In 2019, the government committed to publicly funding infertility services, including IVF. Lynn Enright asks if it will happen this year and speaks to some people about the costs financial, medical and emotional of funding the process privately

Amy Gallagher and James Rowan have always known they would need help to conceive. Rowan had cancer first at age 15, then at 20 and the high-dose chemotherapy used to treat it destroyed his fertility. Before the first course of chemotherapy began, he banked sperm which remained frozen for the best part of two decades. When he and Gallagher got together and decided they wanted to complete their family she has a son from a previous relationship to whom Rowan is a loving stepfather they faced a dearth of information and options.

I asked my GP about it and he just pointed me in the direction of a private clinic, Rowan says. Thats all he could do for me.

The World Health Organisation is clear: infertility is a disease. It affects the male or female reproductive system and is defined by the failure to achieve a pregnancy after 12 months or more of regular unprotected sexual intercourse. In those of reproductive age, it affects men and women equally, with male-factor infertility accounting for 50 per cent of cases, according to Prof Mary Wingfield, clinical director of the Merrion Fertility Clinic in Dublin.

Yet, in Ireland, people who cant conceive without turning to assisted reproductive technology (ART) receive little or no support within the public health system. Those who need in-vitro fertilisation (IVF) and other fertility treatments to start a family will find themselves immediately paying for treatment, a situation that compares unfavourably with most of our European neighbours. In Scotland, for example, eligible patients are offered up to three free cycles of IVF the number most experts agree gives a fair chance of conception. In Ireland, there is no comprehensive State-funded fertility treatment, even when patients are receiving care and treatment for a condition or disease that affects their fertility, such as cancer, colitis or endometriosis.

Forty-year-old Natalie Doyle needed to pursue IVF after her Fallopian tubes became encased in scar tissue following complications relating to colitis. She had been receiving expert care within the public health system but once it came to looking into ART options, a situation she found herself in as a direct result of the disease, she felt completely adrift.

Youre just left on your own to choose a clinic and theres no communication between your fertility clinic and your other doctors, she says. Theres not even a link between your GP and the clinic its just nuts, I cant get my head around it.

Doyle and her partner postponed moving in together, both staying with family while they funded cycle after cycle of failed IVF. Eventually, they conceived their daughter but Doyle is adamant that the Government needs to step in. The costs are too much for many couples to bear, she says.

It feels like youre spending money, just sitting in the waiting room. It bleeds you dry. The Government needs to help with the costs, she says. But they also need to help medically, so that patients like me have a continuity of care. There have to be more regulations, there has to be more support, the mind boggles that nothing has been done yet.

In Ireland, fertility clinics are regulated by the Health Products Regulatory Authority (HPRA) but there is no regulatory body that specifically oversees the fertility industry. In the UK, the Human Fertilisation and Embryology Authority (HFEA) performs that role, ensuring fertility clinics and research centres comply with the law, as well as providing free, clear and unbiased information on all fertility clinics operating within the jurisdiction. Without such a body here, patients can find themselves feeling bewildered.

Amy Gallagher says she got most of her information from Google, Facebook and Instagram.

I just think there should be some form of support for people, not only financially but emotionally, she says. For people who experience infertility as a result of childhood cancer, theres nothing out there. Theres one Facebook group, thats all Ive found. There needs to be something like the citizens information service, somewhere you can get information. People have no one to turn to. Your GP doesnt know and a fertility doctor will charge at least 250 for a consultation, just to ask them questions. The situation is, she says, deeply frustrating and upsetting.

Prof Wingfield says Ireland desperately needs an equivalent of the HFEA. The industry is regulated by the HPRA but its more from the point of view of the quality procedures surrounding the management of human tissues and cells. Its not about the social, medical, ethical and legal realities. There are plans afoot to introduce such a body as part of an overhaul of the provision of fertility treatment but it is not clear when that will happen.

In October 2017, the cabinet approved the Assisted Human Reproduction (AHR) Bill, a piece of draft legislation that laid out regulations for AHR and the need for the establishment of a regulatory body.

Two years on, in late 2019, details of a model of care for infertility developed by the Department of Health in conjunction with the HSEs National Women & Infants Health Programme were announced, with the then minister for health Simon Harris receiving Government approval to publicly fund infertility services. The announcement a clear commitment from the then Government was hugely significant and it looked as though Ireland was finally set to join most other wealthy and developed nations in providing care and treatment for infertile people. Harris told reporters at the time that he expected publicly funded IVF to be available in 2021.

The planned scheme would comprise three stages: the first stage would involve patients seeing their GP and if it was deemed necessary, they would proceed to the second stage and be referred to a newly established regional fertility hub (there are plans for six hubs, one in each of Irelands six maternity networks), where tests, diagnostic surgery and some non-invasive forms of ART would take place. The third stage would involve the provision of free IVF.

Now, another year has passed and there has been little progress with this ambitious undertaking.

The commitment is ongoing and the current Minister for Health, Stephen Donnelly, confirmed in public statements on the most recent Budget that additional funding is being made available in 2021.

Womens health and our maternity services must get more attention, Donnelly said in the Dil last October, noting that, We will . . .open two new regional fertility hubs in Galway and Cork.

In response to questions from The Irish Times, a Department of Health spokesperson said that 2 million has been made available to allow for the establishment of the first four hubs and a further 1 million has been allocated for the final two hubs.

However, while Covid-19 has not impacted the funding available for the project, the establishment of the hubs has been slowed by the pandemic and its impact on the HSE and the provision of elective health services. None of the six regional hubs are operational at present. Meanwhile, the AHR Bill has still not been signed into law - and without that, publicly funded IVF will not take place.

The Department of Health spokesperson says that it is intended that, in line with available resources, [the] model of care for infertility will be rolled out on a phased basis over the course of the coming years. When pushed for a more specific timeframe, the spokesperson said it is not possible at this juncture to give a definitive timeline.

Rowan and Gallagher arent holding their breath. Weve been promised this Government money for years but its just not coming, Rowan says. Every time you hear about it, you think: Oh maybe that will be through soon. But it seems to be taking years. You cant rely on it, you cant put your hope in it. Gallagher fears that any change will come too late for her: It sounds mad because Im only 32, but every year that Im older, our chances are lower.

Prof Wingfield says Ireland absolutely lags behind other developed countries when it comes to the provision of fertility treatment. The cost of fertility drugs prescribed by a consultant are covered by the Drugs Payment Scheme or a Medical Card and private patients can claim tax relief on the costs of fertility treatment but even so, Irish patients receive significantly less support than those in the UK, Germany, Turkey and most European nations. When asked why that is, she says the answer is complicated. In the past, it would have been because it was a difficult subject to discuss from a religious and moral point of view, but thats no longer the case.

However, when you remove any religious concerns from the discussion of fertility treatment, there remains two very powerful taboos: money and womens reproductive systems.

Because, over the years, its only been available privately not just in Ireland but in most parts of the world and the treatment is expensive. There was a perception that it was a luxury, something that only rich people can afford, Prof Wingfield says.

Rowan says that he and Gallagher have encountered an attitude that suggests fertility treatment is somehow extravagant: We have no choice but to do IVF if we want to have a child but sometimes it feels like people dont understand that. Its nearly treated as though Amy is going in for a boob job. People think its a luxury as opposed to a necessity.

A cycle of IVF usually costs between 6,000 and 10,000 depending on which treatment is required and which clinic you are using. There is not always evidence to support expensive add-ons, such as endometrial scratching and assisted hatching, but if you are already spending huge sums of money, it can seem churlish not to attempt to boost your chances by opting in. Treatment can be accessed at a cheaper cost abroad (most Irish patients go to the Czech Republic or Spain) but flights and accommodation will add up and being hundreds of miles from your doctor if something goes wrong is stressful and potentially dangerous.

Generally, only the most expensive private health insurance packages cover infertility treatment and even then, they do not cover the entire cost. The most comprehensive packages at Irish Life and VHI cover up to 2,000 towards a cycle of IVF, which can be accessed only twice per lifetime.

The vast expense can make patients feel that their clinics are rapacious. You have to pay 160 for a blood test to tell you that youre not pregnant. Its horrendous. It can feel like its just about money to them. says Gallagher. Prof Wingfield, however, makes the point that it is a very expensive treatment because its very labour intensive.

