Short Branch Lengths (Y chromosome)

In my last post I mentioned the issue of shorter branches for contemporary Africans in the Y-chromosome phylogenetic tree. This means that starting from the fork that leads on one side to Africans, and the other to non-Africans, the latter contains more mutations than the former, but we are all the same age and equally distant from our common ancestor. So why do the Africans have fewer mutations? Do Eurasians accumulate more mutations? Are the branches built incorrectly? This post will try to shed some light on this matter.

Y-chromosomes and haplogroups

The accepted haplogroup structure for chromosome Y, just like that of mtDNA, is rooted in Africa, where the most basal lineages are found.

Using the phylogenetic tree analogy, all other variants, found outside of Africa are branches that stem from this African origin. Outlier branches, even closer to the root, include our ancestor-relatives, the Denisovans and Neanderthals.

Back in 2014 I posted about Neanderthal Y chromosomes, and used the following image, which I have updated to add Denisovans.

The Denisovan and Neanderthal Y-chromosomes were studied by Martin Petr et al. (2020) in their paper The evolutionary history of Neanderthal and Denisovan Y chromosomes (Science 369, 1653-1656 (2020). doi:10.1126/science.abb6460 🔒- free access on Biorxiv🔓), which I will comment in depth in a future post. The authors of this paper mention that their Y-chromosome phylogenetic trees display shorter branch lengths for Africans.

This is interesting! They state "Importantly, we discovered that the branch-lengths in Africans are as much as 13% shorter compared to non-Africans (Figure S7.3), which is consistent with significant branch length variability discovered in previous studies and suggested to be a result of various demographic and selection processes."

Below is Figure S7.3 mentioned above. You can see that all these African samples have ratios, except for the S_Mbuti_1 sample, that are lessr than 1, meaning the branches are shorter than the European ones. Furthermore, the most diverged samples (A00) are even shorter :

Original caption:Branch length differences between African Y chromosomes and a panel of 13 non-African Y chromosomes. Ratios were calculated by creating an alignment of chimpanzee, African and non-African Y chromosomes and taking the ratio of the number of derived alleles observed in an African (x-axis) and the number of derived alleles in each of the individual non-Africans (dots, Table S7.1). “A00” represents a merge of sequences of two lower coverage Y chromosomes, A00-1 and A00-2 (Table S4.3). Fig S7.3 in Petr et al. (2020)

The branch lengths refer to the number of accumulated mutations in the branches of phylogenetic-trees. Africans have fewer mutations than non-Africans, so their branches are shorter, yet they are supposedly older! This is an anomaly, because it impliles a slower mutation rate in Africa, or a quicker one outside of Africa. The explanation offered by the authors is a classic one. This explanation is that leaving Africa caused population bottlenecks and forced adaptation to new environments which speed up mutations, or so the theory goes! Below is Fig. S1.7 from this paper.

Branches. Fig. S1.7

The values of the branches a, d, e, and f are given in the paper's Table S7.1 and are the following (I adapted the image and included a new column, a+d the branch leading to non-Africans, which, as you can see, has more mutations than the African ones -compare the values of a+d with f.

Branch lengths. Table S7.1

The difference seems small but it is significant. Furthermore since Ust'Ishim, who died 45,000 years ago, non-Africans added an average of d-e mutations, ~200 of them. Africans added ~180-190 mutations. Hence, the "shorter branch" issue.

Shorter or Longer?

However, an earlier paper that studied Neanderthal and H. sapiens Y chromosomes by Mendez F, Poznik G, Castellano S, Bustamante C, (2016) (The Divergence of Neandertal and Modern Human Y Chromosomes. The American Journal of Human Genetics, 98, 728-734) showed different branch lengths, but with an opposite skew! This work included two figures (Fig. 1B, and Fig. 2) which I have combined and adapted in the image below. (the filters are different regions used to compare the DNA strands, some are more restrictive than others).

The branch lengths leading to the most divergent Africans with haplogroup A00, Mbo people from Cameroon, has a length e, which is longer than the one leading to the Reference (European men), branch d. But both share the same root. Why have the Mbo men accumulated more mutations than Europeans during the same time span?

