Felipe E. Silva

Adaptive potential in Amazonian primates: connecting genomics, climate change, and adaptive evolution


In this project, I will integrate genomics and ecological niche modelling to investigate how the paleoclimatic changes in the Amazon Rainforest influenced the evolutionary history of primates. I will investigate the demographic history, genetic diversity, and adaptive evolution of uakari monkeys, genus Cacajao. Uakaris are considered as flagship species for conservation in the Amazon Rainforest being a successful case where the conservation efforts directed to one species also promoted the conservation of other species, and their habitats (see, for example, https://www.mamiraua.org/). They have their geographic distribution influenced by the flooded forest of western Amazonia and may be sensitive to climate change. Therefore, understanding how the paleoclimatic changes in the Amazon Rainforest influenced the evolutionary history of uakaris will also allow us to understand how adapted they are to the anthropogenic climate change in future scenarios.


I am a primatologist interested in the ecology, evolution, and conservation of Neotropical primates. I am a licentiate in Biological Sciences (2005), I have an MSc degree in Zoology (2008), and a PhD in Evolutionary Biology (2020). I started my research with Neotropical primates in 2003, and since 2012, I have investigated primate ecology, diversity, evolution, and conservation in the Amazon rainforest. In my research projects, I organized field trips to remote areas of the Brazilian Amazon. I have expertise in researching flagship species for conservation (for example, uakari monkeys, genus Cacajao). I have integrated my field experience with ecological niche modelling and genomics data analysis.

During my PhD in Evolutionary Biology and Conservation at the University of Salford, UK (awarded on July 31, 2020), I collected new information on the occurrence and distribution of uakaris (genus Cacajao) throughout the Amazon, and I used molecular analyses to investigate their genetic diversity, and ecological analyses to reassess their conservation status. In particular, I used the reduced representation of the genome (ddRADseq) to investigate their diversity and phylogenetic relationship; and geographic information system (GIS) and ecological niche modelling techniques to predict the synergistic effects of deforestation and climate change in the habitat of uakaris in the future. Based on that, I developed a research and conservation framework for bald-headed uakaris that may be a baseline for its long-term conservation. I am an IUCN Red List assessor for several Amazonian primate species.

In March 2020, I started a research project on the ecology, evolution, and conservation of uakari monkeys in the Research Group on Primate Biology and Conservation at Mamirauá Institute for Sustainable Development (https://www.mamiraua.org/). Mamirauá Institute is a social organisation supported mainly by the Ministry of Science, Technology and Innovation. It has integrated research and management of natural resources to improve the social and environmental conditions in protected areas in the middle of the Solimões River.


Publications (Credit Authorship Role Taxonomy)

26 papers published, two in press, and one under revision. Eight papers as 1st author, five as 2nd author, and one as senior

In press/Under Review

29. Rashid, S., Kuderna LFK, Cox AJ, Ulirsch JC, Gao H, Aguet F, Christmas MJ, Janiak MC, Kuhlwilm M, Orkin JD, Manu S, Valenzuela A, Bergman J, Rouselle M, SILVA FE et al. (under revision) Identification of conserved sequence elements across 230 primate genomes with deep learning. Science (Investigation, Validation, Writing – review & editing).

28. Gao H, Hamp T, Ede J, Schraiber JG, McRae J, Singer-Berk M, Yang Y, Dietrich A, Fiziev P, Kuderna L, Sundaram L, Wu Y, Adhikari A, Field Y, Chen S, Batzoglou S, Aguet F, Lemire G, Reimers R, Balick D, Janiak MC, Kuhlwilm M, Orkin JD, Manu S, Valenzuela A, Bergman J, Rouselle M, SILVA FE et al. (In press). The landscape of tolerated genetic variation in humans and primates. Science (Investigation, Validation, Writing – review & editing).

27. Kuderna LFK, Gao G, Janiak MC, Kuhlwilm M, Orkin JD, Manu S, Valenzuela A, Bergman J, Rouselle M, Silva FE et al. (In press). A global catalog of whole-genome diversity from 233 primate species. Science (Investigation, Validation, Writing – review & editing).



26. SILVA FE, Pacca L, Lemos L, Gusmão A, da Silva O, Dalponte JC, Franco CLB, Santana MI, Buss G, El Bizri H (2022). Using habitat loss predictive models and population surveys to re-assess the conservation status of an Amazonian titi monkey (Plecturocebus bernhardi) in a deforestation hotspot. Oryx 56 (6): 846–853 (Conceptualization, Formal Analysis, Funding Acquisition, Investigation, Methodology, Validation, Writing). https://doi.org/10.1017/S0030605322000655

