Carnivora genomic testing: Hassanin et al. 2021

From the abstract:
“The order Carnivora, which currently includes 296 species classified into 16 families, is distributed across all continents. The phylogeny and the timing of diversification of members of the order are still a matter of debate. Here, complete mitochondrial genomes were analysed to reconstruct the phylogenetic relationships and to estimate divergence times among species of Carnivora.”

Genomic tests too often do not and can not test fossil taxa leading to a problem with taxon exclusion. Moreover, genomic testing in deep time too often delivers false positives relative to phenomic (trait-based) traits that are designed to produce tree topologies in which all sister taxa greatly resemble one another, modeling micro-evolutionary events. Why this is so remains an unsolved problem. A phenomic cladogram (the LRT, subset Fig. x) that includes fossil taxa is found online here: http://reptileevolution.com/reptile-tree.htm

Figure 2. Talpa the Eastern mole nests in the LRT with Herpestes the mongoose.

Figure 1. Talpa the Eastern mole nests in the LRT with Herpestes the mongoose.

Talpa, the mole (Fig. 1), was excluded here, but nests within Carnivora in the phenomic analysis, the large reptile tree (LRT, 1803+ taxa, subset Fig. x).

Figure 1. Nandinia, the palm civet, nests as the proximal outgroup taxon to the Carnivora and all other placental mammals.

Figure 2 Nandinia, the palm civet, nests as the proximal outgroup taxon to the Carnivora and all other placental mammals.

Nandinia, the palm civet sure looks like it, but is not a basal member of Carnivora in the LRT, but a basal placental outgroup taxon to the clade Carnivora.

Figure 1. Mammals at the base of the Placentalia include the outgroup taxon: Caluromys, a basal placental: Genetta, a basal Carnivora: Eupleres, a basal Volitantia: Ptilocercus, a basal Primates: Microcebus, and basal Glires: Tupaia.

Figure 3. Mammals at the base of the Placentalia include the outgroup taxon: Caluromys, a basal placental: Genetta, a basal Carnivora: Eupleres, a basal Volitantia: Ptilocercus, a basal Primates: Microcebus, and basal Glires: Tupaia.

Carnivora is the first major clade to split off
from basal Placentalia (Fig. x). Therefore, the proximal outgroup taxon, the woolly oppossum, Caluromys (Fig. 3) , should be included as the outgroup next time.

Figure 2. Subset of the LRT focusing on the Carnivora.

Figure x. Subset of the LRT focusing on the Carnivora.

By chilling contrast,
in the Hassanin et al. 2021 genomic analysis, a hoofed placental, the tapir (Tapirus), was used as the outgroup taxon. Given all other placentals for their choice of outgroup for Carnivora, why did they choose a relative of horses and rhinos? We’ve seen this sort of confused mayhem before and recently in genomic studies. Let’s all pray that the ghost of Alfred Sherwood Romer will come visit Hassanin et al. and all others who think this is a good idea.


References
Hassanin A, Veron G, Ropiquet A, Jansen van Vuuren B, Le´cu A, Goodman SM, et al. 2021. Evolutionary history of Carnivora (Mammalia, Laurasiatheria) inferred from mitochondrial genomes. PLoS ONE 16(2): e0240770. https://doi.
org/10.1371/journal.pone.0240770

Macrauchenia: the good and bad of genomic studies

From the Wesbury et al. 2021 abstract
“The unusual mix of morphological traits displayed by extinct South American native ungulates (SANUs) confounded both Charles Darwin, who first discovered them, and Richard Owen, who tried to resolve their relationships. Here we report an almost complete mitochondrial genome for the litoptern Macrauchenia (Fig. 1). Our dated phylogenetic tree (Fig. 2) places Macrauchenia as sister to Perissodactyla, but close to the radiation of major lineages within Laurasiatheria. This position is consistent with a divergence estimate of B66Ma.”

Note they don’t ask us to pay as much attention to the proximal outgroup for Macrauchenia: the clade Carnivora (Fig. 2).

Figure 1. Macrauchenia museum mount.

Figure 1. Macrauchenia museum mount.

According to Wikipedia
Laurasiatheria is a gene-based clade “that includes that includes hedgehogs, even-toed ungulates, whales, bats, odd-toed ungulates, pangolins, and carnivorans, among others.”

Isn’t that an odd assemblage? 
Think about it. According to Wesley et al. (Fig. 2), sabertooth cats are closer to horses, rhinos and Macrauchenia than other long-legged, placental herbivores. By the way, in gene studies elephants appear in an unrelated major clade, Afrotheria.

Figure 1. Gene-based cladogram from Westbury et al. 2021 (slightly compressed to fit). Note the close relationship between Carnivora and Macrauchenia here. That is not replicated in a trait-based study (Fig. 2).

Figure 2. Gene-based cladogram from Westbury et al. 2021 (slightly compressed to fit). Note the close relationship between Carnivora and Macrauchenia here. That is not replicated in a trait-based study (Fig. 2).

A more reasonable, trait-based, phylogenetic analysis
(the large reptile tree, LRT, 1794+ taxa, subset Fig. 3) also nests the Macrauchenia clade basal to tapirs, rhinos and horses. The outgroup is the hyrax + elephant + manatee clade, then the artiodactyls, then the mesonychids + hippos + desmostylians + mysticetes. Off this chart (Fig. 3), the clade Carnivora is the basalmost placental clade, not the proximal outgroup to Macrauchenia.

