I don’t think it matters what genes are suppressed in humans with Y chromosomes and humans without Y chromosomes.
If Janet and John are siblings, then Janet may have genes ABCDef and John may have genes aCEgHI, where lower case are inactive, but they still share 50% of the same genes. Their offspring will have a 50% chance of sharing each of genes Aa, Cc, and Ee; their daughters will have A and/or C active, and their sons will have C and E active, but there’s still going to be a boosted chance of bad reinforcements.
The fact that gene e isn’t active in Janet doesn’t mean that it’s not still present in her gametes, and still potentially able to mess up her sons if it’s a bad recessive.
You seem to be thinking in terms of epigenetics and development, where genes can be suppressed. But for reproduction, genetics is crucial, and genetically those genes are still present; making them inactive doesn’t delete them. And because of that, if you’re deciding whether to mate with someone, the genes that are inactive still figure into the degree of relatedness.
The problem of index-of-relatedness being non-commutative is familiar from haplodiploid insects. It leads to some strange predictions for differences of reproductive strategy among social, solitary, and slave-taking wasps, bees, and ants, and amazing confirmations from fieldwork. The key to successful analysis seems to be recognising that the issue for any organism in an evolutionarily successful strategy is how to get copies of its rare genes back to the same point in the life-cycle that it is at. For a gametophyte, how to get copies of its rare genes into a proliferation of new gametophytes; for a sporophyte, how to get them into a proliferation of new sporophytes.
For a diplosessile the obvious possibilities are to bear and nourish haplomotiles or to engage in some sort of parthenovegetative reproduction. If you bud or sucker you produce new diplosessiles each with 100% of your rare genes; if you set fruit you make haplomotiles they go on to produce new diplosessiles that each have only 50% of your rare genes. There seems to be an obvious advantage to vegetative reproduction, but a great many types of plants on Earth engage prolifically in sexual reproduction, so we can be confident that there is something to it.
For a haplomotile the obvious possibilities are
to encourage/help/assist your parent in producing more haplomotile siblings, each of which will have on average 50% of your rare genes
to propagate your parent vegetatively, resulting in a proliferation of diplosessiles that will produce haplomotiles each with an average of 50% of your rare genes.
to seek another haplosessile, mate, and produce disessiles that will produce haplomotiles each of which has on average half your genes.
to bud, producing a haplomotile with identical genes.
The first three strategies result in producing future haplomotiles with a random ~half of the organism’s rare genes, from parent or child diplosessiles that contains all of them. The first has the advantage that one’s parent is already grown, so that a large proportion of resources invested in a parent will go into siblings rather that initial growth. The second means putting a lot of effort into the scion before it becomes reproductively mature, but it buys you insurance against the death of your parent, and dispersal into extra space to gather light and nutrients. I can see it becoming the superior strategy as ones parent grows large and accumulates a plethora of offspring to cultivate and defend it. The third has the advantages of the second, with the additional advantages of sexual reproduction, whatever those are (genetically varied descendants might be have less chance of all being wiped out by the same parasite or pathogen?). The fourth would seem to have the advantage of getting more or you genes into each descendant, but that hasn’t resulted in parthenogenesis sweeping Earth, so there’s obviously something to keep it in check.
So, what do we see organisms doing in this biosphere?
Diplosessiles photosynthesise and grow.
Some species (or in some circumstances they) spread vegetatively like aspen groves.
Most [species | times they] bear haplomotiles.
Some [species | times they] produce parthenogenetic zygotes for clonal propagation.
Haplomotiles scurry about, eating food bodies from their parent trees (especially when they are young), eating diplosessiles other than their close relatives, eating mature and maturing haplomotiles other than their relatives, and clearing land for their family.
Some [species | times they] stay close to their parent, depending mostly on food bodies, defending their parent tree and unripe siblings, and clearing unrelated neighbours to allow their parent to grow. This activity is especially common where the parent can freely increase its reproductive capacity by vegetative growth,
Some [species | times they] wander off with buds or scions of their parent, to find or clear a place to plant a clone of their parent. When they do that they leave behind the food supply that they parent produces, so must rob other diplosessiles of food, browse on unrelated diplosessiles, and/or prey on other haplomotiles. This activity would seem common when the parent is approaching constraints on local growth, and has a surfeit of offspring to feed and plenty to defend it. This is a project that a “war party” or assarting team of sibling haplomotiles might co-operate on.
Some [species | times they] wander off like fertile bees of ants to find unrelated mates, couple, plant their seed, and then cultivate or defend it until its first offspring ripen. Then, it seems to me, their interest may be either to cultivate and defend their offspring, or seek another mate and produce another seed with another ticket in the genetic lottery. To produce a second seed with the same mate results in a clone of offspring, less resilient than a variety of them. And whereas diploid animals produce offspring with an index of relatedness of 50% between pairs, haplomotile “animals” do that only by changing mates.
Some produce parthenogenetic duplicates.
Is there a major problem with any of those strategies? What are the other strategies that I haven’t thought of and listed? Does any of them dominate the others, so that we see only, say, cows each defending a calf-tree, or only plants producing a swarm of animal offspring to defend them like ants on an acacia?
