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APPENDIX 12 in Detangling the effects of patch attributes on bryophyte diversity in fragmented subtropical secondary forests - a case study of land-bridge islands
APPENDIX 12. — Relationships of accumulative species number with accumulative sampling efforts for eight largest islands.
FIG. 2 in Detangling the effects of patch attributes on bryophyte diversity in fragmented subtropical secondary forests - a case study of land-bridge islands
FIG. 2. — Relationships of species richness with number of habitat types, area, elevation, shape irregularity, vegetative cover, and ISW for five bryophyte categories in 168 forest fragments of the Thousand Island Lake, China. The regression equations are derived from GLMMs. Note: ISW, the relative proportion of water within a circle of a diameter of 1000 m centered on a given island.
Data from: "Fragmentation and detachment of hot copper and silver dimer anions: a comparison"
<p>The files found here are text files with data related to the article: "Fragmentation and detachment of hot copper and silver dimer anions: a comparison" published in Phys Rev A (DOI: 10.1103/PhysRevA.107.062824). The files contain the information necessary to reproduce all figures containing data from the experiment or from the described calculations. Each file contains a header explaining the data sets which follow.</p>
Breeding season forest fragment size does not create negative carry-over for adult Wood Thrushes on fall migration timing or apparent annual survival
<p>Although carry-over effects related to wintering habitat quality are known to influence population dynamics of migratory songbirds, the presence of breeding season carry-over is under-studied in full annual cycle models. To test whether forest fragment size on the breeding grounds can impose negative carry-over effects on a migratory songbird, we fitted adult Wood Thrushes with one-year coded radio-tags in forest fragments ranging from 11–499 ha in southwestern Ontario during the 2016–2019 breeding seasons and utilized automated telemetry via the Motus Wildlife Tracking System to record fall migration timing and returns the following spring (apparent annual survival). To examine short-term effects of fragment size on breeding females, during the 2018 and 2019 breeding seasons, we collected blood samples during incubation to measure corticosterone levels and tracked complete reproductive success and nest timing. We found that Wood Thrushes breeding in small forest fragments were not subject to strong negative effects on body condition (mass, corticosterone), reproductive success, or timing of the last nest of the season. Next, we found that the onset of fall migration departure was not delayed for birds nesting in small fragments and that apparent annual survival was not linked to breeding fragment size. This suggests that habitat differences linked to fragment size were not strong enough to trigger the kinds of negative carry-over effects (delayed migration, lower reproductive success) that have been documented in other species as a result of poor wintering ground habitat quality. The strength of breeding fragment size-induced seasonal carry-over remains a critical gap in full annual cycle models for other declining migratory songbirds. Our findings suggest that while the importance of preserving large forested areas is often prioritized in conservation projects, small forest fragments can also have high conservation value.</p>
Methods to pick up overlapping small fragment pairs from two libraries
<p>PIWI-interacting (pi)RNA pathways control transposable elements (TEs) and endogenous genes, playing important roles in animal gamete formation. However, the underlying piRNA biogenesis mechanisms remain elusive. Here, we show endogenous protein-coding sequences (CDSs), that are normally used for translation, serve as origins of non-coding piRNA biogenesis in<em> Drosophila melanogaster</em> testes. The product, namely CDS-piRNAs, formed silencing complexes with Aubergine (Aub) in germ cells. Proximity proteome and functional analyses show CDS-piRNAs and cluster/TE-piRNAs are distinct species occupying Aub, the former loading selectively relies on chaperone Cyclophilin 40. Moreover, Argonaute-2 (Ago2) and Dicer-2 activities were found critical for CDS-piRNA production. We provide evidence that Ago2-bound short interfering (si)RNAs and micro(mi)RNAs specify precursors to be processed into piRNAs. We further demonstrate that Aub is crucial in spermatid differentiation, regulating chromatins through mRNA cleavage. Collectively, our data illustrate a unique strategy employed by male germline, expanding piRNA repertoire for silencing of endogenous genes during spermatogenesis.</p>
Experimental data for "Fragmentation of ice particles: laboratory experiments on graupel-graupel and graupel-snowflake collisions"