25. Janiak MC, SILVA FE, Beck RMD, Vries D, Kuderna LFK, Torosin NS, Melin AD, Marquès-Bonet T, Goodhead IB, Messias M, da Silva MNF, Sampaio I, Farias IP, Rossi R, Melo FR, Valsecchi J, Hrbek T, Boubli JP (2022). 205 newly-assembled mitogenomes from the speciose Amazonian primates provide mixed evidence for rivers as drivers of speciation. Molecular Ecology 31(14): 3888–3902 (Funding Acquisition, Investigation, Methodology, Validation, Writing). https://doi.org/10.1111/mec.16554

24. SILVA FE, Valsecchi J, Roos C, Bowler M, Röhe F, Sampaio R, Janiak MC, Bertuol F, Santana MI, Silva Jr JS, Rylands AB, Gubili C, Hrbek T, McDevitt AD, Boubli J. (2022). Molecular phylogeny and systematics of bald uakaris genus Cacajao (Lesson, 1840), with the description of a new species. Molecular Phylogenetics and Evolution 173: 107509 (Conceptualization, Formal Analysis, Funding Acquisition, Investigation, Methodology, Validation, Writing). https://doi.org/10.1016/j.ympev.2022.107509

23. Vieira KRA, Weber HA, de Sant’Ana FJF, Blume GR, SILVA FE,  Santana MIS (2022) Male genital organs of the black-crowned dwarf marmoset (Callibella humilis). Anatomia, Histologia, Embryologia, 00:1–9. (Funding Acquisition, Investigation, Validation, Writing).https://doi.org/10.1111/ahe.12866

22. Boubli JP, Janiak MC, Porter LM, de la Torre S, Cortés-Ortiz L, Da Silva MNF, Rylands AB, Nash S, Bertuol F, Byrne H, SILVA FE et al. (2021). Ancient DNA of the pygmy marmoset type specimen Cebuella pygmaea (Spix, 1823) resolves a taxonomic conundrum. Zoological Research 42(6): 761–771 (Investigation, Validation, Writing).

21. SILVA FE, Lemos LP, Ravetta AL, Röhe F, Sampaio R, Franco CLP, Santos PMRS, Santana MI, Valsecchi JA, Endo W, Haugaasen T, Peres CA, Boubli JP (2021). On the geographic distribution of the bald uakaris (Cacajao calvus ssp.) in Brazilian Amazonia. Primate Conservation 35: 66–83 (Conceptualization, Formal Analysis, Funding Acquisition, Investigation, Methodology, Validation, Writing).

20. Costa-Araújo R, Silva-Jr JS, Boubli JP, Rossi RV, Canale GR, Melo FR, Bertuol F, SILVA FE et al. (2021). An integrative analysis uncovers a new, pseudo-cryptic species of Amazonian marmoset (Primates: Callitrichidae: Mico) from the arc of deforestation. Scientific Reports 11: 15665 (Validation, Writing).

19. Lebrão C, Rosa LMV, Paim FP, Nassar PM, SILVA FE (2021). Community-based tourism as a window for primate conservation in Mamirauá Sustainable Development Reserve, Amazon Rainforest, Brazil. International Journal of Primatology 42(4): 523-527 (Formal Analysis, Investigation, Methodology, Validation, Writing)

18. Costa-Araújo R, de Melo FR, Canale GR, Hernández-Rangel SM, Messias MR, Rossi RV, SILVA FE et al. (2020). The Munduruku marmoset: a new monkey species from southern Amazonia. PeerJ 7:e7019 (Validation, Investigation, Writing).

17. Rabelo RM, Gonçalves JR, SILVA FE et al. (2020). Predicted distribution and habitat loss for the endangered black-faced black spider monkey (Ateles chamek) in the Amazon. Oryx 54: 699–705 (Conceptualization, Investigation, Methodology, Validation, Writing – review & editing).

16. SILVA FE, El Bizri H, Gonçalves J, Lemos L, Costa-Araújo R, Lima I, Santos AT, Santana MI, Franco CLB, Boubli J (2020). The Roosevelt–Rondon expedition marmoset (Mico marcai): unveiling the conservation status of a data deficient species. Oryx 54:539–545 (Conceptualization, Formal Analysis, Funding Acquisition, Investigation, Methodology, Validation, Writing).

15. Boubli JP, Byrne H, da Silva MNF, Silva-Júnior JS, Costa-Araújo R, Bertuol F, Gonçalves J, Melo F, Rylands AB, Mittermeier RA, SILVA FE et al. (2019). On a new species of titi monkey (Primates: Plecturocebus Byrne et al., 2016), from Alta Floresta, southern Amazon, Brazil. Molecular Phylogenetics and Evolution 132: 117–137 (Methodology, Validation, Writing).

14. SILVA FE et al. (2018). In search of a meaningful classification for Amazonian marmosets: should dwarf marmosets be considered Mico congenerics? Zoologica Scripta 47: 133–143 (Conceptualization, Formal Analysis, Funding Acquisition, Writing).

