Arbuscular Mycorrhizal Fungi Alleviate Drought Stress in C3 (Leymus chinensis) and C4 (Hemarthria altissima) Grasses via Altering Antioxidant Enzyme Activities and Photosynthesis

As one of the most important limiting factors of grassland productivity, drought is predicted to increase in intensity and frequency. Greenhouse studies suggest that arbuscular mycorrhizal fungi (AMF) can improve plant drought resistance. However, whether AMF can improve plant drought resistance in field conditions and whether the effects of AMF on drought resistance differ among plants with different photosynthetic pathways remain unclear. To evaluate the effect of indigenous AMF on plant drought resistance, an in situ rainfall exclusion experiment was conducted in a temperate meadow in northeast China. The results showed that AMF significantly reduced the negative effects of drought on plant growth. On average, AMF enhanced plant biomass, photosynthetic rate (A), stomatal conductance (g s), intrinsic water use efficiency (iWUE), and superoxide dismutase (SOD) activity of the C3 species Leymus chinensis by 58, 63, 38, 15, and 45%, respectively, and reduced levels of malondialdehyde (MDA) by 32% under light and moderate drought (rainfall exclusion of 30 and 50%, respectively). However, under extreme drought (rainfall exclusion of 70%), AMF elevated only aboveground biomass and catalase (CAT) activities. Averagely, AMF increased the aboveground biomass, A, and CAT activity of Hemarthria altissima (C4) by 37, 28, and 30%, respectively, under light and moderate droughts. The contribution of AMF to plant drought resistance was higher for the C3 species than that for the C4 species under both light and moderate drought conditions. The results highlight potential photosynthetic type differences in the magnitude of AMF-associated enhancement in plant drought resistance. Therefore, AMF may determine plant community structure under future climate change scenarios by affecting the drought resistance of different plant functional groups.

Water Use Efficiency as a Constraint and Target for Improving the Resilience and Productivity of C3 and C4 Crops

The ratio of plant carbon gain to water use, known as water use efficiency (WUE), has long been recognized as a key constraint on crop production and an important target for crop improvement. WUE is a physiologically and genetically complex trait that can be defined at a range of scales. Many component traits directly influence WUE, including photosynthesis, stomatal and mesophyll conductances, and canopy structure. Interactions of carbon and water relations with diverse aspects of the environment and crop development also modulate WUE. As a consequence, enhancing WUE by breeding or biotechnology has proven challenging but not impossible. This review aims to synthesize new knowledge of WUE arising from advances in phenotyping, modeling, physiology, genetics, and molecular biology in the context of classical theoretical principles. In addition, we discuss how rising atmospheric CO₂ concentration has created and will continue to create opportunities for enhancing WUE by modifying the trade-off between photosynthesis and transpiration.

Tracking temporal shifts in area, biomes, and pollinators in the radiation of Salvia (sages) across continents: leveraging anchored hybrid enrichment and targeted sequence data

PREMISE OF THE STUDY

A key question in evolutionary biology is why some clades are more successful by being widespread geographically, biome diverse, or species-rich. To extend understanding of how shifts in area, biomes, and pollinators impact diversification in plants, we examined the relationships of these shifts to diversification across the mega-genus Salvia.

METHODS

A chronogram was developed from a supermatrix of anchored hybrid enrichment genomic data and targeted sequence data for over 500 of the nearly 1000 Salvia species. Ancestral areas and biomes were reconstructed using BioGeoBEARS. Pollinator guilds were scored, ancestral pollinators determined, shifts in pollinator guilds identified, and rates of pollinator switches compared.

KEY RESULTS

A well-resolved phylogenetic backbone of Salvia and updated subgeneric designations are presented. Salvia originated in Southwest Asia in the Oligocene and subsequently dispersed worldwide. Biome shifts are frequent from a likely ancestral lineage utilizing broadleaf and/or coniferous forests and/or arid shrublands. None of the four species diversification shifts are correlated to shifts in biomes. Shifts in pollination system are not correlated to species diversification shifts, except for one hummingbird shift that precedes a major shift in diversification near the crown of New World subgen. Calosphace. Multiple reversals back to bee pollination occurred within this hummingbird clade.

CONCLUSIONS

Salvia diversified extensively in different continents, biomes, and with both bee and bird pollinators. The lack of tight correlation of area, biome, and most pollinator shifts to the four documented species diversification shifts points to other important drivers of speciation in Salvia.

Metabolite profiles reveal interspecific variation in operation of the Calvin-Benson cycle in both C4 and C3 plants

Low atmospheric CO2 in recent geological time led to the evolution of carbon-concentrating mechanisms (CCMs) such as C4 photosynthesis in >65 terrestrial plant lineages. We know little about the impact of low CO2 on the Calvin-Benson cycle (CBC) in C3 species that did not evolve CCMs, representing >90% of terrestrial plant species. Metabolite profiling provides a top-down strategy to investigate the operational balance in a pathway. We profiled CBC intermediates in a panel of C4 (Zea mays, Setaria viridis, Flaveria bidentis, and F. trinervia) and C3 species (Oryza sativa, Triticium aestivum, Arabidopsis thaliana, Nicotiana tabacum, and Manihot esculenta). Principal component analysis revealed differences between C4 and C3 species that were driven by many metabolites, including lower ribulose 1,5-bisphosphate in C4 species. Strikingly, there was also considerable variation between C3 species. This was partly due to different chlorophyll and protein contents, but mainly to differences in relative levels of metabolites. Correlation analysis indicated that one contributory factor was the balance between fructose-1,6-bisphosphatase, sedoheptulose-1,7-bisphosphatase, phosphoribulokinase, and Rubisco. Our results point to the CBC having experienced different evolutionary trajectories in C3 species since the ancestors of modern plant lineages diverged. They underline the need to understand CBC operation in a wide range of species.

Leaf shape and size track habitat transitions across forest-grassland boundaries in the grass family (Poaceae)

Grass leaf shape is a strong indicator of their habitat with linear leaves predominating in open areas and ovate leaves distinguishing forest-associated grasses. This pattern among extant species suggests that ancestral shifts between forest and open habitats may have coincided with changes in leaf shape or size. We tested relationships between habitat, climate, photosynthetic pathway, and leaf shape and size in a phylogenetic framework to evaluate drivers of leaf shape and size variation over the evolutionary history of the family. We also estimated the ancestral habitat of Poaceae and tested whether forest margins served as transitional zones for shifts between forests and grasslands. We found that grass leaf shape is converging toward different shape optima in the forest understory, forest margins, and open habitats. Leaf size also varies with habitat. Grasses have smaller leaves in open and drier areas, and in areas with high solar irradiance. Direct transitions between linear and ovate leaves are rare as are direct shifts between forest and open habitats. The most likely ancestral habitat of the family was the forest understory and forest margins along with an intermediate leaf shape served as important transitional habitat and morphology, respectively, for subsequent shifts across forest-grassland biome boundaries.

