The thing about evolution that distinguishes it from intelligent design is that evolution is utilitarian. It settles for something that works better than what preceded it, which is different from designing a perfect solution to a problem. Near enough is good enough because anything which is an improvement gets pushed up the frequency listing in the gene pool. So, organisms over time have accumulated sub-optimal systems that sometimes fail and cause other problems.
One of those systems is the way DNA is replicated - which is so error prone that error correction mechanisms have evolved over time, but they don't always work either, so we have the phenomenon of the 'jumping genes' that get inserted in the wrong place in the genome, sometime in the middle of a functional gene or in a control section adjacent to a functional gene, causing genetic defects.
So, in the best Heath-Robinson approach to design, rather than abandoning that design and starting again, the way any intelligent designer would do, another layer of complexity is needed to try to mitigate the occasion when the system fails.
So, what organisms have evolved over the years is a process for neutralising these 'jumping genes' by attaching methyl groups to one of the bases which prevents it being transcribed. This is a part of the epigenetic system by which the specialised cells of multicellular organisms turn of unwanted genes and only allow the genes for their speciality to be active - a layer of complexity needed because the way cells replicate was inherited from their single-celled ancestors where the whole genome needs to be included in every daughter cell.
Animals, such as mammals have two enzymes which attach this methyl group depending on the DNA 'context', but plants have multiple enzymes for doing the same thing. The question is why do plants need these multiple enzymes?
On problem with believing a myth that Earth was made out of nothing by magic 6-10,000 years ago is that there are paintings in caves in France that are older than that, showing animals that were around before then.
And a problem with believing that the same magician created all living things just as they are today without any ancestors, is that those same cave paintings show species that were ancestral to some of the animals that are around today, such as domestic cattle.
And a problem with believing that the same magician created all the animals for the benefit of humans is the evidence that all our domestic animals, with almost no exceptions, have been improved by selective breeding from wild ancestors. Did their putative creator not know what humans would need or how they would use the animals it created for them?
Aurochs, their evolution and relationship to domestic cattle.
Aurochs (Bos primigenius) were large wild cattle that roamed parts of Europe, Asia, and North Africa. They are considered the ancestors of modern domestic cattle, playing a significant role in human history and agriculture. Here's an overview of the aurochs, their characteristics, history, and their relationship to modern cattle.
Physical Characteristics
Size: Aurochs were significantly larger than modern cattle, with bulls standing up to 6 feet (1.8 meters) at the shoulder and weighing up to 1,500 pounds (700 kg) or more. Cows were generally smaller than bulls.
Appearance: They had a muscular build with long legs and a slender body, which allowed them to move quickly. They possessed a distinctive hump over their shoulders.
Color: Bulls were typically dark with a lighter "eel stripe" down the back, while cows were generally reddish-brown.
Horns: Aurochs had large, forward-curving horns, which could reach up to 31 inches (80 cm) long. These horns were crucial for defense against predators and in fights between males.
Evolution and Extinction
Evolution: The aurochs evolved around 2 million years ago in India and spread across Europe, Asia, and North Africa. Over time, isolated populations adapted to their environments.
Extinction: The last recorded aurochs died in 1627 in Poland due to hunting, habitat loss, and diseases spread by domesticated cattle. Their extinction marked the end of the species, but they live on genetically through domestic cattle, which were bred from aurochs around 8,000 to 10,000 years ago.
Relationship to Domestic Cattle
Domestication: Modern domestic cattle (Bos taurus and Bos indicus) were domesticated from different auroch populations. Early humans domesticated aurochs in two main areas:
Bos taurus was domesticated in the Fertile Crescent (modern-day Middle East).
Bos indicus (zebu cattle) was domesticated in the Indian subcontinent.
Genetic Influence: Domestic cattle have inherited many traits from their auroch ancestors. Selective breeding by humans introduced variations in size, color, horn shape, and other physical traits to better suit agricultural needs.
Behavior: Domestic cattle have been bred for docility and other traits that make them manageable for farming. Aurochs, on the other hand, were more aggressive and less tolerant of human presence.
Breeding Back Efforts
In recent years, there have been efforts to "breed back" cattle that resemble the aurochs. Breeding back does not resurrect the aurochs genetically but seeks to produce cattle that resemble aurochs in appearance and behavior.
Heck Cattle: In the early 20th century, German zoologists Heinz and Lutz Heck attempted to recreate aurochs by selectively breeding European cattle breeds with certain aurochs-like features.
TaurOs Project: Launched in 2008, this project uses selective breeding of various cattle breeds to produce animals that physically and behaviorally resemble aurochs, focusing on rewilding European landscapes.
Role in Ecosystems and Rewilding
Aurochs once played a critical role in their ecosystems by grazing on grasses, which helped maintain the balance of plant species and created habitats for other animals. In rewilding efforts, cattle resembling aurochs are introduced to landscapes where their grazing patterns help to maintain open grasslands and support biodiversity.
Cultural Significance
Aurochs appear in ancient art, mythology, and folklore across many cultures. They were revered as symbols of strength and vitality and often featured in prehistoric cave paintings, such as those in Lascaux, France, which date back over 17,000 years.
Summary
Ancestors of Domestic Cattle: Aurochs are the wild progenitors of domestic cattle, with genetic links to both Bos taurus and Bos indicus.
Distinctive Features: Large, muscular, and possessing large horns, aurochs were much larger than modern cattle.
Rewilding and Conservation: Through efforts like the Heck Cattle and TaurOs Project, conservationists attempt to restore the ecological impact that aurochs once had on European landscapes.
Legacy: Although extinct, the aurochs' genetic legacy continues in domestic cattle, and they remain an iconic symbol in history and conservation.
The story of the aurochs highlights the powerful connection between humans and wild animals, showcasing how our ancestors' choices shaped the landscapes and species we see today.
And all these questions come from a paper published recently in Nature which reports on the analysis of the genome of 38 Aurochs from bones stretching back over some 50,000 years from sites across Eurasia from the UK to Siberia. The team of geneticists from Trinity College and other universities have explained their findings in a Trinity College press release:
Ancient DNA brings to life history of the iconic aurochsGeneticists from Trinity, together with an international team of researchers, have deciphered the prehistory of aurochs – the animals that were the focus of some of the most iconic early human art, and whose tale is intertwined with climate change and human culture.
The team analysed 38 genomes harvested from bones dating across 50 millennia and stretching from Siberia to Britain in this work.
The aurochs roamed in Europe, Asia and Africa for hundreds of thousands of years. Adorned as paintings on many a cave wall, their domestication to create cattle gave us a harnessed source of muscle, meat and milk. Such was the influence of this domestication that today their descendants make up a third of the world’s mammalian biomass.
We normally think of the European aurochs as one common form or type, but our analyses suggest there were three distinct auroch populations alone in Europe – a Western European, an Italian, and a Balkan. There was thus a greater diversity in the wild forms than we had ever imagined.
Dr Mikkel-Holger S. Sinding, co-author
Department of Biology
University of Copenhagen, Copenhagen, Denmark.
Intriguingly, climate change also wrote its signature in aurochs genomes in two ways:
First, European and north Asian genomes separated and diverged at the beginning of the last ice age, around 100,000 years ago, and did not seem to mix until the world warmed up again at its end.
And second, genome-estimated population sizes dropped in the glacial period, with a more pronounced hard time endured by European herds. These lost the most diversity when they retreated to separated refugia in southern parts of the continent before repopulating it again afterwards.
The most pronounced drop in genetic diversity occurs between the period when the aurochs of southwest Asia were domesticated in the north of the Fertile Crescent, just over 10,000 years ago, to give the first cattle.
Remarkably only a handful of maternal lineages (as seen via mitochondrial DNA which is handed down via mothers to their offspring) come through this process into the cattle gene pool.
A Pleistocene aurochs from the Upper Rhine Valley, around 50,000 years old.
Image credit Staatliche Schlosser and Garten Hessen.
Although Caesar exaggerated when he said it was like an elephant, the wild ox must have been a highly dangerous beast and this hints that its first capture and taming must have happened with only a very few animals. However, the narrow genetic base of the first cattle was augmented as they first travelled with their herders west, east and south. It is clear that there was early and pervasive mating with wild aurochs bulls, leaving a legacy of the four separate preglacial aurochs ancestries that persists among the domestic cattle of today.
Professor Dan Bradley, senior author
Smurfit Institute of Genetics
Trinity College Dublin, Dublin, Ireland.