For one couple to do IVF, she says, youll have several nurses involved, one or two doctors and several scientists. Then youll have all the administrative staff because record-keeping is so critical. It is a very expensive treatment to provide. The Merrion Clinic is run as a not-for-profit organisation and has charitable status but costs there are not significantly lower than at the private clinics, which are run for profit.

Infertility often has an impact on mental health a study in the United States found that women with infertility felt as anxious or depressed as those diagnosed with cancer, hypertension, or who were recovering from a heart attack and stress about money adds to feelings of anxiety and helplessness.

Louise Hazlett (37) has private health insurance that has covered the surgeries and treatments she needed to treat her endometriosis, but it does not extend to fertility treatment, which she needs as a direct result of the disorder. Over the last four years, she and her husband, Kevin, have had five cycles of IVF. In 2017, she discovered she was pregnant with twins but she went into labour at 22 weeks and her sons died shortly after birth. Since then, she has had three more cycles of IVF.

She explains that they got a loan from the credit union for 20,000 and that went fairly rapidly.

We had to get another loan last year, she says. And we just save. Any spare money goes to fertility. We both work but its not easy. But I feel lucky that we are in a position to save and to pay back loans. Not all couples have that.

People assume that once you get married or reach a certain age that youre going to have kids. They assume its going to be easy. And people say things like, Oh still no sign? And at this stage, I just say, Well, Ive done five cycles of IVF. We hope the sixth one is going to be our lucky one. That shuts people up.

Prof Wingfield says: Most people grow up thinking that they will be able to have children and unless they run into problems, they dont realise that it is such a big issue. People who have not experienced infertility according to the HSE, 85 per cent of people conceive within one year will perhaps struggle to realise just how distressing and expensive the process can be.

Its like an obsession, Doyle says. You see all the people around you getting pregnant and having kids. I had to become distant for the sake of my own mental health I couldnt go to baby showers. People can say that they understand but unless you go through it yourself, you dont, you cant really.

This isolation can be compounded by silence around the subject. People who cant get pregnant sometimes feel that there is something wrong with them and it affects peoples self-esteem, says Prof Wingfield. So its hard to be vocal about it and people can be very private about it. Often peoples friends or family dont even know about it. That is changing and people are becoming more open about it and with that will come the realisation that it is a medical issue.

The people interviewed for this piece said they were keen to speak openly because they believe that raising awareness is vital. Gallagher says she didnt tell her employer during her first cycle because she felt there was a stigma and a lack of compassion: People ask Is it you or him? and How much is it? Those are the two questions I get asked all the time. When going through her second cycle, she was open about it in her workplace but felt like they didnt understand.

It was like: Youre not sick, why do you need time off?

Hazlett hopes publicly-funded infertility treatment will help to improve awareness of infertility and its causes and treatments.

There will be huge challenges to creating a functional and fair State-sponsored system of providing fertility treatment. It will be necessary to decide who is eligible for free fertility treatment and to establish criteria and cut-offs. In the UK, for example, gay women who are in a relationship can access free IVF with a sperm donor but single women are ineligible. The financial, legal and logistical concerns relating to the implementation of the Governments planned three stages will be complex, but if it is achieved it will be a huge step forward for our health system. Prof Wingfield laments the existing system: As a doctor, it is unacceptable to me that medical healthcare should be preferentially available to those in our society who can find the money to pay for it and not available to all.

Doyles daughter Sadie is just about to turn three. When she was 10 months old, Doyle and her partner David Smith could finally move into their own home after years of spending almost everything they earned on fertility treatment. They consider themselves the lucky ones and wish more people could get to experience their joy.

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Infertility treatment: When will free IVF be introduced in Ireland? - The Irish Times

Genetics

Fionas genetics are hugely valuable in species rebound – WLWT Cincinnati

January 22, 2021 medical

Fiona the hippopotamus could play a major role in her species' rebound. The world-famous hippo, who turns 4 this week at the Cincinnati Zoo, has genetics that are pretty valuable, her zookeepers said. She could play a critical role in bringing back a threatened species. Hippos are listed as a vulnerable, meaning they face a high risk of extinction in the wild. Officially, threatened species are those listed as critically endangered, endangered or vulnerable. Hippos are listed as vulnerable due to widespread poaching for meat and ivory, as well as human encroachment. It is the eventual goal to have Fiona breed in an effort to increase her species' numbers, but the timeline on when she will be able to breed remains murky.We anticipate that she will not be sexually mature until about 5 or 6 years old maybe even later than that because Fiona was a preemie, said Wendy Rice, head keeper of Africa Department at Cincinnati Zoo.Fiona was thrust into the spotlight due to her remarkable survival story. Born six weeks premature at the Cincinnati Zoo on Jan. 24, 2017, Fiona weighed only 29 pounds at birth 25 pounds less than the lowest recorded birth weight for her species. But she has rebounded from near-death, now weighing a whopping 1,600 pounds, consistent with a normal hippo her age. Fiona has a long way to go until shes considered full grown. But shes on track and making gains every day, Rice said.Already, Cincinnati's once-baby hippo has reached a certain level of maturity. And, when she's ready, Fiona will likely attempt to breed.Her fate and her love interest will likely be determined by the Hippo Species Survival Plan, a cooperation of all zoos across the United States that house hippos and breed them. The group shares information about captive populations in order to maintain genetic diversity.With Fiona being Henrys only living offspring, her genetics are fairly valuable in that theyre not well represented in the population that we have," Rice said. "Its very likely that she will get a recommendation to breed someday.So what happens then? It's highly unlikely that Fiona would move away from Cincinnati, Rice said. Instead, expect a male suitor to arrive in the Queen City.If and when she gets a recommendation for a breeding partner, theres a really good chance that the boy would have to come to Cincinnati. We do not want to have our princess leave Cincinnati, and the whole city would probably riot if she moved away.But we're still talking at least a year -- probably more -- down the road. In the meantime, Fiona will focus on growing. Right now, Rice said Fiona is probably the human equivalent of a pre-teen girl. She's growing out of her sassy phase and becoming more and more independent of her mother. In the past, wherever Bibi was, thats where Fiona was. Just this past year, shes gotten a little bit braver and bolder. Shes also starting to read boundaries a little bit better with mom. She was pushing the envelope, trying to see what she could get away with. But shes kind of settled down a bit and matured, and she can now read mama really well, Rice said. Even as the hippo matures, Rice said her personality is here to stay.Shes still full of personality and shell still come out here and put a show on for her guests," Rice said." Shell come right up to the glass and make eye contact with people. She understands that theyre here for her and that shes kind of a big deal. I think she appreciates her fandom and tries to give them the best experience possible.

Fiona the hippopotamus could play a major role in her species' rebound.

The world-famous hippo, who turns 4 this week at the Cincinnati Zoo, has genetics that are pretty valuable, her zookeepers said. She could play a critical role in bringing back a threatened species.

Hippos are listed as a vulnerable, meaning they face a high risk of extinction in the wild. Officially, threatened species are those listed as critically endangered, endangered or vulnerable. Hippos are listed as vulnerable due to widespread poaching for meat and ivory, as well as human encroachment.

It is the eventual goal to have Fiona breed in an effort to increase her species' numbers, but the timeline on when she will be able to breed remains murky.

We anticipate that she will not be sexually mature until about 5 or 6 years old maybe even later than that because Fiona was a preemie, said Wendy Rice, head keeper of Africa Department at Cincinnati Zoo.

Fiona was thrust into the spotlight due to her remarkable survival story. Born six weeks premature at the Cincinnati Zoo on Jan. 24, 2017, Fiona weighed only 29 pounds at birth 25 pounds less than the lowest recorded birth weight for her species.

But she has rebounded from near-death, now weighing a whopping 1,600 pounds, consistent with a normal hippo her age.

Fiona has a long way to go until shes considered full grown. But shes on track and making gains every day, Rice said.

Already, Cincinnati's once-baby hippo has reached a certain level of maturity. And, when she's ready, Fiona will likely attempt to breed.

Her fate and her love interest will likely be determined by the Hippo Species Survival Plan, a cooperation of all zoos across the United States that house hippos and breed them. The group shares information about captive populations in order to maintain genetic diversity.

With Fiona being Henrys only living offspring, her genetics are fairly valuable in that theyre not well represented in the population that we have," Rice said. "Its very likely that she will get a recommendation to breed someday.

