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1. PanAf20K: A Large Video Dataset for Wild Ape Detection and Behaviour Recognition

Author

Brookes, Otto, Mirmehdi, Majid, Stephens, Colleen, Angedakin, Samuel, Corogenes, Katherine, Dowd, Dervla, Dieguez, Paula, Hicks, Thurston C., Jones, Sorrel, Lee, Kevin, Leinert, Vera, Lapuente, Juan, McCarthy, Maureen S., Meier, Amelia, Murai, Mizuki, Normand, Emmanuelle, Vergnes, Virginie, Wessling, Erin G., Wittig, Roman M., Langergraber, Kevin, Maldonado, Nuria, Yang, Xinyu, Zuberbuhler, Klaus, Boesch, Christophe, Arandjelovic, Mimi, Kuhl, Hjalmar, and Burghardt, Tilo

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

We present the PanAf20K dataset, the largest and most diverse open-access annotated video dataset of great apes in their natural environment. It comprises more than 7 million frames across ~20,000 camera trap videos of chimpanzees and gorillas collected at 14 field sites in tropical Africa as part of the Pan African Programme: The Cultured Chimpanzee. The footage is accompanied by a rich set of annotations and benchmarks making it suitable for training and testing a variety of challenging and ecologically important computer vision tasks including ape detection and behaviour recognition. Furthering AI analysis of camera trap information is critical given the International Union for Conservation of Nature now lists all species in the great ape family as either Endangered or Critically Endangered. We hope the dataset can form a solid basis for engagement of the AI community to improve performance, efficiency, and result interpretation in order to support assessments of great ape presence, abundance, distribution, and behaviour and thereby aid conservation efforts., Comment: Accepted at IJCV

Published
2024

3. Potentially Zoonotic Enteric Infections in Gorillas and Chimpanzees, Cameroon and Tanzania

Author

Strahan, Emily K., Witherbee, Jacob, Bergl, Richard, Lonsdorf, Elizabeth V., Mwacha, Dismas, Mjungu, Deus, Arandjelovic, Mimi, Ikfuingei, Romanus, Terio, Karen, Travis, Dominic A., and Gillespie, Thomas R.

Subjects
Chimpanzees, Infection, Phylogeny, Zoonoses, Resveratrol, Disease susceptibility, Adenoviruses, Escherichia coli, Health
Abstract

The close phylogenetic relationship between humans and great apes results in similarities in infection susceptibility and a high potential for pathogen exchange (2,2). Despite this zoonotic potential, previous studies of [...]

Published
2024
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4. Automatic Individual Identification of Patterned Solitary Species Based on Unlabeled Video Data

Author

Suessle, Vanessa, Arandjelovic, Mimi, Kalan, Ammie K., Agbor, Anthony, Boesch, Christophe, Brazzola, Gregory, Deschner, Tobias, Dieguez, Paula, Granjon, Anne-Céline, Kuehl, Hjalmar, Landsmann, Anja, Lapuente, Juan, Maldonado, Nuria, Meier, Amelia, Rockaiova, Zuzana, Wessling, Erin G., Wittig, Roman M., Downs, Colleen T., Weinmann, Andreas, and Hergenroether, Elke

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

The manual processing and analysis of videos from camera traps is time-consuming and includes several steps, ranging from the filtering of falsely triggered footage to identifying and re-identifying individuals. In this study, we developed a pipeline to automatically analyze videos from camera traps to identify individuals without requiring manual interaction. This pipeline applies to animal species with uniquely identifiable fur patterns and solitary behavior, such as leopards (Panthera pardus). We assumed that the same individual was seen throughout one triggered video sequence. With this assumption, multiple images could be assigned to an individual for the initial database filling without pre-labeling. The pipeline was based on well-established components from computer vision and deep learning, particularly convolutional neural networks (CNNs) and scale-invariant feature transform (SIFT) features. We augmented this basis by implementing additional components to substitute otherwise required human interactions. Based on the similarity between frames from the video material, clusters were formed that represented individuals bypassing the open set problem of the unknown total population. The pipeline was tested on a dataset of leopard videos collected by the Pan African Programme: The Cultured Chimpanzee (PanAf) and achieved a success rate of over 83% for correct matches between previously unknown individuals. The proposed pipeline can become a valuable tool for future conservation projects based on camera trap data, reducing the work of manual analysis for individual identification, when labeled data is unavailable.

Published
2023

5. Discovery of Novel Herpes Simplexviruses in Wild Gorillas, Bonobos, and Chimpanzees Supports Zoonotic Origin of HSV-2

Author

Wertheim, Joel O, Hostager, Reilly, Ryu, Diane, Merkel, Kevin, Angedakin, Samuel, Arandjelovic, Mimi, Ayimisin, Emmanuel Ayuk, Babweteera, Fred, Bessone, Mattia, Brun-Jeffery, Kathryn J, Dieguez, Paula, Eckardt, Winnie, Fruth, Barbara, Herbinger, Ilka, Jones, Sorrel, Kuehl, Hjalmar, Langergraber, Kevin E, Lee, Kevin, Madinda, Nadege F, Metzger, Sonja, Ormsby, Lucy Jayne, Robbins, Martha M, Sommer, Volker, Stoinski, Tara, Wessling, Erin G, Wittig, Roman M, Yuh, Yisa Ginath, Leendertz, Fabian H, and Calvignac-Spencer, Sébastien

Subjects
Biochemistry and Cell Biology, Evolutionary Biology, Genetics, Biological Sciences, Infectious Diseases, Sexually Transmitted Infections, Aetiology, 2.2 Factors relating to the physical environment, Infection, Good Health and Well Being, Animals, Herpesvirus 2, Human, Hominidae, Humans, Phylogeny, Sequence Analysis, DNA, Simplexvirus, Viral Zoonoses, phylogenetics, zoonosis, herpesvirus, molecular clock, ape, Biochemistry and cell biology, Evolutionary biology
Abstract

Viruses closely related to human pathogens can reveal the origins of human infectious diseases. Human herpes simplexvirus type 1 (HSV-1) and type 2 (HSV-2) are hypothesized to have arisen via host-virus codivergence and cross-species transmission. We report the discovery of novel herpes simplexviruses during a large-scale screening of fecal samples from wild gorillas, bonobos, and chimpanzees. Phylogenetic analysis indicates that, contrary to expectation, simplexviruses from these African apes are all more closely related to HSV-2 than to HSV-1. Molecular clock-based hypothesis testing suggests the divergence between HSV-1 and the African great ape simplexviruses likely represents a codivergence event between humans and gorillas. The simplexviruses infecting African great apes subsequently experienced multiple cross-species transmission events over the past 3 My, the most recent of which occurred between humans and bonobos around 1 Ma. These findings revise our understanding of the origins of human herpes simplexviruses and suggest that HSV-2 is one of the earliest zoonotic pathogens.

Published
2021

6. Limited evidence of C4 plant consumption in mound building Macrotermes termites from savanna woodland chimpanzee sites

Author

Phillips, Seth, Scheffrahn, Rudolf H, Piel, Alex, Stewart, Fiona, Agbor, Anthony, Brazzola, Gregory, Tickle, Alexander, Sommer, Volker, Dieguez, Paula, Wessling, Erin G, Arandjelovic, Mimi, Kühl, Hjalmar, Boesch, Christophe, and Oelze, Vicky M

Subjects
Climate Change Impacts and Adaptation, Physical Geography and Environmental Geoscience, Biological Sciences, Ecology, Earth Sciences, Environmental Sciences, Climate Change Science, Africa, Animals, Behavior, Animal, Carbon, Carbon Isotopes, Diet, Feeding Behavior, Forests, Grassland, Isoptera, Nitrogen, Nitrogen Isotopes, Pan troglodytes, Plants, General Science & Technology
Abstract

Stable isotope analysis is an increasingly used molecular tool to reconstruct the diet and ecology of elusive primates such as unhabituated chimpanzees. The consumption of C4 plant feeding termites by chimpanzees may partly explain the relatively high carbon isotope values reported for some chimpanzee communities. However, the modest availability of termite isotope data as well as the diversity and cryptic ecology of termites potentially consumed by chimpanzees obscures our ability to assess the plausibility of these termites as a C4 resource. Here we report the carbon and nitrogen isotope values from 79 Macrotermes termite samples from six savanna woodland chimpanzee research sites across equatorial Africa. Using mixing models, we estimated the proportion of Macrotermes C4 plant consumption across savanna woodland sites. Additionally, we tested for isotopic differences between termite colonies in different vegetation types and between the social castes within the same colony in a subset of 47 samples from 12 mounds. We found that Macrotermes carbon isotope values were indistinguishable from those of C3 plants. Only 5 to 15% of Macrotermes diets were comprised of C4 plants across sites, suggesting that they cannot be considered a C4 food resource substantially influencing the isotope signatures of consumers. In the Macrotermes subsample, vegetation type and caste were significantly correlated with termite carbon values, but not with nitrogen isotope values. Large Macrotermes soldiers, preferentially consumed by chimpanzees, had comparably low carbon isotope values relative to other termite castes. We conclude that Macrotermes consumption is unlikely to result in high carbon isotope values in either extant chimpanzees or fossil hominins.

