Find research datasets worth reusing

opencc-zeroSep 2020View details →

Code and data from: A mobile sex-determining region, male-specific haplotypes, and rearing environment influence age at maturity in Chinook salmon.

Variation in age at maturity is an important contributor to life history and demographic variation within and among species. The optimal age at maturity can vary by sex, and the ability of each sex to evolve towards its fitness optimum depends on the genetic architecture of maturation. Using GWAS of RAD sequencing data, we show that age at maturity in Chinook salmon exhibits sex-specific genetic architecture, with age at maturity in males governed by large (up to 20Mb) male-specific haplotypes. These regions showed no such effect in females. We also provide evidence for translocation of the sex-determining gene between two different chromosomes. This has important implications for sexually antagonistic selection, particularly that sex-linkage of adaptive genes may differ within and among populations based on chromosomal location of the sex-determining gene. Our findings will facilitate research into the genetic causes of shifting demography in Chinook salmon as well as a better understanding of sex-determination in this species and Pacific salmon in general.

opencc-zeroSep 2020View details →

Data from: Interactive effects of social environment, age and sex on immune responses in Drosophila melanogaster

Social environments have been shown to have multiple effects on individual immune responses. For example, increased social contact might signal greater infection risk and prompt a prophylactic upregulation of immunity. This differential investment of resources may in part explain why social environments affect ageing and lifespan. Our previous work using Drosophila melanogaster showed that single-sex social contact reduced lifespan for both sexes. Here, we assess how social interactions (isolation or contact) affect susceptibility to infection, phagocytotic activity and expression of a subset of immune and stress related genes in young and old flies of both sexes. Social contact had a neutral, or even improved, effect on post-infection lifespan in older flies and reduced the expression of stress response genes in females, however it reduced phagocytotic activity. Together, these findings indicate that social contact in D. melanogaster does not have a predictable impact on immune responses and does not simply trade-off immune investment with lifespan.

opencc-zeroOct 2020View details →

Inselberg, taxa, environment data for Inselberg floristics exemplify coast to inland OCBIL transition in a global diversity hotspot

We examined floristics of granitoid inselbergs in the hitherto poorly documented southeastern region of the Southwest Australian Floristic Region (SWAFR) and adjacent Great Western Woodlands, addressing several hypotheses of OCBIL theory. We found exceptional taxon richness (1,550 taxa on 89 inselbergs, with 58 well-sampled inselbergs and 1493 taxa chosen for detailed analyses). Granite inselberg endemism declines towards the arid inland, though taxon richness does not. OCBILs are likely found up to 500 km inland, not ca. 300 km as previously hypothesized. Hybrids are extremely rare on the 58 inselbergs analysed, whereas rare species, including singletons, are abundant. Conversely, exotic weeds are less common than in the whole SWAFR flora (8.2% vs 12.8%). Granite plant communities are distributed in parallel bands to the south coast, approximating the general transition from the Esperance and Boylya Floristic Districts across the SWAFR boundary north into the Arid Zone's Great Western Woodlands. Positive correlations exist between several plant life forms and inselberg area, save for geophytes. There is a decrease from the coast inland for most life forms, except for annual and graminoid herbs that increase in taxa inland. Thus, inselberg floristics exemplify the coast-to-inland OCBIL transition in this global biodiversity hotspot.

opencc-by-4.0Oct 2020View details →

Performance Curves for better Performance Predictions of Parallel Applications in Multicore Environments

Model-based performance prediction for parallel applications on architectural models suffers from significant inaccuracies.  A major reason is that current model-based performance prediction approaches consider CPU speed as a single metric for multicore performance.  Thus, in this paper, we investigate performance-influencing factors for multicore environments, execute extensive experiments to determine their impact on the performance, and extract performance curves for characteristic behaviours. As a result, we present a set of performance curves to software engineers which enables them to increase the performance prediction power in an easy to use manner.  Further, we evaluate the approach using 13 SPEC Benchmarks and could show that our approach reduces the prediction error by up to 60% and increases the accuracy by up to 98% for certain scenarios.

