In an example of how the environment, and in this case probably the availability of different food items, can cause changes on which natural selection can act, a study by an international team or reserchers led by Pablo Salmón of Lund University, Sweden, has shown that great tits, Parus major living in an urban environment have paler breasts than those living in a forest environment.
Although this is probably not an evolutionary change, i.e., a change in the frequency of alleles in the population gene pools, as the cause is probably dietary difference, it illustrates how an environmental change can produce changes in features on which natural selection can act to bring about true evolutionary changes, and so begin the process of allopatric speciation.
Of course, there will be creationists who will misrepresent the scientific fact of evolution, either deliberately, or mendaciously in order to mislead others, who will dismiss this as "not evolution", not for the reason given above but because "they're still great tits/still birds" and haven't grown a new structure or turned into an unrelated taxon.
The research is explained in a Lund University press release:
Bilaterians are a group of animals characterized by bilateral symmetry, which means they have a left and right side that are mirror images of each other. This symmetry allows for a clear front and back end, as well as distinct top and bottom surfaces. Bilaterians are among the most diverse and successful animal groups on Earth.
The emergence of bilaterians marked a significant milestone in the evolution of life. They evolved during the Cambrian explosion, a period around 541 million years ago when there was a rapid diversification of complex animal life in the fossil record.
Bilaterians gave rise to a wide array of animal lineages, many of which are still present today. Some of the major groups that evolved from bilaterians include:
Deuterostomes: One of the major branches of bilaterians, deuterostomes include several important animal groups, such as vertebrates (fish, amphibians, reptiles, birds, and mammals) and echinoderms (starfish, sea urchins, and sea cucumbers).
Protostomes: Another major branch of bilaterians, protostomes include diverse groups such as arthropods (insects, spiders, crustaceans), mollusks (snails, clams, squids), annelids (earthworms, leeches), and many others.
Bilaterians were crucial in shaping the animal kingdom and played a pivotal role in the complex ecological relationships that emerged throughout Earth's history. They eventually diversified into the incredible variety of animal species that we see today.
ChatGPT3 "What were bilaterians and what did they evolve into?" [Response to user question] Retrieved from https://chat.openai.com
Imagine, you're a creationist fool whose cult leaders have made to feel smugly self-important because a supernatural magic man created your ancestors specially with uniquely humans abilities that set you apart from the other animals, just a few thousand years ago, like the ability to learn, remember and have complex social interactions.
Then along comes a bunch of those spoil-sport scientists who shows that the genes for those things evolved in some very primitive ancestors, the bilaterians, 650 million years ago and so are shared with all the multitude of descendants of those primitive organisms.
How do you handle this new information while still feeling the smugly self-important special creation of the creator of the universe?
You can't allow yourself to think you could be wrong, because that would spoil the whole delusion, so you ignore the science, abuse the scientists, or simply declare it all wrong, and carry on believing the myth of your special importance.
But the problem is the research findings are still there and won't go away just because you've ignored them or declared them wrong, so, whatever you do, avoid reading what follows because it is from a press release from the university of Leicester, UK, where the leaders of the research team were from, and the open access paper in Nature Communications where they published their findings:
How a 'Macro-Evolutionary' Change can be Produced by Changes to a Few Genes.
A transient change in expression of one gene (Shh) can produce a cascade of developmental events leading to the formation of feathers instead of scales
Lurk a while in any Evolution vs Creationism group in the social media and you can guarantee a creationist will try to argue that a given example of evolution which they have probably just deamnded be provided, and which conforms to the scientific definition of evolution - any change in allele frequency over time - is not real evolution because it wasn't 'macro-evolution' which they will define as a change in 'kind' or the evolution of a new species, even the evolution of new structures - whichever definition they think stands the best chance of winning.
I've been at this for long enough to remember how, when the early internet 'bulletin boards' on CompuServe had morphed into thriving debate 'forums', creationists would simply argue that there was no such thing as evolution, full stop! It simply never happened; not in the slightest. No Way! Everything was created exactly as it is today during 'Creation Week' a few thousand years ago! Any evidence to the contrary was a forgery by evil scientists or had been planted by Satan.
