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Daily Archives: November 28, 2021
Leadership in the time of Covid is a thankless job, in politics and in sport – Stuff.co.nz
Posted: November 28, 2021 at 9:53 pm
OPINION: Assuming you have the required skills, would you want to be Prime Minister or All Black rugby coach? Really?
Its a wonder they can find anyone to do either job, given leadership means abuse, insinuations, and accusations. Opposition leader is said to be even worse.
PM Jacinda Ardern and Ian Foster must wonder what they were thinking when they stuck their heads above the parapet; two Waikato kids now being widely compared with a by-product from the back end of cows.
Neither will be having a great time, both are likely to be cursing Covid. OK, Ardern had Whakaari/White Island and the mosque shootings to deal with as well, but for two years Covid has stalked their every move.
READ MORE:* New political puppets unveiled at Wellington's Backbencher pub* Which prime ministers oversaw the biggest house price increases?* Limited travel bubble gives All Blacks extra hope to be home by Christmas but one massive hurdle remains
Photosport
All Blacks head coach Ian Foster, dejected after losing to France.
Public doubts are rising. Ardern is maintaining her smile as she slips in the polls, and a potpourri of disaffected Kiwis protest in the streets.
Foster has never won a popularity poll, even before consecutive losses to Ireland and France. You wouldnt rule out an anti-Fozzie march, the way things are going in Aotearoa.
Why lump Ardern and Foster together, you ask? Stints as a Press Gallery and sports reporter have revealed they have more parallels, than differences.
In Australia, its said the cricket captain is the second-most important person, after prime minister. Former PM John Howard even put it the other way around.
Rachael Kelly/Stuff
Werner Marx and Phil Gerritson of Tapanui were at Groundswell's Mother Of All Protests in Gore.
And so it is in Godzone, where rugby is the national game and politics has five sides on the Parliamentary pitch at the same time.
A PM must manage the unmanageable, whether the country or her own MPs, as does the All Blacks coach, harnessing an array of talents and mindsets into a cohesive whole.
After an election, one political team is given the ball, while the others complain about how they want it, how unfair the rules are, and what they would do if they only had the ball (always much better).
And just like Super Rugby, political parties have fans who will go nowhere else, or even see any merit in their rivals. A small percent of voters might switch, but only to the next-door party on the political spectrum.
No-one is going from the Greens to ACT, or vice versa, that would be like a Crusaders fan switching to the Blues. A decade after Foster left the Chiefs, there are still accusations of bias, with every selection seen through a Chiefs filter.
When the All Blacks get rucked over, the coach is a target of frustrated fans, powerless to vote him out, and with employer New Zealand Rugby usually as supportive as an international front-row forward.
My point is (yes, I know it has been a long wait) no normal person could handle either job, and both Ardern and Foster are more talented than normal people; which is not to say they are flawless, or even the best.
Yes, there is the money - the prime minister gets $471,049 and annual allowances for travel and lodging, and a lifetime annuity.
DAVID WHITE/Stuff
John Key was one prime minister who got to choose the timing of his own exit.
For that, prime ministers work endlessly, irrespective of the colour of their rosettes. I say this as someone who has been phoned by a PM after 11pm, and before 7.30am. Exhausting.
Fosters salary is a state secret. Top All Blacks earn more than a million.
So there is the money, but when did money ever make you less tired, or less stressed? Your body doesnt know how much youre being paid. It just knows it is exhausted, and youre not looking after it. The same goes for your brain.
And at the end of it all it can (and usually does) end in tears; Helen Clark, Jenny Shipley, Laurie Mains, John Hart, Grizz Wyllie, Bill English, John Mitchell, Jim Bolger, Mike Moore - did any stop being top gun on their own terms?
Or maybe they did. Maybe they (and their families) were simply relieved the war was over.
Whod blame them?
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Leadership in the time of Covid is a thankless job, in politics and in sport - Stuff.co.nz
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Interpretation: The Fourth Amendment | The National …
Posted: at 9:53 pm
Imagine youre driving a car, and a police officer spots you and pulls you over for speeding. He orders you out of the car. Maybe he wants to place you under arrest. Or maybe he wants to search your car for evidence of a crime. Can the officer do that?
The Fourth Amendment is the part of the Constitution that gives the answer. According to the Fourth Amendment, the people have a right to be secure in their persons, houses, papers and effects, against unreasonable searches and seizures. This right limits the power of the police to seize and search people, their property, and their homes.
The Fourth Amendment has been debated frequently during the last several years, as police and intelligence agencies in the United States have engaged in a number of controversial activities. The federal government has conducted bulk collection of Americans telephone and Internet connections as part of the War on Terror. Many municipal police forces have engaged in aggressive use of stop and frisk. There have been a number of highly-publicized police-citizen encounters in which the police ended up shooting a civilian. There is also concern about the use of aerial surveillance, whether by piloted aircraft or drones.
The application of the Fourth Amendment to all these activities would have surprised those who drafted it, and not only because they could not imagine the modern technologies like the Internet and drones. They also were not familiar with organized police forces like we have today. Policing in the eighteenth and early nineteenth centuries was a responsibility of the citizenry, which participated in night watches. Other than that, there was only a loose collection of sheriffs and constables, who lacked the tools to maintain order as the police do today.
The primary concerns of the generation that ratified the Fourth Amendment were general warrants and writs of assistance. Famous incidents on both sides of the Atlantic gave rise to placing the Fourth Amendment in the Constitution. In Britain, the Crown employed general warrants to go after political enemies, leading to the famous decisions in Wilkes v. Wood (1763) and Entick v. Carrington (1765). General warrants allowed the Crowns messengers to search without any cause to believe someone had committed an offense. In those cases the judges decided that such warrants violated English common law. In the colonies the Crown used the writs of assistancelike general warrants, but often unbounded by time restraintsto search for goods on which taxes had not been paid. James Otis challenged the writs in a Boston court; though he lost, some such as John Adams attribute this legal battle as the spark that led to the Revolution. Both controversies led to the famous notion that a persons home is their castle, not easily invaded by the government.
Today the Fourth Amendment is understood as placing restraints on the government any time it detains (seizes) or searches a person or property. The Fourth Amendment also provides that no warrants shall issue, but upon probable cause, supported by oath or affirmation, and particularly describing the place to be searched and the persons or things to be seized. The idea is that to avoid the evils of general warrants, each search or seizure should be cleared in advance by a judge, and that to get a warrant the government must show probable causea certain level of suspicion of criminal activityto justify the search or seizure.
To the extent that a warrant is required in theory before police can search, there are so many exceptions that in practice warrants rarely are obtained. Police can search automobiles without warrants, they can detain people on the street without them, and they can always search or seize in an emergency without going to a judge.
The way that the Fourth Amendment most commonly is put into practice is in criminal proceedings. The Supreme Court decided in the mid-twentieth century that if the police seize evidence as part of an illegal search, the evidence cannot be admitted into court. This is called the exclusionary rule. It is controversial because in most cases evidence is being tossed out even though it shows the person is guilty and, as a result of the police conduct, they might avoid conviction. The criminal is to go free because the constable has blundered, declared Benjamin Cardozo (a famous judge and ultimately Supreme Court justice). But, responded another Supreme Court justice, Louis Brandeis, If the government becomes the lawbreaker, it breeds contempt for the law.
One of the difficult questions today is what constitutes a search? If the police standing in Times Square in New York watched a person planting a bomb in plain daylight, we would not think they needed a warrant or any cause. But what about installing closed circuit TV cameras on poles, or flying drones over backyards, or gathering evidence that you have given to a third party such as an Internet provider or a banker?
Another hard question is when a search is acceptable when the government has no suspicion that a person has done something wrong. Lest the answer seem to be never, think of airport security. Surely it is okay for the government to screen people getting on airplanes, yet the idea is as much to deter people from bringing weapons as it is to catch themthere is no cause, probable or otherwise, to think anyone has done anything wrong. This is the same sort of issue with bulk data collection, and possibly with gathering biometric information.
What should be clear by now is that advancing technology and the many threats that face society add up to a brew in which the Fourth Amendment will continue to play a central role.
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When Can’t the Fourth Amendment Protect My Privacy? | Nolo
Posted: at 9:53 pm
Learn when the government can invade your privacy to hunt for evidence of a crime.
The Fourth Amendment to the U.S. Constitution places limits on the power of the police to make arrests, search people and their property, and seize objects and contraband (such as illegal drugs or weapons). These limits are the bedrock of search-and-seizure law. This article covers basic issues you should know, beginning with an overview of the Fourth Amendment itself.
The Fourth Amendment to the U.S. Constitution reads as follows:
"The right of the people to be secure in their persons, houses, papers, and effects, against unreasonable searches and seizures, shall not be violated, and no Warrants shall issue, but upon probable cause, supported by Oath or affirmation, and particularly describing the place to be searched, and the persons or things to be seized."
The search-and-seizure provisions of the Fourth Amendment are all about privacy. To honor this freedom, the Fourth Amendment protects against "unreasonable" searches and seizures by state or federal law enforcement authorities.
The flip side is that the Fourth Amendment does permit searches and seizures that are reasonable. In practice, this means that the police may override your privacy concerns and conduct a search of you, your home, barn, car, boat, office, personal or business documents, bank account records, trash barrel, or whatever, if:
The Fourth Amendment applies to a search only if a person has a "legitimate expectation of privacy" in the place or thing searched. If not, the amendment offers no protection because there are, by definition, no privacy issues.
Courts generally use a two-part test (fashioned by the U.S. Supreme Court) to determine whether, at the time of the search, a defendant had a legitimate expectation of privacy in the place or things searched:
For example, a person who uses a public restroom expects not to be spied upon (the person has an expectation of privacy), and most peopleincluding judgeswould consider that expectation to be objectively reasonable. Therefore, the installation of a hidden video camera by the police in a public restroom would be considered a "search" and would be subject to the Fourth Amendment's requirement of reasonableness.
On the other hand, if an officer stops a car and, when talking to the driver, happens to notice a weapon on the passenger seat, there's been no search under the Fourth Amendment. That's because, even if the driver somehow considered the passenger seat to be a private place, society isn't willing to extend privacy protections to that particular location. In other words, there's no objectively reasonable expectation of privacy with respect to the gun because it was in plain view.
A good example of how this works comes from a U.S. Supreme Court case in which the court held that a bus passenger had a legitimate expectation of privacy in an opaque carry-on bag positioned in a luggage rack above the passenger's head. The Court held that the physical probing by the police of the bag's exterior for evidence of contraband constituted a search subject to Fourth Amendment limitations. (Bond v. U.S., 529 U.S. 334 (2000).)
If it turns out the police conducted an illegal search, does that mean the criminal case is over? Not necessarily, but consequences do exist.