Life history is a key factor explaining functional trait diversity among subtropical grasses, and its influence differs between C3 and C4 species

Life history and photosynthetic type both affect the economics of leaf physiological function. Annual plants have lower tissue densities and resource-use efficiencies than perennials, while C4 photosynthesis, facilitated in grasses by specific changes in leaf anatomy, improves photosynthetic efficiency and water-use efficiency, especially in hot climates. This study aimed to determine whether C4 photosynthesis affects differences in functional traits between annual and perennial species. We measured 26 traits and characterised niche descriptors for 42 grasses from subtropical China. Differences in the majority of traits were explained by life history. The ranges of annual species (particularly C4 annuals) extended to regions with greater temperature seasonality and lower precipitation, and annuals had less-negative turgor-loss points, higher specific leaf areas, and lower water-use efficiencies, stomatal conductances, and leaf areas per stem area than perennials. Photosynthetic type largely affected leaf physiology as expected, but interacted with life history in determining specific traits. Leaf hydraulic conductance was intermediate in perennials, highest in C4-annuals, and lowest in C3-annuals. Densities of stomata and stem vessels were similar across C3-perennials and C4 species, but stomatal densities were lower and stem vessel densities higher in C3-annuals. Phylogenetic principal component analysis confirmed that in this subtropical environment life history is the predominant axis separating species, and annuals and perennials were more different within C3 than C4 grasses. The interplay between life history and photosynthetic type may be an overlooked factor in shaping the physiological ecology of grasses.

Shared extremes by ectotherms and endotherms: Body elongation in mustelids is associated with small size and reduced limbs

An elongate body with reduced or absent limbs has evolved independently in many ectothermic vertebrate lineages. While much effort has been spent examining the morphological pathways to elongation in these clades, quantitative investigations into the evolution of elongation in endothermic clades are lacking. We quantified body shape in 61 musteloid mammals (red panda, skunks, raccoons, and weasels) using the head-body elongation ratio. We also examined the morphological changes that may underlie the evolution toward more extreme body plans. We found that a mustelid clade comprised of the subfamilies Helictidinae, Guloninae, Ictonychinae, Mustelinae, and Lutrinae exhibited an evolutionary transition toward more elongate bodies. Furthermore, we discovered that elongation of the body is associated with the evolution of other key traits such as a reduction in body size and a reduction in forelimb length but not hindlimb length. This relationship between body elongation and forelimb length has not previously been quantitatively established for mammals but is consistent with trends exhibited by ectothermic vertebrates and suggests a common pattern of trait covariance associated with body shape evolution. This study provides the framework for documenting body shapes across a wider range of mammalian clades to better understand the morphological changes influencing shape disparity across all vertebrates.

Chlorophyll Fluorescence, Photoinhibition and Abiotic Stress: Does it Make Any Difference the Fact to Be a C3 or C4 Species?

Chlorophyll fluorescence analysis is one of the most powerful and widely used techniques to study the effect of stresses on the photosynthetic process. From the first utilization, the F v/F m ratio has been largely used as a sensitive indicator of plant photosynthetic performance. Decreases of this index are indicative of the reduction of photosystem II (PSII) efficiency, namely photoinhibition. In the last 20 years, application of chlorophyll fluorescence has been largely improved, and many other informative parameters have been established to detect PSII photochemical efficiency and the partitioning of light energy to alternative dissipative mechanisms (qE, energy-dependent quenching; qZ, zeaxanthin-dependent quenching and qI, photoinhibitory quenching; qH, sustained photoprotective antenna quenching; qM, quenching dependent to chloroplast movement; qT, light harvesting complexes II-I state-transition) such as the recently developed "photoprotective power" of non-photochemical quenching (pNPQ). This review reports a brief description of the main chlorophyll fluorescence parameters and a wide analysis of the current bibliography on the use of different parameters which are useful to detect events of PSII photoinhibition. In addition, in view of the inherent differences in morpho-anatomical, physiological and biochemical features between C3 and C4 metabolism, possible differences in terms of photoinhibition between C3 and C4 plant species under stress conditions are proposed. The attempt is to highlight the limits of their comparison in terms of susceptibility to photoinhibition and to propose direction of future research which, assisted by chlorophyll fluorescence, should improve the knowledge of the different sensitivity of C3 and C4 to abiotic stressors.

Effects of drought and fire on resprouting capacity of 52 temperate Australian perennial native grasses

It remains uncertain how perennial grasses with different photosynthetic pathways respond to fire, and how this response varies with stress at the time of burning. Resprouting after fire was examined in relation to experimentally manipulated pre-fire watering frequencies. We asked the following questions: are there response differences to fire between C₃ and C₄ grasses? And, how does post-fire resprouting vary with pre-fire drought stress? Fifty-two perennial Australian grasses (37 genera, 13 tribes) were studied. Three watering frequencies were applied to simulate increasing drought. Pre-fire tiller number, tiller density, specific leaf area and leaf dry matter content were measured as explanatory variables to assess response. Most species (90%) and individuals (79%) resprouted following experimental burning. C₄ grasses had higher probabilities of surviving fire relative to C₃ grasses. Responses were not related to phylogeny or tribe. High leaf dry matter content reduced the probability of dying, but also reduced the re-emergence of tillers. Post-fire tiller number increased with increasing drought, regardless of photosynthetic type, suggesting that drought plays a role in the ability of grasses to recover after fire. This has implications for understanding the persistence of species in landscapes where fire management is practiced.

Overexpression of the Rieske FeS protein of the Cytochrome b6f complex increases C4 photosynthesis in Setaria viridis

C₄ photosynthesis is characterised by a CO₂ concentrating mechanism that operates between mesophyll and bundle sheath cells increasing CO₂ partial pressure at the site of Rubisco and photosynthetic efficiency. Electron transport chains in both cell types supply ATP and NADPH for C₄ photosynthesis. Cytochrome b₆f is a key control point of electron transport in C₃ plants. To study whether C₄ photosynthesis is limited by electron transport we constitutively overexpressed the Rieske FeS subunit in Setaria viridis. This resulted in a higher Cytochrome b₆f content in mesophyll and bundle sheath cells without marked changes in the abundances of other photosynthetic proteins. Rieske overexpression plants showed better light conversion efficiency in both Photosystems and could generate higher proton-motive force across the thylakoid membrane underpinning an increase in CO₂ assimilation rate at ambient and saturating CO₂ and high light. Our results demonstrate that removing electron transport limitations can increase C₄ photosynthesis.

