Phylogenetic reconstructions are often plagued by difficulties in distinguishing phylogenetic signal (due to shared ancestry) from phylogenetic noise or homoplasy (due to character-state convergences or reversals). We use a new interpretive hypothesis, termed hemiplasy, to show how random lineage sorting might account for specific instances of seeming ''phylogenetic discordance'' among different chromosomal traits, or between karyotypic features and probable species phylogenies. We posit that hemiplasy is generally less likely for underdominant chromosomal polymorphisms (i.e., those with heterozygous disadvantage) than for neutral polymorphisms or especially for overdominant rearrangements (which should tend to be longer-lived), and we illustrate this concept by using examples from chiropterans and afrotherians. Chromosomal states are especially powerful in phylogenetic reconstructions because they offer strong signatures of common ancestry, but their evolutionary interpretations remain fully subject to the principles of cladistics and the potential complications of hemiplasy.cladistics ͉ gene trees ͉ lineage sorting ͉ phylogeny ͉ species trees I n phylogenetic analyses, systematists routinely strive to distinguish homology (trait similarity due to shared ancestry) from homoplasy (trait similarity arising from evolutionary convergence, parallelism, or character-state reversals). Homology can offer valid phylogenetic signal, whereas homoplasy is regarded as evolutionary noise that, if not properly accommodated, jeopardizes phylogenetic reconstructions. Homology itself has distinct components, as first emphasized by Hennig (1) in his insightful distinction between symplesiomorphies (traits showing sharedancestral homology) and synapomorphies (traits with sharedderived homology). From a Hennigian perspective, only valid synapomorphies properly earmark clades.The critical distinctions between homoplasy and homology and between different kinds of homology have served the field of systematics well. However, a difficulty arises when a sharedderived genetic trait that from mechanistic considerations should be homoplasy-free nonetheless recurs in two or more taxa that seem to be unrelated. For example, suppose that a derived chromosomal inversion with presumably unique (monophyletic) endpoint breaks is present in two or more species that belong to disparate clades. Under the traditional interpretive framework outlined above, this phylogenetic dilemma could only be resolved in either of two ways: by supposing that the inversion has evolved multiple times independently, notwithstanding mechanistic karyotypic arguments to the contrary; or by supposing that the shared trait does earmark a bona-fide organismal clade, notwithstanding independent phylogenetic evidence to the contrary.Here, we raise another potential explanation for this kind of phylogenetic enigma, and illustrate its application to karyotypic data involving chromosomal syntenies in mammals. Each synteny is a large conserved block of DNA, i.e., a linked assembla...