Category Archives: Genetics

Genetics

Events tomorrow SEPTEMBER 9: Department of Studies (DoS) in Genetics and Genomics, Mysore University – Star of Mysore

Valedictory of IABSCON-South Zone-2022 and International Symposium on Translational Research, Dr. H. Basavana Gowdappa, Principal, JSS Medical College, chief guest, Dr. T. Venkatesh, St. Johns Medical College, Bengaluru, Dr. R. Medha, JIPMER, Puducherry and Dr. H.P. Gurushankara, Central University of Kerala, Kasaragod, will be present, Vijnana Bhavan, Manasagangothri, 4 pm.

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Events tomorrow SEPTEMBER 9: Department of Studies (DoS) in Genetics and Genomics, Mysore University - Star of Mysore

Genetics

In Brief This Week: Illumina, Interpace, Genetic Signatures, Guardant Health, More – GenomeWeb

NEW YORK Illumina said this week that it has opened its first manufacturing site in China. The Shanghai-based facility will initially produce 16 clinical sequencing reagents. In a statement, the firm said it plans to "achieve complete localized production for its gene sequencing instruments and consumables within the next five years."

Interpace Biosciences this week announced the closing of the sale of its Pharma Services business to Flagship Biosciences for an undisclosed amount. Parsippany, New Jersey-based Interpace will use the proceeds of the transaction for working capital requirements and investments to help drive the growth of its molecular diagnostics business. The company said the disposition of its pharma services business is expected to improve operating cash flow by nearly $5 million annually.

The American Society of Human Genetics said this week that the Illumina Corporate Foundation has awarded it a one-year, $175,000 grant to support the ASHG learning center.

The web portal offers scientists access to professional education videos, webinars, workshops, and other content. ASHG said it would use the grant to implement closed captioning across its live and on-demand content. Other details were not disclosed.

Genetic Signatures this week reported fiscal year 2022 revenues of A$35.4 million, a 25 percent increase from A$28.3 million in FY 2021. The growth was driven by demand for the firm's EasyScreen SARS-CoV-2 Detection Kit, although the company said in a statement that demand for other non-COVID-19 tests has increased. The company's net income for the full year was A$3.3 million, or A$2.11 per share, compared to A$1.8 million, or A$1.23 per share, in the previous year. The Australian firm had A$36.9 million in cash and cash equivalents at the end of the fiscal year.

OpGen has been granted a 180-day extension from the Listing Qualifications Department of Nasdaq to regain compliance with the exchange's minimum bid price requirement. If at any time until Feb. 27, 2023, the bid price for OpGen's common stock closes at or above $1.00 per share for a minimum of 10 consecutive trading days, the firm will regain compliance with the rule. The firm's share price hasn't closed at $1 or higher since mid-January.

Ochsner Health this week became the first healthcare system to incorporate Epic Systems' Orders and Results Anywhere integration with its genomic module. Physicians at New Orleans-based Ochsner, through the system's Precision Medicine Program, will now be able to order Tempus Health genomic tests for patients within the electronic health record system. Through the Epic EHRs, physicians can order genomic tests to identify actionable variants, in turn informing therapeutic decisions and clinical trial eligibility. In addition to Tempus, Epic has also partnered with Caris Life Sciences, Guardant Health, and Myriad Genetics to integrate biomarker testing into EHRs.

Guardant Health said this week that it has expanded its collaboration with Merck KGaA to further leverage the GuardantINFORM real-world evidence platform to help accelerate development efforts for the pharma firm's precision oncology pipeline. The expanded strategic collaboration will focus on therapy development for core cancer indications with significant unmet need.

Caris Life Sciences said this week that the Medical College of Wisconsin Cancer Center has joined its Precision Oncology Alliance, a growing network of leading cancer centers that collaborate to advance precision oncology and biomarker-driven research. MCW is the largest private research institution in Wisconsin, and its cancer center serves a distinct region that includes large, underserved populations of patients who experience significant disparities in cancer incidence and outcomes.

POA members gain access to a growing portfolio of biomarker-directed trials as well as Caris' CODEai, an industry-leading dataset with cancer treatment information and clinical outcomes data for over 275,000 patients.

