A classic biogeographic pattern is the alignment of diploid, tetraploid and hexaploid races of creosote bush (Larrea tridentata) across the Chihuahuan, Sonoran and Mohave Deserts of western North America. We used statistically robust differences in guard cell size of modern plants and fossil leaves from packrat middens to map current and past distributions of these ploidy races since the Last Glacial Maximum (LGM). Glacial/early Holocene (26–10 14C kyr bp or thousands of radiocarbon years before present) populations included diploids along the lower Rio Grande of west Texas, 650 km removed from sympatric diploids and tetraploids in the lower Colorado River Basin of south‐eastern California/south‐western Arizona. Diploids migrated slowly from lower Rio Grande refugia with expansion into the northern Chihuahuan Desert sites forestalled until after ~4.0 14C kyr bp. Tetraploids expanded from the lower Colorado River Basin into the northern limits of the Sonoran Desert in central Arizona by 6.4 14C kyr bp. Hexaploids appeared by 8.5 14C kyr bp in the lower Colorado River Basin, reaching their northernmost limits (~37°N) in the Mohave Desert between 5.6 and 3.9 14C kyr bp. Modern diploid isolates may have resulted from both vicariant and dispersal events. In central Baja California and the lower Colorado River Basin, modern diploids probably originated from relict populations near glacial refugia. Founder events in the middle and late Holocene established diploid outposts on isolated limestone outcrops in areas of central and southern Arizona dominated by tetraploid populations. Geographic alignment of the three ploidy races along the modern gradient of increasingly drier and hotter summers is clearly a postglacial phenomenon, but evolution of both higher ploidy races must have happened before the Holocene. The exact timing and mechanism of polyploidy evolution in creosote bush remains a matter of conjecture.

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Aim The absence of Sonoran Desert plants in late Pleistocene‐aged packrat middens has led to speculation that they survived glacial episodes either in refugia as intact associations (Clementsian community concept) or in dry microsites within chaparral or woodland according to individualistic species responses (Gleasonian community concept). To test these hypotheses, we developed a midden record from one likely refugium in north‐eastern Baja California, Mexico. We also measured stomatal guard cell size in fossil leaves to further evaluate site‐level individualistic responses of Larrea tridentata (creosote bush) ploidy races to climatic changes, including monsoonal history, over the late Quaternary. Location Sierra Juárez, Lower Colorado River Basin, north‐eastern Baja California, Mexico. Methods Packrat (Neotoma) middens were collected from ˂ 300 m elevation on the eastern piedmont of the Sierra Juárez. Plant macrofossils and pollen were analysed from 50 dated middens, including determination of Larrea tridentata ploidy races. Results Pleistocene middens dating back to > 55,000 cal. yr bp contained a mix of extralocal species characteristic of chaparral and pinyon–juniper–oak woodland, along with some modern desert elements. Many other desert taxa were absent during the Pleistocene, although most had arrived by the beginning of the Holocene 11,700 years ago. Main conclusions The assemblage of chaparral, woodland and select desert elements refutes the hypothesis that the Lower Colorado River Basin served as a late Pleistocene refugium for Sonoran Desert flora. The rapid arrival of most missing desert species by the early Holocene suggests they did not have far to migrate. They probably survived the last glacial period as smaller, disparate populations in dry microsites within chaparral and pinyon–juniper–oak woodlands. Diploid and tetraploid races of Larrea tridentata were present during the Pleistocene, but hexaploids did not appear until the mid‐Holocene. This demonstrates that individualistic responses to climate involved genetic variants, in this case cytotypes, and not just species.

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