Unintelligent Design - How Evolution Rescued an Unintelligent Heath-Robinson Design Blunder

A WashU researcher hand pollinates Arabidopsis.

Photo: Joe Angeles/WashU

How plants evolved multiple ways to override genetic instructions - The Source - Washington University in St. Louis

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?

Refuting Creationism - How A Beetle Evolved To Eat Toxic Plants

Red milkweed beetle, Tetraopes tetrophthalmus

CC BY 2.5, Link

Red milkweed beetle, Tetraopes tetrophthalmus

Red milkweed beetle genome sequence offers plant-insect co-evolutionary insights

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.

Refuting Creationism - Wind Dispersal of Seeds - 370 Million Years Before 'Creation Week'.

A fossil of the winged-seed, Alasemenia, sourced from the Jianchuan mine in Xinhang Town, China.

Image credit: Deming Wang (CC BY 4.0)

Figure 1

Fertile branches and seeds of Alasemenia tria gen. et sp. nov.
(a) Thrice dichotomous branch with a terminal ovule. Arrow indicating boundary between ovule and ultimate axis (PKUB21721a). (b, f, g, i) Once dichotomous branch with a terminal ovule (PKUB21781, PKUB23132, PKUB19338a, PKUB17899). (c) Twice dichotomous branch with a terminal ovule (PKUB19713a). (d, e) Ovule with three integumentary wings (PKUB19321, PKUB19316). (h) Ovule showing two integumentary wings (PKUB19282). (j, k) Ovule terminating short ultimate axis (PKUB23114, PKUB23129). Scale bars, 1 cm (a–c, h), 5 mm (d–g, i–k).

New seed fossil sheds light on wind dispersal in plants | For the press | eLife The problem creationists have is that so much of Earth's history happened before their cult's dogma says it was created by magic just 10,000 years ago.

In fact, 99.9975% of Earth's history occurred during that long pre-'Creation Week' period, that just about any scientific paper dealing with fossils casually refutes creationism.

In fact the entire fossil record refutes creationism because nowhere in it are fossils found without ancestors and the geological column simply doesn't contain the evidence of a whole range of modern species suddenly appearing. It shows exactly the opposite - species evolving and diverging from common ancestors with modern forms having intermediate forms between them and common ancestors with other species in the same clade.

There is a clear progression in the fossil record of plants, for example, from simple single-celled algae, through primitive terrestrial mosses and liverworts followed by ferns, and eventually the angiosperms with their flowers and seeds.

Within the angiosperms there is again a fossil record or two main functions:

1. Ferilisation of seeds, which included co-evolution between flowers and pollinators - bees, moths, birds, etc. - or wind pollination.
2. Dispersal of seeds - wind, birds, mammals, etc.

And each of those fossil records is matched by the co-evolution of the pollinators and the seed dispersers.

Tell me about wind seed dispersal in plants, when it evolved, etc. Wind seed dispersal, also known as anemochory, is a widespread adaptation in plants to ensure the spread of their seeds over large distances, increasing their chances of finding suitable environments for growth. This dispersal mechanism relies on wind to transport seeds that are often lightweight and have specialized structures to aid their movement through the air.

Key Features of Wind-Dispersed Seeds:

1. Lightweight: Wind-dispersed seeds are typically small and light, allowing them to be carried long distances.
2. Structures for Flight: Many of these seeds have adaptations like wings, hairs, or other structures that catch the wind. Examples include:
   • Pappus: In species like dandelions (Taraxacum), the seed has a parachute-like structure called a pappus.
   • Wings: In trees like maples (Acer), seeds have wing-like structures called samaras.
   • Tumbleweeds: Some plants, like Salsola spp., disperse seeds by breaking off entirely and rolling in the wind.

Evolution of Wind Seed Dispersal:
Wind dispersal is a relatively ancient mechanism in plants, evolving as plants colonized terrestrial habitats. The earliest land plants likely relied on wind to disperse spores before the evolution of seeds. Once seeds evolved, various adaptations for wind dispersal followed. This trait has evolved independently across many plant lineages, making it an example of convergent evolution. Some key evolutionary timelines include:

• Early Seed Plants: The gymnosperms, which appeared around 350 million years ago, often use wind for seed dispersal, as seen in conifers with winged seeds.
• Angiosperms: Flowering plants, which diversified during the Cretaceous (about 125 million years ago), also show multiple independent evolutions of wind dispersal traits. Many families of angiosperms, such as Asteraceae (the daisy family) and Poaceae (the grasses), have specialized wind-dispersal mechanisms.

Factors Driving the Evolution of Wind Dispersal:

• Open Habitats: Wind dispersal is particularly advantageous in open, windy environments such as grasslands, deserts, and mountainous regions.
• Resource Efficiency: Wind dispersal doesn't require the plant to invest energy in producing fleshy fruit to attract animals for seed dispersal, making it resource-efficient.
• Competition and Colonization: It allows plants to colonize new areas and reduce competition by spreading seeds far from the parent plant.

In conclusion, wind seed dispersal has evolved multiple times in both ancient and modern plant lineages, driven by the need to disperse seeds efficiently in open or windy environments. Its prevalence in diverse plant families highlights its evolutionary success.

And now a group of researchers have found the second-earliest known record of wind dispersal of seeds from roughly 360–385 million years ago, during the Late Devonian. The fossils were found in the Jianchuan mine in Xinhang Town, Anhui Province, China.

The team were led by Professor Deming Wang of the Key Laboratory of Orogenic Belts and Crustal Evolution, Department of Geology, Peking University, Beijing, China. Their findings are the subject of a paper in the on-line, open access journal, eLife, and are explained in an eLife press release:

New seed fossil sheds light on wind dispersal in plants

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Scientists have discovered one of the earliest examples of a winged seed, granting insight into the origin and early evolution of wind dispersal strategies in plants.

