Florida dolphin found with highly pathogenic avian flu: Report

by University of Florida

Credit: Pixabay/CC0 Public Domain

The case of a Florida bottlenose dolphin found with highly pathogenic avian influenza virus, or HPAIV—a discovery made by University of Florida researchers in collaboration with multiple other agencies and one of the first reports of a constantly growing list of mammals affected by this virus—has been published in Communications Biology

The report documents the discovery, the first finding of HPAIV in a cetacean in North America, from the initial response by UF's Marine Animal Rescue team to a report of a distressed dolphin in Dixie County, Florida, to the subsequent identification of the virus from brain and tissue samples obtained in a postmortem examination.

Analyses initially performed at UF's zoological medicine diagnostic laboratory ruled out the presence of other potential agents at play in the dolphin's disease, with the Bronson Animal Disease Diagnostic Laboratory in Kissimmee, Florida, verifying the presence of HPAI virus in both the lung and brain.

Those results were confirmed by the National Veterinary Services Laboratory in Ames, Iowa, which characterized the virus subtype and pathotype. The virus was confirmed to be HPAI A (H5N1) virus of HA clade 2.3.4.4b. Subsequent tissue analysis was performed at the Biosafety Level 3 enhanced laboratory at St. Jude Children's Research Hospital in Memphis.

Allison Murawski, D.V.M., a former intern with UF's aquatic animal medicine program, was first author on the study and developed a case report on the dolphin as part of her research project. She traveled to Memphis and worked closely with Richard Webby, Ph.D., who directs the World Health Organization Collaborating Center for Studies on the Ecology of Influenza in Animals and Birds at St. Jude's and served as corresponding author on the paper

Webby's laboratory investigates avian influenza cases in many species and was key in determining where the virus may have originated, what unique RNA characteristics or mutations were present that could suggest its ability to infect other mammals, and how the virus could be tracked from this source.

The researchers sequenced the genomes from local birds and looked at viruses isolated from Northeast seal populations.

"We still don't know where the dolphin got the virus and more research needs to be done," Webby said.

"This investigation was an important step in understanding this virus and is a great example where happenstance joins with curiosity, having to answer the 'why' and then seeing how the multiple groups and expertise took this to a fantastic representation of collaborative excellence," said Mike Walsh, D.V.M., an associate professor of aquatic animal health, who served as Murawski's faculty mentor.

More information: Allison Murawski et al, Highly pathogenic avian influenza A(H5N1) virus in a common bottlenose dolphin (Tursiops truncatus) in Florida, Communications Biology (2024). DOI: 10.1038/s42003-024-06173-x

Journal information: Communications Biology 

Provided by University of Florida Experts warn bird flu virus changing rapidly in largest ever outbreak

NEWS RELEASE 26-APR-2024

Florida dolphin found with highly pathogenic avian flu: Report

UNIVERSITY OF FLORIDA

The case of a Florida bottlenose dolphin found with highly pathogenic avian influenza virus, or HPAIV — a discovery made by University of Florida researchers in collaboration with multiple other agencies and one of the first reports of a constantly growing list of mammals affected by this virus — has been published in Communications Biology.

The report documents the discovery, the first finding of HPAIV in a cetacean in North America, from the initial response by UF’s Marine Animal Rescue team to a report of a distressed dolphin in Dixie County, Florida, to the subsequent identification of the virus from brain and tissue samples obtained in a postmortem examination.

Analyses initially performed at UF’s zoological medicine diagnostic laboratory ruled out the presence of other potential agents at play in the dolphin’s disease, with the Bronson Animal Disease Diagnostic Laboratory in Kissimmee, Florida, verifying the presence of HPAI virus in both the lung and brain.

Those results were confirmed by the National Veterinary Services Laboratory in Ames, Iowa, which characterized the virus subtype and pathotype. The virus was confirmed to be HPAI A (H5N1) virus of HA clade 2.3.4.4b. Subsequent tissue analysis was performed at the Biosafety Level 3 enhanced laboratory at St. Jude Children’s Research Hospital in Memphis.

