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Figure 3 in The effects of forest fragmentation on the population ecology and natural history of a funnel-web spider
Figure 3. Simple linear regressions between the sheet area of the web and the cephalothorax length of Aglaoctenus lagotis individuals in two vegetation fragments (JKW: John Kennedy Woodland; PCC: Pica-Pau Country Club) in Araguari, Minas Gerais, Brazil. The correlation is positive for both sites (p <0.0001).
Figure 1 in The effects of forest fragmentation on the population ecology and natural history of a funnel-web spider
Figure 1. Map of the municipality of Araguari, Minas Gerais, Brazil. 1. The John Kennedy Woodland (JKW; 18°38′35″ S, 48°11′19″ W). 2. The Permanent Preservation Area of the Pica- Pau Country Club (PCC; 18°36′38″ S, 48°11′17″ W).
Figure 2 in The effects of forest fragmentation on the population ecology and natural history of a funnel-web spider
Figure 2. Schematic diagram of the methodology used to measure the volume of the capture web of Aglaoctenus lagotis. See the text for details of the calculation.
Dataset for Capturing roaming molecular fragments in real-time
<p>experimental data (ion and electron)</p> <p>quasi-classical trajectory data</p> <p>potential energies and gradients of triply charged state</p>
Fragmentation and translocation distort the genetic landscape of ungulates: red deer in the Netherlands
<p>Many ungulate populations have a complex history of isolation and translocation. Consequently, ungulate populations may have experienced substantial reductions in the level of overall gene flow, yet simultaneously have augmented levels of long distance gene flow. To investigate the effect of this dual anthropogenic effect on the genetic landscape of ungulates, we genotyped 35K SNPs in 47 red deer (Cervus elaphus) of Netherlands, including putative autochthonous relic populations as well as allochthonous populations established in private estates and rewilding areas. We applied FST and ordination analyses to determine the meta-population genetic structure and thereby the occurrence of hybridization. At population level, we investigated levels of inbreeding through individual-based diversity measures, including Runs of Homozygosity. We documented that both spatial genetic structure and within-population genetic variation differed markedly from patterns assumed from present-day abundance and distribution. Notwithstanding the small spatial scale, red deer populations formed distinct genetic clusters, and some had higher genetic similarity to distant than to nearby populations. Moreover, the putative autochthonous relic deer populations had much reduced levels of polymorphism and multi-locus heterozygosity, despite relatively large current population sizes. Accordingly, genomes of these deer contained a high proportion of long (>5 Mb) Runs of Homozygosity. Whereas the observed high levels of inbreeding warrant defragmentation measures, the presence of adjacent autochthonous and allochthonous genetic stocks imply that facilitation of gene flow would cause genetic homogenization. Such distortions of the genetic landscape of ungulates creates management dilemmas that cannot be properly anticipated without baseline genetic monitoring.</p>
Using multiple seedlots in restoration planting enhances genetic diversity compared to natural regeneration in fragmented tropical forests
<p>Catastrophic degradation of forests is ongoing worldwide and leads to severe forest fragmentation. Restoration plantings are often necessary to restore fragmented forests, complementing the limited natural regeneration. High genetic diversity is critical for the long-term viability of restored forests. However, there is limited knowledge of whether planted populations capture a genetic variation comparable to natural populations. We measured the efficiency of two forest restoration strategies using the common tropical oak <em>Quercus bambusifolia</em>. The multi-seedlot planting was established over ten years by collecting seeds from several locations in fragmented secondary forests of Hong Kong, while the single seedlot planting was established in just one year with seeds from a single natural location. We analysed the genetic diversity and genetic structure from both plantings and compared them with natural populations. The multi-seedlot planting exhibited a higher rate of genetic recovery, greater genetic diversity (He = 0.69), and higher effective population size (Ne_p = 86.5) compared to natural populations (He = 0.66, Ne_p = 64.3, on average) and the single seedlot planting (He = 0.50, Ne_p = 30.8). The multi-seedlot planting erased the effect of seed shadows which was detected in natural populations while the single seedlot planting strengthened the effect. We conclude that capturing high levels of genetic diversity in the collection of propagules is a standard requirement to ensure the long-term viability of forest restoration. Propagule collection over multiple years is required when only a few parental trees are available to avoid founder effects.</p>
