F Rosa Rubicondior: Creationism in Crisis - A New Look at Bird Evolution - Not Whether, But How!

Thursday 4 April 2024

Creationism in Crisis - A New Look at Bird Evolution - Not Whether, But How!

A greater flamingo, Mallorca, Spain.
Credit: Daniel J. Field
We’ve had bird evolution all wrong - News - University of Florida

To a child-like black vs white creationist, science changing its mind is science admitting it was wrong - which means it's probably wrong this time too, so all of science can be dismissed as wrong. Unless of course, it's some pseudo-science purporting to support creationism, then it's absolutely incontrovertible proof of creationism, because there is nothing a creationist craves more than proof of creationism provided by the same science they despise so much when it refutes creationism yet again.

So, news that a team of researchers at Florida University have re-examined the genetic evidence for the evolution of birds and revised the family tree will be music to the ears of any creationist fraud looking for some science to misrepresent. However, this research does nothing of the sort, and merely confirms what we already know - that birds diversified from a common ancestor by an evolutionary process. The debate is never about whether that happened, but how and exactly when.

What misled taxonomists was a chunk of DNA that has remained more or less unchanged for some 60 million years. By a process which is poorly understood, this large chunk of DNA avoids recombination during the process of egg and sperm production. Using this section alone gave one family tree, which put doves and flamingoes as close cousins, but using the whole genome gave a different family tree which makes doves and flamingoes much more distantly related (though of course, still related by common ancestry).

The research team have published their findings, open access, in Proceedings of the National Academy of Science (PNAS) and explain them in a University of Florida news release:
A frozen chunk of genome rewrites our understanding of the bird family tree.

An enormous meteor spelled doom for most dinosaurs 65 million years ago. But not all. In the aftermath of the extinction event, birds — technically dinosaurs themselves — flourished.

Scientists have spent centuries trying to organize and sort some 10,000 species of birds into one clear family tree to understand how the last surviving dinosaurs filled the skies. Cheap DNA sequencing should have made this simple, as it has for countless other species.

But birds were prepared to deceive us.

In a pair of new research papers released today, April 1, scientists reveal that another event 65 million years ago misled them about the true family history of birds. They discovered that a section of one chromosome spent millions of years frozen in time, and it refused to mix together with nearby DNA as it should have.

This section, just two percent of the bird genome, convinced scientists that most birds could be grouped into two major categories, with flamingos and doves as evolutionary cousins. The more accurate family tree, which accounts for the misleading section of the genome, identifies four main groups and identifies flamingos and doves as more distantly related.

My lab has been chipping away at this problem of bird evolution for longer than I want to think about. We had no idea there would be a big chunk of the genome that behaved unusually. We kind of stumbled onto it.

Professor Edward Braun, Ph.D., senior author
Department of Biology
University of Florida, Gainesville, FL, USA
Braun supervised an international team of collaborators led by Siavash Mirarab, a professor of computer engineering at the University of California San Diego, to publish their evidence that this sticky chunk of DNA muddied the true history of bird evolution. Mirarab and Braun also contributed to a companion paper published in Nature that outlines the updated bird family tree, which was led by Josefin Stiller at the University of Copenhagen.
Two mutually exclusive bird family trees. The top family tree lumps flamingos and doves, in blue and teal respectively, closely together, while the bottom family tree does not. The top family tree was built around distortions in bird genomes that date back to the extinction of the dinosaurs. The bottom family tree is likely more accurate, after accounting for these genomic anomalies.

Credit: Edward Braun
Both papers are part of the B10K avian genomics project led by Guojie Zhang of Zhejiang University, Erich Jarvis of Rockefeller University, and Tom Gilbert of the University of Copenhagen.

Ten years ago, Braun and his collaborators pieced together a family tree for the Neoaves, a group that includes the vast majority of bird species. Based on the genomes of 48 species, they split the Neoaves into two big categories: doves and flamingos in one group, all the rest in the other. When repeating a similar analysis this year using 363 species, a different family tree emerged that split up doves and flamingos into two distinct groups.

With two mutually exclusive family trees in hand, the scientists went hunting for explanations that could tell them which tree was correct.

When we looked at the individual genes and what tree they supported, all of a sudden it popped out that all the genes that support the older tree, they’re all in one spot. That’s what started the whole thing.

Professor Edward Braun, Ph.D
Investigating this spot, Braun’s team noticed it was not as mixed together as it should have been over millions of years of sexual reproduction. Like humans, birds combine genes from a father and a mother into the next generation. But birds and humans alike first mix the genes they inherited from their parents when creating sperm and eggs. This process is called recombination, and it maximizes a species’ genetic diversity by making sure no two siblings are quite the same.