This paper calculates the split age for both Modern Human branches (Mbo and Europeans) at 280 thousand years ago (kya), and dates the Neanderthals split at ∼588 kya. The Neanderthal man that was analyzed, died ∼49,000 years ago, in El Sidrón, Spain, and is located on branch f. His lineage contains 49,000 years of fewer mutations because we mutated while he remained static, yet, the total line f contains far more mutations than either modern human line: the A00 (a+e) or European lineage (a+d), who, by the way have had an added 50 ky of mutations on them!

This shows that the Neanderthal Y chromosome mutated faster than Homo sapiens Y chromosome, or that the timeline calculated in the paper is inaccurate.

Back and Recurring mutations

The paper noted that "The 17 sites that are incompatible with the tree are principally due to recurrent and back mutations". So these are not as infrequent as imagined.

Reference Bias

Janet Kelso, co-author of Petr et al.'s paper investigated branch lengths and published her research in 2024: Resolving the source of branch length variation in the Y chromosome phylogeny, Yaniv Swiel, Janet Kelso, Stéphane Peyrégne. bioRxiv 2024.07.05.602100; doi: https://doi.org/10.1101/ 2024.07.05.602100.

This paper admits that population size, and reproductive age, accumulated deleterious mutations due to bottlenecks in the out of Africa group, may play a role, but the main cause of branch length differences is the reference human Y chromosome used for comparison, that lacks mutations that appear in more diverged haplogroups: "branch length variation amongst human Y chromosomes cannot solely be explained by differences in demographic or biological processes. Instead, reference bias results in mutations being missed on Y chromosomes that are highly diverged from the reference used for alignment."

Reference bias is an error caused by using a certain benchmark (in this case the reference haplogroup, which is European, known as the Homo sapiens (human) genome assembly GRCh37 (hg19) from the Genome Reference Consortium), that favors genetic "reads" that match it, over those in alternative alleles. The reference Y haplogroup is R1b.

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Comment on A00, the most ancient Y chromosome

For those interested in the deepest root of Y-chromosomes, the one named A00, you can find the original paper describing it by Mendez F., et al., (2013) (An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree. AJHG, Vol 92:3 3, 7 March 2013, pp 454-459, https://doi.org/10.1016/j.ajhg.2013.02.002). An interesting critique to the findings, especially the extreme old age of this "basal" root, can be found in this paper: Elhaik E, Tatarinova TV, Klyosov AA, Graur D., (2013). The 'extremely ancient' chromosome that isn't: a forensic bioinformatic investigation of Albert Perry's X-degenerate portion of the Y chromosome. (Eur J Hum Genet. 2014 Sep;22(9):1111-6. doi: 10.1038/ejhg.2013.303. Epub 2014 Jan 22. PMID: 24448544; PMCID: PMC4135414).

San, the oldest humans?

Sometimes the media, and websites mention "the oldest" or "the earliest" people pointing at the Mbo or the Khoisan (San) groups, but in fact nobody alive nowadays is "older" than other populations. We have all been evolving since the first Homo sapiens appeared. We are all equally distant from him or her, nobody is closer or more similar to those original modern humans.

This is why I dislike phylogenetic trees like the one shown below (source) that implies a direct link from the ancient root to nowadays for the San people, and a series of steps to a short fork for Asians and Europeans. (Hss: H. sapiens, Hsnn: Neanderthals, Hsnd: Denisovan)

When I read that the Khoisan separated from all other humans 150,000 years ago, I get the impression that it is a false statement. The Khoisan were not isolated since then, they also have admixture of other humans, but having lived in isolation in the deep past, and admixing with other diverse, divergent, isolated groups, they acquired a higher diversity themselves, as a population, while humans living outside of Africa lost diversity due to bottlenecks and founder effects. But the genes we retained in America, Asia, Oceania and Europe are mostly as old as the ones found in Africans.

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Back to differing branch lengths

Hallast P, Batini C, Zadik D, et al. (2015). (The Y-chromosome tree bursts into leaf: 13,000 high-confidence SNPs covering the majority of known clades. Molecular Biology and Evolution. 2015 Mar;32(3):661-673. DOI: 10.1093/molbev/msu327. PMID: 25468874; PMCID: PMC4327154. 🔓) mentioned that "Different clades within the tree show subtle but significant differences in branch lengths to the root." Fig. 3 in this paper (above is part of the figure) gives a clear image on how the branch lengths differ.

