FIELD RESEARCH
Night Monkey Phylogenomics, Evolutionary History, and Taxonomy
The classification and evolutionary history of night monkeys (owl monkeys; Aotus spp.) have long been central challenges in Neotropical primate systematics. Despite decades of study, their taxonomy remains unsettled, shaped by partially discordant signals from cytogenetic variation, cranial morphology, vocalization patterns, and increasingly, molecular datasets. Recent work, including Helenbrook (In Review), has further emphasized that much of this instability reflects not only incomplete lineage sorting and historical hybridization, but also uneven geographic sampling and the continued absence of dense, range-wide genomic datasets. As a result, species boundaries within Aotus remain fluid, and competing phylogenetic hypotheses continue to coexist.
Our research addresses these limitations by applying a museum-integrated phylogenomic framework designed to resolve deep and shallow evolutionary structure within Aotus. We combine high-throughput sequencing of modern non-invasive samples with genome recovery from museum-preserved material, enabling geographically comprehensive sampling across taxa that are otherwise difficult to obtain in the wild.
We employ a combination of mitochondrial genome sequencing and genome-wide nuclear markers generated through next-generation sequencing (NGS) platforms, including Illumina-based short-read sequencing for degraded DNA. A central component of our work is the incorporation of environmental DNA (eDNA) and non-invasive genetic sampling (e.g., fecal DNA), which expands spatial and ecological coverage while minimizing disturbance to wild populations. These methods enable detection of Aotus presence in fragmented and inaccessible habitats, particularly in rapidly changing Amazonian and Andean landscapes where traditional sampling is logistically or ethically constrained. When combined with museum genomics, this creates a temporally stratified dataset spanning historical, contemporary, and environmental sources of genetic material.
We further leverage deep genomic coverage to identify cryptic diversity within Aotus, evaluate lineage divergence across major biogeographic barriers (e.g., Amazonian rivers and Andean foothills), and reconstruct population-level structure across the genus. From a conservation perspective, this integrated framework provides a critical advance for a genus that inhabits some of the most rapidly transforming ecosystems in South America. Extensive deforestation, agricultural expansion driven by fire and land conversion, and increasing habitat fragmentation are reshaping Aotus distributions, particularly in the Amazon Basin and adjacent forest systems. By combining eDNA detection with genome-wide inference from both contemporary and museum samples, our approach enables fine-scale monitoring of population persistence and genetic connectivity in degraded landscapes.
Ultimately, this research advances a more resolved and evolutionarily informed taxonomy of Aotus, while simultaneously generating actionable conservation units grounded in genomic evidence. By integrating phylogenomics, museum-based sequencing, and non-invasive sampling, and building on the conceptual synthesis of Helenbrook (in press), we provide a framework for disentangling long-standing taxonomic uncertainty in night monkeys and for supporting evidence-based conservation strategies across their range.
Conservation Parasitology
Conservation parasitology is an emerging field that recognizes parasites as integral components of biodiversity and essential contributors to ecosystem function, rather than simply agents of disease. Parasites influence host population dynamics, mediate species interactions, and contribute to energy flow and nutrient cycling within ecological networks. Despite their critical ecological roles, parasites are often overlooked in conservation planning, particularly in captive breeding, translocation, and reintroduction programs, where disease management typically prioritizes parasite removal. Such approaches risk disrupting coevolved host-parasite relationships, altering immune function, and creating ecologically incomplete or maladapted populations upon reintroduction.
Our research in conservation parasitology seeks to address these gaps by examining the dual roles of parasites. While parasites can contribute to population decline under altered environmental conditions, they also play a vital role in maintaining ecological stability when kept within natural regulatory limits. We explore how parasite loss, amplification, or community restructuring can impact species recovery, population viability, and ecosystem health in both managed and wild systems. This is particularly relevant for rehabilitation and reintroduction NGOs, where our work helps integrate parasite dynamics into species recovery efforts.
