Rosa Rubicondior: Refuting Creationism - Diverging Sloth Genomes

Deforested genomes: scientists find signs of environmental degradation in the genomes of the endangered Maned Sloths - Leibniz Institute for Zoo and Wildlife Research

The discovery fits seamlessly within the framework of Darwinian evolution. Two once-connected populations became isolated and exposed to different ecological conditions, followed their own evolutionary paths. Over time, their genomes accumulated distinct mutations reflecting adaptation, genetic drift, and local environmental pressures. The result is two clearly defined species whose divergence can be explained entirely by natural processes acting over generations — a textbook demonstration of evolution in action.

Yet this same process now drives both species along a far more perilous trajectory. As their habitats continue to shrink and fragment, their populations are losing genetic diversity and becoming increasingly inbred. Evolution has no foresight or purpose; it cannot plan for the future or reverse the consequences of environmental destruction. The very mechanism that once diversified life on Earth can, under relentless human pressure, just as readily lead to extinction.

There is no sign of “intelligent design” in this grim reality — only the blind, natural workings of selection, drift, and chance operating within a degraded environment. If a designer were guiding life towards some higher purpose, it would hardly produce a situation where its own creations are being driven to extinction by the ecological collapse of their habitats. The plight of the maned sloths stands as a vivid reminder that life’s diversity, beauty, and tragedy arise not from supernatural intent, but from the impersonal and unyielding logic of evolution.

As world leaders prepare for COP30 in Brazil, the message from the maned sloths’ genomes could not be clearer: conservation must be guided by evolutionary science and ecological understanding, not by comforting myths of divine oversight. Only by recognising the true, natural processes that shape life can we hope to protect what remains of it.

Background^ The Maned Sloths.

Bradypus torquatus
Bradypus crinitus

Photos: Instituto Tamanduá

Taxonomy & Species Split

The maned sloths belong to the three-toed sloth genus Bradypus, family Bradypodidae (order Pilosa). [1]
Until very recently the population along Brazil’s Atlantic Forest was treated as one species — the northern form, Bradypus torquatus. [2]
A taxonomic revision in 2022 revalidated the southern form as a distinct species: the Bradypus crinitus (southern maned sloth). [2]
The two species are geographically separated by different coastal-forest strips in Brazil and show genetic divergence consistent with long-term isolation. [2]

Evolutionary History & Divergence

The genus Bradypus is part of a larger group of arboreal and ground-dwelling xenarthrans whose fossil record includes the giant ground sloths. [3]
Molecular studies indicate that three-toed sloths and two-toed sloths did not evolve their arboreal, hanging habits from a common sloth ancestor in one go — rather, their lineages diverged millions of years ago and developed tree-living independently. [1]
For the maned sloths specifically: analyses suggest that B. crinitus and B. torquatus diverged during the Early Pliocene, some millions of years ago (exact timing still refining). [4]
Genomic and demographic work (including whole-genome resequencing) recently shows how both long-term historical forces (such as climate shifts) and recent habitat change have shaped these species’ genetic diversity. [5]

Biology, Ecology & Adaptations

Maned sloths are specialised folivores — adapted to a diet of tree leaves, with low energy intake, slow metabolism, and canopy-living behaviour. [6]
They inhabit the canopy of Brazil’s Atlantic coastal rainforest, often in evergreen or semi-deciduous forests. B. torquatus is endemic to regions in Bahia, Espírito Santo and Rio de Janeiro. [6]
Their morphology is distinctive: coarse, long fur often hosting algae and arthropods; a “mane” of darker hairs on the neck/shoulders (hence “maned”). [7]
Behaviourally, they descend to the ground rarely (for defaecation or tree-to-tree transfer) and move slowly. Their energy-saving adaptations reflect their niche. [8]

Conservation & Genetic Diversity Concerns

Both species face major threats from habitat loss, fragmentation and degradation of the Atlantic Forest. The smaller, isolated forest patches reduce gene flow and increase inbreeding risk. [9]
The southern species (B. crinitus) shows lower genetic diversity overall; the northern species (B. torquatus) is already showing signs of rapid inbreeding.
This genetic vulnerability compounds the evolutionary narrative: populations that diverged via natural isolation now face anthropogenic isolation — accelerating genetic risks.

Why It Matters

The maned sloths are living examples of evolutionary divergence through isolation and adaptation, which reinforces the core Darwinian principle: isolation + distinct pressures → genomic divergence.
Their plight also underscores how human-caused changes (habitat loss) add a layer of evolutionary pressure — often far faster and harsher than natural processes, making conservation genomic studies especially vital.