Allison Murawski, D.V.M., a former intern with UF’s aquatic animal medicine program, was first author on the study and developed a case report on the dolphin as part of her research project. She traveled to Memphis and worked closely with Richard Webby, Ph.D., who directs the World Health Organization Collaborating Center for Studies on the Ecology of Influenza in Animals and Birds at St. Jude’s and served as corresponding author on the paper

Webby’s laboratory investigates avian influenza cases in many species and was key in determining where the virus may have originated, what unique RNA characteristics or mutations were present that could suggest its ability to infect other mammals, and how the virus could be tracked from this source.

The researchers sequenced the genomes from local birds and looked at viruses isolated from Northeast seal populations.

“We still don’t know where the dolphin got the virus and more research needs to be done,” Webby said.

“This investigation was an important step in understanding this virus and is a great example where happenstance joins with curiosity, having to answer the ‘why’ and then seeing how the multiple groups and expertise took this to a fantastic representation of collaborative excellence,” said Mike Walsh, D.V.M., an associate professor of aquatic animal health, who served as Murawski’s faculty mentor.

---

JOURNAL

Communications Biology

DOI

10.1038/s42003-024-06173-x 

METHOD OF RESEARCH

Case study

SUBJECT OF RESEARCH

Animals

ARTICLE TITLE

Highly pathogenic avian influenza A(H5N1) virus in a common bottlenose dolphin (Tursiops truncatus) in Florida

ARTICLE PUBLICATION DATE

18-Apr-2024

Study suggests host response needs to be studied along with other bacteriophage research

Bacteriophage (magenta) attack Pseudomonas aeruginosa (teal) biofilms grown in 

association with respiratory epithelial cells (nuclei, yellow). Credit: Paula Zamora, 

A team of micro- and immunobiologists from the Dartmouth Geisel School of Medicine, Yale University, and the University of Pittsburgh has found evidence suggesting that future research teams planning to use bacteriophages to treat patients with multidrug-resistant bacterial infections need to also consider how cells in the host's body respond to such treatment.

In their paper published in the open-access journal PLOS Biology, the group describes experiments they conducted that involved studying the way epithelial cells in the lungs respond to bacteriophages.

Over the past decade, medical scientists have found that many of the antibiotics used to treat bacterial infections are becoming resistant, making them increasingly useless. Because of this, other scientists have been looking for new ways to treat such infections. One possible approach has involved the use of bacteriophages, which are viruses that parasitize bacteria by infecting and reproducing inside of them, leaving them unable to reproduce.

To date, most of the research involving use of bacteriophages to treat infections has taken place in Eastern Europe, where some are currently undergoing clinical trials. But such trials, the researchers involved in this new study note, do not take into consideration how cells in the body respond to such treatment. Instead, they are focused on determining which phages can be used to fight which types of bacteria, and how well they perform once employed.

The reason so little attention is paid to host cell interaction, they note, is that prior research has shown that phages can only replicate inside of the bacterial cells they invade; thus, there is little opportunity for them to elicit a response in human cells.

In this new study, the research team suggests such thinking is misguided because it fails to take into consideration the immune response in the host. To demonstrate their point, the team conducted a series of experiments involving exposing human epithelial cells from the lungs (which are the ones that become infected as part of lung diseases) to bacteriophages meant to eradicate the bacteria causing an infection.

They found that in many cases, the immune system responded by producing proinflammatory cytokines in the epithelial cells. They noted further that different phages elicited different responses, and there exists the possibility that the unique properties of some phages could be used to improve the results obtained from such therapies. They conclude by suggesting that future bacteriophage research involve inclusion of host cell response.

More information: Paula F. Zamora et al, Lytic bacteriophages induce the secretion of antiviral and proinflammatory cytokines from human respiratory epithelial cells, PLOS Biology (2024). DOI: 10.1371/journal.pbio.3002566

Journal information: PLoS Biology 

© 2024 Science X NetworkMammalian cells may consume bacteria-killing viruses to promote cellular health

Study details a common bacterial defense against viral infection

Complex of 2 proteins enhances blockage of phage replication

Peer-Reviewed Publication

OHIO STATE UNIVERSITY

COLUMBUS, Ohio – One of the many secrets to bacteria’s success is their ability to defend themselves from viruses, called phages, that infect bacteria and use their cellular machinery to make copies of themselves.

