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 Melendez 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).

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.

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

Y-Chromosome Haplogroup P in America

<>In yesterday's post about the Yana River site in northern Siberia, I mentioned that the remains of two men discovered there, dated to ~30 kya, who carried haplogroup P as a marker in their Y-chromosomes. This is a rare variant, and is not considered a founding lineage of Native American people. This means that when found in America it is considered as a later arrival, after the 1492 discovery of America by Europeans.

Y-chromosome Haplogroup P

These two men from Yana River dated to 31,000 years ago, carried P haplogroup in their Y-chromosome. This variant is not considered as a founding lineage in America.

Amerindian men are almost 100% haplogroup Q (Y-chromosome), with some rare C3 haplogroup individuals. No P haplogroup is ever mentioned in any of the studies involving Native Americans, so, if the Yana people moved to America and carried P haplogroup with them, it is nowhere to be seen. It has vanished, or, the lack of it is probably proof that they never reached the New World.

However, a thesis discussing the peopling of Patagonia from a genetic point of view (Poblamiento de la Patagonia: una aproximación genética en poblaciones indígenas actuales de Chile y Argentina, Michelle de Saint Pierre Barrera, p. 146), has an interesting entry: IV.5.2 P haplogroup: an Amerindian marker?, argues that "it is peculiar that the native populations of all America have one main Amerindian haplogroup, Qla3al, and only two rare haplogroups, Qla and C3b... So the question is if the low diversity observed could be due to an undertypification of rare haplogroups, assign them erroneously in non-Amerindian category haplogroups. Since for most of Amerindian tribes have between a 5-25% of non-Amerindian haplogroups, it is not difficult to assign erroneously. In this work we show an average of 3.6% for the marker M45 in Amerindian samples both M242 and M207 negatives, which discards them belonging to the Q or R haplogroups and assigning them to P. The fact that we had not found the P marker in any of rural populations and only found the marker in natives populations with high level of Amerindian haplogroups, together with Asiatic provenance of P (Mitchell et al., 1997), allow us to put in the category Amerindian haplogroups."

This is thought provoking. Samples that can't be assimilated to the native Q or to R, which is Eurasian, and brought to America by the European discovery) are roughly 3.6% of the total, and to make matters worse, samples from Amerindians that don't conform to the Q haplogroup are assigned to non-native introgression!

The author suggests that "The information showed here allows us to propose a revision of this lineage and it reassignation like a proper haplogroup, analog to Q1a-M242 description by Seielstad et al. (2003). We show the presence of this haplogroup only in northern Chilean native samples with high levels of the other Amerindian haplotype, Q1a3al. Like P marker is the ancestry of two lineages very common in Europe (R) and Asia (Q), a more carefully revision on P it is necessary to determine its real presence in both continents."

The paper cites some authors who have studied the presence of P haplogroup among South American natives:

Bortolini et al. (2003) "They obtained variable percentage of P haplogroup in several populations.". Bolnick et al. (2006) "found P positive samples in Cheyenne and Cheroke in percentages between 2-4%". Blanco-Verea et al. (2010) "found P positive in Colla, Diaguita and Mapuche" but Toscanini et al. (2010) failed to confirm this among Colla and Tobas. Bailliet et al. (2008) "found possible P (assign it within K haplogroup) in Ayoreo, Lengua, Wichi, Mocovi, Huilliche and Tehuelche".

Regarding the latter study, Baillet et al. (see p. 299 in their article) consider P as allochtonous (imported, originated in some other, non-American location) and found it at high levels: "K(xQ,R) did not exceed values of ~7%" they place P withing K excluding Q and R haplos. As usual, any genetic markers that don't fit into the expected Q haplogroup for Amerindian males is considered as having been brought to America after is European discovery in 1492!

Baillet et al. also argue that "K(xQ,R) is a minor haplogroup among South American samples and involves subhaplogroups of Asian origin (Su et al. 2000; Hammer et al. 2001; Su et al. 1999; Underhill et al. 2001"

Looking into other P-haplogroup studies in America, I found a paper by M. Saõ-Bento et al., (2009) reported P haplogroup at 1.23% frequency in a Brazilian study in the interior of Sao Paulo state, but remarked that it could be a mistaken identification: "the presence of the haplogroup P(xR1,T) is most probably due to the Native American haplogroup Q, which cannot be identified with the chosen Y-SNPs, even though it may also be related to the Asian input."

The ISOGG website from their now obsolete 2018 webpage on P haplogroup, states that "appearance. Haplogroup P is best represented by its two immediate subclades, haplogroups Q and R, which expanded to become the dominant haplogroups in, respectively, the Americas and Europe. P1-M74 or M45 has been found in n. Philippines, India, China (Maks, Ai Cham, Biao, Then, Uygurs, Tibetans, Hans), Taiwan (Pyuma), Indonesia (Batak, Malay, Minangkabau, Kaili, Alor), Romania (Szeklers), Scandinavia, Iran (Bakhtiari, Arabs) Pakistan (Burushos), Melanesia, Jordan, It is not clear that all these men were verified negative for the haplogroup Q subgroup. P2-B253 was identified in the Philippines (Agtas)" This is a wide geographic range, spanning many people of different ethnic origins, from Romania and Scandinavia, across the Middle East, Southern, Eastern, and Southeast Asia, Siberia, and Melanesia! This is a clear hint of antiquity, an original group that was widespread in that area, and possible presence elsewhere at low frequencies. The ISOGG 2019-2020 current version repeats this information. But no values for prevalence frequencies are provided.