Figure 2. Subset of the LRT focusing on derived placentals. Yellow highlights the Macrauchenia clade.

Figure 3. Subset of the LRT focusing on derived placentals. Yellow highlights the Macrauchenia clade.

Perhaps taxon exclusion is at fault here.
On the other hand, gene studies too often produce such odd interrelationships (Carnivora nesting closer to Macrauchenia than other herbivore clades). Gene studies too often deliver false positives in deep time studies. That’s a fact, not a hypothesis.

If your professor is asking you to help out on a deep time genomic study,
run.


References
Westbury M et al. (21 co-authors) 2021. A mitogenomic timetree for Darwin’s enigmatic South American mammal Macrauchenia patachonica. Nature Communications | 8:15951 | DOI: 10.1038/ncomms15951 |www.nature.com/naturecommunications

https://en.wikipedia.org/wiki/Laurasiatheria
reptileevolution.com/macrauchenia.htm

SVP abstracts 2: Barrett and Hopkins mishandle hyaena taxonomy

Cherry-picking taxa
(leading to both taxon exclusion and inappropriate taxon inclusion mars this otherwise earnest study.

From the Barrett and Hopkins abstract:
“The family Hyaenidae today is represented by only four living species, but this constitutes only a small fraction of known taxa from the fossil record. Results from both molecular and morphological analyses have shown disagreement in relationships, while certain hypothesized stem hyaenids and viverroids have received little to no phylogenetic assessment.”

First red flag: In the large reptile tree (LRT, 1749+ taxa; subset Fig. 3) viverroids (= civets), like Nandinia (Fig. 2) nest outside the clade Carnivora. Hyaenas, like Crocuta (Fig. 1), are highly derived carinvorans. Barrett and Hopkins think these two are related to one another based on Gray 1821 and gene studies. In the LRT civets are closer to their marsupial ancestors than to hyaenas, nesting with cats and dogs.

This taxonomic problem goes back to Gray 1821
who created the following clades of unrelated taxa. 

Viverridae (Gray 1821) defined as consisting of the genera Viverra (= large Indian civet), Genetta (= genet), Herpestes (= mongoose), and Suricata (= meerkat).

Viverroidea (Gray 1821, civets, mongooses, hyenas and aardwolves) is not supported by the LRT. Adding taxa lumps and separates these taxa.

Essentially viverroids were neither cat-like (= Felliformes) nor dog-like (Caniformes) carnivorans, a split still accepted by many mammal workers due to genomic results. The LRT (subset Fig. 3) does not agree with these lumps and splits.

Figure 3. Crocuta (hyena) skeleton. Note similarities to Canis (figure 2)

Figure 1. Crocuta (hyena) skeleton. Note similarities to Canis (figure 2)

Continuing from the Barrett and Hopkins abstract:
“These taxa include the percrocutids (bone-crushing, hyena-like viverroids), lophocyonids (extremely hypocarnivorous feliforms), and additional well-preserved, yet unassessed Miocene viverroids.”

Second red flag: Nandina, the palm civet (Fig. 2), and other vivveroids are small, mink-like arboreal taxa with short legs and a long tail. Percrocutids and hyaenas are terrestrial gallopers with a distinctly different morphology from head to toe.

Figure 1. Nandinia, the palm civet, nests as the proximal outgroup taxon to the Carnivora and all other placental mammals.

Figure 2. Nandinia, the palm civet, nests as the proximal outgroup taxon to the Carnivora and all other placental mammals.

Continuing from the Barrett and Hopkins abstract:
“Thus, to combine all available datasets, we performed a total-evidence Bayesian phylogenetic analysis inclusive of a sample of stem-to-derived hyaenids, herpestids, viverrids and other unassessed viverroid taxa.”

This is a classic case of taxon exclusion based on genomic studies. In other words, this study was doomed from the start.

Figure 2. Subset of the LRT focusing on the Carnivora.

Figure 3. Subset of the LRT focusing on the Carnivora.

Continuing from the Barrett and Hopkins abstract:
“The analyzed dataset includes stratigraphic occurrences, 257 morphological characters and mitochondrial genes of all living taxa in the analysis and ancient DNA from the cave hyena (Crocuta crocuta spelaea).”

“All living taxa in the analysis” = which living taxa? Hyaenas and palm civets? The genomic taxon list makes Gray 1821 quite a prognosticator, but neither study is supported when fossil taxa and traits are tested.  Let’s get back to trait (= phenomic) analysis. Genomes yield false positives too often and exclude too many extinct taxa.

Figure 1. Mammals at the base of the Placentalia include the outgroup taxon: Caluromys, a basal placental: Genetta, a basal Carnivora: Eupleres, a basal Volitantia: Ptilocercus, a basal Primates: Microcebus, and basal Glires: Tupaia.

Figure 1. Mammals at the base of the Placentalia include the outgroup taxon: Caluromys, a basal placental: Genetta, a basal Carnivora: Eupleres, a basal Volitantia: Ptilocercus, a basal Primates: Microcebus, and basal Glires: Tupaia.

The transition from marsupial to placental was documented 
here (Figs. 3, 4) where viverrids, like Genetta nested at the base of the Placentalia, far from highly derived hyaenas and separated by ALL OTHER carnivorans.