Abstract
Now extinct, the aurochs (Bos primigenius) was a keystone species in prehistoric Eurasian and North African ecosystems, and the progenitor of cattle (Bos taurus), domesticates that have provided people with food and labour for millennia1. Here we analysed 38 ancient genomes and found 4 distinct population ancestries in the aurochs—European, Southwest Asian, North Asian and South Asian—each of which has dynamic trajectories that have responded to changes in climate and human influence. Similarly to Homo heidelbergensis, aurochsen first entered Europe around 650 thousand years ago2, but early populations left only trace ancestry, with both North Asian and European B. primigenius genomes coalescing during the most recent glaciation. North Asian and European populations then appear separated until mixing after the climate amelioration of the early Holocene. European aurochsen endured the more severe bottleneck during the Last Glacial Maximum, retreating to southern refugia before recolonizing from Iberia. Domestication involved the capture of a small number of individuals from the Southwest Asian aurochs population, followed by early and pervasive male-mediated admixture involving each ancestral strain of aurochs after domestic stocks dispersed beyond their cradle of origin.
One interesting finding is that the aurochs split and diversified during a glacial period when different populations were in different refugia, where they diversified genetically. This is reflected in the DNA inherited by domestic cattle and shows allopatric speciation in progress.
Another interesting finding is how the domesticated cattle and the wild aurochs continued to interbreed with domestic cattle, with auroch bulls mating with domestic cows, showing how diverging species can interbreed for a period until barriers to hybridization evolve.
All this paints a much more interesting picture of the origins of domestic cattle from wild ancestors than the childish one involving magic that creationists find easier to understand. It also poses the question for creationists - why didn't their putative designer design domestic cattle fit for purpose - docile and a high milk yield - that had to be bred into them through an extended period of selective breeding because their wild ancestors were too big and dangerous?
Being parochial Bronze Age pastoralists who knew about nothing and nowhere that was more than a day or two's walk from their hill pastures in Canaan, those who made up the Hebrew creation myths could not possibly have been aware that there were other cultures in far-away places like China, Korea and Japan, which had ancient histories going way back before the myth-makers thought Earth was created, and which were unscathed by an global flood at the time in which they set that tale.
Had they been aware of them, they could have made up slightly more plausible myths with a more realistic timeline, instead of requiring their believers to try to compress everything that's happened in the entire 14-billion-year-old Universe into 10,000 years.
But how could they have done so when they had no-one to teach them the real history of the planet and the people living on it? All they had was their own limited imagination and a handful if inherited myths from neighbouring culture, like Egypt and Sumeria, for theirs was a backward, illiterate culture from the fearful infancy of our species, dependent on oral traditions and superstitions.
How could they possibly have known, for example, that a population of humans had been more or less isolated for about 6,500 years, ending at about the time the myth-makers believed Earth was made out of nothing by magic, complete with a dome over it to cover the small, flat place they called home? They would have known nothing about immigration from China or from the Korean Peninsula into the Japanese archipelago that brought this period of isolation to an end and probably resulted in the present-day population of Japan.
So, of course, they saw nothing wrong with inventing a tale about a genocidal flood killing everyone apart from 8 related survivors, or of building a tower to reach above the dome or about a panicking god making them all speak different languages so they couldn't work in cooperative groups any more, and yet, if their tale is to be believed, the descendants of those few survivors, all speaking different languages, migrated to places like China, Korea and Japan where they all adopted the local language and writing that had been used for several thousand years, forgot all about Noah and his flood and invented new gods and religions, whereas the myth-makers of Canaan remembered it all word-perfect in every detail...
So, how do we know the record they left was wrong?
It has often been a theme of my blog posts how, if we regard cells as the result of conscious (I won't use the term 'intelligent' as that's singularly inappropriate, as we shall see) design then the picture quickly emerges of a bungling incompetent, cobbling together Heath-Robinson solutions to problems of its own incompetent making and lack of foresight.
The entire system of epigenetics, for example, is only necessary in a multicellular organism with its cell specialisation because specialised cells only need a small subset of the entire genome, yet, because cells replicate using exactly the same process that single-celled organisms use, where the entire genome needs to be replicated in every daughter cell, the cells of multicellular organisms such as humans each receive the entire species genome. So, most of it needs to be turned off.
This is where the epigenetic system comes in where methyl groups are attached to key bases in the DNA which prevents that section being transcribed into RNA, effectively switching the gene off. There are other components to the epigenetic system, but that is the pertinent component as far as this particular blunder is concerned.
The problem starts when a methyl group is attached to a cytosine base (C in the CGTA genetic code) which is next to a guanine(G) base.
We are continually being assurd by gullible cretionists that the Theory of Evolution (TOE) is 'a theory in crisis' becase a growing body of biologisdts have abandonned it in favour of the creationists superstition of intelligent [sic] design.
This has been a creationist fantasy for at least the last 50 years since when it is supposedly about to happen, any day now, real soon (a bit like The Second Coming of Christ - something which, despite regular announcements that it will happen next Wednesday at noon, never happens - but its gunna, you see!)
However, when we read the scientific publications of these biologists who are allegedly abandoning the TOE, we see no signs whatever of any abandonment; quite the opposite. We see the TOE as firmly embedded in biological science as the Laws of Thermodynamics and the Theory of Gravity are embedded in physics, Atomic Theory is embedded in chemistry and Germ Theory is embedded in epidemiology. It forms the bedrock of the science, without which very little makes any sense.
For example, when a bunch of entomologists wanted to understand how a species of herbivorous beetle can eat a toxic plant, they compared it genomically with a related species that doesn't eat the toxic plant to see how the ability to proccess the toxins evolved.
Of course, being scientists, they reject the idea that the beetle was magically created that way by an unproven supernatural entity because none of that can be falsified and the existence of such an entity can't be established, so there is no logical reason to include one in any answer. The fact that their mummies and daddies might have believed in it is irrelevent to their science, because belief doesn't create facts.
Plants like Arabidopsis, seen here, have two options to ensure accurate chromosome division—a molecule called DDM1 and a process known as RNAi. If Arabidopsis loses one of these, it’s fine. But if it loses both, it’s in trouble.
Developmental defects of double, triple and quadruple mutants in RNA-dependent RNA polymerase (rdr1, rdr2, rdr6) and DNA methylation (ddm1) in floral organ identity, leaf shape and fertility (silique length).
The secret to being a good designer or planner is to always have a Plan B. I say that as a former emergency operations centre manager where the future is unpredictable, so I needed to keep as many options open as possible because, as I used to joke, my Plan B was to tear up Plan A and start again.
Now, you can play the percentages game, for example, I could be fairly sure town centres would be fairly busy around 11 pm, especially on a Friday and Saturday night, when in the UK the pubs close, or as we call it, 'chucking out time', and a lot of inebriated people would be out on the streets, fighting over available taxis, over girl/boyfriends or who had got served at the bar out of turn (queue-jumping is a big no-no in the UK).
I also knew from 17 years operational experience that most of the calls would require little more than smoothing ruffled feathers, running checks to exclude underlying medical problems and sending them on their way, so turnover time would be relatively short, and I would get a crew back fairly quickly.
Another peak would be around 1 am when the nightclubs closed, but with a few exceptions such as those the rest of the week would resemble a system in chaos where medical emergencies, traffic accidents and every other imaginable emergency occurred more or less randomly, with statistical patterns only being noticeable over time with a sufficiently large database.
Later on, I became the data analyst who looked for those patterns and used them to devise deployment plans to minimise average emergency response times, but that's another story.
Juggling acts were the daily routine for an emergency operations centre like mine, as we tried to maintain as much emergency cover as possible while getting help to people who needed it as quickly as possible. And you never knew you had made the right decision until it turned out not to have been the wrong one.
Our major handicap was of course being unable to accurately forecast the future, not just weeks or days ahead but hours and minutes. What we singularly lacked was omniscience for which educated guesses were a poor substitute.
So, to a creationist it might come as something of a shock to learn that their putative designer behaves like a designer/planner who can't foretell the future because, if nothing else, it is allegedly omniscient, and its designs are perfect. As such it shouldn't need a Plan B because Plan A will be perfectly designed for the precise future needs of the species. There should never be an occasion where it needs to tear up Plan A and starts again; it shouldn’t need to consult a large database to look for patterns then work out the probability of that pattern repeating itself and planning its responses accordingly, never knowing if it was the right plan until it turned out not to be.
And yet a team of researchers from Cold Spring Harbor Laboratory, New York, USA has found that the plant, Arabidopsis has a Plan B for when Plan A fails. Plan A is all about making the ramshackle, Heath Robinson process for ensuring mistakes in DNA replication get attended to. In a design which seems to be a characteristic of creationism putative intelligent [sic] designer, a shoddy process needs another layer of complexity to try to make it works, but even that fix breaks and the result of growth defects, sterility and, in many cases in animals, cancers or developmental disorders.