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The study, published today as the final Version of Record after previously appearing as a Reviewed Preprint in eLife, details the second-earliest known winged seed – Alasemenia – from the Late Devonian epoch, roughly 360–385 million years ago. The authors use what the editors call solid mathematical analysis to demonstrate that Alasemenia’s three-winged seeds are more adapted to wind dispersal than one, two and four-winged seeds.

Wind dispersal in plant seeds is a natural mechanism that allows plants to spread their seeds through the air to new areas. This helps reduce competition for resources, increasing the plant’s chances of survival. Examples of wind dispersal strategies include tumbleweeds, parachutes such as dandelions and milkweeds, and winged seeds like those of the maple tree, often called ‘helicopter’ seeds.

The earliest-known plant seeds date back to the Late Devonian epoch.

This period marks a significant evolutionary milestone in plant history, as they transitioned from spore-based reproduction, as with ferns and mosses, to seed-based reproduction. However, little is known about wind dispersal in seeds during this time, as most fossils lack wings and are typically surrounded by a protective cupule.

Professor Deming Wang, lead author
Key Laboratory of Orogenic Belts and Crustal Evolution
Department of Geology
Peking University, Beijing, China.

Cupules are cup-shaped structures that partly enclose seeds, much like in acorns or chestnuts (although the Devonian cupules do not share the same origin with these modern ones), and could be associated with other dispersal methods, such as water transport.

To better understand early wind dispersal mechanism, Wang and colleagues studied several seed fossils from the Late Devonian, sourced from the Jianchuan mine in Xinhang Town, Anhui Province, China. From this, they identified a new fossil seed, Alasemenia.

They first described the characteristics of Alasemenia by carefully analysing the fossil samples, including making slices to view the seed’s internal structures. They found that Alasemenia seeds are about 25–33 mm long and clearly lack a cupule, unlike most other seeds of the period. In fact, this is one of the oldest-known records of a seed without a cupule, 40 million years earlier than previously believed. Each seed is covered by a layer of integument, or seed coat, which radiates outwards to form three wing-like lobes. These wings taper toward the tips and curve outward, creating broad, flattened structures that would have helped the seeds catch the wind.

The team then compared Alasemenia to the other known winged seeds from the Late Devonian: Warstenia and Guazia. Both of these seeds have four wings – Guazia’s being broad and flat, and Warstenia’s being short and straight. They performed a quantitative mathematical analysis to determine which seed had the most effective wind dispersal. This revealed that having an odd number of wings, as in Alasemenia, grants a more stable, high spin rate as the seeds descend from their branches, allowing them to catch the wind more effectively and therefore disperse further from the parent plant.

Our discovery of Alasemenia adds to our knowledge of the origins of wind dispersal strategies in early land plants. Combined with our previous knowledge of Guazia and Warsteinia, we conclude that winged seeds as a result of integument outgrowth emerged as the first form of wind dispersal strategy during the Late Devonian, before other methods such as parachutes or plumes.

Pu Huang, senior author
Nanjing Institute of Geology and Paleontology
Chinese Academy of Sciences, Nanjing, China.

The three-winged seeds seen in Alasemenia during the Late Devonian would have subsequently been followed by two-winged seeds during the Carboniferous period, and then single-winged seeds during the Permian.

Professor Deming Wang.

Abstract
The ovules or seeds (fertilized ovules) with wings are widespread and especially important for wind dispersal. However, the earliest ovules in the Famennian of the Late Devonian are rarely known about the dispersal syndrome and usually surrounded by a cupule. From Xinhang, Anhui, China, we now report a new taxon of Famennian ovules, Alasemenia tria gen. et sp. nov. Each ovule of this taxon possesses three integumentary wings evidently extending outwards, folding inwards along abaxial side and enclosing most part of nucellus. The ovule is borne terminally on smooth dichotomous branches and lacks a cupule. Alasemenia suggests that the integuments of the earliest ovules without a cupule evolved functions in probable photosynthetic nutrition and wind dispersal. It indicates that the seed wing originated earlier than other wind dispersal mechanisms such as seed plume and pappus, and that three- or four-winged seeds were followed by seeds with less wings. Mathematical analysis shows that three-winged seeds are more adapted to wind dispersal than seeds with one, two or four wings under the same condition.

eLife assessment This useful study describes the second earliest known winged ovule without a capule in the Famennian of Late Devonian. Using solid mathematical analysis, the authors demonstrate that three-winged seeds are more adapted to wind dispersal than one-, two- and four-winged seeds. The manuscript will help the scientific community to understand the origin and early evolutionary history of wind dispersal strategy of early land plants.

https://doi.org/10.7554/eLife.92962.3.sa0

eLife digest
Many plants need seeds to reproduce. Seeds come in all shapes and sizes and often have extra features that help them disperse in the environment. For example, some seeds develop wings from seed coat as an outer layer, similar to fruits of sycamore trees that have two wings to help them glide in the wind.

The first seeds are thought to have evolved around 372-359 million years ago in a period known as the Famennian (belonging to the Late Devonian). Fossil records indicate that almost all these seeds were surrounded by an additional protective structure known as the cupule and did not have wings. To date, only two groups of Famennian seeds have been reported to bear wings or wing-like structures, and one of these groups did not have cupules. These Famennian seeds all had four wings.

Wang et al. examined fossils of seed plants collected in Anhui province, China, which date to the Famennian period. The team identified a new group of seed plants named the Alasemenia genus. The seeds of these plants each had three wings but no cupules. The seeds formed on branches that did not have any leaves, which indicates the seeds may have performed photosynthesis (the process by which plants generate energy from sunlight). Mathematical modelling suggested that these three-winged seeds were better adapted to being dispersed by the wind than other seeds with one, two or four wings. These findings suggest that during the Famennian the outer layer of some seeds that lacked cupules evolved wings to help the seeds disperse in the wind. It also indicates that seeds with four or three wings evolved first, followed by other groups of seed plants with fewer seed wings. Future studies may find more winged seeds and further our understanding of their evolutionary roles in the early history of seed plants.

