Abstract Rare species present a challenge under changing environmental conditions as the genetic consequences of rarity may limit species ability to adapt to environmental change. To evaluate the evolutionary potential of a rare species, we assessed variation in traits important to plant fitness using multigenerational common garden experiments. Torrey pine, Pinus torreyana Parry, is one of the rarest pines in the world, restricted to one mainland and one island population. Morphological differentiation between island and mainland populations suggests adaptation to local environments may have contributed to trait variation. The distribution of phenotypic variances within the common garden suggests distinct population‐specific growth trajectories underlay genetic differences, with the island population exhibiting substantially reduced genetic variance for growth relative to the mainland population. Furthermore, F1 hybrids, representing a cross between mainland and island trees, exhibit increased height accumulation and fecundity relative to mainland and island parents. This may indicate genetic rescue via intraspecific hybridization could provide the necessary genetic variation to persist in environments modified as a result of climate change. Long‐term common garden experiments, such as these, provide invaluable resources to assess the distribution of genetic variance that may inform conservation strategies to preserve evolutionary potential of rare species, including genetic rescue.

Torrey pine (Pinus torreyana) is one of the rarest pine species in the world. Restricted to one mainland and one island population in California, Torrey pine is a species of conservation concern under threat due to low population sizes, lack of genetic variation, and environmental stochasticity. Previous research points to a lack of within population variation that is unprecedented among conifer species, although a few fixed genetic differences between the populations contribute to subspecies classification. Given this, development of best conservation practices requires a combination of genetic and trait evaluation tools to conserve this keystone species. To evaluate phenotypic differences between populations, a provenance trial was established in 2007 at the Santa Barbara Botanic Garden. The trial consists of seeds established from cones collected within a mainland progeny trial of mainland and island individuals and includes mainland, island, and hybrid individuals, the result of natural hybridization within the progeny trial. Genetic ancestry of individuals was evaluated using allozyme markers as fixed genetic differences were observed between populations. We evaluated phenotypic differences between mainland, island and hybrid individuals, comparing early germination traits and annual fitness metrics height and fecundity following establishment. Preliminary results indicate admixed individuals exhibit increased fitness relative to mainland and island individuals at all development stages, suggesting a potential role for genetic rescue via intraspecific hybridization in this genetically depauperate species. However, unidirectional hybridization within the F1s indicates extrinsic or intrinsic barriers to reproduction have evolved between these populations, indicating between-population crosses may not represent a viable option to conserve evolutionary potential. This long term dataset provides an invaluable resource to test predictions regarding the use of genetic rescue in rare, long-lived species.

Provenance studies are an increasingly important analog for understanding how trees adapted to particular climatic conditions might respond to climate change. Dendrochronological analysis can illuminate differences among trees from different seed sources in terms of absolute annual growth and sensitivity to external growth factors. We analyzed annual radial growth of 567 36-year-old pitch pine (Pinus rigida Mill.) trees from 27 seed sources to evaluate their performance in a New Jersey Pine Barrens provenance experiment. Unexpectedly, missing rings were prevalent in most trees, and some years-1992, 1999, and 2006-had a particularly high frequency of missing rings across the plantation. Trees from local seed sources (<55 km away from the plantation) had a significantly smaller percentage of missing rings from 1980-2009 (mean: 5.0%), relative to northernmost and southernmost sources (mean: 9.3% and 7.9%, respectively). Some years with a high frequency of missing rings coincide with outbreaks of defoliating insects or dry growing season conditions. The propensity for missing rings synchronized annual variations in growth across all trees and might have complicated the detection of potential differences in interannual variability among seed sources. Average ring width was significantly larger in seed sources from both the southernmost and warmest origins compared to the northernmost and coldest seed sources in most years. Local seed sources had the highest average radial growth. Adaptation to local environmental conditions and disturbances might have influenced the higher growth rate found in local seed sources. These findings underscore the need to understand the integrative impact of multiple environmental drivers, such as disturbance agents and climate change, on tree growth, forest dynamics, and the carbon cycle.

