Nor climate nor human impact factors: Chytrid infection shapes the skin bacterial communities of an endemic amphibian in a biodiversity hotspot.

The bacterial communities of the amphibian skin (i.e., the bacteriome) are critical to the host's innate immune system. However, it is unclear how different drivers can alter this function by modulating the bacteriome's structure. Our aim was to assess the extent to which different host attributes and extrinsic factors influence the structure of the bacterial communities of the skin. Skin bacterial diversity was examined in 148 individuals of the four-eyed frog (Pleurodema thaul) from 16 localities spanning almost 1800 km in latitude. The richness and beta diversity of bacterial families and the richness and abundance of Bd-inhibitory bacterial genera were used to describe their structure. Predictors associated with the host (developmental stage, genetic lineage, individual Batrachochytrium dendrobatidis [Bd] infection status) and the landscape (current climate, degree of anthropogenic disturbance) were used in the statistical modeling in an information theoretical approach. Bd infection and host developmental stage were the only predictors affecting bacteriome richness, with Bd+ individuals and postmetamorphic stages (adults and juveniles) having higher richness than Bd- ones and tadpoles. High diversity in Bd+ individuals is not driven by bacterial genera with known anti-Bd properties. Beta diversity was not affected by Bd infection and was mainly a consequence of bacterial family turnover rather than nestedness. Finally, for those bacterial genera known to have inhibitory effects on chytrid, Bd+ individuals had a slightly higher diversity than Bd- ones. Our study confirms an association between Bd infection and the host developmental stage with the bacterial communities of the skin of P. thaul. Unexpectedly, macroclimate and human impact factors do not seem to play a role in shaping the amphibian skin microbiome. Our study exemplifies that focusing on a single host-parasite system over a large geographic scale can provide essential insights into the factors driving host-parasite-bacteriome interactions.

Heat tolerance variation reveals vulnerability of tropical herbivore-parasitoid interactions to climate change.

Assessing the heat tolerance (CTmax) of organisms is central to understand the impact of climate change on biodiversity. While both environment and evolutionary history affect CTmax, it remains unclear how these factors and their interplay influence ecological interactions, communities and ecosystems under climate change. We collected and reared caterpillars and parasitoids from canopy and ground layers in different seasons in a tropical rainforest. We tested the CTmax and Thermal Safety Margins (TSM) of these food webs with implications for how species interactions could shift under climate change. We identified strong influence of phylogeny in herbivore-parasitoid community heat tolerance. The TSM of all insects were narrower in the canopy and parasitoids had lower heat tolerance compared to their hosts. Our CTmax-based simulation showed higher herbivore-parasitoid food web instability under climate change than previously assumed, highlighting the vulnerability of parasitoids and related herbivore control in tropical rainforests, particularly in the forest canopy.

Patterns of genome size variation in caridean shrimps: new estimates for non-gambarelloides Synalpheus species.

Genome size (GS) or DNA nuclear content is considered a useful index for making inferences about evolutionary models and life history in animals, including taxonomic, biogeographical, and ecological scenarios. However, patterns of GS variation and their causes in crustaceans are still poorly understood. This study aimed to describe the GS of five Neotropical Synalpheus non-gambarelloides shrimps (S. apioceros, S. minus, S. brevicarpus, S. fritzmueller, and S. scaphoceris) and compare the C-values of all Caridea infraorder in terms of geography and phylogenetics. All animals were sampled in the coast of São Paulo State, Brazil, and GS was assessed by flow cytometry analysis (FCA). The C-values ranged from 7.89 pg in S. apioceros to 12.24 pg in S. scaphoceris. Caridean shrimps had higher GS than other Decapoda crustaceans. The results reveal a tendency of obtaining larger genomes in species with direct development in Synalpheus shrimps. In addition, a tendency of positive biogeographical (latitudinal) correlation with Caridea infraorder was also observed. This study provides remarkable and new protocol for FCA (using gating strategy for the analysis), which led to the discovery of new information regarding GS of caridean shrimps, especially for Neotropical Synalpheus, which represents the second-largest group in the Caridea infraorder.

Year-round high abundances of the world's smallest marine vertebrate (Schindleria) in the Red Sea and worldwide associations with lunar phases.