The Malaysian Genomics Resource Centre Berhad said this week that it has signed a memorandum of understanding to explore opportunities for the distribution of biopharmaceutical and genomics products and services with Ajlan & Bros Medical Company. Under the MoU, the parties will explore the feasibility of Riyadh, Saudi Arabia-based Ajlan becoming a marketing and distribution representative for Malaysian Genomics for genetic screening tests, mesenchymal stem cell products, and exosome products. Ajlan will also identify commercial R&D opportunities for genome sequencing and analysis in the Middle East and North Africa region for areas such as agriculture, aquaculture, plantations, healthcare, and industrial biotechnology. In turn, Malaysian Genomics will analyze samples for genetic screening tests as well as provide Ajlan with genomic and bioinformatics expertise to bid for projects.

BioEcho Life Sciences, a Cologne, Germany-based biotech company specializing in nucleic acid extraction technology, has opened a US subsidiary in Boston. In a statement, BioEcho General Manager Lydia Willing noted that the company will provide an extensive portfolio of its products in the US and have the ability to work on specific customer needs around nucleic acid research.

In Brief This Week is a selection of news items that may be of interest to our readers but had not previously appeared on GenomeWeb.

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In Brief This Week: Illumina, Interpace, Genetic Signatures, Guardant Health, More - GenomeWeb

Genetics

ClinVar Miner

The content on this website is current as of 1 August 2022. On that date, ClinVar had 2,404,889 submissions on 1,543,902 variants. When referencing data from this website, please cite the 2018 Human Mutation article "ClinVar Miner: Demonstrating utility of a Webbased tool for viewing and filtering ClinVar data" .

ClinVar Miner was developed by Alex Henrie in the Eilbeck Lab with support from the NHGRI's ClinGen Resources (grants U41 HG006834-01A1 to Heidi Rehm and U01 HG007437-01 to Jonathan Berg). Use of the NCBI logo represents use of NCBI data but does not constitute an approval or endorsement of this application. Source code is available on GitHub under the GNU General Public License.

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.

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ClinVar Miner

Genetics

Investing in the genetics of Scotland’s trout sector – The Fish Site

According to Xelect, the agreement marks the start of the first selective breeding programme for sea-grown rainbow trout (which are often referred to as steelhead) in the UK and is designed to provide Kames with a major boost to the quality of their production faster growing fish, with high survival rates, that thrive in seawater.

The project started with an initial genetic evaluation of Kames broodstock to ensure that the selective breeding programme would be based on a highly diverse population, with strong potential for future gains.

In the next stage, Xelect will combine genetic analysis of the fish (genotypes) with real world performance data (phenotypes). By using the latest breeding programme management techniques and our highly sophisticated software, OptiMate, Xelect can then identify the optimal crosses to provide Kames with major trait improvements every generation, said Xelect programme manager, Lidia de los Rios Perez in a press release.

Were really delighted to be working with Kames. They are an institution in Scottish aquaculture, and whilst our customers are spread all over the world, weve always been committed to developing aquaculture in Scotland too, said Xelects CEO, Ian Johnston.

This is an exciting stage of development for Kames as we launch into the next fifty years with fully integrated production. Partnering with Xelect is an obvious choice as it not only preserves our Scottish provenance but offers access to a great team of specialists dedicated to enhancing our own unique strain of steelhead trout, said Kames managing director, Neil Manchester.

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Investing in the genetics of Scotland's trout sector - The Fish Site

Genetics

Considerations for Policymakers to Improve Healthcare through Telegenetics: A Points to Consider Statement of the American College of Medical Genetics…

BETHESDA, Md., Aug. 30, 2022 /PRNewswire/ -- Telemedicine has skyrocketed during the COVID-19 pandemic, but what actions are needed for more patients to have equitable, fair access to genetics services via telegenetics? To address this urgent problem, the Advocacy and Government Affairs Committee of the American College of Medical Genetics and Genomics (ACMG) has just released a new Points to Consider statement that will assist policymakers tasked with improving appropriate, broad access to genetics services via telehealth: "Considerations for Policymakers to Improve Healthcare through Telegenetics: A Points to Consider Statement of the American College of Medical Genetics and Genomics."