One thing you can depend on with creationism's putative designer is that there will never be a simple solution when there is a more complicated way to solve the problem it just created, and just like William Heath-Robinson, it will try to use pre-existing structures that were designed for an entirely different function, like a pile of books under the legs of a ladder to make it tall enough, and every piece of string holding things together will have knots in it.
And when we look beneath the superficial resemblance of design in, for example, a living cell, we find all manner of if-it-works-it'll-do solutions to problems, like the solution to the problem of breaking DNA that a team of scientists, led by Kaspar Burger, from Julius-Maximilians-Universität Würzburg (JMU) in Bavaria, Germany, have discovered.
The problem arises of course because the method for replicating DNA as cells divide is poorly designed and unnecessarily complicated in the first place. If the putative designer had devised a more sensible method for replicating cells in multicellular organisms than that used for replicating single cells where the whole genome needs to be replicated, many of the problems of erroneous copying wouldn't arise because only a small subset of the genome is needed for specialised cells.
A lower-fungus-farming worker of the rare fungus-farming ant species Mycetophylax asper, collected in Santa Catarina, Brazil, in 2014, on its fungus garden.
One of the 'uniquely human' abilities that creationists traditionally cite in support of their childish superstition that humans were magically created out of dirt as a species separate from other animals, is the fact that humans for the most part, indulge in agriculture - i.e., we grow plants as food - or at least other people do. Most of us in the developed economies buy their produce in shops.
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Like all their other claims of human exceptionalism, it's a nonsense fairy tale, of course. Humans have some unique characteristics that make them a distinct species, but then so does every other species, by definition. There is nothing materially different about humans that makes them subject to different laws of chemistry and physics than other species, of course.
And in respect of agriculture, we are far from unique - ants have been at it for about 66 million years - well before creationists imagine the entire Universe was magically created from nothing by a magic god made of nothing. But this is hardly surprising, since some 99.9975% of the history of life on Earth happened before creationism's legendary 'Creation Week'.
Imagine you're a design engineer tasked to design part of a manufacturing process to be used in two different factories. You produce a solution which works in one factory, so what do you do for the second factory?
If you're creationism putative designer, you forget all about the solution that works, and you design a completely different method for the second factory. It would be far too simple to use the first method you designed for the second factory, obviously. It would be as though there is no communication between the two factories and no sharing of ideas or testing to see which method was the most efficient in terms of time, materials and labor. Each factory would work to its own methods, oblivious of anywhere else or any better solutions.
And that just what creationism's alleged creator appears to have done with two populations of a common coastal plant in Catalonia - a wild member of the cabbage family, Brassica fruticulosa - where different populations have adapted to soil salinity in two different ways.
What can you tell me about the plant Brassica fruticulosa, its distribution and adaptation to different soil conditions?
Brassica fruticulosa, commonly known as Mediterranean cabbage, is a wild species within the Brassicaceae family. It is native to the Mediterranean region, where it thrives in a variety of habitats, including rocky, disturbed, and coastal areas. The species is highly adapted to different environmental conditions, including poor, dry, and calcareous soils, which is a key feature of its resilience.
Distribution: Brassica fruticulosa is primarily found in Southern Europe, North Africa, and parts of the Middle East. Its distribution spans countries like Spain, Italy, Greece, Turkey, and Algeria, extending into coastal regions with Mediterranean climates.
Adaptation to Soil Conditions:
Drought Resistance: The plant is well-suited to dry and nutrient-poor soils, a characteristic of Mediterranean ecosystems. Its deep root system allows it to access water in arid environments, contributing to its drought tolerance.
Calcareous Soils: The species is adapted to alkaline soils, often thriving in limestone-rich areas. It can tolerate high pH levels, which would limit the growth of less adapted species.
Disturbed and Rocky Soils:Brassica fruticulosa also thrives in disturbed habitats, such as roadsides and rocky outcrops. Its ability to grow in these challenging environments shows its resilience to various soil types and disturbances.
This adaptation to different soil conditions is likely linked to its ecological strategy of thriving in marginal habitats, where competition from other plants is less intense.
This was discovered by three researchers from the Universitat Autònoma de Barcelona (UAB) Plant Physiology Lab, in collaboration with researchers from the University of Nottingham (UK), the Max Planck Institute for Biology (Germany), and Charles University in Prague (Czech Republic).
Their findings are the subject of a recent open access research paper in Proceedings of the National Academy of Science (PNAS) and a UAB news release.
Different adaptation strategies to saline soils identified in neighbouring populations of the same plant speciesResearchers from the Faculty of Biosciences have identified two divergent adaptive responses to soil salinity in populations of the same wild species found in the Catalonia’s coastal area, the Brassica fruticulosa, and have pinpointed the genes involved. The study will help to investigate the ways to improve resilience in agricultural species of the same plant family, such as rapeseed and mustard, in the face of a globally relevant stressor as is soil salinization.
The study was recently published in Proceedings of the National Academy of Sciences (PNAS) and is signed by researchers Sílvia Busoms, Glòria Escolà and Charlotte Poschenrieder from the UAB Plant Physiology Lab, in collaboration with researchers from the University of Nottingham (UK), the Max Planck Institute for Biology (Germany), and Charles University in Prague (Czech Republic).
Over the past few years, UAB researchers have worked in close collaboration with members of the University of Nottingham to develop a study model along the Catalan coast to understand the interaction between environmental factors such as salinity and the adaptation of wild populations of the Brassicaceae family. They developed several studies focused on populations of Arabidopsis thaliana, a model organism for biological research, but in this case, they focused on Brassica fruticulosa, a species genetically and morphologically closer to cultivated brassicas such as rapeseed (Brassica napus) and mustard (Sinapis alba).
This research has allowed them to demonstrate that in Catalonia coastal populations of B. fruticulosa use two different strategies to tolerate soil salinity: those from the north (Cap de Creus region) are able to restrict root-to-shoot sodium transport, preventing the damage of the aerial parts. In contrast, those from the centre accumulate sodium in the leaves, but they use efficient mechanisms of osmotic adjustment and compartmentalisation that allow them to tolerate high concentrations of this compound.
The fact that two populations of the same plant species located so close geographically have evolved differently under the same environmental conditions surprised the researchers.
“In general, in all organisms it is expected that species adapting to similar stressors also evolve in a similar way. In our case, however, although in the coastal habitats of the Catalan coast soil salinity can be considered the main selective agent, there must be other factors that have altered the recent evolutionary process of this Brassicaceae species.
Sílvia Busoms, lead author
Department of Plant Physiology
Universitat Autònoma de Barcelona, Barcelona, Spain
This divergence in plant populations so close to each other has rarely been described, not so much because it is an exception, but because in many cases the studies are carried out at the macro-scale.
The Tramontane wind may explain this divergence
In their study, researchers examined in detail the characteristics of the soils and the climatology of all the populations’ location. The only parameter that showed significant differences was evapotranspiration, which was higher in the north due to the Tramontane wind that regularly blows there.
When there is high evapotranspiration, plants absorb more water and at the same time more sodium if they do not have mechanisms to exclude it. Therefore, the strategies used by the plants of the central coastal areas may be insufficient in the conditions of the northern coast. In the study we hypothesise that although they are neighbouring populations, the northern B. fruticulosa evolved differently in order to tolerate both high salinity levels and high evapotranspiration.
Charlotte Poschenrieder, co-author
Department of Plant Physiology
Universitat Autònoma de Barcelona, Barcelona, Spain
To characterise the genetic basis of the two adaptive strategies identified, researchers first created the reference genome of B. fruticulosa, which will contribute to the expansion of the catalogue of reference genomes of eukaryotic species from the Catalan-speaking territories (within the Earth Biogenome Project) and will allow further research with this species. Subsequently, the sequencing of 18 populations and the subsequent genetic and transcriptomic analyses validated the two strategies observed and allowed researchers to propose candidate genes involved in the mechanisms of salinity tolerance.
Salinity is a threat to the planet's agricultural soils and its consequences are greater when it affects impoverished soils such as those found in the Mediterranean basin. A better understanding of the mechanisms of salt tolerance used by plants living there and which have adapted to these conditions is essential to improve the resilience of cultivars that must adapt to the new environmental conditions. “This study, therefore, establishes B. fruticulosa as a promising source of desirable alleles, and the population diversity present in Catalonia as a powerful model for the study of adaptations to saline soils,” researchers conclude.
Original article:
Silvia Busoms, Ana C. da Silva, Glòria Escolà and Levi Yant. Local cryptic diversity in salinity adaptation mechanisms in the wild outcrossing Brassica fruticulosa.