So what happens then? It's highly unlikely that Fiona would move away from Cincinnati, Rice said. Instead, expect a male suitor to arrive in the Queen City.

If and when she gets a recommendation for a breeding partner, theres a really good chance that the boy would have to come to Cincinnati. We do not want to have our princess leave Cincinnati, and the whole city would probably riot if she moved away.

But we're still talking at least a year -- probably more -- down the road. In the meantime, Fiona will focus on growing.

Right now, Rice said Fiona is probably the human equivalent of a pre-teen girl. She's growing out of her sassy phase and becoming more and more independent of her mother.

In the past, wherever Bibi was, thats where Fiona was. Just this past year, shes gotten a little bit braver and bolder. Shes also starting to read boundaries a little bit better with mom. She was pushing the envelope, trying to see what she could get away with. But shes kind of settled down a bit and matured, and she can now read mama really well, Rice said.

Even as the hippo matures, Rice said her personality is here to stay.

Shes still full of personality and shell still come out here and put a show on for her guests," Rice said." Shell come right up to the glass and make eye contact with people. She understands that theyre here for her and that shes kind of a big deal. I think she appreciates her fandom and tries to give them the best experience possible.

Originally posted here:
Fionas genetics are hugely valuable in species rebound - WLWT Cincinnati

Genetics

Sanford genetics group shares benefits of custom kids’ care – Sanford Health News

January 22, 2021 medical

Pharmacogenetics, or precision medicine, is still new to many pediatric providers despite its documented benefits, according to an article the Sanford Childrens Genomic Medicine Consortium published recently in The Pharmacogenomics Journal.

Pharmacogenetics uses a persons DNA to help providers choose the best medicine and dosage of medicine. And there are plenty of opportunities to use genetic traits in pediatrics, the group wrote.

Theres evidence that pharmacogenetics benefit pediatric oncology, pain management, organ transplantation, and immunosuppression, according to the journal article. Additionally, advances in technology have made it easier to study complete genomes, and providers can use that information to improve health care for children.

Ten hospitals have signed on to the consortium to rapidly integrate genetics and genomics into primary and specialty pediatric care.

Above all, the mission of the consortium is to efficiently manage resources in genetics and genomics, perform cutting-edge research and education and bring genomic medicine into pediatric practice. This will help set the standard for precision medicine in childrens health care.

The 10 member hospitals are:

A previous innovation project funded by the consortium was a study of the outcomes of rapid whole genomic sequencing in critically ill newborn infants. Another previous study evaluated the routine use of an extensive, pediatric-focused, next generation sequencing panel in the diagnosis of childhood cancers.

Posted In Children's, Company News, Genetics

Genetics

Spatial patterns and conservation of genetic and phylogenetic diversity of wildlife in China – Science Advances

January 22, 2021 medical

Abstract

Genetic diversity and phylogenetic diversity reflect the evolutionary potential and history of species, respectively. However, the levels and spatial patterns of genetic and phylogenetic diversity of wildlife at the regional scale have largely remained unclear. Here, we performed meta-analyses of genetic diversity in Chinese terrestrial vertebrates based on three genetic markers and investigated their phylogenetic diversity based on a dated phylogenetic tree of 2461 species. We detected strong positive spatial correlations among mitochondrial DNA-based genetic diversity, phylogenetic diversity, and species richness. Moreover, the terrestrial vertebrates harbored higher genetic and phylogenetic diversity in South China and Southwest China than in other regions. Last, climatic factors (precipitation and temperature) had significant positive effects while altitude and human population density had significant negative impacts on levels of mitochondrial DNA-based genetic diversity in most cases. Our findings will help guide national-level genetic diversity conservation plans and a post-2020 biodiversity conservation framework.

Biodiversity loss and conservation are among the most concerning global issues. The Convention on Biological Diversity (CBD) was established to develop national strategies for the conservation and sustainable use of biological diversity. An endangerment status assessment of worldwide vertebrates showed that approximately 20% of vertebrates have become threatened (1). In China, the situation is even worse: 21.4% of vertebrates are threatened, including 43.1% of amphibians, 29.7% of reptiles, 26.4% of mammals, 20.4% of fishes, and 10.6% of birds (2). Thus, it is urgent to protect biodiversity regionally and globally. As the most fundamental dimension of biodiversity, genetic diversity is a key basis for species survival and ecosystem functions (3). Higher genetic diversity means higher evolutionary potential and a greater ability to respond to environmental changes (4). An increasing number of studies have shown that genetic factors play a critical role in species endangerment and extinction (57). Thus, assessment and protection of genetic diversity are becoming essential and high-priority strategies for biodiversity conservation (4). However, under the current CBD framework, the goal proposed for genetic diversity focuses mainly on the conservation of farmed and domestic animals and cultivated plants and neglects that of wild animals and plants, which would overlook genetic erosion and harm the evolutionary potential of wildlife (8). Therefore, to better conserve the genetic diversity of wildlife, it is necessary to assess genetic diversity at regional and global scales for use in the scientific designs of natural protected areas and biodiversity conservation strategies. Miraldo et al. (9) presented the first global distribution of genetic diversity for mammals and amphibians using mitochondrial cytochrome b (Cytb) and cytochrome oxidase subunit I (Co1) gene sequences. However, the grid cell size (~150,000 km2) that they used was so large that it was difficult to determine the national- or regional-level pattern of genetic diversity in detail, including in China.

Phylogenetic diversity is the sum of phylogenetic branch lengths for all of the species in an area (10). Phylogenetic diversity measures the time scale of species evolution and reflects the evolutionary history of species (11), which contributes to the selection of biodiversity conservation priority areas (1214). Higher phylogenetic diversity excluding the effect of taxonomic richness indicates a higher proportion of distantly related and anciently diverged taxa (11, 15). Previous studies have shown that regions with higher phylogenetic diversity may not necessarily have higher species diversity, which would result in neglecting the conservation of the regions (11, 16). In this case, the conservation of older evolutionary lineages might be neglected. Thus, monitoring the level and spatial distribution of phylogenetic diversity is also important for effective conservation of biodiversity.

China is one of the countries with the richest biodiversity in the world, harboring more than 3000 terrestrial vertebrates (2). In recent years, with the development of molecular genetics, genetic diversity of many species has been assessed and numerous DNA sequences have been accumulated. In this study, we focus on the patterns of genetic and phylogenetic diversity in Chinese terrestrial vertebrates, using meta-analyses of a large published dataset and a robust dated phylogenetic tree as well as species distribution. We aim to (i) reveal whether positive spatial correlation existed among species richness, genetic diversity, and phylogenetic diversity; (ii) identify hotspot regions of high genetic diversity and high phylogenetic diversity; and (iii) explore the influences of abiotic (precipitation, temperature, and altitude) and biotic (human population) factors on the levels of genetic and phylogenetic diversity. We found that, on the whole, species richness predicted phylogenetic diversity and mitochondrial DNA-based genetic diversity in a positive direction, and higher phylogenetic diversity predicted higher genetic diversity. We identified that the terrestrial vertebrates in South China and Southwest China harbored higher genetic and phylogenetic diversity than in other regions, and central South China was identified as an evolutionary museum, while the Hengduan Mountains was identified as an evolutionary cradle. We also revealed that both mean annual precipitation and temperature had significant positive effects, while altitude and human population density had significant negative impacts on levels of mitochondrial DNA-based genetic diversity in most cases. Our findings provide insights into the spatial patterns and influencing factors of genetic and phylogenetic diversity at a regional scale.

We surveyed the population-level genetic diversity data of Chinese terrestrial vertebrates (mammals, birds, reptiles, and amphibians) based on three molecular markers (mitochondrial Cytb gene sequence, mitochondrial D-loop sequence, and nuclear microsatellites). A total of 287 terrestrial vertebrate species (103 mammals, 59 birds, 31 reptiles, and 94 amphibians) were assessed for population-level genetic diversity with at least one molecular marker, accounting for 9.3% of the 3075 terrestrial vertebrates distributed in China (figs. S1 to S4 and tables S1 to S9). Two unbiased genetic diversity indices, nucleotide diversity () for the Cytb and D-loop sequences and expected heterozygosity (HE) for microsatellite, were used as measures of population-level genetic diversity. In this study, the Cytb-, D-loop, and microsatellite-based genetic diversity measures were analyzed separately (tables S1 to S9). Furthermore, the species-level genetic diversity for three genetic markers was obtained by averaging the population-level genetic diversity values (tables S10 to S12).