Very little is known about the ecology and biology of the smallest marine vertebrates, fishes in the genus Schindleria. Even though over half of named Schindleria species have been identified in the Red Sea, the collection of only very few specimens has been documented. Here, we assessed abundance patterns of nearly two thousand Red Sea long dorsal fin (LDF) adults and found evidence for putative seasonal and spatial differences, likely related to differing habitat and environmental conditions. The highest abundances were outside local seasonal temperature extremes and decoupled from peaks of coral reef fish recruitment. We also found evidence for global trends in abundances related to lunar cycles using our Red Sea data and that from a recently published large collection of specimens from the DANA Expedition (1928-1930). The abundance of adult LDF Schindleria in relation to lunar phases differed significantly, with most Schindleria caught outside the full moon, and mostly during the new moon in the Red Sea and the 3rd quarter moon in the DANA collection. We further suggest that the abundances of Schindleria at coral reefs may be related to reproductive cycles and that these cycles may be timed with the moon as back-calculations of hatch dates from otoliths from the Red Sea significantly resulted after the new moon, making Schindleria the fastest-lived coral reef fish with the shortest generation times. Schindleria could be the most numerous coral reef fish in the world, for which we encourage increased research.

Amphibian responses in experimental thermal gradients: Concepts and limits for inference.

The interpretation of thermal-gradient data depends on the behavioral drives reported or assumed, and on the underlying behavioral models explaining how such drives operate. The best-known example is positive thermotaxis, a thermoregulatory behavioral drive frequently linked to a dual set-point model of thermoregulation around a target range. This behavioral drive is often assumed as dominant among 'ectotherms', including amphibians. However, we argue that, because amphibians are extremely diverse, they may exhibit alternative behavioral drives in thermal gradients, and tackle this idea from two perspectives. First, we provide a historical review of original definitions and proposed limits for inference. Second, although caveats apply, we propose that a cross-study analysis of data of temperature settings of gradients and the temperatures selected by amphibians would corroborate alternative behavioral drives, including negative thermotaxis. Therefore, we analyzed published data focusing on such relationships and show that gradient temperature settings influence the temperatures selected by amphibians, with further effects of phylogeny and ontogeny. We conclude that thermal gradient experiments are outstanding tools to investigate behavioral drives, but no given drive can be assumed a priori unless additional information about thermoregulation is available. Based on the historical debate, we propose using selected temperatures and preferred temperatures as different concepts, the former merely operational and the second explicitly linked to positive thermotaxis (and thus compatible with dual set-point thermoregulation). Under this view, thermal preferences would stand for a hypothesis of a behavioral drive (positive thermotaxis) requiring formal testing. These considerations impact the scope for inference based on thermal gradient experiments, particularly ecological modeling and emerging disease.

Performance, genomic rearrangements, and signatures of adaptive evolution: Lessons from fermentative yeasts.

The capacity of some yeasts to extract energy from single sugars, generating CO2 and ethanol (=fermentation), even in the presence of oxygen, is known as the Crabtree effect. This phenomenon represents an important adaptation as it allowed the utilization of the ecological niche given by modern fruits, an abundant source of food that emerged in the terrestrial environment in the Cretaceous. However, identifying the evolutionary events that triggered fermentative capacity in Crabtree-positive species is challenging, as microorganisms do not leave fossil evidence. Thus, key innovations should be inferred based only on traits measured under culture conditions. Here, we reanalyzed data from a common garden experiment where several proxies of fermentative capacity were recorded in Crabtree-positive and Crabtree-negative species, representing yeast phylogenetic diversity. In particular, we applied the "lasso-OU" algorithm which detects points of adaptive shifts, using traits that are proxies of fermentative performance. We tested whether multiple events or a single event explains the actual fermentative capacity of yeasts. According to the lasso-OU procedure, evolutionary changes in the three proxies of fermentative capacity that we considered (i.e., glycerol production, ethanol yield, and respiratory quotient) are consistent with a single evolutionary episode (a whole-genomic duplication, WGD), instead of a series of small genomic rearrangements. Thus, the WGD appears as the key event behind the diversification of fermentative yeasts, which by increasing gene dosage, and maximized their capacity of energy extraction for exploiting the new ecological niche provided by single sugars.

Testing the metabolic homeostasis hypothesis in amphibians.