For captive populations, we emphasize the need for evidence-based parasite management strategies that balance disease risk with the preservation of native parasite diversity. This includes targeted screening, selective treatment, and post-release monitoring to ensure the health and ecological integrity of reintroduced populations. For wild populations, we advocate for the incorporation of parasite ecology into long-term monitoring, habitat restoration, and ecosystem health assessments, recognizing that parasites are vital to the functioning of natural ecosystems.
By including parasites in conservation frameworks, recovery plans, and biodiversity assessments, our research aims to provide a more holistic approach to species reintroduction and ecosystem management. In an era of rapid environmental change, "conservation parasitology" offers a critical lens through which to assess and manage the health and viability of both wildlife populations and ecosystems. This work supports rehabilitation and reintroduction efforts, helping NGOs address the complex health challenges of parasitic infections and contributing to the long-term survival of endangered species.
Applied Conservation Biology
Primate species across the globe face mounting threats from habitat loss, fragmentation, hunting, and human-wildlife conflict, making effective conservation strategies essential for their survival. The application of integrated conservation biology is crucial for addressing these threats, particularly in biodiversity hotspots where species are increasingly restricted to fragmented and isolated habitats. Our research applies cutting-edge genomic, phylogeographic, and ecological techniques to inform conservation planning for primates, with a focus on enhancing population viability and fostering long-term ecological sustainability.
Langurs, a diverse group of primates, face significant conservation challenges due to habitat loss, fragmentation, hunting, and human-wildlife conflict. These threats are particularly severe for species such as several species found from India down to the Sundra Shelf, all of which are endemic to rapidly degrading habitats in the tropical rainforests of South and Southeast Asia. While some aspects of the taxonomy and phylogeny of these langurs are well-understood, there remains a significant knowledge gap regarding their population structure, genetic diversity, and contemporary connectivity. This lack of information hinders effective conservation planning, especially as these species face increasing pressures from anthropogenic disturbances such as deforestation, climate change, and agricultural expansion.
To address these critical gaps, we employ an integrative approach that combines genomic research with spatial and environmental modeling. Through phylogeographic analyses, we aim to reconstruct the historical distribution of langur species, assess past population connectivity, and identify key ecological corridors and refugia. Understanding the historical dynamics of their range is crucial for identifying areas that may have historically supported genetic exchange and movement between populations. This knowledge is key for implementing habitat restoration efforts and ensuring the long-term viability of langur populations in fragmented landscapes.
Our research also focuses on genetic diversity, population structure, and gene flow across fragmented habitats. We can obtain high-resolution genetic data that informs population health and connectivity. These tools allow us to study both mitochondrial and nuclear DNA to identify potential signs of inbreeding, genetic isolation, and adaptive differentiation between populations. This information is critical for prioritizing conservation actions, such as translocations, habitat restoration, or the creation of protected corridors to link isolated populations.
In parallel to the scientific research, we emphasize community-centered conservation strategies to ensure that conservation actions are sustainable and contextually relevant. Local communities are central to the success of conservation efforts, and we work to engage them in habitat restoration, corridor protection, and conflict mitigation strategies. By promoting sustainable livelihoods, such as eco-tourism, non-timber forest products, and community-based forest management, we aim to build local ownership of conservation initiatives. Additionally, addressing human-wildlife conflict is essential for minimizing negative interactions between langurs and local populations. Conflict mitigation strategies, including compensation for crop damage and education programs that promote coexistence, will help to foster a more harmonious relationship between humans and wildlife.
Our ultimate goal is to ensure the long-term survival of threatened species and their habitats by applying a holistic, science-driven approach to conservation. By integrating evolutionary biology with landscape-scale conservation and community engagement, our research provides a comprehensive model for addressing the unique conservation challenges faced by langurs and other primates in rapidly changing ecosystems. This approach can be adapted to other regions and species facing similar threats, such as habitat destruction, climate change, and human encroachment, and will contribute to the broader effort to preserve primate biodiversity and promote sustainable ecosystems in biodiversity hotspots worldwide.