References
Barrett PZ and Hopkins SS 2020. First total-evidence phylogeny of the hyaenidae and enigmatic viverroids reveals novel relationships. SVP abstracts 2020.
Gray JE 1821. On the natural arrangement of vertebrose animals. The London Medical Repository Monthly Journal and Review 15:296-310

SVP abstracts 1 Asher et al. trust genomics over phenomics

From the Asher et al. 2020 abstract:
“Paleontology’s fundamental contribution to science includes understanding how extinct species relate to the living. Major questions about antiquity and diversification all depend on accurately reconstructing fossils on the Tree of Life.”

As longtime readers know already, an accurate (= self-healing due to taxon inclusion) Vertebrate Tree of Life, from headless Cambrian chordates to naked bipedal primates, can be found online here.

“However, fossils are poorly known compared to living species, having degraded with usually no traces of DNA or soft tissues.”

Yeah, but…if you don’t have fossils, many interrelationships will evade your studies. So don’t put the downer on fossils, especially in an SVP abstract.

“Molecular data are sometimes recovered from very recent fossils, but in general are exceedingly rare and will remain so for the foreseeable future. Here, we apply a method that incorporates genomic data from living species and, in turn, fundamentally reshapes the phylogenetic tree of living and fossil species alike.”

A bit of advice for Asher et al.: Stop what you’re doing. Go back to fossils. Genomics don’t work in deep time time studies. False positives are possible.

“This method does not require direct access to fossil biomolecules, but can nonetheless change our understanding of the evolutionary affinities of long-extinct fossil groups. We incorporate genomic signal by using morphology reconstructed from predicted ancestors on well-corroborated trees of living species, and re-include such ancestors as terminal taxa in phylogenetic analyses of fossils.”

I have not yet seen a deep time genomic study that makes sense or corroborates a phenomic study. No one has.

“With examples from Mesozoic mammals and maniraptoran dinosaurs, we show that this method recovers a signal supported by genomic data for living taxa using only morphological data. Examples from mammals include monophyletic Laurasiatheria, Afrotheria, Xenarthra, and Euarchontoglires, as well as glirids and Aplodontia among sciuromorph rodents.”

First, let’s define clades:

  1. Laurasiatheria = hedgehogs, even-toed ungulates, whales, bats, odd-toed ungulates, pangolins, and carnivorans
  2. Afrotheria = golden moles, elephant shrews (also known as sengis), tenrecs, aardvarks, hyraxes, elephants, and sea cows.
  3. Xenarthra = anteaters, tree sloths and armadillos.
  4. Euarchontoglires = rodents, lagomorphs, treeshrews, colugos and primates.

The LRT confirms some of these interrelationships (e.g. rodents and lagomorphs), but refutes others (e. g. whates and bats).

“For fossils, our results indicate that at least some anatomically well-known North American “condylarths” are more closely related to Laurasiatheria than Afrotheria.”

Stop right there. Three fourths of the above genomic clades are not supported.

“In addition, we demonstrate that morphological datasets applied to mammalian and maniraptoran phylogenetics vary in their ability to reconstruct well-corroborated clades. Some morphological datasets improve congruence of topologies derived from subsampled sequence alignments with the well-corroborated tree; others decrease congruence.”

Stop right there. The ‘well-corroborated tree’ means their genomic results match other genomic results (e.g. Flynn et al. 2005), not realizing that bats and whales cannot be closely related to one another. That’s bonkers! Stops that sort of thinking. You went to college! Genomics produce bogus results that must be rejected.

“We provide a set of criteria which we hope will be of use to the wider community in vetting the relative information content of morphological datasets relevant for paleontology, and hope to end at least some, seemingly intractable, debates about the phylogenetic affinities of long-extinct species lacking genomic data.”

If you really want to end the debate, add extinct and extant taxa to phenomic (= trait-based) studies that include fossils. In the LRT all sister taxa actually look alike down to the details, and all convergent clades nest apart from each other. The LRT provides a framework for this task.


References
Asher R, Beck R, Field D and  Benson R 2020. Fossils and the tree of life: Making genomic data informative for extinct vertebrates without direct access to molecules. SVP abstracts.
Flynn JJ, et al. 2005. Molecular phylogeny of the Carnivora (Mammalia): assessing the impact of increased sampling on resolving enigmatic relationships. Syst Biol 54:317–37.

A new genomic study of the Carnivora

Beware colleagues.
We learned long ago that genomic studies produce false positives in deep time studies. Genomic studies recover clades named for continents like Afrotheria and Laurasiatheria. So why are workers still dabbling in the dark art of deep time genomics?

From the Hassanin et al. 2020 abstract:
“The order Carnivora, which currently includes 296 species classified into 16 families, is distributed across all continents. The phylogeny and the timing of diversifications are still a matter of debate.”

Not true. The large reptile tree (LRT, 1747+ taxa) confidently nests Carnivora at the base of the Placentalia with outgroups extending to headless Cambrian chordates. The proximal outgroups and sisters to basal Carnivora look quite similar (Fig. 1) inside and out, even allowing for 200 million years of evolution since their radiation.

Figure 1. Mammals at the base of the Placentalia include the outgroup taxon: Caluromys, a basal placental: Genetta, a basal Carnivora: Eupleres, a basal Volitantia: Ptilocercus, a basal Primates: Microcebus, and basal Glires: Tupaia.

