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opencc-by-4.0Mar 2022View details →

Data archive for the publication: Multi-variable compensated quantum yield measurements of upconverting nanoparticles with high dynamic range: a systematic approach

The two compressed repositories contain raw and analysed data for the following publication on Optics Express:  <a href="https://doi.org/10.1364/OE.452874">Multi-variable compensated quantum yield measurements of upconverting nanoparticles with high dynamic range: a systematic approach</a> The code for processing and analysing these data is available on GitHub and it has its own DOI.  To access the code and for instructions on how to run the it follow the link: <a href="https://github.com/Biophotonics-Tyndall/QY-System-paper">Biophotonics-Tyndall/QY-System-paper (github.com)</a>.

opencc-zeroMar 2022View details →

Demographic, physiological, and genetic factors linked to poleward range expansion along the shoreline of China

Distribution range expansion is one of the most significant consequences of climate change in the Anthropocene. During range expansion, the former biogeographic barrier can be broken and then a new biogeographic pattern might appear. A comprehensive study, including demographic pattern, physiological performance and genetic features, is crucial for understanding how the expanding population occupies and survives in the new habitat, within which it formerly did not occur. In the present study, we investigated the demographic, physiological, and genetic features of the intertidal gastropod Nerita yoldii, which has extended its northern limit by ~200 km into areas that are warming up faster than the historical distribution over the former biogeographic break of the Yangtze River Estuary (YRE) during recent decades. The neutral SNPs data showed that the new marginal populations formed a distinct cluster established by a few founders. Demographic modeling analysis revealed that the new marginal populations experienced strong genetic bottlenecks followed by recent demographic expansion. Successful expansion that overcomes the founder effect (reduced genetic variation) might be attributed to its high capacity of rapid population growth and multiple introductions. According to the non-neutral SNPs under diversifying selection, there were high levels of heterozygosity in the new marginal populations, which might be beneficial for adapting to the novel thermal conditions. The common garden experiment showed that the new marginal populations have evolved divergent transcriptomic and physiological responses to heat stress, allowing them to occupy and survive in the novel environment. Our study also reveals a fast loss of transcriptional plasticity in the new marginal populations, potentially contributing to local adaptation. These results suggest a new biogeographic pattern for the snail N. yoldii has formed with the occurrence of demographic, physiologic and genetic changes, and emphasize the roles of adaptation of marginal populations during distribution range expansion.

opencc-zeroMar 2022View details →

Black-capped and mountain chickadee range-wide condition

Both abiotic and biotic drivers influence species distributions. Abiotic drivers, such as climate, have received considerable attention, even though biotic drivers, such as hybridization, often interact with abiotic drivers. We sought to explore the (1) costs of co-occurrence for ecologically similar species that hybridize and (2) associations between ecological factors and condition to understand how abiotic and biotic factors influence species distributions. For two closely related and ecologically similar songbirds, black-capped and mountain chickadees, we characterized body condition, as a proxy for fitness, using a 1,358 individual range-wide dataset. We compared body condition in sympatry and allopatry with several abiotic and biotic factors using species-specific generalized linear mixed models. We generated genomic data for a subset of 217 individuals to determine the extent of hybridization-driven admixture in our dataset. Within this data subset, we found that ~11% of the chickadees had hybrid ancestry, and all hybrid individuals had typical black-capped chickadee plumage. In the full data set, we found that birds of both species, independent of demographic and abiotic factors, had significantly lower body condition when occurring in sympatry than birds in allopatry. This could be driven by either the inclusion of cryptic, likely poor condition, hybrids in our full dataset, competitive interactions in sympatry, or be due to range edge effects. We are currently unable to discriminate between these mechanisms. Our findings have implications for mountain chickadees in particular, which will encounter more black-capped chickadees as black-capped chickadee ranges shift upslope and could lead to local declines in mountain chickadee populations.

opencc-zeroDec 2021View details →

Combining climatic and genomic data improves range-wide tree height growth prediction in a forest tree

Population response functions based on climatic and phenotypic data from common gardens have long been the gold standard for predicting quantitative trait variation in new environments. However, prediction accuracy might be enhanced by incorporating genomic information that captures the neutral and adaptive processes behind intra-population genetic variation. We used five clonal common gardens containing 34 provenances (523 genotypes) of maritime pine (Pinus pinaster Aiton) to determine whether models combining climatic and genomic data capture the underlying drivers of height-growth variation, and thus improve predictions at large geographical scales. The plastic component explained most of the height-growth variation, probably resulting from population responses to multiple environmental factors. The genetic component stemmed mainly from climate adaptation, and the distinct demographic and selective histories of the different maritime pine gene pools. Models combining climate-of-origin and gene pool of the provenances, and positive-effect height-associated alleles (PEAs) captured most of the genetic component of height-growth and better predicted new provenances compared to the climate-based population response functions. Regionally-selected PEAs were better predictors than globally-selected PEAs, showing high predictive ability in some environments, even when included alone in the models. These results are therefore promising for the future use of genome-based prediction of quantitative traits.

