Creationism in Crisis - Scientists Have Worked Out The Time Scale for the Evolution of Placental Mammals

Creationism in Crisis

Scientists Have Worked Out The Time Scale for the Evolution of Placental Mammals

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A genomic timescale for placental mammal evolution | Science

It's another dreadful day for creationism as scientists involved in the Zoonomia Project publish yet another paper that refutes creationist dogma and the disinformation that is used to recruit more scientifically illiterate dupes into the money-making and extremist political cult.

This paper, published in Science concerns the gaps in the palaeontological record of the diversification of mammals from a single stem species. The gaps are filled with genetic evidence, made possible by the systematic comparison of 241 whole genomes from different existing mammals.

To make matters worse for creationism, the major periods of diversification coincides with major environmental changes as evidenced from geology and show changes over several millions of years - on an Earth that creationists believe is only a few thousand years old!

The work was made possible by the work of the Zoonomia Consortium, which should be keeping creationist cult leaders awake at night, if they grasped the significance of the work:

The Zoonomia Consortium was formed in 2015 by a group of scientists from several institutions, including the University of California, Davis, the University of California, Berkeley, the University of California, Santa Cruz, and the Broad Institute of MIT and Harvard. The goal of the consortium was to develop a comprehensive database of animal genomes that could be used to study and compare the genetic basis of traits across different species.

In 2020, the Zoonomia Consortium published a paper in the journal Nature describing the results of their work. The paper, entitled "Zoonomia Consortium, A comparative genomics multitool for scientific discovery and conservation," provides an overview of the consortium's approach and the tools they developed.

The Zoonomia database includes genomic data from over 100 species of animals, including mammals, birds, reptiles, and fish. The database is freely available to researchers and includes a variety of tools for analyzing and comparing genomic data, such as genome browsers, alignment tools, and gene expression analysis tools.

The Zoonomia Consortium's work has significant implications for conservation biology, as it allows researchers to compare the genetic basis of traits across different species and identify genetic factors that may be important for species survival. For example, researchers could use the Zoonomia database to identify genes that are associated with disease resistance or tolerance to environmental stressors, which could inform conservation efforts.

Reference:

Lewin, H.A., Robinson, G.E., Kress, W.J. et al. Zoonomia Consortium, A comparative genomics multitool for scientific discovery and conservation. Nature 587, 240–245 (2020). https://doi.org/10.1038/s41586-020-2876-6

Tell me about the Zonomia Consortium, please

According to the international team of scientists, led by William J Murphy, of Veterinary Integrative Biosciences, Texas A&M University:

Placental mammals display a staggering breadth of morphological, karyotypic, and genomic diversity, rivaling or surpassing any other living vertebrate clade (1,2,3). This variation represents the culmination of 100 million years (Ma) of diversification and parallel adaptation to tumultuous changes in Earth’s environments, including catastrophic events such as the Cretaceous-Paleogene (K-Pg) bolide impact. These different measures of diversity have impeded a complete reckoning of how and why modern placental mammal orders suddenly appeared in the Paleocene with scant paleontological signal preceding the KPg impact.

Details of the research and their main conclusions are given in the structured abstract to the team's paper in Science:

Structured Abstract

INTRODUCTION

Resolving the role that different environmental forces may have played in the apparent explosive diversification of modern placental mammals is crucial to understanding the evolutionary context of their living and extinct morphological and genomic diversity.

RATIONALE

Limited access to whole-genome sequence alignments that sample living mammalian biodiversity has hampered phylogenomic inference, which until now has been limited to relatively small, highly constrained sequence matrices often representing <2% of a typical mammalian genome. To eliminate this sampling bias, we used an alignment of 241 whole genomes to comprehensively identify and rigorously analyze noncoding, neutrally evolving sequence variation in coalescent and concatenation-based phylogenetic frameworks. These analyses were followed by validation with multiple classes of phylogenetically informative structural variation. This approach enabled the generation of a robust time tree for placental mammals that evaluated age variation across hundreds of genomic loci that are not restricted by protein coding annotations.

