New examination of fish considered a ‘living fossil’ changes our understanding of vertebrate skull evolution

Researchers reanalyzed the skull musculature of coelacanths, a group of fish that has existed for 400 million years, and concluded that many structures had been incorrectly described.

Fundação de Amparo à Pesquisa do Estado de São Paulo

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One of the authors of the study, Aléssio Datovo, poses next to a coelacanth specimen on display at the Smithsonian Institution’s National Museum of Natural History 

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Credit: Museum of Zoology (MZ), USP

The coelacanth is known as a “living fossil” because its anatomy has changed little in the last 65 million years. Despite being one of the most studied fish in history, it continues to reveal new information that could transform our understanding of vertebrate evolution. This is revealed in a study published in the journal Science Advances by researchers from the University of São Paulo (USP) in Brazil and the Smithsonian Institution in the United States.

Upon re-examining the cranial musculature of the African coelacanth (Latimeria chalumnae), the authors discovered that only 13% of the previously identified evolutionary muscle novelties for the largest vertebrate lineages were accurate. The study also identified nine new evolutionary transformations related to innovations in feeding and respiration in these groups.

“Ultimately, it’s even more similar to cartilaginous fish [sharks, rays, and chimaeras] and tetrapods [birds, mammals, amphibians, and reptiles] than previously thought. And even more distinct from ray-finned fish, which make up about half of living vertebrates,” says Aléssio Datovo, a professor at the Museum of Zoology (MZ) at USP supported by FAPESP, who led the study.

Among the evolutionary novelties erroneously identified as present in coelacanths are muscles responsible for actively expanding the buccopharyngeal cavity, which extends from the mouth to the pharynx. This set of muscles is directly related to food capture and respiration. However, the study showed that these supposed muscles in coelacanths were actually ligaments, which are structures incapable of contraction.

Ray-finned fish (actinopterygii) and lobe-finned fish (sarcopterygii) diverged from a common ancestor approximately 420 million years ago. The sarcopterygii include fish such as coelacanths and lungfish, as well as all other tetrapods, because they evolved from an aquatic ancestor. These include mammals, birds, reptiles, and amphibians.

In ray-finned fish, such as aquarium carp, it is easy to see how the mouth moves to suck in food. This ability gave actinopterygii a significant evolutionary advantage; today, they comprise about half of all living vertebrates.

This is a fundamental difference from other fish, such as coelacanths and sharks, which primarily feed by biting their prey.

“In previous studies, it was assumed that this set of muscles that would give greater suction capacity was also present in coelacanths and, therefore, would have evolved in the common ancestor of bony vertebrates, which we now show isn’t true. This only appeared at least 30 million years later, in the common ancestor of living ray-finned fish,” points out Datovo.

Behind the scenes

Coelacanths are extremely rare fish that live about 300 meters below the surface of the water and spend their days in underwater caves.

One reason they have changed so little since the extinction of the dinosaurs is that they have few predators and live in a relatively protected environment. This has resulted in slow changes to their genome, as shown by a 2013 study published in the journal Nature. 

Coelacanths were first known only from fossils from about 400 million years ago. It was not until 1938 that a living animal was discovered, much to the astonishment of scientists. In 1999, another species (Latimeria chalumnae) was discovered in Asian waters.

Due to the rarity of specimens in museums, researchers from USP and the Smithsonian Institution’s National Museum of Natural History had to persevere to find an institution willing to lend animals for dissection.

The Field Museum in Chicago and the Virginia Institute of Marine Science, both in the United States, finally agreed to lend one specimen each. According to Datovo, G. David Johnson, co-author of the article, deserves credit for obtaining the loan.

Johnson, born in 1945, was “probably the greatest fish anatomist of his time,” according to Datovo. He died in November 2024 after a domestic accident while the study was under review.

Contribution

“Contrary to what it may seem, dissecting a specimen does not mean destroying it as long as it’s done properly,” says Datovo.

The researcher, who has been conducting this type of study for over 20 years, spent six months separating all the muscles and skull bones of the coelacanth. These structures are now preserved and can be studied individually by other scientists, eliminating the need to dissect a new animal.

