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Stone Age bear genome reconstructed from DNA in Mexican cave

Cam ac uk zoology department feed - 5 hours 3 min ago

A team of scientists led by Professor Eske Willerslev in the University of Cambridge’s Department of Zoology and the Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, have recreated the genomes of animals, plants and bacteria from microscopic fragments of DNA found in the remote Chiquihuite Cave in Mexico.

The findings have been described as the ‘moon landings of genomics’, because researchers will no longer have to rely on finding and testing fossils to determine genetic ancestry and connections.

The results, published today in the journal Current Biology, are the first time environmental DNA has been sequenced from soil and sediment. They include the ancient DNA profile of a Stone Age American black bear taken from samples in the cave.

Working with highly fragmented DNA from soil samples means scientists no longer have to rely on DNA samples from bone or teeth for enough genetic material to recreate a profile of ancient DNA.

The samples included faeces and droplets of urine from an ancestor of the American black bear, which allowed the scientists to recreate the entire genetic code of two species of the animal: the Stone Age American black bear, and a short-faced bear called Arctodus simus that died out 12,000 years ago. 

Professor Willerslev said: “When an animal or a human urinates or defecates, cells from the organism are also excreted. We can detect the DNA fragments from these cells in the soil samples and have now used these to reconstruct genomes for the first time. We have shown that hair, urine and faeces all provide genetic material which, in the right conditions, can survive for much longer than 10,000 years.

“Analysis of DNA found in soil could have the potential to expand the narrative about everything from the evolution of species to developments in climate change – fossils will no longer be needed.”

Chiquihuite Cave is a high-altitude site, situated 2,750 metres above sea level. DNA of mice, black bears, rodents, bats, voles and kangaroo rats was also found. The scientists say that DNA fragments in sediment will now be able to be tested in many former Stone Age settlements around the world.

Professor Willerslev said: “Imagine the stories those traces could tell. It’s a little insane – but also fascinating – to think that, back in the Stone Age, these bears urinated and defecated in the Chiquihuite Cave and left us the traces we’re able to analyse today.”

Reference

Petersen, M.K. et al, Environmental genomics of Late Pleistocene black bears and giant short-faced bears. Current Biology, April 2021. DOI: 10.1016/j.cub.2021.04.027

Adapted from a press release by St John's College, Cambridge.

 

Scientists have reconstructed ancient DNA from soil for the first time, in an advance that will significantly enhance the study of animal, plant and microorganism evolution.

Analysis of DNA found in soil could have the potential to expand the narrative about everything from the evolution of species to developments in climate change – fossils will no longer be needed.Eske WillerslevDevlin A. GandyAssistant Professor Mikkel Winther Pedersen with team members sampling the different cultural layers in the cave.


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Stepwide - promoting the next generation of female researchers

News from this site - 8 hours 11 min ago

A new website created by 3 female postdocs shines a light on early career talent at the University of Cambridge and affiliated institutes. The StepWide website launched last month aims to support female postdoctoral researchers, or those who identify as such, from any discipline, to showcase their expertise and grow their...

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Conservationists may be unintentionally spreading pathogens between threatened animal populations

Cam ac uk zoology department feed - Mon, 12/04/2021 - 10:00

The new report published today in the journal Conservation Letters focuses on freshwater mussels, which the researchers have studied extensively, but is applicable to all species moved around for conservation purposes. 

Mussels play an important role in cleaning the water of many of the world’s rivers and lakes, but are one of the most threatened animal groups on Earth. There is growing interest in moving mussels to new locations to boost threatened populations, or so they can be used as ‘biological filters’ to improve water quality. 

A gonad-eating parasitic worm, Rhipidocotyle campanula, which can leave mussels completely sterile, was identified as a huge risk for captive breeding programmes where mussels from many isolated populations are brought together.  

“We need to be much more cautious about moving animals to new places for conservation purposes, because the costs may outweigh the benefits,” said Dr David Aldridge in the Department of Zoology at the University of Cambridge, senior author of the report.

