Data from: Nonlinear effects of intraspecific competition alter landscape-wide scaling up of ecosystem function
Contributors: Little, Chelsea Jean, Fronhofer, Emanuel A., Altermatt, Florian
... A major focus of ecology is to understand and predict ecosystem function across scales. Many ecosystem functions are only measured at local scales, while their effects occur at a landscape level. Here, we investigate how landscape-scale predictions of ecosystem function depend on intraspecific competition, a fine-scale process, by manipulating intraspecific density of shredding macroinvertebrates and examining effects on leaf litter decomposition, a key function in freshwater ecosystems. For two species, we found that per-capita leaf processing rates declined with increasing density following power functions with negative exponents, likely due to interference competition. To demonstrate consequences of this nonlinearity, we scaled up estimates of leaf litter processing from shredder abundance surveys in 10 replicated headwater streams. In accordance with Jensen’s inequality, applying density-dependent consumption rates reduced estimates of catchment-scale leaf consumption by an order of magnitude relative to density-independent rates. Density-dependent consumption estimates aligned closely with metabolic requirements in catchments with large, but not small, shredder populations. Importantly, shredder abundance was not limited by leaf litter availability and catchment-level leaf litter supply was much higher than estimated consumption. Thus leaf litter processing was not limited by resource supply. Our work highlights the need for scaling-up which accounts for intraspecific interactions.
Data from: Evidence for individual discrimination and numerical assessment in collective antipredator behaviour in wild jackdaws (Corvus monedula)
Contributors: Coomes, Jenny R., McIvor, Guillam E., Thornton, Alex
... Collective responses to threats occur throughout the animal kingdom but little is known about the cognitive processes underpinning them. Antipredator mobbing is one such response. Approaching a predator may be highly risky, but the individual risk declines and the likelihood of repelling the predator increases in larger mobbing groups. The ability to appraise the number of conspecifics involved in a mobbing event could therefore facilitate strategic decisions about whether to join. Mobs are commonly initiated by recruitment calls, which may provide valuable information to guide decision-making. We tested whether the number of wild jackdaws responding to recruitment calls was influenced by the number of callers. As predicted, playbacks simulating three or five callers tended to recruit more individuals than playbacks of one caller. Recruitment also substantially increased if recruits themselves produced calls. These results suggest that jackdaws use individual vocal discrimination to assess the number of conspecifics involved in initiating mobbing events, and use this information to guide their responses. Our results show support for the use of numerical assessment in antipredator mobbing responses and highlight the need for a greater understanding of the cognitive processes involved in collective behaviour.
Data from: Social spider webs harbor largely consistent bacterial communities across broad spatial scales
Contributors: Keiser, Carl N., Hammer, Tobin J., Pruitt, Jonathan N.
... Social animals that live in domiciles constructed from biomaterials may facilitate microbial growth. Spider webs are one of the most conspicuous biomaterials in nature, yet almost nothing is known about the potential for webs to harbor microbes, even in social spiders that live in dense, long-term aggregations. Here, we tested whether the dominant bacteria present in social spider webs vary across sampling localities and whether the more permanent retreat web harbors compositionally distinct microbes from the more ephemeral capture webs in the desert social spider Stegodyphus dumicola. We also sampled spider cuticles and prey items in a subset of colonies. We found that spider colonies across large spatial scales harbored similar web-associated bacterial communities. We also found substantial overlap in bacterial community composition between spider cuticle, prey, and web samples. These data suggest that social spider webs can harbor characteristic microbial communities and potentially facilitate microbial transmission among individuals, and this study serves as the first step towards understanding the microbial ecology of these peculiar animal societies.
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Data from: Antibodies to Plasmodium vivax Reticulocyte binding protein 2b are associated with protection against P. vivax malaria in populations living in low malaria transmission regions of Brazil and Thailand
Contributors: He, Wen-Qiang, Karl, Stephan, White, Michael, Nuitragool, Wang, Monteiro, Wuelton, Kuehn, Andrea, Gruszczyk, Jakub, Franca, Camila, Sattabongkot, Jetsumon, Lacerda, Marcus
... Background. The Plasmodium vivax Reticulocyte Binding Protein (PvRBP) family is involved in red blood cell recognition and members of this family are potential targets for antibodies that may block P. vivax invasion. To date, the acquisition of immunity against PvRBPs in low malaria transmission settings and in a broad age group of exposed individuals has not been investigated. Methodology/Principal Findings. Total IgG antibody levels to six members of the PvRBP family (PvRBP1a, PvRBP1b, PvRBP2a, PvRBP2b, a non-binding fragment of PvRBP2c (PvRBP2cNB) and PvRBP2-P2) were measured in samples collected from individuals living in two regions of low P. vivax endemicity in Brazil and Thailand. In both settings, levels of total IgG to PvRBP1a, PvRBP2b, PvRBP2cNB, and PvRBP2P-2 increased statistically significantly with age as shown by the correlation coefficient, denoted as rho (rho=0.17-0.49; P<0.001), and those to PvRBP1a, PvRBP2b and PvRBP2cNB were significantly higher in infected individuals than those in uninfected individuals by using Wilcoxon's signed-rank test (P<0.001). Of the six PvRBPs examined, only antibodies to PvRBP2b were associated with protection against clinical malaria in both settings (Hazard Ratio=0.45-0.50, P≤0.032). Conclusion/Significance. Our results indicate that PvRBP2b warrants further preclinical development as a blood-stage vaccine candidate against P. vivax. Total IgG responses to PvRBPs were also shown to be promising immunological markers of exposure to P. vivax infection.
