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opencc-by-4.0Sep 2020View details →

Figure 3 from: Li Y, Liu C, Lin L, Li Y, Xiao J, Loh K-H (2020) Pleistocene isolation caused by sea-level fluctuations shaped genetic characterization of Pampus minor over a large-scale geographical distribution. ZooKeys 969: 137-154. https://doi.org/10.3897/zookeys.969.52069

Figure 3 NJ tree and distribution of Cytb haplotypes among populations for P. minor. Bootstrap supports of > 50 in 1000 replicates are shown.

opencc-zeroSep 2020View details →

Predictive multi-scale occupancy models at range-wide extents: effects of habitat and human disturbance on distributions of wetland birds

Aim: Predicting distributions is fundamental to ecology, yet hindered by spatially-restricted sampling, scale-dependent relationships, and detection error associated with field surveys. Predictive species distribution models (SDMs) are nonetheless vital for conservation of many species. We developed a framework for building predictive SDMs with multi-scale data, and used it to develop range-wide breeding-season SDMs for 14 marsh bird species of concern. Location: USA. Methods: We built SDMs using data from range-wide surveys conducted over 14 years, and habitat and disturbance covariates measured at multiple spatial scales. We built hierarchical occupancy models that included heterogeneity in detectability during sampling, and used Bayesian model selection to regulate model complexity (covariates and scales) based explicitly on spatial predictive abilities. We thus integrated model selection for optimizing out-of-sample prediction, range-wide sampling over broad conditions, multi-scale analyses and scale-optimization, and species-specific detectability for a suite of wide-ranging species. Results: Distributions of marsh birds were affected by local wetland conditions, but also by agricultural, urban, and hydrologic disturbances operating from local scales (100 – 500 m) to the watershed level. Variables measuring human disturbances improved prediction for most species, and every species was affected by attributes at > 1 scale. Five species showed evidence for continental-scale range contraction during the study. Main conclusions: We demonstrate how hierarchical occupancy models can be optimized for prediction across a species' range at the extent of a continent while also accounting for imperfect detection, and thus describe a generalizable approach that can be used for any species. We provide the first data-driven, empirical SDMs built at the range-wide extent for most of our 14 study species and demonstrate that previous studies focused on local distributions and the effects of fine-scale wetland vegetation missed important broad-scale drivers of occupancy for marsh birds.

opencc-by-4.0Oct 2020View details →

A Large Scale Study On the Effectiveness of Manual and Automatic Unit Test Generation

Recently, an increasingly large amount of effort has been devoted to implementing tools to generate unit test suites automatically. Previous studies have investigated the effectiveness of these tools by comparing automatically generated test suites (ATSs) to manually written test suites (MTSs). Most of these studies report that ATSs can achieve higher code coverage, or even mutation coverage, than MTSs, particularly when suites are generated from defective code. However, these studies usually consider a limited amount of classes or subject programs, while the adoption of such tools in the industry is still low. This work aims to compare the effectiveness of ATSs and MTSs when applied as regression test suites. We conduct an empirical study, using ten programs (1368 classes), written in Java, that already have MTSs and apply two sophisticated tools that automatically generate test cases: Randoop and EvoSuite. To evaluate the test suites’ effectiveness, we use line and mutation coverage. Our results indicate that MTSs are, in general, more effective than ATSs regarding the investigated metrics. Moreover, the number of generated test cases may not indicate test suites’ effectiveness. Furthermore, there are situations when ATSs are more effective, and even when ATSs and MTSs can be complementary.