Technological advances have enabled recent identification of the proteins involved in these systems, but scientists are still digging deeper into what those proteins do.

In a new study, a team from The Ohio State University has reported on the molecular assembly of one of the most common anti-phage systems – from the family of proteins called Gabija – that is estimated to be used by at least 8.5%, and up to 18%, of all bacteria species on Earth.

Researchers found that one protein appears to have the power to fend off a phage, but when it binds to a partner protein, the resulting complex is highly adept at snipping the genome of an invading phage to render it unable to replicate.

“We think the two proteins need to form the complex to play a role in phage prevention, but we also believe one protein alone does have some anti-phage function,” said Zhangfei Shen, co-lead author of the study and a postdoctoral scholar in biological chemistry and pharmacology at Ohio State’s College of Medicine. “The full role of the second protein needs to be further studied.”

The findings add to scientific understanding of microorganisms’ evolutionary strategies and could one day be translated into biomedical applications, researchers say.

Shen and co-lead author Xiaoyuan Yang, a PhD student, work in the lab of senior author Tianmin Fu, assistant professor of biological chemistry and pharmacology at Ohio State.

The study was published April 16 in Nature Structural & Molecular Biology.

The two proteins that make up this defense system are called Gabija A and Gabija B, or GajA and GajB for short.

Researchers used cryo-electron microscopy to determine the biochemical structures of GajA and GajB individually and of what is called a supramolecular complex, GajAB, created when the two bind to form a cluster consisting of four molecules from each protein.

In experiments using Bacillus cereus bacteria as a model, researchers observed the activity of the complex in the presence of phages to gain insight into how the defense system works.

Though GajA alone showed signs of activity that could disable a phage’s DNA, the complex it formed with GajB was much more effective at ensuring phages would not be able take over the bacterial cell.

“That’s the mysterious part,” Yang said. “GajA alone is sufficient to cleave the phage nucleus, but it also does form the complex with GajB when we incubate them together. Our hypothesis is that GajA recognizes the phage’s genomic sequence, but GajB enhances that recognition and helps to cut the phage DNA.”

The large size and elongated configuration of the complex made it difficult to get the full picture of GajB’s functional contributions when bound to GajA, Shen said, leaving the team to make some assumptions about protein roles that have yet to be confirmed.

“We only know GajB helps enhance GajA activity, but we don’t yet know how it works because we only see about 50% of it on the complex,” Shen said.

One of their hypotheses is that GajB may influence the concentration level of an energy source, the nucleotide ATP (adenosine triphosphate), in the cellular environment – specifically, by driving ATP down upon detection of the phage’s presence. That would have the dual effect of expanding GajA’s phage DNA-disabling activity and stealing energy that a phage would need to start replicating, Yang said.

There is more to learn about bacterial anti-phage defense systems, but this team has already shown that blocking virus replication isn’t the only weapon in the bacterial arsenal. In a previous study, Fu, Shen, Yang and colleagues described a different defense strategy: bacteria programming their own death rather than letting phages take over a community.

This work was supported by the National Institute of General Medical Sciences.

Additional co-authors are Jiale Xie, Jacelyn Greenwald, Ila Marathe, Qingpeng Lin and Vicki Wysocki of Ohio State, and Wenjun Xie of the University of Florida.

#

Contact: Tianmin Fu, Fu.978@osu.edu

Written by Emily Caldwell, Caldwell.151@osu.edu; 614-292-8152

---

JOURNAL

Nature Structural & Molecular Biology

DOI

10.1038/s41594-024-01283-w 

ARTICLE TITLE

Molecular basis of Gabija anti-phage supramolecular assemblies

ARTICLE PUBLICATION DATE

16-Apr-2024

Porcelain Gallbladder Found in Human Remains in Mississippi Asylum Cemetery

A rare secret was taken to the grave in an unmarked, 100-year-old burial ground.

BY HANNAH SEO

APRIL 24, 2024


The hardened organ was found in a grave of a mental asylum cemetery. 