Published
2021

7. Population dynamics and genetic connectivity in recent chimpanzee history

Author

Fontsere, Claudia, Kuhlwilm, Martin, Morcillo-Suarez, Carlos, Alvarez-Estape, Marina, Lester, Jack D., Gratton, Paolo, Schmidt, Joshua M., Dieguez, Paula, Aebischer, Thierry, Álvarez-Varona, Paula, Agbor, Anthony, Angedakin, Samuel, Assumang, Alfred K., Ayimisin, Emmanuel A., Bailey, Emma, Barubiyo, Donatienne, Bessone, Mattia, Carretero-Alonso, Andrea, Chancellor, Rebecca, Cohen, Heather, Danquah, Emmanuel, Deschner, Tobias, Dunn, Andrew, Dupain, Jef, Egbe, Villard E., Feliu, Olga, Goedmakers, Annemarie, Granjon, Anne-Céline, Head, Josephine, Hedwig, Daniela, Hermans, Veerle, Hernandez-Aguilar, R. Adriana, Imong, Inaoyom, Jones, Sorrel, Junker, Jessica, Kadam, Parag, Kaiser, Mike, Kambere, Mbangi, Kambale, Magloire V., Kalan, Ammie K., Kienast, Ivonne, Kujirakwinja, Deo, Langergraber, Kevin, Lapuente, Juan, Larson, Bradley, Laudisoit, Anne, Lee, Kevin, Llana, Manuel, Llorente, Miquel, Marrocoli, Sergio, Morgan, David, Mulindahabi, Felix, Murai, Mizuki, Neil, Emily, Nicholl, Sonia, Nixon, Stuart, Normand, Emma, Orbell, Chris, Ormsby, Lucy J., Pacheco, Liliana, Piel, Alex, Riera, Laura, Robbins, Martha M., Rundus, Aaron, Sanz, Crickette, Sciaky, Lilah, Sommer, Volker, Stewart, Fiona A., Tagg, Nikki, Tédonzong, Luc Roscelin, Ton, Els, van Schijndel, Joost, Vergnes, Virginie, Wessling, Erin G., Willie, Jacob, Wittig, Roman M., Yuh, Yisa G., Yurkiw, Kyle, Zuberbuehler, Klaus, Hecht, Jochen, Vigilant, Linda, Boesch, Christophe, Andrés, Aida M., Hughes, David A., Kühl, Hjalmar S., Lizano, Esther, Arandjelovic, Mimi, and Marques-Bonet, Tomas

Published
2022
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8. Threat of mining to African great apes

Author

Junker, Jessica, primary, Quoss, Luise, additional, Valdez, Jose, additional, Arandjelovic, Mimi, additional, Barrie, Abdulai, additional, Campbell, Geneviève, additional, Heinicke, Stefanie, additional, Humle, Tatyana, additional, Kouakou, Célestin Y., additional, Kühl, Hjalmar S., additional, Ordaz-Németh, Isabel, additional, Pereira, Henrique M., additional, Rainer, Helga, additional, Refisch, Johannes, additional, Sonter, Laura, additional, and Sop, Tenekwetche, additional

Published
2024
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9. PanAf20K: A Large Video Dataset for Wild Ape Detection and Behaviour Recognition

Author

Brookes, Otto, primary, Mirmehdi, Majid, additional, Stephens, Colleen, additional, Angedakin, Samuel, additional, Corogenes, Katherine, additional, Dowd, Dervla, additional, Dieguez, Paula, additional, Hicks, Thurston C., additional, Jones, Sorrel, additional, Lee, Kevin, additional, Leinert, Vera, additional, Lapuente, Juan, additional, McCarthy, Maureen S., additional, Meier, Amelia, additional, Murai, Mizuki, additional, Normand, Emmanuelle, additional, Vergnes, Virginie, additional, Wessling, Erin G., additional, Wittig, Roman M., additional, Langergraber, Kevin, additional, Maldonado, Nuria, additional, Yang, Xinyu, additional, Zuberbühler, Klaus, additional, Boesch, Christophe, additional, Arandjelovic, Mimi, additional, Kühl, Hjalmar, additional, and Burghardt, Tilo, additional

Published
2024
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10. Threat of mining to African great apes

Author

Junker, Jessica, Quoss, Luise, Valdez, Jose, Arandjelovic, Mimi, Barrie, Abdulai, Campbell, Geneviève, Heinicke, Stefanie, Humle, Tatyana, Kouakou, Célestin Y, Kühl, Hjalmar S, Ordaz-Németh, Isabel, Pereira, Henrique M, Rainer, Helga, Refisch, Johannes, Sonter, Laura, Sop, Tenekwetche, Junker, Jessica, Quoss, Luise, Valdez, Jose, Arandjelovic, Mimi, Barrie, Abdulai, Campbell, Geneviève, Heinicke, Stefanie, Humle, Tatyana, Kouakou, Célestin Y, Kühl, Hjalmar S, Ordaz-Németh, Isabel, Pereira, Henrique M, Rainer, Helga, Refisch, Johannes, Sonter, Laura, and Sop, Tenekwetche

Abstract

The rapid growth of clean energy technologies is driving a rising demand for critical minerals. In 2022 at the 15th Conference of the Parties to the Convention on Biological Diversity (COP15), seven major economies formed an alliance to enhance the sustainability of mining these essential decarbonization minerals. However, there is a scarcity of studies assessing the threat of mining to global biodiversity. By integrating a global mining dataset with great ape density distribution, we estimated the number of African great apes that spatially coincided with industrial mining projects. We show that up to one-third of Africa's great ape population faces mining-related risks. In West Africa in particular, numerous mining areas overlap with fragmented ape habitats, often in high-density ape regions. For 97% of mining areas, no ape survey data are available, underscoring the importance of increased accessibility to environmental data within the mining sector to facilitate research into the complex interactions between mining, climate, biodiversity, and sustainability.

Published
2024

12. CD4 receptor diversity in chimpanzees protects against SIV infection

Author

Bibollet-Ruche, Frederic, Russell, Ronnie M., Liu, Weimin, Stewart-Jones, Guillaume B. E., Sherrill-Mix, Scott, Li, Yingying, Learn, Gerald H., Smith, Andrew G., Gondim, Marcos V. P., Plenderleith, Lindsey J., Decker, Julie M., Easlick, Juliet L., Wetzel, Katherine S., Collman, Ronald G., Ding, Shilei, Finzi, Andrés, Ayouba, Ahidjo, Peeters, Martine, Leendertz, Fabian H., van Schijndel, Joost, Goedmakers, Annemarie, Ton, Els, Boesch, Christophe, Kuehl, Hjalmar, Arandjelovic, Mimi, Dieguez, Paula, Murai, Mizuki, Colin, Christelle, Koops, Kathelijne, Speede, Sheri, Gonder, Mary K., Muller, Martin N., Sanz, Crickette M., Morgan, David B., Atencia, Rebecca, Cox, Debby, Piel, Alex K., Stewart, Fiona A., Ndjango, Jean-Bosco N., Mjungu, Deus, Lonsdorf, Elizabeth V., Pusey, Anne E., Kwong, Peter D., Sharp, Paul M., Shaw, George M., and Hahn, Beatrice H.

Published
2019

13. Recent genetic connectivity and clinal variation in chimpanzees

Author

Lester, Jack D., Vigilant, Linda, Gratton, Paolo, McCarthy, Maureen S., Barratt, Christopher D., Dieguez, Paula, Agbor, Anthony, Álvarez-Varona, Paula, Angedakin, Samuel, Ayimisin, Emmanuel Ayuk, Bailey, Emma, Bessone, Mattia, Brazzola, Gregory, Chancellor, Rebecca, Cohen, Heather, Danquah, Emmanuel, Deschner, Tobias, Egbe, Villard Ebot, Eno-Nku, Manasseh, Goedmakers, Annemarie, Granjon, Anne-Céline, Head, Josephine, Hedwig, Daniela, Hernandez-Aguilar, R. Adriana, Jeffery, Kathryn J., Jones, Sorrel, Junker, Jessica, Kadam, Parag, Kaiser, Michael, Kalan, Ammie K., Kehoe, Laura, Kienast, Ivonne, Langergraber, Kevin E., Lapuente, Juan, Laudisoit, Anne, Lee, Kevin, Marrocoli, Sergio, Mihindou, Vianet, Morgan, David, Muhanguzi, Geoffrey, Neil, Emily, Nicholl, Sonia, Orbell, Christopher, Ormsby, Lucy Jayne, Pacheco, Liliana, Piel, Alex, Robbins, Martha M., Rundus, Aaron, Sanz, Crickette, Sciaky, Lilah, Siaka, Alhaji M., Städele, Veronika, Stewart, Fiona, Tagg, Nikki, Ton, Els, van Schijndel, Joost, Vyalengerera, Magloire Kambale, Wessling, Erin G., Willie, Jacob, Wittig, Roman M., Yuh, Yisa Ginath, Yurkiw, Kyle, Zuberbuehler, Klaus, Boesch, Christophe, Kühl, Hjalmar S., and Arandjelovic, Mimi

Published
2021
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14. Author Correction: Environmental variability supports chimpanzee behavioural diversity

Author

Kalan, Ammie K., Kulik, Lars, Arandjelovic, Mimi, Boesch, Christophe, Haas, Fabian, Dieguez, Paula, Barratt, Christopher D., Abwe, Ekwoge E., Agbor, Anthony, Angedakin, Samuel, Aubert, Floris, Ayimisin, Emmanuel Ayuk, Bailey, Emma, Bessone, Mattia, Brazzola, Gregory, Buh, Valentine Ebua, Chancellor, Rebecca, Cohen, Heather, Coupland, Charlotte, Curran, Bryan, Danquah, Emmanuel, Deschner, Tobias, Dowd, Dervla, Eno-Nku, Manasseh, Fay, J. Michael, Goedmakers, Annemarie, Granjon, Anne-Céline, Head, Josephine, Hedwig, Daniela, Hermans, Veerle, Jeffery, Kathryn J., Jones, Sorrel, Junker, Jessica, Kadam, Parag, Kambi, Mohamed, Kienast, Ivonne, Kujirakwinja, Deo, Langergraber, Kevin E., Lapuente, Juan, Larson, Bradley, Lee, Kevin C., Leinert, Vera, Llana, Manuel, Marrocoli, Sergio, Meier, Amelia C., Morgan, Bethan, Morgan, David, Neil, Emily, Nicholl, Sonia, Normand, Emmanuelle, Ormsby, Lucy Jayne, Pacheco, Liliana, Piel, Alex, Preece, Jodie, Robbins, Martha M., Rundus, Aaron, Sanz, Crickette, Sommer, Volker, Stewart, Fiona, Tagg, Nikki, Tennie, Claudio, Vergnes, Virginie, Welsh, Adam, Wessling, Erin G., Willie, Jacob, Wittig, Roman M., Yuh, Yisa Ginath, Zuberbühler, Klaus, and Kühl, Hjalmar S.