opencc-zeroSep 2020View details →

Data from: Regional response of grassland productivity to changing environment conditions influenced by limiting factors

Regional differences and regulatory mechanisms of vegetation productivity response to changing environmental conditions constitute a core issue in macroecological researches. To verify the main limiting factors of different macrosystems [temperature-limited Tibetan Plateau (TP), precipitation-limited Mongolian Plateau (MP), and nutrient-limited Loess Plateau (LP)], we conducted a comparative survey of the east-west grassland transects on the three plateaus and explored the factors limiting regional productivity and their underlying mechanisms. The results showed that aboveground net primary productivity (ANPP) of LP (109.10 ± 16.76 g m−2 yr−1) was significantly higher than that of MP (66.71 ± 11.11 g m−2 yr−1) and TP (57.02 ± 10.59 g m−2 yr−1). The response rate of ANPP with environmental changes was different among different plateaus, being closely related to the main limiting factors. On MP, this was precipitation, on LP it was temperature and nutrients, and on TP, it was non-specific, reflecting restriction by the extremely low temperature. After autocorrelation screening of environmental factors, different regions exhibited different productivity response mechanisms. MP was mainly influenced by temperature and precipitation, LP was influenced by temperature and nutrient, and TP was influenced by nutrient, reflecting the modifying effect of the main limiting factors. The effect of each regional environment on ANPP was 72.56% on average and only 27.18% after simple regional integration. The regional model could optimize the simulation error of the integrated model, and the relative deviations in MP, LP, and TP were reduced by 31.76%, 17.22%, and 2.23%, respectively. These findings indicate that the grasslands on the three plateaus may have different or even the opposite mechanisms to control productivity.

opencc-zeroOct 2020View details →

Going with the flow: corals in high-flow environments can beat the heat

Coral reefs are experiencing unprecedented declines in health on a global scale leading to severe reductions in coral cover. One major cause of this decline is increasing sea surface temperature. However, conspecific colonies separated by even small spatial distances appear to show varying responses to this global stressor. One factor contributing to differential responses to heat stress is variability in the coral's micro-environment, such as the amount of water flow a coral experiences. High flow provides corals with a variety of health benefits, including heat stress mitigation. Here, we investigate how water flow affects coral gene expression and provides resilience to increasing temperatures. We examined host and photosymbiont gene expression of Acropora cf. pulchra colonies in discrete in situ flow environments during a natural bleaching event. In addition, we conducted controlled ex situ tank experiments where we exposed A. cf. pulchra to different flow regimes and acute heat stress. Notably, we observed distinct flow-driven transcriptomic signatures related to energy expenditure, growth, heterotrophy and a healthy coral host-photosymbiont relationship. We also observed disparate transcriptomic responses during bleaching recovery between the high- and low-flow sites. Additionally, corals exposed to high flow showed "frontloading" of specific heat-stress related genes such as heat shock proteins, antioxidant enzymes, genes involved in apoptosis regulation, innate immunity, and cell adhesion. We posit that frontloading is a result of increased oxidative metabolism generated by the increased water movement. Gene frontloading may at least partially explain the observation that colonies in high-flow environments show higher survival and/or faster recovery in response to bleaching events.

opencc-zeroOct 2020View details →

Evolution in alternating environments with tunable inter-landscape correlations

Natural populations are often exposed to temporally varying environments. Evolutionary dynamics in varying environments have been extensively studied, though understanding the effects of varying selection pressures remains challenging. Here we investigate how cycling between a pair of statistically related fitness landscapes affects the evolved fitness of an asexually reproducing population. We construct pairs of fitness landscapes that share global fitness features but are correlated with one another in a tunable way, resulting in landscape pairs with specific correlations. We find that switching between these landscape pairs, depending on the ruggedness of the landscape and the inter-landscape correlation, can either increase or decrease steady-state fitness relative to evolution in single environments. In addition, we show that switching between rugged landscapes often selects for increased fitness in both landscapes, even in situations where the landscapes themselves are anti-correlated. We demonstrate that positively correlated landscapes often possess a shared maximum in both landscapes that allows the population to step through sub-optimal local fitness maxima that often trap single landscape evolution trajectories. Finally, we demonstrate that switching between anti-correlated paired landscapes leads to ergodic-like dynamics where each genotype is populated with nonzero probability, dramatically lowering the steady-state fitness in comparison to single landscape evolution.

