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, H_e, 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 H_e was closely related to the logarithm of the number of mature trees in the population (r_He,N = 0.93). Diversity among populations, F_ST, was 24.8% of the total diversity, which is higher than that observed in almost all conifer species studied. Nei's genetic distance, D, was not related to geographic distance between populations, and D? was 0.033, which is higher than estimates for most wide-ranging species. Most populations had excess homozygosity and the fixation index, F_IS, 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.     

Understory physical structures reduce browsing damage to palatable shrubs in a dry conifer forest,western North America

High densities of cattle (Bos taurus) and wild ungulates (Rocky Mountain elk, Cervus canadensis; mule deer, Odocoileus hemionus) have impacted the abundance and population dynamics of palatable woody species in forests of the interior Pacific Northwest, USA. As a result, large shrubs are functionally absent from some forest stands. Physical structures can provide safe sites for browsed species to persist within forests. We evaluated the role of coarse woody debris and conifer trees in protecting a common, yet heavily browsed species, serviceberry (Amelanchier alnifolia) from elk, deer and cattle. We measured height and architecture of individuals and the degree to which they were protected by coarse woody debris and unpalatable conifers in areas exposed to ungulates and in ungulate exclosures. Multiple linear regression and quantile regression were used to test for the effects of protection and foliar overlap on plant height. Results showed that increased protection and foliar overlap resulted in a lower proportion of shrubs exhibiting arrested architecture. Shrub height increased as foliar overlap and protection increased, with effects primarily restricted to high levels of protection (>?300° surrounded by nearby conifer trees and/or coarse woody debris). Taller shrubs were most associated with intermediate levels of foliar overlap. Results support the hypothesis that understory structural elements can act as protective barriers. Forest management actions (e.g., prescribed fire, understory thinning) that reduce the prevalence of structures may unintentionally suppress browsed shrub species and contribute to the continued functional absence of tall deciduous species in dry conifer forests.

     

针叶小爪螨不同种群在针叶树和阔叶树上的生长发育和繁殖及其生殖隔离

报道丁针叶小爪螨Oligonychus ununguis (Jacobi）的4个种群在针叶树和阔叶树上的生长发育和繁殖及其生殖隔离的研究结果。饲养试验证明,针叶树(杉木)种群不能在板栗、麻栎等阔叶树上存活;阔叶树(板栗、麻栎)种群也不能在杉木、黑松、赤松等针叶树上存活。交配试验证明,针叶树种群和阔叶树种群虽有交配行为,但不能正常繁衍后代,两种群间存在着明显的生殖隔离。据此认为针叶树种群和阔叶树种群有可能为两个不同种。     

Genetic and environmental contributions to the winter hardiness of conifers

Summary

Both genetic and environmental components are involved in the processes of winter hardening and dehardening which permit needles of conifers like Norway spruce to survive very low temperatures (< - 30°C) over winter and to recover fully in time for the following and subsequent seasons. One of the major environmental effects of increasing concentrations of atmospheric ozone (O₃) in recent summers has been to affect detrimentally the ability of conifer needles to harden properly and at the correct rate the following autumn. Part of the mechanism by which this occurs in the cytoplasm of needle cells has been traced to detrimental effects on both the Δ¹² fatty acid desaturase and the unusual Δ⁵ desaturase which appears to be part of the low temperature survival mechanism of conifers. The genetic component of winter hardening also involves needle lipids. Studies of lipids in the needles of Norway spruce trees of different provenances growing for many years in the UK have shown that they change during winter hardening as though they were still on trees in the original sites throughout Europe from which the seeds of these trees were initially collected.     

