Coral Adaptation and Epigenetics

By Rud Istvan

WUWT has posted several excellent articles by Jim Steele on how global warming alarmism uses corals as the poster child for warming and acidifying oceans, none of which is scientifically justified. A brief review follows, calling attention to a recently discovered additional adaptation mechanism not covered AFAIK by Jim Steele’s posts. The motivation for this post was triggered by a recent lunch with newish neighbor Charles the Moderator (CtM), and his sharing many wonderful underwater photographs of the coral reef he now dives frequently off Pompano Beach (same reef system as off Fort Lauderdale, just a few miles further north and more conveniently onshore). If any coral reef images appear in this post, CtM added them and gets the photocredits.

Snorkeling in the neighborhood. Click for larger image. ~ctm

I have had a longstanding interest in corals, since have been recreationally diving coral reefs for several decades, including those off my Fort Lauderdale beach condo since 2000. Even took my dive uncertified teenagers to the US Virgin Islands, where we snorkeled the reefs at the Carambola resort on St. Croix, and did the Virgin Islands National Park snorkel trail at Buck Island. It is the only underwater ‘hiking’ trail in the entire US National Park system.


Corals are now known to have three, not two, evolutionary adaptation systems. This fact alone refutes any coral climate alarmism such as regularly coming out of Australia concerning the Great Barrier Reef.

The first adaptation mechanism is simply Darwinian evolution. Corals are ancient animals and very diverse. They have been around since the Cenozoic era. You would correctly surmise that as an animal group, corals have already survived a LOT of climate change. Corals are part of the Cnidara phylum, in the class Anthoza, comprising 5 orders of which four exist and one is extinct. There are over 2400 known coral species.

From a global warming alarm perspective, Darwinian evolution probably works too slowly for corals to adapt to ‘sudden’ anthropogenic global warming and associated ocean acidification. (For more on that overblown ocean alarm, CtM has a separate possible post on seawater chemistry and ocean pH biology, excerpted and adapted from essay Shell Games in my ebook Blowing Smoke.)

The second major coral adaptation mechanism is bleaching, which Jim Steele has previously explained in detail here. In sum, corals are filter feeders. All shallow water corals in the ocean photic zone have evolved a secondary food source provided by symbiont zooxanthellae, which are photosynthetic dinoflagellate algae of the genus Symbiodinum. These live within the coral polyp body, and photosynthesize food for themselves and the host polyp. In return, the polyp provides its symbionts with ‘fertilizer’ from its metabolic waste products. Symbionts provide the profusion of coral colors seen when diving live reefs. Coral polyps are translucent, so without symbionts appear white against their calcium carbonate exoskeletons, which we incorrectly think of as ‘coral’. Broad variation in zooxanthellae species means each is exquisitely adapted to local temperature and pH. If seawater conditions change, corals have evolved the ability to bleach. They expel their current symbionts (thus appearing ‘bleached’ white), and then wait for better ones to come along. That happens naturally since better adapted zooxanthellae differentially multiply in abundance.

This adaptation mechanism is biologically fast, less than a year. Coral alarmists argue that if the polyps do not repopulate symbionts within a few months, they can starve to death (typically about a year or a bit more depending on local seawater fertility). That is true. In which case the dead reef will be eventually be repopulated from new coral larvae after the annual spawning. As prophetically said in Jurassic Park, “Life finds a way.”

Snorkeling in the neighborhood. Click for larger image. ~ctm

Since about 2015, a third coral adaptation mechanism has been shown, epigenetics. Recent references are too numerous to link here. Interested readers can find dozens of papers and articles by simply googling ‘coral epigenetics’. Jean-Baptiste LaMarck was correct after all! Environmentally adapted traits CAN be passed down the generations. Especially in corals, which not only reproduce sexually by spawning, but also asexually by budding that directly transfers epigenetics to progeny.

Technically, the ‘noncoding’ DNA around each gene’s DNA (we skip the intron/exon ‘gene’ complication) determines when and how often a gene is expressed in relation to its cell’s ‘environment’. That is how embryos develop. The main method for ‘permanently’ turning off genes no longer needed as an embryo develops is DNA methylation, discovered by embryologists.