Seeing each muscle and nerve firsthand allowed the authors to identify what was actually in the coelacanth’s head with certainty, point out previously undescribed structures, and correct errors that had been repeated in the scientific literature for over 70 years.

“There were many contradictions in the literature. When we finally got to examine the specimens, we detected more errors than we’d imagined. For example, 11 structures described as muscles were actually ligaments or other types of connective tissue. This has a drastic consequence for the functioning of the mouth and breathing, because muscles perform movement, while ligaments only transmit it,” he explains.

Due to the position of coelacanths in the vertebrate tree of life, the discovery impacts our understanding of cranial evolution in all other large vertebrate groups.

With this information, the researcher used three-dimensional microtomography images of the skulls of other groups of fish, both extinct and living. These images are made available by other researchers who study fish anatomy when they perform 3D scans.

From images of the skull bones of other fish from completely extinct lineages, Datovo and Johnson were able to infer where the muscles found in coelacanths would fit, elucidating the evolution of these muscles in the first jawed vertebrates. In future work, Datovo intends to analyze similarities with the muscles of tetrapods, such as amphibians and reptiles.

About São Paulo Research Foundation (FAPESP)
The São Paulo Research Foundation (FAPESP) is a public institution with the mission of supporting scientific research in all fields of knowledge by awarding scholarships, fellowships and grants to investigators linked with higher education and research institutions in the State of São Paulo, Brazil. FAPESP is aware that the very best research can only be done by working with the best researchers internationally. Therefore, it has established partnerships with funding agencies, higher education, private companies, and research organizations in other countries known for the quality of their research and has been encouraging scientists funded by its grants to further develop their international collaboration. You can learn more about FAPESP at www.fapesp.br/en and visit FAPESP news agency at www.agencia.fapesp.br/en to keep updated with the latest scientific breakthroughs FAPESP helps achieve through its many programs, awards and research centers. You may also subscribe to FAPESP news agency at http://agencia.fapesp.br/subscribe. 

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Journal

Science Advances

DOI

10.1126/sciadv.adt1576 

Article Title

Coelacanths illuminate deep-time evolution of cranialmusculature in jawed vertebrates

 

Study identifies gene clusters in rhizobia linked to robust legume growth

University of Illinois at Urbana-Champaign, News Bureau

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Legumes like clover form root nodules that harbor symbiotic soil microbes known as rhizobia. These nodules are the site of exchange of nutrients that benefit the plants and the rhizobia. 

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Credit: Graphic by Julie McMahon

CHAMPAIGN, Ill. — In a new study, scientists used nearly every tool in their toolkit — genomics, transcriptomics, greenhouse experiments and advanced statistical methods — to gain new insight into the complex chemical interactions that take place in underground root nodules, where legumes like soybeans exchange vital nutrients with soil microbes called rhizobia.

Reported in the Proceedings of the National Academy of Sciences, their study identified clusters of rhizobial genes that appear to move rapidly through bacterial populations and drive greater plant biomass in the host plants. Understanding the interplay of host and bacterial genomes will help efforts to optimize plant growth by improving the rhizosphere, the researchers said.

“Just like us, plants are full of microbes, and some form these tightly co-evolved symbioses where a lot of evolutionary history has shaped a very intimate interaction,” said Katy Heath, a professor of plant biology at the University of Illinois Urbana-Champaign who led the study with Illinois plant biology professor Amy Marshall-Colón. “Legumes like soybeans, peas or peanuts develop these special relationships with rhizobia.”

Rhizobial bacteria “fix” nitrogen from the atmosphere by converting it into a form the plants can use, Heath said. In exchange, the legumes give the rhizobia carbon-rich sugars, “which is what plants make when they do photosynthesis.”

Rather than exploring the role of one or two genes at a time, Heath and her colleagues wanted to get a more global sense of the variation in these exchanges. They turned to a model system for studying such interactions, pairing the legume Medicago truncatula, a close relative of alfalfa that looks like clover, with the rhizobial bacterium Sinorhizobium meliloti.

In a greenhouse experiment, the team inoculated each M. truncatula plant with one of 20 strains of the rhizobium. The S. meliloti strains differ from one another genetically but still belong to the same species. Some of the strains consistently resulted in greater plant growth, Heath said. Once the plants and microbes formed root nodules, the site of exchange, the researchers plucked off the nodules and froze them for further analysis.