RESULTS

Coalescent and concatenation phylogenies inferred from multiple treatments of the data were highly congruent, including support for higher-level taxonomic groupings that unite primates+colugos with treeshrews (Euarchonta), bats+cetartiodactyls+perissodactyls+carnivorans+pangolins (Scrotifera), all scrotiferans excluding bats (Fereuungulata), and carnivorans+pangolins with perissodactyls (Zooamata). However, because these approaches infer a single best tree, they mask signatures of phylogenetic conflict that result from incomplete lineage sorting and historical hybridization. Accordingly, we also inferred phylogenies from thousands of noncoding loci distributed across chromosomes with historically contrasting recombination rates. Throughout the radiation of modern orders (such as rodents, primates, bats, and carnivores), we observed notable differences between locus trees inferred from the autosomes and the X chromosome, a pattern typical of speciation with gene flow. We show that in many cases, previously controversial phylogenetic relationships can be reconciled by examining the distribution of conflicting phylogenetic signals along chromosomes with variable historical recombination rates.

Lineage divergence time estimates were notably uniform across genomic loci and robust to extensive sensitivity analyses in which the underlying data, fossil constraints, and clock models were varied. The earliest branching events in the placental phylogeny coincide with the breakup of continental landmasses and rising sea levels in the Late Cretaceous. This signature of allopatric speciation is congruent with the low genomic conflict inferred for most superordinal relationships. By contrast, we observed a second pulse of diversification immediately after the Cretaceous-Paleogene (K-Pg) extinction event superimposed on an episode of rapid land emergence. Greater geographic continuity coupled with tumultuous climatic changes and increased ecological landscape at this time provided enhanced opportunities for mammalian diversification, as depicted in the fossil record. These observations dovetail with increased phylogenetic conflict observed within clades that diversified in the Cenozoic.

CONCLUSION

Our genome-wide analysis of multiple classes of sequence variation provides the most comprehensive assessment of placental mammal phylogeny, resolves controversial relationships, and clarifies the timing of mammalian diversification. We propose that the combination of Cretaceous continental fragmentation and lineage isolation, followed by the direct and indirect effects of the K-Pg extinction at a time of rapid land emergence, synergistically contributed to the accelerated diversification rate of placental mammals during the early Cenozoic.

The timing of placental mammal evolution.
Superordinal mammalian diversification took place in the Cretaceous during periods of continental fragmentation and sea level rise with little phylogenomic discordance (pie charts: left, autosomes; right, X chromosome), which is consistent with allopatric speciation. By contrast, the Paleogene hosted intraordinal diversification in the aftermath of the K-Pg mass extinction event, when clades exhibited higher phylogenomic discordance consistent with speciation with gene flow and incomplete lineage sorting.

Abstract

The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis of genetic variation across an alignment of 241 placental mammal genome assemblies, addressing prior concerns regarding limited genomic sampling across species. We compared neutral genome-wide phylogenomic signals using concatenation and coalescent-based approaches, interrogated phylogenetic variation across chromosomes, and analyzed extensive catalogs of structural variants. Interordinal relationships exhibit relatively low rates of phylogenomic conflict across diverse datasets and analytical methods. Conversely, X-chromosome versus autosome conflicts characterize multiple independent clades that radiated during the Cenozoic. Genomic time trees reveal an accumulation of cladogenic events before and immediately after the Cretaceous-Paleogene (K-Pg) boundary, implying important roles for Cretaceous continental vicariance and the K-Pg extinction in the placental radiation.

Nicole M. Foley et al.
A genomic timescale for placental mammal evolution.
Science 380,eabl8189(2023).DOI:10.1126/science.abl8189

© 2023 The Authors, Published by American Association for the Advancement of Science. Reprinted with kind permission under licence #5540151116953

With this evidence, biologists are becoming less and less dependent upon the fossil record, so the childish creationists objections to the TOE based on the gaps in the fossil record are carrying less and less weight with those who understand the basics of biology and the genetic basis of evolution.

Never do we find scientists declaring that the evidence is casting doubt on the TOE as the best explanation for the evidence, and each discovery such as this comparison of the genomes of over 240 species of placental mammals simply adds yet more evidence to the mountain that already exists.

The scientists never set out to confirm the TOE, or destroy creationism, yet, simply by revealing the facts about mammalian genetic evolution, they did both.

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