Estimating demographic parameters is fundamental for conservation programs. Inferences are generally derived from the variation of unlinked nuclear genomic regions, which are often unavailable for non-model species. These limitations can be circumvented using universal polymorphic markers that can be easily transferred across taxa, such as cytoplasmic single sequence repeats (SSRs). These markers are sensitive to population expansions, but no formal test has been conducted to explore if they can be used to infer and distinguish between competing bottleneck scenarios. Herein, we simulated the evolution of ten linked haploid SSRs in populations submitted to different bottleneck regimes (θ 1 = 1, 10, 50 and 90 % of θ 0) at different times (τ = 0.5, 1 and 10). The variation of these markers, as compiled with six summary statistics, allowed to detect severe population collapses independently of τ, and as long as populations kept roughly constant effective sizes after the size reduction. Mild declines became difficult to infer as τ increased, and small bottlenecks were virtually undetectable with these markers. More complex frameworks, such as bottlenecks followed by expansions, were also difficult to infer. Comparisons with chloroplast SSR variation in the Mexican relict Picea mexicana and the eastern North American Picea rubens suggested that these species went through bottlenecks of different intensities. While P. mexicana suffered a severe population decline that could be dated back to the last interglacial, P. rubens went through a more recent (i.e. late Pleistocene) and milder bottleneck. These results indicate that linked SSRs can be used as proxies to infer basic parameters related to strong population declines in species that lack adequate genomic resources.

PREMISE OF THE STUDY:Variation in a species is a blend of adaptive, random, and migratory responses. Pitch pine (Pinus rigida), a highly variable eastern conifer, has occupied multiple glacial refugia, whose harsh conditions favored adaptations enhancing subsequent dispersal and recolonization of newly deglaciated sites. We assessed phenotypic diversity in long-term growth trials to elucidate both the adaptations and likely refugia.METHODS:Pitch pine progeny from 31 areas were grown in common gardens in six locations, from eastern Massachusetts to Korea.KEY RESULTS:Survival increased with source latitude, but seedlings from southern latitudes were tallest in the first (postplanting) year, but that advantage dissipated in later years. Progeny from northern latitudes were precocious, highly fecund, had smaller seeds, and more seeds per cone. Seed mass decreased with latitude in both parents and progeny. Serotinous cones were notably common in the New Jersey Pine Plains and Acadia National Park. Various disease agents and frost burn exhibited latitudinal trends that were nonlinear, with a break in the regression slope at about 40°N latitude. Cluster analysis identified both northern and southern groups, largely split between unglaciated and deglaciated terrain, but with Acadia and the Pine Plains as unique outliers. Within the southern group, provenances were organized into contiguous subgroups, but geographic structure was less evident in the northern group.CONCLUSIONS:The present range of pitch pine was colonized by migrants from at least three different refugia, including at least one on the exposed continental shelf during the Last Glacial Maximum.

Premise of the study: Fire in the New Jersey Pine Plains has selectively maintained a dwarf growth form of pitch pine (Pinus rigida), which is distinct from the surrounding tall forest of the Pine Barrens and has several other inherited adaptations that enable it to survive in an environment dominated by fire.Methods: Pitch pine progeny from two Pine Plains sites, the West and East Pine Plains, were grown in common garden environments with progeny from two Pine Barrens stands, Batsto and Great Egg Harbor River. The tests were replicated in five locations: in New Jersey, Connecticut, two sites in Massachusetts, and Korea. One of the tests was monitored for up to 36 yr.Key results: Progeny of Pine Plains origin were, in general, shorter, more crooked, precocious, bore more cones, had a higher frequency of serotinous cones, and had a higher frequency of stem cones than did Pine Barrens progeny, wherever they were grown.Conclusions: The Pine Plains is an ecotype that has evolved in response to disturbance. The several characters that distinguish it from the surrounding tall forest of the Pine Barrens are inherited. The dwarf stature and crooked form not only enable the ecotype to persist in an environment of frequent fires but also increase its flammability.