This timely discovery, especially in light of the upcoming COP30 meeting in Brazil, has just been published in the journal Molecular Ecology, accompanied by a press release from the Leibniz Institute for Zoo and Wildlife Research.

Deforested genomes: scientists find signs of environmental degradation in the genomes of the endangered Maned Sloths
The Northern and Southern Maned Sloths may look very similar from the outside, but their genomes reveal different stories: the two species have faced very distinct conditions in Brazil’s Atlantic Forest in the past and confront different conservation threats today. In an article recently published in the journal “Molecular Ecology”, scientists from the Leibniz Institute for Zoo and Wildlife Research (Leibniz-IZW) in partnership with the Brazilian NGO Instituto Tamanduá show that the southern, currently more endangered lineage displays lower genetic diversity than the northern lineage, which however shows a rapid rise in inbreeding in recent decades. The findings demonstrate that genomic studies can offer critical insights for conservation of endangered species.
From 10 to 21 November, conservation leaders from across the globe meet in Brazil at the 30th Conference of the Parties (COP30) of the United Nations Framework Convention on Climate Change (UNFCCC). The country is home to several biodiversity hotspots of global importance, regions that not only boast with species diversity but also contribute to a stable global climate – if sufficiently protected. A new study by the Leibniz-IZW and the Instituto Tamanduá offers important insights for biodiversity conservation in tropical forests in Brazil.

The Atlantic Forest, South America’s highly diverse coastal tropical forest, used to cover a significant portion of Brazil’s territory. Owing to human activities such as clearing for agriculture and urbanization, today only about 8 percent of its original extent remains. Even though severely reduced and fragmented, the Atlantic Forest still serves as habitat for a multitude of fascinating – and resilient – species. Among these species are the Maned Sloths, which can be found nowhere else on the planet.

Collaborating closely with the Brazilian conservation NGO Instituto Tamanduá, scientists from Leibniz-IZW were able to sequence whole genomes of two closely related sloth species from Brazil’s Atlantic Forest: the Northern Maned Sloth (Bradypus torquatus) and the Southern Maned Sloth (Bradypus crinitus). A species genome is equivalent to its genetic “blueprint” and the process of genome sequencing consists of converting the information contained in the DNA to data scientists can analyse. By studying the sloth’s genomes, the goal was to investigate how ancient climatic shifts and recent human-driven habitat changes have shaped the species genetic diversity, population history and current conservation status.

Genomic insights for conservation

Some of the studies’ key results show that the Southern Maned Sloth, which currently is more endangered, displays lower genetic diversity and also lower historical population sizes compared to the Northern relatives. This finding likely reflects the distinct environmental and climatic conditions the two areas have experienced in the past.

But the situation is also worrisome for the Northern Maned Sloth: despite its higher genetic diversity and larger current population sizes, there has been a rapid rise in inbreeding – characterised by the mating of related individuals – in recent decades. This is likely owing to recent deforestation and habitat fragmentation in the Northern region. The study also shows that the Northern lineage carries a higher genetic load (i.e., more disadvantageous gene variants) which could be dangerous if the trend of population decline is not reversed. “By revealing key aspects of the species’ genetic health, these findings allow us to design conservation actions that are truly focused on what the species needs most”, said Larissa Arantes, scientist at Leibniz-IZW who led the work.

These key finds buried deep in the sloth’s genomes show that each lineage has unique conservation needs, shaped by both deep-time environmental change and modern threats to their tropical habitat.

Why it matters

This study provides genomic insight into a species living in one of the world’s most threatened biodiversity hotspots. Despite the importance of these mega diverse regions, this kind of data is only available for a very limited number of species found there. The work offers actionable genetic information for managing vulnerable populations. In particular, the findings highlight the urgency of preserving genetic diversity, mitigating inbreeding, and maintaining habitat connectivity for the long-term survival of these sloths.

Genomic erosion poses a serious threat to populations under pressure, especially with rising inbreeding. This should serve as a warning that fragmentation is reducing the Maned Sloth’s chances of survival, particularly in the northern region of Bahia. We will continue our close partnership with Instituto Tamanduá to assess the extent of the impact on the Maned Sloth’s genomic health.

Camila Mazzoni, senior author
Department of Evolutionary Genetics
Leibniz Institute for Zoo and Wildlife Research (IZW)
Berlin, Germany.

