February 2025

Resolving the taxonomic puzzle of bush babies

“When I reached England in the spring of 1862, I found myself surrounded by a room full of packing-cases, containing the collections that I had from time to time sent home for my private use. These comprised nearly three thousand bird-skins, of about a thousand species; and at least twenty thousand beetles and butterflies, of about seven thousand species; besides some quadrupeds and landshells. A large proportion of these I had not seen for years; and in my then weak state of health, the unpacking, sorting, and arranging of such a mass of specimens occupied a long time.” (From Wallace’s 1869 Preface of his book The Malay Archipelago) [1].  

Alfred Russel Wallace reflected the above lines several years after his return from the Malay Archipelago (1854-1862), an expedition that took him 8 years of innumerable anecdotes and field trips in the mission of collecting, classifying and describing the flora and fauna of distant lands mostly unknown to science back then. Around half a century later, two other brave expeditioners embarked in a similar adventure, this time through the Congo tropical forest, where they mainly explored the basins and nearby jungles to the Congo river. As explained in the American Museum of Natural History (AMNH) registries, The American Museum Congo Expedition, which took place from 1909 to 1915, was composed by a rather small team of only two men: Herbert Lang, a German-born expert in taxidermy and mammals who led the expedition and served as photographer, and James Paul Chapin, an ornithologist and Museum employee who assisted him. Their primary mission was to broaden the Museum’s collection of African animal specimens, while Lang also collected ethnographic items. Alongside the successful collection of okapis and white rhinoceroses, the expedition contributed an extensive variety of specimens: 5800 mammals, 6241 birds, 4800 reptiles and amphibians, 5400 fish, 110000 invertebrates, 3800 ethnographic artifacts, and 9500 photographs organized into 40 albums. Initial scientific reports were published throughout the following decade, with research continuing well into the 1920s and 1930s.  

Chapin kept extensive daily records on his diaries about the many collected specimens along their journey. Among them, a brief mentioning to mysterious brown-coated small lemur-like monkeys given to them can be read through the following lines: “Large bats […], were very common here, coming out in numbers at dusk. Four specimens were shot […]. Three small brownish lemurs were warmly welcomed; but only a single monkey, one of the common red-tailed Cercopithecus was collected.” (From James Paul Chapin diaries, book 3, Nov. 1, 1909 to Feb. 5, 1910) [2].  

Despite such a brief mentioning, the expedition collected several specimens that were lately classified as belonging to the Galagidae family, a group of small cryptic strepsirrhine primates native to continental sub-Saharan Africa, also known as bush babies or nagapies. A total of 6 genera with multiple species within are currently recognized, although their phylogenetic structure has been subjected to extensive reconfiguration since the XIX century [3]. Bush babies, or galagos (Galagidae), were conventionally divided just into 6 species [6] but throughout the 1980s and 1990s the number was increased, in particular because studies of vocalizations had alerted researchers to the coexistence of sympatric species pairs, whereby two or more distinct species sharing the same natural habitat would coexist maintaining independent genetic pools without interbreeding [5].  

Inspired by the need to better understanding the diversity of these evasive yet abundant nocturnal animals, Dr. Anna Penna embarked herself in a dire task: to go across the museum collections analyzing the morphology and genetics of galagos in order to bring light to their evolutionary history and taxonomic relationships. In a recent review, Dr. Penna, in collaboration with Dr. Pozzi, revisited the past and current knowledge of Galagids phylogeny, combining evidence from morphology, acoustics and genetics [3]. As she mentions, a subgroup of small galagos got her particular interest. Among these, two main geographical populations could be distinguished: Eastern and Western dwarf galagos. Although classified under the “dwarf” category, genetics and acoustic data revealed that these dwarf forms diverged more than 20 million years ago and do not form a monophyletic group, as the Eastern species are more closely related to non-dwarf forms [6]. Within the Western populations, two species are found (Galagoides thomasi and Galagoides demidoff) occurring in sympatry as far west as Senegal and west to Uganda, and down to north-western Angola, as well as the newly described and isolated Galagoides kumbirensis, which is limited to the western mountainous areas of Angola.  

Dr. Anna Penna collecting 3D-landmarks in subfossil lemurs deposited at the Duke University Division of Fossil Primates, Raleigh, NC, USA.

 

In her project, Dr. Penna has collected new substantial genetic and morphological evidence from over a hundred specimens of dwarf galagos, allowing the reconstruction of phylogenetic relationships based on mitochondrial and whole genomes comparing thousands of polymorphic sites. She has found two very distinct but broadly co-distributed groups with minimal to no genetic admixture, each of which subdivided in two major subclusters. However, neither species nor subspecies classification of the three Western dwarf galagos currently recognized match the genetic clusters she found. The apparent subcluster division is influenced by the Sanaga river in Cameroon, which seems to play an important role in their geographical isolation leading to genetic differentiation. Interestingly, this effect has also been observed in other primates such as chimpanzees [7]. This genetic structure appears consistent at both nuclear and mitochondrial level, and it is also supported by morphological differences in skulls.  