Data from: Lack of activity of recombinant HIF prolyl hydroxylases (PHDs) on reported non-HIF substrates
Contributors: Cockman, Matthew E., Lippl, Kerstin, Tian, Ya-Min, Pegg, Hamish B., Figg, William D., Abboud, Martine I., Heilig, Raphael, Fischer, Roman, Myllyharju, Johanna, Schofield, Christopher J.
... Human and other animal cells deploy three closely related dioxygenases (PHD 1, 2 and 3) to signal oxygen levels by catalysing oxygen regulated prolyl hydroxylation of the transcription factor HIF. The discovery of the HIF prolyl-hydroxylase (PHD) enzymes as oxygen sensors raises a key question as to the existence and nature of non-HIF substrates, potentially transducing other biological responses to hypoxia. Over 20 such substrates are reported. We therefore sought to characterise their reactivity with recombinant PHD enzymes. Unexpectedly, we did not detect prolyl-hydroxylase activity on any reported non-HIF protein or peptide, using conditions supporting robust HIF-α hydroxylation. We cannot exclude PHD-catalysed prolyl hydroxylation occurring under conditions other than those we have examined. However, our findings using recombinant enzymes provide no support for the wide range of non-HIF PHD substrates that have been reported.
Data from: Nature and significance of intraspecific variation in the early Cambrian oryctocephalid trilobite Oryctocephalites palmeri Sundberg and McCollum, 1997
Contributors: Webster, Mark, Sundberg, Frederick
... Oryctocephalid trilobites are seldom abundant and often tectonically deformed, creating problems for robust species delimitation and compromising their utility in biostratigraphic and evolutionary studies. By studying more than 140 specimens recovered from the upper portion of the Combined Metals Member (Pioche Formation, Nevada; Cambrian Stage 4, Series 2), we exploit a rare opportunity to explore how morphological variation among oryctocephalid specimens is partitioned into intraspecific variation versus interspecific disparity. Qualitative and quantitative analyses reveal that two species are represented: Oryctocephalites palmeri Sundberg and McCollum, 1997 and Oryctocephalites sp. A, the latter known from a single cranidium stratigraphically below all occurrences of the former. In contrast to the conclusions of a previous study, there is no evidence of cranidial dimorphism in O. palmeri. However, that species exhibits considerable variation in cranidial shape and pygidial spine arrangement and number. Cranidial shape variation within O. palmeri is approximately one-half of the among-species disparity within the genus. Comparison of cranidial shape between noncompacted and compacted samples reveals that compaction causes significant change in mean shape and an increase in shape variation; such changes are interpretable in terms of observed fracture patterns. Nontaphonomic variation is partitioned into ontogenetic and nonallometric components. Those components share similar structure with each other and with interspecific disparity, suggesting that ontogenetic shape change might be an important source of variation available for selection. This highlights the importance of ontogenetic and taphonomic sources of variation with respect to species delimitation, morphospace occupation, and investigation of evolutionary patterns and processes.
Data from: The biodiversity benefit of native forests and mixed-species plantations over monoculture plantations
Contributors: Wang, Xiaoyang, Hua, Fangyuan, Wang, Lin, Wilcove, David, Yu, Douglas W
... Aim: China’s Grain for Green Program (GFGP) is the largest reforestation program in the world and has been operating since 1999. The GFGP has promoted the establishment of tree plantations over the restoration of diverse native forests. In a previous study, we showed that native forests support higher species richness and abundance of birds and bees than GFGP plantations and that mixed-species GFGP plantations support a higher level of bird diversity than other GFGP monocultures. Here, we use metabarcoding of arthropod diversity to test the generality of these results. Location: Sichuan, China Methods: We sampled arthropod communities using pan traps in the land-cover types concerned under the GFGP. These land-use types include croplands, native forests, and the dominant GFGP reforestation outcomes: monoculture and mixed-species plantations. We used COI-amplicon sequencing (‘metabarcoding’) of the arthropod samples to quantify and assess the arthropod community profiles associated with each land-cover type. Results: Native forests support the highest levels of arthropod species diversity, followed by mixed-species plantations, followed by bamboo and other monocultures. Also, the arthropod community in native forests shares more species with mixed-species plantations than it does with any of the monocultures. Together, these results broadly corroborate our previous conclusions on birds and bees but show a higher arthropod biodiversity value of mixed-species plantations than previously indicated by bees alone. Main conclusion: In our previous study, we recommended that GFGP should prioritize the conservation and restoration of native forests, and where plantations are to be used, we recommended promote mixed-species arrangements over monocultures. Both these recommendations should result in more effective protection of terrestrial biodiversity, which is an important objective of China’s land-sustainability spending. The results of this study strengthen these recommendations because our policy prescriptions are now also based on a dataset that includes over 500 species-resolution taxa, ranging across the Arthropoda.
