On the thread entitled “Species Kinds”, commenter phoodoo asks:
What’s the definition of a species?
A simple question but hard to answer. Talking of populations of interbreeding individuals immediately creates problems when looking at asexual organisms, especially the prokaryotes: bacteria and archaea. How to delineate a species temporally is also problematic. Allan Miller links to an excellent basic resource on defining a species and the Wikipedia entry does not shy away from the difficulties.
In case phoodoo thought his question was being ignored, I thought I’d open this thread to allow discussion without derailing the thread on “kinds”.
Ah, but there are a great many stretches. Over the long haul, linkage groups can be quite small. And coalescence for any particular bit can take millions of years. I think you overstate the case. The present population is descended from a great many members of a preceding population (even more if we count genealogical descent rather than possession of particular DNA fragments, but still many regardless).
I don’t think your original claim, that members of a species are similar because they have only a few ancestors, is right at all.
John Harshman,
You don’t just stop there though, at the coalescence of a given historically undivided haplotype. Recombination does not set the maximum width of a coalescent stretch. If a recombinational event takes place in the middle of a wider stretch, the two sub-stretches are still themselves expected to be commonly descended from even further back. Genetic stretches are constantly meeting themselves, sometimes mutated, sometimes sliced and travelling via different routes.
Can, but that does not render the entire argument void. We can still cluster in-the-main on characters from more recent ancestors even if (say) our blood groups go back beyond the human-chimp split. And there is in any case still clustering at higher taxonomic levels, in which these ‘millions-of-years’ coalescences play a part.
I was specifically talking about ancestors who actually contribute material. We could hardly cluster on the characters of those that don’t!
I don’t know if the dispute is between those vague terms ‘a great many’ and ‘few’. Nonetheless, it seems beyond dispute to me that we have a particular fixed allele now because there was a ‘cone of fixation’ from its origin to the present, and that cone’s apex is in an individual, recombination or no. If that fixed locus is one of the things on which we can be said to cluster, common ancestry on one individual is the fundamental source of that clustering. This multiplies up for multiple characters to bring in more individuals, but essentially the processes of selection and drift involve the gradual elimination of ancestors, to leave the same ‘few’ at a given remove at the head of the family tree. As one ascends, they get fewer still – till you hit the first sexual eukaryote at least.
This is without considering selective sweeps, bottlenecks and inbreeding, of course, all of which tend to reduce the effective population size. [eta – and gene conversion]
It’s only subjective if it’s the opinion of a particular finite individual. If it’s the opinion of God it’s objective by definition
peace
I quoted this mostly because I like the phrase ‘cone of fixation’ but also to point out that if the cause of clustering in species is reproductive isolation it seems a little like question begging for reproductive isolation to be the determining factor in defining a species.
But Ive already said that 😉
peace
And what is the opinion of god on the red wolf?
I don’t know, but I know he has one.
The enterprise of science is all about gleaning what his opinion is. That is true whether you acknowledge his existence or not
peace
fifthmonarchyman,
I never even mentioned reproductive isolation. I think you might not be fully grasping the argument.
It’s odd how your god seems happy to explicitly tell us it’s opinion on all sorts of things, from when to eat fish to who to stone to death and why.
If two groups of people have differing opinions on what his opinion is, what are our options?
A holy war?
Do tell how we can determine who is wrong and who is right via god.
OMagain,
In some other thread, preferably! 😉
Unfortunately we only have your opinion of His opinion
Allan Miller,
Sure, each fixation has a source in one individual (or actually Nµ individuals). But different fixations, different individuals. Even a selective sweep only carries a small part of the genome with it, and most fixations are neutral anyway. And if we’re talking about humans, there seem to be no bottlenecks within the past few million years.
If. Assuming there is such a person, and assuming you have any clue about his opinion, two huge and dubious assumptions on which to hang an idea of species.
peace
It was a rhetorical question. I already know the answer!
WARRRRRRRRR!
John Harshman,
Indeed. The point at issue is whether this number of individuals, for the diagnostic characters in question, can be considered ‘a great many’ or ‘few’. I still contend that the winnowing of genetic contribution by drift (which includes random gamete sampling) and selection means that, for species-diagnostic characters, the number is closer to the ‘few’ end of the spectrum. Incidental coalescence for the numerically greater number of ancestor alleles that were already fixed anyway does not count. It’s the characters that contribute to divergence and distinction that matter for my contention, and they tend (IMO) to come from ‘few’ even without invoking isolational founder effects or accelerated elevation of inbreeding coefficients.
I wasn’t talking about any species in particular. My statement was a general one. I wasn’t relying on bottlenecking to rescue my assertion, it’s just one of the several factors that increase ‘clustering’ due to their effect on distance to most-recent ancestors, and on the number of those with some genetic contribution still extant.
In unconstrained, fully panmictic populations with no gene conversion, having a Ne closer to their census size, there is more within-population divergence, and hence somewhat less ‘clustering’. The less variation there is, the more clustering, but also the fewer ancestral individuals contributing to the current genetic landscape. The two correlate.
