Rosa Rubicondior: Unitelligent Design - How The Giant Clam Has a Needlessly Complex Way To Get Nutrients

How tiny algae shaped the evolution of giant clams | CU Boulder Today | University of Colorado Boulder

You can depend on creationism's idiot designer to never do something the obvious uncomplicated way when there is an obscure and much more complicated way to achieve the same result. It's almost exactly like it's a mindless fool, blundering about without a plan who sometimes happens across something that works and sticks with it, trying to make the best of it with more blundering.

Quite the opposite of what anyone other than a creationist would call intelligent, in fact.

For example, having designed a giant clam to live in nutrient poor coral reefs, it then designed them to have algae living symbiotically inside them, supplementing their megre diet got by filtering the seawater, with sugars manufactured by photosynthesis. This enables the giant clam to grow up to 4.5 feet (1.4 metres) in length and weigh over 700 pound (317 Kg).

Any intelligent designer could have either designed them to live in a less nutrient-poor environment or given them the chloroplasts the algae have to achieve the same result far more simply.

But of course, the giant clam wasn't intelligently designed; it evolved by the utilitarian evolutionary process that is constrained by its evolutionary history and so finds suboptimal but functional processes that a needlessly complex. This complexity impresses creationists because, not understanding how evolution works, they imagine it reflects intelligent design, instead of refuting it.

What can you tell me about giant clams, Tridacna maxima? The species Tridacna maxima, commonly known as the small giant clam or maxima clam, is a marine bivalve mollusc belonging to the family Cardiidae. It is one of the most widely distributed species of giant clams, found in warm, shallow waters of the Indo-Pacific region, including the Red Sea, the Indian Ocean, and the central and western Pacific.

Physical Characteristics

Tridacna maxima is smaller thanTridacna gigas (the true giant clam), typically reaching a maximum length of about 30 cm (12 inches), though some individuals can grow slightly larger.
It has a thick, heavy shell with prominent ridges and folds, often encrusted with algae and other marine organisms.
The mantle, which is the soft tissue visible when the shell is open, is highly colourful, displaying patterns of iridescent blue, green, brown, or gold. These colours come from symbiotic algae (zooxanthellae) living in the clam’s tissues.
Ecology and Behaviour

T. maxima is a sessile species that embeds itself in coral reefs or sandy substrates, often in shallow waters less than 20 meters deep.
Like other giant clams, it has a mutualistic relationship with photosynthetic zooxanthellae, which provide the clam with nutrients via photosynthesis.
The clam also filters plankton and organic matter from the water using its gills.
It is a long-lived species, with some individuals surviving for several decades.
Reproduction

T. maxima is a hermaphrodite, meaning it possesses both male and female reproductive organs.
It reproduces via external fertilization, releasing eggs and sperm into the water column.
Larvae go through a free-swimming stage before settling on a suitable substrate and developing into juveniles.
Conservation Status

Although Tridacna maxima is not currently considered endangered, it faces threats from overharvesting for the aquarium trade, food consumption, and habitat destruction due to coral reef degradation.
Many countries regulate their collection, and some populations are protected in marine reserves.

How giant clams have evolved to accommodate symbiotic algae is the subject of a research paper published, open access, in Communications Biology by a team of researchers led by Professor Jingchun Li of the Department of Ecology and Evolutionary Biology, Colorado University, Boulder, Colorado, USA. Their work os explained in an article in CU Boulder Today by Yvaine Ye

How tiny algae shaped the evolution of giant clams
Giant clams, some of the largest mollusks on Earth, have long fascinated scientists. These impressive creatures can grow up to 4.5 feet in length and weigh over 700 pounds, making them icons of tropical coral reefs. But these animals don’t bulk up on a high-protein diet. Instead, they rely largely on energy produced by algae living inside them. In a new study led by CU Boulder, scientists sequenced the genome of the most widespread species of giant clam, Tridacna maxima, to reveal how these creatures adapted their genome to coexist with algae.

The findings, published Jan. 4 in the journal Communications Biology, offer clues about how such evolution may have contributed to the giant clam’s size.

Giant clams are keystone species in many marine habitats. Understanding their genetics and ecology helps us better understand the coral reef ecosystem.

Professor Jingchun Li, senior author
Department of Ecology and Evolutionary Biology
Colorado University Boulder, Colorado, USA.

A symbiotic relationship
Unlike popular myths—like the one in Disney’s “Moana 2” where the giant clam eats humans—these vegetarian mollusks rely on algae living within their bodies for energy. If giant clams ingest the right algae species while swimming through the ocean as larvae, they develop a system of tube-like structures coated with these algae inside their body. These algae can turn sunlight into sugar through photosynthesis, providing nutrients for the clams.

It’s like the algae are seeds, and a tree grows out of the clam’s stomach.