Dynamics of forests with Araucariaceae in the western Pacific

Abstract. Several species of Araucaria and Agathis (Araucariaceae) occur as canopy emergents in rain forests of the western pacific region, often representing major components of total stand biomass. New data from permanent forest plots (and other published work) for three species (Araucaria hunsteinii from New Guinea, A. laubenfelsii from New Caledonia, and Agathis australis from New Zealand) are used to test the validity of the temporal stand replacement model proposed by Ogden (1985) and Ogden & Stewart (1995) to explain the structural and compositional properties of New Zealand rain forests containing the conifer Agathis australis. Here we propose the model as a general one which explains the stand dynamics of rain forests with Araucariaceae across a range of sites and species in the western Pacific. Forest stands representing putative stages in the model were examined for changes through time in species recruitment, growth and survivorship, and stand richness, density and basal area. Support for the model was found on the basis of: 1. Evidence for a phase of massive conifer recruitment following landscape-scale disturbances (e.g. by fire at the Huapai site, New Zealand for Agathis australis); 2. Increasing species richness of angiosperm trees in the pole stage of forest stand development (i.e. as the initial cohort of conifers reach tree size; >10 cm DBH); 3. A high turnover rate for angiosperms (<100 yr), and low turnover for conifers (≥ 100 yr) in the pole stage, but similar turnover rates for both components (50–100 yr) as forests enter the mature to senescent phase for the initial conifer cohort; 4. Very low rates of recruitment for conifers within mature stands, and projected forest compositions which show increasing dominance by angiosperm tree species; 5. A low probability of conifer recruitment in large canopy gaps created by conifer tree falls during the initial cohort senescent phase, which could produce a second generation low density stand in the absence of landscape scale disturbance; 6. Evidence that each of the three species examined required open canopy conditions (canopy openness > 10 %) for successful recruitment. The evidence presented here supports the temporal stand replacement model, but more long-term supporting data are needed, especially for the phase immediately following landscape level disturbance.     

Characterization of EST-SSRs in loblolly pine and spruce

In the first large study of conifer expressed sequence tag-simple sequence repeats (EST-SSRs), two large conifer EST databases were characterized for EST-SSRs. One database was from “interior spruce” (white and Engelmann spruce in Southern British Columbia) and Sitka spruce, while the other was from loblolly pine. We found 475 and 629 unique EST-SSRs in loblolly pine and spruce, respectively. 3′ ESTs contained 14% more SSRs than 5′ EST reads in loblolly pine and 41% more in spruce. Conifer EST-SSRs differed conspicuously from angiosperm EST-SSRs in several aspects. EST-SSRs were considerably less frequent in conifers (one EST-SSR every ∼50 kb) than in angiosperms (one EST-SSR every ∼20 kb). Dinucleotide repeats were the most abundant repeat class in conifers, while in angiosperms, trinucleotides were most common. Finally, the AT motif was the dominant motif recovered in both conifer species, whereas AG was the most common dinucleotide repeat in angiosperms. Also, as these EST-SSRs in conifers could be developed into useful genetic markers, our work demonstrates the value of large-scale EST sequencing projects for in-silico approaches for marker development.     

Prospects for genomic selection in conifer breeding: a simulation study of Cryptomeria japonica

Genomic selection (GS) can be a powerful technology in conifer breeding because conifers have long generation intervals, protracted evaluation times, and high costs of breeding inputs. To elucidate the potential of GS for conifer breeding, we simulated 60-year breeding programs in Cryptomeria japonica with and without GS. In conifers, the rapid decay of linkage disequilibrium (LD) can constitute a severe barrier to application of GS. For overcoming that barrier, we proposed an idea to leverage a seed orchard system, which has been used commonly in conifers, because some degree of LD exists in progenies derived from the limited number of elite trees in a seed orchard. The base population used for simulations consisted of progenies from 25 elite trees. Results show that GS breeding (GSB) done without model updating outperformed phenotypic selection breeding (PSB) during the first 30 years, but the genetic gain achieved over the 60 years was smaller in GSB than in PSB. However, GSB with model updating outperformed PSB over the 60 years. The genetic gain achieved over the 60 years of GSB with model updating was nearly twice that of PSB. Advantages of GSB over PSB prevailed, even for a low heritability polygenic trait. The number of markers necessary for efficient GS was a realistic level (e.g., one in every 1 cM), although higher marker density engendered higher accuracy of selection. These results suggest that GS can be useful in C. japonica breeding. Updating of the prediction model was, however, indispensable for attaining the large genetic gain.     

