Question for John

[Oxyaena]

John, were you able to gain access to Gatesy et al (2013) yet? I could
ask Peter to link us to a non-pay-walled version of it, given that he
works at a university. Or maybe Pandora, given their uncanny ability to
find any paper whatsoever with seemingly no paywall, even if it comes
from a pay-walled journal (I should mention than *PNAS* is an
interesting case, given that any paper published over six months ago is
free, and papers published now will be free in six months).

In case readers can't find the thread where the paper is cited, I have
the citation below:

Gatesy, J., Geisler, J. H., Chang, J., Buell, C., Berta, A., Meredith,
R. W., ... & McGowen, M. R. (2013). A phylogenetic blueprint for a
modern whale. Molecular Phylogenetics and Evolution, 66(2), 479-506.

Happy hunting!
--
"Biology only makes sense in the light of evolution." - Theodosius
Doubzhansky

[John Harshman]

On 7/28/18 4:41 AM, Oxyaena wrote:
> John, were you able to gain access to Gatesy et al (2013) yet?

No.

[Oxyaena]

On 7/28/2018 9:06 AM, John Harshman wrote:
> On 7/28/18 4:41 AM, Oxyaena wrote:
>> John, were you able to gain access to Gatesy et al (2013) yet?
>
> No.

That was blunt.

>
>> I could ask Peter to link us to a non-pay-walled version of it, given
>> that he works at a university. Or maybe Pandora, given their uncanny
>> ability to find any paper whatsoever with seemingly no paywall, even
>> if it comes from a pay-walled journal (I should mention than *PNAS* is
>> an interesting case, given that any paper published over six months
>> ago is free, and papers published now will be free in six months).
>>
>> In case readers can't find the thread where the paper is cited, I have
>> the citation below:
>>
>> Gatesy, J., Geisler, J. H., Chang, J., Buell, C., Berta, A., Meredith,
>> R. W., ... & McGowen, M. R. (2013). A phylogenetic blueprint for a
>> modern whale. Molecular Phylogenetics and Evolution, 66(2), 479-506.
>>
>> Happy hunting!
>

[John Harshman]

On 7/28/18 7:39 AM, Oxyaena wrote:
> On 7/28/2018 9:06 AM, John Harshman wrote:
>> On 7/28/18 4:41 AM, Oxyaena wrote:
>>> John, were you able to gain access to Gatesy et al (2013) yet?
>>
>> No.
>
> That was blunt.

It was an answer to the question. What else were you looking for?

[Oxyaena]

True.

[Peter Nyikos]

The url is here:
https://www.sciencedirect.com/science/article/pii/S1055790312004186

The abstract is here:
The emergence of Cetacea in the Paleogene represents one of the most profound macroevolutionary transitions within Mammalia. The move from a terrestrial habitat to a committed aquatic lifestyle engendered wholesale changes in anatomy, physiology, and behavior. The results of this remarkable transformation are extant whales that include the largest, biggest brained, fastest swimming, loudest, deepest diving mammals, some of which can detect prey with a sophisticated echolocation system (Odontoceti – toothed whales), and others that batch feed using racks of baleen (Mysticeti – baleen whales). A broad-scale reconstruction of the evolutionary remodeling that culminated in extant cetaceans has not yet been based on integration of genomic and paleontological information. Here, we first place Cetacea relative to extant mammalian diversity, and assess the distribution of support among molecular datasets for relationships within Artiodactyla (even-toed ungulates, including Cetacea). We then merge trees derived from three large concatenations of molecular and fossil data to yield a composite hypothesis that encompasses many critical events in the evolutionary history of Cetacea. By combining diverse evidence, we infer a phylogenetic blueprint that outlines the stepwise evolutionary development of modern whales. This hypothesis represents a starting point for more detailed, comprehensive phylogenetic reconstructions in the future, and also highlights the synergistic interaction between modern (genomic) and traditional (morphological + paleontological) approaches that ultimately must be exploited to provide a rich understanding of evolutionary history across the entire tree of Life.

Does the url give you free access, or do you still need my assistance?

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina

[erik simpson]

Paywalled as usual.

[Peter Nyikos]

So tell me what you would like to know about the article.


Since nobody has given me a clue so far, I'll post the "highlights"
and the "Summary and Conclusions." The latter is LONG!


Highlights

► The origin of Cetacea (whales) represents a key macroevolutionary transition within Mammalia. ► We assess the distribution of support among molecular datasets for Artiodactyla relationships. ► Three supermatrices of molecular and fossil data yield a composite phylogenetic hypothesis. ► We infer a phylogenetic blueprint that outlines the stepwise evolution of modern whales.