Braun’s team found evidence that one section of one bird chromosome had suppressed this recombination process for a few million years around the time the dinosaurs disappeared. Whether the extinction event and the genomic anomalies are related is unclear.

The result was that the flamingos and doves looked similar to one another in this chunk of frozen DNA. But taking into account the full genome, it became clear that the two groups are more distantly related.

What’s surprising is that this period of suppressed recombination could mislead the analysis. And because it could mislead the analysis, it was actually detectable more than 60 million years in the future. That's the cool part. We discovered this misleading region in birds because we put a lot of energy into sequencing birds’ genomes. I think there are cases like this out there for other species that are just not known right now.

Professor Edward Braun, Ph.D
Such a mystery could be lurking in the genomes of other organisms as well.
As usual, the technical details are in the abstract and background in the team’s paper in PNAS:

Genomes are mosaics of evolutionary histories, and over time, regions of shared history shrink due to recombination. We typically observe frequent changes in evolutionary trees across the genome, especially for rapid radiations. We have found an exception across 21 Mb of neoavian genomes. Unexpectedly, this region shows a consistent history for the first divergence among Neoaves circa 65 Mya. Moreover, the history strongly supported in this region differs from the inferred species tree. We show that the cause of this surprising pattern may be an ancient rearrangement that remained polymorphic across multiple speciation events. We demonstrate that this single region can interact with limited taxon sampling to mislead phylogenomic analyses.


Genomes are typically mosaics of regions with different evolutionary histories. When speciation events are closely spaced in time, recombination makes the regions sharing the same history small, and the evolutionary history changes rapidly as we move along the genome. When examining rapid radiations such as the early diversification of Neoaves 66 Mya, typically no consistent history is observed across segments exceeding kilobases of the genome. Here, we report an exception. We found that a 21-Mb region in avian genomes, mapped to chicken chromosome 4, shows an extremely strong and discordance-free signal for a history different from that of the inferred species tree. Such a strong discordance-free signal, indicative of suppressed recombination across many millions of base pairs, is not observed elsewhere in the genome for any deep avian relationships. Although long regions with suppressed recombination have been documented in recently diverged species, our results pertain to relationships dating circa 65 Mya. We provide evidence that this strong signal may be due to an ancient rearrangement that blocked recombination and remained polymorphic for several million years prior to fixation. We show that the presence of this region has misled previous phylogenomic efforts with lower taxon sampling, showing the interplay between taxon and locus sampling. We predict that similar ancient rearrangements may confound phylogenetic analyses in other clades, pointing to a need for new analytical models that incorporate the possibility of such events.

The potential for conflicting evolutionary histories across the genome, often called gene tree–species tree discordance (1), has now been fully incorporated into evolutionary theory (2). This change reflects the plethora of genome-wide analyses that have documented discordance across the genome, starting from early such analyses (3). Besides inference error (46), there are several causes for true biological discordance. Incomplete lineage sorting (ILS) is an omnipresent source of discordance (710), and it can be exacerbated by hybridization (11). ILS is a by-product of neutral evolution and the presence of polymorphisms in populations that undergo successive speciations. The random sorting of polymorphisms into descendent lineages may not match the species tree (12). Thus, ILS, which occurs with a nonzero probability for every recombining genome, has been the default biological explanation for observed discordance and has been targeted by many methods of species tree inference (13). Discordance due to hybridization does not impact all branches of the tree but can be very common in some clades (14, 15) and is observed in birds (16); however, hybridization is not strictly an alternative to ILS as deep coalescences can occur on phylogenetic networks just as they do on trees.

An important signature of ILS is its randomness. Evolutionary trees for individual loci represent different realizations of a stochastic process, captured by the multi-species coalescence (MSC) model (17). ILS is expected to be present across the genome, and contiguous windows with the same history are expected to be short due to accumulated recombinations, reaching an expected equilibrium of 1/(2Ner) base pairs (bp). While estimates of recombination rate r and effective population size Ne vary, using reasonable ranges for birds (e.g., 105Ne106 and 1.2×109r107 per bp; see refs. 18 and 19), these windows can range between 5 bp and 4,000 bp. Thus, at the higher end, the recombination-free window sizes measure in thousands of base pairs and not millions. As a consequence, for sufficiently short branches of the species tree (which have experienced high levels of ILS), we expect the evolutionary history to change frequently as we move along the genome; for such branches, it would be exceedingly unlikely that long stretches of the genome (e.g., > 1 Mbp) would have evolved under the same topology, displaying no discordance. Note that genomic segments with different histories do not necessarily follow the boundaries between genes, and hence, we will use the term “locus trees,” as opposed to the typically used gene tree.