Night Monkey Phylogenomics, Evolutionary History, and Taxonomy
The classification and evolutionary history of night monkeys (owl monkeys; Aotus spp.) have long been central challenges in Neotropical primate systematics. Despite decades of study, their taxonomy remains unsettled, shaped by partially discordant signals from cytogenetic variation, cranial morphology, vocalization patterns, and increasingly, molecular datasets. Recent work, including Helenbrook (In Review), has further emphasized that much of this instability reflects not only incomplete lineage sorting and historical hybridization, but also uneven geographic sampling and the continued absence of dense, range-wide genomic datasets. As a result, species boundaries within Aotus remain fluid, and competing phylogenetic hypotheses continue to coexist.
Our research addresses these limitations by applying a museum-integrated phylogenomic framework designed to resolve deep and shallow evolutionary structure within Aotus. We combine high-throughput sequencing of modern non-invasive samples with genome recovery from museum-preserved material, enabling geographically comprehensive sampling across taxa that are otherwise difficult to obtain in the wild.
We employ a combination of mitochondrial genome sequencing and genome-wide nuclear markers generated through next-generation sequencing (NGS) platforms, including Illumina-based short-read sequencing for degraded DNA. A central component of our work is the incorporation of environmental DNA (eDNA) and non-invasive genetic sampling (e.g., fecal DNA), which expands spatial and ecological coverage while minimizing disturbance to wild populations. These methods enable detection of Aotus presence in fragmented and inaccessible habitats, particularly in rapidly changing Amazonian and Andean landscapes where traditional sampling is logistically or ethically constrained. When combined with museum genomics, this creates a temporally stratified dataset spanning historical, contemporary, and environmental sources of genetic material.
We further leverage deep genomic coverage to identify cryptic diversity within Aotus, evaluate lineage divergence across major biogeographic barriers (e.g., Amazonian rivers and Andean foothills), and reconstruct population-level structure across the genus. From a conservation perspective, this integrated framework provides a critical advance for a genus that inhabits some of the most rapidly transforming ecosystems in South America. Extensive deforestation, agricultural expansion driven by fire and land conversion, and increasing habitat fragmentation are reshaping Aotus distributions, particularly in the Amazon Basin and adjacent forest systems. By combining eDNA detection with genome-wide inference from both contemporary and museum samples, our approach enables fine-scale monitoring of population persistence and genetic connectivity in degraded landscapes.
Ultimately, this research advances a more resolved and evolutionarily informed taxonomy of Aotus, while simultaneously generating actionable conservation units grounded in genomic evidence. By integrating phylogenomics, museum-based sequencing, and non-invasive sampling, and building on the conceptual synthesis of Helenbrook (in press), we provide a framework for disentangling long-standing taxonomic uncertainty in night monkeys and for supporting evidence-based conservation strategies across their range.
Conservation Parasitology
Conservation parasitology is an emerging field that recognizes parasites as integral components of biodiversity and essential contributors to ecosystem function, rather than simply agents of disease. Parasites influence host population dynamics, mediate species interactions, and contribute to energy flow and nutrient cycling within ecological networks. Despite their critical ecological roles, parasites are often overlooked in conservation planning, particularly in captive breeding, translocation, and reintroduction programs, where disease management typically prioritizes parasite removal. Such approaches risk disrupting coevolved host-parasite relationships, altering immune function, and creating ecologically incomplete or maladapted populations upon reintroduction.
Our research in conservation parasitology seeks to address these gaps by examining the dual roles of parasites. While parasites can contribute to population decline under altered environmental conditions, they also play a vital role in maintaining ecological stability when kept within natural regulatory limits. We explore how parasite loss, amplification, or community restructuring can impact species recovery, population viability, and ecosystem health in both managed and wild systems. This is particularly relevant for rehabilitation and reintroduction NGOs, where our work helps integrate parasite dynamics into species recovery efforts.
