Patterns of genotype-environment association in the eastern North American yellow birch (Betula alleghaniensis Britt.)

Opportunities and challenges in assessing climate change vulnerability through genomics

� Springer-Verlag 2005 Abstract Tree-ring characteristics in four species were ex- amined to address whether co-occurring mature trees of dif- ferent successional status respond differently to drought, and whether saplings of these species have a greater re- sponse to drought than mature trees. We examined saplings and mature trees of paper birch, yellow birch, red maple and sugar maple, which varied in successional status (shade- tolerance) and co-occurred at Harvard Forest, Petersham, Mass., USA. Three drought events in 1964-1966, 1981 and 1995 were identified using climate data. For mature trees, there was no significant interspecific difference in relative changes in ring-width index (RWI) during the 1964-1966 and 1995 drought events. However, the interspecific differ- ence was significant in the 1981 drought event. Response function analysis for mature trees showed that the radial growth of sugar maple was mainly controlled by spring and summer precipitation, red maple by spring and sum- mer precipitation and temperature, yellow birch by winter and summer precipitation, and spring and summer tem- perature, and paper birch by spring and summer precipita- tion and spring temperature. Saplings of sugar maple and yellow birch, but not red maple and paper birch, showed significant positive correlations between RWI and annual total precipitation. In the 1995 drought event, saplings and

The observed winter (DJF) precipitation in Southeast China (1961–2010) is characterized by a monopole pattern of the 3-monthly Standardized Precipitation Index (SPI-3) whose interannual variability is related to the anomalies of East Asian Winter Monsoon (EAWM) systems. Dynamic composites and linear regression analysis indicate that the intensity of EAWM and Siberia High (SH), the position of East Asian Trough (EAT), and El Nino events and sea surface temperature (SST) anomalies over South China Sea (SCS) influence different regions of anomalous Southeast China winter precipitation on interannual scales. The circulation indices (EAWM index, SH index, and EAT index) mainly affect the winter precipitation in the eastern part of Southeast China. El Nino events affect the South China winter precipitation due to the anticyclone anomalies over Philippines. The effect of SCS SST anomalies on the winter precipitation is mainly in the southern part of Yangtze River. Thus, a set of circulation regimes, represented by a handful indices, provide the basis for modeling precipitation anomalies or extremes in future climate projections.

Adaptation to climate in five eastern North America broadleaf deciduous species: Growth clines and evidence of the growth-cold tolerance trade-off

The declining health of high-elevation red spruce (Picea rubens Sarg.) and Fraser fir (Abies fraseri (Pursh) Poir.) in the southern Appalachian region has long been linked to nitrogen (N) deposition. Recently, N deposition has also been proposed as a source of negative health impacts in lower elevation deciduous forests. In 1998 we established 46 plots on six sites in North Carolina and Virginia dominated by American beech (Fagus grandifolia Ehrh.), sugar maple (Acer saccharum Marsh.), and yellow birch (Betula alleghaniensis Britt). We evaluated several response variables across an N deposition gradient, including annual basal area growth; foliage percent N, Al, P, K, Mg, and Ca; and forest floor percent N, Mg, and C, pH, and potential net nitrification and N mineralization rates. We found a significant linear relationship between N deposition and basal area growth in sugar maple, but not in American beech or yellow birch. In addition, we found a significant relationship between N deposition and foliar chemistry (foliar %N in all species, foliar Mg/N and %K in sugar maple, and %P in sugar maple and yellow birch). Foliar %N of the three studied species was high relative to values reported in other studies in the United States and Canada. Several forest floor response variables (%N, C/N, pH, Mg/N, and potential net nitrification and N mineralization rates and nitrification/mineralization fractions) were also correlated with N deposition. The correlations between the above response variables and N deposition are consistent with the influence of chronic N deposition on forested ecosystems measured in other regions and suggest that chronic N deposition may be influencing forest structure and chemistry within the southern region.

