Creationism in Crisis - Rhino Retroviruses Provide Evidence of Evolution

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Female black rhinoceros, Diceros bicornis bicornis.

Wikipedia
User: Bernard DUPONT

African rhinos share retroviruses not found in Asian rhinos or other related species - Leibniz Institute for Zoo and Wildlife Research

Endogenous retroviruses have long been a bugbear for creationists in that they show convincing evidence of evolutionary phylogeny and common ancestry, so this paper which reveals the recent entry into the genome of the African rhinoceroses but not the Asian rhinoceroses, shows that the African rhinos share a common ancestor more recently than they share a common ancestor with the Asian species. That African ancestor became infected after it split from the common ancestor of the African and Asian rhinos.
The research team was led by Alex D. Greenwood of the Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany.

First, a little about ERV's:

Endogenous retroviruses (ERVs) Endogenous retroviruses (ERVs) are remnants of ancient retroviral infections that have become permanently integrated into the genome of the host organism. They are found in the genomes of most vertebrates, including humans. ERVs are considered "endogenous" because they are passed from generation to generation and are inherited in a Mendelian fashion, just like other genes. The life cycle of a retrovirus involves the reverse transcription of its RNA genome into DNA, which is then integrated into the host genome. Occasionally, retroviruses infect germ cells (cells that give rise to eggs or sperm) and their DNA is inserted into the genome of the offspring. Over time, these integrated viral sequences can become fixed in the population and passed on to future generations.

ERVs provide evidence for evolution in several ways:

1. Shared ERVs among species: ERVs are found in the genomes of different species, and the presence of the same ERV at the same genomic location in different species suggests a common ancestor. For example, scientists have identified a specific retroviral sequence called "HERV-K" that is present in the genomes of humans, chimpanzees, and other primates. The shared presence of this ERV provides strong evidence for a common evolutionary history.
2. ERV distribution and phylogenetic relationships: The distribution of ERVs across different species can be used to construct phylogenetic trees, which illustrate the evolutionary relationships between species. By comparing the presence or absence of specific ERVs in different genomes, scientists can infer the evolutionary history and relatedness of species. This approach has been used to study the evolutionary relationships between primates and other mammals.
3. ERVs as "molecular fossils": ERVs can act as "molecular fossils" that provide insights into ancient viral infections and evolutionary events. By studying the DNA sequences of ERVs, scientists can gain information about the timing of viral integration events and the evolutionary relationships between different ERVs. This information helps reconstruct the evolutionary history of the host species.
4. Functional remnants of ERVs: Although most ERVs have accumulated mutations over time and lost their ability to produce functional viral particles, some ERVs retain functional elements. These functional remnants can have important roles in the regulation of gene expression and embryonic development. For example, certain ERVs have been co-opted by the host organism to play a role in placenta formation in mammals. This co-option of ERV sequences for new functions illustrates the process of exaptation, where existing genetic material is repurposed for novel functions during evolution.

References:

1. Mager, D. L., & Stoye, J. P. (2015). Mammalian endogenous retroviruses. Microbiology spectrum, 3(1), MDNA3-0009-2014. doi: 10.1128/microbiolspec.MDNA3-0009-2014
2. Griffiths, D. J. (2001). Endogenous retroviruses in the human genome sequence. Genome biology, 2(6), reviews1017.1. doi: 10.1186/gb-2001-2-6-reviews1017

chatGPT3, "Tell me all about endogenous retroviruses (ERV's), how they enter the genome and why they are evidence for evolution, with references, please. [Response to user question]
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The press release from the Leibniz Institute for Zoo and Wildlife Research explains the research and its significance:

Rhinoceros belong to a mammalian order called odd-toed ungulates that also include horses and tapirs. They are found in Africa and Asia. Until recently, evidence suggested that throughout their evolutionary history, gammaretroviruses such as Murine leukemia virus had not colonised their genomes, unlike most other mammalian orders. The colonisation process is called retroviral endogenisation and has resulted in most mammalian genomes being comprised of up to ten percent retroviral like sequences. An analysis of modern and extinct rhino genomes headed by the German Leibniz Institute for Zoo and Wildlife Research (Leibniz-IZW) now found that African rhinos have dozens of gammaretroviruses in their genomes absent from the genomes of Asian rhino species, such as the Sumatran and Javan rhino, and that the African black rhino has two related groups, one missing from the white rhinos. The restriction of gammaretroviruses to African rhinos and the close relatedness of the viruses to rodent viruses, particularly those of African rodents, suggests that African rhinos were infected by an exogenous viral variant and their genomes colonised in Africa. The work is published in the scientific “Journal of Virology”.

We had data from several rhino species where we kept finding large portions of gammaretroviruses. When we used much newer and more complete reference genomes from modern and extinct rhinos we found that only African rhinos had been colonised

Dr Kyriakos Tsangaras, lead author
Department of Life and Health Sciences
University of Nicosia, Nicosia, Cyprus

This ultimately comes down to lack of high-quality reference sequences of wildlife. While things have improved a lot since the first human genome was sequenced, you miss things such as viral history when the databases lack so many species or high-quality reference genomes from many species. It is really another example of why we need more genome reference sequences from wildlife because we don’t know what other things we are missing and which conclusions we draw about presence and absence of sequences that may turn out to be a consequence of too little information.

Professor Alex Greenwood, Senior author
Head of the Wildlife Disease Department. Leibniz Institute for Zoo and Wildlife Research
Berlin, Germany

Retroviruses such as the causal agent of aids, HIV-1, are unique among viruses in that they have to integrate into the DNA of the host as part of their replication cycle. If this happens in the germline in spermatocytes or oocytes, they can become a part of the host genome that is inherited by the following generation and then are present in every cell of offspring bodies. This evolutionary process has happened so often that on average up to ten per cent of the mammalian genome is made up of retroviruses or their remnants. A previous study of available genomes from horses and their relatives suggested that they, along with rhinos and tapirs, had not been invaded by gammaretroviruses, a group of viruses related to mouse and bird viruses that have successfully colonised most mammalian genomes.