The team analyzed the “transcriptome” of each nodule. Transcriptomes contain all the RNA produced by an organism — or in this case, two organisms — offering a clear picture of every gene that is being expressed.

Once the researchers determined which plant and bacterial genes were being expressed at higher levels in nodules associated with the most vigorous plant growth, they sequenced high-quality reference genomes of each bacterial strain.

Interpreting the data was a formidable task, Heath said.

“Bacteria have genetic processes that are different from ours,” she said. “We think a lot in classic genetics about that vertical line of inheritance from parents to offspring — and they do that, too. But then they are also swapping genes horizontally when they bump into other bacteria — within the same species or between different species. The complexity of horizontal gene transfer is massive.”

S. meliloti have two sources of DNA: a large primary chromosome, which is inherited from a “parent” bacterium when it divides; and two giant plasmids, each containing roughly half as many genes as the chromosome. Plasmids are circular chunks of DNA that are more mobile than chromosomal DNA and are the site of horizontal gene transfer, allowing bacteria to acquire new genes from their neighbors. Horizontal gene transfer even allows bacteria to pick up the genes required for them to become rhizobia, Heath said.

Marshall-Colón and postdoctoral researcher Rizwan Riaz conducted detailed statistical analyses and gene network modeling to identify which rhizobial genes correlated with more robust plant growth. The reference genomes were useful to understanding which genes were present and where they were located in the chromosomal or plasmid DNA. This resulted in the discovery that many of the genes of interest were clustered together in plasmids.

Further experiments, led by North Dakota State microbiological sciences professor and study co-author Barney Geddes, involved deleting the specified genes. U. of I. microbiology graduate student Ivan Sosa Marquez tested the effects of these deletions on plant growth, confirming that the identified genes were important for enhanced plant growth.

“We’re not trying to say these are the important genes in all rhizobia in all the legumes,” Heath said. “But we’re gaining an understanding of the level of variation on which natural selection acts.”

The study offers a broad picture of one set of S. meliloti genes, “which only some strains have and which appear to boost the growth of one legume species. The genes themselves are less universally applicable than the approach we’ve developed, which likely be applicable to many other fields,” Heath said.

“These aspects of microbial genetics that we’re tapping into are the ones that matter for agricultural productivity, for livestock growth and for human health,” she said. “It’s these genes that are moving around and we don’t know why. And they’re working with the rest of the genome in really complicated ways.”

Heath and Marshall-Colón are affiliates of the Carl R. Woese Institute for Genomic Biology at the U. of I.

The National Science Foundation, the IGB and Consejo Nacional de Ciencia y Tecnologia, Mexico, supported this work.

Editor’s note:  

To reach Katy Heath, email kheath@illinois.edu.  

The paper “Mobile gene clusters and co-expressed plant-rhizobium pathways drive partner quality variation in symbiosis” is available online (after publication) or from pnasnews@nas.edu. 

DOI: 10.1073/pnas.2411831122

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Journal

Proceedings of the National Academy of Sciences

DOI

10.1073/pnas.2411831122 

Method of Research

Experimental study

Subject of Research

Not applicable

Article Title

Mobile gene clusters and co-expressed plant-rhizobium pathways drive partner quality variation in symbiosis

Article Publication Date

28-Jul-2025

 

Remapping the evolutionary tree of butterflies

Wellcome Trust Sanger Institute

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Some butterflies can smell others of the same species, allowing them to identify each other in areas where multiple species all look the same, new research finds.

A large international team has genetically mapped glasswing butterflies found across Central and South America, rewriting the evolutionary tree and highlighting six new species.

The team includes experts at the Wellcome Sanger Institute, Universidad Regional Amazónica Ikiam in Ecuador, Universidade Estadual de Campinas in Brazil, the University of Cambridge, and others1.

The research, published today (28 July) in the Proceedings of the National Academy of Sciences (PNAS), starts to uncover new insights about these butterflies as well as factors involved in the rapid diversification of species and why some species are more capable of this. The findings help experts to understand more about how has life evolved until now and possibly suggest how it might change in the future.