If, upon review, a court finds that an unreasonable search occurred, any evidence seized as a result of it cannot be used as direct evidence against the defendant in a criminal prosecution. This principle, established by the U.S. Supreme Court in 1961, has come to be known as the exclusionary rule.
To this day, many commentators criticize the exclusionary rule on the ground that it unfairly "lets the criminal go free because the constable has erred." But the rule's supporters argue that excluding illegally seized evidence is necessary to deter police from conducting illegal searches. According to this deterrence argument, the police are less likely to conduct improper searches if the resulting evidence can't be used to convict the defendant. (There are, however, exceptions to the exclusionary rulefor one, see Police Searches and the Good Faith Exception.)
Not only is evidence that's the product of an illegal search generally inadmissible in court, but so too is additional evidence derived from the initial evidence. This principle is colorfully known as the "fruit of the poisonous tree" doctrine. The "tree" is the evidence that the police illegally seized in the first place; the "fruit" is the second-generation product of the illegally seized evidence. Both tree and fruit are typically inadmissible at trial. (For more, see Fruit of the Poisonous Tree.)
Some defendants believe that if they can show that a search was illegal, the case must be dismissed. Not true. If a prosecutor has enough other evidence to prove the defendant guilty, the case can continue. Also, the illegally-seized evidence can generally be considered by a judge when deciding on an appropriate sentence following conviction and admitted in civil and deportation cases. In some circumstances, a prosecutor can use such evidence to impeach (attack the credibility of) a defendant who testifies at trial.
To learn more about search-and-seizure law, get The Criminal Law Handbook: Know Your Rights, Survive the System, by Paul Bergman (Nolo). If you might need to talk to a criminal defense attorney or want to know how the law may differ slightly in your state, you can turn to Nolo's trusted Lawyer Directory to find a lawyer near you.
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When Can't the Fourth Amendment Protect My Privacy? | Nolo
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Time for the National Party to embrace kindness – Stuff.co.nz
Posted: at 9:53 pm
OPINION: I know some people would be rolling their eyes at the thought of the National Party embracing the kindness brand.
These are the same people who continually and openly mock Jacinda Ardern for her advocacy for kindness, seeing it as virtue-signalling and a coy attempt at garnering domestic and international popularity.
I dont buy these criticisms because they are simply not consistent with the inner character and behaviour of the prime minister, whose propensity for empathy seems as natural as Donald Trumps propensity for self-adulation.
ROBERT KITCHIN/Stuff
Donna Miles says interim National Party leader Shane Reti is an obvious permanent choice as a leader who displays, communicates and prioritises the values of decency and kindness, rather than domination and power.
But there are other criticisms of Labours kindness brand worth mentioning. It is said that Kiwis living in poor neighbourhoods of South Auckland, with large Mori and Pasifika populations, whose problems have been exacerbated by Covid and lockdowns, have not felt much kindness.
READ MORE:* Populism from the Brexit and Trump playbooks enters the New Zealand election campaign but its a risky strategy* Boochani and Collins raise unsettling questions about refugees* Iranian writer Behrouz Boochani granted refugee status in NZ* We are lucky Behrouz Boochani is here to tell his story * Celebrated author Behrouz Boochani, detained on Manus Island for six years, arrives in New Zealand
The housing crisis, child poverty and rising inequality have also left many New Zealanders feeling neglected and uncared for.
But these are not arguments against kindness - if anything, these are good reasons for thinking deeper about what a kind New Zealand should really look like, and how a healthy, empathetic society can ensure no-one is left behind.
People who belittle kindness as a value in politics and business often do so to justify their own selfishness and cruelty. But times are changing and even businesses are thinking and committing to kindness, wanting it to become an everyday thought and a consistent part of their mindset and communication.
It all makes sense. Kindness, its argued, is highly recognisable, especially when it happens directly to us - and all of us, bar sociopaths, are capable of exhibiting kindness.
To my Iranian mum, whose English is not good enough to follow New Zealand politics in great detail, the kindness of Jacinda Ardern has always been too obvious to miss. It is in her mannerism and countenance, Mum says of the way the PM conducts and carries herself.
ROBERT KITCHIN/Stuff
Donna Miles: Even I cannot help but like our PM for her decorum and decency.
She also openly says that she loves Jacinda Ardern. I firmly believe political leaders should not be idolised in any way, lest they be exempt from scrutiny and accountability, but even I cannot help but like our PM for her decorum and decency. I think it is a human condition to be more forgiving of people that we like, and to be overly critical of people we don't like.
This brings me to the National Partys current leadership crisis. As I write this, there is no clear indication of whom the future leader of the party will be.
But I do hope that this new change will bring with it a discontinuation of past practices and a departure from the party's current image. From dirty politics to wanting to appear tough on important issues such as crime and asylum response to these issues should be guided by evidence, not fleeting populism the National Partys anti-kindness approach has not only been detrimental to ordinary Kiwis, it clearly has also led to continual division and spite within the party.
I will never forget how the National Party behaved after high-profile Kurdish refugee author Behrouz Boochani was granted asylum in New Zealand. When Boochani arrived in Christchurch for a speaking engagement at the Word festival, he called the Christchurch welcome a reminder of kindness.
joseph johnson/Stuff
Donna Miles says she will never forget the National Partys treatment of Kurdish-Iranian refugee and journalist Behrouz Boochani after his arrival in New Zealand last year.
But soon after he was granted asylum, the National Party suggested political interference because, they said, the author had connections in the Greens and the Labour Party. All of it was untrue, of course, and the allegations seemed to many, including some National supporters, entirely pointless and mean-spirited.
National, having underestimated Boochanis support, quietly changed tack. If National had kindness as its guiding principle, it would have not made those allegations without any evidence, or consideration of their impact on Boochani, who had already suffered prolonged cruelty in Australian offshore detention centres on Manus Island.
Almost all modern crises faced by humanity require a departure from a selfish approach, which prioritises the individual, to an approach which considers the collective interest as paramount.
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Donna Miles: Almost all modern crises faced by humanity require a departure from a selfish approach, which prioritises the individual ...
The hard reality is that without a great deal of altruism and self-sacrifice, serious issues such as the climate change crisis, housing crisis, refugee crisis, inequality crisis and even the pandemic will not be resolved. But there is another just as urgent reason for more politicians to embrace the kindness brand and that is the growing mental health crisis.
Constant nastiness and bickering in politics is disengaging for voters and detrimental to everyones mental wellbeing, including the politicians themselves.
National now has a chance to appoint a leader who displays, communicates and prioritises the values of decency and kindness, rather than domination and power.
There is an obvious choice in Dr Shane Reti. The question is, will the National Party take it?
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Time for the National Party to embrace kindness - Stuff.co.nz
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‘Disappointing’ National Party needs ‘new vision’ – Former PM – RNZ
Posted: at 9:53 pm
Former Prime Minister Jim Bolger has weighed in on the National Party's leadership race, saying that the party he once led needs to have a serious think about where it wants to go.
Former Prime Minister Jim Bolger. Photo: RNZ/Rebekah Parsons-King
Leader Judith Collins lost a vote of confidence this week and deputy leader Shane Reti was named acting leader.
The party is scheduled to meet Tuesday to select a new leader, with former leader Simon Bridges and MP Christopher Luxon among the top candidates.
Reti is the fifth leader the National Party has had since Jacinda Ardern was elected Prime Minister in 2017.
The former National leader, who was Prime Minister from 1990 to 1997, spoke to TVNZ's Q + A today and did not mince words when it came to evaluating the current state of his party.
"Disappointing is a very gentle way of putting it," Bolger said. "The electors gave their verdict at the last election."
"What the National Party needs to be doing ... is actually saying what are we going to do different. What's our new vision?"
Bolger would not be drawn on whether he thought Bridges or Luxon should be the next leader.
"I'm sure the qualities are in the caucus," he said. "The caucus has to decide which of them can meet some of the challenges."
"I'm not going to nominate them. I just think they have to look at presenting the National vision much better than they did before the last election."
Simon Bridges and Chris Luxon may contest Tuesday's National Party leadership vote. Photo: Dom Thomas
The National Party suffered a landslide defeat last year and won the party vote in only one electorate.
"You can't get much lower than that," Bolger said.
Bolger said society is currently divided on many levels, noting "the divisions that are occurring in New Zealand now between the vaccinated and the unvaccinated," and National needs a leader who can bridge that gap.
"We want a leader in the opposition as well as in government. We want a leader that can bring people together."
Bolger said that a kind of "reimagining capitalism" needs to be done, not just in Aotearoa but globally.
"Clearly the model that's been pursued across the world now is dividing societies. Some are getting obscenely rich and others are going to the food kitchens. That's a dangerous position for a society."
"We've got to do a lot of hard thinking as a society, not only the National Party."
Bolger said the caucus should remember they will not just be selecting a new leader, but possibly a future prime minister.
"What vision do they have? What new ideas do they have?"
Bolger noted that transitions from a popular leader are hard in any party.
"The Labour Party were exactly the same when Helen Clark left."
National should not think that Labour is unbeatable in 2023, he said.
"There is no reason the Labour Party can't be defeated at the next election two years away."
But he said National needs to be more than just naysayers.
"They've got to do much more than just be critics.
"What people want to know is if you don't like it, what would you do instead?
Bolger led National through three elections in the 1990s, and told Q + A that the party has to keep changing.
"It really needs a person who has a vision that they can sell that's inclusive, that understands the stresses and strains of a modern society."
"I want to encourage whoever is the leader to think bigger than they've been thinking for the last little while."
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'Disappointing' National Party needs 'new vision' - Former PM - RNZ
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Evolutionary change in the construction of the nursery environment when parents are prevented from caring for their young directly – pnas.org
Posted: at 9:53 pm
Significance
Parents can care for offspring directly by giving them food or warmth, for example, or they can help them without direct contact via an extended phenotype by manipulating the nursery environment in which offspring develop. Using an experimental evolution approach, we prevented parents from directly supplying care to their offspring and observed how the extended care phenotype and offspring traits evolved in response. We found that depriving offspring of direct care caused rapid adaptive change in the construction of the nursery environment, which rescued offspring from otherwise poor developmental conditions. Overall, offspring tended to perform better when transplanted to a nursery environment constructed by parents of their own lineage, suggesting that offspring adapt to the evolved extended parental phenotype.
Parental care can be partitioned into traits that involve direct engagement with offspring and traits that are expressed as an extended phenotype and influence the developmental environment, such as constructing a nursery. Here, we use experimental evolution to test whether parents can evolve modifications in nursery construction when they are experimentally prevented from supplying care directly to offspring. We exposed replicate experimental populations of burying beetles (Nicrophorus vespilloides) to different regimes of posthatching care by allowing larvae to develop in the presence (Full Care) or absence of parents (No Care). After only 13 generations of experimental evolution, we found an adaptive evolutionary increase in the pace at which parents in the No Care populations converted a dead body into a carrion nest for larvae. Cross-fostering experiments further revealed that No Care larvae performed better on a carrion nest prepared by No Care parents than did Full Care larvae. We conclude that parents construct the nursery environment in relation to their effectiveness at supplying care directly, after offspring are born. When direct care is prevented entirely, they evolve to make compensatory adjustments to the nursery in which their young will develop. The rapid evolutionary change observed in our experiments suggests there is considerable standing genetic variation for parental care traits in natural burying beetle populationsfor reasons that remain unclear.
