Paul D. Hodgskiss

RECENT EVOLUTION AND DIVERGENCE AMONG POPULATIONS OF A RARE MEXICAN ENDEMIC, CHIHUAHUA SPRUCE, FOLLOWING HOLOCENE CLIMATIC WARMING

Fragmentation and reduction in population size are expected to reduce genetic diversity. However, examples from natural populations of forest trees are scarce. The range of Chihuahua spruce retreated northward and fragmented coincident with the warming climate that marked the early Holocene. The isolated populations vary from 15 to 2441 trees, which provided an opportunity to test whether census number is a good predictor of genetic diversity. Mean expected heterozygosity, He, based on 24 loci in 16 enzyme systems, was 0.093 for 10 sampled populations, which is within the range reported for conifers. However, estimates varied more than twofold among populations and He was closely related to the logarithm of the number of mature trees in the population (rHe,N = 0.93). Diversity among populations, FST, was 24.8% of the total diversity, which is higher than that observed in almost all conifer species studied. Neis genetic distance, D, was not related to geographic distance between populations, and D̄ was 0.033, which is higher than estimates for most wide‐ranging species. Most populations had excess homozygosity and the fixation index, FIS, was higher than that reported for all but one species of conifer. Nm, the number of migrants per generation, was 0.43 to 0.76, depending on estimation procedure, and is the smallest observed in conifers. The data suggest that populations of Chihuahua spruce have differentiated by drift and that they are effectively isolated. The results illustrate how a combination of paleontological observation and molecular markers can be used to illuminate recent evolutionary events. Multilocus estimates of outcrossing for two small populations were zero (complete selfing) and 0.153, respectively, which are in striking contrast to the near complete outcrossing observed in most conifers. The high fixation index and a high proportion of empty seeds (45%) suggest that inbreeding may be a serious problem for conservation of Chihuahua spruce.

Population structure, genetic diversity, and clone formation in Quercus chrysolepis (Fagaceae).

Stands of canyon live oak (Quercus chrysolepis, Fagaceae) are maintained for fuelwood, fire management, recreation, and as habitat for wildlife. Information about the link between the oaks reproductive ecology and its extent of genetic diversity is important in developing land management policies that will maintain the long-term viability of populations. Basal sprouting is the primary means of reproduction following fire or cutting, and stands frequently include groups of visibly connected trees in a clustered distribution that suggests cloning. We determined the extent to which clusters of trees were clonal and defined the spatial pattern and diversity of genotypes for six populations across nearly the entire east-west extent of the San Bernardino Mountains in southern California. We mapped over 100 trees at each of five sites and genotyped each tree for allozymes at seven polymorphic loci. We identified clones using these multilocus genotypes and detected an average of 34.4 ± 7.3 (SD) clones per site, most of which had unique genotypes. In general, clustered trees belong to single clones and most clones consist of few trees (mean = 3.4 ± 0.6 trees per clone). However, clone size increased significantly with increased individual heterozygosity, suggesting that selection may favor highly heterozygous clones. Clonal diversity and evenness were high relative to reports for most other clonal species; an average of 97% of clones had distinct genotypes, and Simpsons index of diversity averaged 0.95 ± 0.02. Population genetic analyses of 319 clones from six sites revealed high genetic diversity within sites (mean HS = 0.443). Only a small proportion of the total genetic diversity was explained by variation among sites (mean GST = 0.018), which is consistent with high gene flow among sites (Nm = 9.5). We found no significant substructure among plots within sites, and fixation indices within sites were generally small, suggesting that either little inbreeding occurs, and/or few inbred progeny survive. However, spatial autocorrelation analysis of clones indicated fine-scale genetic structure at distances under 4 m, possibly due to limited seed dispersal. Our data suggest that guidelines for seed collection of canyon live oak for use in restoration can be specified in a manner similar to that recommended for conifer species within the region studied.

