Zhejiang University

Genomic anamolies dating back to the time of the dinosaurs misled scientists about the evolutionary history of birds. An enormous meteor spelled doom for most dinosaurs 65 million years ago. But not all. In the aftermath of the extinction event, birds -- technically dinosaurs themselves -- flourished. Scientists have spent centuries trying to organize and sort some 10,000 species of birds into one clear family tree to understand how the last surviving dinosaurs filled the skies. Cheap DNA sequencing should have made this simple, as it has for countless other species. But birds were prepared to deceive us. In a pair of new research papers released today, April 1, scientists reveal that another event 65 million years ago misled them about the true family history of birds. They discovered that a section of one chromosome spent millions of years frozen in time, and it refused to mix together with nearby DNA as it should have. This section, just two percent of the bird genome, convinced scientists that most birds could be grouped into two major categories, with flamingos and doves as evolutionary cousins. The more accurate family tree, which accounts for the misleading section of the genome, identifies four main groups and identifies flamingos and doves as more distantly related. "My lab has been chipping away at this problem of bird evolution for longer than I want to think about," said Edward Braun, Ph.D., the senior author of the paper published in the Proceedings of the National Academy of Sciences and a professor of biology at the University of Florida. "We had no idea there would be a big chunk of the genome that behaved unusually. We kind of stumbled onto it." Braun supervised an international team of collaborators led by Siavash Mirarab, a professor of computer engineering at the University of California San Diego, to publish their evidence that this sticky chunk of DNA muddied the true history of bird evolution. Mirarab and Braun also contributed to a companion paper published in Nature that outlines the updated bird family tree, which was led by Josefin Stiller at the University of Copenhagen. Both papers are part of the B10K avian genomics project led by Guojie Zhang of Zhejiang University, Erich Jarvis of Rockefeller University, and Tom Gilbert of the University of Copenhagen. Ten years ago, Braun and his collaborators pieced together a family tree for the Neoaves, a group that includes the vast majority of bird species. Based on the genomes of 48 species, they split the Neoaves into two big categories: doves and flamingos in one group, all the rest in the other. When repeating a similar analysis this year using 363 species, a different family tree emerged that split up doves and flamingos into two distinct groups. With two mutually exclusive family trees in hand, the scientists went hunting for explanations that could tell them which tree was correct. "When we looked at the individual genes and what tree they supported, all of a sudden it popped out that all the genes that support the older tree, they're all in one spot. That's what started the whole thing," Braun said. Investigating this spot, Braun's team noticed it was not as mixed together as it should have been over millions of years of sexual reproduction. Like humans, birds combine genes from a father and a mother into the next generation. But birds and humans alike first mix the genes they inherited from their parents when creating sperm and eggs. This process is called recombination, and it maximizes a species' genetic diversity by making sure no two siblings are quite the same. Braun's team found evidence that one section of one bird chromosome had suppressed this recombination process for a few million years around the time the dinosaurs disappeared. Whether the extinction event and the genomic anomalies are related is unclear. The result was that the flamingos and doves looked similar to one another in this chunk of frozen DNA. But taking into account the full genome, it became clear that the two groups are more distantly related. "What's surprising is that this period of suppressed recombination could mislead the analysis," Braun said. "And because it could mislead the analysis, it was actually detectable more than 60 million years in the future. That's the cool part." Such a mystery could be lurking in the genomes of other organisms as well. "We discovered this misleading region in birds because we put a lot of energy into sequencing birds' genomes," Braun said. "I think there are cases like this out there for other species that are just not known right now." This work was supported in part by the National Science Foundation.

