On a mission on Independence Day

Independence Day, anniversary no. 241 is upon us, a holiday surely on the short list of important ones in the United States. There’s no end to the philosophical and political ideas that can be, and have been, expounded upon. But as for me, I’m thinking about connections inspired by the research and personal reading I’ve been doing lately. Bear with me grizzlies, while I attempt to connect genetic research on rare California plants to American history.

I started graduate school in genetics, not ecology, and that field has always been the most fascinating to me. I’m in fact currently working on a topic that bridges the two fields, referred to as genetic biocontrol, the aim of which is to use genetic methods to reduce fitness, and hence population sizes, of harmful or otherwise unwanted species. So, I was sad to learn in a recent special issue devoted to the work of Dr. Leslie Gottlieb of UC Davis, on polyploid genetics, that he had passed away five years ago. The major focal taxon of Gottlieb’s work was the genus Clarkia, and I had some good conversations with him when I was doing restoration and propagation work on a very rare Clarkia (C. lingulata) endemic to the Merced River canyon, the main river flowing into, and through, Yosemite Valley. This is a famous species in plant genetics, cited in textbooks as an example of instantaneous speciation (see here and here), derived from it’s progenitor, Clarkia biloba. Clarkia lingulata is found in only two populations near the junction of the South Fork Merced with its main stem, a few miles west of the western boundary of Yosemite National Park.

Said River of Mercy is not merciful this year though, or any time at high water, should you happen to be in it. It is uncontrolled, and at high water rages through a steep, boulder filled death sieve as it leaves Yosemite Valley and heads for the San Joaquin. I still remember well the day that a woman, with her three kids, fell asleep at the wheel after driving all night, and drove off the road and into the river at daybreak, just above this location, drowning them all. When I was kayaking, the Merced was the only river that ever scared me off the river, although part of that was due to being solo and exhausted, which is a full-on recipe for disaster. There is also some very interesting history regarding Clarkia lingulata‘s location, one involving the cause of the American discovery of Yosemite Valley in 1851, but I won’t go into that here.

In one of our discussions, Les discussed some aspects of another rare Clarkia species he was working with, Clarkia franciscana. The species is so named because it is found only in the immediate area of the San Francisco Presidio–and this makes for a segue from genetics to history, involving the SF Presidio, Spain, Mexico and the United States, Upper (or New) California, and July of 1776.

The history of what is now the state of California has, I think, to rank as one of the most interesting of any in the world, and especially so from 1846 to 1850. Just a week before the momentous event in Philadelphia, a small group of Spanish Franciscans, with a small military escort, arrived from the Carmel River area (just south of present Monterey, CA), to extend the Spanish Upper California dominion northward by establishing their third presidio (military base and/or fort, the first two being at San Diego and Monterey in 1769/1770), and with it another mission of course. These establishments were significant because both were to carry the name of the order’s founder, Saint Francis of Assisi.

On June 27 1776, this group came upon a small creek draining the peninsular hills east (toward San Francisco Bay), which they named Dolores, and decided that this would serve as the future mission site. On June 29 they established an altar and consecrated the site, and then began looking for a strategic location for the presidio and fort, which they located on a high bluff commanding the narrow entrance to the bay (the “Golden Gate”), just to the water side of what is now the southern anchorage of the Golden Gate Bridge.

A depiction of Mission Dolores circa 1893 by Edward Borein

At this point, books worth of material could be inserted discussing the Spanish (and after 1822, Mexican) discovery, settlement and management of Upper California, and with jaw fairly agape at both the process and the end result (circa 1848), for much of it. And we, with the benefit of 20/20 hindsight, wouldn’t be the first to do so either–the Russians, the British, and especially the Americans, of that time, did so also. It’s documented in various writings, which are for me at least, entirely fascinating. Some of it seems to defy logic. If anyone could write an authoritative book titled “Imperial expansion: how not to do it”, it would have to be the Spanish and/or Mexicans.

To say that things went downhill for the Spanish from 1776 to 1848 would be the understatement of the century. Twenty-one missions were established in Upper California during the “mission period” from 1769 to the American conquest in 1846, but for various reasons including Russian presence starting around 1805, only two north of Mission Dolores (Missions San Rafael and Solano), and both of those quite late in the game. The events in Philadelphia five days after consecration of the Mission San Francisco de Assis (= Dolores) site, caused the Spanish to pull back on several intended plans in northwestern New Spain, now the western United States, including expansion north of San Francisco Bay and another plan for a series of missions in the interior lands east and south of it.