The species-level phylogenetic diversity of Chinese terrestrial vertebrates was surveyed on the basis of the coding sequences of five mitochondrial genes (Cytb, Co1, Nd1, 12S rRNA, and 16S rRNA). A total of 2461 terrestrial vertebrates were assessed for phylogenetic diversity with at least one available mitochondrial gene sequence, accounting for 80% of the Chinese terrestrial vertebrates (figs. S5 to S7 and table S13). On the basis of a constructed maximum likelihood phylogenetic tree and 391 available divergence times from the TimeTree database (table S14), we estimated the divergence times of these vertebrates. The results showed that the amphibians first diverged from the fishes and then the reptiles evolved from the amphibians. Both the mammals and birds evolved from the reptiles, with the mammals diverging first. These results are consistent with the general conclusion about the divergence order of the terrestrial groups (17). In this study, we used divergence time as the measure of phylogenetic diversity for further analysis.

We first divided the map of China into 0.5 0.5 (~50 km by 55 km) grid cells and then calculated the species richness, genetic diversity, and phylogenetic diversity within each grid cell. The spatial correlation tests showed that the genetic diversity measures based on mitochondrial Cytb and D-loop sequences were significantly correlated [correlation coefficient (r) = 0.385, P = 0.012]. However, no significant correlation was observed for Cytb versus microsatellites (r = 0.128, P = 0.475) and for D-loop versus microsatellites (r = 0.084, P = 0.463) (fig. S8 and table S15). The inconsistencies in spatial correlations among the three genetic markers were most likely due to different measure rationales (nucleotide diversity versus expected heterozygosity) and evolutionary rates (slowly versus rapidly evolving). The differences in correlation among the different markers were similar to that of Miraldo et al. (9).

The tests for spatial correlations between genetic diversity and species richness revealed a significant positive correlation for Cytb genetic diversity (r = 0.728, P = 0.008), and a marginally significant correlation for D-loop genetic diversity (r = 0.320, P = 0.072) (Fig. 1, A and B). These results were consistent with those of global terrestrial mammals (18) and global marine and freshwater fishes (19). However, a nonsignificant correlation for microsatellite genetic diversity (r = 0.138, P = 0.499) was detected (Fig. 1C and table S15), which was similar to AFLP marker-based genetic diversity assessment of alpine plant communities (20). The differences in correlation showed that the widely discussed correlation relationship between genetic and species diversity was genetic marker dependent.

(A to C) Correlation tests between species richness (SR) and Cytb-, D-loop, and microsatellite-based genetic diversity (GD). (D) Correlation test between SR and phylogenetic diversity (PD). (E to G) Correlation tests between PD and Cytb-, D-loop, and microsatellite-based GD.

The tests for spatial correlations between genetic diversity and phylogenetic diversity showed a significant positive correlation for Cytb (r = 0.722, P = 0.013) and a marginally significant positive correlation for D-loop (r = 0.306, P = 0.089) (Fig. 1, E and F). The results were similar to those of global terrestrial mammals (18). However, the correlation was not significant for microsatellites (r = 0.123, P = 0.566) (Fig. 1G and table S15). In addition, we selected a set of abundant terrestrial vertebrate species with a threatened status rank of LC (Least-Concern) (table S16) and tested the spatial correlations between genetic and phylogenetic diversity. The results were similar to those for all the terrestrial vertebrates (table S17).

A significant positive correlation was detected between phylogenetic diversity and species richness (r = 0.99, P < 0.001) (Fig. 1D and table S15), implying that the regions with high species richness often had high phylogenetic diversity. The significant positive correlation pattern between phylogenetic diversity and species richness may be common, as shown in different large-scale analyses focusing on birds, mammals, and angiosperms (16, 18, 21).

It is generally accepted that Chinas zoogeographical regionalization is divided into the Palaearctic and Oriental realms, including seven zoogeographical regions (22, 23). The Palaearctic realm includes the Northeast China, North China, Inner Mongolia-Xinjiang, and Qinghai-Tibet Plateau regions, while the Oriental realm consists of the Southwest China, Central China, and South China regions. We mapped the genetic diversity data onto the zoogeographical region map of China using a grid size of 0.5 0.5. Overall, the terrestrial vertebrates distributed in the Oriental realm had higher genetic diversity than those in the Palaearctic realm for all three markers (Fig. 2, A to C; fig. S9; and table S18). In the case of zoogeographical regions, the vertebrates in South China harbored the highest genetic diversity for Cytb and microsatellites, suggesting a hotspot region of genetic diversity, whereas those in North China had the lowest genetic diversity for D-loop and microsatellites (table S18). In addition, the Southwest China and west Central China harbored relatively high genetic diversity. The spatial pattern of species richness across the Palaearctic and Oriental realms was similar to that of genetic diversity (Fig. 2D). However, within the zoogeographical regions, the spatial patterns of species richness were somewhat different from those of genetic diversity. The South China region had the highest species richness, whereas the Qinghai-Tibet Plateau and Inner Mongolia-Xinjiang regions harbored the lowest species richness (Fig. 2D). These results suggest that regions with low species richness do not necessarily have low genetic diversity, such as the Qinghai-Tibet Plateau, which should be given more conservation attention. To determine the possible effects of different sample sizes of the grid cells, we examined the frequency distribution of the proportion of species with surveyed genetic diversity data in the grid cells based on the classification of seven zoogeographical regions and found similar frequency distributions on the whole across the seven regions (figs. S10 to S12).

Northeast China (NE), North China (NC), Inner Mongolia-Xinjiang (IX), Qinghai-Tibet Plateau (QT), Southwest China (SW), Central China (CC), and South China (SC). The red line indicates the boundary between the Palaearctic and Oriental realms. (A and B) Spatial patterns of Cytb- and D-loopbased GDs. measured by nucleotide diversity. (C) Spatial pattern of microsatellite-based GD measured by expected heterozygosity. (D) Spatial pattern of SR measured by number of species.

The province-level distributions of genetic diversity based on the three markers demonstrated similar patterns on the whole (figs. S13 and S14). The terrestrial vertebrates distributed in Yunnan, Guangxi, Sichuan, and Guizhou provinces harbored the highest genetic diversity. In contrast, the terrestrial vertebrates distributed in Shanxi, Shandong, Hebei, Liaoning, Jilin, Heilongjiang, and part of Xinjiang had lower genetic diversity. The terrestrial vertebrates in Qinghai and Tibet had intermediate genetic diversity. These results could help guide province-level conservation plans for genetic diversity.

The terrestrial vertebrates in the Oriental realm had significantly higher phylogenetic diversity (PD = 10,390.25 2029.43) than those in the Palaearctic realm (PD = 4942.60 1402.09) (Fig. 3, A and B). The terrestrial vertebrates in South China harbored the highest phylogenetic diversity (PD = 12,327.46 2111.27), and those in Central China and Southwest China had the second highest phylogenetic diversity. The terrestrial vertebrates on the Qinghai-Tibet Plateau had the lowest phylogenetic diversity (PD = 3936.66 1162.35) (Fig. 3B and table S18). The province-level distribution of phylogenetic diversity showed a clear pattern, in which the terrestrial vertebrates in south China had notably higher phylogenetic diversity than those in north China (fig. S15). Specifically, the vertebrates in Yunnan and Guangxi provinces had the highest phylogenetic diversity, and those in Tibet, Xinjiang, and Qinghai had the lowest phylogenetic diversity (fig. S15). These results could help guide province-level conservation plans for phylogenetic diversity.

(A) A dated phylogenetic tree of Chinese terrestrial vertebrates based on five mitochondrial genes (Cytb, Co1, Nd1, 12S rRNA, and 16S rRNA). Ma, million years. (B) Spatial pattern of PD measured by species divergence time. The red line indicates the boundary between the Palaearctic and Oriental realms. (C) Areas with significantly higher or lower PD after controlling for the confounding effect of SR. The red line indicates the boundary between the Palaearctic and Oriental realms.