3.4. Summary and conclusions

The current analysis represents a first attempt at combining genomic and paleontological data to derive a wide-ranging phylogenetic hypothesis for Cetacea (Fig. 7) and a unified reconstruction of the many evolutionary novelties that characterize this group (Fig. 2). Crown cetaceans such as Physeter macrocephalus and Balaenoptera musculus (Fig. 1) are highly derived outliers relative to the majority of extant mammalian species, most of which are furry, four-limbed, terrestrial, and miniscule in comparison (Fig. 4). The phenotypic divide between extant cetaceans and even their closest living relatives (Figs. 1C and 5) indicates that extinction has erased much of the historical evidence of whale evolution. Luckily, recent fossil finds have contributed to a rapidly growing inventory of extinct taxa that fill in wide anatomical gaps (Fig. 3). To make sense of this diversity, however, the fossil record of whales must be organized phylogenetically to distinguish primitive from derived states and to reconstruct long sequences of anatomical transformation. Many paleontologists have attacked this problem through phylogenetic analysis of morphological characters, the only systematic evidence that can be garnered from whale fossils (e.g., Geisler and Sanders, 2003, Theodor and Foss, 2005, Thewissen et al., 2007, Fitzgerald, 2010, Marx, 2010), but the results often have been incongruent with trees based on large matrices of molecular data (e.g., Gatesy, 1998, McGowen et al., 2009, Steeman et al., 2009; Zhou et al., 2011a, Zhou et al., 2012).

The past two decades have seen the emergence and pre-eminence of genomic data in systematics (Delsuc et al., 2005), perhaps due to the sheer quantity of available data, the simplicity of nucleotide characters, as well as the tractability of molecular evolution models utilized in phylogenetic analysis, but a sole reliance on DNA sequences has limitations as a general approach to reconstructing the history of Life. Molecular systematic hypotheses that place cetaceans in the context of extant mammalian diversity (Fig. 4, Fig. 5) represent ‘phylogenetic skeletons’ that are woefully incomplete in terms of documenting key anatomical transitions, and ironically must be fleshed out by the addition of fossilized bones. DNA sequences cannot be recovered from most extinct taxa, making genetic data relatively impotent with regard to the placement of fossils. Furthermore, despite the huge weight of character evidence provided by genomic information, morphological data can overturn phylogenetic hypotheses based on large compilations of molecular data. Although likely to be rare in the age of comparative genomics, this possibility was demonstrated here; the addition of only 115 phenotypic characters overturned a topology for Mysticeti supported by analysis of >30,000 molecular characters (Fig. 6).

Our research group and collaborators have therefore committed the past decade to merging morphology and molecules in combined supermatrix studies of Cetacea to reconcile paleontological and genomic evidence (Gatesy and O’Leary, 2001, O’Leary et al., 2004, Deméré et al., 2005, Deméré et al., 2008, Geisler and Uhen, 2005, Geisler et al., 2007, Geisler et al., 2011, O’Leary and Gatesy, 2008, Geisler and Theodor, 2009, Spaulding et al., 2009). In this more inclusive approach to systematics, phenotypic characters coded from extant taxa provide the critical link of homologies that connect phenotypic characters from fossils to molecular data from extant taxa. We have examined whale phylogeny at several hierarchical scales. Here, results from these supermatrix studies were merged to yield a single composite phylogenetic tree that encompasses the early derivation of whales as well as the subsequent diversification of crown group cetaceans (Fig. 7). The overall topology represents a phylogenetic blueprint for modern cetaceans, a hypothesis that summarizes the approximate age and relative sequence of changes that have occurred in the evolutionary construction of extant whales over the Cenozoic (Fig. 8, Fig. 9; Table 1). Due to the inclusion of genomic data, our hypothesis disagrees with trees based on morphology alone in the deep nesting of Cetacea within Artiodactyla as well as contrasting relationships within both Odontoceti and Mysticeti. The rearrangement of extant lineages, in turn, forces a reinterpretation of anatomical homologs and alters the placement of extinct taxa in the tree.