Figure 1. Mammals at the base of the Placentalia include the outgroup taxon: Caluromys, a basal placental: Genetta, a basal Carnivora: Eupleres, a basal Volitantia: Ptilocercus, a basal Primates: Microcebus, and basal Glires: Tupaia.

Continuing from the Hassanin et al. 2020 abstract:
“Here, complete mitochondrial genomes were analysed to reconstruct the phylogenetic relationships and to estimate divergence times among species of Carnivora.”

Hold on to your hats. Here comes a load of genomic misdirection.

“According to our divergence time estimates, crown carnivorans appeared during or just after the Early Eocene Climatic Optimum; all major groups of Caniformia (Cynoidea/Arctoidea; Ursidae; Musteloidea/Pinnipedia) diverged from each other during the Eocene,”

Phenomic studies, like the LRT, do not recover this clade.

“while all major groups of Feliformia (Nandiniidae; Feloidea; Viverroidea) diversified more recently during the Oligocene, with a basal divergence of Nandinia at the Eocene/Oligocene transition; intrafamilial divergences occurred during the Miocene, except for the Procyonidae, as Potos separated from other genera during the Oligocene.”

 Phenomic studies, like the LRT, do not recover this clade. In the LRT, dogs and cats are highly derived sister taxa, along with hyenas and aardwolves. Seals and sea lions arise from separate terrestrial ancestors. Not all bears are related to Ursus. Weasels are basal to all of the above, including a long list of fossil taxa ignored by genomics. Potos flavus is the extant kinkajou, which was just added to the LRT, nesting between Procyon and the pandas, as expected.

Figure 2. Subset of the LRT focusing on the Carnivora.

Figure 2. Subset of the LRT focusing on the Carnivora. Genetta was just added to the LRT, nesting with Paleocenee Protictis.

In the LRT
Vulpavus, Protictis + Genetta and Nandinia are basalmost Placentalia, and the only tested placental outgroups to the Carnivora. Talpa, the mole, is an overlooked extant member of the Carnivora. Ursus arises apart from dogs + cats, which find last common ancestors in Tremarctos, Speothos and Borophagus. The short-faced bear, Arctodus, is a giant wolverine (Gulo). Seals and sea lions have separate terrestrial ancestors and became aquatic by convergence. The rest of the online LRT is here: reptileevolution.com/reptile-tree.htm


References
Hassanin A, et al. (7 co-authors) 2020. Evolutionary history of Carnivora (Mammalia, Laurasiatheria) inferred from mitochondrial genomes. bioRxiv 2020.10.05.326090 (preprint)
doi: https://doi.org/10.1101/2020.10.05.326090
https://www.biorxiv.org/content/10.1101/2020.10.05.326090v1

Genomic studies:
Flynn JJ, et al. 2005. Molecular phylogeny of the Carnivora (Mammalia): assessing the impact of increased sampling on resolving enigmatic relationships. Syst Biol 54:317–37.

Woltering et al. 2020 study genes to elucidate finger origins

Woltering et al. 2020
attempted to elucidate the transition from fins to fingers by studying the genes of extant lungfish, which don’t have fingers and their ancestors never had fingers.

From the abstract
“How the hand and digits originated from fish fins during the Devonian fin-to-limb transition remains unsolved.

No. The large reptile tree (LRT; subset Fig. 1) solved that problem in 2019 following the work of Boisvert, Mark-Kurik and Ahlberg 2008. These authors found four finger buds on Panderichthys. Thereafter four fingers appear on all basalmost tetrapods in the LRT, like Trypanognathus (Fig. 2), a taxon found in Carboniferous strata with Middle Devonian origins. Taxon exclusion is once again the problem here.

Late Devonian taxa with supernumerary digits, like Acanthostega and Ichthyostega, are the traditional ‘go-to’ taxa for the fin-to-finger transition. That was supplanted in 2019 by phylogenetic analysis in the LRT (subset Fig. 1). Simply adding taxa recovers Acanthostega and Ichythyostega as terminal taxa. They have more derived skulls and bodies sporting larger limbs and more digits.

Figure 4. Subset of the LRT focusing on basal tetrapods. Colors indicate number of fingers known. Many taxa do not preserve manual digits.

Figure 4. Subset of the LRT focusing on basal tetrapods. Colors indicate number of fingers known. Many taxa do not preserve manual digits.

Woltering et al. 2020 report,
“Controversy in this conundrum stems from the scarcity of ontogenetic data from extant lobe-finned fishes. We report the patterning of an autopod-like domain by hoxa13 during fin development of the Australian lungfish, the most closely related extant fish relative of tetrapods.”

In other words, Woltering et al. looked at genes in lungfish that never had digits.

Figure 6. Dorsal and ventral views of Panderichthys and several basal tetrapods demonstrating the low, flat skulls and bodies with small limbs and relatively straight ribs.

Figure 2. Dorsal and ventral views of Panderichthys and several basal tetrapods demonstrating the low, flat skulls and bodies with small limbs and relatively straight ribs at the fin-to-finger transition. Acanthostega and Ichythyostega have more derived bodies with larger limbs and more digits.

