[Taxacom] Molecular evidence (in 2017) supports my 2014 theory about rafting killifish

[John Grehan]

Hi Roland

"And still, annoyingly, animals move and seeds are dispersed, even over
long distances. Who could imagine that this ever would have an effect on
anything"

Not sure why it's annoying. Every species had to disperse one way or
another to be where they are, even over 'long' distances. That is why one
sees some species with near global ranges. And that is consistent with taxa
that have global ranges with allopatric sub-clades - the ancestor was
global (more or less) and differentiated allopatrically (in other words
vicariance).

Your host-parasite outline is quite interesting. If one views hosts as
'island habitats' then I think the situation is comparable to the idea of
metapopulations of taxa on physical islands, where the islands may be
geographically isolated, but are temporally connected by past islands and
island interactions. But even with that interchange between islands,
vicariance may occur as tectonic events isolate particular island sectors.
That is why one gets, for example, different taxa that are reciprocally
allopatric in the Pacific despite each spanning multiple islands. Just as
you outline for parasites that there is no 1:1 relationship between the
animal host and parasite phylogenies, so too one usually finds the same
situation with  plant host and parasite (phytophage) phylogenies, and yet
both can provide informative biogeographic patterns. Also, just as one
cannot assume that a host 'endemic' to a particular host originated with
that host, one cannot assume that an island endemic originated with that
island (and one sees the irony of some molecular studies using island age
as a calibration point when at the same time others find other taxa on the
same island calibrated by fossils to be older than the island).

Cheers, John Grehan

On Sun, Jan 3, 2021 at 12:39 AM Roland Bergman-Sun via Taxacom <
taxacom at mailman.nhm.ku.edu> wrote:

> And still, annoyingly, animals move and seeds are dispersed, even over
> long distances. Who could imagine that this ever would have an effect
> on anything?
>
> As fascinating as these interminable reruns are, I can't help but
> notice the parallel between this and Fahrenholz' rule.
>
> Fahrenholz' rule states that ectoparasitic animals that do not have a
> free-living stage are bound definitely to their hosts, and thus will
> speciate in parallel to these. Stated differently, it predicts that
> dispersal from one host to another is of no practical or evolutionary
> importance, and that vicariance on a single host lineage is the
> exclusive mechanism that dominates louse evolution. This results in
> the famous "Parasite phylogeny should mirror host phylogeny", which
> inevitably lead to the idea that *any* louse species found on a novel
> host species must represent a new species; if on a new host family or
> host order, it may represent a new louse genus. Morphology was
> speedily disregarded by the maxim "It is methodologically more correct
> to say that we don't know the morphological differences than to state
> that there are none" (Eichler, 1942 I think). Multitudes of species
> were then described based on host associations (or with the regular
> phrase "Species X is well separated from other species by characters
> of the head", with no details or detailed illustrations). This
> artificial host specificity was subsequently taken as evidence for
> Fahrenholz' rule, in an excellent example of circular reasoning.
>
> In recent decades, both morphological revisions and molecular work has
> been very unkind to Fahrenholz. Both lines of evidence have
> independently shown that host specificity varies greatly and some
> species of lice occur on great numbers of hosts with few or no
> morphological and genetic differences between populations on different
> host species. The same species of lice is known to be well established
> on host species belonging to different orders in many cases (e.g.
> buzzard, falcons, and pigeons). In other cases, of course, there are
> high degrees of co-speciation and host specificity; it all depends on
> the groups examined. In general, the more louse species there are in a
> genus, the more likely it is that there will be some species that
> break Fahrenholz' rule. We recently published an example of a species
> that is known (genetically, it is not described yet) from over a dozen
> different host families ranging from Australia and the Philippines
> through South China all the way to Malawi. Specimens from across this
> range are genetically more or less identical, and there are no real
> morphological differences other than what may be expected within a
> species. From morphological samples, we have found about 50 more host
> species, which include more or less the whole Old World tropics, and
> about 20 different host families.
>
> Similarly, groups of genera that are morphologically and genetically
> very similar occur on widely distantly related hosts. We recently
> realised that lice on pigeons, penguins, sandpipers, and grebes form a
> monophyletic group genetically, and share at least two morphological
> characters that are not found in any other lice. Yet these bird groups
> are not very closely related at all. Similarly, the
> Degeeriella-complex occurs on a range of distantly related bird
> groups, with no obvious patterns (e.g. some but not all kingfishers,
> grouse and pheasants but not other galliforms, some New Guinean
> passerines and pittas, but barely any other passerines, etc.). At the
> time of writing, there is not a single published example that has been
> studied in any detail during the last 30 years in which Fahrenholz'
> rule applies without exception.
>
> Thus, even millimetre-long lice, that live their whole life on the
> host, and have no free-living stage and no intermediary hosts, and
> cannot move even a centrimetre on a non-feather surface, can somehow
> move between hosts, including over vast distances and between
> distantly related hosts and establish viable populations there. There
> are many different mechanisms known for this (water walking, phoresy
> on flies, etc.), and many of these have been dismissed by adherents of
> Fahrenholz' as having no or little impact. Yet obviously they have.
> Comparisons with animals that can actually move longer than a few
> millimeters on their own volition are perhaps obvious to all.
>
> These days, Fahrenholz' rule is all but abandoned, except in the sense
> of a null hypothesis that can be tested. The great adherents to this
> rule (Eichler, Zlotorzycka, etc.) are all gone. Of all the louse
> researchers in the world, there seems to be only one person who gives
> this idea any credence any longer; he published a half-hearted defence
> of this rule last year, reiterating Eichler's comment from 1942
> paraphrased above. The pretty pattern so dogmatically adhered to by
> would-be-theoreticians is ruined completely by the fact that animals
> move.
>
> ---
>
> Now I am off to work on my 2021 bird list. Interestingly, on my
> wish-list for the day is the Japanese Grosbeak, which normally breeds
> in the north of China, Japan, and Korea, but which winters here in
> Guangzhou. In recent years, they have attempted to breed here as well,
> in a sort of microcosm of dispersal. At least one pair got fledged
> chicks the year before last, so it remains to be seen if they will be
> able to establish a viable population. Yet to my knowledge -- and this
> is perhaps illuminating -- Japan did not split from South China