The tips of all haplogroups should all align, justified on the right side, as all the tips are contemporary, however, they have different lengths. I took R2 as the reference and drew a black vertical line. This makes the shorter branches stand out: haplogroups A, B, H, I1, Q, and R, and also the longer ones like C, G, J, or T. As you can see in the image above (I recommend visiting Fig 3 following the link, because it has far more detail than the simplified version I included above.)

Replication timing

A very thorough analysis on the causes of branch length differences can be found in Qiliang Ding , Ya Hu , Amnon Koren , Andrew G Clark, (2021). Mutation Rate Variability across Human Y-Chromosome Haplogroups. Molecular Biology and Evolution, Vol 38:3, March 2021, pp 1000–1005, https://doi.org/10.1093/molbev/msaa268.🔓.

The paper used data from over 1,700 men and "uncovered substantial variation (up to 83.3%) [in the] mutation rate among haplogroups. This rate positively correlates with phylogenetic branch length, indicating that interhaplogroup mutation rate variation is a likely cause of branch length heterogeneity."

The authors remarked that "Previous studies suggested that branch length heterogeneity might be caused by nongenetic factors, for example, paternal age variation across populations, acting over many generations. Another possibility is variation in mutation rate among Y-chromosome haplogroups.... [but] It was suggested that variation in Y-chromosome mutation rate across haplogroups was unlikely (Jobling and Tyler-Smith 2017)."

They disagree with the nongenetic factors and with Jobling and Tyler-Smith's dismissal of varying mutation rates, and prove that both are mistaken. This paper confirms that something known as replication timing varies across haplogroups, and this difference is linked to higher mutation rates (later replication causing more mutations than early replication timing).

Replication timing is the sequence in which the DNA of a chromosome is duplicated during cellular division. It involves unwinding and unzipping the DNA strand in a specific orer, in different places, some of them simultaneously.

Due to these differing mutation rates, branch lengths are different, and this impacts on the timing and dating of haplogroups. The paper's supplementary file states that the divergence time of haplogroups E1b, R1a, and R1b may be underestimated, while that of haplogroup B is overestimated, as the former have shorter branches, and the latter, longer ones. See Fig. 3 C and D in the paper.

The explanation sounds good, but why do different haplogroups have different replication timing? Alas, no answer is provided!

Population factors

Nevertheless, Barbieri, C., Hübner, A., Macholdt, E. et al. (2016) (Refining the Y chromosome phylogeny with southern African sequences. Hum Genet 135, 541–553 (2016). https://doi.org/10.1007/s00439-016-1651-0 🔓) attribute branch length in Southern African haplogroups to paternal age: "there is pronounced variation in branch length between major haplogroups; in particular, haplogroups associated with Bantu speakers have significantly longer branches. Technical artifacts cannot explain this branch length variation, which instead likely reflects aspects of the demographic history of Bantu speakers, such as recent population expansion and an older average paternal age. The influence of demographic factors on branch length variation has broader implications both for the human Y phylogeny and for similar analyses of other species." (Sure! it affects the calculation of dates along the branches of phylogenetic trees!).

This paper finds "The shortest branches in the Y chromosome phylogeny are for haplogroups A and B... E1b1a lineages have significantly longer branches than E1b1b or E2 lineages." Taking a look at the mutations marked along the phylogenetic tree shown in the paper's Fig 1, it confirms the comment branch lengths variability (below is the number of mutations from the tip to the root at the A2—T node).

• A2a: 17
• A2b: 7
• A2c:22
• A3b1b: 21
• B2B1: 113
• E1b1a: 208
• E1b1b: 138
• E2: 105

These people, living today have an extremely wide variation in mutation numbers between their common ancestor at the A2—T root and themselves: 7 to 208 mutations!! They are all Africans, and should be equally distant to the R1b reference genome, meaning that Kelso's reference bias does not apply in this case. This could be due to paternity age (older men have more mutations in their sperm as they sire children and pass on mutations in their Y chromosomes to their sons), or to the different replication times of different haplogroups.