I dug a bit deeper into some of the groups mentioned above. Interestingly, it includes dark skinned, short statured Negrito people like the Agta, where P is found at frequencies of 4.62% (Source), white Indoeuropeans like the Pakistani Burushos, and Asian people like the European Romanian Szeklers, who are said to descend from Atila's central Siberian Huns (as stated by Csány et al., (2008): "...the presence of the haplogroup P*(xM173) in Szekler samples, which may reflect a Central Asian connection".

An interesting point is to look at the distribution of haplogroups Q and R and try to figure out the location of their source (the root is haplogroup P). The map is from Chiaroni J, Underhill PA, Cavalli-Sforza LL. (2010) (Y chromosome diversity, human expansion, drift, and cultural evolution. Proc Natl Acad Sci U S A. 2009 Dec 1;106(48):20174-9. doi: 10.1073/pnas.0910803106. Epub 2009 Nov 17. Erratum in: Proc Natl Acad Sci U S A. 2010 Jul 27;107(30):13556. PMID: 19920170; PMCID: PMC2787129.)

Haplogroups R and Q, distribution and frequency maps. Adapted from: Source

Below are two images showing R and Q haplogroup distribution in Eurasia (it did not include America for haplogroup Q) it is four years newer than the previous image; they appear in the Supplementary information files of Raghavan, M., Skoglund, P., Graf, K. et al. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature 505, 87–91 (2014). https://doi.org/10.1038/nature12736.

Haplogroups R and Q, distribution and frequency maps (excl. America) Source

It would seem that R originated in Central Asia (somewhere between Afghanistan, Pakistan, and Tajikistan and moved west across Western Asia, Europe, and into northern Africa. Q, on the other hand could have originated in North-Central Asia, and moved east into America. But if that was the case why is it absent in Western Siberia? Could Q in Asia be a backflow from America?

Where is the geographic location for haplogroup P, the root of both Q and R? The maps in Chiaroni, Underhill, and Cavalli-Sforza (2009) don't show P or the root from which P originated (haplogroup K), neither does the 2014 paper.

However, I found a non-scholarly online source posted in 2013, that says:

"Haplogroup K... was the parent of haplogroup P which is the parent of both haplogroups Q and R.
It has always been believed that haplogroup R made its way into Europe before the arrival of Neolithic farmers about 10,000 years ago. However, that conclusion has been called into question, also by the use of Ancient DNA results... in a nutshell, he said that there is no early evidence in burials, at all, for haplogroup R being in Europe at an early age. In about 40 burials from several location, haplogroup R has never been found. If it were present, especially in the numbers expected given that it represents more than half of the haplogroups of the men of Europe today, it should be represented in these burials, but it is not. Hammer concludes that evidence supports a recent spread of haplogroup R into Europe about 5000 years ago. Where was haplogroup R before spreading into Europe? In Asia.
It appears that haplogroup K diversified in Southeast Asian, giving birth to haplogroups P, Q and R. Dr. Hammer said that this new information, combined with new cluster information and newly discovered SNP information over the past two years requires that haplogroup K be significantly revised. Between the revision of haplogroup K, the parent of both haplogroup R, previously believed to be European, and haplogroup Q, known to be Asian, European and Native, we may be in for a paradigm shift in terms of what we know about ancient migrations and who is whom. This path for haplogroup R into Europe really shouldn’t be surprising. It’s the exact same distribution as haplogroup Q, except haplogroup Q is much less frequently found in Europe than haplogroup R."

This is quite revealing, (see Dr. Hammer's conference and its map showing K, P, R and Q, here).

Other maps found online show R and Q splitting from P somewhere in Central Asia: see the map below (source) where I added the "P" in red to highlight it. Notice however, how this map shows K splitting in Northern Iran (?) and not in Southeast Asia, P spits into R and Q somewhere close to the Altai region west of Lake Balkhash.

There does not seem to be a consensus for the location of K or P roots of the Q and R lineages. The information from yfull.com shown below (online here), shows the two samples mentioned at the top of this post, from Yana River, and modern ones from Malaysia, the Andaman Islands in India, the Philippines, and an ancient one ~1100 BP from Austria (maybe a remnant of Huns?). The tree then splits into Q and R.

This tree seems to confirm a contemporary prevalence in Southern and Southeastern Asia.

A paper by Karafet TM, Mendez FL, Sudoyo H, Lansing JS, Hammer MF. (Improved phylogenetic resolution and rapid diversification of Y-chromosome haplogroup K-M526 in Southeast Asia. Eur J Hum Genet. 2015 Mar;23(3):369-73. doi: 10.1038/ejhg.2014.106. Epub 2014 Jun 4. PMID: 24896152; PMCID: PMC4326703), suggests an origin in that area. It also (See Table 1), gives the following frequencies (all other locations in Asia, Europe, and America have 0%) for haplogroup P-P295*: Aeta, 28%; Sulawesi, 0.6%; Sumba, 3.2%; Timor, 10.8%. This study calls Haplogroup P-P295, K2b2, and mentions its "sister clades Q and R" adding that "The P295 mutation, previously assumed to be equivalent to 18 other mutations defining the haplogroup P, is derived in a broader group of chromosomes. In our worldwide sample of 7462 Y chromosomes, we observe the newly defined paragroup P-P295* in 83 chromosomes from Island Southeast Asia (Timor, Sumba, Sulawesi) and the Negrito Aeta population from Philippines." Clearly a lineage set in the insular part of Sundaland! The paper continues:

"...This pattern leads us to hypothesize a southeastern Asian origin for P-P295 and a later expansion of the ancestor of subhaplogroups R and Q into mainland Asia. An alternative explanation would involve an extinction event of ancestral P-P295* chromosomes everywhere in Asia. These scenarios are equally parsimonious. They involve either a migration event (P* chromosomes from Indonesia to mainland Asia) or an extinction event of P-P295* paragroup in Eurasia. However, given the geographic distribution of the P331 mutation, the immediate predecessor of P lineage and its likely origin in Southeast Asia/Indonesia, the existing evidence favors the first scenario."