<p>Graupel-graupel and graupel-snowflake collisions<br> experiments were carried out in still air conditions in the cold room of the Wind tunnel laboratory of the<br> Johannes Gutenberg University, Mainz. Graupel particles were first exposed to supersaturated air conditions, under which dendritic ice crystals have grown on their surface.<br> All fragments resulting from graupel-graupel collisions were<br> collected and investigated under a digital microscope. Fragments resulting from graupel-snowflake collisions were observed and recorded instantly after collision using a<br> holographic instrument. Number, size, area, and aspect ratio distributions of fragments were derived. </p> <p>These files contain data collected during the graupel-graupel and graupel-snowflake collisions. These data served for generating the figures in the publication.</p> <p>The files Graupel_graupel_number_CKE_mass_size.csv and Graupel_snowflake_CKE_mass_size give information on the experimental properties of the graupel-graupel and graupel-snowflake collisions, respectively.<br> For these two files, the first column gives the name of the experiment (e.g. snow1). Each line is corresponding to one collision experiment.</p> <p>The concrete data for each collision experiment is provided in the data file having the corresponding name, e.g., snow_data1.csv contains the data of collision experiment snow1, etc.</p> <p>Readme_graupel_data.txt and Readme_snow_data.txt contain collision kinetic energies of graupel-graupel and graupel-snowflake collisions, respectively.</p> <p>Graupel_crystal_surface.csv gives the estimated number of crystal for defined bins (Fig. 12 dashed line) on the surface of the 2 mm graupel before the collision.</p> <p> </p>
Demography of the understory herb Heliconia acuminata (Heliconiaceae) in an experimentally fragmented tropical landscape
<p>Habitat fragmentation remains a major focus of research by ecologists decades after being put forward as a threat to the integrity of ecosystems. While studies have documented myriad biotic changes in fragmented landscapes, including the local extinction of species from fragments, the demographic mechanisms underlying these extinctions are rarely known. However, many of them – especially in lowland tropical forests – are thought to be driven by one of two mechanisms: (1) reduced recruitment in fragments resulting from changes in the diversity or abundance of pollinators and seed dispersers or (2) increased rates of individual mortality in fragments due to dramatically altered abiotic conditions, especially near fragment edges. Unfortunately, there have been few tests of these potential mechanisms due to the paucity of long-term and comprehensive demographic data collected in both forest fragments and continuous forest sites. Here we report 11 years (1998-2009) of demographic data from populations of the Amazonian understory herb Heliconia acuminata (LC Rich.) found at Brazil's Biological Dynamics of Forest Fragments Project (BDFFP). The resulting data set comprises >66000 plant×year records of 8586 plants, including 3464 seedlings that became established after the initial census. Seven populations were in experimentally isolated fragments (one in each of four 1-ha fragments and one in each of three 10-ha fragments), with the remaining six populations in continuous forest. Each population was in a 50×100m permanent plot, with the distance between plots ranging from 500 m-60 km. The plants in each plot were censused annually, at which time we recorded, identified, marked, and measured new seedlings, identified any previously marked plants that died, and recorded the size of surviving individuals. Each plot was also surveyed 4-5 times during the flowering season to identify reproductive plants and record the number of inflorescences each produced. These data have been used to investigate topics ranging from the way fragmentation-related reductions in germination influence population dynamics to statistical methods for analyzing reproductive rates. This breadth of prior use reflects the value of these data to future researchers. In addition to analyses of plant responses to habitat fragmentation, these data can be used to address fundamental questions in plant demography, the evolutionary ecology of tropical plants, and for developing and testing demographic models and tools. Though we welcome opportunities to collaborate with interested users, there are no restrictions on the use this data set. However, we do request that those using the data for teaching or research inform us of how they are doing so and cite this paper and the data archive when appropriate. Any publication using the data must also include a BDFFP Technical Series Number in the Acknowledgments. Authors can request this series number upon the acceptance of their article by contacting the BDFFP's Scientific Coordinator or E. M. Bruna.</p>
Capacity for recovery in Bornean orangutan populations if both forest fragmentation and offtake are limited
<p>Spatial layers to run RangeShifter for orangutan populations across Borneo for the three subspecies (<em>Pongo pygmaeus pygmaeus, P. p. wurmbii </em>and <em>P. p. morio</em>).</p> <p>Each subspecies has four associated layers, defined for two fragmentation scenarios Status quo (current levels of fragmentation) and Extreme fragmentation (fragments less than 5,000 ha removed). 1). Habitat, defines the 1/b values for populations intersecting the specific habitat types. 2). Patches, delineates discrete areas of suitable orangutan habitat, each with a unique ID. 3). Resistance, accumulative cost to an orangutan of moving across that landscape and 4). Start_patches, specifies which patches should be initialised with orangutans present at year 0 of the model run. </p>
Frugivore-mediated seed dispersal in fragmented landscapes: Compositional and functional turnover from forest to matrix
