Evolutionary pathways to lower biomass allocation to the seed coat in crops: insights from allometric scaling.

Crops generally have seeds larger than their wild progenitors´ and with reduced dormancy. In wild plants, seed mass and allocation to the seed coat (a proxy for physical dormancy) scale allometrically so that larger seeds tend to allocate less to the coats. Larger seeds and lightweight coats might thus have evolved as correlated traits in crops. We tested whether 34 crops and 22 of their wild progenitors fit the allometry described in the literature, which would indicate co-selection of both traits during crop evolution. Deviations from the allometry would suggest that other evolutionary processes contribute to explain the emergence of larger, lightweight-coated seeds in crops. Crops fitted the scaling slope but deviated from its intercept in a consistent way: Seed coats of crops were lighter than expected by their seed size. The wild progenitors of crops displayed the same trend, indicating that deviations cannot be solely attributed to artificial selection during or after domestication. The evolution of seeds with small coats in crops likely resulted from a combination of various pressures, including the selection of wild progenitors with coats smaller than other wild plants, further decreases during early evolution under cultivation, and indirect selection due to the seed coat-seed size allometry.

Early human selection of crops' wild progenitors explains the acquisitive physiology of modern cultivars.

Crops have resource-acquisitive leaf traits, which are usually attributed to the process of domestication. However, early choices of wild plants amenable for domestication may also have played a key role in the evolution of crops' physiological traits. Here we compiled data on 1,034 annual herbs to place the ecophysiological traits of 69 crops' wild progenitors in the context of global botanical variation, and we conducted a common-garden experiment to measure the effects of domestication on crop ecophysiology. Our study found that crops' wild progenitors already had high leaf nitrogen, photosynthesis, conductance and transpiration and soft leaves. After domestication, ecophysiological traits varied little and in idiosyncratic ways. Crops did not surpass the trait boundaries of wild species. Overall, the resource-acquisitive strategy of crops is largely due to the inheritance from their wild progenitors rather than to further breeding improvements. Our study concurs with recent literature highlighting constraints of crop breeding for faster ecophysiological traits.

Disparities among crop species in the evolution of growth rates: the role of distinct origins and domestication histories.

Growth rates vary widely among plants with different strategies. For crops, evolution under predictable and high-resource environments might favour rapid resource acquisition and growth, but whether this strategy has consistently evolved during domestication and improvement remains unclear. Here we report a comprehensive study of the evolution of growth rates based on comparisons among wild, landrace, and improved accessions of 19 herbaceous crops grown under common conditions. We also examined the underlying growth components and the influence of crop origin and history on growth evolution. Domestication and improvement did not affect growth consistently, that is growth rates increased or decreased or remained unchanged in different crops. Crops selected for fruits increased the physiological component of growth (net assimilation rate), whereas leaf and seed crops showed larger domestication effects on morphology (leaf mass ratio and specific leaf area). Moreover, climate and phylogeny contributed to explaining the effects of domestication and changes in growth. Crop-specific responses to domestication and improvement suggest that selection for high yield has not consistently changed growth rates. The trade-offs between morpho-physiological traits and the distinct origins and histories of crops accounted for the variability in growth changes. These findings have far-reaching implications for our understanding of crop performance and adaptation.

Incorporating phylogenetic metrics to microbial co-occurrence networks based on amplicon sequences to discern community assembly processes.

Co-occurrence network analysis based on amplicon sequences is increasingly used to study microbial communities. Patterns of co-existence or mutual exclusion between pairs of taxa are often interpreted as reflecting positive or negative biological interactions. However, other assembly processes can underlie these patterns, including species failure to reach distant areas (dispersal limitation) and tolerate local environmental conditions (habitat filtering). We provide a tool to quantify the relative contribution of community assembly processes to microbial co-occurrence patterns, which we applied to explore soil bacterial communities in two dry ecosystems. First, we sequenced a bacterial phylogenetic marker in soils collected across multiple plots. Second, we inferred co-occurrence networks to identify pairs of significantly associated taxa, either co-existing more (aggregated) or less often (segregated) than expected at random. Third, we assigned assembly processes to each pair: patterns explained based on spatial or environmental distance were ascribed to dispersal limitation (2%-4%) or habitat filtering (55%-77%), and the remaining to biological interactions. Finally, we calculated the phylogenetic distance between taxon pairs to test theoretical expectations on the linkages between phylogenetic patterns and assembly processes. Aggregated pairs were more closely related than segregated pairs. Furthermore, habitat-filtered aggregated pairs were closer relatives than those assigned to positive interactions, consistent with phylogenetic niche conservatism and cooperativism among distantly related taxa. Negative interactions resulted in equivocal phylogenetic signatures, probably because different competitive processes leave opposing signals. We show that microbial co-occurrence networks mainly reflect environmental tolerances and propose that incorporating measures of phylogenetic relatedness to networks might help elucidate ecologically meaningful patterns.