Why study lungfish
when we have fossil taxa (Fig. 3) in the lineage of tetrapods? Why study genes when genomic studies produce false positives in deep time? Taken together the Woltering et al. study seems like a waste of effort on both fronts, but they didn’t realize this at the time. Paleontologists love genomics like Isaac Newton loved alchemy.

Figure 3. Forelimb of several basal tetrapods rearranged to more closely fit the LRT. Four fingers turns out to be the primitive number. Five is a recent mutation. Six was a short-lived experiment in Tulerpeton.

Figure 3. Forelimb of several basal tetrapods rearranged to more closely fit the LRT. Four fingers turns out to be the primitive number. Five is a recent mutation. Six was a short-lived experiment in Tulerpeton.

Woltering et al. 2020 report,”
“Differences from tetrapod limbs include the absence of digit-specific expansion of hoxd13 and hand2 and distal limitation of alx4 and pax9, which potentially evolved through an enhanced response to shh signaling in limbs. These developmental patterns indicate that the digit program originated in postaxial fin radials and later expanded anteriorly inside of a preexisting autopod-like domain during the evolution of limbs. Our findings provide a genetic framework for the transition of fins into limbs that supports the significance of classical models proposing a bending of the tetrapod metapterygial axis.”

Be wary of genetic studies over deep time. They have been shown to deliver false positives way too often to be trusted, or even attempted. Fossils and phenomic studies are better in all respects because they recover cladograms in which all taxa demonstrate a gradual accumulation of derived traits.


References
Boisvert CA, Mark-Kurik E and Ahlberg PE 2008.
 The pectoral fin of Panderichthys and the origin of digits. Nature 456:636–638.
Woltering JM et al. (5-co-authors) 2020. Sarcopterygian fin ontogeny elucidates the origin of hands with digits. Science Advances 6(34): eabc3510 DOI: 10.1126/sciadv.abc3510
https://advances.sciencemag.org/content/6/34/eabc3510

Kuhl et al. 2020: an ‘unbiased, resolved’ avian tree of life?

Similar to other traditional myths,
Kuhl et al. 2020 repeat a traditional myth that will never be validated.

From the abstract
“In this tree, grebes and flamingos are the sister clade of all other Neoaves,”

Kuhl et al. is a genomic study. These two bird types do not resemble each other (Fig. 1) and do not nest together in phenomic studies, like the large reptile tree (LRT, Subset Fig. 2). Prum et al. 2015 recovered the same false positive relationship. If a study cannot be validated by traits, it is invalid and worthless.

The unanswered question here is, “Why do certain genes resemble one another in these two unrelated taxa?” Now there’s another subject for a PhD thesis.

Figure 2. Flamingo and grebe illustration from Nat Geo article on birds.

Figure 1. Flamingo and grebe illustration from Nat Geo article on birds.

Earlier we looked at grebes and flamingoes
here in 2017. Apparently there has been no enlightenment among paleontologists since then. Where is the critical thinking?

Continuing from the Kuhl et al. abstract:
“All non-passerine taxa were placed with robust statistical support including the long-time enigmatic hoatzin (Opisthocomiformes), which was found being the sister taxon of the Caprimulgiformes.” [= nightjars, sailors [= barn swallows?], hummingbirds, unrelated taxa in the LRT]

In the LRT the hoatzin nests between sparrows and parrots because they look alike, both overall, and in detail, location and diet. Relatives

If you have not learned this already,
genomic studies over deep time lead one to madness.

From the press release:
“For the first time, they have been able to clarify the relationship of all families of non-passerine birds and almost all families of passerine birds.  The new family tree is based on gene sections that do not code for proteins, but contain sequences that are specific to the families and their genera.”

Better to stick with a phenomic study that makes sense, like the LRT. Chickens and ducks are not related in the LRT.  That makes sense because they don’t resemble each other. Parrots and hawks are not related in the LRT. That also makes sense, but genomic studies put each of these two pairs of taxa together.

As mentioned above, we looked at Prum et al 2015
earlier in a three-part series ending here demonstrating several times that genomic studies do not replicate phenomic studies in the sort of deep time that brought us birds (Late Jurassic to the Present).

Genomic studies are EXCELLENT
over short phylogenetic time. For this reason genomic studies are used by the judicial system. For this reason paleontologists think genomic studies should supersede phenomic  studies. However, tests document the fact that genomic studies produce mismatches (taxa that do not look alike, Fig. 1) over deep time. Paleontologists realize this, but continue to put their faith in genomic studies, hoping that someday the last common ancestor of flamingoes (genus: Phoenicopterus) and grebes (genus: Aechmophorus) will someday be discovered in the fossil record.

The LRT has already recovered that last common ancestor,
a taxon close to the late-surviving, but extant megapodes, Megapodius and Early Cretaceous Juehuaornis. You’ll notice (Fig. 1) that clade includes nearly all crown birds.

Figure 3. Subset of the LRT focusing on birds. Note the separation of the duck clade from the chicken clade.

Figure 1. Subset of the LRT focusing on birds. Note the separation of the duck clade from the chicken clade.

The hallmarks of the Scientific Method include:

  1. asking a specific question
  2. devising a hypothesis
  3. experimenting to gather data
  4. analyzing the data, and then
  5. evaluating whether the hypothesis is correct based on the experimental data.

When the data support the hypothesis, the findings can be published or shared.
What happens if the findings do not confirm the hypothesis? Answers here.