<p>Seed dispersal by frugivores is a fundamental function for plant community dynamics in fragmented landscapes, where forest remnants are typically embedded in a matrix of anthropogenic habitats. Frugivores can mediate both connectivity among forest remnants and plant colonization of the matrix. However, it remains poorly understood how frugivore communities change from forest to matrix due to the loss or replacement of species with traits that are less advantageous in open habitats, and whether such changes ultimately influence the composition and traits of dispersed plants via species interactions. Here, we close this gap by using a unique dataset of seed-dispersal networks that were sampled in forest patches and adjacent matrix habitats of seven fragmented landscapes across Europe. We found a similar diversity of frugivores, plants and interactions contributing to seed dispersal in forest and matrix, but a high turnover (replacement) in all these components. The turnover of dispersed seeds was smaller than that of frugivore communities because different frugivore species provided complementary seed dispersal in forest and matrix. Importantly, the turnover involved functional changes towards larger and more mobile frugivores in the matrix, which dispersed taller, larger-seeded plants with later fruiting periods. Our study provides a trait-based understanding of frugivore-mediated seed dispersal through fragmented landscapes, uncovering non-random shifts that can have cascading consequences for the composition of regenerating plant communities. Our findings also highlight the importance of forest remnants and frugivore faunas for ecosystem resilience, demonstrating a high potential for passive forest restoration of unmanaged lands in the matrix.</p>
Natal forest fragment size does not predict fledgling, pre-migration, or apparent annual survival in Wood Thrushes
<p>Determining the drivers and mechanisms for first-year survival of migratory songbirds has been an understudied area in population dynamics due to the difficulty in tracking juveniles once they have dispersed from the natal site. With the advancement in miniaturization of radio-tags (battery life ~400 days) and the development of the Motus Wildlife Tracking System, we tracked 189 Wood Thrush nestlings through independence and to fall migration departure, and their return the following spring. Natal forest fragment size was not a good predictor of survival at any of the main life stages and onset of fall migration was predicted by fledge date but not natal fragment size. The percent forest cover in the landscape (at 2-km scale) had only a weak effect on fledgling survival. Survival probability was lowest for fledglings on their natal territory (70%, or 0.86 weekly survival probability), very high for juveniles as they explored the local landscape prior to fall migration (89%, or 0.99 weekly survival probability) and low during their first migration and wintering season (26%, or 0.95 weekly survival probability). To our knowledge, this is the first study to directly estimate annual apparent juvenile survival in a migratory songbird using year-round radio-tracking. Our study suggests that small forest fragments are important for the conservation for forest songbirds because they can support high survival of juveniles. </p>
Transliterated Fragments of the Electronic Babylonian Literature Project (eBL)
<pre>Data from Paper "Transliterated Fragments of the Electronic Babylonian Literature Project (eBL, https://www.ebl.lmu.de/)</pre> <p>Use together with code https://github.com/ElectronicBabylonianLiterature/tansliterated-fragments</p>
Fig. 2. Ornithocheiroidea indet. PIN 5028−3, left humerus distal end. Melovatka 3 in Two bone fragments of ornithocheiroid pterosaurs from the Cenomanian of Volgograd Region, southern Russia
Fig. 2. Ornithocheiroidea indet. PIN 5028−3, left humerus distal end. Melovatka 3, Volgograd Region, Russia; Upper Cretaceous, upper Cenomanian; in anterior (A), dorsal (B), posterior (C), ventral (D), and distal (E) views. D1 and E1 are stereo−photographs with explanatory drawings (D2, E2). The oval opening seen in right upper corner of the stereo−photograph in Fig. D1 is a postmortem bone breakage and therefore it is not shown in explanatory drawing.
Fig. 3. Ornithocheiroidea indet. PIN 5028−1, left femur distal end. Melovatka 3 in Two bone fragments of ornithocheiroid pterosaurs from the Cenomanian of Volgograd Region, southern Russia
Fig. 3. Ornithocheiroidea indet. PIN 5028−1, left femur distal end. Melovatka 3, Volgograd Region, Russia; Upper Cretaceous, upper Cenomanian. Cross−section of the diaphysis (A), medial view (B), anterior view (C), lateral view (D), posterior view (E), and distal view (F). F1 is a stereo−photograph with explanatory drawing (F2).
Data and code for: Plastic and quantitative genetic divergence mirror environmental gradients among wild, fragmented populations of Impatiens capensis
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Frugivore-mediated seed dispersal in fragmented landscapes: Compositional and functional turnover from forest to matrix
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Suturing fragmented landscapes: Mosaic hybrid zones in plants may facilitate landscape restoration
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Data from: Genetic effects of anthropogenic habitat fragmentation on remnant animal and plant populations: a meta-analysis
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Data from: Individual energetics scale up to community coexistence: Movement, metabolism and biodiversity dynamics in fragmented landscapes
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Data and code from: The continuity-contiguity problem in fragmentation-biodiversity research
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Data from: A shift to metapopulation genetic management for persistence of a species threatened by fragmentation: the case of an endangered Australian freshwater fish
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