Long-term demographic decline and late glacial divergence in a Californian paleoendemic: Sequoiadendron giganteum (giant sequoia)

Worldwide Late Pleistocene and Early Holocene population declines in extant megafauna are associated with Homo sapiens expansion rather than climate change

The worldwide extinction of megafauna during the Late Pleistocene and Early Holocene is evident from the fossil record, with dominant theories suggesting a climate, human or combined impact cause. Consequently, two disparate scenarios are possible for the surviving megafauna during this time period - they could have declined due to similar pressures, or increased in population size due to reductions in competition or other biotic pressures. We therefore infer population histories of 139 extant megafauna species using genomic data which reveal population declines in 91% of species throughout the Quaternary period, with larger species experiencing the strongest decreases. Declines become ubiquitous 32-76 kya across all landmasses, a pattern better explained by worldwide Homo sapiens expansion than by changes in climate. We estimate that, in consequence, total megafauna abundance, biomass, and energy turnover decreased by 92-95% over the past 50,000 years, implying major human-driven ecosystem restructuring at a global scale.

Bioclimatic Characterisation of Specific Native Californian Pinales and Their Future Suitability under Climate Change

Rising temperatures and changes in precipitation patterns under climate change scenarios are accelerating the depletion of soil moisture and increasing the risk of drought, disrupting the conditions that many plant species need to survive. This study aims to establish the bioclimatic characterisation, both qualitative and quantitative, of ten native Californian Pinales for the period 1980-2019, and to determine their habitat suitability by 2050. To achieve this, an exhaustive search of the Gbif database for records of ten conifer taxa was carried out. To conduct the bioclimatic characterisation of the studied taxa, we worked with the monthly values of average temperature and precipitation for the period 1980-2019 from 177 meteorological stations. Linear regressions was performed in order to compile the future evolution of California's climate. Suitable areas and optimal areas were defined at the present time (1980-2019) and its future projection (2050). We applied Boolean logic and, in this investigation, the Conditional Logic Operator (CON) was used to determine the possible species presence (one) or absence (zero) for each of the 15 variables analysed. In general, most of the conifers studied here will experience a reduction in their habitat range in California by the year 2050 due to climate change, as well as the displacement of species towards optimal areas. Furthermore, the results have highlighted the applicability of bioclimatology to future conditions under climate change. This will aid conservation managers in implementing strategic measures to ameliorate the detrimental impacts of climate change, thereby ensuring the ecological integrity and sustainability of the affected conifer species.

Genome-wide association identifies candidate genes for drought tolerance in coast redwood and giant sequoia

Drought is a major limitation for survival and growth in plants. With more frequent and severe drought episodes occurring due to climate change, it is imperative to understand the genomic and physiological basis of drought tolerance to be able to predict how species will respond in the future. In this study, univariate and multitrait multivariate genome-wide association study methods were used to identify candidate genes in two iconic and ecosystem-dominating species of the western USA, coast redwood and giant sequoia, using 10 drought-related physiological and anatomical traits and genome-wide sequence-capture single nucleotide polymorphisms. Population-level phenotypic variation was found in carbon isotope discrimination, osmotic pressure at full turgor, xylem hydraulic diameter, and total area of transporting fibers in both species. Our study identified new 78 new marker × trait associations in coast redwood and six in giant sequoia, with genes involved in a range of metabolic, stress, and signaling pathways, among other functions. This study contributes to a better understanding of the genomic basis of drought tolerance in long-generation conifers and helps guide current and future conservation efforts in the species.

Selective Sweeps and Polygenic Adaptation Drive Local Adaptation along Moisture and Temperature Gradients in Natural Populations of Coast Redwood and Giant Sequoia

Dissecting the genomic basis of local adaptation is a major goal in evolutionary biology and conservation science. Rapid changes in the climate pose significant challenges to the survival of natural populations, and the genomic basis of long-generation plant species is still poorly understood. Here, we investigated genome-wide climate adaptation in giant sequoia and coast redwood, two iconic and ecologically important tree species. We used a combination of univariate and multivariate genotype-environment association methods and a selective sweep analysis using non-overlapping sliding windows. We identified genomic regions of potential adaptive importance, showing strong associations to moisture variables and mean annual temperature. Our results found a complex architecture of climate adaptation in the species, with genomic regions showing signatures of selective sweeps, polygenic adaptation, or a combination of both, suggesting recent or ongoing climate adaptation along moisture and temperature gradients in giant sequoia and coast redwood. The results of this study provide a first step toward identifying genomic regions of adaptive significance in the species and will provide information to guide management and conservation strategies that seek to maximize adaptive potential in the face of climate change.