Diversification, adaptation, and community assembly of the American oaks (Quercus), a model clade for integrating ecology and evolution

Contents Summary 669 I. Model clades for the study and integration of ecology and evolution 670 II. Oaks: an important model clade 671 III. Insights from the history of the American oaks for understanding community assembly and ecosystem dominance 673 IV. Bridging the gap between micro- and macroevolutionary processes relevant to ecology 679 V. How do we reconcile evidence for adaptive evolution with niche conservatism and long-term stasis? 682 VI. High plasticity and within-population genetic variation contribute to population persistence 683 VII. Emerging technologies for tracking functional change 685 VIII. Conclusions 685 Acknowledgements 686 References 686 SUMMARY: Ecologists and evolutionary biologists are concerned with explaining the diversity and composition of the natural world and are aware of the inextricable linkages between ecological and evolutionary processes that maintain the Earth's life support systems. Yet examination of these linkages remains challenging due to the contrasting nature of focal systems and research approaches. Model clades provide a critical means to integrate ecology and evolution, as illustrated by the oaks (genus Quercus), an important model clade, given their ecological dominance, remarkable diversity, and growing phylogenetic, genomic, and ecological data resources. Studies of the clade reveal that their history of sympatric parallel adaptive radiation continues to influence community assembly today, highlighting questions on the nature and extent of coexistence mechanisms. Flexible phenology and hydraulic traits, despite evolutionary stasis, may have enabled adaptation to a wide range of environments within and across species, contributing to their high abundance and diversity. The oaks offer fundamental insights at the intersection of ecology and evolution on the role of diversification in community assembly processes, on the importance of flexibility in key functional traits in adapting to new environments, on factors contributing to persistence of long-lived organisms, and on evolutionary legacies that influence ecosystem function.

The Grass was Greener: Repeated Evolution of Specialized Morphologies and Habitat Shifts in Ghost Spiders Following Grassland Expansion in South America

While grasslands, one of Earth's major biomes, are known for their close evolutionary ties with ungulate grazers, these habitats are also paramount to the origins and diversification of other animals. Within the primarily South American spider subfamily Amaurobioidinae (Anyphaenidae), several species are found living in the continent's grasslands, with some displaying putative morphological adaptations to dwelling unnoticed in the grass blades. Herein, a dated molecular phylogeny provides the backbone for analyses revealing the ecological and morphological processes behind these spiders' grassland adaptations. The multiple switches from Patagonian forests to open habitats coincide with the expansion of South America's grasslands during the Miocene, while the specialized morphology of several grass-dwelling spiders originated at least three independent times and is best described as the result of different selective regimes operating on macroevolutionary timescales. Although grass-adapted lineages evolved towards different peaks in adaptive landscape, they all share one characteristic: an anterior narrowing of the prosoma allowing spiders to extend the first two pairs of legs, thus maintaining a slender resting posture in the grass blade. By combining phylogenetic, morphological, and biogeographic perspectives we disentangle multiple factors determining the evolution of a clade of terrestrial invertebrate predators alongside their biomes.

Pliocene and Eocene provide best analogs for near-future climates

As the world warms due to rising greenhouse gas concentrations, the Earth system moves toward climate states without societal precedent, challenging adaptation. Past Earth system states offer possible model systems for the warming world of the coming decades. These include the climate states of the Early Eocene (ca. 50 Ma), the Mid-Pliocene (3.3-3.0 Ma), the Last Interglacial (129-116 ka), the Mid-Holocene (6 ka), preindustrial (ca. 1850 CE), and the 20th century. Here, we quantitatively assess the similarity of future projected climate states to these six geohistorical benchmarks using simulations from the Hadley Centre Coupled Model Version 3 (HadCM3), the Goddard Institute for Space Studies Model E2-R (GISS), and the Community Climate System Model, Versions 3 and 4 (CCSM) Earth system models. Under the Representative Concentration Pathway 8.5 (RCP8.5) emission scenario, by 2030 CE, future climates most closely resemble Mid-Pliocene climates, and by 2150 CE, they most closely resemble Eocene climates. Under RCP4.5, climate stabilizes at Pliocene-like conditions by 2040 CE. Pliocene-like and Eocene-like climates emerge first in continental interiors and then expand outward. Geologically novel climates are uncommon in RCP4.5 (<1%) but reach 8.7% of the globe under RCP8.5, characterized by high temperatures and precipitation. Hence, RCP4.5 is roughly equivalent to stabilizing at Pliocene-like climates, while unmitigated emission trajectories, such as RCP8.5, are similar to reversing millions of years of long-term cooling on the scale of a few human generations. Both the emergence of geologically novel climates and the rapid reversion to Eocene-like climates may be outside the range of evolutionary adaptive capacity.

Opposite macroevolutionary responses to environmental changes in grasses and insects during the Neogene grassland expansion

The rise of Neogene C4 grasslands is one of the most drastic changes recently experienced by the biosphere. A central - and widely debated - hypothesis posits that Neogene grasslands acted as a major adaptive zone for herbivore lineages. We test this hypothesis with a novel model system, the Sesamiina stemborer moths and their associated host-grasses. Using a comparative phylogenetic framework integrating paleoenvironmental proxies we recover a negative correlation between the evolutionary trajectories of insects and plants. Our results show that paleoenvironmental changes generated opposing macroevolutionary dynamics in this insect-plant system and call into question the role of grasslands as a universal adaptive cradle. This study illustrates the importance of implementing environmental proxies in diversification analyses to disentangle the relative impacts of biotic and abiotic drivers of macroevolutionary dynamics.

Grassland fire ecology has roots in the late Miocene

That fire facilitated the late Miocene C4 grassland expansion is widely suspected but poorly documented. Fire potentially tied global climate to this profound biosphere transition by serving as a regional-to-local driver of vegetation change. In modern environments, seasonal extremes in moisture amplify the occurrence of fire, disturbing forest ecosystems to create niche space for flammable grasses, which in turn provide fuel for frequent fires. On the Indian subcontinent, C4 expansion was accompanied by increased seasonal extremes in rainfall (evidenced by δ18Ocarbonate), which set the stage for fuel accumulation and fire-linked clearance during wet-to-dry seasonal transitions. Here, we test the role of fire directly by examining the abundance and distribution patterns of fire-derived polycyclic aromatic hydrocarbons (PAHs) and terrestrial vegetation signatures in n-alkane carbon isotopes from paleosol samples of the Siwalik Group (Pakistan). Two million years before the C4 grassland transition, fire-derived PAH concentrations increased as conifer vegetation declined, as indicated by a decrease in retene. This early increase in molecular fire signatures suggests a transition to more fire-prone vegetation such as a C3 grassland and/or dry deciduous woodland. Between 8.0 and 6.0 million years ago, fire, precipitation seasonality, and C4-grass dominance increased simultaneously (within resolution) as marked by sharp increases in fire-derived PAHs, δ18Ocarbonate, and 13C enrichment in n-alkanes diagnostic of C4 grasses. The strong association of evidence for fire occurrence, vegetation change, and landscape opening indicates that a dynamic fire-grassland feedback system was both a necessary precondition and a driver for grassland ecology during the first emergence of C4 grasslands.