As shown by the correlation analysis above, the phylogenetic diversity pattern was highly correlated with the species richness pattern (Fig. 1D). To control for the confounding effect of species richness, we detected areas with significantly higher or lower phylogenetic diversity than expected using a randomization method. The result showed that significantly higher phylogenetic diversity occurred in the central South China region, mainly including Hainan and Guangxi provinces, suggesting that these areas harbored many older terrestrial vertebrate lineages, serving as an evolutionary museum (Fig. 3C and fig. S16) (9). This result is similar to that for the phylogenetic diversity of genus-level angiosperms in China, in which the top 5% highest phylogenetic diversity and standard effective size of phylogenetic diversity were mainly located in Guangdong, Guangxi, Guizhou, and Hainan provinces (15). These results suggested that the above areas are phylogenetic diversity hotspots not only for terrestrial vertebrates but also for angiosperms in China, which deserve more conservation efforts. In contrast, significantly lower phylogenetic diversity occurred in the Southwest China region, i.e., the Hengduan Mountains, suggesting that these areas were the centers of recent speciation events and thus contained many younger lineages, serving as an evolutionary cradle (Fig. 3C and fig. S16) (15, 24). This divergence pattern is similar to that of a study on global terrestrial birds (16).

The above correlation results showed that the mitochondrial DNA-based genetic diversity was strongly correlated with species richness. Therefore, to reveal the effects of abiotic and biotic factors on genetic diversity, we performed the semi-part spatially explicit generalized linear mixed modeling (spaGLMM) analysis by regressing genetic diversity against species richness and then using the residuals of models to evaluate the effects of abiotic (mean annual precipitation, mean annual temperature, and altitude) and biotic (human population density) factors. The results showed that most of the genetic diversity measures were well predicted by these factors (Table 1). In detail, mean annual precipitation had a significant positive effect on Cytb-based genetic diversity; mean annual temperature had a significant positive effect on D-loopbased genetic diversity; and altitude and human population density had significant negative impacts on Cytb- and D-loopbased genetic diversity (Table 1). In addition, the spaGLMM analysis with the species richness included as an explanatory variable gave similar results to the semi-part spaGLMM analysis (table S19). Because the relationships between most of the factors and microsatellite-based genetic diversity were different from theoretically expected, here we did not discuss microsatellite-related results.

MAP, mean annual precipitation; MAT, mean annual temperature; ALT, mean altitude; HPD, human population density.

Because the phylogenetic diversity was very strongly correlated with species richness, we also performed the semi-part spaGLMM analysis for phylogenetic diversity. The results showed that the above abiotic and biotic factors had no significant impacts on phylogenetic diversity (Table 1), suggesting that the species richness had a much higher effect on phylogenetic diversity compared to other factors. To test this, we performed the spaGLMM analysis with species richness as an independent variable. The results showed that the importance of species richness was far more than those of other factors, indicating that phylogenetic diversity was mainly affected by species richness (table S19).

This is the first study to assess the correlation between genetic diversity and phylogenetic diversity for all the terrestrial vertebrate groups at a large spatial scale. The findings revealed a significant correlation between genetic and phylogenetic diversity for Cytb-based genetic diversity measure and a marginally significant correlation for D-loopbased measure at a grid cell scale, demonstrating the important role of phylogenetic diversity in predicting level of genetic diversity. In addition, we also found a significant positive correlation between genetic diversity and species richness for Cytb-based genetic diversity measure and a marginally significant correlation for D-loopbased measure. However, no significant correlations were detected between genetic diversity and phylogenetic diversity (or species richness) for microsatellite-based measure, suggesting that these correlations are genetic marker dependent.

Our study is also the first region-level survey and assessment of the genetic and phylogenetic diversity of Chinese terrestrial vertebrates that demonstrated the spatial distribution pattern of diversity and identified the regions of high and low genetic/phylogenetic diversity. The spatial patterns showed that the terrestrial vertebrates in South China and Southwest China harbored not only higher genetic diversity but also higher phylogenetic diversity, highlighting the high conservation priority for these hotspot regions. We also identified key areas with significantly higher or lower phylogenetic diversity after controlling for the effects of species richness and discerned the evolutionary museum and cradle for Chinese terrestrial vertebrates. In particular, we found inconsistencies among the regions in terms of genetic and species diversity. Although the terrestrial vertebrates on the Qinghai-Tibet Plateau had the lowest species richness, they had intermediate genetic diversity, possibly because of less human activity and heterogeneous abiotic effects in this region. The terrestrial vertebrates in North China and Northeast China, which are exposed to more human activity and located in north further in latitude, harbored intermediate species richness but lower genetic diversity. These results were supported by the semi-part spaGLMM analyses, which revealed that abiotic (precipitation, temperature, and altitude) and biotic factors (human population) played important roles in the spatial patterns of genetic diversity.

We investigated the effects of abiotic and biotic factors driving the spatial patterns of genetic and phylogenetic diversity at a grid cell scale. On the whole, the effects of these factors on Cytb- and D-loopbased genetic diversity were consistent with ecological and evolutionary expectations. Mean annual precipitation and temperature had significant positive effects on genetic diversity, because higher precipitation and temperature most likely provide more suitable conditions for species survival, population expansion, and speciation. In contrast, altitude had significant negative impacts on genetic diversity, because higher elevation means harsher living conditions especially for terrestrial vertebrates. For biotic factor, human population density had significant negative impacts on genetic diversity, because higher density means more human activities and more possible interference with wildlife and their habitats.

Our study summarizes the findings of genetic/phylogenetic diversity studies, revealing the basic background of genetic resources in Chinese terrestrial vertebrates, which could facilitate genetic resource protection under the CBD framework and guide future genetic/phylogenetic diversity research and conservation. In addition, compared with the total number of Chinese terrestrial vertebrates, the number of species with surveyed genetic diversity data is relatively small. To better conserve genetic diversity, scientists and managers should cooperate to perform genetic diversity surveys for more species, especially those with an unclear genetic status. Furthermore, the genetic and phylogenetic diversity of freshwater and marine vertebrates should be surveyed and assessed to protect gradually decreasing aquatic genetic resources. Last, our study is the first to use nuclear microsatellite markers to assess large-scale genetic diversity pattern and explore the relationship between genetic and phylogenetic diversity. However, it is worth noting that microsatellite-based correlation and model analyses produced different results from those based on mitochondrial DNA, which cautions us to carefully interpret results from different genetic markers.

We retrieved published literatures of population-level genetic diversity studies from public academic databases. For the English literature, we searched the Web of Science database (http://apps.webofknowledge.com/) using the search rule TS = (species Latin name OR species English name) AND TS = genetic diversity AND TS = population. For the Chinese literature, we searched the CNKI database (www.cnki.net), CQVIP database (www.cqvip.com), and Chinese Science Citation Database (http://sciencechina.cn) using the search rule species Latin name AND genetic diversity. Then, to search the literature as comprehensively as possible, we searched only the species Latin name again for species without related references or with few related references.

We screened the retrieved literature following several steps. First, we used only the literature about wild animal studies and discarded the literature studying captive populations. Second, we focused on population-level studies based on microsatellite, mitochondrial Cytb, or D-loop markers. These three markers have been widely used in population genetics and phylogeographic studies of vertebrates. For microsatellite-based studies, we extracted the expected heterozygosity (HE) values for each population of species as the measure of microsatellite genetic diversity. HE is an unbiased measure and thus insensitive to small sample sizes (25). For mitochondrial Cytb gene and D-loop sequence-based studies, we extracted Neis nucleotide diversity () values for each population of species as the measure of Cytb or D-loop genetic diversity (26). is also unbiased and thus insensitive to small sample sizes (26). If the same population had more than one HE or from different references, we used the mean value as the genetic diversity measure of this population. Last, on the basis of population-level genetic diversity data, we estimated species-level genetic diversity by averaging the population-level genetic diversity values (9). Mean genetic diversity metric has been widely applied in large-scale studies (9, 18, 19).

In total, we compiled a dataset of 287 terrestrial vertebrates, which included 103 mammals, 59 birds, 31 reptiles, and 94 amphibians, accounting for 15.6, 4.1, 6.7, and 18.6% of the respective total numbers of species (figs. S1 and S2). Overall, the assessment proportions for genetic diversity of mammals and amphibians were higher than those of birds and reptiles, with the proportion of birds being the lowest. The number of terrestrial vertebrate species with population-level genetic diversity data based on microsatellite marker (n = 151) was higher than those based on Cytb gene (n = 142) and D-loop (n = 105), accounting for 4.9, 4.6, and 3.4% of the 3075 Chinese terrestrial vertebrates, respectively (figs. S3 and S4).

