Richard Buggs

Tag: genomics

  • More on human-chimp genomic similarity

    More on human-chimp genomic similarity

    The Live Science website has just published an article on Do humans and chimps really share nearly 99% of their DNA? subtitled: “The frequently cited 99% similarity between human and chimp DNA overlooks key differences in the genomes.“

    This includes an email interview with a leading figure in the field, Tomas Marques-Bonet. Tomas was the final author of the 2013 Nature paper Great ape genetic diversity and population history. Since then he has published numerous papers on both ape and human genomes.

    The Live Science article reports:

    But the 99% figure is misleading because it focuses on stretches of DNA where the human and chimp genomes can be directly aligned and ignores sections of the genomes that are difficult to compare, Tomas Marques-Bonet, head of the Comparative Genomics group at the Institute of Evolutionary Biology (CSIC/UPF) in Barcelona, Spain, told Live Science in an email.


    Sections of human DNA without a clear counterpart in chimp DNA make up approximately 15% to 20% of the genome, Marques-Bonet said. For example, some bits of DNA are present in one species but missing in the other; these are known as “insertions and deletions.” In the course of evolution from a common ancestor, some pieces of DNA in one species broke off and reattached elsewhere along the chromosome.


    So, while earlier studies suggested a 98% to 99% similarity, comparisons that include harder-to-align regions push that difference closer to 5% to 10%, Marques-Bonet said. “And if we account for the regions still too complex to align properly with current technology, the true overall difference is likely to exceed 10%,” he said.


    In fact, a 2025 study found that human and chimpanzee genomes are approximately 15% different when compared directly and completely. But if this direct method is used, then there is even a lot of variability within species themselves — up to 9% among chimpanzees, the 2025 study found.”

    Another article reporting Tomas Marques-Bonet’s comments can be found on primatology.net.

    For more on the 2025 study, see my earlier blog post here.

  • How much of a human genome is identical to a chimpanzee genome?

    How much of a human genome is identical to a chimpanzee genome?

    Back in 2018 I wrote a blog post entitled “How similar are human and chimpanzee genomes?” This reported my analysis of the data available at the time, concluding:

    “The percentage of nucleotides in the human genome that had one-to-one exact matches in the chimpanzee genome was 82.34%.”

    This was based on human and chimpanzee genome assemblies hg38 and pantro6.

    Critics of my analysis said that this figure could not be trusted because both the human and chimpanzee genome assemblies were incomplete at the time.

    Since then, much more complete genome assemblies have been published for both species.

    Last month, the Nature paper “Complete sequencing of ape genomes” reported various comparisons of telomere-to-telomere genome assemblies.

    When the latest human genome assembly was used as a target, and the latest chimpanzee assembly was aligned to it, the authors report gap divergence of 13.3% and single nucleotide variant divergence of 1.6% (these results can be found in Supplementary Figure III.11 and 12 respectively, for hg0002 vs PanTro3).

    As I understand their methods, gap divergence was based on counting base (A, T, G or C) positions in the human genome that have no aligning base from the chimp genome in the whole genome alignment. Single nucleotide variant divergence was based on counting bases that align to a different base (e.g. an A aligning to a T). The authors calculated these divergences for each 1 million base segment of the human genome then averaged them all to get a genome-wide figure.

    Adding the average gap divergence and average single nucleotide variant divergence together gives a total difference of 14.9%.

    Thus, as I understand it, for the latest assemblies, 85.1 % of the nucleotides in the human genome have one-to-one exact matches in the chimpanzee genome.

    This is clearly a slightly higher figure than the 82.3% that I calculated in 2018. But it is not far off.

    The new result of 85.1% is just for autosomes (non-sex chromosomes). The same Nature paper reports 4.18% and 75.6% gap divergence and 1.15% and 3.98% single nucleotide variant divergence for X and Y chromosomes respectively.

    At some point I would like to repeat exactly the same analysis as I did in 2018 on the 2025 data. But until then, the figures reported by the authors of the Nature paper provide a helpful comparison.

  • Interview on science and faith

    Interview on science and faith

    For a summary of my group’s latest research on UK broadleaved trees, and a discussion of the positive interaction between my science and Christianity, listen to this week’s episode of the ECO Chamber podcast, from the ENDS Report. My interview starts 30 minutes in.

    Also on Spotify, Apple, Podbean.

  • Public lecture “Trees of Life: Do they exist?”

    Public lecture “Trees of Life: Do they exist?”

    In gave my inaugural lecture as Professor of Evolutionary Genomics at Queen Mary University of London on 16th November 2022, the film of which can be viewed below.

    Inaugural lectures are a chance to give a personal view on one’s research field, at a level that will be understood by the whole university and the general public.

    My Vice-Principal asked me to be more personal than usual in this inaugural, speaking about my Christian faith as well as my research as a biologist.

    I decided to do this by placing side-by-side “tree-of-life” concepts from the Bible and from The Origin of Species. By comparing and contrasting the evidence for these very different trees of life, I tried to help the audience understand how I think through things as both a biologist and a Christian.

    Whether or not this worked, you can judge for yourself.