Then, in the face of so much evidence, particularly the very large number of living and extinct species and the impossibility of them all being collected together in a few days, herded onto a wooden boat and surviving for a year, they began to concede that there had indeed been evolution, but only limited to evolution withing species, and evolution moreover at a phenomenal rate, far exceeding anthing proposed by biologists, so as to produce the millions of species from a few 'kinds' that survived the genocidal flood their putative creator had inflicted on its creation, just a few thousand years ago.
What creationists are doing is moving the goal-posts by redefining a well-understood scientific term to place it beyond what science actually claims, so they can demand evidence of something that no evolutionary biologist ever claimed - that a single mutation produced a new species or that one species gave birth to another in a single event, ignoring the fact that evolutionary biologists understand the evolution is normally a slow process which takes place in the species gene pool, with the instances of new species arising by, for example, hybridization, being rare exceptions, but nevertheless, natural processes, not requiring supernatural entities to explain.
So, ask a creationist now wedded to the notion that real evolution needs to be 'macro-evolution' to define a reptile 'kind' and a bird 'kind' and they will normally define a reptile 'kind' as having scales and a bird 'kind' as having feathers, ignoring the fact that paleontologists have discovered several feathered dinosaurs (reptiles).
Now, present a creationist with an example such as the one in this research paper, where changes to a small number of genes resulted in what they would define as 'macro-evolution', i.e., a change in 'kind' because that change in chickens results in them growing feathers where they normally grow scales, showing the feathers are simply evolved scales.
A rather beautiful large spider is rapidly spreading across the southern USA, aided by a couple of attributes that enable it to adapt to human habitation, in a stunning example of how the environment can select for species fitted to live and thrive in it. A related species, T. clavipes, has already established itself in southern USA.
The spider, Trichonephila clavata, is a very large, but harmless (to humans), Jorō spider, the subject of a recent research paper in the journal Arthropoda. The research, carried out by researchers, by Andrew K. Davis and Amitesh V. Anerao of Odum School of Ecology, University of Georgia, Athens, GA, USA.
The study shows that, in a classic example of how particular traits can enable a species to extend its range, T. clavata is good at living alongside humans. Rather than being aggressive, which most people would assume is the reason it is out-competing native American spiders, T. clavate is particularly shy and non-aggressive. Despite their size and warning colouration, they are harmless to humans and pets. They will only attempt to bite if picked up and trapped and even then, their fangs aren't large enough to pierce human skin.
Interestingly, their avoidance strategy is to remain completely motionless for about an hour when disturbed, unlike most spiders which normally resume activity after few minutes, leading the researchers to classify them as 'shy' rather than aggressive.
The research is explained in a University of Georgia press release:
New study suggests the massive spiders are gentle giants, mean people no harm
One of the ways that people think this spider could be affecting other species is that it’s aggressive and out-competing all the other native spiders, so we wanted to get to know the personality of these spiders and see if they’re capable of being that aggressive. It turns out they’re not.
They basically shut down and wait for the disturbance to go away. Our paper shows that these spiders are really more afraid of you than the reverse.
One thing this paper tells me is that the Joros’ rapid spread must be because of their incredible reproductive potential,” Davis said. “They’re simply outbreeding everybody else. It’s not because they’re displacing native spiders or kicking them out of their own webs.
Dr. Andrew Davis, lead author
Odum School of Ecology,
University of Georgia, Athens, GA, USA.
Despite their intimidating appearance, the giant yellow and blue-black spiders spreading across the Southeastern U.S. owe their survival to a surprising trait: They’re rather timid.
According to a new study from the University of Georgia, the Jorō (Joro) spider may be the shyest spider ever documented.
The researchers compared more than 450 spiders’ responses to a brief and harmless disturbance across 10 different species.
While most spiders froze for less than a minute before resuming their normal activities, the Joro spiders remained motionless for more than an hour.
