Diego R. Barneche

BAAD: a biomass and allometry database for woody plants

Understanding how plants are constructed—i.e., how key size dimensions and the amount of mass invested in different tissues varies among individuals—is essential for modeling plant growth, carbon stocks, and energy fluxes in the terrestrial biosphere. Allocation patterns can differ through ontogeny, but also among coexisting species and among species adapted to different environments. While a variety of models dealing with biomass allocation exist, we lack a synthetic understanding of the underlying processes. This is partly due to the lack of suitable data sets for validating and parameterizing models. To that end, we present the Biomass And Allometry Database (BAAD) for woody plants. The BAAD contains 259 634 measurements collected in 176 different studies, from 21 084 individuals across 678 species. Most of these data come from existing publications. However, raw data were rarely made public at the time of publication. Thus, the BAAD contains data from different studies, transformed into standard units and variable names. The transformations were achieved using a common workflow for all raw data files. Other features that distinguish the BAAD are: (i) measurements were for individual plants rather than stand averages; (ii) individuals spanning a range of sizes were measured; (iii) plants from 0.01–100 m in height were included; and (iv) biomass was estimated directly, i.e., not indirectly via allometric equations (except in very large trees where biomass was estimated from detailed sub-sampling). We included both wild and artificially grown plants. The data set contains the following size metrics: total leaf area; area of stem cross-section including sapwood, heartwood, and bark; height of plant and crown base, crown area, and surface area; and the dry mass of leaf, stem, branches, sapwood, heartwood, bark, coarse roots, and fine root tissues. We also report other properties of individuals (age, leaf size, leaf mass per area, wood density, nitrogen content of leaves and wood), as well as information about the growing environment (location, light, experimental treatment, vegetation type) where available. It is our hope that making these data available will improve our ability to understand plant growth, ecosystem dynamics, and carbon cycling in the worlds vegetation.

Diet and diversification in the evolution of coral reef fishes.

The disparity in species richness among evolutionary lineages is one of the oldest and most intriguing issues in evolutionary biology. Although geographical factors have been traditionally thought to promote speciation, recent studies have underscored the importance of ecological interactions as one of the main drivers of diversification. Here, we test if differences in species richness of closely related lineages match predictions based on the concept of density-dependent diversification. As radiation progresses, ecological niche-space would become increasingly saturated, resulting in fewer opportunities for speciation. To assess this hypothesis, we tested whether reef fish niche shifts toward usage of low-quality food resources (i.e. relatively low energy/protein per unit mass), such as algae, detritus, sponges and corals are accompanied by rapid net diversification. Using available molecular information, we reconstructed phylogenies of four major reef fish clades (Acanthuroidei, Chaetodontidae, Labridae and Pomacentridae) to estimate the timing of radiations of their subclades. We found that the evolution of species-rich clades was associated with a switch to low quality food in three of the four clades analyzed, which is consistent with a density-dependent model of diversification. We suggest that ecological opportunity may play an important role in understanding the diversification of reef-fish lineages.

Ten new records of reef fish on the coast of Santa Catarina State, Brazil

We present a list with 10 new records of reef fish on the coast of Santa Catarina State, the southernmost site of tropical reef fish occurrence on the Brazilian coast. We also comment on the distribution-range of the recently described Halichoeres sazimai (Labridae).

Energetic and ecological constraints on population density of reef fishes

Population ecology has classically focused on pairwise species interactions, hindering the description of general patterns and processes of population abundance at large spatial scales. Here we use the metabolic theory of ecology as a framework to formulate and test a model that yields predictions linking population density to the physiological constraints of body size and temperature on individual metabolism, and the ecological constraints of trophic structure and species richness on energy partitioning among species. Our model was tested by applying Bayesian quantile regression to a comprehensive reef-fish community database, from which we extracted density data for 5609 populations spread across 49 sites around the world. Our results indicate that population density declines markedly with increases in community species richness and that, after accounting for richness, energetic constraints are manifested most strongly for the most abundant species, which generally are of small body size and occupy lower trophic groups. Overall, our findings suggest that, at the global scale, factors associated with community species richness are the major drivers of variation in population density. Given that populations of species-rich tropical systems exhibit markedly lower maximum densities, they may be particularly susceptible to stochastic extinction.