BackgroundIntrogressive hybridization is common in natural birch woodlands in Iceland, where two birch (Betula) species (diploid dwarf birch B. nana and tetraploid tree birch B. pubescens) coexist and hybridize readily. Our previous morphological, cytogenetic and palynological studies show that triploid hybrids are likely to have mediated gene flow between the two species. Our previous molecular study based on chloroplast haplotyping confirms the hybrid introgression and provides information about the genetic origin of Betula species in Iceland. The question remains, however, as to what extent nuclear gene flow is involved in this hybrid introgression process. The objective of the present study was therefore to use nuclear markers to probe birch introgressive hybridization.ResultsAFLP (Amplified Fragment Length Polymorphism) analysis was performed on genomic DNA isolated from 169 individual Betula plants (67 diploid B. nana, 82 tetraploid B. pubescens and 20 triploid hybrids), from birch woodlands in Iceland in comparison to those from northern Scandinavia. The generated 115 polymorphic markers were subjected to analysis of molecular variance across ploidy groups, locations, and major chloroplast haplotypes. A new R package, Linarius, was developed for use with this mixed ploidy dataset. All markers were considered nuclear as no allele specific to any chloroplast haplotypes was detected. The results were to a certain extent congruent with those from our previous chloroplast study. No ploidy- or species-specific alleles were detected. Almost all alleles were shared among all three ploidy groups, indicating gene flow via hybridization. The difference, however, was that the nuclear markers clearly differentiated between diploid B. nana and tetraploid B. pubescens, whereas the chloroplast haplotype variation between species was non-significant. The triploid hybrid group was scattered within both ploidy clusters, in line with its role as a bridge to introgression. This nuclear separation between the two species is comparable to that from our previous analysis based on species- specific morphological characters, implying that the whole genomes may be selected for species adaptability in their different habitats. Furthermore, the present AFLP study depicted a clear east–west geographical separation among Icelandic Betula populations, based on both genetic distance analysis and anamorphosis modelling. This geographical separation is prominent in B. nana while B. pubescens is more genetically homogeneous.ConclusionThe present study shows that despite extensive gene flow, Betula species maintain their species integrity and ploidy stability. This in turn allows the long-term survival of the species in their local habitats.

The relative alkalinity tolerances of yellow birch, sweet birch, river birch, paper birch, and Japanese white birch were evaluated by comparing foliar chlorosis and growth of seedlings irrigated for 56 days with either a pH 6.0 nutrient solution (control) or K2CO3-amended solutions adjusted to pH 7.3 or 8.3. Both visual ratings and SPAD-502 chlorophyll meter measurements were effective methods of quantifying the severity of alkalinity-induced foliar chlorosis. Eight weeks of the pH 8.3 treatment was more effective than 4 weeks of the same treatment or 4 or 8 weeks of the pH 7.3 treatment for detecting differences in alkalinity tolerance among the species. Treatment for 8 weeks with either pH 7.3 or 8.3 solutions increased foliar chlorosis of sweet, river, paper, and Japanese white birch seedlings relative to the control treatment, whereas yellow birch seedlings exhibited mild chlorosis only in the pH 8.3 treatment. Based upon severity of chlorosis, yellow birch was most tolerant of soil alkalinity, sweet birch was least tolerant, and river, paper and Japanese white birch were intermediate in tolerance. Stem relative growth rates and shoot and root cumulative dry mass values did not consistently corroborate the relative alkalinity tolerances of the birch species indicated by the chlorosis and chlorophyll data, possibly because of container restriction of root growth of the more rapidly growing species. Results of this study indicate that yellow birch may be valuable for developing new birch cultivars adapted to alkaline soils.

Exotic insect species are an increasing concern with international trade. Detecting and removing any insect are thus important for any imported/exported product, including wood products. For example, wood transportation is known to be an important pathway for the introduction and dispersal of the Emerald Ash Borer, Agrilus planipennis (Coleoptera: Buprestidae). This Asian species is causing high mortality of ash trees in its introduced range because of the weak natural defense of trees and the virtual absence of natural enemies. For similar reasons, there are concerns in Europe that the Bronze Birch Borer, A. anxius, native to North America, could be introduced and cause important birch mortality. Having efficient detection methods and phytosanitary measures to prevent introducing it is thus important. In this study, we evaluated tomodensitometry—or CT-scan—as a detection method for detecting these two Agrilus spp. using debarking as the method of reference. Using CT-scan, we were also able to precisely measure the depth of insects in ash and birch trees in order to recommend proper phytosanitary measures for exportation and importation of wood products. Both techniques efficiently detect the presence of insects in ash, paper birch, and yellow birch. However, the number of A. anxius detected depended on both the technique and the diameter of the sample. The depth of insects depended on tree species, sample diameter, and life-stage. Globally, A. planipennis are deeper in ash trees than A. anxius in birch trees, and prepupae are deeper than larvae. The maximal depth in the sapwood (excluding bark thickness) for ash, paper birch, and yellow birch was 21.9 mm, 6.30 mm, and 3.22 mm, respectively. While CT-scan is more expensive and requires access to expensive equipment, debarking is more time-consuming, especially if the number of insects needs to be determined.