A number of hypotheses about compensatory mechanisms that allow ectothermic animals to cope with the latitudinal decrease in ambient temperature ( TA) have been proposed during the last century. One of these hypotheses, the 'metabolic homeostasis' hypothesis (MHH), states that species should show the highest thermal sensitivity of the metabolic rate ( Q10-SMR) at the colder end of the range of TAs they usually experience in nature. This way, species should be able to minimize maintenance costs during the colder hours of the day, but quickly take advantage of increases in TA during the warmer parts of the day. Here, we created a dataset that includes Q10-SMR values for 58 amphibian species, assessed at four thermal ranges, to evaluate three predictions derived from the MHH. In line with this hypothesis, we found that: (i) Q10-SMR values tended to be positively correlated with latitude when measured at lower TAs, but negative correlated with latitude when measured at higher TAs, (ii) Q10-SMR measured at lower TAs were higher in temperate species, whereas Q10-SMR measured at higher TAs were higher in tropical species, and (iii) the experimental TA at which Q10-SMR was maximal for each species decreased with latitude. This is the first study to our knowledge showing that the relationship between Q10-SMR and latitude in ectotherms changes with the TA at which Q10-SMR is assessed, as predicted from an adaptive hypothesis. This article is part of the theme issue 'Physiological diversity, biodiversity patterns and global climate change: testing key hypotheses involving temperature and oxygen'.

Exploring the evolution of multicellularity in Saccharomyces cerevisiae under bacteria environment: An experimental phylogenetics approach.

There have been over 25 independent unicellular to multicellular evolutionary transitions, which have been transformational in the complexity of life. All of these transitions likely occurred in communities numerically dominated by unicellular organisms, mostly bacteria. Hence, it is reasonable to expect that bacteria were involved in generating the ecological conditions that promoted the stability and proliferation of the first multicellular forms as protective units. In this study, we addressed this problem by analyzing the occurrence of multicellularity in an experimental phylogeny of yeasts (Sacharomyces cerevisiae) a model organism that is unicellular but can generate multicellular clusters under some conditions. We exposed a single ancestral population to periodic divergences, coevolving with a cocktail of environmental bacteria that were inoculated to the environment of the ancestor, and compared to a control (no bacteria). We quantified culturable microorganisms to the level of genera, finding up to 20 taxa (all bacteria) that competed with the yeasts during diversification. After 600 generations of coevolution, the yeasts produced two types of multicellular clusters: clonal and aggregative. Whereas clonal clusters were present in both treatments, aggregative clusters were only present under the bacteria treatment and showed significant phylogenetic signal. However, clonal clusters showed different properties if bacteria were present as follows: They were more abundant and significantly smaller than in the control. These results indicate that bacteria are important modulators of the occurrence of multicellularity, providing support to the idea that they generated the ecological conditions-promoting multicellularity.

Aerobic power and flight capacity in birds: a phylogenetic test of the heart-size hypothesis.

Flight capacity is one of the most important innovations in animal evolution; it only evolved in insects, birds, mammals and the extinct pterodactyls. Given that powered flight represents a demanding aerobic activity, an efficient cardiovascular system is essential for the continuous delivery of oxygen to the pectoral muscles during flight. It is well known that the limiting step in the circulation is stroke volume (the volume of blood pumped from the ventricle to the body during each beat), which is determined by the size of the ventricle. Thus, the fresh mass of the heart represents a simple and repeatable anatomical measure of the aerobic power of an animal. Although several authors have compared heart masses across bird species, a phylogenetic comparative analysis is still lacking. By compiling heart sizes for 915 species and applying several statistical procedures controlling for body size and/or testing for adaptive trends in the dataset (e.g. model selection approaches, phylogenetic generalized linear models), we found that (residuals of) heart size is consistently associated with four categories of flight capacity. In general, our results indicate that species exhibiting continuous hovering flight (i.e. hummingbirds) have substantially larger hearts than other groups, species that use flapping flight and gliding show intermediate values, and that species categorized as poor flyers show the smallest values. Our study reveals that on a broad scale, routine flight modes seem to have shaped the energetic requirements of birds sufficiently to be anatomically detected at the comparative level.

Studying the evolutionary significance of thermal adaptation in ectotherms: The diversification of amphibians' energetics.

