Although reconstruction of the phylogeny of living birds has progressed tremendously in the last decade, the evolutionary history of Neoaves--a clade that encompasses nearly all living bird ...species--remains the greatest unresolved challenge in dinosaur systematics. Here we investigate avian phylogeny with an unprecedented scale of data: >390,000 bases of genomic sequence data from each of 198 species of living birds, representing all major avian lineages, and two crocodilian outgroups. Sequence data were collected using anchored hybrid enrichment, yielding 259 nuclear loci with an average length of 1,523 bases for a total data set of over 7.8 × 10(7) bases. Bayesian and maximum likelihood analyses yielded highly supported and nearly identical phylogenetic trees for all major avian lineages. Five major clades form successive sister groups to the rest of Neoaves: (1) a clade including nightjars, other caprimulgiforms, swifts, and hummingbirds; (2) a clade uniting cuckoos, bustards, and turacos with pigeons, mesites, and sandgrouse; (3) cranes and their relatives; (4) a comprehensive waterbird clade, including all diving, wading, and shorebirds; and (5) a comprehensive landbird clade with the enigmatic hoatzin (Opisthocomus hoazin) as the sister group to the rest. Neither of the two main, recently proposed Neoavian clades--Columbea and Passerea--were supported as monophyletic. The results of our divergence time analyses are congruent with the palaeontological record, supporting a major radiation of crown birds in the wake of the Cretaceous-Palaeogene (K-Pg) mass extinction.
The production of artificial fertilizers, fossil fuel use and leguminous agriculture worldwide has increased the amount of reactive nitrogen in the natural environment by an order of magnitude since ...the Industrial Revolution1. This reorganization of the nitrogen cycle has led to an increase in food production2, but increasingly causes a number of environmental problems1, 3. One such problem is the accumulation of nitrate in both freshwater and coastal marine ecosystems. Here we establish that ecosystem nitrate accrual exhibits consistent and negative nonlinear correlations with organic carbon availability along a hydrologic continuum from soils, through freshwater systems and coastal margins, to the open ocean. The trend also prevails in ecosystems subject to substantial human alteration. Across this diversity of environments, we find evidence that resource stoichiometry (organic carbon:nitrate) strongly influences nitrate accumulation by regulating a suite of microbial processes that couple dissolved organic carbon and nitrate cycling. With the help of a meta-analysis we show that heterotrophic microbes maintain low nitrate concentrations when organic carbon:nitrate ratios match the stoichiometric demands of microbial anabolism. When resource ratios drop below the minimum carbon:nitrogen ratio of microbial biomass4, however, the onset of carbon limitation appears to drive rapid nitrate accrual, which may then be further enhanced by nitrification. At low organic carbon:nitrate ratios, denitrification appears to constrain the extent of nitrate accretion, once organic carbon and nitrate availability approach the 1:1 stoichiometry5 of this catabolic process. Collectively, these microbial processes express themselves on local to global scales by restricting the threshold ratios underlying nitrate accrual to a constrained stoichiometric window. Our findings indicate that ecological stoichiometry can help explain the fate of nitrate across disparate environments and in the face of human disturbance.
Nitrogen (N) availability is thought to frequently limit terrestrial ecosystem processes, and explicit consideration of N biogeochemistry, including biological N
2
fixation, is central to ...understanding ecosystem responses to environmental change. Yet, the importance of free-living N
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fixation-a process that occurs on a wide variety of substrates, is nearly ubiquitous in terrestrial ecosystems, and may often represent the dominant pathway for acquiring newly available N-is often underappreciated. Here, we draw from studies that investigate free-living N
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fixation from functional, physiological, genetic, and ecological perspectives. We show that recent research and analytical advances have generated a wealth of new information that provides novel insight into the ecology of N
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fixation as well as raises new questions and priorities for future work. These priorities include a need to better integrate free-living N
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fixation into conceptual and analytical evaluations of the N cycle's role in a variety of global change scenarios.