The big newish epigenetics realization is that DNA methylation can also ‘evolve’ in response the external environment, altering patterns of gene expression without evolutionary changes to the genes themselves. This alters the phenotype but not the genotype.

There is also a second epigenetic mechanism not found in embryology but recently found in many organism’s environmental responses. Since a cell’s nucleus chromosomes have their DNA strands bunched up like a yarn tangle, the tangle has to unfold for interior genes to be expressed into RNA. RNA in turn is the template cellular cytoplasm machinery uses to make the protein the gene encodes. For conservation of ‘energy’, cells evolved DNA refolding where the most frequently used genes eventually get located on the DNA tangle’s outside.

Coral epigenetics has now been show to use both methods, and provides neither a very fast nor very slow adaptation response. It may take decades—just the right time frame to adapt to global warming and climate change.

Since I am leaving any coral images to CtM (and those would not show epigenetics anyway), illustrating how powerful epigenetic adaptation is uses an example more familiar to all, and verifiable in any grocery store, dried beans.


Modern genetic analysis of dried beans (all P. vulgaris) tells a fascinating epigenetics story. All the many domestic food phenotypes pictured above emerged near simultaneously from a single wild plant. As a result, they today still have very little genotypic variation amongst beans that superficially appear to come from different plants. Nope, all are P. vulgaris, no different than hundreds of dog breeds are all Canus lupus subspecies familiaris (translation, domesticated wolves).

Archeology shows that domesticated P. vulgaris emerged independently in Peru, (landrace kidney beans), in the Mexican highlands (landraces pinto and red beans), and once more in lowland MesoAmerica (landraces black and navy beans), all between 10000BCE and 8000BCE. These distinctly different bean phenotypes all emerged together during the emergence of sedentary agriculture and domesticated plants and animals. The DNA analysis proves bean phenotypes emerged through epigenetic selection rather than through genetic selective breeding—which would have introduced more genetic variation.

I agree with Jim Steele. Coral alarmism doesn’t amount to a hill of beans.


71 thoughts on “Coral Adaptation and Epigenetics

  1. and………

    “Coccolithophores need carbon dioxide dissolved in seawater for photosynthesis, and bicarbonate ions, in equilibrium with carbon dioxide, to build their calcium shells. But it was assumed that too much carbon dioxide would jeopardise the delicate balance of this two-way chemical reaction.

    Not so, it seems, with the coccolithophore, or at least with the most abundant species, called Emiliania huxleyi. The latest study into this species shows that it appears to thrive on high levels of carbon dioxide. Instead of finding it difficult to make its calcium carbonate plates, as some scientists had expected, the organism can, in fact, make bigger and bigger plates as carbon dioxide concentrations are increased artificially, according to a study published in the current issue of the journal Science.”…ld-813915.html


    “More acidic water may be a sign of healthy corals, says a new study, muddying the waters still further on our understanding of how coral reefs might react to climate change.

    Andreas Andersson of the Scripps Institution of Oceanography in San Diego, California, and his colleagues carefully monitored a coral reef in Bermuda for five years, and found that spikes in acidity were linked to increased reef growth.

    The team found that coral growth itself made the water more acidic as the corals sucked alkaline carbonate out of the water to build their skeletons. The corals also ate more food during these high-activity periods and pumped more CO2 into the water, increasing acidity further.

    These corals didn’t seem to mind the fluctuations in local acidity that they created,,,,,,,,,

    /////which were much bigger than those we expect to see from climate change.////

    This may mean that corals are well equipped to deal with the lower pH levels.…fering-damage/

    • 1. if global warming kills corals….why did they bother to develop a way to deal with it
      2. If CO2 makes sea water ‘acidification’…and that dissolves calcium carbonate shells, etc….how did the White Cliffs of Dover form when CO2 was ~3000ppm

      epigenetics ….right now looking at a very simple one….corals selective preference for zoox…so far, that’s seems to be it…the few clades of zoox have a wide overlapping range of tolerance…some corals show a preference for one over the others

    • “More acidic” or less alkaline? The term “acidic” in relation to seawater seems oxymoronic.

      • …and the take home was

        “These corals didn’t seem to mind the fluctuations in local acidity that they created,,,,,,,,,

        /////which were much bigger than those we expect to see from climate change.”