C4 photosynthesis and climate through the lens of optimality

CO2, temperature, water availability, and light intensity were all potential selective pressures that determined the competitive advantage and expansion of the C4 photosynthetic carbon-concentrating mechanism over the last ∼30 My. To tease apart how selective pressures varied along the ecological trajectory of C4 expansion and dominance, we coupled hydraulics to photosynthesis models while optimizing photosynthesis over stomatal resistance and leaf/fine-root allocation. We further examined the importance of nitrogen reallocation from the dark to the light reactions. We show here that the primary selective pressures favoring C4 dominance changed through the course of C4 evolution. The higher stomatal resistance and leaf-to-root ratios enabled by C4 led to an advantage without any initial difference in hydraulic properties. We further predict a reorganization of the hydraulic system leading to higher turgor-loss points and possibly lower hydraulic conductance. Selection on nitrogen reallocation varied with CO2 concentration. Through paleoclimate model simulations, we find that water limitation was the primary driver for a C4 advantage, with atmospheric CO2 as high as 600 ppm, thus confirming molecular-based estimates for C4 evolution in the Oligocene. Under these high-CO2 conditions, nitrogen reallocation was necessary. Low CO2 and high light, but not nitrogen reallocation, were the primary drivers for the mid- to late-Miocene global expansion of C4 We also predicted the timing and spatial distribution for origins of C4 ecological dominance. The predicted origins are broadly consistent with prior estimates, but expand upon them to include a center of origin in northwest Africa and a Miocene-long origin in Australia.

Insights into the historical assembly of global dryland floras: the diversification of Zygophyllaceae

BACKGROUND

Drylands cover nearly 41% of Earth's land surface and face a high risk of degradation worldwide. However, the actual timeframe during which dryland floras rose on a global scale remains unknown. Zygophyllaceae, an important characteristic component of dryland floras worldwide, offers an ideal model group to investigate the diversification of dryland floras. Here, we used an integration of the phylogenetic, molecular dating, biogeographic, and diversification methods to investigate the timing and patterns of lineage accumulation for Zygophyllaceae overall and regionally. We then incorporated the data from other dominant components of dryland floras in different continents to investigate the historical construction of dryland floras on a global scale.

RESULTS

We provide the most comprehensive phylogenetic tree for Zygophyllaceae so far based on four plastid and nuclear markers. Detailed analyses indicate that Zygophyllaceae colonized Africa, Asia, Australia, and the New World at different periods, sometimes multiple times, but Zygophyllaceae lineages in the four regions all experienced a rapid accumulation beginning at the mid-late Miocene (~ 15-10 Ma). Other eleven essential elements of dryland floras become differentiated at the same time.

CONCLUSIONS

Our results suggest that the rise of global dryland floras is near-synchronous and began at the mid-late Miocene, possibly resulting from the mid-Miocene global cooling and regional orogenetic and climate changes. The mid-late Miocene is an essential period for the assembly and evolution of global dryland floras.

Investigating the NAD-ME biochemical pathway within C4 grasses using transcript and amino acid variation in C4 photosynthetic genes

Expanding knowledge of the C₄ photosynthetic pathway can provide key information to aid biological improvements to crop photosynthesis and yield. While the C₄ NADP-ME pathway is well characterised, there is increasing agricultural and bioengineering interest in the comparably understudied NAD-ME and PEPCK pathways. Within this study, a systematic identification of key differences across species has allowed us to investigate the evolution of C₄-recruited genes in one C₃ and eleven C₄ grasses (Poaceae) spanning two independent origins of C₄ photosynthesis. We present evidence for C₄-specific paralogs of NAD-malic enzyme 2, MPC1 and MPC2 (mitochondrial pyruvate carriers) via increased transcript abundance and associated rates of evolution, implicating them as genes recruited to perform C₄ photosynthesis within NAD-ME and PEPCK subtypes. We then investigate the localisation of AspAT across subtypes, using novel and published evidence to place AspAT3 in both the cytosol and peroxisome. Finally, these findings are integrated with transcript abundance of previously identified C₄ genes to provide an updated model for C₄ grass NAD-ME and PEPCK photosynthesis. This updated model allows us to develop on the current understanding of NAD-ME and PEPCK photosynthesis in grasses, bolstering our efforts to understand the evolutionary 'path to C₄' and improve C₄ photosynthesis.

Fire spread and the issue of community-level selection in the evolution of flammability

Whether plants can evolve to promote flammability is controversial. Ecologically, fire only spreads in landscapes when many plants are flammable, but collective behaviours among large groups are difficult to evolve at the individual level. Here, we formulate a model that examines how flammability can spread from rarity, combining individual-level costs and payoffs of flammability with landscape-level fire spread, sufficiently generic to analogize flammability among grasses, Mediterranean systems, and others. We found that fire-prone and fire-suppressing landscapes, composed of flammable and non-flammable plants, respectively, were alternatively stable in some environments, and flammability therefore only increased from rarity in environments when fire-proneness was the only stable state. Thus, fire-vegetation feedbacks alone probably did not drive the evolution and spread of flammability. However, evolution of flammability did promote fire-proneness in temporally and spatially heterogeneous environments: when flammable plants already occupied some substantial fraction of a fire-prone landscape, a positive feedback with fire could maintain flammability in a decreasingly favourable environment, and fire feedbacks could expand the distribution of flammability traits from fire-prone into fire-suppressing areas in a heterogeneous landscape. Thus, fire feedbacks could potentially have promoted the widespread invasion and persistence of flammability traits to their current widespread prominence.

Human impacts in African savannas are mediated by plant functional traits

Tropical savannas have a ground cover dominated by C₄ grasses, with fire and herbivory constraining woody cover below a rainfall-based potential. The savanna biome covers 50% of the African continent, encompassing diverse ecosystems that include densely wooded Miombo woodlands and Serengeti grasslands with scattered trees. African savannas provide water, grazing and browsing, food and fuel for tens of millions of people, and have a unique biodiversity that supports wildlife tourism. However, human impacts are causing widespread and accelerating degradation of savannas. The primary threats are land cover-change and transformation, landscape fragmentation that disrupts herbivore communities and fire regimes, climate change and rising atmospheric CO₂ . The interactions among these threats are poorly understood, with unknown consequences for ecosystem health and human livelihoods. We argue that the unique combinations of plant functional traits characterizing the major floristic assemblages of African savannas make them differentially susceptible and resilient to anthropogenic drivers of ecosystem change. Research must address how this functional diversity among African savannas differentially influences their vulnerability to global change and elucidate the mechanisms responsible. This knowledge will permit appropriate management strategies to be developed to maintain ecosystem integrity, biodiversity and livelihoods.

