F Rosa Rubicondior: Genetics
Showing posts with label Genetics. Show all posts
Showing posts with label Genetics. Show all posts

Sunday 10 March 2024

Unintelligent Design - How Epigenetic Settings Are Passed To Daughter Cells - Even William Heath Robinson Would Be Impressed


Cracking Epigenetic Inheritance: HKU Biologists Discovered the Secrets of How Gene Traits are Passed on - Press Releases - Media - HKU

It all started when single-celled organisms started to form colonies of like-minded individuals. The easiest way to do it was for the two daughter cells of a dividing cell to stick together instead of going their own way. They in turn would have had more daughter cells until they formed large clump of cells, but, unless the cells began to perform distinct functions, there was no advantage to forming clumps like that instead of each cell going its own way and fending for itself. Fortunately, there were no large predators around, otherwise a clump of cells would have made a tasty snack and the whole idea would have been abandoned as too risky by half, and we would be stuck now with a world of single-celled organisms and nothing else.

However, with the trial and error which characterises biological development, some of the cells in the clump began to perform specialist functions. For example, as the clump got larger, specialist cells would have been needed to exchange gasses with the environment or the cells at the centre would have been deprived of oxygen and their waste in the form of carbon dioxide would have accumulated because diffusing across a large mass of cells would be too slow to keep up with production and the supply of oxygen would be too slow to keep up with the demand. The same thing applied to getting nutrients into the center of the clump.

So, the clumps which had specialist cells fared better in the competition for resources than those which were just undifferentiated clumps. In fact, the clumps with specialised cells would probably have eaten the undifferentiated clumps and become predators. And with predators there was pressure for increased specialisation for movement, ingestion and excretion, for more efficient respiration and for reproduction. And predation also produced pressure for more motility, for senses like sight and smell and maybe hearing and as the organisms became more complex so they needed nervous systems to coordinate their activities and process and respond to the stimuli their senses were receiving from their environment and some would have evolved defensive armour such as scales and spikes and hard shells and internal structures like cartilage and bone to give their bodies shape and form and to make their swimming apparatus stiffer and more powerful.

But what they never managed to do was find a different way to produce all the different specialist cells by a different method to that used by their single-celled ancestors, so every cell in their body had the full genome whether they needed it or not, and more often than not, they didn't need most of it. A bone cell doesn't need to do what a nerve cell does, and a nerve cell doesn't need to do what a muscle cell does, and neither muscle nor nerve cells need to make bone, and what else needs to make elbow skin other than an elbow skin cell, except perhaps a scrotum skin cell? Yet they all have the genes for doing everything any one cell needs to do.

So, cue creationism's intelligent [sic] designer who has been designing and modifying all these different clumps of specialised cells but who, for some reason, seems incapable of recognising that its designs are heading for disaster unless it can think up a way to make sure each specialised cell has only the genes it needs. For reasons which no creationist apologist has ever managed to explain, their putative designer always behaves as though it can't undo a bad design and start again but is compelled to try to make the best of what it has muddled through with so far. In every way, creationism’s 'intelligent [sic] designer' behaves just like a mindless process operating without a plan, handicapped by acute amnesia, and constantly surprising itself with a new problem it designed just yesterday.

Just like the eccentric British designer and cartoonist, William Heath Robinson, no solution to a problem can be too complex even if it creates a new problem for which another overly complex solution has to be found. Unlikely objects, designed for a completely different purpose, will be pressed into service; a stepladder will be balanced precariously on top of a piano and an umbrella will be used to push a button when prodded by a sink plunger swinging on a length of knotted string. A labour-saving device for peeling potatoes will take half a dozen, intense and serious-looking men to operate it and peeling the potatoes will take considerably longer than had each man been given a potato peeler and left to get on with it. Eggs will be fried in a frying pan held over a candle lit by a match rubbed against a matchbox which swings into action when released by a lever when the scuttle-full of coal, or the boulder suspended on knotted string, lands on it.
Every hot-air ballon will have had several leaks mended with patches in a different fabric as will every set of bellows used to blow out the candle at the right time or make the fire burn up when needed to make the hot air balloon rise, which will be held down by a coal-scuttle full of coal until a man with nothing else to do, cuts the string with a pair of scissors when prodded in the back by an umbrella operated by a wheel with broken spokes joined together with sticks tied on with more string or held together with bent nails.

And the whole 'irreducibly complex', 'intelligently designed' machine would fail if just one component was taken away or a piece of knotted string broke.
So, what did creationism's intelligent designer produce to solve the problem of too many genes for the specialised cells? It produced the overly complex solution of epigenetics of course! There was no going back and starting again for our intrepid, muddle through, mend and make do, near-enough-is-good-enough utilitarian designer. Going back and starting again would have been far too simple.

So complex is this system, that a team of researchers has only just worked out how cells pass on their epigenetic settings to their daughter cells.

Their findings are the subject of a paper in Nature and a news release from the University of Hong Kong:

Figure 2.The cryo-EM structure of the yeast replisome in complex with FACT and parental histones (A) and its atomic model (B).
Modified from Li et al, Nature (2004)
Figure 2. The cryo-EM structure of the yeast replisome in complex with FACT and parental histones (A) and its atomic model (B).
Modified from Li et al, Nature (2004)
A research team led by Professor Yuanliang ZHAI at the School of Biological Sciences, The University of Hong Kong (HKU) collaborating with Professor Ning GAO and Professor Qing LI from Peking University (PKU), as well as Professor Bik-Kwoon TYE from Cornell University, has recently made a significant breakthrough in understanding how the DNA copying machine helps pass on epigenetic information to maintain gene traits at each cell division. Understanding how this coupled mechanism could lead to new treatments for cancer and other epigenetic diseases by targeting specific changes in gene activity. Their findings have recently been published in Nature.

Background of the Research

Our bodies are composed of many differentiated cell types. Genetic information is stored within our DNA which serves as a blueprint guiding the functions and development of our cells. However, not all parts of our DNA are active at all times. In fact, every cell type in our body contains the same DNA, but only specific portions are active, leading to distinct cellular functions. For example, identical twins share nearly identical genetic material but exhibit variations in physical characteristics, behaviours and disease susceptibility due to the influence of epigenetics. Epigenetics functions as a set of molecular switches that can turn genes on or off without altering the DNA sequence. These switches are influenced by various environmental factors, such as nutrition, stress, lifestyle, and environmental exposures.