ASYLUM HILL PROJECT, UNIVERSITY OF MISSISSIPPI MEDICAL CENTER

In This Story

WHEN THE MISSISSIPPI STATE LUNATIC Asylum closed in 1935, its cemetery was unceremoniously forgotten. The plant life became tangled overgrowth, wooden grave markers deteriorated, and the thousands of marked and unmarked graves there lay untouched for decades.

The land eventually became part of the grounds of the University of Mississippi Medical Center. When the institution rediscovered the graves during construction on campus in 2012, it started the Asylum Hill Project to research the history of the cemetery while respectfully studying, memorializing, and moving the deceased to a more suitable location on campus. As researchers began excavating the first 100 burials, they discovered an archaeological oddity among the remains of one individual: a stony-beige colored object, about the size and shape of a quail egg (about two inches long and one inch wide), sat in the soil, right in the middle of this person’s torso. It was oddly light for its shape and size.

The object inside the woman’s grave looked like an egg. 

DEPARTMENT OF BIOMEDICAL MATERIALS SCIENCE, UNIVERSITY OF MISSISSIPPI MEDICAL CENTER

Initially, no one knew what it was. “Everyone just stood around and had theories,” says Jennifer Mack, the lead bioarchaeologist at The University of Mississippi Medical Center and the Asylum Project. “Someone thought it was a calcified cyst, someone else thought it was a gallstone, and I thought, ‘that’s way too big to be a gallstone.’” Mack took the object back to her office. Later, a retired surgeon on the team visited her. “I said, ‘hey, we found something interesting,’” Mack recalls. “He came over, and as I was opening the bag, he said ‘I think that’s a calcified gallbladder.’ Because as a surgeon, he had seen them on multiple occasions before.”

The team later confirmed it to be a perfectly preserved calcified gallbladder, also known as a “porcelain gallbladder.” The team recently published their discovery in The International Journal of Osteoarchaeology. It’s the first porcelain gallbladder to be published in an academic journal as an archaeological finding.

A porcelain gallbladder is a relatively rare and irreversible condition where parts or all of your gallbladder, the organ that stores the bile made by your liver and aids with digestion, calcifies and hardens. It’s named that way not because the organ becomes ceramic, but because in living or recently deceased individuals, a calcified gallbladder takes on a whitish blue color. It’s entirely possible for a person with porcelain gallbladder to not know they have it—people with it are often asymptomatic and can live with the condition. Though, people with a porcelain gallbladder often have it removed, as it can be a risk factor for cancer.

An X-ray of a different porcelain gallbladder from 2010 shows where they normally sit within the body. HERBERT L. FRED, MD, HENDRIK A. VAN DIJK/CC BY 2.0

Researchers haven’t come to a consensus on why or how a porcelain gallbladder occurs, but it’s thought that chronic inflammation can trigger the calcification process. Interestingly, even though there are plenty of other places throughout your body and in the gastrointestinal tract where chronic inflammation can happen, “it’s not like we get ‘porcelain esophagus’ or ‘porcelain stomach,’” says Kurt Schaberg, an anatomic pathologist at the University of California, Davis. “We don’t know specifically why the gallbladder turns porcelain, but it famously does.”

Mack and her team know that the individual with the porcelain gallbladder was an adult of middle to old age, but not much else. “The classic scenario of a porcelain gallbladder would be an older woman,” says Schaberg—statistically, that would make the most sense.

Normally after death, all parts of a gastrointestinal tract would decay and rot away. Schaberg says, “It’s kind of interesting to see a part of the GI tract survive due to these calcifications.”

'Incredibly Rare' Prehistoric Finds May Have Marked Path To Afterlife

Published Apr 24, 2024

By Aristos Georgiou
Science and Health Reporter
NEWSWEEK

An archaeological survey has identified traces of hundreds of previously unknown monuments—including five "incredibly rare" prehistoric structures that may have once marked "routes for the dead" into the afterlife.

James O'Driscoll with the Department of Archaeology at the University of Aberdeen in the United Kingdom conducted the survey using LiDAR technology in the Baltinglass landscape of County Wicklow, Ireland, which is renowned for its prehistoric remains. The results have been published in the journal Antiquity.

LiDAR is a remote sensing method that involves the use of laser pulses fired at the ground to generate 3D models of a given landscape. This method can map the topography of the land while also revealing hidden man-made features that may not normally be visible.