Botryosphaeria Dothidea and Neofusicoccum Yunnanense Causing Canker and Die-Back of Sequoiadendron Giganteum in Croatia

Sequoiadendron giganteum Lindl. [Buchholz] is a long-lived tree species endemic to the Sierra Nevada Mountains in California. Due to its massive size and beauty, S. giganteum is a popular ornamental tree planted in many parts of the world, including Europe. Since 2017, scattered branch die-back has been observed on S. giganteum trees in Zagreb, Croatia. Other symptoms included resinous branch cankers, reddish-brown discoloration of the sapwood and, in severe cases, crown die-back. Branches showing symptoms of die-back and cankers were collected from six S. giganteum trees in Zagreb and the aim of this study was to identify the causal agent of the disease. The constantly isolated fungi were identified using morphology and phylogenetic analyses based on the internal transcribed spacer (ITS) of the ribosomal DNA (rDNA), and partial sequencing of two housekeeping genes, i.e., translation elongation factor 1-α (TEF 1-α), and β tubulin 2 (TUB2). The fungi were identified as Botryosphaeria dothidea (Moug.) Ces. and De Not. and Neofusicoccum yunnanense G.Q. Li & S.F. Chen. The pathogenicity test was conducted in a plant growth chamber on S. giganteum seedlings and revealed that N. yunnanense was more aggressive compared to B. dothidea. N. yunnanense was able to reproduce symptoms of canker and die-back and kill plants seven weeks after inoculation whereas B. dothidea produced cankers. To the best of our knowledge, this is the first report of B. dothidea and N. yunnanense causing canker and die-back disease of S. giganteum in Croatia. It is also the first record on the identity and pathogenicity of any fungal species associated with S. giganteum in this country. The study expended the known host range of N. yunnanense to include S. giganteum, which is a valuable ornamental tree in Croatian landscapes. Disease management strategies should be developed to mitigate or reduce the impact of the disease.

A Reference Genome Sequence for Giant Sequoia

The giant sequoia (Sequoiadendron giganteum) of California are massive, long-lived trees that grow along the U.S. Sierra Nevada mountains. Genomic data are limited in giant sequoia and producing a reference genome sequence has been an important goal to allow marker development for restoration and management. Using deep-coverage Illumina and Oxford Nanopore sequencing, combined with Dovetail chromosome conformation capture libraries, the genome was assembled into eleven chromosome-scale scaffolds containing 8.125 Gbp of sequence. Iso-Seq transcripts, assembled from three distinct tissues, was used as evidence to annotate a total of 41,632 protein-coding genes. The genome was found to contain, distributed unevenly across all 11 chromosomes and in 63 orthogroups, over 900 complete or partial predicted NLR genes, of which 375 are supported by annotation derived from protein evidence and gene modeling. This giant sequoia reference genome sequence represents the first genome sequenced in the Cupressaceae family, and lays a foundation for using genomic tools to aid in giant sequoia conservation and management.

Association of genetic and climatic variability in giant sequoia, Sequoiadendron giganteum, reveals signatures of local adaptation along moisture-related gradients

Uncovering the genetic basis of local adaptation is a major goal of evolutionary biology and conservation science alike. In an era of climate change, an understanding of how environmental factors shape adaptive diversity is crucial to predicting species response and directing management. Here, we investigate patterns of genomic variation in giant sequoia, an iconic and ecologically important tree species, using 1,364 bi-allelic single nucleotide polymorphisms (SNPs). We use an F _ST outlier test and two genotype-environment association methods, latent factor mixed models (LFMMs) and redundancy analysis (RDA), to detect complex signatures of local adaptation. Results indicate 79 genomic regions of potential adaptive importance, with limited overlap between the detection methods. Of the 58 loci detected by LFMM, 51 showed strong correlations to a precipitation-driven composite variable and seven to a temperature-related variable. RDA revealed 24 outlier loci with association to climate variables, all of which showed strongest relationship to summer precipitation. Nine candidate loci were indicated by two methods. After correcting for geographic distance, RDA models using climate predictors accounted for 49% of the explained variance and showed significant correlations between SNPs and climatic factors. Here, we present evidence of local adaptation in giant sequoia along gradients of precipitation and provide a first step toward identifying genomic regions of adaptive significance. The results of this study will provide information to guide management strategies that seek to maximize adaptive potential in the face of climate change.