He added: “We’ve seen that mixing different populations of mussels can allow widespread transmission of gonad-eating worms – it only takes one infected mussel to spread this parasite, which in extreme cases can lead to collapse of an entire population.”

Pathogens can easily be transferred between locations when mussels are moved. In extreme cases, the pathogens may cause a population of mussels to completely collapse. In other cases infections may not cause a problem unless they are present when other factors, such as lack of food or high temperatures, put a population under stress leading to a sudden outbreak.

The report recommends that species are only relocated when absolutely necessary and quarantine periods, tailored to stop transmission of the most likely pathogens being carried, are used. 

It identifies four key factors that determine the risk of spreading pathogens when relocating animals: proportion of infected animals in both source and recipient populations; density of the resulting population; host immunity; and the life-cycle of the pathogen. Pathogens that must infect multiple species to complete their life-cycle, like parasitic mites, will only persist if all of the species are present in a given location.

“Moving animals to a new location is often used to protect or supplement endangered populations. But we must consider the risk this will spread pathogens that we don’t understand very well at all, which could put these populations in even greater danger,” said Josh Brian, a PhD student in the Department of Zoology at the University of Cambridge and first author of the report.

Different populations of the same species may respond differently to infection with the same pathogen because of adaptations in their immune system. For example, a pack of endangered wolves moved to Yellowstone National Park died because the wolves had no immunity to parasites carried by the local canines.

The researchers say that stocking rivers with fish for anglers, and sourcing exotic plants for home gardens could also move around parasites or diseases. 

“Being aware of the risks of spreading diseases between populations is a vital first step towards making sure we avoid unintentional harm in future conservation work,” said Isobel Ollard, a PhD student in the Department of Zoology at the University of Cambridge, who was also involved in the study.

This research was funded by the Woolf Fisher Trust.

Reference
Brian, J.I., Ollard, I.S., & Aldridge, D.C. ‘Don’t move a mussel? Parasite and disease risk in conservation action.’ Conservation Letters, April 2021. DOI: 10.1111/conl.12799

Moving endangered species to new locations is often used as part of species conservation strategies, and can help to restore degraded ecosystems. But scientists say there is a high risk that these relocations are accidentally spreading diseases and parasites.

We’ve seen that mixing different populations of mussels can allow widespread transmission of gonad-eating worms.David Aldridge David AldridgeAt-risk species of river mussel


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Economic benefits of protecting nature now outweigh those of exploiting it

Cam ac uk zoology department feed - Mon, 08/03/2021 - 16:19

The largest study of its kind finds that in most cases economic value is higher when habitats are conserved or restored, rather than converted to uses such as farming.

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Lead shot still prevalent in pheasant shooting

News from this site - Fri, 26/02/2021 - 09:22

During the 2020-2021 pheasant shooting season 99.4% of 180 pheasants from which shotgun pellets were recovered had been killed using toxic lead shotgun ammunition . This is despite a call by nine UK shooting and rural organisations who joined together a year ago to issue a statement saying that they wanted to see a...

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Climate change may have driven the emergence of SARS-CoV-2

Cam ac uk zoology department feed - Fri, 05/02/2021 - 12:03

A new study published today in the journal Science of the Total Environment provides the first evidence of a mechanism by which climate change could have played a direct role in the emergence of SARS-CoV-2, the virus that caused the COVID-19 pandemic.

The study has revealed large-scale changes in the type of vegetation in the southern Chinese province of Yunnan, and adjacent regions in Myanmar and Laos, over the last century. Climatic changes including increases in temperature, sunlight, and atmospheric carbon dioxide - which affect the growth of plants and trees - have changed natural habitats from tropical shrubland to tropical savannah and deciduous woodland. This created a suitable environment for many bat species that predominantly live in forests.