Abstract - Conserving forest genetic resources and, indeed, preventing species extinctions will be complicated by the expected changes in climate projected for the next century and beyond. This paper uses case examples from rare spruces (Picea sp.) from North America to discuss the interplay of conservation, genetics, and climate change. New models show how climate change will affect these spruces, making it necessary to relocate them if they are to survive, a tool known as assisted migration or, preferably, assisted colonization. The paper concludes with some speculation on the broader implications of climate change, and the relevance of conservation to preserving the necessary ecological services provided by forests.

PREMISE OF THE STUDY:Climate change may threaten endemic species with extinction, particularly relicts of the Arcto-Tertiary Forest, by elimination of their contemporary habitat. Projections of future habitat are necessary to plan for conservation of these species.METHODS:We used spline climatic models and modified Random Forests statistical procedures to predict suitable habitats for Brewer spruce (Picea breweriana), which is endemic to the Klamath Region of California and Oregon. We used three general circulation models and two sets of carbon emission scenarios (optimistic and pessimistic) for future climates.KEY RESULTS:Our procedures predicted present occurrence of Brewer spruce perfectly. For the decades 2030, 2060, and 2090, its projected range within the Klamath Region progressively declined, to the point of disappearance in the decade 2090. The climate niche was projected to move north to British Columbia, the Yukon Territory, and southeastern Alaska.CONCLUSION:The results emphasize the necessity of assisted colonization and trans-boundary movement to prevent extinction of Brewer spruce. The projections provide a framework for formulating conservation plans, but planners must also consider regulations regarding international plant transfers.

UNLABELLEDPREMISE OF THE STUDYModeling the contemporary and future climate niche for rare plants is a major hurdle in conservation, yet such projections are necessary to prevent extinctions that may result from climate change. •METHODSWe used recently developed spline climatic models and modified Random Forests statistical procedures to predict suitable habitats of three rare, endangered spruces of Mexico and a spruce of the southwestern USA. We used three general circulation models and two sets of carbon emission scenarios (optimistic and pessimistic) for future climates. •KEY RESULTSOur procedures predicted present occurrence perfectly. For the decades 2030, 2060, and 2090, the ranges of all taxa progressively decreased, to the point of transient disappearance for one species in the decade 2060 but reappearance in 2090. Contrary to intuition, habitat did not develop to the north for any of the Mexican taxa; rather, climate niches for two taxa re-materialized several hundred kilometers southward in the Trans-Mexican Volcanic Belt. The climate niche for a third Mexican taxon shrank drastically, and its two mitotypes responded differently, one of the first demonstrations of the importance of intraspecific genetic variation in climate niches. The climate niche of the U.S. species shrank northward and upward in elevation. •CONCLUSIONThe results are important for conservation of these species and are of general significance for conservation by assisted colonization. We conclude that our procedures for producing models and projecting the climate niches of Mexican spruces provide a way for handling other rare plants, which constitute the great bulk of the world's endangered and most vulnerable flora.

Electrophoretic techniques permit population biologists to analyze genetic structure of natural populations by using large numbers of allozyme loci. Several methods of analysis have been applied to allozyme data, including chi-square contingency tests, F- statistics, and genetic distance. This paper compares such statistics for pitch pine (Pinus rigida Mill.) with those gathered for other plants and animals. On the basis of these comparisons, we conclude that pitch pine shows significant differentiation across its range, but appears to be less differentiated than many other organisms. Data for other forest trees indicate that they, in general, conform to the pitch pine model. An open breeding system and a long life cycle probably are responsible for the limited differentiation observed in forest trees. These conclusions pertain only to variation at allozyme loci, a class that may be predominantly neutral with respect to adaptation, although gene frequencies for some loci were correlated with climatic variables. D uring the last 40 years, a considerable body of information has been assembled on genetic variabil­ ity in forest tree species. Measurements of growth rate, cold-hardiness, phenology, and related traits have provid­ ed tree breeders with much useful knowledge, and have indicated in a general way how tree species have adapted to a spatially variable habitat (Wright 1976). Most informa­ tion has come from studies designed to assess relative differences in metric traits among provenances represent­ ing a wide geographic range. When the identification of suitable seed sources for use in reforestation is a primary objective, provenance tests (that is, common garden studies) may be indispensible. However, such studies are expensive to conduct, require large areas of land, yield useful data only after many years, and use traits of unknown inheritance. The development of electrophoretic techniques during the last two decades provided an alternative to common garden techniques for estimating levels of genetic variation in natural populations (Lewontin 1974). Electrophoretic techniques are now widely used in studies of plant and animal populations and have produced a large body of data on the levels and patterns of genic variability charac­ teristic of many species. Although the difficulties inherent in the large size and late reproductive maturity of trees somewhat delayed their study, there is in recent years a rapid accumulation of useful data from the application of electrophoretic techniques to several conifers.