Published
2021
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15. Chimpanzee ethnography reveals unexpected cultural diversity

Author

Boesch, Christophe, Kalan, Ammie K., Mundry, Roger, Arandjelovic, Mimi, Pika, Simone, Dieguez, Paula, Ayimisin, Emmanuel Ayuk, Barciela, Amanda, Coupland, Charlotte, Egbe, Villard Ebot, Eno-Nku, Manasseh, Michael Fay, J., Fine, David, Adriana Hernandez-Aguilar, R., Hermans, Veerle, Kadam, Parag, Kambi, Mohamed, Llana, Manuel, Maretti, Giovanna, Morgan, David, Murai, Mizuki, Neil, Emily, Nicholl, Sonia, Ormsby, Lucy Jayne, Orume, Robinson, Pacheco, Liliana, Piel, Alex, Sanz, Crickette, Sciaky, Lilah, Stewart, Fiona A., Tagg, Nikki, Wessling, Erin G., Willie, Jacob, and Kühl, Hjalmar S.

Published
2020
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18. Chimpanzee behavioural diversity is spatially structured and negatively associated with genetic variation

Author

Barratt, Christopher, primary, Gratton, Paolo, additional, Marta, Silvio, additional, Onstein, Renske, additional, Fontsere, Claudia, additional, Lester, Jack, additional, Kalan, Ammie, additional, Kulik, Lars, additional, Bocksberger, Gaelle, additional, Dieguez, Paula, additional, McCarthy, Maureen, additional, Kuhlwilm, Martin, additional, Abwe, Ekwoge, additional, Agbor, Anthony, additional, Angedakin, Samuel, additional, Assumang, Alfred, additional, Aubert, Floris, additional, Ayimisin, Emmanuel, additional, Bailey, Emma, additional, Barciela, Amanda, additional, Barubiyo, Donatienne, additional, Bessone, Mattia, additional, Brazzola, Gregory, additional, Buh, Valentine Ebua, additional, Chancellor, Rebecca, additional, Cohen, Heather, additional, Corogenes, Katherine, additional, Coupland, Charlotte, additional, Danquah, Emmanuel, additional, Deschner, Tobias, additional, Dunn, Andrew, additional, Dupain, Jef, additional, Egbe, Villard, additional, Granjon, Anne-Céline, additional, Hedwig, Daniela, additional, Hermans, Veerle, additional, Hernandez-Aguilar, R. Adriana, additional, Imong, Inaoyom, additional, Jeffery, Kathryn, additional, Jones, Sorrel, additional, Junker, Jesscia, additional, Kambere, Mbangi, additional, Kambi, Mohamed, additional, Kienast, Ivonne, additional, Kujirakwinja, Deo, additional, Langergraber, Kevin, additional, Lapuente, Juan, additional, Larson, Bradley, additional, Lee, Kevin, additional, Llana, Manuel, additional, Martin, Rumen, additional, Mbi, Tanyi, additional, Meier, Amelia, additional, Morgan, Bethan, additional, Morgan, David, additional, Neil, Emily, additional, Nicholl, Sonia, additional, Nixon, Stuart, additional, Niyigaba, Protais, additional, Normand, Emmanuelle, additional, Orbell, Christopher, additional, Ormsby, Lucy, additional, Orume, Robinson, additional, Pacheco, Liliana, additional, Piel, Alex, additional, Preece, Jodie, additional, Robbins, Martha, additional, Rundus, Aaron, additional, Sanz, Crickette, additional, Schijndel, Joost van, additional, Sommer, Volker, additional, Stewart, Fiona, additional, Tagg, Nikki, additional, Tédonzong, Luc Roscelin, additional, Tickle, Alexander, additional, Vendras, Elleni, additional, Vergnes, Virginie, additional, Vyalengerera, Magloire, additional, Welsh, Adam, additional, Wessling, Erin, additional, Willie, Jacob, additional, Wittig, Roman, additional, Yuh, Yisa Ginath, additional, Yurkiw, Kyle, additional, Zuberbühler, Klaus, additional, Andres, Aida, additional, Marques-Bonet, Tomas, additional, Boesch, Christophe, additional, Arandjelovic, Mimi, additional, and Kühl, Hjalmar, additional

Published
2023
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19. Environmental variability supports chimpanzee behavioural diversity

Author

Kalan, Ammie K., Kulik, Lars, Arandjelovic, Mimi, Boesch, Christophe, Haas, Fabian, Dieguez, Paula, Barratt, Christopher D., Abwe, Ekwoge E., Agbor, Anthony, Angedakin, Samuel, Aubert, Floris, Ayimisin, Emmanuel Ayuk, Bailey, Emma, Bessone, Mattia, Brazzola, Gregory, Buh, Valentine Ebua, Chancellor, Rebecca, Cohen, Heather, Coupland, Charlotte, Curran, Bryan, Danquah, Emmanuel, Deschner, Tobias, Dowd, Dervla, Eno-Nku, Manasseh, Michael Fay, J., Goedmakers, Annemarie, Granjon, Anne-Céline, Head, Josephine, Hedwig, Daniela, Hermans, Veerle, Jeffery, Kathryn J., Jones, Sorrel, Junker, Jessica, Kadam, Parag, Kambi, Mohamed, Kienast, Ivonne, Kujirakwinja, Deo, Langergraber, Kevin E., Lapuente, Juan, Larson, Bradley, Lee, Kevin C., Leinert, Vera, Llana, Manuel, Marrocoli, Sergio, Meier, Amelia C., Morgan, Bethan, Morgan, David, Neil, Emily, Nicholl, Sonia, Normand, Emmanuelle, Ormsby, Lucy Jayne, Pacheco, Liliana, Piel, Alex, Preece, Jodie, Robbins, Martha M., Rundus, Aaron, Sanz, Crickette, Sommer, Volker, Stewart, Fiona, Tagg, Nikki, Tennie, Claudio, Vergnes, Virginie, Welsh, Adam, Wessling, Erin G., Willie, Jacob, Wittig, Roman M., Yuh, Yisa Ginath, Zuberbühler, Klaus, and Kühl, Hjalmar S.

Published
2020
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20. Historical sampling reveals dramatic demographic changes in western gorilla populations

Author

Thalmann, Olaf, Wegmann, Daniel, Spitzner, Marie, Arandjelovic, Mimi, Guschanski, Katerina, Leuenberger, Christoph, Bergl, Richard A, and Vigilant, Linda

Abstract

Abstract Background Today many large mammals live in small, fragmented populations, but it is often unclear whether this subdivision is the result of long-term or recent events. Demographic modeling using genetic data can estimate changes in long-term population sizes while temporal sampling provides a way to compare genetic variation present today with that sampled in the past. In order to better understand the dynamics associated with the divergences of great ape populations, these analytical approaches were applied to western gorillas (Gorilla gorilla) and in particular to the isolated and Critically Endangered Cross River gorilla subspecies (G. g. diehli). Results We used microsatellite genotypes from museum specimens and contemporary samples of Cross River gorillas to infer both the long-term and recent population history. We find that Cross River gorillas diverged from the ancestral western gorilla population ~17,800 years ago (95% HDI: 760, 63,245 years). However, gene flow ceased only ~420 years ago (95% HDI: 200, 16,256 years), followed by a bottleneck beginning ~320 years ago (95% HDI: 200, 2,825 years) that caused a 60-fold decrease in the effective population size of Cross River gorillas. Direct comparison of heterozygosity estimates from museum and contemporary samples suggests a loss of genetic variation over the last 100 years. Conclusions The composite history of western gorillas could plausibly be explained by climatic oscillations inducing environmental changes in western equatorial Africa that would have allowed gorilla populations to expand over time but ultimately isolate the Cross River gorillas, which thereafter exhibited a dramatic population size reduction. The recent decrease in the Cross River population is accordingly most likely attributable to increasing anthropogenic pressure over the last several hundred years. Isolation of diverging populations with prolonged concomitant gene flow, but not secondary admixture, appears to be a typical characteristic of the population histories of African great apes, including gorillas, chimpanzees and bonobos.

Published
2011

21. Camera traps unveil demography, social structure, and home range of six unhabituated Western chimpanzee groups in the Moyen Bafing National Park, Guinea.

Author

Debetencourt, Benjamin, Barry, Mamadou Moussa, Arandjelovic, Mimi, Stephens, Colleen, Maldonado, Nuria, and Boesch, Christophe

Subjects
SOCIAL structure, CHIMPANZEES, SOCIAL dynamics, NATIONAL parks & reserves, HOMINIDS, WILDLIFE conservation, CRITICALLY ill children
Abstract

Precise estimates of population dynamics and social grouping patterns are required for effective conservation of wild animal populations. It is difficult to obtain such information on non‐human great apes as they have slow reproductive rates. To gain a better understanding of demography in these populations, previous research has typically involved habituation\, a process that requires years. Here, we collected data continuously over year‐long periods to monitor an unhabituated population of critically endangered Western chimpanzees (Pan troglodytes verus) in the Moyen Bafing National Park, Guinea. We used two arrays of 100 camera traps that were placed opportunistically in two distinct 100 km2 sites, named Bakoun and Koukoutamba. We identified 227 individuals in Bakoun and 207 in Koukoutamba through their unique facial features. Our camera trap data make clear that these individuals belong to six and seven closed groups, respectively. Six of those groups were near‐completely sampled with an average minimum size of 46.8 individuals (range: 37–58), and a mean adult sex ratio of 1.32 (range: 0.93–2.10). We described the demographic composition of these groups and use Bayesian social network analysis to understand population structure. The network analyses suggested that the social bonds within the two populations were structured by sex homophily, with male chimpanzees being more or equally likely to be observed together than other adult associations. Through estimation of minimum convex polygons, we described the minimum home range for those groups. Compared to other chimpanzee groups living in a similar environment (mosaic savanna‐forest), the Moyen Bafing region seems to host a high‐density of chimpanzees with small home ranges for their group size. Our research highlights the potential of camera traps for studying the demographic composition of chimpanzee populations with high resolution and obtaining crucial information on several groups in a time‐efficient and cost‐effective way. Research highlights: Using an array of 100 camera traps for a year in two different 100 km2 study sites, we were able to identify individually more than 400 chimpanzees and assigned them in 13 different closed groups.From the identification, we could study demography, social structure, and home range of six unhabituated groups in a savanna‐forest mosaic landscape where few chimpanzee studies took place.From the identification, we could study demography, social structure, and home range of six unhabituated groups in a savanna‐forest mosaic landscape where few chimpanzee studies took place. [ABSTRACT FROM AUTHOR]