> tectonically at any point during the last three years since I arrived
> here. Of course, I don't read Chinese so I may have overlooked it, but
> I would imagine that that sort of thing would be mentioned in the
> international press as well.
>
> Cheers!
>
> On Sun, Jan 3, 2021 at 6:03 AM John Grehan via Taxacom
> <taxacom at mailman.nhm.ku.edu> wrote:
> >
> > Hi Ken,
> >
> > Understand that you feel that way since it seems that you and Jason are
> > frustrated when your claims or interpretations are contested. But
> > regardless, the bottom line remains the same:
> >
> > 1) fossil calibrated molecular divergence estimates are minimums only
> > (claims for anything else is indeed transmogrification)
> > 2) Priors are just guesses
> > 3) molecular clocks are not set in stone as the only arbiter of
> > phylogenetic age
> > 4) Older tectonic ages are not falsified by fossil calibrated ages (since
> > the latter are just minimums)
> > 5) tectonic correlations are empirically observable
> > 6) No one (to my knowledge) has provided an empirically grounded
> > falsification of any proposed tectonic correlation (i.e. demonstrated
> that
> > taxa are younger than the correlated tectonics)
> > 7) Panbiogeographic studies have generated novel geological predictions
> > that have subsequently been corroborated by geologists - its one case
> where
> > evolutionary theory is not simply a matter of belief, but an actual means
> > of predicting new knowledge that was later found to be true (I notice
> those
> > who dismiss panb biogeography step around this one :)
> >
> > Cheers, John Grehan
> >
> > On Sat, Jan 2, 2021 at 4:52 PM Kenneth Kinman via Taxacom <
> > taxacom at mailman.nhm.ku.edu> wrote:
> >
> > > Thank you Jason,
> > >         You present an excellent critique of "CP" panbiogeographers
> > > arguments.   Almost always the same old rigmarole of cherry-picking,
> > > quoting out of context, sophistry, circular argumentation, and other
> > > methods of muddying the waters.  And it is often cloaked within a
> barrage
> > > of other verbiage, so I agree that it is important to warn newcomers.
> > >
> > > ________________________________
> > > From: Taxacom <taxacom-bounces at mailman.nhm.ku.edu> on behalf of JF
> Mate
> > > via Taxacom <taxacom at mailman.nhm.ku.edu>
> > > Sent: Saturday, January 2, 2021 12:35 AM
> > > To: Taxacom <taxacom at mailman.nhm.ku.edu>
> > > Subject: Re: [Taxacom] Molecular evidence (in 2017) supports my 2014
> > > theory about rafting killifish
> > >
> > > I think that Rob was on the right track but not precise enough. It is
> not
> > > that panbiogeography is akin to creationism, it is that the defence
> John
> > > and Michael are mounting is reminiscent of creationists. I may be
> wrong in
> > > your intention but the arguments I hear are cherry-picking, sophistry,
> > > circular argumentation and in general muddying the waters so as to
> create a
> > > gap for a "Panbiogeography of the gaps". This, however, is a mistake
> and
> > > has left you holding an untenable arcane view of biogeography whilst
> > > ignoring the last 60 years of advances in phylogenetics. The debate
> > > strategy seems to me to be a kafkaesque attempt to neutralize any
> > > possibility of criticizing Croizat or panbiogeography by labelling as
> > > suspect all other contenders, molecular phylogenetics (you call it
> > > phenetics), fossil calibration (using minimum age as a the fine edge
> of the
> > > wedge to push arguments such as confusing point calibration with log
> > > distributions), molecular clocks (your definition is "strict clock"
> from
> > > the 1960´s but you don´t care), and generally weaponizing the widely
> > > acknowledged limitations of all of these and more fields.
> > >
> > > John, you asked me to argue why I said that your position on Croizatian
> > > Panbiogeography (CP) was untenable. Succinctly, because of two main
> > > reasons. Firstly because Croizat quite simply rejected cladistics, and
> if
> > > you accept cladistics you are a vicariance cladist by definition and
> > > arguing otherwise is rejecting reality Secondly, because CP rejects
> > > dispersal (“Interestingly it is dispersalism that invokes miracles and
> > > mysteries.”) in spite of evidence that demonstrates that, however
> > > infrequently, it happens. Trying to relabel cases of dispersal as
> "range
> > > expansion" is sophistry aimed at making panbiogeography unfalsifiable.
> > >
> > > This pattern of muddying the waters is particularly noticeable when you
> > > selectively quote, for example with Donoghue and De Baets. From the
> same
> > > 2016 publication: "Biogeographic and fossil calibrations are
> complementary,
> > > not competing, approaches to constraining molecular clock analyses,
> > > providing alternative constraints on the age of clades that are vital
> to
> > > avoiding circularity in investigating the role of biogeographic
> mechanisms
> > > in shaping modern biodiversity." (2016). I don´t think any
> biogeographer
> > > would disagree with this statement, but it is anathema with CP
> because, as
> > > John has said: “If molecular clock models incorporating a tectonic
> > > correlation result in unacceptable results, that does not invalidate
> the
> > > tectonic correlation. But it does raise questions about the molecular
> > > model. Nothing ridiculous about it at all.”  The unfalsifiability of
> CP in
> > > all its glory. If something disagrees with CP, CP is not at fault
> because
> > > it is perfect. Other examples of cherry-picking involve the numerous
> out of
> > > context quotes of researchers acknowledging the caveats of