"We have seen a dramatic increase in telemedicine use during the COVID-19 pandemic, but research suggests access is not equitable across different population groups," said lead author Heather E. Williams, PhD, MS. "Policy efforts to ensure equitable access to genetics services via telehealth are necessary. We can continue to address disparities by eliminating barriers to accessing the medical genetics workforce."

The statement, the first published by ACMG's Advocacy and Government Affairs (AGA) Committee, is intended to be used by policymakers to consider as they pursue legislative, regulatory, or other policies related to telegenetics or reducing disparities in access to genetic services. It describes telegenetics services, the need for these services, existing barriers to technology access, actions needed to ensure equitable access and the current state of reimbursement for these services.

A few of the specific points to consider include:

The statement concludes that while the COVID-19 pandemic expedited the expanded integration of telemedicine into genetic services, only a concerted effort will ensure that all Americans can benefit from these services. The points discussed in this statement should be viewed as considerations for federal, state and institutional policymakers as well as payers that are tasked with ensuring equitable access to telemedicine, including telegenetics. Improved telehealth policies are necessary to enhance patient care and reduce disparities in accessing genetics healthcare to patients throughout the United States.

About the American College of Medical Genetics and Genomics

Founded in 1991, the American College of Medical Genetics and Genomics (ACMG) is a prominent authority in the field of medical genetics and genomics and the only nationally recognized medical professional organization solely dedicated to improving health through the practice of medical genetics and genomics. The only medical specialty society in the US that represents the full spectrum of medical genetics disciplines in a single organization, the ACMG provides education, resources and a voice for more than 2,500 clinical and laboratory geneticists, genetic counselors and other healthcare professionals. ACMG's mission is to improve health through the clinical and laboratory practice of medical genetics as well as through advocacy, education and clinical research, and to guide the safe and effective integration of genetics and genomics into all of medicine and healthcare, resulting in improved personal and public health. Genetics in Medicine is the official ACMG journal. ACMG's website, http://www.acmg.net, offers resources including policy statements, practice guidelines, and educational programs. The ACMG Foundation for Genetic and Genomic Medicine works to power ACMG educational and public health programs through charitable gifts from corporations, foundations and individuals.

Kathy Moran, MBA[emailprotected]

SOURCE American College of Medical Genetics and Genomics

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Considerations for Policymakers to Improve Healthcare through Telegenetics: A Points to Consider Statement of the American College of Medical Genetics...

Genetics

Ambry Genetics Publishes 43000 Patient Study Showing Combined RNA and DNA Analysis Identifies Patients Who Are High-Risk for Cancer but Would Have…

ALISO VIEJO, Calif.--(BUSINESS WIRE)--Ambry Genetics, a leader in clinical diagnostic testing and a subsidiary of REALM IDx, Inc., announced today the findings of a study that showed paired RNA and DNA genetic testing, conducted at the same time, detected elusive pathogenic variants in 1 of every 950 patients that were missed by DNA testing alone. The findings, published in npj Genomic Medicine, highlight the importance of combining RNA and DNA analysis in hereditary cancer testing to give clinicians and their patients the most accurate and comprehensive genetic data needed to inform patient care and achieve the best outcomes.

According to the National Library of Medicine, as of August 2017, there were approximately 75,000 genetic tests on the market, representing 10,000 unique test types. Unfortunately, many of these DNA-only tests exclude large portions of DNA such as introns, a sequence of DNA that is spliced out before an RNA molecule is translated into a protein. In addition to omitting large portions of introns, DNA-only testing lacks the functional context to determine whether a variant increases cancer risk, which can lead to inconclusive results. These limitations may prevent patients and their families from getting accurate results to inform their preventative or therapeutic care.

Concurrent RNA and DNA testing helps identify more patients at risk by determining if an uncertain result from DNA testing is normal or disease-causing, and expands the range of genetic testing to identify mutations that DNA-only testing misses.