Professor Jingchun Li.

At the same time, the clams shield the algae from the sun’s radiation and give them other essential nutrients. This mutually beneficial relationship is known as photosymbiosis.

Overfishing and climate change are major threats to giant clams.
Credit: Ruiqi Li/CU Boulder.

Giant clams live in a symbiotic relationship with algae.

Credit: Ruiqi Li/CU Boulder.

It’s interesting that many of giant clams’ cousin species don’t rely on symbiosis, so we want to know why giant clams are special.

Professor Jingchun Li.

In collaboration with researchers at the University of Guam and the Western Australian Museum, the team compared the genes of T. maxima with closely related species — such as the common cockle—that lack symbiotic partners. The researchers found that T. maxima have evolved more genes coded for sensors to distinguish friendly algae from harmful bacteria and viruses. At the same time, T. maxima tuned down some of its immune genes in a way that likely helps the animal tolerate algae living in their body long term, according to Ruiqi Li, the paper’s first author and postdoctoral researcher at the CU Museum of Natural History.

As a result of the clam’s weakened immune system, its genome contains a large number of transposable elements, which are bits of genetic material left behind by ancient viruses.

These aspects highlight the tradeoffs of symbiosis. The host has to accommodate a suppressed immune system and potentially more viral genome invasions.

Dr. Ruiqi Li, first author.
Department of Ecology and Evolutionary Biology
Colorado University Boulder, Colorado, USA.

The study also discovered that giant clams have fewer genes related to body weight control, known as the CTRP genes. Having fewer CTRP genes might have allowed giant clams to grow larger.

Conservation concerns
Last year, a giant clam population assessment by Ruiqi Li, prompted the International Union for Conservation of Nature (IUCN) to update the conservation status of multiple giant clam species. Tridacna gigas, the largest and most well-known species, is now recognized as “critically endangered,” the highest level before a species becomes extinct in the wild.

T. maxima, because of its wide distribution, is currently classified as “least concern.” But Ruiqi Li said it’s possible that different species are lumped into one category simply because they look similar.

If you think these giant clams are all the same species, you might underestimate the threat they face. Genetic studies like this can help us distinguish between species and assess their true conservation needs.

Dr. Ruiqi Li.

The team hopes to sequence the genomes of all 12 known species of giant clams to better understand their diversity.

Similar to corals, giant clams are facing increasing threats from climate change. When the ocean water becomes too warm, the clams expel the symbiotic algae from their tissues. Without the algae, the giant clams can starve.

The giant clams are very important for the stability of the marine ecosystem and support biodiversity [many creatures living in the shallow waters rely on their shells for shelter, and giant clams also provide food for other organisms.] Protecting them is essential for the health of coral reefs and the marine life that depends on them.

Professor Jingchun Li.

Abstract
Symbioses are major drivers of organismal diversification and phenotypic innovation. However, how long-term symbioses shape whole genome evolution in metazoans is still underexplored. Here, we use a giant clam (Tridacna maxima) genome to demonstrate how symbiosis has left complex signatures in an animal’s genome. Giant clams thrive in oligotrophic waters by forming a remarkable association with photosymbiotic dinoflagellate algae. Genome-based demographic inferences uncover a tight correlation between T. maxima global population change and major paleoclimate and habitat shifts, revealing how abiotic and biotic factors may dictate T. maxima microevolution. Comparative analyses reveal genomic features that may be symbiosis-driven, including expansion and contraction of immunity-related gene families and a large proportion of lineage-specific genes. Strikingly, about 70% of the genome is composed of repetitive elements, especially transposable elements, most likely resulting from a symbiosis-adapted immune system. This work greatly enhances our understanding of genomic drivers of symbiosis that underlie metazoan evolution and diversification.

Introduction
Photosymbiosis, wherein heterotrophic hosts establish relationships with photoautotrophic symbionts, has played an essential role in the evolution of life, shaping the ancient origins of the eukaryotic cell and organelles. It is also the foundation of coral reefs, one of the most biodiverse and productive ecosystems¹. It involves efficient photosynthetic energy exchanges between autotrophs and heterotrophs, and can be found in a variety of animal hosts, ranging from sponges, cnidarians, to mollusks and amphibians². Symbiosis requires complex crosstalk among the partners at multiple levels, such as chemical signaling, immune recognition, metabolic exchange, and host-symbiont population dynamics³. These interactions can trigger co-evolutionary dynamics among distantly related lineages⁴, generate strong selection pressures on certain genomic regions⁵, or relax pressure on other parts of the genome⁶. Growing work has started to uncover molecular mechanisms behind symbiosis through the lens of gene evolution. Such genes include putative pattern-recognition receptors involved in symbiont recognition, as well as transporters for carbon, nitrogen, phosphorus, and trace metals that facilitate host-symbiont metabolic exchange^7,8,9.