"I have been working on the Baltinglass landscape for over a decade. It formed the core component of my PhD," O'Driscoll told Newsweek.

"While my PhD focused on targeted geophysical and remote sensing surveys and excavations, what was sorely missing was a large-scale topographical model of the landscape, which would not only help to knit together all of the research that had previously been undertaken, but also help to discover new archaeological sites that were either hidden under trees and scrub overgrowth, or had been mostly levelled by thousands of years of ploughing," he said.

A view of the Baltinglass landscape in County Wicklow, Ireland. An archaeological survey of the region has revealed various previously unknown monuments. JAMES O’DRISCOLL/ANTIQUITY PUBLICATIONS LTD

The detailed topographical survey O'Driscoll undertook using LiDAR almost doubled the number of known archaeological sites in the landscape, revealing previously unknown monuments such as a "massive" Bronze Age hillfort, early medieval ringforts and a large number of burial structures from various periods of prehistory.

But the "most significant" findings of the survey, according to the researcher, were a cluster of up five previously unknown "cursus" monuments. These prehistoric monuments, found on the islands of Great Britain and Ireland, are typically long and relatively narrow earthwork enclosures. While poorly understood, they tend to be defined by an enclosing bank with a ditch on the outside. While relatively well-known in Britain, they are poorly documented in Ireland.

"The discovery of the cursus monuments is particularly significant, as these are incredibly rare in Ireland," O'Driscoll said. "There are less than 20 recorded cursus monuments in Ireland, and they typically occur in isolation or pairs."

"This makes the identification of five examples in Baltinglass the largest cluster of these sites in the country—but also, the detailed topographical model of the sites and their surrounding landscape provided an opportunity to 'digitally' investigate these monuments in detail," he said.

Using his new data, the archaeologist was able to demonstrate that at least four of the five newly identified cursus monuments were aligned with important solar events. These events were linked to yearly farming cycles, as well as death and rebirth, shedding light on the purpose of these mysterious monuments.

For O'Driscoll, these examples may have symbolized the ascent of the dead into the heavens and their perceived rebirth.

"The function of these types of monuments has always been a thorny topic, as we simply don't have enough information. But given that some of the Baltinglass sites can also be linked with burial monuments, this suggested to me that they may have been ceremonial monuments used in burial practices, where the cursus marked the physical route in which the dead moved from the living into the afterlife," O'Driscoll said.

The cursus monuments of Baltinglass uncovered by the LiDAR survey. These types of monuments are "incredibly rare" in Ireland. JAMES O’DRISCOLL/ANTIQUITY PUBLICATIONS LTD

As well as casting light on their purpose, the cursus discoveries could also help to fill a chronological gap in the settlement record of the area. According to O'Driscoll, the new monuments suggest that the Baltinglass landscape remained an important region for developing farming communities in the region during the Neolithic (or New Stone Age) archaeological period, which in Ireland lasted from roughly 4000–2400 B.C., according to some definitions.

Baltinglass was previously known for its Early Neolithic monuments, as well as those dating from the Middle to Late Bronze Age (around 1400–800 B.C.). However, evidence for human activity and occupation between the Early Neolithic and Middle-Late Bronze Age was almost non-existent, leading experts to conclude that the area may have been abandoned for roughly two millennia.

The latest study may help to challenge this narrative, given that cursus monuments typically date to the Middle Neolithic, although the newly uncovered Irish examples have yet to be comprehensively dated.

"The implications for the study are significant, as it provides an explanation for the function of this monument type in Ireland, and allows us to understand the ritual and ceremonial practices of our ancestors who lived over 5,000 years ago," O'Driscoll said.

"It is the first focused investigation of this monument type in Ireland, and it provides a platform for future study—key to which will be excavation and scientific dating of these monuments, if we can find the funding!"

 Archaeologists reveal hundreds of ancient monuments using LiDAR

Image Credit : Antiquity

By:Mark Milligan

Date:

April 25, 2024

A new study published in the journal Antiquity has revealed hundreds of previously unrecorded monuments at Baltinglass in County Wicklow, Ireland.

