Generalized permutahedra are polytopes that arise in combinatorics, algebraic geometry, representation theory, topology, and optimization. They possess a rich combinatorial structure. Out of this structure we build a Hopf monoid in the category of species.

Species provide a unifying framework for organizing families of combinatorial objects. Many species carry a Hopf monoid structure and are related to generalized permutahedra by means of morphisms of Hopf monoids. This includes the species of graphs, matroids, posets, set partitions, linear graphs, hypergraphs, simplicial complexes, and building sets, among others. We employ this algebraic structure to define and study polynomial invariants of the various combinatorial structures.

We pay special attention to the antipode of each Hopf monoid. This map is central to the structure of a Hopf monoid, and it interacts well with its characters and polynomial invariants. It also carries information on the values of the invariants on negative integers. For our Hopf monoid of generalized permutahedra, we show that the antipode maps each polytope to the alternating sum of its faces. This fact has numerous combinatorial consequences.

We highlight some main applications:

We obtain uniform proofs of numerous old and new results about the Hopf algebraic and combinatorial structures of these families. In particular, we give optimal formulas for the antipode of graphs, posets, matroids, hypergraphs, and building sets. They are optimal in the sense that they provide explicit descriptions for the integers entering in the expansion of the antipode, after all coefficients have been collected and all cancellations have been taken into account.

We show that reciprocity theorems of Stanley and Billera–Jia–Reiner (BJR) on chromatic polynomials of graphs, order polynomials of posets, and BJR-polynomials of matroids are instances of one such result for generalized permutahedra.

We explain why the formulas for the multiplicative and compositional inverses of power series are governed by the face structure of permutahedra and associahedra, respectively, providing an answer to a question of Loday.

We answer a question of Humpert and Martin on certain invariants of graphs and another of Rota on a certain class of submodular functions.

We hope our work serves as a quick introduction to the theory of Hopf monoids in species, particularly to the reader interested in combinatorial applications. It may be supplemented with Marcelo Aguiar and Swapneel Mahajan’s 2010 and 2013 works, which provide longer accounts with a more algebraic focus.