13. Lemos LP; el Bizri HR; Amaral JV; Santos AS; Koga DM; SILVA FE (2018). Vertebrate hunting in the Serra do Divisor National Park, Acre, Brazil. Biodiversidade Brasileira 8(1): 69–88 (Conceptualization, Formal Analysis, Funding Acquisition, Investigation, Methodology, Validation, Writing).

12. Boubli JP; da Silva MNF; Rylands AB; Nash SD; Bertuol F; Nunes M; Mittermeier RA; Byrne H; SILVA FE et al. (2018). How many pygmy marmosets (Cebuella Gray 1870) species are there? A taxonomic re-appraisal based on new molecular evidence. Molecular Phylogenetics and Evolution 120:170–182, 2018 (Methodology, Validation, Investigation, Writing).

11. Siqueira GHL; SILVA FE; Santana MIS (2018). Morphological description of male genital organs of Marca's marmoset (Mico marcai). Anatomia Histologia Embryologia 47: 372–384 (Conceptualization, Funding Acquisition, Investigation, Validation, Writing).

10. SILVA FE, Endo W, Silva Jr JS, Santos Jr MA (2018). New insights into the distribution and conservation status of the golden–white tassel–ear marmoset Mico chrysoleucos (Primates Callitrichidae). Primates 59: 347–353 (Conceptualization, Funding Acquisition, Investigation, Methodology, Validation, Writing).

09. Marsh LK; Duarte A; Gomez JPB; Selby C; da Silva IB; Whitaker S; Lemos LP; SILVA FE; Santana MIS (2017). Missing monkey found: Vanzolini's bald–faced saki monkey. Pithecia vanzolinii, Oryx 51: 584–585 (Conceptualization, Methodology, Investigation, Validation).

08. Cortés–Ortiz L; Agostini I; Aguiar LM; Kelaita M; SILVA FE; Bicca–Marques JC. (2015). Hybridization in howler monkeys: current understanding and future directions.in: Kowalewski MM; Garber PA; Cortés–Ortiz L; Urbani B; Youlatos D (Org) Howler Monkeys 1st ed New York: Springer New York, p.107–131 (Methodology, Investigation, Validation, Writing).

07. Boyle SA; Thompson CL; Deluycker A; Alvarez SJ; Alvim THG; Aquino R; Bezerra BM; Boubli JP; Bowler M; Caselli CB; Chagas RRD; Ferrari SF; Fontes IP; Gregory T; Haugaasen T; Heiduck S; Hores R; Lehman S; de Melo FR; Moreira LS; Moura VS; Nagy-Reis MB; Palacios E; Palminteri S; Peres CA; Pinto L; Port-Carvalho M; Rodríguez A; dos Santos RR; Setz EZF; Shaffer CA; SILVA FE et al. (2015). Geographic comparison of plant genera used in frugivory among the pitheciids. American Journal of Primatology 78: 493–506 (Methodology, Investigation, Validation).

06. Rabelo RM; SILVA FE, Vieira T, Ferreira-Ferreira J, Paim FP, Dutra W, de Souza e Silva Júnior J, Valsecchi J et al. (2014). Extension of the geographic range of Ateles chamek (Primates Atelidae): evidence of river-barrier crossing by an Amazonian primate. Primates 55: 167–171 (Conceptualization, Funding Acquisition, Investigation, Methodology, Validation, Writing).

05. Dalponte JC; SILVA FE; Silva JR JS (2014). New species of titi monkey genus Callicebus Thomas 1903 (Primates Pitheciidae) from Southern Amazonia Brazil. Papéis Avulsos de Zoologia 54:457–472 (Conceptualization, Funding Acquisition, Investigation, Methodology, Validation, Writing).

04. Garbino GST; SILVA FE; Davis BJW (2013). Range extension of the vulnerable dwarf marmoset Callibella humilis (Roosmalen et al. 1998) and first analysis of its long call structure Primates 35: 529–546 (Funding Acquisition, Investigation Validation, Writing).

03. SILVA FE, Nunes HGL, Bastos A (2013). Rediscovery of Marca's marmoset and the challenges for its conservation. Oryx 47: 327 (Conceptualization, Formal Analysis, Funding Acquisition, Investigation, Methodology, Validation, Writing).

02. Monteiro FOB; Kugelmeier T; do Valle RR; Lima AB; SILVA FE. et al. (2013). Evaluation of the fecal steroid concentrations in Alouatta belzebul (Primates Atelidae) in the National Forest of Tapirape-Aquiri in Pará Brazil. Journal of Medical Primatology 42: 325–332 (Formal Analysis, Investigation, Methodology, Validation, Writing).

01. SILVA FE; Bicca–Marques JC. (2013). Do patch size and interpatch distance influence the distribution of brown howler monkeys (Alouatta guariba clamitans) in a fragmented landscape in south Brazil? In: Marsh LK; Chapman CA (Org) Primates in Fragments 1st ed New York: Springer New York v2, p.137–145 (Conceptualization, Formal Analysis, Funding Acquisition, Investigation, Methodology, Validation, Writing)