Introduction
Since plants colonized the land, wind dispersal (anemochory) became common with the seed wing representing a key dispersal strategy through geological history (Taylor et al., 2009; Ma, 2009.1; McLoughlin and Pott, 2019). Winged seeds evolved numerous times in many lineages of extinct and extant seed plants (spermatophytes) (Schenk, 2013; Stevenson et al., 2015). Lacking wings as integumentary outgrowths, the earliest ovules in the Famennian (372–359 million years ago [Ma], Late Devonian) rarely played a role in wind dispersal (Rowe, 1997). Furthermore, nearly all Famennian ovules are cupulate, i.e., borne in a protecting and pollinating cupule (Prestianni et al., 2013.1; Meyer-Berthaud et al., 2018).

Warsteinia was a Famennian ovule with four integumentary wings, but its attachment and cupule remain unknown (Rowe, 1997). Guazia was a Famennian ovule with four wings and it is terminally borne and acupulate (devoid of cupule) (Wang et al., 2022). This paper documents a new Famennian seed plant with ovule, Alasemenia tria gen. et sp. nov. It occurs in Jianchuan mine of China, where Xinhang fossil forest was discovered to comprise in situ lycopsid trees of Guangdedendron (Wang et al., 2019.1). The terminally borne ovules are three-winged and clearly acupulate, thus implying additional or novel functions of integument. Based on current fossil evidence and mathematical analysis, we discuss the evolution of winged seeds and compare the wind dispersal of seeds with different number of wings.

Figure 2

Fertile branches and seeds of Alasemenia tria gen. et sp. nov.
(a–c) Once dichotomous branch with a terminal ovule (PKUB16876a, b, PKUB17767). a, b, Part and counterpart. (d, e) Part and counterpart, arrow showing the third integumentary wing (PKUB19322a, b). (f) Ovule on ultimate axis (PKUB21752). (g, h, k–m) Ovules lacking ultimate axis (PKUB16788, PKUB21631, PKUB16522, PKUB21647, PKUB21656). (i, j) Part and counterpart, showing limit (arrows) between nucellus and integument (PKUB19339a, b). (n) Four detached ovules (arrows 1–4) (PKUB19331). (o) Enlarged ovule in n (arrow 2), showing three integumentary wings (arrows). Scale bars, 1 cm (n), 5 mm (a–h, k–m, o), 2 mm (i, j).

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Figure 3

Seeds of Alasemenia tria gen. et sp. nov.
(a, b) Part and counterpart, enlarged ovule in Figure 1a (PKUB21721a, b). (c) Enlarged ovule in Figure 1c. (d) Counterpart of ovule in c (PKUB19713b). (e) Dégagement of ovule in d, exposing the base of the third integumentary wing (arrow). (f) Enlarged ovule in Figure 1d. (g, h) Enlarged ovule in Figure 2i and j, respectively. Scale bars, 5 mm (a–e), 2 mm (f–h).

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Figure 4 with 5 supplements

Transverse sections of seeds of Alasemenia tria gen. et sp. nov.
(a, b) Part and counterpart. (c–e) Sections of seed in a and b (at three lines, in ascending orders). Arrow in d indicating probable nucellar tip (Slide PKUBC17913-12b, 10a, 9b). (f, g) Part and counterpart. (h–k) Sections of seed in f and g (at four lines, in ascending orders) (Slide PKUBC19798-8b, 6b, 4a, 4b). (l, m) Part and counterpart. (n–r) Sections of seed in l and m (at five lines, in ascending orders), showing three wings departing centrifugally (Slide PKUBC17835-5a, 7b, 8b, 9a, 10a). (s, v, A), One seed sectioned. (t, u) Sections of seed in s (at two lines, in ascending orders) (Slide PKUBC18716-8b, 7a). (w–z) Sections of seed in v (at four lines, in ascending orders) (Slide PKUBC20774-7a, 6b, 3a, 3b). (B–E) Sections of seed in A (at four lines, in ascending orders), showing three wings departing centrifugally (Slide PKUB17904-5b, 4a, 4b, 3b). Scale bars, 2 mm (a, b, f, g, l, m, s, v, A), 1 mm (c–e, h–k, n–r, t, u, w–z, B–E).

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Figure 5

Reconstruction of two acupulate ovules with integumentary wings.
(a) Alasemenia tria with three wings distally extending outwards. (b), A. tria with one of three wings partly removed to show nucellar tip. (c) Guazia dongzhiensis with four wings distally extending inwards (Wang et al., 2022). Scale bars, 5 mm.

Deming Wang, Jiangnan Yang, Le Liu, Yi Zhou, Peng Xu, Min Qin, Pu Huang (2024)
Alasemenia, the earliest ovule with three wings and without cupule
eLife 13: RP92962. https://doi.org/10.7554/eLife.92962.3

Copyright: © 2024 The authors.
Published by eLife Sciences Publications Ltd. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

And yet, despite this this daily refutation of creationism, the cult manages to stagger on, albeit shedding members as they reach the age of reason and realize they've neem fooled, and parasitic frauds like Ham and Kovind still cream off millions of dollars from their gullible and scientifically illiterate following in a desperate attempt to prove their inherited superstation gives them a better insight into the workings of the world around them than those clever-dicky, elitists scientists with their big words have.

Who needs facts and evidence, and all that bothersome learning when you have a mummy and daddy, and a preacher in a pulpit to tell you what to believe?

Unintelligent Design - How Creationism's 'Designer' Needs Plan B For When Plan A Fails To Mend Its Previous Design Blunder

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).

Shimada, A., et al (2024)

Plants have a backup plan | Cold Spring Harbor Laboratory

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.

Unintelligent Design - Doing The Same Thing In Two Different Ways

Brassica fruticulosa

Photo: Sílvia Busoms, UAB.

Brassica fruticulosa

Photo: Sílvia Busoms, UAB.