Parental care encompasses all parental traits that enhance offspring fitness and that have evolved for this purpose (1). Direct forms of care have been analyzed extensively in previous work. They involve parents engaging directly with their young by defending their offspring from attack, for example, or by brooding them when they are cold or feeding them (2). Yet, parental care can also take the form of an extended phenotype. Before their offspring even exist, parents can manipulate the nursery environment in which their future young will develop by carefully choosing the territory within which the nursery is sited, by constructing a nursery or nest, and by stockpiling it with food for the newly hatched offspring (3). In some species, such as dung beetles, beewolves, skates, and jacky dragons, parents and their offspring never meet again after egg laying. Nevertheless, the extended parental care phenotype in these species endures to influence offspring fitness (47).
Here, we are interested in the evolutionary relationship between the extent of direct care and the extended parental care phenotype and how that, in turn, influences the evolution of offspring traits. Each form of care is understood to generate a fitness benefit for the offspring, usually at some fitness cost to the parent that supplies it (1, 2). Any existing fitness costs limit the supply of care, but the relative benefits derived from each form of care presumably determine the relative level of investment in each of them. If the relative fitness benefits derived from direct care suddenly decline, for example, then we might expect a corresponding adaptive increase in the extended parental care phenotype to compensate for any loss in fitness experienced by the offspring. Previous studies have produced correlational evidence that is consistent with this possibility (e.g., refs. 810). Furthermore, recent work has investigated whether such compensatory changes can be induced via phenotypic plasticity within the lifetime of an individual (11, 12). However, we are unaware of any work that has considered how changes in one form of care cause evolutionary change in other forms of care or how that could causally influence the evolution of offspring traits.
To address this question, we took advantage of the natural variation in parental care found in the burying beetle Nicrophorus vespilloides, which comprises both direct care and an extended parental care phenotype. Burying beetles use small dead vertebrates, such as mice or small birds, to rear their larvae (13, 14). The extended parental care phenotype is expressed when parents transform the carcass into an edible nest. They scissor off the fur or feathers, roll it into a ball, cover the flesh with antimicrobial exudates, and bury it in a shallow grave (1416). Eggs are laid in the soil surrounding the carcass, and when larvae hatch, they crawl to the carcass. Parents assist the offspring in colonizing the carcass by biting small holes in the flesh, which are used by larvae to penetrate the carcass. Parents may stay to supply their offspring with direct care, which involves defending them and feeding them via oral trophallaxis (17). Larvae can also feed themselves and can survive without any posthatching care (17, 18). Approximately 1 wk after hatching, larvae disperse to pupate in the soil. Parental presence during larval development increases larval survival (19), yet the duration of posthatching parental care is highly variable, with a range spanning from no posthatching care at all to the whole period of larval development (13, 2022). Thus, the extent of direct parental care experienced by burying beetle larvae in early life is highly variable.
We used experimental evolution to investigate how a change in the supply of direct parental care affects the evolution of an extended parental care phenotype: that is, construction of the nursery environment through the conversion of the carcass into an edible nest. Both types of care have been shown to improve offspring survival (19, 23) and incur life span costs in burying beetles (2426). We established experimental populations that evolved either with Full Care (FC; i.e., direct care plus extended parental care) or No Care (NC; i.e., only extended parental care but no direct contact with parents).
We have reported some of the outcomes of this experimental evolution work previously. We found that preventing direct posthatching care in experimental NC populations for generation after generation initially resulted in lower breeding success and larval survival (27). However, this was followed by a rapid increase in fitness in subsequent generations so that FC and NC populations had similar measures of fitness by generation 13 (27). We have also investigated how the evolution of larval traits, such as their morphology (22) and social interactions on the carcass (18, 28), contributed to this recovery in fitness in the NC populations. Here, we focus more on the evolution of parental traits in the NC populations by examining how changes in the parental extended phenotype of carcass preparation promote and interact with offspring fitness in the absence of direct care.
To disentangle the fitness consequences of changes in the parental traits from changes in larval traits, we cross-fostered larvae within and between FC and NC after multiple generations of experimental evolution (18, 22, 27, 29). By measuring correlates of larval fitness in the absence of direct care, we further determined whether evolved change in the extended parental care phenotype compensated for the loss of direct parental care (in our laboratory environment). Our results demonstrate that there is rapid adaptive evolution of the extended parental care phenotype when parents are prevented from interacting with their offspring and that offspring adapt rapidly to this changed nursery environment.
The experimental populations were founded from four wild populations of N. vespilloides collected in Cambridgeshire, United Kingdom (Byrons Pool, Gamlingay Woods, Overhall Grove, and Waresley Woods) in the summer of 2014. Further details of these wild populations are given in refs. 22 and 28. The populations were interbred to create a genetically diverse stock laboratory population from which the experimentally evolving populations could be derived. This allowed us to avoid potential confounding effects of inbreeding depression, which is masked by direct parental care (30). Two selective regimes were established, one with full posthatching parental care, FC, and the other without any posthatching parental care, NC. Two independent replicates (hereafter referred to as block 1 and block 2) of the FC and NC regimes were maintained, with block 2 breeding a week after block 1.
At each generation, males and females were paired within each experimental population, excluding sibling and cousin pairings. Each pair was placed in a breeding box (17 12 6 cm) half filled with moistened compost, and a small, thawed dead mouse (8 to 14 g, obtained frozen from LiveFoods Direct) was placed on top of the soil. Breeding boxes were kept in dark cabinets to simulate natural underground conditions. In the FC populations, a minimum of 30 pairs of unrelated beetles were bred at each generation. Parents were allowed to remain in the box throughout larval development and so, were able to provide posthatching care. In the NC populations, we set up a minimum of 50 pairs each generation to compensate for the increased number of failed broods (27), and both parents were removed from the breeding box 53 h after pairing, before larvae started hatching. This allowed parents sufficient time to convert the mouse body into a carrion nest and for females to lay eggs in the surrounding soil, but it deprived larvae of any posthatching care (31, 32).
Eight days after pairing, dispersing larvae were placed into individual cells (2 2 2 cm) in an eclosion box (10 10 2 cm), with one brood per eclosion box. They were covered with moistened peat and left undisturbed to pupate. Newly eclosed adults were then removed and housed individually until breeding a minimum of 17 d after eclosion. All adult beetles were fed raw ground beef twice a week.
In generation 11, we created a third type of experimental population (from here on, known as Nmstanding for No Care, maternal) from each of the two replicates of the NC population. The two replicate Nm populations were bred in parallel with each of the two FC and NC replicates. The Nm population passed through one generation of full posthatching parental care to eliminate potential maternal and/or other environmental effects in the NC population. To create each Nm population, we thus followed the same protocol as for the FC populations and bred an additional 30 pairs of unrelated beetles from each NC replicate population. The Nm populations were discontinued after the experimental analysis described below.
In generation 13 of the FC and NC populations (corresponding to generation 1 of Nm), we collected newly eclosed adults from all three populations. We housed all beetles individually in plastic boxes (12 8 2 cm) until pairing for the experiment described below.
We randomly selected males and females from each population to set up 450 pairs (75 pairs per population per block) and placed them in a breeding box (17 12 6 cm) with a 10- to 12-g thawed mouse carcass. After 53 h, before any larvae hatched, we removed the parents and measured the parents pronotum width, which is standardly used as a proxy for adult body size. As a measure of reproductive investment, we counted the number of eggs visible on the bottom of the breeding boxes, which is a noninvasive accurate method for deducing clutch size (33). Eggs were left in situ, in the soil in the breeding boxes, to hatch into larvae.
Before the eggs hatched, carcasses were swapped between breeding boxes to create a fully factorial 3 3 experimental design, such that larvae from each experimental population were allowed to develop on carcasses prepared by adults either from the larvaes own natal population or from the other two experimental populations (SI Appendix, Fig. S1). Larvae were, therefore, always unrelated to the adults that had prepared the carcass whereupon they developed. Furthermore, since the adults were removed, no broods received any direct parental care. After 8 d, we counted and weighed surviving larvae to derive correlates of offspring fitness on the different carcasses.
Using this experimental design, we were able to separate contributions to larval fitness due to the extended parental care phenotype from any contributions to larval fitness made by larval traits (22, 28).
Burying beetles typically roll the denuded flesh of the carcass into a ball to create a nest for their larvae. The first measure we made of the nursery environment was the roundness of the carrion nest. Although no correlation between development on a rounder carcass and larval mass at dispersal has yet been found, rounder carcasses correlate negatively with paternal life span, indicating a cost to nest construction (25), and are also less hospitable to rival blowfly larvae (34). Burying beetles also smear costly antimicrobial exudates on the carcass surface (35, 36), which improves larval survival (23). A rounder carcass would minimize the surface area to volume ratio, thus potentially reducing defense costs and the possibility of carcass desiccation. This could be particularly advantageous to offspring in the absence of posthatching parental care.
We measured carcass roundness 53 h after pairing adults and presenting them with a dead mouse, following methods described in ref. 25. Briefly, we took two photographs of each carcass from perpendicular positions 30 cm away with identical cameras and settings (Fujifilm av200). When visible, we digitally removed the mouses tail from all photos with GIMP (v. 2.8.16; The GIMP Development Team; https://www.gimp.org/), as the tail strongly influences roundness estimates. We then calculated carcass roundness with a custom-written script (SI Appendix) in ImageJ (1.49v, Wayne Rasband; NIH; https://imagej.nih.gov/ij). By applying this process to a ping-pong ball, we established that a perfect sphere has a roundness score of 0.9. We, therefore, adjusted subsequent measures of roundness by dividing by 0.9, meaning that a value of 1.0 intuitively equaled a sphere.
Second, we recorded whether small holes were visible on the surface of the carcass at 53 h after pairing. There is individual variation in the timing of these holes. In previous work, we found that only 26% of wild-caught N. vespilloides, breeding in laboratory conditions, made a visible hole in the surface of the carcass before larval hatching (22). In the absence of posthatching care, the presence of a hole in the carcass is critical for larval survival (19). We hypothesized that NC populations might make these entrance holes earlier than FC populations. Some of these data, namely the presence of a hole in the carcass in FC and NC populations at 53 h after pairing, were published in ref. 22. Here, we present a different analysis of these data, including examining the fitness consequences of the presence of a hole for different experimental populations, as well as data regarding Nm populations.
