Rangewide Genetic Diversity in Natural Populations of Chinese Pine (Pinus tabulaeformis)

Thirteen natural populations from throughout the range of the Chinese pine (Pinus tabulaeformis Carr.) were examined using inter-simple sequence repeat markers to characterize the genetic structure at the species level and to compare the extent and distribution of genetic variation among central, intermediate, and marginal populations. Although the total genetic variation in the Chinese pine was mainly maintained within populations, the genetic differentiation among populations was significant (P < 0.001). The genetic divergence was significantly correlated with geographic distance (P < 0.05). Genetic diversity tended to decrease from the central to intermediate and marginal populations. The marginal populations had significantly lower intrapopulation genetic diversity than central populations (P < 0.05). Cluster analysis based on Nei’s unbiased genetic distances confirmed the difference among four central populations and the rest. Both historical and contemporary factors may have played key roles in shaping the spatial genetic structure of this species.     

Genetic Conservation of Insular Populations of Monterey Pine (Pinus Radiata D. Don)

Monterey pine (Pinus radiata D. Don) has only five extant native populations: three disjunct populations along the coast of California, USA and two on Mexican islands. All populations have been influenced by human activity, but the island populations in particular have been affected by introduced biota. On Guadalupe Island, the pine population has suffered drastically from overgrazing by introduced goats. We visited both island populations and described their status, took measurements, and made seed collections. We counted approximately 200 mature pine trees and virtually no seedlings on Guadalupe Island: a reduction of approximately half the population in the last 50 years. The trees are all large (mean diameter of 144 cm) –considerably larger than trees from the other four populations – and arguably near the end of their natural lifespan. The population on Cedros Island is much more robust, with thousands of trees. None sampled were as large as those on Guadalupe Island (mean diameter of 20 cm) and many groves were young and even-aged – presumably the consequence of natural regeneration after a recent fire. Tissue samples from trees on both islands did not show evidence of infection from the pitch canker pathogen, Fusarium circinatum, that has caused significant mortality in the three mainland populations. Caution is recommended in any restoration activity for the Guadalupe Island pines. Inbreeding levels could indicate the need for some planting or seeding intervention but there are also risks associated with this. Natural regeneration – after goat removal – is preferred.     

Genetic Divergence and Fitness Convergence under Uniform Selection in Experimental Populations of Bacteria

Replicate populations of bacteria were propagated for 1000 generations in the laboratory. The growth substrate was periodically renewed, so that during most generations (cell doublings) it was not limiting. The final clones demonstrated about a 40% fitness increase when competed against their common ancestor. This increase was uniform both among and within populations despite extensive differentiation in correlated traits: cell size, resistance to starvation and dry mass of culture. It is suggested that genetic diversity developed because selection promoted any changes directing cell activity toward a higher maximum growth rate. Evolution of this trait halted at a similar level when some basic constraints on bacterial metabolism were met. The selective values of emerging mutations must have depended on the genetic background. They would be beneficial early in evolution but ineffective near the limit of adaptation. This hypothesis was tested for one mutation that affected both fitness and colony morphology. In some clones it was the first adaptive mutation and provided a third of the total fitness increase, but it was not assimilated by the clones that reached the adaptive ceiling in some other way. Near the limit of adaptation, epistasis levels off the fitnesses of genetically variable clones.     

Microsatellite DNA analysis of genetic effects of harvesting in old-growth eastern white pine (Pinus strobus) in Ontario, Canada

Microsatellite DNA markers from 13 simple sequence repeat (SSR) loci were used to compare genetic diversity between preharvest pristine and postharvest residual gene pools of two adjacent virgin, old-growth ( approximately 250 years) stands of eastern white pine (Pinus strobus L.) in Ontario. There was concurrence in genetic diversity changes in the postharvest gene pools of the two stands. The total and mean numbers of alleles detected in each stand were reduced by approximately 26% after tree density reductions of approximately 75%. Approximately 18 and 21% of the low-frequency (0. 25 > P > or = 0.01) alleles and 76 and 92% of the rare (P < 0.01) alleles were lost from residual stands A and B, respectively, after harvesting. Multilocus gametic diversity was reduced by 38 and 85% and genotype additivity by approximately 50% in the residual stands after harvesting. Latent genetic potential of each stand was reduced by approximately 40%. Although heterozygosity was reduced (1-5%) in the postharvest residual stands, the reductions were not substantial and not comparable to those using other genetic diversity measures. The reductions in genetic diversity measures were slightly higher than those theoretically expected in postbottleneck populations according to drift theory. In the absence of substantial gene migration that could ameliorate the genetic losses, the ability of the postharvest white pine gene pools to adapt to changing environmental and disease conditions may have been compromised. The microsatellite DNA results for genetic effects of harvesting in old-growth eastern white pine stands were similar to those that we reported earlier from allozyme analysis (Buchert et al. 1997). The results indicate that silvicultural practices should ensure that the gene pools of remaining pristine old-growth stands are reconstituted in the regenerating stands.     