Seasonal and age-related variation in the needle quality of five conifer species

Summary Age changes of foliage resource quality (water, nitrogen, fibre, phenolics and toughness) were studied in five species of conifer (Pinus sylvestris L.), Picea abies (L.) Karsten, Tsuga heterophylla (Rafinesque) Sargent (all Pinaceae), Chamaecyparis lawsonian (Murray) Parlatore and Thuja plicata D. Don (both Cupressaceae) over a 2-year period in an English forest.Mature foliage of Pinus sylvestris was characterized by higher levels of nitrogen, fibre and toughness, and lower phenolics, and that of Tsuga heterophylla by higher levels of phenolics, and lower fibre and toughness levels, than the mature needles of the other species studied. Immature needles had higher levels of water and nitrogen, and lower levels of fibre and toughness, than older needles. Immature needles of Picea abies and Tsuga heterophylla had a high concentration of phenolics, which decreased with needle maturity. By mid-August, the levels of most of the foliar constituents in current-year needles had stabilized at levels maintained for the next year. Sampling revealed a fall in the concentration of phenolics, fibre and water in mature needles between March and June. Possible reasons for this seasonal trend are discussed. The levels of conifer foliar constituents were compared with levels recorded in broadleaf trees. Conifers had greater concentrations of all measured foliar constituents, but, with the exception of the six fold greater toughness of conifer needles, the differences between broadleaves and conifers were less than those between the immature and mature conifer needles. Previous studies have related the abundance of Lepidoptera on conifers to hostplant taxonomic relationships. However, the foliar constituents measured in this study were poor predictors of taxonomic relationships between the conifers. It is suggested that the abundance of Lepidoptera on conifers is not determined by levels of general foliar constituents and the role of other hostplant factors in shaping lepidopteran utilization of conifers is discussed.     

An Improved Protocol for Intact Chloroplasts and cpDNA Isolation in Conifers

Background

Performing chloroplast DNA (cpDNA) isolation is considered a major challenge among different plant groups, especially conifers. Isolating chloroplasts in conifers by such conventional methods as sucrose gradient and high salt has not been successful. So far, plastid genome sequencing protocols for conifer species have been based mainly on long-range PCR, which is known to be time-consuming and difficult to implement.

Methodology/Principal Findings

We developed a protocol for cpDNA isolation using three different conifer families: Araucaria angustifolia and Araucaria bidwilli (Araucariaceae), Podocarpus lambertii (Podocarpaceae) and Pinus patula (Pinaceae). The present protocol is based on high salt isolation buffer followed by saline Percoll gradient. Combining these two strategies allowed enhanced chloroplast isolation, along with decreased contamination caused by polysaccharides, polyphenols, proteins, and nuclear DNA in cpDNA. Microscopy images confirmed the presence of intact chloroplasts in high abundance. This method was applied to cpDNA isolation and subsequent sequencing by Illumina MiSeq (2×250 bp), using only 50 ng of cpDNA. Reference-guided chloroplast genome mapping showed that high average coverage was achieved for all evaluated species: 24.63 for A. angustifolia, 135.97 for A. bidwilli, 1196.10 for P. lambertii, and 64.68 for P. patula.

Conclusion

Results show that this improved protocol is suitable for enhanced quality and yield of chloroplasts and cpDNA isolation from conifers, providing a useful tool for studies that require isolated chloroplasts and/or whole cpDNA sequences.     

