[Taxacom] More junk science in phylogenomic timing

[John Grehan]

Kawahara et al 2019. Phylogenomics reveals the evolutionary timing and
pattern of butterflies and moths

https://www.pnas.org/content/early/2019/10/15/1907847116/tab-figures-data

As noted by some Taxacomers, the following critique is not of interest to
everyone and is here posted only for those interested in the nature of
timing and arguments for transmogrifying fossil calibrated estimates from
minimums to maximums and their consequences. So for anyone for whom this
topic is dead wood, please read no further and use the delete button to
avoid unnecessary aggravation. For anyone still interested in this topic
either way, I am always happy to read further responses and commentary, and
I am not immune from making errors in critique.

John Grehan

Declaring something as 'junk science' is probably harsh wording, but it is
justified here in terms of 'junk' being the magical creation of maximum age
boundaries out of nothing. And out of nothing, nothing comes.

In this paper the authors dated lepidopteran phylogeny with “carefully
evaluated synapomorphy based fossils”. So calibrations are fossil based –
which is where the junk science comes in. In their supplemental data they
note:

“Fossil calibrations were introduced as minimum bounds of uniform priors
and with the maximum root age as a hard maximum bound”

In other words, fossils provide minimum ages, but they are going to use
'uniform priors' to magically dream up an upper maximum. This is where
science becomes magic.

They note that “maximum calibration bounds (which must be applied to the
root age) are notoriously difficult to specify, as they rely on the absence
of evidence (79)” Exactly – they cannot be scientifically designated so
they are not just 'notoriously difficult,' they are not empirically
possible in the first place!

So what did they dream up? The dreamed that a “conservative age constraint
on the Amphiesmenoptera (Lepidoptera + Trichoptera) root between 201 Ma
(based on stem Glossata scale fossils (80), see Dataset S5) and 314.4 Ma
based on the absence of amphiesmenopteran fossils in the late
Carboniferous.”

Here they admit that they are fossil record literalists – that absence of
fossils is absence of existence – which they later contradict when their
molecular dating precedes the age of fossils (see further below). This is
where magic creates an artificial reality. The only scientifically
defensible content of this paper is where divergence dates are recognized
as being minimums only, nothing more nothing less.

Back to the abstract.

“The oldest members of the Lepidoptera crown group appeared in the Late
Carboniferous” (no, the appeared *by* the Late Carboniferous)

“Lepidoptera evolved the tube-like proboscis in the Middle Triassic (241
Ma)” (*not before or by*)

“proboscis....allowed them to acquire nectar from flowering plants.”

Finally some recognize that structure determines function and not the other
way around!

“our results indicate that butterflies became day-flying in the Late
Cretaceous (∼98 Ma).” No they do not. The only indicate that they become
day-flying *by the Late Cretaceous*.

“Our study provides an essential framework for future comparative studies
on butterfly and moth evolution” Excellent propaganda statement (which is
OK as all scientists engage in propaganda, but its good to recognize is and
consider its context). Here I would agree that the paper is essential for
keeping track of phylogenetic outcomes, and also as an excellent example of
misrepresenting minimums as actual or maximal ages of clades..

P. 2. “Previous phylogenetic studies that examined macroevolutionary
patterns of Lepidoptera (e.g., refs. 6 and 12–17) lacked sufficient genetic
data and carefully evaluated fossil sampling to confidently resolve the
evolutionary history of the order.” Seems to imply that these earlier
studies were a waste of time and money?

P. 2. “Using different dating schemes and a set of critically evaluated
fossils, we conducted multiple fossil-calibrated phylogenetic analyses” So
here it is again – fossil ‘calibrated’

“Our results indicate that the most recent common ancestor of crown
Lepidoptera appeared in the Late Carboniferous, ~299.5” No they did not,
the results only indicate that this group appeared at this time *or earlier*
.

“significantly predating the oldest known lepidopteran fossil from the
Triassic-Jurassic boundary” Which is of course the whole point – fossils
and fossil calibrated estimates are all minimums and absence of fossils is
not evidence of absence (contradicting their claims in the supplemental
data as noted above).

“Micropterigoidea, which are detritivores or bryophyte feeders (7), as the
sister group to all other Lepidoptera (280.6 Ma” Again – *by or before
280.6 Ma.*

“The crown age of Angiospermivora is dated at 257.7 Ma (CI, 276.7to 234.5
Ma)”Actually dated to 257 Ma or anytime earlier (*including earlier than
276 Ma*)

“suggesting that moths were internal plant tissue feeders in the Late
Permian” *By* the Late Permian.

“there is general agreement that some angiosperm lineages, which are in
part now extinct, were present >300 Ma (24)” Finally a statement of a
minimum!

“Large body size, a characteristic of some extant butterflies and moths,
may be an ecological consequence of being freed from the constraints of
living within plants” Or may not – this is a rhetorical exercise as some
ghost moths which are internal feeders are among the larger bodied (and
winged) Lepidoptera.

“thereby allowing greater access to nectar sources and the ability to fly
far distances.” But some molecular dispersalists believe that ghost moths
without any such ability can fly thousands of miles across oceans.

“of the ancient Nothofagus tree (19)” This is a sort of rhetorical device.
How ancient is ancient? It implies that they feed on Nothofagus because
they were sufficiently ancient – as if there were no other alternatives
around.

“ The common ancestor of nectar-feeding Lepidoptera first appeared in the
Middle Triassic (241.4 Ma; CI, 261.1 to 218.9 Ma). *Or earlier.*

“The clade Ditrysia, which is estimated to have a late-Jurassic crown age
(154.7 Ma; CI, 172.1 to 137.5 Ma)” *Or earlier*

“Apoditrysia have additional sensilla on the proboscis (19), implying that
further specialization on adult food resources may have arisen in the Early
Cretaceous (118.5 Ma; CI, 132.1 to 105.6 Ma).” *Or earlier.*

“This result confidently shows that butterflies are diurnalmoths with a
Late Cretaceous crown age (98.3 Ma; CI, 110.3 to86.9 Ma),” *Or earlier.*

“slightly younger than other published estimates using butterfly fossils
and host-plant maximum age calibrations” Since they are all minimums this
is of no account.

“neotropical nocturnal moth-like butterflies (Hedylidae) were sister groups
(84.4 Ma; CI, 96.6 to 72.2 Ma).” *Or earlier.*

“(Pieridae; 51.7 Ma; CI, 63.9 to 40.4 Ma) *or earlier.*

“Nocturnality in Lepidoptera dates back to at least the ancestor of
Heteroneura, in the Jurassic (209.7Ma; CI, 249.9 to 208.1 Ma)”. *By the
Jurassic.*

“the ancestor of Papilionoidea (98.3 Ma; CI, 110.3 to 86.9 Ma)”. *At least
110 Ma*