opencc-by-4.0Jan 2019View details →

Fig. 2 in Home Ranges Of The Red Fox, Vulpes Vulpes (Carnivora, Canidae) And European Badger, Meles Meles (Carnivora, Mustelidae), In Oak Forests Of Slobozhanshchyna, Ukraine

Fig. 2. Examples of determination the family home range boundaries in 1) foxes and 2) badgers.

opencc-by-4.0Jan 2019View details →

Fig. 5 in Home Ranges Of The Red Fox, Vulpes Vulpes (Carnivora, Canidae) And European Badger, Meles Meles (Carnivora, Mustelidae), In Oak Forests Of Slobozhanshchyna, Ukraine

Fig. 5. Fox family home ranges in May–June in 2007-2009 and 2011 in Gomilshanski Lisy NNP.

opencc-by-4.0Oct 2017View details →

Fig. 2 in Interspecific Interactions as a Factor of Limitation of Geographical Distribution: Evidence Obtained by Modeling Home Ranges of Vole Twin Species Microtus Arvalis – M. Levis (Rodentia, Microtidae)

Fig. 2. Potential distribution of the East European vole (Microtus levis). Captions as in fig.1.

opencc-by-4.0Jan 2017View details →

Fig. 2 in Home Range Of The Spur-Thighed Tortoise, Testudo Graeca (Testudines, Testudinidae), In The National Park Of El-Kala, Algeria

Fig. 2. View of the study area with different habitats.

opencc-by-4.0Jan 2017View details →

Fig. 1 in Home Range Of The Spur-Thighed Tortoise, Testudo Graeca (Testudines, Testudinidae), In The National Park Of El-Kala, Algeria

Fig. 1. Location of the study site in the National Park of El Kala, in north-eastern Algeria.

opencc-by-4.0Jan 2017View details →

Fig. 3 in Home Range Of The Spur-Thighed Tortoise, Testudo Graeca (Testudines, Testudinidae), In The National Park Of El-Kala, Algeria

Fig. 3. Tortoises locations (A) in relation to Dwarf palm distribution (B) on the study site.

Mechanisms underlying altitudinal and horizontal range contraction: The western black crested gibbon

Aim: Species ranges in mountain areas may shift both horizontally and altitudinally, resulting from climate change and anthropogenic impact. Two hypotheses (the abundant center hypothesis and the contagion hypothesis) have been proposed to account for patterns of horizontal range contraction. However, undulating topograph causes a mosaic of unsuitable habitats, which may complicate the spatial pattern of range contraction. We develop a framework incorporating horizontal and altitudinal range contraction patterns of a species living in mountain areas, to better understand the underlying mechanisms of species range contraction. Location: China, North Laos, and North Vietnam Taxon: Western black crested gibbon, Nomascus concolor Methods: We collected occurrence data of the gibbons from various sources and modelled their potential distribution range in the 1950s, 1980s, and 2010s, using ecological niche modelling. We compared distances from the center point of the potential range in 1950s to center points of the largest 100 patches in the 1950s and the 2010s to understand the patterns of horizontal range contraction. We also calculated potential distribution within different altitudinal range for six populations in each period to understand the patterns of altitudinal range contraction. Results: Potential horizontal distribution of the gibbons decreased by 69% from the 1950s to the 2010s. We found the 100 largest patches in 2010s were further apart from the center point of the potential range in 1950s compared to the 100 largest patches in 1950s, supporting the contagion hypothesis. No populations extended their range to higher altitude, suggesting climate change did not have a profound effect on gibbon range upward shift. All populations lost a substantial proportion of their ranges in lower altitude (500 – 1,500 m) but to different degrees, suggesting that populations experienced different anthropogenic pressures. Main conclusions: Anthropogenic threats probably including human population increase, agricultural expansion and hunting, were more likely than climate change to have caused range contraction in western black-crested gibbons. This study highlights the importance of studying horizontal and altitudinal range contraction simultaneously.