In fact, Joros are relatively harmless to people and pets. Joros won’t bite unless cornered. And even if you did manage to somehow annoy a Joro into biting you, its fangs likely wouldn’t be large enough to pierce your skin.
A female Joro spider spins its web. The 30mm scale bar is included for size reference.
Credit: Jeremy Howell
Most spiders begin moving quickly after stress, Joros remain immobile for 60-plus minutes
To examine the spiders’ reaction to stress, the researchers used a turkey baster to gently blow two rapid puffs of air onto individual spiders. This minor disturbance causes the spiders to “freeze” for a period of time, going absolutely still.
The researchers tested more than 30 garden spiders, banded garden spiders and marbled orb weavers. They also analyzed similar data from previously published, peer-reviewed papers that assessed the response of 389 more spiders, comprising five additional species.
All of those spiders began moving again after an average of about a minute and half of stillness.
The Joros, however, stayed frozen with no body or leg movement for over an hour in most cases.
The only other spider species that exhibited a similarly extended response was the Joro spider’s cousin, the golden silk spider. Known as Trichonephila clavipes, the golden silk spider and the Joro spider are from the same genus.
A Joro spider feasts on a caterpillar.
Joros may be invasive, but they’re not aggressive
Most people think ‘invasive’ and ‘aggressive’ are synonymous. People were freaking out about the Joro spiders at first, but maybe this paper can help calm people down.
They’re so good at living with humans that they’re probably not going away anytime soon.
Amitesh Anerao, co-author of the study,
Undergraduate researcher,
Georgia University, Athens, GA, USA
Officially known as Trichonephila clavata, the East Asian Joro spider first arrived in Georgia around 2013. The species is native to Japan, Korea, Taiwan and China, and likely hitched a ride stateside on a shipping container.
The species has since rapidly spread across the state and much of the Southeast. Joro spiders easily number in the millions now. And there’s not much we can do to stop them from increasing their range.
Davis’ previous research even suggested the invasive arachnids could spread beyond their current habitats and through most of the Eastern Seaboard.
Sunlight streams through the elaborate webs made by Joro spiders
Joro spiders built to withstand human activity
Joros are regularly spotted in areas native Georgia spiders don’t typically inhabit.
They build their golden webs between powerlines, on top of stoplights and even above the pumps at local gas stations—none of which are particularly peaceful spots.
The researchers believe the Joro spiders’ shyness may help them better endure the barrage of noise, vibrations and visual stimuli they consistently encounter in urban settings. Their prolonged freeze response to being startled could help conserve the Joro spiders’ energy.
If you’re wondering how something so mild-mannered could spread the way Joro spiders have, you aren’t the only one.
Arachnophobes can take solace in the Joro spiders’ meek and gentle temperament. But the spiders are likely here to stay.
Figure 2. Behavioral responses of spiders to a mild disturbance stimulus (air puff), from our tests, plus from data presented in published studies (see Table 1). Shown are the mean durations of time spent in a “thanatosis” state after receiving the stimulus.
The researcher’s paper is available, open access, in the journal,Arthropoda:
Abstract
The jorō spider (Trichonephila clavata, originally from east Asia) has been introduced in the southeastern United States, and is rapidly expanding this range, leading to questions about what facilitates this spread. Meanwhile, its cousin, the golden silk spider (T. clavipes), already has a range that covers most of the southeast. In an ongoing effort to understand the behavior of jorō spiders in their introduced range, we undertook the current project to evaluate how they react to perceived threats, which can inform us on how a species interacts with conspecifics, or how well it can tolerate anthropogenic disturbances. We collected mature females of both Trichonephila species, plus three locally common orb-weaving species in Georgia, and we evaluated the time spent immobile after experiencing a mild disturbance (a brief puff of air). We also collected similar “air puff response” data for five other North American species from the published literature. Collectively, the dataset totaled 453 observations of freezing behavior across 10 spider species. Comparing these data across species revealed that most spiders remained immobile for under a minute after the stimulus. Meanwhile, both Trichonephila spiders remained immobile for over an hour, which appears to be unprecedented, and suggests that spiders in this genus are the “shyest” ever documented. This reaction could also allow Trichonephila spiders to tolerate urban environments by remaining motionless throughout each disturbance instead of fleeing.