Together with colleagues from Australia and Germany the scientific team found that in fact two different viral groups had colonised African rhinos. One of them had only colonised the black rhino (Diceros bicornis) and not the white rhino (Ceratotherium simum) and was evolutionarily younger than the one shared by both. As both groups are restricted to African rhinos the study suggests that the African rhino lineage was infected and their genomes colonised in Africa, and that is why the respective gammaretroviruses are not found in Asian rhinoceros and other rhino relatives.

More detail is given in the team's paper in the Journal of Virology, which sadly lies behind a paywall. However, the abstract is freely available:

ABSTRACT

High-throughput sequences were generated from DNA and cDNA from four Southern white rhinoceros (Ceratotherium simum simum) located in the Taronga Western Plain Zoo in Australia. Virome analysis identified reads that were similar to Mus caroli endogenous gammaretrovirus (McERV). Previous analysis of perissodactyl genomes did not recover gammaretroviruses. Our analysis, including the screening of the updated white rhinoceros (Ceratotherium simum) and black rhinoceros (Diceros bicornis) draft genomes identified high-copy orthologous gammaretroviral ERVs. Screening of Asian rhinoceros, extinct rhinoceros, domestic horse, and tapir genomes did not identify related gammaretroviral sequences in these species. The newly identified proviral sequences were designated SimumERV and DicerosERV for the white and black rhinoceros retroviruses, respectively. Two long terminal repeat (LTR) variants (LTR-A and LTR-B) were identified in the black rhinoceros, with different copy numbers associated with each (n = 101 and 373, respectively). Only the LTR-A lineage (n = 467) was found in the white rhinoceros. The African and Asian rhinoceros lineages diverged approximately 16 million years ago. Divergence age estimation of the identified proviruses suggests that the exogenous retroviral ancestor of the African rhinoceros ERVs colonized their genomes within the last 8 million years, a result consistent with the absence of these gammaretroviruses from Asian rhinoceros and other perissodactyls. The black rhinoceros germ line was colonized by two lineages of closely related retroviruses and white rhinoceros by one. Phylogenetic analysis indicates a close evolutionary relationship with ERVs of rodents including sympatric African rats, suggesting a possible African origin of the identified rhinoceros gammaretroviruses.

IMPORTANCE:Rhinoceros genomes were thought to be devoid of gammaretroviruses, as has been determined for other perissodactyls (horses, tapirs, and rhinoceros). While this may be true of most rhinoceros, the African white and black rhinoceros genomes have been colonized by evolutionarily young gammaretroviruses (SimumERV and DicerosERV for the white and black rhinoceros, respectively). These high-copy endogenous retroviruses (ERVs) may have expanded in multiple waves. The closest relative of SimumERV and DicerosERV is found in rodents, including African endemic species. Restriction of the ERVs to African rhinoceros suggests an African origin for the rhinoceros gammaretroviruses.

Tsangaras K, Mayer J, Mirza O, Dayaram A, Higgins DP, Bryant B, Campbell-Ward M, Sangster C, Casteriano A, Höper D, Beer M, Greenwood AD (2023)
Evolutionarily young African rhinoceros gammaretroviruses.
J VIROL 97, e0193222. https://doi.org/10.1128/jvi.01932-22.

© 2023 American Society for Microbiology.
Reprinted under the terms of s60 of the Copyright, Designs and Patents Act 1988.

To any normal person, evidence like this would confirm evolutionary divergence, firstly between the African and Asian rhinoceroses, then, later between the African rhinoceroses.

It would also show that the scientists are in no doubt that evolution is the fundamental explanation for their findings, with no hint that they believe magic and supernatural magicians were involved, like creationist frauds fool their dupes into believing they increasingly are. Indeed, why would they? What rational, educated adult, with a mental age greater than about 9, believes in magic or supernatural magicians and thinks they should play any part in scientific explanations of real-world evidence?

Creationism in Crisis - How African Mammals Evolved

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Bull African bush elephant, Loxodonta africana

From enormous elephants to tiny shrews: how mammals shape and are shaped by Africa's landscapes

The thing about evolution is that it explains how and why an ecosystem shapes and changes the evolution of the species within it and why the evolution of the species within it shapes and changes the ecosystem, all driven in the longer term by changing climate and geology and migration of new species into it.

The key to understanding that is understanding how environmental selectors favour certain variants over others, whether those variants are size, color, ability to find food and mates, or avoid being the prey of predators.

Given that then, we can us the Theory of evolution to predict that the reason Africa's fauna is the way it is today will be found in African geological and geological history and the history of migration into Africa from, mostly, Eurasia.

In his new book, African Ark: Mammals, landscape and the ecology of a continent, Professor Ara Monadjem of the Department of Biological Sciences, University of Eswatini, describes where the African megafauna came from and how they have shaped the African ecosystems, even influencing the evolution of humans, and in so doing have created an environment on which many plants and small animals depend.

His article in The Conversation explains the background to his book. His article is reprinted here under a Creative Commons license, reformatted for stylistic consistency.

Published: May 2, 2023 3.05pm BST
Updated: May 8, 2023 1.09pm BST

From enormous elephants to tiny shrews: how mammals shape and are shaped by Africa’s landscapes

The African elephant is the world’s largest terrestrial mammal.

Ara Monadjem, Author provided

Ara Monadjem, University of Eswatini

Africa is the world’s most diverse continent for large mammals such as antelopes, zebras and elephants. The heaviest of these large mammals top the scales at over one ton, and are referred to as megafauna. In fact, it’s the only continent that has not seen a mass extinction of these megafauna.

The continent’s megafauna community includes the world’s largest terrestrial mammal, the African elephant. Adult African bush elephants can weigh as much as 6 tons. Other giants across African continent include hippopotamuses, rhinoceroses and giraffes.

So, it is only in Africa that ecological interactions and dynamics can be studied as they would have been before the sudden and profound flourishing of Homo sapiens over the past 12 000 years; before then, megafauna would have dominated all terrestrial landscapes on all continents. A visit to Africa is, in other words, a visit to our planet’s past.