The P lineage originated in Indonesia and migrated into Asia. This paper mentions that the K haplogroup "arose somewhere in the Middle East shortly after anatomically modern humans dispersed from Africa" It then split into two families, one leading to Haplogroups T and L, with limited geographic distribution, and the other, characterized by the M526 mutation which leads to several sublineages of K named a to d. By far, K2b is the largest, and it comprises two sub-groups, K2b1 and K2b2. The first leads to haplogroups M, S, K-P60 and K-P79. The second is the one that we are interested in, because it leads directly to haplogroup P and its branches Q and R. This paper says: "the monophyletic group formed by haplogroups R and Q, which make up the majority of paternal lineages in Europe, Central Asia and the Americas, represents the only subclade with K2b that is not geographically restricted to Southeast Asia and Oceania."

Karafet et al. suggest a rapid diversification, just 3,000 years between the appearance of K and its split into K2b1 and K2b2, and another 2,000 years to the split leading to P-P295. Then another 12,300 years to the root from which Q and R split (95% CI: 6.6–20 ky). So if K originated after the OOA event some 70 kya, the appearance of P was very early.

Denisovans

Anomalies in geographic distribution open the door to new questions. In this case, why does P have such a strange distribution? Interestingly, the Australasian signal detected in Native Americans is shared with people living in Island Southeast Asia!

I think that the answer may lie with our ancestor-cousins, the Denisovans.

They lived in this region, and admixed with modern humans as they crossed Asia to the north, and also and in this area. Furthermore, there were different groups of Denisovans exchanging body fluids with humans. At least two Denisovan lineages, D1 and D2 interbred with humans here in Southeast Asia, the Negritos of the Philippines may have met another Denisovan group that lived there (source).

The rapid spread of the mutation leading to P →Q, R, may have been induced by this intermixing with Denisovans. But, considering the "tree" of human Y-chromosome haplogroups, Denisovan Y-chromosome should have split off from the branch leading to H. sapiens long ago, and it would have different markers. A Denisovan man would not belong tho haplogroup P, his markers would differ.

In a future post I will look into the Y-chromosomes of Denisovans and Neanderthals.

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

Siberian Yana people and Native Americans (38-24 kya)

The site at Yana River in Russia is the oldest and northernmost (70°43'N 135°25'E) site discovered, to date in Northeastern Siberia. The people who lived there used a distinct type of stone tools, replaced by later waves of humans who reached the region. It has been dated to 32,000 years ago.

The Yana site was disvovered and studied by Vladimir Pitulko et al., (2004); the team followed up on a discovery that took place in 1993, when a spear foreshaft, crafted from the horn of a wolly rhinoceros was discovered, by chance, on the bank of Yana River by a local scientist named Mikhail Dashtzeren. Dashtzeren led Pitulko's team th the spot, and a methodical search of the area led to the 2001 discovery of the Yana Rhinoceros Horn Site (Yana RHS); Pitulko et al., also found mammoth tusk foreshafts.

The interesting part, is that the wooly-rhino horn foreshaft is very similar to the mammoth ivory foreshafts used by the American natives of the Clovis culture dating back 14,000 years. Foreshafts made of rhino horn were tough and flexible, and not as rigid as the Clovis ones. There were no wolly rhinos in America, so the Clovis had to use mammoth ivory. The foreshaft allowed hunters to replace broken stone points quickly when they broke while hunting megafauna. This implies that there was a shared know-how concerning spear-making, that spanned 18,000 years across two continents. But, as we will see below, the Yana people had vanished in Siberia, replaced by others, long before the Clovis appeared in America. How was this know-how shared?

The people who lived in Yana also shared genes with Amerindians. More recent research (Sikora M, Pitulko VV, et al. The population history of northeastern Siberia since the Pleistocene. Nature. 2019 Jun;570(7760):182-188. doi: 10.1038/s41586-019-1279-z. Epub 2019 Jun 5. PMID: 31168093; PMCID: PMC7617447) noted their specific stone tool technology and that there are no other sites in northeastern Siberia until the final part of the Last Glacial Maximum or LGM: "Following the occupation at Yana RHS, there is an absence of archaeological sites in northeastern Siberia until the latter part of the LGM, when groups bearing a very distinctive stone tool technology appear (~20 kya). It was within that intervening period that the ancestral Native American population emerged, but to date no genomes from individuals of this age have been recovered in northeastern Siberia."

Clearly, the Yana people who had been living there 32 kya had vanished 20 kya. Their stone tool style had also vanished: "by the time of the Last Glacial Maximum (LGM) ~23-19 kya, the Yana-related assemblage had disappeared. LGM and later artefact assemblages are dominated by a distinctive microblade stone tool technology, which spread in a time-transgressive manner north and east out of the Amur region, but did not reach Chukotka or cross the Bering Land Bridge (Beringia) until the end of the Pleistocene, and thus later than the earliest known sites in the Americas." This suggests that those who replaced the Yana came from the southeast, and did not move on, into America until it was already inhabited.