Data from: Scale-dependent intraspecific competition of Taurus cedar (Cedrus libani A. Rich.) saplings in the Southern Turkey

Better understanding of the competitive interaction at the early development stages of the stand is crucial to help schedule silvicultural treatments for young stands and for the better management of the future stands. We used scale-dependent analysis to improve our understanding of sapling dynamics in the pure Taurus cedar (Cedrus libani A. Rich.) stands in Southern Turkey. Using data from nine plots established at the western Taurus Mountains; diameter, height and crown radii of saplings were compared, and spatial point pattern analyses were performed. We found significant differences for the mean diameter and height, and crown radii of saplings among the plots. Univariate pair correlation function showed that sapling pattern was regular only at small scales (r < 0.4 m) but was predominantly random. Bivariate pair correlation function revealed no evidence of spatial interaction between tall saplings and short saplings. Univariate mark correlation function revealed that strong intraspecific competition was detected at small scales (up to 0.55m). This distance is reasonable for the juvenile age tending of Taurus cedar saplings and should be under consideration during silvicultural treatments to use the site productivity more efficiently.

Data for: The scales of coevolution: comparative phylogeography and genetic demography of a locally adapted venomous predator and its prey

Coevolutionary theory predicts that differences in the genetic demography of interacting species can influence patterns of local adaptation by affecting the potential of local populations to respond to selection. We conducted a comparative phylogeographic study of venomous rattlesnakes and their venom-resistant ground squirrel prey across California, and assessed how effective population size (Ne) estimates correspond with a previously documented pattern of rattlesnake local adaptation. Using RAD-seq markers, we detected lineage relationships among both the rattlesnakes (Crotalus oreganus ssp.) and ground squirrels (Otospermophilus sp.) that are incongruent with previous phylogenetic hypotheses. Both rattlesnakes and squirrels share a deep divergence at the Sacramento-San Joaquin River Delta. At this broad phylogeographic scale, we found that the locally adapted rattlesnakes had higher Ne than squirrels. At the population scale, snakes also had larger Ne accompanied by larger values of several metrics of population genetic diversity. However, the specific magnitude of local adaptation of venom activity to ground squirrel venom resistance was not significantly correlated with local differences in Ne or other diversity statistics between predator and prey populations, suggesting other factors in the geographic mosaic of coevolution contribute to the specific local-scale outcomes of this interaction. These results suggest an evolutionary mechanism that may explain some (but clearly not all) of rattlesnake local adaptation in this coevolutionary interaction – larger population sizes raise adaptive potential of rattlesnakes compared to ground squirrels.

The diversification and evolution of niche breadth across spatial scales in western North American monkeyflowers

Species show remarkable variation in ecological niche breadth, but the directionality of niche breadth evolution remains a question for niche axes across spatial scales. Testing the association between niche breadth evolution and the process of diversification could shed light on the role of ecology in the formation and maintenance of biodiversity. Here we applied Cladogenetic State change Speciation and Extinction models in western North American monkeyflowers (Mimulus sensu lato), with two states of niche breadth (generalist and specialist). We aimed to estimate the effects of niche breadth along broad-scale bioclimatic and local-scale microhabitat axes on diversification rate, and the evolutionary trend and mode of niche breadth. We found opposite patterns across spatial scales, with higher speciation rates detected for generalists along broad-scale bioclimatic axes and for specialists along local-scale microhabitat axes. Furthermore, we found weak trends towards specialization for bioclimatic niche breadth, but generalization for microhabitat niche breadth. Both cladogenetic and anagenetic changes were comparable and thus important in the evolution of niche breadth in this group. Together, these findings suggest that the underlying mechanisms of niche breadth evolution might differ across spatial scales, and that change in niche breadth could be tightly associated with the diversification process.

Climatic and Vegetational Drivers of Insect Beta Diversity at the Continental Scale