T Naidoo et al., (2020) in their analysis of Khoe-San men in South Africa also found the branch issue: " Branch Length Heterogeneity Several earlier studies (Scozzari et al. 2014; Hallast et al. 2015; Barbieri et al. 2016) found evidence of branch length heterogeneity among Y-chromosome haplogroups, and provided possible reasons for its occurrence. We also noted significant differences in branch length heterogeneity among the major African haplogroups (supplementary tables S2 and S3, Supplementary Material online). A reduced mean branch length for haplogroup A, noted previously by Scozzari et al. (2014), was again apparent from our data. Although most major haplogroups differed significantly (with the exception of the E1b1a subclades), we found that haplogroup B did not appear to have as reduced a mean branch length, relative to haplogroup E, as found previously (Hallast et al. 2015; Barbieri et al. 2016). Within haplogroup E, E1b1b1 was found to have the highest mean branch length; though this may have been due to a lower sample size compared with haplogroup E1b1a." It seems to me, as a layman, that the branch length issue perplexes even the smartest scholars.

Closing comments

This post shows that scholars don't agree on why the African branches, the most diverged, and "archaic", leading to the root, and origin of our H. sapiens species, contain fewer mutations than those found in Eurasian people. Since the basis of calculating the splits between modern humans and archaic relatives like Neanderthals and Denisovans is the assumption that there is a "mutation clock" that ticks at a regular pace, so if we know the ticking rate, and the number of mutations, we can calculate when species split from others, and people diverged from others. Short branches on supposedly ancient lineages are incongruent.

We are all equally ancient, Africans, Eurasians, and Americans, yet we have accumulated mutations in our Y chromosome at different rates. This is something that should be clearly analyzed. Software issues, methodology, sampling, reference bias, replication times, older reproductive ages, larger population sizes, bottlenecks, etc. have been put forward to explain this anomaly. None of these answers seems satisfactory. Chromosome Y is peculiar, it is small, and critical; any mutations here can have disruptive effects. We are overlooking something. When we find it, we will know why some branches are longer than others.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2026 by Austin Whittall © 

An intro to Y chromosome haplogroups

My last post mentioned the possibility of Denisovans being linked to Haplogroup P of the Y chromosome, and the possible presence of haplogroup P in America. I thought that it would be straightforward to associate Denisovans with haplogroup P. But after giving it some thought, it isn't. So I decided to recap and go back to the basics and try to find out if it is feasible to associate Denisovans with any human Y chromosome haplogroup.

Transmission and Mutations of Chromosome Y

Chromosome Y is inherited in a patrilineal manner. All men carry one chromosome X and one chromosome Y, they inherit the X from their mothers and the Y from their fathers. In human beings, carrying a pair of X and Y means you are a man. If you inherit the X from both parents, you are a woman.

Base Pairs

Like all chromosomes, Y is made up of DNA (Deoxyribonucleic acid) a molecule that is made up of two counter-spiraling helicoids (like a winding circular stairway), both strands are made up of sugar-phosphate and are the backbone onto which four different compounds (bases) attach. These are Adenine (A), Cytosine (C), Guanine (G), and Thymine (T); these are the steps of the stairway. The bases bind in a particular way, A with T and G with C.

DNA carries the instructions that the cells can read and use it as a template to build proteins.

The bases are laid down in a certain sequence along the spirals, for instance one strand could have: A T G C C T A G T... and the opposing one would have the complementary bases (a T for every A, a C for each G, and viceversa): T A C G G A T C A...

Each pair of linked bases (the rungs of the stairway) is a base pair, for instance A—T. There are 60 to 300 million base pairs in each of our 46 chromosomes, a total of around 3 billion of them in our genome.

Chromosome Y is the smallest in terms of base pairs: roughly 60 million on average.

Genes

Genes are a specific sequence of aligned base pairs in one chromosome. They are the basic unit of heredity. A gene has the codes required to produce special molecules known as RNA or specific proteins.

When cells replicate, or in the case of our sexual gametes (ovarian eggs and sperm), the chromosomes undergo a process of splitting and the DNA strands unwind and replicate. With 3 billion base pairs, copying the new strands can lead to alterations in the base pairs: mutations.