What happened to the Yana? Why did they vanish without a trace? The 2019 paper offers a timeline for the Ancient Siberian population or ANS: "The initial movement into the region represents a now-extinct ANS population diversifying ~38 kya, soon after the basal West Eurasian and East Asian split, represented by the archaeological culture found at Yana RHS... The arrival of people carrying ancestry from East Asia, and their admixture with descendants of the ANS lineage ~20-18 kya, led to the rise of the AP and Native American lineages. In the archaeological record this is reflected by the spread of microblade technology that accompanies the post-LGM contraction of the once-extensive mammoth steppe10. This group was, in turn, largely replaced by Neosiberians in the early and mid-Holocene... We find that, despite the complex pattern of population admixture throughout the last 40,000 years, the first inhabitants of northeastern Siberia, represented by Yana, were not the direct ancestors of either Native Americans or present-day Siberians, although traces of their genetic legacy can be observed in ancient and modern genomes across America and northern Eurasia. These earliest ancient Siberians (ANS), who are known from a handful of other ancient genomes (Mal'ta and Afontova Gora), are the descendants of one of the early modern human populations that diversified as Eurasia was first settled by our species, and thus highly distinct."

The Mal'ta and Afontova Gora remains are much younger, and dated to 25 kya and 17 kya, respectively, and also further south and west from Yana River. They came from central Siberia. The Mal'ta remains carry the U haplogroup (mtDNA) like Yana people, it is rare nowadays in Eurasia and has not yet been detected among Amerindians or ancient Native American remains, Mal'ta's Y-chromosome was haplogroup R, close to its root (Source) so it was also different to the Amerindian Q and Yana River's P haplogroups.

Could the Yana people have moved on, heading east, and entered America? This would explain their sudden disappearance from Siberia, and the transfer of the ivory foreshafts technology used much later by the Clovis people.

In Northwestern Canada 24,000 years ago?

If modern humans were in northern Siberia, 100 km from the frozen Arctic sea, ~71° latitude north, the earliest and northernmost people to have been yet detected in such a northern climate, what stopped them from moving further east and entering America at that time? Nothing.

Research from 2017 (Bourgeon, Lauriane; Burke, Ariane; and Higham, Thomas, Earliest Human Presence in North America Dated to the Last Glacial Maximum: New Radiocarbon Dates from Bluefish Caves, Canada (2017). KIP Articles. 1595. https://digitalcommons.usf.edu/kip_articles/1595), though supporting the Beringian Standstill hypothesis (which I do not agree with), describes radiocarbon dating of bones found in America (Bluefish Caves, Yukon, Canada, 67°09'N 140°45'W, right beside the border with Alaska) which according to the authors "confirm that Bluefish Caves is the oldest known archaeological site in North America ", adding that, "in conclusion, while the Yana River sites indicate a human presence in Western Beringia ca. 32,000 cal BP, the Bluefish Caves site proves that people were in Eastern Beringia during the LGM, by at least 24,000 cal BP" This is an early date for human presence in America.

Y-chromosome Haplogroup P

The 2019 paper on the Yana site (see Suppl. Table 1) mentions that the remains of two men unearthed in the Yana region, dated to ~30 kya, were sequenced. They carried U2 mtDNA (a maternal haplogroup which is not found in among Native Americans). Their Y-chromosome Haplogroup was P1, which is ancestral to two main haplogroups: (1) haplogroup Q, preponderant among Amerindians, and (2) haplogroup R, which very frequent across Eurasia.

These two men from Yana River dated to 31,000 years ago, carried P haplogroup in their Y-chromosome. This variant is not considered a founding lineage in America, where it is found, it is regarded as "imported" after the European discovery in 1492. Only Q, which descends from haplogroup P, is considered a founding Amerindian lineage.

I believe that a deeper look into haplogroup P would be interesting, and that will be the subject of my next post.

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

Neanderthals: they dispersed across Asia in 2000 years

When I look at the long distances covered by our ancestors across the Old World and the Americas, I often wonder how long did it take them to trek across the continents. Today I found a paper that modelled how long it took the Neanderthals to move from Western Europe, in the Caucasus, to Altai.

I was surprised to find that it could have taken around 2,000 years.

The paper by Coco E, and Iovita R (2025) (Agent-based simulations reveal the possibility of multiple rapid northern routes for the second Neanderthal dispersal from Western to Eastern Eurasia. PLoS One 20(6): e0325693. https://doi.org/10.1371/journal.pone.0325693) used a computer simulation to find out how a group of hunter-gatherers would move from a starting point into new territories without any previous knowledge of what lies ahead. The program places "cost barriers" like deserts, glaciers, wider rivers, that slow down progress and require detours or more effort to cross them. The simulation did not consider sites where Neanderthal remains have been found, yet the routes it traced coincide with many of them!. Below is a map from this paper (Fig. 2) of these paths during different periods. The authors consider that advancing and retreating ice shields during glacial periods pushed the Neanderthals into refugia further south, to warmer climates, and that they pushed north during the warmer periods.

The simulations end at Altai, where we know that Denisovans and Neanderthals mixed.

How long did it take?

The paper states that "it is possible that Neanderthal dispersals would have taken slightly longer than 2000 years. However, the model still suggests dispersal could have occurred relatively quickly. Such a dispersal may have left few vestiges along the route, as Neanderthals would have spent relatively little time in any one location."

The authors find that their arrival to Altai was inevitable, forged by the geographic constraints and landscape: "This suggests that Neanderthal dispersal to the Altai is an inevitable outcome of local movement decisions defined by geography."