For captive populations, we emphasize the need for evidence-based parasite management strategies that balance disease risk with the preservation of native parasite diversity. This includes targeted screening, selective treatment, and post-release monitoring to ensure the health and ecological integrity of reintroduced populations. For wild populations, we advocate for the incorporation of parasite ecology into long-term monitoring, habitat restoration, and ecosystem health assessments, recognizing that parasites are vital to the functioning of natural ecosystems.
By including parasites in conservation frameworks, recovery plans, and biodiversity assessments, our research aims to provide a more holistic approach to species reintroduction and ecosystem management. In an era of rapid environmental change, "conservation parasitology" offers a critical lens through which to assess and manage the health and viability of both wildlife populations and ecosystems. This work supports rehabilitation and reintroduction efforts, helping NGOs address the complex health challenges of parasitic infections and contributing to the long-term survival of endangered species.
Applied Conservation Biology
Primate species across the globe face mounting threats from habitat loss, fragmentation, hunting, and human-wildlife conflict, making effective conservation strategies essential for their survival. The application of integrated conservation biology is crucial for addressing these threats, particularly in biodiversity hotspots where species are increasingly restricted to fragmented and isolated habitats. Our research applies cutting-edge genomic, phylogeographic, and ecological techniques to inform conservation planning for primates, with a focus on enhancing population viability and fostering long-term ecological sustainability.
Langurs, a diverse group of primates, face significant conservation challenges due to habitat loss, fragmentation, hunting, and human-wildlife conflict. These threats are particularly severe for species such as several species found from India down to the Sundra Shelf, all of which are endemic to rapidly degrading habitats in the tropical rainforests of South and Southeast Asia. While some aspects of the taxonomy and phylogeny of these langurs are well-understood, there remains a significant knowledge gap regarding their population structure, genetic diversity, and contemporary connectivity. This lack of information hinders effective conservation planning, especially as these species face increasing pressures from anthropogenic disturbances such as deforestation, climate change, and agricultural expansion.
To address these critical gaps, we employ an integrative approach that combines genomic research with spatial and environmental modeling. Through phylogeographic analyses, we aim to reconstruct the historical distribution of langur species, assess past population connectivity, and identify key ecological corridors and refugia. Understanding the historical dynamics of their range is crucial for identifying areas that may have historically supported genetic exchange and movement between populations. This knowledge is key for implementing habitat restoration efforts and ensuring the long-term viability of langur populations in fragmented landscapes.
Our research also focuses on genetic diversity, population structure, and gene flow across fragmented habitats. We can obtain high-resolution genetic data that informs population health and connectivity. These tools allow us to study both mitochondrial and nuclear DNA to identify potential signs of inbreeding, genetic isolation, and adaptive differentiation between populations. This information is critical for prioritizing conservation actions, such as translocations, habitat restoration, or the creation of protected corridors to link isolated populations.
In parallel to the scientific research, we emphasize community-centered conservation strategies to ensure that conservation actions are sustainable and contextually relevant. Local communities are central to the success of conservation efforts, and we work to engage them in habitat restoration, corridor protection, and conflict mitigation strategies. By promoting sustainable livelihoods, such as eco-tourism, non-timber forest products, and community-based forest management, we aim to build local ownership of conservation initiatives. Additionally, addressing human-wildlife conflict is essential for minimizing negative interactions between langurs and local populations. Conflict mitigation strategies, including compensation for crop damage and education programs that promote coexistence, will help to foster a more harmonious relationship between humans and wildlife.
Our ultimate goal is to ensure the long-term survival of threatened species and their habitats by applying a holistic, science-driven approach to conservation. By integrating evolutionary biology with landscape-scale conservation and community engagement, our research provides a comprehensive model for addressing the unique conservation challenges faced by langurs and other primates in rapidly changing ecosystems. This approach can be adapted to other regions and species facing similar threats, such as habitat destruction, climate change, and human encroachment, and will contribute to the broader effort to preserve primate biodiversity and promote sustainable ecosystems in biodiversity hotspots worldwide.
