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Fossil Friday: The Big Bang of Tertiary Birds and a Phylogenetic Mess

February 23, 2024, 6:45 AM
Photo; Haplochromis, CC BY-SA 3.0 , via Wikimedia Commons.

This Fossil Friday we look into the abrupt origin of birds, which is just one of the many discontinuities in the fossil record of life on Earth. The image features a fossil bird of the genus Rhychaetites from the famous Eocene Messel pit in Germany. It is similar and also related to modern ibises.

While feathered dinosaurs and primitive toothed birds were abundant during the Cretaceous period, only the chicken and duck clade (Galloanserae) appeared in the Late Cretaceous (Field et al. 2020), while all the other groups of modern birds (Neoaves) appeared suddenly and with great diversity in the Lower Tertiary (today called Paleogene). Indeed, modern crown group birds appear and diversify so abruptly that it has been called a “Big Bang of Tertiary birds” by some paleo-ornithologists (Feduccia 1995, 2003a, 2014, Ksepka et al. 2017). Some of their colleagues did not like such an explosive view for obvious reasons (e.g. Dyke 2003, van Tuinen et al. 2003), but Alan Feduccia addressed and rebutted all critics (Feduccia 2003b), and emphasized that “a rapid, explosive Tertiary radiation best explains why resolving phylogenetic relationships of modern orders remains intractable.” James (2005) reviewed the Paleogene fossil record of birds and found that

before the Paleogene, fossils of putative neornithine birds are sparse and fragmentary (Hope 2002), and their phylogenetic placement is all the more equivocal. … The weak molecular genetic signal found so far for relationships among many higher-level taxa of birds could be explained if there was an early, explosive radiation of birds into diverse ecological niches. … Perhaps the greatest unsolved problem in avian systematics is the evolutionary relationships among modern higher-level taxa.

Rocks vs Clocks

Molecular clock studies, which suggested that modern birds might have originated more early in the Cretaceous, were thoroughly rejected as incompatible with the fossil record (Benton 1999), which could rather suggest that the molecular clock is running faster during the phases of rapid diversification in the major radiations. Nevertheless, van Tuinen (2009) estimated for the Timetree of Life that Neoaves initially diversified already 95 million years ago, followed by another diversification 87-75 million years ago and in the Tertiary (van Tuinen 2009). The author hoped that “more Cretaceous and Paleocene fossil material” may resolve the conflict but admitted that “phylogenetic resolution among the main divergences within Neoaves continues to remain a major hurdle, with most neoavian orders appearing to have diverged in close succession … indicating a rapid evolutionary radiation.” Six years later new fossil discoveries did not come to rescue yet: A fossil calibrated time line of animal evolutionary history (Benton et al. 2015; also see Fossil Calibration Database) suggested an age 86.8-60.2 million years for crown group Neoaves, even though the authors explicitly acknowledged the Paleocene penguin Waimanu from New Zealand as oldest unequivocal neoavian fossil record. Clearly, the molecular clock studies still do not agree with the empirical data of paleontological research.

A few scientists claimed that the problem can be resolved, such as the study by Ericson et al. (2006), which presented “the first well-resolved molecular phylogeny for Neoaves, together with divergence time estimates calibrated with a large number of stratigraphically and phylogenetically well-documented fossils.” According to these authors their results “do not contradict palaeontological data and show that there is no solid molecular evidence for an extensive pre-Tertiary radiation of Neoaves.” However, their result was quickly critiqued and refuted by Brown et al. (2007), who found that “nuclear DNA does not reconcile ‘rocks’ and ‘clocks’ in Neoaves”. They mentioned that “the discrepancy between fossil- and molecular-based age estimates for the diversification of modern birds has persisted despite increasingly large datasets on both sides”, and their reanalysis of Ericson’s data documented “that there is no reliable molecular evidence against an extensive pre-Tertiary radiation of Neoaves.” In the same year Zhang (2007) confirmed that “paleontological studies showed that modern avian groups probably first appeared in the Paleocene and experienced an explosive radiation in the early Cenozoic.”