Sadly, 
Kuhl et al. 2020 was a complete waste of time for the nine co-authors, the editors, referees and innumerable readers who all believed the flawed premise of this genomic hypothesis of interrelations. Where is the genomic study that replicates phenomic studies like the LRT? When that happens, we’ll have that long sought validation.


Pertinent Carl Sagan – ‘A way of thinking’ YouTube video.

References
Kuhl H, et al. (8 co-authors) 2020. An unbiased molecular approach using 3″UTRs resolves the avian family-level tree of life. Molecular Biology and Evolution, msaa191 (advance online publication) doi: https://doi.org/10.1093/molbev/msaa191
https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msaa191/5891114

Tuatara genes provide false-positive links to mammals

Preamble:
Genomic (gene) studies think they are unlocking secret doors

to understanding vertebrate interrelationships. Sometimes they do the opposite. Wide gamut phenomic (trait) studies show that gene studies over deep time introduce invalid hypotheses of interrelationships. So, worse than useless, gene studies (like today’s example) confuse readers and workers with false positives, false hopes that claim to be true, but are not valid when put to the test.

So why are they published?
Because gene studies work great over shallow time. Ask any prosecutor or Ancestry.com.

The dorsal spines of Tuatara (Sphenodon).

Figure 1. The dorsal spines of Tuatara (Sphenodon).

Gemmell and Rutherford et al. 2020 report:
“The tuatara (Sphenodon punctatus)… [is] A key link to the now-extinct stem reptiles (from which dinosaurs, modern reptiles, birds and mammals evolved), the tuatara provides key insights into the ancestral amniotes.”

In a competing phenomic study (the large reptile tree, LRT, 1717+ taxa; Fig. 2) the lepidosaur, Sphenodon (Fig. 1), is simply the last living proximal outgroup taxon to living squamates. On the other hand, tuataras and mammals share a last common ancestor all the way back in the Viséan, at the last common ancestor of all reptiles, Silvanerpeton.

Figure 1. Gemmell and Rutherford cladogram compared to LRT (with taxon list reduced to match Gemmell and Rutherford).

Figure 2. Gemmell and Rutherford cladogram compared to LRT (with taxon list greatly reduced to match Gemmell and Rutherford).

Gemmell and Rutherford et al. continue:
“Here we analyse the genome of the tuatara, which—at approximately 5 Gb—is among the largest of the vertebrate genomes yet assembled. Our analyses of this genome, along with comparisons with other vertebrate genomes, reinforce the uniqueness of the tuatara. Phylogenetic analyses indicate that the tuatara lineage diverged from that of snakes and lizards around 250 million years ago [Earliest Triassic].”

This timing is confirmed by the LRT, but fossils generally represent periods of wide radiations, not moments of origin.

“This lineage also shows moderate rates of molecular evolution, with instances of punctuated evolution. Our genome sequence analysis identifies expansions of proteins, non-protein-coding RNA families and repeat elements, the latter of which show an amalgam of reptilian and mammalian features.”

Phenomic studies do not support a mammal connection other than at the very base of the Reptilia (see the LRT).

“The sequencing of the tuatara genome provides a valuable resource for deep comparative analyses of tetrapods, as well as for tuatara biology and conservation.”

False positives are not valuable resources. They steer readers and workers wrong. Gene studies too often deliver false p;positives compared to trait-based studies over deep time.

From an online story from phys.org with quotes from the authors.
“The tuatara genome contained about 4% jumping genes that are common in reptiles, about 10% common in monotremes (platypus and echidna) and less than 1% common in placental mammals such as humans,” said Professor Adelson.

“This was a highly unusual observation and indicated that the tuatara genome is an odd combination of both mammalian and reptilian components.”

“The unusual sharing of both monotreme and reptile-like repetitive elements is a clear indication of shared ancestry albeit a long time ago,” said Dr. Bertozzi.”

Or… this is a false positive. Not sure why false positives keep creeping in to gene studies, but they do.

Colleagues: Don’t publish genomic studies unless they are confirmed by phenomic studies.


References
Gemmell NJ, Rutherford K., Prost, S. et al. 2020. The tuatara genome reveals ancient features of amniote evolution. Nature (2020). https://doi.org/10.1038/s41586-020-2561-9 DOI: 10.1038/s41586-020-2561-9 , www.nature.com/articles/s41586-020-2561-9

https://phys.org/news/2020-08-dinosaur-relative-genome-linked-mammals.html?fbclid=IwAR1VjTxtCI8Yd9VrUIAbuwxDmEhOM1q27WFueBbt1KIo062qKi2UqNnvzX0

https://www.researchgate.net/publication/342666056_Bird_phylogeny_false_positives_detected_in_a_gene_sequencing_study

Recalibrating clade origins, part 2

Marjanovic 2019 reports on
the origin of several clades based on fossils and molecules. Yesterday we looked at part 1, which focused on the abstract. Today: the origin of several more listed clades.

Gnathostomata (Chondrichthyes + Osteichichthyes)
Marjanovic cautiously proposes the mid-Florian (Early Ordovician, 475 mya) for the origin using traditional taxa and cladograms.

