Robert D. Westfall

Gene movement and genetic association with regional climate gradients in California valley oak (Quercus lobata Née) in the face of climate change

Rapid climate change jeopardizes tree populations by shifting current climate zones. To avoid extinction, tree populations must tolerate, adapt, or migrate. Here we investigate geographic patterns of genetic variation in valley oak, Quercus lobata Née, to assess how underlying genetic structure of populations might influence this species’ ability to survive climate change. First, to understand how genetic lineages shape spatial genetic patterns, we examine historical patterns of colonization. Second, we examine the correlation between multivariate nuclear genetic variation and climatic variation. Third, to illustrate how geographic genetic variation could interact with regional patterns of 21st Century climate change, we produce region‐specific bioclimatic distributions of valley oak using Maximum Entropy (MAXENT) models based on downscaled historical (1971–2000) and future (2070–2100) climate grids. Future climatologies are based on a moderate‐high (A2) carbon emission scenario and two different global climate models. Chloroplast markers indicate historical range‐wide connectivity via colonization, especially in the north. Multivariate nuclear genotypes show a strong association with climate variation that provides opportunity for local adaptation to the conditions within their climatic envelope. Comparison of regional current and projected patterns of climate suitability indicates that valley oaks grow in distinctly different climate conditions in different parts of their range. Our models predict widely different regional outcomes from local displacement of a few kilometres to hundreds of kilometres. We conclude that the relative importance of migration, adaptation, and tolerance are likely to vary widely for populations among regions, and that late 21st Century conditions could lead to regional extinctions.

Distribution and Climatic Relationships of the American Pika (Ochotona princeps) in the Sierra Nevada and Western Great Basin, U.S.A.; Periglacial Landforms as Refugia in Warming Climates

Abstract We used a rapid assessment to survey American pika (Ochotona princeps) populations and documented 420 pika site occurrences in southwestern U.S.A. These included 329 sites from the Sierra Nevada (SN), California; 67 from six southwestern Great Basin (swGB) ranges, California and Nevada; 16 from three central Great Basin ranges, Nevada; and 8 from the central Oregon Cascades. Of these, 67% were currently occupied, 27% modern (indirectly scored active), and 6% old. Sites were grouped into 148 demes, 88 regions, and 11 mountain ranges. Current elevations ranged from 1645 m (1827 m excluding Oregon) to 3887 m, extending the lower elevational range of the species at the study latitude. Sites were distributed on all slope aspects with a preference for north to easterly aspects, and without preference for substrate. Rock-ice-feature (RIF) till, notably rock-glacier and boulder-stream landforms, accounted for 83% of the sites. Climatic relationships from the PRISM model for the SN and swGB sites showed wide tolerance, with average precipitation 910 mm, average minimum temperature −3.9 °C, and average maximum temperature 8.7 °C. Average minimum temperatures for old sites were not significantly different from recent sites, whereas average maximum temperatures were significantly higher in old sites. Unusual features of RIF landforms make them important refugia for pikas as climates warm. In contrast to studies that document species vulnerability elsewhere, pikas in the SN and swGB appear to be thriving and tolerating a wide range of thermal environments.

Allozyme differentiation and biosystematics of the Californian closed-cone pines ( Pinus subsect. Oocarpae )

Allozyme differentiation at 32 loci was studied in the three Californian species of Pinus subsect. Oocarpae: P. attenuata, P. muricata, and P. radiata, and in a small sample of a Latin American species of the subsection, P. oocarpa. The Californian species were previously known to comprise highly differentiated, disjunct populations, but with uncertain phylogenetic relationships among several populations and species. All populations had clear affinities for single species. The controversial Channel Islands (Santa Cruz Island) population of P. muricata and the Mexican Island (Guadalupe and Cedros islands) populations of P. radiata were distinct within their respective species, but clearly fell within each species complex. Con- to evidence from other traits, the Californian species were equally differentiated from one another allozymically, with no evidence of close relationships among pairwise comparisons of the three species. Pinus oocorpa, the putative ancestral species, was about two times more variable, and at substantial and approximately equal genetic distance from each of the three Californian species. Divergence of populations within species was generally clinal. The initial radiation of P. attenuata was in the Sierra Nevada, and subsequent divergence was toward the coast in the Siskiyou Mountains, and then south through the coast range to southern California. Divergence in both P. muricata and P. radiata occurred northward along the coast, with the southern island populations retaining ancestral alleles, and differentiation from P. oocarpa increasing northward within species. Genetic differentiation among species was twice that among populations within species.