EVIDENCE FOR AN EXTREME BOTTLENECK IN A RARE MEXICAN PINYON: GENETIC DIVERSITY, DISEQUILIBRIUM, AND THE MATING SYSTEM IN PINUS MAXIMARTINEZII

Maxipiñon (Pinus maximartinezii Rzedowski), which is confined to a single population of approximately 2000 to 2500 mature trees, covers about 400 ha in southern Zacatecas, Mexico. Genetic diversity measured by expected heterozygosity was 0.122, which is moderate for pines. However, percentage polymorphic loci was low, 30.3%. The fixation index (F) of 0.081 indicated only slight heterozygote deficiency. Mating system analysis indicated a significant but low level of selling; the multilocus outcrossing rate, tm, was 0.816. The mean of single locus estimates, ts, was smaller (0.761), perhaps suggesting mating among relatives, although the difference between tm and ts was not statistically significant.

Genetic diversity, mating system, and conservation of a Mexican subalpine relict, Picea mexicana Martínez

Mexican spruce (Picea mexicana Martínez), an endangered species of the highest sky islands in Méxicos 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, Wrights FST, the proportion of total genic diversity among populations, was only 6.9%. Neis 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; Wrights 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.

Genetic diversity and the mating system of a rare Mexican pinon, Pinus pinceana, and a comparison with Pinus maximartinezii (Pinaceae).

Weeping piñon (Pinus pinceana) has a restricted and fragmented range, trees are widely scattered within populations, and reproduction is limited. Nevertheless, genetic diversity was high; based on 27 isozyme loci in 18 enzyme systems, unbiased expected heterozygosity averaged 0.174. Differentiation also was high (F(ST) = 0.152), reflecting isolation between southern, central, and northern fragments of the range. Among populations in the northern fragment, F(ST) was only 0.056, and the number of migrants per generation (Nm) was 4.21, which should preclude fixation. Nm between central and southern populations or between them and populations in the northern fragment was lower, 0.99-1.66, indicating a degree of genetic isolation. Multilocus outcrossing rates (t(m)) ranged from 0.836 in the south to 0.897 in the north. Therefore, selfing is low but statistically significant. The equilibrium inbreeding coefficient (F(e)) calculated from t(m) was in good agreement with observed inbreeding coefficients, suggesting that weeping piñon may be near equilibrium with respect to inbreeding and selection against selfed trees. Weeping piñon was variable at all loci polymorphic in maxipiñon (Pinus maximartinezii) and, therefore, qualifies as a possible progenitor of maxipiñon. Because of the high level of diversity, reasonable levels of gene flow within the northern fragment of weeping piñons range, high rates of outcrossing, and, perhaps, only weak selection against inbred trees, protection in reserves would be a viable option for conservation.

Genic diversity, genetic structure, and mating system of Brewer spruce (Pinaceae), a relict of the Arcto-Tertiary forest

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 spruces narrow, fragmented distribution, the outlook for its conservation was good, with the exception of possible negative effects of logging.

Relationships among the Spruces (Picea, Pinaceae) of Southwestern North America

Abstract Numerous populations from six spruce taxa, including four relict endemics, Picea chihuahuana (Chihuahua spruce), P. martinezii (Martínez 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 Neis 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 morphology.

Applying landscape genomic tools to forest management and restoration of Hawaiian koa (Acacia koa) in a changing environment

Identifying and quantifying the importance of environmental variables in structuring population genetic variation can help inform management decisions for conservation, restoration, or reforestation purposes, in both current and future environmental conditions. Landscape genomics offers a powerful approach for understanding the environmental factors that currently associate with genetic variation, and given those associations, where populations may be most vulnerable under future environmental change. Here, we applied genotyping by sequencing to generate over 11,000 single nucleotide polymorphisms from 311 trees and then used nonlinear, multivariate environmental association methods to examine spatial genetic structure and its association with environmental variation in an ecologically and economically important tree species endemic to Hawaii, Acacia koa. Admixture and principal components analyses showed that trees from different islands are genetically distinct in general, with the exception of some genotypes that match other islands, likely as the result of recent translocations. Gradient forest and generalized dissimilarity models both revealed a strong association between genetic structure and mean annual rainfall. Utilizing a model for projected future climate on the island of Hawaii, we show that predicted changes in rainfall patterns may result in genetic offset, such that trees no longer may be genetically matched to their environment. These findings indicate that knowledge of current and future rainfall gradients can provide valuable information for the conservation of existing populations and also help refine seed transfer guidelines for reforestation or replanting of koa throughout the state.

Genetic conservation and management of the California endemic, Torrey pine (Pinus torreyana Parry): Implications of genetic rescue in a genetically depauperate species

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.