Ecology, not host phylogeny, shapes the oral microbiome in closely related species of gorillas

Moraitou, Markella; Forsythe, Adrian; Yates, James A. Fellows; Brealey, Jaelle C.; Warinner, Christina; Guschanski, Katerina

doi:10.1101/2022.06.06.494923

Cited by 3 publications

(1 citation statement)

References 166 publications

(332 reference statements)

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“…To date, studies on the ancient Neolithic microbiome have mostly relied on small groups of samples distributed over a broad geographical area characterised by distinct ecological conditions and subsistence strategies, thus introducing possible geographical and dietary bias. Indeed, as observed for different microbiome sources, the microbial communities that inhabit dental plaque appear to be influenced by diet, ecology and living conditions [17][18][19] . Moreover, archaeological evidence suggests that the Neolithic transition was not a monolithic event, but differences occurred in the adopted subsistence strategies across coeval communities [20][21][22] .…”

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confidence: 94%

Ancient oral microbiomes support gradual Neolithic dietary shifts towards agriculture

et al. 2022

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The human microbiome has recently become a valuable source of information about host life and health. To date little is known about how it may have evolved during key phases along our history, such as the Neolithic transition towards agriculture. Here, we shed light on the evolution experienced by the oral microbiome during this transition, comparing Palaeolithic hunter-gatherers with Neolithic and Copper Age farmers that populated a same restricted area in Italy. We integrate the analysis of 76 dental calculus oral microbiomes with the dietary information derived from the identification of embedded plant remains. We detect a stronger deviation from the hunter-gatherer microbiome composition in the last part of the Neolithic, while to a lesser extent in the early phases of the transition. Our findings demonstrate that the introduction of agriculture affected host microbiome, supporting the hypothesis of a gradual transition within the investigated populations.

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confidence: 94%

Ancient oral microbiomes support gradual Neolithic dietary shifts towards agriculture

et al. 2022

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Ghost admixture in eastern gorillas

Pawar

Cuadros-Espinoza

Manuel

et al. 2022

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Archaic admixture has had a significant impact on human evolution with multiple events across different clades, including from extinct hominins such as Neanderthals and Denisovans into modern humans. Within the great apes archaic admixture has been identified in chimpanzees and bonobos, but the possibility of such events has not been explored in other species. Here, we address this question using high-coverage whole genome sequences from all four extant gorilla subspecies, including six newly sequenced eastern gorillas from previously unsampled geographic regions. Using Approximate Bayesian Computation (ABC) with neural networks to model the demographic history of gorillas, we find a signature of admixture from an archaic 'ghost' lineage into the common ancestor of eastern gorillas, but not western gorillas. We infer that up to 3% of the genome of these individuals is introgressed from an archaic lineage that diverged more than 3 million years ago from the common ancestor of all extant gorillas. This introgression event took place before the split of mountain and eastern lowland gorillas, likely more than 40 thousand years ago, and may have influenced perception of bitter taste in eastern gorillas. When comparing the introgression landscapes of gorillas, humans and bonobos, we find a consistent depletion of introgressed fragments on the X chromosome across these species. However, depletion in protein-coding content is not detectable in eastern gorillas, possibly as a consequence of stronger genetic drift in this species.

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Ecology-relevant bacteria drive the evolution of host antimicrobial peptides in Drosophila

Hanson

Grollmus

Lemaître

2022

Preprint

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Antimicrobial peptides are host-encoded antibiotics that combat invading microbes and help shape the microbiome in plants and animals. However, little is known about how the host antimicrobial peptide repertoire is evolutionarily adapted to its microbiome. Here we characterize the function and evolution of the Diptericin antimicrobial peptide family of Diptera. Using mutations affecting the two Diptericins (Dpt) of D. melanogaster, we reveal the specific role of DptA against the pathogen Providencia rettgeri and DptB against the gut mutualist Acetobacter. Strikingly, presence of DptA- or DptB-like genes across Diptera correlates with the presence of Providencia and Acetobacter in their environment. Moreover, presence of DptA- and DpB-like genes is sufficient to predict host resistance against infection by these bacteria across a broad range of fly species. Our study explains the evolutionary logic behind the bursts of rapid evolution of an antimicrobial peptide family, and reveals how the host immune repertoire adapts itself to changing microbial environments.

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Ecology, not host phylogeny, shapes the oral microbiome in closely related species of gorillas

Cited by 3 publications

References 166 publications

Ancient oral microbiomes support gradual Neolithic dietary shifts towards agriculture

Ancient oral microbiomes support gradual Neolithic dietary shifts towards agriculture

Ghost admixture in eastern gorillas

Ecology-relevant bacteria drive the evolution of host antimicrobial peptides in Drosophila

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