A classic study showing how traits can facilitate the spread of a species into new territories provided the local environment provides the right selectors, if not, of course, introduction won't succeed. And once again confirming the relationship between a species and its environment and how the latter selects for traits which produce more copies than other alleles.
All perfectly understandable in terms of natural processes, with not a hint that supernatural magic had to be involved at some point.
And yet creationism is still managing to recruit new scientifically illiterate fools into the cult, despite all its counter-factual claims and readily available evidence refuting them.
Butterflies first began to diverge from moths about 100 million years ago. It had been assumed that this was to avoid nocturnal bats by flying during the day, but a group of geneticists led by Akito Y. Kawahara, of the McGuire Center for Lepidoptera and Biodiversity in the Florida Museum of Natural History, FL, USA, have now shown that a diurnal existence was made possible by the evolving relationship between flowering plants and bees, which provided an energy-rich source of nectar.
By analysising the DNA from more than 2,000 species representing all butterfly families and 92% of genera, the world-wide team of scientists have traced the movements and feeding habits of butterflies through time in a four-dimensional puzzle that led back to North and Central America. Their results were published, open access, a couple of days ago, in the journal Nature, Ecology & Evolution.
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:
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.
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.
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.
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.”
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 data1,2. 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 regions3,4. 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 sequences5,6.
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.
Slideshow code developed in collaboration with ChatGPT3 at https://chat.openai.com/
Fossils from the Lower Cambrian Yu'anshan Formation at Mafang (Figs. A-K) and Ercaicun (Fig. L) near Haikou, Kunming. All bar scales 10 mm except: C, I, 5 mm; L, 1 mm. Abbreviations: an, antenna; ap, appendage; as, axial spine; ex, exopodite; eye, compound eye; fc, free cheek; hs, head shield; leg, tentacle-like leg; te, trunk end. A) Three lobopodians (arrowed separately in different colors) of Microdictyon sinicum coexisting with their host Eldonia eumorpha (RCCBYU 10414). B) Fuxianhuia protensa (RCCBYU 10192), an adult with three juveniles (arrows). C) Eoredlichia intermedia with one free cheek detached (RCCBYU 10199). D) Four laterally compressed Leanchoilia illecebrosa (RCCBYU 10193). E) Concentration of exoskeletons of Yunnanocephalus yunnanensis (RCCBYU 10366). F) Dense accumulation of Yunnanozoon lividum (RCCBYU 10418). G) Eoredlichia intermedia (RCCBYU 10190). H) Xandarella spectaculum (RCCBYU 10191), with head shield, antennae and appendages preserved in separate laminae. I) Naraoia longicaudata (RCCBYN 10367) with nonsymmetry gut fillings (arrow). J) Dorsoventrally compressed Leanchoilia illecebrosa (RCCBYU 10194). K) Paucipodia inermis (RCCBYU 10186) preserved across two thin layers marked by the dark shadow. L) Kunmingella douvillei (RCCBYU 10196) with outstretched appendages and trunk.
The bad news for creationism continues with the publication of yet another paper refuting one of their central dogmas - the lie that the so-called 'Cambrian Explosion' was a sudden creation of all the basic body plans of the major phyla, without ancestors, in a single act of magical design and creation.
The creationist argument of course depends on a deliberate misrepresentation of the metaphorical use of the word 'explosion' in this context, which is used in biology to describe a relatively rapid radiation of new taxa such as frequently happens when the potential evolutionary landscape changes due either to a major geological/cosmological event, or due to the evolution of new capabilities such as air-breathing and terrestrial existence or flight, or, in plants, new methods of fertilisation such as pollen, resulting in the explosive radiation of flowering plants.
Creationist frauds pretend it is used literally, to mean a sudden single event.
There was a lesser-known but similar 'explosive' increase in biodiversity during the Ordovician (approximately 485 to 443 million years ago) - the Great Ordovician Biodiversification ‘Event’ (GOBE).