Further research would be required, in Afghanistan and Turkmenistan to locate sites and provide additional data. The paper did not model beyond Altai. I wonder what direction would the simulation take into China, or even towards the northeast, into the tip of Asia and across Bering, into America.<7p>

Could these same paths have been used by the H. Georgicus of Dmanisi, Georgia, in the Caucasus, ~2 million years ago, to reach East Asia?

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

Mosquitoes with a taste for human blood evolved first in Asia than in Africa, and did so 2.9 to 1.6 Ma

A research paper published in Nature on February 26, 2026, used some interesting genetic studies to support the idea that mosquitoes in Southeast Asia evolved a taste for human blood (anthropophily) at the time that the first hominins reached the area (Homo erectus). It is an interesting paper as it used data from the study of insects to confirm some ancient anthropological dates.

These are the details of this recent paper published in Nature on Feb. 26, 2026: Singh, U.S., Harbach, R.E., Hii, J. et al. Early hominin arrival in Southeast Asia triggered the evolution of major human malaria vectors. Sci Rep 16, 6973 (2026). https://doi.org/10.1038/s41598-026-35456-y

An ancient relationship: homo and mosquitoes. Source

In the abstract, it mentions that some species belonging to a group called Leucosphyrus, part of the Anopheles mosquitoes that live in Southeast Asia not only transmit malaria, they are also fine tuned to drinking human blood. Other mosquitoes in the region occupy different niches, feeding off other monkeys (non-human primates or NHP) and transmit NHP malaria variants. This study analyzed the genes of mosquitoes from 11 species (including their mtDNA) and built dated phylogenetic trees for them.

The paper found that the original, basal species of mosquitoes in this region were monkey-feeding ones, living in what is now Malaysia, Borneo, and the Indonesian islands of Java and Sumatra, when this area was linked by a now submerged continental shelf, into Sundaland. During that time (Pliocene) the area was covered by a lush rainforest. The authors believe that "anthropophily most likely evolved once, involving adaptive introgression, in the early Pleistocene in Sundaland, giving rise to multiple descendent anthropophilic species. Such early origination of anthropophily must necessarily have been in response to the arrival of early hominins (Homo erectus) rather than anatomically modern humans, likely associated with loss and fragmentation of rainforests during the early Pleistocene. The early origination of anthropophily also provides independent non-archaeological evidence supporting the limited fossil record of early hominin colonization in Southeast Asia around 1.8 Mya." This date is roughly when Homo erectus reached the area.

The article reveals that mosquitoes are host-specific and that many genes are involved in this specificity. So "multiple genetic changes at these and other genes are required for the evolution of anthropophily, i.e. a strong, evolved preference for human blood. It is not surprising therefore that anthropophily is uncommon amongst the ~ 3500 known mosquito species. It is therefore more parsimonious to consider that anthropophily within a taxon has a single origin. Accordingly, it is improbable that there were multiple independent switches to anthropophily in the human-preferring species of the Dirus and Balabacensis Clades, which diverged around 1.3–0.5 Mya. Even taking into account some uncertainty in the molecular clock used for these divergence estimates these clades far predate the arrival of anatomically modern humans in SE Asia 76,000–63,000 years ago. We therefore reject with confidence the hypothesis that anthropophily in the Leucosphyrus Subgroup evolved in response to the arrival of modern humans in SE Asia."

Therefore it was an ancient event, long before human beings appeared in Africa.

The article adds that "Using the same molecular clock rate as applied in this study and a species tree, anthropophily would be inferred to have evolved ~ 509,000–61,000 years ago in the lineage leading to the major African malaria vectors, An. gambiae and An. coluzzii... Since An. gambiae originates in West African forests the switch to anthropophilly may instead have occurred in response to modern humans entering this forested region ~ 150,000 years ago. The emergence of anthropophily in the domestic form of Aedes aegypti and the molestus ecotype of Culex pipiens, both date to within the last 10,000 years, apparently in response to growing human populations and environmental change." So, the African human-feeding mosquitoes took place independently, and later than the SE Asian event(

Finally, the article "indicates that anthropophily in the Leucosphyrus Subgroup emerged much earlier than in other anthropophilic mosquito species. If a strictly bifurcating tree were assumed, anthropophily could have evolved either: by the time of node N1 [95% CI: 2.9–1.8 Mya] and subsequently been lost in the lineage leading to An. nemophilous and An. introlatus; or evolved twice along the lineages leading to the Dirus Clade (N3, 1.6 Mya [95% CI: 2.0–1.2 Mya]) and the Balabacensis Clade (N5, 0.5 Mya [95% CI: 0.7–0.4 Mya]).... We therefore consider the most parsimonious argument for the evolution of anthropophily in the Leucosphyrus Subgroup to be that it evolved once only through the process of adaptive introgression at nodes N1/N2 as this accommodates the multiplicity of genes underlying the trait and negates any need to invoke loss of this trait. According to this hypothesis, anthropophily would have evolved between the extremes of the N1 and N2 confidence intervals i.e. between 2.9 and 1.6 mya (Fig. 3) when all the lineages were in Sundaland, and prior to the divergence of the Dirus Clade (node N3, 1.6 Mya [95% CI: 2.0–1.2 Mya]) further north in Indochina. This hypothesis could be tested against the above alternatives by identifying the genes underlying anthropophily and characterizing their evolutionary history."

The interesting part in the preceding text is that dates, which on the "older" tip of the scale reach 2.9 and 2 million years back. This is in line with the recent findings in Eurasia about an early Homo erectus dispersal across Asia.

