phaidra.vetmeduni.ac.at o:5132 DOI 10.1186/s13059-025-03868-0 Unraveling genome- and immunome-wide genetic diversity in modern and historical Jaguars Background The jaguar (Panthera onca) is a keystone species within diverse ecosystems ranging from dense rainforests to open grasslands across Central and South America. However, its populations are declining rapidly due to anthropogenic actions, such as deforestation and poaching. Here we investigate the effects of this decline on genetic diversity and genetic health. Utilizing both modern and historical museum samples, we infer population structure and immunome variability in 25 jaguars to identify unique genetic diversity that can inform targeted conservation efforts. Results Our genome-wide analyses identifies three distinct geographic populations: Central America, South American lowlands, and South American highlands. Modern samples that exhibit lower levels of heterozygosity also show higher levels of inbreeding. The South American lowland population shows the lowest levels of inbreeding, while the highland population exhibits the lowest overall immunome-wide variability. However, the innate (Natural Killer Cell Complex, Toll-Like Receptor) and adaptive (Major Histocompatibility Complex Class II) immune genes, which are crucial for adaptive responses and disease resilience, show high diversity in terms of heterozygosity and haplotype diversity in individuals of all three populations. Conclusions South American highland and Central American jaguars face significant threats from habitat loss and fragmentation. The observed genome- and immunome-wide diversity in historical and modern jaguars reflect their recent demographic decline and challenges of local adaptation. We recommend re-evaluating evolutionarily significant units to prioritize conservation strategies, ensuring the preservation of unique genetic and adaptive diversity crucial for the species’ resilience and long-term survival. eng Jaguar Conservation Genetic Diversity Population Structure Evolutionarily Significant Units Immune Response Genes NKC TLR MHC 2026-05-15T08:52:12.380Z LOMv1.0 Author BEGIN:VCARD VERSION:3.0 N:Meißner;René; FN:René Meißner X-ORCID:https://orcid.org/0000-0003-2829-1607 END:VCARD BEGIN:VCARD VERSION:3.0 N:Winter;Sven; FN:Sven Winter X-ORCID:https://orcid.org/0000-0002-1890-0977 END:VCARD BEGIN:VCARD VERSION:3.0 N:Elbers;Jean Pierre; FN:Jean Pierre Elbers END:VCARD BEGIN:VCARD VERSION:3.0 N:Plášil;Martin; FN:Martin Plášil END:VCARD BEGIN:VCARD VERSION:3.0 N:Futas;Ján; FN:Ján Futas END:VCARD BEGIN:VCARD VERSION:3.0 N:Mohandesan;Elmira; FN:Elmira Mohandesan END:VCARD BEGIN:VCARD VERSION:3.0 N:Sharif;Muhammad Bilal; FN:Muhammad Bilal Sharif END:VCARD BEGIN:VCARD VERSION:3.0 N:Horin;Petr; FN:Petr Horin END:VCARD BEGIN:VCARD VERSION:3.0 N:Prost;Stefan; FN:Stefan Prost END:VCARD BEGIN:VCARD VERSION:3.0 N:Burger;Pamela; FN:Pamela Burger X-ORCID:https://orcid.org/0000-0002-6941-0257 END:VCARD https://w3id.org/kim/hcrt/scheme https://w3id.org/kim/hcrt/text Textdokument Text LOMv1.0 yes https://creativecommons.org/licenses/by/4.0 application/pdf 3203198 https://phaidra.vetmeduni.ac.at/o:5132 https://phaidra.vetmeduni.ac.at/api/object/o:5132/thumbnail LOMv1.0 discipline