Arlo Hinckley is a postdoctoral researcher at the Smithsonian National Museum of Natural History and Universidad de Sevilla. He is an evolutionary biologist with a focus on the origin, maintenance, and distribution of mammalian diversity. Here, Arlo shares his recent work on the evolutionary history and divergence patterns of Asian squirrels.
Picture of Arlo Hinckley taken at his office, at the Mammals Division of the National Museum of Natural History.
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Institute. Smithsonian National Museum of Natural History & Universidad de Sevilla
Academic life stage. Postdoc
Major research themes. I am primarily interested in the study of the evolutionary origin, maintenance, and distribution of mammalian diversity in Tropical East Asia (TEA).
Current study system. TEA is a major biodiversity hotspot with a complex geography, and geological and climatic history, providing an excellent system to study evolution. Despite recent advances, the underlying evolutionary mechanisms driving this region’s high levels of biodiversity are still poorly understood. To gain insights into such drivers, I reconstruct the evolutionary history of small mammals (rodents, eulipotyphlans, and treeshrews). These taxa can be locally abundant, highly diverse, have short generation times and are frequently habitat specialists with low dispersal abilities. Their sensitivity to environmental change and low dispersal abilities makes them great models to evaluate how past and present climatic and geological events shape speciation processes and biogeographic patterns, while their fast generation times generally makes these inferences informative even at short timescales. I however do not consider small mammals’ mere models, I am genuinely interested in their systematics, ecology, and conservation, and love sampling them in the field.
Recent JBI paper. Hinckley, A., Hawkins, M. T., Maldonado, J. E., & Leonard, J. A. (2023). Evolutionary history and patterns of divergence in three tropical east Asian squirrels across the Isthmus of Kra. Journal of Biogeography, 50(6), 1090-1102. https://doi.org/10.1111/jbi.14598
The Himalayan Striped Squirrel (Tamiops mcclellandii) is a largely insectivorous and strictly arboreal squirrel lives on the trunks and main branches of tall trees and has a wide distribution range that spans the Isthmus of Kra biogeographic transition. Photo Credit: Andaman Kaosung. Location: Kaeng Krachan District, Thailand.
Motivation behind this paper. Understanding the biotic and abiotic mechanisms underlying the generation and maintenance of biogeographic transitions represents a long-standing topic in evolutionary biology. Biogeographic transition is the gradual change in species distribution due to climate, geology, and even human activities, resulting in ecosystem and biodiversity shifts. The Isthmus of Kra (IOK) is a terrestrial biogeographic transition in the Thai-Malay peninsula, which divides Sundaland and Indochina. Despite intriguing biogeographers since Alfred R. Wallace first noted it in 1876, the IOK still constitutes a poorly characterized biogeographic transition. This is possibly due to challenges associated with sampling across such a large and geographically (and politically) complex region as TEA, but also due to a scarcity of species with distributions spanning this region, and a lack of appropriate molecular markers and/or fossil calibrations for divergence dating. This is why my co-authors and I decided to focus on three squirrel species that are distributed across the IOK, belonging to a subfamily for which we had already developed a panel of genetic markers and that has several fossils. This allowed us to look at population structure across the IOK and the drivers that have shaped this transition and regional diversification patterns by integrating divergence dating analyses with geological and paleoclimatic evidence.
Key methodologies. We generated complete mitochondrial genomes and sequences of eleven nuclear genes fragments from museum specimen samples. We studied how different populations are connected by looking at their genetic information from mitochondrial DNA and other molecular markers. We used advanced methods to estimate when these populations started to evolve separately, considering the influence of climate and geological changes over time. This research was possible thanks to the work of historical naturalists, in combination with the recent advances in high throughput sequencing, which allowed us to yield the molecular data this study was based on. I expect museum genomics to revolutionize the field of historical biogeography, since researchers can now sample very large/remote regions with much less time/funding investment. Still, field surveys and specimen collection will remain pivotal to fill geographical gaps, complement museum-based data, and to support future research with new methodological approaches that still do not exist. Just as the historical collectors I mentioned did not collect our study specimens for the purpose of this research, who knows what information researchers will extract from museum specimens in 50 years!