September 24, 2024. Proc Natl Acad Sci. https://doi.org/10.1073/pnas.2407821121
Significance
One might expect that closely related populations of a given species should adapt to the same environmental stressor in the same way due to genetic or physiological constraints. However, this is not commonly tested due to practical limitations. Here, we show that, even at the level of neighboring populations, contrasting adaptive strategies control adaptive responses to high coastal salinity in Brassica fruticulosa, a close wild relative of many crops of worldwide importance. This indicates multiple options for engineering an agriculturally crucial adaptation: soil salinization. These results will be of interest to not only those studying fundamental mechanisms of adaptation, but also resilience improvement in Brassica species.
Abstract
It is normally supposed that populations of the same species should evolve shared mechanisms of adaptation to common stressors due to evolutionary constraint. Here, we describe a system of within-species local adaptation to coastal habitats, Brassica fruticulosa, and detail surprising strategic variability in adaptive responses to high salinity. These different adaptive responses in neighboring populations are evidenced by transcriptomes, diverse physiological outputs, and distinct genomic selective landscapes. In response to high salinity Northern Catalonian populations restrict root-to-shoot Na+ transport, favoring K+ uptake. Contrastingly, Central Catalonian populations accumulate Na+ in leaves and compensate for the osmotic imbalance with compatible solutes such as proline. Despite contrasting responses, both metapopulations were salinity tolerant relative to all inland accessions. To characterize the genomic basis of these divergent adaptive strategies in an otherwise non-saline-tolerant species, we generate a long-read-based genome and population sequencing of 18 populations (nine inland, nine coastal) across the B. fruticulosa species range. Results of genomic and transcriptomic approaches support the physiological observations of distinct underlying mechanisms of adaptation to high salinity and reveal potential genetic targets of these two very recently evolved salinity adaptations. We therefore provide a model of within-species salinity adaptation and reveal cryptic variation in neighboring plant populations in the mechanisms of adaptation to an important natural stressor highly relevant to agriculture.
Today’s accumulation of high-profile cases detailing repeated evolution capture the fascination of biologists. Independently evolved adaptive coloring shifts in mammals and insects, defensive armor in fish, and serpentine and altitude adaptation in plants: these all present not only additional evidence for candidate mechanisms underlying adaptations, but also an optimistic outlook toward “predicting” the course of evolution and inspiring expositions for the public (1–6). Given these iconic cases, an expectation may arise that even at the functional level, neighboring populations of the same species should, due to genetic or developmental constraints and mutation limitation, share evolved strategies of adaptation to the same stressors (7). The logical extension is that natural selection might be expected to predictably drive the origin and maintenance of adaptations at strategic or mechanistic levels. However, this idea has not been sufficiently tested due to restraints on study systems, sampling, resolution, and scale (8). We thus lack a clear understanding of how often an expectation of uniform or repeatable species-wide adaptation strategies is violated in favor of diversity even within single species.
Here, we test this expectation by taking a “hyperlocal” approach in the study of plant adaptation to coastal stressors, focusing on adaptation to high coastal salinity in a strip of coastline in Catalunya, Northern Spain. Previous work on local adaptation of Arabidopsis thaliana in this region detailed geographically and temporally fine-scale adaptive variation in fitness-related traits across environmental salinity gradients, even at the scale of a few kilometers (9, 10). This region is characterized by a positive gradient of soil salinity from inland to the coast, shaping plant species communities and driving the evolution of salinity tolerance mechanisms at the local population- (deme-) level (11). Plant evolutionary responses to these conditions have been observed even in the selfer A. thaliana at fine (3 to 5 km) scale, resulting in functionally adaptive variation (12). Functional confirmation of this is evidenced by selective sweep of a hypomorphic ion transporter HKT1;1, which modulates Na+ leaf concentrations in response to rapid (monthly) temporal and spatial variation in rainfall and soil salinity (9).
Unfortunately, work in A. thaliana has two major limitations: first, due to its overwhelmingly selfing reproductive mode, relative to its outcrossing relatives A. thaliana has 10-fold lower genetic diversity and high rates of spontaneous, population-specific mutations (13). This low diversity also has important consequences in respect to increased homozygosity and effective population size, resulting in genetic drift, reduced effective recombination rates, genomic background effects, and the fixation of maladaptive alleles (reviewed in ref. 14). Second, Arabidopsis is substantially divergent from important Brassica crops, limiting the translational potential of discoveries in this otherwise convenient lab model. Wild outcrossing Brassicas, on the other hand, harbor higher levels of genetic diversity, directly facilitating studies of adaptation (15). Motivated by these considerations, we searched for wild Brassicaceae species with contrasting, recently evolved (within-species) phenotypes in complex coastal adaptations, focusing specifically on salinity tolerance. This resulted here in the identification of a model for local adaptation to coastal salinity, Brassica fruticulosa, and allows us to test hypotheses regarding the scale of local adaptation to high coastal salinity.
The genus Brassica belongs to the Brassicaceae (mustard) family and contains nearly 100 species, many of which are grown globally as vegetables like cabbage, broccoli, kale, and radish, as mustards, as oil crops (placing 3rd after palm and soy), and as fodder for animal feed (16). Brassicas are widely proficient at adapting to new habitats due to recent and recurrent polyploidy events, hybridization, and plastic genomes. These characteristics also make them great targets for genetic manipulation to further enhance resilience (17).
Here, we first perform a large-scale, genus-wide natural variation survey of diverse, wild outcrossing Brassicas in coastal Northeast Spain, eventually testing six candidate species for within-species adaptation to high salinity. From these, we identify and develop one particularly promising model of within-species variation in adaptation to extreme salinity and complex coastal stressors, B. fruticulosa. First described in 1792 by Cirillo (18), B. fruticulosa has not yet been recognized as harboring population-specific salinity adaptation. This has been a missed opportunity, as B. fruticulosa is closely related to Brassica rapa (19, 20) and shares many affinities with this global crop. We then assemble the B. fruticulosa genome using Oxford Nanopore long read sequencing polished with Illumina short reads, and sequence 90 individuals from 18 populations (nine coastal, nine inland) contrasting in salinity and soil parameters defined by ionome levels in leaves and soil in the root space of every individually sequenced wild plant. Using transcriptome data of leaves and roots, we reveal divergent adaptive strategies in response to high salinity in neighboring plant populations. We then perform common garden, physiological, and ion homeostasis experiments to detail these different strategies that evolved in closely neighboring adapted plant populations. Finally, we perform environmental association analysis (EAA) (with soil ionome as phenotype) and genome scans by ecotype to seek a genomic basis of divergent adaptative strategies to high salinity in neighboring B. fruticulosa populations. Taken together, these experiments reveal contrasting adaptive responses to extreme salinity, at the local scale, differing mechanistically at the scale of kilometers.
Fig 6.
Overview of the contrasting salinity tolerance strategies of the North and Central B. fruticulosa coastal metapopulations. Hypothetical model of genes, ion transport, and signaling pathways involved in salinity tolerance mechanisms. Gene symbols are shown in bold letters. Ion fluxes are indicated with black arrows. Gene activation/repression and molecule increase/decrease are indicated with red arrows. Star-framed symbols denote signaling pathways and hormone molecules are circled in green. “ST” = Salt tolerant.
Silvia Busoms, Ana C. da Silva, Glòria Escolà and Levi Yant. Local cryptic diversity in salinity adaptation mechanisms in the wild outcrossing Brassica fruticulosa.
September 24, 2024. Proc Natl Acad Sci. https://doi.org/10.1073/pnas.2407821121
This example is interesting in that it shows the process of allopatric speciation in progress even though the two populations are still regarded as the same species. It's not clear from this paper whether the two population can or do interbreed, but if they do, what would be the consequences for the hybrids? Depending on the mode of inheritance, the offspring's genes could express in three different ways:
Adapted like the northern population.
Adapted like the southern population.
Adapted like both populations.
In the case pf 1 and 2, 50% of the offspring would be maladapted for the local conditions and in the case of 3, it would be adapted for neither and could be non-viable. We can exclude any advantage from being adapted for both locations otherwise there would not be two different populations since they would both carry the same dual adaptation.
So, hybridization would be wasteful with reduced survival of the hybrids. This is environmental pressure to establish barriers to hybridization because plants that don't hybridize will tend to produce more successful offspring than those which do.
From an intelligent [sic] design perspective, this example of doing the same thing in two different ways makes no sense as the work of the same designer. However, given that there is no mechanism for isolated populations to share information and make informed decisions about the best way to adapt to local conditions, then ensure they evolved that way, this makes perfect sense from an evolutionary perspective.
Again, the detail behind a superficial appearance of designs reveals that there was no intelligence involved in the process; instead, the process was a mindless utilitarian process that produced two different solutions to the same problem.
Just as creationism's legendary creator god was creating a small flat planet with a dome over it in the Middle East, there were modern humans living (or rather dying) in South Africa.