Sequences of five mitochondrial genes (Cytb, Co1, 12S rRNA, 16S rRNA, and Nd1) were used to reconstruct the phylogeny of Chinese terrestrial vertebrates. The sequences of the five mitochondrial genes were searched in GenBank with the following steps. First, the available mitochondrial reference genomes were downloaded, and the corresponding coding sequences of these genes were extracted. Then, the available coding sequences for the remaining species were directly downloaded from GenBank using the species Latin name and gene name. If more than one sequence was available for the same locus of a species, the sequence with a length similar to that of the corresponding gene was selected. Last, the short genes whose coding sequence length was <300 base pairs were discarded from the dataset. After these steps, we compiled a total of 2461 species including 573 mammals, 1170 birds, 359 reptiles, and 359 amphibians, representing 87.0, 81.0, 77.2, and 71.0% of the respective total numbers of species. Our dataset covered 46 orders, 204 families, and 847 genera. For each gene, the coding sequences of 973 species were extracted from their mitochondrial genomes, while others were directly downloaded from the GenBank database. The numbers of species with Cytb and Co1 sequences were higher than those with Nd1, 12S rRNA, and 16S rRNA sequences (fig. S7).

The coding sequences of each gene were concatenated and aligned by MAFFT (27) with default parameters, and the poorly aligned sites at the beginning and the end were trimmed. Then, the aligned sequences of these five genes were imported into SequenceMatrix software (28) to construct a supermatrix with the gaps treated as missing data. A phylogenetic analysis was performed on this supermatrix using the maximum likelihood method implemented in RAxML 8.2.12 (29) with the ASC_GTRGAMMA model and 1000 bootstrap replicates. Each gene was treated as a partition, and the zebrafish was used as outgroup. On the basis of this phylogenetic tree, we used the penalized likelihood method implemented in treePL (30) to date the divergence times of these vertebrates. A total of 391 available divergence times from TimeTree (31) were selected as calibration points for the dating analysis (table S14). The prime option and through analysis were implemented with optimal parameters.

On the basis of our dated phylogenetic tree and species distribution data, we calculated Faiths phylogenetic diversity of Chinese terrestrial vertebrates using the picante package (32) in R, as widely used in phylogenetic diversity studies (33). In this study, we used divergence time as the measure of phylogenetic diversity of each species.

The distributional ranges of terrestrial vertebrate species (including mammals, amphibians, reptiles, and birds) were derived from the IUCN spatial database (www.iucnredlist.org/resources/spatial-data-download). The range of each species was originally in a vectorized shapefile format and was rasterized into a grid system with a 0.5 0.5 resolution (~50 km by 55 km). We double-checked the rasterized maps to confirm that they matched the original vectorized distributional range maps. The resultant rasterized map of each species was always conservative relative to the original vectorized map, as many margins of species fragmented distributions might not have been recorded as the presence of the species in our 0.5 0.5 grid cells. This is because the areas of these margins were too small in the corresponding grid cells. The map of China used in this study was from Resource and Environment Science and Data Center (www.resdc.cn/data.aspx?DATAID=200). The Latin name of each species was checked to avoid potential synonyms. In total, our gridded distribution database included the occurrence records for 1941 species. After matching with the genetic and phylogenetic data, the final distribution dataset used for the diversity assessment included a total of 180 species for the genetic diversity analysis and 1685 species for the phylogenetic diversity analysis.

Climate data with a 2.5 spatial resolution were collected from the WorldClim database (https://worldclim.org/). We used the two most important climatic variables, mean annual temperature and mean annual precipitation that were calculated for the climate data from 1970 to 2000, as predictors of spatial patterns of genetic and phylogenetic diversity of terrestrial vertebrates in China. Human population density in 2010 in China (in persons per square kilometer) was derived from the Gridded Population of the World collection (https://sedac.ciesin.columbia.edu/data/collection/gpw-v4). Digital elevation data with a 2.5 spatial resolution in China were originally derived from the NASA Shuttle Radar Topographic Mission and downloadable from the WorldClim database. Because we mapped the genetic and phylogenetic diversity using a grid cell size of 0.5 0.5 for each variable (including altitude), we took the average of all values within each grid cell as the variables value for the grid cell.

In many cases in which biodiversity data are collected associated with spatial information (e.g., sampling location coordinates), conventional correlation tests are not valid because the assumption of total independence of samples is violated. For spatial biodiversity data, neighboring locations can present similar biodiversity features (e.g., genetic diversity or phylogenetic diversity as investigated here), which is a phenomenon known as spatial autocorrelation, resulting in nonindependent association of biodiversity information between neighboring locations. To this end, conventional correlation tests can be misleading. To cope with this issue, we used a modified t test to account for spatial autocorrelation (34, 35) when testing the spatial associations between genetic diversity, phylogenetic diversity, and species richness. The test is based on the adjustment of the sample correlation coefficient between the two spatially correlated quantities and requires the estimation of an effective sample size (degrees of freedom).

We performed spatial correlation tests between genetic diversity based on different markers, between genetic diversity and species richness, between genetic diversity and phylogenetic diversity, and between phylogenetic diversity and species richness. In addition, we selected a set of abundant terrestrial vertebrate species with a threatened status rank of LC (2) to further explore the relationship between genetic diversity and phylogenetic diversity. The set of abundant terrestrial vertebrates included 39 species for Cytb, 25 species for D-loop, and 45 species for microsatellite (table S16). We performed the correlation analyses for Cytb-, D-loop, and microsatellite-based genetic diversity separately.

We divided the map of China into 0.5 0.5 grid cells using R software. Then, we mapped the spatial distributional patterns of species richness, genetic diversity, and phylogenetic diversity based on the diversity values calculated for each grid cell. For species richness, we summed the total number of species occurring in the grid cell. For genetic diversity, we summed the genetic diversity values of each species present within the grid cell and divided the total value by the number of species surveyed in the grid cell, as used in (9). For phylogenetic diversity, we summed the divergence times of all species surveyed within the grid cell following the definition of Faiths phylogenetic diversity (10, 15).

To detect grid cells with significantly higher or lower phylogenetic diversity than expected controlling for the confounding effect of species richness, we used a randomization protocol (36). In detail, we first computed the phylogenetic diversity for each grid cell and divided this value by the species richness found in the cell. Then, we used a random swapping algorithm to randomize the species-site binary matrix while fixing the species richness of each grid cell and the range size of each species. The randomization procedure was repeated 1000 times, and the following effective size of phylogenetic diversity-species richness was computedZPD=ObsPDMean(RandPD)SD(RandPD)where ObsPD is the observed phylogenetic diversity-species richness ratio for each grid cell. RandPD represents the random phylogenetic diversity-species richness ratio calculated for each grid cell derived from the randomized species-site matrix. Mean(RandPD) and SD(RandPD) denote the mean and standard deviation of the 1000 random phylogenetic diversity-species richness ratio values, respectively. ZPD approximately followed a standard normal distribution; as such, at the significance level of 0.05, a grid cell was identified as having statistically significantly high phylogenetic diversity given the associated species richness if ZPD > 1.96. Conversely, a grid cell was identified as having statistically significantly low phylogenetic diversity given the associated species richness if ZPD < 1.96.

Species richness might have strong associations with genetic and phylogenetic diversity (37, 38). To explore the effects of factors affecting the spatial patterns of genetic and phylogenetic diversity of Chinese terrestrial vertebrates, we performed a semi-part spaGLMM implemented in the spaMM package (39) in the R environment (40), in which the influence of species richness on genetic or phylogenetic diversity was explicitly partialled out. To do so, we firstly constructed a spaGLMM model in which species richness is the only explanatory variable of genetic or phylogenetic diversity and then we used the residuals of this model for evaluating the impacts of other abiotic and biotic factors on genetic or phylogenetic diversity. In addition, to assess the effect of species richness on genetic and phylogenetic diversity, we also performed the spaGLMM analyses with the species richness as an explanatory variable as well as other factors.