Soil Moisture, Grass Production and Mesquite Resprout Architecture Following Mesquite Above-Ground Mortality

Honey mesquite (Prosopis glandulosa) is an invasive native woody plant in the southern Great Plains, USA. Treatments used to slow the invasion rate have either killed the plant (“root-kill”) or killed above-ground tissue (“top-kill”). Top-killing provides temporary suppression, but stimulates multi-stemmed regrowth. This study from north central Texas quantified soil moisture, grass production and mesquite resprout architecture following a mechanical clearing treatment that top-killed mesquite (cleared) compared to untreated mesquite woodland (woodland) over a 10-year period. During an extreme drought at 5 and 6 years post-clearing, soil moisture at 60-cm depth became lower in cleared than in woodland, suggesting that, as early as 5 years after top-kill, water use by regrowth mesquite could be greater than that by woodland mesquite. Perennial grass production was greater in cleared treatments than in woodland treatments in all years except the extreme drought years. Mesquite regrowth biomass increased numerically each year and was independent of annual precipitation with one exception. During the year 5 and 6 drought, mesquite stopped lateral expansion of larger stems and increased growth of smaller stems and twigs. In summary, top-killing mesquite generated short-term benefits of increased grass production, but regrowth created potentially negative consequences related to soil moisture.

Understanding the Genetic Basis of C4 Kranz Anatomy with a View to Engineering C3 Crops

One of the most remarkable examples of convergent evolution is the transition from C₃ to C₄ photosynthesis, an event that occurred on over 60 independent occasions. The evolution of C₄ is particularly noteworthy because of the complexity of the developmental and metabolic changes that took place. In most cases, compartmentalized metabolic reactions were facilitated by the development of a distinct leaf anatomy known as Kranz. C₄ Kranz anatomy differs from ancestral C₃ anatomy with respect to vein spacing patterns across the leaf, cell-type specification around veins, and cell-specific organelle function. Here we review our current understanding of how Kranz anatomy evolved and how it develops, with a focus on studies that are dissecting the underlying genetic mechanisms. This research field has gained prominence in recent years because understanding the genetic regulation of Kranz may enable the C₃-to-C₄ transition to be engineered, an endeavor that would significantly enhance crop productivity.

Stomatal and non-stomatal limitations in savanna trees and C4 grasses grown at low, ambient and high atmospheric CO2

By the end of the century, atmospheric CO₂ concentration ([CO₂]_a) could reach 800 ppm, having risen from ∼200 ppm ∼24 Myr ago. Carbon dioxide enters plant leaves through stomata that limit CO₂ diffusion and assimilation, imposing stomatal limitation (L_S). Other factors limiting assimilation are collectively called non-stomatal limitations (L_NS). C₄ photosynthesis concentrates CO₂ around Rubisco, typically reducing L_S. C₄-dominated savanna grasslands expanded under low [CO₂]_a and are metastable ecosystems where the response of trees and C₄ grasses to rising [CO₂]_a will determine shifting vegetation patterns. How L_S and L_NS differ between savanna trees and C₄ grasses under different [CO₂]_a will govern the responses of CO₂ fixation and plant cover to [CO₂]_a - but quantitative comparisons are lacking. We measured assimilation, within soil wetting-drying cycles, of three C₃ trees and three C₄ grasses grown at 200, 400 or 800 ppm [CO₂]_a. Using assimilation-response curves, we resolved L_S and L_NS and show that rising [CO₂]_a alleviated L_S, particularly for the C₃ trees, but L_NS was unaffected and remained substantially higher for the grasses across all [CO₂]_a treatments. Because L_NS incurs higher metabolic costs and recovery compared with L_S, our findings indicate that C₄ grasses will be comparatively disadvantaged as [CO₂]_a rises.

Climate and host-plant associations shaped the evolution of ceutorhynch weevils throughout the Cenozoic

Using molecular phylogenetic data and methods we inferred divergence times and diversification patterns for the weevil subfamily Ceutorhynchinae in the context of host‐plant associations and global climate over evolutionary time. We detected four major diversification shifts that correlate with both host shifts and major climate events. Ceutorhynchinae experienced an increase in diversification rate at ∼53 Ma, during the Early Eocene Climate Optimum, coincident with a host shift to Lamiaceae. A second major diversification phase occurred at the end of the Eocene (∼34 Ma). This contrasts with the overall deterioration in climate equability at the Eocene‐Oligocene boundary, but tracks the diversification of important host plant clades in temperate (higher) latitudes, leading to increased diversification rates in the weevil clades infesting temperate hosts. A third major phase of diversification is correlated with the rising temperatures of the Late Oligocene Warming Event (∼26.5 Ma); diversification rates then declined shortly after the Middle Miocene Climate Transition (∼14.9 Ma). Our results indicate that biotic and abiotic factors together explain the evolution of Ceutorhynchinae better than each of these drivers viewed in isolation.

Genetics of lineage diversification and the evolution of host usage in the economically important wheat curl mite, Aceria tosichella Keifer, 1969

BACKGROUND

Understanding the mechanisms that underlie the diversification of herbivores through interactions with their hosts is important for their diversity assessment and identification of expansion events, particularly in a human-altered world where evolutionary processes can be exacerbated. We studied patterns of host usage and genetic structure in the wheat curl mite complex (WCM), Aceria tosichella, a major pest of the world's grain industry, to identify the factors behind its extensive diversification.

RESULTS

We expanded on previous phylogenetic research, demonstrating deep lineage diversification within the taxon, a complex of distinctive host specialist and generalist lineages more diverse than previously assumed. Time-calibrated phylogenetic reconstruction inferred from mitochondrial DNA sequence data suggests that lineage diversification pre-dates the influence of agricultural practices, and lineages started to radiate in the mid Miocene when major radiations of C4 grasses is known to have occurred. Furthermore, we demonstrated that host specificity is not phylogenetically constrained, while host generalization appears to be a more derived trait coinciding with the expansion of the world's grasslands. Demographic history of specialist lineages have been more stable when compared to generalists, and their expansion pre-dated all generalist lineages. The lack of host-associated genetic structure of generalists indicates gene flow between mite populations from different hosts.

CONCLUSIONS

Our analyses demonstrated that WCM is an unexpectedly diverse complex of genetic lineages and its differentiation is likely associated with the time of diversification and expansion of its hosts. Signatures of demographic histories and expansion of generalists are consistent with the observed proliferation of the globally most common lineages. The apparent lack of constrains on host use, coupled with a high colonization potential, hinders mite management, which may be further compromised by host range expansion. This study provides a significant contribution to the growing literature on host-association and diversification in herbivorous invertebrates.