Like I say, a football crowd is stuffed full of relatives, sharing extensive common ancestry, and this must be the ultimate source of their ‘clustering’. Less so if it’s an international …
I suppose we might be talking at cross purposes? If one takes all the differences that have accumulated since a common ancestral node, then indeed a larger (and increasing) number of mutations in individuals contributes to those differences. But as regards why each member of a species more closely resembles the rest of its conspecifics than anything else, that is due to their more recent within-population common ancestry, regardless of time since a branching node.
I’d say that every character fixed since the split from its closest living relative is a species-diagnostic character. In our case, there are some millions of those. Certainly, if we limit the pool to a few characters, there will be few coalescents of those few characters — one each, if we are counting individual nucleotides. But I’d still say that individuals in a species resemble each other because of interbreeding and selection for a similar environment rather than because they share a small set of ancestors.
John Harshman,
I don’t get this distinction. Interbreeding and selection cause loss of the genetic contribution of ancestors!
I most closely resemble my kin because of common ancestry. I don’t see something else taking over from that as we broaden out the set considered, even though these other things do have an effect on the specific characters encountered.
It’s a population genetic fact that a population at equilibrium can only sustain the retention of ancestry of a subset of any given ancestral population. This does not go away when adding in perturbations from equilibrium. Very few of those perturbations increase the ‘carrying capacity’ of the population for the number of ancestors’ DNA.
John Harshman,
I’d agree, but they are not the reason why members of a population resemble each other. They are, granted, a reason for the extent to which they differ from others.
More than the inbreeding, I’m concerned about the outbreeding! 😉
I don’t understand this statement. Aren’t those the same thing? Resemblance can only be relative to something else.
Tallness, for instance?
No I think understand the argument.
I used your comments as a spring board but my response was more generally about the definition of species.
peace
I find it funny that the moment a higher power is merely mentioned the swarm commences.
It’s amazing how something so innocuous can cause such a stir. It’s almost like people here are obsessed with the topic
😉
peace
Oh shut up.
Said the guy whose definition of species includes a quality unknowable except to his god. Obsessed much?
which quality is that?
Here is my definition again.
species- a group of organisms that are relatively similar genetically and phenotypically share a relatively recent ancestor and occupy the same ecological niche.
Is it perhaps possible that you are imagining something about God that is not there?
I don’t think so, but then again I don’t usually see things about the knowledge of the almighty in definitions that are not actually there.
peace
fifthmonarchyman,
This may be a good point to remind you that while you claim to have three criteria for species status, your definition mentions four. It’s also unworkable unless you can define, in each case, what “relatively” means.
John Harshman,
The ‘something else’ can be coffee cups or motor vehicles, it doesn’t have to be other organisms. If things are produced from a template, they resemble each other, without (I would say) specific reference to anything else.
Of course, we were talking of species, which have a divergent history. But, this is a history of templates.
If one has a population, it derives from relatively few ancestral individuals. It does! It does! This fact is surely undeniable, from population genetics? If one took a population at equilibrium, and called that point t1, then allowed it to carry on to time t2 when neutral mutations generated at t1 are fixing, the number of individuals from t1 still with genetic representation at t2 must be ‘few’, and getting ‘fewer’. Surely? Perhaps Joe could set me straight on that.
Now, if one brings in other species, extending back from t1 to a prior common branch point B, there are obviously many more mutations, originating in many more individuals, involved in the path from B to t1. But, they all go through the same ‘few’ individuals at t1. So as far as coalescence is concerned, from the point of view of t2 individuals, they got all their alleles via the same few individuals in t1. Even those alleles generated between B and t1.
At t2, individuals resemble each other because of their common descent from those few t1 individuals. But they differ from a second cluster of individuals descended from B by much more – all the mutations from B to t2, plus those down the equivalent segments of the second line, contribute to the difference. But as far as why each individual species broadly seems to be produced to a common ‘theme’, that is due to their within-population common descent from ‘few’ ancestral templates, which was the point I was trying to make.
Here is another example of the harm our current definition of species as reproductively compatible organisms could cause.
check it out
http://phys.org/news/2016-08-elephants-knowledgenot-mutationsto-survive.html
peace
If you are making a claim, explain why that article supports your viewpoint.
My definition is tri-perspectivial.
past
present
potential future
The criteria of ecological niche and phenotype are both subsumed under the perspective of a snap shot of current state
The criteria of recent common ancestor is looking from the historic perspective of the past
The criteria of genetic similarity is looking at potential. It’s meant to more a more fluid perspective than is given with the present phenotype and ecological niche.
I hope that makes sense I can elaborate further if need be
“relatively” means compared to other organisms.
The precise values would change depending on our measurement and level of resolution we want to achieve.
peace
Do I really need to spell it out.
If a species is defined by only reproductive compatibility then Namibian desert elephants are the same as African savanna elephants.
The article makes the case that Namibian desert elephants are a unique population that should be preserved, irrespective of reproductive compatibility.