Habitat fragmentation shapes natal dispersal and sociality in an Afrotropical cooperative breeder
<p>It remains poorly understood how effects of anthropogenic activity, such as large-scale habitat fragmentation, impact sociality in animals. In cooperatively breeding species, groups are mostly formed through delayed offspring dispersal, and habitat fragmentation can affect this process in two opposite directions. Increased habitat isolation may increase dispersal costs, promoting delayed dispersal. Alternatively, reduced patch size and quality may decrease benefits of philopatry, promoting dispersal. Here, we test both predictions in a cooperatively breeding bird (placid greenbul, Phyllastrephus placidus) from an Afrotropical cloud forest archipelago. Males born in fragmented forest dispersed about one year earlier than those born in continuous forest. Contrary to females, males also started to reproduce earlier and mostly settled within their natal patch. Females only rarely delayed their dispersal for more than one year, both in fragmented and continuous forests. Our results suggest that early male dispersal and reproduction is jointly driven by a decrease in the value of the natal territory and an increase in local breeding opportunities in fragmented forest. While plasticity in dispersal strategies of cooperative breeders in response to anthropogenic change is believed to optimize reproduction-survival trade-offs, to what extent it shapes the ability of species to respond to rapid environmental change remains to be studied.</p>
Data Set "Systematic partitioning of proteins for quantum-chemical fragmentation methods using graph algorithms"
<p>Data set accompanying the publication "Systematic partitioning of proteins for quantum-chemical fragmentation methods using graph algorithms"</p> <p>The data set contains:</p> <p>- Input script for PyADF (v0.97) for calculating (a) all two body terms to use as graph weights and (b) fragmentation error for all k and nmax (aspf)</p> <p>- PDB files of proteins and the "regions of interest" (RoI) used in this work.</p> <p>- Raw data: protein graph representations, resulting partitions, data underlying all figures shown in our article.</p> <p>- Jupiter notebook to create all figures shown in the article and in the supporting information from data in the results folder.</p> <p>- Images of protein structures and graph representations of ubiquitin.</p>
Figures 1-3 from: Ribeiro PVA, Baesse CQ, Cury MC, de Melo C (2020) Leukocyte profile of the helmeted manakin, Antilophia galeata (Passeriformes: Pipridae) in a Cerrado forest fragment. Zoologia 37: 1-9. https://doi.org/10.3897/zoologia.37.e46441
Figures 1-3 Number of lymphocytes for Antilophia galeata in relation to sex (1), presence/absence of incubation patch (2) and presence/absence of ticks (3). Boxes represent mean values while bars represent the standard error.
Data from: Rapid assessment of conformational preferences in biaryl and aryl carbonyl fragments
The ability to rapidly assess the preferred conformation of key fragments in a structure "by visual inspection" is a very useful starting point in the process of drug design. With the ability to do so, one could address questions like: "How could we avoid planarity in a molecule?", "Will a molecule change its conformational preference if we make it more or less basic?" or "How does this electronic repulsion affect the conformational preference in the system?" in timely fashion. In this paper, we describe how the conformational energy profile (CEP, plot of energy as a function of dihedral bond angle) of a fragment can be interpreted through the understanding the interplay between resonance stabilization, steric effects and electrostatic interactions. Fifty-nine biaryl and aryl carbonyl fragments present in oral drugs or which are close derivatives thereof were selected. Calculation of their CEPs using ab initio methodology allowed us to conclude the relative importance of these factors in the conformational preference of these fragments as follows: steric repulsion > lone pair - lone pair repulsion > lone pair - fluorine repulsion > resonance stabilization and, to formulate "rules of thumb" that the practicing medicinal/organic chemist can apply when analysing molecules that contain these fragments.