Climate-smart crops with enhanced photosynthesis

The potential of enhanced photosynthetic efficiency to help achieve the sustainable yield increases required to meet future demands for food and energy has spurred intense research towards understanding, modeling, and engineering photosynthesis. These current efforts, largely focused on the C3 model Arabidopsis thaliana or crop plants (e.g. rice, sorghum, maize, and wheat), could be intensified and broadened using model systems closely related to our food, feed, and energy crops and that allow rapid design-build-test-learn cycles. In this outlooking Opinion, we advocate for a concerted effort to expand our understanding and improve our ability to redesign carbon uptake, allocation, and utilization. We propose two specific research directions that combine enhanced photosynthesis with climate-smart metabolic attributes: (i) engineering pathways for flexible (facultative) C3-C4 metabolism where plants will operate either C3 or C4 photosynthesis based on environmental conditions such as temperature, light, and atmospheric CO2 levels; and (ii) increasing rhizospheric sink strength for carbon utilization, including strategies that allow for augmented transport of carbon to the soil for improved soil properties and carbon storage without jeopardizing aboveground crop biomass. We argue that such ambitious undertakings be first approached and demonstrated by exploring the full genomic potential of two model grasses, the C3Brachypodium distachyon and the C4Setaria viridis. The development of climate-smart crops could provide novel and bold solutions to increase crop productivity while reducing atmospheric carbon and nitrogen emissions.

Some like it hot: the physiological ecology of C4 plant evolution

The evolution of C₄ photosynthesis requires an intermediate phase where photorespiratory glycine produced in the mesophyll cells must flow to the vascular sheath cells for metabolism by glycine decarboxylase. This glycine flux concentrates photorespired CO₂ within the sheath cells, allowing it to be efficiently refixed by sheath Rubisco. A modest C₄ biochemical cycle is then upregulated, possibly to support the refixation of photorespired ammonia in sheath cells, with subsequent increases in C₄ metabolism providing incremental benefits until an optimized C₄ pathway is established. 'Why' C₄ photosynthesis evolved is largely explained by ancestral C₃ species exploiting photorespiratory CO₂ to improve carbon gain and thus enhance fitness. While photorespiration depresses C₃ performance, it produces a resource (photorespired CO₂) that can be exploited to build an evolutionary bridge to C₄ photosynthesis. 'Where' C₄ evolved is indicated by the habitat of species branching near C₃-to-C₄ transitions on phylogenetic trees. Consistent with the photorespiratory bridge hypothesis, transitional species show that the large majority of > 60 C₄ lineages arose in hot, dry, and/or saline regions where photorespiratory potential is high. 'When' C₄ evolved has been clarified by molecular clock analyses using phylogenetic data, coupled with isotopic signatures from fossils. Nearly all C₄ lineages arose after 25 Ma when atmospheric CO₂ levels had fallen to near current values. This reduction in CO₂, coupled with persistent high temperature at low-to-mid-latitudes, met a precondition where photorespiration was elevated, thus facilitating the evolutionary selection pressure that led to C₄ photosynthesis.

Unexpected reversal of C3 versus C4 grass response to elevated CO2 during a 20-year field experiment

Theory predicts and evidence shows that plant species that use the C₄ photosynthetic pathway (C₄ species) are less responsive to elevated carbon dioxide (eCO₂) than species that use only the C₃ pathway (C₃ species). We document a reversal from this expected C₃-C₄ contrast. Over the first 12 years of a 20-year free-air CO₂ enrichment experiment with 88 C₃ or C₄ grassland plots, we found that biomass was markedly enhanced at eCO₂ relative to ambient CO₂ in C₃ but not C₄ plots, as expected. During the subsequent 8 years, the pattern reversed: Biomass was markedly enhanced at eCO₂ relative to ambient CO₂ in C₄ but not C₃ plots. Soil net nitrogen mineralization rates, an index of soil nitrogen supply, exhibited a similar shift: eCO₂ first enhanced but later depressed rates in C₃ plots, with the opposite true in C₄ plots, partially explaining the reversal of the eCO₂ biomass response. These findings challenge the current C₃-C₄eCO₂ paradigm and show that even the best-supported short-term drivers of plant response to global change might not predict long-term results.

Mitochondrial introgression and interspecies recombination in the Fusarium fujikuroi species complex

The Fusarium fujikuroi species complex (FFSC) is an economically important monophyletic lineage in the genus Fusarium. Incongruence observed among mitochondrial gene trees, as well as the multiple non-orthologous copies of the internal transcribed spacer region of the ribosomal RNA genes, suggests that the origin and history of this complex likely involved interspecies gene flow. Based on this hypothesis, the mitochondrial genomes of non-conspecific species should harbour signatures of introgression or introgressive hybridization. The aim of this study was therefore to search for recombination between the mitochondrial genomes of different species in the FFSC. Using methods based on mt genome sequence similarity, five significant recombinant regions in both gene and intergenic regions were detected. Using coalescent-based methods and the sequences for individual mt genes, various ancestral recombination events between different lineages of the FFSC were also detected. These findings suggest that interspecies gene flow and introgression are likely to have played key roles in the evolution of the FFSC at both ancient and more recent time scales.

Shade compromises the photosynthetic efficiency of NADP-ME less than that of PEP-CK and NAD-ME C4 grasses

The high energy cost and apparently low plasticity of C4 photosynthesis compared with C3 photosynthesis may limit the productivity and distribution of C4 plants in low light (LL) environments. C4 photosynthesis evolved numerous times, but it remains unclear how different biochemical subtypes perform under LL. We grew eight C4 grasses belonging to three biochemical subtypes [NADP-malic enzyme (NADP-ME), NAD-malic enzyme (NAD-ME), and phosphoenolpyruvate carboxykinase (PEP-CK)] under shade (16% sunlight) or control (full sunlight) conditions and measured their photosynthetic characteristics at both low and high light. We show for the first time that LL (during measurement or growth) compromised the CO2-concentrating mechanism (CCM) to a greater extent in NAD-ME than in PEP-CK or NADP-ME C4 grasses by virtue of a greater increase in carbon isotope discrimination (∆P) and bundle sheath CO2 leakiness (ϕ), and a greater reduction in photosynthetic quantum yield (Φmax). These responses were partly explained by changes in the ratios of phosphoenolpyruvate carboxylase (PEPC)/initial Rubisco activity and dark respiration/photosynthesis (Rd/A). Shade induced a greater photosynthetic acclimation in NAD-ME than in NADP-ME and PEP-CK species due to a greater Rubisco deactivation. Shade also reduced plant dry mass to a greater extent in NAD-ME and PEP-CK relative to NADP-ME grasses. In conclusion, LL compromised the co-ordination of the C4 and C3 cycles and, hence, the efficiency of the CCM to a greater extent in NAD-ME than in PEP-CK species, while CCM efficiency was less impacted by LL in NADP-ME species. Consequently, NADP-ME species are more efficient at LL, which could explain their agronomic and ecological dominance relative to other C4 grasses.