Tropical forests dominate global terrestrial carbon (C) exchange, and recent droughts in the Amazon Basin have contributed to short‐term declines in terrestrial carbon dioxide uptake and storage. ...However, the effects of longer‐term climate variability on tropical forest carbon dynamics are still not well understood. We synthesised field data from more than 150 tropical forest sites to explore how climate regulates tropical forest aboveground net primary productivity (ANPP) and organic matter decomposition, and combined those data with two existing databases to explore climate – C relationships globally. While previous analyses have focused on the effects of either temperature or rainfall on ANPP, our results highlight the importance of interactions between temperature and rainfall on the C cycle. In cool forests (< 20 °C), high rainfall slowed rates of C cycling, but in warm tropical forests (> 20 °C) it consistently enhanced both ANPP and decomposition. At the global scale, our analysis showed an increase in ANPP with rainfall in relatively warm sites, inconsistent with declines in ANPP with rainfall reported previously. Overall, our results alter our understanding of climate – C cycle relationships, with high precipitation accelerating rates of C exchange with the atmosphere in the most productive biome on earth.
Humans continue to transform the global nitrogen cycle at a record pace, reflecting an increased combustion of fossil fuels, growing demand for nitrogen in agriculture and industry, and pervasive ...inefficiencies in its use. Much anthropogenic nitrogen is lost to air, water, and land to cause a cascade of environmental and human health problems. Simultaneously, food production in some parts of the world is nitrogen-deficient, highlighting inequities in the distribution of nitrogen-containing fertilizers. Optimizing the need for a key human resource while minimizing its negative consequences requires an integrated interdisciplinary approach and the development of strategies to decrease nitrogen-containing waste.
Nutrient resorption is a fundamental process through which plants withdraw nutrients from leaves before abscission. Nutrient resorption patterns have the potential to reflect gradients in plant ...nutrient limitation and to affect a suite of terrestrial ecosystem functions.
Here, we used a stoichiometric approach to assess patterns in foliar resorption at a variety of scales, specifically exploring how N : P resorption ratios relate to presumed variation in N and/or P limitation and possible relationships between N : P resorption ratios and soil nutrient availability.
N : P resorption ratios varied significantly at the global scale, increasing with latitude and decreasing with mean annual temperature and precipitation. In general, tropical sites (absolute latitudes < 23°26′) had N : P resorption ratios of < 1, and plants growing on highly weathered tropical soils maintained the lowest N : P resorption ratios. Resorption ratios also varied with forest age along an Amazonian forest regeneration chronosequence and among species in a diverse Costa Rican rain forest.
These results suggest that variations in N : P resorption stoichiometry offer insight into nutrient cycling and limitation at a variety of spatial scales, complementing other metrics of plant nutrient biogeochemistry. The extent to which the stoichiometric flexibility of resorption will help regulate terrestrial responses to global change merits further investigation.
Terrestrial biosphere-atmosphere carbon dioxide (CO2) exchange is dominated by tropical forests, where photosynthetic carbon (C) uptake is thought to be phosphorus (P)-limited. In P-poor tropical ...forests, P may also limit organic matter decomposition and soil C losses. We conducted a field-fertilization experiment to show that P fertilization stimulates soil respiration in a lowland tropical rain forest in Costa Rica. In the early wet season, when soluble organic matter inputs to soil are high, P fertilization drove large increases in soil respiration. Although the P-stimulated increase in soil respiration was largely confined to the dry-to-wet season transition, the seasonal increase was sufficient to drive an 18% annual increase in CO2 efflux from the P-fertilized plots. Nitrogen (N) fertilization caused similar responses, and the net increases in soil respiration in response to the additions of N and P approached annual soil C fluxes in mid-latitude forests. Human activities are altering natural patterns of tropical soil N and P availability by land conversion and enhanced atmospheric deposition. Although our data suggest that the mechanisms driving the observed respiratory responses to increased N and P may be different, the large CO2 losses stimulated by N and P fertilization suggest that knowledge of such patterns and their effects on soil CO2 efflux is critical for understanding the role of tropical forests in a rapidly changing global C cycle.
