Rosa Rubicondior: Refuting Creationism - How The Centromere Evolved

26-02-19Uncovering evolution at the center of cell division | Max Planck Institute

AI-generated infographic (ChatGPT Auto)

A paper recently published in Nature by a research team led by Andrea Musacchio, Director at the Max Planck Institute of Molecular Physiology in Dortmund, Germany, and Jef Boeke from the NYU Grossmann School of Medicine, refutes a number of creationism's sacred dogmas. It shows how evolution at the cellular level progresses through intermediate stages and how new genetic information can arise and be repurposed. It also shows how complex specified information can evolve naturally by a Darwinian process.

The paper goes some way towards solving the ‘centromere paradox’. This is the observation that although the mechanism of cell replication, which is common to all eukaryotic cells, is highly conserved, the centromere — the specialised point on a chromosome to which proteins attach and pull the chromosomes apart during cell division — appears to mutate freely. This results in a wide variety of centromeres, ranging from large, repeat-rich centromeres in some species to the tiny, minimalist ‘point centromeres’ of yeast.

The team showed that the tiny centromere in yeast evolved through intermediate stages and began as a ‘jumping gene’, or retrotransposon — an essentially parasitic chunk of DNA that can relocate within a chromosome, thereby creating new genetic material. In yeast, this appears to have been repurposed by evolution to create the precise minimalist centromere — an example of what William A. Dembski would call complex specified information and designate as evidence for a creator.

The Centromere Paradox and Evolutionary Innovation. Every time a cell divides, its chromosomes must be accurately separated so that each new cell receives a complete copy of the genome. This crucial task depends on a specialised region of each chromosome known as the centromere. At this site, protein structures called kinetochores attach to the spindle fibres that pull duplicated chromosomes apart during cell division.

Because this process is so fundamental to life, one might expect the DNA sequences that define centromeres to be highly conserved across species. Yet biologists have long known that the opposite appears to be true. Centromere DNA varies enormously between organisms. Some species possess large regions packed with repetitive DNA, while others — such as budding yeast — have extremely small and simple centromeres known as point centromeres.

This puzzling combination of functional conservation but genetic variability is known as the centromere paradox.

The paradox highlights an important feature of evolution: biological functions can remain stable even while the underlying genetic components change dramatically. Evolution often works not by designing structures from scratch but by repurposing existing genetic elements.

One source of such innovation is transposable elements, sometimes called “jumping genes”. These are pieces of DNA capable of copying or inserting themselves elsewhere in the genome. Although they were once dismissed as useless or parasitic DNA, scientists now know that transposable elements frequently provide raw material for evolutionary innovation. Genes, regulatory sequences, and even entire functional systems have evolved from these mobile DNA fragments.

The new research suggests that the minimalist centromere found in yeast may have originated from such a transposable element. Over evolutionary time, what began as a mobile genetic parasite was co-opted and refined into a highly precise chromosome-segregation system.

This is a striking example of how evolutionary tinkering — modifying and repurposing existing components — can produce complex biological systems without the need for external design.

The team's work is explained in the form of a Q&A interview with first author Max Haase, released as a news item by the Max Planck Institute of Molecular Physiology:

Uncovering evolution at the center of cell division
Max Planck scientists discover the evolutionary “missing link” explaining the dramatic transition of the yeast centromere
Centromeres play virtually the same central role across the entire tree of life: They ensure the faithful segregation of chromosomes during cell division. Yet the striking diversity in centromere architecture – from large, repeat-rich DNA arrays to the minimalistic “point” centromeres in yeast – combined with their rapid evolution has puzzled scientists for decades. A research team led by Andrea Musacchio, Director at the Max Planck Institute of Molecular Physiology in Dortmund, and Jef Boeke from the NYU Grossmann School of Medicine have now solved the enduring mystery about the yeast centromere’s origin and evolution. They have identified a “proto-point” centromere that bridges the gap between the actual tiny “point” centromere and its more elaborate ancestor that incorporated fragments of parasitic DNA. This discovery reveals one of the most dramatic evolutionary transitions at DNA level.