Dataset supporting the findings of Alleon et al. "Inherited geochemical diversity of 3.4 Ga organic films from the Buck Reef Chert, South Africa.." published in Communications Earth & Environment

Raman, SEM, TEM, and XANES data supporting the findings reported by Alleon et al. in Communications Earth & Environment.

Alligator Reef Fishes species checklist 2020.xlsx Spreadsheet of the checklist of fish species documented in the study area of Alligator Reef & environs, Florida Keys, USA, by Starck, Estapé & Estapé (2017), updated with 14 additional species records

Alligator Reef Fishes species checklist 2020.xlsx  Spreadsheet of the checklist of fish species documented in the study area of Alligator Reef & environs, Florida Keys, USA, by Starck, Estapé & Estapé (2017), updated with 14 additional species records

Alligator Reef Fishes species photographs 2020: updated version of Fishes of Alligator Reef & environs, Florida Keys, USA. Starck, Estapé & Estapé (2017) obtained 323 images of 318 fish species, now we add 33 additional photographs of species listed in 2017, plus 13 photographs of new records

Alligator Reef Fishes species photographs 2020: updated version of Fishes of Alligator Reef & environs, Florida Keys, USA. Starck, Estapé & Estapé (2017) obtained 323 images of 318 fish species, now we add 33 additional photographs of species listed in 2017, plus 13 photographs of new records since 2017, to make a total of 369 images of 364 fish species in the study area (all but 4 taken by Carlos Estapé and Allison Morgan Estapé).

opencc-zeroNov 2020View details →

Data from: The effect of social environment on bird song: listener-specific expression of a sexual signal

Animal signals should consistently differ among individuals to convey distinguishable information about the signalers. However, behavioral display signals, such as bird song are also loaded with considerable within-individual variance with mostly unknown function. We hypothesized that the immediate social environment may play a role in mediating such variance component, and investigated in the collared flycatcher (Ficedula albicollis) if the identity and quality of listeners could affect song production in signalers. After presenting territorial males with either a female or male social stimulus, we found in the subsequent song recordings that the among-stimulus effects corresponded to non-zero variance components in several acoustic traits indicating that singing males are able to plastically adjust their songs according to stimulus identity. Male and female stimuli elicited different responses as the identity of the female stimuli affected song complexity only, while the identity of male stimuli altered also song length, maximum frequency and song rate. The stimulus-specific effect on song in some cases decreased with time, being particularly detectable right after the removal of the stimulus and ceasing later, but this pattern varied across the sex of the stimulus and the song traits. We were able to identify factors that can explain the among-stimulus effects (e.g. size and quality of the stimuli) with roles that also varied among song traits. Our results confirm that the variable social environment can raise considerable variation in song performance, highlighting that within-individual plasticity of bird song can play important roles in sexual signaling.

opencc-zeroNov 2020View details →

Hybridization between Felis silvestris silvestris and Felis silvestris catus in two contrasted environments in France

European wildcat (Felis silvestris silvestris) populations are fragmented throughout most of the whole range of the sub-species, and may be threatened by hybridization with the domestic cat F.s. catus. The underlying ecological processes promoting hybridization, remain largely unknown. In France, wildcats are mainly present in the North-East and signs of their presence in the Pyrenees have been recently provided. However, no studies have been carried out in the French Pyrenees to assess their exposure to hybridization. We compared two local populations of wildcats, one living in a continuous forest habitat in the French Pyrenees, the other living in a highly fragmented forest-agricultural landscape in Northeastern France to get insights into the variability of hybridization rates. Strong evidence of hybridization was detected in Northeastern France and not in the Pyrenees. Close kin in the Pyrenees were not found in the same geographic location contrary to what was previously reported for females in the Northeastern wildcat population. The two wildcat populations were significantly differentiated (Fst = 0.072) to an extent close to what has been reported (Fst = 0.103) between the Iberian population, from which the Pyrenean population may originate, and the German population, which is connected to the Northeastern population. The genetic diversity of the Pyrenean wildcats was lower than that of Northeastern wildcat populations in France and in other parts of Europe. The lower hybridization in the Pyrenees may result from the continuity of natural forest habitats. Further investigations should focus on linking landscape features to hybridization rates working on local populations.