Essential Oil Variability in Natural Populations of Picea omorika,a Rare European Conifer

This study is the first report on the composition and variability of essential oil in the relic, endemic, and vulnerable tree species Serbian spruce, Picea omorika, in its natural populations. In the needles of 108 trees of four natural populations, 49 components of essential oils were identified. The main compounds were bornyl acetate (29.2%), camphene (18.7%), and α‐pinene (12.9%). Fourteen additional components had the contents of up to 0.5%: α‐cadinol (6.1%), limonene (5.8%), santene (3.5%), (E)‐hex‐2‐enal (2.9%), T‐cadinol (2.9%), δ‐cadinene (2.3%), tricyclene (2.1%), myrcene (1.6%), β‐pinene (1.2%), borneol (0.9%), germacrene D (0.9%), α‐muurolene (0.6%), and two unidentified compounds. Population IV from Mile?evka Canyon had a much higher content of bornyl acetate (42.9%). Populations I–III from Mt. Tara were more abundant in sesquiterpenes (up to 18.2%). The content of bornyl acetate, the multi‐variation analyses according to seven selected components, especially the cluster analysis and genetic analysis of α‐cadinol, which suggested the monogenic type of heredity, showed a clear differentiation of the two geographic areas, the similarity of populations I–III from the area of Mt. Tara, and the separation of the population IV from Mile?evka Canyon.     

Identifying Signatures of Natural Selection in Tibetan and Andean Populations Using Dense Genome Scan Data

High-altitude hypoxia (reduced inspired oxygen tension due to decreased barometric pressure) exerts severe physiological stress on the human body. Two high-altitude regions where humans have lived for millennia are the Andean Altiplano and the Tibetan Plateau. Populations living in these regions exhibit unique circulatory, respiratory, and hematological adaptations to life at high altitude. Although these responses have been well characterized physiologically, their underlying genetic basis remains unknown. We performed a genome scan to identify genes showing evidence of adaptation to hypoxia. We looked across each chromosome to identify genomic regions with previously unknown function with respect to altitude phenotypes. In addition, groups of genes functioning in oxygen metabolism and sensing were examined to test the hypothesis that particular pathways have been involved in genetic adaptation to altitude. Applying four population genetic statistics commonly used for detecting signatures of natural selection, we identified selection-nominated candidate genes and gene regions in these two populations (Andeans and Tibetans) separately. The Tibetan and Andean patterns of genetic adaptation are largely distinct from one another, with both populations showing evidence of positive natural selection in different genes or gene regions. Interestingly, one gene previously known to be important in cellular oxygen sensing, EGLN1 (also known as PHD2), shows evidence of positive selection in both Tibetans and Andeans. However, the pattern of variation for this gene differs between the two populations. Our results indicate that several key HIF-regulatory and targeted genes are responsible for adaptation to high altitude in Andeans and Tibetans, and several different chromosomal regions are implicated in the putative response to selection. These data suggest a genetic role in high-altitude adaption and provide a basis for future genotype/phenotype association studies necessary to confirm the role of selection-nominated candidate genes and gene regions in adaptation to altitude.     

Genetic Diversity and Divergence in Chinese Yak (Bos grunniens) Populations Inferred from Blood Protein Electrophoresis

In 6 Chinese yak (Bos. Grunniens) populations including 177 yaks, 34 blood protein loci were studied by horizontal starch gel electrophoresis, four of these loci (AKP, ALB, LDH-1, TF) were found to be polymorphic. The percentage of polymorphic loci(P) is 0.118, the mean individual heterozygosity(H) is 0.015, which means a low level of genetic diversity in the whole Chinese yak population. The coefficient of gene differentiation (G _ST ) is 0.0625, which indicated an almost-indistinguishable divergence among different populations at the level of blood protein electrophoresis.     