Data from: Spatial and temporal genetic structure at the fourth trophic level in a fragmented landscape
A fragmented habitat becomes increasingly fragmented for species at higher trophic levels, such as parasitoids. To persist, these species are expected to possess life-history traits, such as high dispersal, that facilitate their ability to use resources that become scarce in fragmented landscapes. If a specialized parasitoid disperses widely to take advantage of a sparse host, then the parasitoid population should have lower genetic structure than the host. We investigated the temporal and spatial genetic structure of a hyperparasitoid (fourth trophic level) in a fragmented landscape over 50 × 70 km, using microsatellite markers, and compared it with the known structures of its host parasitoid, and the butterfly host which lives as a classic metapopulation. We found that population genetic structure decreases with increasing trophic level. The hyperparasitoid has fewer genetic clusters (K = 4), than its host parasitoid (K = 15), which in turn is less structured than the host butterfly (K = 27). The genetic structure of the hyperparasitoid also shows temporal variation, with genetic differentiation increasing due to reduction of the population size, which reduces the effective population size. Overall, our study confirms the idea that specialized species must be dispersive to use a fragmented host resource, but that this adaptation has limits.
Data from: Individual behaviour mediates effects of warming on movement across a fragmented landscape
Global warming and habitat fragmentation impose dramatic and potentially interactive impacts on ecosystems. Warming induces shifts in species' distributions as they track temperature changes, but this can be hindered in fragmented landscapes. Corridors connecting habitat patches might ameliorate the combined effects of fragmentation and global warming. Using novel automated tracking methods, the movement of woodlice (Oniscus asellus) ranging in body size from 15·3 to 108·6 mg was quantified across a temperature range from 15 to 25 °C as they moved around an experimental fragmented landscape. We used confirmatory path analysis to test causal effects of temperature and body size on individual movement and corridor crossing rates between two habitat patches. Results showed that woodlice behaved differently in corridors than patches by moving, on average, faster and more often. This is congruent with natural systems where corridors generally provide lower quality habitat than patches. Although metabolic theory suggests positive scaling of movement with body temperature (up to a peak) and body size, we found that corridor crossing rate was (i) not directly affected by body size and (ii) negatively influenced by temperature, possibly due to its indirect effects via humidity. Our path model revealed that metabolic scaling could only explain temperature effects on maximum body velocity, but decision-based behaviour explained most variation in corridor crossing rates. This led to direct and indirect effects of temperature and size on individual movement between habitat patches. Our findings suggest that increasing mean global temperatures, coupled with increasing habitat fragmentation, could have synergistic negative impacts on populations through a combination of physiological and behavioural factors that mediate individual responses to temperature and fragmentation.