The Baltinglass area (known as ‘Ireland’s Hillfort Capital’) has a high density of Early Neolithic and Late Bronze Age monuments, however, very little evidence has been recorded that dates from the Middle Neolithic period.

According to Dr James O’Driscoll from the University of Aberdeen, the ancient landscape around Baltinglass was incredibly important to the Early Neolithic people, however, the lack of Middle Neolithic evidence suggests that this importance was lost until the Late Bronze Age.

Using advanced LiDAR technology, archaeologists have created detailed three-dimensional models, revealing hundreds of ancient sites that that been destroyed by thousands of years of ploughing.

Image Credit : Antiquity

Light Detection and Ranging (LiDAR), is a method of remote sensing using light in the form of a pulsed laser to measure ranges (variable distances) to the Earth. The differences in the laser return times and wavelengths can be used to compile a 3-D digital map of the landscape.

The most significant discovery from the survey is a cluster of five cursus monuments, the largest example found in both Britain and Ireland. The purpose of such monuments are speculative, but some theories propose that they were used in rituals connected with ancestor veneration, that they follow astronomical alignments, or that they served as buffer zones between ceremonial and occupation landscapes.

Image Credit : Antiquity

According to the study authors: “These five cursus monuments are clearly aligned with burial monuments in the landscape, as well as the rising and setting sun during major solar events such as the solstice.”

“This may have symbolised the ascent of the dead into the heavens and their perceived rebirth, with the cursus physically setting out the final route of the dead, where they left the land of the living and joined the ancestors beyond the visible horizon,” said Dr O’Driscoll.

Header Image Credit : Antiquity

Sources : Antiquity | Exploring the Baltinglass cursus complex: routes for the dead? – James O’Driscoll. https://doi.org/10.15184/aqy.2024.39

Ancient nomads you’ve probably never heard of disappeared from Europe 1,000 years ago. Now, DNA analysis reveals how they lived


Burial with a horse at the Rákóczifalva site, Hungary (8th century AD). Sándor Hegedűs, Hungarian National Museum

THE CONVERSATION
Published: April 24, 2024 

How do we understand past societies? For centuries, our main sources of information have been pottery sherds, burial sites and ancient texts.

But the study of ancient DNA is changing what we know about the human past, and what we can know. In a new study, we analysed the genetics of hundreds of people who lived in the Carpathian Basin in southeastern central Europe more than 1,000 years ago, revealing detailed family trees, pictures of a complex society, and stories of change over centuries.
Who were the Avars?

The Avars were a nomadic people originating from eastern central Asia. From the 6th to the 9th century CE, they wielded power over much of eastern central Europe.

A gold earring from a 7th-century female grave at the Rákóczifalva site, Hungary. Hungarian National Museum, CC BY

The Avars are renowned among archaeologists for their distinctive belt garnitures, but their broader legacy has been overshadowed by predecessors such as the Huns. Nevertheless, Avar burial sites provide invaluable insights into their customs and way of life. To date, archaeologists have excavated more than 100,000 Avar graves.

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Now, through the lens of “archaeogenetics”, we can delve even deeper into the intricate web of relationships among individuals who lived more than a millennium ago.
Kinship patterns, social practices and population dynamics

Much of what we know about Avar society comes from descriptions written by their enemies, such as the Byzantines and the Franks, so this work represents a significant leap forward in our understanding.

We combined ancient DNA data with archaeological, anthropological and historical context. As a result, we have been able to reconstruct extensive pedigrees, shedding light on kinship patterns, social practices and population dynamics of this enigmatic period.
Excavations at the cemetery of Rákóczifalva, Hungary in 2006. Hungarian National Museum, CC BY

We sampled all available human remains from four fully excavated Avar-era cemeteries, including those at Rákóczifalva and Hajdúnánás in what is now Hungary. This resulted in a meticulous analysis of 424 individuals.

Around 300 of these individuals had close relatives buried in the same cemetery. This allowed us to reconstruct multiple extensive pedigrees spanning up to nine generations and 250 years.
Communities were organised around main fathers’ lines

Our research uncovered a sophisticated social framework. Our results suggest Avar society ran on a strict system of descent through the father’s line (patrilineal descent).