Different adaptation strategies to saline soils identified in neighbouring populations of the same plant species - Universitat Autònoma de Barcelona - UAB Barcelona

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:

1. 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.
2. 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.
3. 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 species

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Researchers 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.

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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

Copyright: © 2024 The authors.
Published by National Academy of Science. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

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:

1. Adapted like the northern population.
2. Adapted like the southern population.
3. 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.

Refuting Creationism - Evolutionary History of the Grape is Enough to Make Creationists Wine

Nekemias mucronata sp. nov. Complete leaflet
Scale bar: 1 cm.

Tosal, A. Vicente, A. & Denk, T. (2024)

Nekemias mucronata fossil lateral leaflets from the collection of the Natural Science Museum of Barcelona.

Reconstructing the evolutionary history of the grape family

For today's refutation of creationism, we have the history of the grape, stretching back to between 40 and 23 million years before creationists think Earth was created.

Like almost everything else about the history of life in Earth, the evolution of the modern grape took place in the 99.9975% of time that preceded 'Creation Week' when creationism's little god made a small, flat planet with a dome over it in the Middle East.

This history has now been reconstructed by a team of three palaeontologists led by Aixa Tosal, from the Faculty of Earth Sciences and the Biodiversity Research Institute (IRBio) of the University of Barcelona, with Alba Vicente, also from the University of Barcelona, and Thomas Denk from the Swedish Museum of Natural History (Stockholm).

Refuting Creationism - How Daisies Speciated On Isolated Islands

Top: Pleurophyllum speciosum
Bottom: Pulicaria canariensis

Top: Bidens mooreensis
Bottom: Argyroxiphium sandwicense

Pleurophyllum speciosum - Campbell Island.

Credit Phil Garnock-Jones.

Isolated daisies have the greatest diversity | Naturalis

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.

Refuting Creationism - Evolution By Hybridization May Be Commonplace in Plants

DR Lionel Di Santo samples black cottonwood, Populus trichocarpa in the coastal regions of the Pacific Northwest.

Credit: Penn State. CC BY-NC-ND 4.0

The team found the black cottonwood-balsam poplar stable hybrid lineage after analyzing the genetic makeup of 546 poplar tree cuttings collected along seven transects ranging from Alaska to Wyoming, with collections in British Columbia and Alberta, Canada, in between.

Credit: Penn State. CC BY-NC-ND 4.0

Discovery of a hybrid lineage offers clues to how trees adapt to climate change | Penn State University

Despite creationist dogma that say otherwise, evolution in a population can occur hybridization, especially in plants, where it may be commonplace. Two related plants hybridize and the resulting offspring acquires additional genes which extend its capabilities, enabling it to survive environmental change or move into new niches, and forming a stable population with new allele frequencies.

And as though to rub salt into creationist wounds, some of these happened hundreds of thousands of years before creationism's legendary 'Creation Week', before which, on the say-so of some ignorant Bronze Age pastoralists who were unaware of anything more than a day or two's walk from the Canaanite Hills, creationists think there was once nothing out of which everything was created by some magic words, just a few thousand years ago.

They also hold the diametrically opposite views simultaneously, that evolution is impossible because the Second Law of Thermodynamics [sic] forbids it, and that evolution occurred as a massively accelerated rate in the last few thousand years, unnoticed by anyone, in which several whole new species arose in a single generation by magic.

Now a team led by Penn State University paleobotanists led by Associate Professor Jill Hamilton, from Penn State’s College of Agricultural Sciences, have shown that a hybrid between black cottonwood, or Populus trichocarpa, and balsam poplar, Populus balsamifera, was able to move out of the wet coastal region to which most black cottonwood trees are restricted, into the arid lands to the east. This movement started about 800,000 years ago.

Refuting Creationism - Now It's 60-Million-Year-Old Grape Seed Fossils!

Lithouva - the earliest fossil grape from the Western Hemisphere, ~60 million years old from Colombia. Top figure shows fossil accompanied with CT scan reconstruction. Bottom shows artist reconstruction.

Photos by Fabiany Herrera, art by Pollyanna von Knorring.

Sixty-million-year-old grape seeds reveal how the death of the dinosaurs may have paved the way for grapes to spread - Field Museum

If you're a creationist cult leader whose livelihood depends on fooling scientifically illiterate simpletons into thinking Earth is just 10,000 years old and the creation myth in the Bible is literal science and history, about the last thing you need is a bunch of paleontologists to find 60-million-year-old fossil grape seeds and publish their findings in a peer-reviewed science journal.

Actually, the publication is the least of your worries because your dupes will never read anything remotely scientific in case it makes them begin to wonder if they could be wrong, but what do you do about the 60-million-year date? You lie about the scientists, obviously.

You tell your dupes that scientists just make up dates to suit their 'anti-God' agenda because they are all part of a massive Satanic conspiracy, confident that the same thinking defect that causes creationism in an adult also causes conspiracism. So you can be sure they'll fall for it, no matter the absurdity of the idea that millions of biomedical scientists and their assistants, the managers of all the major universities and research establishment around the world, the editors of science journals and all their staff, are in on the conspiracy and never break ranks and blow the whistle on it.

Creationism in Crisis - Scientists Have Shown How Fruits of the Solanacea Evolved

Different Solanum species

Cultivated tomatoes, Solanum lycopersicum

New tomato, potato family tree shows that fruit color and size evolved together | Penn State University

The Solanaceae is a large family of plants which includes potatoes, tomatoes, aubergines and peppers/capsicums, and some highly poisonous plants such as deadly nightshade and thornapple. Some of them are economically and nutritionally important food crops.

A feature of the family is the high level of toxicity of most parts of the plants, even important crops like potatoes, all parts of which, apart from the tubers, are highly poisonous, even the small green tomato-like fruits. Similarly, all parts of the closely related tomato plant, apart from the fruits, are highly toxic.