By contrast, the LRT splits off quasi-jawless sturgeons before the appearance of jawed sharks + other bony fish. It also splits off the jawed Loganellia + Rhincodon + Manta clade before the Polyodon + ratfish + sharks + skates clade and the Pachycormus + Hybodus clade before the dichotomy that resulted in the rest of the bony fish (the now polyphyletic ‘Osteichthyes‘)… so direct comparisons are not apples and apples here. Sturgeons first appear much later in the fossil record. Loganellia appears in the Early Silurian with an earlier genesis. So Marjanovic’s estimate may be a little early.

Osteichthyes (Actnopterygii + Sarcopterygii)
Marjanovic reports, “The oldest known uncontroversial crown-group osteichthyan is the oldest known dipnomorph, Youngolepis.” He suggests, “the minimum age for this calibration is the same as that for the next node,” the Silurian/Devonian boundary, 420 mya.

The LRT includes placoderms within one branch of the bony fish, so Entelognathus along with the stem-lungfish Guiyu, both in the Late Silurian are older than Marjanovic suggests with an earlier genesis. Sturgeons, which traditional workers consider a member of the Osteichyes, phylogenetically preceded Longanellia, which is known from Early Silurian strata. So, again we’re not comparing similar cladograms here. The LRT tests a wider gamut of taxa, which is an advantage in that it opens further possibilities than tradition dictates.

Dipnomorpha + Tetrapodomorpha (lungfish + lobe fin ancestors of tetrapods)
Marjanovic reports, “I suggest a hard minimum age of 420mya.” (See above).

The LRT includes Late Siluirian Guiyu within the stem-lungfish clade. so the split occurred earlier.

Tetrapoda (Amphibia + total group of Amniota)
Marjanovic reports, “the richer and better studied Famennian (end-Devonian) record, which has not so far yielded tetrapods close to the crown-group but has yielded more stemward tetrapods and other tetrapodomorphs (Marjanović and Laurin, 2019), should be used to place a soft maximum age around very roughly 365 Ma.”

Figure 3. Tersomius texensis, an amphibamid lepospondyl close to Dendrerpeton.

Figure 1. Tersomius texensis, an amphibamid lepospondyl close to Dendrerpeton.

In the LRT the last common ancestor of Amphibia + Amniota is Tersomius (Fig. 1), a late survivor in the Early Permian of an earlier genesis and radiation. The oldest taxa from this clade in the LRT are the basal amniotes / amphibian-like reptiles, Silvanerpeton and Eldeceeon from the Viséan (335 mya), with a long list of late surviving taxa between them and Tersomius, some eight nodes beyond the Late Devonian Acanthostega and Ichthyostega (365 mya). So the Tournaisian (355 mya) split suggested by Marjanovic seems about right.

Amniota (Theropsida + Sauropsida)
Marjanovic reports, “I refrain from recommending a maximum age other than that of the preceding Node, even though such an early age would imply very slow rates of morphological evolution in the earliest thero- and sauropsids.”

The LRT recovers a different basal dichotomy (Archosauromorpha + Lepidosauromorpha) and a different last common ancestor for all amniotes (Silvanerpeton) than Marjanovic is working with. Silvanerpeton is Viséan in age (~335 mya). In the LRT ‘Amniota’ is a junior synonym for Reptilia.

Crown group of Diapsida (Lepidosauromorpha + Archosauromorpha)
Marjanovic reports, “I cannot express confidence in a maximum age other than that of  Node 106, which I cannot distinguish from the maximum age of Node 105 as explained above. This leaves Node 107 without independent calibrations in the current taxon sample.”

The LRT finds two origins for reptiles with a diapsid skull architecture. So the tradtional clade ‘Diapsida’ is also a junior synonym for Reptilia and Marjanovic is using an outdated and under represented cladogram. Lepidosauromorph diapsids first appear with Paliguana in the earliest Triassic. Archosauromorph diapsids first appear with Erpetonyx and Petrolacosaurus in the Late Carboniferous with an earlier genesis. These taxa are not mentioned by Marjanovic.

Archosauria (Crocodile total group + Bird total group)
Marjanovic reports, “I accept the Permian-Triassic boundary (251.902 ± 0.024 Ma: ICS; rounded to 252) as the soft maximum age on the grounds that a major radiation of archosauromorphs at the beginning of the Triassic seems likely for ecological reasons.”

The LRT restricts membership within the Archosauria to just Crocodylomorpha + Dinosauria. So the maximum age for this dichotomy is younger and the last common ancestor is the PVL 4597 specimen (late Middle Triassic, 230mya) traditionally assigned to Gracilisuchus, but nesting apart from the holotype.

The LRT finds the Archosauriformes first appeared in the Late Permian (260mya), arising from a sister to Youngoides romeri (FMNH UC1528) thereafter splitting into clades arising from the larger Proterosuchus and the smaller Euparkeria.

Alligatoridae (Alligatorinae + Caimaninae)
Marjanovic reports, “Given this uncertainty, I have used a hard minimum age of 65 Ma for present purposes, but generally recommend against using this cladogenesis as a calibration for time trees.”

The LRT does not include pertinent taxa surrounding this split.

Figure 1. Megapodius is the extant bird nesting at the base of all neognathae (all living birds except ratites).

Figure 2. Megapodius is the extant bird nesting at the base of all neognathae (all living birds except ratites). And it looks like a basal bird. It also looks a bit like the Solnhofen bird, Jurapteryx. It is easy to imagine diverse forms arising from this bauplan and the LRT indicates that is exactly what happened.