Centromeres are regions of DNA where the cell’s machinery grabs each chromosome and pulls it into the two daughter cells. Centromeres are essential for accurate chromosome segregation in every dividing cell, from yeast to humans. Although the machinery that governs chromosome segregation is deeply conserved, centromeric DNA evolves rapidly – a phenomenon known as the “centromere paradox”. A particular striking example of this rapid evolution is the “point” centromere in yeast. In their new study, the teams from the MPI and NYU provide the first mechanistic route explaining the transition of the yeast centromere and identified its genetic origin.

First author Max Haase explains the new findings in the following interview.

What is the discovery you made?

Our paper explains how a very important chromosome feature - the centromere - in brewer’s yeast came to be. In yeast they are extremely small and precise - a striking oddity in the tree of life that has puzzled chromosome biologists for decades. In this work, we show a likely intermediate stage in their evolution and trace where the DNA for these special centromeres originally came from.

Why is it so exciting?

We found previously unknown centromeres in related yeast species that look like halfway stages between large, repeat-rich centromeres and the tiny ones in brewer’s yeast. The DNA at these centromeres is related to a class of “jumping genes” (mobile pieces of DNA) called retrotransposons, suggesting that these elements provided the raw material that evolution reshaped into modern yeast centromeres. This gives a concrete genetic explanation for how yeast ended up with this unusual centromere type.

Why are your findings important for the scientific community?

Yeast centromeres were the first centromeres whose functional DNA sequence was isolated and worked out in detail, beginning with work by Clarke and Carbon in the early 1980s, yet it has remained a mystery how such tiny, precisely defined centromeres could have evolved. By showing how one kind of centromere can be rebuilt from another, our work addresses this long-standing question and shows how bits of “selfish” or parasitic DNA can be tamed and turned into DNA that cells now rely on to organize their chromosomes. This provides a concrete example of how a core part of the chromosome can be completely restructured over evolution by repurposing DNA that once looked like genomic “junk”.

What are the next steps you will take?

Next, we want to understand how the kinetochore—the protein machinery that recognizes centromeres—can accommodate such dramatic changes in centromere DNA over evolutionary time. As part of this, we are tackling the open question of how centromeres assemble the kinetochore. We are also looking for additional cases where transposons have been re-used to build chromosome structures like centromeres, to see how common this kind of genome innovation is.

Publication:
Haase, M.A.B., Lazar-Stefanita, L., Baudry, L. et al.
Ancient co-option of LTR retrotransposons as yeast centromeres.
Nature (2026). https://doi.org/10.1038/s41586-025-10092-0

Abstract
Centromeres ensure accurate chromosome segregation, yet their DNA evolves rapidly across eukaryotes leaving the origins of new centromere architectures unclear^1,2,3,4. The brewer’s yeast Saccharomyces cerevisiae exemplifies this long-standing puzzle. Its centromeres shifted ancestrally from large, repeat-rich, epigenetically specified forms to the compact, genetically defined ‘point’ centromeres^1,5. How this transition occurred has remained unresolved6. Here we identify evolutionarily related ‘proto-point’ centromeres that provide a resolution to the evolutionary origins of point centromeres. Proto-point centromeres contain a single centromeric nucleosome positioned over an AT-rich core, accompanied by relaxed organization and sequence variability of flanking cis-elements. In two species, these proto-point centromeres lie within retrotransposon-derived repeat clusters, linking ancestral repeat-rich centromeres to genetically encoded ones. Comparative and phylogenetic analyses indicate that proto-point and point centromeres evolved in an ancestor with retrotransposon-rich centromeres. These results identify long-terminal-repeat retrotransposons, specifically Ty5 sequences, as the genetic substrate for point-centromere evolution and provide a mechanistic route by which an epigenetic centromere can become genetically specified. More broadly, they show how selfish elements can be co-opted to perform essential chromosomal functions.