  2. Epigenetics is not Lamarkian. No environmentally acquired characteristics are passed on. Look up “lac operon” for a simple example. Environmental signals trigger what genes are expressed. Those sequences being preserved (part of DNA that used to be termed “junk”) from previous eras of good, old-fashioned natural selection.

    • KML,

      I would not quibble regards the term Lamarkian. But in contrast to Darwinian evolution where different alleles (i.e. altered DNA sequences) are passed on and maintained via natural selection, Epigenetic changes do not change the DNA sequence, but pass on the ability of that gene to be expressed or not. An epigenetic change arises in response to factors encountered during the parent’s life span, so it can be deemed Lamarkian.

      Epigenetic controls can be passed on erased.

      Read about genetic imprinting .

      The dogma of genetic determinism does not adequately represent organismal flexibility.

      • Jim, what’s expressed is what was encountered in their ancestors’ life spans, not their own. That is why it’s not Lamark. The past is re-emerging, so-to-speak. Were an entirely new environment to arise (not sure how that could occur), there wouldn’t be anything the genes could do. If there wasn’t the right tool in the tool kit already, most would die. But if a few among the many happened to have a new tool…well, you know,that’s what NS is.

        • That is one hypothesis. I am not arguing for a creationism, just pointing out that you are assuming a viewpoint, one which, perhaps just in my lack of education, is not supported by much evidence. Epigenetics is a rather new discovery itself. One other possibility is that (somehow) the genes were engineered for a wide variety of possibilities, some or many of which have never yet been experienced.

          Are Darwin’s finches proven to be different species (different genes) rather than just different epigenetic expressions?

    • Yeah, it think the term “epigenetics” may be used in an odd way here. I was of the impression it only applied to the non-heritable expression of genes, rather than heritable selection of variant regulatory genes (i. e. those not coding for proteins). This may just be an example of differing usages of the same word.

      • No, it is how the genes are expressed that is the topic at hand, not mutations in the genes themselves. The question is whether the expression can be transmitted to offspring as well as the raw genetic material. One would think that it should be, from an engineering point of view, anyways.

        • I think you may be defining “gene” as the portion of DNA that codes for protein. DNA also controls the portion that codes for protein, contained in what was called “junk DNA”. Used in a broad sense, both are genes.

          • I think the term junk DNA is used incorrectly here when it is used to include genes that are not currently being expressed. Gene regulation (expression vs inhibition) is accomplished by several mechanisms including methylation/de-methylation of DNA, and as suggested in the article, this may be recruited by environmental factors.

            If an organism born in the old environment finds itself in the new environment and methylates some gene as it adapts, does its progeny born in the new environment inherit the methylated gene or does it merely respond quickly, methylating the base gene for itself?

          • Guido, as noted in the main post for corals the answer is yes, directly inherited. Perhaps not when new coral larvae arise from the annual spawning (dunno), but definitely by definition when coral polyps reproduce asexually by simply budding. Interestingly, budding is the more common way for a reef to ‘repair itself’ continuously, while annual spawning forms a new reef or repopulates a dead one.

          • The original definition didn’t include heritability, but gradually that has changed. Now it can be used either way. Makes things rather confusing.

    • To a dispassionate observer, it looks like acquired characteristics are passed on. The mechanism is a quibble.

      Anyway … I stumbled on this:

      Perhaps extinction is wiping out species at high latitudes at a fast rate, but new species are forming to fill those ecological niches not too long after they are emptied out by extinction … link

      It seems like the harsh environment of the polar seas promotes faster evolution than tropical seas. The alarmists love to worry about species extinction or extirpation. Any ecological niche will be filled somehow. If a species does become extinct, something else will replace it. That’s nature’s way, the alarmists should embrace it. Fat chance.

      Another question is about the amount of genetic difference it takes to define a species. Consider a group of birds that has practically the same dna. If one of that group goes extinct, have we truly lost a species? link Another example is the genetic variation in chimps vs. that of humans.

      While the genetic difference between individual humans today is minuscule – about 0.1%, on average – study of the same aspects of the chimpanzee genome indicates a difference of about 1.2%. link

      Does that imply that there are many species of chimps? Most people don’t think so.

      When it comes to nature vs. nurture, DNA, and epigenetics, things are complicated. Dogma isn’t helpful.

