Spatial distribution of conspecific genotypes within chimeras of the branching coral Stylophora pistillata

Chimerism is a coalescence of conspecific genotypes. Although common in nature, fundamental knowledge, such as the spatial distribution of the genotypes within chimeras, is lacking. Hence, we investigated the spatial distribution of conspecific genotypes within the brooding coral Stylophora pistillata, a common species throughout the Indo-Pacific and Red Sea. From eight gravid colonies, we collected planula larvae that settled in aggregates, forming 2–3 partner chimeras. Coral chimeras grew in situ for up to 25 months. Nine chimeras (8 kin, 1 non-related genotypes) were sectioned into 7–17 fragments (6–26 polyps/fragment), and genotyped using eight microsatellite loci. The discrimination power of each microsatellite-locus was evaluated with 330 ‘artificial chimeras,’ made by mixing DNA from three different S. pistillata genotypes in pairwise combinations. In 68% of ‘artificial chimeras,’ the second genotype was detected if it constituted 5–30% of the chimera. Analyses of S. pistillata chimeras revealed that: (a) chimerism is a long-term state; (b) conspecifics were intermixed (not separate from one another); (c) disproportionate distribution of the conspecifics occurred; (d) cryptic chimerism (chimerism not detected via a given microsatellite) existed, alluding to the underestimation of chimerism in nature. Mixed chimerism may affect ecological/physiological outcomes for a chimera, especially in clonal organisms, and challenges the concept of individuality, affecting our understanding of the unit of selection.

Combining the Seed Endophytic Bacteria and the Back to the Future Approaches for Plant Holonbiont Breeding

Given the limits of intensive agriculture (pollution, degradation of biodiversity, or soil desertification), it is necessary to develop sustainable alternatives to respond to future agricultural demand. Among these sustainable alternatives is the use of microbial biostimulants. Despite convincing scientific studies on them, their agricultural use remains minor. This can be explained by the lack of efficiency and reliability of their use. This review proposes to develop efficient microbial biostimulants based on the combination of two approaches, namely that of endophytic bacteria from seeds and the Back to the Future approach. Seed endophytic bacteria have a major agroindustrial potential insofar as they stand out from other microbial agents by their resistance, competitiveness, efficiency, and vertical transmission. Contrary to modern cultivars, non-domesticated plants harbor microbiomes which have not been impacted by the processes of domestication and agriculture intensification. The Back to the Future suggests therefore to use interesting microorganisms isolated from non-domesticated plants and to integrate them into modern cultivars. This could result in the rehabilitation of modern microbiomes and lead to make crop cultures more resistant and resilient. The idea consisting in the combination of both approaches aims at obtaining optimized microbiomes. Particular emphasis is placed on integrating these innovative microbiomes into variety breeding programs. Indeed, given the importance of plant-microorganism interactions, particularly from an agronomic point of view, taking the hologenome into account as a unit of selection in breeding programs is essential. This integrative and unprecedented approach to designing breeding programs is promising with a view to reconciling productivity and preservation of agroecosystems.

Genomic Prediction in Family Bulks Using Different Traits and Cross-Validations in Pine

Genomic prediction integrates statistical, genomic and computational tools to improve the estimation of breeding values and increase genetic gain. Due to the broad diversity in mating systems, breeding schemes, propagation methods, and unit of selection, no universal genomic prediction approach can be applied in all crops. In a genome-wide family prediction (GWFP) approach, the family is the basic unit of selection. We tested GWFP in two loblolly pine (Pinus taeda L.) datasets: a breeding population composed of 63 full-sib families (5-20 individuals per family), and a simulated population with the same pedigree structure. In both populations, phenotypic and genomic data was pooled at the family level in silico. Marker effects were estimated to compute genomic estimated breeding values at the individual (GEBV) and family (GWFP) levels. Less than six individuals per family produced inaccurate estimates of family phenotypic performance and allele frequency. Tested across different scenarios, GWFP predictive ability was higher than those for GEBV in both populations. Validation sets composed of families with similar phenotypic mean and variance as the training population yielded predictions consistently higher and more accurate than other validation sets. Results revealed potential for applying GWFP in breeding programs whose selection unit are family, and for systems where family can serve as training sets. The GWFP approach is well suited for crops that are routinely genotyped and phenotyped at the plot-level, but it can be extended to other breeding programs. Higher predictive ability obtained with GWFP would motivate the application of genomic prediction in these situations.

Genomic Prediction in Family Bulks Using Different Traits and Cross-Validations in Pine

Genomic prediction (GP) integrates statistical, genomic and computational tools to improve the estimation of breeding values and increase genetic gain. Due to the broad diversity in biology, breeding scheme, propagation method, and unit of selection, no universal GP approach can be applied in all crops. In a genome-wide family prediction (GWFP) approach, the family bulk is the basic unit of selection. We tested GWFP in two loblolly pine (Pinus taeda L.) datasets: a breeding population composed of 63 full-sib families (5-20 individuals per family), and a simulated population with the same pedigree structure. In both populations, phenotypic and genomic data was pooled at the family level in silico. Marker effects were estimated to compute genomic estimated breeding values at the individual (GEBV) and family (GWFP) levels. Less than six individuals per family produced inaccurate estimates of family phenotypic performance and allele frequency. Tested across different scenarios, GWFP predictive ability was higher than those for GEBV in both populations. Validation sets composed of families with similar phenotypic mean and variance as the training population yielded predictions consistently higher and more accurate than other validation sets. Results revealed potential for applying GWFP in breeding programs whose selection unit are family bulks, and for systems where family can serve as training sets. The GWFP approach is well suited for crops that are routinely genotyped and phenotyped at the plot-level, but it can be extended to other breeding programs. Higher predictive ability obtained with GWFP would motivate the application of GP in these situations.