Changes in seedlings’ composition and abundance following soil scarification and amendments in a northern hardwood forest

Until recently, natural dynamics of mixedwood stands have been largely ignored, resulting in the transformation of many North American mixedwoods into conifer- or hardwood-dominated stand types. The goal of this study was to examine canopy gap dynamics in balsam fir ( Abies balsamea (L.) Mill.) – yellow birch ( Betula alleghaniensis Britt.) mixedwoods to better understand possible mechanisms for species coexistence. Gap proportion in 12 study stands varied between 9% and 30% of the total stand area, while gap size varied from 20 to 2100 m2. Balsam fir mortality was the primary cause of gap formation. Balsam fir and mountain maple ( Acer spicatum Lamb.) dominated the tree and shrub regeneration layers, respectively. Shrub competition slows the natural filling of gaps by tree species. Our results indicate that yellow birch is most abundant in gaps over 800 m2 and balsam fir in those under 200 m2. Transition models showed that the greater longevity of yellow birch than balsam fir ensured its maintenance as a dominant. Dominant species coexistence thus results from divergent use of available resources through time and space. Forest management should maintain variability in harvest timing and size because the use of one gap size or a single rotation age will lead to an imbalance in species proportion relative to natural stands.

Local adaptation patterns have been found in many plants and animals, highlighting the genetic heterogeneity of species along their range of distribution. In the next decades, global warming is predicted to induce a change in the selective pressures that drive this adaptive variation, forcing a reshuffling of the underlying adaptive allele distributions. For species with low dispersion capacity and long generation time such as trees, the rapidity of the change could impede the migration of beneficial alleles and lower their capacity to track the changing environment. Identifying the main selective pressures driving the adaptive genetic variation is thus necessary when investigating species capacity to respond to global warming. In this study, we investigate the adaptive landscape of Fagus sylvatica along a gradient of populations in the French Alps. Using a double-digest restriction-site-associated DNA (ddRAD) sequencing approach, we identified 7,000 SNPs from 570 individuals across 36 different sites. A redundancy analysis (RDA)-derived method allowed us to identify several SNPs that were strongly associated with climatic gradients; moreover, we defined the primary selective gradients along the natural populations of F.sylvatica in the Alps. Strong effects of elevation and humidity, which contrast north-western and south-eastern site, were found and were believed to be important drivers of genetic adaptation. Finally, simulations of future genetic landscapes that used these findings allowed identifying populations at risk for F.sylvatica in the Alps, which could be helpful for future management plans.

La classe de cime et le diametre de 1862 bouleaux jaunes (Betula alleghaniensis Britton) de 1,5 cm et plus ont ete inventories a intervalle de 10 ans depuis 1927. L'âge nominal du peuplement etait de 25 ans en 1927. La survie et la croissance du bouleau jaune dans les peuplements de 25 a 85 ans etaient influencees pas la classe de cime et les perturbations anterieures. La mortalite etait negativement correlee avec la croissance anterieure en diametre et, a un degre moindre, avec la classe de cime. La mortalite parmi les arbres supprimes etait 2x a 4x plus elevee que chez les arbres de l'etage superieur. La mortalite etait 8x plus elevee parmi les arbres dont la croissance etait inferieure a 1 cm par decennie au dhp que parmi ceux dont la croissance etait egale ou superieure a 2 cm par decennie au dhp. La mortalite et la croissance en diametre etaient independantes du diametre des arbres lorsque les effets de la croissance anterieure en diametre et de la classe de cime etaient enleves. La diminution de la croissance en diametre du bouleau jaune dans les peuplements de 35 a 55 ans etait reliee a la stratification verticale. La croissance en diametre augmentait apres une periode de defoliation et de secheresse dans les peuplements de 55 a 65 ans, vraisemblablement a cause de la mortalite accrue du chene pendant cette periode. Simultanement, la persistance dans l'etage superieur augmentait et la regression dans la classe de cime ralentissait. Apres un delai de 10 ans, la progression dans la classe de cime des arbres intermediaires augmentait. Le recrutement de bouleaux jaunes et le passage des arbres supprimes dans la classe de cime intermediaire a atteint un sommet apres un delai de 20 ans. Les methodes de coupe qui imitent la mortalite due a la defoliation devraient augmenter la densite du bouleau jaune dans le sud de la Nouvelle-Angleterre.