      • I read the 1.2 percent as chimp vs human, not within chimps, so variation across the species divide is 12 x the intraspecific figure for humans.

          • Yup. Even setting aside bonobos, common chimps have far more genetic diversity than do humans. And most of the relatively little diversity our species can boast remains in Africa.

      • A lot of the so-called “junk” DNA is also actually used during embryonic development and not during the adult lifetime.

    • Maybe not where they started out.

      Bill In Oz November 17, 2018 at 12:54 am

      Ummmmm. Eight thousand years ago before the last ice age ended, the coast of Qld was another 40-80ks out to sea of where it is now.

      The coral that was present during the last glaciation moved up hill as the sea level rose. OK, maybe that’s a nit pick. 🙂

      • commieBob – a good point – the coral in the GBR certainly ‘moved uphill’ – by 40-80 kilometres! An alternate view is that the previous reef died (because the rising sea level meant that they ‘drowned’), and a new reef was built in the newly created shallows 40-80 km away. Maybe we could settle this – is there any evidence of substantial coral growing between the previous reef and the current reef? I guess it depends on the rate of sea level change – was it over years, decades or centuries? Either way, due to the well documented SLR after the last ice age, the current GBR is less than 20,000 years old. Just a baby, really, in geological time.

  3. Good post Rud,

    Indeed coral are highly resilient and adaptable. Darwinian natural selection, epigenetics that determine when and what gees are turned on and off, as well realizing coral well being is determined by manipulating the holobiont- i.e. the genetics of all their symbiotic partners.

    In contrast to alarmists who portray all organisms as fragile beings susceptible to deadly consequences from the slightest of environmental changes, our growing scientific knowledge of biology reveals tremendous organismal resilience to an always evolving climate.

  4. An excellent post. It missed one way that corals can survive changes in oceanic alkalinity (not “acidity”, the ocean is alkaline).

    It turns out that coral reefs affect the alkalinity of the water in a couple of ways. One is through reef growth, where they are removing carbonates from the water to build the reef from.

    The other is that coral produces CO2 as part of its daily changes. From my post on the subject entitled “The Reef Abides“, q.v. …

    The pH of the water over a reef is not driven by chemistry, nor by the partial pressure of CO2 in the air. It is driven by the reef itself, which is a net producer of CO2. In other words, the biological products of the reef creatures themselves cause the water over the reef to move from more to less alkaline, often on a short time span. In one study the pH of the reef water changed by one full pH unit (1000% change) in 12 hours … and yet climate researchers breathlessly forecast dire consequences from much smaller pH changes than that spread out over a century, not 12 hours.


    • An excellent post. It missed one way that corals can survive changes in oceanic alkalinity (not “acidity”, the ocean is alkaline).

      Just a technical point Willis, ocean alkalinity is the sum of all the proton acceptors it isn’t a measure of the ocean’s pH being in the alkaline range. It actually is a constant even when the pH changes.

  5. I think Epigenetics is mostly fancy sounding pseudoscience, which falls flat when the basic mechanisms involved are examined in detail.

    • Jeff,

      There is such a thing as epigrnetics, but IMO way too much is made of it by eco-devo advocates.

      Genes are protein-coding sequences. Latest estimate in humans is about 19,000, but the guess keeps getting lowered. For how long and when genes operate is determined by control sequences, i.e. epigrnetically.

      For instance, humans and chimps have the same number of follicles per sq in. of skin, but in most places chimp hair grows longer than on humans.

      Corn (maize) and its wild ancestor teosinte are genetically identical. The vast difference between them is all down to control sequences in the genome, i.e. epigenetics.

      • That should be “evo-devo”. My iPhone thrice tried to make it Eco-Debo and partially succeeded on the fourth try.

      • Yes genes are certainly turned on and off in any organism, but the mechanisms of how changes due to experience are transmitted through egg or sperm cell, which are mainly DNA, seem very sketchy at best.

        • Hi Jeff, – Maybe you have a technical reason to reject epi-genetics, I can’t assume your expertise. I’ll link a mechanism that recieved a lot of attention when it was published in case of interest to you & not already known to you.

          Back in 2014 researchers described how a sperm chromosome histone (a protein) can undergo methyl-ation (interaction) that in simple wording “marked” the histone. Unlike the sperm, egg cells have the enzyme (a protein) named Polycomb repressive complex 2. That ezyme keeps replicating the same “mark” on successive divided cells; the epi-genetic modification of the gene. As per published report titled “H3K27me and PRC2 transmit a memory of repression across generations and during development.”

