Soundscapes and deep learning enable tracking biodiversity recovery in tropical forests.

Tropical forest recovery is fundamental to addressing the intertwined climate and biodiversity loss crises. While regenerating trees sequester carbon relatively quickly, the pace of biodiversity recovery remains contentious. Here, we use bioacoustics and metabarcoding to measure forest recovery post-agriculture in a global biodiversity hotspot in Ecuador. We show that the community composition, and not species richness, of vocalizing vertebrates identified by experts reflects the restoration gradient. Two automated measures - an acoustic index model and a bird community composition derived from an independently developed Convolutional Neural Network - correlated well with restoration (adj-R² = 0.62 and 0.69, respectively). Importantly, both measures reflected composition of non-vocalizing nocturnal insects identified via metabarcoding. We show that such automated monitoring tools, based on new technologies, can effectively monitor the success of forest recovery, using robust and reproducible data.

Assessing the Viability of the Methylsulfinyl Radical-Ozone Reaction.

Although integral to remote marine atmospheric sulfur chemistry, the reaction between methylsulfinyl radical (CH3 SO) and ozone poses challenges to theoretical treatments. The lone theoretical study on this reaction reported an unphysically large barrier of 66 kcal mol-1 for abstraction of an oxygen atom from O3 by CH3 SO. Herein, we demonstrate that this result stems from improper use of MP2 with a single-reference, unrestricted Hartree-Fock (UHF) wavefunction. We characterized the potential energy surface using density functional theory (DFT), as well as multireference methodologies employing a complete active-space self-consistent field (CASSCF) reference. Our DFT PES shows, in contrast to previous work, that the reaction proceeds by forming an addition adduct [CH3 S(O3 )O] in a deep potential well of 37 kcal mol-1 . An O-O bond of this adduct dissociates via a flat, low barrier of 1 kcal mol-1 to give CH3 SO2 +O2 . The multireference computations show that the initial addition of CH3 SO+O3 is barrierless. These results provide a more physically intuitive and accurate picture of this reaction than the previous theoretical study. In addition, our results imply that the CH3 SO2 formed in this reaction can readily decompose to give SO2 as a major product, in alignment with the literature on CH3 SO reactions.

Parasites in space and time: a case study of haemosporidian spatiotemporal prevalence in urban birds.

Prevalence responses to anthropic factors differ across hosts and parasite species. We here analyzed the spatiotemporal variation of avian haemosporidian prevalence in bird assemblages of the Mooswald forest (i.e., urban greenspace; Freiburg, Germany), in response to local environmental features (e.g., water sources, human presence (visited)/absence (unvisited)) and bird-level traits (e.g., body condition, age, sex) in 2 years. We used a nested PCR protocol (mitochondrial (mt)DNA cytochrome b (cyt b) gene) and microscopy to determine haemosporidian infections. Prevalence was analyzed using a general linear multi-model (glmulti) approach with Akaike information criterion corrected for small samples (AICc), with subsequent model inferences using a GLMM on the best selected model, considering bird species as a random factor. Analyses were conducted for the main understory bird species (Blackcap - Sylvia atricapilla, Chaffinch - Coereba flaveola, Great Tit - Parus major, Blue Tit - Cyanistes caeruleus, European Robin - Erithacus rubecula, Blackbird - Turdus merula, Song Thrush - Turdus philomelos). We further conducted spatial autocorrelation analyses for all haemosporidian infections, and classification and regression trees (CARTs) for focal species. We analyzed a total of 544 samples of seven bird species. In 2011 prevalence for Haemoproteus/Plasmodium was 25.8% and 11.7% for Leucocytozoon. In 2013 prevalence for Haemoproteus/Plasmodium was 26.5% and 35.5% for Leucocytozoon. Haemosporidian prevalence was significantly different between some focal species. There was a negative association between distance to the nearest water source and prevalence in the year 2011, and the opposite pattern for the year 2013. However, when analyzed for the six focal species separately, such a relationship could change from a negative to a positive one, or there could be no relationship at all. For Leucocytozoon there was higher prevalence in the section of the forest visited by humans. We did not find spatial autocorrelation for prevalence across the study site, but there were statistically significant local spatial clusters in the visited section. Although there were similar responses of prevalence to some factors, infection patterns were generally bird species-specific. Thus, prevalence is a labile epidemiological parameter, varying spatiotemporally in an idiosyncratic way.