It’s exactly the same situation as with the red wolf
peace
Not spelling it out is the first mistake. You have reduced uncertainty. I know understand what your point was.
I now can make the following point. Nobody is making any argument that they should not be preserved. Not in that article or elsewhere, as far as I can see. Except hunters might want to hunt them. Well, they are always going to want to do that irrespective of the rarity or otherwise of the prey.
So I really don’t understand your point after all. Is it that conservation decisions should be taken above the species level?
One comment moved to Guano. Please address the ideas, not the person.
Roger Wilco.
Yeah, no-one makes any decisions on conservation based on criteria of reproductive compatibility, as far as I am aware. It is but one way of subsetting things, and not a particularly useful one in many instances.
No, it made no sense at all. You have arbitrarily divided your four categories into three groups, and the explanations for which categories go into which groups are senseless. I fear that further elaboration would only be more senseless.
This too seems senseless. “Compared to other organisms” is so vague as to be useless. “Level of resolution we want to achieve” seems to mean that choice of what fits a species category is capricious. Collies could be a species. Dogs could be a species. The genus Canis could be a species. The family Canidae could be a species. Your criteria offer no guidance.
peace
I’ve posted this before in relation to this – How To Do It. Next week – taxonomy.
quote:
If Wayne’s team is correct, it could spell trouble for the red wolf. The US Endangered Species Act makes no mention of hybrids, so the red wolf might lose its protected status – and the millions of dollars spent on captive breeding and recovery programmes.
end quote:
Check it out
https://www.newscientist.com/article/2099192-red-wolf-may-lose-endangered-status-because-its-just-a-hybrid/
peace
quote:
Namibia, however, does not see its desert elephants as animals that are any different from the other elephants within its borders. In a press release (pdf) sent at the beginning of June, Simeon N. Negumbo, permanent secretary of Namibia’s Ministry of Environment and Tourism, wrote that the country is home to more than 20,000 elephants and the region where the hunts will take place has a total of 391 elephants with a 55 percent sex ratio. He called desert elephants “tourist attractions” and said all elephants in the country are “no longer rare…but only potentially valuable.” He noted that human–wildlife conflict is increasing, and that some humans have been killed by elephant attacks.
end quote:
check it out
http://blogs.scientificamerican.com/extinction-countdown/why-is-namibia-killing-its-rare-desert-elephants/
peace
1) you really like the word “arbitrarily” don’t you. I’m not sure it means what you think it means. 😉
2) When I am having trouble understanding why something is I ask clarifying questions before assuming that It is all senseless.
It seems to help me. Just saying
quote:
For Kant, concepts are higher “so far as they have other concepts under them, which in relation to them are called lower concepts”. Genus and species is defined in terms of this relation between concepts: “the higher concept in regard to its lower concept is called genus, the lower in respect of its higher, species”.
end quote:
from here
http://www.philosophy-dictionary.org/GENUS_AND_SPECIES
My criteria in not meant to offer guidance on the level of resolution we want to explore. It is only meant as a guide for comparing organisms within a level that we choose.
Choosing how closely we want to look at populations of organisms is up to us. Just as it is with all classification.
I can separate the same group of objects into
1) red and blue piles
or
2) Red, purple and blue piles
or
3) Red, reddish purple,bluish purple and blue piles.
It’s really up to the folks doing the categorization to decide and defend their choice.
Once we decide we are going to stop at red and blue piles and pick a point to draw the line between the two sets there is no ambiguity at all.
We have a clear explicit standard and no “species” problem at all.
peace
fifthmonarchyman,
I don’t like the word “arbitrarily” all that much; it just seems to come up when talking about your ideas of species. That’s a problem for you.
“Species”, when talking about organisms, at least in the past few hundred years, does not refer to the philosophical categories you want to talk about. Your idea of multiple levels of species is one more point at which one would have to make arbitrary decisions. Sorry to use that word again, but your ideas demand it. Rather than just mention that, why not explain why the decisions either are not arbitrary, or why arbitrariness is a good thing.
Disclaiming all responsibility for making and defending choices is just a way to avoid confronting the fact the choices you demand can’t be defended. Why? Because they’re — wait for it — arbitrary. A perfectly useful word, aptly applied.
fifthmonarchyman,
‘Making no mention’ is hardly a policy decision.
Massive effort is put into preserving domestic rare breeds, which are perfectly capable of matings with other members of their species. As far as conservation is concerned, people either think a lineage is worth saving or they don’t. They don’t apply an objective razor to this decision, and it’s certainly not based on the BSC.
Hybrids, imported to the argument as posing a difficulty for an ‘evolutionary’ view of species, are something of a problem for the essentialist.
Allan,
I didn’t recognize ‘BSC’ as an acronym for ‘biological species concept’ and had to Google it. One of the hits was the Bristol Stool Chart:
Feces species.
That’s a different reference! You really don’t get how this works do you?
keiths,
Yes, that’s what I meant … !