Conserving the evolutionary potential of California valley oak (Quercus lobata Née): a multivariate genetic approach to conservation planning

California valley oak (Quercus lobata Née) is a seriously threatened endemic oak species in California and a keystone species for foothill oak ecosystems. Urban and agricultural development affects a significant fraction of the species’ range and predicted climate change is likely to dislocate many current populations. Here, we explore spatial patterns of multivariate genotypes and genetic diversity throughout the range of valley oak to determine whether ongoing and future patterns of habitat loss could threaten the evolutionary potential of the species by eradicating populations of distinctive genetic composition. This manuscript will address three specific questions: (i) What is the spatial genetic structure of the chloroplast and nuclear genetic markers? (ii) What are the geographical trends in the distribution of chloroplast and nuclear genotypes? (iii) Is there any part of the species’ range where allelic diversity in either the chloroplast or nuclear genomes is particularly high? We analysed six chloroplast and seven nuclear microsatellite genetic markers of individuals widespread across the valley oak range. We then used a multivariate approach correlating genetic markers and geographical variables through a canonical trend surface analysis, followed by GIS mapping of the significant axes. We visualized population allelic richness spatially with GIS tools to identify regions of high diversity. Our findings, based on the distribution of multivariate genotypes and allelic richness, identify areas with distinctive histories and genetic composition that should be given priority in reserve network design, especially because these areas also overlap with landscape change and little degree of protection. Thus, without a careful preservation plan, valuable evolutionary information will be lost for valley oak.

Allozyme markers in breeding zone designation

Early studies of allozyme variation in plant populations suggested that allelic frequencies in some loci vary by geography. Since then, the expectation that allozymes might be useful in describing geographic patterns has generally not been borne out by single locus analyses, except on the broadest scale. Multi-locus analyses reveal the converse: canonical correlation analysis of individual, uniformly-spaced genotypes describe statistically-significant, complex patterns with geography. Multi-locus scores in four major species, Abies concolor, Pinus lambertiana, P. ponderosa, and Pseudotsuga menziesii, of the mixed conifer forest in the Sierra Nevada correlate 0.40 or greater with the first canonical vector of a geographical trend surface equation. The different species follow similar patterns by latitude and elevation. In contrast with patterns in the Sierra Nevada, large-scale differentiation is weak (R2 < 0.20) among populations of Pseudotsuga menziesii in the Coast Ranges and Siskyou Mountains of northern California and southern Oregon, where differentiation may be local. For the purpose of forming zones, we subdivided scores of the first two to four canonical vectors into groups and plotted them as multidimensional contour intervals. Reclassification by discriminant analysis serves as an approximate guide to transfer risks within and among these groups.

Allozyme markers in forest genetic conservation

Genetic diversity is important in tree-breeding, in managing rare and endangered tree species, and in maintaining healthy populations of widespread native tree species. Allozymes are useful in determining genetic relationships among species, where they can be used to assess affiliations of rare taxa and predict relative endangerment among species. Because allozymes sometimes yield different information about genetic variation within species than revealed by other traits, when estimates of total or adaptive genetic variation are important, allozymes are best used in conjunction with other traits. Allozymes are useful for measuring direct allelic diversity when designing ex-situ and in-situ conservation strategies. We demonstrate an application of canonical trend-surface analysis for determining locations of in-situ genetic conservation areas. Allozymes also serve as useful markers in monitoring the effects of forest management and other environmental changes on genetic diversity.

New Records of Marginal Locations for American Pika (Ochotona princeps) in the Western Great Basin

Abstract. We describe 46 new site records documenting occupancy by American pika (lOchotona princeps) at 21 locations from 8 mountain regions in the western Great Basin, California, and Nevada. These locations comprise a sub- set of sites selected from regional surveys to represent marginal, isolated, or otherwise atypical pika locations, and to provide information for assessing environmental tolerance limits. Several locations are known from historic observations (Madeline Plain, Bodie Mtns., Wassuk Mtns., Mono Craters) and are included here to update current status. Site eleva- tions range from 1848 m to 3392 m; relative to the broad range of pika sites in the region, the new locations have cli- mates that are 2—4 °C warmer and receive approximately half the annual precipitation. Sites are located in lava flows and domes, inselbergs (isolated, rocky exposures on a small hill), eroding bedrock, rock-glacier till, talus slopes, and anthro- pogenic roadbed armaments and mining ore dumps. Several sites are situated in uncommon vegetation contexts, for example, montane desert scrub communities or locations where vegetation adjacent to taluses is sparse or lacking. Prox- imity to surrounding pika habitats (as a measure of marginality) was evaluated based on relative talus distribution pat- terns for 0.5-km, 2.5-km, and 5.0-km circular areas nested around each site. Seven idealized, schematic spatial patterns were used to assess potential connectivity among sites, ranging from “island” (no other talus within the respective areas) to “even” (many talus patches regularly distributed). Applying this approach to the 21 sites demonstrated a simple method for qualitatively assessing pika habitat relative to dispersal potential and metapopulation viability and also revealed complexities of biogeographic patterns related to marginality.