A team of scientists led by the Max Planck Institute for Evolutionary Anthropology and including palaeoanthropologists from University of Cape Town, Cape Town, South Africa, have now succeeded in reconstructing the genomes from the remains of 13 individuals who died between 1,300 and 10,000 years ago, including the oldest human genome from South Africa to date.
If the creation myth had any element of truth in it, humans would have radiated from the legendary founder couple to form a thriving community living in a rock shelter in South Africa's Cape Province. Moreover, the evidence now shows that these people were isolated from the rest of humanity for many thousands of years.
Creationists try to get round the absurdity of the Bible myth which has two (or seven) of every species being packed into a wooden boat small enough to survive turbulent seas for a year, by introducing a new element to the myth that their god forgot to include - that there were just two (or seven) of each 'kind' and all of them underwent a period of warp-speed evolution (that non-one seemed to have noted) with several new species popping into existence each generation to give the many millions of known terrestrial species we have today.
Understandably, creationists are reticent to put any numbers on their claim. They won't say how many different 'kinds' there were on the boat, how many new species arose at each generation and for how long this period of fantastical speciation lasted. Nor will they define 'kind' in any meaningful way that matches any recognisable taxon. I have even been told it can mean 'animal kind' and 'plant kind'. It seems to vary according to the needs of the argument.
And they won't say why some 'kinds' have just one or two species while others have hundreds, or in the case of the Asteraceae family of plants, some 34,000 distinct species, so some must have been speciating much faster then other while some hardly bothered if at all.
In the later case, we now have a substantial database compiled by a team at the Naturalis Biodiversity Center, Leiden, The Netherlands which catalogues all 34,000 different species with their geographical distribution, showing how they radiated and diversified into new species, colonising isolated islands and, like Darwin's finches, radiating into different species on each island in an archipelago.
Four researchers working at the University of Arkansas have found a natural mechanism by which new genes can arise, which gives the lie to creationist claims that this is impossible.
Before moving on to the details of their discovery which has just been published, open access, in the Oxford University Press journal Molecular Biology And Evolution, I'll first discuss the current state of understanding of how new genetic information arises naturally, without the need for magic.
The History of dogs and their co-evolution with humans as they diverged from their wolf ancestors is a fascinating and complex story, most of which, like 99.9975% of all of the history of life on Earth occurred before creationist's legendary 'Creation Week'.
'Creation Week' is when creationists believe a magic god made of nothing magicked a small universe consisting of a single flat planet with a dome over it, centred on the Middle East, all out of nothing, in just 6 days about 10,000 years ago, (although why an omnipotent god couldn't have done it all in an instant and needed 6 full days, with a day to recover from the effort, is never explained).
Had the ancient inhabitants of the Iberian Peninsula contrived to get their oral history and origin myths written down in the same way that the Bronze Age Canaanite pastoralists did, we might have had a slightly more accurate and less implausible history. It certainly wouldn't have had daft tales about a global genocidal flood just at the time newcomers with new ideas, a new language and new techniques of animal husbandry were migrating into the area having traversed Western Europe from the Steppes of Central Asia.
Unlike the parochial Canaanite nonsense, it might well have had people, places and animals from more than a day or two's walk from the Canaanite Hills.
Archaeological evidence shows that, at the time when creationist superstition says everyone had been drowned in a genocidal, global flood several thousand feet deep, by a vindictive god, people originating on the Steppes of Central Asia were migrating across western Europe and into the Iberian Peninsula, as though nothing unusual was happening.
Heliconius erato with one wing (right) altered by CRISPR gene. Dorsal view
Luca Livraghi.
Heliconius erato with one wing (right) altered by CRISPR gene. Ventral view
Luca Livraghi.
This is one of those research papers that creationists traditionally misrepresent as 'proving' that something biologists have long known about is wrong, and so it somehow discredits the entire body of science, and, in this specific case, that the existence of RNA that is non-coding but functional, somehow proves there is no such thing as 'junk' DNA.
In reality, of course, it simply shows us that sometimes, evolution happens in unexpected ways.
The assumption, which is almost always valid and based on sound scientific evidence, is that DNA is transcribed into messenger RNA (mRNA) that mRNA is transcribed by ribosomes into proteins. Proteins then serve functions such as structural proteins or as enzymes catalysing chemical processes in the cell. In the special case of so-called homeobox genes (hox genes) these have a regulatory function in a developing embryo, stimulating groups of cells to organise into specific tissues such as limbs, eyes and other specialised tissues, by switching other genes off and on at certain times.
Although both have evolved from a segmented ancestor, as can still be seen in the larvae of insects, spiders and mites differ from insects in the number of major body-parts. While insects have well-defines head, thorax (to which wings and legs are attached) and an abdomen, where the reproductive organs or normally located, spiders, scorpions, tics and mites (arachnids or chelicerates) have just two - a cephalothorax, combining the head and thorax, and an abdomen.
Now scientists have discovered a gene in the chelicerates that controls the development of the 'waist' between the cephalothorax and the abdomen, which is missing in insects. The loss of this gene could be the reason the two groups of arthropods evolved in different directions.
The team of scientists, led by Emily V. W. Shetton, of the Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA, have just published their findings, open access, in PLOS Biology and explained it in a press release reprinted in Science Daily:
The research team also included: Jesús A. Ballesteros of the Department of Biology, Kean University, Union, New Jersey, USA and Pola O. Blaszczyk, Benjamin C. Klementz, and Prashant P. Sharma all of Department of Integrative Biology, University of Wisconsin-Madison.
A favourite creationists straw man parody of science says that evolutionary biologists believe evolution is a process of increasing complexity, leading eventually to humans - the most complex of all species.
This is utter nonsense, of course, being intelligently designed to easily attack and make evolutionary biology look like something no rational person would believe, so creationists dupes can feel smugly superior to scientists without bothering to learn any real science.
Creationists dogma also says that a genome was intelligently designed, so does not contain any redundant or non-coding DNA, since an intelligent designer would not have designed needless complexity and prolific waste (both characteristics of a mindless evolutionary process).
So, it leaves creationists floundering when science discovers genomes many times larger (for larger read 'more complex', in creationist terminology) than the human genome. In fact, the human genome is about average for the number of genes and size of the genome compared to other animals and very much smaller than that of many animals and plants.
News that a team of evolutionary biologists are reassessing what we thought we knew about the dodo, Raphus cucullatus, is a good excuse to look at what the dodo teaches us about evolution.
The dodo was a species of pigeon which had spread to the Indian Ocean island of Mauritius, where in common with many island birds had lost the ability to fly. In the context of an island with no mammalian predators, any advantage of flight is balanced against the greater disadvantage of occasionally being blown out to sea. Natural selection, with no foresight and no plan, results in a flightless bird, and, as events transpire, extinction.
The arrival of Europeans with their rats, cats and dogs and need for supplies for a long sea voyage, was an environmental change that the dodo could not adapt to because evolution has no reverse gear and rarely reinvents what was lost earlier. The ground-nesting dodo like its close relative, on a neighbouring island, the Rodriguez Island Solitaire, Pezophaps solitaria, were doomed. They were extinct by the late 17th century.
Evolution is an unintelligent process. This would not be so, if species like the dodo had been intelligently designed by an omniscient designer, who could have foreseen and prepared for the coming of Europeans with their rats, cats and dogs. It is not an intelligent act to design a species headed for inevitable extinction because it can't adapt to what can be anticipated.
What information do you have on the 'Oxford dodo' and it's role in literature and biology?
The "Oxford dodo" is a significant artifact in both biological and literary history. Here's an overview of its importance:
Historical Background
The Dodo: The dodo (Raphus cucullatus) was a flightless bird native to Mauritius, an island in the Indian Ocean. It became extinct in the late 17th century due to overhunting by humans and the introduction of non-native animals.
Oxford Dodo: The Oxford dodo refers to the most complete known specimen of the dodo, which is housed at the Oxford University Museum of Natural History. This specimen includes the only remaining soft tissue (a dried head and a foot) from any dodo in the world.
Role in Biology
Scientific Study: The Oxford dodo has played a crucial role in scientific studies on the species. Since it includes soft tissue, researchers have been able to extract DNA, providing insights into the dodo's genetic makeup and its relationship to other bird species.
Extinction Studies: The dodo is often cited as one of the earliest recorded examples of human-caused extinction. The Oxford specimen has contributed to studies on extinction, illustrating the impact of human activity on isolated ecosystems.
Role in Literature
Lewis Carroll's "Alice's Adventures in Wonderland": One of the most famous literary references to the dodo is in Lewis Carroll's 1865 novel *Alice's Adventures in Wonderland*. The dodo in the story is believed to represent Carroll himself, who had a stammer and sometimes introduced himself as "Do-do-Dodgson" (Carroll's real name was Charles Dodgson). The character of the dodo in the story is depicted as a wise figure who proposes the "Caucus-race," where everyone wins and all must have prizes—a satire on political processes.