Evolution of thermal physiology alters the projected range of threespine stickleback under climate change

Species distribution models (SDMs) are widely used to predict range shifts but could be unreliable under climate change scenarios because they do not account for evolution. The thermal physiology of a species is a key determinant of range and thus incorporating thermal trait evolution into SDMs might be expected to alter projected ranges. We identified a genetic basis for physiological and behavioural traits that evolve in response to temperature change in natural populations of threespine stickleback (Gasterosteus aculeatus). Using these data, we created geographic range projections using a mechanistic niche envelope approach under two climate change scenarios. Under both scenarios, trait data was either static ('no evolution' model), allowed to evolve at observed evolutionary rates for the trait ('evolution' model), or allowed to evolve at a rate of evolution scaled in association with the variance that is explained by quantitative trait loci (QTL; 'scaled evolution' models). We show that incorporating these traits and their evolution substantially altered the projected ranges for a widespread panmictic marine population, with over 7-fold increases in area under climate change projections when traits are allowed to evolve. Evolution-informed SDMs should improve the precision of forecasting range dynamics under climate change, and aid in their application to management and the protection of biodiversity.

Data supporting: Environmental RNA degrades more rapidly than environmental DNA across a broad range of pH conditions

Although the use and development of molecular biomonitoring tools based on environmental nucleic acids (eDNA and eRNA; collectively known as eNAs) have gained broad interest for the quantification of biodiversity in natural ecosystems, studies investigating the impact of site-specific physicochemical parameters on eNA-based detection methods (particularly eRNA) remain scarce. Here, we used a controlled laboratory microcosm experiment to comparatively assess the environmental degradation of eDNA and eRNA across an acid-base gradient following complete removal of the progenitor organism (Daphnia pulex). Using water samples collected over a 30-day period, eDNA and eRNA copy numbers were quantified using a droplet digital PCR (ddPCR) assay targeting the mitochondrial cytochrome c oxidase subunit I (COI) gene of D. pulex. We found that eRNA decayed more rapidly than eDNA at all pH conditions tested, with detectability—predicted by an exponential decay model—for up to 57 hours (eRNA; neutral pH) and 143 days (eDNA; acidic pH) post organismal removal. Decay rates for eDNA were significantly higher in neutral and alkaline conditions than in acidic conditions, while decay rates for eRNA did not differ significantly among pH levels. Collectively, our findings provide the basis for a predictive framework assessing the persistence and degradation dynamics of eRNA and eDNA across a range of ecologically relevant pH conditions, establish the potential for eRNA to be used in spatially and temporally sensitive biomonitoring studies (as it is detectable across a range of pH levels), and may be used to inform future sampling strategies in aquatic habitats.

Data from: Demographic and ecogeographic factors limit wild grapevine spread at the southern edge of its distribution range - wild grapevine sampling locations, Maxent input files, morphological and microsatellite data

This dataset contains raw data described in the paper: "Rahimi O., Ohana-Levi N., Brauner H., Inbar N., Hübner S. and Drori E. (2021) "Demographic and ecogeographic factors limit wild grapevine spread at the southern edge of its distribution range", accepted for publication in "Ecology and Evolution". The spatial distribution of plants is constrained by demographic and eco-geographic factors that determine the range and abundance of the species. In this study, we performed genetic and morphological analyzes based on SSR and OIV datasets. In addition, according to the spatial distribution model performed by Maxent software we found that distance to water sources, Normalized difference vegetation index, and precipitation are the main environmental factors constraining V.v. sylvestris distribution at its southern distribution range. All raw data used for this study can be found in this deposit which contains a table with grapevine locations, Maxent input files, morphological and microsatellite data.

Publication release: How well do species distribution models predict occurrences in exotic ranges?

<div class="record-description"> Species distribution models (SDMs) are widely used predictive tools to forecast potential biological invasions. However, the reliability of SDMs extrapolated to exotic ranges remains understudied, with most analyses restricted to few species and equivocal results. We examined the spatial transferability of SDMs for 647 non-indigenous species extrapolated across 1,867 invaded ranges, and identify what factors may help differentiate predictive success from failure. We performed a large-scale assessment of the transferability of SDMs using two modelling approaches: generalized additive models (GAMs) and MaxEnt. We fitted SDMs on the native ranges of species and extrapolated them to exotic ranges. We examined the influence of general factors and factors related to biological invasions on spatial transferability. Here, we provide the code and data for publication in Global Ecology and Biogeography as part of Nguyen and Leung 2022 "How well do species distribution models predict occurrences in exotic ranges?". Provided are the files and scripts necessary to fit and validate the SDMs using distirbutional data from their native and exotic ranges, respectively, formulated as generalized additive models (GAMs) or MaxEnt models. Additionally, provided is a script to validate the SDMs on their native fitting range using 10-fold cross-validation, and to fit the transferability model, as a linear mixed model (LMM), with a provided cleaned data.frame. The dataset provided includes a full species list with GBIF occurrence records, target-group background (TGB) records to use with model fitting and validation, as well as environmental data associated with the sightings. </div>