The Cambrian explosion is a term used to describe a rapid diversification of animal life that occurred approximately 541 million years ago during the Cambrian Period. It is considered to be one of the most significant events in the history of life on Earth, as it marked the appearance of the first complex animal forms
The Cambrian Period, which lasted from approximately 541 to 485 million years ago, was characterized by a rapid increase in biodiversity, with the emergence of a wide variety of animal phyla. Fossil evidence from this period shows the appearance of many new body plans, including those of arthropods, mollusks, echinoderms, and chordates. The diversification of these groups was likely driven by a combination of environmental and evolutionary factors, including the availability of new ecological niches and the evolution of new genetic and developmental pathways.
In yet another rebuttal of the Creationist claim that the Theory of Evolution is being discarded by mainstream biologists as an explanation for observable evidence, an international team of researchers led by scientists from Aarhus University, Denmark have investigated the beta diversity of woodlands worldwide to assess the effects of climate change since the last ice age, 21,000 years ago.
Incidentally, 21,000 years is more than twice as long ago as creationists believe Earth was magicked into existence by a magic man using magic words. Also, there was no sign of a global flood a few thousand years ago.
Beta diversity is a measure of how diversity differs between locations.
Beta diversity is a term used in ecology to describe the variation in species composition among different habitats or ecosystems. It refers to the differences in species richness (the number of species) and species composition (the identity of the species present) among different communities or sites.
Beta diversity can be measured in different ways, including using indices such as the Jaccard index, the Simpson index, or the Bray-Curtis index. These indices provide a measure of the degree of dissimilarity between communities based on their species composition.
Beta diversity is important in ecology because it provides insights into the distribution of species and the factors that influence their distribution. For example, if beta diversity is high between two habitats, it suggests that the environmental conditions in those habitats are different and may support different sets of species. Conversely, if beta diversity is low, it suggests that the environmental conditions are similar and may support similar sets of species.
Beta diversity can also be used to assess the effects of human activities on biodiversity. For example, if beta diversity is lower in an area that has been impacted by human activities, it suggests that those activities have homogenized the habitat and reduced the diversity of species that can survive there.
In summary, beta diversity is a key concept in ecology that helps us understand the variation in species composition among different habitats or ecosystems, and can provide insights into the factors that influence species distribution and the impacts of human activities on biodiversity.
References:
Baselga, A. (2010). Partitioning the turnover and nestedness components of beta diversity. Global Ecology and Biogeography, 19(1), 134-143.
Ferrier, S., & Guisan, A. (2006). Spatial modelling of biodiversity at the community level. Journal of Applied Ecology, 43(3), 393-404.
Jost, L. (2007). Partitioning diversity into independent alpha and beta components. Ecology, 88(10), 2427-2439.
Legendre, P., & De Cáceres, M. (2013). Beta diversity as the variance of community data: dissimilarity coefficients and partitioning. Ecology Letters, 16(8), 951-963.
Vellend, M. (2016). The conceptual foundations of ecological diversity revisited. Ecology Letters, 19(8), 912-923.
ChatGPT. (20 Apr 2023). Tell me about beta diversity in the science of ecology. [Response to a user question].
Retrieved from https://chat.openai.com/
The team found a close link between the global pattern of tree biodiversity and global temperature changes since the peak of the last ice age.
The Aarhus University News release explains the study:
With 99% of all known species having gone extinct, creationists still like to imagine an omniscient god created them. One must assume, therefore, that they believe it created them to go extinct!
It's a strange sort of intelligence that would intelligently design something to fail, but that's the sort of double think creationists need to be capable of to be members of their anti-science cults.
But the good news is that one of these 'creations', the Mediterranean Monk seal, is making something of a comeback, having been reduced to about 800 individuals, mostly around the coast of Greece.
The Mediterranean monk seal (Monachus monachus) is one of the world's most endangered marine mammals and is the only seal species endemic to the Mediterranean Sea. The species is characterized by its monk-like hood, and its gray-brown fur with lighter colored undersides.