针叶树基因组特征及其序列资源挖掘进展

针叶树是裸子植物中最大也是分布最广的一支。作为多年生木本植物,针叶树不仅为工业提供建筑、造纸等重要原料和其它可再生能源,而且在北半球的生态平衡中也起着重要作用。因其独特的分类地位、重要的经济价值和生态价值,针叶树序列资源挖掘备受重视。然而其庞大且复杂的基因组阻碍了这一进程,截至2013年4月,尚无获得全基因组序列的针叶树种。随着第2代测序技术的出现及生物信息学的快速发展,针叶树序列资源挖掘也从转录组过渡到全基因组测序,后者己在松属（Pinus）、云杉属（Picea）和黄杉属（Pseudotsuga）部分树种中开展。该文首次归纳了针叶树基因组特征．回顾了针叶树序列资源挖掘进程,并重点介绍了火炬松（Pinustaeda）、欧洲云杉（Piceaabies）和白云杉（Piceaglauca）的全基因组测序项目。     

Foraging behaviour, host plant and host location in the aphid hyperparasitoid Euneura augarus

Euneura augarusis a specialized ectohyperparasitoid of conifer lachnids, which causes considerable mortality in mummies of conifer lachnid parasitoids. For the search on a large scale, E. augarusfemales rely mainly on volatile secondary plant compounds of conifers to locate potential host plants. In the medium-range (i.e., on a given host plant), females detect the presence of hosts either during spiral search flights or during search by walking. Search flights were more effective when mummies were dispersed, while clumped mummies were mainly found by walking. On ant-attended trees, E. augaruswas not able to forage successfully. Choice experiments with Aphidius ervi-mummies showed that E. augarusis able to develop in species that are not attacked in the field. We hypothesize that the proximate mechanism of host plant specificity, and as a consequence, host aphid specificity seems to be the use of typical conifer volatiles for host finding which provide the `search image' for the species.     

Conifer colonization of a 350-year old rock fall at Lassen Volcanic National Park in northern California

Montane conifers of western North America commonly colonize mineral surfaces resulting from landslides, lahars, mudflows, and rock avalanches. This colonization can include shade-tolerant conifers that may eventually dominate the forest in a pattern termed “direct” succession. Documenting examples of this long-term successional process are useful for identifying alternative successional trajectories and indicating potential controlling mechanisms for subsequent experimental analysis. This study (1) analyzes the 1992 status of the conifer colonization on the coarse-textured surface of a 1650 AD rock avalanche in northern California and (2) measures individual growth and survivorship in permanent plots between 1992 and 2003. Increment cores of large trees indicated initial conifer colonization before 1700 AD with continuous subsequent colonization. Mean conifer density in 1992 was 725 (SD = 747) ha⁻¹ with densities increasing with decreasing rock sizes. Densities were not correlated with distances to possible seed sources. Median heights were <1 m, and the mean proportional height growth rate for healthy individuals was 0.0166 year⁻¹. The mortality rate for individuals ≥0.1-m tall was <0.007 year⁻¹. The conifers were more numerous than shrubs, and there was little apparent evidence of facilitation or inhibition of conifers. The species assemblage is mostly (89%) Abies concolor, Pinus monticola, and Pinus ponderosa individuals dispersed across an elevation range of 1870–2040 m a. s. l. This is an atypical species mix for these elevations in this location, and this mix is not readily predicted from species properties such as seed mass, seed flight distance, or drought tolerance.     

Understory responses to restoration in aspen‐conifer forests around the Lake Tahoe Basin: residual stand attributes predict recovery

The removal of conifers from aspen (Populus tremuloides) stands is being undertaken throughout the western United States to restore aspen for local‐ and landscape‐level biodiversity. Current practices include mechanically removing conifers or hand thinning, piling, and burning cut conifers in and adjacent to aspen‐conifer stands. To evaluate the effectiveness of restoration treatments, we examined tree regeneration and herbaceous vegetation cover in thinned, thinned and pile burned, and non‐thinned control stands. Growth rates of small conifer saplings threatening to outcompete and replace aspen were also measured. Two to four years after pile burning, herbaceous vegetation cover within the footprint of burned piles (i.e. burn scars) was 35–73% of that in adjacent areas. Aspen was more likely to regenerate inside burn scars where fewer surrounding trees were true firs. Conifer seedlings were more likely to regenerate in burn scars where more of the surrounding trees were conifers (pine or fir) as opposed to aspen. Fir saplings had much slower growth than did aspen saplings. Overall, our findings show that restoration treatments are promoting desirable outcomes such as enhancing aspen regeneration but that follow‐up treatments will be needed to remove numerous conifer seedlings becoming established after restoration activities. Eliminating conifers, while they are small, growing slowly, and contributing little to fuel loads may be an economical way to prolong restoration treatment effectiveness.     