Using cutting-edge computational methods and supercomputing infrastructure, researchers have built the largest and most detailed bird family tree to date -- an intricate chart delineating 93 million years of evolutionary relationships between 363 bird species, representing 92% of all bird families. The updated tree reveals sharp increases in effective population size, substitution rates and relative brain size in early birds in the aftermath of the mass extinction event that wiped out the dinosaurs 66 million years ago. And by closely examining one of the branches of this tree, researchers found that flamingos and doves are more distantly related than previous genome-wide analyses had shown. Using cutting-edge computational methods and supercomputing infrastructure at UC San Diego, researchers have built the largest and most detailed bird family tree to date -- an intricate chart delineating 93 million years of evolutionary relationships between 363 bird species, representing 92% of all bird families. The updated tree reveals sharp increases in effective population size, substitution rates and relative brain size in early birds in the aftermath of the mass extinction event that wiped out the dinosaurs 66 million years ago. And by closely examining one of the branches of this tree, researchers found that flamingos and doves are more distantly related than previous genome-wide analyses had shown. An international team of scientists has built the largest and most detailed bird family tree to date -- an intricate chart delineating 93 million years of evolutionary relationships between 363 bird species, representing 92% of all bird families. The advance was made possible in large part thanks to cutting-edge computational methods developed by engineers at the University of California San Diego, combined with the university's state-of-the-art supercomputing resources at the San Diego Supercomputer Center. These technologies have enabled researchers to analyze vast amounts of genomic data with high accuracy and speed, laying the groundwork for the construction of the most comprehensive bird family tree ever assembled. The advance is detailed in two complementary papers published on April 1 in Nature and the Proceedings of the National Academy of Sciences (PNAS). The updated family tree, reported in Nature, revealed patterns in the evolutionary history of birds following the cataclysmic mass extinction event that wiped out the dinosaurs 66 million years ago. Researchers observed sharp increases in effective population size, substitution rates and relative brain size in early birds, shedding new light on the adaptive mechanisms that drove avian diversification in the aftermath of this pivotal event. In the companion paper published in PNAS, researchers closely examined one of the branches of the new family tree and found that flamingos and doves are more distantly related than previous genome-wide analyses had shown. The work is part of the Bird 10,000 Genomes (B10K) Project, a multi-institutional effort led by University of Copenhagen, Zhejiang University and UC San Diego that aims to generate draft genome sequences for about 10,500 extant bird species. "Our goal is to reconstruct the entire evolutionary history of all birds," said Siavash Mirarab, professor of electrical and computer engineering at the UC San Diego Jacobs School of Engineering, who is a co-senior author on the Nature paper, as well as first and co-corresponding author on the PNAS paper. Piecing together the past At the heart of these studies lies a suite of algorithms known as ASTRAL, which Mirarab's lab developed to infer evolutionary relationships with unprecedented scalability, accuracy and speed. By harnessing the power of these algorithms, the team integrated genomic data from over 60,000 genomic regions, providing a robust statistical foundation for their analyses. The researchers then examined the evolutionary history of individual segments across the genome. From there, they pieced together a mosaic of gene trees, which were then compiled into a comprehensive species tree. This meticulous approach enabled the researchers to construct a new and improved bird family tree that delineates complex branching events with remarkable precision and detail, even in cases of historical uncertainty. "We found that our method of adding tens of thousands of genes to our analysis was actually necessary to resolve evolutionary relationships between bird species," said Mirarab. "You really need all that genomic data to recover what happened in this certain period of time 65-67 million years ago with high confidence." The team's ability to conduct these analyses on massive datasets was made possible because Mirarab's lab designed their computational methods to run on powerful GPU machines. They ran their calculations on the Expanse supercomputer at the San Diego Supercomputer at UC San Diego. "We were fortunate to have access to such a high-end supercomputer," said Mirarab. "Without Expanse, we would not have been able to run and rerun our analyses on such large datasets in a reasonable amount of time." The researchers also looked at the effects of different genome sampling methods on the accuracy of the tree. They showed that two strategies -- sequencing many genes from each species, as well as sequencing many species -- combined together are important for reconstructing this evolutionary history. "Because we used a mixture of both strategies, we could test which approach has stronger impacts on phylogenetic reconstruction," said Josefin Stiller, professor of biology at the University of Copenhagen and lead author of the Nature paper. "We