Understanding how environmental variation influences population genetic structure is important for conservation management because it can reveal how human stressors influence population connectivity, genetic diversity and persistence. We used riverscape genetics modelling to assess whether climatic and habitat variables were related to neutral and adaptive patterns of genetic differentiation (population-specific and pairwise FST ) within five metapopulations (79 populations, 4583 individuals) of steelhead trout (Oncorhynchus mykiss) in the Columbia River Basin, USA. Using 151 putatively neutral and 29 candidate adaptive SNP loci, we found that climate-related variables (winter precipitation, summer maximum temperature, winter highest 5% flow events and summer mean flow) best explained neutral and adaptive patterns of genetic differentiation within metapopulations, suggesting that climatic variation likely influences both demography (neutral variation) and local adaptation (adaptive variation). However, we did not observe consistent relationships between climate variables and FST across all metapopulations, underscoring the need for replication when extrapolating results from one scale to another (e.g. basin-wide to the metapopulation scale). Sensitivity analysis (leave-one-population-out) revealed consistent relationships between climate variables and FST within three metapopulations; however, these patterns were not consistent in two metapopulations likely due to small sample sizes (N = 10). These results provide correlative evidence that climatic variation has shaped the genetic structure of steelhead populations and highlight the need for replication and sensitivity analyses in land and riverscape genetics.

Understanding how ecotypic divergence persists under extensive gene flow is critical for predicting adaptive responses in long-lived conifers. Mongolian Scots pine (Pinus sylvestris var. mongolica) occupies contrasting mountain and sandy-dune habitats in northeastern China, forming two ecotypes with distinct environmental adaptations. Using reference-free Specific Locus Amplified Fragment sequencing (SLAF-seq) data and genome-wide SNPs, we explored patterns of genomic differentiation and genotype-environment associations to determine whether adaptive divergence is driven by few large-effect loci or polygenic shifts. Despite weak population structure, we identified ~ 3% of the genome as adaptive outliers with strong differentiation between ecotypes. These loci exhibited significant environmental associations indicating that both adaptive genomic islands and polygenic shifts are dominated by large-effect variants rather than minor-effect alleles. Furthermore, phenotypic differentiation between ecotypes reflected a dual mechanism: adaptive genetic divergence shaping hydraulic traits and mechanical support, and genotype-by-environment (G×E) interactions enabling phenotypic plasticity in physiological responses, such as water-use efficiency and stress tolerance. The interplay between hard genetic adaptation and plasticity highlights how Mongolian Scots pine can simultaneously preserve ecotypic differentiation and respond flexibly to environmental heterogeneity. Importantly, such plasticity may provide a critical buffer against rapid climate change, allowing populations to persist despite ongoing gene flow and delayed genomic divergence. Our study highlights how divergent selection and plasticity together maintain ecotypic divergence in wind-pollinated pine variety with high gene flow and demonstrates a novel reference-free approach for dissecting adaptive architectures in non-model genomes.

Silvicultural restoration measures have been implemented in the northern hardwoods forests of southern Quebec, Canada, but their financial applicability is often hampered by the depleted state of the resource. To help identify sites most suited for the production of high quality timber, where the potential return on silvicultural investments should be the highest, this study assessed the impact of stand and site characteristics on timber quality in sugar maple (Acer saccharum Marsh.) and yellow birch (Betula alleghaniensis Britt.). For this purpose, lumber value recovery (LVR), an estimate of the summed value of boards contained in a unit volume of round wood, was used as an indicator of timber quality. Predictions of LVR were made for yellow birch and sugar maple trees contained in a network of more than 22000 temporary sample plots across the Province. Next, stand-level variables were selected and models to predict LVR were built using the boosted regression trees method. Finally, the occurrence of spatial clusters was verified by a hotspot analysis. Results showed that in both species LVR was positively correlated with the stand age and structural diversity index, and negatively correlated with the number of merchantable stems. Yellow birch had higher LVR in areas with shallower soils, whereas sugar maple had higher LVR in regions with deeper soils. The hotspot analysis indicated that clusters of high and low LVR exist across the province for both species. Although it remains uncertain to what extent the variability of LVR may result from variations in past management practices or in inherent site quality, we argue that efforts to produce high quality timber should be prioritized in sites where LVR is predicted to be the highest.