**1. Introduction**

Phylogeny refers to the evolutionary history of a taxonomic group of organisms. Phylogeny is essential in understanding the biodiversity, genetics, evolution, and ecology among groups of organisms [1, 2]. Functional morphology involves the study of the relationships between the structure of an organism and the function of the various parts of an organism. The old adage "form follows function" is a guiding principle of functional morphology. It helps in understanding the ways in which body structures can be used to produce a wide variety of different behaviors, including moving, feeding, fighting, and reproducing. It thus, integrates concepts from physiology, evolution, anatomy and development, and synthesizes the diverse ways that biological and physical factors interact in the lives of organisms [3].

The order Diptera includes all true flies. These insects are distinctive because their hind wings are modified into small, club-shaped structures called halters. Diptera flies are the most ecologically diverse group of insects, and probably have a greater economic impact on humans than any other group of insects [4, 5]. Several families of Diptera are involved in the transmission of disease pathogens to humans and other animals. Biting flies cause annoyance that impacts negatively on tourism, recreation, land development, and industrial productivity. Some flies are pests of agricultural plants especially those that infest fruit crops in the field. On the other hand, many flies are beneficial; particularly those that pollinate flowering plants, assist in the decomposition of organic matter, or serve as biocontrol agents of insect pests [6].

Diptera is one of the most species-rich, anatomically varied and ecologically innovative orders of insects, making up 10–15% of known animal species. An estimated 195,000 species of Diptera have been described [7, 8], however, the actual total number of extant fly species is many times that number. The living dipteran species have been classified into about 17,000 genera, 190 families, 28–39 superfamilies and 12–15 infraorders, and around 3100 fossil species have been described [9]. The monophyly of Diptera is well established with a number of complex morphological modifications recognized as synapomorphies, including the transformation of the hindwings into halteres, and the development of the mouthpart elements for sponging liquids.

Recent research into the phylogeny of Diptera has been characterized by more sophisticated and consistent methods of analyzing traditional phylogenetic and morphological characters [10], and the inclusion of ever larger volumes of molecular sequence data. The greatest advances in dipteran phylogenetics over the past few decades have been made by a relatively small number of authors attempting to synthesize phylogenetic data across large components of it, by the use of quantitative methods. A clearer understanding of the bioecological processes of Diptera would necessitate a more robust estimate of their phylogenetics and functional morphology, which will serve as an organizing framework for fly classification and nomenclature and as the context for understanding the pattern of evolutionary change, tracing the origin of morphological and ecological adaptations, and documenting diversification itself. In this chapter, the current status of Diptera phylogenetics and functional morphology is reviewed with emphasis on newer contributions and progress in understanding these group of insects [11].
