Phylogeny and species traits predict bird detectability

Avian acoustic communication has resulted from evolutionary pressures and ecological constraints. We therefore expect that auditory detectability in birds might be predictable by species traits and phylogenetic relatedness. We evaluated the relationship between phylogeny, species traits, and field‐based estimates of the two processes that determine species detectability (singing rate and detection distance) for 141 bird species breeding in boreal North America. We used phylogenetic mixed models and cross‐validation to compare the relative merits of using trait data only, phylogeny only, or the combination of both to predict detectability. We found a strong phylogenetic signal in both singing rates and detection distances; however the strength of phylogenetic effects was less than expected under Brownian motion evolution. The evolution of behavioural traits that determine singing rates was found to be more labile, leaving more room for species to evolve independently, whereas detection distance was mostly determined by anatomy (i.e. body size) and thus the laws of physics. Our findings can help in disentangling how complex ecological and evolutionary mechanisms have shaped different aspects of detectability in boreal birds. Such information can greatly inform single‐ and multi‐species models but more work is required to better understand how to best correct possible biases in phylogenetic diversity and other community metrics.     

Using basic plant traits to predict ungulate seed dispersal potential

Habitat fragmentation contributes to the decline of plant species by decreasing gene flow among populations. Restoring connectivity among habitat patches is therefore a major issue for plant conservation. However, deciding where to focus restoration efforts requires identifying suitable dispersers for each target plant species. We collected data from the literature on wild and domesticated ungulates, known to be effective seed dispersers, and on the plants they dispersed in Europe via epi‐ and/or endozoochory. We performed a systematic literature review to identify plant and animal traits relevant for seed dispersal. We first modeled the relationships between epi‐ or endozoochory and a priori selected plant traits (diaspore releasing height, length, shape and morphology, and habitat openness). The differences we underlined between the two dispersal mechanisms justified splitting our analyses accordingly. Then, for each dispersal mechanism, we asked whether basic plant traits could be used to predict specific traits of ungulates as endozoochorous or epizoochorous seed dispersers. We modeled the relationships between a priori selected ungulate traits for epizoochory (habitat openness, shoulder height, hair curliness, and hair length) and for endozoochory (habitat openness, body mass, feeding type and digestive system) and plant traits. Plant habitat openness and diaspore morphology were the predictors that most often explained differences among ungulates for epizoochory, whereas plant habitat openness and diaspore releasing height most often explained differences for endozoochory. Our trait‐based predictive models can help improve our ability to propose more precise management decisions for the conservation of plant populations worldwide by taking into account ungulate dispersers.     

Murine susceptibility to street rabies virus is unrelated to induction of host lymphoid depletion

The mechanism and cellular targets of mononuclear cell depletion were investigated in strains of mice susceptible or resistant to lethal infection with a virulent street rabies virus (SRV). Significant depletion was evident in the thymus of all infected animals at approximately 5 days postinfection and subsequently involved the spleen and lymph nodes in mice developing clinical signs of rabies. Immunofluorescent analyses of lymphocyte subsets in depleted spleens revealed that cell losses were non-selective since the relative proportions of K+, Thy-1+, Lyt-1+, and Lyt-2+ cells remained unchanged. Diminished expression of I-A membrane glycoproteins on spleen lymphocytes was noted, however, perhaps reflecting reduced availability of I-A-inducing lymphokines. Adrenal hormone toxicity was identified as the cause of mononuclear cell depletion in that mice adrenalectomized before SRV infection showed no evidence of lymphoid depletion. The failure of adrenalectomy to alter anti-rabies antibody responses or SRV lethality also indicates that involution of the lymphoid system is a consequence and not a cause of genetically controlled host susceptibility to SRV. The mechanism of adrenal gland stimulation in rabies-infected mice appears to involve a virus-induced dysfunction in the pituitary gland rather than a stress response to paralysis-induced starvation, based on results of kinetic studies on weight loss, appetite depression, and paralysis in these animals and previous reports of pituitary infection during rabies disease. The relationship of these observations to current theories on rabies virus pathogenicity is discussed.     