In our cells, DNA is organised into chromatin. The nucleosome forms a fundamental repeating unit of chromatin. Each nucleosome consists of approximately 147 base pairs of DNA wrapped around a histone octamer which is composed of two H2A-H2B dimers and one H3-H4 tetramer. During DNA replication, parental nucleosomes carrying the epigenetic tags, also known as histone modifications, are dismantled and recycled, ensuring the accurate transfer of epigenetic information to new cells during cell division. Errors in this process can alter the epigenetic landscape, gene expression and cell identity, with potential implications for cancer and ageing. Despite extensive research, the molecular mechanism by which epigenetic information is passed down through the DNA copying machine, called the replisome, remains unclear. This knowledge gap is primarily due to the absence of detailed structures that capture the replisome in action when transferring parental histones with epigenetic tags. Studying the process is challenging because of the fast-paced nature of chromatin replication, as it involves rapid disruption and restoration of nucleosomes to keep up with the swift DNA synthesis.

In previous studies, the research team made significant progress in understanding the DNA copying mechanism, including determining the structures of various replication complexes. These findings laid a solid foundation for the current research on the dynamic process of chromatin duplication.

Summary of Research Findings

This time, the team achieved another breakthrough by successfully capturing a key snapshot of parental histone transfer at the replication fork. They purified endogenous replisome complexes from early-S-phase yeast cells on a large scale and utilised cryo-electron microscopy (cryo-EM) for visualisation.

They found that a chaperone complex FACT (consisting of Spt16 and Pob3) interacts with parental histones at the front of the replisome during the replication process. Notably, they observed that Spt16, a component of FACT, captures the histones that have been completely stripped off the duplex DNA from the parental nucleosome. The evicted histones are preserved as a hexamer, with one H2A-H2B dimer missing. Another protein that involved in DNA replication, Mcm2, takes the place of the missing H2A-H2B dimer on the vacant site of the parental histones, placing the FACT-histone complex onto the front bumper of the replisome engine, called Tof1. This strategic positioning of histone hexamer on Tof1 by Mcm2 facilitates the subsequent transfer of parental histones to the newly synthesised DNA strands. These findings provide crucial insights into the mechanism that regulates parental histone recycling by the replisome to ensure the faithful propagation of epigenetic information at each cell division.

This study, led by Professor Zhai, involved a collaborative effort that spanned nearly eight years, starting at HKUST and concluding at HKU. He expressed his excitement about the findings, ‘It only took us less than four months from submission to Nature magazine to the acceptance of our manuscript. The results are incredibly beautiful. Our cryo-EM structures offer the first visual glimpse into how the DNA copying machine and FACT collaborate to transfer parental histone at the replication fork during DNA replication. This knowledge is crucial for elucidating how epigenetic information is faithfully maintained and passed on to subsequent generations. But, there is still much to learn. As we venture into uncharted territory, each new development in this field will represent a big step forward for the study of epigenetic inheritance.’

The implications of this research extend beyond understanding epigenetic inheritance. Scientists can now explore gene expression regulation, development, and disease with greater depth. Moreover, this breakthrough opens up possibilities for targeted therapeutic interventions and innovative strategies to modulate epigenetic modifications for cancer treatment. As the scientific community delves deeper into the world of epigenetics, this study represents a major step towards unravelling the complexities of replication-coupled histone recycling.

About the Research Team

Apart from Professor Yuanliang Zhai’s lab, the research team also includes Professor Xiang David Li from Department of Chemistry of HKU, Professor Yang Liu and Professor Keda Zhou from School of Biomedical Sciences of HKU, Professor Shangyu Dang from Division of Life Science of HKUST, and others. Learn more about Professor Yuanliang Zhai’s work and his research team: https://www.scifac.hku.hk/people/zhai-yuanliang or https://zhai95.wixsite.com/mysite-1

Co-authors include Mr Yuan Gao, Mr Jian Li, Dr Zhichun Xu from School of Biological Sciences (SBS) of HKU; Dr Ningning Li, Ms Yujie Zhang, Dr Jianxun Feng from School of Life Sciences of PKU, Dr Daqi Yu and Dr Jianwei Lin from Department of Chemistry of HKU, and Dr Yingyi ZHANG from Biological Cryo- EM Center of HKUST.

The journal paper can be accessed here: https://www.nature.com/articles/s41586-024-07152-2

Abstract

In eukaryotes, DNA compacts into chromatin through nucleosomes1,2. Replication of the eukaryotic genome must be coupled to the transmission of the epigenome encoded in the chromatin3,4. Here we report cryo-electron microscopy structures of yeast (Saccharomyces cerevisiae) replisomes associated with the FACT (facilitates chromatin transactions) complex (comprising Spt16 and Pob3) and an evicted histone hexamer. In these structures, FACT is positioned at the front end of the replisome by engaging with the parental DNA duplex to capture the histones through the middle domain and the acidic carboxyl-terminal domain of Spt16. The H2A–H2B dimer chaperoned by the carboxyl-terminal domain of Spt16 is stably tethered to the H3–H4 tetramer, while the vacant H2A–H2B site is occupied by the histone-binding domain of Mcm2. The Mcm2 histone-binding domain wraps around the DNA-binding surface of one H3–H4 dimer and extends across the tetramerization interface of the H3–H4 tetramer to the binding site of Spt16 middle domain before becoming disordered. This arrangement leaves the remaining DNA-binding surface of the other H3–H4 dimer exposed to additional interactions for further processing. The Mcm2 histone-binding domain and its downstream linker region are nested on top of Tof1, relocating the parental histones to the replisome front for transfer to the newly synthesized lagging-strand DNA. Our findings offer crucial structural insights into the mechanism of replication-coupled histone recycling for maintaining epigenetic inheritance.

This Heath-Robinson solution to a problem which no intelligent designer would design in the first place, is repeated in every one of your 17 trillion cells and in every cell of every multicellular organism on the planet. A hugely wasteful and error-prone, needlessly complex system of which any intelligent designer would be ashamed, but which creationist frauds fool their ignorant dupes into believing is evidence of intelligence. In reality of course, it's evidence of exactly the opposite.

It's not even humorous and entertaining like William Heath-Robinson's ridiculously complicated, irreducibly complex, machines.

Saturday 9 March 2024

Creationism in Crisis - How Genomic Imprinting Evolved - Unintelligently


Revealing the evolutionary origin of genomic imprinting 
Caenorhabditis elegans

Genomic imprinting is the process by which genes are suppressed by epigenetic settings that differ depending on whether the genes come from the father or the mother in a sexually-reproducing species.

This is an example of the sort of Heath Robinson machine which a natural, mindless evolutionary process can and does produce and which distinguishes evolved systems from intelligently designed processes. It comes from the fact that multicellular organism uses the same method to replicate their cells as their single-celled ancestors used, yet only need a small selection of the genes depending on how specialised the particular cells are.

But the reason for genomic imprinting involves something even more embarrassing to any creationists who understand it - it probably evolved out of an arms race not between the organism and a foreign parasite but between the organism and one of its genes that had gone rogue and turned into a 'jumping' gene or 'selfish genetic element':
What exactly are 'selfish genetic elements' and what do they do? Selfish genetic elements are DNA sequences that have evolved to enhance their own transmission to the next generation, often at the expense of the organism's overall fitness. These elements can manipulate various cellular and reproductive processes to increase their own propagation within a population, sometimes even if it is detrimental to the host organism.