The authors continue (highlight is mine): "Dating of the evolution of anthropophily in the Leucosphyrus Group to 2.9–1.6 mya overlaps with the earliest proposed date for the arrival of early hominins (Homo erectus) into Sundaland at 1.8 Mya, but not with the more recent proposed date of 1.3 Mya. Our findings suggest that anthropophily in the Leucosphyrus Group emerged in Sundaland in the early Pleistocene in response to the arrival of early hominins who must have not only been present in this region by this time but must have been in substantial numbers to drive adaptation to human host preference. This supports the hypothesis of Husson et al. that early hominins were present and abundant in Sundaland ~ 1.8 Mya, prior to their dispersal via land bridges to Java. Middle Pleistocene fossils of Homo erectus indicate their prolonged occupation on the exposed Sundaland landmass, likely associated with extensive river systems. In the context of the very fragmentary nature of the fossil record in tropical SE Asia our findings contribute an important piece of evidence to the broader puzzle of the colonization of hominins in insular Southeast Asia".

Closing Comments

These findings add up to the other evidence mentioned in recent posts, suggesting a very early out of Africa (or even an Eurasian origin of hominins!). I have tried to learn more about American mosquitoes that feed on humans, but research seems to be scarce in this area other than focusing on the main vectors of malaria, dengue, yellow fever, Zika, and chikungunya (see this 2022 paper as an example). If there are anthropophilic mosiquitoes in America that could be dated, what dates would they provide? (several strains reached America after the European discovery, from Africa and Eurasia, the Aedes aegypti vector of yellow fever and Zika) originated in Africa and arrived with the slave trade, and Aedes albopictus, the "Asian tiger mosquito" arrived 40 years ago, from Asia, in used tires! Would other local strains shed light on the date of the peopling of America?

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

Early discovery of Brazil and its relationship with St. Brendan (Brandaõ)

As mentioned in a previous post, Brazil, in South America, was officialy discovered by chance, by the Portuguese navigator Cabral in the year 1500 AD, eight years after Columbus discovered America. However, several authors in the 1800s and 1900s have suggested that the Portuguese knew about Brazil's existence from much earlier, and in an interesting twist it has a link with the story of St. Brendan mentioned in yesterday's post.

In the Historia de la Nación Argentina, Vol 2, p. 355, published in 1936, Max Fleiuss wrote about the discovery of Brazil and included the following comments a letter written by Master John (Maese Juan), to the King of Portugal informing him of the discovery of Brazil, he wrote it in Vera Cruz, an island, where Cabral landed in 1500:

"This letter, dated like that of the scribe of the Calcutta trading post, in Veracruz on May 1, 1500, was found by Varnhagen in the archives of the Torre do Tombo and published in the Revista del Instituto Histórica Brasileira in 1843. The following paragraph perfectly elucidates the question of the prior knowledge that the Portuguese discoverers had of Brazil: «As for the location of this land, Your Highness should order a world map to be drawn, which Pero Vaz Bisagudo has, and in this way Your Highness will be able to see the location of this land.»
That planisphere by Pero Vaz de Cunha, the Bisagudo, is one of the oldest, as Master Juan points out to the king; and it was traced on the "Portuguese Map of the Vatican Secret Archives" of 1343. Emperor Charles V of France ordered it to be reproduced in 1375 by one of the most skilled Spanish cartographers from Majorca and ordered it to be corrected and enlarged according to the explorations made from that year 1343 onwards. A copy of it is now in the National Library of Paris."

Maese Joao is telling the king to look at the map owned by Pero Vaz de Cunha known as The Bisagudo, one of his navigators and officers. Bisagudo as a nickname referred to Pero Vaz de Cunha's shap features, from the Portuguese words viso agudo, acute face. He had been sent by King John II of Portugal to build a fortress in Senegal, Africa, but the mission took a nasty turn involving Pero executing one of his comrades. The Crown never again required his services after this. (Source) another reference says his nickname was due to his cunning and sharp intelligence.

The letter of Maese Joao says that an ancient map from 1343, showed where Brazil was located.

Max Fleiuss then adds that the map was traced from the secret Vatican files, and also copied in 1375 by the French King, Charles V, and that a copy can be found in the French National Library in Paris!

Fleiuss continues (highlight is mine, because Sancho Brandão, is, as we will see further down, linked by his same-sounding name, to St. Brendan).