Mission Dolores circa 1842 by Henry Miller

One argument has it that in so doing the Spanish were hoping to marshall their energies to re-claim parts of Spanish Florida lost initially to the French, and hence to the British after 1763, thinking that the Revolutionary War might offer their best chance to do so. But this plan, along with apparently about everything the Spanish and Mexicans did from 1800-1850, backfired. Not only did they not increase Spanish Florida, they quickly lost what they already had. This was followed later (1822) by the entire loss of New Spain, i.e. Mexican independence. The fracturing of the once vast Spanish empire then continued as the Mexicans in turn quickly lost Texas to independence, whose annexation by the United States about a decade later thus led to the Mexican-American war. In amazingly short order therein, they then managed to not only not reclaim Texan territory, but instead to astoundingly quickly lose both California and New Mexico. This was followed in less than a year by surrender, and with it the additional loss of what are now roughly the states of Utah, Nevada and Arizona. The total area is a large and very valuable chunk of real estate, by any standard.

I’m no historian, though I read my fair share, but compared to the serious difficulties and drain of two wars with the British spanning 40 years, and the even more extended and often ferocious wars with various Native American tribes, this sudden acquisition of a vast, important territory without much of a fight stands out. James Marshall discovered gold in the tail race of John Sutter’s sawmill east of what is now Sacramento just about two weeks before the Treaty of Guadalupe-Hidalgo officially ceded all this territory to the United States. That this should happen to a people who had historically been obsessed and sometimes deluded by various fantastic stories regarding that material, kind of says it all. Marshall and Sutter tried to keep the discovery secret for a couple of months but that was a lost cause, and they likely knew it–it was a virtual certainty that the gold veins and placer deposits that ran up and down half the Sierra Nevada, and elsewhere, would be found in almost no time by those about to pour unobstructed into what was now the United States. And so they poured. And the rest as they say…

12 thoughts on “On a mission on Independence Day

  1. Hi Jim,
    Just saw this. I really appreciate you mentioning and linking to the Gottlieb special issue. As you may recall, the topic of speciation and autogamy in plants is one I am interested in. The first paper in the special issue directly addresses my primary interest in population bottlenecks and founder effects. The paper summarizes the evidence as not supporting bottlenecks during speciation, but I have more work to do to figure out how that is substantiated. I will be digging into the references for that. There is a brave new world of molecular analysis on the topic since I last dove into this.
    I was not aware of the Clarkia lingulata work (big holes in my knowledge since I am self-taught). It is a good example of the plants that interest me most, rare and endemic colonizing annuals with high rates of autogamy that seem to have recently evolved from outcrossing species. It differs from the plants that have adapted to serpentine in that it lacks habitat specialization when compared to the progenitor, which is an interesting twist. I am still at a loss in trying to figure out why any competitive/selective phase with the progenitor needs to be invoked in the life history.

    • I am still at a loss in trying to figure out why any competitive/selective phase with the progenitor needs to be invoked in the life history

      Don’t try too hard. I think you’re right to be puzzled. Could it be habit? [Habitat habit??] I think there are many circumstances where conspecific taxa inhabit a common or pseudo-common habitat and are faced with competing for resources (light, for example) with ancestors. And in these circumstances it makes sense that selection acting on new and novel differences could lead to speciation. But is this a necessary condition? I’m not persuaded. At the margins of habitat types there is likely lots of room for new and different phenotypes to explore and potentially colonize without going head to head with the old man.

    • Yeah, I know this is right within your wheelhouse of interest Matt. The genetic concepts involved also relate directly to what I’m working on now.

      You’re referring to the paper by Barret et al.?

    • I too would have to read the Barrett paper, and refs therein, to assess the claimed evidence for a lack of bottlenecks. That’s an unexpected result, but it also depends on exactly how one defines a bottleneck, in particular the level of required homozygosity.

      I can confirm, from my own work, Lewis and Roberts’ statements (2nd “here” link above) that there is no obvious or clear difference in either biological characteristics, or habitat conditions, between C. lingulata and C. biloba ssp australis. As a generalization however, such differences are not required for speciation, even though the classical description of the evolutionary process, sensu Darwin, has selection on phenotypic variation as a central element. But that’s largely because Darwin pre-dated genetics as a science and so had incomplete ideas about genetic isolating mechanisms. It was obvious that spatial separation could act as an isolator, but not at all that cytogenetic (chromosome) processes can do so even for immediate neighbors.

      If we jump now to mid 20th C Mayr and others, we get the fuller, genetically based definition of a species, i.e. anything that is reproductively isolated from its near relative(s)–no other criteria are invoked. And we know that plants in particular have come up with all these interesting genetic and mating systems that allow them to achieve Mayr’s criteria without necessarily involving any phenotypic differentiation or selective advantage at all: polyploidy/aneuploidy, apomixis, bisexuality, and autogamy in particular. For all the major evolutionary advantages of sexual reproduction and unisexuality–long expounded upon–there are also major drawbacks. These show up in particular in small populations, or for that matter any situation in which allogamy is a potential difficulty, e.g. in large but low density, wind pollinated populations.