Crown group of Neognathae (Gallanseres + Neoaves)
Marjanovic further defines this clade as, “The last common ancestor of Anas, Gallus and Meleagris on one side and Taeniopygia.” More commonly Marjanovic nests a duck, a chicken and a turkey on one side and a zebra finch on the other as the basal dichotomy of all living birds, sans ostriches, kiwis and kin. Marjanovic reports, “As the soft maximum age I tentatively suggest 115 Ma, an estimate of the mid-Aptian age of the (likewise terrestrial) Xiagou Fm of northwestern China, which has yielded a diversity of stem-birds but no particularly close relatives of the crown.”

Taxa listed by Marjanovic are all highly derived taxa in the LRT where the scrub fowl, Megapodius (Fig. 2) and the tinamou, Crypturus, are basal neognaths. These would have had their genesis in the Earllest Cretaceous given that Early Cretaceous clades that redevelop or retain teeth are more derived.

More tomorrow…


References
Marjanovic D 2019. Recalibrating the transcriptomic timetree of jawed vertebrates.
bioRxiv 2019.12.19.882829 (preprint)
doi: https://doi.org/10.1101/2019.12.19.882829
https://www.biorxiv.org/content/10.1101/2019.12.19.882829v1

Mutation vs. natural selection

Gemma Tarlach, writing in Discover Magazine online 2014 wrote:
“Mutation, Not Natural Selection, Drives Evolution. Molecular evolutionary biologist Masatoshi Nei (2013) says Darwin never proved natural selection is the driving force of evolution — because it isn’t.”

“In 1972, he devised a now widely used formula, Nei’s standard genetic distance, which compares key genes of different populations to estimate how long ago the groups diverged. In the early ’90s, Nei was a co-developer of free software that creates evolutionary trees based on genetic data. Molecular Evolutionary Genetics Analysis, or MEGA.”

So that’s the scientist who brought us genomics. Perhaps there were others, too.

Nei continues:
“Natural selection occurs sometimes, of course, because some types of variations are better than others, but mutation created the different types. Natural selection is secondary.”

Someone is forgetting sexual selection, which encourages certain phenomic changes over others. Someone is forgetting extinction by disease, comet impact, etc., which clears the Earth for survivors.

Nei continues:
“My position is mutation creates variation, then natural selection may or may not operate, it may or may not choose the good variation and eliminate the bad one, but natural selection is not the driving force.”

Nei continues:
“I had developed the genetic distance theory [in the ’70s] because I wanted to make a phylogenetic tree, and distance can be used for making trees. But I was also interested in statistics. So I combined the two methods. To test it, first we did computer simulations: We generated a DNA sequence for an evolutionary tree where we already knew where the tree branched.

Or did they? The large reptile tree (LRT, 1596+ taxa) upsets many traditional relationships among the taxa its tests. The LRT cladogram was not available to Nei in 2011 and was probably overlooked in 2013.

Nei continues:
“Then we used statistics, the neighbor-joining method, to reconstruct the tree and test whether it resembled the actual phylogenetic tree. It did, and that’s how we knew this method gave a pretty good idea of how species evolved and diverged.”

So, false positives matched false positives. Think Afrotheria. Laurasiatheria. And remember no fossil taxa are used in genomic studies. Think what a difference fossil taxa make.

Nei continues:
“But any time a scientific theory is treated like dogma, you have to question it. The dogma of natural selection has existed a long time. Most people have not questioned it. Most textbooks still state this is so. Most students are educated with these books.”

“You have to question dogma. Use common sense. You have to think for yourself, without preconceptions. That is what’s important in science.”

You also have to add fossil taxa. And where was the common sense that nested elephants and kin as basal placentals? And who would nest flamingoes with grebes, except genomic workers?

In the comments section of this online article,
medical laboratory scientist James Kohl wrote: “In “Roles of Mutation and Selection in Speciation: From Hugo de Vries to the Modern Genomic Era” (2011), Nei ignored ecological factors as he did in his book “Mutation-Driven Evolution”. He also ignored the biophysical constraints on protein folding that prevent mutation-driven evolution. Instead, in his book he evoked ‘constraint-breaking mutation” as the source of all biological innovations and species diversity in the world. Now, with the lesser role for natural selection, mutation-driven evolution “just happens” due to constraint-breaking mutations. Is there a model for that? Is there a model organism that exemplifies it?”

“Species diversity is is obviously nutrient-dependent and it is controlled by the metabolism of nutrients to species-specific pheromones, which control the physiology of reproduction in species from microbes to man. Chemical ecology and olfactory/pheromonal input link the epigenetic landscape to the physical landscape of DNA in the organized genome of species from microbes to man. There is no reason to add the biologically implausible role of constraint-breaking mutation until experimental evidence ecologically validates the earlier versions of untested theories about evolution that are still based on population genetics instead of on experimental evidence of conserved molecular mechanisms sans mutations.”


References
Nei M 2013. Mutation-Driven Evolution.
Nei M and Nozawa M 2011. In “Roles of Mutation and Selection in Speciation: From Hugo de Vries to the Modern Genomic Era”,

http://discovermagazine.com/2014/march/12-mutation-not-natural-selection-drives-evolution

https://www.nature.com/scitable/knowledge/library/speciation-the-origin-of-new-species-26230527/