Novel application of species richness estimators to predict the host range of parasites

Host range is a critical life history trait of parasites, influencing prevalence, virulence and ultimately determining their distributional extent. Current approaches to measure host range are sensitive to sampling effort, the number of known hosts increasing with more records. Here, we develop a novel application of results-based stopping rules to determine how many hosts should be sampled to yield stable estimates of the number of primary hosts within regions, then use species richness estimation to predict host ranges of parasites across their distributional ranges. We selected three mistletoe species (hemiparasitic plants in the Loranthaceae) to evaluate our approach: a strict host specialist (Amyema lucasii, dependent on a single host species), an intermediate species (Amyema quandang, dependent on hosts in one genus) and a generalist (Lysiana exocarpi, dependent on many genera across multiple families), comparing results from geographically-stratified surveys against known host lists derived from herbarium specimens. The results-based stopping rule (stop sampling bioregion once observed host richness exceeds 80% of the host richness predicted using the Abundance-based Coverage Estimator) worked well for most bioregions studied, being satisfied after three to six sampling plots (each representing 25 host trees) but was unreliable in those bioregions with high host richness or high proportions of rare hosts. Although generating stable predictions of host range with minimal variation among six estimators trialled, distribution-wide estimates fell well short of the number of hosts known from herbarium records. This mismatch, coupled with the discovery of nine previously unrecorded mistletoe-host combinations, further demonstrates the limited ecological relevance of simple host-parasite lists. By collecting estimates of host range of constrained completeness, our approach maximises sampling efficiency while generating comparable estimates of the number of primary hosts, with broad applicability to many host-parasite systems.     

Using functional traits to predict species growth trajectories,and cross‐validation to evaluate these models for ecological prediction

Modeling plant growth using functional traits is important for understanding the mechanisms that underpin growth and for predicting new situations. We use three data sets on plant height over time and two validation methods—in‐sample model fit and leave‐one‐species‐out cross‐validation—to evaluate non‐linear growth model predictive performance based on functional traits. In‐sample measures of model fit differed substantially from out‐of‐sample model predictive performance; the best fitting models were rarely the best predictive models. Careful selection of predictor variables reduced the bias in parameter estimates, and there was no single best model across our three data sets. Testing and comparing multiple model forms is important. We developed an R package with a formula interface for straightforward fitting and validation of hierarchical, non‐linear growth models. Our intent is to encourage thorough testing of multiple growth model forms and an increased emphasis on assessing model fit relative to a model's purpose.     

Attenuated rabies virus activates, while pathogenic rabies virus evades, the host innate immune responses in the central nervous system

Rabies virus (RV) induces encephalomyelitis in humans and animals. However, the pathogenic mechanism of rabies is not fully understood. To investigate the host responses to RV infection, we examined and compared the pathology, particularly the inflammatory responses, and the gene expression profiles in the brains of mice infected with wild-type (wt) virus silver-haired bat RV (SHBRV) or laboratory-adapted virus B2C, using a mouse genomic array (Affymetrix). Extensive inflammatory responses were observed in animals infected with the attenuated RV, but little or no inflammatory responses were found in mice infected with wt RV. Furthermore, attenuated RV induced the expression of the genes involved in the innate immune and antiviral responses, especially those related to the alpha/beta interferon (IFN-alpha/beta) signaling pathways and inflammatory chemokines. For the IFN-alpha/beta signaling pathways, many of the interferon regulatory genes, such as the signal transduction activation transducers and interferon regulatory factors, as well as the effector genes, for example, 2'-5'-oligoadenylate synthetase and myxovirus proteins, are highly induced in mice infected with attenuated RV. However, many of these genes were not up-regulated in mice infected with wt SHBRV. The data obtained by microarray analysis were confirmed by real-time PCR. Together, these data suggest that attenuated RV activates, while pathogenic RV evades, the host innate immune and antiviral responses.     

Functional traits predict drought performance and distribution of Mediterranean woody species

Water availability is one of the key environmental factors that affect plant establishment and distribution. In many regions water availability will decline with climate change, exposing small seedlings to a greater likelihood of drought. In this study, 17 leaves, stem, root, and whole-plant traits of ten woody Mediterranean species were measured under favourable growing conditions and seedling drought survival was evaluated during a simulated dry-down episode. The aims of this study were: i) to assess drought survival of different species, ii) to analyse which functional traits predict drought survival time, and iii) to explain species distribution in the field, based on species drought survival and drought strategies. Drought survival time varied ten-fold across species, from 19 to 192 days. Across species, drought survival was positively related to the rooting depth per leaf area, i.e., the ability to acquire water from deeper soil layers while reducing transpiring leaf area. Drought survival time was negatively related to species ability to grow quickly, as indicated by high relative growth and net assimilation rates. Drought survival also explained species distribution in the field. It was found that species were sorted along a continuum, ranging between two contrasting species functional extremes based on functional traits and drought performance. One extreme consisted of acquisitive fast-growing deciduous species, with thin, soft metabolically active leaves, with high resource use and vulnerability to drought. The opposite extreme consisted of conservative slow-growing evergreen species with sclerophyllous leaves, deep roots, a low transpiring area, and low water use, resulting in high drought survival and drought tolerance. The results show that these drought strategies shape species distribution in this Mediterranean area.     