Given her recent results, a revision of the current three-species subdivision of Western dwarf galagos seems necessary, where geographical barriers and sympatric coexistence might be shaping the cryptic evolution of these nocturnal small primates, both genetically and morphologically.  

As part of her project, Dr. Penna, in collaboration with Dr. Alexander Salis and other researchers in the field of conservation has also been working on facilitating access to teaching resources for students interested in museomics and the paleogenetics field, which she would like to share with us:  

Applications of Museum Collections and Genomics to Biodiversity Conservation

Designing a Conservation Genomics Project Incorporating DNA from Museum Specimens

The Application of Conservation Museomics Approaches to the Protection of the Iberian Lynx (Lynx pardinus)

 

References

1. Wallace, A. R. The Malay Archipelago: The Land of the Orangutan, and the Bird of Paradise (Macmillan, 1869).
2. Chapin, J. P. The diaries of James Chapin: Book 3 (November 1, 1909 to February 5, 1910). American Museum Congo Expedition. AMNH Archival Resources.
3. Penna, A. & Pozzi, L. Hidden in the dark: A review of galagid Systematics and phylogenetics. Int J Primatol 45, 1320–1353 (2024).
4. Napier, J. R. & Napier, P. H. A Handbook of Living Primates. (Academic Press, 1967).
5. Bush, G. L. Sympatric speciation in animals: new wine in old bottles. Trends Ecol Evol 9, 285–288 (1994).
6. Masters, J. C. et al. A new genus for the eastern dwarf galagos (Primates: Galagidae). Zool J Linn Soc 181, 229–241 (2017).
7. Fontsere, C. et al. Population dynamics and genetic connectivity in recent chimpanzee history. Cell Genomics 2, None (2022).

 

Below, Anna shared with us further details about her profile, career, prospects and future projects:  

1. Briefly introduce yourself. What is your origin story for how you got into science?
I am a postdoctoral researcher at Lund University (Sweden) and a Research Associate at the Smithsonian National Museum of Natural History (USA). My scientific journey began in Brazil, where I spent my undergraduate years conducting fieldwork on capuchin monkeys—studying their behavior, feeding ecology, and even parasitology in the wild. Those were incredible years! I had the chance to visit breathtaking locations in the Brazilian Atlantic Forest and the dry Caatinga, observing primates in their natural habitats. But everything changed during my senior year when I took a class on evolutionary biology. I became fascinated by the idea that the way traits are interconnected—what we call morphological integration—can shape the evolution of form and shape in nature. That realization set me on a path toward studying how primates evolved their incredible diversity in skull morphology, a question that has guided my research ever since.  

2. How and/or why did you start working on this project?
For my master’s thesis, I set out to understand what evolutionary processes gave rise to the stunning morphological diversity of strepsirrhine primates (lemurs, galagos, and lorises). I used a quantitative genetics framework to test whether genetic drift or natural selection played a stronger role in shaping cranial variation. But to do this properly, I needed a large dataset, comprising thousands of skulls from different species, in order to quantify trait variation and correlations. That meant visiting museums across Europe and the U.S. to 3D-landmark and photograph specimens. However, as I examined more and more skulls, I realized that many specimens, especially the species of nocturnal, small-bodied primates like mouse lemurs and dwarf galagos, were nearly impossible to identify by morphology alone. Their skulls looked almost identical, making it hard to ensure I was grouping specimens in the right way. This issue wasn’t just a minor inconvenience for my research, but a much larger problem. If we struggle to tell species apart using traditional methods, how can we accurately document biodiversity? And if our species classifications are unclear, how reliable are the evolutionary trees we build to study primate evolution? These problems kept me up at night! Then, I learned about ancient DNA technologies and how researchers were using museum specimens to extract and sequence DNA, even from century-old specimens. I knew right then that I wanted to apply these techniques to improve the primate tree of life. For my PhD, I shifted gears to focus on species delimitation and genetic diversity in cryptic nocturnal primates from Sub-Saharan Africa and Southeast Asia, particularly galagos, lorises, and angwantibos. My work combines museum genomics and an integrative taxonomy approach to uncover hidden diversity, refine species classifications, and shed light on the evolutionary history of these fascinating primates.  