      The production of non-reduced gametes (2N instead of 1N, due to meiotic first division failure) appears to be common in plant taxa, and especially in their pollen. If this also occurs in the ovules, then polyploid offspring can be a regular, albeit low frequency, event. And polyploidy can also arise through mitotic failure in the zygote, after fertilization (i.e. 4N instead of 2N cells). We also know from both molecular evidence, and cytogenetics, that the vast majority of plant taxa have experienced a genome duplication event, i.e. polyploidy, sometime in their history, even though they currently display disomic (diploid) meiosis and inheritance.

      Polyploids, no matter how originating, are almost always largely sterile when mated with their progenitor species, and hence satisfy Mayr’s biological species criterion. Their ability to survive long term then boils down to their ability to avoid “demographic swamping”, which will rapidly drive them to extinction, due to the low polyploid to polyploid fertilization event frequency, given that the very few polyploid individuals produced, are swimming in a vast sea of diploids. Hence, very strong selection for autogamy will exist, which is the only possible antidote to a very strong extinction vortex process that will otherwise result. Only the strongly self-fertilizing will make it out alive.

      Make sense?

  2. I was referring to the Barrett et al paper. Although in re-reading, I see they only consider selective mechanisms for autogamy.

    “Hence, very strong selection for autogamy will exist, which is the only possible antidote to a very strong extinction vortex process that will otherwise result.”
    Yes! I more or less worked this out on my own in my work on autogamy in serpentine endemics, while of course realizing that I was very unlikely to have been the first to do so. This is the first time I have seen someone else make the same argument. But look what that means: autogamy in a nascent polyploid species confers no competitive advantage, but is rather merely facilitative for speciation by preventing backcrossing. So it is selective but not adaptive.

    In obligate selfing serpentine-tolerant taxa, a simple thought experiment eliminates most possible speciation routes. First of all, I have never been able to comprehend how serpentine tolerance can arise gradually involving any sort of sympatric process. There just are no plants lurking at the periphery of an ultramafic outcrop with partial tolerance, diligently winnowing the genome towards full tolerance. There are of course bodenvag species, but that is not the same thing. We are not evolving a complex eye from a light-sensing cell here. If that is not the route, then we are left with a mutation that provides for tolerance more or less all at once. When that happens to an outcrossing species on a nearby substrate, the mutant plant is suddenly freed from all competition for resources (having visited ultramafic exposures throughout the West, I can personally attest that space and light are always available). The only risk that our nascent, tolerant species faces is loss of tolerance though backcrossing, i.e. demographic swamping.

    Under these circumstances, I have trouble envisioning autogamy evolving sympatrically on serpentine. The problem that needed to be solved, genetic isolation to fix the tolerance, would have to have been already solved. If an individual (tolerant but outcrossing) plant has a mutation that causes obligate autogamy, that plant has embarked on its own route to speciation. Then you have to evoke biotype depletion to fit with the patterns of speciation that we actually see, where the outcrossing progenitor dies out. It is not impossible, and in fact that sort of biotype depletion has been invoked, but it is just a lot of arm-waving that is not really necessary.

    Goldschmidt had a much more parsimonious idea. What if a single mutation affects a homeotic gene? In agreement with the neo-Darwinian synthesis, we can assume that homeotic mutations (“macromutations”) are almost always dead ends resulting in plants that cannot survive. But what if a homeotic mutation creates both a metabolic change that confers serpentine tolerance, and a morphological change to the flower that causes obligate autogamy? Even a weak plant with no chance of competing can become a new species on serpentine, free of competition on the open substrate, and immune to backcrossing with the non-tolerant progenitor species. Hypothesizing more than one individual plant being created from the progenitor species with a homeotic mutation is just more arm waving and not parsimonious, so we are left with a true “founder.”

    This begs the question: can the pattern of autogamy in plants be fully explained by this mechanism? If so, autogamy is not selective at all but rather facilitative – and only facilitative – for speciation. I think there is good evidence that autogamy can be adaptive for colonizers through reproductive assurance. So it is most likely sometimes selective and sometimes merely facilitative, the latter occurring when the mating system is neutral for selection due to a lack of both intra- and inter-specific competition.

    I have to think some more about the Clarkia situation, where there is no evidence of a difference in fitness between the outcrossing progenitor and the autogamous descendent. I’m also going to work a bit on what you wrote, some of the words and concepts are above my proverbial pay grade.