Some base pairs are lost (deletions) others are copied twice (duplications). This alters the blueprint and may have an impact on how the gene that contains these mutations functions. Mutations can be negative (deleterious), neutral, or even positive. As we will see below, mutations in chromosome Y are problematic, as they accumulate.

Hominin Evolution

Our closest primate relative is the common ancestor that we share with chimpanzees, who lived between 6 and 8 million years ago.

This distant ancestor evolved, through a series of mutations into our homo ancestors: Homo habilis and Homo erectus, and others, reaching the common ancestor of Neanderthals, Denisovans, and Homo sapiens.

The original male hominins living 3 or 4 million years ago, carried certain base pair sequences in their Y chromosomes. We can imagine a small population with a few hundred males sharing identical base pairs (this is of course an over simpification, they differed). These "men" then passed their Y chromosomes with these same sequences to their sons. Some of them probably died in their childhood and did not mate, others only had daughters, so their Y chromosomes were lost, only those who had sons passed them on to the next generation.

Mutations

Each generation went through the same process, but the sequences that were passed on, changed over time as chance and external factoes introduced random mutations in the base pairs of the DNA strands of the Y chromosome.

Below are some of the factors that cause mutations:

• Chance, random mutations.
• Age of conception, those men who reproduce later will have more male germ-cell divisions, and each division entails the risk of a failed copy in the sequence. Formation of sperm (or spermatogenesis) implies constant cellular division over a man's lifespan. Female oocytes that result in eggs are all produced at birth, in one go.
• Methylation, the addition of a methyl group (—CH₃) to the DNA strand due to epigenetic (lifestyle or external) factors such as stress, famine, or toxins (alcohol, chemicals, smoking).
• Oxidative stress. Sperm are also modified by inflammation, heat, radiation (cosmic rays) which can produce free radicals which are oxidants and degrade the DNA.
• Inadequate repair systems, although the Y chromosome has limited repair mechanisms as it is mostly non-recombining (it has no partner like the other non-sexual chromosomes and does not recombine with the X chromosome). It has limited ability to fix glitches due to its high content of repeat sequences called palindromes.

Unlike other chromosomes, mutations can't be purged in Y chromosomes, so if they are harmful, they will accumulate and lead to genetic malfunction (sterility, illness, death, stillborn boys, and miscarriages). The chromosome will not work as expected. Mutations can reverse, undoing the original variation, but it is an unusual event.

The hominins evolved, but the basic structure of their Y chromosomes was similar, only the accumulated mutations, those that had allowed viable offspring survived, the others vanished as those who carried them died.

The whole genome is subjected to mutations, the X chromosome, and the other chromosomes, and natural selection acts, promoting the survival of the mutations that provide an advantage to those carrying them. It is possible that certain Y chromosomes, even though they were fit and possibly provided survival benefits, were eclipsed by deleterious mutations in other chromosomes. This led to the loss of many Y chromosome variants that had evolved over millennia.

The image Below shows an extremely oversimplified version of a Y chromosome. The original, ancestral version is (1) it has 50 million base pairs (not shown), but one mutated, say an A for a T (shown with the red band). It survives in the following generation and after many generations during which othe over the years, and today, when we look at the global population and sample the men, we find the variants marked (2) to (8), each one carries the original "red" mutation but have added others, each identified with a different color (blue, black, orange, green, violet, and gray).

Y Chromosome markers explained. Austin Whittall ©2026

Haplogroups

Here is where modern geneticists and anthropologists use their computer software tools, algorithms, and theory to build phylogenetic trees. They choose certain base pair mutations known as SNPs as "markers" that define "haplogroups" that split populations into branches from a main trunk (the basal one). Assuming that there are no back-mutations, and that repeat mutations are extremely uncommon, they propose that each marker (a mutation at a given base pair) that is fixed in a given population arose in a sequential manner.

In the example shown above, the phylogenetic tree would be the one shown below, assuming that mutations accumulate and don't reverse:

Caveats

We could argue that (8) resulted from (4) that lost its "blue" mutation, but as mentioned further up, orthodoxy considers that back mutations are rare so they ignore them. Problems also arise when we ask which mutation came first, (2), (7), or (8) they are all just one mutation away from the ancestral root.