Symbol of Extinction: In literature and popular culture, the dodo has come to symbolize obsolescence and extinction, often representing something that is outdated or doomed to disappear. The Oxford dodo, as a physical reminder of a lost species, has reinforced this symbolism.
Cultural and Educational Impact
Exhibitions: The Oxford dodo has been featured in various exhibitions, not just as a scientific specimen but also as a cultural icon. It serves as a powerful educational tool about biodiversity loss and conservation.
Inspiration for Research and Art: The dodo has inspired a wide range of research, from studies in paleontology and conservation biology to its portrayal in art, literature, and even in discussions about colonialism and its impact on indigenous species.
Recent Developments
DNA Analysis: Advances in DNA technology have allowed scientists to conduct more detailed studies on the Oxford dodo's remains, leading to a better understanding of its biology and the causes of its extinction. These studies are crucial for understanding the dynamics of extinction and the evolution of island species.
Conservation Lessons: The story of the dodo, as illustrated by the Oxford specimen, is frequently used in discussions about conservation and the need to protect endangered species today. It serves as a cautionary tale about the consequences of human activity on the environment.
In summary, the Oxford dodo is more than just a biological specimen; it is a symbol of extinction and a cultural icon that has influenced literature, conservation science, and our understanding of human impact on the natural world.
Is there any evidence for the story that it was rescued from a bonfire of 'rubbish' at either the Ashmolean or the Oxford University Natural History Museum?
The story that the Oxford dodo was rescued from a bonfire of "rubbish" at the Ashmolean Museum, or the Oxford University Museum of Natural History is a widely circulated anecdote, but its accuracy is somewhat debated. Here's what is known:
Origins of the Story
Historical Context: The story typically claims that the dodo specimen, or parts of it, were nearly discarded during a clean-up or reorganization at one of the Oxford museums, likely the Ashmolean Museum, where the dodo was initially housed. The account suggests that someone recognized the value of the remains just in time to save them from being burned as rubbish.
Attribution: This anecdote is often linked to John Tradescant the Younger, an early naturalist and collector, whose collection formed the core of the Ashmolean Museum's early holdings. It is also sometimes associated with Elias Ashmole, the museum's founder.
Supporting Evidence
Lack of Concrete Records: There is no definitive archival evidence or documentation to substantiate the bonfire rescue story. The tale seems to have been passed down through oral history and later written accounts, but without solid documentary support.
Museum Records: Some records suggest that by the late 18th century, parts of the dodo specimen were discarded because they had decayed. The surviving head and foot were kept, while the rest of the body, which had likely decomposed significantly, was disposed of. This might have contributed to the myth that the specimen was almost entirely lost.
Plausibility and Scholarly Opinions
Scholarly Views: Historians and museum curators generally agree that while the story is plausible, it is likely an exaggeration or a simplification of events. It is plausible that during a period of reorganization or decay of the specimen, parts of the dodo were discarded, and someone recognized the importance of preserving the head and foot.
Interpretation: The bonfire story has become part of the dodo's lore, serving as a dramatic reminder of how close we came to losing this invaluable specimen. Whether or not it is literally true, the story underscores the precarious nature of historical artifacts and the importance of preservation.
Cultural Impact
Moral of the Story: The bonfire rescue tale is often used to highlight the fragility of historical artifacts and the importance of vigilance in preservation. It also serves to enhance the mystique of the dodo, a species already surrounded by a sense of loss and extinction.
In summary, while the story of the Oxford dodo being rescued from a bonfire at either the Ashmolean or the Oxford University Museum of Natural History is an intriguing one, it remains an anecdote with limited concrete evidence. The story has likely been embellished over time, though it reflects the real dangers historical specimens face when not properly cared for.
The extinction of the dodo on Mauritius had a long-lasting effect on the island's ecosystem of which the dodo was an essential part, but its contribution to the history of Oxford and it's literary heritage that is perhaps as interesting, coming as it does from the fact that the 'New' Ashmolean Museum became the depository of the only known remains of a dodo, which, when the collection in the Ashmolean was shared with the Oxford University Natural History Museum, and Pitt Rivers museum, was housed there, where it fascinated the Oxford Academic, Charles Ludwig Dodgson, aka Lewis Carroll (the Latinized form of Charles Ludwig).
Dodgson had a stammer and would introduce himself as Charles Do-Do-Dodgson, earning him the nickname Dodo Dodgson. When he wrote Alice in Wonderland, he based the Dodo on the 'Oxford dodo' and himself.
Part of the Oxford story concerning the Oxford dodo is probably apocryphal but serves to illustrate the importance of conservation, the fragility of specimens and recognising the importance of specimens which may not seem important at the time. The story is that it was saved from destruction at the last minute when it was destined for a bonfire of 'rubbish' that was being thrown out. The story varies as to who rescued it and whether it was the Ashmolean or the Natural History Museum that was about to burn it. What is probably true, and probably contributed to the story, is the fact that there was initially much more of the dodo but much of it decayed and was destroyed, leaving only the beak, feet and skin of the head and face.
The new study by researchers from the University of Southampton and Oxford University Museum is the subject of an open access paper in the Zoological Journal of the Linnean Society, and a University of Southampton News release:
Rethinking the Dodo Researchers are setting out to challenge our misconceptions about the Dodo, one of the most well-known but poorly understood species of bird.
In a paper published today in the Zoological Journal of the Linnean Society researchers from the University of Southampton, Natural History Museum (NHM) and Oxford University Museum of Natural History have undertaken the most comprehensive review of the taxonomy of the Dodo and its closest relative, the Rodriguez Island Solitaire.
They’ve painstakingly gone through 400 years’ worth of scientific literature and visited collections around the UK to ensure this iconic species, embodying humanity’s destructive potential, is correctly classified.
The Dodo was the first living thing that was recorded as being present and then disappeared. Before this, it hadn’t been thought possible for human beings to influence God’s creation in such a way. This was a time before the scientific principles and systems we rely on to label and classify a species were in place. Both the Dodo and the Solitaire were gone before we had a chance to understand what we were looking at.
Dr Neil J. Gostling, co-corresponding author
School of Biological Sciences
Faculty of Environmental and Life Sciences
University of Southampton, Southampton, UK.
Correcting the record
Much of what was written about the Dodo and the Solitaire was based on accounts from Dutch sailors, representations by artists, and incomplete remains.
The lack of a definitive reference point (type specimen) or convention to label species (zoological nomenclature) led to a series of misidentifications in the centuries following their extinction. New species such as the Nazarene Dodo, the White Dodo, and the White Solitaire were named, but the paper confirms that none of these creatures existed. Still, these erroneous ‘pebbles’ sent ripples through the waters of zoological literature.
By the 18th and early 19th centuries, the Dodo and the Solitaire were considered to be mythological beasts. It was the hard work of Victorian-era scientists who finally proved that the Dodo and the Solitaire were not mythological but were giant ground doves. Unfortunately, no one could agree how many species there had been. Throughout most of the 19th and 20th centuries, researchers thought there were three different species, although some people thought there had been four or even five different species.
Dr. Mark T. Young, co-corresponding author
School of Biological Sciences
Faculty of Environmental and Life Sciences
University of Southampton, Southampton, UK.
To unpick this confusion, researchers went through all the literature on the Dodo and Rodriguez Solitaire encompassing hundreds of accounts dating back to 1598 and visited specimens around the UK, including the world’s only surviving soft tissue from the Dodo, in the Oxford Museum.
More has been written about the Dodo than any other bird, yet virtually nothing is known about it in life. Based on centuries of nomenclatural confusion, and some 400 years after its extinction, the Dodo and Solitaire, continue to prompt heated debate. We’ve gone from where the first statements were made, seen how these have developed, and identified various rabbit holes to correct the record, as best we can.
Dr Julian Hume, co-author
Bird Group
Natural History Museum
Tring Hertfordshire, UK.
Through this work, researchers were able to confirm that both birds were members of the columbid (pigeon and dove) family.
Understanding its wider relationships with other pigeons is of taxonomic importance, but from the perspective of conservation, the loss of the dodo and the solitaire a few decades later means a unique branch of the pigeon family tree was lost. There are no other birds alive today like these two species of giant ground dove.
Dr Neil J. Gostling.
Challenging our misconceptions
The Dodo was an integral part of the ecosystem of Mauritius.
Artwork by Julian Pender Hume.
The researchers believe the popular idea of the Dodo as a fat, slow animal, predestined for extinction is flawed.
Even four centuries later, we have so much to learn about these remarkable birds. Was the Dodo really the dumb, slow animal we’ve been brought up to believe it was? The few written accounts of live Dodos say it was a fast-moving animal that loved the forest.
