasting microbial biogeographical patterns between anthropogenic subalpine grasslands and natural alpine grasslands
The effect of plant species composition on soil microbial communities was studied at the multiregional level. We compared the soil microbial communities of alpine natural grasslands dominated by Carex curvula and anthropogenic subalpine pastures dominated by Nardus stricta. We conducted paired sampling across the Carpathians and the Alps and used Illumina sequencing to reveal the molecular diversity of soil microbes. We found that bacterial and fungal communities exhibited contrasting regional distributions and that the distribution in each grassland is well discriminated. Beta diversity of microbial communities was much higher in C. curvula grasslands due to a marked regional effect. The composition of grassland-type core microbiomes suggest that C. curvula, and N. stricta to a lesser extent, tend to select a cohort of microbes related to antibiosis/exclusion, pathogenesis and endophytism. We discuss these findings in light of the postglacial history of the studied grasslands, the habitat connectivity and the disturbance regimes. Human-induced disturbance in the subalpine belt of European mountains has led to homogeneous soil microbial communities at large biogeographical scales. Our results confirm the overarching role of the dominant grassland plant species in the distribution of microbial communities and highlight the relevance of biogeographical history.
Data from: Genome-wide markers untangle the green-lizard radiation in the Aegean Sea and support a rare biogeographical pattern
Aim: The Aegean Sea constitutes a major biogeographic barrier between the European and Asian continents and several models of diversification in the Aegean have been documented. Here we test three of those models for the Aegean green-lizards (Lacerta trilineata–pamphylica group): Vicariance vs. Overland Dispersal vs. Island Stepping-stone Dispersal. We investigate these hypotheses and complement our knowledge on the impact of the Aegean Barrier on east Mediterranean taxa. Location: Aegean Sea, east Mediterranean Taxon: Lacerta lizards Methods: We analysed ddRAD loci (double-digest restriction-site-associated DNA) to estimate species-trees under coalescent models and maximum likelihood trees using concatenation. We performed hierarchical population structure analyses and inferred ancestral distribution-areas. We also sequenced the complete cytochrome b gene and produced a time-calibrated mtDNA gene-tree tree to conduct a critical comparison with previous studies. Results: Aegean green-lizards diverged into four main groups in parallel during the Late Pliocene with distributions to the East and West of the Aegean. The Eastern group includes Lacerta pamphylica and East Aegean L. trilineata, while the Western group contains the Central Cyclades populations and the remaining populations of the Balkan Peninsula. The Aegean green-lizards' ancestor occurred in Anatolia, while the West lineage ancestor occurred in the Central Cyclades islands, revealing a dispersal between the two regions. The radiations of all major green-lizard groups, including trilineata+pamphylica, occurred in parallel in the Late Pliocene. Main Conclusions: In contrast to previously suggested biogeographical hypotheses for the group, based on mtDNA, the Island Stepping-stone Dispersal scenario is strongly supported. Green lizards offer a rare paradigm of diversification in the Aegean, where populations largely expanded their geographical distribution and crossed the Aegean Barrier by using the central Aegean islands as stepping stones.
Data from: The world's biogeographical regions revisited: global patterns of endemism in Tipulidae (Diptera)
This paper explores the distributional data of 4,224 Tipulidae (Insecta: Diptera) species to search for endemism patterns in a worldwide scale and to test the extent to which the global patterns of endemism of the group fit into previously proposed regionalization schemes, particularly Wallace's system and recent revisions of it. Large scale areas of endemism are assessed using the grid-based method implemented in VNDM. VNDM depends on the prior definition of the grid size for analysis, but a criterion for choosing beforehand a particular grid size is not clear. The same holds for the choice of the level of similarity in species composition selected for the calculation of consensus areas. In our study, we developed a methodological approach that helped defining objective criteria for choosing suitable values for these critical variables. Large-scale areas of endemism around the globe are identified and ranked according to endemicity levels: 1—West Palaearctic, 2—Nearctic, 3—East Palaearctic-Oriental, 4—West North America, 5—Australia, 6—Neotropical, 7—Sub-Saharan Africa, 8—Palaearctic, and 9—Middle East. Our main conclusion is that there are still some limitations in applying biogeographical classifications proposed mostly on the basis of vertebrate distribution to other taxonomic groups, such as the Tipulidae. While there is a general congruence of the broad-scale areas of endemism of tipulids with previously proposed regionalization schemes, for some areas, the sharpness of boundaries between traditional regions is not so acute, due to a great level of overlap of part of its biotic elements.
Data from: Crossing the uncrossable: novel trans-valley biogeographic patterns revealed in the genetic history of low dispersal mygalomorph spiders (Antrodiaetidae, Antrodiaetus) from California
Antrodiaetus riversi is a dispersal-limited, habitat specialized mygalomorph spider species endemic to mesic woodlands of northern and central California. Here we build upon prior phylogeographic research using a much larger geographic sample and include additional nuclear genes, providing more detailed biogeographic insights throughout the range of this complex. Of particular interest is the uncovering of unexpected and replicated trans-valley biogeographic patterns, where in two separate genetic clades western haplotypes in the California south Coast Ranges are phylogenetically closely-related to eastern haplotypes from central and northern Sierran foothills. In both instances, these trans-valley phylogenetic patterns are strongly supported by multiple genes. These western and eastern populations are currently separated by the Central Valley, a well-recognized modern-day and historical biogeographic barrier in California. For one clade the directionality is clearly northeast to southwest, and all available evidence is consistent with a jump dispersal event estimated at 1.2-1.3 million years ago. During this time period, paleogeographic data indicate that northern Sierran rivers emptied to the ocean in the south Coast Ranges, rather than at the San Francisco Bay. For the other trans-valley clade genetic evidence is less conclusive regarding the mechanism and directionality of biogeographic exchange, although the estimated timeframe is similar (approximately 1.8 Ma). Despite the large number of biogeographic studies previously conducted in central California, to the best of our knowledge no prior studies have discussed or revealed a northern Sierran to south Coast Range biogeographic connection. This uniqueness may reflect the low-dispersal biology of mygalomorph spiders, where "post-event" gene exchange rarely erases historical biogeographic signal.
FIGURES 18, 19 & 20. Hermippus spp., Female opisthosoma showing the characteristic dorsal pattern. 18 H in On the genus Hermippus Simon, 1893 (Araneae: Zodariidae, Zodariinae) in India with the description of three new species from the Western Ghats and proposing a new biogeographical hypothesis for the distribution of the genus
FIGURES 18, 19 & 20. Hermippus spp., Female opisthosoma showing the characteristic dorsal pattern. 18 H. globosus sp. nov. 19 H. inflexus sp. nov. 20 H. gavi sp. nov. Scale bars: 18, 0.47 mm; 19, 0.48 mm; 20, 0.53 mm.
FIGURE 11 in The Eastern Arc Mountains and coastal forests of East Africa—an archive to understand large-scale biogeographical patterns: Pseudotomias, a new genus of African Pseudophyllinae (Orthoptera: Tettigoniidae)
FIGURE 11. Distribution of Pseudotomias species in Tanzania. Square: P. kisarawe n. sp. Circle: P. usambaricus n. sp.
FIGURE 10 in The Eastern Arc Mountains and coastal forests of East Africa—an archive to understand large-scale biogeographical patterns: Pseudotomias, a new genus of African Pseudophyllinae (Orthoptera: Tettigoniidae)
FIGURE 10. Morphological details of female Pseudotomias kisarawe n. sp. A. Lateral view on ovipositor B. Subgenital plate.
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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.