Then, as you say, there is the strategy of skipping or reducing a step. Most plants on Earth alternate their generations between diploid sporophytes and haploid gametophytes. In some algae the two forms are equally prominent, but among land plants one stage or the other has been reduced to an inconspicuous and dependent form that seems a mere organ in the other. In mosses and liverworts the macroscopic plant is a haploid gametophyte on which the diploid sporophyte grows briefly and depends for nutrition. In seed plants the diploid sporophyte is the familiar plant, and the sporophytes are microscopic and ephemeral incidents in the course of fertilisation.
If something of the sort happened in some species or orders of organisms in my suggested biosphere that would merely add interest. But if the reduction of either generation to an inconspicuous state were evolutionarily inevitable it would spoil the scheme. Also, if there seemed to be a compelling pressure to express motility in the diploid generation or photosynthesis and sessile growth in the haploid one the scheme would be unstable.
I think Plantae come fairly close to all employing an alternation of generations between haploid and diploid forms. But in nearly every case one or the other is reduced to an inconspicuous form that is much more interesting to science than science fiction. I am worried about that seeming to be too inevitable for my scheme to be plausible.
I think that you might need to go back a step in the analysis. That is, it’s important to ask not merely what it is in the interest of the haploid to do [note that I’m defining “interest” in Darwinian terms, as gaining genetic representation in future generations], but what it is in the interest of the diploid to have the haploid do as its agent. Of course this is subject to principal/agent problems!
Here is your haploid, and it’s in its interest to do X. But X confers no benefit on your diploid. At this point the diploid has three choices:
It can go ahead and produce haploids, gaining no benefit from doing so. As this consumes resources, diploids that do it will be less fit and will be outcompeted by diploids that follow other strategies.
It can simply not produce haploids. Instead it has to produce new diploids, clones of itself. This is commonly called vegetative propagation (cf. your reference to Plantae) and will produce a world of clones.
It can produce haploids, but find ways to constrain their actions so that they can’t act in certain ways that would otherwise be in their interest.
The second strategy is obviously simple to follow. But we don’t inhabit a world of clones. Why not? For one thing, a clone may be well adapted to one environment, but less able to thrive in a different environment; mixis, achieved through haploid/diploid alternation, produces more varied offspring that can exploit more diverse environments. For another, the environment may be actively changing; for example, parasites may acquired the ability to infest a particular diploid strain—genetically uniform populations (as in plant breeding) are notoriously vulnerable to new diseases, but if you keep mixing up the genes you have hedged your bets against parasite outbreaks. I also suggest that clones are vulnerable to copying errors that will degrade the accuracy of their genomes over time, reducing their biochemical toolkits (in a fashion akin to Tasmanians’ loss of technologies over the millennia); mixis provides a way of importing nondegraded genes to replace ones you’ve lost. (The degraded genes are, in effect, “bad recessives.”)
So how can a diploid constrain its haploids?
One obvious method is to provide them with few nutrients, and limited ways of acquiring more. Sperm and eggs are relatively small (and eggs, which are bigger, are less motile); they don’t have much time to pursue their own interests. It might also be possible to subsidize the haploids through “parental” behavior, but with a price tag in behavioral constraints. Both of these strategies limit haploid ability to disperse, either through lack of stored energy, or through needing to stay close to Mother Diploid. The first of these strategies, at least, seems to be very widespread.
So a thing that could make for more autonomous haploids is an environment that puts a premium on wider dispersal. Maybe there is some resource that is needed but exists in scattered clumps; or some hazardous condition that prevents vegetative propagation, with safe spaces being far apart.
If you have haploids with some degree of autonomy, they might gain the ability to split off bits of Mother Diploid and carry them along on their travels, ensuring their own supply of essential resources. Or they might learn to steal diploids from other strains or even other species.
Have you read Olaf Stapledon’s Star Maker? He has vegetative races on planets with intense solar radiation, which have enough energy to get up and move about, detaching themselves from their roots. You might view the “roots” as the mother diploids, and the motile parts as the haploids. As I recall, he has a predictable crisis when the motile plants learn to synthesize necessary substances chemically and stop bothering with roots, which are allowed to die. . . .
I also want to note that, looking up coelenterates, I find that they don’t actually do diploid/haploid alternation. Rather, they have a diploid polyp that reproduces asexually, producing a diploid medusa that reproduces sexually, producing haploid gametes that have only a brief separate existence. It’s rather as if children didn’t reach puberty, but propagated pubescent adolescents that then produced more children.
Coming back to this one, the likeliest answer is “insurance.” Yes, you’re kin to your diploid mother, 100%. But your diploid mother could die. Then if you can’t reproduce, you’re out of luck in the Darwinian lottery. On the other hand, if you have reproduced, your diploid daughter is 100% your kin, and is just as good a bet. Surely two tickets in the lottery are better than one!
(It could be said, I suppose, that you still have kin in your siblings. But if none of them can reproduce, either—presumbly all haploids are fertile or all are sterile, to a first approximation—then the long-run value of all of them as kin is zero.)
This suggests, by the way, that you might have haploids who have no desire to mate as long as their mother is alive; they become fertile or sexually motivated after their mother dies, and disperse to seek mates.
For some reason this is making me think about Kipling’s antisocialist allegory “The Mother Hive” . . .