Here are some key facts about the Mediterranean monk seal:
Habitat: Mediterranean monk seals are found in the Mediterranean Sea and the eastern Atlantic Ocean, primarily along the coastlines of Greece, Turkey, and North Africa.
Population: According to the International Union for Conservation of Nature (IUCN), the Mediterranean monk seal population is estimated to be between 500 and 700 individuals, making it one of the rarest mammals in the world.
Threats: The primary threats to Mediterranean monk seals include habitat loss, human disturbance, entanglement in fishing gear, and hunting. The species has been heavily exploited for its fur, oil, and meat, and has suffered from a decline in its prey species due to overfishing.
Conservation Efforts: The Mediterranean monk seal is protected under various national and international laws, including the Convention on the Conservation of Migratory Species of Wild Animals and the Convention on the Conservation of European Wildlife and Natural Habitats. Several conservation organizations are also working to protect the species, including the Mediterranean Monk Seal Conservation Society and the Hellenic Society for the Study and Protection of the Monk Seal.
ChatGPT. (10 Apr 2023). Tel me about the Mediterranean Monk seal, with references, please. [Response to a user question]. OpenAI.
The Monk seal was once abundant around the Greek coast and used to breed on the beaches but evolved a change of habit due to persecution by humans who saw it as competition for fish. It now breeds in sea caves and tends to stay in them when not in the sea.
The Greek poet, Homer, mentioned what is probably the monk seal in his Odyssey:
Homer, the ancient Greek poet, mentioned the Mediterranean monk seal in his epic poem, the Odyssey. In Book 4, lines 345-347, he describes the sea-monsters that inhabit the waters around the island of Pharos:
…and the great seal (phoke) was in attendance upon her from the bottom of the sea, even the seal that was wont to come forth last from his lair to bask upon the shore.
In this passage, the Greek word "phoke" is used to refer to the seal, which is believed to be the Mediterranean monk seal. It is interesting to note that the word "phoke" is also the origin of the English word "phocid," which refers to the family of true seals that includes the Mediterranean monk seal.
It is worth noting that the Odyssey was written in the 8th century BCE, long before the Mediterranean monk seal became endangered. At the time, the species was likely abundant and well-known to the ancient Greeks.
It is a sign of cultural evolution that humans are now more inclined to protect endangered species than to persecute them, consequently, the monk seal population has rebounded, and they are now present in Croatia and Albania from where they had disappeared. When a female monk seal, nicknamed Argyro, who became so familiar with humans on the island of Samos that she would lounge in beach chairs and hang out in a cafe, was shot, it caused an outrage throughout Greece. In earlier times, Greek fishermen would boast that they had killed a monk seal as this was considered a good thing to do.
This cultural evolution in humans, where the primitive notion that a god had given all the animals on Earth to humankind to use or abuse as they wished, to one where we realise we all share this one planet and depend on maximising biodiversity if we are all to survive, has allowed the monk seal to reverse its cultural evolution and once again start to come out of the sea caves and appear in numbers on beaches. This is another example of how Humanism is replacing the old, harmful religious superstitions as human ethical evolution rids itself of the regressive influence of religion.
When scientists from the Field Museum of Natural History, Chicago, Illinois, USA, discovered a hummingbird with an iridescent gold throat, they thought they had discovered a new species, but DNA evidence revealed that it was a hybrid between two closely related species - the Pink-throated Brilliant, Heliodoxa gularis and the Rufous-webbed Brilliant, H. branickii.
The problem was that the two parent species both had pink throats, so you might expect a hybrid to have a pink throat also, not glittering gold.
It's not often these days that we have some good news about biodiversity and the mass extinction now underway due to human interference with the environment, climate change, competition for living space and food production, etc, but here are a few small crumbs from Australia, where recent surveys have shown that 29 species which were once critically endangered, are now back from the brink of extinction.
The following article reprinted from The Conversation under a Creative Commons license is by five leading Australian conservationists. The article has been reformatted for stylistic consistence. The original can be read here.
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