For example, researchers found that in glasswing butterflies, even the most closely related species produce different pheromones, indicating that they can smell others of the same species. Given that all of these butterflies look the same to teach birds that they are all toxic, this allows the butterflies to find a compatible mate.

By untangling the taxonomy of these butterflies, the team provides answers to questions that have remained unknown for at least 150 years. The researchers also present ten freely available reference genomes that can help to monitor and maintain insect populations in some of the most biodiverse areas of the world.

Butterflies are used in conservation as an indicator species, meaning they are used to track and monitor the levels of biodiversity and other insects in an area.

Glasswing (Ithomiine) butterflies are found across Central and South America and make up a substantial part of the butterfly species found there, making them good indicators of biodiversity in incredibly biodiverse areas, like the Amazon rainforest.

However, there are over 400 species of glasswing butterfly, and all species in an area look incredibly similar to discourage birds from eating them, with colouring that implies they are toxic.

Additionally, glasswing butterflies can undergo rapid radiation, where many new species arise from the same ancestor in a short period of time. As they are very closely related, it makes it difficult to visually identify and track the different species of butterflies.

To genetically untangle these butterflies, an international team including Sanger Institute scientists sequenced the genomes of almost all species of two particularly fast radiations of glasswing butterflies to remap their evolutionary trees. Of those species, 10 were sequenced to the gold standard of “reference quality” genomes that are freely available to the research community.

By genetically mapping these butterflies, the team highlighted that six subspecies were more genetically distinct than previously thought, leading to them being classified as new individual species. Also, understanding the species from a genomic perspective enables experts to highlight any visual differences that could be used to identify and track the different species, now that they are confirmed as genetically distinct.

The team also investigated if the genomes held clues as to why these butterflies had so many species, and what allowed them to develop so quickly. While most butterflies have 31 chromosomes, they found that in these glasswing butterflies, the number of chromosomes varies a lot, ranging between 13 and 28. While they have largely the same genes, these genes are packaged into chromosomes in different ways in each species, a process known as chromosomal rearrangement.  

These chromosomal rearrangements have knock-on effects when it comes to mating. In order to reproduce, butterflies must produce eggs and sperm, but this relies on the butterfly's chromosomes lining up. This means that if two butterflies with different chromosomal rearrangements mated, their offspring would be sterile because they would be unable to produce sperm or eggs. As a result, the butterflies have evolved a new mechanism using pheromones to detect potential mates with a chromosome arrangement that matches their own and therefore avoid producing sterile offspring.

The researchers suggest that the high level of chromosomal rearrangement in these butterflies is key to their ability to rapidly form new species, as once a population changes its chromosome number and thus forms its own species, it can more quickly adapt to different altitudes or host plants. Why they have such high levels of rearrangements remains a mystery and is something the scientists are working to uncover.

Understanding rapid radiation in insects could have implications for conservation research, understanding how species adapt to climate change, as well as possible implications for agriculture and pest control.

Dr Eva van der Heijden, first author at the Wellcome Sanger Institute and the University of Cambridge, said: “Glasswing butterflies are an incredibly adaptive group of insects that have been valuable in ecology research for around 150 years. However, until now, there was no genetic resource that allowed us to robustly identify different species, and it is difficult to monitor and track something that you can’t identify easily. With this new genetically informed evolutionary tree, and multiple new reference genomes, we hope that it will be possible to advance biodiversity and conservation research around the world, and help protect the butterflies and other insects that are crucial to many of Earth’s ecosystems.”

Dr Caroline Bacquet, senior author at the Universidad Regional Amazónica Ikiam in Ecuador, said: “Having the reference genomes for the two groups of glasswing butterflies, Mechanitis and Melinaea, allowed us to take a closer look at how they have adapted to life in such close proximity to their relatives. These butterflies share the responsibility of warding off predators by displaying similar colour patterns, and by producing different pheromones they can successfully find mates and reproduce. Now that we have clarity on glasswing butterfly species, we can look for specific markings or differences between them, giving new ways to track them during fieldwork.”