Third, we measured antimicrobial activity in male and female anal exudates at 53 h after pairing. Adults deposit these exudates all over the carrion nest during carcass preparation. The presence of these exudates improves larval survival (23) and affects the composition of bacterial communities growing on prepared carcasses (16, 37). Lytic activity is heritable in N. vespilloides (38), with significant positive maternal effects, and therefore, it is feasible that selection could act to increase it in NC and Nm populations, where parents cannot maintain the carcass after larval hatching.
Burying beetles readily produce a redbrown liquid when gently tapped on the back of the abdomen. However, in some cases, individuals did not produce exudates. The total numbers of successfully sampled individuals were 398 males (131 FC, 130 NC, and 137 Nm) and 401 females (133 FC, 129 NC, and 139 Nm). We collected exudates with Pasteur pipettes, stored them in 1.5-mL Eppendorf tubes, and kept them frozen at 20C until further analysis. Lytic activity was measured in an automated plate reader (Biotek ELx808) by a microplate turbidity assay that quantifies the degradation rate of bacterial cell walls (adapted from ref. 23). Briefly, we diluted exudates 25-fold in potassium phosphate buffer (pH 6.4, 0.02 M). We added 10 L of diluted exudates per well to 96-well microtiter plates filled with 100 L per well of a 1.3-mg mL1 suspension of lyophilized Micrococcus luteus (Sigma-Aldrich) in potassium phosphate buffer. Samples were initially incubated in the plate reader at 25C for 30 s with continuous shaking. Absorbance at 450 nm was measured every 10 min for 60 min, with continuous shaking for 10 min at 25C between measurements. We calculated lytic activity as the percentage change in absorbance relative to control wells, with 10 L of potassium phosphate buffer and 100 L of M. luteus suspension. We report here results for change in absorbance at 450 nm after 60 min.
All analyses were performed using the statistical program R version 4.1.1 (39). Mixed effects models were performed with the package lme4 version 1.1-27.1 (40). Seventeen breeding pairs were removed from the analysis either because a parent died or was damaged before adult removal (FC = 2, NC = 3, Nm = 3) or because no eggs were observed in the box upon adult removal (FC = 2, NC = 5, Nm = 2). Therefore, 433 breeding pairs were included in the analysis (FC = 146, NC = 142, Nm = 145).
A further seven breeding pairs were removed from the analysis of carcass preparation traits because we could not measure pronotum width for both parents, and body size is an important explanatory variable for carcass roundness and lytic activity. Therefore, 426 breeding pairs were included in the analysis of carcass preparation traits (FC = 143, NC = 140, Nm = 143). To analyze the presence of a hole in the carcass, we initially fitted a generalized linear mixed model (GLMM) with a binomial distribution and a population per block random effect to account for variation between the independent replicates due to founder effects and asynchronous maintenance. No variance was explained by the random effect, and therefore, we used a generalized linear model (GLM) with a binomial distribution to analyze the presence of a hole. Carcass roundness and lytic activity were analyzed with linear mixed models. Lytic activity was log transformed to ensure that model residuals met the assumptions of normality for regression. In these and subsequent models with mixed effects, we included a population per block random effect.
To compare brood performance between experimental populations, we analyzed breeding success (i.e., survival of at least one larva to dispersal), brood size, and brood mass. Offspring mass is a known correlate of fitness in burying beetles (19, 26). Brood success was initially analyzed with a binomial GLMM. Again, the random effect population per block did not explain any variance, and we, therefore, used a binomial GLM to model brood success. Brood size and brood mass were analyzed with linear mixed models (LMMs). We removed brood failures (i.e., no larvae survived to dispersal) from the analysis of brood size and brood mass. To evaluate the relative contribution of parental and larval traits on larval survival to dispersal, we fitted a linear regression model on brood size, with the number of eggs as a covariate. We then used regression residuals as a measure of offspring survival from egg laying to larval dispersal. We included the residuals as the response variable in a LMM with population, carcass type (i.e., population that prepared the carcass), presence of a hole, female size, and carcass roundness as explanatory factors/covariates. Post hoc comparisons were performed with the package emmeans version 1.6.3 in R (41).
Model selection in all analyses was performed by comparing nested models with the Akaike Information Criterion (AIC) and ANOVA (42). Here, we report the minimal adequate models, where nonsignificant terms (P > 0.05, as reported by ANOVA of nested models) were dropped when this resulted in a decrease of AIC by two units. The significance of interaction terms was determined by performing ANOVAs on nested models (with and without the interaction terms). To validate models, we inspected residuals of all minimal adequate models. Female and male sizes, as well as carcass mass, were included as covariates in all the initial models. For LMMs, we used Satterthwaites approximation to calculate degrees of freedom and P values with the package lmerTest version 3.1-3 (43). To check whether approximating degrees of freedom alters statistical results, we ran all minimal adequate models with and without random effects. All models maintained the same qualitative results, and most variables showed P values and effect sizes of the same magnitude whether we included or excluded random effects. Only in the models for brood mass and offspring mortality did we find lower P values when the random effect population per block was excluded (reported in Results).
We found significant differences in the extended parental care phenotype across the different populations we sampled. Carcasses prepared by NC and Nm beetles were twice as likely to have a hole as carcasses prepared by FC beetles (Table 1). At the time of the removal of parents (53 h after pairing), the percentages of carcasses with a visible hole were 30% in FC carcasses, 61% in NC carcasses, and 59% in Nm carcasses.
Summary of minimal adequate models of carcass preparation traits in FC, NC, and Nm populations
Carcasses prepared by NC and Nm beetles were also rounder (Table 1) (overall effect of population: 2 = 25.80, P = 2.5 106). There was a complex, significant interaction between population type and both female and male body sizes (Fig. 1 and Table 1). In FC lines, carcass roundness was positively associated with both male and female sizes. In NC and Nm lines, the slope of the relationship between carcass roundness and body size was significantly shallower than in FC lines, with beetles across a range of sizes producing similarly well-rounded carcasses.
The predicted partial effects of the experimental population of origin and female (Left) and male (Right) pronotum width on carcass roundness. Each data point represents a carcass prepared by a pair of beetles (n = 426). Lines represent adjusted carcass roundness values predicted by a linear mixed model.
Lytic activity in anal exudates at 53 h was similar across the three populations, for both males and females (Table 1). The main predictors of lytic activity, for both sexes, were the individuals size and the lytic activity of their breeding partner. Larger individuals produced higher lytic activity, and individuals paired with beetles that had higher lytic activity also showed higher lytic activity themselves. Lytic activity did not differ significantly between males and females (ANOVA: F1,722 = 1.245, P = 0.265).
Across all populations, the presence of a hole on the surface of the carcass was the best predictor of breeding success (i.e., whether at least one larva would survive to dispersal; absence of hole: 79% successful [169 of 214]; presence of hole: 96% successful [211 of 219]) (Table 2). The number of successful broods did not differ across the three experimental populations, nor were broods more likely to be successful on FC-, NC-, or Nm-prepared carcasses after the effect of hole presence was controlled for statistically by including it in the model (Table 2).
Summary of minimal adequate models explaining differences in the success, size, and mass of broods from FC, NC, and Nm populations on carcasses prepared by FC, NC, and Nm parents
The number of eggs observed at the bottom of breeding boxes, a proxy measure for clutch size, was significantly larger in the FC populations than in the NC and Nm populations (on average, FC clutches had 4.21 and 4.15 more eggs than NC and Nm clutches, respectively) (SI Appendix, Fig. S2 and Table S1). Brood size varied across populations and also depended on which populations had prepared the carcasses that the larvae developed upon (Table 2). Despite FC females laying larger clutches, FC broods were not larger overall at dispersal. The presence of a hole was, of all the factors considered, the one with the largest positive effect on the number of larvae that survived to dispersal (Fig. 2 and Table 2) across all three populations. There was, however, a significant interaction between population and the presence/absence of a hole. In carcasses where no hole could be seen, FC broods were significantly smaller than both NC and Nm broods (Fig. 2 and SI Appendix, Table S2). There was no effect of carcass roundness on brood size (ANOVA between nested models with and without carcass roundness as a fixed effect: 2 = 2.16, P = 0.14).
Brood size and brood mass of larvae at dispersal from FC, NC, and Nm broods (red, blue, and green box plots, respectively) developing on carcasses with and without a hole. Sample sizes: FC = 125, NC = 127, and Nm = 128. Box plots depict the first quartile, median, and third quartile. Whiskers on the box plots range from the samples lowest to highest value within 1.5 interquartile range. Points depict sample outliers. Significant differences between populations are indicated with asterisks (post hoc analyses with emmeans using the Tukey method; *P < 0.05; **P < 0.01; ***P < 0.001) (SI Appendix, Tables S2 and S4).
A significant interaction was also found between the broods population of origin and the population of origin of the beetles that prepared the carcass (population carcass) (Fig. 3 and Table 2). There was a tendency for broods to be larger at dispersal on carcasses prepared by parents of their own population of origin (Fig. 3 and SI Appendix, Table S3). FC larvae performed significantly better on carcasses prepared by FC parents than on carcasses prepared by NC and Nm parents (post hoc tests and 95% CIs) (SI Appendix, Table S3). NC and Nm larvae showed a nonsignificant tendency to perform better on carcasses prepared by NC and Nm parents, respectively (SI Appendix, Table S3).
Brood size and brood mass of larvae at dispersal from FC, NC, and Nm broods developing on carcasses prepared by FC, NC, or Nm parents (red, blue, and green box plots, respectively). Sample sizes: FC = 125, NC = 127, and Nm = 128. Box plots depict the first quartile, median, and third quartile. Whiskers on the box plots range from the samples lowest to highest value within 1.5 interquartile range. Points depict sample outliers. Significant differences between populations are indicated with asterisks (post hoc analyses with emmeans using the Tukey method; *P < 0.05; **P < 0.01; ***P < 0.001) (SI Appendix, Tables S3 and S5).
Brood mass varied across populations and carcasses prepared by different populations, in a similar way to brood size, with presence of a hole having the largest positive effect (Fig. 2 and Table 2). There was a significant interaction between the presence of a hole and the population of origin, with FC broods having significantly smaller mass than NC and Nm broods in the absence of a hole (post hoc tests and 95% CIs) (SI Appendix, Table S4). Again, there was a tendency for brood mass to be highest in broods reared on carcasses from their own parental population (Fig. 3) (post hoc tests and 95% CIs) (SI Appendix, Table S5). The minimal adequate model for brood mass also included a marginally significant interaction between the presence of a hole and the carcass of origin; post hoc tests suggest that the presence of a hole leads to broods attaining a greater mass at dispersal when reared on NC and Nm carcasses than on FC carcasses (post hoc tests and 95% CIs) (SI Appendix, Table S6). When running the minimal adequate model without random effects, the P values for population were lower than in the mixed model with Satterthwaites approximated degrees of freedom (LMM: P = 0.01 and P = 0.02 for NC and Nm, respectively; LM: P = 0.006 and P = 0.007 for NC and Nm, respectively).