The number of coronaviruses in an area is closely linked to the number of different bat species present. The study found that an additional 40 bat species have moved into the southern Chinese province of Yunnan in the past century, harbouring around 100 more types of bat-borne coronavirus. This ‘global hotspot’ is the region where genetic data suggests SARS-CoV-2 may have arisen. 

“Climate change over the last century has made the habitat in the southern Chinese Yunnan province suitable for more bat species,” said Dr Robert Beyer, a researcher in the University of Cambridge’s Department of Zoology and first author of the study, who has recently taken up a European research fellowship at the Potsdam Institute for Climate Impact Research, Germany.

He added: “Understanding how the global distribution of bat species has shifted as a result of climate change may be an important step in reconstructing the origin of the COVID-19 outbreak.”

To get their results, the researchers created a map of the world’s vegetation as it was a century ago, using records of temperature, precipitation, and cloud cover. Then they used information on the vegetation requirements of the world’s bat species to work out the global distribution of each species in the early 1900s. Comparing this to current distributions allowed them to see how bat ‘species richness’, the number of different species, has changed across the globe over the last century due to climate change.

“As climate change altered habitats, species left some areas and moved into others - taking their viruses with them. This not only altered the regions where viruses are present, but most likely allowed for new interactions between animals and viruses, causing more harmful viruses to be transmitted or evolve,” said Beyer.

The world’s bat population carries around 3,000 different types of coronavirus, with each bat species harbouring an average of 2.7 coronaviruses - most without showing symptoms. An increase in the number of bat species in a particular region, driven by climate change, may increase the likelihood that a coronavirus harmful to humans is present, transmitted, or evolves there.

Most coronaviruses carried by bats cannot jump into humans. But several coronaviruses known to infect humans are very likely to have originated in bats, including three that can cause human fatalities: Middle East Respiratory Syndrome (MERS) CoV, and Severe Acute Respiratory Syndrome (SARS) CoV-1 and CoV-2. 

The region identified by the study as a hotspot for a climate-driven increase in bat species richness is also home to pangolins, which are suggested to have acted as intermediate hosts to SARS-CoV-2. The virus is likely to have jumped from bats to these animals, which were then sold at a wildlife market in Wuhan - where the initial human outbreak occurred. 

The researchers echo calls from previous studies that urge policy-makers to acknowledge the role of climate change in outbreaks of viral diseases, and to address climate change as part of COVID-19 economic recovery programmes. 

“The COVID-19 pandemic has caused tremendous social and economic damage. Governments must seize the opportunity to reduce health risks from infectious diseases by taking decisive action to mitigate climate change,” said Professor Andrea Manica in the University of Cambridge’s Department of Zoology, who was involved in the study. 

“The fact that climate change can accelerate the transmission of wildlife pathogens to humans should be an urgent wake-up call to reduce global emissions,” added Professor Camilo Mora at the University of Hawai‘i at Manoa, who initiated the project.

The researchers emphasised the need to limit the expansion of urban areas, farmland, and hunting grounds into natural habitat to reduce contact between humans and disease-carrying animals.

The study showed that over the last century, climate change has also driven increases in the number of bat species in regions around Central Africa, and scattered patches in Central and South America.

This research was supported by the European Research Council.

Reference
Beyer, R.M. et al: ‘Shifts in global bat diversity suggest a possible role of climate change in the emergence of SARS-CoV-1 and SARS-CoV-2.’ Science of the Total Environment, Feb 2021. DOI: 10.1016/j.scitotenv.2021.145413

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Hear from other University of Cambridge researchers who are investigating how to reduce the risk of animal viruses jumping to humans.    

Global greenhouse gas emissions over the last century have made southern China a hotspot for bat-borne coronaviruses, by driving growth of forest habitat favoured by bats.

