Creationism in Crisis - Scientists Have Reconstructed the Genome of the Earliest Mammalian ancestor

Morganucodon, one of the oldest known mammal-like species

Source: FunkMonk (Michael B. H.), CC BY-SA 3.0
via Wikimedia Commons

Revealing the Genome of the Common Ancestor of All Mammals - Leibniz Institute for Zoo and Wildlife Research

The creationist delusion that the Theory of Evolution is a theory in crisis, about to be replaced in mainstream biology with their childish, evidence free superstition based on the ludicrous idea that nothing evolves and everything is made by magic, took another blow today when an international team of scientists led by scientists from the University of California Davis and the Leibniz Institute for Zoo and Wildlife Research (Leibniz-IZW), Berlin, Germany, published their computed genome of the stem species from which all mammals evolved.

Such a project would not have been mooted had the scientists had the slightest doubt about evolution being the explanation for biodiversity, nor would it have been possible to compute this ancestral genome if the DNA of mammals did not form consistent hierarchy of nested clades resulting in evidence that the genomes of the ancestors of modern mammals form a family tree with a single origin, which lived about 200 million years ago.

The scientists' work is published in the scientific journal Proceedings of the National Academy of Sciences (PNAS).

As the scientists explain in the news release from Leibniz-IZW:

Every modern mammal, from a platypus to a blue whale, is descended from a common ancestor that lived about 180 million years ago. We don’t know a great deal about this animal, but the organization of its genome has now been computationally reconstructed by an international team of scientists.

Our results have important implications for understanding the evolution of mammals and for conservation efforts

Professor Harris Lewin, senior author
Department of Evolution and Ecology,
University of California, Davis, CA, USA.

The scientists drew on high-quality genome sequences from 32 living species representing 23 of the 26 known orders of mammals. They included humans and chimps, wombats and rabbits, manatees, domestic cattle, rhinos, bats and pangolins. The analysis also included the chicken and Chinese alligator genomes as comparison groups. Some of these genomes are being produced as part of the Earth BioGenome Project and other large-scale biodiversity genome sequencing efforts. Lewin chairs the Working Group for the Earth BioGenome Project.

The reconstruction shows that the mammal ancestor had 19 autosomal chromosomes, which control the inheritance of an organism’s characteristics outside of those controlled by sex-linked chromosomes, (these are paired in most cells, making 38 in total) plus two sex chromosomes

Dr Joana Damas, first author
Postdoctoral scientist
Genome Center University of California, Davis, CA, USA

The team identified 1,215 blocks of genes that consistently occur on the same chromosome in the same order across all 32 genomes. These building blocks of all mammal genomes contain genes that are critical to developing a normal embryo.

Chromosomes stable over 300 million years The scientists found nine whole chromosomes, or chromosome fragments in the mammal ancestor whose order of genes is the same in modern birds’ chromosomes.

This remarkable finding shows the evolutionary stability of the order and orientation of genes on chromosomes over an extended evolutionary timeframe of more than 320 million years

Professor Harris Lewin

. In contrast, regions between these conserved blocks contained more repetitive sequences and were more prone to breakages, rearrangements and sequence duplications, which are major drivers of genome evolution.

Ancestral genome reconstructions are critical to interpreting where and why selective pressures vary across genomes. This study establishes a clear relationship between chromatin architecture, gene regulation and linkage conservation. This provides the foundation for assessing the role of natural selection in chromosome evolution across the mammalian tree of life.

Professor William Murphy, (not one of the authors)
Texas A&M University, Galveston, Texas, USA.

The scientists were able to follow the ancestral chromosomes forward in time from the common ancestor. They found that the rate of chromosome rearrangement differed between mammal lineages. For example, in the ruminant lineage (leading to modern cattle, sheep and deer) there was an acceleration in rearrangement 66 million years ago, when an asteroid impact killed off the dinosaurs and led to the rise of mammals.

The results will help understanding the genetics behind adaptations that have allowed mammals to flourish on a changing planet over the last 180 million years

Dr Camilla Mazzoni, co-author
Head of Evolutionary and Conservation Genetics
Berlin Center for Genomics in Biodiversity Research
and Research Group Leader in Evolutionary and Conservation Genomics
Department of Evolutionary Genetics, Leibniz-IZW.

No doubt there then that (mammals and birds) evolved and that this work is strong evidence for the scientific theory. Creationists might like to ignore the fact that at no point did the scientists find any evidence of magic or supernatural intervention in the process.

They give more detail in their statement of significance and the abstract to the open access paper in PNAS. I've highligted the parts Creationists should ignore if they want to retain their delusion:

Significance

Computational reconstruction of ancestral mammalian karyotypes revealed a comprehensive picture of the chromosome rearrangements that occurred over the evolutionary history of mammals. Ancient gene order, in some cases extending to full chromosomes, was found conserved for more than 300 My, demonstrating strong evolutionary constraint against rearrangements in some regions. Conserved segments of chromosomes are enriched for genes that control developmental processes. Therefore, Darwinian selection likely maintains ancient gene combinations while allowing for genomic innovations within or near chromosomal sites that break and rearrange over evolutionary time. The revealed relationship between the three-dimensional structure of chromosomes and the evolutionary stability of chromosome segments provides additional insights into the mechanisms of chromosome evolution and diseases associated with genome rearrangements.

Abstract

Decrypting the rearrangements that drive mammalian chromosome evolution is critical to understanding the molecular bases of speciation, adaptation, and disease susceptibility. Using 8 scaffolded and 26 chromosome-scale genome assemblies representing 23/26 mammal orders, we computationally reconstructed ancestral karyotypes and syntenic relationships at 16 nodes along the mammalian phylogeny. Three different reference genomes (human, sloth, and cattle) representing phylogenetically distinct mammalian superorders were used to assess reference bias in the reconstructed ancestral karyotypes and to expand the number of clades with reconstructed genomes. The mammalian ancestor likely had 19 pairs of autosomes, with nine of the smallest chromosomes shared with the common ancestor of all amniotes (three still conserved in extant mammals), demonstrating a striking conservation of synteny for ∼320 My of vertebrate evolution. The numbers and types of chromosome rearrangements were classified for transitions between the ancestral mammalian karyotype, descendent ancestors, and extant species. For example, 94 inversions, 16 fissions, and 14 fusions that occurred over 53 My differentiated the therian from the descendent eutherian ancestor. The highest breakpoint rate was observed between the mammalian and therian ancestors (3.9 breakpoints/My).Reconstructed mammalian ancestor chromosomes were found to have distinct evolutionary histories reflected in their rates and types of rearrangements. The distributions of genes, repetitive elements, topologically associating domains, and actively transcribed regions in multispecies homologous synteny blocks and evolutionary breakpoint regions indicate that purifying selection acted over millions of years of vertebrate evolution to maintain syntenic relationships of developmentally important genes and regulatory landscapes of gene-dense chromosomes. [my highlighting]

Damas, Joana; Corbo, Marco; Kim, Jaebum, et al.(2022)
Evolution of the ancestral mammalian karyotype and syntenic regions
Proceedings of the National Academy of Sciences (PNAS) 119 (40), e2209139119. DOI: 10.1073/pnas.2209139119

Copyright: © 2022 The authors.
Published by PNAS. Open access
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

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