Published
2024
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22. Chimpanzee culture in context

Author

Koops, Kathelijne, primary, Arandjelovic, Mimi, additional, Hobaiter, Catherine, additional, Kalan, Ammie, additional, Luncz, Lydia, additional, Musgrave, Stephanie, additional, Samuni, Liran, additional, Sanz, Crickette, additional, and Carvalho, Susana, additional

Published
2023
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23. Mammal mitogenomics from invertebrate-derived DNA

Author

Danabalan, Renita, Merkel, Kevin, Schnell, Ida Bærholm, Arandjelovic, Mimi, Boesch, Christophe, Brazzola, Gregory, Dieguez, Paula, Dupain, Jef, Kambale-Vyalengerera, Magloire, Kühl, Hjalmar S., Hoffmann, Constanze, Lapuente, Juan, Thinh, Van Ngoc, Zimmermann, Fee, Leendertz, Fabian H., Gilbert, M. Thomas P., Roos, Christian, Mazzoni, Camila, Gogarten, Jan F., Calvignac-Spencer, Sébastien, Danabalan, Renita, Merkel, Kevin, Schnell, Ida Bærholm, Arandjelovic, Mimi, Boesch, Christophe, Brazzola, Gregory, Dieguez, Paula, Dupain, Jef, Kambale-Vyalengerera, Magloire, Kühl, Hjalmar S., Hoffmann, Constanze, Lapuente, Juan, Thinh, Van Ngoc, Zimmermann, Fee, Leendertz, Fabian H., Gilbert, M. Thomas P., Roos, Christian, Mazzoni, Camila, Gogarten, Jan F., and Calvignac-Spencer, Sébastien

Abstract

The metabarcoding of vertebrate DNA found in invertebrate-derived DNA (iDNA) has proven a powerful tool for monitoring biodiversity. To date, iDNA has primarily been used to detect the presence/absence of particular taxa using metabarcoding, though recent efforts demonstrated the potential utility of these data for estimating relative animal abundance. Here, we test whether iDNA can also be used to reconstruct complete mammalian mitogenomes and therefore bring the field closer to population-level analyses. Specifically, we used mitogenomic hybridization capture coupled with high-throughput sequencing to analyze individual (N = 7) or pooled (N = 5) fly-derived DNA extracts, and individual (N = 7) or pooled (N = 1) leech-derived DNA extracts, which were known a priori to contain primate DNA. All sources of iDNA showed their ability to generate large amounts of mammalian mitogenomic information and deeper sequencing of libraries is predicted to allow for even more complete recovery of primate mitogenomes from most samples (90%). Sixty percent of these iDNA extracts allowed for the recovery of (near) complete mammalian mitochondrial genomes (hereafter mitogenomes) that proved useable for phylogenomic analyses. These findings contribute to paving the way for iDNA-based population mitogenomic studies of terrestrial mammals.

Published
2023

24. Chimpanzee genomic diversity reveals ancient admixture with bonobos

Author

de Manuel, Marc, Kuhlwilm, Martin, Frandsen, Peter, Sousa, Vitor C., Desai, Tariq, Prado-Martinez, Javier, Hernandez-Rodriguez, Jessica, Dupanloup, Isabelle, Lao, Oscar, Hallast, Pille, Schmidt, Joshua M., Heredia-Genestar, José María, Benazzo, Andrea, Barbujani, Guido, Peter, Benjamin M., Kuderna, Lukas F. K., Casals, Ferran, Angedakin, Samuel, Arandjelovic, Mimi, Boesch, Christophe, Kühl, Hjalmar, Vigilant, Linda, Langergraber, Kevin, Novembre, John, Gut, Marta, Gut, Ivo, Navarro, Arcadi, Carlsen, Frauds, Andres, Aida M., Siegismund, Hans. R., Scally, Aylwyn, Excoffier, Laurent, Tyler-Smith, Chris, Castellano, Sergi, Xue, Yali, Hvilsom, Christina, and Marques-Bonet, Tomas

Published
2016

25. Persistent anthrax as a major driver of wildlife mortality in a tropical rainforest

Author

Hoffmann, Constanze, Zimmermann, Fee, Biek, Roman, Kuehl, Hjalmar, Nowak, Kathrin, Mundry, Roger, Agbor, Anthony, Angedakin, Samuel, Arandjelovic, Mimi, Blankenburg, Anja, Brazolla, Gregory, Corogenes, Katherine, Couacy-Hymann, Emmanuel, Deschner, Tobias, Dieguez, Paula, Dierks, Karsten, Dx, Ariane, Dupke, Susann, Eshuis, Henk, Formenty, Pierre, Yuh, Yisa Ginath, Goedmakers, Annemarie, Gogarten, Jan F., Granjon, Anne-Cline, McGraw, Scott, Grunow, Roland, Hart, John, Jones, Sorrel, Junker, Jessica, Kiang, John, Langergraber, Kevin, Lapuente, Juan, Lee, Kevin, Leendertz, Siv Aina, Lguillon, Floraine, Leinert, Vera, Lhrich, Therese, Marrocoli, Sergio, Mtz-Rensing, Kerstin, Meier, Amelia, Merkel, Kevin, Metzger, Sonja, Murai, Mizuki, Niedorf, Svenja, De Nys, Hlne, Sachse, Andreas, van Schijndel, Joost, Thiesen, Ulla, Ton, Els, Wu, Doris, Wieler, Lothar H., Boesch, Christophe, Klee, Silke R., Wittig, Roman M., Calvignac-Spencer, Sbastien, and Leendertz, Fabian H.

Subjects
Anthrax -- Environmental aspects, Animal populations -- Environmental aspects -- Health aspects, Rain forests -- Environmental aspects -- Health aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Constanze Hoffmann [1]; Fee Zimmermann [1, 2]; Roman Biek [3]; Hjalmar Kuehl [4]; Kathrin Nowak [1]; Roger Mundry [4]; Anthony Agbor [4]; Samuel Angedakin [4]; Mimi Arandjelovic [4]; Anja [...]

Published
2017
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26. Author Correction: Chimpanzee ethnography reveals unexpected cultural diversity

Author

Boesch, Christophe, Kalan, Ammie K., Mundry, Roger, Arandjelovic, Mimi, Pika, Simone, Dieguez, Paula, Ayimisin, Emmanuel Ayuk, Barciela, Amanda, Coupland, Charlotte, Egbe, Villard Ebot, Eno-Nku, Manasseh, Fay, J. Michael, Fine, David, Hernandez-Aguilar, R. Adriana, Hermans, Veerle, Kadam, Parag, Kambi, Mohamed, Llana, Manuel, Maretti, Giovanna, Morgan, David, Murai, Mizuki, Neil, Emily, Nicholl, Sonia, Ormsby, Lucy Jayne, Orume, Robinson, Pacheco, Liliana, Piel, Alex, Sanz, Crickette, Sciaky, Lilah, Stewart, Fiona A., Tagg, Nikki, Wessling, Erin G., Willie, Jacob, and Kühl, Hjalmar S.

Published
2020
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28. The complex Y-chromosomal history of gorillas

Author

Staedele, Veronika, Arandjelovic, Mimi, Nixon, Stuart, Bergl, Richard A., Bradley, Brenda J., Breuer, Thomas, Cameron, Kenneth N., Guschanski, Katerina, Head, Josephine, Kyungu, Jean C., Masi, Shelly, Morgan, David B., Reed, Patricia, Robbins, Martha M., Sanz, Crickette, Smith, Vincent, Stokes, Emma J., Thalmann, Olaf, Todd, Angelique, Vigilant, Linda, Staedele, Veronika, Arandjelovic, Mimi, Nixon, Stuart, Bergl, Richard A., Bradley, Brenda J., Breuer, Thomas, Cameron, Kenneth N., Guschanski, Katerina, Head, Josephine, Kyungu, Jean C., Masi, Shelly, Morgan, David B., Reed, Patricia, Robbins, Martha M., Sanz, Crickette, Smith, Vincent, Stokes, Emma J., Thalmann, Olaf, Todd, Angelique, and Vigilant, Linda

Abstract

Studies of the evolutionary relationships among gorilla populations using autosomal and mitochondrial sequences suggest that male-mediated gene flow may have been important in the past, but data on the Y-chromosomal relationships among the gorilla subspecies are limited. Here, we genotyped blood and noninvasively collected fecal samples from 12 captives and 257 wild male gorillas of known origin representing all four subspecies (Gorilla gorilla gorilla, G. g. diehli, G. beringei beringei, and G. b. graueri) at 10 Y-linked microsatellite loci resulting in 102 unique Y-haplotypes for 224 individuals. We found that western lowland gorilla (G. g. gorilla) haplotypes were consistently more diverse than any other subspecies for all measures of diversity and comprised several genetically distinct groups. However, these did not correspond to geographical proximity and some closely related haplotypes were found several hundred kilometers apart. Similarly, our broad sampling of eastern gorillas revealed that mountain (G. b. beringei) and Grauer's (G. b. graueri) gorilla Y-chromosomal haplotypes did not form distinct clusters. These observations suggest structure in the ancestral population with subsequent mixing of differentiated haplotypes by male dispersal for western lowland gorillas, and postisolation migration or incomplete lineage sorting due to short divergence times for eastern gorillas.