    The lecture drew on articles I have published in Nature Ecology and Evolution, Nature Plants, and American Journal of Botany. I describe work by others in Nature and Nature Communications. The Origin of Species provided my starting point on Darwin’s tree of life simile. The works of Richard Dawkins, especially The Greatest Show on Earth and The God Delusion, provided helpful material in both sections of the lecture. On the Biblical tree of life, I used an argument by Peter J. Williams, (whose research recently featured in Nature) developed in his book Can We Trust the Gospels? I also refer to research by Elizabeth Barnes on inclusion in the biological sciences.

    I have been a full professor at Queen Mary for over four years now, but there is a back-log of inaugural lectures, and many never happen at all. So it was a great privilege to be invited to give this.

  • Natural v. Artificial Selection

    Natural v. Artificial Selection

    Last week I published a short article in Molecular Ecology on evidence for natural selection. It has proven difficult to show natural selection occurring in real time in wild populations. New approaches may help, and these are being pioneered in studies of Soay sheep. While commenting on these new approaches, I make several general points about the evidential case for natural selection.

    Perhaps the more broadly interesting of these is a critique of the argument by analogy to natural selection. I suggest that, although widely used, the analogy has severe limitations. You can read this critique from the second to the seventh paragraph of my article, which is available open access here.

  • How similar are human and chimpanzee genomes?

    How similar are human and chimpanzee genomes?

    I recently participated in a discussion on the Biologos forum on the degree of similarity between the human and chimpanzee genomes. I was asked for my current view on this issue by Dennis Venema, who had found a old quote online from a newspaper article that I had written in 2008 on this issue. In 2008, in a couple of newspaper articles, I did some simple calculations based on the 2005 Chimpanzee genome paper. On the basis of these, I had come to the surprising conclusion that these data suggested that the human and chimpanzee genomes in their entirety could be only 70% identical. Dennis Venema asked me if this was still my view. You can read the whole discussion here. It is rather long, with lots of tangential contributions. If you want a quick summary of my perspective,  here is my final closing statement (which I originally posted here):

    “How similar are the human and chimpanzee genomes?” is a relatively straightforward scientific question. We are hindered by the still somewhat incomplete nature of both the human and the chimpanzee reference genome assemblies, but we can make this clear in our assessments and allow for the uncertainties that it raises.

    The best way to assess the similarity of two genomes is to take complete genome assemblies of both species, that have been assembled independently, and align them together. The alignment process involves searching the contents of the two genomes against each other.

    (more…)
  • Adam and Eve: lessons learned

    Adam and Eve: lessons learned

    This blog was first posted at Nature Ecology & Evolution Community on 14 April 2018

    Preliminary conclusions about the possibility of a short, sharp human bottleneck

    A few months ago I asked this community if modern genome science had tested an “Adam and Eve” hypothesis that the human lineage has passed through short, sharp bottleneck of two at some point in its history. While this question may sound bizarre to some, it is one that is often asked by those with a background in Abrahamic faiths. My post has therefore been taken up and discussed extensively on the Skeptical Zone and Biologos Forum over the past few months, as well as by various blogs.

    The claim that genomic methods have been used to test and reject an “Adam and Eve” hypothesis was central to the recent book Adam and the Genome. My post, which critiqued the arguments made in that book, has received a broad level of explicit or tacit agreement in subsequent online discussions. More adequate ways of testing the hypothesis have been suggested, and preliminary results have been obtained.

    Here I will share some of the lessons I have learned from these discussions and from further reading. These are somewhat tentative, and not all are based on published peer reviewed literature. In a short blog I cannot do not do full justice to all the contributions that have been made by various scientists within the online fora, so as far as possible I will try to provide direct links to the contributions of others.

    Here are the lessons I have learned so far:

    (more…)

  • Responding to Felsenstein, Schaffner and Harshman at The Skeptical Zone

    Here is the text of a comment I posted at The Skeptical Zone in response to comments by Joe Felsenstein, Steve Schaffner and John Harshman on my Nature Ecology and Evolution blog on human bottlenecks:

    Thank you all for interacting with my Nature Ecology and Evolution Community blog, and thanks to Vincent Torley for posting here. Vincent kindly sent me a personal email pointing out this thread to me and asking me to specifically interact with comments made by Steve Schaffner and Joe Felsenstein. I will also comment on John Harshman’s comments as he is making the strongest case against a bottleneck of two, which was not mentioned explicitly by Dennis Venema in his book chapter. (more…)

  • Adam and Eve: a tested hypothesis?

    Does genomic evidence make it scientifically impossible that the human lineage could have ever passed through a population bottleneck of just two individuals? This is a question I am asked semi-frequently by religious friends. With my current understanding of the genetic evidence, I can’t state categorically that it’s impossible. In this view, I find I differ from a recent book chapter on the topic. I’m writing this blog to run my thoughts past other biologists, and check I am not missing something. (more…)

  • “Abundant bioactivity” of random DNA sequences?

    This blog was written for the Nature Ecology and Evolution Community where it is posted here.

    Probing the claims of a recent study

    Readers of this blog will be aware of the recent Nature Ecology and Evolution paper entitled “Random sequences are an abundant source of bioactive RNAs or peptides”. Rafik Neme, the first author, posted an engaging Behind the Paper blog here.

    On a quick look, I thought the study might be the beginnings of the solution to the mystery of orphan genes. (I posted about orphan genes here a few months ago.) The paper appears to demonstrate that an unexpectedly high percentage of random 150 base-pair DNA sequences are functional when expressed in E. coli. If true, this would suggest that de novo gene evolution could occur easily from junk DNA. (more…)