Far beyond collecting the samples that made this genomic study possible, the NGO Instituto Tamanduá has years of experience leading a wide range of hands-on actions to protect these and other species of sloths and anteaters. From describing a new species of Maned sloth to restoring its native habitat through reforestation, all of the organization’s actions are guided by science and generate new scientific knowledge, including studies like this one.

Publication:
Arantes LS, De Panis D, Miranda FR, Santos FR, Hiller M, Mazzoni CJ (2025) Genomic Signatures in Maned Three‐Toed Sloths From Ancient to Recent Environmental Changes in Brazil's Threatened Atlantic Forest.
Molecular Ecology, e70148. DOI: 10.1111/mec.70148

ABSTRACT
Environmental and climatic changes have shaped the evolutionary trajectories of natural populations, leaving genomic signatures that reflect how species respond to these shifts and their impacts on genetic health. While these insights are essential for unravelling evolutionary histories and informing conservation strategies, studies on Neotropical species remain largely underrepresented. Maned Three-Toed Sloths, endemic to the fragmented Atlantic Forest of Brazil, were recently reclassified into two distinct species: the Northern and Southern Maned Sloths. Our study investigates the genomic imprints left by ancient and recent environmental changes in the Atlantic Forest in these two sloth lineages, using whole-genome resequencing data. Our analysis reveals that the Southern Maned Sloth exhibits a smaller historical population size than the Northern Maned Sloth. This disparity likely stems from differing climatic changes along the Atlantic Forest distribution during the Pleistocene, characterised by greater climatic stability and larger refugia areas in the north. Consequently, the southern lineage presents a lower genetic diversity and higher overall inbreeding level. Nonetheless, the northern population has experienced a fast increase in inbreeding levels in the last few decades, likely associated with extensive recent deforestation in the northeast region of Bahia State. The distinct demographic trajectories also resulted in the northern lineage carrying a higher genetic load, implying higher fitness costs for this lineage if inbreeding persists. Together, our findings confirm the independent evolutionary paths of these two lineages and underscore the unique conservation challenges posed by both historical climatic changes and ongoing deforestation of the Atlantic Forest.

1 Introduction
Ancient and recent environmental and climatic changes shape the evolutionary trajectories of natural populations, leaving lasting genomic signatures. Changes in population demography, such as population decline and isolation, directly impact genetic diversity, inbreeding levels, and genetic load. As populations shrink or become fragmented, both inbreeding levels and genetic drift increase, leading to a loss of genetic variability and making species more vulnerable to genomic erosion and extinction (Pinto et al. 2024). Genomic erosion refers to the harmful genomic imprints that threaten small populations, including genome-wide diversity loss, increase of expressed genetic load, and maladaptation (Dussex et al. 2023). There has been a recent surge in genomic studies of small and threatened populations, leveraging whole-genome data to estimate multiple metrics of genomic erosion. This holds great promise for advancing conservation genomics by helping to identify vulnerable populations and design targeted conservation strategies to ensure long-term species viability (Bosse and van Loon 2022). However, such efforts remain largely underrepresented for Neotropical species (Vilaça et al. 2024.1), emphasising the need for broader taxonomic and geographic sampling to better understand the interconnections between environmental changes and genetic health.

Maned Three-toed Sloths (Xenarthra: Bradypodidae), the only xenarthrans endemic to Brazil's Atlantic Forest, are characterised by a black mane on the hindneck of the adults (Hayssen 2009). Like other sloths, they are strictly arboreal and have low metabolic rates due to their diet composed of leaves and shoots, causing them to remain immobile in trees for extended periods (Chiarello 1998). As a result, they are difficult to observe in the dense forest canopy, contributing to limited knowledge about their biology (Chiarello 2008). Additionally, their behavioural traits and arboreal habits make them highly vulnerable to deforestation and fires.

The Maned Three-Toed Sloths' habitat is facing alarming conservation threats. Despite being one of the most important biodiversity hotspots Mittermeier et al. 2011, the Atlantic Forest has suffered extensive deforestation due to anthropogenic activities. Only about 8% of its original extent remains (Brown et al. 2020), with the current landscapes mostly composed of small and fragmented patches surrounded by open habitats, such as pastures and agricultural fields (Ribeiro et al. 2009.1; Vancine et al. 2024.2). However, restoration projects implemented over the last years are responsible for an increase in the forest cover in specific areas (Romanelli, 2022.1). These new forest formations are crucial for biodiversity conservation, especially for sloths, which depend on the presence of high and connected canopies for their survival. The challenges posed by habitat fragmentation underscore the need to evaluate its impact on the genetic health of sloth populations, which can offer valuable insights to inform more effective conservation strategies.