One well-known example of selfish genetic elements is transposable elements, also known as jumping genes. These DNA sequences have the ability to move or copy themselves within the genome, potentially disrupting genes or regulatory sequences in the process. While transposable elements can sometimes contribute to genetic variation and evolution, they can also cause harmful mutations or genomic instability.

Another example of selfish genetic elements is meiotic drive elements. These elements bias their own transmission during meiosis, the process by which gametes (sperm and eggs) are formed. Meiotic drive can result in the preferential transmission of one allele (variant of a gene) over another, leading to distortions in genetic inheritance patterns within a population.

Selfish genetic elements can have significant implications for evolutionary processes, population genetics, and genome stability. They can influence patterns of genetic diversity, contribute to speciation, and even drive the evolution of complex biological systems. However, they can also pose challenges for organisms by causing genetic disorders or reducing overall reproductive success.
In the case of the nematode, Caenorhabditis elegans, this arms race has produced a truly bizarre result, and something only an unintelligent, mindless designer, or a malevolent designer, could come up with, known as toxic ascaris, or TAs:

Thursday 29 February 2024

Creationism in Crisis - Evolution By Loss Of Complexity - How A Mutation Cost Our Ancestors Their Tails


Change in Genetic Code May Explain How Human Ancestors Lost Tails | NYU Langone News

In that distant, pre-'Creation Week' history of Life On Earth, 25 million years before creationists think Earth was created out of nothing, and all living things on it were magicked into existence without ancestors, a 'jumping gene' inserted a short length of DNA termed AluY, into the gene which controls tail length in monkeys, and the resulting tailless monkeys went on to diversify into the apes - gibbons, siamangs, orangutans, gorillas, chimpanzees, bonobos, and the hominins which were to evolve into the Australopithecines and the Homo genus, including Homo sapiens, all of which still possess that short insertion in the TBXT gene, which otherwise is identical to one of the gene which grow the tail of the simians.

As an example of design, it is one of the least intelligent, since, instead of removing all the genes required to grow a tail, the 'designer' simply broke an essential gene and left all the others to do nothing apart from having to be replicated in every cell in every ape that ever lived, as an example of the massive waste and unnecessary complexity that characterises an evolved process and gives the lie to any notion of any intelligence being involved.

By inserting the AluY snippet into a mouse BBXT gene the researchers found a variety of tail effects, including mice born without tails. They also showed that there was a small increase in the incidence on neural tube defects (spina bifida) in mice.

Quite why tailless would have been selected for during the evolution of these ancestors of the modern apes is a matter for speculation; maybe a tail was becoming an encumbrance for a brachiating mode of locomotion as opposed to running along the top of branches and jumping from branch to branch, which the smaller monkeys used, where a tail was an important balance organ. For a heavier ape hanging beneath the branches by its arms, there would have been less need for a balance organ and a tail would have been liable to damage and infection.

How this was discovered by a team led by researchers at New York University Grossman School of Medicine, is the subject of an open access paper in Nature and a NYU Langone Health news release:

Sunday 25 February 2024

Creationism in Crisis - What Made Snakes Able To Evolve So Quickly 100 Million Years Before 'Creation Week'?


A false boa, Pseudoboa nigra, eating a lava lizard, Tropidurus hispidus.
Image credit: Ivan Prates, University of Michigan.
Snakes do it faster, better: How a group of scaly, legless lizards hit the evolutionary jackpot | University of Michigan News

100 million years ago the ancestral snake was just another lizard but then suddenly (on the evolutionary timescale) something happened that enables snakes to diversify into thousands of different species while the other lizards plodded along slowly, diversifying at a much slower rate than the snakes.

But what was it that allowed this sudden radiation into so many species and why did it give the snakes the edge over their cousins the lizards? It was an event that an international team led by University of Michigan biologists have called an evolutionary singularity, in an analogy with whatever was at the start of the Big Bang.

The team has estimated that snakes have evolved up to three times faster than lizard, an ability that was facilitated by three things - an elongated body and loss of legs; enhanced sensory detection enabling them to find and track prey, and a flexible skull that enabled them to swallow large prey.

In an attempt to understand this, the team assembled a large database of lizard and snake diets from examining the stomach contents of tens of thousands of museum specimens. They also sequenced the partial genomes of almost 1,000 species from which they were able to construct the evolutionary trees of lizards and snakes.

Their findings are the subject of a paper in Science and of a news release from the University of Michigan:

Friday 23 February 2024

Creationism in Crisis - 250 Million Years of Butterfly And Moth Evolution


Butterfly and moth genomes mostly unchanged despite 250 million years of evolution

It'll no doubt come as a surprise to those creationists who believe Earth was created from nothing by magic just about 10,000 years ago to learn that the butterflies and moths have been evolving for 250 million years.

It'll maybe come as a bigger surprise to those creationists who have been fooled into believing that the Theory of Evolution is being discarded by mainstream biologists in favour of their childish fairy tale of magic and supernatural spirits, that yet another group of mainstream biologists regard it as the foundation of modern biology, and are participating in the Darwin Tree of Life Project, which aims to sequence the genome of 70,000 eukaryote species from Britain and Ireland, to learn their evolutionary relationships.

This project also contributes to the much larger, Earth BioGenome Project.

One of the teams taking part in this project, based at the Wellcome Sanger Institute and the University of Edinburgh, Scotland, has just completed the sequencing of 200 high-quality genome of the Lepidoptera order of insects (moths and butterflies) and discovered some interesting facts about the evolution of the order, including that there are some elements in the genomes, which they term 'Merian elements' after the 17th century entomologist Maria Sibylla Merian, which have remained relatively stable over the 250 million years the order has been evolving.

The research is published in the journal Nature Ecology & Evolution and is described in a Welcome Sanger Institute news release:

Wednesday 21 February 2024

Creationism in Crisis - 275 Million New Human Genetic Variants in USA Alone - Why So Many?


275 Million New Genetic Variants Identified in NIH Precision Medicine Data | All of Us Research Program | NIH

Researchers at the American NIH have identified 275 million previously unknown genetic variants in samples from 250,000 representative American adults who participated in their All of Us research program. Half the participants were of non-European ancestry. Nearly 4 million of these newly discovered variants are from areas of the genome tied to known disease risks.

Let's consider that from the point of view of someone who believes in intelligent [sic] design:

Why on Earth would an intelligent designer design so many variations on the same theme? An intelligent designer, especially one endowed with the foresight of omniscience and unlimited powers and who is omnibenevolent and perfect, would design the perfect solution to every problem, and stick with it, not design lots of different solutions to the same problem. And every iteration through the cycle of replication would produce an exact copy of that perfect design, so there is no logical way all those variations could be the result of random mutations which all happened to be equally good at whatever they did, so there was no element of selection involved.