The importance of morphological characters, particularly fossil data, is evident in a summary topology that tracks the evolutionary lineage that terminates at Balaenoptera musculus (Fig. 10). Based on molecular data alone, it is impossible to discern the relative order of the many important evolutionary modifications (Fig. 2) that have culminated in this remarkable species. The ancestral lineage that connects the basal node of Artiodactyla to the extant blue whale traverses 30 branch points in our composite tree, but only 9 of the 30 side branches include lineages that extend to the living biota (Fig. 7). Numerous extinct side branches permit reconstruction of a more fine-grained sequence of evolutionary change (Gauthier et al., 1988, Donoghue et al., 1989). Our summary of the available evidence (Fig. 7, Fig. 8, Fig. 9, Fig. 10; Table 1) implies that a double-trochelated astragalus, the fibro-elastic penis, and a multi-chambered stomach evolved deep in the history of Cetacea over 60 million years ago (branches A–B), and that these changes were followed by the derivation of several “aquatic” specializations (sparse hair, loss of sebaceous glands, ability to nurse and birth underwater) in the common ancestor of Cetacea and Hippopotamidae (branch C) (Fig. 8). Over the next ∼20 million years, the involucrum (branch D), simplification of the dentition (branch E), a robust tail (branch E), an enlarged mandibular foramen (branch F), the transition to saltwater (branches F–G), shortened neck vertebrae (branch H), separation of the pelvis from the vertebral column (branch L), posterior migration of the external nares (branch L), vestigial hindlimbs (branches K–M), reduction of elbow flexion (branch O), and many additional specializations evolved sequentially on the stem lineage to crown Cetacea (Table 1). From ∼35–28 million years ago, the key anatomical traits that characterize filter-feeding whales were derived in succession on the stem to crown Mysticeti (Fig. 9): a broad rostrum (branch a), an unsutured mandibular symphysis (branches b–c), palatal nutrient foramina and by inference baleen (branch c), loss of mineralized teeth (branch d), and bowed mandibles (branch e). Features that are unique to the engulfment feeding apparatus of balaenopterids (pleated throat pouch, reduced tongue, fibrous temporomandibular joint) and unprecedented body size evolved later, within crown group Mysticeti (branches g and h; Fig. 9). Balaenoptera musculus displays a mosaic of features acquired at various time depths over the past ∼60 million years of artiodactyl evolution; our composite tree summarizes the age and phylogenetic generality of the various traits that characterize this highly derived species (Fig. 10).

Our hypothesis should be considered a starting point toward a more comprehensive phylogenetic analysis of whale origins and diversification. We see several obvious ways that improvements can be achieved. First, taxonomic sampling can be expanded. Several recent supermatrix studies have included nearly all extant species of Cetacea, but these efforts focused on molecular data (McGowen et al., 2009, Steeman et al., 2009; Slater et al., 2010). DNA sequences have been published for over 90 extant species, but effective integration of these data with the fossil record of Cetacea will require coding morphological characters from many more extant taxa to provide an overlap of systematic information. In terms of fossils, the sampling of extinct taxa in our composite tree focused on filling gaps on the stem lineages of Odontoceti, Mysticeti, Cetacea, Ruminantia, Suina, and Camelidae (Fig. 7). However, >700 wholly extinct artiodactyl genera have been described (McKenna and Bell, 1997, O’Leary et al., 2004). Many additional extinct taxa should be coded to yield a more detailed evolutionary reconstruction. Second, it would be preferable to compile a single supermatrix with a broadly applicable set of phenotypic characters that characterizes variation across both deep and shallow divergences within Artiodactyla. The present supertree of three supermatrix topologies (Fig. 7) is based on several assumptions of monophyly that would not be required if the same phenotypic characters were coded for all relevant taxa. This is a challenging task, but a recent effort to compile a morphological matrix across all mammalian orders demonstrates that several thousand phenotypic characters from diverse taxa can be scored with the aid of modern web-based tools (O’Leary and Kaufman, 2007) and cooperation among taxonomic specialists (Novacek et al., 2008). Third, genomic resources now permit a mapping of critical molecular changes that correlate with the unique specializations and degenerative features of whales. Recent studies of DNA sequences from Cetacea have documented convergent changes in the auditory genes of echolocating cetaceans and bats (Li et al., 2010, Liu et al., 2010, Davies et al., 2012), as well as adaptive evolution of brain development genes (McGowen et al., 2011, McGowen et al., 2012, Xu et al., 2012) and Hox loci involved in forelimb development (Wang et al., 2009). Other work has characterized patterns of pseudogenization in Cetacea that parallel evolutionary losses at the phenotypic/behavioral level, including mutational decay of genes related to color vision (Levenson and Dizon, 2003), enamel formation (Deméré et al., 2008, Meredith et al., 2009, Meredith et al., 2011b), olfaction (Kishida et al., 2007, McGowen et al., 2008, Hayden et al., 2010), taste (Jiang et al., 2012), and vomeronasal chemoreception (Yu et al., 2010). Further efforts that tie particular anatomical transformations to underlying molecular change will contribute to the emerging macroevolutionary synthesis.