Using species distribution models to predict new occurrences for rare plants

Aim  To evaluate a suite of species distribution models for their utility as predictors of suitable habitat and as tools for new population discovery of six rare plant species that have both narrow geographical ranges and specialized habitat requirements.
Location  The Rattlesnake Creek Terrane (RCT) of the Shasta-Trinity National Forest in the northern California Coast Range of the United States.
Methods  We used occurrence records from 25 years of US Forest Service botanical surveys, environmental and remotely sensed climate data to model the distributions of the target species across the RCT. The models included generalized linear models (GLM), artificial neural networks (ANN), random forests (RF) and maximum entropy (ME). From the results we generated predictive maps that were used to identify areas of high probability occurrence. We made field visits to the top-ranked sites to search for new populations of the target species.
Results  Random forests gave the best results according to area under the curve and Kappa statistics, although ME was in close agreement. While GLM and ANN also gave good results, they were less restrictive and more varied than RF and ME. Cross-model correlations were the highest for species with the most records and declined with record numbers. Model assessment using a separate dataset confirmed that RF provided the best predictions of appropriate habitat. Use of RF output to prioritize search areas resulted in the discovery of 16 new populations of the target species.
Main conclusions  Species distribution models, such as RF and ME, which use presence data and information about the background matrix where species do not occur, may be an effective tool for new population discovery of rare plant species, but there does appear to be a lower threshold in the number of occurrences required to build a good model.     

Nucleotide sequence and host La protein interactions of rabies virus leader RNA.

Rabies virus leader RNA was detected in infected BHK-21 cell extracts by hybridization to end-labeled genomic RNA. Similar to the leader RNA of vesicular stomatitis virus, the leader RNA of rabies virus was also found to be associated with the La protein by specific immunoprecipitation with antisera from lupus patients. The 3' end of the genomic RNA of rabies virus was sequenced, and the size and termination site of leader RNA were determined. In addition, extension of the sequence into the nucleocapsid gene of rabies virus showed an open reading frame for at least 37 amino acid residues. Sequence relationships between rabies virus and vesicular stomatitis virus leader genes and the possible involvement of the La protein in rhabdovirus biology are discussed.     

Life‐history traits predict perennial species response to fire in a desert ecosystem

The Mojave Desert of North America has become fire‐prone in recent decades due to invasive annual grasses that fuel wildfires following years of high rainfall. Perennial species are poorly adapted to fire in this system, and post‐fire shifts in species composition have been substantial but variable across community types. To generalize across a range of conditions, we investigated whether simple life‐history traits could predict how species responded to fire. Further, we classified species into plant functional types (PFTs) based on combinations of life‐history traits and evaluated whether these groups exhibited a consistent fire‐response. Six life‐history traits varied significantly between burned and unburned areas in short (up to 4 years) or long‐term (up to 52 years) post‐fire datasets, including growth form, lifespan, seed size, seed dispersal, height, and leaf longevity. Forbs and grasses consistently increased in abundance after fire, while cacti were reduced and woody species exhibited a variable response. Woody species were classified into three PFTs based on combinations of life‐history traits. Species in Group 1 increased in abundance after fire and were characterized by short lifespans, small, wind‐dispersed seeds, low height, and deciduous leaves. Species in Group 2 were reduced by fire and distinguished from Group 1 by longer lifespans and evergreen leaves. Group 3 species, which also decreased after fire, were characterized by long lifespans, large non‐wind dispersed seeds, and taller heights. Our results show that PFTs based on life‐history traits can reliably predict the responses of most species to fire in the Mojave Desert. Dominant, long‐lived species of this region possess a combination of traits limiting their ability to recover, presenting a clear example of how a novel disturbance regime may shift selective environmental pressures to favor alternative life‐history strategies.     

