Rosa Rubicondior: Unintelligent Design - When Snakes Borrow Genes from the Sea

A Western Brown snake, Pseudonaja nuchalis

By Andy - originally posted to Flickr as Western Brown, CC BY-SA 2.0, Link

New study unlocks mystery origin of iconic Aussie snakes | Newsroom | University of Adelaide

Intrigued by the information I unearthed while researching for my recent blog post about Australia's elapsid snakes and how skinks have evolved resistance to their venom, I discovered that these snakes have evolved from a common ancestor that once lived in the sea, and, while there, picked up a number of 'jumping genes' that are only found in marine animals as diverse as fish, sea squirts, sea urchins, bivalve molluscs and turtles.

The more we learn about genomes, the clearer it becomes that evolution is not a neat or predictable process—it is messy, opportunistic, and deeply influenced by historical contingency. A striking example of this comes from a recent genomic study that traced the origins of Australia’s iconic elapid snakes—not just through their DNA, but through the foreign DNA embedded within it. Researchers have identified at least 14 distinct horizontal gene transfer (HGT) events in these snakes, in which transposable elements—“jumping genes” — from unrelated marine organisms such as fish, tunicates, molluscs, and turtles have been incorporated into the snake genome.

This is compelling evidence that the ancestors of modern Australian elapids passed through a marine environment, acquiring genetic material from the organisms they encountered there. The transfers are not random. They show ecological specificity, temporally sequenced occurrence, and a nested pattern of inheritance — hallmarks of an evolutionary process rather than the actions of an intelligent designer.

For proponents of Intelligent Design creationism, this presents a serious interpretive problem. The idea that different species share features because of a “common designer” does not explain why Australian elapids should contain such a unique suite of genes from marine animals—genes absent in closely related snakes that remained on land. Nor does it account for the fact that many of these sequences serve no obvious function, are neutral or even mildly deleterious, and resemble the genetic detritus typical of unguided evolution.

ID advocates will likely claim this is just more evidence of “design reuse” or “genetic toolkits.” But such claims are not only ad hoc; they fail to explain the clear environmental and phylogenetic patterns observed in the data. The evolutionary explanation, by contrast, is both predictive and parsimonious: snakes dispersed through a marine environment, interacted with marine organisms, and as a result, their genomes bear the signature of that history.
In what follows, we will explore how this discovery not only sheds light on the evolutionary past of Australian elapids, but also exposes the weaknesses in ID’s core explanatory framework. The genome of a snake tells a story—and it's not the story of design.

About Australian Elapids. Australian elapids are a remarkable group of front-fanged venomous snakes belonging to the family Elapidae, which also includes cobras, kraits, and mambas. What makes the Australian clade extraordinary is not just its venom potency, but its evolutionary success across an astonishing range of habitats.

Diversity

Australia is home to over 100 species of elapid snakes, making it one of the most diverse snake radiations on the continent. This group includes:

Terrestrial hunters like the Eastern brown snake (Pseudonaja textilis)
Fossorial (burrowing) species such as the small-eyed snakes (Cryptophis spp.)
Semi-aquatic and fully marine snakes, including the beaked sea snake (Hydrophis schistosus) and olive sea snake (Aipysurus laevis)

The radiation includes both highly venomous and more cryptic species, adapted to deserts, forests, grasslands, wetlands, and coral reefs.

Distribution

Australian elapids are found throughout the Australian mainland and offshore islands, extending into New Guinea, parts of Indonesia, and across the Indo-Pacific via their marine representatives. Their success in both terrestrial and marine environments is unparalleled among snakes.

The marine elapids (commonly referred to as sea snakes) are especially interesting—they are the only group of snakes to have become fully marine, breathing air but living entirely in the ocean.

Evolutionary Significance

Genetic studies place Australian elapids within a subfamily called Hydrophiinae, which includes both land and sea snakes. They are believed to have originated from a single Asian ancestor that dispersed to Australia via a marine route around 25–30 million years ago, before undergoing rapid adaptive radiation.