[beautiful Fig. 10 with long caption omitted]

As phylogenetics proceeds into the twenty-first century, a focus has been rightly placed on genome-scale datasets because of the nearly limitless supply of discrete systematic characters (Delsuc et al., 2005). Regardless, many neontologists recently have come to the realization that, moving forward, paleontological data will be essential for phylogenetic analysis, divergence dating, estimation of diversification and extinction rates, biogeography, and the mapping of particular phenotypic traits (Wiens, 2009, Losos, 2011, Pyron, 2011, Slater et al., 2012). These revelations are not really new (Gauthier et al., 1988, Donoghue et al., 1989, Novacek, 1992, Novacek and Wheeler, 1992, Smith and Littlewood, 1994, Smith, 1998), but instead indicate that even with the development of ‘sophisticated’ likelihood models, genomic data can advance the field only so far. We predict a blossoming relationship between paleontology and genomics in the coming years, with the hope that a more complete phylogenetic reconstruction of Life, including its many extinct lineages, will be achieved.

[erik simpson]

What I would really like is a copy of the article itself. Thanks for what you
did copy. It looks to be very interesting.

<Clip long quote>

[Peter Nyikos]

To what end? Nobody but you has shown any interest in the article
since I offered to post from it, and you haven't commented on
anything in the long Conclusion. If you can't do that in this
online medium, I can hardly expect you to type out the parts
that you find interesting from the printed copy.

> Thanks for what you
> did copy. It looks to be very interesting.
>
> <Clip long quote>

I would have thought that at least the concluding part of the Conclusions
might prompt some comment. Here it is again, broken up into three
paragraphs, with a comment by me after each:

As phylogenetics proceeds into the twenty-first century, a focus has been
rightly placed on genome-scale datasets because of the nearly limitless
supply of discrete systematic characters (Delsuc et al., 2005).

And this is a trap: the temptation is that, whenever morphology and
paleontology conflict with genomic evidence, the sheer bulk of the latter
will win out. The case of turtles is a prime example. Once classed
as anaspsids, they are now put closer to birds than are snakes, lizards,
and perhaps even *Sphenodon*. Diapsids that somehow closed up both
two fenestrae -- a change without parallel in the fossil record
nor nor in living amniotes.

And why? because no one has ever found a way of weighting
morphological characters, the way DNA gives no-brainer ways
of assigning weight to genomic characters.

Regardless, many neontologists recently have come to the realization that,
moving forward, paleontological data will be essential for phylogenetic
analysis, divergence dating, estimation of diversification and extinction
rates, biogeography, and the mapping of particular phenotypic traits
(Wiens, 2009, Losos, 2011, Pyron, 2011, Slater et al., 2012).

Developmental biology will have to play a role, especially for
that "mapping."

These revelations are not really new (Gauthier et al., 1988, Donoghue et
al., 1989, Novacek, 1992, Novacek and Wheeler, 1992, Smith and Littlewood,
1994, Smith, 1998), but instead indicate that even with the development of
`sophisticated' likelihood models, genomic data can advance the field only
so far. We predict a blossoming relationship between paleontology and
genomics in the coming years, with the hope that a more complete
phylogenetic reconstruction of Life, including its many extinct lineages,
will be achieved.

I'm afraid this will turn out to be a voice crying in the wilderness
of no-brainer computer programming.


Peter Nyikos
Professor of Mathematics -- standard disclaimer--
Univ. of South Carolina
http://people.math.sc.edu

[John Harshman]

Turtles were classed as anaspids? But they have jaws! (OK, it's a simple
typo; but who can resist a spelling flame?)

Anyway, do you disagree? Do you think the molecular data are wrong on
this matter? On what basis? Let's note that there is morphological
support for turtles being diapsids, and that it came before the
molecular data. This is the first publication I know of: Rieppel O.
Osteology of Simosaurus gaillardoti and the Relationships of Stem-Group
Sauropterygia. Fieldiana: Geology New Series 1994; 28:1-85. But what if
there weren't?

> And why? because no one has ever found a way of weighting
> morphological characters, the way DNA gives no-brainer ways
> of assigning weight to genomic characters.

Not true. There are plenty of proposals for weighting morphological
characters, and DNA doesn't automatically assign weight to genomic
characters, whatever that means. Now what you mean is that you think
morphological characters should count for more than molecular ones. But
what's your justification for that, if any?