Dr Joana Meier, senior author at the Wellcome Sanger Institute, said: “We are in the middle of an extinction crisis and understanding how new species evolve, and evolve quickly in some cases, is important for preserving species. Comparing butterflies that rapidly form new species to others that do not could benchmark how common this is in insects and highlight the factors involved. This, in turn, could identify any species that require closer conservation and possibly identify genes that are important in the adaptation process and might have uses in agriculture, medicine, or bioengineering. This research would not have been possible without global collaboration. We have one planet, and we must work together to understand and protect it.”

ENDS

Notes to Editors:

1. This study was made possible by a large international collaboration. As well as those already mentioned, this work included researchers at Harvard University, USA, the Federal University of Pernambuco, Brazil, Technische Universität Braunschweig, Germany, the University of York, the University of Bristol, Université de Guyane, France, Universidad Nacional Mayor de San Marcos, Lima, Peru, Smithsonian Tropical Research Institute, Panama, University of Florida, USA, and Université des Antilles, Paris, France. A full list of contributors and affiliations can be found in the publication.

Publication:

E. van der Heijden, K. Näsvall, F. Seixas, et al. (2025) ‘Genomics of Neotropical biodiversity indicators: two butterfly radiations with rampant chromosomal rearrangements and hybridisation.’ PNAS. DOI: 10.1073/pnas.2410939122

Funding:

This research includes funding from Wellcome and others. A full list of funding acknowledgements can be found in the publication.

Selected websites:

University of Cambridge

The University of Cambridge is one of the world’s top ten leading universities, with a rich history of radical thinking dating back to 1209. Its mission is to contribute to society through the pursuit of education, learning and research at the highest international levels of excellence.

The University comprises 31 autonomous Colleges and 150 departments, faculties and institutions. Its 24,450 student body includes more than 9,000 international students from 147 countries. In 2020, 70.6% of its new undergraduate students were from state schools and 21.6% from economically disadvantaged areas.

Cambridge research spans almost every discipline, from science, technology, engineering and medicine through to the arts, humanities and social sciences, with multi-disciplinary teams working to address major global challenges. Its researchers provide academic leadership, develop strategic partnerships and collaborate with colleagues worldwide.

The University sits at the heart of the ‘Cambridge cluster’, in which more than 5,300 knowledge-intensive firms employ more than 67,000 people and generate £18 billion in turnover. Cambridge has the highest number of patent applications per 100,000 residents in the UK. www.cam.ac.uk

The Wellcome Sanger Institute

The Wellcome Sanger Institute is a world leader in genomics research. We apply and explore genomic technologies at scale to advance understanding of biology and improve health. Making discoveries not easily made elsewhere, our research delivers insights across health, disease, evolution and pathogen biology. We are open and collaborative; our data, results, tools, technologies and training are freely shared across the globe to advance science.

Funded by Wellcome, we have the freedom to think long-term and push the boundaries of genomics. We take on the challenges of applying our research to the real world, where we aim to bring benefit to people and society.

Find out more at www.sanger.ac.uk or follow us on Twitter, Instagram, Facebook, LinkedIn and on our Blog.

About Wellcome

Wellcome supports science to solve the urgent health challenges facing everyone. We support discovery research into life, health and wellbeing, and we’re taking on three worldwide health challenges: mental health, infectious disease and climate and health. https://wellcome.org/

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Journal

Proceedings of the National Academy of Sciences

DOI

10.1073/pnas.2410939122 

Article Title

Genomics of Neotropical biodiversity indicators: Two butterfly radiations with rampant chromosomal rearrangements and hybridization

Article Publication Date

28-Jul-2025

DESANTISLAND

On a Florida bombing range, endangered woodpeckers get a second chance

The rockets’ red glare clears the way for a major comeback.

Michigan State University

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Alex Lewanski releases a banded red-cockaded woodpecker. Bird banding allows researchers to track and monitor individuals, helping create a detailed population record over years or decades. 

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Credit: Greg Thompson

Florida’s Avon Park bombing range is teeming with life. Over 40 at-risk species occupy this 106,000-acre expanse used by the U.S. Air Force for training exercises. 

Conservation biologists from Michigan State University are using the range to test something other than weapons: innovative strategies to save threatened species. 

Using decades’ worth of monitoring data, researchers are looking back through time to understand the outcome of interventions designed to rescue a population of imperiled red-cockaded woodpeckers. 