Fig. 1: Proto-point centromeres in Saccharomycodales yeasts reveal diversity in genetic centromere organization.

a, A time-calibrated phylogeny of the 12 orders of Saccharomycotina (from ref. ²⁶) showing known centromere (CEN) types and the number of species in each order (Extended Data Fig. 1a). b, Closer view of the sister orders Saccharomycetales and Saccharomycodales, highlighting representative species and the inferred LCA of point centromeres. c, Hi-C contact map of H. uvarum, showing characteristic cross-shaped interaction patterns at centromeres (magenta arrow); the ribosomal DNA cluster (grey) and telomeres (black) are also indicated. d, Genome-wide Cse4–mNeonGreen ChIP–seq signal for chromosome 1, with the centromere position identified by Hi-C marked in magenta (full maps in Extended Data Fig. 2). e, Fine-scale view of the centromeric region showing inferred Cse4 nucleosome dyads (green bars), GC composition (brown line) and mononucleosome occupancy (blue line), revealing a single well-positioned centromeric nucleosome. f, Consensus sequence logos of the conserved CDEI and CDEIII motifs defining point centromeres in Saccharomycetales. g, Sequence logo of the H. uvarum CAM that flanks its AT-rich CDEII-like core. h, Sequence logo of the Sa. ludwigii CAM that flanks its AT-rich CDEII-like core. i, Comparative summary of centromere organization between the sister orders, illustrating the shift from flexible proto-point architectures in Saccharomycodales to the strict tripartite structure of point centromeres in Saccharomycetales. CPM, counts per million; ORF, open reading frame. ^aAdditional centromere structures are presented in Extended Data Fig. 6d–g.

Fig. 2: Proto-point centromeres in Saccharomycodes are embedded within ancient Ty5 retrotransposon clusters.

a, Schematic of Sa. ludwigii centromere structures, showing a compact CDEII + CAM core flanked by Ty5 LTRs. b, Whole-genome comparison of Sa. ludwigii strains differing by up to 8% sequence divergence, with a heat map below showing pairwise percentage identity of core centromeric regions. c, Detailed comparison of the core CEN2 region from Japanese and South African strains, with the e value profile of a local alignment across the full centromere. d, Phylogenetic relationships among Sa. ludwigii core centromeric sequences. e, Sequence divergence across CEN2 and flanking genes between Japanese and South African strains, highlighting a pronounced peak at the centromere. f, DNA dot plot comparing JP and SA CEN2 regions; only alignments with e < 10−10 are shown, revealing Ty5-associated rearrangements. g, Alignment of Ty5 LTRs from the indicated strains and elements, showing LTRs of recent and degenerate insertions. Note, the element SaCENTy5-1 is at a non-centromeric position, roughly 40 kb from the centromere. h, Estimated insertion times of Sa. ludwigii centromeric LTRs, inferred assuming 65 or 150 doublings a year (doublings per year; dt yr⁻¹; n = 861 pairwise comparisons). JP, Japanese; NA, not assembled; SA, South African.

Fig. 3: Ty5 retrotransposon clusters mark ancient centromeric regions across yeast lineages.

a, Time-calibrated phylogeny of the sister classes Pichiomycetes and Saccharomycetes (from ref. 26), showing their respective orders and associated centromere types (filled circles). The distribution of centromere sizes—measured as the intergenic distance between flanking genes—is shown for each species, revealing broad variation from compact proto-point to large Ty5-rich centromeres. b, Parsimony reconstruction of centromere-type evolution across both classes under alternative ancestral-state assumptions. Models initiating from Ty5-cluster centromeres require the fewest transitions, supporting their presence in the common ancestor. c, Representative examples of conserved gene synteny surrounding centromeres between species from Pichiomycetes and Saccharomycetes, illustrating shared centromere-linked genomic neighbourhoods. d–f, Conservation of centromere linkages of Saccharomycetales–Saccharomycodales CEN–ALG genes across Pichiomycetes and Saccharomycetes. Histograms show the distribution of distances from each gene to its nearest centromere. Centromere-proximal genes (≤30 kb from the nearest centromere) are shown as green bars. n indicates the number of genes examined in each panel; the percentage gives the fraction classified as centromere proximal. d, Genes unlinked to centromeres show no positional conservation. e,f, By contrast, genes linked to point centromeres in Saccharomycetales remain significantly associated with centromeres in Saccharomycodales and in species possessing Ty5-cluster centromeres (P < 0.0001 for within Saccharomycodales test (e), and P < 0.0001 for outside Saccharomycodales test (f)). Distances from each gene to its nearest centromere were computed, and empirical cumulative distributions (e,f) were compared with a null distribution (d) using a two-sided Kolmogorov–Smirnov test. These conserved linkages indicate that Ty5-cluster centromeres are ancient genomic features inherited from a common ancestor predating the split of Pichiomycetes and Saccharomycetes.