Aim We construct a framework for mapping pattern and drivers of insect diversity at the continental scale, and use it to test whether and which environmental gradients drive insect beta diversity. Location Global; North and Central America; Western Europe Time period 21st century Major taxa studied Insects Methods An informatics system was developed to integrate terrestrial data on insects with environmental parameters. We mined repositories of data for distribution, climatic data was retrieved (WorldClim), and vegetation parameters inferred from remote sensing analysis (MODIS Vegetation Continuous Fields). Beta diversity between sites was calculated and then modelled with two methods, Mantel test with Multiple Regression and Generalized Dissimilarity Modelling. Results Geographic distance was usually the main driver of insect beta diversity. Independent of geographic distance, bioclimate variables explained more variance in dissimilarity than vegetation variables, although the particular variables found to be significant were more consistent in the latter, particularly, tree cover. Tree cover gradients drove compositional dissimilarity at denser coverages, in both continental case studies. For climate, gradients in temperature parameters were significant in driving beta diversity more so than gradients in precipitation parameters. Main conclusions Although environmental gradients drive insect beta diversity independently of geography, the relative contribution of different climatic and vegetational parameters is not expected to be consistent in different study systems. With further incorporation of additional temporal information and variables, this approach will enable development of a predictive framework for conserving insect biodiversity at the global-scale.

openmit-licenseOct 2020View details →

Scale and Space Dependent Horizontal Eddy Diffusivity at the Global Surface Ocean

Sea surface temperature (SST) and idealized temperature tracer based estimates of horizontal diffusivity at the ocean surface. See https://doi.org/10.5281/zenodo.4126315 for the code to reproduce these estimates. There are two files which include the following KxKy_SST_MITGCM_025.nc SST based estimates are based on 35 years of satellite SST data (1982-2017) and we have divided the data in 30 chuncks, both using a 5 year and 10 year sub-sampling. The 'ens' dimension marks these chuncks whereas 'lat' and 'lon' mark the two Cartesian directions (latitude and longitude). Note that 'ens' can be also viewed as time. There are two fields 'Kx' and 'Ky' for each dataset ('SST' for the OI-SST based estimates or 'MITGCM' for the tracer simulation based estimates) and length of sub-sampling. 'Kx' is the diffusivity in 'lon' direction whereas 'Ky' is the diffusivity in 'lat' direction. Data is given at 0.25° resolution, but the effective resolution is twice that i.e. 0.5°. K_SST_MITGCM_2deg.nc Scale dependent estimate of the diffusivity magnitude i.e. \(K= \sqrt{K_xK_y}\) . As for the other data, here as well the estimates are done using 5 year and 10 year sub-sampling, and all the data is interpolated to a common 2° by 2° global grid. The coordinate 'dg' defines the scale in degrees. Note that again the effective resolution of the estimates is twice the 'dg'.

opencc-by-4.0Oct 2020View details →

Updated dataset for the manuscript - "Pore-scale Water Vapor Condensation Behaviors in Shales: An Experimental Study"

Updated dataset for the manuscript entitled "Pore-scale Water Vapor Condensation Behaviors in Shales: An Experimental Study".

opencc-zeroDec 2019View details →

Climate drives community-wide divergence within species over a limited spatial scale: evidence from an oceanic island

Geographic isolation substantially contributes to species endemism on oceanic islands when speciation involves the colonisation of a new island. However, less is understood about the drivers of speciation within islands. What is lacking is a general understanding of the geographic scale of gene flow limitation within islands, and thus the geographic scale and drivers of geographical speciation within insular contexts. Using a community of beetle species, we show that when dispersal ability and climate tolerance are restricted, microclimatic variation over distances of only a few kilometres can maintain strong geographic isolation and drive incipient speciation. Further to this, we demonstrate congruent diversification with gene flow across species, mediated by Quaternary climate oscillations that have facilitated a dynamic of isolation and secondary contact. The unprecedented scale of parallel species responses to a common environmental driver for evolutionary change has profound consequences for understanding past and future species responses to climate variation.

opencc-zeroNov 2020View details →

Data from: Latitudinal variation of arrival and breeding phenology of the pied flycatcher Ficedula hypoleuca using large-scale citizen science data.

