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opencc-zeroAug 2020View details →

Data from: Developing extruded seed pellets to overcome soil hydrophobicity and seedling emergence barriers

Globally soil water repellency is a major constraint to plant establishment, restricting water infiltration and moisture retention in the seed zone, resulting in poor germination and seedling emergence. To address this problem within an ecosystem restoration context, we investigated the use of a surfactant in extruded seed pellets to improve native plant recruitment in water repellent topsoils of two proteaceous woodland species, Banksia menziesii R.Br (glasshouse trial) and Lambertia inermis R.Br (field trial). In this two-part study, we first examined B. menziesii seedling performance in detail under glasshouse conditions for differences in survival between the extruded pelleting formulations after an induced drought at 12 weeks. We demonstrated that there was no difference in seedling emergence, amongst control seed and pellet treatments in B. menziesii. Initially B. menziesii seedlings emerged faster in the control treatment (non-pelleted control seeds) and had greater initial plant growth (leaf and root production), however by week 12, seedlings generated from pellets were not significantly different from the control seeds, and pellets + surfactant had the greatest number of leaf establishment. Survival after drought of B. menziesii seedlings ranged from 14 to 31 days with pellet + surfactant surviving approximately 2.6 days (11.8%) longer than the control seeds. For the second species, L. inermis, seedling emergence under field conditions was approximately 24% greater in seedlings derived from extruded pellets, however there was no difference in overall survival due to post-emergence predation. This study provides a proof of concept that seedling emergence in water repellent soils can be enhanced with extruded pellets containing surfactants. Our demonstration under in situ and ex situ conditions confirms the prospective use of seed enhancement technologies with future development and field-testing warranted.

opencc-by-4.0Sep 2020View details →

Dataset for "Edge Defects and Energy Barriers in Skyrmion Monolayers"

Dataset for "Edge Defects and Energy Barriers in Skyrmion Monolayers" This dataset provides data from a series of atomistic simulations from experiments on the effects of varying the size of defects on a monolayer of Cobalt, where defects of three shapes (square, triangle and bezier) are varied in size, and the effect of the demagnetising interaction viewed. The simulations were performed with the open-source software Fidimag (10.5334/jors.223, 10.5281/zenodo.2650286). The dataset is split into several directories, and the data is either stored in VTK files (which can be opened by a variety of free tools, for e.g. Paraview and MayaVi, TecPlot), and CSV files and NDT files, which can be opened in standard numerical data libraries and software (e.g. Pandas, NumPy, Excel, LibreOffice Calc) or opened in a text editor for viewing directly. energy-barrier-data This folder contains space delimited NDT files which give the energy information history across a set of simulations. This contains 6 folders: squ-nd, tri-nd, bez-nd and squ-wd, tri-wd, bez-wd which correspond to data for the square, triangle and bezier defects, calculated without and with the demagnetising interaction respectively. For the triangle datasets, the files are labelled with the width of the defect. For the square datasets, the files are labelled with the width and height of the defect. For the bezier datasets, the files are labelled with the width, and the height of the control point for a bezier curve. Each row in the data file gives the energy of a set of images in the Nudged Elastic Band Method at a given iteration; thus, the final row is the converged energy data. energy-term-data-triangles This folder contains more detailed energy information calculated for the converged triangle images. These CSV files are labelled with the width of the defect, and 'nd' for no demagnetising interaction, and 'wd' if the demagnetistaion is present (e.g. 'w_0.5_nd.csv' is the file for a width 0.5nm triangular defect with no demagnetising interaction). These files have columns corresponding to the different magnetic energies (Exchange, Anisotropy, DMI, Demagnetising) in Joules for each image in the NEBM calculation, along with the total energy of each state. vtks This folder contains VTK files of some of the states used to create figures. There are six folders  * no-defect and no-defect-wd which correspond to the set of images from simulations of the nanostructure with no defect present * squ-5.0_5.0 and squ-wd-5.0_5.0 which are for the sample with a 5.0nm by 5.0nm defect * tri-7.0 and tri-wd-7.0 which are for the sample with a triangular defect of width 7.0nm.

opencc-zeroSep 2020View details →

How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels

The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study "replicated" instances of secondary contact between closely-related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry-informative panel of such SNPs. We then compared their frequencies in newly-sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi-stable variants (Dobzhansky-Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact.

opencc-zeroNov 2020View details →

Data from: Modelling species distributions limited by geographic barriers: a case study with African and American primates