Publications (ORCID ID)
Helenbrook, W. D. (In Review). Shedding light on Amazonian phylogeographic patterns and evolutionary history of night monkeys (Genus: Aotus) using reconstructed fecal metagenomic shotgun sequencing. bioRxiv (2025): 2025-11.
Helenbrook, W. D., & Valdez, J. (2025). Role of Rivers as Geographical Barriers in Shaping Molecular Divergence of Neotropical Primates. Biotropica, 57(3), e70028.
Helenbrook, W.D. and Valdez, J. (2021). Species distribution and conservation assessment of the black-headed night monkey (Aotus nigriceps): a species of Least Concern that faces widespread anthropogenic threats. Primates
Helenbrook, W.D. and Whipps, C. (2021). Molecular characterization of Blastocystis in captive and free-ranging New World Primates. Acta Parasitologica.
Helenbrook, W.D. and Valdez, J. (2020). Species distribution modeling and conservation assessment of the black-headed night monkey (Aotus nigriceps) – A species of Least Concern that faces widespread anthropogenic threats. PrePrint bioRxiv
Helenbrook, W.D., Nelson, A., and Solorzano, B. (2020). Intestinal parasitism in the black-headed night monkey, Aotus nigriceps. International Journal of Primatology.
Helenbrook, W.D., Wilkinson, M., and Suarez, J. (2020). Habitat use, fruit consumption, and population density of the black-headed night monkey, Aotus nigriceps, in Southeastern Peru. Acta Amazonica.
Helenbrook, W.D., Linck, N., Pardo, M., and Suarez, J. (2019). Spatial variation in black headed night monkey (Aotus nigriceps) vocalizations. PrePrint bioRxiv
Helenbrook, W.D., Preston, L., Linck, N., Quirk, M., and Suarez, J. (2018). Bioacoustics of the black-headed night monkey, Aotus nigriceps. Neotropical Primates 24: 29-33
Helenbrook, W.D., Stehman, S.V., Shields, W.M., & Whipps, C.M. (2017). Association of anthropogenic disturbances and intestinal parasitism in Ecuadorian mantled howler monkeys, Alouatta palliata aequatorialis. Folia Primatologica 88: 307-322.
Helenbrook, W. D., Shields, W. M., & Whipps, C. M. (2015). Characterization of Blastocystis species infection in humans and mantled howler monkeys, Alouatta palliata aequatorialis, living in close proximity to one another. Parasitology Research 114: 2517-2525.
Helenbrook, W.D., Wade, S.E., Shields, W.M., Stehman, S.V., & Whipps, C.M. (2015). Gastrointestinal parasites of Ecuadorian mantled howler monkeys (Alouatta palliata aequatorialis) based on fecal analysis. The Journal of parasitology 101: 341-350.
Helenbrook, W. (2015). Evaluation of mandrill monkey fecal preservation and extraction methodologies reveal ideal combinations for maximum DNA yields. Report. Tropical Conservation Fund.
Helenbrook, W.D. (2014). Effects of ecological disturbance on parasite communities in both people and mantled howler monkeys (Alouatta palliata aequatorialis) living in Ecuador. State University of New York College of Environmental Science and Forestry.
Helenbrook, W.D. (2014). Risk factors associated with endoparasitism in two rural Ecuadorian communities. State University of New York College of Environmental Science and Forestry.
Searing, K.B. , Shoemaker, K.T., Helenbrook, W.D., Schlaepfer, M.A. (2010). Move It? An assessment tool and ranking system for assisted colonization. PS 56-96: Move It? An assessment tool and ranking system for assisted colonization. In The 95th ESA Annual Meeting.
Schlaepfer, M.A., Helenbrook, W. D., Searing, K. B., & Shoemaker, K. T. (2009). Assisted colonization: evaluating contrasting management actions (and values) in the face of uncertainty. Trends in Ecology & Evolution, 24(9), 471-472.
Helenbrook, W.D. (2006). Non-invasive sampling of mandrill and drill monkeys for use in genetic analyses. In American Journal of Primatology 68, pp. 88-88).