In the real world, this is far more complicated, especially when we sequence the Y-chromosome of Neanderthals and Denisovans, which have degraded, decayed, and are incomplete. The strands of DNA of ancient remains are full of voids, and bases that have switched, or flipped. Comparing them with modern strands is done with software that "matches" them and points out the differences.

Toomas Kivisild (2017) highlights the complexity of analyzing haplogroups in ancient Y-chromosome samples: "it can be challenging to distinguish true mutations from those induced by damage, particularly in case of C to T and G to A substitutions", contamination is another factor, and the errors caused by low quality readings caused by "coverage" (how many sites were measured in a sample for comparison with a reference genome) and "sequencing depth" (how many reads covered the sample). All of them can lead to incorrect branch lengths, tree inferences, and dating.

SNPs

And mutations can appear in markers leading to mistaken identifications, like the ones reported by A.T. Fernandes, R. Goncalves, and A. Brehm (2004), in the Azores, where "It was found that some individuals share the same haplotype but belong to different Y-chromosome haplogroup suggesting that SNP mutations may occur frequently." SNPs are Single Nucleotide Polymorphisms (a switch in one base, like an A for a T). This paper notes that "The human Y-chromosome haplogroups are characterized by several mutations according to the phylogeny and nomenclature proposed by the Y-chromosome Consortium. Haplogroups are considered to be stable due to the very low mutation rate of most binary markers (SNPs), around 10⁻⁹ per base per generation, showing evidence of recurrent mutation at only 6 of 240 SNPs." This study involved 240 unrelated men and found "three individuals that share an haplotype with a double duplication suggest[ing] that a recurrent mutation occurred in SNP M78 because the duplication event is rare and it is unlikely to occur twice. For the individuals sharing the same haplotype but belonging to different haplogroups two explanations can be possible: recurrent mutations in several SNP namely in M78 and M81 (E3b1/E3b2) and M172 (J/J*) or several STR mutations may have occurred." So much for haplogroups and the assumptions that they are based on! 6 in 240 may seem a low frequency but it is high, 2.5%.

STR, mentioned above is a Short Tandem Repea, a snip of 2 to 6 base pairs long that is repeated two or more times in a location along the DNA strand.

The Branches of the Haplogroup tree

Another factor to consider when looking at ancient and modern DNA is that a man who died 50,000 years ago shows us a picture of a lineage that stopped accumulating mutations then. During the following 50,000 years all other lineages continued adding mutations to their DNA strands at a rate of 10^-9 per base per generation (I am using the SNP haplogroup marker value given above). So assuming generations of 25 years, in 50 ky, there are 2000 generatons, and with 50 million base pairs in a Y chromosome, we can calculate 50 x 10⁶ x 2 x 10³ x 10^-9 = 100 mutations.

When we look at our last shared common ancestor with the Denisovan group who lived ~550,000 years ago, if we assume no mixing with these people since then. After 500 ky, when we met them again in Asia during the Out of Africa migration, each branch, ours, and theirs would have accumulated an average of 1000 mutations (1000 in 50 million base pairs is a very low proportion: 0.002%). With Neanderthals from who we split later, around 350 kya, and met during our first Out of Africa 150 kya, only 400 mutations would have accumulated during the 200 ky we remained apart.

Intra Homo sapiens comparisons like the ones that compare a modern Chinese or a Native American from the Amazon, with an African San, are comparing lineages that have accumulated mutations since they split, probably 60 ky (Chinese and Amerindian) ago from the African line, accumulating mutations separately since then ~120 mutations in each line. And Native Americans with a 30 ky split from Chinese would have added 60 mutations.

Branch Shortening

Finally, and this will be the subject of my next post, mutations do not accumulate at the same rate. Africans have "shorter branches" on the phylogenetic trees. A paper by Petr et al, (2020) using data from an ancient man found in Siberia, Ust’-Ishim, 45,000 years old and modern humans noticed that the number of mutations from the root of each "branche" that leads to Africans and Non-Africans differed, implying different mutation rates (or, in my opinion, incorrect dating of the root, or fork): "Importantly, we discovered that the branch-lengths in Africans are as much as 13% shorter compared to non-Africans, which is consistent with significant branch length variability discovered in previous studies and suggested to be a result of various demographic and selection processes. Notice how they attempt to explain the issue away with "various" processes.

