▪ Abstract  The proliferation of molecular data in systematics has opened a Pandora's box of alternate approaches to inferring hierarchical patterns of relationship among taxa. In this review, we examine practical and theoretical reasons for employing some methods and avoiding others. We offer a philosophical overview of the relationship between systematics patterns and evolutionary processes, and we discuss the differential emphasis given to each of these areas by opposing methodological camps. We review the sources and types of incongruence between data partitions from different sources and recommend a specific procedure for contending with incongruence. We then focus on inference of relationships among closely related taxa, with particular emphasis on mtDNA as a source of characters, its advantages and potential pitfalls. We conclude with a review of several widely cited empirical studies and suggest that the gene tree–species tree problem may be less severe than its prevalence in the literature would suggest.

Conservation genetics has expanded its purview such that molecular techniques are now used routinely to prioritize populations for listing and protection and infer their historical relationships in addition to addressing more traditional questions of heterozygosity and inbreeding depression. Failure to specify whether molecular data are being used for diagnosis‐related questions or for population viability questions, however, can lead either to misinterpretation of character data as adaptive information or to misinterpretation of frequency or distance data as diagnostic or historical information. Each of these misinterpretations will confound conservation programs. The character‐based approach to delimiting phylogenetic species is both operationally and logically superior to “diagnostic” methods that involve distance‐ or frequency‐based routines, which are unstable over time. Tree‐based criteria for the diagnosis of conservation “units” are also inappropriate because they can depend on patterns inferred without reference to diagnostic characters. Intraspecific studies, conservation‐related or otherwise, that adopt terminology and methods designed to infer nested hierarchic relationships confuse diagnosis with historical inferences by treating diagnoses as outcomes rather than as precursors to phylogeny reconstruction. A character‐based diagnostic approach recognizes the analytical dichotomy between species hierarchies and population statistics and provides a framework for the understanding of each. No species concept, however, should be viewed as an absolute criterion for protecting populations, but as part of a framework from within which identification of protection and management goals can be achieved effectively and defensibly.

The Atacama Desert in Chile—hyperarid and with high–ultraviolet irradiance levels—is one of the harshest environments on Earth. Yet, dozens of species grow there, including Atacama-endemic plants. Herein, we establish the Talabre–Lejía transect (TLT) in the Atacama as an unparalleled natural laboratory to study plant adaptation to extreme environmental conditions. We characterized climate, soil, plant, and soil–microbe diversity at 22 sites (every 100 m of altitude) along the TLT over a 10-y period. We quantified drought, nutrient deficiencies, large diurnal temperature oscillations, and pH gradients that define three distinct vegetational belts along the altitudinal cline. We deep-sequenced transcriptomes of 32 dominant plant species spanning the major plant clades, and assessed soil microbes by metabarcoding sequencing. The top-expressed genes in the 32 Atacama species are enriched in stress responses, metabolism, and energy production. Moreover, their root-associated soils are enriched in growth-promoting bacteria, including nitrogen fixers. To identify genes associated with plant adaptation to harsh environments, we compared 32 Atacama species with the 32 closest sequenced species, comprising 70 taxa and 1,686,950 proteins. To perform phylogenomic reconstruction, we concatenated 15,972 ortholog groups into a supermatrix of 8,599,764 amino acids. Using two codon-based methods, we identified 265 candidate positively selected genes (PSGs) in the Atacama plants, 64% of which are located in Pfam domains, supporting their functional relevance. For 59/184 PSGs with an Arabidopsis ortholog, we uncovered functional evidence linking them to plant resilience. As some Atacama plants are closely related to staple crops, these candidate PSGs are a “genetic goldmine” to engineer crop resilience to face climate change.