Rosa Rubicondior: Creationism Refuted - Recovering DNA from Extinct Galápagos Giant Tortoises

Dome-shelled Galápagos giant tortoise, Chelonoidis nigra

By Mfield, Matthew Field, http://www.photography.mattfield.com - Own work,
CC BY-SA 3.0, Link

Reading the giant tortoise DNA that time forgot | Yale News

Few places are more closely associated with evolutionary biology than the Galápagos Islands. Their isolation has repeatedly divided colonising populations into smaller groups, allowing mutation, genetic drift and natural selection to produce distinct island lineages. Yet their subsequent history has not always resembled a neatly branching tree. Occasional migration—and, more recently, the deliberate movement of animals by humans—has brought formerly isolated populations back into contact, permitting them to interbreed and exchange genes.

The evolutionary radiation of the Galápagos giant tortoises is a particularly striking example. Thirteen living and four extinct lineages are currently recognised within the Chelonoidis complex, each descended from the same ancestral colonisation but subsequently differentiated by geographical isolation. Unfortunately, centuries of exploitation by sailors and settlers devastated many populations, leaving some lineages represented only by bones preserved in museums.

Those remains retain a record of their evolutionary history, but reading it is difficult. DNA begins to fragment and chemically deteriorate after death, while contamination from microorganisms and people can overwhelm the surviving genetic material. In some of the museum specimens examined in a new study, researchers could read less than one per cent of the original genome—far too little for many conventional methods of genomic comparison.

However, a team led by researchers at Yale University has now developed a computational approach capable of extracting reliable evolutionary information from such exceptionally incomplete genomes. As described in Proceedings of the Royal Society B, the researchers analysed dried bones from five historical specimens and placed their surviving DNA fragments upon a reference phylogeny constructed from high-quality genomes belonging to living and other historical tortoises.

Importantly, the researchers did not manufacture plausible sequences to fill the gaps. Their analytical pipeline was designed to recover the phylogenetic and population-genetic signal present in ultra-low-coverage genomes without imputing the missing genotypes. Even at sequencing depths as low as 0.008 times the genome, the surviving fragments contained enough mutually consistent information to reveal where the specimens belonged.

The results confirmed that the bones represented two evolutionarily distinct, now-extinct lineages: the former tortoises of Santa Fe and an extinct San Cristóbal lineage different from the population still living on that island. These were not merely unusual individuals belonging to surviving populations but genetically distinguishable branches of the wider Galápagos tortoise radiation.

Yet extinction may not have erased their genetic legacy completely. Sailors commonly transported living tortoises between islands as a convenient supply of fresh meat. Some escaped or were released and subsequently bred with local tortoises. Consequently, fragments of genomes belonging to ostensibly extinct lineages may still survive within living hybrids, raising the possibility that carefully managed breeding could preserve—and perhaps concentrate—more of that lost ancestry.

This is evolution written simultaneously as a branching and reconnecting history: populations became isolated and diverged, but some later met and exchanged genes. There is nothing here resembling separately created “kinds”, each possessing an inviolable identity. Instead, there are changing populations, incomplete reproductive barriers, extinction and hybridisation—the untidy, reticulated pattern expected when biodiversity is the product of evolutionary processes rather than discrete acts of creation.

The research also vindicates the often-underappreciated value of natural-history collections. Bones gathered more than a century ago, long before genome sequencing was imaginable, can now disclose evolutionary relationships that appeared to have vanished with the animals themselves. As analytical methods improve, museum drawers do not merely preserve relics of the past; they preserve evidence awaiting the technology capable of reading it.

Extinct—but not necessarily genetically erased. Extinction normally means that the last recognisable member of a species or population has died. It does not necessarily mean, however, that every fragment of that lineage’s genome has disappeared.

When two differentiated populations meet and interbreed, their offspring inherit DNA from both. If those hybrids reproduce, segments of the introduced DNA—known as introgressed DNA—may pass through many subsequent generations. Recombination breaks the segments into progressively smaller pieces, while natural selection, genetic drift and chance determine which survive.

Consequently, a lineage can become extinct as a distinct population while portions of its genetic ancestry persist in members of another. Evolutionary history therefore does not always resemble a tree whose branches separate permanently. Sometimes branches reconnect and exchange genes, producing a network-like, or reticulated, pattern.

Modern humans provide a familiar example. Neanderthals and Denisovans disappeared as distinct human populations, but both interbred with ancestors of living Homo sapiens. As a result, many people today carry fragments of Neanderthal DNA, while Denisovan ancestry is especially prominent in some populations of Oceania and parts of Asia. Genomic studies have also detected signs of contributions from other archaic human populations for which no securely identified fossils or complete genomes may yet be available. These are sometimes informally described as “ghost” populations.