Brown et al. (2008) called this problem the “rock-clock gap” and said that “determining an absolute timescale for avian evolutionary history has proven contentious. The two sources of information available, paleontological data and inference from extant molecular genetic sequences (colloquially, ‘rocks’ and ‘clocks’), have appeared irreconcilable; … These two sources of data therefore appear to support fundamentally different models of avian evolution.” Their own study of mitochondrial DNA did “fail to reconcile molecular genetic divergence time estimates with dates taken from the fossil record; instead, we find strong support for an ancient origin of modern bird lineages.” Thus, the problem turned out to be quite stubborn and refused to go away with more data. On the contrary, each new study reenforced the problem. For example, the attempt by Pratt et al. (2008) to resolve the deep phylogeny of Neoaves produced molecular datings from mitochondrial genomes that “support a major diversification of at least 12 neoavian lineages in the Late Cretaceous.” Another example is the study by Pacheco et al. (2011), who used several molecular dating approaches and conservative calibration points, but still “found time estimates slightly younger than those reported by others, most of the major orders originated prior to the K/T boundary.” But even more interestingly, these authors revealed the secret reason why so many evolutionary biologists do not like the Big Bang model: “proponents of this hypothesis do not provide viable genetic mechanisms for those changes” (Pacheco et al. 2011). In other words, if there were such Big Bangs then Darwinism cannot plausibly explain them. This is why these abrupt appearances in the history of life fascinate me and will be subject of my book project called “The Big Bangs of Life.”

Phylogenomics vs Clocks

But it gets worse. Not just that rocks and clocks conflicted, but phylogenomic studies increasingly supported the Big Bang of Tertiary birds so that now molecular trees conflicted with molecular clocks. The Big Bang view was most strongly confirmed by the seminal study of Jarvis et al. (2014), a genome scale phylogenetic analysis by more than 100 authors (!), who found that “even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.” This result was widely reported by the popular science media with sensational headlines about the mapping of the “‘Big Bang’ of Bird Evolution” (AMNH 2014, Duke University 2014, BGI Shenzen 2014, Smithsonian Insider 2014), or as Time Magazine titled “There was a Big Bang for Birds” (Kluger 2014), or “Rapid bird evolution after the age of dinosaurs unprecedented, study confirms” (University of Sydney 2014). Casey Luskin (2014) then also reported for Evolution News how this “massive genetic study confirms birds arose in Big Bang-type of explosion.”

Another comprehensive phylogenetic study more recently again confirmed such an extremely rapid “major radiation of crown birds in the wake of the Cretaceous–Palaeogene (K–Pg) mass extinction” (Prum et al. 2015; also see Wink et al. 2023 for a perfect visualization of Prum’s results). Claramunt & Cracraft (2015) “combined DNA sequences of clock-like genes for most avian families with 130 fossil birds to generate a new time tree for Neornithes” and concluded that “it was not until the Cretaceous-Paleogene transition (66 million years ago) that Neornithes began to diversify rapidly around the world.” Brusatte et al. (2015) concluded in their review article on the origin and diversification of birds that “after the mass extinction, modern birds (members of the avian crown group) explosively diversified, culminating in more than 10,000 species distributed worldwide today.” Braun et al. (2019) still acknowledged that Neoaves “appears to have undergone a rapid radiation near the end Cretaceous mass extinction (the K-Pg boundary).” Looks like a solid scientific consensus, but not so fast. After all, we are dealing with evolutionary biology, where almost anything can happen.

A New Study

Indeed, this month a new paper by Wu et al. (2024) came to a totally different result from the consensus of virtually all previous studies. The press release (Yirka 2024) says that this “new study suggests birds began diversifying long before dinosaurs went extinct” and “the research team found evidence that the Neoaves divergence path began long before the asteroid struck.” The team of mainly Chinese authors analyzed the genomes of hundreds of species of birds and arrived at a new tree of Neoaves. The authors concluded that “the evolution of modern birds followed a slow process of gradualism rather than a rapid process of punctuated equilibrium, with limited interruption by the KPg catastrophe”. They dated the common ancestor of Neoaves to 130 million years ago in the Early Cretaceous and their diversification to the Late Cretaceous, even though there exists not a single Cretaceous fossil of this group, which had already led the worlds foremost expert on the fossil record, Michael Benton (1999), to strongly reject such hypotheses as impossible.

Unsurprisingly, other experts are not convinced either, and said that “if the new study was right, there should be fossils of all major groups of living birds from well before the asteroid impact. But almost none have been found. The signal from the fossil record is not ambiguous” (Berv quoted in Zimmer 2024 for the New York Times). Likewise another comment in the prestigious journal Science said that “if major bird groups really did emerge before the asteroid impact, then why have almost no ancient bird fossils from that time period been found?” (Jacobs 2024). Spot on, but still we have a conflict between molecular evidence and the fossil record, which should agree if Darwinism is correct.