Tropical forests play a substantial role in the global carbon (C) cycle and are projected to experience significant changes in climate, highlighting the importance of understanding the factors that ...control organic matter decomposition in this biome. In the tropics, high temperature and rainfall lead to some of the highest rates of litter decomposition on earth, and given the near-optimal abiotic conditions, litter quality likely exerts disproportionate control over litter decomposition. Yet interactions between litter quality and abiotic variables, most notably precipitation, remain poorly resolved, especially for the wetter end of the tropical forest biome. We assessed the importance of variation in litter chemistry and precipitation in a lowland tropical rain forest in southwest Costa Rica that receives >5000 mm of precipitation per year, using litter from 11 different canopy tree species in conjunction with a throughfall manipulation experiment. In general, despite the exceptionally high rainfall in this forest, simulated throughfall reductions consistently suppressed rates of litter decomposition. Overall, variation between species was greater than that induced by manipulating throughfall and was best explained by initial litter solubility and lignin:P ratios. Collectively, these results support a model of litter decomposition in which mass loss rates are positively correlated with rainfall up to very high rates of mean annual precipitation and highlight the importance of phosphorus availability in controlling microbial processes in many lowland tropical forests.
Trait-based studies can help clarify the mechanisms driving patterns of microbial community assembly and coexistence. Here, we use a trait-based approach to explore the importance of rRNA operon copy ...number in microbial succession, building on prior evidence that organisms with higher copy numbers respond more rapidly to nutrient inputs. We set flasks of heterotrophic media into the environment and examined bacterial community assembly at seven time points. Communities were arrayed along a geographic gradient to introduce stochasticity via dispersal processes and were analyzed using 16 S rRNA gene pyrosequencing, and rRNA operon copy number was modeled using ancestral trait reconstruction. We found that taxonomic composition was similar between communities at the beginning of the experiment and then diverged through time; as well, phylogenetic clustering within communities decreased over time. The average rRNA operon copy number decreased over the experiment, and variance in rRNA operon copy number was lowest both early and late in succession. We then analyzed bacterial community data from other soil and sediment primary and secondary successional sequences from three markedly different ecosystem types. Our results demonstrate that decreases in average copy number are a consistent feature of communities across various drivers of ecological succession. Importantly, our work supports the scaling of the copy number trait over multiple levels of biological organization, ranging from cells to populations and communities, with implications for both microbial ecology and evolution.
Global changes such as variations in plant net primary production are likely to drive shifts in leaf litterfall inputs to forest soils, but the effects of such changes on soil carbon (C) cycling and ...storage remain largely unknown, especially in C‐rich tropical forest ecosystems. We initiated a leaf litterfall manipulation experiment in a tropical rain forest in Costa Rica to test the sensitivity of surface soil C pools and fluxes to different litter inputs. After only 2 years of treatment, doubling litterfall inputs increased surface soil C concentrations by 31%, removing litter from the forest floor drove a 26% reduction over the same time period, and these changes in soil C concentrations were associated with variations in dissolved organic matter fluxes, fine root biomass, microbial biomass, soil moisture, and nutrient fluxes. However, the litter manipulations had only small effects on soil organic C (SOC) chemistry, suggesting that changes in C cycling, nutrient cycling, and microbial processes in response to litter manipulation reflect shifts in the quantity rather than quality of SOC. The manipulation also affected soil CO ₂ fluxes; the relative decline in CO ₂ production was greater in the litter removal plots (−22%) than the increase in the litter addition plots (+15%). Our analysis showed that variations in CO ₂ fluxes were strongly correlated with microbial biomass pools, soil C and nitrogen (N) pools, soil inorganic P fluxes, dissolved organic C fluxes, and fine root biomass. Together, our data suggest that shifts in leaf litter inputs in response to localized human disturbances and global environmental change could have rapid and important consequences for belowground C storage and fluxes in tropical rain forests, and highlight differences between tropical and temperate ecosystems, where belowground C cycling responses to changes in litterfall are generally slower and more subtle.
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