Genetic diversity and genetic structure in Engelmann spruce (Picea engelmannii Parry ex Engelm.) were interpreted with respect to the effects of glacial and interglacial displacement and compared with patterns in blue spruce (Picea pungens Engelm.), which occupies a range well south of the last glacial front. On average, Engelmann spruce populations were polymorphic at 80% of 24 isozyme loci, with 2.4 alleles per locus and expected heterozygosity of 0.255. The respective means for four populations of blue spruce were 42.7%, 1.6 alleles, and 0.138. Of total diversity, 14.7% was among populations in Engelmann spruce and 8.6% in blue spruce. In Engelmann spruce, numbers of alleles increased from south to north. Recent bottlenecks were indicated in the three southernmost populations of Engelmann spruce and in the northernmost population of blue spruce. Cluster analysis divided Engelmann spruce into a northern group and a Southwestern group; however, populations from Utah were distributed among both clusters. Genetic distance was correlated with geographic distance between northern populations but not between Southwestern populations, where drift predominated over gene flow. In two Engelmann spruce populations from Utah, multilocus outcrossing rates were 0.951 (±0.016) and 0.940 (±0.071). At Flys Peak, Arizona, the southernmost location of Engelmann spruce, outcrossing was also high, 0.899 (±0.017). Thus, inbreeding coefficients observed for parental (–0.104 to 0.047) and filial (0.011 to 0.026) generations were low. Although Engelmann spruce seemed genetically robust, the evidence of bottlenecks in the southern extreme of its range suggested future problems in an era of global warming.

Chihuahua spruce (Picea chihuahuana Martínez) is a montane subtropical conifer endemic to the Sierra Madre Occidental in northwestern México. Range‐wide variation was investigated using maternally inherited mitochondrial (mtDNA) and paternally inherited chloroplast (cpDNA) DNA markers. Among the 16 mtDNA regions analysed, only two mitotypes were detected, while the study of six cpDNA microsatellite markers revealed eight different chlorotypes. The average cpDNA diversity (H = 0.415) was low but much higher than that for mtDNA (H = 0). The distribution of mitotypes revealed two clear nonoverlapping areas (GST = NST = 1), one including northern populations and the second one including the southern and central stands, suggesting that these two regions may represent different ancestral populations. The cpDNA markers showed lower population differentiation (GST = 0.362; RST = 0.230), implying that the two ancestral populations continued to exchange pollen after their initial geographic separation. A lack of a phylogeographic structure was revealed by different spatial analyses of cpDNA (GST > RST; and samova), and reduced cpDNA gene flow was noted among populations (Nm = 0.873). Some stands deviated significantly from the mutation–drift equilibrium, suggesting recent bottlenecks. Altogether, these various trends are consistent with the hypothesis of a population collapse during the Holocene warming and suggest that most of the modern P. chihuahuana populations are now effectively isolated with their genetic diversity essentially modelled by genetic drift. The conservation efforts should focus on most southern populations and on the northern and central stands exhibiting high levels of genetic diversity. Additional mtDNA sequence analysis confirmed that P. martinezii (Patterson) is not conspecific with P. chihuahuana, and thus deserves separate conservation efforts.