Following marriage, men typically remained within their paternal community, preserving the lineage continuity. In contrast, women played a crucial role in fostering social ties by marrying outside their family’s community. This practice, called female exogamy, underscores the pivotal contribution of women in maintaining social cohesion.

Additionally, our study identified instances where closely related male individuals, such as siblings or a father and son, had offspring with the same female partner. Such couplings are called “levirate unions”.

Read more: In a Stone Age cemetery, DNA reveals a treasured 'founding father' and a legacy of prosperity for his sons

Despite these practices, we found no evidence of pairings between genetically related people. This suggests Avar societies meticulously preserved an ancestral memory.

These findings align with historical and anthropological evidence from societies of the Eurasian steppe.

Our study also revealed a transition in the main line of descent within Rákóczifalva, when one pedigree took over from another. This occurred together with archaeological and dietary shifts likely linked to political changes in the region.

The transition, though significant, cannot be detected from higher-level genetic studies. Our results show an apparent genetic continuity can mask the replacement of entire communities. This insight may have far-reaching implications for future archaeological and genetic research.
Future direction of research

Our study, carried out with researchers from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany and at Eötvös Loránd University in Budapest, Hungary, is part of a larger project called HistoGenes funded by the European Research Council.

This project shows we can use ancient DNA to examine entire communities, rather than just individuals. We think there is a lot more we can learn.
An expert at work harvesting ancient DNA from a human bone. Max Planck Institute for Evolutionary Anthropology

Now we aim to deepen our understanding of ancestral Avar society by expanding our research over a wider geographical area within the Avar realm. This broader scope will allow us to investigate the origins of the women who married into the communities we have studied. We hope it will also illuminate the connections between communities in greater detail.

Additionally, we plan to study evidence of pathogens and disease among the individuals in this research, to understand more about their health and lives.

Read more: Ancient DNA reveals children with Down syndrome in past societies. What can their burials tell us about their lives?

Another avenue of research is improving the dating of Avar sites. We are currently analysing multiple radiocarbon dates from individual burials to reveal a more precise timeline of Avar society. This detailed chronology will help us pinpoint significant cultural changes and interactions with neighbouring societies.

The authors would like to acknowledge the contributions to this work of Zsófia Rácz, Tivadar Vida, Johannes Krause and Zuzana Hofmanová.

Authors   

Magdalena M.E. Bunbury
Postdoctoral Researcher, James Cook University

Guido Alberto Gnecchi-Ruscone
Postdoctoral Researcher, Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology

Disclosure statement

Magdalena M.E. Bunbury receives funding from the Australian Research Council (ARC) (project number CE170100015). She currently carries out a cadetship at the Reef and Rainforest Research Centre, a non-profit organisation in Cairns. Previously, she received funding from the German Academic Exchange Service (DAAD) (project number D0850554) and the Erasmus scheme of the European Union.

Guido Alberto Gnecchi-Ruscone receives funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme under grant agreement No 856453.

 

The story of the first Alor people adapting to climate change 43,000 years ago

by Shimona Kealy, Hendri A. F. Kaharudin and Sue O'Connor, The Conversation

Marine shell and coral fishing (at left) and ornamentation (at right) technologies from 

Makpan. (A) rotating fishhook; (B) jabbing fishhook; (C) small jabbing fishhook; 

(D) possible shell lure; (E) large jabbing fishhook; (F) perforated coral sinker; 

(G) finger-coral tool; (H) selection of single-holed disc beads and two-holed oval beads

 made on Nautilus pompilius.

As humans, our greatest evolutionary advantage has always been our ability to adapt and innovate. When people first reached the expanded coastline of Southeast Asia around 65,000 years ago, and faced the sea crossings necessary to continue east into the islands of the Wallacean archipelago (the migration of Homo sapiens out of Africa to Australia), these abilities were put to use like never before.

Our study reports new evidence that humans reached and settled on the island of Alor, East Nusa Tenggara, around 43,000 years ago.

Alor is a smaller island lying between the larger islands of Flores and Timor, on the southern migratory pathway between mainland Southeast Asia and Australia.

Traces of settlements from that time demonstrate that once people began to move into the islands, they did so very quickly, and rapidly adjusted to their new island homes, especially in terms of acquiring food.