The early radiation of Neoaves, the clade comprising ca. 95% of bird species (20), has extensive phylogenetic discordance, often attributed to abundant ILS (10, 21). Quantifying levels of ILS has been difficult due to the confounding effect of stochastic error and systematic bias in locus tree estimation (46). Nevertheless, the signatures of ILS among early divergences of Neoaves are observed regardless of the data type (e.g., both coding and noncoding sequences) used for phylogenetic estimation. Analyses of other genomic changes, such as insertions and deletions, also provide strong evidence for ILS in the early branches of Neoaves (10, 22, 23). Although rare genomic changes can exhibit homoplasy (see ref. 24.for a transposable element example), most conflicts between these low homoplasy characters and the species tree are likely to reflect ILS. This combination of challenges has motivated genome-wide studies of bird evolution (2527), including whole-genome analyses by Jarvis et al. (10), which included 48 species representing most bird orders, and a recent study by Stiller et al. (21), which included 363 species representing most bird families.

Among key findings by Jarvis et al. (10) was the division of Neoaves into two strongly supported clades: Columbea and Passerea (Fig. 1), a topology (called J2014 henceforth) found in their analyses dominated by noncoding DNA. Columbea comprises Columbimorphae (doves, mesites, and sandgrouse) and Mirandornithes (also called Phoenicopterimorphae; flamingos and grebes). Passerea includes all other Neoaves. The division of Neoaves into Columbea and Passerea has been the subject of intense debate (5, 25, 26, 28). The new analyses by Stiller et al. (21) recovered Mirandornithes alone as the earliest diverging Neoaves, thus breaking Columbea (Fig. 1). Columbimorphae was united with Otidimorphae as the sister to all other Neoaves except Mirandornithes. This placement of Mirandornites as sister to all other Neoaves (called the S2024 topology henceforth) has been proposed before (26, 28). It was recovered by Jarvis et al. (10) when analyses were limited to ultra-conserved element (UCE) sequence data, although later analyses of UCEs with more filtering resulted in Columbea again (29). It is remarkable that the two whole-genome-based analyses disagree on this fundamental relationship, each with strong statistical support. Unfortunately, morphological data do not provide any way to resolve this disagreement because there are essentially no characters that unite clades deep in the avian tree (27).
Fig 1.
The topologies recovered by Jarvis et al. (10) (J2014) using 48 species and Stiller et al. (21) using 363 species (S2024). J2014 splits Neoaves into Columbea (Columbimorphae and Mirandornithes) and Passerea (all other Neoaves). S2024 places Mirandornithes as the sister to other Neoaves and puts Columbimorphae as the sister to Otidimorphae within the other Neoaves.

A plausible explanation for the conflict between Jarvis et al. (10) and Stiller et al. (21) is the impact of improved taxon sampling, though in the context of species tree estimation rather than the traditional arguments that focused on only a few genes (30). In this study, we show that while taxon sampling plays a role, what makes it especially relevant in this case is the existence of a striking outlier region of a single chromosome (Chr 4 in chicken). The locus trees in this region (21 Mb long; Table 1) show uncharacteristically low levels of discordance and consistently support J2014. This is in profound contrast to the rest of the genome that shows abundant and stochastic discordance with frequent changes in the topology, as expected under ILS; genome-wide analyses, on aggregate, support the S2024 topology as the species tree. Our results suggest that there was a period around the early diversification of Neoaves when recombination was strongly suppressed in the chromosome 4 outlier region across more than one speciation event. Remarkably, the strong phylogenetic signal of that event has persisted in extant genomes. These patterns dramatically diverge from ILS expectations based on the rest of the genome and require invoking more complex processes.

Creationists will need to ignore the detailed genetic analysis behind this revised taxonomy for birds and how it compares with the hopelessly muddled and contradictory classification of birds in the Bible, which appears to include bats but 'forgets' to mention many major orders of birds and has several different 'kinds' of hawk and owl (Leviticus 11: 13-20) and even has some fowl with four feet (Leviticus 11:21). But then the authors knew nothing of genetics, nor of any birds outside their small area of the Middle East in which they set their tales.

Creationists will also need to ignore the fact that these biologists have no doubt about the explanatory power of the Theory of Evolution and the fact that the genetic analysis reveals that birds have been around for many millions of years longer than creationists dogma says Earth has existed for.

Just another casual and unintentional refutation of the counter-factual superstition of creationism by scientists who simply revealed the facts.

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