Further reading. Though old and dated, it is short, clear, and comprehenisive. Mark A. Jobling and Chris Tyler-Smith, (2003). The human Y Chromosome an evolutionary marker comes of age, Nat Rev Genet. 2003 Aug;4(8):598-612. doi: 10.1038/nrg1124.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2026 by Austin Whittall © 

On the direction and root of phylogenetic trees

When I see a phylogenetic tree (also known as an evolutionary tree), I always wonder why do we believe that those branches, trunk and the root which anchors it, are correct. I ask myself why is it assumed that the mutation took place in one direction and not the other. And this trivial question is fundamental because the branches open up from other branches based on the differences between the DNA as you move along them.

Below is a very simple example of what I mean. Imagine we reach a planet, and come across a species whose DNA is sequenced and reveals the folowing genes: A, B and C.

We then take a sample of individuals, and sequence their genome. The nine individuals in our sample come from different continents and the "order" of the genes is different in each individual:

AAAAA, AACAA, BAAAA, BAAAB, BBAAA, CACAA, AACAB, BAACB and BABAB.

We assume that mutations take place at random so a B can spontaneously mutate into C or A, an A into B or C and a C into A or B. So, a group of scientists after looking at the genomes assumes that AAAAA is the oldest group of that species and that the other populations are the result of mutations that modified the original genome. They build tree (1) shown below. The most distant population is the one with the BABAB genome.

The red arrow marks the "founding" population and the green arrow the "newest" group, descended from them.

But another group of scientist based on some ancient remains and other assumptions, says "No, the original population is not AAAAA, it is the people carrying the BABAB genes" (exactly the opposite to what the first group of scientists have proposed and proven in Tree (1).

The second group builds Tree 2, where as we can see (the green arrow shows the original population and the red one shows us where they place the population AAAAA. For this second group of scholars, populations AACAB and CACAA are the "most recent" populations. The tree below shows the mutated gene in red:

Two different trees built from the same genome samples. Copyright © 2018 by Austin Whittall

The scholars could then identify haplogroups where the A to C or the B to A mutation marks a haplogroup and theorize on how these haplogroups evolved one from the other... Does this sound familiar? Yes, it is how the mtDNA and the Y chromosome DNA haplogroups were created -by adopting certain mutations as key indicators for branches and defining that it took place in a certain way (in our DNA, for instance, an aadenine (A) switch for a cytosine (C) may mark a haplogroup. A for C but, we could also -as in our thoretical planet imagine that the C switched for an A and that the supposed parent genome is actually the child and not the other way round.

Thus the "new" American genomes could actually be the oldest and the African ones the youngest (like switching from tree 1 to 2 above).

This is of course an oversimplification, but we do have the DNA of Neanderthals, Denisovans, Homo sapiens from different sites around the world, and anchors from our ape relatives, the chimps. But often, when I look at the sequences (CGACGGAATACG... and so on - see this image below (from Nature where a standard human sequence -top row "Reference"- is compared to Neandertal sequences in the bottom two rows), I wonder how true and accurate are our "reconstructions". Which base mutated first, which later?...

And also See this image, which compares Denisovan, Neandertal and some apes and monkeys.

Trees are created by computer programs that use "assumptions" and theoretical considerations built into them by the scientists that programmed them. They supposedly work using statistically sound calculations, which are so complex that I doubt anyone can verify them without the help of computer software... so maybe some bias is built into them, for instance assuming that AAAAA is the "original" genome in our distant planet, or here, assuming that the DNA of an African is "older" than that of an Amerindian...

I don't believe in snake oil, but I do believe that we should look at facts with open eyes (like the two trees that can be built using those nine sequences in our distant planet. Same data different conclusions) and not be biased by a prejudice (prejudice = Pre Judgement, we use the data to prove what we believe to be true, not to prove the facts...).

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2014 by Austin Whittall ©