Life traces in Makpan Cave

Our collaborative research project, involving Australian and Indonesian archaeologists, excavated Makpan cave on Alor's south-west coast in mid-2016.

We identified the presence of human occupants in Makpan cave by discovering various tools made from stone, shell, and coral, as well as the remains of marine shell and sea urchins, for which humans are the only likely transport agents from coast to cave.

We used radiocarbon dating of preserved charcoal and marine shell to determine the period of human occupation at Makpan. The presence of both these materials in the cave is a direct result of human activity, so their dates can be directly connected to when people were living at Makpan.

The Makpan dates push back the record for human occupation on Alor island, doubling the initial occupation date of 21,000 years previously recovered from Tron Bon Lei, excavated in 2014.

This new find shows that Alor was occupied at the same time as Flores to the west, and Timor to the east—confirming Alor's position as a 'stepping-stone' between these two larger islands.

The deepest levels of the Makpan deposit recovered evidence for human occupation (such as stone tools and food waste) but in very low numbers. This suggests that when people first arrived at Makpan, they did so in low numbers.

During the 43,000 years of human occupation, Makpan witnessed a series of significant rises and falls in sea levels. This was caused by extreme climate changes during the last ice age. These environmental changes led the inhabitants of Makpan cave to undergo several phases of adaptation to environmental changes.

1. Early habitation phase

During the period from 43,000 to 14,000 years ago, when sea levels were lower, the inhabitants of Makpan relied more on coastal resources as they were more easily accessible.

During the Late Pleistocene (ice age), the lower sea level meant Alor Island was still connected to Pantar Island to the west. This created a mega-island that was nearly twice its size.

This condition eliminated the Pantar Strait between Pantar and Alor. The Pantar Strait is a passage for strong ocean currents connecting the Flores and Savu seas. Instead, the strait was replaced by a large sheltered bay.

Falling sea levels as the last ice age reached its maximum extent, also increased the distance from the site of Makpan to the coast.

This increased distance likely encouraged people to broaden their diet away from an intensely marine focus, to include a variety of land-based fruits and vegetables and perhaps make more use of giant rats, which were the only terrestrial fauna of any size available on the island at this time. This scenario is supported by isotopic analysis of human teeth from Makpan.

2. Pleistocene-Holocene transition phase

As the ice age began to wane around 14,000 years ago (the transition period from the Pleistocene to the early Holocene), bringing Makpan back within less than 1km of the coast, we see evidence for increased use of marine resources and foraging in the sheltered bay region, rocky coastline, reefs and deeper waters off Alor's south coast.

This increased access to a variety of marine protein sources is represented by the veritable smorgasbord of seafoods forming the dense midden deposits between around 12,000–11,000 years ago.

It is no surprise that the site sees significant evidence for fishing at this time, not just the bones of a wide variety of fish and shark species, but also in the form of shell fishhooks in different shapes and sizes. It also has the other items needed for fishing such as sinkers, and files made of coral used to make the hooks. The hooks were made from highly nacreous (i.e., shiny) shell species—which may have assisted in attracting the fish.

Although we do not find perishable organic materials, the diversity of fish hook types found in Makpan implies the use of fiber lines and nets, and the ability to fish in both shallow and deep water.

3. Late habitation phase

As sea levels continued to rise in the Early-Middle Holocene, the Pantar Strait opened up once more and we see the loss of the sheltered bay resources from the Makpan diet alongside an increase in reliance on terrestrial foods.

This coincided with a decline in occupation intensity, culminating in the abandonment of Makpan about 7,000 years ago. Why Makpan was abandoned at this time we do not know. Perhaps these final sea level increases made other areas around Alor island more attractive settlement locations, encouraging people to relocate.

The cave was reoccupied in the Neolithic (about 3,500 years ago), after sea-levels had stabilized, and we see a significant change in technology and lifestyle—evidenced by the appearance of pottery and domestic animals in the deposits. The Makpan archaeological record shows just how inventive and adaptive modern humans were in response to global climate change.

Provided by The Conversation 

This article is republished from The Conversation under a Creative Commons license. Read the original article.40,000 years of adapting to sea-level change on Alor Island