Many species have advanced the timing of annual reproductive cycles in response to climatic warming, sometimes leading to asynchrony between trophic levels, with negative population consequences. Long-distance migratory birds, reliant on short seasonal food pulses for breeding, are considered particularly susceptible to such disjunction because late arrival may preclude optimal timing of egg-laying. It is unknown whether the relative timing of arrival and egg-laying is sufficiently plastic, in time and space, to enable an adaptive response when arrival times change relative to local food resources. We used citizen science data, describing pied flycatcher Ficedula hypoleuca arrival and egg-laying dates, to explore temporal (2013-2016) and spatial (across Great Britain) variation in the phenology of arrival, laying and their difference. To assess the long-term trend in arrival and laying at a single location, we used data from a long-term field study. The arrival-laying interval was consistently shorter in the north, driven by the contrast between spatial variation in arrival date and spatial invariance in laying date. To understand whether a short arrival-laying interval may have consequences for productivity, we assessed the association between this interval and clutch size. We found no statistically significant correlation between these two variables. To examine long-term changes in arrival and laying dates, we focussed on a single location in southwestern England. Both dates of first male arrival and first egg laid in a season advanced since 1986, with no evidence of interval shortening. Together, our results demonstrate spatial and annual variation in the arrival-laying interval, with no detected effect on fecundity. Thus, the interval from arrival to laying is likely dictated by spatially and temporally varying local conditions, suggesting these migrant birds may have the ability to adapt this interval to align with local conditions and mitigate potential mismatch impacts.

Figure 1 from: Antoł A, Kozłowski J (2020) Scaling of organ masses in mammals and birds: phylogenetic signal and implications for metabolic rate scaling. ZooKeys 982: 149-159. https://doi.org/10.3897/zookeys.982.55639

Figure 1 PGLS (solid lines) and OLS (dashed lines) interspecific scaling of tissue/organ masses in mammals with log fat-free-body mass as the independent variable. For the scaling with log body mass as an independent variable, see Suppl. material 1: Figure S3

Figure 2 from: Antoł A, Kozłowski J (2020) Scaling of organ masses in mammals and birds: phylogenetic signal and implications for metabolic rate scaling. ZooKeys 982: 149-159. https://doi.org/10.3897/zookeys.982.55639

Figure 2 PGLS (solid lines) and OLS (dashed lines) interspecific scaling of tissue/organ masses in birds with log fat-free-body mass as the independent variable. For the scaling with log body mass as an independent variable, see Suppl. material 1: Figure S5.

opencc-zeroNov 2020View details →

Strong genetic differentiation on a small geographic scale in the Neotropical rainforest understory tree Paypayrola blanchetiana (Violaceae)

Self-incompatible plants as well as common plant species are expected to be especially vulnerable to the deleterious effects of fragmentation on genetic diversity. Paypayrola blanchetiana (Violaceae) is a common, self-incompatible understory tree in the East Brazilian Atlantic forest. Its autochorous seed dispersal and occurrence in dense, well-separated clusters makes it an interesting model for studies of gene flow and genetic structuring on a small geographic scale. A previous study has found remarkably low fruit set and frequent seed abortions in this species in several populations situated in forest fragments. We tested the hypothesis that P. blanchetiana is affected by inbreeding and loss of genetic diversity in a fragmented landscape. Nine nuclear and three plastid microsatellite loci were genotyped for 285 individuals (149 adult trees and 136 saplings) across seven populations in five forest fragments in a 240 km2 sugarcane-rainforest matrix. We found a low to moderate genetic diversity in nuclear loci of P. blanchetiana, population structuring on a small geographical scale and high levels of inbreeding. Haplotype distributions confirmed that seed dispersal is very limited. There were, however, no signs for lower genetic diversity or higher inbreeding in populations situated in the smallest forest fragments. Furthermore, genetic diversity was not lower in the sapling cohort, which was created in post-fragmentation condition. Therefore, we may be witnessing the genetic consequences of this species biology, rather than immediate effects of fragmentation.

opencc-zeroNov 2020View details →

Data from: Altitude shapes the environmental drivers of large-scale variation in abundance of a widespread mammal species