Data from: The conservation genomics of the endangered distylous gypsophile Oreocarya crassipes (Boraginaceae)
Contributors: Cohen, James I.
... The Chihuahuan Desert includes many endemic angiosperm species, some having very restricted geographic ranges. One of these species is Oreocarya crassipes (I. M. Johnst.) Hasenstab & M. G. Simpson, an endangered distylous gypsophile from the Trans-Pecos region in southern Brewster County, Texas, USA. The species is known from 10 populations, and this small number of populations, human development in the area, a distylous breeding system, and edaphic requirements threaten the long-term viability of the species. Using both hundreds of single nucleotide polymorphisms identified via tunable genotyping-by-sequencing (tGBS) and 10 microsatellite loci, patterns of genetic diversity, demography, selection, and migration were examined for 192 individuals from four populations of O. crassipes. From the sampled individuals, two populations (clusters) were identified via multiple methodologies and with both types of data. With SNP data, population substructure was further resolved among one of these populations to identify two distinct groups of individuals. Multiple individuals recognized as having mixed ancestry, along with Fst values and AMOVA results, provide evidence of genetic exchange among populations, which is less common for gypsophiles than non-gypsophiles, and the rate of migration among populations has been increasing recently. The Fst values for O. crassipes are more similar to those of other rare species than to other gypsophiles. Additionally, while distyly specifically does not necessarily impact the population genetics of the species, allogamy, which is facilitated by distyly, seems to have played a role in the genetic structure of O. crassipes.
Contributors: Hill, Geoffrey, Hood, Wendy, Ge, Zhiyuan, Grinter, Rhys, Greening, Chris, Johnson, James, Park, Noel, Taylor, Halie, Andreasen, Victoria, Powers, Matthew
... Carotenoid coloration is widely recognized as a signal of individual condition in various animals, but despite decades of study, the mechanisms that link carotenoid coloration to condition remain unresolved. Most birds with red feathers convert yellow dietary carotenoids to red carotenoids in an oxidation process requiring the gene encoding the putative cytochrome P450 enzyme CYP2J19. Here, we tested the hypothesis that the process of carotenoid oxidation and feather pigmentation is functionally linked to mitochondrial performance. Consistent with this hypothesis, we observed high levels of red ketolated carotenoids associated with the hepatic mitochondria of molting wild house finches (Haemorhous mexicanus), and upon fractionation, we found the highest concentration of ketolated carotenoids in the inner mitochondrial membrane. We further found that the redness of growing feathers was positively related to the performance of liver mitochondria. Structural modeling of CYP2J19 supports a direct role of this protein in carotenoid ketolation that may be functionally linked to cellular respiration. These observations suggest that feather coloration serves as a signal of core functionality through inexorable links to cellular respiration in the mitochondria.
Data from: The ecology and evolution of seed predation by Darwin's finches on Tribulus cistoides on the Galápagos Islands
Contributors: Carvajal-Endara, Sofía, Hendry, Andrew P., Emery, Nancy C., Neu, Corey P., Carmona, Diego, Gotanda, Kiyoko M., Davies, T. Jonathan, Chaves, Jaime A., Johnson, Marc T. J
... Predator-prey interactions play a key role in the evolution of species traits through antagonistic coevolutionary arms-races. The evolution of beak morphology in the Darwin’s finches in response to competition for seed resources is a classic example of evolution by natural selection. The seeds of Tribulus cistoides are an important food source for the largest ground finch species (Geospiza fortis, G. magnirostris, and G. conirostris) in dry months, and the hard spiny morphology of the fruits are a potent agent of selection that drives contemporary evolutionary change in finch beak morphology. Although the effects of these interaction on finches are well known, how seed predation affects the ecology and evolution of the plants is poorly understood. Here we examine whether seed predation by Darwin’s finches affects the ecology and evolution of T. cistoides. We ask whether the intensity of seed predation and the strength of natural selection by finches on fruit defense traits varies among populations, islands, years, or with varying finch community composition (i.e., the presence/absence of the largest beaked species, which feed on T. cistoides most easily). We then further test whether T. cistoides fruit defenses have diverged among islands in response to spatial variation in finch communities. We addressed these questions by examining seed predation by finches in 30 populations of T. cistoides over three years. Our study reveals three key results. First, Darwin’s finches strongly influence T. cistoides seed survival, whereby seed predation varies with differences in finch community composition among islands and in response to inter-annual fluctuations in precipitation. Second, finches impose phenotypic selection on T. cistoides fruit morphology, whereby smaller and harder fruits with longer or more spines exhibited higher seed survival. Variation in finch community composition and precipitation also explains variation in phenotypic selection on fruit defense traits. Third, variation in the number of spines on fruits among islands is consistent with divergent phenotypic selection imposed by variation in finch community composition among islands. These results suggest that Darwin’s finches and T. cistoides are experiencing an ongoing coevolutionary arms-race, and that the strength of this coevolution varies in space and time.