Dr. Mark T. Young.
Evidence from bone specimens suggests that the Dodo’s tendon which closed its toes was exceptionally powerful, analogous to climbing and running birds alive today. The dodo was almost certainly a very active, very fast animal. These creatures were perfectly adapted to their environment, but the islands they lived on lacked mammalian predators. So, when humans arrived, bringing rats, cats, and pigs, the Dodo and the Solitaire never stood a chance.
Dodos held an integral place in their ecosystems. If we understand them, we might be able to support ecosystem recovery in Mauritius, perhaps starting to undo the damage that began with the arrival of humans nearly half a millennium ago.
Dr Neil J. Gostling.
Learning ‘valuable lessons’
The study marks the beginning of a wider project to understand the biology of these iconic animals.
The mystery of the Dodo bird is about to be cracked wide open. We have assembled a fantastic team of scientists to uncover the true nature of this famous extinct bird. But we are not just looking back in time - our research could help save today's endangered birds too.
Using cutting-edge computer technology, we are piecing together how the Dodo lived and moved. This isn't just about satisfying our curiosity. By understanding how birds evolved in the past, we are learning valuable lessons that could help protect bird species today. It's like solving a 300-year-old puzzle, and the solution might just help us prevent more birds from going the way of the Dodo.
Professor Marcus O Heller, co-author
Bioengineering Research Group
Faculty of Engineering and Physical Sciences
University of Southampton, Southampton, UK.
Palaeoartist Karen Fawcett’s Dodo sculpture
The project will include work with palaeoartist Karen Fawcett , who has created a detailed, life-size model of the Dodo to bring the words on the pages of books and journal articles to life.
This work has been the merging of science and art to achieve accuracy and realism so that these creatures come back from the dead, real and tangible for people to touch and see.
Karen Fawcett
Palaeoartist
The work is supported by the University of Southampton’s Institute for Life Sciences.
The Institute was delighted to support this exciting work which exemplifies Southampton’s strength in interdisciplinary research and advanced scholarship.
Professor Max Crispin.
Director
Institute for Life Sciences.
University of Southampton, Southampton, UK.
Creationists might want to ignore or prepare to lie about the following, especially the section on the terminology and nomenclature background, which contains a description of how taxonomy has adapted to the modern synthesis of evolutionary theory, cladistics, shared common ancestry and monophyletics as it will make distressing reading for those who have been fooled into believing that biologists are abandoning the TOE as not fit for purpose, since nothing could be further from the truth, as this paper shows:
Abstract
The Dodo and its extinct sister species, the Solitaire, are iconic exemplars of the destructive capabilities of humanity. These secondarily terrestrial columbids became extinct within a century of their first encounter with humanity. Their rapid extinction, with little material retained in natural history collections, led 18th and some early 19th century naturalists to believe that these aberrant birds were mythological. This meant that the nomenclatural publications in which their scientific nomina were established were based on accounts written before the species became extinct. As such, no type specimens were designated for either the Dodo or the Solitaire. Our in-depth historical overview of both species and associated family-group nomina found that the nominal authority of the Dodo-based family group is not what is reported in the literature. Moreover, our detailed review of the family-group nomina based on columbid genera ensures that the current columbid family-group systematization is valid. Changing nomenclatural norms between the 19th and 20th centuries had a profound impact on Dodo nomenclature; so much so that the Dodo is an example of how pervasive nomenclatural ‘ripples’ can be and a warning for our current world of multiple nomenclatural codes.
INTRODUCTION
The Mauritian Dodo, †Raphus cucullatus (Linnaeus, 1758) (Fig. 1), and the Rodrigues Solitaire, †Pezophaps solitaria (Gmelin, 1789) (Fig. 2), are textbook examples of evolutionary transitions and of human-made extinctions. Their morphologies were so aberrant that for a time, during the 18th and early 19th centuries, they were considered mythological (Duncan 1828, de Blainville 1835, Strickland 1844, 1848, Hume 2006; see Figs 1, 2). As said by Strickland (1848: 4): ‘So rapid and so complete was their extinction that the vague descriptions given of them [Dodo and Solitaire] by early navigators were long regarded as fabulous or exaggerated, and these birds, almost contemporaries of our great-grandfathers, became associated in the minds of many persons with the Griffin and the Phœnix of mythological antiquity’. The existence of the Solitaire, in particular, was long doubted, because for several decades it was known solely from the descriptions by Leguat (1708). Strickland (1844: 324) mentioned that the Solitaire had been considered either ‘fictitious, or to be founded on an imperfect description of the true Dodo’.
Dodo (†Raphus cucullatus) mounted composite skeleton [NHMUK S/1988.50.1 (PV A 3302)]. A, cranial view. B, left lateral view.
Solitaire (†Pezophaps solitaria) mounted skeletons (on display at the Royal College of Surgeons, London, UK in 2023). A, female individual. B, male individual. Note the difference in skeleton size and robusticity between the sexes.
A series of key papers during the early 19th century ‘resurrected’ the Dodo and the Solitaire from the realm of the mythological to the material (Duncan 1828, de Blainville 1835, Strickland 1844). The seminal work of Strickland (1848) and Melville (1848.1), in their shared volume, described in detail the anatomy of specimens still found in European collections at that time, in addition to giving an authoritative account of the history of the two species. However, it was not until new expeditions to the islands of Mauritius and Rodrigues during the 1860s that new incomplete skeletons of both species were discovered. The skeletal remains discovered in the ‘Mare aux Songes’ marsh during 1865 (Clark 1866, Hume et al. 2009) allowed the Dodo to be described more fully (Owen 1866.1), and the Solitaire was described by Newton and Newton (1868, 1869) after the Jenner excavations of 1865 discovered skeletal remains (Parish 2013: 234; Hume et al. 2015).
There has been renewed interest in the biology of the Dodo and the Solitaire in the 21st century. Studies have explored Dodo body mass (Brassey et al. 2016, van Heteren et al. 2017) and bone histology (Angst et al. 2017.1), and the endocranial anatomy of both species has been reconstructed digitally from computed tomography scans (Gold et al. 2016.1). New Dodo material has been discovered from Mare aux Songes, and the ecosystem of the Mare aux Songes Lagerstätte has been studied (see Rijsdijk et al. 2009.1, 2015.1, Meijer et al. 2012). The remarkable ‘Thirioux Dodos’ have been described in-depth, which includes the most complete Dodo skeleton known (Claessens and Hume 2015.2; Claessens et al. 2015.3). There have even been attempts to reconstruct digitally how these animals would have looked (Rodríguez-Pontes 2016.2). With each decade, our understanding of these aberrant birds is being revolutionized. To ensure that this work is on a firm basis, we need to ensure that the alpha and beta taxonomy (and accompanying nomenclature) of both species is stable. As we will show, there are no known type specimens for either species. Moreover, given that the use of Dodo-based (i.e. †Raphus) family-group nomina is now accepted within columbid systematics, we need to ensure that these names are themselves valid, in order to maintain the nomenclatural stability of extant pigeons and doves. To those ends, we provide an in-depth historical overview of the Dodo, the Solitaire, and the family-group nomina based upon them. We also establish a new nomen to unite both species: †Raphina.
Terminology and nomenclatural background
Before starting our historical overview, it is worth stating that the current rules of zoological nomenclatural are ‘relatively’ recent and have evolved from prior rules/suggestions made during the 19th century. We wish this to be clear from the outset, in order that readers will not mistake our comments hereafter as undue criticisms of past workers. There have also been dramatic shifts in both systematics (the paradigms and methods used to hypothesize clades) and nomenclature (the establishment of names for said clades, and the rules governing those names) between the 18th and 21st centuries. During the 18th and 19th centuries, the rules and norms of zoological nomenclature were being developed (e.g. Linnaeus 1758, Kirby 1815, Westwood 1836, 1837a, 1837.1b, Strickland 1837.2, 1878, Strickland et al. 1843, Dall 1878.1, Société Zoologique de France 1881, Douvillé 1882, American Ornithologists’ Union 1886, Blanchard 1889, Bütschli et al. 1893), prior to their widespread formulation and promulgation during the 20th century (ICZN 1905, 1961, 1964, 1985, 1999). Moreover, the paradigms used to hypothesize taxa were distinctly different, with the transition from a pre-evolutionary paradigm to an acceptance of paraphyletic groupings and groups united based on shared similarity, which then shifted to our current paradigm based on shared common ancestry and monophyletic groups (for a general overview of thought, see Mayr 1942, 1965, 1982, Hennig 1966, Nelson 1973, de Queiroz 1988, Mishler 2009.2; and for some clade-specific examples, see Allard et al. 1999.1, Dornburg and Near 2021, Cotterill et al. 2014 and the references therein).