What can you tell me about the Solanaceae and the time-scale of their evolution? The Solanaceae, commonly known as the nightshade family, is a diverse and economically significant family of flowering plants. This family includes well-known species such as tomatoes, potatoes, eggplants, bell peppers, and tobacco. Understanding the evolution and diversification of the Solanaceae involves looking at their origin, diversification events, and the adaptive radiation that led to the variety of species we see today.

Evolutionary Origin and Timeline

• Early Origins: The Solanaceae family is believed to have originated during the late Cretaceous period, around 80-90 million years ago (mya). This timing is based on molecular clock estimates and fossil records.
• Diversification: Significant diversification within the family occurred during the Paleocene and Eocene epochs (about 66-34 mya), likely driven by climatic changes and the availability of new ecological niches.

Key Evolutionary Events

1. Initial Diversification: The early diversification of Solanaceae likely took place in South America, which is considered the primary center of origin for the family. The varied climates and geographies of this region provided multiple ecological niches.
2. Dispersal and Adaptation: As members of the Solanaceae spread to different parts of the world, they adapted to a wide range of environments. This includes the arid regions of Australia and the temperate climates of North America and Europe.
3. Radiation of Major Genera: Key genera within the family, such as Solanum (which includes tomatoes and potatoes), diversified significantly during the Miocene epoch (23-5 mya). This period was marked by further climatic changes that created new habitats.

Morphological and Genetic Diversification

• Morphological Adaptations: Solanaceae species exhibit a wide range of growth forms, from herbaceous plants to shrubs and small trees. They have also developed various fruit types, including berries, capsules, and drupes.
• Genetic Studies: Advances in molecular genetics have provided insights into the evolutionary relationships within the family. Phylogenetic studies based on DNA sequencing have helped clarify the lineage and divergence times of different genera and species.

Ecological and Economic Importance

• Agricultural Significance: Many Solanaceae species are essential crops with significant agricultural value. Tomatoes, potatoes, and peppers are staple foods in many cultures.
• Medicinal and Toxic Properties: Some members of the Solanaceae family produce alkaloids that have medicinal properties, such as atropine and scopolamine, used in various treatments. However, some species are also toxic and have been used historically as poisons.

Evolutionary Challenges and Research Directions

• Hybridization and Polyploidy: Hybridization and polyploidy (having multiple sets of chromosomes) have played a role in the evolution of some Solanaceae species, contributing to their genetic diversity.
• Conservation and Study: Preserving the genetic diversity of wild Solanaceae species is important for both conservation and potential agricultural benefits. Continued research on their genetics and evolutionary history can provide valuable insights into plant evolution and adaptation.

In summary, the Solanaceae family has a rich evolutionary history that spans tens of millions of years. Its members have adapted to a wide range of ecological niches, leading to the diverse array of species we see today. This evolutionary journey has been shaped by climatic changes, geographical dispersal, and genetic diversification.

Which species are the result of hybridization and/or polyploidy?

Hybridization and polyploidy have played significant roles in the evolution of many species within the Solanaceae family. Here are some notable examples:

Hybridization

Hybridization has contributed to the genetic diversity and speciation within the Solanaceae family. Some examples include:

1. Tomato (Solanum lycopersicum):
   • The cultivated tomato (Solanum lycopersicum) has undergone hybridization with wild relatives, leading to the development of various cultivars with different desirable traits such as disease resistance, fruit size, and flavor.
   • Wild species such as Solanum pimpinellifolium and Solanum cheesmaniae have contributed genetic material to cultivated tomatoes through both natural hybridization and intentional breeding.
2. Potato (Solanum tuberosum):
   • The cultivated potato (Solanum tuberosum) is a complex hybrid species. It has hybridized with various wild potato species, such as Solanum demissum and Solanum acaule, which have contributed to its genetic makeup and provided resistance to diseases like late blight.
3. Pepper (Capsicum species):
   • Hybridization among different Capsicum species has been common in the cultivation of peppers. For instance, Capsicum annuum (bell pepper, chili pepper) has hybridized with other species such as Capsicum frutescens and Capsicum chinense to produce new varieties with different heat levels and flavors.
   
   Polyploidy
   
   Polyploidy has been an important mechanism in the evolution of certain Solanaceae species. Polyploid species often exhibit greater genetic diversity and adaptability.
   1. Potato (Solanum tuberosum):
      • The cultivated potato is a tetraploid species (4 sets of chromosomes, 2n = 4x = 48), resulting from the polyploidization of diploid ancestors. This polyploid nature has contributed to its genetic complexity and adaptability.
   2. Tobacco (Nicotiana tabacum):
      • Nicotiana tabacum, the species used for commercial tobacco, is an allotetraploid (4 sets of chromosomes, 2n = 4x = 48). It originated from the hybridization of two diploid species, Nicotiana sylvestris and Nicotiana tomentosiformis, followed by chromosome doubling.
   3. Wild Potatoes:
      • Several wild potato species are polyploids. For example, Solanum demissum is a hexaploid species (6 sets of chromosomes, 2n = 6x = 72), and it has been used in breeding programs to introduce disease resistance genes into cultivated potatoes.
   Importance of Hybridization and Polyploidy
   
4. Genetic Diversity: Both hybridization and polyploidy contribute to genetic diversity, providing a broader range of traits that can be selected for in breeding programs.
5. Adaptability: Polyploid species often have greater genetic variability, which can enhance their adaptability to different environmental conditions and stresses.
6. Crop Improvement: Understanding the genetic contributions from hybridization and polyploidy is crucial for crop improvement efforts, allowing for the development of new varieties with desirable traits such as increased yield, disease resistance, and improved nutritional content.

Overall, hybridization and polyploidy have been vital in shaping the evolution and diversity of the Solanaceae family, leading to the development of many economically important species and cultivars.

Now researchers at Penn State University, have produced a new evolutionary tree of the family which explains how the fruits of the plants evolved their size and colour together and that fruit-eating animals were probably not the main drivers of their evolution, as was previously thought.