Human-induced habitat fragmentation effects on connectivity, diversity and population persistence of an endemic fish, Percilia irwini, in the Biobío river basin (Chile)
<p> </p> <p>An understanding of how genetic variability is distributed in space is fundamental for the conservation and maintenance of diversity in spatially fragmented and vulnerable populations. While fragmentation can occur from natural barriers it can also be exacerbated by anthropogenic activities such as hydroelectric power plant development. Whatever the source, fragmentation can have significant ecological effects, including the disruptions of migratory processes and gene flow among populations. In Chile, the Biobío river basin exhibits a high degree of habitat fragmentation due to the numerous hydroelectric power plants in operation, the number of which is expected to increase following new renewable energy use strategies. Here, we assessed the effects of different kinds of barriers on the genetic structure of the endemic freshwater fish <em>Percilia irwini</em>, knowledge that is critically needed to inform conservation strategies in light of current and anticipated further fragmentation initiatives in the system. We identified 8 genetic units throughout the entire Biobío system with high effective sizes. A reduced effective size estimate was however observed in a single population located between two impassable barriers. Both natural waterfalls and human made dams were important drivers of population differentiation in this system, however, dams affect genetic diversity differentially depending on their mode of operation. Evidence of population extirpation was found in two river stretches limited by upstream and downstream dams. Significant gene flow in both directions was found among populations not separated by natural or anthropogenic barriers. Our results suggest a significant vulnerability of <em>P. irwini </em>populations to future dam development and demonstrate the importance of studying basin-wide data sets with genetic metrics to understand the strength and direction of anthropogenic impacts on fish populations.</p>
Data from: Reserve size and fragmentation alters community assembly, diversity and dynamics
Researchers have disputed whether a single large habitat reserve will support more species than many small reserves. However, relatively little is known from a theoretical perspective about how reserve size affects competitive communities structured by spatial abiotic gradients. We investigate how reserve size affects theoretical communities whose assembly is governed by dispersal limitation, abiotic niche differentiation, and source-sink dynamics. Simulations were conducted with varying scales of dispersal across landscapes with variable environmental spatial autocorrelation. Landscapes were inhabited by simulated trees with seedling and adult stages. For a fixed total area in reserves, we found that small reserve systems increased the distance between environments dominated by different species, diminishing the effects of source-sink dynamics. As reserve size decreased, environmental limitations to community assembly became stronger, α-species richness decreased, and γ-richness increased. When dispersal occurred across short distances, a large reserve strategy caused greater stochastic community variation, greater α-richness, and lower γ-richness than in small reserve systems. We found that reserve size variation trades off between preserving different aspects of natural communities, including α versus γ-diversity. Optimal reserve size will depend on the importance of source-sink dynamics and the value placed on different characteristics of natural communities. Anthropogenic changes to the size and separation of remnant habitats can have far reaching effects on community structure and assembly.
Data from: Effects of mis-alignment between dispersal traits and landscape structure on dispersal success in fragmented landscapes
Dispersal is fundamental to population dynamics and hence extinction risk. The dispersal success of animals depends on the biophysical structure of their environments and their biological traits; however, comparatively little is known about how evolutionary trade-offs among suites of biological traits affect dispersal potential. We developed a spatially explicit agent-based simulation model to evaluate the influence of trade-offs among a suite of biological traits on the dispersal success of vagile animals in fragmented landscapes. We specifically chose traits known to influence dispersal success: speed of movement, perceptual range, risk of predation, need to forage during dispersal, and amount of suitable habitat required for successful settlement in a patch. Using the metric of relative dispersal success rate, we assessed how the costs and benefits of evolutionary investment in these biological traits varied with landscape structure. In heterogeneous environments with low habitat availability and scattered habitat patches, individuals with more equal allocation across the trait spectrum dispersed most successfully. Our analyses suggest that the dispersal success of animals in heterogeneous environments is highly dependent on hierarchical interactions between trait trade-offs and the geometric configurations of the habitat patches in the landscapes through which they disperse. In an applied sense, our results indicate potential for ecological mis-alignment between species' evolved suites of dispersal-related traits and altered environmental conditions as a result of rapid global change. In many cases identifying the processes that shape patterns of animal dispersal, and the consequences of abiotic changes for these processes, will require consideration of complex relationships among a range of organism-specific and environmental factors.
Data from: Mitochondrial genome fragmentation unites the parasitic lice of eutherian mammals
Organelle genome fragmentation has been found in a wide range of eukaryotic lineages; however, its use in phylogenetic reconstruction has not been demonstrated. We explored the use of mitochondrial (mt) genome fragmentation in resolving the controversial suborder-level phylogeny of parasitic lice (order Phthiraptera). There are ~5,000 species of parasitic lice in four suborders (Amblycera, Ischnocera, Rhyncophthirina and Anoplura), which infest mammals and birds. The phylogenetic relationships among these suborders are unresolved despite decades of studies. We sequenced the mt genomes of eight species of parasitic lice and compared them with 17 other species of parasitic lice sequenced previously. We found that the typical single-chromosome mt genome is retained in the lice of birds but fragmented into many minichromosomes in the lice of eutherian mammals. The shared derived feature of mt genome fragmentation unites the eutherian mammal lice of Ischnocera (family Trichodectidae) with Anoplura and Rhyncophthirina to the exclusion of the bird lice of Ischnocera (family Philopteridae). This novel clade is also supported by phylogenetic analysis of mt genome and cox1 gene sequences. Our results demonstrate, for the first time, that organelle genome fragmentation is informative for resolving controversial high-level phylogenies.