Quite simply, lots of variations on the same theme are evidence not of intelligent design, but of utilitarian, mindless 'design' working without a plan and with no conception of the ideal or perfection. Variation is kept because it works; maybe not exactly as well as other alleles, but well enough for the carrier to survive and reproduce. Even if the differences are too small to play a significant part in evolution by natural selection, unless they are serious deleterious, genetic drift can account for them being a significant part of the species genome.

Thursday 25 January 2024

Unintelligent Design - How Ovulation Goes Wrong Because It Wasn't Intelligently Designed


Gene expression atlas captures where ovulation can go awry | Cornell Chronicle

Back in the late 1960s and early 1970, in what seems like a different lifetime now, I was a senior research assistant in the Oxford University/MRC Neuroendocrinology Research Unit, researching the hormonal control of ovulation in guinea pigs. Two of our tools were radioimmunoassays I had adapted for measuring extremely low levels of a hormone in guinea pig anterior pituitary glands known as luteinizing hormone (LH), and another similar assay for measuring the level of the steroid progesterone in guinea pig blood.

Sadly, having worked for close on two years towards producing a research paper with hundreds of assay results, thousands of microscope slides, hundreds of electron micrographs and a freezer full of samples waiting to be assayed, the government pulled the rug from under our feet by withdrawing our research funding, and I was made redundant, so my work was never published. Disillusioned and with a young family to support, I left research and perused a career in the NHS Ambulance Service instead - but that's a different story, and not relevant to the subject of this blogpost, which illustrates how much science has progressed in the last 50-60 years.

Researchers are no longer researching the hormonal control of ovulation but the fine details of the genetic control of the process of ovulation at the cell level, and what they've found is that the process is far from intelligently designed by anything resembling a perfect, omniscient, omnipotent designer. It is a process that is so complex that it can, and does, go wrong. An intelligent designer who didn't want random women to be unable to shed viable eggs, could have designed a less complicated process, but you can depend on creationism's putative intelligent[sic] designer to never do something simple when there is a far more complicated and wasteful way to achieve the same result.

The research, published a few days ago in Proceedings of the National Academy of Sciences, was led by Iwijn De Vlaminck, associate professor of biomedical engineering in Cornell Engineering, and Yi Athena Ren, assistant professor of animal science in the College of Agriculture and Life Sciences. The paper’s lead author is Madhav Mantri, Ph.D., now a postdoctoral researcher at Stanford University.

The team used a form of RNA tagging to map the gene expressions that occur during ovarian follicle maturation and ovulation in mice.

This spatial transcriptomics map depicts the cell types of a mouse ovary undergoing hormone-induced ovulation
The research is explained in a Cornell University Press release:

Tuesday 23 January 2024

Creationism in Crisis - Hagfish Genome Shows How Genetic Information Arises Without Magic


Hagfish, until now the only vertebrate that hadn't had its genome sequenced.
Image credit: Juan Pascual Anaya
January: Hagfish | News and features | University of Bristol

One of the mysteries of vertebrate evolution is from where did all the genetic information come, but a recently completed sequencing of the hagfish genome has solved that mystery.

Creationists traditionally parrot the claim that information can't increase without magic because of some half-baked notion that it is like energy, so is subject to the third law of thermodynamics, which states that energy can neither be created nor destroyed.

But it only takes a moment's thought to realise that every time a cell replicates, the amount of genetic information normally doubles, without the help of magic, because it is simply a controlled organisation of existing matter. Similarly, if the genome gets doubled, or lengths of DNA get accidentally duplicated, this is simply the incorporation of existing matter into the resulting genome. No new matter is created yet the amount of information in the genome increases.

The other source of creationist confusion stems from them not understanding the difference between information and meaning. Meaning is information in the context of the environment. I'll illustrate this with a simple analogy:

Monday 22 January 2024

Creationism in Crisis - No Doubt That Lycophytes Evolved, The Question is How?


Marsh Clubmoss, Lycopodiella inundata, with sundew, Drosera rotundifolia.
Credit: Christian Fischer via Wikipedia (CC BY-SA 3.0)
A Window into Plant Evolution: The Unusual Genetic Journey of Lycophytes - Boyce Thompson Institute

Creationists who are desperate to believe they are winning the argument against evolution in the science community and converting biologists to believing in magic and a supernatural magician or two, will not want to read about the discovery by an international team of researchers concerning the evolution of a small group of plants known as lycophytes.

First, a brief introduction to lycophytes, courtesy of ChatGPT 3.5:

Friday 19 January 2024

Creationism in Crisis - How Mammoths Evolved During The 700,000 Years They Lived in Siberia Prior To 'Creation Week'


Woolly mammoths evolved smaller ears and woolier coats over the 700,000 years that they roamed the Siberian steppes | ScienceDaily
What could the authors of Gensis know about the fauna of Alaska when they thought Earth was a small, flat planet centered on the Canaanite hill country? They didn't even know much about the history of their close neighbours in Egypt and Mesopotamia, let alone the remote areas of Asia.

So, they were oblivious of the fact that there were woolly mammoths there and had been for some 700,000 years. This is why there are no mammoths in the Bible, nor their relatives, Asian and African elephants, for that matter. To Bronze Age Canaanite hill farmers these animals, and where they lived and the people who lived alongside them, simply didn't exist. So, they concocted tales which to us are ludicrously unrealistic, such as tales about a magic man magically making stuff from nothing with magic words, about 5,000 years before they were making the tales up, followed by an equally ludicrous tale of a genocidal flood about two thousand years later with two of all known species surviving for a year, sealed in a wooden box with no ventilation. They thought breath was something to do with 'life' and didn't know about oxygen or why the animals would have needed it, so didn't see anything wrong with a tale about hundreds of animals and 8 humans being sealed in a floating wooden box for a year.

But now, thanks to science, we know better and can see what they got wrong, and why they could not have privy to real scientific knowledge, or knowledge about real geography and history.

One of the things they got spectacularly wrong was the childish belief that all the animals around them and the planet they lived on, were all created in a few days and none of the animals had ancestors, because they didn't even know their domestic animals like goats, sheep, cattle, doves and pigs had all been selectively bred from wild ancestors.

And of course, they couldn't even have guessed that there were mammoths in Siberia which had been evolving there for 700,000 years until going extinct about 9,000 years earlier.