In my latest book, African Ark: Mammals, Landscape and the Ecology of a Continent, I tell the story of how Africa’s mammal fauna arose.

It’s not just a tale of megafauna and other well-known large mammals. I pay particular attention to small mammals, such as mice, bats and shrews. That’s partly because I have been studying these creatures for the past three decades.

These animals are also generally overlooked by both scientists and the public. But without them, and the ways in which they’ve interacted with each other and with their larger cousins over tens of thousands years, Africa wouldn’t have the richly varied landscapes it does today.

Africa’s mammals are a global treasure that must be protected. However, the lives of local communities are inextricably linked with these mammals and the remaining natural landscapes that harbour their dwindling populations; conservation solutions will require these communities’ active participation and blessing.

In some areas, nature-based tourism may be a viable solution. However, much of the rest of the continent – where no tourists go – will require other, perhaps novel, approaches. What we cannot afford is the extinction of any of these beautiful creatures or the continued loss and reduction of the ecosystem services that they freely provide.

Early mammal history

The history of African mammals begins with an apparently unrelated group of creatures. They’re so dissimilar from each other today that taxonomists didn’t work out their true relationships until about two decades ago. These are the elephants, manatees, elephant shrews, African golden moles, hyraxes and tenrecs. Collectively they make up the super-order Afrotheria.

Today, this group accounts for only a small fraction of the mammal species on the continent. But that is only because Africa – which formed part of the prehistoric southern supercontinent of Gondwana – was colonised, in stages and over millions of years, by ‘invaders’ from the northern supercontinent of Laurasia.

Large mammals shaped the evolution of humans: here’s why it happened in Africa

These colonists include nearly all the mammals that we normally associate with Africa, including rhinoceroses, zebras, antelopes, primates, bats and even rodents. In return, some Afrotherians, including elephants, roamed out of Africa to colonise other lands further north.

Other mammals, including monkeys and caviomorph rodents (such as guinea pigs and capybaras), used Africa as a stepping stone to colonise South America, as did lemurs to colonise Madagascar.

Shaped by geography

The variables of physical geography have worked hand in hand with the tectonic forces of prehistory.

Africa is not a uniform landscape that enjoys the same climate and habitat throughout. Some parts, such as Madagascar, are not even connected to the mainland but appear as offshore islands. Terrestrial mammals typically reach islands in two ways: they either raft across the intervening sea, or cross by foot during periods of drier weather or lower sea levels that connect the islands to the mainland.

Kenyan fossil shows chameleons may have 'rafted' from mainland Africa to Madagascar

In the continent’s interior, other formidable barriers restrict and determine mammal movement. Long, deep, fast-flowing rivers, such as the Congo in central Africa, can be almost as effective a barrier as open oceans. Mountain ranges can form inland ‘islands’ that are as ecologically isolated as their ocean equivalents.

By providing barriers, geographical features limit the movement of animals across the landscape, thereby affecting the composition of mammal communities in different parts of the continent.

Population shifts

Another element that’s crucial to telling the story of Africa’s mammals is an understanding of how species and population groups are formed and fluctuate over time.

For example, megafauna play important roles in shaping the landscape and its plant communities. This in turn shapes many smaller animals’ habitats. Hippopotamuses in the Okavango Delta create and maintain open water channels, which serve as critical habitat for fishes. And, by defecating in water, hippos also introduce vast amounts of organic fertiliser into this aquatic ecosystem, helping to enrich it.

Smaller animals, too, shape landscapes.

Some species of rats and mice, such as pouched mice in the genus Saccostomus, are granivores that feed on seeds, including those of trees responsible for bush encroachment in savannas such as the sicklebush. Colleagues and I have shown experimentally that various species of mice in Eswatini actually prefer the seeds of this encroaching plant and hence can assist in controlling its spread. But these rodents require good grass cover for persistence, and hence can’t provide this ecological service in over-grazed, degraded landscapes.

The numbers of animals naturally fluctuate over time, typically reflecting fluctuations in food supply brought about by, for example, droughts or floods. A key determinant of these population fluctuations is also the inherent life history characteristics of a species: short-lived, fast reproducing species such as rats and mice will, by definition, experience greater fluctuations in their numbers than long-lived, slow reproducing species like elephants.

Conservation

My book concludes by looking at human interactions with African mammals and the need to conserve these mammals, both for their own sake and for ours. The ecosystem services provided by many mammals are crucial to a healthy environment for all species. Humans evolved in Africa and have interacted with other African mammals for millions of years here.

This is not true on other continents, where humans are – in geological timescales – a recent addition. It may well be that this long relationship between humans and other African mammals is the reason why, despite the losses wrought by humankind, so many large mammals persist on the continent: they have ‘learnt’ through natural selection how to survive with us.

The book was written in conjunction with wildlife journalist Mike Unwin and is published by Wits University Press.
Ara Monadjem, Full Professor in the Department of Biological Sciences, University of Eswatini

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Published by The Conversation.
Open access. (CC BY 4.0)

It happens with such monotonous regularity, with practically every biology paper ever published, that the fact that this article refutes creationist claims is hardly worth mentioning. One day, maybe, someone will tell the cult that they are living in a counter-factual wonderland, completely disconnected from the real world.

Creationism in Crisis - Australian Megafauna From 15 Million Years Before God Created the Universe!

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Reconstruction of Nimbadon lavarackorum mother and juvenile (detail)

Peter Schouten.
Source: PLOS ONE

These giant 'drop bears' with opposable thumbs once scaled trees in Australia. But how did they grow so huge?

The thing about having a counter-factual superstition like creationism is that you need to concoct increasingly unlikely explanation for your rejection of the sort of real-world evidence that normal people base their opinions on.

For example, we have in the following example, evidence that 15 million years ago, there were large marsupials living in Australia, one of which, known to science as Nimbadon, weighed about 70Kg and climbed about in trees. The evidence is in the form of fossils, 24 of which were found in a few square metres of each other at one site within the Riversleigh World Heritage site, Gregory, Queensland, Australia.