Published
2022
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29. Population dynamics and genetic connectivity in recent chimpanzee history

Author

Fundación la Caixa, Ministerio de Ciencia, Innovación y Universidades (España), Ministerio de Economía y Competitividad (España), European Commission, Vienna Science and Technology Fund, European Research Council, Howard Hughes Medical Institute, Generalitat de Catalunya, Wellcome Trust Centre for Human Genetics, Max Planck Society, Heinz L. Krekeler Foundation, Fontsere, Claudia, Kuhlwilm, Martin, Morcillo-Suárez, Carlos, Alvarez-Estape, Marina, Lester, Jack D., Gratton, Paolo, Schmidt, Joshua M., Dieguez, Paula, Aebischer, Thierry, Álvarez-Varona, Paula, Agbor, Anthony, Angedakin, Samuel, Assumang, Alfred K., Ayimisin, Emmanuel Ayuk, Bailey, Emma, Barubiyo, Donatienne, Bessone, Mattia, Carretero-Alonso, Andrea, Chancellor, Rebecca, Cohen, Heather, Danquah, Emmanuel, Deschner, Tobias, Dunn, Andrew, Dupain, Jef, Egbe, Villard E., Feliú, Olga, Goedmakers, Annemarie, Granjon, Anne‐Céline, Head, Josephine, Hedwig, Daniela, Hermans, Veerle, Hernandez-Aguilar, R. Adriana, Imong, Inaoyom, Jones, Sorrel, Junker, Jessica, Kadam, Parag, Kaiser, Mike, Kambere, Mbangi, Kambale, Magloire V., Kalan, Ammie K., Kienast, Ivonne, Kujirakwinja, Deo, Langergraber, Kevin E., Lapuente, Juan, Larson, Bradley, Laudisoit, Anne, Lee, Kevin, Llana, Manuel, Llorente, Miquel, Marrocol, iSergio, Morgan, David, Mulindahabi, Felix, Murai, Mizuki, Neil, Emily, Nicholl, Sonia, Nixon, Stuart, Normand, Emma, Orbell, Chris, Ormsby, Lucy Jayne, Pacheco, Liliana, Piel, Alex, Riera, Laura, Robbins, Martha M., Rundus, Aaron, Sanz, Crickette, Sciaky, Lilah, Sommer, Volker, Stewart, Fiona, Tagg, Nikki, Tédonzong, Luc Roscelin, Ton, Els, van Schijndel, Joost, Vergnes, Virginie, Wessling, Erin G., Willie, Jacob, Wittig, Roman M., Yuh, Yisa G., Yurkiw, Kyle, Zuberbuehler, Klaus, Hecht, Jochen, Vigilant, Linda, Boesch, Christophe, Andrés, Aida M., Hughes, David A., Kühl, Hjalmar, Lizano, Esther, Arandjelovic, Mimi, Marqués-Bonet, Tomàs, Fundación la Caixa, Ministerio de Ciencia, Innovación y Universidades (España), Ministerio de Economía y Competitividad (España), European Commission, Vienna Science and Technology Fund, European Research Council, Howard Hughes Medical Institute, Generalitat de Catalunya, Wellcome Trust Centre for Human Genetics, Max Planck Society, Heinz L. Krekeler Foundation, Fontsere, Claudia, Kuhlwilm, Martin, Morcillo-Suárez, Carlos, Alvarez-Estape, Marina, Lester, Jack D., Gratton, Paolo, Schmidt, Joshua M., Dieguez, Paula, Aebischer, Thierry, Álvarez-Varona, Paula, Agbor, Anthony, Angedakin, Samuel, Assumang, Alfred K., Ayimisin, Emmanuel Ayuk, Bailey, Emma, Barubiyo, Donatienne, Bessone, Mattia, Carretero-Alonso, Andrea, Chancellor, Rebecca, Cohen, Heather, Danquah, Emmanuel, Deschner, Tobias, Dunn, Andrew, Dupain, Jef, Egbe, Villard E., Feliú, Olga, Goedmakers, Annemarie, Granjon, Anne‐Céline, Head, Josephine, Hedwig, Daniela, Hermans, Veerle, Hernandez-Aguilar, R. Adriana, Imong, Inaoyom, Jones, Sorrel, Junker, Jessica, Kadam, Parag, Kaiser, Mike, Kambere, Mbangi, Kambale, Magloire V., Kalan, Ammie K., Kienast, Ivonne, Kujirakwinja, Deo, Langergraber, Kevin E., Lapuente, Juan, Larson, Bradley, Laudisoit, Anne, Lee, Kevin, Llana, Manuel, Llorente, Miquel, Marrocol, iSergio, Morgan, David, Mulindahabi, Felix, Murai, Mizuki, Neil, Emily, Nicholl, Sonia, Nixon, Stuart, Normand, Emma, Orbell, Chris, Ormsby, Lucy Jayne, Pacheco, Liliana, Piel, Alex, Riera, Laura, Robbins, Martha M., Rundus, Aaron, Sanz, Crickette, Sciaky, Lilah, Sommer, Volker, Stewart, Fiona, Tagg, Nikki, Tédonzong, Luc Roscelin, Ton, Els, van Schijndel, Joost, Vergnes, Virginie, Wessling, Erin G., Willie, Jacob, Wittig, Roman M., Yuh, Yisa G., Yurkiw, Kyle, Zuberbuehler, Klaus, Hecht, Jochen, Vigilant, Linda, Boesch, Christophe, Andrés, Aida M., Hughes, David A., Kühl, Hjalmar, Lizano, Esther, Arandjelovic, Mimi, and Marqués-Bonet, Tomàs

Abstract

Knowledge on the population history of endangered species is critical for conservation, but whole-genome data on chimpanzees (Pan troglodytes) is geographically sparse. Here, we produced the first non-invasive geolocalized catalog of genomic diversity by capturing chromosome 21 from 828 non-invasive samples collected at 48 sampling sites across Africa. The four recognized subspecies show clear genetic differentiation correlating with known barriers, while previously undescribed genetic exchange suggests that these have been permeable on a local scale. We obtained a detailed reconstruction of population stratification and fine-scale patterns of isolation, migration, and connectivity, including a comprehensive picture of admixture with bonobos (Pan paniscus). Unlike humans, chimpanzees did not experience extended episodes of long-distance migrations, which might have limited cultural transmission. Finally, based on local rare variation, we implement a fine-grained geolocalization approach demonstrating improved precision in determining the origin of confiscated chimpanzees.

Published
2022

30. Using nonhuman culture in conservation requires careful and concerted action

Author

Carvalho, Susana, Wessling, Erin G; https://orcid.org/0000-0001-9661-4354, Abwe, Ekwoge E, Almeida‐Warren, Katarina; https://orcid.org/0000-0002-7634-9466, Arandjelovic, Mimi, Boesch, Christophe, Danquah, Emmanuel, Diallo, Mamadou Saliou, Hobaiter, Catherine; https://orcid.org/0000-0002-3893-0524, Hockings, Kimberley, Humle, Tatyana, Ikemeh, Rachel Ashegbofe, Kalan, Ammie K, Luncz, Lydia, Ohashi, Gaku, Pascual‐Garrido, Alejandra, Piel, Alex, Samuni, Liran, Soiret, Serge; https://orcid.org/0000-0001-6773-500X, Sanz, Crickette, Koops, Kathelijne; https://orcid.org/0000-0001-7097-2698, Carvalho, Susana, Wessling, Erin G; https://orcid.org/0000-0001-9661-4354, Abwe, Ekwoge E, Almeida‐Warren, Katarina; https://orcid.org/0000-0002-7634-9466, Arandjelovic, Mimi, Boesch, Christophe, Danquah, Emmanuel, Diallo, Mamadou Saliou, Hobaiter, Catherine; https://orcid.org/0000-0002-3893-0524, Hockings, Kimberley, Humle, Tatyana, Ikemeh, Rachel Ashegbofe, Kalan, Ammie K, Luncz, Lydia, Ohashi, Gaku, Pascual‐Garrido, Alejandra, Piel, Alex, Samuni, Liran, Soiret, Serge; https://orcid.org/0000-0001-6773-500X, Sanz, Crickette, and Koops, Kathelijne; https://orcid.org/0000-0001-7097-2698

Abstract

Discussions of how animal culture can aid the conservation crisis are burgeoning. As scientists and conservationists working to protect endangered species, we call for reflection on how the culture concept may be applied in practice. Here, we discuss both the potential benefits and potential shortcomings of applying the animal culture concept, and propose a set of achievable milestones that will help guide and ensure its effective integration existing conservation frameworks, such as Adaptive Management cycles or Open Standards.