Santa Lucia fir ( Abies bracteata ), is a unique fir, the sole member of the subgenus Pseudotorreya . It is a relict of the Miocene broadleaved evergreen sclerophyll forest, and is now restricted to a highly fragmented range in the Santa Lucia Mountains of central coastal California. Expected heterozygosity for 30 isozyme loci in 18 enzyme systems, averaged over six populations that spanned the species’ north–south range, was only 0.036. Despite a fragmented range and isolated populations, differentiation ( F ST ) was only 0.080 for mature trees, and the number of migrants per generation ( Nm ) was 2.88 or 3.83, depending on the method of estimation. F ST for embryos was lower, 0.025, and Nm correspondingly higher, 9.75. Nei’s genetic distances were small and unrelated to geographic distances between populations. The proportion of full seeds per cone was only 0.082–0.488, depending on population, which suggests a high incidence of selfing followed by embryo abortion. However, the level of accumulated inbreeding, F IS , in mature trees was low, only 0.049. By contrast, F IS for embryos was 0.388, which indicates a high proportion of selfed progeny, in agreement with the low seed yields. The difference in inbreeding coefficients between seed trees and their progeny suggest that most inbreds are eliminated before maturity and, therefore, seed production, already low, overestimates the true potential for regeneration of these populations. These results have implications for conservation.

Brewer spruce (Picea breweriana), a relict of the widespread Arcto-Tertiary forests, is now restricted to a highly fragmented range in the Klamath Region of California and Oregon. Expected heterozygosity for 26 isozyme loci, averaged over 10 populations, was 0.121. More notable than the relatively high level of diversity when compared to other woody endemics was the strong decrease in expected heterozygosity with latitude. Differentiation (F(ST)) was 0.152, higher than values for many north temperate conifers with larger distributions. The number of migrants per generation (Nm) was 1.34 or 2.70, depending on the method of estimation. Inbreeding appeared low; F(IS) was only 0.003, in agreement with multilocus population outcrossing rates (t(m)), which were generally well above 0.90. No difference in t(m) was found between isolated vs. clustered trees. However, the number of seeds per cone was greatest in the densest populations; t(m) is a measure of effective outcrossing after mortality in the embryonic stage, whereas a reduced number of seeds per cone indicates self pollination. Selfing increased after logging; outcrossing rate before logging was 0.961 and after logging, 0.756. Despite Brewer spruce's narrow, fragmented distribution, the outlook for its conservation was good, with the exception of possible negative effects of logging.

Numerous populations from six spruce taxa, including four relict endemics, Picea chihuahuana (Chihuahua spruce), P. martinezii (Martinez spruce), P. mexicana (Mexican spruce), and P. breweriana (Brewer spruce), and two widespread species, P. engelmannii (Engelmann spruce) and P. pungens (blue spruce), were compared at homologous isozyme loci to test various hypotheses about their affinities and origins. Each of the species was clearly separated, and Neighbor-Joining and Unweighted Pair Group analyses of Nei's genetic distance grouped all populations within a taxon into their own clusters. Spruces from Flys Peak, Chiricahua Mountains, Arizona, joined a P. engelmannii cluster and were not a bridge to P. mexicana as previously believed. Spruces from Cerro Mohinora, Chihuahua, were clearly P. mexicana, not phantom hybrids of P. chihuahuana and P. pungens. Nuclear random amplified polymorphic DNA and chloroplast simple sequence repeat and cleaved amplified polymorphic genetic markers were compared in a smaller sample of populations, using distance and parsimony approaches. DNA markers, like isozymes, clearly identified spruces from Cerro Mohinora as P. mexicana. In contradiction to the most recent taxonomic treatment, P. chihuahuana and P. martinezii were separated as distinct species by both isozyme and DNA markers, and formed a sister-species group. Picea engelmannii and P. mexicana formed a separate cluster, and the genetic distance between them was similar to values associated with closely related species but greater than distances typical of subspecies or varieties in conifers. Picea pungens, which is so similar to P. engelmannii that the two are frequently misidentified, was clearly distinguished from it, sometimes joining a P. chihuahuana-martinezii group and sometimes a P. engelmannii-mexicana group, depending on analysis. Picea breweriana was well isolated from all other taxa. Both DNA and isozyme phylogenies agreed with results from crossability studies and contradicted intrageneric relationships constructed largely on cone mor- phology.