These fossils show that Nimbadon belongs to an extinct group of marsupials called diprotodontoids, whose closest living relatives are wombats and Koalas.

Australian diprotodontoids
Australian diprotodontoids refer to a diverse group of marsupials that belong to the superfamily Diprotodontoidae. These unique animals are endemic to Australia and have a rich fossil record spanning several million years. They exhibit a wide range of body sizes, from small, rat-like forms to massive, herbivorous giants.

One prominent member of the Australian diprotodontoids is the extinct genus Diprotodon. Diprotodon was the largest known marsupial to have ever lived, reaching the size of a rhinoceros. It lived during the Pleistocene epoch and is often referred to as the "giant wombat" due to its resemblance to modern wombats. Diprotodon had a robust build, powerful limbs, and a specialized skull adapted for herbivorous feeding.

Another notable diprotodontoid is Zygomaturus, which lived during the late Miocene to the late Pleistocene. Zygomaturus was a large, herbivorous marsupial characterized by its elongated snout and peculiar cheek teeth. It is believed to have inhabited wetland and riparian environments.

Other diprotodontoids include Nototherium, Palorchestes, and Procoptodon. Nototherium was a medium-sized herbivore with an elongated skull, while Palorchestes was a peculiar genus with long arms and a unique grasping hand. Procoptodon, also known as the "short-faced kangaroo," had a short, robust face and incredibly long hind limbs.

References:

1. Archer, M., Hand, S. J., & Godthelp, H. (1991). Riversleigh: The Story of Animals in Ancient Rainforests of Inland Australia. Reed Books.
2. Long, J. A., Archer, M., Flannery, T. F., & Hand, S. J. (2002). Prehistoric Mammals of Australia and New Guinea: One Hundred Million Years of Evolution. University of New South Wales Press.
3. Mackness, B. (2008). Australian Megafauna: Diprotodontoidae. In Janis, C., Gunn, A., & Uhen, M. (Eds.), Evolution of Tertiary Mammals of North America (Volume 2: Small Mammals, Xenarthrans, and Marine Mammals) (pp. 425-436). Cambridge University Press.

ChatGPT3. (2023). "Tell me about the Australian diprotodontoids."
[Retrieved from https://chat.openai.com/]

Now all that, of course, is entirely inconsistent with creationist belief in an Earth that is just a few thousand years old and on which all living and extinct creatures, including dinosaurs and extinct Australian megafauna such as Nimbadon, were created in the first week and lived contemporaneously until a genocidal global flood killed them all bar a few selected ones from whom all modern species are descended, and all fossils are of animals drowned in that flood just 4000 years ago.

So, how do creationists cope with the resulting cognitive dissonance between the real-world evidence and what they need to believe because not believing it would be a terrifying existential threat? They claim:

• All the dating methods palaeontologists and geologists use are wrong (by many orders of magnitude), even, bizarrely citing the fact that carbon dating has an accepted limitation to the age at which it can date objects accurately, when in fact, carbon dating isn't used to date fossils (because of that very limitation and also because any carbon in the fossil will be due to minerlisation and not derived from the body of the animal).
• The scientists are part of a conspiracy, often a Satanic or even Zionist conspiracy, of which all the scientists' assistants and all the staff of the publishing houses that publish the scientific journals are part, and none of whom has ever broken ranks and blown the whistle on the deception.
• The facts must be wrong because they are at odds with what the Bible says and the Bible is the inerrant word of God, so the Bible says.
• Scientists all hate God and want to turn people away from 'him'.

That bizarre and highly unlikely 'explanation' for the evidence is so much more convoluted and involving so many more entities, than the simple explanation - the scientists are telling the truth and the Bible is not literal truth - that any rational person would go with the most vicarious explanation as being the one most likely to be correct, especially since scientists keep producing more and more evidence for the latter alternative while creationists can find no evidence for the former.

What creationists can never admit is what is obvious to most normal people: that when their religion disagrees with science, their religion is wrong; science is a tool for discovering the truth.

and that was by way of introduction to a recent article in The Conversation in which four palaeontologists describe Nimbadon and discuss why they grew so large. The palaeontologists are:

• Anusuya Chinsamy-Turan, Professor, Biological Sciences Department, University of Cape Town
• Karen Black, Leading Education Professional, UNSW Sydney
• Mike Archer, Professor, Pangea Research Centre, UNSW Sydney
• Sue Hand, Professor emeritus, UNSW Sydney

Their article is reprinted here under a Creative Commons Licence, reformatted for stylistic consistency:

These giant ‘drop bears’ with opposable thumbs once scaled trees in Australia. But how did they grow so huge?

Peter Schouten, Author provided

Anusuya Chinsamy-Turan, University of Cape Town; Karen Black, UNSW Sydney; Mike Archer, UNSW Sydney, and Sue Hand, UNSW Sydney

Although long dead, fossil skeletons provide an incredible window into the lifestyle and environment of an extinct animal.

By analysing the various features of fossil bones we can reveal not only the overall size and shape of the animal, but also what kind of movement the animal was capable of, its lifestyle, and the environment in which it lived.

But what if we looked inside fossil bones? What secrets would it reveal about the growth and development of an extinct animal? In a newly published paper in the Journal of Paleontology, we have done just that, using 15 million-year-old skeletons of a giant bear-like marsupial from the world-famous Riversleigh World Heritage Area (Boodjamulla) in Waanyi country of northwest Queensland.

Tree-dwelling wombat relatives

Reconstruction of a mother and baby Nimbadon. They had powerful arms, large hands and feet and huge claws to assist climbing through the rainforest tree tops.

Peter Schouten, Author provided

The huge tree-dwelling herbivorous marsupials, known as Nimbadon, weighed about 70kg, making them the largest arboreal (tree dwelling) mammals known from Australia.

Nimbadon belongs to a diverse group of long extinct, large-bodied marsupials known as diprotodontoids, the likes of which include the largest marsupial to have ever lived, the 2.5 tonne megafaunal Diprotodon, and bizarre trunked marsupials reminiscent of modern-day tapirs.