Reward regulation in plant-frugivore networks requires only weak cues.

Theory assumes that fair trade among mutualists requires highly reliable communication. In plant-animal mutualisms the reliability of cues that indicate reward quality is often low. Therefore, it is controversial whether communication allows animal mutualists to regulate their reward intake. Here we show that even loose relationships between fruit brightness and nutritional rewards (r2 = 0.11-0.35) allow birds to regulate their nutrient intake across distinct European plant-frugivore networks. Resident, over-wintering generalist frugivores that interact with diverse plant species select bright, lipid-rich fruits, whereas migratory birds select dark, sugar- and antioxidant-rich fruits. Both nutritional strategies are consistent with previous physiological experiments suggesting that over-wintering generalists aim to maximize their energy intake, whereas migrants aim to enhance the build-up of body fat, their immune response and oxidative status during migration. Our results suggest that animal mutualists require only weak cues to regulate their reward intake according to specific nutritional strategies.

Projected impacts of climate change on habitat availability for an endangered parakeet.

In tropical montane cloud forests, climate change can cause upslope shifts in the distribution ranges of species, leading to reductions in distributional range. Endemic species with small ranges are particularly vulnerable to such decreases in range size, as the population size may be reduced significantly. To ensure the survival of cloud forest species in the long term, it is crucial to quantify potential future shifts in their distribution ranges and the related changes in habitat availability in order to assure the long-term effectiveness of conservation measures. In this study, we assessed the influence of climate change on the availability of forested habitat for the endemic El Oro parakeet. We investigated the future range shift by modelling the climatic niche of the El Oro parakeets and projecting it to four different climate change scenarios. Depending on the intensity of climate change, the El Oro parakeets shift their range between 500 and 1700 m uphill by the year 2100. On average, the shift is accompanied by a reduction in range size to 15% and a reduction in forested habitat to only 10% of the original extent. Additionally, the connectivity between populations in different areas is decreasing in higher altitudes. To prevent a population decline due to habitat loss following an upslope range shift, it will be necessary to restore habitat across a large elevational span in order to allow for movement of El Oro parakeets into higher altitudes.

A2 to B Blood Type Incompatible Deceased Donor Kidney Transplantation in a Recipient Infected with the Human Immunodeficiency Virus: A Case Report.

BACKGROUND: With the introduction of the Kidney Allocation System in the United States in December 2014, transplant centers can list eligible B blood type recipients for A2 organ offers. There have been no prior reports of ABO incompatible A2 to B deceased donor kidney transplantation in human immunodeficiency virus-positive (HIV+) recipients to guide clinicians on enrolling or performing A2 to B transplantations in HIV+ candidates. We are the first to report a case of A2 to B deceased donor kidney transplantation in an HIV+ recipient with good intermediate-term results. METHODS AND RESULTS: We describe an HIV+ 39-year-old African American man with end-stage renal disease who underwent A2 to B blood type incompatible deceased donor kidney transplantation. Prior to transplantation, he had an undetectable HIV viral load. The patient was unsensitized, with his most recent anti-A titer data being 1:2 IgG and 1:32 IgG/IgM. Induction therapy of basiliximab and methylprednisolone was followed by a postoperative regimen of plasma exchange, intravenous immunoglobulin, and rituximab with maintenance on tacrolimus, mycophenolate mofetil, and prednisone. He had delayed graft function without rejection on allograft biopsy. Nadir serum creatinine was 2.0 mg/dL. He continued to have an undetectable viral load on the same antiretroviral therapy adjusted for renal function. CONCLUSIONS: To our knowledge, this is the first report of A2 to B deceased donor kidney transplantation in an HIV+ recipient with good intermediate-term results, suggesting that A2 donor kidneys may be considered for transplantation into HIV+ B-blood type wait list candidates.