Data on where and why species' range shifts are hampered by unsuitable landscapes: for moth species in Great Britain

This dataset concerns moth (Lepidoptera) species in Great Britain and was compiled to address the question: Which landscape attributes have caused differential speeds of range expansion since 1985, both between landscapes and between species? More specifically, does the 'conductance' measured across a network of habitat help to predict the speed of range expansion? Conductance is a modelled measure of the speed at which a species could colonise a defined 'target' from a defined 'source' via a network of habitat patches. If it is predictive of real range expansion rates, it could be used to pinpoint the best places to target habitat conservation and restoration efforts. Our analysis leverages climate and landcover data alongside two exceptional spatio-temporal databases for moth species in Britain. The Rothamsted Insect Survey is a scattered network of traps that are continuously monitored, which provides ideal "target" locations to test when each species arrived. The National Moth Recording Scheme collates verified records of species from all locations, providing the most complete picture possible of the "source" distribution where expanding species could have originated. We used previous studies (Fox et al., 2014) and these databases to select 54 species that were southerly distributed in Britain and showed some sign of range expansion. Then we tested how attributes of both the species and the landscapes affected the observed arrival times.

Data from: Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing

Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different tissue types. We find that no single method is best for all cases. Instead, the optimal storage and extraction methods vary by taxa, by tissue, and by down-stream application. Therefore, we provide sample preservation guidelines that ensure sufficient DNA integrity and amount required for use with long-read and long-range sequencing technologies across vertebrates. Our best practices generate the uHMW DNA needed for the high-quality reference genomes for Phase 1 of the Vertebrate Genomes Project (VGP), whose ultimate mission is to generate chromosome-level reference genome assemblies of all ~70,000 extant vertebrate species.

Evolution in response to climate in the native and introduced ranges of a globally distributed plant

The extent to which species can adapt to spatiotemporal climatic variation in their native and introduced ranges remains unresolved. To address this, we examined how clines in cyanogenesis (HCN production—an antiherbivore defense associated with decreased tolerance to freezing) have shifted in response to climatic variation in space and time over a 60-year period in both the native and introduced ranges of Trifolium repens. HCN production is a polymorphic trait controlled by variation at two Mendelian loci (Ac and Li). Using phenotypic assays, we estimated within-population frequencies of HCN production and dominant alleles at both loci (i.e., Ac and Li) from 10,575 plants sampled from 131 populations on 5 continents, and then compared these frequencies to those from historical data collected in the 1950s. There were no clear relationships between changes in the frequency of HCN production, Ac, or Li and changes in temperature between contemporary and historical samples. We did detect evidence of continued evolution to temperature gradients in the introduced range, whereby the slope of contemporary clines for HCN and Ac in relation to winter temperature became steeper than historical clines and more similar to native clines. These results suggest that cyanogenesis clines show no clear changes through time in response to global warming, but introduced populations continue to adapt to their contemporary environments.

opencc-zeroMay 2022View details →

Data from: Lineage-specific trait variations and plasticity of obligate parthenogenetic animals following the expansion of distribution range to a continental archipelago.

Two asexual lineages, JPN1 and JPN2, of panarctic Daphnia pulex expanded the distribution range to Japan from North America, independent of each other. According to the mutation rates within these lineages, JPN1 lineage colonized Japan earlier than JPN2 lineage. Moreover, the ratio of nonsynonymous to synonymous mutation rates (dN/dS) was lower in JPN1 than in JPN2 lineage. Accordingly, it is hypothesized that variations of phenotypic traits differ between these two lineages. In addition, since they are obligate parthenogenetic animals, the lineage occupying a larger distribution range should have a larger phenotypic plasticity. To test these hypotheses, we experimentally examined the phenotypic variations of fitness-related traits, including digestive, life history and morphological traits, among several genotypes of these lineages. We found that within-lineage variations of most traits were smaller in JPN1 than in JPN2. In addition, the overall phenotypic variations were also smaller within the JPN1 lineage than within the JPN2 lineage. These results support the idea that the JPN1 lineage has been more efficiently subjected to negative selection, as expected from the lower dN/dS ratio. However, the magnitude of the phenotypic plasticity to changing food levels was at the same level for both the JPN1 and JPN2 lineages, while variations found in the phenotypic plasticity were smaller in the JPN1 lineage. The difference in the variations of the phenotypic traits and plasticity between the two lineages suggests that these two lineages have evolved under somewhat different environmental conditions and that genotypes of the JPN2 lineage may have exploited niches that differed somewhat from that of the JPN1 genotypes.