"On February 12, 1343, during the reign of Alfonso IV, the Valiant, son of King Dinis, in Portugal, he informed Pope Clement VI, in a letter written from Montemayor-el-Novo (Vatican Archives), that Captain Sancho Brandão had reached a land he believed to be an island and that he was taking wild animals, livestock, and brazilwood back to Lisbon, and that he had had it surveyed by several ships. On maps from the 15th and 16th centuries, the legend "Isla de Brandam" [Brandam's Island] is also applied to "Isla del Brasil." [Brazil Island] This island appeared in the Medici Atlas as early as 1351.
Capistrano de Abreu tells us that some medieval maps give the name to a single island, in the shape of a perfectly regular circle... or in the shape of a crescent moon; others give the name to two semicircular islands separated by a strait. In Pisigano's map of 1367, there are three Bracir islands. Nenrod Krestalimer, in his study of medieval maps, found the word Brazil written with the following variants: Brazí, Braciri, Brazil, Brasiel. Brasil, Brazile, Braziele, Braziel, Bracil, Bracill, Bcrsill, Braxil, Braxiili, Braxiel, Braxyiili and Brigilge.
On the map of Charles V [the one mentioned further up, from 1375] and on the world map of Banulph Hyggeden, designed in 1360 (British Museum, London), that island has more or less the same shape as it does on the map of Bisagudo; an island that is still found on the geographical charts of Nicoló Zeno (1380), of Becario (1435) and of André Bianco, original of 1436 and copy of 1448. In the latter, it includes the legend according to which its maritime distance from the Cape Verde archipelago is calculated at 1500 miles, or approximately the distance between Cape Verde and Cape St. Augustine.[more on Bianco's map further down]
In addition, this information appears in Paulo Toscanelli's letter. Furthermore, on Martin Behaim's globe, dated 1487, the "Island of Sancho Brandõo or Brazil" is marked. This astronomer and cartographer from Nuremberg resided for a long time in Lisbon and died there in 1507. Sancho Brandõo, captain of the 1343 expedition, would therefore be, chronologically, the original discoverer of Brazil.
Among the autographs that belonged to Lord Charles Stuart's archive, there was found the letter from Pedro Alvarez to Dom Manuel in which he announced, along with the scribe, the astronomer, and all the ship commanders, the discovery of the Brazilian land. These letters were sent by the vessel under the command of Gaspar de Lemos. Cabral addresses the king in the following passage: «Obeying Your Highness’s instructions, we sailed west, and took possession, with authentic title, of Your Highness’s land, which the ancients called Brandam or Brazil» (Torre do Tombo Archive, Lord Stuart Archive Register).
Renowned authors, such as Luciano Pereira, Faustino da Fonseca, Lopes de Mendonga, Brito Rebello, Jayme Cortezão, Capistrano de Abreu, João Ribeiro, Pandiá Calogeras, Rodolfo García, and the American Henry Vignaud, considered one of Columbus’s best biographers, acknowledge that Duarte Pacheco Pereira was Cabral’s predecessor."

Andrea Bianco's Map

Plenty has been written about Bianco's maps. See this excellent reproduction of the 1436 map (Zoomable), in it, Brazil Island can be seen west of Portugal, at the latitude of Cape St. Vincent in southern Portugal, half way across the ocean towards Antillia Island (the map has the text upside down, rotate it to read some of the names). Regarding the 1448 map you can see it here, also zoomable (requires free registration to view). Below is a copy of it, from Fleiuss' article. His original caption is included.

Land located in the Portolan chart of Andrea Bianco (1448), 1500 miles west of Cape Verde Islands.

The map shows Cape Verde (the two points on the right), two islands, Dos Ermanes Islands (Two Brothers? Islands, which probably depict the Cape Verde Islands), and on the lower left side, cut by the end of the parchment is a piece of land, possibly an island, or the coast of some continental area, with a rather illegible text written in ancient Venetian. This text has been interpreted in many different ways, as we will see below

Bianco's Text

Below is a detail of Bianco's 1448 map, showing the text written on the island Source. The upper line gives the name of the island, the bottom line its location.

Fleiuss says the inscriptian reads "Authenticated Island, 1,500 miles away to the west" and asserts that "Portuguese navigators apparently found a land located 1,500 miles west of the Cape Verde Islands—more or less where the South American coast is located—which they later named Authentic Island."

A very interesting online source written by Michael Ferrar reads this text as: "Ixola A(n)tarticha, Xe longo a ponente 1500 mia" and gives it the following interpretation (I summarize his text): While reading Gavin Menzies book ("1421, the year China discovered the world") he read on page 277 that the text «Andrea Bianco’s map of 1448 referred to, “Ixola Otinticha. Xe longa a ponente 1500 mia” with a translation reading “a genuine island is 1500 miles west of here (West Africa)”» Ferrar consulted an expert on ancient Venetian writing who read "Ixola A(n)tarticha. Xe longo a ponente 1500 mia”, that could be translated from Venecian to English as: “The Antarctic Island. It has 1500 miles long to the west”." This expert suggests that the island is a reference to the mythical Antarctic continent or Terra Incognita Australis, legendary like the dos ermanes islands.

An older version, from 1895 (A Pre-Columban Discovery of America, by H. Yule Oldham, The Geographical Journal, Vol. 5, No. 3 (Mar., 1895), pp. 221-233, http://www.jstor.org/stable/1773930) shows this same map and refers to the mysterious text as follows: "at the lower edge of the map, south-west from Cape Verde-that is, in the direction of Brazil— there is to be seen a long stretch of coast-line with this singular inscription in the Venetian dialect: "isola otinticha," that is authentic or authenticated island. It is difficult to believe that this can refer to anything but Brazil... Owing to lack of room on the parchment on which the map is drawn, only a corner of this island is shown, on the very edge of the skin, but still much closer to Cape Verde than Brazil actually is. As if, however, to prevent any misconception, the cartographer has added under the words "ixola otinticha" the qualifying statemen, "xe longa a ponente 1500 mia.""

Oldham argues, with a lengthy explanation in the footnote, that "longa" in old Venetian means "distant" and that the text should be interpreted as: "authentic island is distant 1500 miles to the west."

Opposing View

A publication (Um suposto descobrimento do Brasil antes de 1448 —A supposed discovery of Brazil before 1448— by Tomás Oscar Marcondes de Souza in the Revista do Instituto Historico e Geografico de Sao Paulo, vol XLVI, p. 211, 1948, suggests that the idea of a pre-Cabral discovery is a fantasy. Among other things, it analyzes Bianco's map, and includes two images of the relevant text, that we show below, and adds the following comments about these texts.