Among living animals, Nimbadon is most closely related to wombats. Yet surprisingly, in terms of body size and lifestyle, they are more comparable to sun bears, which today can be found scaling the rainforest canopies of Southeast Asia.

When we first uncovered jawbones of Nimbadon at Riversleigh in 1993, we thought we were looking at very large leaf-eating marsupials who foraged for food on the forest floor.

Modern-day sun bears climb trees and lounge there much like sloths do.

Shutterstock

But like many of the species we’ve unearthed from Riversleigh, the closer we look at these animals, the more bizarre and fascinating they become.

Nimbadon is now known from its complete skeleton, including material representing developmental ages ranging from tiny pouch-young to mature adults. It had strong arms with very mobile shoulder and elbow joints. Its hands and feet had specially adapted opposable thumbs with huge curved claws for climbing, penetrating bark and grasping branches.

These animals were highly specialised climbers and lived vastly different lifestyles compared to their closest living relatives – the land-dwelling, burrowing wombats.

Our initial research showed that Nimbadon was not only a “tree-hugger”, but also a “tree-hanger”, spending some of its time suspended from tree branches like a sloth.

Fossil skeleton of a mature adult Nimbadon.

Karen Black, Author provided

Nimbadon lived 15 million years ago in the canopy of lowland Australian rainforests. These biodiverse, lush forests were home to some equally strange animals: flesh-eating kangaroos, tree-climbing crocodiles, ancestral thylacines, cat- to leopard-sized marsupial lions, huge anaconda-like snakes, giant toothed platypuses and mysterious marsupials so strange they have been called “Thingodonta”. It was a very different Australia than the one we see today.

Sectioning the bones

Despite the wealth of information we have gleaned from Nimbadon skeletons, until now we hadn’t fully understood the growth patterns of these ancient marsupials.

Were they affected by seasonality? How long did they take to grow to adult body size in the canopies of the ancient forest? Clues to these questions lay in the bones’ microscopic structure.

To look inside the fossil bones, we needed to select the right material. Long bones, such as the bones of the leg, are known to preserve a good record of growth, so we analysed ten long bones of several different-sized individuals.

Articulated fossilised Nimbadon skeletons in a large slab of limestone recovered from a 15 million year old fossil cave deposit in the Riversleigh World Heritage Area, northwestern Queensland.

Anna Gillespie, Author provided

We began by removing a section from the shaft of the bone, and embedded it in resin. Using a diamond-edged blade, we cut our samples into thin sections and polished them further until light could pass through them. These thinned sections were mounted on glass microscope slides to be studied.

Remarkably, even after millions of years of fossilisation, the microscopic structure of the fossil bones had remained intact. We were amazed to discover that Nimbadon grew in periodic spurts. Individuals had fast growth periods, each followed by a slow growth period, often associated with a band of arrested growth.

Seasonal growers

Cyclical growth patterns have previously been documented for marsupials such as in the living western grey kangaroo. However, our results indicate that, overall, the limbs of Nimbadon had a much slower, more extenuated growth than kangaroo limbs.

One individual recorded at least seven to eight growth cycles, which suggests this arboreal giant needed at least this amount of time – and probably more – to become a fully-grown, sexually mature adult.

Based on these alternating cycles of fast and slow growth, Nimbadon may have been affected by seasonal conditions such as food availability. However, exactly how long it took for eight growth cycles to develop remains a mystery. If indeed they represent annual cycles, it would be at least eight years until sexual maturity, which is unusual in the modern marsupial world.

For example, kangaroos are sexually mature at one to two years. That being said, Nimbadon is an unusual beast and a very large one at that, so an extended developmental period (and lifespan) is not unlikely.

Real-life drop bears

We have come to think about these strange arboreal marsupials as real versions of the legendary “drop bears” of Australian folklore – mysterious tree-dwelling creatures that would drop down on unsuspecting animals below.

Reconstruction of Nimbadon’s palaeoenvironment of lush rainforest with underground caves.

Karen Black, Author provided

While moving in herds through the rainforest canopy, both young and adult Nimbadon would have occasionally lost their grip before dropping down from the treetops. Sometimes they would end up in forest floor caves, which is where we have been finding their still-articulated skeletons.

Given the constant surprises that research into this extraordinary, extinct Riversleigh mammal has already produced, we are eager and prepared for still more.

Currently we are looking into wear in the enamel microstructure of Nimbadon’s teeth to determine this legendary drop bear’s diet. We expect that what we find down the track will continue to upend our naïve first presumptions about the lifestyles of this and many of the other strange inhabitants of the ancient inland rainforests of Riversleigh.
Anusuya Chinsamy-Turan, Professor, Biological Sciences Department, University of Cape Town; Karen Black, Leading Education Professional, UNSW Sydney; Mike Archer, Professor, Pangea Research Centre, UNSW Sydney, and Sue Hand, Professor emeritus, UNSW Sydney

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Published by The Conversation.
Open access. (CC BY 4.0)

Copyright: © 2023 The authors.
Published by Cambridge University Press on behalf of The Paleontological Society. Open access. (CC BY 4.0)

The authors of that article have recently published their findings, open access, in the Journal of Paleontology:

Abstract

Despite the recognition that bone histology provides much information about the life history and biology of extinct animals, osteohistology of extinct marsupials is sorely lacking. We studied the bone histology of the ca. 15-million-year-old Nimbadon lavarackorum from Australia to obtain insight into its biology. The histology of thin sections of five femora and five tibiae of juveniles, subadult, and adult Nimbadon lavarackorum was studied. Growth marks in the bones suggest that N. lavarackorum took at least 7–8 years (and likely longer) to reach skeletal maturity. The predominant bone tissue during early ontogeny is parallel-fibered bone, whereas an even slower rate of bone formation is indicated by the presence of lamellar bone tissue in the periosteal parts of the compacta in older individuals. Deposition of bone was interrupted periodically by lines of arrested growth or annuli. This cyclical growth strategy indicates that growth in N. lavarackorum was affected by the prevailing environmental conditions and available resources, as well as seasonal physiological factors such as decreasing body temperatures and metabolic rates.