We compared genetic diversity estimated from allozymes and from random amplified polymorphic DNA (RAPDs) in a sample of 210 Great Basin bristlecone pines (Pinus longaeva Bailey) from three groves in the White Mountains, California, USA. The White Mountains are the most westerly extension of bristlecone pine and home to the oldest known living trees. We assayed two forks of each tree to determine whether they originated from multiple seed caches of the Clark’s nutcracker. Despite the limited and fragmented distribution of bristlecone pine, its level of genetic diversity was comparable to that of other pines, but lower than that reported for eastern populations of Great Basin bristlecone pine. Twenty-six of 36 allozymes were polymorphic (p95 5 38.9%; p 5 63.0%), with observed heterozygosity (Ho) of 0.122 and expected heterozygosity (He) of 0.134. The proportion of the total variation among populations (GST) was only 0.011. The high proportion of trees with multiple stems was not due to germination in seed caches; only six of 210 forked trees had multiple allozyme genotypes. Of the 42 RAPD loci scored, 27 were monomorphic. Genetic diversity for RAPDs was nearly the same as that for allozymes (p95 5 34.1%, He 5 0.130). However, the estimates of diversity and differentiation were much higher (He 5 0.321, GST 5 0.039) after excluding monomorphic loci.

Mexican spruce (Picea mexicana Martínez), an endangered species of the highest sky islands in México’s Sierra Madre Oriental and Sierra Madre Occidental, is threatened by fire, grazing, and global warming. Its conservation depends on whether it also is threatened by inbreeding and loss of genic diversity. We used 18 isozyme markers in 12 enzyme systems to assay genic diversity, characterize the mating system, and test for recent bottlenecks in three known populations. Unbiased, expected heterozygosity (He) averaged 0.125. Despite a separation of 676 km between populations in the Sierra Madre Oriental and the Sierra Madre Occidental, Wright’s FST, the proportion of total genic diversity among populations, was only 6.9%. Nei’s genetic distance was 0.001 between the populations in the Sierra Madre Oriental and more than an order of magnitude greater, 0.019, between the Sierra Madre Oriental and Sierra Madre Occidental. However, both values point to relatively recent divergence. Mating systems were predominantly outcrossing, but with significant selfing. Multilocus estimates of selfing varied from 19% to 41%, and the means of single-locus estimates were higher, suggesting that additional inbreeding occurred by mating among relatives. Despite significant inbreeding, observed heterozygosity was as high as or higher than He; Wright’s fixation index, FIS, was −0.107. Under the observed level of selfing, positive values of FIS were expected. Therefore, selection against inbreds and homozygotes must be intense. Cornuet-Luikart tests indicate recent bottlenecks in at least two of the three populations. The results suggest that Mexican spruce is a genetically viable species, and threats are primarily environmental.

We compared genetic diversity estimated from allozymes and from random amplified polymorphic DNA (RAPDs) in a sample of 210 Great Basin bristlecone pines (Pinus longaeva Bailey) from three groves in the White Mountains, California, USA. The White Mountains are the most westerly extension of bristlecone pine and home to the oldest known living trees. We assayed two forks of each tree to determine whether they originated from multiple seed caches of the Clark's nutcracker. Despite the limited and fragmented distribution of bristlecone pine, its level of genetic diversity was comparable to that of other pines, but lower than that reported for eastern populations of Great Basin bristlecone pine. Twenty-six of 36 allozymes were polymorphic (p(95) = 38.9%; p = 63.0%), with observed heterozygosity (H(o)) of 0.122 and expected heterozygosity (H(e)) of 0.134. The proportion of the total variation among populations (G(ST)) was only 0.011. The high proportion of trees with multiple stems was not due to germination in seed caches; only six of 210 forked trees had multiple allozyme genotypes. Of the 42 RAPD loci scored, 27 were monomorphic. Genetic diversity for RAPDs was nearly the same as that for allozymes (p(95) = 34.1%, H(e) = 0.130). However, the estimates of diversity and differentiation were much higher (H(e) = 0.321, G(ST) = 0.039) after excluding monomorphic loci.