> Regardless, many neontologists recently have come to the realization that,
> moving forward, paleontological data will be essential for phylogenetic
> analysis, divergence dating, estimation of diversification and extinction
> rates, biogeography, and the mapping of particular phenotypic traits
> (Wiens, 2009, Losos, 2011, Pyron, 2011, Slater et al., 2012).
>
> Developmental biology will have to play a role, especially for
> that "mapping."

I'm not sure you know what "mapping" means in that sentence.
Developmental biology might play a role in character coding (i.e.
assessment of primary homology and transformation series), but that
isn't mapping.

> These revelations are not really new (Gauthier et al., 1988, Donoghue et
> al., 1989, Novacek, 1992, Novacek and Wheeler, 1992, Smith and Littlewood,
> 1994, Smith, 1998), but instead indicate that even with the development of
> `sophisticated' likelihood models, genomic data can advance the field only
> so far. We predict a blossoming relationship between paleontology and
> genomics in the coming years, with the hope that a more complete
> phylogenetic reconstruction of Life, including its many extinct lineages,
> will be achieved.
>
> I'm afraid this will turn out to be a voice crying in the wilderness
> of no-brainer computer programming.

Why are you afraid?

[John Harshman]

On 8/9/18 4:43 AM, Peter Nyikos wrote:

> Diapsids that somehow closed up both
> two fenestrae -- a change without parallel in the fossil record
> nor nor in living amniotes.

Are you sure? There are certainly cases in which one temporal fenestra
was completely eliminated. The euryapsid condition is not uncommon, and
some thalattosaurs have no upper fenestrae.

[erik simpson]

To what end? I want to read it, of course. Your editorial remarks seem strange
to me, but I suppose they're in keeping with your dislike of current systematic
practices. You alse seem to asking me to "type out" parts that interest me, but
I obviously can't do that if I can't see the article.

[John Harshman]

On 7/28/18 4:41 AM, Oxyaena wrote:

Incidentally, you could probably go to ResearchGate and ask for a pdf.
It's likely that Gatesy or one of the other authors would send it.
Here's a link:

https://www.researchgate.net/publication/232720076_A_Phylogenetic_Blueprint_for_a_Modern_Whale

[erik simpson]

Just filed my request. Thanks.

[Peter Nyikos]

Even now, no one but me seems to be interested in discussing what
I've posted so far from the article that is the topic of this thread.

Gatesy, J., Geisler, J. H., Chang, J., Buell, C., Berta, A., Meredith,
R. W., ... & McGowen, M. R. (2013). A phylogenetic blueprint for a
modern whale. Molecular Phylogenetics and Evolution, 66(2), 479-506.

On Thursday, August 9, 2018 at 10:23:29 AM UTC-4, John Harshman wrote:
> On 8/9/18 4:43 AM, Peter Nyikos wrote:
>
> > Diapsids that somehow closed up both
> > two fenestrae -- a change without parallel in the fossil record
> > nor nor in living amniotes.

Also, I know of no synapsid ever losing its temporal opening. Our
own zygyomatic arch is testimony to its existence in mammals, for
example.

> Are you sure? There are certainly cases in which one temporal fenestra
> was completely eliminated.

Looks like even the clumsily redundant "both two" didn't make much
of an impression on you.

> The euryapsid condition is not uncommon,

In fact, it's essentially what one sees in lizards and snakes.
But it consists of eliminating most or all of the lower bar
of the lower fenestra, typically leaving an arch bounded on the sides
by what's left of the squamosal and jugal, and above partly
by the postorbital.

In contrast, the situation in turtles would have to be one of
complete closure, judging from the second oldest known turtle,
*Proganochelys.* All reproductions I have seen of its skull
show no sign of any arch there, and the squamosal is high up,
with massive quadratojugal and jugal where one would expect
the lower fenestral bar to be.

The one picture I've found so far of the skull of the oldest
(AFAIK) turtle, tells a similar story. I'm referring to that
"turtle on the half shell," Odontochelys.

And so, morphologically at least, Carroll's words still seem spot on:

There is no evidence for the prior existence of temporal openings,
which precludes their close relationship to earlier synapsids or diapsids.
-- Vertebrate Paleontology and Evolution, p. 207.


I know of no such example of complete closure, except perhaps
in Araeoscelis, and one picture does seem to show a small arch
bounded by jugal and squamosal on the sides AND above.

But you may have found some:

> and
> some thalattosaurs have no upper fenestrae.

Which ones? And where is the evidence that they are descended
from diapsids? In the absence of living members, molecular
evidence is nonexistent.

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina

http://www.math.sc.edu/~nyikos