Studies on the population genetics, phylogenetic relationships, systematics and evolution of arthropods that inhabit necrotic tissue of cacti in the Sonoran Desert of North America are reviewed. These studies have focused upon several species of insects (orders Diptera and Coleoptera) and arachnids (order Pseudoscorpiones). For most taxa studied, little genetic structure and high dispersal ability are found in populations inhabiting the mainland and Baja California peninsula regions of the Sonoran Desert, consistent with the availability of the rotting cactus microhabitat which is patchily distributed and ephemeral. There is evidence, however, that the Gulf of California, which bisects the Sonoran Desert, has played a role in limiting gene flow and promoting speciation in several taxa, including histerid beetles, whereas other taxa, especially Drosophila nigrospiracula and D. mettleri, apparently are able to freely cross the Gulf, probably by taking advantage of the Midriff Islands in the northern Gulf as dispersal “stepping stones”. Genetic evidence has also been found for historical population expansions dating to the Pleistocene and late Pliocene in several taxa. Overall, these studies have provided important insights into how arthropods with different life history traits, but generally restricted to a necrotic cactus microhabitat, have evolved in an environmentally harsh and tectonically active region. In addition, they suggest some taxa for further, and more detailed, hypothesis driven studies of speciation.

DNA barcoding has resulted in the ‘discovery’ of a vast number of new species and subspecies. Assigning formal scientific names to these taxa remains a major challenge. Names sometimes are newly designated. Alternatively, available valid names can be resurrected from synonymy, based on barcode analyses together with classical taxonomic characters. For the most part, however, new putative species revealed by barcoding studies go undescribed. This situation is most often attributed to insufficient taxonomic expertise with the authors conducting the study, together with a critical lack of formally trained taxonomists. However, even with formal training, and additional supportive data from morphological, ecological or life history characters, other factors can arise that impede new species descriptions. In the present paper, several specific taxonomic challenges that have arisen from barcode analyses in two groups of skipper butterflies (Lepidoptera: Hesperiidae), the Sootywings (Pholisora catullus and P. mejicanus) and the Coyote Cloudywing (Achalarus toxeus) are highlighted and discussed. Both P. catullus and A. toxeus show relatively large intraspecific genetic divergences of barcodes (2–3%) which suggests the possibility of previously unrecognized cryptic speciation within each group. Some of the challenges to providing formal names and clarifying taxonomic status of these cryptic taxa could be largely overcome by (1) barcoding type specimens, (2) clarifying imprecise and often vague or suspect type localities, and (3) by conducting in-depth comparative studies on genitalic morphology.

The population genetics and phylogenetic relationships of Culex mosquitoes inhabiting the Sonoran Desert region of North America were studied using mitochondrial DNA and microsatellite molecular markers. Phylogenetic analyses of mitochondrial cytochrome c oxidase subunit I (COI) from mosquitoes collected over a wide geographic area, including the Baja California peninsula, and mainland localities in southern Arizona, USA and Sonora, Mexico, showed several well‐supported partitions corresponding to Cx. quinquefasciatus, Cx. tarsalis, and two unidentified species, Culex sp. 1 and sp. 2. Culex quinquefasciatus was found at all localities and was the most abundant species collected. Culex tarsalis was collected only at Tucson, Arizona and Guaymas, Sonora. The two unidentified species of Culex were most abundant at Navojoa in southern Sonora. Haplotype and nucleotide diversities in the COI gene segment were substantially lower in Cx. quinquefasciatus compared with the other three species. Analysis of molecular variance revealed little structure among seven populations of Cx. quinquefasciatus, whereas significant structure was found between the two populations of Cx. tarsalis. Evidence for an historical population expansion beginning in the Pleistocene was found for Cx. tarsalis. Possible explanations for the large differences in genetic diversity between Cx. quinquefasciatus and the other species of Culex are presented.

A number of insect species undergo annual and strikingly long-distance migrations. While the census sizes appear to be very large in many of these species, our understanding of their population genetics and interpopulation connectivity remains elusive. Here, we summarize the utility and limitations of mitochondrial DNA barcodes to assess migratory patterns and genetic connectivity among populations of four well-known species of long-distance, multigenerational insect migrants, the butterflies Danaus plexippus and Vanessa cardui, and the dragonflies Pantala flavescens and Anax junius. We contrast the differences between the two butterfly species, which show low genetic diversity and little or no phylogeographic structuring, with the two dragonfly species which show an intriguing pattern of high genetic diversity and no apparent phylogeographic structure. Although a recent population genetic study of P. flavescens reported high gene flow and reduced (or diminished) COI genetic diversity across widely separated geographic regions, suggesting global panmixia, reanalysis of the data from that study revealed high genetic diversity in agreement with other studies on both P. flavescens and A. junius. The presence of isolated populations of P. flavescens, such as found on Easter Island that appear non-migratory, as well as evidence for significant structure among some migratory populations, suggest that concluding global panmixia in P. flavescens may be premature. We also suggest that cost-effective barcode analyses would be the method of choice for preliminary analyses of large data sets required to assess migratory routes and connectivity among populations on a global scale.

Nucleotide sequence data from a segment of the mitochondrial cytochrome c oxidase subunit I (COI) gene, known as the barcode segment, were used to examine phylogenetic relationships and systematics of buckeye butterflies (Nymphalidae: Nymphalinae: Junonia) from the New World, with emphasis on taxa from western North America. Three nominal species have been recognized for North America, J. evarete (Cramer), J. genoveva (Cramer), and J. coenia Hübner, with additional species recently proposed for the West Indies and northern South America. The distinctive Andean buckeye, J. vestina C. Felder & R. Felder, along with J. evarete and J. genoveva, are also components of the South American fauna. With the exception of J. vestina, butterflies comprising the New World Junonia have had a confused taxonomic history, and species assignments are often problematic. Our results show that the barcode segment resolves the two major clades of New World Junonia, referred to here as clades A and B, with similar high support seen in an earlier phylogenetic study using both mitochondrial and nuclear genes. Within clade A, J. vestina resolved in a basal position to J. evarete from South America and the Caribbean. The data further suggest that species assignments in some populations of New World Junonia clustering in clade B (J. coenia + J. genoveva) need to be reevaluated. DNA barcodes, although failing to resolve all recognized species and subspecies level taxa of New World Junonia, probably owing to relatively recent divergences, can provide valuable tools for identifying the two major lineages, and when used in conjunction with morphological, ecological, behavioral and life history information can provide insights into the taxonomy and evolution of this difficult group.