Phthalides produced by Coccomyces strobi (Rhytismataceae,Rhytismatales) isolated from needles of Pinus strobus

As part of a broad survey of the metabolites produced by foliar endophytes of conifers, a strain was isolated from surface-sterilized needles collected from eastern white pine on the north shore of Lake Huron, Ontario. The isolate was sterile in culture. Species identity was not resolved by ITS sequence because of the absence of corresponding sequences in public sequence databases, however the strain was placed in Rhytismataceae (Rhytismatales). Field collections targeting Rhytismataceae species on Pinus strobus were conducted enabling the isolate to be identified as Coccomyces strobi. An extract of the culture filtrate demonstrated moderate antifungal activity. Two new phthalides, (±)-strobides A-B (1-2) and the known phytotoxin cyclopaldic acid (3) were characterized from C. strobi DAOMC 251937. This is the first record of the occurrence of this species as a foliar endophyte. Previous reports have suggested that it is a cambium endophyte associated with small cankers on branches. The production of the phytotoxin cyclopaldic acid suggests that C. strobi is a weak opportunistic pathogen, switching from an endophytic to a pathogenic phase when the host tissue becomes weakened.     

Divergent Selection and Local Adaptation in Disjunct Populations of an Endangered Conifer,Keteleeria davidiana var. formosana (Pinaceae)

The present study investigated the genetic diversity, population structure, F _ST outliers, and extent and pattern of linkage disequilibrium in five populations of Keteleeria davidiana var. formosana, which is listed as a critically endangered species by the Council of Agriculture, Taiwan. Twelve amplified fragment length polymorphism primer pairs generated a total of 465 markers, of which 83.74% on average were polymorphic across populations, with a mean Nei’s genetic diversity of 0.233 and a low level of genetic differentiation (approximately 6%) based on the total dataset. Linkage disequilibrium and HICKORY analyses suggested recent population bottlenecks and inbreeding in K. davidiana var. formosana. Both STRUCTURE and BAPS observed extensive admixture of individual genotypes among populations based on the total dataset in various clustering scenarios, which probably resulted from incomplete lineage sorting of ancestral variation rather than a high rate of recent gene flow. Our results based on outlier analysis revealed generally high levels of genetic differentiation and suggest that divergent selection arising from environmental variation has been driven by differences in temperature, precipitation, and humidity. Identification of ecologically associated outliers among environmentally disparate populations further support divergent selection and potential local adaptation.     

Genetic diversity and spatial genetic structure of Pinus strobus (Pinaceae) across an island landscape inferred from allozyme and cpDNA markers

The Beaver Island Archipelago (BIA) provides a model system to address the impact of long-term isolation on genetic diversity and gene flow. Low lake levels are assumed to have caused the BIA to be attached to mainland Michigan for at least 4000 years (10000 yr B.P.- 6000 yr B.P.), eventually, rising lake levels would have kept the islands isolated since 6000 yr B.P. If the island populations of a plant species in the BIA were indeed once continuous with the mainland of Michigan, then we would expect similar levels of genetic diversity in populations of such a species on the islands vs. the mainland. We compared levels of allozyme genetic diversity of 20 plots of Pinus strobus in the BIA with two mainland populations in northern Michigan. In addition, if pollen is a primary agent of gene flow across islands, a low degree of allozyme differentiation among the island populations of P. strobus in the BIA would be evident. Furthermore, since seed dispersal is more limited than pollen dispersal in P. strobus, a more pronounced spatial genetic structure (SGS) is expected in allozymes than in cpDNA markers. To gain insights on the pattern of seed and pollen dispersal among the 20 plots, we further analyzed spatial autocorrelation using Moran's I-statistics for both data sets [biparentally inherited, allozymes and paternally inherited, cpDNA microsatellites (cpDNA SSR)]. We found a similar level of allozyme variability in both the BIA (mean H _e = 0.080) and the two mainland populations (mean H _e = 0.078). As predicted, we observed a low but significant degree of genetic divergence among populations for allozymes (mean F _ST = 0.033 across 20 plots). Our allozyme-based SGS analysis revealed significant evidence of SGS (i.e. isolation-by-distance; slope β = ?0.194 from regression analysis of observed averaged Moran's I values against the logarithm of the upper bound of six distance classes). In contrast, little evidence of SGS was found in cpDNA SSR data across the BIA (β = 0.013). These results suggest that although gene flow via seed dispersal is somewhat limited, pollen flow has been sufficient to maintain genetic diversity and prevent differentiation across the island landscape over several thousand years of isolation.     