The team have just published their findings, open access, in the journal New Phytologist. It is explained in the press release from Penn State:

Fruits of Solanum plants, a group in the nightshade family, are incredibly diverse, ranging from sizable red tomatoes and purple eggplants to the poisonous green berries on potato plants. A new and improved family tree of this group, produced by an international team led by researchers at Penn State, helps explain the striking diversity of fruit colors and sizes and how they might have evolved.

The team found that the size and color of fruits evolved together and that fruit-eating animals were like not the primary drivers of the fruits’ evolution, as had been previously thought. The study, published in the journal New Phytologist, may also provide insight into breeding agriculturally important plants with more desirable traits, the researchers said.

“There are about 1,300 species in the genus Solanum, making it one of the most diverse plant genera in the world,” said João Vitor Messeder, graduate student in ecology and biology in the Penn State Eberly College of Science and Huck Institutes for the Life Sciences and lead author of the paper. “Since the 1970s and ‘80s, researchers have suggested that birds, bats and other fruit-eating animals have driven the evolution of fruits like those in Solanum. However, the importance of the evolutionary history of the plants has been underestimated or rarely considered when evaluating the diversification of fleshy fruits. To better test this hypothesis, we needed first to produce a more robust phylogeny, or family tree, of this plant group to improve our understanding of the relationships between species.”

Plants in the genus Solanum produce fruits with a wide variety of sizes, colors and nutritional values. They can appear black, purple, red, green, yellow or orange and range in size from less than a quarter of an inch to as much as 8 inches, or 0.5 to 20 centimeters. In addition to agriculturally important plants, some plants in the group are cultivated for their ornamental flowers, and the fruits of many of these plants are eaten by humans and a large diversity of animals, including birds, bats, reptiles, primates and other land mammals.

The researchers collected samples of plants from across the world, including wild plants from Brazil, Peru and Puerto Rico and plants from botanical gardens, and sequenced their genes from RNA. They supplemented with previously collected samples and publicly available data, ultimately comparing the sequences of 1,786 genes from a total of 247 species to reconstruct the Solanum family tree. This included representatives from all 10 of the major clades — the branches of the tree — and 39 of 47 minor clades within the genus.

“By using thousands of genes shared among species that effectively represented the entire genus, we significantly improved the Solanum family tree, making it the most comprehensive to date,” said Messeder, who conducted the research in the lab of Hong Ma, Huck Chair in Plant Reproductive Development and Evolution and professor of biology at Penn State and a co-corresponding author of the paper. “Recent advances in technology allowed us to use more genes than previous studies, which faced many challenges in resolving relationships between species and clades. This improved tree helps us understand when different fruit colors and sizes originated or how they changed as new plant species came about.”

The researchers added considerable resolution of the smaller branches in the group that includes potatoes and tomatoes, as well as their closely and more distantly related wild species. The insights gained, the researchers said, could support crop improvement programs for these species and other crops in the genus.

“If the closest wild relatives of important agricultural crops have desirable traits, it is possible to breed crops with those species or borrow their genes, for example to improve resistance to temperature or pests or to produce larger fruits or fruits of a certain color,” Messeder said.

The researchers found that the color and size of Solanum fruits was fairly conserved over evolutionary history, meaning that closely related species tend to have similar fruits. The evolution of fruit color and size is also correlated, with changes in one trait often corresponding to changes in the other, leading fruits of certain colors to be bigger than fruits of other colors.

“These results suggest that physiological and molecular mechanisms may play a role in keeping the evolution of fruit color and size tied together,” Messeder said. “While frugivores — or animals that primarily eat fruit — and seed dispersers may influence diversification, we need to consider all of the possibilities when studying how fruits became so diverse.”

The researchers also clarified the origin and diversification timeline of this genus, in part by including recent information from the oldest nightshade family fossil — from a different genus in the Nightshade family whose fossil was dated to about 52 million years ago — and from particular genes that improved estimates of the length of evolutionary branches. The researchers dated the origin of Solanum to about 53.1 million years ago — a full 30 million years earlier than prior estimates that were based on genes from other parts of the plant cell. This paints a new picture of the environment that might have shaped how these plants diversified into new groups and species.

“The Earth’s environment changed dramatically during the 30 million years in terms of temperature, carbon dioxide in the atmosphere, geography and animal diversity,” Messeder said. “Now that we know when Solanum and its subgroups originated, we can think about the conditions that might have promoted the diversification of that group, as well as how other organisms might have played a role.”

The team found that the earliest members of Solanum had medium-sized berries that remained green when ripe, and that green and yellow fruits of this group became more diverse around 14 million years ago. The researchers speculated that bats might have played a role in this diversification, given their similar evolutionary timeline and that they are the primary dispersers of modern green and yellow Solanum fruits. As new bat species arose and expanded where they were living during this time, they ate Solanum fruits and carried their seeds to new environments.

Next, the researchers plan to explore how modern interactions between animals and the fruit they eat may shed light on the evolution of both groups as well as explore the evolution of certain genes relevant to fruit color and size.

In addition to Messeder and Ma, the research team includes Tomás Carlo, professor of biology at Penn State; Guojin Zhang, postdoctoral researcher at Penn State at the time of the research; Juan David Tovar at the National Institute of Amazonian Research in Brazil; César Arana at the National University of San Marcos in Peru; and Jie Huang and Chien-Hsun Huang at Fudan University in China.