Community structure of reef fishes on a remote oceanic island (St Peter and St Paul’s Archipelago, equatorial Atlantic): the relative influence of abiotic and biotic variables

This study investigates the reef fish community structure of the world’s smallest remote tropical island, the St Peter and St Paul’s Archipelago, in the equatorial Atlantic. The interplay between isolation, high endemism and low species richness makes the St Peter and St Paul’s Archipelago ecologically simpler than larger and highly connected shelf reef systems, making it an important natural laboratory for ecology and biogeography, particularly with respect to the effects of abiotic and biotic factors, and the functional organisation of such a depauperate community. Boosted regression trees were used to associate density, biomass and diversity of reef fishes with six abiotic and biotic variables, considering the community both as a whole and segregated into seven trophic groups. Depth was the most important explanatory variable across all models, although the direction of its effect varied with the type of response variable. Fish density peaked at intermediate depths, whereas biomass and biodiversity were respectively positively and negatively correlated with depth. Topographic complexity and wave exposure were less important in explaining variance within the fish community than depth. No effects of the predictor biotic variables were detected. Finally, we notice that most functional groups are represented by very few species, highlighting potential vulnerability to disturbances.

Isolation drives taxonomic and functional nestedness in tropical reef fish faunas

&NA; Taxonomic nestedness, the degree to which the taxonomic composition of species‐poor assemblages represents a subset of richer sites, commonly occurs in habitat fragments and islands differing in size and isolation from a source pool. However, species are not ecologically equivalent and the extent to which nestedness is observed in terms of functional trait composition of assemblages still remains poorly known. Here, using an extensive database on the functional traits and the distributions of 6316 tropical reef fish species across 169 sites, we assessed the levels of taxonomical vs functional nestedness of reef fish assemblages at the global scale. Functional nestedness was considerably more common than taxonomic nestedness, and generally associated with geographical isolation, where nested subsets are gradually more isolated from surrounding reef areas and from the center of biodiversity. Because a nested pattern in functional composition implies that certain combinations of traits may be represented by few species, we identified these groups of low redundancy that include large herbivore‐detritivores and omnivores, small piscivores, and macro‐algal herbivores. The identified patterns of nestedness may be an outcome of the interaction between species dispersal capabilities, resource requirements, and gradients of isolation among habitats. The importance of isolation in generating the observed pattern of functional nestedness within biogeographic regions may indicate that disturbance in depauperate and isolated sites can have disproportionate effects on the functional structure of their reef fish assemblages.

Do low oxygen environments facilitate marine invasions? Relative tolerance of native and invasive species to low oxygen conditions

Biological invasions are one of the biggest threats to global biodiversity. Marine artificial structures are proliferating worldwide and provide a haven for marine invasive species. Such structures disrupt local hydrodynamics, which can lead to the formation of oxygen-depleted microsites. The extent to which native fauna can cope with such low oxygen conditions, and whether invasive species, long associated with artificial structures in flow-restricted habitats, have adapted to these conditions remains unclear. We measured water flow and oxygen availability in marinas and piers at the scales relevant to sessile marine invertebrates (mm). We then measured the capacity of invasive and native marine invertebrates to maintain metabolic rates under decreasing levels of oxygen using standard laboratory assays. We found that marinas reduce water flow relative to piers, and that local oxygen levels can be zero in low flow conditions. We also found that for species with erect growth forms, invasive species can tolerate much lower levels of oxygen relative to native species. Integrating the field and laboratory data showed that up to 30% of available microhabitats within low flow environments are physiologically stressful for native species, while only 18% of the same habitat is physiologically stressful for invasive species. These results suggest that invasive species have adapted to low oxygen habitats associated with manmade habitats, and artificial structures may be creating niche opportunities for invasive species.