This history is not just a tale of migration—it’s written into their DNA.

These 'jumping genes' were discovered by a team, led by Professor David Adelson from the University of Adelaide’s School of Biological Sciences. Their research was published in the journal, Genes in 2022 and was described in a University of Adelaide news item:

New study unlocks mystery origin of iconic Aussie snakes
New research led by the University of Adelaide has found the first tangible evidence that the ancestors of some of Australia’s most venomous snakes arrived by sea rather than by land – the dispersal route of most other Australian reptiles.
In a paper published in Genes , the researchers analysed the genomes of two Australian elapids (front fanged snakes), a tiger and a brown snake, and compared them to marine and semi-marine elapid sea snakes and Asian elapids.

They inferred that the ancestor of all Australian elapids had accumulated self-replicating and self-mobilising genes (jumping genes) that were not present in their land relatives but came from another source altogether.

While we know all marine and semi-marine sea snakes descended from a common Australian land-based ancestor, the origin of Australian elapids has been debated for some time. Some believe their ancestors travelled by land, whereas others hold the more contentious view that a marine or semi-marine ancestor swam here. In our research we found a number of genes that were present in the ancestor of all Australian elapids but could not be traced to a snake ancestor; instead they could be traced to similar transposable gene sequences found in marine life, including fish, sea squirts, sea urchins, bivalves and turtles. This indicates the marine environment transferred the new genetic material into the snakes and offers new support to the argument that the first Australian elapids swam to our shores. They must have previously acquired the new genetic material during an ancestral period when they were adapted to marine life.

Professor David L Adelson, co-corresponding author.
School of Biological Sciences
University of Adelaide, Adelaide, SA, Australia.

The researchers identified 14 distinct transfer events of the new genetic material from other marine organisms, with eight genes uniquely present in the marine and semi-marine sea snake genomes. In the case of the semi-marine snake genome, the acquired genes accounted for as much as 8-12% of the total genome sequence.

This meant that we could unambiguously determine the major genetic differences between land and marine/semi-marine snakes were a consequence of migration into a marine environment. This is the first time that jumping genes have been used to confirm the evolutionary history of any animal species, and this research definitively proved that the common ancestor of all Australian elapids adapted to a marine environment. It may also have made it easier for the subsequent land to marine transition of sea snakes.

Professor David L Adelson

Publication:
Galbraith, J.D.; Ludington, A.J.; Sanders, K.L.; Amos, T.G.; Thomson, V.A.; Enosi Tuipulotu, D.; Dunstan, N.; Edwards, R.J.; Suh, A.; Adelson, D.L.
Horizontal Transposon Transfer and Its Implications for the Ancestral Ecology of Hydrophiine Snakes. Genes (2022), 13, 217. https://doi.org/10.3390/genes13020217

Abstract
Transposable elements (TEs), also known as jumping genes, are sequences able to move or copy themselves within a genome. As TEs move throughout genomes they often act as a source of genetic novelty, hence understanding TE evolution within lineages may help in understanding environmental adaptation. Studies into the TE content of lineages of mammals such as bats have uncovered horizontal transposon transfer (HTT) into these lineages, with squamates often also containing the same TEs. Despite the repeated finding of HTT into squamates, little comparative research has examined the evolution of TEs within squamates. Here we examine a diverse family of Australo–Melanesian snakes (Hydrophiinae) to examine if the previously identified, order-wide pattern of variable TE content and activity holds true on a smaller scale. Hydrophiinae diverged from Asian elapids ~30 Mya and have since rapidly diversified into six amphibious, ~60 marine and ~100 terrestrial species that fill a broad range of ecological niches. We find TE diversity and expansion differs between hydrophiines and their Asian relatives and identify multiple HTTs into Hydrophiinae, including three likely transferred into the ancestral hydrophiine from fish. These HTT events provide the first tangible evidence that Hydrophiinae reached Australia from Asia via a marine route.