Colour spaces in ecology and evolutionary biology.

The recognition that animals sense the world in a different way than we do has unlocked important lines of research in ecology and evolutionary biology. In practice, the subjective study of natural stimuli has been permitted by perceptual spaces, which are graphical models of how stimuli are perceived by a given animal. Because colour vision is arguably the best-known sensory modality in most animals, a diversity of colour spaces are now available to visual ecologists, ranging from generalist and basic models allowing rough but robust predictions on colour perception, to species-specific, more complex models giving accurate but context-dependent predictions. Selecting among these models is most often influenced by historical contingencies that have associated models to specific questions and organisms; however, these associations are not always optimal. The aim of this review is to provide visual ecologists with a critical perspective on how models of colour space are built, how well they perform and where their main limitations are with regard to their most frequent uses in ecology and evolutionary biology. We propose a classification of models based on their complexity, defined as whether and how they model the mechanisms of chromatic adaptation and receptor opponency, the nonlinear association between the stimulus and its perception, and whether or not models have been fitted to experimental data. Then, we review the effect of modelling these mechanisms on predictions of colour detection and discrimination, colour conspicuousness, colour diversity and diversification, and for comparing the perception of colour traits between distinct perceivers. While a few rules emerge (e.g. opponent log-linear models should be preferred when analysing very distinct colours), in general model parameters still have poorly known effects. Colour spaces have nonetheless permitted significant advances in ecology and evolutionary biology, and more progress is expected if ecologists compare results between models and perform behavioural experiments more routinely. Such an approach would further contribute to a better understanding of colour vision and its links to the behavioural ecology of animals. While visual ecology is essentially a transfer of knowledge from visual sciences to evolutionary ecology, we hope that the discipline will benefit both fields more evenly in the future.

Decline in territory size and fecundity as a response to carrying capacity in an endangered songbird.

Density-dependent processes are fundamental mechanisms for the regulation of populations. Ecological theories differ in their predictions on whether increasing population density leads to individual adjustments of survival and reproductive output or to dominance and monopolization of resources. Here, we use a natural experiment to examine which factors limit population growth in the only remaining population of the endangered pale-headed brush finch (Atlapetes pallidiceps). For three distinct phases (a phase of population suppression, 2001-2002; expansion due to conservation management, 2003-2008; and equilibrium phase, 2009-2014), we estimated demographic parameters with an integrated population model using population size, the proportion of successfully breeding pairs and their productivity, territory size, and mark-recapture data of adult birds. A low proportion of successful breeders due to brood parasitism (0.42, 95% credible interval 0.26-0.59) limited population growth before 2003; subsequent culling of the brood parasite resulted in a two-fold increase of the proportion of successful breeders during the 'expansion phase'. When the population approached the carrying capacity of its habitat, territory size declined by more than 50% and fecundity declined from 1.9 (1.54-2.27) to 1.3 (1.12-1.53) chicks per breeding pair, but the proportion of successful breeders remained constant (expansion phase: 0.85; 0.76-0.93; equilibrium phase: 0.86; 0.79-0.92). This study demonstrates that limiting resources can lead to individual adjustments instead of despotic behavior, and the individual reduction of reproductive output at high population densities is consistent with the slow life-history of many tropical species.

Limited Dispersal and Significant Fine - Scale Genetic Structure in a Tropical Montane Parrot Species.

