April 1, 2021 | David F. Coppedge

Evolutionists Fool Themselves with Darwin Trees

The methods evolutionists use are almost guaranteed to give wrong results a vast majority of the time.

The cornerstone of evolution is the phylogenetic tree: the iconic diagram that links all organisms to common ancestors in the distant past. The universal Darwin tree purports to show when all the major groups branched off from a universal common ancestor—the root of the tree. Evolutionists proudly display their tree diagrams for branches within the universal tree. Here is one example of an evolutionary tree for dinosaurs and birds exhibited in a museum:

How the Wyoming Dinosaur Center uses its Archaeopteryx specimen for evolutionary propaganda. (Credit: DFC)


A preprint on bioRxiv gives a stern warning to evolutionists who like to connect the dots between organisms, both fossil and living, to construct phylogenetic trees. They’re fooling themselves, and not just on April 1. It looks like another case of a common proverb about Darwinians: “everything you know is wrong.”

Ghosts in the Tree

The paper by Ticou, Tannier and de Vienne is titled, “Ghost lineages deceive introgression tests and call for a new null hypothesis.” It appeared on the biology preprint server bioRxiv on March 30, 2020. Here is the Abstract. Watch for the error that occurs in “the vast majority of cases.”

The data that is known and sampled in any evolutionary study is always a small part of what exists, known or not, or what has existed in the past and is extinct. Therefore it is likely that all detected past horizontal gene fluxes, hybridization, introgressions, admixtures or transfers, involve “ghosts”, that is, extinct or unsampled lineages. The presence of these ghosts is acknowledged by all scientists, but almost all wish that and make as if their blurring influence would be low, like a background noise that, with a reasonable approximation, can be ignored. We assess this undervalued hypothesis by qualifying and quantifying the effect of ghost lineages on introgression detection by the popular D-statistics method.* We use a genomic dataset of bears to illustrate and circumscribe the possibility of misinterpretation and show on simulated data that under certain conditions, far from unrealistic, most results interpreted from D-statistics, concerning the existence of introgression and the identity of donors and recipients of horizontal gene flows, are erroneous. In particular, the use of a distant outgroup, usually given as a solid ground for these tests, leads in fact to an increase in the error probability, and to false interpretations in a vast majority of the cases. We argue for a switch of the null hypothesis: the results of detection methods for gene fluxes should be interpreted with the full and visible participation of the unknown ghosts.

*(For information on D-statistics, see this Avian Hybrids blog post).

Introgression refers to flow of genetic data across groups, either by hybridization or backcrossing from previously hybridized individuals. The authors cite evidence that introgression is common among eukaryotes, including mammals, fish, insects, plants and fungi. It provides the evidence that Neanderthals and other humans interbred. What does this do to phylogenetic inference?

Because there are so many species that have never been identified or are extinct, the possibility exists for many “ghost lineages” unaccounted for in phylogenetic studies. A ghost lineage is a chain of ancestral species (“extinct or unsampled”) inferred by evolutionists who draw Darwin trees. They don’t know if such ancestors exist, but they draw lines between distant species simply because they believe they are related. Those ghosts must be there, they think. Such thinking is a fool’s errand.

Accounting for these “ghost lineages” (extinct and unsampled) is particularly relevant when studying horizontal fluxes of genetic material across taxa, because many inferred such events are likely to involve these lineages. This was repeatedly acknowledged, especially in studies of introgression between populations, but was considered in this context either a source of noise, or at best a problem that could be worked out by sampling more or performing multiple tests. Very recently Hibbins and Hahn (2021) advised to “keep in mind” this possibility of misinterpretation but as far as we know, the real impact of ghost lineages on the capacity of gene flow detection methods has not been properly evaluated and quantified.

Introgression can be confused with incomplete lineage sorting (ILS), in which similar alleles are inherited by species that are thought to be further apart genetically. Geneticists thought that using a distant outgroup would clear that up, and allow the expected tree to be preserved. Hibbins and Hahn warned in EcoEvoRxiv just two months ago that a possibility of misinterpretation exists. The current paper explains, “Working on a subset of the species logically leads to an underestimation of the true frequency of introgression and thus an inflated role of ILS.” What did most evolutionists do with the warning? They ignored it.


The three authors decided to quantify the potential for misinterpretation. They took data from lineages of bears.

In this study, we first analyse a genomic dataset from a phylogenetic study of bears to show how the interpretation of introgression tests can depend on the presence or absence of relevant lineages in the sampled data. We then quantify the effect of ghost lineages on the misidentification of donors and recipients lineages using simulations. In particular we explore the effect of the choice of the outgroup, the size of the tree and the effect of preferential transfers to closely related species on this misidentification.

They took five species of bears with known topology and took turns removing one, seeing what the D-statistics did with the tree. What did they find? They showed that a “wrong identification of the lineages involved (donors and recipients) in the majority of the cases, notably when the distance between the ingroup and the outgroup is big.” In other words, the very procedure though to eliminate noise in the data actually made it noisier. None of the tests produced errors below 25%, and that was when all the intervening species were known. The more the unknown species in the tree, the greater the misinterpretation.

We simulated species trees with N = 20, 40, 60, 80 and 100 species in total, and randomly sampled 20 species each time. This allowed simulating sampling efforts between 100% (20 species out of 20) and 20% (20 species out of 100). We observe that low sampling contributes to an increase in the amount of misinterpreted D-statistics due to ghost introgression (fig. 5). While the mean proportion of erroneous interpretation is around 25% when 100% of extant lineages are sampled, this error is close to 60% when only 20% of the lineages are known.

No Way Around It

Surprisingly, their results seemed more favorable when extinct species were chosen. But that does not remove the deception. Due to the inability of knowing what unknown groups experienced hybridization or introgression, “a detectable signal” may be lost. In cases where there is no a priori information on ghost lineages, resulting trees may look good but be fictional. Sampling more species would help, but that is not possible for evolutionary lineages assumed to stretch deep into the past: “it is not reasonable to assume that the whole extinct and extant diversity is known.” The authors point out that two other popular methods for inferring trees “were shown recently to be subject to misinterpretation because of ghost introgression as well.”

The impact of ghost lineages on the detection of introgression thus goes much beyond the simple question of the tool used. It is a problem that we, as a community, are only starting to recognize.

Another geneticist had warned last year, “the presence of ghost introgression has important consequences for the study of evolutionary processes.” These three authors of the preprint have shown the consequences are very damaging: phylogenetic interpretations are more wrong than they are right.

What do these authors advise going forward? Assume ghosts! “the results of detection methods for gene fluxes should be interpreted with the full and visible participation of the unknown ghosts.” Ha! Evolutionists believe in ghosts! It’s the only way they can preserve their precious Darwin trees they trust in.

Evolutionists: everything you know is wrong. That is not an April Fool joke.

Humpty Darwin sits on a wall of foam bricks held together by decayed mortar. Cartoon by Brett Miller commissioned for CEH. All rights reserved.



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