Molecular Proxies for Climate Maladaptation in a Long-Lived Tree (Pinus pinaster Aiton,Pinaceae)

Understanding adaptive genetic responses to climate change is a main challenge for preserving biological diversity. Successful predictive models for climate-driven range shifts of species depend on the integration of information on adaptation, including that derived from genomic studies. Long-lived forest trees can experience substantial environmental change across generations, which results in a much more prominent adaptation lag than in annual species. Here, we show that candidate-gene SNPs (single nucleotide polymorphisms) can be used as predictors of maladaptation to climate in maritime pine (Pinus pinaster Aiton), an outcrossing long-lived keystone tree. A set of 18 SNPs potentially associated with climate, 5 of them involving amino acid-changing variants, were retained after performing logistic regression, latent factor mixed models, and Bayesian analyses of SNP–climate correlations. These relationships identified temperature as an important adaptive driver in maritime pine and highlighted that selective forces are operating differentially in geographically discrete gene pools. The frequency of the locally advantageous alleles at these selected loci was strongly correlated with survival in a common garden under extreme (hot and dry) climate conditions, which suggests that candidate-gene SNPs can be used to forecast the likely destiny of natural forest ecosystems under climate change scenarios. Differential levels of forest decline are anticipated for distinct maritime pine gene pools. Geographically defined molecular proxies for climate adaptation will thus critically enhance the predictive power of range-shift models and help establish mitigation measures for long-lived keystone forest trees in the face of impending climate change.     

Characterization of pollen tube development in Pinus strobus (Eastern white pine) through proteomic analysis of differentially expressed proteins

The differentially expressed proteins in pollen tubes indicate their specific roles in this stage of male gametophyte development. To isolate these proteins, 2-DE was done using ungerminated pollen and 2-day-old pollen tubes of Pinus strobus. Results show that 645 and 647 protein spots were clearly resolved from pollen grains and pollen tubes, respectively. Thirty-eight protein spots were expressed only in pollen tubes, while 19 increased in intensity. MALDI-TOF MS was used to generate tryptic peptide masses that were submitted to Mascot for identification. Of the differentially expressed proteins, 12% matched with hypothetical proteins, 33% did not hit any protein, and for the 55%, a putative function was assigned based on similarity of sequences with previously characterized proteins. Therefore, pollen tube development can be characterized by the cellular activities that involve metabolism, stress/defense response, gene regulation, signal transduction, and cell wall formation. This study expands our understanding of the changes in protein expression associated with pollen tube development and provides insights into the molecular programs that separate the development of the pollen tubes from pollen grains. This is the first report that describes a global analysis of differentially expressed proteins from the pollen tube of any seed plant.     

Genetic,Ecological and Morphological Divergence between Populations of the Endangered Mexican Sheartail Hummingbird (Doricha eliza)

The Mexican Sheartail (Doricha eliza), an endangered hummingbird, is endemic to Mexico where two populations have a disjunct distribution. One population is distributed along the northern tip of the Yucatan Peninsula whereas the other is mostly restricted to central Veracruz. Despite their disjunct distribution, previous work has failed to detect morphological or behavioral differences between these populations. Here we use variation in morphology, mtDNA and nuDNA sequences to determine the degree of morphological and molecular divergence between populations, their divergence time, and historical demography. We use species distribution modeling and niche divergence tests to infer the relative roles of vicariance and dispersal in driving divergence in the genus. Our Bayesian and maximum likelihood phylogenetic analyses revealed that Doricha eliza populations form a monophyletic clade and support their sister relationship with D. enicura. We found marked genetic differentiation, with reciprocal monophyly of haplotypes and highly restricted gene flow, supporting a history of isolation over the last 120,000 years. Genetic divergence between populations is consistent with the lack of overlap in environmental space and slight morphological differences between males. Our findings indicate that the divergence of the Veracruz and Yucatan populations is best explained by a combination of a short period of isolation exacerbated by subsequent divergence in climate conditions, and that rather than vicariance, the two isolated ranges of D. eliza are the product of recent colonization and divergence in isolation.     