Tropical montane ecosystems are biodiversity hotspots harbouring many endemics that are confined to specific habitat types within narrow altitudinal ranges. While deforestation put these ecosystems under threat, we still lack knowledge about how heterogeneous environments like the montane tropics promote population connectivity and persistence. We investigated the fine-scale genetic structure of the two largest subpopulations of the endangered El Oro parakeet (Pyrrhura orcesi) endemic to the Ecuadorian Andes. Specifically, we assessed the genetic divergence between three sites separated by small geographic distances but characterized by a heterogeneous habitat structure. Although geographical distances between sites are small (3-17 km), we found genetic differentiation between all sites. Even though dispersal capacity is generally high in parrots, our findings indicate that dispersal is limited even on this small geographic scale. Individual genotype assignment revealed similar genetic divergence across a valley (~ 3 km distance) compared to a continuous mountain range (~ 13 km distance). Our findings suggest that geographic barriers promote genetic divergence even on small spatial scales in this endangered endemic species. These results may have important implications for many other threatened and endemic species, particularly given the upslope shift of species predicted from climate change.

Geographical distance and barriers explain population genetic patterns in an endangered island perennial.

Island plants are frequently used as model systems in evolutionary biology to understand factors that might explain genetic diversity and population differentiation levels. Theory suggests that island plants should have lower levels of genetic diversity than their continental relatives, but this hypothesis has been rejected in several recent studies. In the Azores, the population level genetic diversity is generally low. However, like in most island systems, there are high levels of genetic differentiation between different islands. The Azores lettuce, Lactuca watsoniana, is an endangered Asteraceae with small population sizes. Therefore, we expect to find a lower level of genetic diversity than in the other more common endemic Asteraceae. The intra- and interpopulation genetic structure and diversity of L. watsoniana was assessed using eight newly developed microsatellite markers. We included 135 individuals, from all 13 known populations in the study. Because our microsatellite results suggested that the species is tetraploid, we analysed the microsatellite data (i) in codominant format using PolySat (Principal Coordinate Analysis, PCoA) and SPAgedi (genetic diversity indexes) and (ii) in dominant format using Arlequin (AMOVA) and STRUCTURE (Bayesian genetic cluster analysis). A total of 129 alleles were found for all L. watsoniana populations. In contrast to our expectations, we found a high level of intrapopulation genetic diversity (total heterozigosity = 0.85; total multilocus average proportion of private alleles per population = 26.5 %, Fis = -0.19). Our results show the existence of five well-defined genetic groups, one for each of the three islands São Miguel, Terceira and Faial, plus two groups for the East and West side of Pico Island (Fst = 0.45). The study revealed the existence of high levels of genetic diversity, which should be interpreted taking into consideration the ploidy level of this rare taxon.

Energetics and transition-state dynamics of the F + HOCH3 → HF + OCH3 reaction.

The F + HOCH3 → HF + OCH3 reaction is a system with 15 internal degrees of freedom that can provide a benchmark for the development of theory for increasingly complex chemical reactions. The dynamics of this reaction were studied by photoelectron-photofragment coincidence (PPC) spectroscopy carried out on the F-(HOCH3) anion, aided by a computational study of both the anion and neutral potential energy surfaces, with energies extrapolated to the CCSDT(Q)/CBS level of theory. Photodetachment at 4.80 eV accesses both the reactant and product channels for this reaction. In the product channel (HF + OCH3 + e-) of the neutral potential energy surface, vibrationally excited HF products in addition to the stable product-channel hydrogen-bonded complex (FH-OCH3) are observed in the PPC and photoelectron spectra. In addition, experimental evidence is observed for the reactant-channel van der Waals complex (F-HOCH3), in good agreement with the theoretical predictions. The relative stability of these long-lived complexes was probed by reducing the ion beam energy, increasing the product time-of-flight, indicating lifetimes on the microsecond timescale for the reactant- and product-channel complexes as well as providing evidence for long-lived vibrational Feshbach resonances associated with the HF(v > 0) + OCH3 product states. This system will provide a model for extending full-dimensionality quantum dynamics to larger numbers of degrees of freedom.

Biodiversity at multiple trophic levels is needed for ecosystem multifunctionality.