To deduce the extent of larval mortality, we applied a best-fit regression on the entire dataset of brood size on clutch size (F1,378 = 148.5, P < 0.001, R2 = 0.28) (SI Appendix, Fig. S3 and Table S7) and used the residuals as a response variable in a GLMM (Table 3).
Generalized linear mixed model of offspring mortality between egg laying and larval dispersal for FC, NC, and Nm populations reared on FC, NC, and Nm carcasses
Overall, there was a population effect on larval mortality, with FC populations showing higher mortality than NC or Nm populations, thus potentially explaining why FC broods were not on average larger, despite having larger clutch sizes. Again, we found a significant interaction between the larval population of origin and the presence of a hole in the carcass. On carcasses without a hole, FC populations showed greater offspring mortality between egg laying and larval dispersal than NC and Nm populations (Table 3 and SI Appendix, Table S8). An interaction between the larval population of origin and the carcass population of origin (population carcass) (Table 3) was retained in the minimal adequate model, despite being only marginally significant, because removing it did not decrease AIC. Post hoc tests revealed that FC offspring were most likely to die between egg laying and larval dispersal across all types of carcasses (Tables 4 and 5). There was again a tendency for larvae to perform better on carcasses prepared by parents of their own parental population (Fig. 4 and Tables 4 and 5). Offspring were equally likely to survive on FC-prepared carcasses, regardless of their population of origin. However, FC populations were significantly more likely to die between egg laying and larval dispersal than NC and Nm populations when they developed on NC-prepared carcasses. On Nm-prepared carcasses, FC populations differed significantly only from Nm populations in the likelihood that larvae would die between egg laying and larval dispersal (Tables 4 and 5). When running the minimal adequate model without random effects, the P values for population were lower than in the mixed model with approximated degrees of freedom (LMM: P = 0.045 and P = 0.009 for NC and Nm, respectively; LM: P = 0.009 and P = 0.0002 for NC and Nm, respectively).
Variation in offspring mortality between egg laying and larval dispersal due to the interaction between population and carcass type: least-square means (LS) and 95% confidence levels (CL)
Number of larvae that survived from egg laying to larval dispersal in relation to clutch size (estimated from the number of eggs on the bottom of the breeding box). Figures show the FC, NC, and Nm populations (red, blue, and green circles and box plots, respectively) developing on FC- (Top), NC- (Middle), or Nm-prepared carcasses (Bottom). Each data point in Right represents a different brood. Sample sizes: FC = 125, NC = 127, and Nm = 128. A regression model for brood size was fit to all the data (black lines in Left; R2 = 0.28) (SI Appendix, Fig. S2 and Table S7), and the residuals from those lines (Right) were used as response variables in linear mixed models (i.e., this was our measure of relative offspring mortality). Box plots depict the first quartile, median, and third quartile. Whiskers on the box plots range from the samples lowest to highest value within 1.5 interquartile range. Points depict sample outliers. Significant differences between populations (indicated with an asterisk; *P < 0.05; **P < 0.01; ***P < 0.001) were found in NC- and Nm-prepared carcasses but not FC-prepared carcasses. Post hoc analyses were performed with emmeans using the Tukey method (Tables 4 and 5).
Variation in offspring mortality between egg laying and larval dispersal due to the interaction between population and carcass type: estimated differences between populations within carcass types
We found that when experimental populations were prevented from supplying care directly to their young for several generations, individuals adapted by modifying the way they constructed the nursery in which their offspring developed. Even though they could no longer meet their larvae, parents were still able to enhance their offsprings fitness through this modified form of indirect care. Importantly, Nm parents, which were reared with posthatching care, showed the same response as NC parents, which had not experienced parental care themselves. Hence, the differences we observed between FC and NC parents were not a result of phenotypic plasticity in response to their own early life environment but represented evolved divergence in this trait.
We measured change in several facets of nursery construction, and the results offer preliminary insights into the modular nature of carcass preparation and the extent to which the different elements are subject to different selection pressures and are genetically uncorrelated. The prehatching care trait with the strongest fitness consequences to the brood was the timing of insertion of a hole in the carcass. When we tested the adaptive value of the new nursery environment, in a previous study, by inserting a hole in the carcass ourselves and forcing larvae to develop with no posthatching care, we observed increased brood survival, brood size, and mass and more surviving larvae for a given clutch sizeregardless of the population from which larvae were drawn (22). By biting this hole in the carcass before they were removed, parents probably enabled larvae to enter the carcass, to feed upon it, and to take up residence there (19, 22), even in the parents absence. Furthermore, the fitness gained by the evolution of this extended parental care phenotype helped to compensate for the fitness lost from the experimental removal of direct care; by generation 13, parents from the NC and FC populations produced similar numbers of larvae per gram of carrion, as shown in ref. 27.
If the presence of a hole has such strong fitness consequences when parents are absent, why did roughly 70% of FC and 40% of NC and Nm parents still not bite a hole before larval hatching? The results for FC parents are unsurprising because they typically remain with their brood under their selective regime. Unlike NC parents, FC parents had the opportunity to make entrance holes in the carcass after their larvae hatched, as they crawled through the soil to the carcass. The proportion of FC parents making a hole in the carcass before larval hatching is close to the proportion found in wild-caught beetles breeding in the laboratory (26%) (22). As for the NC parents, it is possible that the accompanying evolution of morphological and behavioral larval traits (22, 28) helped to decrease selective pressure on accelerated hole biting by parents, or it may be that this trait was still under selection and spread further through the NC population in subsequent generations. Either possibility can explain why we did not observe all NC parents biting a hole prior to their removal by the 13th generation of experimental evolution.
Focusing on carcass roundness, we found that carcasses prepared by parents from the NC populations were rounder by the time we removed parents. In FC populations, by contrast, only larger parents were able to produce rounder carrion nests. However, just as in a previous study (25), we found no evidence that carcass roundness affected brood performance directly. Why, then, did we observe a change in this trait?
One possibility is that the shape of the carcass itself is not the trait under selection but that it changes as a by-product of selection on the pace of carcass preparation. Our experimental protocol placed NC beetles under selection to complete carcass preparation within 53 h to ensure they had bitten a hole for their larvae before they were removed and perhaps thereby incidentally favored beetles that had prepared rounder nests. FC parents, by contrast, are not under selection to complete this task as quickly. Furthermore, converting the dead body into a carrion nest is likely to be energetically costly because it involves rolling the corpse around and pushing it against the soil. This might explain why smaller beetles, with fewer energy reserves, engaged in carcass preparation less vigorously and, consequently, produced less rounded carcasses in the same timeframe in the FC lines (and also as observed in ref. 25). The strong fitness consequences of the presence of a hole contrast with the seeming lack of fitness consequences of carcass roundness, and suggest that both traits belong to the same behavioral module. Strong selection on the timing of the hole could, therefore, have dragged the rest of the behavioral module with it as a correlated response, resulting in rounder carcasses. It would be interesting to test whether this speculation is correct or whether carcass rolling is in fact a distinct behavioral module.
We found no difference between our experimental populations in a third trait associated with carcass preparationthe lytic activity of the anal exudateswhich is again consistent with the suggestion that carcass preparation comprises distinct behavioral modules. Our results imply that the different modules evolve under different selection pressures and are not strongly genetically correlated, much as has been found in the extended parental phenotypes of bees (44) and mice (45). This could explain why some elements of carcass preparation have evolved in response to the elimination of posthatching care, while others have not.
An additional explanation for the lack of differences in lytic activity between experimental populations, which does not exclude the suggestion of modularity, is that the NC larvae have evolved stronger lytic activity in their antimicrobial exudates (4648). A further explanation is that the lytic activity of the anal exudates is a highly plastic trait (24), and its plasticity prevented any evolutionary change. All these interpretations remain to be tested in future work.
We detected evolved change in the way that parents constructed the nursery environment after only 13 generations of experimental evolution. The most likely explanation is that we selected on existing standing genetic variation in the mix of wild populations that founded the experimental populations. By mixing different wild populations, we intentionally increased the genetic variation in our experimental laboratory populations. We must, therefore, be cautious not to directly extrapolate our results to wild populations and risk overestimating their ability to respond to similar selective pressures. Nevertheless, the question remains of how so much genetic variation is able to persist naturally over relatively small geographic distances. One possibility is that there is genetic differentiation between the different wild populations that we sampled originally (49). We have recently found that even nearby populations can be divergently adapted to the specific local conditions within their woodland (50). It is also possible that there is considerable genetic variation in parental care within populations, which is maintained by variation in key environmental conditions governing each breeding attempt, such as the species of the dead animal, the density of carrion, and the extent of competition within and among species for the opportunity to breed upon it (51).
The extended parental care phenotype was not the only trait to diversify across populations. NC populations had smaller clutch sizes than FC populations. Typically, burying beetles lay more eggs than can successfully be reared on a carcass and then, cull the hatchlings to adjust brood size to the existing resources (52). It is possible that NC populations are selected to lay fewer eggs that more accurately match the existing resources because they are removed before they can cull any hatchlings. This hypothesis is currently under investigation in our laboratory.
Furthermore, the cross-fostering experiment suggests that larvae were divergently and locally adapted to develop under NC vs. FC. FC larvae not only suffered higher mortality in the absence of posthatching care than NC larvae, they were also more likely than NC larvae to die when developing in carcasses prepared by parents from other lineages. NC larvae also tended to perform better in carcasses prepared by their own lineage, although this was not statistically significantperhaps because our experiment did not have enough statistical power to detect very small effects, despite a large sample size. Why is the effect size larger for FC larvae than for NC larvae? One possibility is that NC larvae mostly rely on their own traits to secure access to the carcass, whereas FC larvae are more locally adapted to a particular extended parental phenotype. We know from previous work that NC larvae have evolved relatively larger mandibles (22), a propensity to hatch more synchronously (53), and an inclination to behave more cooperatively toward siblings (28). However, further work is needed to fully understand the extent and mechanisms of local adaptation to the extended parental phenotype in FC vs. NC larvae.
