The University of Edinburgh

Researchers have recovered remarkably preserved microbiomes from two teeth dating back 4,000 years, found in an Irish limestone cave. Genetic analyses of these microbiomes reveal major changes in the oral microenvironment from the Bronze Age to today. The teeth both belonged to the same male individual and also provided a snapshot of his oral health. Researchers at Trinity College Dublin have recovered remarkably preserved microbiomes from two teeth dating back 4,000 years, found in an Irish limestone cave. Genetic analyses of these microbiomes reveal major changes in the oral microenvironment from the Bronze Age to today. The teeth both belonged to the same male individual and also provided a snapshot of his oral health. The study, carried out in collaboration with archaeologists from the Atlantic Technological University and University of Edinburgh, was published today in journal Molecular Biology and Evolution. The authors identified several bacteria linked to gum disease and provided the first high-quality ancient genome of Streptococcus mutans, the major culprit behind tooth decay. While S. mutans is very common in modern mouths, it is exceptionally rare in the ancient genomic record. One reason for this may be the acid-producing nature of the species. This acid decays the tooth, but also destroys DNA and stops plaque from fossilising. While most ancient oral microbiomes are retrieved from fossilised plaque, this study targeted the tooth directly. Another reason for the scarcity of S. mutans in ancient mouths may be the lack of favorable habitats for this sugar-loving species. An uptick of dental cavities is seen in the archaeological record after the adoption of cereal agriculture thousands of years ago, but a far more dramatic increase has occurred only in the past few hundred years when sugary foods were introduced to the masses. The sampled teeth were part of a larger skeletal assemblage excavated from Killuragh Cave, County Limerick, by the late Peter Woodman of University College Cork. While other teeth in the cave showed advanced dental decay, no cavities were visible on the sampled teeth. However, one tooth produced an unprecedented amount of S. mutans DNA, a sign of an extreme imbalance in the oral microbial community. "We were very surprised to see such a large abundance of S. mutans in this 4,000-year-old tooth," said Dr Lara Cassidy, an assistant professor in Trinity's School of Genetics and Microbiology, and senior author of the study. "It is a remarkably rare find and suggests this man was at a high risk of developing cavities right before his death." The researchers also found that other streptococcal species were virtually absent from the tooth. This indicates the natural balance of the oral biofilm had been upset -- mutans had outcompeted the other streptococci leading to the pre-disease state. The team also found evidence to support the "disappearing microbiome" hypothesis, which proposes modern microbiomes are less diverse than those of our ancestors. This is cause for concern, as biodiversity loss can impact human health. The two Bronze Age teeth produced highly divergent strains of Tannerella forsythia, a bacteria implicated in gum disease. "These strains from a single ancient mouth were more genetically different from one another than any pair of modern strains in our dataset, despite the modern samples deriving from Europe, Japan and the USA," explained Iseult Jackson, a PhD candidate at Trinity, and first author of the study. "This represents a major loss in diversity and one that we need to understand better." Very few full genomes from oral bacteria have been recovered prior to the Medieval era. By characterising prehistoric diversity, the authors were able to reveal dramatic changes in the oral microenvironment that have happened since. Dr Cassidy added: "Over the last 750 years, a single lineage of T. forsythia has become dominant worldwide. This is the tell-tale sign of natural selection, where one strain rises rapidly in frequency due to some genetic advantage it holds over the others. T. forsythia strains from the industrial era onwards contain many new genes that help the bacteria colonise the mouth and cause disease. "S. mutans has also undergone recent lineage expansions and changes in gene content related to pathogenicity. These coincide with humanity's mass consumption of sugar, although we did find that modern S. mutans populations have remained more diverse, with deep splits in the S. mutans evolutionary tree pre-dating the Killuragh genome." The scientists believe this is driven by differences in the evolutionary mechanisms that shape genome diversity in these species. "S. mutans is very adept at swapping genetic material between strains," said Dr Cassidy. "This means an advantageous innovation can be spread across S. mutans lineages like a new piece of tech. This ability to easily share innovations may explain why this species retains many diverse lineages without one becoming dominant and replacing all the others." In effect, both these disease-causing bacteria have changed dramatically from the Bronze Age to today, but it appears that very recent cultural transitions in the industrial era have had an inordinate impact.