Many experiments have shown that loss of biodiversity reduces the capacity of ecosystems to provide the multiple services on which humans depend. However, experiments necessarily simplify the complexity of natural ecosystems and will normally control for other important drivers of ecosystem functioning, such as the environment or land use. In addition, existing studies typically focus on the diversity of single trophic groups, neglecting the fact that biodiversity loss occurs across many taxa and that the functional effects of any trophic group may depend on the abundance and diversity of others. Here we report analysis of the relationships between the species richness and abundance of nine trophic groups, including 4,600 above- and below-ground taxa, and 14 ecosystem services and functions and with their simultaneous provision (or multifunctionality) in 150 grasslands. We show that high species richness in multiple trophic groups (multitrophic richness) had stronger positive effects on ecosystem services than richness in any individual trophic group; this includes plant species richness, the most widely used measure of biodiversity. On average, three trophic groups influenced each ecosystem service, with each trophic group influencing at least one service. Multitrophic richness was particularly beneficial for 'regulating' and 'cultural' services, and for multifunctionality, whereas a change in the total abundance of species or biomass in multiple trophic groups (the multitrophic abundance) positively affected supporting services. Multitrophic richness and abundance drove ecosystem functioning as strongly as abiotic conditions and land-use intensity, extending previous experimental results to real-world ecosystems. Primary producers, herbivorous insects and microbial decomposers seem to be particularly important drivers of ecosystem functioning, as shown by the strong and frequent positive associations of their richness or abundance with multiple ecosystem services. Our results show that multitrophic richness and abundance support ecosystem functioning, and demonstrate that a focus on single groups has led to researchers to greatly underestimate the functional importance of biodiversity.

Floral colour change as a potential signal to pollinators.

Colour change in flowers (with age and/or after pollination) is taxonomically widespread, has evolved repeatedly, and has a range of putative selective benefits linked to modifying pollinator behaviour; however, this phenomenon seems paradoxically uncommon. We explore this paradox by reviewing the empirical evidence and argue that the evolution and maintenance of floral colour change as a signal to modify pollinator behaviour require special ecological circumstances that will often not be met across a plant population for a sustained number of generations, which potentially explains the scarcity of this phenomenon. We discuss alternative explanations for floral colour change and potentially fruitful lines of future research.

Forests of opportunities and mischief: disentangling the interactions between forests, parasites and immune responses.

Habitat characteristics determine the presence of individuals through resource availability, but at the same time, such features also influence the occurrence of parasites. We analyzed how birds respond to changes in interior forest structures, to forest management regimes, and to the risk of haemosporidian infections. We captured and took blood samples from blackcaps (Sylvia atricapilla) and chaffinches (Fringilla coelebs) in three different forest types (beech, mixed deciduous, spruce). We measured birds' body asymmetries, detected avian haemosporidians, and counted white blood cells as an immune measure of each individual per forest type. We used, to our knowledge for the first time, continuous forest structural parameters to quantify habitat structure, and found significant effects of habitat structure on parasite prevalence that previously have been undetected. We found three times higher prevalence for blackcaps compared with chaffinches. Parasite intensity varied significantly within host species depending on forest type, being lowest in beech forests for both host species. Structurally complex habitats with a high degree of entropy had a positive effect on the likelihood of acquiring an infection, but the effect on prevalence was negative for forest sections with a south facing aspect. For blackcaps, forest gaps also had a positive effect on prevalence, but canopy height had a negative one. Our results suggest that forest types and variations in forest structure influence the likelihood of acquiring an infection, which subsequently has an influence on host health status and body condition; however, responses to some environmental factors are host-specific.

Photodissociation of Cerium Oxide Nanocluster Cations.

Cerium oxide cluster cations, CexOy(+), are produced via laser vaporization in a pulsed nozzle source and detected with time-of-flight mass spectrometry. The mass spectrum displays a strongly preferred oxide stoichiometry for each cluster with a specific number of metal atoms x, with x ≤ y. Specifically, the most prominent clusters correspond to the formula CeO(CeO2)n(+). The cluster cations are mass selected and photodissociated with a Nd:YAG laser at either 532 or 355 nm. The prominent clusters dissociate to produce smaller species also having a similar CeO(CeO2)n(+) formula, always with apparent leaving groups of (CeO2). The production of CeO(CeO2)n(+) from the dissociation of many cluster sizes establishes the relative stability of these clusters. Furthermore, the consistent loss of neutral CeO2 shows that the smallest neutral clusters adopt the same oxidation state (IV) as the most common form of bulk cerium oxide. Clusters with higher oxygen content than the CeO(CeO2)n(+) masses are present with much lower abundance. These species dissociate by the loss of O2, leaving surviving clusters with the CeO(CeO2)n(+) formula. Density functional theory calculations on these clusters suggest structures composed of stable CeO(CeO2)n(+) cores with excess oxygen bound to the surface as a superoxide unit (O2(-)).

