Influence of phylogeny on the estimation of diet from dental morphology in the Carnivora

Because teeth are the most easily preserved part of the vertebrate skeleton and are particularly morphologically variable in mammals, studies of fossil mammals rely heavily on dental morphology. Dental morphology is used both for systematics and phylogeny as well as for inferences about paleoecology, diet in particular. We analyze the influence of evolutionary history on our ability to reconstruct diet from dental morphology in the mammalian order Carnivora, and we find that much of our understanding of diet in carnivorans is dependent on the phylogenetic constraints on diet in this clade. Substantial error in estimating diet from dental morphology is present regardless of the morphological data used to make the inference, although more extensive morphological datasets are more accurate in predicting diet than more limited character sets. Unfortunately, including phylogeny in making dietary inferences actually decreases the accuracy of these predictions, showing that dietary predictions from morphology are substantially dependent on the evolutionary constraints on carnivore diet and tooth shape. The “evolutionary ratchet” that drives lineages of carnivorans to evolve greater degrees of hypercarnivory through time actually plays a role in allowing dietary inference from tooth shape, but consequently requires caution in interpreting dietary inference from the teeth fossil carnivores. These difficulties are another reminder of the differences in evolutionary tempo and mode between morphology and ecology.

Reconstruction of nitrogenase predecessors suggests origin from maturase-like enzymes

The evolution of biological nitrogen fixation, uniquely catalyzed by nitrogenase enzymes, has been one of the most consequential biogeochemical innovations over life's history. Though understanding the early evolution of nitrogen fixation has been a longstanding goal from molecular, biogeochemical, and planetary perspectives, its origins remain enigmatic. In this study, we reconstructed the evolutionary histories of nitrogenases, as well as homologous maturase proteins that participate in the assembly of the nitrogenase active-site cofactor but are not able to fix nitrogen. We combined phylogenetic and ancestral sequence inference with an analysis of predicted functionally divergent sites between nitrogenases and maturases to infer the nitrogen-fixing capabilities of their shared ancestors. Our results provide phylogenetic constraints to the emergence of nitrogen fixation and suggest that nitrogenases likely emerged from maturase-like predecessors. Though the precise functional role of such a predecessor protein remains speculative, our results highlight evolutionary contingency as a significant factor shaping the evolution of a biogeochemically essential enzyme.

Disentangling the roles of inter and intraspecific variation on leaf trait distributions across the eastern United States

Functional traits are central to how organisms perform and influence ecosystem function. Although phylogenetic constraints and environmental conditions are both known to affect trait distributions, data limitations have resulted in large scale studies modeling traits either as species weighted averages (ignoring intraspecific variation) or as a function of the environment (ignoring phylogenetic constraints). As a result, large scale predictions for trait distributions do not include key drivers, likely resulting in biased predictions, and cannot be used to assess the relative contributions of inter- and intraspecific variation. To address these limitations, we developed a joint model integrating phylogenetic and environmental information to understand and predict the distribution of eight leaf traits across the eastern United States. This joint model explained 68% of trait variation, outperforming both species-only and environment-only models, with variance attributable to phylogeny alone (23%), the environment alone (18%), and their overlapping effects (26%). The importance of phylogenetic constraints and the environment varied by trait, with some traits associated predominantly with environmental variation and others with phylogeny. To make predictions more continuously across the eastern USA we combined this model with data from the large-scale Forest Inventory and Analysis survey to estimate traits for ~1.2 million trees. The combined model exhibited significant deviations in predictions from both species-only and environment-only models with variation in the direction and magnitude of these differences among ecoregions. These predictions demonstrate the importance of modeling both intra- and interspecific variation to understand and predict large scale gradients in species and ecosystem traits.