Life history traits predict insect species responses to large herbivore overabundance: a multitaxonomic approach

There is increasing concern over the ecological impact of markedly increasing numbers of large herbivores (hereafter large herbivore overabundance) on forest ecosystems. To predict the ecological consequences of large herbivore overabundance, it is first necessary to understand how biological communities respond to large herbivore overabundance. Here, we examined the relationships between the life history traits of five insect taxonomic groups (moths, dung beetles, longicorn beetles, carabid beetles, and carrion beetles) and their responses to deer overabundance in Hokkaido, northern Japan. Insects were collected from three study sites: enclosure (20 deer/km²), control (10 deer/km²), and exclosure (0 deer/km²). The different taxonomic and functional insect species differed in their response to deer overabundance. The abundance (number of individuals) of longicorn beetles, dung beetles, and arbor-feeding moths was higher in the enclosure site than in the control site, whereas that of carabid beetles, carrion beetles, and herb- or shrub-feeding moths was higher in the control site than in the enclosure site. These results suggest that the type of food and the level of dependence on the understory are key traits determining insect sensitivity to deer overabundance. In addition, large or flightless species responded negatively to deer overabundance. Overall, this study demonstrated a significant change in insect communities following experimental deer overabundance, suggesting that large herbivore overabundance leads to the homogenization of biological communities. Unfortunately, because insects have diverse functions in forest ecosystems, such marked changes in both abundance and composition of insect communities will decrease ecosystem functions and resilience.     

Experimental Lagos bat virus infection in straw-colored fruit bats: A suitable model for bat rabies in a natural reservoir species

Rabies is a fatal neurologic disease caused by lyssavirus infection. Bats are important natural reservoir hosts of various lyssaviruses that can be transmitted to people. The epidemiology and pathogenesis of rabies in bats are poorly understood, making it difficult to prevent zoonotic transmission. To further our understanding of lyssavirus pathogenesis in a natural bat host, an experimental model using straw-colored fruit bats (Eidolon helvum) and Lagos bat virus, an endemic lyssavirus in this species, was developed. To determine the lowest viral dose resulting in 100% productive infection, bats in five groups (four bats per group) were inoculated intramuscularly with one of five doses, ranging from 10^0.1 to 10^4.1 median tissue culture infectious dose (TCID₅₀). More bats died due to the development of rabies after the middle dose (10^2.1 TCID₅₀, 4/4 bats) than after lower (10^1.1, 2/4; 10^1.1, 2/4) or higher (10^3.1, 2/4; 10^4.1, 2/4) doses of virus. In the two highest dose groups, 4/8 bats developed rabies. Of those bats that remained healthy 3/4 bats seroconverted, suggesting that high antigen loads can trigger a strong immune response that abrogates a productive infection. In contrast, in the two lowest dose groups, 3/8 bats developed rabies, 1/8 remained healthy and seroconverted and 4/8 bats remained healthy and did not seroconvert, suggesting these doses are too low to reliably induce infection. The main lesion in all clinically affected bats was meningoencephalitis associated with lyssavirus-positive neurons. Lyssavirus antigen was detected in tongue epithelium (5/11 infected bats) rather than in salivary gland epithelium (0/11), suggesting viral excretion via the tongue. Thus, intramuscular inoculation of 10^2.1 TCID₅₀ of Lagos bat virus into straw-colored fruit bats is a suitable model for lyssavirus associated bat rabies in a natural reservoir host, and can help with the investigation of lyssavirus infection dynamics in bats.     

Leaf habit does not predict leaf functional traits in cerrado woody species

Plant species with a high leaf life span (LLS) commonly have a low specific leaf area (SLA), leaf nitrogen per unit mass (N), and phosphorous concentration (P), whereas species with low LLS have a high SLA, N and P. However, LLS tends to be longer in species growing in low-nutrient soils and, therefore, differences in LLS and other leaf traits may not be consistent with a plant classification according to leaf habit. Here we investigated whether leaf habit is consistent with leaf economic spectrum trade-offs in cerrado (a Neotropical savanna) woody species. We analyzed the SLA, N and P of 125 woody species with a distinct leaf habit (deciduous, semideciduous, brevideciduous or evergreen). We also gathered data on the LLS (33 species), maximum net photosynthesis per leaf area (A_area, 56 species) and per leaf mass (A_mass, 31 species), comprising the most extensive database analyzed so far for the cerrado. Differences among leaf habit groups were tested using generalized linear mixed models and ANOVA. We did not find differences in SLA and N among species with a distinct leaf habit, but deciduous species had a higher leaf P concentration than evergreens. Species did not differ in LLS and A_mass, but A_area varied among groups. Semideciduous species had higher A_area values than deciduous and brevideciduous species, but all other groups had similar A_area values. Because of the small difference in the LLS, SLA, leaf N, leaf P and maximum net photosynthesis, we argue that deciduous, brevideciduous, semideciduous and evergreen species may not constitute different functional groups in cerrado woody species.