But a team of Swedish and Russian scientists, led by David Díez-del-Molino of the Centre for Palaeogenetics and Department of Zoology, Stockholm University, Stockholm, Sweden, has now examined the genomes of 23 woolly mammoths, including that of the oldest known remains from 700,000 years ago, and compared them to 28 genomes of modern Asian and African elephants, to gain an understanding of the evolution of this species of mammoth. Their findings are published in an open access paper in Current Biology and explained in a Cell press release (taken here from the copy in Science Daily):

Tuesday 16 January 2024

Creationism in Crisis - How Human Skin Colour Evolved in Africa Long Before 'Creation Week'


1996 map of the major ethnolinguistic groups of Africa, by the Library of Congress Geography and Map Division (substantially based on G.P. Murdock, Africa, its peoples and their cultural history, 1959).

Source: Wikipedia
A molecular look at the mechanisms behind pigmentation variation | Penn Today

While creationism's god was creating a small flat Earth with a dome over it to keep the water above the sky out, the people of Africa were evolving and diversifying according to local conditions and gene flow between populations that has resulted in a whole range of skin tones and a genetic variance that is greater in a small population of Africans than in the whole of the extra-African population of the world, reflecting the genetic bottleneck of a small band of migrants moving out of Africa into Eurasia.

Africans had of course had several hundred thousand years to diversify prior to the mythical 'Creation Week' when creationists believe a magic man made of nothing came from nowhere and magicked a universe out of nothing with some magic words, spoken in a language that no-one understood because there was no-one to understand it.

Saturday 13 January 2024

Creationism in Crisis - Scientists Have Worked Out How The Vertebrate Head Evolved - It wasn't Created By Magic


Figure 3
Dynamics of head mesoderm cell clusters during individualization of the head muscles See also Figures S4 and S5.

(A–L) 3D reconstructions and laser scanning images of stage 24 (A–D), 25 (E–H), and 26 (I–L) lamprey embryos. The area enclosed by the white dotted line in (K) indicates velum mesoderm. Pink, mesoderm; light blue, dorsal inner mandibular mesoderm; green, ventral mandibular arch mesoderm; yellow, cavity in the mandibular mesoderm. Images show sagittal views.

(M) Comparison of rosettes and head mesoderm cell clusters in lamprey and amphioxus embryos. Right blue, somite rosette; blue, distinct head mesodermal cell clusters. DIMM, dorsal inner mandibular mesoderm; EOM, extraocular muscle; GS, gill slit; GV, ganglion trigeminal; HyAM, hyoid arch mesoderm; HyM, hyoid mesoderm; LLM, lower lip mesoderm; LPM, lateral plate mesoderm; MM, mandibular mesoderm; NHP, nasohypophyseal plate; Op, optic vesicle; OPM, oropharyngeal membrane; OV, otic vesicle; PHM, pharyngeal mesoderm; PMM, premandibular mesoderm; PP, pharyngeal pouch; S, somite; ULM, upper lip mesoderm; Vel, velum; VMAM, ventral mandibular arch mesoderm.

Study on Lamprey Embryos Sheds Light on the Evolutionary Origin of Vertebrate Head | UNIVERSITY OF FUKUI

Despite the almost daily claims in the social media by creationist dupes that mainstream biologists are abandoning the Theory of Evolution (TOE) in favour of creationism because it doesn't explain the facts, there is no sign whatsoever in the scientific literature of that happening. No serious biologist has ever published a peer-reviewed paper proposing that magic by a supernatural designer better explains the facts than the TOE.

Instead, just about every paper dealing with origins and development of species and their relationship to other species, has evolution firmly and inextricably embedded within it and the conclusions only ever make sense as the result of an evolutionary process. The belief that the TOE has been or is in the process of being, overthrown by creationism is a lie promulgated by the Deception Institute to claim success for the 'Wedge Strategy', which has been a monumental failure as fewer Americans now believe in creationism than did at the start of the campaign.

The paper recently published with open access in iScience illustrates just have firmly embedded the TOE is in biology. It concerns the early development of the vertebrate head, which has been a matter of conjecture in biology:
Some believe that the vertebrate head has developed as a result of modification of the segmental elements of the trunk, such as the vertebrae and somites. On the other hand, others believe that the vertebrate head has evolved as a new, unsegment body part, unrelated to other widely observed embryonic segments somites. Interestingly, previous studies on embryos have revealed the presence of some vestiges of somites in the head mesoderm (e.g., head cavities and somitomeres). However, homology between trunk somites and such head segments has been controversial.
Note the complete absence of any notion of magic creation in the controversy. The issue is over which tissues evolved into the beginnings of the vertebrate head.

The paper, by Japanese scientists led by Assistant Professor Takayuki Onai, of the Department of Anatomy, University of Fukui, School of Medical Sciences, Fukui, Japan, resolves that controversy by showing how the head of a lamprey embryo develops.

As the University of Fukui news release explains:

Friday 12 January 2024

Unintelligent Design - Neurodegenerative Diseases Such As MS & Alzheimer's Traced Back To Early North European Farmers - 24,000 Years Before 'Creation Week'


Life in Bronze Age Britain (artist's impression)
Ancient DNA reveals reason for high MS and Alzheimer's rates in Europe

Researchers have just completed a massive gene bank for ancient humans who lived in Eurasia up to 34,000 years ago (i.e., up to 24,000 years before creationist dogma says the universe and everything in it was magicked out of nothing by a god made of nothing who self-assembled out of nothing before there was time and space to self-assemble in.

The gene bank has enabled researchers to trace the historical and geographical spread of genes and diseases, producing four papers published in Nature. This article deals with just one of them; others will follow.

The results should disturb any creationists who has the courage to read about them because, not only did it all occur long before the mythical 'Creation Week' that is central to their superstition, but is shows that any designer either could not have been omniscient, or must have been malevolent, because it shows how the genes for Multiple Sclerosis (MS) arose in North Europe, probably as a side-effect of evolving genes to increase resistance to the diseases carried by domestic animals. An omniscient designer who deigned them should have been aware of what they would also cause, so either isn't omniscience and didn't know what its design would do, or created MS deliberately.

As the University of Cambridge News release explains:

Tuesday 2 January 2024

Creationism in Crisis - The Evolution of African Primates


Complex Evolutionary History With Extensive Ancestral Gene Flow in an African Primate Radiation | Molecular Biology and Evolution | Oxford Academic

Mustached guenon,
Cercopithecus cephus
De Brazza's guenon,
Cercopithecus neglectus
Stuhlmann's Blue monkey,
Cercopithecus mitis stuhlmanni,
Crowned Guenon
Cercopithecus pogonias

12 years ago, I wrote a blog post to explain why, because speciation is a process, not an event, we often don't even know it's happened until well after the event when we can see we have a new population with distinct characteristics. I illustrated this with a hypothetical example of monkeys in a forest being split into isolated populations by climate change.

In it I said:
But, gradually, due to climate change or continental drift, or maybe a change in ocean currents, the forest begins to get drier and turn into grasslands, with trees surviving only close to rivers. In other words, the monkey population is broken up into isolated groups which can no longer interbreed because they simply don't come into contact any more. Each group will be free to evolve according to the local conditions in its woodland. Eventually, maybe after a few hundred thousand years, maybe a million or two, these groups may evolve to the point where they not only look different to each other but may not be able to interbreed even if they do meet up.