Published
2022

31. The complex Y‐chromosomal history of gorillas

Author

Städele, Veronika, primary, Arandjelovic, Mimi, additional, Nixon, Stuart, additional, Bergl, Richard A., additional, Bradley, Brenda J., additional, Breuer, Thomas, additional, Cameron, Kenneth N., additional, Guschanski, Katerina, additional, Head, Josephine, additional, Kyungu, Jean C., additional, Masi, Shelly, additional, Morgan, David B., additional, Reed, Patricia, additional, Robbins, Martha M., additional, Sanz, Crickette, additional, Smith, Vincent, additional, Stokes, Emma J., additional, Thalmann, Olaf, additional, Todd, Angelique, additional, and Vigilant, Linda, additional

Published
2022
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32. Using nonhuman culture in conservation requires careful and concerted action

Author

Carvalho, Susana, primary, Wessling, Erin G., additional, Abwe, Ekwoge E., additional, Almeida‐Warren, Katarina, additional, Arandjelovic, Mimi, additional, Boesch, Christophe, additional, Danquah, Emmanuel, additional, Diallo, Mamadou Saliou, additional, Hobaiter, Catherine, additional, Hockings, Kimberley, additional, Humle, Tatyana, additional, Ikemeh, Rachel Ashegbofe, additional, Kalan, Ammie K., additional, Luncz, Lydia, additional, Ohashi, Gaku, additional, Pascual‐Garrido, Alejandra, additional, Piel, Alex, additional, Samuni, Liran, additional, Soiret, Serge, additional, Sanz, Crickette, additional, and Koops, Kathelijne, additional

Published
2022
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33. Using non-human culture in conservation requires careful and concerted action

Author

Carvalho, Susana, primary, Wessling, Erin, additional, Abwe, Ekwoge E., additional, Almeida-Warren, Katarina, additional, Arandjelovic, Mimi, additional, Boesch, Christophe, additional, Danquah, Emmanuel, additional, Diallo, Mamadou Saliou, additional, Hobaiter, Cat, additional, Hockings, Kimberley, additional, Humle, Tatyana, additional, Ikemeh, Rachel Ashegbofe, additional, Kalan, Ammie K., additional, Luncz, Lydia, additional, Ohashi, Gaku, additional, Pascual-Garrido, Alejandra, additional, Piel, Alex, additional, Samuni, Liran, additional, Sanz, Crickette, additional, and Koops, Kathelijne, additional

Published
2021
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34. Quantitative estimates of glacial refugia for chimpanzees ( Pan troglodytes ) since the Last Interglacial (120,000 BP)

Author

Barratt, Christopher D., primary, Lester, Jack D., additional, Gratton, Paolo, additional, Onstein, Renske E., additional, Kalan, Ammie K., additional, McCarthy, Maureen S., additional, Bocksberger, Gaëlle, additional, White, Lauren C., additional, Vigilant, Linda, additional, Dieguez, Paula, additional, Abdulai, Barrie, additional, Aebischer, Thierry, additional, Agbor, Anthony, additional, Assumang, Alfred K., additional, Bailey, Emma, additional, Bessone, Mattia, additional, Buys, Bartelijntje, additional, Carvalho, Joana S., additional, Chancellor, Rebecca, additional, Cohen, Heather, additional, Danquah, Emmanuel, additional, Deschner, Tobias, additional, Dongmo, Zacharie N., additional, Doumbé, Osiris A., additional, Dupain, Jef, additional, Duvall, Chris S., additional, Eno‐Nku, Manasseh, additional, Etoga, Gilles, additional, Galat‐Luong, Anh, additional, Garriga, Rosa, additional, Gatti, Sylvain, additional, Ghiurghi, Andrea, additional, Goedmakers, Annemarie, additional, Granjon, Anne‐Céline, additional, Hakizimana, Dismas, additional, Head, Josephine, additional, Hedwig, Daniela, additional, Herbinger, Ilka, additional, Hermans, Veerle, additional, Jones, Sorrel, additional, Junker, Jessica, additional, Kadam, Parag, additional, Kambi, Mohamed, additional, Kienast, Ivonne, additional, Kouakou, Célestin Y., additional, N′Goran, Kouamé P., additional, Langergraber, Kevin E., additional, Lapuente, Juan, additional, Laudisoit, Anne, additional, Lee, Kevin C., additional, Maisels, Fiona, additional, Mirghani, Nadia, additional, Moore, Deborah, additional, Morgan, Bethan, additional, Morgan, David, additional, Neil, Emily, additional, Nicholl, Sonia, additional, Nkembi, Louis, additional, Ntongho, Anne, additional, Orbell, Christopher, additional, Ormsby, Lucy Jayne, additional, Pacheco, Liliana, additional, Piel, Alex K., additional, Pintea, Lilian, additional, Plumptre, Andrew J., additional, Rundus, Aaron, additional, Sanz, Crickette, additional, Sommer, Volker, additional, Sop, Tenekwetche, additional, Stewart, Fiona A., additional, Sunderland‐Groves, Jacqueline, additional, Tagg, Nikki, additional, Todd, Angelique, additional, Ton, Els, additional, Schijndel, Joost, additional, VanLeeuwe, Hilde, additional, Vendras, Elleni, additional, Welsh, Adam, additional, Wenceslau, José F. C., additional, Wessling, Erin G., additional, Willie, Jacob, additional, Wittig, Roman M., additional, Yoshihiro, Nakashima, additional, Yuh, Yisa Ginath, additional, Yurkiw, Kyle, additional, Boesch, Christophe, additional, Arandjelovic, Mimi, additional, and Kühl, Hjalmar, additional

Published
2021
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35. Structure of Chimpanzee Gut Microbiomes across Tropical Africa

Author

Bueno de Mesquita, Clifton P., primary, Nichols, Lauren M., additional, Gebert, Matthew J., additional, Vanderburgh, Caihong, additional, Bocksberger, Gaëlle, additional, Lester, Jack D., additional, Kalan, Ammie K., additional, Dieguez, Paula, additional, McCarthy, Maureen S., additional, Agbor, Anthony, additional, Álvarez Varona, Paula, additional, Ayimisin, Ayuk Emmanuel, additional, Bessone, Mattia, additional, Chancellor, Rebecca, additional, Cohen, Heather, additional, Coupland, Charlotte, additional, Deschner, Tobias, additional, Egbe, Villard Ebot, additional, Goedmakers, Annemarie, additional, Granjon, Anne-Céline, additional, Grueter, Cyril C., additional, Head, Josephine, additional, Hernandez-Aguilar, R. Adriana, additional, Jeffery, Kathryn J., additional, Jones, Sorrel, additional, Kadam, Parag, additional, Kaiser, Michael, additional, Lapuente, Juan, additional, Larson, Bradley, additional, Marrocoli, Sergio, additional, Morgan, David, additional, Mugerwa, Badru, additional, Mulindahabi, Felix, additional, Neil, Emily, additional, Niyigaba, Protais, additional, Pacheco, Liliana, additional, Piel, Alex K., additional, Robbins, Martha M., additional, Rundus, Aaron, additional, Sanz, Crickette M., additional, Sciaky, Lilah, additional, Sheil, Douglas, additional, Sommer, Volker, additional, Stewart, Fiona A., additional, Ton, Els, additional, van Schijndel, Joost, additional, Vergnes, Virginie, additional, Wessling, Erin G., additional, Wittig, Roman M., additional, Ginath Yuh, Yisa, additional, Yurkiw, Kyle, additional, Zuberbühler, Klaus, additional, Gogarten, Jan F., additional, Heintz-Buschart, Anna, additional, Muellner-Riehl, Alexandra N., additional, Boesch, Christophe, additional, Kühl, Hjalmar S., additional, Fierer, Noah, additional, Arandjelovic, Mimi, additional, and Dunn, Robert R., additional

Published
2021
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36. Maximizing the acquisition of unique reads in noninvasive capture sequencing experiments

Author

La Caixa, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Max Planck Society, Heinz L. Krekeler Foundation, Fundación la Caixa, European Research Council, European Commission, Howard Hughes Medical Institute, Generalitat de Catalunya, Fontsere, Claudia, Alvarez-Estape, Marina, Lester, Jack D., Arandjelovic, Mimi, Kuhlwilm, Martin, Dieguez, Paula, Agbor, Anthony, Angedakin, Samuel, Ayimisin, Emmanuel Ayuk, Bessone, Mattia, Brazzola, Gregory, Deschner, Tobias, Eno-Nku, Manasseh, Granjon, Anne‐Céline, Head, Josephine, Kadam, Parag, Kalan, Ammie K., Kambi, Mohamed, Langergraber, Kevin E., Lapuente, Juan, Maretti, Giovanna, Ormsby, Lucy Jayne, Piel, Alex, Robbins, Martha M., Stewart, Fiona, Vergnes, Virginie, Wittig, Roman M., Kühl, Hjalmar, Marqués-Bonet, Tomàs, Hughes, David A., Lizano, Esther, La Caixa, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Max Planck Society, Heinz L. Krekeler Foundation, Fundación la Caixa, European Research Council, European Commission, Howard Hughes Medical Institute, Generalitat de Catalunya, Fontsere, Claudia, Alvarez-Estape, Marina, Lester, Jack D., Arandjelovic, Mimi, Kuhlwilm, Martin, Dieguez, Paula, Agbor, Anthony, Angedakin, Samuel, Ayimisin, Emmanuel Ayuk, Bessone, Mattia, Brazzola, Gregory, Deschner, Tobias, Eno-Nku, Manasseh, Granjon, Anne‐Céline, Head, Josephine, Kadam, Parag, Kalan, Ammie K., Kambi, Mohamed, Langergraber, Kevin E., Lapuente, Juan, Maretti, Giovanna, Ormsby, Lucy Jayne, Piel, Alex, Robbins, Martha M., Stewart, Fiona, Vergnes, Virginie, Wittig, Roman M., Kühl, Hjalmar, Marqués-Bonet, Tomàs, Hughes, David A., and Lizano, Esther

Abstract

Noninvasive samples as a source of DNA are gaining interest in genomic studies of endangered species. However, their complex nature and low endogenous DNA content hamper the recovery of good quality data. Target capture has become a productive method to enrich the endogenous fraction of noninvasive samples, such as faeces, but its sensitivity has not yet been extensively studied. Coping with faecal samples with an endogenous DNA content below 1% is a common problem when prior selection of samples from a large collection is not possible. However, samples classified as unfavourable for target capture sequencing might be the only representatives of unique specific geographical locations, or to answer the question of interest. To explore how library complexity may be increased without repeating DNA extractions and generating new libraries, in this study we captured the exome of 60 chimpanzees (Pan troglodytes) using faecal samples with very low proportions of endogenous content (<1%). Our results indicate that by performing additional hybridizations of the same libraries, the molecular complexity can be maintained to achieve higher coverage. Also, whenever possible, the starting DNA material for capture should be increased. Finally, we specifically calculated the sequencing effort needed to avoid exhausting the library complexity of enriched faecal samples with low endogenous DNA content. This study provides guidelines, schemes and tools for laboratories facing the challenges of working with noninvasive samples containing extremely low amounts of endogenous DNA.