A fundamental problem in evolutionary biology is the understanding of the factors that promote or constrain adaptive evolution, and assessing the role of natural selection in this process. Here, comparative phylogenetics, that is, using phylogenetic information and traits to infer evolutionary processes has been a major paradigm . In this study, we discuss Ornstein-Uhlenbeck models (OU) in the context of thermal adaptation in ectotherms. We specifically applied this approach to study amphibians's evolution and energy metabolism. It has been hypothesized that amphibians exploit adaptive zones characterized by low energy expenditure, which generate specific predictions in terms of the patterns of diversification in standard metabolic rate (SMR). We complied whole-animal metabolic rates for 122 species of amphibians, and adjusted several models of diversification. According to the adaptive zone hypothesis, we expected: (1) to find "accelerated evolution" in SMR (i.e., diversification above Brownian Motion expectations, BM), (2) that a model assuming evolutionary optima (i.e., an OU model) fits better than a white-noise model and (3) that a model assuming multiple optima (according to the three amphibians's orders) fits better than a model assuming a single optimum. As predicted, we found that the diversification of SMR occurred most of the time, above BM expectations. Also, we found that a model assuming an optimum explained the data in a better way than a white-noise model. However, we did not find evidence that an OU model with multiple optima fits the data better, suggesting a single optimum in SMR for Anura, Caudata and Gymnophiona. These results show how comparative phylogenetics could be applied for testing adaptive hypotheses regarding history and physiological performance in ectotherms.

Phylogenetic Analysis Supports the Aerobic-Capacity Model for the Evolution of Endothermy.

The evolution of endothermy is a controversial topic in evolutionary biology, although several hypotheses have been proposed to explain it. To a great extent, the debate has centered on the aerobic-capacity model (AC model), an adaptive hypothesis involving maximum and resting rates of metabolism (MMR and RMR, respectively; hereafter "metabolic traits"). The AC model posits that MMR, a proxy of aerobic capacity and sustained activity, is the target of directional selection and that RMR is also influenced as a correlated response. Associated with this reasoning are the assumptions that (1) factorial aerobic scope (FAS; MMR/RMR) and net aerobic scope (NAS; MMR - RMR), two commonly used indexes of aerobic capacity, show different evolutionary optima and (2) the functional link between MMR and RMR is a basic design feature of vertebrates. To test these assumptions, we performed a comparative phylogenetic analysis in 176 vertebrate species, ranging from fish and amphibians to birds and mammals. Using disparity-through-time analysis, we also explored trait diversification and fitted different evolutionary models to study the evolution of metabolic traits. As predicted, we found (1) a positive phylogenetic correlation between RMR and MMR, (2) diversification of metabolic traits exceeding that of random-walk expectations, (3) that a model assuming selection fits the data better than alternative models, and (4) that a single evolutionary optimum best fits FAS data, whereas a model involving two optima (one for ectotherms and another for endotherms) is the best explanatory model for NAS. These results support the AC model and give novel information concerning the mode and tempo of physiological evolution of vertebrates.

A phylogenetic analysis of macroevolutionary patterns in fermentative yeasts.

When novel sources of ecological opportunity are available, physiological innovations can trigger adaptive radiations. This could be the case of yeasts (Saccharomycotina), in which an evolutionary novelty is represented by the capacity to exploit simple sugars from fruits (fermentation). During adaptive radiations, diversification and morphological evolution are predicted to slow-down after early bursts of diversification. Here, we performed the first comparative phylogenetic analysis in yeasts, testing the "early burst" prediction on species diversification and also on traits of putative ecological relevance (cell-size and fermentation versatility). We found that speciation rates are constant during the time-range we considered (ca., 150 millions of years). Phylogenetic signal of both traits was significant (but lower for cell-size), suggesting that lineages resemble each other in trait-values. Disparity analysis suggested accelerated evolution (diversification in trait values above Brownian Motion expectations) in cell-size. We also found a significant phylogenetic regression between cell-size and fermentation versatility (R (2) = 0.10), which suggests correlated evolution between both traits. Overall, our results do not support the early burst prediction both in species and traits, but suggest a number of interesting evolutionary patterns, that warrant further exploration. For instance, we show that the Whole Genomic Duplication that affected a whole clade of yeasts, does not seems to have a statistically detectable phenotypic effect at our level of analysis. In this regard, further studies of fermentation under common-garden conditions combined with comparative analyses are warranted.