Fig. 4: Tempo and mode of point-centromere evolution in Saccharomycotina.

a, Mapping of centromere-related genes onto a time-calibrated phylogeny (from ref. ²⁶) reveals three major evolutionary transitions: (1) early loss of H3K9 methylation and associated heterochromatin proteins Swi6 and Clr4, retained only in Lipomycetales; (2) subsequent loss of Mis18, disrupting canonical CENP-A deposition and epigenetic centromere maintenance and (3) emergence of the F-box protein Ctf13—via duplication of DAS1/YDR130C—and the CBF3c in the common ancestor of Saccharomycetales and Saccharomycodales (Extended Data Fig. 5g–i). Core kinetochore adaptors (Ndc10, Cep3 and Skp1) are deeply conserved, indicating that the CBF3c predated the appearance of point-centromere DNA. Green dashed circles mark orders with experimentally validated centromeres; percentages indicate the fraction of species within each order encoding the corresponding gene. RNAi components are abbreviated as follows: RdRP, Argonaute (Ago), Dicer (Dcr) and the yeast-specific Dicer-like (Dcr*). Timing of events are based on secondary divergence times of previous subphylum-wide studies^26,65. b, Model for the evolutionary transition from repeat-based epigenetic to genetic point centromeres. In the common ancestor of Pichiomycetes and Saccharomycetes, loss of Mis18 coincided with the emergence of Ty5-cluster centromeres, Ty5 elements may have integrated at or near ancestral centromeric loci. Over hundreds of millions of years, Ty5 LTR sequences were co-opted as core centromeric DNA—giving rise to CDEII and flanking CAMs—whereas transcriptional regulators Cbf1 and Cep3 evolved into structural centromere-binding factors. This gradual remodelling of both DNA and protein components culminated in the genetically defined point centromeres characteristic of modern Saccharomycetales.

Haase, M.A.B., Lazar-Stefanita, L., Baudry, L. et al.
Ancient co-option of LTR retrotransposons as yeast centromeres.
Nature (2026). https://doi.org/10.1038/s41586-025-10092-0

Copyright: © 2026 The authors.
Published by Springer Nature Ltd. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

Research such as this illustrates something that biologists have recognised for decades but which creationists continue to deny: complex biological systems do not appear fully formed. They arise gradually through a series of intermediate stages, often by repurposing existing genetic elements that originally served entirely different roles. What began as a mobile, parasitic fragment of DNA has, through evolutionary tinkering, become an essential component of the machinery that ensures accurate chromosome segregation during cell division.

Far from requiring the intervention of a supernatural designer, this process demonstrates the remarkable creative power of ordinary evolutionary mechanisms. Mutation generates variation, natural selection preserves what works, and over time biological systems become refined and integrated into the complex networks that sustain life. The result may appear exquisitely precise — as the yeast point centromere does today — but the pathway to that precision is gradual, opportunistic, and entirely natural.

This discovery also exposes a fundamental flaw in claims made by advocates of Intelligent Design such as William Dembski. What they label “complex specified information” is not evidence of design at all, but simply the predictable outcome of evolutionary processes operating over vast spans of time. Once again, the evidence shows that what creationists present as proof of supernatural intervention is in fact another example of evolution doing exactly what the theory predicts.

Advertisement

Amazon