Published
2021

37. Structure of chimpanzee gut microbiomes across tropical Africa

Author

Bueno de Mesquita, Clifton P., Nichols, Lauren M., Gebert, Matthew J., Vanderburgh, Caihong, Bocksberger, Gaëlle, Lester, Jack D., Kalan, Ammie K., Dieguez, Paula, McCarthy, Maureen S., Agbor, Anthony, Varona, Paula Álvarez, Ayimisin, Ayuk Emmanuel, Bessone, Mattia, Cohen, Heather, Coupland, Charlotte, Deschner, Tobias, Egbe, Villard Ebot, Goedmakers, Annemarie, Granjon, Anne Céline, Grueter, Cyril C., Head, Josephine, Hernandez-Aguilar, R.A., Jeffery, Kathryn J., Jones, Sorrel, Kadam, Parag, Kaiser, Michael, Lapuente, Juan, Larson, Bradley, Marrocoli, Sergio, Morgan, David, Mugerwa, Badru, Mulindahabi, Felix, Neil, Emily, Niyigaba, Protais, Pacheco, Liliana, Piel, Alex K., Robbins, Martha M., Rundus, Aaron, Sanz, Crickette M., Sciaky, Lilah, Sheil, Douglas, Sommer, Volker, Stewart, Fiona A., Ton, Els, Van Schijndel, Joost, Vergnes, Virginie, Wessling, Erin G., Wittig, Roman M., Yuh, Yisa Ginath, Yurkiw, Kyle, Zuberbühler, Klaus, Gogarten, Jan F., Heintz-Buschart, Anna, Muellner-Riehl, Alexandra N., Boesch, Christophe, Kühl, Hjalmar S., Fierer, Noah, Arandjelovic, Mimi, Dunn, Robert R., Bueno de Mesquita, Clifton P., Nichols, Lauren M., Gebert, Matthew J., Vanderburgh, Caihong, Bocksberger, Gaëlle, Lester, Jack D., Kalan, Ammie K., Dieguez, Paula, McCarthy, Maureen S., Agbor, Anthony, Varona, Paula Álvarez, Ayimisin, Ayuk Emmanuel, Bessone, Mattia, Cohen, Heather, Coupland, Charlotte, Deschner, Tobias, Egbe, Villard Ebot, Goedmakers, Annemarie, Granjon, Anne Céline, Grueter, Cyril C., Head, Josephine, Hernandez-Aguilar, R.A., Jeffery, Kathryn J., Jones, Sorrel, Kadam, Parag, Kaiser, Michael, Lapuente, Juan, Larson, Bradley, Marrocoli, Sergio, Morgan, David, Mugerwa, Badru, Mulindahabi, Felix, Neil, Emily, Niyigaba, Protais, Pacheco, Liliana, Piel, Alex K., Robbins, Martha M., Rundus, Aaron, Sanz, Crickette M., Sciaky, Lilah, Sheil, Douglas, Sommer, Volker, Stewart, Fiona A., Ton, Els, Van Schijndel, Joost, Vergnes, Virginie, Wessling, Erin G., Wittig, Roman M., Yuh, Yisa Ginath, Yurkiw, Kyle, Zuberbühler, Klaus, Gogarten, Jan F., Heintz-Buschart, Anna, Muellner-Riehl, Alexandra N., Boesch, Christophe, Kühl, Hjalmar S., Fierer, Noah, Arandjelovic, Mimi, and Dunn, Robert R.

Abstract

Understanding variation in host-associated microbial communities is important given the relevance of microbiomes to host physiology and health. Using 560 fecal samples collected from wild chimpanzees (Pan troglodytes) across their range, we assessed how geography, genetics, climate, vegetation, and diet relate to gut microbial community structure (prokaryotes, eukaryotic parasites) at multiple spatial scales. We observed a high degree of regional specificity in the microbiome composition, which was associated with host genetics, available plant foods, and potentially with cultural differences in tool use, which affect diet. Genetic differences drove community composition at large scales, while vegetation and potentially tool use drove within-region differences, likely due to their influence on diet. Unlike industrialized human populations in the United States, where regional differences in the gut microbiome are undetectable, chimpanzee gut microbiomes are far more variable across space, suggesting that technological developments have decoupled humans from their local environments, obscuring regional differences that could have been important during human evolution.

Published
2021

39. The Internal, External and Extended Microbiomes of Hominins

Author

Dunn, Robert R., Amato, Katherine R., Archie, Elizabeth A., Arandjelovic, Mimi, Crittenden, Alyssa N., Nichols, Lauren M., Dunn, Robert R., Amato, Katherine R., Archie, Elizabeth A., Arandjelovic, Mimi, Crittenden, Alyssa N., and Nichols, Lauren M.

Published
2020

40. Geographically structured genomic diversity of non-human primate-infecting Treponema pallidum subsp. pertenue

Author

Mubemba, Benjamin; https://orcid.org/0000-0002-5266-3602, Gogarten, Jan F; https://orcid.org/0000-0003-1889-4113, Schuenemann, Verena J; https://orcid.org/0000-0002-8593-3672, Düx, Ariane; https://orcid.org/0000-0003-1819-8556, Lang, Alexander; https://orcid.org/0000-0002-1259-4315, Nowak, Kathrin; https://orcid.org/0000-0001-7537-5200, Pléh, Kamilla; https://orcid.org/0000-0002-2528-5482, Reiter, Ella, Ulrich, Markus, Agbor, Anthony, Brazzola, Gregory, Deschner, Tobias, Dieguez, Paula; https://orcid.org/0000-0002-6951-2771, Granjon, Anne-Céline; https://orcid.org/0000-0003-1426-523X, Jones, Sorrel; https://orcid.org/0000-0002-3579-7254, Junker, Jessica, Wessling, Erin; https://orcid.org/0000-0001-9661-4354, Arandjelovic, Mimi, Kuehl, Hjalmar, Wittig, Roman M; https://orcid.org/0000-0001-6490-4031, Leendertz, Fabian H; https://orcid.org/0000-0002-2169-7375, Calvignac-Spencer, Sébastien; https://orcid.org/0000-0003-4834-0509, Mubemba, Benjamin; https://orcid.org/0000-0002-5266-3602, Gogarten, Jan F; https://orcid.org/0000-0003-1889-4113, Schuenemann, Verena J; https://orcid.org/0000-0002-8593-3672, Düx, Ariane; https://orcid.org/0000-0003-1819-8556, Lang, Alexander; https://orcid.org/0000-0002-1259-4315, Nowak, Kathrin; https://orcid.org/0000-0001-7537-5200, Pléh, Kamilla; https://orcid.org/0000-0002-2528-5482, Reiter, Ella, Ulrich, Markus, Agbor, Anthony, Brazzola, Gregory, Deschner, Tobias, Dieguez, Paula; https://orcid.org/0000-0002-6951-2771, Granjon, Anne-Céline; https://orcid.org/0000-0003-1426-523X, Jones, Sorrel; https://orcid.org/0000-0002-3579-7254, Junker, Jessica, Wessling, Erin; https://orcid.org/0000-0001-9661-4354, Arandjelovic, Mimi, Kuehl, Hjalmar, Wittig, Roman M; https://orcid.org/0000-0001-6490-4031, Leendertz, Fabian H; https://orcid.org/0000-0002-2169-7375, and Calvignac-Spencer, Sébastien; https://orcid.org/0000-0003-4834-0509

Abstract

Many non-human primate species in sub-Saharan Africa are infected with Treponema pallidum subsp. pertenue, the bacterium causing yaws in humans. In humans, yaws is often characterized by lesions of the extremities and face, while T. pallidum subsp. pallidum causes venereal syphilis and is typically characterized by primary lesions on the genital, anal or oral mucosae. It remains unclear whether other T. pallidum subspecies found in humans also occur in non-human primates and how the genomic diversity of non-human primate T. pallidum subsp. pertenue lineages is distributed across hosts and space. We observed orofacial and genital lesions in sooty mangabeys (Cercocebus atys) in Taï National Park, Côte d'Ivoire and collected swabs and biopsies from symptomatic animals. We also collected non-human primate bones from 8 species in Taï National Park and 16 species from 11 other sites across sub-Saharan Africa. Samples were screened for T. pallidum DNA using polymerase chain reactions (PCRs) and we used in-solution hybridization capture to sequence T. pallidum genomes. We generated three nearly complete T. pallidum genomes from biopsies and swabs and detected treponemal DNA in bones of six non-human primate species in five countries, allowing us to reconstruct three partial genomes. Phylogenomic analyses revealed that both orofacial and genital lesions in sooty mangabeys from Taï National Park were caused by T. pallidum subsp. pertenue. We showed that T. pallidum subsp. pertenue has infected non-human primates in Taï National Park for at least 28 years and has been present in two non-human primate species that had not been described as T. pallidum subsp. pertenue hosts in this ecosystem, western chimpanzees (Pan troglodytes verus) and western red colobus (Piliocolobus badius), complementing clinical evidence that started accumulating in Taï National Park in 2014. More broadly, simian T. pallidum subsp. pertenue strains did not form monophyletic clades based on host species

Published
2020

41. Maximizing the acquisition of unique reads in noninvasive capture sequencing experiments

Author

Fontsere, Claudia, primary, Alvarez‐Estape, Marina, additional, Lester, Jack, additional, Arandjelovic, Mimi, additional, Kuhlwilm, Martin, additional, Dieguez, Paula, additional, Agbor, Anthony, additional, Angedakin, Samuel, additional, Ayuk Ayimisin, Emmanuel, additional, Bessone, Mattia, additional, Brazzola, Gregory, additional, Deschner, Tobias, additional, Eno‐Nku, Manasseh, additional, Granjon, Anne‐Céline, additional, Head, Josephine, additional, Kadam, Parag, additional, Kalan, Ammie K., additional, Kambi, Mohamed, additional, Langergraber, Kevin, additional, Lapuente, Juan, additional, Maretti, Giovanna, additional, Jayne Ormsby, Lucy, additional, Piel, Alex, additional, Robbins, Martha M., additional, Stewart, Fiona, additional, Vergnes, Virginie, additional, Wittig, Roman M., additional, Kühl, Hjalmar S., additional, Marques‐Bonet, Tomas, additional, Hughes, David A., additional, and Lizano, Esther, additional