Fig. 4. A–C in A new Dicranophragma (Diptera: Limoniidae) from a hypogeous environment in Catalonia (Iberian Peninsula)

Fig. 4. A–C. Male terminalia of Dicranophragma (B.) relictum Mederos sp. nov. A. Dorsal view. B. Ventral view. C. Lateral view. D–I. Detail of inner and outer gonostylus (dorsal view) and aedeagal complex (lateral view). D, G. D. (B.) relictum Mederos sp. nov. E, H. D. (B.) nemorale (Meigen, 1818). F, I. D. (B.) adjunctum (Walker, 1848). Scale bars = 0.25 mm (images E–F, H–I after Starý & Reusch 2009).

Figs 51–58 in New fossil genus and new extant species of diatoms (Stephanodiscaceae, Bacillariophyceae) from Pleistocene sediments in the Neotropics (Guatemala, Central America): adaptation to a changing environment?

Figs 51–58 (next page). Type material of fossil lacustrine diatom Discostella gabinii Paillès & Sylvestre sp. nov., Lake Petén-Itzá (Guatemala); SEM valve views. 51. External valve view showing a colliculate central area with scattered areolae, knots and papillae, and a marginal area with finely punctuated radiating striae. 52. External view of a large specimen with numerous areolae in the central area; the striae have rounded ends near the margin. 53. Valve view of a complete corroded frustule showing valve interior with medium sized alveoli and marginal fultoportulae located in the middle of every 3rd to 5th alveoli; open valvocopula present. 54. External openings of marginal fultoportulae located just below the crescent end of the striae (white arrowheads). 55. Internal valve view with medium sized alveoli and a large expansion of the smooth central lamina; marginal fultoportulae located on every 3rd to 5th alveoli. 56. Internal valve view with smooth central area with a single areola; open valvocopula present. 57. Detail view of valve margin; marginal fultoportulae composed of one tube with two satellite pores positioned on the external ends of the alveoli; rimoportula with vertically orientated lips, located between two costae at the edge of an alveolus and within the ring of marginal fultoportulae. 58. Detail view of the valve margin with an eroded marginal fultoportula at the edge of the alveolus; note a row of fine pores on the interior of the girdle band (white arrowheads). Scale bars = 51–56 = 2 µm; 57–58 = 1 µm.

Figs 33–40 in New fossil genus and new extant species of diatoms (Stephanodiscaceae, Bacillariophyceae) from Pleistocene sediments in the Neotropics (Guatemala, Central America): adaptation to a changing environment?

Figs 33–40 (next page). Type material of fossil lacustrine diatom Cyclocostis rolfii Paillès gen. et sp. nov.; SEM internal valve views. 33. Broken valve revealing internal structure; note the reduced cell cavity (white arrowhead). 34. Valve interior showing strong anastomosing ribs merging to a central siliceous ring; central lamina absent; marginal fultoportulae located on every 2nd recessed costa; note the slightly deflected rimoportula (white arrow). 35. Valve interior of a small specimen with strong thick ribs and reduced alveoli, central lamina absent; note the single valve face fultoportula (white arrowhead) located near the valve margin on the raised central area; open valvocopula in place. 36. Broken valve margin showing complex alveolar structure: two thick ribs with a median recessed costa, more inwardly bent, carrying marginal fultoportula composed of one tube and three satellite pores. 37. Valve interior of a small specimen with valvocopula. 38. Heart shaped alveoli due to the marginal fultoportula located on median recessed costa. 39. Internal valve view with marginal fultoportulae and rimoportula arranged in a ring below the valve margin; the single valve face fultoportula (double white arrowhead) is always on the opposite side from the rimoportula (single white arrowhead). 40. Detail of the single valve face fultoportula composed of a short tube and three satellite pores always in an eccentric position. Scale bars: 33, 34 = 5 µm; 35, 39 = 2 µm; 36–38 = 1 µm; 40 = 0.5 µm.