    • Lots to say but not a lot of time.

      First to clear up a misconception, C. lingulata is not an autogamous descendent of an outcrossing progenitor. The breeding systems of both taxa are about identical; the individual flowers are protandrous, and therefore largely infertile, but selfing can and does occur between different flowers on the same plant.

      I think in general you’re laying too much emphasis on breeding system and not enough on enviro adaptation. Autogamy is not a particularly hard thing to achieve in bisexual (moneocious) species, and in fact most taxa self pollinate to some degree, due to flowering time differences between flowers on a developing individual. Obligate autogamy does of course occur but it’s not a requirement for reproductive isolation.

      Environmental adaptation can be a quite difficult thing to achieve however, and serpentine soil might well be a good example, though I’m not up on the biochemical adaptations involved. You’ve got, just off hand, at least high levels of Magnesium, Chromium, Nickel, and Iron to deal with, all of which may well require a distinct biochemical process to neutralize. So the idea of an instantaneous, single homeotic mutation along the lines of Goldschmidt, conferring tolerance to all those, plus altering floral morphology at the same time, is well…a bit of a huge leap.

      If instead I reproductively isolate a population from it’s parent, by say polyploidy, space or whatever, I can then let that population take it’s time to develop whatever env. tolerances are required to put it into a new niche over time. No need for catastrophic hopeful mutants. And also no necessary bottlenecks either, although I’ve still not read Barrett et al and I don’t know if they discuss that.

      Another point is that single- and multi-gene traits are different in terms of how big of a problem outcrossing is; favorable multi-gene trait allele combos are more fragile and thus aided by selfing.

  3. Looking forward to your response.
    I forgot a paragraph in my post above. I am not sure that modern genetic testing has supported Goldschmidt’s idea of homeotic mutations. Barrett et al does mention single mutations that have a profound affect on the structure of the flower, so that is pretty close. The same result can also be achieved with a “slot machine payoff” (my own term although once again I am sure others have thought of it). This is where a colonizing species has a highly variable genome that facilitates (that word again!) adaptation to novel conditions. So the species may have certain mutations that occur with some regularity. A slot machine payoff occurs stochastically when a single plant has multiple macromutations, and the combination somehow manages to allow it to both fill a new niche and avoid demographic swamping. Even if it remains an outcrosser, sympatric selection under a new set of conditions can quickly cause enough divergence from the progenitor to create a new species. As has been noted going back to Darwin, isolation can substitute for traits like autogamy in avoiding demographic swamping.

  4. Been off backpacking and seeing a total eclipse. Then had to go back and read some stuff only dimly remembered. I should be putting less emphasis on Goldschmidt and more on my general confusion with how speciation results in serpentine tolerance.

    Jim wrote:

    “If instead I reproductively isolate a population from it’s parent, by say polyploidy, space or whatever, I can then let that population take it’s time to develop whatever env. tolerances are required to put it into a new niche over time.”

    The problem is that I cannot make saltational speciation work here. Is the isolated population on or off serpentine? If it is off, nothing of interest has happened. If it is on, everything of interest has already happened. So how does it happen? I cannot apply a single aspect of Darwinian survival of the fittest. The Darwinian might invoke a gradual accumulation of tolerance. But where? Last I looked, there was zero evidence of plants on the periphery of serpentine, gradually developing tolerance as they slowly migrate across the boundary. The boundary on the tops and sides of serpentine outcrops are very abrupt. Down below there might be some gradational sites, but the idea of a plant lurking on the far side, plodding away at tolerance by launching offspring partway – but not all the way – across the divide…how does that work? A thin line of marginally tolerant plants? With all the neo-endemics, how come we never see anything like that happening? Why is autogamy overrepresented?

    There is an odd juxtaposition of autogamy, rarity, and serpentine tolerance in both Hesperolinon and Streptanthus. It must be telling us something, and I am keeping an open mind, but the insights of the neo-Darwinian synthesis are not helping.

    Prof. Art Kruckeberg threw up his hands trying to understand the origin of Streptanthus polygaloides: “the origin of this bizarre species is an abominable mystery.” That was written in 1984. Not sure any progress has been made since then.

  5. Just discovered that this is no longer paywalled, and read it for the first time:

    Click to access Saltational-evolution-of-form-in-vascular-plants-a-neoGoldschmidtian-synthesis.pdf

    All my ideas that I have been blabbing about are in here plus a bunch more that are above my pay grade. Autogamy is “ancillary” but facilitative due to creating reproductive isolation. This paper is over 20 years old, not sure how it has fared since then.

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