Typhlichthys subterraneus
Matthew Niemiller
Some days there are so many papers in which the authors casually — and with no intention of doing so — comprehensively refute basic creationist claims, that there just aren’t enough hours in the day to keep up with them. For creationists, of course, the task is simple: never read a scientific publication. The last thing any dedicated creationist wants is those pesky, “Satanic” scientists trying to make them lose ‘faith’, or worse, consider the possibility of being wrong when confronted with nasty, toxic facts.
In the bizarre world of faith, things must be true if you believe them by faith. After all, faith is the sure and certain way to “just know” the truth without all that bothersome learning. It’s also the sure and certain way to know that yours is the only true faith and that all other faiths are wrong.
So this new research about the convergent evolution of blind cavefish will need to be kept firmly behind the impregnable shield of faith, because faith must be protected from cold, harsh reality at all times — even at the cost of personal integrity. A creationist would much rather be thought of as intellectually dishonest than wrong.
The news comes from researchers at Yale, who have discovered how blind cavefish lost their eyes through something creationists insist can’t happen because it is invariably fatal: loss of genetic information. And not just once, but in several species of blind cavefish — all of which lost their eyes by essentially the same mechanism.
The researchers showed, using a new “mutational clock,” that the oldest blind cavefish, the Ozark cavefish (Troglichthys rosae), began degenerating up to 11 million years ago. This technique also establishes a minimum age for the caves these fish inhabit, since the caves must have existed before the fish colonised them.
In a nice confirmation of the Theory of Evolution — which predicts that environmental change will drive evolutionary change and that species will evolve towards greater fitness in that environment — several species of cavefish exhibit broadly similar adaptations such as a flattened skull, a long, thin body, and the loss or reduction of pelvic fins.
Why “Loss of Information” Is Evolution in Action. Creationists often claim that mutations which reduce or eliminate a function are always harmful. In reality, when a trait is no longer useful — such as eyes in total darkness — natural selection can favour mutations that switch it off, saving energy. This isn’t “devolution,” it’s adaptation.The discovery is published open access in Molecular Biology and Evolution and also explained in Yale News.
Blind cavefish aren’t alone: many species have independently evolved for life without light. The Texas blind salamander (Eurycea rathbuni), cave beetles, and certain spiders and crabs have lost eyes and pigmentation. Even entire ecosystems adapt to permanent darkness. In Movile Cave in Romania, sealed off for ~5.5 million years, dozens of unique species survive without sunlight, relying instead on chemosynthetic bacteria as the base of their food web.
Far from showing “decay,” these systems illustrate evolution’s power to produce thriving life forms in extreme environments — often by losing functions that would be wasteful in their new world.
Here’s a visual overview showing how blind cavefish populations — particularly the Mexican tetra (Astyanax mexicanus) — are distributed across cave clusters in Mexico, illustrating multiple independent colonisations.
Image credit: Richard Borowsky
Overview of Blind Cavefish Species and Their Occurrence
- Mexican Tetra (Astyanax mexicanus) – Multiple Cave Populations (Mexico)
- This species exists in both surface-dwelling, sighted forms and blind, cave-dwelling forms. They are interfertile and highly studied for evolutionary research [1, 2].
- There are at least 29 known cave populations, each isolated and evolving independently—a classic case of convergent evolution [2].
- Population distribution within caves is non-uniform and clumped, typically clustering around nutrient sources like bat guano, which makes estimating total population sizes tricky [3].
- Ozark Cavefish (Troglichthys rosae) – USA (Ozark Highlands)
- Found in about 83 locations across the Ozark Highlands ecoregion (northwestern Arkansas, northeastern Oklahoma, southwestern Missouri) [4].
- Listed as Near Threatened on the IUCN Red List, and protected under US endangered-species regulations [5].
- The earliest onset of eye gene degeneration dates back up to 11 million years ago, according to a new mutational clock analysis [6].
- Hoosier Cavefish (Amblyopsis hoosieri) – Indiana, USA
- Newly described (2014), this species was previously grouped under A. spelaea but is now recognised as a distinct taxon north of the Ohio River [7].
- Falls within the same Amblyopsidae family and shows typical troglomorphic features — loss of pigment and eyes.
- Other Notable Cavefish Around the World
- Omani blind cavefish (Garra barreimiae – cave form): A subspecies in Oman that loses pigmentation and eye function in specific cave populations – genetically similar to its surface counterpart [4, 8].
- Madagascan species (Typhleotris madagascariensis and T. mararybe): Endemic to southwestern Madagascar. T. madagascariensis is blind and unpigmented; T. mararybe is blind but darkly pigmented, adapted for partly lit cave zones [9].
