Scherson, R. A. (Section of Evolution and Ecology, University of California, Davis, CA 95616, U.S.A.; rascherson@ucdavis.edu), H.-K. Choi (Department of Plant Pathology, University of California, Davis, CA 95616, U.S.A.; hchoi@ucdavis.edu), D. R. Cook (Department of Plant Pathology, University of California, Davis, CA 95616, U.S.A.; drcook@ucdavis.edu) & M. J. Sanderson (Section of Evolution and Ecology, University of California, Davis, CA 95616, U.S.A.; mjsanderson@ucdavis.edu). Phylogenetics of New World Astragalus: Screening of novel nuclear loci for the reconstruction of phylogenies at low taxonomic levels. Brittonia 57: 354–366. 2005.—This study explores methods to use information gathered from genomics technology to understand evolutionary relationships in the hyperdiverse legume group Neo-Astragalus. These species inhabit deserts and mountains of North and South America, and even though the monophyly of the group is well established, relationships within it are still poorly understood. Plastid genes, commonly used to infer phylogenies in plants, are usually not useful for closely related taxa because of low levels of genetic variation. The Medicago truncatula genome project provided a suite of candidate nuclear loci with high levels of variation that might prove suitable for low-level phylogenetics. This paper reports the development of methods for screening a large number of these nuclear loci, and detailed analysis of four of them. Four different patterns of phylogenetic diversification occur in the loci sampled from these genomes of Astragalus species. One locus (CNGC4) was single copy and could be directly used in phylogenetic analyses. Two loci (ARG10 and FENR) showed patterns strongly suggestive of duplication events in some taxa, and one locus (tRALS) has apparently undergone a cryptic duplication, making it very difficult to diagnose. Potential methods for using the information provided by these loci are discussed.