There is no federal standard or international standard, and it is not illegal to use Ne in unusual ways. But all population geneticists I know would use it for the effective population size (after subscripting the “e”). This is definable as the size of an idealized population in a diploid hermaphroditic population that is random-mating, which in that case means having gametes contributed to an infinite gamete pool from which they are drawn at random to make offspring. The idealized population chosen is one which has the same rate of inbreeding (or the same rate of increase of variance of gene frequency among replicates) per generation as the actual population being discussed. Populations (ideal and real) matched by effective population size have nearly identical outcomes in cases of selection, migration, and mutation in the presence of genetic drift. So it is very useful to compute Ne because we can then see how an idealized population behaves in models that we can analyze mathematically.
The selection process was the thing that got me as well. I’ve actually looked at the code, and it is… odd. In some areas, I feel the oddness is intentional obfuscation. In others it may be legitimate confusion or just really ugly code.
Nice to see our UW GS friends checking in 
Thanks.
Does this idealized population also exclude selection? As I understand it (and want to know if I’m wrong), this population does not exhibit fitness differences.
So, the Ne of haploid populations is not based on a haploid population?
Are you from UW GS? I am also affiliated with UW Biology.
Does this idealized population also exclude selection? As I understand it (and want to know if I’m wrong), this population does not exhibit fitness differences.You're right, it does not.
So, the Ne of haploid populations is not based on a haploid population?The idealized diploid population of size N that I described has the same amount of genetic drift as an idealized haploid population of size 2N. You can also think of an idealized haploid population where they each contribute equal, but infinitely large, contributions to a pool of offpspring and then they mate at rancom and have offspring, and N random ones of those survive to adulthood. The idealized haploid population will behave exactly like an idealized diploid one that has half as many individuals.
I’m a student at another institution, but interviewed a few years back for the GS PhD program and had visited before.
Harmit Malik gave a talk at our department retreat in September. Good stuff.
As a New Zealander, this issue is of considerable interest to me. A number of our endemic bird species have gone through severe population bottlenecks. Takehe (118 individuals), Kakapo (49), and the Catham Island Robin (5, with all of the current population being descended from a single male, ‘Old Blue’) come immediately to mind.
The unexpectedly mild impact of inbreeding on the latter species has apparently been the focus of two articles:
Kennedy, Euan S.; Grueber, Catherine E.; Duncan, Richard P.; Jamieson, Ian G. (April 2014). “Severe inbreeding depression and no evidence of purging in an extremely inbred wild species—the Chatham Island black robin”. Evolution. 68 (4): 987–995. doi:10.1111/evo.12315. PMID 24303793.
Weiser, Emily L.; Grueber, Catherine E.; Kennedy, Euan S.; Jamieson, Ian G. (January 2016). “Unexpected positive and negative effects of continuing inbreeding in one of the world’s most inbred wild animals”. Evolution. 70 (1): 154–166. doi:10.1111/evo.12840. PMID 26683565.
The Human-Assisted Spread of a Maladaptive Behavior in this species has also been documented.
Can these species be taken as disproof of MA’s implicit claims about small populations? Or is there still a ‘Sword of Damocles’ hanging over them?
Can these species be taken as disproof of MA’s implicit claims about small populations? Or is there still a ‘Sword of Damocles’ hanging over them?
The negative effects of inbreeding have been studied intensively at least since the 1910s and are massively documented.
However the GA argument seems to sometimes involve excessive mutational load, sometimes involve Muller’s Ratchet, and sometimes involve genetic drift fixing slightly deleterious mutations. They aren’t very clear about this. And these are different phenomena. For example, when they cite Alexey Kondrashov they are citing excessive mutational load, not Muller’s Ratchet.
I don’t understand 1/10th of what you guys are talking about, but I’m going to butt in and be annoying anyway. It seems like what I was trying to argue FOR GE on the other thread. Bacteria probably aren’t really subject to GE, and humanity had far too low of a population size in the past in the current theory for selection to be possible.
Where’s your math?
True. It’s a real shame about all the completely penetrant sterility mutations that are drifting through the population as a result…
I wish I had some 
Darn. I thought scientists understood this stuff better than me. 
It is a shame indeed… 
I wish you had too.
To my knowledge, humans and our ancestors had a fairly constant effective population size of ~2500 or so for the past 2 Ma, only ramping up to the current ~25000 in the past 20-30ka. GE-like (that is, including the real ones) processes are only an issue for species with effective population sizes under 100-200, ‘maybe’ as high as 500 depending on the details.Ironically, it would be a problem for the YEC model.
I don’t get the joke, and that’s a shame since your emojis suggest it’s a really good one. Could you explain it to me, so I can laugh, too?
He was being sarcastic. So I made a joke back by acting like I took him literally.
Apparently it didn’t work. Oh well. 
Oh.
Is there a reason you made a bad joke, rather than responding to the serious point he made?
It wasn’t a serious point. If he wants to explain it was, and wasn’t just sarcasm, then he can.
My (perhaps overly opaque) point was that you seemed to be saying that natural selection is impossible in humans. That is a ridiculous notion that is completely at odds with observed reality.
I was attempting a sort of facetious reductio ad absurdum scenario in which mutations with selection coefficients of 1.0 are inherited across generations in order to point this out, but clearly my attempt fell flat.