For all the above spaGLMM analyses, a correlation matrix according to the Matrn correlation function was assumed and fitted on the basis of the longitude and latitude information of the center point of each grid cell when fitting the mixed model. The Matrn correlation function, containing a scale parameter and a smoothness parameter, is widely applied to model spatial correlation by including exponential and squared exponential models as special cases (41, 42). For the modeling results of semi-part spaMM analyses, when the confidence interval of the estimated coefficient for an explanatory variable was significantly deviated from zero, the variable was considered to have a significant effect on levels of genetic or phylogenetic diversity.

R. Frankham, J. D. Ballou, D. A. Briscoe, Introduction to Conservation Genetics (Cambridge Univ. Press, 2002).

D. J. Futuyma, Evolution (Oxford Univ. Press, 2013).

R. Z. Zhang, China Animal Geography (Science Press, 1999).

M. L. Stein, Interpolation of Spatial Data: Some Theory for Kriging (Springer Press, 2012).

Acknowledgments: We thank Jiekun He for providing the map of zoogeographical regionalization. Funding: This study was supported by the National Natural Science Foundation of China (31821001); the Strategic Priority Research Program of Chinese Academy of Sciences (XDB31000000); the Biodiversity Survey, Monitoring and Assessment Project of Ministry of Ecology and Environment of China (2019HB2096001006); the National Natural Science Foundation of China (31672319); the Youth Innovation Promotion Association, CAS (2016082); and the Special Research Assistant Program of CAS. Author contributions: F.W. conceived and supervised the project. Y.H., H.F., J.C., X.Z., H.W., B.Z., L.Y., X.H., X.S., T.P., W.W., and J.L. performed the data collection. Y.H., H.F., Y.C., J.C., M.W., W.Z., L.Y., and H.H. performed the data analysis. Y.H., H.F., and Y.C. wrote the manuscript with input from F.W. Competing interests: The authors declare that they have no competing interests. Data and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. Additional data related to this paper may be requested from the authors.

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Spatial patterns and conservation of genetic and phylogenetic diversity of wildlife in China - Science Advances

Genetics

Midlothian bug genetics innovator launches insect breeding facility and creates jobs – The Scotsman

January 22, 2021 medical

BusinessA Midlothian-based agri-food biotech business that specialises in bugs has launched a new insect breeding facility and created several jobs.

Friday, 22nd January 2021, 12:30 pm

Founded by entrepreneur and PhD graduate Thomas Farrugia, Beta Bugs develops and distributes insect breeds as a source of protein for animal feed. It has expanded its team from five to ten to help drive into the wider agri-food markets.

Following the completion of his PhD and his first tasting of insects on a trip to Antwerp, Farrugia joined Deep Science Ventures where he began researching how environmentally friendly and versatile insect-based products could be and how they could provide a different source of protein which could change the feeding habits of livestock and fish farms.

He launched Beta Bugs as an insect genetics company in 2017, with the goal of creating high-performance breeds of black soldier fly to accelerate the growth of the insect farming sector.

Over the last 18 months the company based at the Easter Bush Campus has secured 133,000 of private investment alongside 1.2 million in grant funding, including 100,000 from Scottish Governments Unlocking Ambition programme and 84,000 from the Pivotal Enterprise Resilience Fund to help the company grow its operations during the coronavirus restrictions.

Support for the firm from Business Gateway Midlothian has included help with establishing the companys operations within the Science Zone in Midlothian and scaling up its breeding programme at the Easter Bush Campus, which now houses the dedicated insect breeding facility.

Farrugia said: We are delighted to be in a position to expand our team and build a dedicated insect breeding facility thanks to help from various organisations including Business Gateway Midlothian who have been instrumental in our growth since we started out.

Having our own adviser to keep us right along the way and signpost us to other available resources has been invaluable and really helped us to carve out a niche for ourselves in the UK and international genetic insect market.

Annie Watt, Business Gateway Midlothian lead, said: Beta Bugs is an innovative insect-breeding company leading the way in creating genetics for the fast growing insects-as-feed industry, which we are delighted to support.

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Midlothian bug genetics innovator launches insect breeding facility and creates jobs - The Scotsman

Genetics

Some identical twins dont have the exact same DNA – Science News for Students

January 22, 2021 medical

average: (in science) A term for the arithmetic mean, which is the sum of a group of numbers that is then divided by the size of the group.

cell: The smallest structural and functional unit of an organism. Typically too small to see with the unaided eye, it consists of a watery fluid surrounded by a membrane or wall. Depending on their size, animals are made of anywhere from thousands to trillions of cells. Mostorganisms, such as yeasts, molds, bacteria and some algae, are composed of only one cell.

develop: To emerge or to make come into being, either naturally or through human intervention, such as by manufacturing. (in biology) To grow as an organism from conception through adulthood, often undergoing changes in chemistry, size, mental maturity, size or sometimes even shape.

development: (in biology) The growth of an organism from conception through adulthood, often undergoing changes in chemistry, size and sometimes even shape.

DNA: (short for deoxyribonucleic acid) A long, double-stranded and spiral-shaped molecule inside most living cells that carries genetic instructions. It is built on a backbone of phosphorus, oxygen, and carbon atoms. In all living things, from plants and animals to microbes, these instructions tell cells which molecules to make.

egg: The unfertilized reproductive cell made by females.

embryo: The early stages of a developing organism, or animal with a backbone, consisting only one or a few cells. As an adjective, the term would be embryonic and could be used to refer to the early stages or life of a system or technology.

fraternal: Of our relating to brothers, or others with whom people develop close friendships and affection. (in genetics) The term for a type of twin birth where each baby comes from a separate fertilized egg. This is in contrast to identical twins, which result from a single fertilized egg (creating two separate but nearly identical babies).

genetic: Having to do with chromosomes, DNA and the genes contained within DNA. The field of science dealing with these biological instructions is known as genetics. People who work in this field are geneticists.

genome: The complete set of genes or genetic material in a cell or an organism. The study of this genetic inheritance housed within cells is known as genomics.

Iceland: A largely arctic nation in the North Atlantic, sitting between Greenland and the western edge of Northern Europe. Its volcanic island was settled between the late 800s and 1100 by immigrants from Norway and Celtic lands (ones governed by the Scots and Irish). It is currently home to roughly a third of a million people.

mutation: (v. mutate) Some change that occurs to a gene in an organisms DNA. Some mutations occur naturally. Others can be triggered by outside factors, such as pollution, radiation, medicines or something in the diet. A gene with this change is referred to as a mutant.

replicate: (in biology) To copy something. When viruses make new copies of themselves essentially reproducing this process is called replication.

trait: A characteristic feature of something. (in genetics) A quality or characteristic that can be inherited.

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Some identical twins dont have the exact same DNA - Science News for Students

Genetics

Maltese ALS Patients Have Different Genetic Mutations than Northern Europeans – Clinical OMICs News

January 22, 2021 medical

A study carried out by the University of Malta shows that patients with the fatal neurological condition amyotrophic lateral sclerosis have different causative mutations to patients from Northern Europe.

The DNA results caught us by surprise. The most frequently mutated amyotrophic lateral sclerosis (ALS) genes were flawless in Maltese patients, said the studys lead researcher Ruben Cauchi, Ph.D., a senior lecturer at the University.

Instead, some of the 24 patients included in the study had mutations in genes occasionally associated with ALS including ATXN2, DAO, DCTN1, and ERBB4, among others.

As reported in the European Journal of Human Genetics, three of the 24 cases were familial and 21 were sporadic, with no known family history of the disease. Of the mutations seen in the sporadic cases, 40% were in genes with a previous link to ALS, whereas 60% were not. Only one of the familial cases had a mutation in a known ALS-associated gene.

Although Malta is part of Europe it is geographically and culturally isolated island population of just over 500,000 individuals, which makes it ideal for genetic biobanking studies. The Malta Biobank was set up at the university on the island in 1989 and now contains more than 100,000 samples.

Around 4 years ago, a national ALS registry was set up on the island to collect samples and data about those diagnosed with the condition to help scientists understand the condition better and help contribute to global research studies.

ALS is a rapid neurodegenerative condition with a strong genetic component, which currently has no cure. An effective treatment has proved difficult to develop, with many clinical trials failing over the last 10-15 years. However, research continues with the hope of finding a treatment or cure.

