INVITED ARTICLE Practical and Theoretical Considerations for Choice of a DNA Sequence Region in Insect Molecular Systematics, with a Short Review of Published Studies Using Nuclear Gene Regions ANDREW V. Z. BROWER AND ROB DESALLE Department of Entomology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10029-5192 Ann. Entomol. Soc. Am. 87(6): 702-716 (1994) ABSTRACT Simon et al. (Simon, C, F. Frati, A. Beckenbach, B. Crespi, H. Liu & P. Flook. 1994. Evolution, weighting, and phylogenetic utility of mitochondrial gene se- quences and a compilation of conserved polymerase chain reaction primers. Ann. Entomol. Soc. Am. 87: 651—701) examined the dynamics of sequence evolution in mitochondrial DNA with respect to choice of a gene region of the molecule as a source of characters for systematics. Here, we present a brief companion discussion of nuclear genes that are potentially useful for phylogenetic studies in arthropods. Although we are in agreement with most of the Simon et al. discussion on levels of variation and phylogenetic utility of the various available classes of genes, we supplement their discussion of sequence align- ment and character weighting and congruence versus combination of data with our own views on these matters, as they pertain to both nuclear and mitochondrial genes. We also offer some guidelines on nuclear primer design and methods for exploring less well-known parts of the genome. KEY WORDS DNA sequence, molecular systematics, sieving AS POLYMERASE CHAIN REACTION (PCR)-based DNA sequencing for molecular systematics has gained widespread popularity, the variety of gene regions potentially available for study has increased dramatically. Nevertheless, most sys- tematic research has focused on a small subset of genes, especially the 18S nuclear ribosomal RNA (rRNA) gene and mitochondrial rRNA and pro- tein-encoding genes. The reasons for this narrow focus are largely historical and practical. These sequences were the first ones available. In the case of the rRNA genes, this was because RNA sequencing became feasible before DNA se- quencing was easily accomplished and, in the case of mitochondrial DNA (mtDNA), because it occurs in multiple copies per cell and is rela- tively easy to manipulate without recombinant DNA technology. Studies of both via restriction fragment length polymorphisms were popular before the development of Taq polymerase in 1983 (Mullis & Faloona 1987). Because amplification of a specific gene region by means of the PCR depends on a priori knowl- edge of the sequence's end points (for oligonu- cleotide primer attachment), it has been far sim- pler and cheaper to employ known sequence regions to initiate new molecular systematic studies, than to start from scratch by cloning and searching for appropriate target regions at ran- dom. The existence of universal primers con- served among a wide variety of taxa has enabled neophyte researchers to engage in mass sequenc- ing with almost no investment in exploratory se- quencing from cloned libraries or custom primer design. When the goal of a DNA-sequencing study is to understand relationships among taxa better, the choice of a particular piece of DNA matters little, save that its evolutionary history should represent a reasonable apeproximation of the history of the taxa among which relationships are in question. Because time and money are limiting resources, it is eminently sensible to proceed with a proven system, rather than en- deavoring to prove a new one. Of course, it is essential to submit new sequences to an elec- tronic database (e.g., GENBANK [Bilofsky & Burks 1988]) as quickly as possible, to make them available to others for comparative study. Once a gene is established as a paradigm for study at a particular taxonomic level or within a particular group, its popularity tends to snow- ball, not only because it is easy to use for the reasons discussed above, but also because of the accessibility of published and online sequences for use as out-groups or components of more in- clusive analyses. The most familiar examples of this phenomenon are mammalian mitochondrial cytochrome b genes (e.g., Zhang & Ryder 1993; 0013-8746/94/0702-0716$02.00/0 © 1994 Entomological Society of America Downloaded from https://academic.oup.com/aesa/article/87/6/702/19324 by guest on 02 April 2022