Chinsamy, A., Black, K., Hand, S., & Archer, M. (2023).
Paleobiological implications of the bone histology of the extinct Australian marsupial Nimbadon lavarackorum.
Journal of Paleontology, 1-13. doi:10.1017/jpa.2023.22

Copyright: © 2023 The authors.
Published by Cambridge University Press on behalf of The Paleontological Society. Open access
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

Figure 2.
Specimen AR21803. (1) AR21803a, thin section BII; section of partial tibia; arrows indicate growth marks in the compacta; (2) AR21803b, thin section AI; section of partial femur showing a low-magnification overview of the compacta; arrows indicate growth marks in the compacta (note the resorptive endosteal margin of the bone wall); (3) AR21803b, thin section AI showing radial tract of compacted coarse cancellous bone (indicated by the white arrows). Images taken under polarized light with a one-quarter-λ compensator.

Chinsamy, A., Black, K., Hand, S., & Archer, M. (2023).

Not only convincing evidence of the existence of these giant wombat-like marsupials, 15 million years ago, but, as usual, not a hint that the scientists believe the Theory of Evolution is inadequate for explaining the observations, or that magic by an invisible supernatural magician is a better explanation.

In other words, yet another casual and incidental refutation of creationism and the claims made by the scientifically illiterate authors of the Bible.

Creationism in Crisis - Human Genomic Snapshot Shows Evolution Over Hundreds of Thousands of Years

Slideshow code developed in collaboration with ChatGPT3 at https://chat.openai.com/

The Rockefeller University » The clearest snapshot of human genomic diversity ever taken

Creationists hang themselves on a hook by insisting that all humans, and indeed every living thing, were designed by an omniscient, perfect supernatural deity for whom no superlative is enough, because such a designer would design a perfect human species, and a perfect human species would have no genetic diversity because its genome would be the perfect genome with every DNA base the perfect DNA base and every DNA triplet the perfect DNA triplet for the intended purpose.

Save only for a small number of genes for the difference in their sexes, Adam & Eve would have had identical genomes, as would their offspring and their offspring's offspring... down to today's descendants. Indeed, in the biblical myth, Eve was a clone of Adam, so there would not even have been sex chromosomes or genetic sexual differences - which reflects the ignorance of genetics of the authors.

A perfect creator would have no need for genetic diversity. Genetic diversity is the result of an evolutionary process, not of intelligent design!

But even is a slightly less that omnipotent, omniscient creator had lost control of the chemistry and physics that replicates the genome in each new generation, so a little bit of diversity would creep in over time, there is no way the amount of diversity we see today would arise by chance mutation. Even allowing for natural selection which would weed out the less than perfect, there has not been enough time since creationists believe the total human population was reduced to 8 genocidal flood survivors for the present amount of diversity to arise. And what possible mechanism could there be for keeping a mutated form of a perfect gene? Perfection is an absolute, with no possibility of a gene being better than perfect.

The Human Pangenome Reference Consortium.
The Human Pangenome Reference Consortium (HPRC) is a collaborative scientific effort aimed at constructing a comprehensive and representative reference of the human genome. The traditional human genome reference, known as the GRCh38 reference, represents a single individual's genome and does not capture the full genetic diversity of the human population. The HPRC seeks to address this limitation by constructing a pangenome reference that incorporates genetic variation present in different populations.

The HPRC was officially established in 2016 and is composed of researchers from various institutions and organizations, including academic institutions, genome centers, and biotechnology companies. The consortium aims to generate a more complete and accurate representation of the human genome by integrating data from diverse populations worldwide.

The impact of the HPRC's work is significant and has several implications for genomics research and precision medicine. Here are some key points:

1. Capturing Genetic Diversity: The human genome exhibits substantial variation across different populations, and a single reference cannot adequately represent this diversity. The pangenome reference being developed by the HPRC incorporates genetic variants that are absent from the traditional reference, providing a more comprehensive view of human genetic variation.
2. Improved Variant Calling: The pangenome reference enables more accurate variant calling and genotyping in genomic studies. By including a broader range of genetic variants, researchers can better identify and interpret genomic variants specific to different populations. This is particularly relevant for identifying rare or population-specific variants associated with diseases.
3. Precision Medicine: The pangenome reference has implications for personalized medicine and the interpretation of genomic data in clinical settings. It enhances the accuracy of genetic testing and interpretation, especially for underrepresented populations. By considering a broader range of genetic variation, clinicians can provide more precise diagnoses, prognoses, and treatment options tailored to individual patients.
4. Population Genetics and Evolutionary Studies: The pangenome reference facilitates population genetics and evolutionary research. It allows scientists to explore the genetic diversity within and between populations, investigate evolutionary processes, and gain insights into the origins and migration patterns of different human populations.

It's important to note that while the HPRC is actively working on constructing a pangenome reference, as of my knowledge cutoff in September 2021, the consortium had not yet completed and released a final version of the pangenome reference. However, their work has gained recognition and attention within the scientific community due to its potential to revolutionize genomic research and applications.

For more information and updates on the Human Pangenome Reference Consortium, I recommend referring to their official website (https://humanpangenome.org/) and reviewing relevant scientific publications and news articles published after September 2021.

chatGPT3 "Tell me what you know about the Human Pangenome Reference Consortium and the impact of their work, with references, please." [Response to user question]
Retrieved from https://chat.openai.com/

This, of course, is why Michael J Behe's notion of all mutations being deleterious and all change in the genome being 'devolutionary' is nonsensical and unworthy of someone who purports to be a serious biologist, because there is no known mechanism for keeping a gene less well suited for the environment than a perfect gene in the assortative process that is natural selection, so genetic diversity can't possibly arise by accumulation of deleterious genes.

So, if they understood it, the work of the Human Pangenome Reference Consortium should be worrying the frauds who run the creationist cult, because the only plausible mechanism for the present level of human genetic diversity is evolution, by natural selection, genetic drift, horizontal gene transfer and the occasional historical founder effect, all taking place over several hundred thousand years.