The current International Code of Zoological Nomenclature (the Fourth Edition, ICZN 1999, 2003, 2012.1, 2016.3; ‘Zoological Code’ hereafter) is a direct descendent of ‘Blanchard’s Code’ (Blanchard 1889) via the Règles Internationales de la Nomenclature Zoologique [International Rules of Zoological Nomenclature] (ICZN 1905). Raphaël Blanchard, the ‘father of International Zoological Nomenclature’ (Bock 1994: 33), was the Chair of the nomenclatural committee of the International Congress of Zoology, the first President of the International Committee on Zoological Nomenclature, and the Editor of the French edition of the Règles Internationales. For the first International Congress of Zoology, he wrote an overview of zoological nomenclature and outlined what he believed would be an acceptable set of rules for the international corpus of zoologists (‘Blanchard’s Code’; Blanchard 1889). ‘Blanchard’s Code’ did not exist in a vacuum, because a plethora of nomenclatural codes for zoology had been proposed during the 19th century, with the earliest comprehensive code being proposed by the British Association for the Advancement of Science (‘Strickland’s Code’).
‘Strickland’s Code’ (Strickland et al. 1843) was formulated by a committee of British zoologists and palaeontologists (including famous individuals, such as Charles Darwin and Richard Owen, in addition to Hugh Strickland, who was pivotal in our understanding of the Dodo and the Solitaire), who set down many of the norms we recognize today; norms of the so-called ‘Linnean’ system of nomenclature, although this is perhaps more accurately called ‘Linnean–Westwoodian–Stricklandian’ nomenclature (sensuDubois 2011: 4–5). However, there were some important differences between ‘Strickland’s Code’ and the current Zoological Code (ICZN 1999), such as the proposed ‘start date’ for zoological nomenclature, which in ‘Strickland’s Code’ was 1766, beginning with the publication of the 12th edition of Systema Naturæ (Linnaeus 1766). The ensuing controversy over the ‘start date’ for zoological nomenclature cost ‘Strickland’s Code’ support amongst zoologists (Linsley and Usinger 1959: 41), with Dall (1878.1: 15) noting that the starting point used by the British Association had begun ‘admitting to recognition some ichthyological works printed between the dates of the tenth and twelfth editions [of Systema Naturæ]’. Other national societies began proposing their own nomenclatural codes, including the American Association for the Advancement of Science (Dall 1878.1), the Société Zoologique de France (Société Zoologique de France 1881), the American Ornithologists’ Union (American Ornithologists’ Union 1886), and the Deutsche Zoologische Gesellschaft (Bütschli et al. 1893), as did the Congrès international de géologie [International Congress of Geology] (Douvillé 1882). It was ‘Blanchard’s Code’ (Blanchard 1889) and the subsequent Règles Internationales (ICZN 1905) that would begin to bring international stability to zoological nomenclature (for further details, see Linsley and Usinger 1959, Bock 1994).
Zoological nomenclature of the 18th and early 19th centuries did not adhere to the quasi-legal system in place today. The renaming of pre-existing genera and specific epithets was commonplace (particularly up to the 1840s–1850s). Therefore, readers should not be surprised that the principal of priority with regard to nominal authority was not adhered to in Dodo nomenclature during this time period or that the formulation of names does not meet the requirements on the Zoological Code as we understand it today (ICZN 1999). It is also worth noting that when the Dodo and Solitaire were first named (Linnaeus 1766, Gmelin 1789), the concept of nomenclatural types did not exist. Witteveen (2016.4: 156) credited Westwood (1837a) as the originator of this concept, which then became incorporated into ‘Strickland’s Code’ (and subsequent nomenclatural codes). As such, type specimens were not designated for the Dodo or the Solitaire.
Before continuing, we also need to define the terminology we will be using. We will follow the suggestions and recommendations of Dubois and Fitzhugh. Dubois (2021.1: 39) noted that, ‘the term taxonomy is traditionally used in two distinct senses, to designate either a scientific discipline, or any scientific classification of organisms produced by this discipline and adopted as valid by taxonomists’. In order to distinguish between both meanings, Dubois (2005: 406) erected the term ergotaxonomy for the latter (‘classification used by a given author in a given work’, Dubois 2006.1: 250). To remove any ambiguity, we use the term ergotaxonomy to refer to any ‘taxonomic framework’ considered valid by their proposer.
We will use the term ‘systematics’ rather than ‘taxonomy’ throughout. There is disagreement within the field of evolutionary biology regarding whether taxonomy and systematics are different subfields (e.g. Simpson 1961.1, Wiley and Lieberman 2011.1), whether taxonomy is a subdiscipline within systematics (e.g. Michener et al. 1970, Dubois 2006.1, Pavlinov 2013.1, Winsor 2023 and the references therein), or whether systematics is a subfield of taxonomy (e.g. Toepfer 2011.2). However, others, such as Mayr and Ashlock (1991) and Fitzhugh (2008), have proposed that taxonomy is a synonym of systematics. We will follow Fitzhugh (2008: 54) and use the term ‘systematics’ throughout.
We also use the term ‘systematization’ in preference to ‘classification’ following Fitzhugh (2008). Fitzhugh (2008: 54) defined classification as the ‘segregation of objects into classes based on specified properties’, whereas systematization is ‘the organization of observations into a system of concepts, in the form of hypotheses, according to theory’ (the definitions of these terms given by de Queiroz 1988: 241 was similar). We consider the latter to be the best description of systematics, because both species and ‘higher-level’ clades are explanatory hypotheses rather than objects (e.g. see Fitzhugh 2005.1, 2008, Mortimer et al. 2021.2).
Herein, we follow ornithological convention and capitalize English vernacular names of species (Parkes 1978; and the International Ornithological Committee World Bird List v.13.2; https://www.worldbirdnames.org/english-names/spelling-rules/). Moreover, we use the English vernacular names for columbid species that appear in the International Ornithological Committee World Bird List v.13.2 (https://www.worldbirdnames.org/new/bow/pigeons/), but with the following exceptions: (i) Didunculus strigirostris (Jardine, 1845) is referred to as the Samoan Tooth-billed Pigeon, because another species (†Didunculus placopedetesSteadman, 2006.2) was present throughout the islands that constitute the Kingdom of Tonga until ~2850 years ago (Steadman 2006.2; Worthy and Burley 2020) and was also present on Efate Island, Vanuatu (Worthy et al. 2015.4); and (ii) we generally refer to †Pezophaps solitaria as the Solitaire rather than the Rodrigues Solitaire, in order that it is consistent with the use of ‘the Dodo’ for †Raphus cucullatus (i.e. not using Mauritian Dodo). We follow Dubois (2000: 39) in using the term nomen (plural nomina) for any ‘scientific name’ that is formulated in compliance with a nomenclatural code, which, in this case, is the Zoological Code (ICZN 1999, 2003, 2012.2, 2016.5).
Our open nomenclature and synonymy lists follow the recommendations of Richter (1948) (see: Matthews 1973.1, who outlined them in English, and Becker 2001, who gave a recent overview in German), Sigovini et al. (2016.6), and Horton et al. (2021.3). Finally, we use the dagger (†) symbol in front of nomenclatural nomina that denote extinct taxa (except when they appear in quotations).
The dodo was named before biologists understood about evolution and believed species were created without ancestors, so the idea of a systematic nomenclature which reflected the evolutionary relationships between species had not occurred to them, so the dodo and its close relative, the Rodriguez Island Solitaire, were given different family names. This new study proposes a new family name, Raphina, for both species which reflects their evolutionary relationship and puts them in their correct position in the evolutionary tree of the pigeons and doves (the columbids) based on a DNA analysis.
The fact that human agency could drive a species to extinction was a shock to the early biologists who subscribed to the 'creation' mythos and assumed that what God had created mankind would be unable to destroy. We now know that both parts of the superstition were wrong and disastrously so. Not only are species the product of their environment but can be destroyed simply by changing that environment. There is no god playing any part in the process and least of all protecting its 'creation'.
This realisation made the Oxford dodo an object of fascination especially for academics like Do-Do-Dodgson who saw in it a metaphor for revealed wisdom about the nature of reality and the difference between it and human expectations, based on religious mythology.
Creationists might find it distressing to read how modern taxonomy has been revised to reflect the modern evolutionary synthesis, recognising that species can be arranged in clades and family trees based on how they evolved and diversified from common ancestors which themselves were the result of diversification from earlier common ancestors. They will probably find it distressing too how a DNA analysis of an extinct species like the dodo is confirming that view of the origins of biodiversity and no sign of that impending abandonment of the Theory of Evolution that their cult leaders have been assuring them is about to happen, any day now, real soon.