Aim: The boundaries of species distributions are often shaped by natural barriers such as mountains and rivers, but species distribution models usually fail to include these constraints. We tested several approaches that include barriers as explanatory variables in species distribution models. Location: Africa and South America. Time period: Current Major taxa studied: Primates Methods: We modelled the ranges of pairs of species separated by a river taking into account three explanatory components: the environment (ecosystems, topo-hydrography, climate, human pressure), the spatial structure shaped by history and population dynamics (using a trend-surface approach), and rivers as naturals barriers to dispersal (using a binary cis-trans variable that describes both sides of the river). To assess how the addition of a spatial structure and the barrier could improve distribution models, we used a nested approach by comparing models based on: a) the environment; b) the environment and the spatial structure; and c) the environment, the spatial structure and the river. These models were constructed using the favourability functions. Results: There was a decreased occurrence of high-favourability values in the opposite side of the rivers in models that included the spatial structure of distributions, compared to models based on environment alone. This decrease was more marked when the description of the spatial structure was made more flexible. However, model performance was significantly improved by the inclusion of cis-trans variables that identified areas on the opposite side as totally unfavourable. Main conclusions: The performance of distribution models can improve by the use of approaches that describe barriers. Although adding the location of geographic units in relation to a river appears to be the most accurate way to define the presence of a barrier, defining this variable may be challenging. A suitable alternative is to analyse the spatial structure of distributions using a flexible approach.

opencc-by-4.0Nov 2020View details →

Processed data on current events for SDBD units based on Al₂O₃ and AlN barriers (from 1.4 to 2.4 kV)

The dataset contains processed data of current events measured from the reverse electrode of the SDBD units made of Al₂O₃ and AlN, respectively. Each file corresponds to specific material and specific voltage(dset1#{1..6}_cache.npz is for Al₂O₃; dset2#{1..6}_cache.npz is for AlN; from 1.4 to 2.4 kV). Files contain the following NumPy arrays: <ol> <li>    "events" is a processed data of current events approximated by an analytical function, legend: <ul> <li>        'r' is a Pearson's correlation coefficient between the raw signal and analytical approximation;</li> <li>        'ph is a phase of supply voltage (when event occur);</li> <li>        'vm' is a value of supply voltage (when event occur);</li> <li>        'tm' is a time moment of the event's occurrence;</li> <li>        'dq' is a charge transferred in a single event;</li> <li>        'a,b' are the rates of current rise and decay;</li> <li>        'dt' is a peak's half-width;</li> <li>        's'  is a parameter of peak asymmetry.</li> </ul> </li> <li>    "index" determines boundaries between different periods in "events"-array (for example, third period contains events[index[2]:index[3]]).</li> <li>    "oscid" determines boundaries between different measurements in the "index"-array.</li> <li>    "vamps", "vfrqs", "cap0s", "cap1s" are the measurement specific arrays; they contain values of voltage amplitude, frequency, 'cold' and 'plasma' capacities of the system. They should be near-constant.</li> </ol>

FIGURE 4 in Phenotypic divergence in large sized cricket frog species that crossed the geographical barriers within peninsular India

FIGURE 4. Principal Component Analysis for male individuals of F. kalinga (from WG and EG), F. goemchi and F. kudremukhensis using six morphometric characters (Table 2) transformed to their ratio to SVL for from the Western Ghats.

FIGURE 3. Principal Component Analysis for male individuals using 31 in Phenotypic divergence in large sized cricket frog species that crossed the geographical barriers within peninsular India

FIGURE 3. Principal Component Analysis for male individuals using 31 morphometric characters (Table 1) transformed to their ratio to SVL for F. kalinga from the Eastern Ghats and the Western Ghats.

FIGURE 2 in Phenotypic divergence in large sized cricket frog species that crossed the geographical barriers within peninsular India

FIGURE 2. Maximum Likelihood phylogeny for the large sized fejervaryan frogs having predominant distribution in the Western Ghats / Eastern Ghats' (Figure 2, Phuge et al. 2019) with the present data based on 529 bp of mitochondrial 16S rRNA gene.