So, the small flurry of papers published in the last few days by the HPRC should be ringing alarm bells in Creation Central and causing the schemers and planners to come up with strategies for ignoring, misrepresenting of dismissing the work of the Consortium.

As the Rockefeller University news release explains:

For more than 20 years, scientists have relied on the human reference genome, a consensus genetic sequence, as a standard against which to compare other genetic data. Used in countless studies, the reference genome has made it possible to identify genes implicated in specific diseases and trace the evolution of human traits, among other things.

But it has always been a flawed tool. One of its biggest problems is that about 70 percent of its data came from a single man of predominantly African-European background whose DNA was sequenced during the Human Genome Project, the first effort to capture all of a person’s DNA. As a result, it can tell us little about the 0.2 to one percent of genetic sequence that makes each of the seven billion people on this planet different from each other, creating an inherent bias in biomedical data believed to be responsible for some of the health disparities affecting patients today. Many genetic variants found in non-European populations, for instance, aren’t represented in the reference genome at all.

For years, researchers have called for a resource more inclusive of human diversity with which to diagnose diseases and guide medical treatments. Now scientists with the Human Pangenome Reference Consortium have made groundbreaking progress in characterizing the fraction of human DNA that varies between individuals. As they recently published in Nature, they’ve assembled genomic sequences of 47 people from around the world into a so-called pangenome in which more than 99 percent of each sequence is rendered with high accuracy.

Layered upon each other, these sequences revealed nearly 120 million DNA base pairs that were previously unseen.

While it’s still a work in progress, the pangenome is public and can be used by scientists around the world as a new standard human genome reference, says The Rockefeller University’s Erich D. Jarvis, one of the primary investigators.

“This complex genomic collection represents significantly more accurate human genetic diversity than has ever been captured before,” he says. “With a greater breadth and depth of genetic data at their disposal, and greater quality of genome assemblies, researchers can refine their understanding of the link between genes and disease traits, and accelerate clinical research.”

Sourcing diversity

Completed in 2003, the first draft of the human genome was relatively imprecise, but it became sharper over the years thanks to filled-in gaps, corrected errors, and advancing sequencing technology. Another milestone was reached last year, when the final eight percent of the genome—mainly tightly coiled DNA that doesn’t code for protein and repetitive DNA regions—was finally sequenced.

Despite this progress, the reference genome remained imperfect, especially with respect to the critical 0.2 to one percent of DNA representing diversity. The Human Pangenome Reference Consortium (HPRC), a government-funded collaboration between more than a dozen research institutions in the United States and Europe, was launched in 2019 to address this problem.

At the time, Jarvis, one of the consortium’s leaders, was honing advanced sequencing and computational methods through the Vertebrate Genomes Project, which aims to sequence all 70,000 vertebrate species. His and other collaborating labs decided to apply these advances for high-quality diploid genome assemblies to revealing the variation within a single vertebrate: Homo sapiens.

To collect a diversity of samples, the researchers turned to the 1000 Genomes Project, a public database of sequenced human genomes that includes more than 2500 individuals representing 26 geographically and ethnically varied populations. Most of the samples come from Africa, home to the planet’s largest human diversity.

“In many other large human genome diversity projects, the scientists selected mostly European samples,” Jarvis says. “We made a purposeful effort to do the opposite. We were trying to counteract the biases of the past.”

It’s likely that gene variants that could inform our knowledge of both common and rare diseases can be found among these populations.

Mom, dad, and child

But to broaden the gene pool, the researchers had to create crisper, clearer sequences of each individual–and the approaches developed by members of the Vertebrate Genome Project and associated consortiums were used to solve a longstanding technical problem in the field.

Every person inherits one genome from each parent, which is how we end up with two copies of every chromosome, giving us what’s known as a diploid genome. And when a person’s genome is sequenced, teasing apart parental DNA can be challenging. Older techniques and algorithms have routinely made errors when merging parental genetic data for an individual, resulting in a cloudy view. “The differences between mom’s and dad’s chromosomes are bigger than most people realize,” Jarvis says. “Mom may have 20 copies of a gene and dad only two.”

With so many genomes represented in a pangenome, that cloudiness threatened to develop into a thunderstorm of confusion. So the HPRC homed in a method developed by Adam Phillippy and Sergey Koren at the National Institutes of Health on parent-child “trios”—a mother, a father, and a child whose genomes had all been sequenced. Using the data from mom and dad, they were able to clear up the lines of inheritance and arrive at a higher-quality sequence for the child, which they then used for pangenome analysis.

New variations

The researchers’ analysis of 47 people yielded 94 distinct genome sequences, two for each set of chromosomes, plus the sex Y chromosome in males.

They then used advanced computational techniques to align and layer the 94 sequences. Of the 120 million DNA base pairs that were previously unseen or in a different location than they were noted to be in the previous reference, about 90 million derive from structural variations, which are differences in people’s DNA that arise when chunks of chromosomes are rearranged—moved, deleted, inverted, or with extra copies from duplications.

It’s an important discovery, Jarvis notes, because studies in recent years have established that structural variants play a major role in human health, as well as in population-specific diversity. “They can have dramatic effects on trait differences, disease, and gene function,” he says. “With so many new ones identified, there’s going to be a lot of new discoveries that weren’t possible before.”

Filling gaps

The pangenome assembly also fills in gaps that were due to repetitive sequences or duplicated genes. One example is the major histocompatibility complex (MHC), a cluster of genes that code proteins on the surface of cells that help the immune system recognize antigens, such as those from the SARS-CoV-2 virus.

“They’re really important, but it was impossible to study MHC diversity using the older sequencing methods,” Jarvis says. “We’re seeing much greater diversity than we expected. This new information will help us understand how immune responses against specific pathogens vary among people.” It could also lead to better methods to match organ transplant donors with patients, or identify people at risk for developing autoimmune disease.