"While studying the issue related to the discovery of the islands of the Cape Verde archipelago in 1944, we came across, between pages 98 and 99 of the book published by the Ministry of Colonies of the Portuguese Republic, entitled: - "Letters from the islands of Cape Verde, by Vindim Fernandes", by A. Fontoura da Costa, a photographic reproduction of a part of André Bianco's map from 1448, precisely where the much-discussed "Ixola Otinticha" is drawn.
Our surprise was enormous when we verified in this photographic reproduction the existence of another legend, already mentioned by us, on the island under study, with words, partly illegible, but perfectly distinguishable, these final words: "a ponente /500 / mia", which can be verified in the cliché that we publish here." [this is the upper text in the image further up]
As an example, we reproduce here the adulterated legend of "Isla Otinticha" published in volume 1, page XXXII, of "History of the Portuguese Colonization of Brazil". As is easily verified, the falsification consisted of altering the number of miles indicated in the legend of the island in question from 500 to 1500, considering that the real distance between Cape Verde and Cape São Roque in Brazil is approximately 1520 miles." [bottom text in image above]

"

The author concludes: "Thus, the infamous "Ixola Otinticha" from André Bianco's portolan chart of 1448 is perfectly identified with the current island of Santiago, one of the Cape Verde archipelago, and at the same time one of the great proofs that Brazil was discovered by the Portuguese before Columbus's feat and Cabral's voyage to Calicut is annulled."

I took a good look at the map that is shown further up, the original map, Source and it seems that it says 1500, and not 500. But my guess is as good as anyone else's unless the parchment is analyzed in depth (ink samples, etc.). It also seems to say ixola otinticha, which differs from what the expert told Ferrar (Ixola A(n)tarticha).

Saint Brendan and Sancho Brandão

An article published in 1927 (Did St. Brendan Discover Brazil? by Honor Walsh, Records of the American Catholic Historical Society of Philadelphia, Vol. 38, No. 4 (Dec., 1927), pp. 377-384. https://www.jstor.org/stable/pdf/44208689.pdf) mentions, that "Brazil has two names; one, "Ilha de Brasil" (Isle of Brasil), the other, "Ilha de Brandao" (Isle of Brendan?) . Both of these names appear in a letter written under date of February 12, 1343, by King Alfonso IV of Portugal, addressed to the Sovereign Pontiff, although Brazil is supposed to have been terra incognita until its "accidental discovery " by Pedro Alvarez Cabral in the year 1500.". It cites its source as a Brazilian journal, Jorno de Brasil, of Rio de Janeiro, authored by Assis Cintra, who places this letter from the king to the Pope in the be in the secret archives of the Vatican, Book 138, folios 148 and 149.

The discoverer according to Cintra was a man called Sancho Brandaõ, which is very similar to the same-sounding San Brandaõ (St. Brendan)! who was "driven westward by a storm until he reached the shore of a magnificent land, rich in timber yielding a red ink or coloring" (now known as Brazil wood).

The text adds that "Annexed to the letter is a map of the land discovered, with the alternative titles, 'Insula de Brasil' and 'Insula de Brandao'. According to the same Brazilian historian, "In 1375, Charles V, King of France, sent to the Vatican a cartographer from Majorca to copy the Portugese map, with orders to correct and amplify the original in accordance with the explorations carried out from 1343 to 1375. This map is in the Iconographical Section of the National Library in Paris (III, 132, s. XVI) and Brasil Island is shown thereon with more or less the same conformation and position as South America." This is the same information provided by Max Fleiuss.

Walsh then explains that Cabral, after discovering what we now call Brazil, named it "Terra da Santa Cruz" (Holy Cross Land). The name then changed to Brazil due to the red-dye wood of that name. However Walsh repeats a theory put forward by Richard Gumfoleton Daunt, that says that the Portuguese believed they had found the country of Ui Breasail, of the Irish legend, discovered by St. Brendan, so "they were not changing the name from Terra da Santa Cruz to that of a kind of wood, but were reverting to the old name. In this way the Brasil wood would get its name from the country, and not the reverse, as is generally believed." The text adds that Ui Brasil or Ui Breasil, is sometimes written as Hy Brasil. In the Irish Celtic mythology it was an island that could be seen in the western ocean for one day every seven years. It was the Island of the Blessed, also known as the Enchanged Island. (Source)

Regarding the red-dye, known as Brazil, I have mentioned it in a post back in 2011 (Phoenicians, red dye, Ophir, the origin of the name Brazil, etc.)

Assis Cintra

The person mentioned by Walsh, Cintra, existed, and he did write about an early discovery of Brazil. He was Francisco Assis Cintra (1887-1937) was a Brazilian historian, journalist, essayist, and I did find the reference to the letter sent by King Alphonso IV to the Pope Clement VI in 1343 in his book Na Margem da Historia (p.123) —On the Margins of History published in 1930, and in his book O Nome Brasil (com “s” ou com “z”) —The name Brazil (with an “s” or a “z”) (p. 184), published in 1920. They are the source of the text that Walsh and Fleiuss mentioned in their works.

There is another source that mentions correspondence between Alfonso IV and the Pope (who at that time lived in Avignon, France, not in Rome), in this book, published in 1872, but it mentions it in the context of the Fortunate Islands (Canary Islands) and not Brazil, however (see p. xiii) it mentions that this expedition whose pilot was a Genoese, Nicoloso de Recco, brought back " red wood which dyed almost as well as the verzino (Brazil wood) although connoisseurs pronounced it not to be the same; the barks of trees to stain with a red colour...

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