Summary

• Mutualisms between plants and fruit-eating animals were key to the radiation of angiosperms. Still, phylogenetic uncertainties limit our understanding of fleshy-fruit evolution, as in the case of Solanum, a genus with remarkable fleshy-fruit diversity, but with unresolved phylogenetic relationships.
• We used 1786 nuclear genes from 247 species, including 122 newly generated transcriptomes/genomes, to reconstruct the Solanum phylogeny and examine the tempo and mode of the evolution of fruit color and size.
• Our analysis resolved the backbone phylogeny of Solanum, providing high support for its clades. Our results pushed back the origin of Solanum to 53.1 million years ago (Ma), with most major clades diverging between 35 and 27 Ma. Evolution of Solanum fruit color and size revealed high levels of trait conservatism, where medium-sized berries that remain green when ripe are the likely ancestral form. Our analyses revealed that fruit size and color are evolutionary correlated, where dull-colored fruits are two times larger than black/purple and red fruits.
• We conclude that the strong phylogenetic conservatism shown in the color and size of Solanum fruits could limit the influences of fruit-eating animals on fleshy-fruit evolution. Our findings highlight the importance of phylogenetic constraints on the diversification of fleshy-fruit functional traits.

Introduction
The fleshy fruits of angiosperms are key innovations that mediate mutualistic seed dispersal by fruit-eating animals (i.e. frugivores) (Eriksson, 2016). This plant–animal interdependence is central to the development and organization of terrestrial communities (Bascompte & Jordano, 2007; Fleming & Kress, 2013). By encapsulating seeds within nutritious pulp, plants take advantage of foraging animals to effectively disseminate their seeds (Schupp et al., 2010). Thus, frugivores can increase plant fitness, and drive the evolution of fruit types (e.g. fleshy fruits) and fleshy-fruit traits (e.g. color) (Lomáscolo et al., 2010.1; Eriksson, 2016; Xiang et al., 2024). Still, it remains unclear how shared evolutionary history influences the evolution of the functional traits of fleshy fruits among related species. Specifically, to examine how frugivores may affect the evolution of fruit traits, it is crucial to assess whether a trait is conserved and has evolved a few or multiple times within a lineage (Ackerly, 2009).

Differences in fruit traits such as size and color when ripe have been interpreted as adaptations to different types of frugivores (Van Der Pijl, 1982; Valenta & Nevo, 2020). For example, birds typically feed on small brightly colored fruits given their highly developed color vision and narrow bill gapes (Janson, 1983; Wheelwright, 1985; Wheelwright & Janson, 1985.1). In comparison with birds, mammals have more limited color vision but highly developed olfaction, teeth, and forelimbs that aid in the manipulation and use of fruits that are large, tough, dull-colored, and odoriferous (Janson, 1983; Nevo et al., 2018). Such trait-matching suggests that frugivores could drive the evolution of fruit traits through natural selection (i.e. dispersal syndrome hypothesis) (Van Der Pijl, 1982; Janson, 1983; Valenta & Nevo, 2020). For instance, fruit traits of figs (Ficus spp., Moraceae) converge to small brightly colored fruits when birds are the main frugivores, or to larger dull-colored fruits when bats and other mammals are the main frugivores (Lomáscolo et al., 2008, 2010.1). Similarly, other phylogenetic comparative studies have also suggested that frugivores are the main drivers shaping fruit characteristics that lead to general ‘syndromes’ that match distinct frugivore groups (Valenta et al., 2018.1; Nevo et al., 2018; do Nascimento et al., 2020.1; Barnett et al., 2023a,2023.1b). It is expected that when selective pressures from frugivores are convergent, the characteristics of fleshy fruits might be less predictable by phylogenetic relationships (Ackerly, 2009; Valenta & Nevo, 2020).

Although the dispersal syndrome hypothesis offers a compelling explanation for fruit trait diversity rooted in selection theory and adaptation, the evidence remains inconclusive (Valenta & Nevo, 2020). This is because many plant species can be effectively dispersed by animals with distinct morphologies and physiologies, leading to diffuse selective pressures that may preclude adaptation to specific frugivores (Herrera, 1985.2). Furthermore, fruit traits may be phylogenetically determined, limiting the selective pressures from frugivores on fruit trait evolution (Fischer & Chapman, 1993; Jordano, 1995; Ackerly, 2009). In such cases, trait matching is more likely the result of ecological fitting (i.e. pre-existing traits fitting new ecological niches without further modification) rather than the evolution of new traits due to selection (Janzen, 1985.3; Agosta & Klemens, 2008.1). Thus, how much fruit traits are the result of adaptations or of phylogenetic constraints and ecological fitting remains unclear. Advance in this field has been constrained by the use of limited phylogenetic frameworks, poorly resolved phylogenies, and additional challenges posed by hybridization and introgression events among species (e.g. Gardner et al., 2023.2).

Recent studies merging phylogenetics and trait evolution have provided important insights into fleshy-fruit evolution. Fleshy fruits have independently evolved multiple times across angiosperms (Xiang et al., 2017, 2024; Frost et al., 2021; Hilgenhof et al., 2023.3). Studies have shown that fruit color can be associated with long-distance dispersal patterns (Lu et al., 2019) and diversification rates (Spriggs et al., 2015; Lu et al., 2019; L. Zhang et al., 2023.4). Fruit developmental processes have been identified as a mechanism underlying the origin of syndromes (Sinnott-Armstrong et al., 2020.2). Still, in-depth studies assessing the role of shared evolutionary histories on fruit trait evolution remain scarce, especially within highly diverse plant groups.

The genus Solanum L. comprises c. 1300 fleshy-fruited species and is the largest genera of Solanaceae and the second largest genus of fleshy-fruited plants (Frodin, 2004). Regarding fruit traits, Solanum shows a remarkably high diversity, producing berries of various sizes, colors, and pulp with different nutritional and chemical profiles (Cipollini et al., 2002; Knapp et al., 2004.1; Hilgenhof et al., 2023.3). For instance, berry size ranges between 0.5 and 20.0 cm, ripening in many colors, including black, purple, red, green, yellow, and orange. Additionally, Solanum fruits with different colors and sizes are eaten and dispersed by distinct animal groups, including reptiles, birds, bats, primates, and terrestrial mammals (Symon, 1979; Cáceres & Moura, 2003; Arruda Bueno & Motta-Junior, 2004.2; Vasconcellos-Neto et al., 2009.1; Jacomassa & Pizo, 2010.2). This unusual fruit diversity within a single genus makes Solanum an excellent group to investigate a wide range of eco-evolutionary questions (Knapp et al., 2004.1; Moyle, 2008.2). Furthermore, humans have cultivated and domesticated many Solanum species, such as the potato (S. tuberosum), tomato (S. lycopersicum), eggplant (S. melongena), and others (S. betaceum, S. muricatum, and S. quitoense), contributing to the global agriculture (Knapp et al., 2004.1). However, uncertainties in the phylogeny of Solanum limit our understanding of the evolution and diversification patterns of fruit traits relevant to plant–frugivore interactions and agriculture. Unclear phylogenetic relationships make it challenging to determine the ancestral form of a trait and track the number of times and the direction of transitions of the fruit trait over time. Furthermore, assessing the lability of a trait may facilitate its manipulation for agriculture.