The team has also uncovered surprising new characteristics of centromeres, which lie at the cruxes of chromosomes and conduct cell division, pulling apart as cells duplicate. Mutations in centromeres can lead to cancers and other diseases.

Despite having highly repetitive DNA sequences, “centromeres are so diverse from one haplotype to another, that they can account for more than 50 percent of the genetic differences between people or maternal and paternal haplotypes even within one individual,” Jarvis says. “The centromeres seem to be one of the most rapidly evolving parts of the chromosome.”

Relationship building

The current 47-people pangenome is just a starting point, however. The HPRC’s ultimate goal is to produce high-quality, nearly error-free genomes from at least 350 individuals from diverse populations by mid-2024, a milestone that would make it possible to capture rare alleles that confer important adaptive traits. Tibetans, for example, have alleles related to oxygen use and UV light exposure that enable them to live at high altitudes. A major challenge in collecting this data will be to gain trust from communities that have seen past abuses of biological data; for example, there are no samples in the current study from Native American nor Aboriginal peoples, who have been long been disregarded or exploited by scientific studies. One doesn’t have to go far back in time to find examples of unethical use of genetic data: Just a few years ago, DNA samples from thousands of Africans in multiple countries were commercialized without the donors’ knowledge, consent, or benefit. These offenses have sown mistrust against scientists among many populations. But by not being included, some of these groups could remain genetically obscure, leading to a perpetuation of the biases in the data—and to continued disparities in health outcomes. “It’s a complex situation that’s going to require a lot of relationship building,” Jarvis says. “There’s greater sensitivity now.” And even today, many groups are willing to participate. “There are individuals, institutions, and governmental bodies from different countries who are saying, ‘We want to be part of this. We want our population to be represented,’” Jarvis says. “We’re already making progress.”

Copyright: © 2023 The authors.
Published by Springer Nature Ltd. Open access. (CC BY 4.0)

The team's findings are published, open access, in Nature:

Abstract

Single-nucleotide variants (SNVs) in segmental duplications (SDs) have not been systematically assessed because of the limitations of mapping short-read sequencing data^1,2. Here we constructed 1:1 unambiguous alignments spanning high-identity SDs across 102 human haplotypes and compared the pattern of SNVs between unique and duplicated regions^3,4. We find that human SNVs are elevated 60% in SDs compared to unique regions and estimate that at least 23% of this increase is due to interlocus gene conversion (IGC) with up to 4.3 megabase pairs of SD sequence converted on average per human haplotype. We develop a genome-wide map of IGC donors and acceptors, including 498 acceptor and 454 donor hotspots affecting the exons of about 800 protein-coding genes. These include 171 genes that have ‘relocated’ on average 1.61 megabase pairs in a subset of human haplotypes. Using a coalescent framework, we show that SD regions are slightly evolutionarily older when compared to unique sequences, probably owing to IGC. SNVs in SDs, however, show a distinct mutational spectrum: a 27.1% increase in transversions that convert cytosine to guanine or the reverse across all triplet contexts and a 7.6% reduction in the frequency of CpG-associated mutations when compared to unique DNA. We reason that these distinct mutational properties help to maintain an overall higher GC content of SD DNA compared to that of unique DNA, probably driven by GC-biased conversion between paralogous sequences^5,6.

Vollger, M.R., Dishuck, P.C., Harvey, W.T. et al.
Increased mutation and gene conversion within human segmental duplications.
Nature 617, 325–334 (2023). https://doi.org/10.1038/s41586-023-05895-y

Copyright: © 2023 The authors.
Published by Springer Nature Ltd. Open access
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

Scientists from the University of Californis Santa Cruz (UC Santa Cruz) who were involved in the project have produced a video explaining their work:

What's clear from all this is that the Homo sapiens species is not only far from perfectly designed by a perfect designer, but it could not possibly have achieved the present level of genetic diversity starting with 8 individuals, three of whom were sons of one of the couples, in the last 4 thousand years, or even tens of thousands of years, but must have been diversifying for several hundred thousand years since the species diverged from its ancestral species.

In other words, the notion of intelligent design and recent special creation is entirely inconsistent with the observable evidence, which is perfectly explained by an evolutionary process over a very long period of time.

And, to lay another creationist lie, there is no suggestion that any of the scientists involved believe otherwise. There is never a hint that god-magic might have been involved in the process.

Creationism in Crisis - Not a Founder Couple, Not Even a Founder Species!

Slideshow code developed in collaboration with ChatGPT3 at https://chat.openai.com/

Reconstruction of Neanderthal woman

Photo: Bacon Cph; makeup: Morton Jacobsen
https://doi.org/10.1371/journal.pbio.0020449.g001

Nose shape gene inherited from Neanderthals - UCL News

One of the associated dogmas of creationism, with its slavish adherence to Bible literalism, is the legend of Adam & Eve as a single founder couple of the human species without ancestors, together with a genocidal flood 4000 years ago in which the human population was reduced to just eight octogenarians who were the incestuous ancestors of all living humans.

In order to sustain that belief, creationists need to ignore all the evidence that shows several lines of uninterrupted mitochondrial DNA (female) history going back hundreds of thousands of years and several uninterrupted lines of Y chromosome (male) history.

This same genetic evidence also shows that the last common female ancestor and the last common male ancestor of all living humans could not even have lived contemporaneously, let alone met and committed the 'original sin' that we are all supposedly guilty of and need the vicarious redemption by the blood sacrifice of an innocent person to be saved from being punished for by an invisible, mind-reading sky man.

Another major problem for creationists is the evidence that non-African Homo sapiens all carry evidence not only that there never was a severe bottleneck in evolutionary history but that we interbred with at least two other hominin species, especially Neanderthals, so that non-African humans carry something like 1-4% Neanderthal DNA.

Some paleoanthropologists have even suggested that Neanderthals never died out but were simply absorbed into the growing Eurasian Homo sapiens population to the extent that there is now more Neanderthal DNA in the human population than there ever was in the total Neanderthal population.

So, not only not a founding couple who could have committed the original sin, but not even a single founding species!