Conflicting Trees

However, the conflicts are by no means restricted to the timing of bird evolution. Even though Darwinism would predict that all different sources of data should point to one true tree of life, there is fundamental conflict in the various attempts to reconstruct the tree of birds in the 20th and 21st century. This conflict is visible in the results of three general methodological approaches (DNA-DNA-hybridization, morphological cladistics, and phylogenomics), as well as between morphological and molecular data and even between different sets of molecular genetic data.

DNA-DNA-Hybridization

In the 1970s and 1980s the American ornithologists and molecular biologists Charles Sibley and Jon Edward Ahlquist conducted DNA-DNA-hybridization studies of numerous species of modern birds (Sibley & Ahlquist 1990, Sibley 1994; also see Wikipedia). Their revolutionary great tree of 1,100 species of living birds was called “the tapestry” and introduced a major revision of avian classification.

Sibley and Ahlquist’s used the melting temperatures of hybridized strands of DNA of two species as proxy for their overall similarity. Their methods were strongly critiqued as flawed and phenetic (Houde 1987, Lanyon 1992, Harshman 1994, Marks 2011), but even John Harshman found that “the data in Sibley and Ahlquist (1990), properly analyzed, have a strong phylogenetic signal.” Nevertheless, only few of the supraordinal groups from their tree survived later studies, mainly the basal split between Galloanserae and Neoaves.

It is of course a cheap point to say today that the method of DNA-DNA-hybidization is obsolete and was just a short-lived and misguided fad in the early days of phylogenetics, but was it? Think about it. Instead of just comparing arbitrarily selected and arbitrarily defined morphological characters, or instead of just looking into selected sequenced genes, this method compared the overall similarity between complete genomes, the whole shebang of DNA. If anything, it is this very method, which should have recovered the echo of evolutionary history and common descent. That its results failed to agree with the more modern cladistic and phylogenomic studies is basically evidence for the total bankruptcy of Darwinism.

Hennigian Phylogenetics (Cladistics)

Another school of phylogenetic methodology that dominated the pre-phylogenomic era was Hennigian phylogenetic systematics, also known as cladistics. It was mainly based on data from comparative morphology and used only shared derived similarities (called synapomorphies) for the reconstruction of the most parsimonious tree topology. In bird phylogenetics the most prominent representative was certainly the American paleo-ornithologist Joel Cracraft, who was the curator for birds at the American Museum of Natural History in New York (Cracraft 1981, Cracraft & Clarke 2001, Cracraft et al. 2004). Even though Cracraft’s work was not without criticism even from fellow cladists (e.g., Olson 1982), it arguably represents the culmination of traditional cladistic studies on avian phylogeny. Other important cladistic studies based on bird morphology were contributed by Livezey & Zusi (2001, 2006, 2007) and many other works on particular neoavian subgroups. The results differed from each other, from Sibley & Ahlquist’s “tapestry,” and from more modern phylogenomic trees.

By the way: Cracraft (2001) also looked into the rocks vs clocks problem. He acknowledged that “the fossil record has been used to support the origin and radiation of modern birds (Neornithes) in Laurasia after the Cretaceous-Tertiary mass extinction event, whereas molecular clocks have suggested a Cretaceous origin for most avian orders.” He looked into the vicariance biogeography of birds as new source of data to resolve the problem and concluded “that neornithines arose in Gondwana prior to the Cretaceous-Tertiary extinction event.” However, this is fully consistent with the Big Bang hypothesis, which is about the radiation of Neoaves, not of Neornithes. After all, we do have a late Cretaceous fossil record of fowl (Galloanserae). Fifteen years later Claramunt & Cracraft (2015) clarified, as already mentioned above, “that the most recent common ancestor of modern birds inhabited South America around 95 million years ago, but it was not until the Cretaceous-Paleogene transition (66 million years ago) that Neornithes began to diversify rapidly around the world.”

