Phylogenomic Evolution of Trans-Atlantic Dispersal, Ecosystem Function, and Coalescent Population Dynamics Across African and Neotropical Primates (Anthropoidea: Platyrrhini) Under FreeRate and Bayesian Skyline Models

32-chain RuNIE phylogenomic and functional selection analysis across 64 species and 16 loci (L = 23,924 aligned columns; African Catarrhini and Neotropical Pitheciidae, Atelidae, Cebidae, Callitrichidae, and Aotidae) coupled with 10,000-generation (20% burn-in) Bayesian coalescent skyline reconstructions across three independent PopSets (Alouatta spp., Sapajus/Cebus, and Callithrix/Saguinus/Leontopithecus) benchmarked against *MAFFT, *IQ-TREE/*LSD2, *PAML codeml, and *BEAST v1.10.4 The colonization of South America by African anthropoid primates during the Middle to Late Eocene and their subsequent diversification across Neotropical forest strata into five ecologically specialized families (Pitheciidae, Atelidae, Cebidae, Callitrichidae, and Aotidae) represent one of mammalogy's classic trans-oceanic adaptive radiations. Here we execute a 32-chain RuNIE phylogenomic and functional selection analysis across a 16-locus, 64-species primate supermatrix (L = 23,924 aligned columns with 10,254 parsimony-informative sites and 11,093 distinct site patterns) coupled with independent 10,000-generation (20% burn-in) Bayesian coalescent skyline reconstructions across three localized Neotropical population datasets benchmarking Native Rust against *MAFFT v7.526, *IQ-TREE v2.4.0 with *LSD2 v2.4.4, *PAML v4.10.10 codeml, and *BEAST v1.10.4. Our fossil-calibrated chronogram anchors Crown Primates at 74.0 Ma, the trans-Atlantic Simiiformes split between African Catarrhini (crown 28.5 Ma) and Neotropical Platyrrhini at 43.2 Ma (stem rafting window 43.2–24.2 Ma across the Eocene Atlantic), and Crown Platyrrhini at 24.2 Ma, followed by crown radiations of Pitheciidae (19.8 Ma), Atelidae (16.8 Ma), Cebidae (19.5 Ma), Callitrichidae (14.8 Ma), and Aotidae (11.4 Ma). Codon selection modeling (*PAML codeml) reveals strong purifying constraint on Pro8-oxytocin OXT/OXTR neuroendocrine signaling (omega = 0.4905), intermediate selective constraint on TAS2R bitter-taste receptors (omega = 0.7442) and ENAM/GHR dental and phyletic-dwarfism loci (omega = 0.8436), and diversifying and balancing selection on duplicated RNASE1/CHIA folivory-insectivory digestive enzymes (omega = 1.2118) and X-linked OPN1LW spectral-tuning opsin exons (omega = 2.4891). Across the three localized PopSet skyline cohorts, we resolve late Quaternary trans-Andean expansion and contemporary yellow fever epizootic pressure in howler monkeys (Alouatta, Ne = 628,056 to 977,186; *BEAST = 1,007,674), Pleistocene Cerrado/Caatinga dry-corridor colonization and stone-tool nut-cracking persistence in capuchins (Sapajus/Cebus, Ne = 1,042,598 to 1,376,278; *BEAST = 1,411,397), and Atlantic Forest fragmentation followed by metapopulation translocation recovery in callitrichid marmosets and tamarins (Callithrix/Saguinus/Leontopithecus, Ne = 469,859 to 912,085; *BEAST = 940,542), while demonstrating that Native Rust achieves a 29.9-fold end-to-end speedup (13.54 s vs. 404.82 s Hybrid and 3127.88 s full External UFBoot). Canonical Preprint URL: https://crvscience.com/labs/preprints/primate-africa-americas-radiation-preprint Master (Concept) Zenodo DOI: 10.5281/zenodo.24061361 Open-Source Software Repository (GNU GPL-3.0): https://github.com/bpwhite/crvscience-labs