Published
2020
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42. Chimpanzee identification and social network construction through an online citizen science platform

Author

McCarthy, Maureen S., primary, Stephens, Colleen, additional, Dieguez, Paula, additional, Samuni, Liran, additional, Després‐Einspenner, Marie‐Lyne, additional, Harder, Briana, additional, Landsmann, Anja, additional, Lynn, Laura K., additional, Maldonado, Nuria, additional, Ročkaiová, Zuzana, additional, Widness, Jane, additional, Wittig, Roman M., additional, Boesch, Christophe, additional, Kühl, Hjalmar S., additional, and Arandjelovic, Mimi, additional

Published
2020
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44. Novelty Response of Wild African Apes to Camera Traps

Author

Kalan, Ammie K., Hohmann, Gottfried, Arandjelovic, Mimi, Boesch, Christophe, McCarthy, Maureen S., Agbor, Anthony, Angedakin, Samuel, Bailey, Emma, Balongelwa, Cosma Wilungula, Bessone, Mattia, Bocksberger, Gaëlle, Coxe, Sally Jewel, Deschner, Tobias, Després-Einspenner, Marie-Lyne, Dieguez, Paula, Fruth, Barbara, Herbinger, Ilka, Granjon, Anne-Céline, Head, Josephine, Kablan, Yves Aka, Langergraber, Kevin E., Lokasola, Albert Lotana, Maretti, Giovanna, Marrocoli, Sergio, Mbende, Menard, Moustgaard, Jennifer, N’Goran, Paul Kouame, Robbins, Martha M., van Schijndel, Joost, Sommer, Volker, Surbeck, Martin, Tagg, Nikki, Willie, Jacob, Wittig, Roman M., and Kühl, Hjalmar S.

Published
2019
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45. Geographically structured genomic diversity of non-human primate-infecting Treponema pallidum subsp. pertenue

Author

Mubemba, Benjamin, primary, Gogarten, Jan F., additional, Schuenemann, Verena J., additional, Düx, Ariane, additional, Lang, Alexander, additional, Nowak, Kathrin, additional, Pléh, Kamilla, additional, Reiter, Ella, additional, Ulrich, Markus, additional, Agbor, Anthony, additional, Brazzola, Gregory, additional, Deschner, Tobias, additional, Dieguez, Paula, additional, Granjon, Anne-Céline, additional, Jones, Sorrel, additional, Junker, Jessica, additional, Wessling, Erin, additional, Arandjelovic, Mimi, additional, Kuehl, Hjalmar, additional, Wittig, Roman M., additional, Leendertz, Fabian H., additional, and Calvignac-Spencer, Sébastien, additional

Published
2020
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47. Late Quaternary habitat suitability models for chimpanzees (Pan troglodytes) since the Last Interglacial (120,000 BP)

Author

Barratt, Christopher D., primary, Lester, Jack D., additional, Gratton, Paolo, additional, Onstein, Renske E., additional, Kalan, Ammie K., additional, McCarthy, Maureen S., additional, Bocksberger, Gaëlle, additional, White, Lauren C., additional, Vigilant, Linda, additional, Dieguez, Paula, additional, Abdulai, Barrie, additional, Aebischer, Thierry, additional, Agbor, Anthony, additional, Assumang, Alfred Kwabena, additional, Bailey, Emma, additional, Bessone, Mattia, additional, Buys, Bartelijntje, additional, Carvalho, Joana Silva, additional, Chancellor, Rebecca, additional, Cohen, Heather, additional, Danquah, Emmanuel, additional, Deschner, Tobias, additional, Dongmo, Zacharie Nzooh, additional, Doumbé, Osiris A., additional, Dupain, Jef, additional, Duvall, Chris S., additional, Eno-Nku, Manasseh, additional, Etoga, Gilles, additional, Galat-Luong, Anh, additional, Garriga, Rosa, additional, Gatti, Sylvain, additional, Ghiurghi, Andrea, additional, Goedmakers, Annemarie, additional, Granjon, Anne-Céline, additional, Hakizimana, Dismas, additional, Haydar, Nadia, additional, Head, Josephine, additional, Hedwig, Daniela, additional, Herbinger, Ilka, additional, Hermans, Veerle, additional, Jones, Sorrel, additional, Junker, Jessica, additional, Kadam, Parag, additional, Kambi, Mohamed, additional, Kienast, Ivonne, additional, Kouakou, Célestin Yao, additional, N’Goran, Kouamé Paul, additional, Langergraber, Kevin E., additional, Lapuente, Juan, additional, Laudisoit, Anne, additional, Lee, Kevin C., additional, Maisels, Fiona, additional, Moore, Deborah, additional, Morgan, Bethan, additional, Morgan, David, additional, Neil, Emily, additional, Nicholl, Sonia, additional, Nkembi, Louis, additional, Ntongho, Anne, additional, Orbell, Christopher, additional, Ormsby, Lucy Jayne, additional, Pacheco, Liliana, additional, Piel, Alex K., additional, Pintea, Lilian, additional, Plumptre, Andrew J., additional, Rundus, Aaron, additional, Sanz, Crickette, additional, Sommer, Volker, additional, Sop, Tenekwetche, additional, Stewart, Fiona A., additional, Sunderland-Groves, Jacqueline, additional, Tagg, Nikki, additional, Todd, Angelique, additional, Ton, Els, additional, Schijndel, Joost van, additional, VanLeeuwe, Hilde, additional, Vendras, Elleni, additional, Welsh, Adam, additional, Wenceslau, José Francisco Carminatti, additional, Wessling, Erin G., additional, Willie, Jacob, additional, Wittig, Roman M., additional, Yoshihiro, Nakashima, additional, Yuh, Yisa Ginath, additional, Yurkiw, Kyle, additional, Boesch, Christophe, additional, Arandjelovic, Mimi, additional, and Kühl, Hjalmar, additional

Published
2020
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49. Human impact erodes chimpanzee behavioral diversity

Author

Kuhl, Hjalmar S, Boesch, Christophe, Kulik, Lars, Haas, Fabian, Arandjelovic, Mimi, Dieguez, Paula, Bocksberger, Gaëlle, McElreath, Mary Brooke, Agbor, Anthony, Angedakin, Samuel, Ayimisin, Emmanuel Ayuk, Bailey, Emma, Barubiyo, Donatienne, Jeffery, Kathryn J, and Morgan, Bethan

Abstract

Chimpanzees possess a large number of behavioral and cultural traits among non-human species. The ‘disturbance hypothesis’ predicts that human impact depletes resources and disrupts social learning processes necessary for behavioral and cultural transmission. We used an unprecedented data set of 144 chimpanzee communities, with information on 31 behaviors, to show that chimpanzees inhabiting areas with high human impact have a mean probability of occurrence reduced by 88%, across all behaviors, compared to low impact areas. This behavioral diversity loss was evident irrespective of the grouping or categorization of behaviors. Therefore, human impact may not only be associated with the loss of populations and genetic diversity, but also affects how animals behave. Our results support the view that ‘culturally significant units’ should be integrated into wildlife conservation.

Published
2019

50. A roadmap for high-throughput sequencing studies of wild animal populations using noninvasive samples and hybridization capture

Author

White, Lauren C., Fontsere, Claudia, Lizano, Esther, Hughes, David A., Angedakin, Samuel, Arandjelovic, Mimi, Granjon, Anne‐Céline, Hans, Jörg B., Lester, Jack D., Rabanus-Wallace, M. Timothy, Rowney, Carolyn, Städele, Veronika, Marqués-Bonet, Tomàs, Langergraber, Kevin E., Vigilant, Linda, Agencia Estatal de Investigación (España), Max Planck Society, Ministerio de Ciencia, Innovación y Universidades (España), European Commission, Howard Hughes Medical Institute, Fundación 'la Caixa', Generalitat de Catalunya, and La Caixa

Subjects
0106 biological sciences, 0301 basic medicine, Pan troglodytes, Animals, Wild, Sample (statistics), Computational biology, Biology, 010603 evolutionary biology, 01 natural sciences, Target enrichment, DNA sequencing, Population genomics, Feces, 03 medical and health sciences, Exome capture, Genetics, Animals, Chimpanzees, Exome, Ecology, Evolution, Behavior and Systematics, Hybridization capture, High-Throughput Nucleotide Sequencing, Nucleic Acid Hybridization, DNA, Sample quality, Genetics, Population, 030104 developmental biology, Faecal samples, Conservation genomics, Biotechnology
Abstract

Large-scale genomic studies of wild animal populations are often limited by access to high-quality DNA. Although noninvasive samples, such as faeces, can be readily collected, DNA from the sample producers is usually present in low quantities, fragmented, and contaminated by microorganism and dietary DNAs. Hybridization capture can help to overcome these impediments by increasing the proportion of subject DNA prior to high-throughput sequencing. Here we evaluate a key design variable for hybridization capture, the number of rounds of capture, by testing whether one or two rounds are most appropriate, given varying sample quality (as measured by the ratios of subject to total DNA). We used a set of 1,780 quality-assessed wild chimpanzee (Pan troglodytes schweinfurthii) faecal samples and chose 110 samples of varying quality for exome capture and sequencing. We used multiple regression to assess the effects of the ratio of subject to total DNA (sample quality), rounds of capture and sequencing effort on the number of unique exome reads sequenced. We not only show that one round of capture is preferable when the proportion of subject DNA in a sample is above ~2%–3%, but also explore various types of bias introduced by capture, and develop a model that predicts the sequencing effort necessary for a desired data yield from samples of a given quality. Thus, our results provide a useful guide and pave a methodological way forward for researchers wishing to plan similar hybridization capture studies., Funding was provided by the Max Planck Society and the President's Strategic Initiative Fund of ASU. T.M.B. is supported by BFU2017‐86471‐P (MINECO/FEDER, UE), U01 MH106874 grant, Howard Hughes International Early Career, Obra Social “La Caixa” and Secretaria d'Universitats i Recerca and CERCA Programme del Departament d'Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 880) and C.F. is supported by a La Caixa PhD Fellowship.

Published
2019

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