How does carcass preparation in burying beetles compare with other forms of extended parental phenotypes? Despite the widespread occurrence of extended parental phenotypes across taxa, the fitness consequences are likely to depend on the extent of parental presence during offspring development. In species with no direct parental care, such as the mass provisioning beewolves and dung beetles, it is likely that the extended parental phenotype has strong fitness consequences. In dung beetles, the size of the brood mass (the ball of dung with developing larvae) that the mother stockpiles determines many offspring traits (4); in beewolves, the antimicrobial secretions applied by the parent protect the larvae against pathogens during development (5). In other species, direct parental care may mask the adaptive value of extended parental phenotypes. For example, egg size can be considered an extended parental phenotype, yet evidence that avian egg size correlates with offspring survival is inconclusive (reviewed in ref. 54). As pointed out in ref. 54, large eggs can benefit offspring survival in harsh environments, but in good conditions, parental provisioning masks any effect of egg size on survival. Interestingly, the same occurs in burying beetles, where effects of egg size on survival are masked by posthatching care (55). Our findings regarding the timing of carcass preparation parallel results obtained previously for egg size in burying beetles and birds. It suggests that the stability of the environment (whether social or abiotic) affects the evolutionary feedbacks between different forms of parental care. In future work, it will be important to test whether these evolutionary feedbacks exist in natural populations, where the environment is more complex and unpredictable than in the laboratory.
Parental care comprises a suite of traits that are integrated to promote offspring fitness (56). Previous work has emphasized that the wider physical environment and the social environment within the family are each sources of selection on the form and function of parental behavior (5659). Here, we have shown that acts of care are themselves a source of selection on other types of parental traits. Preventing any form of direct care causes parents to evolve modifications in the way in which they construct the nursery environment. Furthermore, coadapted traits in parents and offspring evolved rapidly when we experimentally eliminated direct forms of posthatching care, suggesting that these traits have a high degree of genetic variability in natural populations.
All data, code for image analysis and statistical analysis are available in the SI Appendix.
We thank S. Aspinall and C. Swannack for maintenance of beetle populations and laboratory assistance, J. Troscianko for the ImageJ script, A. Sutter and E. Postma for statistical advice, and B. Kuijper for helpful discussions. We also thank D. Mock and an anonymous reviewer for comments, which greatly improved this manuscript. This work was funded by European Research Council Consolidators Grant 310785 Baldwinian_Beetles (to R.M.K.). R.M.K. was also supported by a Wolfson Merit Award from the Royal Society.
Author contributions: A.D., D.R., and R.M.K. designed research; A.D., D.R., A.C.H., and B.J.M.J. performed research; A.D. and D.R. analyzed data; and A.D., D.R., B.J.M.J., and R.M.K. wrote the paper.
The authors declare no competing interest.
This article is a PNAS Direct Submission.
This article contains supporting information online at https://www.pnas.org/lookup/suppl/doi:10.1073/pnas.2102450118/-/DCSupplemental.
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The Fruit of Evolution Anime Episode 9 Release Date and Time, COUNTDOWN, Where to Watch, News and Everything You Need to Know – Epicstream
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The Fruit of Evolution follows Seiichi Hiragi, who was insulted and bullied because of his appearance. He does not have any friends and was often remarked with harsh words by his classmates. One day, he heard a voice, claiming to be God, saying that he and the rest of his classmates should prepare to be transported to another world.
True enough, Seiichi and his classmates were taken to a fantasy world where stats, levels, and skills are needed to survive. Since he has no one, he was summoned to a different area where he found the Fruit of Evolution that changed his life. The series will follow Seiichis journey in this new world and how he became a champion.
Episode nine of The Fruit of Evolution will be released on November 30, 2021. It is entitled, Black Cat Oliga. It will make its premiere in Japan on Monday at 10:00 PM JST. Of course, for international fans, they can expect the series by Tuesday at 2:30 AM PST.
The series can be streamed on Crunchyroll in English subtitles. For the English dubbed version, fans will have to wait for Cruchyrolls official announcement regarding the matter. While waiting, fans can stream the series on site for free as Crunchyroll has a free trial period for non-members. Members or those who are interested to become members must pay $9.99 per month or $79.99 per year to keep their membership.
Those who signed up can get exclusive perks from the site such as ad-free shows, access to the sites libraries, and simulcasts after Japan. Fans should take note that simulcasts are not available for non-members which means that they must wait for a few days before they can stream The Fruit of Evolution on Crunchyroll, unlike members who will just wait an hour after the episode was released in Japan.
It has been confirmed that the series will have 12 episodes that will run until December 2021, unless there is a delay in production or airing. Those who are curious as to what will happen to Seiichi can stay tuned to find out.
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The UK Government Wants to Sequence Your Babys Genome – WIRED
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In November 2019, Matt Hancock, then the United Kingdoms health secretary, unveiled a lofty ambition: to sequence the genome of every baby in the country. It would usher in a genomic revolution, he said, with the future being predictive, preventative, personalized health care.
Hancocks dreams are finally coming to pass. In October, the government announced that Genomics England, a government-owned company, would receive funding to run a research pilot in the UK that aims to sequence the genomes of between 100,000 and 200,000 babies. Dubbed the Newborn Genomes Programme, the plan will be embedded within the UKs National Health Service and will specifically look for actionable genetic conditionsmeaning those for which there are existing treatments or interventionsand which manifest in early life, such as pyridoxine-dependent epilepsy and congenital adrenal hyperplasia.
It will be at least 18 months before recruitment for participants starts, says Simon Wilde, engagement director at Genomics England. The program wont reach Hancocks goal of including every baby; during the pilot phase, parents will be recruited to join. The results will be fed back to the parents as soon as possible, says Wilde. For many of the rare diseases we will be looking for, the earlier you can intervene with a treatment or therapy, the better the longer-term outcomes for the child are.
The babies genomes will also be de-identified and added to the UKs National Genomic Research Library, where the data can be mined by researchers and commercial health companies to study, with the goal of developing new treatments and diagnostics. The aims of the research pilot, according to Genomics England, are to expand the number of rare genetic diseases screened for in early life to enable research into new therapies, and to explore the potential of having a persons genome be part of their medical record that can be used at later stages of life.
Whole genome sequencing, the mapping of the 3 billion base pairs that make up your genetic code, can return illuminating insights into your health. By comparing a genome to a reference database, scientists can identify gene variants, some of which are associated with certain diseases. As the cost of whole genome sequencing has taken a nosedive (it now costs just a few hundred bucks and can return results within the day), its promises to revolutionize health care have become all the more enticingand ethically murky. Unraveling a bounty of genetic knowledge from millions of people requires keeping it safe from abuse. But advocates have argued that sequencing the genomes of newborns could help diagnose rare diseases earlier, improve health later in life, and further the field of genetics as a whole.
Back in 2019, Hancocks words left a bad taste in Josephine Johnstons mouth. It sounded ridiculous, the way he said it, says Johnston, director of research at the Hastings Center, a bioethics research institute in New York, and a visiting researcher at the University of Otago in New Zealand. It had this other agenda, which isn't a health-based agendait's an agenda of being perceived to be technologically advanced, and therefore winning some kind of race.
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Chloranthus genome provides insights into the early diversification of angiosperms – Nature.com
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Genome sequencing, assembly, and annotation
Chloranthus spicatus has a genome size of 2.97Gb (gigabases) based on K-mer analysis (Supplementary Fig.2, Supplementary Data1); the individual sequenced had a heterozygosity rate of 0.99%, which is possibly associated with the obligate outcrossing system of this species31. Genomic DNA was sequenced using three different methods: 182Gb of Oxford Nanopore Technologies (ONT) long reads, 240Gb of shotgun short reads (BGIseq 2000), and 240Gb of Hi-C data.
The assembled genome was 2,964.14Mb with a contig N50 size of 4.59Mb, covering 99.7% of the genome size as estimated by K-mer analysis (Supplementary Data2,3). Assembled contigs were then clustered into 15 pseudochromosomes, covering 99.9% of the original 2,964.14Mb assembly, with a super-scaffold N50 of 191.37Mb. After performing the Hi-C validation, the genome showed high contiguity, completeness, and accuracy (Supplementary Fig.3) with the 15 pseudochromosomes corroborated by previous chromosome counts of 2n=3032. In all, 21,392 protein-coding genes were predicted using a combination of homology-based and transcriptome-based approaches. The proteome was estimated to be at least 96.8% complete based on BUSCO (benchmarking universal single-copy orthologs) assessment (Supplementary Data4).
The results obtained by Tandem Repeats Finder were mapped to predict coding genes of C. spicatus to estimate the proportion of incorrectly detected paralogous genes (Supplementary Data5). In the C. spicatus genome, repetitive elements accounted for 70.09% of the genome assembly, of which 97.67% were annotated as transposable elements (TEs) (Supplementary Data5). Long terminal-repeat retrotransposons (LTRs) were the major class of TEs and accounted for 58.79% of the genome. Among the LTRs, the most abundant elements were Gypsy (68.03% of the LTRs), followed by Copia (19.01% of the LTRs) (Supplementary Data6). The time of insertion of LTRs in the genome of C. spicatus was estimated based on a peak substitution rate of 0.03 (Supplementary Fig.4). We assumed a synonymous substitution rate of 1.51109 bases per year following two recent studies of the closely related magnoliid lineages Liriodendron and Chimonanthus, resulting in an LTR burst time of approximately 9.9Ma(see methods).
Comparison of the gene and genome characteristics (e.g., genome size, gene size, exon and intron sizes) of C. spicatus and 17 other phylogenetically diverse flowering plants (Supplementary Data7) revealed that long genes and long introns were more prevalent in the genomes of Chloranthales and magnoliids compared to other angiosperms (Fig.2a, b; Supplementary Data8). As the presence of nonfunctional genes and variation in total gene numbers among different species would bias the statistics of gene characteristics, we selected 2,184 high-confidence orthologs from C. spicatus, six magnoliids, and two well-characterized angiosperm genomes, Arabidopsis thaliana and Oryza sativa (Supplementary Fig.5a, Supplementary Data9). Comparison of the lengths of the coding regions and introns revealed that the average coding region lengths in all nine plant genomes were similar (ranging from 1,5331,557bp), whereas the lengths of introns varied greatly (ranging from 1533,681bp; Supplementary Data9). Chloranthus spicatus (3681bp) and the six magnoliid genomes displayed much longer introns (ranging from 1,2702,390bp) than those of A. thaliana (153bp) and O. sativa (372bp), signifying that the presence of longer genes is due to the extension of the intron length rather than coding regions. We separated the 2184 high-confidence orthologs into groups based on length: <5kb (short genes), 510, 1020, and >20kb (long genes). Long genes (>20kb) in C. spicatus (876) were much greater in number than those in Oryza (2) and Arabidopsis (0) (Supplementary Data8,9).
a Comparison of gene and genome characteristics (i.e., genome size, gene size, exon, and intron sizes) of C. spicatus and 17 other flowering plants. b Comparison of the lengths of the coding regions among nine representative plant genomes. c Collinearity patterns between genomic regions of Amborella, Vitis, and Chloranthus. The colored (red/grey) wedges highlight the major syntenic blocks shared among these species. d The number of synonymous substitutions per synonymous site (Ks) distributions confirming the occurrence of a whole-genome duplication (WGD) event in C. spicatus. Source data underlying Fig. 2a are provided as a Source Data file.