This study, which was carried out in collaboration with the University Medical Centre Utrecht in The Netherlands, sought to discover whether Maltese ALS patients had similar genetics and phenotypic characteristics to patients with the condition from elsewhere.

The researchers found that none of the Maltese patients had mutations in the genes C9orf72, SOD1, TARDBP and FUS, where the most common mutations associated with ALS are located, particularly in patients from a Northern European background. This agrees with other studies of Southern European countries, where rates of these mutations are also lower.

This finding confirms the presence of a NorthSouth gradient in the frequency of mutations within these genes across Europe, write the authors.

As with other populations, almost twice as many men were affected by ALS than women on Malta, although the women who were affected were diagnosed about 5 years earlier than the men at an average age of 59.5 years compared with 64 years. The overall incidence of 2-3 cases per 100,000 people was similar on Malta to elsewhere.

More familial cases of ALS (12.5%) were seen on Malta compared with elsewhere. Normally only 5-10% of cases are familial and 90-95% sporadic.

Our results underscore the unique genetics of the Maltese population, shaped by centuries of relative isolation. We also established that genetic factors play a significant role in causing ALS in Malta, noted Cauchi.

The researchers now plan to search for the disease triggers in the patients in the study who did not have mutations in known ALS-related genes.

Our preliminary data excludes the possibility that these patients have deleterious variants in a set of genes associated with other motor neuron disorders including hereditary ataxias, and hereditary motor and sensory neuropathies, writes the team.

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Maltese ALS Patients Have Different Genetic Mutations than Northern Europeans - Clinical OMICs News

Genetics

Genetic Liability to Smoking Linked to Atherosclerotic Cardiovascular Disease – MD Magazine

January 22, 2021 medical

While smoking is linked to atherosclerotic cardiovascular disease (ASCVD), the relative contribution to each subtype is not entirely understood.

A team, led by Michael G. Levin, MD, Division of Cardiovascular Medicine, University of Pennsylvania Perelman School of Medicine, determined the link between genetic liability to smoking and the risk of coronary artery disease (CAD), peripheral artery disease (PAD), and large-artery stroke.

In the mendelian randomization study, the investigators used summary statistics from genome-wide associations of smoking from the UK Biobank (n = 462,690), Coronary Artery Disease Genome Wide Replication and Meta-analysis plus the Coronary Artery Disease Genetics Consortium (n = 60,801 cases, n = 123,504 controls), VA Million Veteran Program (n = 24,009 cases, n = 150,983 controls), and MEGASTROKE (n = 4373 cases, n = 406,111 controls).

The investigators sought main outcomes of risk, defined as odds ratios (OR) of CAD, PAD, and large-artery stroke.

The researchers used 2 measures for smoking throughout the studylifetime smoking index and smoking initiation. The primary measure of smoking was lifetime smoking index, which was previously validated continuous measure that accounts for self-reported smoking status, age at initiation, age at cessation, number of cigarettes smoked per day, and a simulated half-life constant that captures the decreasing effect of smoking on health outcomes following a given exposure.

Link Between ASCV and Smoking

The investigators found genetic liability to smoking was linked to an increased risk of PAD (OR, 2.13; 95% CI, 1.78-2.56;P= 3.61016), CAD (OR, 1.48; 95% CI, 1.25-1.75;P= 4.4106), and stroke (OR, 1.40; 95% CI, 1.02-1.92;P= 0.04).

The team also found the genetic liability to smoking was associated with a greater risk of PAD than risk of large-artery stroke (ratio of OR, 1.52; 95% CI, 1.05-2.19;P= 0.02) or CAD (ratio of OR, 1.44; 95% CI, 1.12-1.84;P= 0.004).

The link between genetic liability to smoking and atherosclerotic cardiovascular diseases was independent from the effects of smoking on traditional cardiovascular risk factors.

In this mendelian randomization analysis of data from large studies of atherosclerotic cardiovascular diseases, genetic liability to smoking was a strong risk factor for CAD, PAD, and stroke, although the estimated association was strongest between smoking and PAD, the authors wrote. The association between smoking and atherosclerotic cardiovascular disease was independent of traditional cardiovascular risk factors.

The Dangers of Smoking

Atherosclerotic cardiovascular disease impacts a number of vascular beds throughout the body, with clinical manifestations. Smoking tobacco is consistently among the leading risk factors for atherosclerotic cardiovascular disease.

Smoking also had independent effects on inflammation, endothelial function, and platelet aggregation, but it is unknown whether the effect of smoking on atherosclerotic cardiovascular disease is primarily mediated through correlated alterations of traditional cardiovascular risk factors or operates through independent mechanisms.

While the detrimental effects of smoking could persist for decades, clarifying the basis of the smoking-atherosclerosis relationship might enable more targeted risk-reduction strategies among both current and former smokers.

The study, Genetics of Smoking and Risk of Atherosclerotic Cardiovascular Diseases, was published online in JAMA Network Open.

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Genetic Liability to Smoking Linked to Atherosclerotic Cardiovascular Disease - MD Magazine

Genetics

For COVID Peace of Mind – and No Swab Up Your Nose – Huntsville Hospital and Kailos Genetics Roll Out Assure Sentinel – Huntsville Business Journal

January 22, 2021 medical

Two issues negatively impacting COVID testing are false readings and the turnaround time it takes for results. False positive results can cause undue concern, whereas false negative readings have the potential to unwittingly add to the continued spread of COVID.

The waiting game is especially difficult; its the kind of time that most people dont really have to spare. They must then play the quarantine game which, in addition to the restrictions, often means a loss of income as they wait for their results.

To overcome these hurdles, Huntsville Hospital and Kailos Genetics have teamed up to offer a COVID-19 test option through its Assure Sentinel and Peace of Mind programs. The programs are designed for non-symptomatic individuals who want to know if they are carrying the COVID-19 virus.

Its the second program weve put into place with Huntsville Hospital, said Troy Moore, chief science officer at Kailos, which is headquartered at the HudsonAlpha Institute for Biotechnology. The first program was focused on a return to work or return to school testing, on a routine basis. Then, we learned there were quite a few people that had a son or daughter going back to school or to college, or theyve been around family members during the holidays, or they have a parent they are taking care of.

This is a place where they could go if they have concerns, but not necessarily a known exposure event.

In this partnership, the hospital staff will administer the test, collect samples, and deliver the results. Kailos will process the tests utilizing its Assure Sentinel program which can detect SARS-CoV-2, the virus that causes COVID-19.

Assure Sentinel testing is painless and affordable and can detect viral infections in individuals before they become symptomatic. By reducing the potential for exposure, Sentinel testing helps to minimize the impact in the workplace, as well as in the community.

The best news is the process is a saline swish and gargle the companys ViraWash to provide a viable sample. No long swab going up your nose and it can be easily done in the workplace.

For more information, contact the Huntsville Hospital Clinical Lab at: 256-265-2LAB (2522).

Original post:
For COVID Peace of Mind - and No Swab Up Your Nose - Huntsville Hospital and Kailos Genetics Roll Out Assure Sentinel - Huntsville Business Journal

Biochemistry

EXPRESS: SARS-CoV-2 (covid-19): a short update on molecular biochemistry, pathology, diagnosis and therapeutic strategies – DocWire News

January 22, 2021 medical

This article was originally published here

Ann Clin Biochem. 2021 Jan 21:4563221992390. doi: 10.1177/0004563221992390. Online ahead of print.

ABSTRACT

The ongoing coronavirus (covid-19) pandemic highlights the need for global scientific cooperation to advance our understanding of the immunological, molecular and biochemical mechanisms causing infection by this virus. Better understanding of key processes has allowed development of vaccines in record time, and of agents with the potential to treat and neutralise current and future coronavirus outbreaks. To date, clinically effective agents for prevention and treatment of covid-19 infections are limited. This review provides a brief synopsis regarding the molecular biology, pathology and laboratory tests commonly used in the diagnosis and prognosis of covid-19, as well as the development of vaccines and therapeutic strategies to manage its current and future mutations.

PMID:33478237 | DOI:10.1177/0004563221992390

Link:
EXPRESS: SARS-CoV-2 (covid-19): a short update on molecular biochemistry, pathology, diagnosis and therapeutic strategies - DocWire News