- Kikori blind gudgeon (Oxyeleotris caeca): Discovered in Papua New Guinea (1996); blind and lacks pigmentation, likely occurs in an extensive underground karst system [10].
- Blind cave eel (Ophisternon candidum): Australia’s longest cavefish, blind and depigmented, found in very restricted subterranean waters of northwestern Australia [11].
- Javan cave barb (Barbodes klapanunggalensis): Recently described (2020–2022) from a karst cave in Java, Indonesia. Likely endemic and threatened due to its limited occurrence [12].
Summary Table Species / Region Distribution / Occurrence Astyanax mexicanus (Mexico) Multiple cave populations; frequent independent colonisations Troglichthys rosae (Ozark Highlands) ~83 cave sites across AR, MO, OK; ~11 mya degeneracy Amblyopsis hoosieri (Indiana, USA) Newly recognised, north of Ohio River Garra barreimiae (Oman cave form) Wadis/caves in Oman; troglomorphic subspecies T. madagascariensis & T. mararybe (Madagascar Distinct cave adaptations in SW Madagascar O. caeca (Papua New Guinea) Karst caves; first known PNG cavefish Ophisternon candidum (Australia) Limited NW Australia; blind, eel-like form B. klapanunggalensis (Java, Indonesia) One Javan karst cave; newly discovered, likely endemic
These species highlight how loss of eyes and pigmentation is a repeated evolutionary response to life in lightless environments—across continents, isolated cave systems, and diverse fish families.
Dark ages: Genomic analysis shows how cavefish lost their eyes
In a new study, Yale researchers used genomic analysis to show when cavefishes lost their eyes, which provides a method for dating cave systems.
Small, colorless, and blind, amblyopsid cavefishes inhabit subterranean waters throughout the eastern United States. In a new study, Yale researchers reveal insights into just how these distinctive cave dwellers evolved — and provide a unique method for dating the underground ecosystems where they reside.
In an analysis of the genomes of all known amblyopsid species, the researchers found that the different species colonized caves systems independently of each other and separately evolved similar traits — such as the loss of eyes and pigment — as they adapted to their dark cave environments.
Their findings are published in the journal Molecular Biology and Evolution.
By studying the genetic mutations that caused the fishes’ eyes to degenerate, the researchers developed a sort of mutational clock that allowed them to estimate when each species began losing their eyes. They found that vision-related genes of the oldest cavefish species, the Ozark cavefish (Troglichthys rosae), began degenerating up to 11 million years ago. The technique provides a minimum age for the caves that the fishes colonized since the cavefish must have been inhabiting subterranean waters when their eyesight began devolving, the researchers said.The ancient subterranean ecosystems of eastern North America are very challenging to date using traditional geochronological cave-dating techniques, which are unreliable beyond an upper limit of about 3 to 5 million years. Determining the ages of cave-adapted fish lineages allows us to infer the minimum age of the caves they inhabit because the fishes wouldn’t have started losing their eyes while living in broad daylight. In this case we estimate a minimum age of some caves of over 11 million years.
Chase D. Brownstein, co-lead author Graduate School of Arts and Sciences Department of Ecology and Evolutionary Biology
Yale University, New Haven, CT, USA.
Maxime Policarpo of the Max Planck Institute for Biological Intelligence and the University of Basel is the co-lead author.
For the study, the researchers reconstructed a time-calibrated evolutionary tree for amblyopsids, which belong to an ancient, species-poor order of freshwater fishes called Percopsiformes, using the fossil record as well as genomic data and high-resolution scans of all living relevant species.
All the cavefish species have similar anatomies, including elongated bodies and flattened skulls, and their pelvic fins have either been lost or severely reduced. Swampfish (Chologaster cornuta), a sister to cavefish lineage that inhabits murky surface waters, also has a flattened skull, elongated body, and no pelvic fin. While it maintains sight and pigment, there is softening of the bones around its eyes, which disappear in cavefishes. This suggests that cavefishes evolved from a common ancestor that was already equipped to inhabit low-light environments, Brownstein said.
To understand when the cavefish began populating caves — something impossible to discern from the branches of an evolutionary tree — the researchers studied the fishes’ genomes, examining 88 vision-related genes for mutations. The analysis revealed that the various cavefish lineages had completely different sets of genetic mutations involved in the loss of vision. This, they said, suggests that separate species colonized caves and adapted to those subterranean ecosystems independently of each other.
From there, the researchers developed a method for calculating the number of generations that have passed since cavefish species began adapting to life in caves by losing the functional copies of vision-related genes.