What they’ve found is a promising story of success.  

Their results, published in a special edition of (Proceedings of the National Academy of Sciences [DOI Link]), demonstrate the potential for translocations — the practice of moving individuals from donor populations to isolated, at-risk ones — to reverse long-term population decline in endangered species. It’s the latest study from MSU’s Fitzpatrick Lab to analyze how translocation efforts can help restore connectivity between isolated populations and bring dwindling species back from the brink. 

These findings emphasize how effective the careful introduction of new individuals can be in the short-term and in the years and decades ahead — presenting a potential boon for threatened and endangered species. 

When used in concert with land protection and management strategies such as controlled burns, interventions at the individual level can help dwindling communities recover. 

Red-cockaded woodpeckers, once abundant from the American South to the Eastern seaboard, have disappeared alongside their pine savannah habitat, now confined to small, disconnected pockets covering only three percent of their historic range. 

The overdevelopment of these ecosystems has placed hundreds of species — including the red-cockaded woodpecker — at risk of disappearing entirely.  

“The only reason that these populations are still around is because of the continued collaborations and long-term investment in these imperiled species,” explained Alex Lewanski, a graduate student at MSU and first author on the study. 

The Avon Park Air Force Range contains over 35,000 acres of pine savannah, providing a well-protected band of habitat for threatened animals and a proving ground for complex conservation strategies. 

The installation is one of 18 Sentinel Landscapes; protected areas around military installations where the Department of Defense and other federal agencies work with state governments and private stakeholders to meet conservation goals. 

Leveraging this rare opportunity, researchers from Archbold Biological Station, in collaboration with the U.S. Fish and Wildlife Service and the U.S. Air Force, introduced fifty-four red cockaded woodpeckers from six donor populations into the range’s pine savannahs between 1998 and 2016. Analyses revealed that translocations provided substantial and extended benefits, improving the population’s size and overall genetic health. 

MSU researchers determined that the introduced birds contributed directly to higher population counts, and that translocated birds and their descendants tended to have higher rates of survival and reproductive success. 

The findings indicate that reproductive success is highly associated with total nesting years — and translocated birds tended to nest for more years than locally hatched ones.  

These positive effects persisted into the future along family lines. About 70 percent of the translocated woodpeckers survived in the population after their release, and many formed breeding pairs with local individuals, providing a boost to the genetic diversity of the population. 

But complex population dynamics, changes which manifest across decades, and the sheer challenge of gathering high-resolution monitoring data makes gauging the effectiveness of translocation efforts difficult. The detail and length of this study, the authors explain, provide rare insights into the long-term effects of these strategies. 

The team hopes that these positive results incentivize land managers to consider the long-term benefits of translocations and continued monitoring.  

“It has the potential to act as an important component of managing many imperiled species,” Lewanski said.  

While the woodpeckers are benefitting from this extensive conservation project, these strategies, and the partnership which support them, have implications for other at-risk species, too. 

In the future, Lewanski expects that genetic insights will play a growing role in tracking and evaluating conservation programs. Analysis of genetic material helps detect and minimize inbreeding and create highly detailed pedigrees for populations, reducing the burden of on-site monitoring programs to track bird nesting and reproduction. 

Using genetic monitoring tools allows scientists and land managers to be more precise when deciding how and when to use translocations, according to Sarah Fitzpatrick, a professor at Michigan State University and  senior author on the study. 

Eventually, a combination of genomic analysis and on-site monitoring could provide tailor-made strategies for managers attempting translocations. 

This study is the product of a partnership between Michigan State University, Archbold Biological Research Station, the U.S. Air Force, Department of Defense and the U.S. Fish and Wildlife Service. 

Funding for managing and monitoring the Avon Park red-cockaded woodpeckers was provided by the DoD, the USAF, and the USFWS. Additional project support was provided by the National Defense Science & Engineering Graduate Fellowship from the Department of Defense and the National Science Foundation. 

By Caleb Hess 

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Journal

Proceedings of the National Academy of Sciences

DOI

10.1073/pnas.2410946122 

Subject of Research

Animals

Article Title

Translocations contribute to population rescue in an imperiled woodpecker

Article Publication Date

28-Jul-2025