FIGURE 1 in Phenotypic divergence in large sized cricket frog species that crossed the geographical barriers within peninsular India

FIGURE 1. Details of the type localities for the species of Fejervarya described from peninsular India (1. F. orissaensis; 2. F. kalinga (from the Eastern Ghats, marked by a star); 3. F. marathi; 4. F. syhadrensis; 5. F. cepfi; 6. F. goemchi; 7. F. gomantaki; 8. New collections of F. kalinga from the Western Ghats (marked by a star); 9. F. krishnan; 10. F. modesta; 11. F. mysorensis;12. F. kudremukhensis; 13. F. sahyadris; 14. F. rufescens; 15.F. sauriceps;16. F. caperata; 17. F. mudduraja; 18. F. murthii; 19. F. nilagirica; 20. F. neilcoxi; 21. F. kadar; 22. F. parambikulamana; 23. F. keralensis; 24. F. manoharani and 25. F. agricola;)

opennotspecifiedNov 2020View details →

FIGURE 1. Helmutneris vadum n in Helmutneris vadum, a new species of Lumbrineridae (Annelida) from Lizard Island, Great Barrier Reef, Australia

FIGURE 1. Helmutneris vadum n. sp. A. Holotype AM W.43952, general view; B. the same, anterior part, ventral view; C. the same, dorsal view; D. Paratype W.46032, maxillary apparatus, dorsal view; E. W.40849, maxilla II, dorsal view; F, the same, maxillae III and IV, dorsal view; G. W.46042, mandibles. Abbreviations: MI—maxilla I, MII—maxilla II, MIII—maxilla III, MIV—maxilla IV, al—attachment lamella, C—maxillary carriers.

opennotspecifiedNov 2020View details →

FIGURE 2. Helmutneris vadum n in Helmutneris vadum, a new species of Lumbrineridae (Annelida) from Lizard Island, Great Barrier Reef, Australia

FIGURE 2. Helmutneris vadum n. sp. Paratype W.46035. A. Anterior part, ventral view; B. Parapodium 1; C. Parapodia 14– 15; D. Parapodia 31–32; E. Simple multidentate hooded hook, parapodium 12; F. Simple multidentate hooded hook, parapodium 17. G. The same, enlarged. Abbreviations: psl—postchaetal lobe.

FIGURE 5 in Phenotypic divergence in large sized cricket frog species that crossed the geographical barriers within peninsular India

FIGURE 5. Fejervarya kalinga in life from A) the Western Ghats (Sirsi, Uttara Kannada, Karnataka); B) the Eastern Ghats (Sileru, Vishakapatanam, Andhra Pradesh).

opencc-zeroDec 2015View details →

Data from: Immigrant inviability produces a strong barrier to gene flow between parapatric ecotypes of Senecio lautus

Speciation proceeds when gene exchange is prevented between populations. Determining the different barriers preventing gene flow can therefore give insights into the factors driving and maintaining species boundaries. These reproductive barriers may result from intrinsic genetic incompatibilities between populations, from extrinsic environmental differences between populations, or a combination of both mechanisms. We investigated the potential barriers to gene exchange between three adjacent ecotypes of an Australian wildflower to determine the strength of individual barriers and the degree of overall isolation between populations. We found almost complete isolation between the three populations mainly due to premating extrinsic barriers. Intrinsic genetic barriers were weak and variable amongst populations. There were asymmetries in some intrinsic barriers due to the origin of cytoplasm in hybrids, which combined with weak selection against hybrids has the potential to facilitate gene flow in the system, specifically from Dune and Headland ecotypes into the Island ecotype. Overall, these results suggest that reproductive isolation between these three populations is almost complete despite the absence of geographic barriers, and that the main drivers of this isolation are ecologically based, consistent with the mechanisms underlying ecological speciation.

opencc-zeroDec 2016View details →

Data from: Dispersal barriers and climate determine the geographic distribution of the helicopter damselfly Mecistogaster modesta

Species' ranges are typically constrained by the interplay of physical barriers to dispersal, environmental requirements such as suitable climatic conditions and biotic constraints such as from predation or competition. However, teasing apart the relative importance of these constraints in determining species distributions still represents a major challenge for ecologists. The Neotropical damselfly Mecistogaster modesta (Coenagrionidae: Odonata) inhabits wet and moist forests in mainland Central America and north-western South America. This habitat specialist spends its larval development exclusively in tank bromeliads, where it acts as a keystone predator within the aquatic food web. Although tank-forming bromeliads occur from the southern United States throughout most of South America, M. modesta is absent from the Caribbean islands and South America south-east of the Andes mountain chain. We employed species distribution models to explore the relative importance of physical barriers (Andes mountain range and oceanic barriers), climate (mean annual temperature and annual precipitation) and biotic interactions (competition from other bromeliad-dwelling odonates) in limiting the geographic distribution of M. modesta. We found that dispersal barriers strongly limit the geographic distribution of M. modesta. In addition, its range is restricted by low temperatures and low precipitation. Competition from other bromeliad-dwelling odonates was not important in limiting the damselfly's range. Because of the physical barriers to dispersal, M. modesta does not occupy its full potential geographic range. Specifically, our model predicted suitable habitat on the Caribbean islands and throughout most of South America, where the species is currently absent. These findings have important conservation implications, particularly as the aridification of rainforests and subsequent localised extinctions due to climate change continue. On the other hand, the species may respond to warming temperatures by tracking climate to higher elevations, with subsequent effects on naïve high-elevation bromeliad food webs. An upwards migration could also increase the probability of M. modesta overcoming the dispersal barrier presented by the Andes, enabling the damselfly to invade large areas of suitable habitat in South America.