Their analysis suggests that cave adaptations occurred between 2.25 and 11.3 million years ago in Ozark cavefish and between 342,000 to 1.70 million years ago (at minimum) and 1.7 to 8.7 million years ago (at maximum) for other cavefish lineages. The findings support the conclusion that at least four amblyopsid lineages independently colonized caves after evolving from surface-dwelling ancestors, the researchers said.
The maximum ages exceed the ranges of traditional cave-dating methods, which includes isotope analysis of cosmogenic nuclides that are produced within rocks and soils by cosmic rays, the researchers noted.
The findings also suggest potential implications for human health, said Thomas Near, professor of ecology and evolutionary biology in Yale’s Faculty of Arts and Sciences (FAS), and senior author of the study.
A number of the mutations we see in the cavefish genomes that lead to degeneration of the eyes are similar to mutations that cause ocular diseases in humans. There is the possibility for translational medicine through which by studying this natural system in cavefishes, we can glean insights into the genomic mechanisms of eye diseases in humans.
Professor Thomas J Near, senior author
Faculty of Arts and Sciences (FAS)
Department of Ecology and Evolutionary Biology
Yale University, New Haven, CT, USA
And Yale Peabody Museum, New Haven, CT, USA.
The other co-authors are Richard C. Harrington of the South Carolina Department of Natural Resources, Eva A. Hoffman of the American Museum of Natural History, Maya F. Stokes of Florida State University, and Didier Casane of Paris-Cité University.
Publication:
What we see with blind cavefish — whether in Mexico, the Ozarks, Madagascar, or Romania’s sealed caverns — is a repeated pattern of evolution producing similar outcomes under similar conditions. Eyes and pigment are costly luxuries in total darkness, so they are pared away by natural selection in population after population. Different lineages, on different continents, separated by millions of years, all converging on the same solution is exactly what evolutionary theory predicts.Abstract
Genomes provide tools for reconstructing organismal evolution and larger Earth system processes. Although genome sequences have been jointly analyzed with geological data to understand links between biological evolution and geological phenomena such as erosion and uplift, genomic and natural history observations have seldom been leveraged to reconstruct the timescale of landscape change in cases where traditional methods from the Earth sciences cannot. Here, we reconstruct the genomic evolution of cave-adapted amblyopsid fishes. Although high-resolution computed tomography reveals the strikingly similar skeletons of cave-adapted lineages, our analyses of the genomes of all species in this clade suggest that amblyopsids independently colonized caves and degenerated their eyes at least four times after descending from populations that already possessed adaptations to low-light environments. By examining pseudogenization through loss-of-function mutations in amblyopsids, we infer that the genomic bases of their vision degenerated over millions of years. We leverage these data to infer the ages of subterranean karstic ecosystems in eastern North America, which are difficult to date using standard geochronologic techniques. Our results support ancient ages for imperiled North American cave biotas and show how genomes can be used to inform the timescale of landscape evolution.
Introduction
The origins of adaptations for life in new environments have captivated evolutionary biologists since the discipline began (Darwin 1859). One of the most striking discoveries has been that lineages across the Tree of Life have convergently modified their phenotypes via strikingly similar genetic and developmental trajectories (Hoekstra 2006; Manceau et al. 2010; Rosenblum et al. 2010.1; Losos 2011; Stern 2013; Gallant et al. 2014; Agrawal 2017).
Caves are a classic system for studying the convergent degeneration of traits under changing selective landscapes. Since the 19th century, thousands of obligate cave-dwelling animals have been described (Rétaux and Casane 2013.1; Culver and Pipan 2019; Niemiller and Taylor 2019.1). These dark, nutrient-limited environments (Poulson and White 1969) often necessitate the evolution of novel features and facilitate the degeneration of traits suited for life at the surface due to the relaxation of selective pressures or selection against metabolically costly structures that are of less use in caves (e.g. eyes). Degenerative evolution has often been examined in cave-adapted model organisms, especially blind populations of Astyanax mexicanus fish (Jeffery et al. 2003; Rétaux and Casane 2013.1; McGaugh et al. 2014.1; Moran et al. 2015; Casane and Rétaux 2016; Krishnan and Rohner 2017.1; Gore et al. 2018). However, the macroevolution of life in caves remains obscure (Niemiller et al. 2013.2a; Yang et al. 2016.1; Hart et al. 2020; Mao et al. 2021, 2022; Balart-García et al. 2023).