松针叶群数量和寿命的水平与垂直变化趋势分析

根据对巴山松针叶群体的水平和垂直变化特征及趋势进行的研究,得到如下结果：(1)单株木的针叶总数和各龄针叶总数随胸径增加而增多,随密度增加而减少;当年生针叶数量所占比例随径阶增加而增大,2年生针叶比例与此相反,而1年生和3年生针叶比例基本保持稳定。(2)单株木的径阶愈小,针叶平均寿命亦愈长;就针叶平均生存期限而言,劣势木最短,优势木次之,而平均木最长。(3)各龄级针叶群体的数量一般在树冠中部所占比例最大,下部所占比例次之,上部比例最小。在林分中处于不同地位的林木表现形式略有差异,与树冠内光照的分布有关。(4)针叶的内禀增长率随着径阶的增大、树高的增加及相对光照强度的增高而增加;树冠中针叶的平均寿命随树高增加而减小。另外,对产生上述结果的原因也进行了部分探讨。     

Reproductive Isolation with Little Genetic Divergence in Sympatric Populations of Brown Trout (SALMO TRUTTA)

Two reproductively isolated demes of brown trout coexist in a small Swedish mountain lake, Lake Bunnersj?rna. We electrophoretically examined 102 specimens from that lake for 27 enzymes encoded by 54 loci. The two demes are fixed for different alleles at a lactate dehydrogenase locus (LDH-1); statistically significant allele frequency differences at five other loci further support the complete lack of gene flow between these demes. There are significant differences in growth rates between fish in the two demes, but no further morphological differentiation h-s been detected.--In light of these findings, the genetic distance between these populations is surprisingly small (Nei's I = 0.975). These demes represent one of the least genetically divergent, reproductively isolated sympatric pair of vertebrate populations that have been identified. The results are discussed from both an evolutionary and ecological perspective.     

The Genetic Structure of Natural Populations of Drosophila Melanogaster. Xxii. Comparative Study of DNA Polymorphisms in Northern and Southern Natural Populations

Restriction map variation in four gene regions (Adh, Amy, Pu and Gpdh) was surveyed for 86 second chromosomes from northern (Aomori) and southern (Ogasawara) Japanese populations of Drosophila melanogaster (43 chromosomes from each population). The regions examined cover a total of 62 kilobases. Estimates of nucleotide diversity (pi) were approximately constant across the gene regions and populations examined. The distribution of restriction site polymorphisms was compatible with the expectation from the neutral mutation-random genetic drift hypothesis, but insertion/deletion polymorphisms were not consistent with it. While the two populations shared a majority of restriction site polymorphisms, frequencies of individual restriction site variants were significantly different between the two populations at 7 out of 35 segregating sites. In addition, an insertion in the Amy region was found in 15 chromosomes from the Ogasawara sample but absent in the Aomori sample. A considerable difference was observed in the number of rare insertions and deletions between the two populations. The numbers of aberrations uniquely represented were 16 in the Ogasawara sample and only 3 in the Aomori sample. These findings suggest that the two populations were differentiated from each other to some degree by means of random genetic drift and/or other factors.     

Genetic Variability and Structuring of Arctic Charr (Salvelinus alpinus) Populations in Northern Fennoscandia

Variation in presumably neutral genetic markers can inform us about evolvability, historical effective population sizes and phylogeographic history of contemporary populations. We studied genetic variability in 15 microsatellite loci in six native landlocked Arctic charr (Salvelinus alpinus) populations in northern Fennoscandia, where this species is considered near threatened. We discovered that all populations were genetically highly (mean F _ST ≈ 0.26) differentiated and isolated from each other. Evidence was found for historical, but not for recent population size bottlenecks. Estimates of contemporary effective population size (N _e) ranged from seven to 228 and were significantly correlated with those of historical N _e but not with lake size. A census size (N _C) was estimated to be approximately 300 individuals in a pond (0.14 ha), which exhibited the smallest N _e (i.e. N _e/N _C = 0.02). Genetic variability in this pond and a connected lake is severely reduced, and both genetic and empirical estimates of migration rates indicate a lack of gene flow between them. Hence, albeit currently thriving, some northern Fennoscandian populations appear to be vulnerable to further loss of genetic variability and are likely to have limited capacity to adapt if selection pressures change.     

High Levels of Genetic Divergence among Populations in a Weedy Fern, Pteris multifida Poir.

Abstract Intragametophytic selfing in the homosporous ferns has been viewed as an advantageous mechanism permitting colonization of distant, open habitats. However, there is little evidence for the generality of colonization through intragametophytic selfing. In this study, the genetic structure of Pteris multifida was determined using Wright's F-statistics in order to detect the occurrence of this type of colonization. A high level of genetic divergence among populations (F_ST= 0.543) was found in P. multifida. This genetic divergence seems to be caused by frequent occurrences of colonization through intragametophytic selfing.