Data from: Diverse reproductive barriers in hybridising crickets suggests extensive variation in the evolution and maintenance of isolation

Reproductive barriers reduce gene flow between populations and maintain species identities. A diversity of barriers exist, acting before, during and after mating. To understand speciation and coexistence, these barriers need to be quantified and their potential interactions revealed. We use the hybridising field crickets Gryllus bimaculatus and G. campestris as a model to understand the full compliment and relative strength of reproductive barriers. We find that males of both species prefer conspecific females, but the effect is probably too weak to represent a barrier. In contrast, prezygotic barriers caused by females being more attracted to conspecific male song and preferentially mounting and mating with conspecifics are strong and asymmetric. Postzygotic barriers vary in direction; reductions in fecundity and egg viability create selection against hybridisation, but hybrids live longer than pure-bred individuals. Hybrid females show a strong preference for G. bimaculatus songs, which together with a complete lack of hybridisation by G. campestris females, suggests that asymmetric gene flow is likely. For comparison, we review reproductive barriers that have been identified between other Gryllids and conclude that multiple barriers are common. Different species pairs are separated by qualitatively different combinations of barriers, suggesting that reproductive isolation and even the process of speciation itself may vary widely even within closely related groups.

Data from: Spatial and temporal genetic structure of Symbiodinium populations within a common reef-building coral on the central Great Barrier Reef

The dinoflagellate photosymbiont Symbiodinium plays a fundamental role in defining the physiological tolerances of coral holobionts, but little is known about the dynamics of these endosymbiotic populations on coral reefs. Sparse data indicate that Symbiodinium populations show limited spatial connectivity; however, no studies have investigated temporal dynamics for in hospite Symbiodinium populations following significant mortality and recruitment events in coral populations. We investigated the combined influences of spatial isolation and disturbance on the population dynamics of the generalist Symbiodinium type C2 (ITS1 rDNA) hosted by the scleractinian coral Acropora millepora in the central Great Barrier Reef. Using eight microsatellite markers, we genotyped Symbiodinium in a total of 401 coral colonies, which were sampled from seven sites across a 12-year period including during flood plume–induced coral bleaching. Genetic differentiation of Symbiodinium was greatest within sites, explaining 70–86% of the total genetic variation. An additional 9–27% of variation was explained by significant differentiation of populations among sites separated by 0.4–13 km, which is consistent with low levels of dispersal via water movement and historical disturbance regimes. Sampling year accounted for 6–7% of total genetic variation and was related to significant coral mortality following severe bleaching in 1998 and a cyclone in 2006. Only 3% of the total genetic variation was related to coral bleaching status, reflecting generally small (8%) reductions in allelic diversity within bleached corals. This reduction probably reflected a loss of genotypes in hospite during bleaching, although no site-wide changes in genetic diversity were observed. Combined, our results indicate the importance of disturbance regimes acting together with limited oceanographic transport to determine the genetic composition of Symbiodinium types within reefs.

opencc-zeroDec 2011View details →

Data from: Role of recent and old riverine barriers in fine scale population genetic structure of Geoffroy's Tamarin (Saguinus geoffroyi) in the Panama Canal Watershed

The role of physical barriers in promoting population divergence and genetic structuring is well known. While it is well established that animals can show genetic structuring at small spatial scales, less well resolved is how the timing of the appearance of barriers affects population structure. This study uses the Panama Canal watershed as a test of the effects of old and novel riverine barriers in creating population structure in Saguinus geoffroyi, a small cooperatively breeding Neotropical primate. Mitochondrial sequences and microsatellite genotypes from three sampling localities revealed genetic structure across the Chagres River and the Panama Canal, suggesting that both waterways act as barriers to gene flow. F-statistics and exact tests of population differentiation suggest population structure on either side of both riverine barriers. Genetic differentiation across the Canal, however, was less than observed across the Chagres. Accordingly, Bayesian clustering algorithms detected between two and three populations, with localities across the older Chagres river always assigned as distinct populations. While conclusions represent a preliminary assessment of genetic structure of S. geoffroyi, this study adds to the evidence indicating that riverine barriers create genetic structure across a wide variety of taxa in the Panama Canal watershed and highlights the potential of this study area for discerning modern from historical influences on observed patterns of population genetic structure.