However, how long-term symbioses shape whole genome evolution in metazoans is still underexplored^8,10,11. Theoretically, symbiosis can alter genomes at multiple levels, including nucleotide substitutions, regulatory adaptations, transposon activity shifts, structure variations, and horizontal gene transfers^11,12,13. Intriguingly, emerging evidence shows that photosymbiotic animal genomes appear to possess higher proportions of transposable elements compared to non-symbiotic relatives^8,11, suggesting that this underexplored aspect of genome architecture may play a significant role in maintaining symbiotic relationships or be influenced by symbiosis.

By forming a remarkable association with photosymbiotic dinoflagellate algae (Symbiodiniaceae), giant clams (subfamily Tridacninae) have secured their position as the largest bivalves on our planet. They possess the heaviest shells among all extant bivalves, with a recorded weight reaching up to 700 pounds. Their mantles display a captivating array of colorful patterns, establishing them as iconic inhabitants of coral reefs. Giant clams originated and diversified in the Indo-west Pacific in warm shallow tropical seas and have always been restricted to these environments^14,15. Genetic evidence suggests that all giant clams are photosymbiotic, and this relationship is thought to have evolved once in their common ancestor at ~27 mya (SD = 4.4)¹⁶, coinciding with the global expansion of modern coral reefs¹⁷. During this period, the emergence of shallow marine habitats dominated by other photosymbiotic organisms likely facilitated the evolution of photosymbiotic traits in giant clams by providing suitable environment and symbiont reservoirs. The genomic adaptations enabling Tridacninae to host photosymbionts likely lead to this subfamily’s radiation (6 mya¹⁶), allowing species and their populations to expand throughout the Indo-Pacific. These same innovations have also closely tied their demographic history and geographic distribution to the fate of coral reef ecosystems. Regrettably, like numerous other remarkable species, wild populations of giant clams face significant threats arising from overfishing and the adverse effects of climate change, which causes them to bleach¹⁸. In 1985, giant clam species were listed on Appendix II of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES).

In contrast to cnidarians that host photosymbionts intracellularly, giant clams harbor symbionts extracellularly, within an elaborate network of tubules derived from the digestive system¹⁹. The tubular system actively engages in transporting immobile symbiont cells across various organs, including the mantle and stomach, which is believed to maximize symbiont photosynthetic efficiency and regulate symbiont populations²⁰. Several molecular mechanisms related to giant clam photosymbiosis have been proposed. For instance, in the tubular system, giant clams can promote symbiont photosynthesis by increasing supply of inorganic carbon through the V-type H⁺ -ATPase-dependent carbon-concentrating mechanism (CCM)²¹. Various transporters have also been identified that play a role in the nutrient exchange between the host and the symbionts, such as the sodium-dependent glucose transporter (SGLT1)²² and the taurine transporter (SLC6A6), which transport exogenous taurine to stimulate photosynthate release²³. In addition, light-induced production of signaling molecules in the symbionts may lead to increased enzymatic activity, which is essential for the host’s calcification²⁴. While substantial progress has been made regarding characterizing individual molecular pathways in giant clam photosymbiosis, a genomic-level comparative framework provides a comprehensive picture of the complexity of genomic signatures of photosymbiosis.

Here, we sequenced a high-quality reference genome for Tridacna maxima, a relatively small but overharvested giant clam species facing conservation challenges. Through comparative genomic analyses with congeners and other non-photosymbiotic mollusks, we demonstrate that its photosymbiotic ecology left unique genomic signatures and resulted in a genome that is distinct from non-symbiotic relatives in many aspects. These include a demographic history mirroring paleoclimate shifts and closely linked to that of coral reefs, a novel repertoire of genes related to immune functions, receptors and metabolism, and an extremely high proportion of transposable elements (Fig. 1).
Fig. 1: Summary of major findings in this study.

Photosymbiosis ecology greatly impacted Tridacna maxima demographic dynamics, genome composition, and gene evolution.

To summarise, giant clams, because they live in a low-nutrient environment, have had to form photosymbiotic relationships with photosynthesising algae that they acquire when free-swimming larvae. To make this symbiosis work, they have had to tone down their immune system and so are prone to viral infections and carry many remnants of old retrovirus infections in their genome.

All typical of a mindless evolutionary process with its sub-optimal solutions and compromises and added layers of complexity to make it work, like a contraption designed by William Heath-Robinson, but unlike anything that an intelligent designer worthy of the adjective, 'intelligent', and the noun 'designer' would produce, even if it lacked the sense to design the giant clams to live in more nutrient-rich environments in the first place.

To a creationist, this sort of needlessly complex arrangement is evidence of a high intelligence at work - which probably explains why they are creationists in the first place.

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