With our +RNAinsight test we were the first company to offer upfront paired DNA and RNA sequencing to give clinicians and their patients the most accurate and comprehensive information about their cancer risk, said Tom Schoenherr, CEO, Ambry Genetics. This study confirms that conducting RNA and DNA testing together is critical to help identify high-risk individuals who would have been missed by DNA-only testing.

Previously, published evidence of the value of RNA sequencing has been limited by studies with small sample sizes and enriched cohorts. This study by Ambry is the largest to examine the impact of paired DNA and RNA analysis in hereditary cancer testing. In the study, tests from 43,524 patients who underwent paired DNA-RNA genetic testing using Ambrys +RNAinsight from March 2019 through April 2020 were examined to determine if the paired sequencing detected more pathogenic variants than DNA testing alone. The analysis identified patients who had disease-causing alterations that DNA testing alone would have misinterpreted. Examining the RNA data resolved variant findings in 549 patients (1 in 79 patients) by providing the required functional data for more accurate interpretation of splicing variants. In addition, the analysis showed that 1 of every 950 patients had a pathogenic deep intronic variant that would not have appeared in DNA testing alone.

The results from the study may underestimate the total clinical impact because some of the patients families who are now eligible for genetic testing were not tested. In addition, the ripple effect created by these updated results extends to past and future patients. These downstream benefits were not quantified in the current study.

This is the largest study of its kind to show the importance of RNA testing in predicting cancer risk, said Carrie Horton, senior clinical research specialist for oncology and first author of the study. Its clear that RNA analysis has the potential to become a standard practice for genetic testing to improve hereditary cancer care.

A webinar, open to the media, genetic counselors, clinicians and other interested parties, will be conducted on Thursday, September 15 at 10 a.m. PT to review the study findings. Registration information is here.

Ambrys +RNAinsight was the first test to provide comprehensive gene coverage for RNA analysis to help classify and detect DNA variants associated with a variety of cancers including breast, ovarian, prostate, colon, pancreatic and uterine. +RNAinsight enables more accurate identification of patients with increased genetic risks for cancer, finds actionable results that may otherwise be missed and decreases the frequency of inconclusive results.

About Ambry Genetics

Ambry Genetics, a subsidiary of REALM IDx, Inc., translates scientific research into clinically actionable test results based upon a deep understanding of the human genome and the biology behind genetic disease. It is a leader in genetic testing that aims to improve health by understanding the relationship between genetics and disease. Its unparalleled track record of discoveries over 20 years, and growing database that continues to expand in collaboration with academic, corporate and pharmaceutical partners, means Ambry Genetics is first to market with innovative products and comprehensive analysis that enable clinicians to confidently inform patient health decisions.

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Ambry Genetics Publishes 43000 Patient Study Showing Combined RNA and DNA Analysis Identifies Patients Who Are High-Risk for Cancer but Would Have...

Genetics

The genetics behind why some people get sicker with COVID-19 than others – ABC News

Norman Swan: One of the common questions that Tegan and I get about Covid is why there's so much variation in how people respond to the infection. One answer is in your genes, and there is a massive ongoing study into comparing people's genomes with how COVID-19 has affected them. Dr Gita Pathak is a team leader in what's called the COVID-19 Host Genetics Initiative. Gita is based at Yale University's School of Medicine in the United States.

Gita Pathak: Thank you for inviting me, I really appreciate it.

Norman Swan: So you're not mapping the virus here, you're mapping the people who were infected with the virus to see what happens to them and whether there are specific genes involved in their experience of the virus.

Gita Pathak: That is correct. The goal of the study is to understand human genetics response to the viral infection which we know as COVID-19. We wanted to look at three different outcomes of COVID-19, specifically people who were critically ill from Covid, then people who were hospitalised due to Covid, and people who tested positive for Covid, so the least severe of the three definitions, and which genes might be associated with these three outcomes.

Norman Swan: And how many genomes have you managed to test?

Gita Pathak: 60 studies from 25 countries, and that resulted in close to 3 million individuals' genetic profiles, and we found a total of 23 genes that show an association with COVID-19.

Norman Swan: So, let's take severity, and this is in a European population, by and large, a Caucasian population. Have you found any consistency in genes for severe disease?