1. Introduction
Variation is the fundamental basis of all evolutionary change, and mobile genetic elements are a major source of genomic variation. A high proportion of animal and plant genome sequences is derived from transposable elements (TE) and TEs are acknowledged drivers of evolutionary change, but their impacts are poorly understood. Understanding how TEs drive evolutionary change requires studying systems that are young, species-rich and ecologically diverse. In these respects, elapid snakes present excellent opportunities for the study of TE dynamics and their contribution to adaptive changes. Elapids are a diverse group of venomous snakes found across Africa, Asia, the Americas and Australia. Following their divergence from Asian elapids ~30 Mya, the Australo–Melanesian elapids (Hydrophiinae) have rapidly diversified into more than 160 species including ~100 terrestrial snakes, ~60 fully marine sea snakes and six amphibious sea kraits [1]. Both the terrestrial and fully marine hydrophiines have adapted to a wide range of habitats and niches. Terrestrial Hydrophiinae are found across Australia, for example, the eastern brown snake (Pseudonaja textilis) in open habitats, the tiger snake (Notechis scutatus) in subtropical and temperate habitats and the inland taipan (Oxyuranus microlepidotus) in inland arid habitats [2]. Sea snakes are phylogenetically closer to tiger snakes than the other terrestrial Hydrophiinae, so share a common ancestor. Since transitioning to a marine habitat, many sea snakes have specialized to feed on a single prey such as fish eggs, catfish, eels or burrowing gobies, while others such as Aipysurus laevis are generalists [3,4] (hereafter, all mentions of these species will use the genus name only, i.e., Aipysurus for A. laevis). Sea kraits (Laticauda) are amphibious and have specialized to hunt various fish including eels and anguilliform-like fish at sea, while digesting prey, mating and shedding on land [5]. Since transitioning to marine environments, both sea snakes and sea kraits have been the recipients of multiple independent horizontal transposon transfer (HTT) events, with adaptive potential [6,7].

Transposable elements (TEs) are mobile genetic elements that can move or copy themselves across the genome, and account for a large portion of most vertebrate genomes [8,9]. Though often given short shrift in genome analyses, TEs are important agents of genome evolution and generate genomic diversity [10,11]. For example, the envelope gene of an endogenous retrovirus was repeatedly exapted by both mammals and viviparous lizards to function in placenta development [12]. In addition, unequal crossing over caused by CR1 retrotransposons led to the duplication, and hence diversification, of the PLA2 venom genes in pit vipers [13].

Transposable elements (TEs) are classified into two major classes based on their structure and replication method [14]. DNA transposons (Class II) mostly proliferate through a “cut and paste” method, possess terminal inverted repeats and are further split based on the transposase sequence used in replication. Retrotransposons (Class I) are split into LTR retrotransposons and non-LTR retrotransposons, which proliferate through “copy and paste” methods. Both subclasses of retrotransposons are split into numerous superfamilies based on both coding and structural features [15,16,17]. Within the diverse lineages of land vertebrates, the evolution of TEs is well described in eutherian mammals and birds. The total repetitive content of both bird and mammal genomes is consistently at 7–10% and 30–50%, respectively. Similarly, most lineages of both birds and eutherian mammals are dominated by a single superfamily of non-LTR retrotransposons (CR1s and L1s, respectively) and a single superfamily of LTR retrotransposons (endogenous retroviruses in both) [8,18]. Some lineages of birds and mammals contain horizontally transferred retrotransposons that have been variably successful (AviRTE and RTE-BovB, respectively) [19,20].

In stark contrast to mammals and birds, squamates have highly variable mobilomes, both in terms of the diversity of their TE superfamilies and the level of activity of said superfamilies within each genome [21]. While these broad comparisons have found significant variation in TEs between distant squamate lineages, none have examined how TEs have evolved within a single family of squamates. The one in-depth study into the mobilome of snakes found that the Burmese python genome is approximately ~21% TE and appears to have low TE expansion, while that of a pit viper is ~45% TE, due to the expansion of numerous TE superfamilies and microsatellites since their divergence ~90 Mya [22,23]. It thus is unclear whether similar expansions have occurred within other lineages of venomous snakes. Here, we examine the TE landscape of the family Hydrophiinae, and in doing so discover horizontal transfer events into the ancestral hydrophiine, sea kraits, sea snakes and tiger snakes.