found that it was more important to sample many genetic sequences from each organism than it was to sample from a broader range of species, although the latter method helped us to date when different groups evolved." Correcting the past With the aid of their advanced computational methods, the researchers were also able to shed light on something unusual that they had discovered in one of their previous studies: a particular section of one chromosome in the bird genome had remained unchanged for millions of years, void of the expected patterns of genetic recombination. This anomaly initially led the researchers to incorrectly group flamingos and doves together as evolutionary cousins, for they appeared closely related based on this unchanged section of DNA. That's because their previous analysis was based on the genomes of 48 bird species. But by repeating their analysis using the genomes of 363 species, a more accurate family tree emerged that moved doves further from flamingos. Moreover, using six high-quality genomes provided by the Vertebrate Genome Project (VGP) -- led by co-author Erich Jarvis, a professor of neurobiology at Rockefeller University -- Mirarab and colleagues were able to detect and putatively explain this surprising pattern. "What's surprising is that this period of suppressed recombination could mislead the analysis," said Edward Braun, professor of biology at the University of Florida and co-corresponding author of the PNAS paper. "And because it could mislead the analysis, it was actually detectable more than 60 million years in the future. That's the cool part." Next steps The impact of this work extends far beyond studying the evolutionary history of birds. The computational methods pioneered by Mirarab's lab have become one of the standard tools for reconstructing evolutionary trees for a variety of other animals. Moving forward, the team is continuing their efforts to construct a complete picture of bird evolution. Biologists are working on sequencing the genomes of additional bird species in the hopes of expanding the family tree to include thousands of bird genera. Meanwhile, computational scientists led by Mirarab are refining their algorithms to accommodate even larger datasets to ensure that analyses in future studies are conducted with high speed and accuracy.

The Establishment of the Facility Demonstrates the Company's Commitment to Delivering Differentiated Solutions to Gynecology and Pediatrics Challenges SHANGHAI, Dec. 22, 2023 /PRNewswire/ -- Changchun GeneScience Pharmaceutical ("GenSci"), a subsidiary of Changchun High-Tech Industries (Group), held a groundbreaking ceremony for its new global headquarters and research & development (R&D) center at Shanghai Zhangjiang International Medical Park on December 15th. With an increasing focus on women`s and children`s health, the Chinese government has been intensifying efforts to improve healthcare services for these demographics, embedding their care within the wider framework of the country's economic and social development policies. The establishment of the R&D center sets the stage for GenSci to further advance the convergence of industry, academia, research and the medical community. By leveraging cutting-edge R&D capabilities and the application of artificial intelligence technologies, GenSci is well-positioned to provide premium health solutions for women and children. The initiative aligns with GenSci's commitment to harnessing science and technology to protect and enhance the health of these vulnerable groups. Continue Reading Changchun GeneScience Pharmaceutical Co., Ltd. The construction of this facility is progressing as planned, and it is expected to be fully operational by 2027, providing a capacity to accommodate up to 2,000 R&D professionals. Supporting the Healthy China Initiative: Focusing on the Health Needs of Women and Children Recognizing the pivotal role of women and children's health in the nation's overall well-being, the government has designated this field as a critical priority. This is evident in the implementation of significant strategic initiatives such as the Healthy China Initiative (2019-2030), the Outline for Children's Development in China (2021-2030), and the Outline for Women's Development in China (2021-2030). These key documents underscore our unwavering commitment to enhancing nationwide awareness regarding the specific needs of women and children, with an overarching objective of safeguarding their health. The health of women and children confronted with new challenges. While the incidence of common childhood diseases has decreased, there is a rise in lifestyle-related health issues in children, including early puberty, myopia, growth deficiencies, body image concerns, immune system abnormalities, and mental health disorders. In addition, women are generally grappling with reproductive health issues and the effects of menopause that can significantly impact their quality of life. Moreover, the periods of pregnancy and early childhood present vital opportunities to avert diseases that can develop later in life. Enhanced health management for women and children during these key stages can help prevent long-term health issues, carrying significant implications for the broader society. Providing Premier Global Maternal and Child Health Solutions through Distinctive Innovation Aligned with national healthcare directives, GenSci has ramped up its R&D investments to address the unmet health needs of women and children. The company has already developed the capability to innovate across various product categories, including biopharmaceuticals, chemical drugs, live