We found a significant correlation between intron length and genome size (R2=0.8869). The highly conserved average length and a number of exons among the nine species compared further indicated that exon structure is mostly consistent among the angiosperms. The average length of introns was approximately 1.66kb, 2.87kb, and 3.35kb for Lauraceae, Magnoliaceae, and Chloranthus, respectively (Supplementary Data8).
LTR-RT represents a major fraction of plant genomes, particularly gymnosperms and magnoliids13. Thus, to understand the constitution of introns in C. spicatus, we looked for repeated elements. LTRs were widely detected in the long introns of C. spicatus and appear to be the major contributor to the long introns in this species. For instance, the gene AT1G04950.1 located on Chromosome 1: 14026061408184 encodes Transcription initiation factor TFIID subunit 6 in A. thaliana. The LTR length of this orthologous gene in C. spicatus (Cspi02386) was significantly longer than that in Lauraceae, Magnoliaceae, O. sativa, and A. thaliana (Supplementary Fig.5b).
We discovered 11,500 intact LTRs and classified them into two groups, Gene-20K LTR (LTRs distributed in genes >20kb length) and ALL LTR (LTRs distributed throughout the genome, Supplementary Fig.6). A similar model distribution of Gene-20K LTR and ALL LTR (Supplementary Figs.7, 8) suggested that the insertion timing of both LTR groups was the same. Further analyses of expression levels revealed that genes with short introns were more likely to exhibit low expression, while genes with long introns exhibited higher expression. However, when the intron length was larger than 40kb, the expression level subsequently declined in C. spicatus (Supplementary Fig.9).
Our investigation of collinearity and synteny patterns between genomic regions of Amborella trichopoda (sister to all other extant angiosperms), Vitis vinifera (sister to all other rosids), and C. spicatus showed highly conserved synteny among these three species (Fig.2c). In addition, this analysis showed clear structural evidence of a single ancient WGD in C. spicatus. The syntenic depth ratio between C. spicatus and A. trichopoda was found to be 1:2, which means that each A. trichopoda region could be matched to two genomic regions in the C. spicatus genome while the comparison of C. spicatus with the ancient hexaploid V. vinifera genome revealed a 2:3 syntenic depth ratio (Fig.2c).
To further investigate the extent of conservation of genome structure between C. spicatus and other angiosperms, we performed pairwise synteny comparisons with several species of magnoliids (Magnolia biondii, Liriodendron chinensis, Persea americana, Cinnamomum kanehirae, Litsea cubeba, Phoebe bournei) (Supplementary Data10). Our results clearly showed that C. spicatus shared a higher number (3,029; i.e., 62.7%) of syntenic blocks (at both the scaffold and chromosome level) with species in its sister clade, the magnoliids, than with Ceratophyllales (2,483, 52.5%), V. vinifera (2,275, 56.5%), or the monocot Oryza sativa (1,700, 45.3%) (Supplementary Fig.10, Supplementary Data10). Amborella trichopoda (1,150, 57%) shared the fewest syntenic blocks with C. spicatus among all the species used for comparative analysis (Supplementary Data10); overall, the number of shared syntenic blocks between these representative genomes generally coincided with phylogenetic relationships.
To further investigate the phylogenetic placement of the C. spicatus WGD, we compared the distribution of Ks values, the number of synonymous substitutions per synonymous site. The Ks distribution for C. spicatus paralogs showed an obvious peak at approximately Ks=0.9, and peaks at similar KS values were identified for other species (Ascarina rubricaulis, Chloranthus japonicus, and Sarcandra glabra) of Chloranthales (Fig.2d); the coincidence of these KS values suggests that an ancient WGD event may be shared among all extant members of this clade. Further, the KS values for orthologs shared by C. spicatus and Phoebe bournei (Lauraceae; magnoliids) show a peak value slightly greater than that observed for paralogs in C. spicatus and other Chloranthales species, which suggests that the Chloranthales WGD occurred after the divergence of Chloranthales and magnoliids (Fig.2d). These observations suggest that the ancient WGD event we detected was specific to Chloranthales.
Although magnoliids also exhibit an ancient WGD event (Supplementary Data11a), this event was not shared with Chloranthales. The age of the Chloranthales WGD is similar to that of a number of ancient polyploidy events that occurred independently in several major clades of angiosperms: the gamma () event (103.67129.35Ma) in the common ancestor of core eudicots; the tau () event (101.82138.82Ma) during the early diversification of monocots; the lambda () event (98.22130.04Ma) during the early diversification of magnoliids; the pi () event (85.78119.82Ma) in Nymphaeales; the kappa () event (98.06130.54Ma) in Chloranthales (this study); and an unnamed event specific to Ceratophyllales33 (Fig.1d). Although these WGD events occurred independently, many of the same stress-related genes were retained independently after these WGD events, including two heat shock transcription factors and Arabidopsis response regulators34. These genes also appear to be retained in Chloranthus (Supplementary Figs.11, 12).
To resolve the long-standing uncertainty regarding the phylogenetic position of Chloranthales and relationships among the five major lineages of Mesangiospermae, 257 single-copy nuclear (SCN) genes were identified using whole-genome sequences from C. spicatus and 17 other flowering plants (strict single-copy genes for each species without missing genes; see Methods for species). The aligned protein-coding regions were analyzed using coalescent and concatenation approaches. Both analyses yielded an identical and highly supported topology (bootstrap values of 100%) (Supplementary Fig.13) in which monocots were sister to all other mesangiosperms; Chloranthales appeared as the sister group to magnoliids, and Chloranthales + magnoliids together were sister to Ceratophyllales + eudicots (Fig.2a, Supplementary Fig.13). We also performed phylogenetic inference based on a 937-SCN gene data set with selection criteria allowing a maximum of three missing species. The phylogenetic results showed an identical topology to that of the 257-SCN gene data set, supporting Chloranthales as the sister to magnoliids (Supplementary Fig.13).
To avoid potential errors caused by sparse gene sampling, we extracted 2,329 low-copy nuclear (LCN) genes, allowing a maximum of three copies for each gene in each species. The phylogenetic trees were then similarly reconstructed by both coalescent and concatenation methods as described above. The resulting species trees were topologically identical to the phylogenetic findings as revealed above based on the 257-SCN and 937-SCN data sets (Supplementary Fig.13). Among the 2,329 LCN gene trees, 61% of the trees (454 out of 742 trees) placed Chloranthales as the sister lineage to magnoliids, with bootstrap support greater than 70% (type I, Fig.1c).
As poor taxon sampling may lead to topological errors, we added a large number of published genomes of the angiosperms and two transcriptomes of Chloranthales to increase our taxon sampling. We extracted 612 mostly single-copy orthologous genes following Yang et al.21and generated a 218-species dataset. The phylogenetic results were congruent with the topologies based on analyses of the 257-SCN, 937-SCN, and 2,329-LCN data sets, supporting monocots and a clade of Chloranthales plus magnoliids as successive sister lineages to a clade of Ceratophyllales plus eudicots (Fig.1d, Supplementary Fig.14).
Phylogenetic analyses were also conducted based on chloroplast DNA sequence data. We selected 80 genes, following a recent study that analyzed 2,881 plastomes1, and obtained two data sets, with 18 species and 134 species, respectively. The resultant topologies using both chloroplast data sets agree with those from the four nuclear data sets in strongly supporting a sister relationship between Chloranthales and magnoliids (Supplementary Figs.15, 16).
Although the same pattern of phylogenetic relationships among the five major groups of Mesangiospermae was consistently recovered in analyses of all four nuclear data sets, phylogenetic incongruence was observed among nuclear gene trees. A major conflict was identified among single-gene trees in all four nuclear gene data sets (257-SCN, 937-SCN, 2,329-LCN, and 612-SCN) involving the placement of the Chloranthales-magnoliids clade relative to monocots and eudicots. We summarized the conflict among gene trees in the 2,329-LCN data set with regard to the proportions of trees supporting three different branching patterns for Chloranthales-magnoliids, monocots, and eudicots. The percentage of gene trees supporting the Chloranthales-magnoliids clade plus eudicots together forming a sister group to monocots (Type II) was higher than percentages for the other two topologies (gene trees with BS>70%: Type I, 30%; Type II, 53%; Type III, 17%; Fig.3a). It is notable that Type I and Type III, the two relationships conflicting with the most likely species tree, are not equal in frequency, suggesting gene tree incongruence patterns not expected under ILS alone (below).
a A summary of the conflicts among gene trees in the 2,329-LCN data set with regard to the proportions of trees supporting three different branching patterns for Chloranthales-magnoliids, monocots, and eudicots.b Gene tree incongruence between nuclear (2,329 LCN genes)and plastid (80 plastid genes) treesin a consensus DensiTree plot.c Aconsensus scenario showingancient gene flow between monocots and eudicots, inferred by QuIBL, PhyloNet, and ABBA-BABA D-statistics. Source data underlying Fig. 3b are provided as a Source Data file.
Furthermore, gene tree discordances were also observed between chloroplast and nuclear gene trees. Phylogenetic analyses of these 18 and 134 flowering plants inferred from 80 concatenated plastid genes strongly supported the placement of the Chloranthales-magnoliids clade as sister to all other Mesangiospermae (Fig.3b and Supplementary Figs.15, 16), which is consistent with the Type I nuclear topology (Fig.3a).
A nonrandom incongruence pattern was observed among different topology types: constituent species of monocots (3 spp.), eudicots (4 spp.), and magnoliids (7 spp.) were assigned to a clade. For each topology type, the majority of genes supported the monophyly of C. spicatus and seven species of magnoliids (Type I: 168/316=53.2%; Type II: 297/496=59.9%; Type III: 122/203=60.1%). We also mapped genes that caused conflict on the chromosomes. Genes that supported both Type I and Type II topologies were found to be evenly distributed on the 15 chromosomes (Supplementary Fig.17). Chi-squared tests showed that gene numbers and locations on each chromosome do not differ significantly (Supplementary Data12, 13).
The observed gene tree incongruence between nuclear and chloroplast trees and among nuclear single-gene trees indicates the possibility of incomplete lineage sorting (ILS) and/or hybridization events during early angiosperm evolution. We first used QuIBL, an approach using branch length distributions across gene trees, to infer putative hybridization patterns35. In all, 100 runs of QuIBL were conducted using 500 randomly selected trees from the 2,329 LCN gene trees. Strong hybridization signals (rate >0.1) were identified in several pairs of major clades of angiosperms (Supplementary Figs.18, 19), including: (i) ancestor of eudicots and ancestor of monocots; (ii) ancestor of eudicots and C. spicatus; (iii) ancestor of the species pair Arabidopsis thaliana-Erythranthe guttata and Vitis vinifera; (iv) Erythranthe guttata and Ceratophyllum demersum. Strong signals of ILS were also detected between Lauraceae and Magnoliaceae (Supplementary Figs.18, 19). Among these events, cases (i) and (ii) can be explained as the causes of gene tree incongruence of the Chloranthales-magnoliids clade relative to monocots and eudicots.