In addition to the recent anthropogenic environmental changes affecting sloth conservation, the Atlantic Forest has also experienced significant historical changes that have influenced the distribution and abundance of its biodiversity. During the climatic oscillations of the Quaternary, the persistence of stable green areas, or refugia, varied across the Atlantic Forest, significantly impacting the spatial patterns of biodiversity and endemism (Carnaval and Moritz 2008.1; Peres et al. 2020.1). The Maned Three-toed Sloths also appear to be affected by this, as the remaining populations exhibit deep genetic divergence that has accumulated over thousands of years (Lara-Ruiz et al. 2008.2; Schetino et al. 2017). Genomic imprints can reveal how these species have adapted to past climatic oscillations, offering valuable insights into their evolutionary history and conservation needs.

Until recently considered a single species, Maned Three-Toed Sloths have been subdivided through a comprehensive integrative taxonomic review (Miranda et al. 2022.2) into two distinct species: the Northern Maned Sloth (Bradypus torquatus Illiger, 1811) inhabiting the states of Bahia and Sergipe, and the Southern Maned Sloth (Bradypus crinitus Gray, 1850) found in the states of Espírito Santo and Rio de Janeiro. Although there are no differences in pelage, size, and body mass, the northern and southern lineages present distinct craniomandibular characters and diverged around 4.2 million years ago (mya), as estimated by coalescent species delimitation analyses using four mitochondrial and nuclear DNA markers. The authors recommended that, along with the taxonomic review, the conservation status of these species should be reassessed to effectively address the conservation challenges of each lineage. An extensive study of the genome-wide diversity and divergence of the Maned Three-Toed Sloths can greatly enhance conservation efforts by providing insights into the unique genetic characteristics and evolutionary history of the northern and southern lineages.

Our research leverages whole-genome resequencing data compared against a chromosome-level reference genome recently assembled by our group (Bein et al. 2024.3) to unravel genomic signatures in Maned Three-Toed Sloths in the context of historical and contemporary environmental and climatic changes in the Atlantic Forest. We test whether genomic metrics—such as genetic diversity, inbreeding levels, genetic load, and historical population sizes—reveal signs of genomic erosion in Maned Three-Toed Sloths, particularly given the extensive fragmentation of the Atlantic Forest, which has occurred both historically and, more acutely, in recent times (Santos et al. 2024.4). Our study is one of the first to demonstrate the power of high-resolution genomic data in revealing the impact of changes to the habitat and environment on the genome-wide diversity of endemic species across the Atlantic Forest. This study presents the framework for other species with similar demographic and ecological traits as the Maned Three-Toed Sloth in such Neotropical ecosystems.

Arantes LS, De Panis D, Miranda FR, Santos FR, Hiller M, Mazzoni CJ (2025) Genomic Signatures in Maned Three‐Toed Sloths From Ancient to Recent Environmental Changes in Brazil's Threatened Atlantic Forest.
Molecular Ecology, e70148. DOI: 10.1111/mec.70148

Copyright: © 2025 The authors.
Published by John Wiley & Sons. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

The discovery fits seamlessly within the framework of Darwinian evolution. Two once-connected populations became isolated and, exposed to different ecological conditions, followed their own evolutionary paths. Over time, their genomes accumulated distinct mutations reflecting adaptation, genetic drift, and local environmental pressures. The result is two clearly defined species whose divergence can be explained entirely by natural processes acting over generations — a textbook demonstration of evolution in action.

Yet this same process now drives both species along a far more perilous trajectory. As their habitats continue to shrink and fragment, their populations are losing genetic diversity and becoming increasingly inbred. Evolution has no foresight or purpose; it cannot plan for the future or reverse the consequences of environmental destruction. The very mechanism that once diversified life on Earth can, under relentless human pressure, just as readily lead to extinction.

There is no sign of “intelligent design” in this grim reality — only the blind, natural workings of selection, drift, and chance operating within a degraded environment. If a designer were guiding life towards some higher purpose, it would hardly produce a situation where its own creations are being driven to extinction by the ecological collapse of their habitats. The plight of the maned sloths stands as a vivid reminder that life’s diversity, beauty, and tragedy arise not from supernatural intent, but from the impersonal and unyielding logic of evolution.

As world leaders prepare for COP30 in Brazil, the message from the maned sloths’ genomes could not be clearer: conservation must be guided by evolutionary science and ecological understanding, not by comforting myths of divine oversight. Only by recognising the true, natural processes that shape life can we hope to protect what remains of it.

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