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University of Copenhagen - Cited by 1,216 - Evolutionary biology - Hologenomics - Biogeography - Behavioural Ecology - Molecular Ecology

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The theory of kin selection is the framework to explain the evolution of social interactions that abound across the diversity of life (1). Observing cooperative behavior posed a challenge to Darwin, but with social insects in mind he proposed that natural selection at the family level can favor helping relatives reproduce (2). His ideas, and the work of Price, built the foundation for Hamilton’s rule, stating that the cost of helping others, in terms of lost reproductive output, may be offset if help is directed toward increasing reproduction of sufficiently close relatives. As such, the investment in passing on genes through relatives contributes to the inclusive fitness of an organism (3). The stark division of labor in some social insects, between sterile workers and reproductive royals, in particular begged an explanation that kin selection provided. Moreover, kin selection has since also helped to explain cooperative behaviors in mammals, birds, algae, and microbes (4). Estimating and analyzing inclusive fitness effects of social traits and applying concepts from kin selection requires the estimation of relatedness between actors and recipients—a challenge in complex microbial communities. In PNAS, Simonet and McNally (5) propose an approach based on the analysis of metagenomes in fecal microbiomes from healthy donors. Their work opens a frontier for kin selection theory by exploring the associations between relatedness and cooperative trait distributions in human gut bacteria. The field of sociomicrobiology has taken off over the last 20 years (6, 7). In microbes, short generation times, tools for their genetic manipulation, and small space requirements have opened a plethora of opportunities to test central tenets of social evolution theory, under controlled conditions that were unattainable using, for example, beehives or ant colonies. With often simple experimental designs it has been shown that production of secreted public goods, such as siderophores … [↵][1]1To whom correspondence may be addressed. Email: sbandersen{at}sund.ku.dk. [1]: #xref-corresp-1-1

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Europe PMC is an archive of life sciences journal literature.

From ontogenesis to homeostasis, the phenotypes of complex organisms are shaped by the bidirectional interactions between the host organisms and their associated microbiota. Current technology can reveal many such interactions by combining multi-omic data from both hosts and microbes. However, explo …

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The hologenome concept of evolution is a hypothesis explaining host evolution in the context of the host microbiomes. As a hypothesis, it needs to be evaluated, especially with respect to the extent of fidelity of transgenerational coassociation of host and microbial lineages and the relative fitnes …

I am a broadly-trained microbial, behavioral, and evolutionary ecologist with interests in hologenomics, evaluating and managing symbiotic microbial influences on human health and disease, especial…

Once upon a time, lions were the world's most widespread mammals. Now we know more about their genealogy – and that could make it easier to help the species survive.

A savory account of how the pursuit of delicious foods shaped human evolution

The hologenome theory of evolution emphasizes the role of microorganisms in the evolution of animals and plants. The theory posits that the holobiont (host plus all of its symbiont microbiota) is a unit of selection in evolution. Genetic variation in the holobiont that can occur either in the host and/or in the microbial symbiont genomes (together termed hologenome) can then be transmitted to offspring. In addition to the known modes of variation, i.e. sexual recombination, chromosomal rearrangement and mutation, variation in the holobiont can occur also via two mechanisms that are specific to the hologenome theory: amplification of existing microorganisms and acquisition of novel strains from the environment. These mechanisms are Lamarckian in that (i) they are regulated by 'use and disuse' (of microbes) and (ii) the variations in the hologenome are transmitted to offspring, thus satisfying also the Lamarckian principle of 'inheritance of acquired characteristics'. Accordingly, the hologenome theory incorporates Lamarckian aspects within a Darwinian framework, accentuating both cooperation and competition within the holobiont and with other holobionts.

The Center for Evolutionary Hologenomics is retelling the story of life by applying the holo-omics approach to both applied and basic research

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Background The MinION Access Program (MAP, 2014–2016) allowed selected users to test the prospects of long nanopore reads for diverse organisms and applications through the rapid development of improving chemistries. In 2014, faced with a fragmented Illumina assembly for the chloroplast genome of the green algal holobiont Caulerpa ashmeadii, we applied to the MAP to test the prospects of nanopore reads to investigate such intricacies, as well as further explore the hologenome of this species with native and hybrid approaches. Results The chloroplast genome could only be resolved as a circular molecule in nanopore assemblies, which also revealed structural variants (i.e. chloroplast polymorphism or heteroplasmy). Signal and Illumina polishing of nanopore-assembled organelle genomes (chloroplast and mitochondrion) reflected the importance of coverage on final quality and current limitations. In hybrid assembly, our modest nanopore data sets showed encouraging results to improve assembly length, contiguity, repeat content, and binning of the larger nuclear and bacterial genomes. Profiling of the holobiont with nanopore or Illumina data unveiled a dominant Rhodospirillaceae (Alphaproteobacteria) species among six putative endosymbionts. While very fragmented, the cumulative hybrid assembly length of C. ashmeadii’s nuclear genome reached 24.4 Mbp, including 2.1 Mbp in repeat, ranging closely with GenomeScope’s estimate (> 26.3 Mbp, including 4.8 Mbp in repeat). Conclusion Our findings relying on a very modest number of nanopore R9 reads as compared to current output with newer chemistries demonstrate the promising prospects of the technology for the assembly and profiling of an algal hologenome and resolution of structural variation. The discovery of polymorphic ‘chlorotypes’ in C. ashmeadii, most likely mediated by homing endonucleases and/or retrohoming by reverse transcriptases, represents the first report of chloroplast heteroplasmy in the siphonous green algae. Improving contiguity of C. ashmeadii’s nuclear and bacterial genomes will require deeper nanopore sequencing to greatly increase the coverage of these larger genomic compartments.

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A paradigm shift has recently transformed the field of biological science; molecular advances have revealed how fundamentally important microorganisms are to many aspects of a host’s phenotype and evolution. In the process, an era of “holobiont” research has emerged to investigate the intricate network of interactions between a host and its symbiotic microbial consortia. Marine sponges are early-diverging metazoa known for hosting dense, specific, and often highly diverse microbial communities. Here we synthesize current thoughts about the environmental and evolutionary forces that influence the diversity, specificity, and distribution of microbial symbionts within the sponge holobiont, explore the physiological pathways that contribute to holobiont function, and describe the molecular mechanisms that underpin the establishment and maintenance of these symbiotic partnerships. The collective genomes of the sponge holobiont form the sponge hologenome, and we highlight how the forces that define a sponge’s phenotype in fact act on the genomic interplay between the different components of the holobiont.