Data from: Defaunation and fragmentation erode small mammal diversity dimensions in tropical forests
Forest fragmentation and defaunation are considered the main drivers of biodiversity loss, yet the synergistic effects of landscape changes and biotic interactions on assemblage structure have been poorly investigated. Here, we use an extensive dataset of 283 assemblages and 105 species of small mammals to understand how defaunation of medium and large mammals and forest fragmentation change the community composition and diversity of rodents and marsupials in tropical forests of South America. We used structured equation models to investigate the relationship between small mammal species, functional and phylogenetic diversity with forest size, forest cover and the occurrence of medium and large mammals. The best-fit model showed that defaunation reduced functional diversity, and that species diversity of small mammals increased with forest patch size. Forest cover did not affect functional and phylogenetic diversity. Our results indicate that occurrence of medium and large sized mammals (probably acting as predators, or competitors of small mammals) and forest patch size help to retain species and functional diversity in small mammal communities. Further, the number of species in a small mammal community was critical to the maintenance of phylogenetic diversity, and may have a pronounced influence on the ecological functions played by small mammals. Identifying how phylogenetic and functional diversity change in function of human pressures allows us to better understand the contribution of extant lineages to ecosystem functioning in tropical forests.
Data from: Predicting local adaptation in fragmented plant populations: implications for restoration genetics
Understanding patterns and correlates of local adaptation in heterogeneous landscapes can provide important information in the selection of appropriate seed sources for restoration. We assessed the extent of local adaptation of fitness components in 12 population pairs of the perennial herb Rutidosis leptorrhynchoides (Asteraceae) and examined if spatial scale (0.7 – 600km), environmental distance, quantitative Q_ST and neutral genetic differentiation F_ST, and size of the local and foreign populations could predict patterns of adaptive differentiation. Local adaptation varied among populations and fitness components. Including all population pairs, local adaptation was observed for seedling survival, but not for biomass, while foreign genotype advantage was observed for reproduction (number of inflorescences). Among population pairs, local adaptation increased with Q_ST and local population size for biomass. Q_ST was associated with environmental distance, suggesting ecological selection for phenotypic divergence. However, low F_ST and variation in population structure in small populations demonstrates the interaction of gene flow and drift in constraining local adaptation in R. leptorrhynchoides. Our study indicates that for species in heterogeneous landscapes, collecting seed from large populations from similar environments to candidate sites is likely to provide the most appropriate seed sources for restoration.
Figure 1 from: Horňák O, Mock A, Šarapatka B, Tuf IH (2020) Character of woodland fragments affects distribution of myriapod assemblages in agricultural landscape. In: Korsós Z, Dányi L (Eds) Proceedings of the 18th International Congress of Myriapodology, Budapest, Hungary. ZooKeys 930: 139-151. https://doi.org/10.3897/zookeys.930.48586
Figure 1 GAM plots evaluating effect of selected measured environmental factors to communities of centipedes and millipedes a relationship between size of wood fragments and number of centipedes' species trapped b relationship between thickness of leaf litter and number of centipedes trapped c relationship between species richness of trees in sites and number of centipedes trapped d relationship between thickness of leaf litter and number of millipedes trapped. Circles on diagram represent individual fragments of woodland.
Fragment and size distribution of green peas upon impact comminution
<p>Raw data of fragments and corresponding morphological descriptors of green peas after impact comminution in a hammer mill.</p>
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Allen Brain Atlas
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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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