opencc-zeroDec 2015View details →

Data from: Barriers to dispersal of rain forest butterflies in tropical agricultural landscapes

Fragmentation of natural habitats can be detrimental for species if individuals fail to cross habitat boundaries to reach new locations, thereby reducing functional connectivity. Connectivity is crucial for species shifting their ranges under climate change, making it important to understand factors that might prevent movement through human-modified landscapes. In tropical regions, rain forests are being fragmented by agricultural expansion, potentially isolating populations of highly diverse forest-dependent species. The likelihood of crossing habitat boundaries is an important determinant of species dispersal through fragmented landscapes, and so we examined movement across rain forest-oil palm plantation boundaries on Borneo by using relatively mobile nymphalid butterflies as our model study taxon. We marked 1666 individuals from 65 species, and 19 percent (100/527) of recaptured individuals crossed the boundary. Boundary crossing was relatively frequent in some species, and net movement of individuals was from forest into plantation. However, boundary crossing from forest into plantation was detected in less than 50 percent (12/28) of recaptured species and was dominated by small-sized butterfly species whose larval host plants occurred within plantations. Thus, while oil palm plantations may be relatively permeable to some species, they may act as barriers to the movement of forest-dependent species (i.e., species that require rain forest habitat to breed), highlighting the importance of maintaining forest connectivity for conserving rain forest species.

Data from: The role of chromosomal rearrangements and geographical barriers in the divergence of lineages in a South American subterranean rodent (Rodentia: Ctenomyidae: Ctenomys minutus)

Identifying factors and the extent of their roles in the differentiation of populations is of great importance for understanding the evolutionary process in which a species is involved. Ctenomys minutus is a highly karyotype- polymorphic subterranean rodent, with diploid numbers ranging from 42 to 50 and autosomal arm numbers ranging from 68 to 80, comprising a total of 45 karyotypes described so far. This species inhabits the southern Brazilian coastal plain, which has a complex geological history, with several potential geographical barriers acting on different time scales. We assessed the geographical genetic structure of C. minutus, examining 340 individuals over the entire distributional range and using information from chromosomal rearrangements, mitochondrial DNA (mtDNA) sequences, and 14 microsatellite loci. The mtDNA results revealed 7 main haplogroups, with the most recent common ancestors dating from the Pleistocene, whereas clustering methods defined 12 populations. Some boundaries of mtDNA haplogroups and population clusters can be associated with potential geographical barriers to gene flow. The isolation by distance pattern also plays an important role in fine-scale genetic differentiation, which is strengthened by the narrowness of the coastal plain and by common features of subterranean rodents (i.e., small fragmented populations and low dispersal rates), which limit gene flow among populations. A step-by-step mechanism of chromosomal evolution can be suggested for this species, mainly associated with the metapopulation structure, genetic drift, and the geographical features of the southern Brazilian coastal plain. However, chromosomal variation plays no or very little role in the diversification of C. minutus populations.

Data from: Barriers to gene flow in the marine environment: insights from two common intertidal limpet species of the Atlantic and Mediterranean

Knowledge of the scale of dispersal and the mechanisms governing gene flow in marine environments remains fragmentary despite being essential for understanding evolution of marine biota and to design management plans. We use the limpets Patella ulyssiponensis and Patella rustica as models for identifying factors affecting gene flow in marine organisms across the North-East Atlantic and the Mediterranean Sea. A set of allozyme loci and a fragment of the mitochondrial gene cytochrome C oxidase subunit I were screened for genetic variation through starch gel electrophoresis and DNA sequencing, respectively. An approach combining clustering algorithms with clinal analyses was used to test for the existence of barriers to gene flow and estimate their geographic location and abruptness. Sharp breaks in the genetic composition of individuals were observed in the transitions between the Atlantic and the Mediterranean and across southern Italian shores. An additional break within the Atlantic cluster separates samples from the Alboran Sea and Atlantic African shores from those of the Iberian Atlantic shores. The geographic congruence of the genetic breaks detected in these two limpet species strongly supports the existence of transpecific barriers to gene flow in the Mediterranean Sea and Northeastern Atlantic. This leads to testable hypotheses regarding factors restricting gene flow across the study area.