One essential aspect of cave ecosystems that has often evaded resolution are the ages of the landforms themselves. The species-rich subterranean ecosystems of eastern North America, for example, are notoriously challenging to date via traditional geochronologic techniques (Granger et al. 2001; Osborne 2005, 2007; Stock et al. 2005.1 ; White 2007.1a). An emerging field, geogenomics, seeks to test hypotheses about landform evolution by studying the history of biological diversification recorded in genomic data (Baker et al. 2014.2; Dawson et al. 2022.1; Dolby et al. 2022.2). Yet, phylogenetic analysis of genome-scale data has not yet been leveraged to investigate the history of cave system formation.
Here, we reconstruct the evolutionary history of cavefishes in the clade Amblyopsidae, which is part of an ancient, species-poor lineage of fishes (Percopsiformes) endemic to North America (Niemiller and Poulson 2010.2, Niemiller et al. 2012, 2013.2a,2013.3b; Armbruster et al. 2016.2; Hart et al. 2020, 2025). Amblyopsid cavefishes include facultative and obligate cave dwellers that show classic adaptations for subterranean life, such as the expansion of sensory structures on the head and body, as well as the degeneration of numerous traits associated with life at the surface, including loss of pigmentation, the degeneration of the eye, and the reduction of hearing capabilities (Niemiller and Poulson 2010.2; Niemiller et al. 2013.2a,2013.4c; Hart et al. 2020). By using genome sequences to produce a new hypothesis of amblyopsid relationships, we demonstrate that at least four lineages with similar skeletal adaptations show genomic evidence for independent cave colonization. Our inferences of cavefish genomic evolution suggest multiple ancient invasions of cave environments by amblyopsids that can be used to inform the ages of the biodiverse subterranean ecosystems of eastern North America (Niemiller and Taylor 2019.1; Niemiller et al. 2021.1).
The timescale of amblyopsid cavefish evolution. Tip-dated Bayesian phylogeny of all recognized species of Percopsiformes including Ambylopsidae inferred from three sets of 50 randomly sampled ultraconserved elements using BEAST2. Colored branches indicate ancestral states inferred under a polymorphic character model in phytools, and pie charts indicate inferred states at nodes with uncertain (<80% probability of a single state) inferred ancestral states. To the right of the phylogeny are high-resolution computed tomography scan renders of percopsiform skulls and skeletons; numbers alongside tip labels indicate the corresponding scan. Colors of bone groups in scans indicate: suspensorium (green), circumorbital series (red), neurocranium (aquamarine), opercular series (light blue), branchiostegal series (dark blue), and pharyngeobranchial series (yellow). Roman numerals at nodes indicate potential cave colonization episodes based solely on the habitat ancestral state reconstruction (solid circle—minimum number of origins; dotted circles—maximum number of origins). Abbreviations: Pal., Paleocene; Olig., Oligocene; N, Northern; S, Southern. Daggers denote extinct species.Illustrations by Julia Johnson (https://www.lifesciencestudios.com/).
For creationism, however, this is a hopelessly awkward fact. Creationist dogma insists that “loss of information” must always be destructive, yet here it is the very means by which organisms adapt and thrive. These fish are not degenerate or failing: they are finely tuned to their environment in a way that makes perfect sense under evolution and no sense at all under the notion of fixed “kinds.”
To accept the evidence would require admitting that the natural world is shaped by gradual, testable processes — not the whims of a designer. And so, predictably, creationists must keep their eyes tightly shut, just like the fish they cannot explain, rather than confront the uncomfortable truth staring them in the face.
Advertisement
What Makes You So Special? From The Big Bang To You
How did you come to be here, now? This books takes you from the Big Bang to the evolution of modern humans and the history of human cultures, showing that science is an adventure of discovery and a source of limitless wonder, giving us richer and more rewarding appreciation of the phenomenal privilege of merely being alive and able to begin to understand it all.
Ten Reasons To Lose Faith: And Why You Are Better Off Without It
This book explains why faith is a fallacy and serves no useful purpose other than providing an excuse for pretending to know things that are unknown. It also explains how losing faith liberates former sufferers from fear, delusion and the control of others, freeing them to see the world in a different light, to recognise the injustices that religions cause and to accept people for who they are, not which group they happened to be born in. A society based on atheist, Humanist principles would be a less divided, more inclusive, more peaceful society and one more appreciative of the one opportunity that life gives us to enjoy and wonder at the world we live in.
Amazon
Amazon
Amazon
Amazon
Amazon
Amazon
Amazon
Amazon
All titles available in paperback, hardcover, ebook for Kindle and audio format.
Prices correct at time of publication. for current prices.
No comments :
Post a Comment
Obscene, threatening or obnoxious messages, preaching, abuse and spam will be removed, as will anything by known Internet trolls and stalkers, by known sock-puppet accounts and anything not connected with the post,
A claim made without evidence can be dismissed without evidence. Remember: your opinion is not an established fact unless corroborated.