Galbraith, J.D.; Ludington, A.J.; Sanders, K.L.; Amos, T.G.; Thomson, V.A.; Enosi Tuipulotu, D.; Dunstan, N.; Edwards, R.J.; Suh, A.; Adelson, D.L.
Horizontal Transposon Transfer and Its Implications for the Ancestral Ecology of Hydrophiine Snakes. Genes (2022), 13, 217. https://doi.org/10.3390/genes13020217

Copyright: © 2025 The authors.
Published by MDPI (Basel, Switzerland). Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

For evolutionary biology, this discovery is a striking affirmation. It confirms not only the long-theorised marine dispersal of elapids to Australia, but also the ecological and molecular mechanisms by which such transitions leave a permanent record in the genome. The presence of marine-derived transposable elements in terrestrial snakes is not just a curiosity—it is a genetic fossil, offering a timestamped glimpse into the evolutionary past.

For Intelligent Design creationism, however, it poses a deeper problem. The theory of a "common designer" might explain superficial similarities between species by appealing to reused blueprints, but it cannot convincingly account for environmentally specific, time-bound, and often functionless genomic features like these. Why would a designer insert sequences from fish, tunicates, and molluscs into the genome of snakes that now live in deserts and forests—especially when those sequences have no clear function and are absent from related terrestrial snakes?

Evolution provides a clear, coherent, and testable explanation: these snakes' ancestors passed through a marine phase during which they were exposed to, and integrated, foreign genetic material from the marine organisms around them. As they colonised the Australian continent and diversified into different habitats, they carried these molecular remnants with them—a legacy of where they had been, not why they were "designed".

Once again, the data aligns with descent, not design. And once again, it is evolution—not Intelligent Design—that proves itself capable of explaining the natural world in all its richness, complexity, and imperfection.

Advertisement

The Unintelligent Designer: Refuting The Intelligent Design Hoax

ID is not a problem for science; rather science is a problem for ID. This book shows why. It exposes the fallacy of Intelligent Design by showing that, when examined in detail, biological systems are anything but intelligently designed. They show no signs of a plan and are quite ludicrously complex for whatever can be described as a purpose. The Intelligent Design movement relies on almost total ignorance of biological science and seemingly limitless credulity in its target marks. Its only real appeal appears to be to those who find science too difficult or too much trouble to learn yet want their opinions to be regarded as at least as important as those of scientists and experts in their fields.

The Malevolent Designer: Why Nature's God is Not Good

This book presents the reader with multiple examples of why, even if we accept Creationism's putative intelligent designer, any such entity can only be regarded as malevolent, designing ever-more ingenious ways to make life difficult for living things, including humans, for no other reason than the sheer pleasure of doing so. This putative creator has also given other creatures much better things like immune systems, eyesight and ability to regenerate limbs that it could have given to all its creation, including humans, but chose not to. This book will leave creationists with the dilemma of explaining why evolution by natural selection is the only plausible explanation for so many nasty little parasites that doesn't leave their creator looking like an ingenious, sadistic, misanthropic, malevolence finding ever more ways to increase pain and suffering in the world, and not the omnibenevolent, maximally good god that Creationists of all Abrahamic religions believe created everything. As with a previous book by this author, "The Unintelligent Designer: Refuting the Intelligent Design Hoax", this book comprehensively refutes any notion of intelligent design by anything resembling a loving, intelligent and maximally good god. Such evil could not exist in a universe created by such a god. Evil exists, therefore a maximally good, all-knowing, all-loving god does not.

Illustrated by Catherine Webber-Hounslow.

Amazon