So where and what was the 'speciation event'? At what point in the process could an observer say, "Hey! I've just seen speciation occur! It happened when...". In fact, we only know that speciation has occurred retrospectively because, according to our rules of taxonomy, failure to interbreed means they are now different species. Maybe if we had been able to examine them a hundred thousand years ago we might have found that they could still interbreed. Maybe we would have found an incompletely speciated 'ring species'.

There was no sudden emergence of a new species; no sudden branching of the 'tree of life'; no mutation which brought a new species into being and no 'macro-evolution' event. There was no event which creation pseudo-scientists proclaim to be impossible and which they claim has never been seen. All there was was a slow accumulation of difference, directed by natural selection with each group doing nothing but struggling to survive and reproduce with the ones which left the most descendant contributing the most genes to the gene-pool.

Now, take the same scenario, only this time the climate changed again after a few tens of thousands of years and the isolated scattered groups could once again mix freely. But this time maybe they had not diverged sufficiently to prevent interbreeding, or maybe one group now had a significant advantage over the others. In these cases, the group with the genes which gave them greater success would come to dominate and possibly replace the others.

Is this speciation? Is this the point at which we can say a new species arose and the 'archaic' form went extinct? Or is this merely evolution of the entire species? Were those groups isolated for a few thousand years new twigs on the monkey branch of the tree of life, or were they merely groups of individuals with the potential to become new species, but which never quite made it? Certainly, the day they came back into contact, nothing happened to their genes. It was not a change on their part which caused them to re-establish contact. It was the environment which changed.

Rosa Rubicondior: Evolution - Making a Monkey (4 July 2012)
And now, as though to confirm my hypothetical example was close to the real thing, a team of archaeologists and geneticists, led by Axel Jens and Katerina Guschanski of the Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden, have carried out a whole genome analysis of 22 species of West African guenons (monkey of the Cercopithecini tribe - one of the world's largest primate radiations) and shown how the different species diverged with frequent gene flow across species boundaries and hybridization events playing a part in the process of radiation and diversification.

The team have published their findings, open access, in the journal Molecular Biology and Evolution. In it they say:

Friday 29 December 2023

Creationism in Crisis - How New Genetic Information Arises Naturally


The 'Christmas tree (Norwegian spruce) Picea abies
Seven times more DNA than a human.
It is a basic axiom of creationism that no new genetic information can arise in a species genome without the assistance of a magic designer. This is based on some half-baked interpretation of 'Shannon Information Theory' and misrepresentation of the second law of thermodynamics in which 'information' is confused with energy and a species genome with a closed system.

Try to get a creationist to explain the science behind that claim and you're likely to get nothing but rehearsed parrot squawks made in response to trigger words, if they don't run away hurling abuse and passive aggressive threats over their shoulder, or quickly change the subject. There will be no understanding of either information theory or thermodynamics.

The natural world is full of examples of how gene or even whole genome duplication creates redundant DNA and copies of genes than can mutate and be selected by natural selection to create new meaning in the genetic information. The Christmas tree, or Norwegian spruce, Picea abies, has about 29,000 functional genes (marginally more than a human) yet it has a genome seven times larger than the human genome, all packed into 12 chromosomes. The reason for this, according to a research team from Umeå universitet, Sweden, is because the mechanism for correcting duplication errors broke millions of years ago, so these duplications have been accumulating in the Picea abies genome ever since.

Creationists seem incapable of understanding the difference between information and the meaning in that information or how meaning is given by the environment. For example, a mutation which gave Streptococcus aureus resistance to the antibiotic, methicillin, would have had no meaning before medical science invented methicillin; now the same information makes MRSA an intractable condition and a highly successful pathogen. The point being that new meaning can arise without any change in the genome simply by a change in the environment, so evolution is not always dependent on change in genetic information.

Sunday 17 December 2023

Creationism in Crisis - The Woolly Dogs Of The American Coast Salish People Predate 'Creation Week'


Researchers, Coast Salish People Analyze 160-Year-Old Indigenous Dog Pelt in the Smithsonian’s Collection | Smithsonian Institution
The reconstructed woolly dog shown at scale with Arctic dogs and spitz breeds in the background to compare scale and appearance; the portrayal does not imply a genetic relationship.
Credit: Karen Carr.
During that long period of Earth's 'pre-Creation Week' history, before anyone told the people of Siberia that they should wait to be created then wiped out in a genocidal flood before forgetting all about it and only then going to live elsewhere, they migrated to North America, taking their domestic dogs with them.

This is the sort of nonsense that creationism requires you to believe in order to reconcile the scientific evidence with the creation myths of a bunch of Bronze Age Canaanite farmers who thought Earth was small, flat and had a dome over it to keep the water above the sky out. Obviously, these people had almost certainly never heard of Siberia or North America or realised that there were other people living there and were as ignorant of most of Earth's long history as they were of cosmology, biology and geology.

One of the things the Bronze Age Canaanites would never have guessed was that some of the domestic dogs the Siberians took with them had genes for a dense wooly fur that could be woven into blankets and other fabrics, but now a team of researchers from the Smithsonian’s National Museum of Natural History have carried out a detailed DNA analysis of the pelt of the last known example of this breed of dog (a dog known as Mutton). Mutton died in 1859 and his pelt was sent to the Smithsonian Institute where it remained until it was rediscovered in the early 2000's.

The analysis has shown that the line diverged from the other dogs about 5,000 years ago (i.e., before creationist superstition says all life on Earth was exterminated in a genocidal flood when their 'all-loving' god flew into a rage because its creation wasn't working as intended).

They have shown that its closes genetic relationship is with the pre-colonial dogs from Newfoundland and British Columbia. The Indigenous Coast Salish communities in the Pacific Northwest (in Washington state and British Columbia) for millennia held these wooly dogs in high esteem, regarding them almost as family members and often keeping them in pens or on islands to prevent them interbreeding with other dogs, to maintain the quality of their wool. This isolation prevented the ingress of genes from other dogs and even from the dogs later colonists brought with them. The genes recovered from Mutton's pelt show that 85% of his genes were from pre-colonial dogs.

The Smithsonian researchers have, with the assistance of Coast Salish Elders, Knowledge Keepers and Master Weavers, now traced the place of the woolly dogs in Coastal Salish culture and the reasons for its decline. Their findings are published in Science and tell a sorry tale of colonial destruction of a people and their culture. Instead of, as has been suggested, the arrival of machinery and woven blankets made the wooly dogs expendable, the truth is that, due to disease and colonial policies of cultural genocide, displacement and forced assimilation, it likely became increasingly difficult or forbidden for Coast Salish communities to maintain their woolly dogs and a 1000 years or more of careful selective breeding was wiped out within a couple of generations.