Scientists have discovered how honeybees can decipher dances by their hive mates that relay directions to food. Scientists have discovered how honeybees can decipher dances by their hive mates that relay directions to food. The findings reveal how, in the complete darkness of the hive, each bee uses its antennae to help interpret the information communicated through the dances. It has been known for decades that honeybees do so-called waggle dances, in which their movements and orientation on the honeycomb signal the direction and distance to food outside the hive. However, until now, it was unclear how the bees gathered around a waggle dancer make sense of the information. Gaining greater insights into how bees communicate could help scientists to better understand the effects of issues such as habitat loss and pesticide use on the insects' ability to find food, researchers say. A team from the University of Edinburgh made the discovery by studying a colony of honeybees at an apiary at the University and using computational models to mimic their brain processes. Researchers from the University's School of Informatics filmed the insects in slow motion and high resolution under infrared light. This enabled them to track the position of the antennae of the surrounding bees in fine detail during each waggle dance -- which are otherwise a blur to the naked human eye. The researchers observed that bees alter the position of their antennae, which are touched repeatedly by the dancer as it waggles by, based on the angle of their body relative to the dancer. The team realised that the bees could decode dances from any angle, or even from constantly changing positions, by combining signals picked up by their antennae with their own sense of gravity. However, this requires the bee to accurately add together the two angles detected from its two sensory systems. Using a computer model that replicates known brain circuits in the bee, the researchers showed that fewer than one hundred neurons are needed to integrate this information and recover the angle and the distance to the food being signalled in a waggle dance. The findings are published in the journal Current Biology. The study was supported by the European Research Council, the Janet Foreman Fund and the Eva Crane Trust. PhD student Anna Hadjitofi, of the University of Edinburgh's School of Informatics, said: "This is particularly exciting because it unveils a remarkably elegant neural mechanism employed by bees to decipher complex information with minimal resources." Professor Barbara Webb, also of the University's School of Informatics, added: "Understanding how the small brains of insects carry out such sophisticated calculations can help us design more compact and energy efficient computers."

Scientists have discovered how female Diadem butterflies have evolved to look like African Queen butterflies to repel predators. Scientists have discovered how female Diadem butterflies have evolved to look like African Queen butterflies to repel predators. African Queens are toxic, making them poor food for predators such as birds. Diadems are actually good prey for birds -- but they have evolved colours and patterns that closely match those of African Queens, making them appear toxic. The new study -- by a team including the universities of Exeter, Edinburgh and Cambridge, and Mpala Research Centre in Kenya -- found that, surprisingly, different genes control these patterns in the two species. "Since the time of Darwin, Wallace and Bates, people have wondered how different butterflies have evolved to appear the same -- and now we know," said Professor Richard ffrench-Constant, from the Centre for Ecology and Conservation on Exeter's Penryn Campus in Cornwall. "Our findings present a compelling instance of convergent evolution, whereby species independently evolve similar traits. "We also find evidence of adaptive atavism in the Diadem -- when a species reverts to a state found in its ancestors. "In this case, Diadem butterflies have re-evolved an ancestral wing pattern and repurposed it to mimic the Africa Queen, providing a major advance in our understanding of how tasty species mimic those that are toxic." Different patterns are found on African Queen butterflies in north, east, south and west Africa -- and the patterns on female Diadem butterflies in each area match these. In contrast, male Diadems have distinctive dark wings with large white patches -- possibly because the need to be recognised by the female outweighs the need to hide. "This is amazing, as the males and females look like totally different butterflies, even though they share the same genome," said Dr Dino Martins, who was the director of Mpala at the time all the butterflies were collected. The study used "haplotagging," a linked-read sequencing technology, and a new analytical tool called Wrath to study the genomes of multiple butterflies from the two different species. "These new techniques can give us unique insights into the molecular population genetics of this fascinating example of Batesian mimicry," said Dr Simon Martin, from the University of Edinburgh, one of the coauthors on the study. Among the different funders was a Discovery Grant from the National Geographic Society, showing how blue skies research into butterflies can fundamentally change our understanding of evolution. The paper, published in the journal Molecular Biology and Evolution, is entitled: "Transposable element insertions are associated with Batesian mimicry in the pantropical butterfly Hypolimnas misippus."