Thermal Regimes and Snowpack Relations of Periglacial Talus Slopes, Sierra Nevada, California, U.S.A.

Abstract Thermal regimes of eight periglacial talus slopes, at contrasting elevations, aspects, and substrates, in the Sierra Nevada, California, had complex microclimatic patterns partially decoupled from external conditions. Over three years, warm seasons showed mean talus matrix temperatures and daily variances lower than surfaces and cooler than free-air; talus surface and matrix positions low in the taluses were colder than higher positions, yielding highly positive altitudinal temperature differentials; ground surface temperatures had greater daily extremes than talus positions; and talus matrix temperatures lagged in response to surface temperature changes. Regulating processes in summer include evaporative cooling, cold-air drainage and Balch effect, and shading effects. In the cold season, talus matrices were warmer than surfaces; low talus positions were warmer than high; isothermal zero-curtain periods occurred before snow disappearance; and snow covered talus low positions more often and longer than higher in the taluses, which were often snow-free. Winter thermal processes likely include insulation from snow cover at talus bases, free exchange between talus matrix and external air in the upper talus, and latent heat from thaw-refreezing in late winter. Permanent ice may occur within high elevation talus slopes. Partially decoupled talus thermal regimes provide buffered habitats for mammals such as American pikas and are likely to be important refugia under future warming.

Radiocarbon dating of American pika fecal pellets provides insights into population extirpations and climate refugia

The American pika (Ochotona princeps) has become a species of concern for its sensitivity to warm temperatures and potential vulnerability to global warming. We explored the value of radiocarbon dating of fecal pellets to address questions of population persistence and timing of site extirpation. Carbon was extracted from pellets collected at 43 locations in the western Great Basin, USA, including three known occupied sites and 40 sites of uncertain status at range margins or where previous studies indicated the species is vulnerable. We resolved calibrated dates with high precision (within several years), most of which fell in the period of the mid-late 20th century bomb curve. The two-sided nature of the bomb curve renders far- and near-side dates of equal probability, which are separated by one to four decades. We document methods for narrowing resolution to one age range, including stratigraphic analysis of vegetation collected from pika haypiles. No evidence was found for biases in atmospheric 14C levels due to fossil-derived or industrial CO2 contamination. Radiocarbon dating indicated that pellets can persist for >59 years; known occupied sites resolved contemporary dates. Using combined evidence from field observations and radiocarbon dating, and the Bodie Mountains as an example, we propose a historical biogeographic scenario for pikas in minor Great Basin mountain ranges adjacent to major cordillera, wherein historical climate variability led to cycles of extirpation and recolonization during alternating cool and warm centuries. Using this model to inform future dynamics for small ranges in biogeographic settings similar to the Bodie Mountains in California, extirpation of pikas appears highly likely under directional warming trends projected for the next century, even while populations in extensive cordillera (e.g., Sierra Nevada, Rocky Mountains, Cascade Range) are likely to remain viable due to extensive, diverse habitat and high connectivity.

Thermal Components of American Pika Habitat—How does a Small Lagomorph Encounter Climate?

ABSTRACT Anticipating the response of small mammals to climate change requires knowledge of thermal conditions of their habitat during times of the day and year when individuals use them. We measured diurnal and seasonal temperatures of free air and of six habitat components for American pikas (Ochotona princeps) over five years at 37 sites in seven mountain ranges in the western Great Basin, United States. Talus matrices (subsurfaces) had low daily variances and, in the warm season, remained cool during the hottest times of the day relative to surfaces and free air. During winter, matrices were warmer than free air. Talus surfaces were warmer than free air in the warm and cold seasons, and had large daily variances. Summer forefield and dispersal environments were warmest of all habitat components. Talus surfaces in summer were highly responsive to solar radiation over the course of the day, warming quickly to high midday temperatures, and cooling rapidly in the evening. By contrast, matrices lagged the daily warm-up and remained warmer than free air at night. These differences afford diurnal and seasonal opportunities for pikas to adapt behaviorally to unfavorable temperatures and suggest that animals can accommodate a wider range of future climates than has been assumed, although warming of the dispersal environment may become limiting. Climate envelope models that use or model only surface air measures and do not include information on individual thermal components of pika habitat may lead to errant conclusions about the vulnerability of species under changing climates.