Habitat quality and heterogeneity directly influence the distribution and abundance of organisms at different spatial scales. Determining the main environmental factors driving the variation in species abundance is crucial to understand the underlying ecological processes and this is especially important for widely distributed species living in contrasting environments. However, the responses to environmental variation are usually described at relatively small spatial scales. Here, we studied the variation in abundance of a widely distributed mustelid, the European badger (Meles meles), across France. We used (1) direct detections of 9,439 dead and living badgers, from 2006 to 2009, to estimate badger relative abundance in 703 small agricultural regions of metropolitan France and (2) a Bayesian modelling approach to identify the main environmental determinants influencing badger abundance. Despite a continuous distribution of badger in France, we found large variation in badger abundance between regions, explained by environmental factors. Among a set of 13 environmental variables, we demonstrated that badger abundance in lowlands (< 400 m a.s.l.) was mostly driven by biotic factors such as potential food resources (earthworm abundance and fruits crops) and forest fragmentation. Conversely, in mountainous areas, abiotic factors (i.e. soil texture and climate) drove the variation in badger relative abundance. These results underline the importance of mapping the abundance of wildlife species based on environmental suitability, and highlight the complexity of drivers influencing species abundance at such large spatial scales. Altitude shaped the environmental drivers (biotic vs. abiotic) that most influenced relative abundance of a widespread species. In the case of badger, such abundance maps are crucial to identify critical areas for species management as this mustelid is a main wild vector of bovine tuberculosis in several countries.

Figure 8 from: Avila-Poveda OH (2020) Large-scale project 'Chiton of the Mexican Tropical Pacific': Chiton articulatus (Mollusca: Polyplacophora). Research Ideas and Outcomes 6: e60446. https://doi.org/10.3897/rio.6.e60446

Figure 8 Schematic diagram of the methodological process through which the chitons will pass to fulfil each of the proposed themes.

Figure 7 from: Avila-Poveda OH (2020) Large-scale project 'Chiton of the Mexican Tropical Pacific': Chiton articulatus (Mollusca: Polyplacophora). Research Ideas and Outcomes 6: e60446. https://doi.org/10.3897/rio.6.e60446

Figure 7 Group of volunteers and collaborators of the QUITÓN PROJECT in FACIMAR-UAS. The project has a logo registration (brand), which is used on the shirts. Shirts used in the field and presentations (congresses, workshops) are shown.

Figure 6 from: Avila-Poveda OH (2020) Large-scale project 'Chiton of the Mexican Tropical Pacific': Chiton articulatus (Mollusca: Polyplacophora). Research Ideas and Outcomes 6: e60446. https://doi.org/10.3897/rio.6.e60446

Figure 6 Locations of Chiton articulatus collection. The star indicates the local headquarters of this project. The base map was taken from Instituto Nacional de Estadística, Geografía e Informática (INEGI). https://www.inegi.org.mx/

Figure 3 from: Avila-Poveda OH (2020) Large-scale project 'Chiton of the Mexican Tropical Pacific': Chiton articulatus (Mollusca: Polyplacophora). Research Ideas and Outcomes 6: e60446. https://doi.org/10.3897/rio.6.e60446

Figure 3 The food menu of some restaurants in Acapulco, Guerrero, including a dish with chiton, common name "Cucaracha/cockroach".

Figure 2 from: Avila-Poveda OH (2020) Large-scale project 'Chiton of the Mexican Tropical Pacific': Chiton articulatus (Mollusca: Polyplacophora). Research Ideas and Outcomes 6: e60446. https://doi.org/10.3897/rio.6.e60446

Figure 2 Example of sale and consumption of meat (foot, in colloquial Spanish "Lengua") of Chiton articulatus. Sale of chitons in beaches of Acapulco (left upper). Sale of chitons in streets of Pochutla, Oaxaca, close to Huatulco (left lower). Dish (Lengua a la Mexicana) in a restaurant in Huatulco (right upper). Artisanal fishing of chitons for a family weekend reunion at Puerto Angel, Oaxaca close to Huatulco (right lower).