Helenbrook, W. D. (In Review). Shedding light on Amazonian phylogeographic patterns and evolutionary history of night monkeys (Genus: Aotus) using reconstructed fecal metagenomic shotgun sequencing. bioRxiv (2025): 2025-11.
Helenbrook, W. D., & Valdez, J. (2025). Role of Rivers as Geographical Barriers in Shaping Molecular Divergence of Neotropical Primates. Biotropica, 57(3), e70028.
Helenbrook, W.D. and Valdez, J. (2021). Species distribution and conservation assessment of the black-headed night monkey (Aotus nigriceps): a species of Least Concern that faces widespread anthropogenic threats. Primates
Helenbrook, W.D. and Whipps, C. (2021). Molecular characterization of Blastocystis in captive and free-ranging New World Primates. Acta Parasitologica.
Helenbrook, W.D. and Valdez, J. (2020). Species distribution modeling and conservation assessment of the black-headed night monkey (Aotus nigriceps) – A species of Least Concern that faces widespread anthropogenic threats. PrePrint bioRxiv
Helenbrook, W.D., Nelson, A., and Solorzano, B. (2020). Intestinal parasitism in the black-headed night monkey, Aotus nigriceps. International Journal of Primatology.
Helenbrook, W.D., Wilkinson, M., and Suarez, J. (2020). Habitat use, fruit consumption, and population density of the black-headed night monkey, Aotus nigriceps, in Southeastern Peru. Acta Amazonica.
Helenbrook, W.D., Linck, N., Pardo, M., and Suarez, J. (2019). Spatial variation in black headed night monkey (Aotus nigriceps) vocalizations. PrePrint bioRxiv
Helenbrook, W.D., Preston, L., Linck, N., Quirk, M., and Suarez, J. (2018). Bioacoustics of the black-headed night monkey, Aotus nigriceps. Neotropical Primates 24: 29-33
Helenbrook, W.D., Stehman, S.V., Shields, W.M., & Whipps, C.M. (2017). Association of anthropogenic disturbances and intestinal parasitism in Ecuadorian mantled howler monkeys, Alouatta palliata aequatorialis. Folia Primatologica 88: 307-322.
Helenbrook, W. D., Shields, W. M., & Whipps, C. M. (2015). Characterization of Blastocystis species infection in humans and mantled howler monkeys, Alouatta palliata aequatorialis, living in close proximity to one another. Parasitology Research 114: 2517-2525.
Helenbrook, W.D., Wade, S.E., Shields, W.M., Stehman, S.V., & Whipps, C.M. (2015). Gastrointestinal parasites of Ecuadorian mantled howler monkeys (Alouatta palliata aequatorialis) based on fecal analysis. The Journal of parasitology 101: 341-350.
Helenbrook, W. (2015). Evaluation of mandrill monkey fecal preservation and extraction methodologies reveal ideal combinations for maximum DNA yields. Report. Tropical Conservation Fund.
Helenbrook, W.D. (2014). Effects of ecological disturbance on parasite communities in both people and mantled howler monkeys (Alouatta palliata aequatorialis) living in Ecuador. State University of New York College of Environmental Science and Forestry.
Helenbrook, W.D. (2014). Risk factors associated with endoparasitism in two rural Ecuadorian communities. State University of New York College of Environmental Science and Forestry.
Searing, K.B. , Shoemaker, K.T., Helenbrook, W.D., Schlaepfer, M.A. (2010). Move It? An assessment tool and ranking system for assisted colonization. PS 56-96: Move It? An assessment tool and ranking system for assisted colonization. In The 95th ESA Annual Meeting.
Schlaepfer, M.A., Helenbrook, W. D., Searing, K. B., & Shoemaker, K. T. (2009). Assisted colonization: evaluating contrasting management actions (and values) in the face of uncertainty. Trends in Ecology & Evolution, 24(9), 471-472.
Helenbrook, W.D. (2006). Non-invasive sampling of mandrill and drill monkeys for use in genetic analyses. In American Journal of Primatology 68, pp. 88-88).