The Gray-bellied Squirrel (Callosciurus caniceps) is an omnivorous, mostly arboreal species that lives in the understory and has a wide distribution range that spans the Isthmus of Kra biogeographic transition. Photo Credit: Jan Ebr. Location: Pahang, Malaysia.
Unexpected challenges. Working with highly degraded DNA from historic museum specimens can be challenging. Requesting destructive sampling tissue loans to 17 museums, along with marker development (intron multiplexes), was highly time-consuming. Furthermore, the lab work had a high degree of uncertainty, as 45% of the samples did not work (possibly due to exposure to formalin or other chemicals). Consequently, we ended up requesting and processing many more samples than what we initially planned to fill certain geographic gaps. Our observations suggest that specimen preparation and storage by the historic collectors might have a greater impact on DNA quality than either their age or the museum where they have been curated. Based on our experience, I would suggest researchers planning a project involving historic DNA to perform target capture (if they can afford it) and target study taxa that have specimens stored in a handful of museums to reduce delays and third-party dependency. If possible, they should also sample specimens collected in expeditions which have yielded molecular data in previous studies on other taxa.
Major results. Populations distributed across the IOK diverged during the Early Pleistocene in all three species, but the precise location of lineage turnovers varied among species. Sundaic and Indochinese populations possibly diverged in allopatric habitat refugia in or around mountains during periods of increased aridity and evergreen forest contraction. Ecological differences and/or topography might have influenced genetic differentiation during periods of rainforest expansion. However, alternative hypotheses remain to be tested with more informative nuclear markers and additional geographic sampling. Finally, two of the study species were paraphyletic and showed ancient Miocene-Pliocene divergences across Indochina. Overall, this research contributes to a better understanding of the evolutionary processes shaping Southeast Asia’s biodiversity, given the robustness and precision that mitochondrial genome and/or nuclear multi-locus datasets provide, its broad geographic scope, and the current shortfall regarding divergence dating studies in this area.
Montane forest of Tropical East Asia. Photo Credit: Daniel Hinckley. Location: Mount Trus Madi, Sabah, Malaysia.
Next steps for this research. We are currently reassessing the taxonomy of these three squirrels through an integrative approach, which includes additional lines of evidence such as morphology. We also look forward to addressing this research hypothesis with phylogenomic evidence and the inclusion of additional taxa with diverse ecological requirements. The combination of improved sampling around the Isthmus of Kra, requiring additional fieldwork, and population genomic approaches, will open the door to exploring potential hybrid/introgression zones in this transition zone. Niche modelling, in combination with population genetic studies, including historic and modern populations, will be pivotal to predicting and tracking potential climate change-driven shifts in the distribution of mammals in this biogeographic transition.
If you could study any organism on Earth, what would it be? One of the best things about working in the largest mammal collection in the world is that you can study almost any species you are interested in, which can sometimes be problematic, since you end up starting too many projects that you must finish. I am currently studying Oriental Giant Squirrels (Ratufa) which I had been longing to work with since I saw them in the field eight years ago. They are highly elusive and understudied taxa due to their canopy-dwelling nature, which makes field sampling highly challenging. The NMNH collection holds specimens from all recognized species and most subspecies of Ratufa, providing a unique opportunity to reconstruct its historical biogeography, integratively review taxonomy, and test the hypothesis that differences in the resilience to forest seasonality of two of its species will be reflected in contrasting evolutionary histories.
Anything else to add? Our research highlights the important role that Tropical East Asian mountains play as forest refugia during the current and future climate-change driven aridification and the necessity to conserve them for the generation and maintenance of this region’s biodiversity in the long term.
Pictures highlighting the logistics, camp/sampling sites, live traps, small mammal sampling, and participants of a biological survey in northern Borneo. Photo Credit: Daniel Hinckley and Arlo Hinckley.