A second analytical approach, PhyloNet, was used to further assess putative hybridization events in our phylogeny. Five network searches were carried out by allowing one to five reticulation events. The species network under the best model (AICs=50.78; BICs=30.52, Supplementary Data14) identified two hybridization events among major clades of angiosperms (Supplementary Fig.20a), supporting ancient hybridization between early members of Nymphaeales and monocots. Ancestral gene flow between monocots and eudicots (Supplementary Fig.20a) was additionally supported by results of QuIBL (Supplementary Fig.19). To test whether the PhyloNet results identified hybridization correctly, we repeated the PhyloNet analyses using coalescent trees simulated without hybridization under the ASTRAL species tree (Supplementary Fig.11). As expected, the species network under the best model (AICs=51.21; BICs=30.25, Supplementary Data14) detected no hybridization events among monocots, eudicots, and magnoliids (Supplementary Fig.20b), suggesting that the analysis using empirical gene trees was not susceptible to false positives.
The unequal frequencies of Type I and Type III topologies discordant with the species tree suggested that ILS alone may not explain the gene tree conflicts in this study; therefore, we also used the ABBA-BABA approach to explicitly model patterns of discordant genealogies. This analysis also inferred frequent hybridization signals (Supplementary Fig.21). Consistent with the other two methods employed, the hybridization event between monocots and eudicots was detected, with the largest absolute Z-value (14.6).
In summary, all three methods used to investigate hybridization (QuIBL, PhyloNet, and ABBA-BABA D-statistics) were unanimous in suggesting ancient gene flow between monocots and eudicots, although with variation among methods in the number of hybridization events and any additional lineages involved in hybridization. A consensus scenario is presented (Fig.3c) showing ancient gene flow between monocots and eudicots.
Terpene synthases (TPSs) are key enzymes that control the production of terpenoids, crucial defense compounds in plants36. To explore the evolution of the TPS family in Magnolia and Chloranthales, as well as to garner a better understanding of terpene evolution in angiosperms, we searched for candidate TPSs in C. spicatus and 17 other flowering plants (the same taxon sampling as in the comparative genomics analyses). Chloranthus spicatus encodes 73 TPSs (Supplementary Data15), similar to V. vinifera (75) and A. coerulea (74), while C. kanehirae exhibited the largest number (95) of TPSs. Particularly, compared to the ANA grade, there was higher diversity in almost all of the magnoliid species and C. spicatus (Supplementary Data16). Furthermore, according to the subfamily classification of TPS genes, TPSs were divided into 6 clades: TPS-a, b, c, e, f, and g (Fig.4b). In Amborella and members of Nymphaeaceae (Euryale ferox and Nymphaea colorata), TPS-a was absent (Supplementary Data16). Furthermore, when we performed GO enrichment analyses using the shared genes between magnoliids and Chloranthales, the genes related to terpene synthase activity (GO:0010333) exhibited a low P-value, indicating that terpene synthase activity was the most enriched of all GO categories (Supplementary Data17). Moreover, our gene family analysis indicates that the TPS-a and TPS-b gene clades expanded remarkably in magnoliids and Chloranthales compared to all other angiosperm clades (Supplementary Data16, Fig.4b); these gene clades primarily consist of angiosperm-specific sesquiterpene and monoterpene synthases, respectively. Several unique Chloranthus-specific sesquiterpenoids, including chlorahololides A, chloranthalactone A, and chlotrichenes A and B with bioactive potential, have been isolated and chemically synthesized in the lab37,38,39.
a A total of 44 genes related to the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway and the mevalonate (MVA) pathway were identified in C. spicatus (left panel). HMGR and DXS exhibited the highest copy numbers in the MEP and MVA pathways, respectively. Differentially expressed genes among seven representative tissues of C. spicatus involved in MEP and MVA pathways are shown in the right panel. b Identification of candidate terpene synthases (TPSs) in C. spicatus and subfamily classification revealed six major clades (TPS-a, b, c, e, f, and g). The gene family tree indicates that TPS-a and TPS-b gene clades are significantly expanded in magnoliids and Chloranthales. c Contraction of R genes in Chloranthales. The nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes were divided into three classes: TIR-NBS-LRR (TNL), CC-NBS-LRR (CNL), and RPW8-NBS-LRR(RNL). In all, 3,518 NBS genes were identified in 28 angiosperm species. * indicates the data were obtained from a previous study40.
To understand the origin of paralog generation of these TPS genes, we compared the numbers of genes in each duplication type among species of magnoliids and Chloranthus (Supplementary Data18). The results showed tandem (23, 33.3%), WGD (18, 26.1%), and transposition (21, 30.4%) duplication events contributed to the expansion of TPSs in C. spicatus, with only a few proximal repeats (7, 10.1%). The 73 CsTPS genes are not evenly distributed across the 15 chromosomes, with Chr2 having the highest concentration of TPS genes. Tandem repeats are mainly present on Chr2 and Chr7 (5 and 6 tandem repeats, respectively), but are also present on chromosomes 4, 5, 9, 14, and 15. We hypothesize that WGD contributed to TPS expansion as well, for instance, the higher copy number of the pairs CsTPS03 and CsTPS33 and CsTPS05 and CsTPS19 (Supplementary Fig.22, Supplementary Data16, 18).
Next, we investigated the genes involved in the production of non-volatile isoprenoids via the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway and the mevalonate (MVA) pathway and identified 44 genes in C. spicatus that may be involved in these pathways (Supplementary Data19, 20). There were multiple copies of the genes encoding enzymes related to the MVA pathway, and the number was approximately double that detected for genes in the MEP pathway. The gene encoding the HMGR enzyme (Hydroxy-3-methylglutaryl) displayed the highest number of gene copies (12) followed by AACT (Acetoacetyl-CoA thiolase) (6 copies). In the MEP pathway, except for DXS (1-deoxy-D-xylulose-5-phosphate synthase), DXR (1-deoxy-D-xylulose 5-phosphate reductoisomerase1-deoxy-D-xylulose 5-phosphate reductoisomerase), and GGPS (geranylgeranyl pyrophosphate synthase), each remaining enzyme had only one corresponding gene copy. In addition, to further validate this observation, a differential gene expression (DE) analysis was also performed using the transcriptome data from different plant parts (stamen, carpel, and peduncle) (Fig.4a). Regardless of the number of gene copies encoding the enzymes of these pathways, at least one gene copy for each enzyme was highly expressed in each tissue. However, for the multiple-copy genes, a few genes were responsible for most of the expression, while the remaining copies were weakly expressed. Altogether, the analyses of expansion and differential expression of TPSs suggest that the appearance of multiple-copy genes in the MVA pathway could be related to the expansion of the TPS-a subfamily, which is probably responsible for the production of sesquiterpenes in Chloranthales.
Nucleotide-binding site-leucine-rich repeat (NBS-LRR, NBS for short) genes encompass more than 80% of the characterized R genes40. The NBS genes were divided into three classes, namely, TIR-NBS-LRR (TNL), CC-NBS-LRR (CNL), and RPW8-NBS-LRR (RNL)40. We identified 3,518 nucleotide-binding site-leucine-rich repeats (NBS-LRR, NBS for short) genes in 28 angiosperm species, and the nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes were classified into three classes: the Toll/interleukin-1 receptor TIR-NBS-LRR (TNL), N-terminal coiled-coil motif CC-NBS-LRR (CNL), and resistance to powdery mildew8 RPW8-NBS-LRR (RNL)40 (Supplementary Data21). The gene copy number in each NBS class showed considerable variation among the analyzed species (Fig.4c). The highest number of TNL genes was found in M. truncatula (of the 28 species examined), while the highest number of CNLs and RNLs were in S. tuberosum and G. max, respectively. Moreover, M. truncatula, G. max, and S. tuberosum contained more R genes than the other angiosperms examined; Chloranthales and magnoliids contained many fewer R genes. TNL and RNL were absent from Chloranthus and the magnoliids (as in the monocot species, O. sativa), and only 19 and 13 CNLs were present in C. spicatus and Magnolia biondii, respectively (Fig.4c, Supplementary Data21). In the species having both TNL and CNL genes, the CNLs are generally more common than the TNLs, with the exception of A. thaliana, V. vinifera, A. trichopoda, E. ferox, and N. colorata.
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Bihar govt directs officials to conduct genome study, increase vaccination to tackle new Covid variant – Hindustan Times
Posted: at 9:53 pm
In wake of the emergence of the new Covid-19 variant Omnicron, the Bihar government on Sunday directed health officials to conduct genome surveillance of all Covid positive samples to ascertain the strain of the virus
ByAnirban Guha Roy/HTC, Patna
In wake of the emergence of the new Covid-19 variant Omnicron, the Bihar government on Sunday directed health officials to conduct genome surveillance of all Covid positive samples to ascertain the strain of the virus.
Chief minister Nitish Kumar during a review meeting of the health department on Sunday directed officials to be alert and ensure that there is adequate stocks of medicines and health facilities at the hospitals.
The chief minister also stressed that people who have returned from abroad should be monitored and those who have tested positive should be screened for the new variant. Kumar who also reviewed the ongoing vaccination programme against Covid-19 laid stress on accelerating the vaccination drive and directed officials to use all modes of publicity to encourage people who have taken the 1st dose to inoculate themselves with the 2nd dose as well. There should be state level monitoring of those districts where the vaccination drive and testing is slow. There should not be any laxity on testing and vaccination drive should be widely publicised , the CM said. Till Sunday, Bihar has inoculated 80 million citizens, according to officials.
During the meeting, Bihar representative of World Health Organisation ( WHO) Dr Subramaniyam apprised the CM about the new Covid variant Omicron and its various aspects. Additional chief secretary (health) Prataya Amrit said the health department is on high alert to tackle the new variant.
Health minister Mangal Pandey, while talking to mediapersons on Sunday, said, Though there has been no positive cases of the new variant in the country so far, the health department is on high alert and directives have been issued to health officials to maintain tight vigil while conducting RT-PCR tests to detect any strain of the new variant so that immediate steps can be taken.
Asked about the central governments directives to conduct tests of around 281 persons who have arrived from foreign countries in last two months in Bihar, the health minister said the health officials have started visiting residences of the persons mentioned in the list.
Health officials have started visiting the persons mentioned in the list who have returned from abroad. There are instances where people have their address in Bihar but live in different parts of the country. So, we will tests of all those people staying in Bihar , the minister said, who also attended the review meeting of health department along with the CM.
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Bihar govt directs officials to conduct genome study, increase vaccination to tackle new Covid variant - Hindustan Times
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