Fragmented and isolated: limited gene flow coupled with weak isolation by environment in the paleoendemic giant sequoia (Sequoiadendron giganteum)

PREMISE

Patterns of genetic structure across a species' range reflect the long-term interplay between genetic drift, gene flow, and selection. Given the importance of gene flow in preventing the loss of diversity through genetic drift among spatially isolated populations, understanding the dynamics of gene flow and the factors that influence connectivity across a species' range is a major goal for conservation of genetic diversity. Here we present a detailed look at gene flow dynamics of Sequoiadendron giganteum, a paleoendemic tree species that will likely face numerous threats due to climate change.

METHODS

We used microsatellite markers to examine nineteen populations of S. giganteum for patterns of genetic structure and to estimate admixture and rates of gene flow between eight population pairs. Also, we used Generalized Dissimilarity Models to elucidate landscape factors that shape genetic differentiation among populations.

RESULTS

We found minimal gene flow between adjacent groves in the northern disjunct range. In most of the southern portion of the range, groves showed a signal of connectivity which degrades to isolation in the extreme south. Geographic distance was the most important predictor of genetic dissimilarity across the range, with environmental conditions related to precipitation and temperature explaining a small, but significant, portion of the genetic variance.

CONCLUSIONS

Due to their isolation and unique genetic composition, northern populations of S. giganteum should be considered a high conservation priority. In this region, we suggest germplasm conservation as well as restoration planting to enhance genetic diversity.

Spatial genetic structure and diversity of natural populations of Aesculus hippocastanum L. in Greece

Horse-chestnut (Aesculus hippocastanum L.) is an endemic and relict species from the Mediterranean biodiversity hotspot and a popular ornamental tree. Knowledge about the evolutionary history of this species remains scarce. Here, we ask what historical and ecological factors shaped the pattern of genetic diversity and differentiation of this species. We genotyped 717 individuals from nine natural populations using microsatellite markers. The influence of distance, topography and habitat variables on spatial genetic structure was tested within the approaches of isolation-by-distance and isolation-by-ecology. Species niche modeling was used to project the species theoretical range through time and space. The species showed high genetic diversity and moderate differentiation for which topography, progressive range contraction through the species’ history and long-term persistence in stable climatic refugia are likely responsible. A strong geographic component was revealed among five genetic clusters that are connected with very limited gene flow. The environmental variables were a significant factor in the spatial genetic structure. Modeling results indicated that future reduction of the species range may affect its survival. The possible impact of climate changes and high need of in situ conservation are discussed.

Coping with gravity: the foliar water relations of giant sequoia

In tall trees, the mechanisms by which foliage maintains sufficient turgor pressure and water content against height-related constraints remain poorly understood. Pressure-volume curves generated from leafy shoots collected crown-wide from 12 large Sequoiadendron giganteum (Lindley) J. Buchholz (giant sequoia) trees provided mechanistic insights into how the components of water potential vary with height in tree and over time. The turgor loss point (TLP) decreased with height at a rate indistinguishable from the gravitational potential gradient and was controlled by changes in tissue osmotica. For all measured shoots, total relative water content at the TLP remained above 75%. This high value has been suggested to help leaves avoid precipitous declines in leaf-level physiological function, and in giant sequoia was controlled by both tissue elasticity and the balance of water between apoplasm and symplasm. Hydraulic capacitance decreased only slightly with height, but importantly this parameter was nearly double in value to that reported for other tree species. Total water storage capacity also decreased with height, but this trend essentially disappeared when considering only water available within the typical range of water potentials experienced by giant sequoia. From summer to fall measurement periods we did not observe osmotic adjustment that would depress the TLP. Instead we observed a proportional shift of water into less mobile apoplastic compartments leading to a reduction in hydraulic capacitance. This collection of foliar traits allows giant sequoia to routinely, but safely, operate close to its TLP, and suggests that gravity plays a major role in the water relations of Earth's largest tree species.