CO2 availability influences hydraulic function of C3 and C4 grass leaves

Atmospheric CO2 (ca) has increased since the last glacial period, increasing photosynthetic water use efficiency and improving plant productivity. Evolution of C4 photosynthesis at low ca led to decreased stomatal conductance (gs), which provided an advantage over C3 plants that may be reduced by rising ca. Using controlled environments, we determined how increasing ca affects C4 water use relative to C3 plants. Leaf gas exchange and mass per area (LMA) were measured for four C3 and four C4 annual, crop-related grasses at glacial (200 µmol mol-1), ambient (400 µmol mol-1), and super-ambient (640 µmol mol-1) ca. C4 plants had lower gs, which resulted in a water use efficiency advantage at all ca and was broadly consistent with slower stomatal responses to shade, indicating less pressure on leaf water status. At glacial ca, net CO2 assimilation and LMA were lower for C3 than for C4 leaves, and C3 and C4 grasses decreased leaf hydraulic conductance (Kleaf) similarly, but only C4 leaves decreased osmotic potential at turgor loss. Greater carbon availability in C4 leaves at glacial ca generated a different hydraulic adjustment relative to C3 plants. At current and future ca, C4 grasses have advantages over C3 grasses due to lower gs, lower stomatal sensitivity, and higher absolute water use efficiency.

Phytoliths indicate significant arboreal cover at Sahelanthropus type locality TM266 in northern Chad and a decrease in later sites

We analyzed phytolith and diatom remains preserved at 45 Miocene and Pliocene localities dated between 8 and 1 Ma in northern Chad (16-17°N). Some of these localities yielded cranial remains, lower jaws, and teeth of the hominin species Australopithecus bahrelghazali (∼3.6 Ma) and Sahelanthropus tchadensis (∼7 Ma). Of the 111 sediment samples analyzed, 41 yielded phytoliths, 20 yielded diatoms, and seven yielded both phytoliths and diatoms. Freshwater planktonic and tychoplanktonic diatom species, indicative of lacustrine conditions, are dominant (>91%) in the samples. The phytolith assemblages indicate an opening of the vegetation and a general trend toward an expansion of grass-dominated environments during the time spanning the two hominin occurrences in Chad. The phytoliths suggest the presence of a mosaic environment, including closed forest patches, palm groves, and mixed/grassland formations, between 7.5 and 7 Ma, the replacement by palm grove-like vegetation at approximately 6.5-5 Ma, and the presence of exclusive grass-dominated formations after 4.5 Ma. The type-locality of S. tchadensis (TM266) was likely similar to modern palm grove formations with an arboreal cover percentage ≥40%. The type locality of A. bahrelghazali (KT12) was a grass-dominated ecosystem (likely savanna) with an unrated percentage of arboreal cover. Furthermore, the grass phytolith data support the existence of a (recurrent) Sahelian-like dry climate in northern Chad since at least 8 Ma. Therefore the local closed vegetation formations in the Djurab region at 7.5-7 Ma were sustained by aquatic systems (such as lakes or related rivers, marshes) rather than by extensive annual precipitation.

The role of diversification in community assembly of the oaks (Quercus L.) across the continental U.S

PREMISE OF THE STUDY

Evolutionary and biogeographic history, including past environmental change and diversification processes, are likely to have influenced the expansion, migration, and extinction of populations, creating evolutionary legacy effects that influence regional species pools and the composition of communities. We consider the consequences of the diversification process in shaping trait evolution and assembly of oak-dominated communities throughout the continental United States (U.S.).

METHODS

Within the U.S. oaks, we tested for phylogenetic and functional trait patterns at different spatial scales, taking advantage of a dated phylogenomic analysis of American oaks and the U.S. Forest Service (USFS) Forest Inventory and Analysis (FIA).

KEY RESULTS

We find (1) phylogenetic overdispersion at small grain sizes throughout the U.S. across all spatial extents and (2) a shift from overdispersion to clustering with increasing grain sizes. Leaf traits have evolved in a convergent manner, and these traits are clustered in communities at all spatial scales, except in the far west, where species with contrasting leaf types co-occur.

CONCLUSIONS

Our results support the hypotheses that (1) interspecific interactions were important in parallel adaptive radiation of the genus into a range of habitats across the continent and (2) that the diversification process is a critical driver of community assembly. Functional convergence of complementary species from distinct clades adapted to the same local habitats is a likely mechanism that allows distantly related species to coexist. Our findings contribute to an explanation of the long-term maintenance of high oak diversity and the dominance of the oak genus in North America.

Constructing a broadly inclusive seed plant phylogeny

PREMISE OF THE STUDY

Large phylogenies can help shed light on macroevolutionary patterns that inform our understanding of fundamental processes that shape the tree of life. These phylogenies also serve as tools that facilitate other systematic, evolutionary, and ecological analyses. Here we combine genetic data from public repositories (GenBank) with phylogenetic data (Open Tree of Life project) to construct a dated phylogeny for seed plants.

METHODS

We conducted a hierarchical clustering analysis of publicly available molecular data for major clades within the Spermatophyta. We constructed phylogenies of major clades, estimated divergence times, and incorporated data from the Open Tree of Life project, resulting in a seed plant phylogeny. We estimated diversification rates, excluding those taxa without molecular data. We also summarized topological uncertainty and data overlap for each major clade.

KEY RESULTS

The trees constructed for Spermatophyta consisted of 79,881 and 353,185 terminal taxa; the latter included the Open Tree of Life taxa for which we could not include molecular data from GenBank. The diversification analyses demonstrated nested patterns of rate shifts throughout the phylogeny. Data overlap and inference uncertainty show significant variation throughout and demonstrate the continued need for data collection across seed plants.

CONCLUSIONS

This study demonstrates a means for combining available resources to construct a dated phylogeny for plants. However, this approach is an early step and more developments are needed to add data, better incorporating underlying uncertainty, and improve resolution. The methods discussed here can also be applied to other major clades in the tree of life.