Gita Pathak: Yes, so genetic ancestry is different than what someone may identify themselves as, like ethnically or geographically. Mostly we do have genetic ancestry of the European descent, but we also had people who are genetically South Asian, East Asian, African ancestry, and that separate from where they are geographically or what they identify as.

Norman Swan: So this is a bit like 23andMe or Ancestry.com where you send off your genes and you find out that you are 50% Greek and you didn't think you were 50% Greek.

Gita Pathak: Correct. When we are looking at genetic profiles, it's really important to adjust for genetic ancestry and not specifically for what somebody identifies as. Some genetic variation is more common in one ancestry over others, and if we include people from these diverse ancestries, we can pick up these signals much more quickly

Norman Swan: So, for example, it was said in the early part of the pandemic that people of South Asian origin had more severe disease and a higher risk of death. Did that pan out in your study?

Gita Pathak: We did find one of the genetic variants that was more common in South Asian populations relative to other populations, but that is just one variant. Genes tend to perform in a similar way across ancestries. They may vary based on their frequency in different ancestries, and that information helps us capture why one ancestry might be exhibiting a higher response or a softer response, but by and large all the genes we saw, they tend to have a similar effect across all ancestries.

Norman Swan: And what with these genes doing to increase your vulnerability to severe disease?

Gita Pathak: Some of the genes that we found were related to different lung functions. So, for example, we found something called SFTPD which is a lung surfactant protein, and it has already been known to be associated with different pulmonary functions, and there are other studies which have shown that this specific gene has been known with respiratory distress syndrome in different populations.

Norman Swan: And just to explain, surfactant is the fluid, if you like, that lines the tubes of your lungs and keeps them open, and it's what is deficient in premature babies, causing the respiratory disease of the premature baby. So, in other words, a deficiency of this in adults may predispose you, unsurprisingly, to severe disease. The question of course on everybody's lips now is why do some people not seem to catch COVID-19? There's a group of people who appear anecdotally to be resistant. Did you find COVID-19 resistance genes?

Gita Pathak: Not in our work. Depending on how we look at the variant, the varients we find are associated with the COVID-19 outcome, but if there are people who may be on the opposite spectrum of these, so let's say who are not carriers of this, they might be generally resistant to Covid but that specific study we haven't performed, but that's a good question for later.

Norman Swan: And just finally, any therapeutic insights that might direct people towards more effective medications to treat people who've got Covid, or prevent it getting worse?

Gita Pathak: One good thing that we understand from this work is that we now have a good number of genes to specifically focus our efforts into, and now this can lead to efforts of drug repurposing or drug development. Did we find a specific drug? No, but we definitely found several targets that now could be investigated for different drugs.

Norman Swan: Gita, thank you very much for joining us.

Gita Pathak: Thank you so much for having me, I really appreciate it.

Norman Swan: Dr Gita Pathak is a team leader in the COVID-19 Host Genetics Initiative at Yale University's School of Medicine.

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The genetics behind why some people get sicker with COVID-19 than others - ABC News

Genetics

The Genetics That Make One Animal Immortal Have Been Revealed – IFLScience

Immortality exists but to get it, you need to be a jellyfish, not a god or a vampire. Moreover, only one species of cnidarian, Turritopsis dohrnii, is known to have found the secret of eternal life. Geneticists hope comparing T. dorniis DNA with its close relative, T. rubra, will help us understand the aging process and how to evade it.

Turritopsis are warm water jellyfish half a centimeter (0.2 inches) long. At least three species of hydra have the capacity to age backwards like Benjamin Button, going from adult to juvenile stage, before eventually growing up again. However, two of these can only go from the hydra equivalent of adolescent to child; like the victim in some uncensored fairytale, sexual reproduction locks them into adulthood. T. dohrnii, on the other hand, appears able to go from its free-floating adult stage to bottom-living polyp, known as life cycle reversal (LCR), as many times as it wants.

A paper in the journal Proceedings of the National Academy of Sciences provides a comparison of T. dorhnii and T. rubra in the hope the differences will prove enlightening, throwing in a few more distantly related types of cnidarians as well.