Friday 15 December 2023

Creationism in Crisis - How Early Humans Caused A Decline In Megafauna Numbers Thousands Of Years Before 'Creation Week'


Peré Davids deer, Elaphurus davidianus. Now extinct in the wild.
People, not the climate, caused the decline of the giant mammals

About 90,000 years before creationist superstition says the Universe was created, humans, who had been evolving in Africa, began to expand their range into Eurasia and eventually into Austronesia and the Americas.

About 500,000 years later most large species show a sudden decline in their numbers, and now researchers led by Professor Jens-Christian Svenning, head of the Danish National Research Foundation's Center for Ecological Dynamics in a Novel Biosphere (ECONOVO) at Aarhus University, believe they have shown that this was due to human predation and habitat destruction.

They reached this conclusion from an analysis of the genomes of 139 species. This involved crunching the data from 3 billion or so data points to build evolutionary trees of the mutations in the genomes. The bigger the population, the more mutations there will be in the species genome, so this data shows the population changes over time.

Their work is published, open access, in Nature and is explained in a news release from Aarhus University:
For years, scientists have debated whether humans or the climate have caused the population of large mammals to decline dramatically over the past several thousand years. A new study from Aarhus University confirms that climate cannot be the explanation.

About 100,000 years ago, the first modern humans migrated out of Africa in large numbers. They were eminent at adapting to new habitats, and they settled in virtually every kind of landscape - from deserts to jungles to the icy taiga in the far north.

Part of the success was human's ability to hunt large animals. With clever hunting techniques and specially built weapons, they perfected the art of killing even the most dangerous mammals.

But unfortunately, the great success of our ancestors came at the expense of the other large mammals.

It is well-known that numerous large species went extinct during the time of the world-wide colonization by modern humans. Now, new research from Aarhus University reveals that those large mammals that survived, also experienced a dramatic decline.
The eastern gorilla is one of the mammals that have declined the most. Today it's only living in small areas in DR Congo.
Foto: Michalsloviak / Creative Commons
By studying the DNA of 139 living species of large mammals, the scientists have been able to show that abundances of almost all species fell dramatically about 50,000 years ago.

This is according to Jens-Christian Svenning, a professor and head of the Danish National Research Foundation's Center for Ecological Dynamics in a Novel Biosphere (ECONOVO) at Aarhus University, and the initiator of the study.

We’ve studied the evolution of large mammalian populations over the past 750,000 years. For the first 700,000 years, the populations were fairly stable, but 50,000 years ago the curve broke and populations fell dramatically and never recovered. For the past 800,000 years, the globe has fluctuated between ice ages and interglacial periods about every 100,000 years. If climate was the cause, we should see greater fluctuations when the climate changed prior to 50.000 years ago. But we don't. Humans are therefore the most likely explanation.

Professor Jens-Christian Svenning, Lead author
Center for Ecological Dynamics in a Novel Biosphere (ECONOVO)
Department of Biology
Aarhus University, Aarhus, Denmark.
Who killed the large mammals?

For decades, scientists have debated what is behind the extinction or rapid decline of large mammals over the past 50,000 years.

On one side are scientists who believe that rapid and severe fluctuations in the climate are the main explanation. For example, they believe that the woolly mammoth went extinct because the cold mammoth steppe largely disappeared.

On the opposite side are a group who believe that the prevalence of modern humans (Homo sapiens) is the explanation. They believe that our ancestors hunted the animals to such an extent that they either became completely extinct or were severely decimated.

So far, some of the most important evidence in the debate has been fossils from the past 50,000 years. They show that the strong, selective extinction of large animals in time and space roughly matches the spread of modern humans around the globe. Therefore, the extinction of animals can hardly be linked to climate. Nevertheless, the debate continues.

The new study presents brand new data that sheds new light on the debate. By looking at the DNA of 139 large living mammals – species that have survived for the past 50,000 years without becoming extinct – the researchers can show that the populations of these animals have also declined over the period. This development seems to be linked to the spread of humans and not climate change.
DNA contains the long-term history of the species

In the past 20 years, there has been a revolution within DNA sequencing. Mapping entire genomes has become both easy and inexpensive, and as a result the DNA of many species has now been mapped.

The mapped genomes of species all over the globe are freely accessible on the internet – and this is the data that the research group from Aarhus University has utilized, explains assistant professor Juraj Bergman, the lead researcher behind the new study.

We’ve collected data from 139 large living mammals and analysed the enormous amount of data. There are approximately 3 billion data points from each species, so it took a long time and a lot of computing power. DNA contains a lot of information about the past. Most people know the tree of life, which shows where the different species developed and what common ancestors they have. We’ve done the same with mutations in the DNA. By grouping the mutations and building a family tree, we can estimate the size of the population of a specific species over time.

The larger the population of an animal, the more mutations will occur. It’s really a question of simple mathematics. Take elephants, for example. Every time an elephant is conceived, there’s a chance that a number of mutations will occur, and it will pass these on to subsequent generations. More births means more mutations.

Assistant professor Juraj Bergman, First author
Center for Ecological Dynamics in a Novel Biosphere (ECONOVO)
Department of Biology
Aarhus University, Aarhus, Denmark.
The large mammals

The 139 large mammals examined in the study are all species that exist today. They include elephants, bears, kangaroos and antelopes, among others.

It is estimated that there are 6,399 species of mammals on the Earth, but the 139 extant megafauna were selected in this study to test how their populations changed over the past 40,000 to 50,000 years, when similar large animals went extinct.

The large mammals are also called megafauna – and are defined as animals weighing more than 44 kg when fully grown. Humans are therefore also considered megafauna. In the study, however, the researchers examined species weighing as little as 22 kg, so that all continents have been represented - except Antarctica.

Source: Journal of Mammalogy
Looking at the neutral parts of the DNA

However, the size of the elephant population is not the only thing that affects the number of mutations.

If the area in which elephants live suddenly dries up, the animals come under pressure – and this affects the composition of mutations. The same applies if two isolated groups of elephants suddenly meet and mix genes.

If not only the size of the population affects how many mutations occur, you would think that the results are rather uncertain. But this is not the case, explains Juraj Bergman.

Only 10 per cent of mammalian genomes consist of active genes. Great selection pressure from the environment or migration will primarily lead to mutations in the genes. The remaining 90 percent, on the other hand, are more neutral. We have therefore examined mutations in those parts of the genome that are least susceptible to the environment. These parts primarily indicate something about the size of the population over time.

Assistant professor Juraj Bergman
Peré Davids deer, shown in this picture, does not live in the wild anymore. The only animals left today is living in Zoos and animal parks.
Foto: Tim Felce / Creative Commons.
The woolly mammoth is an atypical case

Much of the debate about what caused the large animals to either become extinct or decline has centered around the woolly mammoth. But this is a bad example because the majority of the megafauna species that went were associated with temperate or tropical climates, as Jens-Christian Svenning explains.