Phylogenomics

In the 21st century the era of phylogenomics came to dominate the field of bird phylogenetics, which mainly uses maximum likelihood and Bayesian methods for tree reconstruction from DNA sequence data. Within a few years several very extensive phylogenomic studies appeared (e.g., Ericson et al. 2006, Hackett et al. 2008, Pratt et al. 2008, Pacheco et al. 2011, McCormack et al. 2013, Jarvis et al. 2014, Zhang et al. 2014, Prum et al. 2015, Reddy et al. 2017, Houde et al. 2019, Kimball et al. 2019, Braun & Kimball 2021, Kuhl et al. 2021, Yu et al. 2021, Wu et al. 2024; also see the Bird Phylogeny website), which not just conflicted with the previous phylogenies but also with each other (Mayr 2011, Matzke et al. 2012, Braun et al. 2019). This led some experts, such as Poe & Chubb (2004) and Suh (2016), to rather propose a hard polytomy (called “neoavian comb” by Cracraft et al. 2004) based on an explosive evolution, which brings us right back to the Big Bang of birds, because as Feduccia (2014) said: “our continued inability to produce a veracious phylogeny of higher avian taxa is likely related to a Paleogene explosive burst or ‘big bang’ evolution of bird and mammal evolution, resulting in short ordinal internodes.” The resolution of this polytomy has been called “the greatest current challenge of avian systematics” and “last frontier” which “is still elusive” (Pratt et al. 2008). The numerous phylogenomic studies only agree on a few higher clades that were called the “magnificent seven” by Reddy et al. (2017), which already indicates how rare such agreement is, but even those few clades conflict with the older trees based on DNA-DNA-hybridization and morphological cladistics (but see Mayr 2007, 2008 for a few exceptions).

Collapsing Trees

The above-described phylogenetic conflict and incongruent trees of birds exactly confirm a point that I recently made in two other Evolution News articles for Fossil Friday on the phylogeny of arachnids (Bechly 2023) and of insectivore mammals (Bechly 2024): When you look at the numerous published phylogenetic trees of a certain group of organisms and then calculate a strict consensus tree as a kind of common denominator, the result generally tends to be an unresolved polytomy, with basically only the pre-Darwinian Linnean classification of phyla, classes, orders, and families surviving this collapse of phylogenies. This is highly unexpected under Darwinian assumptions but very much resonates with the views of Darwin critics.

This is even implicitly and a bit cryptically acknowledged in mainstream findings like that of Gordon et al. (2021) who said:

Phylogenomic analyses have revolutionized the study of biodiversity, but they have revealed that estimated tree topologies can depend, at least in part, on the subset of the genome that is analyzed. For example, estimates of trees for avian orders differ if protein-coding or non-coding data are analyzed. The bird tree is a good study system because the historical signal for relationships among orders is very weak, which should permit subtle non-historical signals to be identified, while monophyly of orders is strongly corroborated, allowing identification of strong non-historical signals.

Maybe non-history (in the sense of uncommon descent) is the simple reason for a non-historical signal.

Braun et al. (2019) concluded in their review of the phylogenomic era in avian phylogenetics:

Reconstructing relationships among extant birds (Neornithes) has been one of the most difficult problems in phylogenetics, and, despite intensive effort, the avian tree of life remains (at least partially) unresolved. Thus far, the most difficult problem is the relationship among the orders of Neoaves, the major clade that includes the most (~95%) named bird species.

Explaining Away Conflicting Evidence

Of course, this is all reflecting the substantial conflicting data that do not align with an unambiguous nested hierarchy, contrary to the predictions of neo-Darwinism and the bold (and false) claims of its modern popularizers like Richard Dawkins. Something is way off, and mainstream evolutionary biologists simply ignore it and happily produce one conflicting tree after the other without ever questioning the underlying assumptions or even the general Darwinian paradigm. Conflicting evidence is explained away with inexpensive ad hoc hypotheses like convergence, ghost lineages, or incomplete lineage sorting. Torres & Van Tuinen (2013) said “rampant phylogenetic conflict at the ordinal level in modern birds can be explained by ordinal diversification taking place over a short time interval.” However, this is not the explanation of the problem but the description of the problem!

We can conclude that fossil and molecular data conflict in terms of the question when and how quickly modern birds originated, and molecular and morphological data conflict in terms of the reconstruction of the assumed bird tree of life. Why is there such a stark conflict, when Darwinism would naturally predict that different lines of evidence should converge towards one true evolutionary history of birds. Again, a quite obvious explanation could be that there just was no such history, or at least that totally different causal mechanism were at work.

Abrupt Origins

The most important take home message from this article is this: in spite of the new study by Wu et al. (2024), there is overwhelming evidence, recognized by the vast majority of mainstream experts, that there was an explosive diversification of modern birds (Neoaves) in the Lower Tertiary (Paleogene). There was an abrupt origin, a burst of biological creativity with a genuine Big Bang of modern birds, which is best explained by an infusion of new information from an intelligent agent outside the system. What do evolutionary biologists suggest instead? They say that the global collapse of forest ecosystems after the end-Cretaceous impact killed off all arboreal bird lineages and the remaining ground-dwelling ancestors of modern birds experienced a rapid diversification afterwards (Field et al. 2018). Yet another description of the problem, rather than an explanation, which seems to be a recurring theme in evolutionary biology.

References