          • The problem is people quickly leap from epigenetics to Lamarckism, as above.

            “Jean-Baptiste LaMarck was correct after all! Environmentally adapted traits CAN be passed down the generations. ”

            Lamarkism – ” is the hypothesis that an organism can pass on characteristics that it has acquired through use or disuse during its lifetime to its offspring. ”

            Believers have been trying to prove this for hundreds of years, but it has always been disproved.

          • Jeff,

            IMO, if both Lamarckism and epigenetics be properly understood, epigenetics isn’t Lamarckian.

          • Jeff, the first documented case I know of demonstrating the passing on of an acquired trait was published in 1983. It involved the case of a mouse that was infected by a virus to which it created a defense, and that involved the generation of a novel antibody. The ability to create this antibody required the immune system of the mouse to code for it.

            This coding was inserted into the DNA of the mouse and it passed this new capability on to its offspring, which had the genetic coding as an inheritance. Offspring born previous to the infection did not inherit this genetic material nor could they produce that antibody.

            This is a well-documented, published report of pure Lamarkian inheritance of an acquired trait.

            You can therefore drop the claim that it has never been shown to happen and ‘always been disproved’. It has been proven and anyone who wishes can replicate the experiment because that is how the immune system works.

            The human genome has numerous examples of an ability to fight viruses to which ancient humans were exposed. Those capabilities were acquired through exposure and survival, and passed on in the genome to their descendants: us. There is no Darwinian evolutionary element in this example. It is Lamarkian. Both mechanisms exist.

  6. “dried beans (all P. vulgaris) tells a fascinating epigenetics story. ”

    “The DNA analysis proves bean phenotypes emerged through epigenetic selection rather than through genetic selective breeding”

    Rubbish, good old genetic selective breeding explains all the variation.

  7. To Rudd Istvan, Jim Steele and others here !
    A simple big “Thank you” for the post and the commentary. I’m not a coral expert but I am interested in this issue as an Australian.
    The GBR is ‘dying’ is a massive part of the Greenist toolkit here in Oz. It’s good to see that it is complete bull.

  8. Chimeras are formed where coral colonies (sometimes even pieces of live coral) of the same kind of coral with diferent genes are near one another & some fussion together occurs (mechanism of how/when fusion happens is known to be different in different kinds of coral). The chimera thus adds it’s new geno-type to a coral colony; although chimeras usually involve 2 fused there can be chimeras that come from more than 2 different geno-types of the same kind of coral.

    Recovery of coral to some of the environmental alterations it endures is, in some cases, due to the chimera genes added to the colony. For example Great Barrier reef coral chimeras are known; which is not popularly discussed so I point it out here.

    When the chimera occassions greater size in that coral just starting out (again, different for different kinds of coral) not only does it’s survival rate go up, but the chimera subsequently reaches it’s reproductive age quicker than otherwise. In general chimeras boost fertilization outcomes & allay inbreeding limitations; however, it should be understood that in some cases a chimera has been found to have negative impact on it’s coral colony’s robustness.

  9. Rud,

    Corals were around for hundreds of millions of years before our present Cenozoic Era. They evolved in the Cambrian Period of the Paleozoic Era, if not in the Ediacaran Period, last of the Precambrian.

    New groups of them of course have evolved after the mass extinction events of the Phanerozoic Eon.

    • The current evolutionary lineage of scleractinian coral evolved at the beginning of the Mesozoic after the Great Dying at the end of the Permian removed previous reef builders.

      Of note, the current lineages of diatoms and coccolithophores also arose after the Permian extinctions

      • Jim,

        The Permian-Triassic extinction I had in mind, but even Mesozoic and Cenozoic corals still descend from Paleozoic and possibly Ediacaran ancestors.

  10. Rud,
    You said, “Corals are ancient animals and very diverse. They have been around since the Cenozoic era.” Surely you meant to say Paleozoic!