No living person carries an intact Neanderthal or Denisovan genome, and possessing some archaic DNA does not make anyone partly Neanderthal in a taxonomic sense. Rather, different people carry different surviving fragments. Collectively, living humanity preserves considerably more archaic genetic variation than is present in any one individual.

Something similar may have happened among the Galápagos tortoises. Sailors transported tortoises between islands as a source of food, unintentionally bringing together lineages that geographical isolation had previously separated. Some transported animals survived, escaped or were released and bred with local tortoises. Living hybrids may therefore retain genomic fragments inherited from island lineages that no longer survive as distinct populations.

Conservation breeding could bring together individuals carrying different fragments and increase the proportion of ancestry derived from an extinct lineage. It could not resurrect that lineage exactly: much of its genome has probably been lost, and its original population, environment and evolutionary trajectory cannot be reconstructed. Nevertheless, the surviving fragments remain biologically and historically valuable.

The distinction is therefore important: a population may be extinct without being genetically erased. Its evolutionary legacy can persist, scattered through the genomes of living descendants.

The paper in Proceedings of the Royal Society B was accompanied by a Yale News report:

Reading the giant tortoise DNA that time forgot
Using a new computational toolkit, Yale researchers have recovered evolutionary clues from highly degraded DNA and identified two extinct giant tortoise lineages.

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Using a new combination of computational tools to analyze ancient DNA, Yale researchers have discovered two ancient, extinct giant tortoise lineages that once lived on the Galápagos Islands.

The researchers’ pioneering approach, which employs computational genome analysis tools, showed that museum specimens previously considered too genetically degraded to be useful in this type of research can help reveal evolutionary history. The findings could also aid ongoing efforts to expand giant tortoise populations in the Galápagos archipelago.

Results of the study are published in the journal Proceedings of the Royal Society B.

Map of the Galápagos Islands.
Image © stock.adobe.com

For researchers exploring evolutionary lineages, unlocking the DNA of extinct species in ancient samples has always been a challenge, because DNA degrades over time, leaving behind just scattered fragments of genetic information, and researchers struggle to fill in the missing pieces.

But in their new study, the Yale-led researchers developed a computational approach that can maximize the insights gained from the genomes of degraded specimens and then fill in the missing links, bypassing the need for a more complete DNA sample.

The challenge of this study was to reconstruct the genetic relationships of extinct Galápagos giant tortoises, knowing that the DNA we were able to obtain from museum specimens was going to be highly degraded and fragmented and have a high proportion of contamination.

Alexander Ochoa, lead author
Department of Ecology and Evolutionary Biology
Yale University
New Haven, CT, USA.

Ochoa was part of the research team in the lab of Adalgisa Caccone, a senior research scientist and lecturer in Yale’s Department of Ecology and Evolutionary Biology, a member of Yale’s Faculty of Arts and Sciences, and co-author of the new study. The research is part of the lab’s ongoing initiative to understand the genetic diversity of Galápagos giant tortoises.

In their work, researchers sampled these remaining bone fragments from the extinct Santa Fe island giant tortoise lineage.

Photo credit: Van Denburgh, J. 1914. Expedition of the California Academy of Sciences to the Galápagos Islands 1906-1906.
Proceeding of the California Academy of Sciences 2:203-374.

In their work, the researchers extracted DNA from dried bones of historical museum specimens, including five specimens of two extinct tortoise lineages. They then combined the scraps of recovered genetic information and superimposed, or placed, this information onto a reference phylogenetic tree built with high-quality genomes from living and other historical tortoises.

In some of the degraded tortoise specimens studied, less than 1% of the genome could be read. Conventional genomic analyses often discard such samples because the missing information can distort evolutionary relationships. But the researchers’ new computational approach, which combined several powerful computing tools, successfully identified specimens from the extinct San Cristóbal and Santa Fe island lineages.

Southern Isabela giant tortoise native to the volcanoes of southern Isabela Island in the Galápagos and characterized by its dome-shaped shell.
Credit: Evelyn Jensen.

“These are two distinct lineages,” Ochoa said, adding that linking the past with the present underscores current conservation efforts across the Galápagos archipelago. Historically, sailors visiting the Galápagos carried tortoises, which they used as a food source, from one island to another as cargo, Ochoa said. Some of these displaced turtles survived and were able to breed with tortoises from a different island. Due to these human-driven migration events, the genomes of extinct lineages may still be “living” in extant, hybrid tortoises.