Governments must seize the opportunity to reduce health risks from infectious diseases by taking decisive action to mitigate climate change.Andrea ManicaShi bai Xiao/ GreenpeaceForest landscape in Yunnan Province, PRC


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Male butterflies mark their mates with a repulsive smell during sex to ‘turn off’ other suitors

Cam ac uk zoology department feed - Tue, 19/01/2021 - 19:00

Led by Professor Chris Jiggins in the University of Cambridge's Department of Zoology, the team mapped production of the scented chemical compound to the genome of a species of butterfly called Heliconius melponene, and discovered a new gene. They also discovered that the chemical, made in the sex glands of the males, is identical to a chemical produced by flowers to attract butterflies. The study, published today in the journal PLOS Biology, shows that butterflies and flowers independently evolved to make the same chemical for different purposes. 

Dr Kathy Darragh, lead author of the paper and previously a member of Jiggins' research group, said: “We identified the gene responsible for producing this powerful anti-aphrodisiac pheromone called ocimene in the genitals of male butterflies. This shows that the evolution of ocimene production in male butterflies is independent of the evolution of ocimene production in plants.

“For a long time it was thought insects took the chemical compounds from plants and then used them, but we have shown butterflies can make the chemicals themselves – but with very different intentions. Male butterflies use it to repulse competitors and flowers use the same smell to entice butterflies for pollination.”

There are around 20,000 species of butterflies worldwide. Some only live for a month, but the Heliconius melponene butterflies found in Panama that were studied live for around six months. The females typically have few sexual partners and they store the sperm and use it to fertilise their eggs over a number of months after a single mating. 

Male butterflies have as many mates as they can and each time they transfer the anti-aphrodisiac chemical because they want to be the one to fertilise the offspring. This chemical, however, is not produced by all Heliconius butterflies. Whilst Heliconius melpomene does produce ocimene, another closely related species that was analysed – Heliconius cydno – does not produce the strong smelling pheromone. 

If the smell has such a powerful effect, how do the butterflies know when to be attracted or when to steer clear?

Darragh, now based at the University of California, Davis, explained: “The visual cues the butterflies get will be important – when the scent is detected in the presence of flowers it will be attractive but when it is found on another butterfly it is repulsive to the males – context is key.”

This new analysis of the power of smell – also called chemical signalling - sheds new light on the importance of scent as a form of communication. 

Jiggins said: “The butterflies presumably adapted to detect this chemical to find flowers, and then evolved to use it in this very different way. The males want to pass their genes onto the next generation and they don’t want the females to have babies with other fathers, so they use this scent to make them unsexy.

“Male butterflies pester the females a lot so it might benefit the females too if the smell left behind means they stop being bothered for sex after they have already mated.”

Reference

Darragh, K. et al. 'A novel terpene synthase controls differences in anti-aphrodisiac pheromone production between closely related Heliconius butterflies.' Jan 2021, PLOS Biology. DOI: 10.1371/journal.pbio.3001022

Adapted from a press release by St John's College, Cambridge

Butterflies have evolved to produce a strongly scented chemical in their genitals, which they leave behind after sex to deter other males from pursuing their mates.

The males want to pass their genes onto the next generation, and they don’t want the females to have babies with other fathers so they use this scent to make them unsexy.Chris JigginsLuca LivraghiTwo butterflies mating in captivity. Heliconius cydno (left) and Heliconius melpomene (right).


The text in this work is licensed under a Creative Commons Attribution 4.0 International License. Images, including our videos, are Copyright ©University of Cambridge and licensors/contributors as identified.  All rights reserved. We make our image and video content available in a number of ways – as here, on our main website under its Terms and conditions, and on a range of channels including social media that permit your use and sharing of our content under their respective Terms.

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James Croll Medal awarded to Richard Preece

News from this site - Fri, 15/01/2021 - 14:38

The Department is delighted to hear that the Quaternary Research Association (QRA) has awarded Dr Richard Preece the James Croll Medal, their highest honour. The Medal is normally awarded to a member of the Association who has not only made an outstanding contribution to the field of Quaternary science, but whose work has...

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