  11. I wonder what y’all think of this effort:
    “That Australia’s Great Barrier Reef is in serious trouble is no longer subject to debate, but the best way to deal with the problem very much is. An all-out assault on coral predators, giant fans to combat rising sea temperatures and recycling dead corals are all proposals being put on the table. The latest to emerge involves robots playing the role of “the stork” and distributing coral larvae across the Reef to promote new growth.”

  12. Since the average warming is about half a degree, and the 2015/16 Gbr temperatures were about 2-3 degrees above average.. We are obviously talking about bleaching events caused by weather.

    If the Gbr can die from the weather.. How could it possibly have ever have survived changes in climate?

    Well, dying from the weather is exactly how it survives changes in climate. Every bit of coral that now survives after the 2015/16 bleaching events can now pass on their genetics huge distances.

    Where is the problem? Seems an ideal scenario if the oceans do continue to warm.

  13. Evolution may not be as slow as some people imagine. Darwin thought of it as a slow background process over a great deal of time. More recent science has discovered that when a population is put under more stress, and if helpful but rare variations already exist within the population, evolution can proceed very rapidly. The faster the generations are breed, the faster evolution can proceed. (One might wonder is the reason why so many dinosaur species went extinct together was the length of time it took them to breed, so that their evolution was just too slow to keep up)

    Now you might imagine since the variation already existed in the above explanation, this isn’t quite evolution, just selection – but through this selection new successful mutation is focused on this new skewed sample of original population gene expression.

    Think of it this way – if a population is already well adapted, and if competition for most niches is already present, there is little chance that evolution can proceed, so it does so slowly. If the population becomes less well adapted because of environmental change, and if more niches become available, then evolution can proceed much faster – unless the change is so rapid the population first dies out, and then you have an extinction. But again, species that breed faster and more numerous will adapt faster (better odds of a good mutation).

    Most great extinctions (possibly all of them) are followed by rapid evolution (diversification) for this very reason – the populations that survive have lots of possible niches to fill. I think of evolution s main purpose is to create new species to fill new or changed niches in the environment over time.

    Inheriting gene expression is different, and still somewhat controversial (how often does it occur, in what species, and for how many generations). It allows for adaptation in a single generation, much like an existing helpful gene variant of a population would. It can be reversed, which a gene variant for all practical purposes cannot be (it can only be lost in the second generation, but not reversed by the carrier). I think of inheritable gene expression’s main purpose is to adapt an existing species to changes in its environment. It doesn’t create a new species – not by itself.

    As for ejecting symbiotic organisms, the coral has evolved to perform this function in order to stay adapted to a changing environment. Because it evolved this ability, it means the coral has evolved in an environment that changes at least one of its parameters within a certain range. This then implies that the environment that the coral is in, if the coral continues to survive, is still within its Natural boundaries (at least as far as that organism is concerned). Not a big surprise, in fact I would have expected this ability – just not the mechanism which is (or was) a bit of a surprise when I first read of it.

    So, if one is going to study adaptation by organisms to a changing environment, one needs to study many generations – not just one or two. Most biologists seem to panic after one generation seems to collapse in numbers and never go on to study succeeding generations to see if they rebound. You also have to study the organism in its natural environment or you will miss the more complex interactions.

    • biology is constantly throwing out new expressions and seeing if they stick to the wall….most of them are bad choices at the time…those same bad choices might be good choices if the environment changes

  14. Dinoflagellates aren’t technically algae, but do contain plastids of red algal origin, similar to the endosymbiosis in eukaryotes of mitochondria from bacteria and chloroplasts from cyanobacteria.

  15. Development of microbial antibiotic resistance in the laboratory (or the animal) also depends on the size of the test tube as well as the duration of the experiment. The simple explanation is obviously that the test is being carried out on a large population of individuals which may not be genetically homogeneous, and/or are able to make either wholly new changes or changes that are ‘remembered’ somehow in the genome.
    Just as a very small petri-plate cannot adequately represent the scale or scope of changes that can occur within a whole human, a single fish-tank or coral-reef is unlikely to be able to adequately model what happens in the wider environment.

    There are also many other arguments to be considered, such as the rate of change/evolution of symbionts being much faster than that of larger organisms. Some people recognize this may well be helpful, not necessarily harmful.
    As usual, the alarmist argument is woefully incomplete.

  16. Coral Acorpora (a major reef builder) experienced genomic poly-ploidy (more than 2 sets of chromosomes) sometime at least once sometime around 27.9 to 35.7 million years ago. This is categorized as a whole genome duplication circumstance.