Rubisco adaptation is more limited by phylogenetic constraint than by catalytic trade-off

Rubisco assimilates CO2 to form the sugars that fuel life on earth. Correlations between rubisco kinetic traits across species have led to the proposition that rubisco adaptation is highly constrained by catalytic trade-offs. However, these analyses did not consider the phylogenetic context of the enzymes that were analysed. Thus, it is possible that the correlations observed were an artefact of the presence of phylogenetic signal in rubisco kinetics and the phylogenetic relationship between the species that were sampled. Here, we conducted a phylogenetically-resolved analysis of rubisco kinetics and show that there is a significant phylogenetic signal in rubisco kinetic traits. We re-evaluated the extent of catalytic trade-offs accounting for this phylogenetic signal and found that all were attenuated. Following phylogenetic correction, the largest catalytic trade-offs were observed between the Michaelis constant for CO2 and carboxylase turnover (∼21-37%), and between the Michaelis constants for CO2 and O2 (∼9-19%), respectively. All other catalytic trade-offs were substantially attenuated such that they were marginal (<9%) or non-significant. This phylogenetically resolved analysis of rubisco kinetic evolution also identified kinetic changes that occur concomitant with the evolution of C4 photosynthesis. Finally, we show that phylogenetic constraints have played a larger role than catalytic trade-offs in limiting the evolution of rubisco kinetics. Thus, although there is strong evidence for some catalytic trade-offs, rubisco adaptation has been more limited by phylogenetic constraint than by the combined action of all such trade-offs.

The evolution of fruit scent: phylogenetic and developmental constraints

Background Fruit scent is increasingly recognized as an evolved signal whose function is to attract animal seed dispersers and facilitate plant reproduction. However, like all traits, fruit scent is likely to evolve in response to conflicting selective pressures and various constraints. Two major constraints are (i) phylogenetic constraints, in which traits are inherited from ancestors rather than adapted to current conditions and (ii) developmental constraints, if phenotypes are limited by the expression of other traits within the individual. We tested whether phylogenetic constraints play a role in fruit scent evolution by calculating the phylogenetic signal in ripe fruits of 98 species from three study sites. We then estimated the importance of developmental constraints by examining whether ripe fruits tend to emit compounds that are chemically similar to, and share biosynthetic pathways with, compounds emitted by conspecific unripe fruits from which they develop. Results We show that closely related taxa are not more similar to each other than to very distinct taxa, thus indicating that fruit scent shows little phylogenetic signal. At the same time, although ripe and unripe fruits of the same species tend to emit different chemicals, they tend to employ chemicals originating from similar biosynthetic pathways, thus indicating that some developmental constraints determine ripe fruit scent. Conclusions Our results highlight the complex landscape in which fruit scent has evolved. On one hand, fruit scent evolution is not limited by common ancestry. On the other hand, the range of chemicals that can be employed in ripe fruits is probably constrained by the needs of unripe fruits.

RuBisCO adaptation is more limited by phylogenetic constraint than by catalytic trade-off in plants

RuBisCO assimilates CO2 to form the sugars that fuel life on earth. Correlations between RuBisCO kinetic traits across species have led to the proposition that RuBisCO adaptation is constrained by catalytic trade-offs. However, these analyses did not consider the phylogenetic context of the enzymes that were analysed. Thus, it is possible that the observed correlations between RuBisCO kinetic traits are an artefact of the presence of phylogenetic signal in RuBisCO kinetics and the phylogenetic relationship between the species that were sampled. Here, we conducted a phylogenetically resolved analysis of RuBisCO kinetics and show that there is significant phylogenetic signal in all carboxylase kinetic traits, and significant phylogenetic signal in the Michaelis constant for O2 in species that conduct C3 photosynthesis. When accounting for this phylogenetic non-independence between enzymes, we show that the catalytic trade-off between carboxylase turnover and the Michaelis constant for CO2 is weak (~30 % dependency) and that the correlations between all other RuBisCO kinetic traits are either not-significant or marginal (<9 % dependency). Finally, we demonstrate that phylogenetic constraints have limited RuBisCO evolution to a greater extent than catalytic trade-offs. Thus, RuBisCO adaptation in angiosperms is predominantly limited by phylogenetic constraint (most likely caused by a slow rate of molecular evolution) and a partial trade-off between carboxylase turnover and the Michaelis constant for CO2.