> phylogenetics
> > > and calibration as evidence of the inferiority and mendaciousness of
> non CP
> > > researchers (“magic”, “dark art”, “lies”, etc).
> > >
> > > This pattern is so extensive it is tiring pointing out the examples:
> > >
> > > “...keep in mind that some molecular systematists are recognizing that
> > > fossil calibration only provides minimum ages and are looking to
> tectonic
> > > correlates instead - which is another way of saying that they have
> adopted
> > > this panbiogeographic method.” ML or Bayesian models do not assume
> point
> > > dates but a probability distribution into the past. Please stop
> confusing
> > > the terms.
> > >
> > >
> > > “The idea that there has to be a constant molecular clock throughout
> the
> > > phylogenetic history of a group is not an empirical finding. It is a
> model
> > > of evolution that may not be true. … Like priors, molecular clocks are
> also
> > > theoretical models (and there are different models) and open to
> question or
> > > refutation. I would like to see you, Ken, show how a constant molecular
> > > clock” A molecular clock model does not assume monotonic (constant)
> rates
> > > within genes or within lineages nor are clocks assumed a priori.  This
> is a
> > > straw man argument. Nobody assumes the strict clock a priori except in
> very
> > > specific cases like viruses and even then after testing. I can´t
> believe
> > > that this is a mistake when you guys selectively quote dos Reis et al
> 2016:
> > > “Thus, while the clade ages generated in Bayesian studies are extremely
> > > precise and have excellent statistical support, because of the problem
> of
> > > the priors they can be ‘grossly inaccurate’ (dos Reis et al., 2016) and
> > > could be tens or even hundreds of millions of years too young.” Cherry
> > > picked quote: “Errors in the time prior and in the rate prior can lead
> to
> > > very precise but grossly inaccurate time estimates. Great care must
> always
> > > be taken in the construction of fossil calibrations and in the
> > > specification of priors on times and on rates in a dating analysis.”
> Not
> > > quite the same meaning, in particular with the added sentence ending
> “tens
> > > or hundreds of millions of years…”. That is a misquote if I ever saw
> one.
> > >
> > > “We see this in the morphological aspect of molecular genetics where
> > > different groups separated or dislocated by a tectonic feature show
> > > different levels of morphological divergence (for example with the NZ
> > > Alpine fault dislocation where correlated distributions may be
> conspecific
> > > or species level differences even after more than 20 million years. So
> the
> > > panbiogeographic implication of tectonic correlation is that this
> provides
> > > an approximation of age for the correlated groups.”
> > > You are assuming as axiomatic that the taxa on either side of the fault
> > > have been unable to cross since the tectonic event.
> > >
> > > “As Hauenschild et al. (2018) observed, clade ages that are too young
> may
> > > be calculated ‘based on too narrowly set priors, and vicariance
> thereby may
> > > be erroneously ruled out’.”
> > >
> > > Again, cherry-picked, out of context quote. It is followed by: “If the
> > > importance of vicariance in the course of the Gondwanan breakup is to
> be
> > > evaluated via the pragmatic criterion of mismatch between age
> estimates and
> > > geological history, the priors defining the molecular dating analyses
> have
> > > to be solid. As those are predominantly influenced by fossil
> attribution
> > > (Magallón, 2014; Pirie, Litsios, Bellstedt, Salamin, & Kissling, 2015;
> Shen
> > > et al., 2016), taxonomy and phylogeny of the study group are of crucial
> > > importance. Consequently, taxonomically resolved groups with a rich
> fossil
> > > record should constitute ideal model groups, because they are more
> likely
> > > to uncover accurate age estimates (e.g., Favre et al., 2016;
> Muellner‐Riehl
> > > et al., 2016).”
> > > And what did the authors find?
> > > “Results: Our biogeographic analyses illustrate that the ziziphoid
> lineage
> > > was influenced by both long‐distance dispersal and Gondwanan breakup
> > > vicariance events. Yet, these vicariance events cannot explain all
> > > divergence events at the backbone of this lineage.” Shocker, they find
> both
> > > mechanisms at play. I can´t wait to see how you ignore this part of the
> > > paper whilst using the bits that you agree with (usually the necessary
> > > acknowledgement of study limitations).
> > >
> > > This is a pattern. I have kept correspondence for the last 10 years on
> > > these exchanges and it is always the same rigmarole. But I still bite
> > > because it is important to warn newcomers.
> > >
> > > Happy New Year everyone.
> > >
> > > Jason
> > >
> > > On Sat, 2 Jan 2021 at 09:03, John Grehan via Taxacom <
> > > taxacom at mailman.nhm.ku.edu> wrote:
> > >
> > > > p.s. keep in mind that some molecular systematists are recognizing
> that
> > > > fossil calibration only provides minimum ages and are looking to
> tectonic
> > > > correlates instead - which is another way of saying that they have
> > > adopted
> > > > this panbiogeographic method.
> > > >
> > > > John Grehan
> > > >
> > > > >
> > > > _______________________________________________
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> > > 1987-2020.
> > > >
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> > > Nurturing nuance while assaulting ambiguity for about 33 years,
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