Clair LL, Williams L, Wedin M, Lumbsch HT. Multiple, Distinct Intercontinental Lineages but Isolation of Australian Populations in a Cosmopolitan Lichen-Forming Fungal Taxon, Psora decipiens (Psoraceae, Ascomycota)

Multiple drivers shape the spatial distribution of species, including dispersal capacity, niche incumbency, climate variability, orographic barriers, and plate tectonics. However, biogeographic patterns of fungi commonly do not fit conventional expectations based on studies of animals and plants. Fungi, in general, are known to occur across exceedingly broad, intercontinental distributions, including some important components of biological soil crust communities (BSCs). However, molecular data often reveal unexpected biogeographic patterns in lichenized fungal species that are assumed to have cosmopolitan distributions. The lichen-forming fungal species Psora decipiens is found on all continents, except Antarctica and occurs in BSCs across diverse habitats, ranging from hot, arid deserts to alpine habitats. In order to better understand factors that shape population structure in cosmopolitan lichen-forming fungal species, we investigated biogeographic patterns in the cosmopolitan taxon P. decipiens, along with the closely related taxa P. crenata and P. saviczii. We generated a multi-locus sequence dataset based on a worldwide sampling of these taxa in order to reconstruct evolutionary relationships and explore phylogeographic patterns. Both P. crenata and P. decipiens were not recovered as monophyletic; and P. saviczii specimens were recovered as a monophyletic clade closely related to a number of lineages comprised of specimens representing P. decipiens. Striking phylogeographic patterns were observed for P. crenata, with populations from distinct geographic regions belonging to well-separated, monophyletic lineages. South African populations of P. crenata were further divided into well-supported sub-clades. While well-supported phylogenetic substructure was also observed for the nominal taxon P. decipiens, nearly all lineages were comprised of specimens collected from intercontinental populations. However, all Australian specimens representing P. decipiens were recovered within a single well-supported monophyletic clade consisting solely of Australian samples. Our study supports up to 10 candidate species-level lineages in P. decipiens, based on genealogical concordance and coalescent-based species delimitation analyses. Our results support the general pattern of the biogeographic isolation of lichen-forming fungal populations in Australia, even in cases where closely related congeners have documented intercontinental distributions. Our study has important implications for understanding factors influencing diversification and distributions of lichens associated with BSC.

Millions of Years Behind: Slow Adaptation of Ruminants to Grasslands

The Late Cretaceous appearance of grasses, followed by the Cenozoic advancement of grasslands as dominant biomes, has contributed to the evolution of a range of specialized herbivores adapted to new diets, as well as to increasingly open and arid habitats. Many mammals including ruminants, the most diversified ungulate suborder, evolved high-crowned (hypsodont) teeth as an adaptation to tooth-wearing diets and habitats. The impact of different causes of tooth wear is still a matter of debate, and the temporal pattern of hypsodonty evolution in relation to the evolution of grasslands remains unclear. We present an improved time-calibrated molecular phylogeny of Cetartiodactyla, with phylogenetic reconstruction of ancestral ruminant diets and habitats, based on characteristics of extant taxa. Using this timeline, as well as the fossil record of grasslands, we conduct phylogenetic comparative analyses showing that hypsodonty in ruminants evolved as an adaptation to both diet and habitat. Our results demonstrate a slow, perhaps constrained, evolution of hypsodonty toward estimated optimal states, excluding the possibility of immediate adaptation. This augments recent findings that slow adaptation is not uncommon on million-year time scales.

Molecular adaptation in Rubisco: Discriminating between convergent evolution and positive selection using mechanistic and classical codon models

Rubisco (Ribulose-1, 5-biphosphate carboxylase/oxygenase) is the most important enzyme on earth, catalyzing the first step of photosynthetic CO2 fixation. So, without it, there would be no storing of the sun's energy in plants. Molecular adaptation of Rubisco to C4 photosynthetic pathway has attracted a lot of attention. C4 plants, which comprise less than 5% of land plants, have evolved more efficient photosynthesis compared to C3 plants. Interestingly, a large number of independent transitions from C3 to C4 phenotype have occurred. Each time, the Rubisco enzyme has been subject to similar changes in selective pressure, thus providing an excellent model for convergent evolution at the molecular level. Molecular adaptation is often identified with positive selection and is typically characterized by an elevated ratio of non-synonymous to synonymous substitution rate (dN/dS). However, convergent adaptation is expected to leave a different molecular signature, taking the form of repeated transitions toward identical or similar amino acids. Here, we used a previously introduced codon-based differential-selection model to detect and quantify consistent patterns of convergent adaptation in Rubisco in eudicots. We further contrasted our results with those obtained by classical codon models based on the estimation of dN/dS. We found that the two classes of models tend to select distinct, although overlapping, sets of positions. This discrepancy in the results illustrates the conceptual difference between these models while emphasizing the need to better discriminate between qualitatively different selective regimes, by using a broader class of codon models than those currently considered in molecular evolutionary studies.

Extending the scope of Darwin's 'abominable mystery': integrative approaches to understanding angiosperm origins and species richness

Background and aims

Angiosperms are the most species-rich group of land plants, but their origins and fast and intense diversification still require an explanation.

Scope

Extending research scopes can broaden theoretical frameworks and lines of evidence that can lead to solving this 'abominable mystery'. Solutions lie in understanding evolutionary trends across taxa and throughout the Phanerozoic, and integration between hypotheses and ideas that are derived from multiple disciplines.

Key Findings

Descriptions of evolutionary chronologies should integrate between molecular phylogenies, descriptive palaeontology and palaeoecology. New molecular chronologies open new avenues of research of possible Palaeozoic angiosperm ancestors and how they evolved during as many as 200Myr until the emergence of true angiosperms. The idea that 'biodiversity creates biodiversity' requires evidence from past and present ecologies, with changes in herbivory and resource availability throughout the Phanerozoic appearing to be particularly promising.

Conclusions

Promoting our understanding of angiosperm origins and diversification in particular, and the evolution of biodiversity in general, requires more profound understanding of the ecological past through integrating taxonomic, temporal and ecological scopes.

An evaluation of contemporary savanna fire regimes in the Canastra National Park, Brazil: Outcomes of fire suppression policies

Fire has shaped plant evolution and biogeochemical cycles for millions of years in savanna ecosystems, but changes in natural fire regimes promoted by human land use threaten contemporary conservation efforts. In protected areas in the Brazilian savannas (Cerrado), the predominant management policy is fire suppression, reflecting a cultural heritage which considers that fire always has a negative impact on biodiversity. Here we compare resultant fire-regimes in Canastra National Park (CNP), southeast Brazil, associated with areas under and without fire suppression management, based on a 16-year Landsat imagery record. In open grasslands of the Canastra plateau (CP), firefighting is undertaken under government-sanctioned regulation, whereas in the Babilonia sector, non-sanctioned fire management is undertaken by small farmers to promote cattle grazing and cropping. Fire regimes in the Canastra sector are characterized by few, very large, late dry season wildfires recurring at intervals of two years. Fire regimes in lowlands of the Babilonia sector are characterized by many small-scale, starting at the beginning of the dry season (EDS). In Babilonia uplands fire regimes are characterized by higher frequencies of large fires. The study illustrates major challenges for managing fire-prone areas in conflict-of-interest regions. We suggest that management planning in CNP needs to effectively address: i) managing conflicts between CNP managers and local communities; and ii) fire management practices in order to achieve more ecologically sustainable fire regimes. The study has broader implications for conservation management in fire-prone savannas in South America generally.