bacterial preparations (LBPs) and medical devices. The GenSci general manager, Dr. Jin, pointed out that their product innovations are designed to deliver substantial unique benefits. The establishment of the Zhangjiang R&D center is a testament to GenSci's commitment to independent innovation. Since its founding in 1997, GenSci has introduced several groundbreaking therapies, including the GenSci Recombinant Human Growth Hormone, GenSci Heng Recombinant Human Follicle-Stimulating Hormone and Jinfuning Recombinant Human Granulocyte-Stimulating Factor Gel. The company's proprietary innovations and outstanding contribution in the field of child growth and development were recognized when its "Development and Industrialization of Recombinant Human Growth Hormone Series Products" project won the Second Prize of the 2015 National Science and Technology Progress Award. The accolade underscores GenSci's expertise in independent innovation within China's pharmaceutical sector. With an ongoing focus on growth disorders in children, GenSci has expanded its attention to the broader spectrum of children's health. This includes addressing concerns such as abnormal sexual development, obesity, respiratory and digestive health, allergies and autoimmune disorders, neurological and speech development, as well as concerns related to body image. As an illustration, GenSci has been develop an industry-leading ultra-long-acting growth hormone that is administered monthly since 2020, as well as innovative oral treatments for short stature. The company has also been creating comprehensive range of solutions designed to diagnose and treat precocious puberty, including rapid sex hormone tests and long-acting gonadotropin-releasing hormone analogs for treating central precocious puberty. Furthermore, GenSci has been adopting a comprehensive approach that addresses women's health needs throughout their life cycle. This initiative includes support for assisted reproduction, menopausal health, and the treatment of prevalent gynecological conditions. Significantly, the company has been developing the world's first lytic enzyme and live bacterial preparation (LBP) for treating vaginitis caused by drug-resistant bacteria, offering an alternative to antibiotics and addressing the issue of drug resistance. "GenSci has built a globally innovative and competitive R&D product pipeline," Dr. Jin declared. "By 2025, the firm will boast an extensive portfolio, with the expectation of launching more than four top-tier innovative drugs and five novel medical devices annually in the years to come." Enhancing Collaboration Across Industry, Academia, Research, and Healthcare Providers to Tackle Key Issues in Women's and Children's Health GenSci, through a combination of proprietary R&D and collaborative efforts with partners, has developed a suite of sophisticated R&D technology platforms that drive forward-thinking product development. The platforms focus on the protein drug sustained-release technology, mucosal delivery systems for nucleic acid medications, antibody-drug conjugate (ADC) technology, and innovations in ultrasound and hydrogel technologies. Integrating AI technology, GenSci covers the entire drug innovation process, from initial design and screening to process development and formulation. Moreover, the company promotes the introduction and adoption of cutting-edge concepts and technologies by facilitating synergistic integration of industry, academia, research and the medical community, ensuring effective cooperation among these stakeholders. GenSci has formed enduring and robust partnerships with nearly 20 prominent universities, including Shanghai Jiao Tong University and Zhejiang University. The company has also engaged in various scientific research collaborations with institutions such as Shanghai Jiao Tong University, Shandong University, and the Center for Excellence in Brain Science and Intelligence Technology at the Chinese Academy of Sciences. Additionally, GenSci has joined forces with numerous maternity and pediatric departments within both general and specialized hospitals through multicenter clinical trials and joint applications for national projects. As part of these alliances, the company contributes its substantial technical expertise and digital platform capabilities — skills acquired during product development — to these hospitals at no cost. Frontline doctors are engaged to review and provide feedback on these tools, aiding the ongoing enhancement of GenSci's research and digital capabilities in gynecology and pediatrics. Additionally, GenSci has established collaborations with numerous hospitals in the development of digital medical assistance systems，it actively engages in medical research to achieve technological breakthroughs and plays a pivotal role as a high-tech innovation platform in specialized treatment fields. Through deep cooperation and extensive coverage, it truly realizes co-creation and win-win outcomes in medical research. The groundbreaking of GenSci's global innovation hub and R&D center enpowers the company to fully utilize its expertise in gynecology and pediatrics. GenSci intends to introduce innovative therapies for oncology, immunology, hearing loss, and drug-resistant bacterial infections, aiming to address unmet clinical needs. With its advanced strategic positioning, substantial investment in R&D, and unwavering commitment to product innovation, GenSci continues to strive towards tackling significant medical challenges while providing exceptional exceptional treatment options for healthcare professionals and patients. SOURCE Changchun GeneScience Pharmaceutical Co., Ltd.