    These whole genome poly-ploidy gene paradigms are categorized in 3 contexts. The “singleton” consists of core genes maintaining genome integrity & are single copies; “multi-copy” duplicates are genes for signalling, transport & metabolism; while “intermediafe” genes are duplicate genes that over 10s of millions years eventually return to a “singleton” status & are involved in development, growth & transcription regulation.

    Poly-ploidy in some cases, by increasing methyl-ation transposable elements, can selectively reduce nearby gene expression levels (down-regulation) in response to the revised genome. Poly-ploidy can induce differentially methylated regions; in effect there can occur hypo-, as well as hyper- methylation events.

    Not only were there different expressed genes, but potentially insertion-delition poly-morphisms & single nucleotide polymorphisms. Then too the RNA dynamics were likely altered; for example microRNA influence on what is called the “universal stress protein domain”.

    The scope of poly-ploidy extends to genes of mega-gameto-genesis. These can involve embryonic mother cells in the pre-meiotic inter-phase, embryonic mother cell meiosis, nuclear proliferation & even maturation of embryo.

    Coral poly-ploidy different gene expression is integral to response to abiotic conditions, hormone signal transduction & the nucleolus (for brevity skipping nucleolus role as distinct from nucleus). I’ll highlight abiotic stress as a poly-ploidy adaptation (ie: number of gene copies for which genes) here since it is relevant to modern day discussions of coral reef.

      • Edit : Acropora (not acor-pora, sorry I never check comments very well).

        And for Latitude an examplary quote from some scientists about reefs. This from just one report titled Growth anamolies on the coral genera Acropora…”: “… major Indo-Pacific reef-building coral genera, Acropora ….”

  17. The evolutionary hisory of corals is nuanced. Atlantic corals, being more generally descended from the Tethys “mother of all coral worlds”, are older. Atlantic existing genera generally predate the KPg extinction, which was generally very unkind to corals. Below is a contour map of the ages of living coral genera:

    Western Pacific and Indian Ocean existing coral genera tend to be late Cenozoic. There is speculation that closure of the Panama Isthmus is implicated. Maybe. Or maybe new conditions fostered coral evolution in Indo/Indonesia.

  18. You know the more that I read and learn the less it seems that scientists really know and understand about how our climate works and less it seems that they understand how the plants and animals deal with a changing climate. I want to thank all of you for furthering
    my education on both topics.

  19. Nice article Rud. Others have already addressed the Cenozoic vs Paleozoic issue.

    I would point out that corals are said to thrive in the Red Sea at 30C and also in much of the Persian Gulf which is even warmer. I have some doubts that warming per se would have much affect at all on tropical corals except perhaps to enable tropical reefs to expand poleward a bit here and there. CO2? Who the hell knows? Certainly not climate “experts”.

    • Don K, AFAIK the extant coral orders all arose after the Permian extinction. I believe Jim Steel said the same thing differently upthread. Surely their non-calcifying ancestors arose during the Edicarian, and probably began to ‘armor up’ during the Cambrian. One of the big motives for armoring was the Cambrian development of the eye, which actually evolved three separate times with three different architectures. See book In the Blink of an Eye for details.
      Am near certain the corals of the Red Sea are different species than those of our Florida reefs, which are in turn difference species than Australia’s GBR. But all photic zone corals everywhere exhibit symbiont bleaching and epigenetic adaptaion passed down generaltiinally by asexual budding.

      • Rud, Just in case you ever need to know, the late Jack Sepkoski compiled a database of 32000 fossil taxa (marine invertebrates), and when they first and last appear in the fossil record. There’s a searchable copy online at at the U of Wisconsin, Madison — Yes, the Paleozoic orders Tabulata and Rugosa seem to have died out in the PT extinction. Modern corals are mostly (all?) Scleractinia. If that’s wrong, I imagine that one of the resident coral experts will fix it.

        Probably the species names assigned to common coral genera like Acropora and Porites in the Red Sea are different than those in the Pacific and the Atlantic. But species nomenclature for everything looks to me to be a complete shambles. For living critters it may eventually get sorted out by DNA analysis. For fossils where DNA is rarely available, it may never get sorted out.