Feature-based attention is not confined by object boundaries: spatially global enhancement of irrelevant features

Theories of visual attention differ in what they define as the core unit of selection. Feature-based theories emphasize the importance of visual features (e.g., color, size, motion), demonstrated through enhancement of attended features across the visual field, while object-based theories propose that attention enhances all features belonging to the same object. Here we test how within-object enhancement of features interacts with spatially global effects of feature-based attention. Participants attended a set of colored dots (moving coherently upwards or downwards) to detect brief luminance decreases, while simultaneously detecting speed changes in another set of dots in the opposite visual field. Participants had higher speed detection rates for the dot array that matched the motion direction of the attended color array, although motion direction was entirely task-irrelevant. This effect persisted even when it was detrimental for task performance. Overall, these results indicate that task-irrelevant object features are enhanced globally, surpassing object boundaries.

Extended genomes: symbiosis and evolution

Many aspects of an individual's biology derive from its interaction with symbiotic microbes, which further define many aspects of the ecology and evolution of the host species. The centrality of microbes in the function of individual organisms has given rise to the concept of the holobiont—that an individual's biology is best understood as a composite of the ‘host organism’ and symbionts within. This concept has been further elaborated to posit the holobiont as a unit of selection. In this review, I critically examine whether it is useful to consider holobionts as a unit of selection. I argue that microbial heredity—the direct passage of microbes from parent to offspring—is a key factor determining the degree to which the holobiont can usefully be considered a level of selection. Where direct vertical transmission (VT) is common, microbes form part of extended genomes whose dynamics can be modelled with simple population genetics, but that nevertheless have subtle quantitative distinctions from the classic mutation/selection model for nuclear genes. Without direct VT, the correlation between microbial fitness and host individual fitness erodes, and microbe fitness becomes associated with host survival only (rather than reproduction). Furthermore, turnover of microbes within a host may lessen associations between microbial fitness with host survival, and in polymicrobial communities, microbial fitness may derive largely from the ability to outcompete other microbes, to avoid host immune clearance and to minimize mortality through phage infection. These competing selection pressures make holobiont fitness a very minor consideration in determining symbiont evolution. Nevertheless, the importance of non-heritable microbes in organismal function is undoubted—and as such the evolutionary and ecological processes giving rise to variation and evolution of the microbes within and between host individuals represent a key research area in biology.

Why the item will remain the unit of attentional selection in visual search

Hulleman & Olivers (H&O) reject item-based serial models of visual search, and they suggest that items are processed equally and globally during each fixation period. However, neuroscientific studies have shown that attentional biases can emerge in parallel but in a spatially selective item-based fashion. Even within a parallel architecture for visual search, the item remains the critical unit of selection.

Item-based selection is in good shape in visual compound search: A view from electrophysiology

We argue that although the framework put forward by Hulleman & Olivers (H&O) can successfully explain much of visual search behaviour, it appears limited to tasks without precise target identification demands. In particular, we contend that the unit of selection may be larger than a single item in standard detection tasks, whereas the unit may mandatorily be item-based in compound tasks.

Holes in the Hologenome: Why Host-Microbe Symbioses Are Not Holobionts

ABSTRACT The advent of relatively inexpensive tools for characterizing microbial communities has led to an explosion of research exploring the diversity, ecology, and evolution of microbe-host systems. Some now question whether existing conceptual frameworks are adequate to explain microbe-host systems. One popular paradigm is the “holobiont-hologenome,” which argues that a host and its microbiome evolve as a single cooperative unit of selection (i.e., a superorganism). We argue that the hologenome is based on overly restrictive assumptions which render it an approach of little research utility. A host plus its microbiome is more effectively viewed as an ecological community of organisms that encompasses a broad range of interactions (parasitic to mutualistic), patterns of transmission (horizontal to vertical), and levels of fidelity among partners. The hologenome requires high partner fidelity if it is to evolve as a unit. However, even when this is achieved by particular host-microbe pairs, it is unlikely to hold for the entire host microbiome, and therefore the community is unlikely to evolve as a hologenome. Both mutualistic and antagonistic (fitness conflict) evolution can occur among constituent members of the community, not just adaptations at the “hologenome” level, and there is abundant empirical evidence for such divergence of selective interests among members of host-microbiome communities. We believe that the concepts and methods of ecology, genetics, and evolutionary biology will continue to provide a well-grounded intellectual framework for researching host-microbiome communities, without recourse to the limiting assumption that selection acts predominantly at the holobiont level.