opencc-zeroDec 2020View details →

Divergence of responses to variable socio-sexual environments in laboratory populations of Drosophila melanogaster evolving under altered operational sex-ratios

Post-copulatory sexual selection (PSS) is an important selective force that determines fitness in polyandrous species. PSS can be intense in some cases and can drive the evolution of remarkable ejaculate properties. In males, investment in ejaculate plays an important role in the outcome of PSS. Thus, males are expected to adaptively tailor their ejaculate according to the perceived competition in their vicinity. Plastic responses in ejaculate investment to variation in intra-sexual competition are disparate and widespread in males. We investigated the evolution of plasticity in reproductive traits using Drosophila melanogaster populations evolving for more than 150 generations under male- or female-biased sex ratios. When exposed to different numbers of competitors early in their life, males from these two regimes responded differently in terms of their copulation duration and sperm competitive ability. In addition, the effect of this early life experience wore off at different rates in males of male-biased and female-biased regimes with increasing time from the removal of competitive cues. Furthermore, our study finds that males change their reproductive strategies depending upon the identity of rival males. Together, our results provide evidence of the evolution of male reproductive investment that depends on socio-sexual cues experienced early in life.

opencc-zeroJan 2021View details →

Spatial and temporal variation in prey colour patterns for background-matching across a continuous heterogeneous environment

In heterogeneous habitats, camouflage via background-matching can be challenging because visual characteristics can vary dramatically across small spatial scales. Additionally, temporal variation in signalling functions of colouration can affect crypsis, especially when animals use colouration seasonally for intraspecific signalling (e.g. mate selection). We currently have a poor understanding of how wild prey optimise background-matching within continuously heterogeneous habitats, and whether this is affected by requirements of intraspecific signalling across biological seasons. Here, we quantified colour patterns of a wild population of shore skink (Oligosoma smithi), a variably coloured lizard endemic to New Zealand, to 1) investigate whether background-matching varies across a vegetation gradient; 2) assess potential signalling functions of colour; and 3) to determine whether there is a trade-off between requirements for crypsis and intraspecific signalling in colouration across seasons. Although all pattern types occurred throughout the vegetation gradient, we found evidence for background-matching in skinks across the vegetation gradient, where dorsal brightness and pattern complexity corresponded with the proportion of vegetation cover. There was also a significant disparity between ventral colour (saturation) of juveniles and adults, and also between sexes, suggestive of sex recognition. However, there was little indication that colour was condition-dependent in adults. Despite some evidence for a potential role in signalling, crypsis did not greatly differ across seasons. Our study suggests that selection favours a mix of generalist and specialist background-matching strategies across continuously heterogeneous habitats.

opencc-by-4.0Jan 2021View details →

Figure 2 from: Raes N, Casino A, Goodson H, Islam S, Koureas D, Schiller EK, Schulman L, Tilley L, Robertson T (2020) White paper on the alignment and interoperability between the Distributed System of Scientific Collections (DiSSCo) and EU infrastructures - The case of the European Environment Agency (EEA). Research Ideas and Outcomes 6: e62361. https://doi.org/10.3897/rio.6.e62361

Figure 2 The current and required implementation readiness levels for DiSSCo to enter the construction phase of the DiSSCo RI. The grey arrows indicate the tasks for the DiSSCo Prepare project.

opencc-by-4.0Jan 2021View details →

Figure 3 from: Raes N, Casino A, Goodson H, Islam S, Koureas D, Schiller EK, Schulman L, Tilley L, Robertson T (2020) White paper on the alignment and interoperability between the Distributed System of Scientific Collections (DiSSCo) and EU infrastructures - The case of the European Environment Agency (EEA). Research Ideas and Outcomes 6: e62361. https://doi.org/10.3897/rio.6.e62361

Figure 3 An example of a simple Digital Specimen (Hardisty 2020). Arrows point to identifiers of linked information that was derived from or is related to the physical specimen it represents. dissco.tech blog post.