Regeneration in Atlantic oakwoods: has deer management had a beneficial effect?

Summary

The fragmented Atlantic oakwoods of western Europe are a habitat of conservation importance, and in the UK are threatened by browsing of young trees, invasion by exotic species and under-planting with conifers. Previous research showed that small tree saplings were abundant in Scottish oakwoods, but growth was limited by shading and frequent browsing. Within this study, we aimed to assess whether subsequent changes in deer management had resulted in increased sapling growth, and to determine whether planting of oak within lines of brash left after conifer clearance had offered long-term protection from browsing.

Pellet group counts at two sites in Glen Nant, Argyll, indicated that use by red deer, roe deer and sheep was lower than five years previously. Within one site, sapling survival was high despite continued browsing, and some saplings, particularly hazel, had gained substantial height increments. In contrast, at the second site, survival was low and the surviving saplings had managed no net growth. At a third site in Glen Etive, Argyll, partially protected by fencing, survival of oak saplings was high, and two thirds had increased in height. Planting oak saplings amongst lines of conifer brash did not offer long-term protection, but within a fenced exclosure saplings had grown substantially, despite vigorous competition from the field layer.

Deer management policies within these woods are beginning to show some success in promoting regeneration, but they will need to be continued for a long period to overcome the low growth rates of hardwood species.     

Analysis of character correlations among wood decay mechanisms,mating systems,and substrate ranges in homobasidiomycetes

Homobasidiomycetes include the majority of wood-decaying fungi. Two basic forms of wood decay are known in homobasidiomycetes: white rot, in which lignin and cellulose are degraded, and brown rot, in which lignin is not appreciably degraded. An apparent correlation has been noted between production of a brown rot, decay of conifer substrates, and possession of a bipolar mating system (which has a single mating-type locus, in contrast to tetrapolar systems, which have two mating-type loci). The goals of this study were to infer the historical pattern of transformations in decay mode, mating type, and substrate range characters, and to determine if a causal relationship exists among them. Using nuclear and mitochondrial rDNA sequences, we performed a phylogenetic analysis of 130 species of homobasidiomycetes and performed ancestral state reconstructions by using parsimony on a range of trees, with various loss:gain cost ratios. We evaluated pairwise character correlations by using the concentrated changes test (CCT) of Maddison and the maximum likelihood (ML) method of Pagel. White rot, tetrapolar mating systems, and the ability to decay conifers and hardwoods appear to be plesiomorphic in homobasidiomycetes, whereas brown rot, bipolar mating systems, and exclusive decay of conifers appear to have evolved repeatedly. The only significant correlation among characters was that between brown rot (as the independent character) and exclusive decay of conifer substrates (P < 0.03). This correlation was supported by the CCT on a range of plausible trees, although not with every reconstruction of ancestral states, and by the ML test. Our findings suggest that the evolution of brown rot has promoted repeated shifts to specialization for confier substrates.     

Resin-based defenses in conifers

Bark beetle infestation and associated fungal infection are a serious disease problem in conifer species. Conifers have evolved elaborate, constitutive and inducible, terpene-based defense mechanisms to deter insect pests and their symbiotic fungal pathogens. This process involves the secretion of oleoresin, a complex mixture of monoterpenes, sesquiterpenes and diterpenoid acids. Induced oleoresinosis in grand fir (Abies grandis) provides a model system for studying the regulation of defensive terpene biosynthesis and for identifying relevant genes. The ecological relationships between conifers, beetle pests, beetle predators and fungal pathogens present several possible avenues for manipulating oleoresin composition to improve tree resistance. Possible examples include chemically disguising the host, adding toxins and altering the levels of pheromone precursors, attractants for predators or hormone mimics to disrupt insect development. Strategies and prospects for generating transgenic conifers with increased defense capability are discussed.