        That’s my opinion, not that of taxonomists. Taxonomists would, I’m sure, argue differently. Taxonomists love to argue. I don’t.

        Are the animals really different in any meaningful way? Beyond my pay grade.

  20. Final return to a probably dead thread, to clear up some molecular biology confusion/misunderstanding in some comments. Done mainly so the main post can serve as an archived WUWT reference. All of what follows is easily googled.
    Not being critical of comments. It took me four years to grok what my newly hired Ph.D experts were explaining as the basics to the ‘ignorant kiddie’ seniormost executive in charge of Motorola’s multihundred million dollar gene chip initiative-their penultimate boss. And that did not include epigenetics, unknown at the time.

    Genes code for proteins. That is only about 3% by ACTG base pair count of the now fully sequenced human DNA. The rest was thought to be Junk DNA when I ran the business in the 1990’s, a time at which the human genome was speculated fo be 60,000 to 100,000 genes based on identified proteins and a 1:1 presumption.

    The presumption was very wrong. There are ~20000 human genes, so coding is not 1:1 (although interestingly, insulin is). Two reasons have emerged. One is the gene exon/intron complexity noted in the main post ( and intended as a hint that I did not learn all this from a quick cheap google last week). The second is even more complicated. Sometimes a gene codes for a very long protein, and a second gene expresses a protein enzyme cleaves it into one or more functional protein fragments. The important capillary forming protein VEGF is formed this way, and is the target of the blockbuster anticancer monoclonal antibody medicine Avastin.

    Gene portions of DNA can usually be identified by conserved ‘srart/stop’ codons. Everythong outide the codons was deemed junk just 20 years ago. Not so. Many outside codon but adjacent DNA eedions aee now known to in orporate gene promoters, coding where, when, and how much a gene should be expressed.

    In embryology, a methylated gene is never relegated to junk status, and the process of producing haploid eggs and sperm removes all embyological methylation, so each new sexually produced first cell creating the potential for a new organism starts fresh.

    In epigenetics, one of two known mechanisms is promoter region methylation. Whether it is passed sexually, dunno. The other known for sure is DNA folding. Whether this is passed sexually, again dunno.

    But since corals also reproduce asexually by budding, they for sure can pass down environmentally inducted epigenetic modifications. Hence my perhaps misconstrued LaMarck obiter dictum.

    • Good point. i failed to remember the corals also reproduce by budding, just like aphids produce clones asexually during a given year.

  21. This 2017 article calls into question much of the research done on epigenentics in corals. For example,
    “Nevertheless, it remains to be seen whether this divergent methylation causes or is caused by differences in gene expression, whether it responds to environmental cues, and whether it can be passed across generations. In summary, we do not dismiss a potential role for epigenetic inheritance in TGP [transgenerational plasticity] of corals, but evidence is currently largely lacking, and mechanisms other than DNA methylation need increased attention.”

    Another article posted recently on WUWT talked about problems with experimental design in studies of corals. Sure enough, the first article I looked at about epigenetics in corals had this problem: common garden tanks were used. In addition, the samples gathered were very close to one another specifically to minimize genetic diversity. Basically, there was no treatment replication.

    One important consideration in all of this is that coral species vary in their response to environmental change. While it’s probably true that some species will be able to adapt/evolve, diversity is an important part of the function and economic value of coral reefs. And, as I frequently point out, rate of change can be just as important as total amount when it comes to all biotic and ecosystem responses.

    • Kristi,

      It’s highly unlikely that any coral species will go extinct due to alleged ocean “acidification”. Human activities do threaten some reefs, but change in pH and temperature aren’t among them.

      The only family of stony corals (as they all have been since the Triassic) to go extinct in the Cenozoic did so at a time of cooling seas and falling CO2. Corals like it hot, high in CO2 and lower in alkalinity. Such as during the mid-Cretaceous, when they thrived.

      There are deep, cold water species, but less basic seas don’t threaten them either.

      • John Tillman,

        I didn’t say anything about extinction.

        A family going extinct is not the same as a species going extinct.

        Funny that researchers all around the world have noticed reefs dying off when you seem to suggest they should be doing even better. I can understand a few researchers being wrong, but hundreds of them? How do you explain it?

        Are you saying that all corals since the Triassic have been stony corals???

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