Dr Maria Pascual-Torner of Universidad de Oviedo, Spain, and co-authors didnt find any single genetic trick that appears to provide the fountain of youth. Instead, they discovered a wide variety of potential contributors, reporting; We have identified variants and expansions of genes associated with replication, DNA repair, telomere maintenance, redox environment, stem cell population, and intercellular communication.

This polyp of Turritopsis dohrnii is from a colony generated by a single rejuvenated medusa. Image Credit: Maria Pascual-Torner

All of these could eventually prove important, but the study homed in on two significant aspects of T. dohrniis genome absent in its relative. One of these silences the polycomb repressive complexes: 2 families of proteins that regulate gene expression. The other activates pluripotency the capacity of a stem cell to turn into whatever sort of cell it needs to become during life cycle reversal.

Applying these to humans will certainly be a Herculean task if its possible at all. However, while many of T. dorhniis features probably only work in combination, some might provide a few precious extra years of health in more complex creatures, ourselves included.

As the paper notes: Natural selection declines with age. Only in rare cases, such as the orca grandmothers, is there much evolutionary benefit to living long and healthy lives after reproduction ceases. Consequently, nature has done little work to ensure it occurs well have to work out how to make it happen ourselves, with only T. dorhnii to guide us.

Even T. dohrnii does not live forever. Indeed the typical specimen has a much shorter life expectancy than you, this being the sad consequence of a small lifeform with few defenses and tasty to larger jellyfish and fish. Presumably, this is why they have not come to dominate the Earth as we might expect an immortal species to do. Nevertheless, its capacity for rejuvenation makes it theoretically capable of eternal life, something suspected in only one other species and confirmed in none.

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The Genetics That Make One Animal Immortal Have Been Revealed - IFLScience

Genetics

You’re in control: Exercise outweighs genetics when it comes to longer life – Study Finds

SAN DIEGO If living into your 90s seems to run in the family, dont just assume that means you will too.Our genetics make us who we are, but new research from the University of California, San Diego finds exercise trumps genes when it comes to promoting a longer life.

You dont need a medical degree to know that forgoing physical activity in favor of stagnation isnt the wisest choice for your health and longevity. But, certain people are genetically predisposed to live longer than others. The research team at UCSD set out to determine if such individuals dont have to move quite as much as the rest of us to live just as long.

The goal of this research was to understand whether associations between physical activity and sedentary time with death varied based on different levels of genetic predisposition for longevity, says lead study author Alexander Posis, M.P.H., a fourth-year doctoral student in the San Diego State University/UC San Diego Joint Doctoral Program in Public Health, in a university release.

This research project began a decade ago. In 2012, as part of the Womens Health Initiative Objective Physical Activity and Cardiovascular Health study (OPACH), study authors began keeping track of the physical activity habits among 5,446 older U.S. women (ages 63 or older). Subjects were tracked up until 2020, and wore a research-grade accelerometer for up to seven days. That device measured how much time they spent moving, the intensity of that physical activity, and their usual amount of sedentary time.

Sure enough, higher levels of light physical activity and moderate-to-vigorous physical activity were associated with a lower risk of dying during the tracking period. Additionally, more time spent sedentary was associated with a higher risk of mortality. Importantly, this observed connection between exercise and a longer life remained consistent even among women determined to have different levels of genetic predisposition for longevity.

Our study showed that, even if you arent likely to live long based on your genes, you can still extend your lifespan by engaging in positive lifestyle behaviors such as regular exercise and sitting less, explains senior study author Aladdin H. Shadyab, Ph.D., assistant professor at the Herbert Wertheim School of Public Health and Human Longevity Science at UC San Diego. Conversely, even if your genes predispose you to a long life, remaining physically active is still important to achieve longevity.

In conclusion, study authors recommend that older women engage in physical activity of any intensity as regularly as possible. Doing so will lower the risk of both various diseases and premature death.

The study is published in the Journal of Aging and Physical Activity.

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You're in control: Exercise outweighs genetics when it comes to longer life - Study Finds

Genetics

Genetic pattern and demographic history of cutlassfish (Trichiurus nanhaiensis) in South China Sea by the influence of Pleistocene climatic…

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