Temperature effects on mass-scaling exponents in colonial animals: a manipulative test

Body size and temperature are fundamental drivers of ecological processes because they determine metabolic rates at the individual level. Whether these drivers act independently on individual-level metabolic rates remains uncertain. Most studies of intraspecific scaling of unitary organisms must rely on preexisting differences in size to examine its relationship with metabolic rate, thereby potentially confounding size-correlated traits (e.g., age, nutrition) with size, which can affect metabolic rate. Here, we use a size manipulation approach to test whether metabolic mass scaling and temperature dependence interact in four species (two phyla) of colonial marine invertebrates. Size manipulation in colonial organisms allows tests of how ecological processes (e.g., predation) affect individual physiology and consequently population- and community-level energy flux. Body mass and temperature interacted in two species, with one species exhibiting decreased and the other increased mass-scaling exponents with increasing temperature. The allometric scaling of metabolic rate that we observe in three species contrasts with the isometric scaling of ingestion rates observed in some colonial marine invertebrates. Thus, we suggest that the often observed competitive superiority of colonial over unitary organisms may arise because the difference between energy intake and expenditure increases more strongly with size in colonial organisms.

Fish reproductive-energy output increases disproportionately with body size

Big mamas matter for fish The theoretical relationship between reproduction and body size has assumed that total mass relates directly to fecundity, regardless of the number of individuals involved. This assumption leads to fisheries management practices that suggest that one large female fish can be replaced by several smaller females. However, this assumption is incorrect. Barneche et al. show that larger females are far more productive than the same weights worth of smaller females. Management practices that ignore the value of large females could contribute to unexplained declines seen in some fish stocks. Science, this issue p. 642 Reproduction does not scale linearly with body size in fish—bigger females produce many more offspring. Body size determines total reproductive-energy output. Most theories assume reproductive output is a fixed proportion of size, with respect to mass, but formal macroecological tests are lacking. Management based on that assumption risks underestimating the contribution of larger mothers to replenishment, hindering sustainable harvesting. We test this assumption in marine fishes with a phylogenetically controlled meta-analysis of the intraspecific mass scaling of reproductive-energy output. We show that larger mothers reproduce disproportionately more than smaller mothers in not only fecundity but also total reproductive energy. Our results reset much of the theory on how reproduction scales with size and suggest that larger mothers contribute disproportionately to population replenishment. Global change and overharvesting cause fish sizes to decline; our results provide quantitative estimates of how these declines affect fisheries and ecosystem-level productivity.

Nestedness across biological scales

Biological networks pervade nature. They describe systems throughout all levels of biological organization, from molecules regulating metabolism to species interactions that shape ecosystem dynamics. The network thinking revealed recurrent organizational patterns in complex biological systems, such as the formation of semi-independent groups of connected elements (modularity) and non-random distributions of interactions among elements. Other structural patterns, such as nestedness, have been primarily assessed in ecological networks formed by two non-overlapping sets of elements; information on its occurrence on other levels of organization is lacking. Nestedness occurs when interactions of less connected elements form proper subsets of the interactions of more connected elements. Only recently these properties began to be appreciated in one-mode networks (where all elements can interact) which describe a much wider variety of biological phenomena. Here, we compute nestedness in a diverse collection of one-mode networked systems from six different levels of biological organization depicting gene and protein interactions, complex phenotypes, animal societies, metapopulations, food webs and vertebrate metacommunities. Our findings suggest that nestedness emerge independently of interaction type or biological scale and reveal that disparate systems can share nested organization features characterized by inclusive subsets of interacting elements with decreasing connectedness. We primarily explore the implications of a nested structure for each of these studied systems, then theorize on how nested networks are assembled. We hypothesize that nestedness emerges across scales due to processes that, although system-dependent, may share a general compromise between two features: specificity (the number of interactions the elements of the system can have) and affinity (how these elements can be connected to each other). Our findings suggesting occurrence of nestedness throughout biological scales can stimulate the debate on how pervasive nestedness may be in nature, while the theoretical emergent principles can aid further research on commonalities of biological networks.