In this regard, captive breeding programs that mate these hybrids may be able to recover the genomes of the extinct lineages in future generations. The tools developed in our study are not only useful for the discovery of extinct lineages but could also be applied to broader wildlife conservation efforts.

Alexander Ochoa.

Collaborators in the study include researchers from Newcastle University, the University of California, Berkeley, the University of Connecticut, Woods Hole Oceanographic Institution, Pacific Northwest Oceanographic Laboratory, the University of New Mexico, the University of Crete, the Foundation for Research and Technology – Hellas (FORTH), and MacEwan University.

Publication:
Alexander Ochoa, Stephen J. Gaughran, Rachel Gray, Nicole A. Fusco, Johanna N. J. Weston, Cyler Conrad, Nikos Poulakakis, Joshua M. Miller, Adalgisa Caccone, Evelyn L. Jensen;
Integration of ultra-low coverage whole-genome sequences for reconstructing the evolutionary history of Galapagos giant tortoises.
Proc. R. Soc. B 1 July 2026; 293(2075): 20260103. https://doi.org/10.1098/rspb.2026.0103

Abstract
Genomic data from contemporary and historical samples often need to be coupled for evolutionary reconstructions of multitaxon complexes. However, the genetic data recovered from historical samples may result only in ultra-low coverage whole-genome sequences (ulcWGS; <0.15× depth), leading to inaccurate evolutionary inferences given a preponderance of missing data. Using the Galapagos giant tortoise radiation as a study system (Chelonoidis spp., composed of 13 extant and four extinct lineages), we assembled a novel methodological pipeline that removes potential noise introduced by the missing data and enhances the evolutionary signal from ulcWGS samples. We leveraged existing tools for phylogenomic placement (EPA-ng), population genomic structure (smartsnp) and admixture (Admixfrog, NGSadmix) to demonstrate that the evolutionary history of samples can be uncovered with sequencing depths as low as 0.008–0.139×. Importantly, these approaches do not use genotype imputation of the ulcWGS samples, which would require extensive reference datasets. Our application to two cases of extinct lineages of Galapagos giant tortoises, with and without references from the same lineage, demonstrates the general value of the approach. We confirm where the extinct lineages from San Cristóbal and Santa Fe islands fit into the Galapagos giant tortoise radiation, and that these lineages were evolutionarily distinct entities.

Geographical locations of 17 lineages of giant tortoises (Chelonoidis spp.). Distributions of extant lineages are depicted in purple. Extinct lineages are marked with †. Carapace morphology: S, saddleback; D, domed; I, intermediate; ?, unknown. Island names and ages (Ma, inside square brackets) are in the inset map; names of islands where historical tortoise remains were collected are in bold type, and those producing ultra-low coverage whole-genome sequences (ulcWGS) have an asterisk (*). The triangle (▲) on San Cristóbal Island shows where specimens from the Historical San Cristóbal lineage were collected. (Modified from Gaughran et al. [20].)

What the researchers recovered from these museum specimens was not merely a means of attaching names to old bones. It was evidence of an evolutionary history in which ancestral tortoises colonised the Galápagos, became isolated on different islands, diverged into genetically distinct populations and, in some cases, later exchanged genes after human interference brought them together again.

The analysis succeeded because common ancestry leaves an identifiable pattern in the genome. Even when more than 99 per cent of the sequence was unavailable, the surviving fragments could be compared with those of other tortoises and placed consistently within the Galápagos radiation. The missing DNA was not invented to make the specimens fit: the evolutionary relationship emerged from the authentic genetic information that remained.

Nor does hybridisation undermine evolution by blurring supposedly rigid species boundaries. It illustrates how evolution actually operates. Populations can diverge without instantly becoming incapable of interbreeding, and genes can cross between lineages when geographical barriers are removed. Like the archaic hominin DNA carried by modern humans, the ancestry of an extinct tortoise population can persist long after that population has ceased to exist independently.

Creationism contributes nothing to understanding any of this. It cannot explain why the genomes form the nested relationships predicted by descent with modification, why island populations accumulated distinctive genetic differences or why those differences can be traced through later hybrids. Its vague assertion that tortoises were created as some undefined “kind” supplies neither a testable history nor a useful conservation strategy.

Evolutionary biology, by contrast, has transformed a few degraded bones into evidence and that evidence into practical knowledge. Museum specimens collected more than a century ago can now help identify lost genetic diversity and guide efforts to preserve what remains. Once again, the productive explanation is not separate creation but common ancestry, isolation, divergence, extinction and gene flow—natural processes operating without foresight, purpose or supernatural intervention.

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