3. Were there any major challenges in this project? How did you overcome them?
Working with historical museum specimens comes with a unique set of challenges, particularly when it comes to extracting DNA. One unexpected hurdle came when I was working with some specimens collected over a century ago during the American Museum of Natural History’s 1909-1915 Congo Expedition. Some of these specimens produced strange results during DNA extraction—the lysis reactions turned purple, and library preparation completely failed. I reached out to colleagues in ancient DNA research and museum curation to troubleshoot what might be happening. Although I couldn’t fully investigate the issue, we suspect that certain chemical preservatives used in the early 1900s—or even the accumulation of metallic oxides from internal wiring structures used in the taxidermization process—, were interfering with the enzymatic reactions. Interestingly, the smaller dwarf galago specimens from the same expedition yielded much better results, and I was able to generate great genomic libraries for them. This suggests that their diminutive size may have spared them from excessive chemical exposure during preservation. This experience highlighted how little we know about historical specimen preparation techniques and their effects on DNA preservation. It’s a reminder that working with ancient and museum DNA isn’t just about applying cutting-edge sequencing techniques—you also need a deep understanding of the historical context behind the specimens themselves.  

4. What do you think are the main take-home messages of this project?
Our research reveals that the true diversity of nocturnal primates, particularly dwarf galagos, has been vastly underestimated. By sequencing historical DNA from specimens housed in nine natural history collections, we uncovered multiple genetically distinct lineages within what were previously thought to be just two widely distributed species in Central and Western Africa. This means we may be overlooking several hidden species that are distinct at a genetic level but nearly identical in appearance. This discovery has profound implications for conservation. Many of these cryptic species may have smaller ranges and more specific habitat requirements than previously assumed. If we continue to treat them as a single widespread species with stable population trends, we risk misrepresenting their conservation needs. More broadly, our study challenges long-held assumptions about the evolution of dwarf galagos. For instance, their small body size was traditionally thought to be an ancestral trait retained by just a few species. However, our findings suggest that these small-sized radiations are more diverse than we might think. Our study also highlights the power of museum genomics. Traditional taxonomy struggled to resolve the identities of these species based on morphology alone, but by combining DNA analysis with skull measurements, we were able to tease apart different evolutionary lineages. This integrative approach is crucial to refine the primate tree of life. An exciting area for future research is the role of past climate change in shaping African biodiversity. We still know very little about how shifts in habitat distribution over millennia influenced the diversification of primates and other mammals. Similarly, the process of cryptic speciation—where species diverge genetically without obvious morphological changes—is still poorly understood. Why do some groups accumulate significant genetic differences without changing in appearance? What ecological or evolutionary pressures drive this pattern? A comparative approach that examines multiple lineages and environments could help answer these questions.  

5. What do you think is missing in the field that you would like to work on?
While our work has brought clarity to galagid diversity and evolution, many unanswered questions remain. One of the most pressing gaps is the need for broader genetic sequencing of type specimens—the original reference specimens used to describe and name species. By sequencing these historical specimens, we can better link genetic lineages to species names, refining taxonomic classifications that were established decades or even centuries ago. Integrating genetic and morphological data more effectively is definitely something that can benefit our community. By combining genomic, morphometric, and ecological datasets, we can better understand the evolutionary processes that drive species diversity, including the role of developmental constraints and adaptation. Of course, museum genomics has enormous potential beyond taxonomy and systematics. Ancient DNA is a powerful tool for understanding biodiversity loss, tracking genetic erosion in endangered species, and uncovering how populations have changed over time. Currently, a major limitation that we have is the geographic and taxonomic bias in museum genomics research. Most large-scale genetic studies rely on specimens housed in institutions in North America and Europe, while museum specimens housed in collections in the Global South—where biodiversity is highest—remain severely underused for genetic data. This imbalance limits our understanding of species diversity and evolutionary history in regions that are most affected by habitat loss and climate change. The challenges are not just about specimen availability but also about the barriers to conducting historical DNA research in these regions. The cost of reagents, lab supplies, sequencing equipment, and computational resources to analyze the data remains prohibitively high in many countries. Addressing these gaps requires not only greater collaboration between institutions but also direct investment in building local capacity and training students to become independent researchers.  

6. Where do you see yourself in the near future?
Working in a museum collection! I am passionate about the incredible stories that museum specimens can tell—whether it’s uncovering hidden species, tracing evolutionary histories, or informing conservation efforts. Working in a museum allows me to combine my interests in evolutionary biology, bioinformatics, and taxonomy while also contributing to the preservation and study of biodiversity for future generations. As a Brazilian national, I would love to contribute more to the study and protection of the fauna of my home country. I am especially interested in using museum collections to combat illegal wildlife trafficking. DNA from confiscated animals can be compared against museum reference collections to pinpoint their geographic origin, providing critical information for law enforcement and conservation efforts. By building a global reference database of genetic data from museum specimens, we could help pinpoint the geographic origin of confiscated animals, providing critical support for conservation efforts and law enforcement.