Previous studies have made significant progress toward reconstructing the evolutionary history of Solanum (Weese & Bohs, 2007.1; Särkinen et al., 2013.1; Gagnon et al., 2022; Huang et al., 2023.5), with the identification of three deep lineages (we adopted the informal clade nomenclature proposed in previous molecular phylogenetic studies – Bohs, 2005; Stern et al., 2011; Särkinen et al., 2013.1; Tepe et al., 2016.1; Gagnon et al., 2022). The Thelopodium Clade, comprising three species, diverges first, while the remaining species are divided into Clades I and II. Clade I contains c. 350 species, including tomato and potato, whereas Clade II, with c. 900 species, has many spiny shrubs, including eggplant. Clades I and II were further subdivided into nine major and 47 minor clades (Särkinen et al., 2013.1). However, the placement of many clades is inconsistent among studies using various taxa and genes (Särkinen et al., 2013.1; Gagnon et al., 2022; Huang et al., 2023.5) (Supporting Information Fig. S1). Recently, a comprehensive phylogenetic study of 742 Solanum species still found major clades with unresolved relationships (Fig. S1) (Gagnon et al., 2022). For example, the monophyly of Clade I was supported by some analyses using plastid sequences (Fig. S1a–c) but not others using nuclear genes (Fig. S1d,e), and placement of its major clades – especially Regmandra – was uncertain (Fig. S1c–e). These inconsistencies have been described as polytomies near the crown node and reflect difficulties for resolving the deep Solanum relationships (Gagnon et al., 2022). Another recent study (Huang et al., 2023.5) using 1699 genes from 81 Solanum species, along with other members of Solanaceae, presented a well-supported phylogeny, but lacked the Thelopodium Clade and some major clades in Clades I and II, including Regmandra (Fig. S1f–k) and many minor clades. Consequently, a Solanum phylogeny with a more complete lineage representation and well-supported relationships is needed to further understand the ecological factors that shape its evolution, including the drivers behind its remarkable diversity of fruit sizes, shapes, and colors.

Here, we bridge the gap between ecology and phylogenomics using Solanum as study group to examine the tempo and mode of the evolution of fruit traits that are both agriculturally relevant and mediate frugivory and seed dispersal interactions. We used 1786 low-copy nuclear genes across 247 species to reconstruct a highly resolved Solanum phylogeny. We explored the temporal aspects of Solanum's evolutionary history and investigated the phylogenetic effects on the diversification patterns of two important fruit functional traits: size and color when ripe. We evaluated how evolutionarily constrained are fruit size and color in Solanum and discussed implications for the ecology and evolution of seed dispersal mutualisms.

Fig. 2
Divergence time estimation for Solanum indicating its origin in early Eocene and divergence among extant species starting in the middle Eocene. Relevant estimated divergence times of major clade lineages are marked at corresponding nodes. Branch colors match major clade colors of Fig. 1, with their respective names on the right side. Fruit colors and sizes are mapped on terminal tips. At the bottom of the chronogram, geological timescale is shown with periods delimited by vertical lines, the estimated temperature variation for the Cenozoic, and arrows indicating the Mid-Eocene Climatic Optimum and Mid-Miocene Climatic Optimum. Eo, Eocene; LC, late Cretaceous; Mio, Miocene; Ol, Oligocene; Pal, Paleocene; Pli, Pliocene; Q, Quaternary. On the right side, pictures demonstrate some of the variety of colors, sizes, and shapes that can be found in Solanum fruits. Pictures were taken by the authors or downloaded from the internet (Supporting Information Table S6). (Detailed divergence times with species names are shown in Figs S6, S7).

Messeder, J.V.S., Carlo, T.A., Zhang, G., Tovar, J.D., Arana, C., Huang, J., Huang, C.-H. and Ma, H. (2024)
A highly resolved nuclear phylogeny uncovers strong phylogenetic conservatism and correlated evolution of fruit color and size in Solanum L..
New Phytol, 243: 765-780. https://doi.org/10.1111/nph.19849

Copyright: © 2024 The authors.
Published by John Wiley & Sons. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

Of special concern for creationists, is not the technical details, which few would understand even if they read it, but the timeline and the fact that the scientists show no hint of giving up on the Theory of Evolution but instead, use it to explain their findings, with no hint that a magic supernatural entity intervened anywhere in the divergence process.

Additionally, the Introduction section contains links to lots of references to papers dealing with the same or related subjects. None of them show any signs of adopting creationism because the TOE isn't up to the task, either.

The entire range of Solanum species, including many important foods, is the result of evolution, with new genetic information being created by the natural processes of gene and whole genome duplication to give polyploidy, and hybridization. The potatoes, tomatoes, peppers, chilis and aubergines we eat contain evidence of evolution in their genomes.

Many of these plants are the product of cultivation and human selective breeding of course, so creationists might like to explain why plants, like domestic animals, which are the descendants of species the Bible says were created for humankind, have had to be improved to make them fit for purpose. Did their designer not know what humans would need, or did the authors of the Bible not understand about domestication, cultivation and selective breeding to improve on the wild type?