Locally rare species influence grassland ecosystem multifunctionality.

Species diversity promotes the delivery of multiple ecosystem functions (multifunctionality). However, the relative functional importance of rare and common species in driving the biodiversity-multifunctionality relationship remains unknown. We studied the relationship between the diversity of rare and common species (according to their local abundances and across nine different trophic groups), and multifunctionality indices derived from 14 ecosystem functions on 150 grasslands across a land-use intensity (LUI) gradient. The diversity of above- and below-ground rare species had opposite effects, with rare above-ground species being associated with high levels of multifunctionality, probably because their effects on different functions did not trade off against each other. Conversely, common species were only related to average, not high, levels of multifunctionality, and their functional effects declined with LUI. Apart from the community-level effects of diversity, we found significant positive associations between the abundance of individual species and multifunctionality in 6% of the species tested. Species-specific functional effects were best predicted by their response to LUI: species that declined in abundance with land use intensification were those associated with higher levels of multifunctionality. Our results highlight the importance of rare species for ecosystem multifunctionality and help guiding future conservation priorities.

Investment in attending to cues and the evolution of amplifiers.

Signals and cues are extensively used in social interactions across diverse communication systems. Here, we extend an existing theoretical framework to explore investment by emitters and perceivers in the fidelity with which cues and signals associated with the former are detected by the latter. Traits of the emitter that improve cue or signal fidelity without adding information are termed 'amplifiers'. We assume that each party can invest in improving fidelity but that it is increasingly costly the more fidelity is improved. Our model predicts that evolution of amplifier traits of a pre-existing cue occurs over a broader range of circumstances than evolution of signalling in situations where the emitter offered no pre-existing cue to the perceiver. It further predicts that the greater the intrinsic informational value of a cue, the more likely it is that the perceiver (and not the emitter) will invest in the fidelity of detecting that cue. A consequence of this predicted asymmetry is that true communication with reciprocal adaptations in emitters and perceivers to improve signal fidelity is likely to occur predominantly for traits of intermediate reliability. The corollary is that uncertainty of the perceiver will then be a key feature of communication. Uncertainty can arise because perceivers misinterpret signals or do not perceive them correctly, but here we argue that uncertainty is more fundamentally at the root of communication because traits that are intrinsically highly informative will induce only the perceiver and not the emitter to invest in improved fidelity of perception of that trait.

Morphology predicts species' functional roles and their degree of specialization in plant-frugivore interactions.

Species' functional roles in key ecosystem processes such as predation, pollination or seed dispersal are determined by the resource use of consumer species. An interaction between resource and consumer species usually requires trait matching (e.g. a congruence in the morphologies of interaction partners). Species' morphology should therefore determine species' functional roles in ecological processes mediated by mutualistic or antagonistic interactions. We tested this assumption for Neotropical plant-bird mutualisms. We used a new analytical framework that assesses a species's functional role based on the analysis of the traits of its interaction partners in a multidimensional trait space. We employed this framework to test (i) whether there is correspondence between the morphology of bird species and their functional roles and (ii) whether morphologically specialized birds fulfil specialized functional roles. We found that morphological differences between bird species reflected their functional differences: (i) bird species with different morphologies foraged on distinct sets of plant species and (ii) morphologically distinct bird species fulfilled specialized functional roles. These findings encourage further assessments of species' functional roles through the analysis of their interaction partners, and the proposed analytical framework facilitates a wide range of novel analyses for network and community ecology.