One of the major aims of contemporary evolutionary biology is the understanding of the current pattern of biological diversity. This involves, first, the description of character distribution at various nodes of the phylogenetic tree of life and, second, the functional explanation of such changes. The analysis of character distribution is a powerful tool at both the morphological and molecular levels. Recent high-throughput sequencing approaches provide new opportunities to study the genetic architecture of organisms at the genome-wide level. In eukaryotes, one overarching finding is the absence of simple correlations of gene count and biological complexity. Instead, the domain architecture of proteins is becoming a central focus for large-scale evolutionary innovations. Here, we review examples of the evolution of novelty in conserved gene families in insects and nematodes. We highlight how in the absence of whole-genome duplications molecular novelty can arise, how members of gene families have diversified at distinct mechanistic levels, and how gene expression can be maintained in the context of multiple innovations in regulatory mechanisms. 1. Introduction To understand evolutionary novelty and its contribution to the generation of new species, biologists search for character differences between closely related species and try to determine the functional meaning of such changes. Characters range from morphological traits, like the trichome pattern on the cuticle of a fruit fly larva, to molecular characters such as nucleotide sequences. The genomics era is now providing an increasing number and also new kinds of molecular characters, such as gene numbers in multigenic families, gene position on chromosomes, microRNAs, or insertions of mobile elements at various places in a genome. In addition, next-generation sequencing approaches provide genome-wide single-nucleotide polymorphism (SNP) and copy number variation (CNV) data in a number of model organisms [1]. Nonetheless, it remains challenging to articulate knowledge concerning all these characters in a comprehensive functional framework. While there are some cases with a direct link between various levels of character changes, such as the small number of single-nucleotide mutations in a transcriptional enhancer that can modify the trichome pattern on the larval cuticle in Drosophila sechellia [2], there are many other cases where great variation at the molecular level has no simply interpretable effect at the level of the organism. Although this does not mean that such changes are necessarily
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