The classic arguments for the climate as an explanatory model are based on the fact that the woolly mammoth and a number of other species associated with the so-called "mammoth steppe" disappeared when the ice melted and the habitat type disappeared. This is basically an unsatisfactory explanatory model, as the vast majority of the extinct megafauna species of the period did not live at all on the mammoth steppe. They lived in warm regions, such as temperate and tropical forests or savannahs. In our study, we also show a sharp decline during this period in populations of the many megafauna species that survived and come from all sorts of different regions and habitats.

It seems inconceivable that it is possible to come up with a climate model that explains how, across all continents and groups of large animals, there have been extinctions and continuous decline since about 50,000 years ago. And how this selective loss of megafauna is unique for the past 66 million years, despite huge climate change. Given the rich data we now have, it’s also hard to deny that instead it is because humans spread across the globe from Africa and subsequently grew in population.

Professor Jens-Christian Svenning
The final full stop in the debate has probably yet to be set, but Jens-Christian Svenning finds it difficult to see how the arguments for the climate as an explanation can continue.
The team’s findings are explained in detail in their open access paper in Nature:
Abstract

The worldwide extinction of megafauna during the Late Pleistocene and Early Holocene is evident from the fossil record, with dominant theories suggesting a climate, human or combined impact cause. Consequently, two disparate scenarios are possible for the surviving megafauna during this time period - they could have declined due to similar pressures, or increased in population size due to reductions in competition or other biotic pressures. We therefore infer population histories of 139 extant megafauna species using genomic data which reveal population declines in 91% of species throughout the Quaternary period, with larger species experiencing the strongest decreases. Declines become ubiquitous 32–76 kya across all landmasses, a pattern better explained by worldwide Homo sapiens expansion than by changes in climate. We estimate that, in consequence, total megafauna abundance, biomass, and energy turnover decreased by 92–95% over the past 50,000 years, implying major human-driven ecosystem restructuring at a global scale.

Introduction

The late-Quaternary extinction event1,2 is characterised by the selective extinction of large-bodied animals (megafauna) at a global scale. At the present date, only a small fraction of this prehistorically speciose group2,3,4,5 persists in rapidly diminishing communities, many of which face an immediate threat of extinction6,7. The causes of megafauna decline have been subject to long-standing debate, with fluctuations in paleoclimate and the spread of Homo sapiens emerging as the predominant explanatory factors3,5,8,9,10,11,12,13,14,15,16,17,18.

According to the climate-driven hypothesis of megafauna dynamics, a temporal dependency of population sizes on the glacial–interglacial cycle is expected. On the other hand, modern humans are expected to start influencing megafauna densities in recent times, mainly following the Last Interglacial period, corresponding to their worldwide expansion out of Africa19. To distinguish between these two scenarios, previous studies have focused on inferring past species distributions and extinction chronologies based on fossil data3,5,8,9,10,11,12,13,14,15,16,17,18. However, while the fossil record provides valuable insight into species’ histories, its fragmentary nature allows for only a limited temporal resolution of past population dynamics.

An alternative approach to fossil-based analyses is using genomic sequence data to reconstruct time-resolved trajectories of species population sizes20,21. Genomics-based methods commonly provide population size estimates for most of the Quaternary period (consisting of the Pleistocene period between 2.58 million and 11,700 years ago and the Holocene period between 11,700 years ago and present), thereby covering multiple glaciation cycles, as well as recent periods of human expansion22,23,24,25,26,27,28,29,30,31,32. Thus, genomics-based trajectories of population sizes should provide a more comprehensive framework for modelling the impact of climatic shifts and humans on megafauna dynamics compared to fossil-based approaches. However, a global analysis of genomics-based megafauna histories and their driving factors is currently lacking.

We focus our study on the Late Pleistocene and Early Holocene population trajectories of extant megafauna to address the following hypotheses. On the one hand, the surviving species may have experienced similar dynamics as the species undergoing extinction, showing widespread population declines linked to Homo sapiens or climate. Alternatively, surviving megafauna communities may have exhibited compensatory dynamics33, resulting in an increase in population size due to mechanisms such as competitive release. These scenarios have widely different ecological implications, whereby co-occurrence of population declines and extinctions would result in the exacerbation of ecosystem degradation, while compensatory dynamics would stabilise ecosystem functioning34. Thus, studying population dynamics of the surviving megafauna species during the Late Pleistocene and Early Holocene extinction period has major implications for our understanding of past and contemporary biosphere functioning4,35.

We curated a genomic dataset comprising 139 high-quality reference genome assemblies and short-read sequence data of extant terrestrial megafauna and implemented a bioinformatic pipeline to infer their Quaternary population histories. We studied the population dynamics of megafauna as a function of species’ ecology, geographical distribution, climate, and anthropogenic influence. We detect a global, severe decline in megafauna population sizes over the past 50,000 years and show that this observation is best explained by the influence of the worldwide expansion of H. sapiens rather than past climate dynamics. This lack of compensatory dynamics has had major impacts on ecosystem structure and functioning as reflected in a dramatic reduction of wild megafauna abundance, biomass and energy turnover.
Fig. 1: Effective population size (Ne) dynamics of 139 extant megafauna species.
a Each step line represents changes in Ne with respect to time for a single megafauna species, coloured by a gradient based on average adult mass. The dashed line represents the fit of the piecewise linear model, as determined by breakpoint analysis. The grey-shaded area represents the 95% confidence interval of the linear model prediction. The blue rectangle represents the timespan of realm-specific breakpoints (Supplementary Fig. 2). Both axes are log10-transformed. Credit information for photographs of Antilocapra americana, Elephas maximus, Ursus arctos, Macropus giganteus and Giraffa tippelskirschi are available in Supplementary Table 2. All photographs are under CC-BY copyright (https://creativecommons.org/licenses/by/4.0/) and adapted for the purpose of the figure. b Relationship between species’ adult mass and the rate of population size change (slope). The x-axis is log10-transformed. Points are median slope values with 95% HPDI ranges indicated by bars (each distribution is derived using n = 1000 posterior samples). c Distribution of species’ decline severity. Source Data for this figure are in Source Data 14.


During that long period that creationists believe was before 'Creation Week', when they think Earth was magicked up out of nothing by a magic man made of nothing, mammalian megafauna such as elephants and mammoths, giraffes, kangaroos and antelopes had evolved, and the humans (who hadn't been created yet, but had been evolving in Africa for several millions of years) had spread out of Africa and across most of the Earth and were busy hunting and killing these large animals, leaving their descendants to tell the tale in the number of mutations in the neutral parts of the genome.

Creationists will need to ignore this evidence and the fact that the Theory of Evolution is the underpinning theory of biology that explains these observations.
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