So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to

Human biochemical genetics

https://hal.archives-ouvertes.fr/hal-00457602/document

A global overview of drought and heat-induced tree mortality reveals emerging climate change risks for forests

Framework Convention on Climate Change

http://sylvain-delzon.com/wp-content/uploads/2013/02/Lindner-et-al-2010-FEM.pdf

Climate change impacts, adaptive capacity, and vulnerability of European forest ecosystems

Patterns, mechanisms, projections, and consequences of tree mortality and associated broad-scale forest die-off due to drought accompanied by warmer temperatures—“hotter drought”, an emerging characteristic of the Anthropocene—are the focus of rapidly expanding literature. Despite recent observational, experimental, and modeling studies suggesting increased vulnerability of trees to hotter drought and associated pests and pathogens, substantial debate remains among research, management and policy-making communities regarding future tree mortality risks. We summarize key mortality-relevant findings, differentiating between those implying lesser versus greater levels of vulnerability. Evidence suggesting lesser vulnerability includes forest benefits of elevated [CO2] and increased water-use efficiency; observed and modeled increases in forest growth and canopy greening; widespread increases in woody-plant biomass, density, and extent; compensatory physiological, morphological, and genetic mechanisms; dampening ecological feedbacks; and potential mitigation by forest management. In contrast, recent studies document more rapid mortality under hotter drought due to negative tree physiological responses and accelerated biotic attacks. Additional evidence suggesting greater vulnerability includes rising background mortality rates; projected increases in drought frequency, intensity, and duration; limitations of vegetation models such as inadequately represented mortality processes; warming feedbacks from die-off; and wildfire synergies. Grouping these findings we identify ten contrasting perspectives that shape the vulnerability debate but have not been discussed collectively. We also present a set of global vulnerability drivers that are known with high confidence: (1) droughts eventually occur everywhere; (2) warming produces hotter droughts; (3) atmospheric moisture demand increases nonlinearly with temperature during drought; (4) mortality can occur faster in hotter drought, consistent with fundamental physiology; (5) shorter droughts occur more frequently than longer droughts and can become lethal under warming, increasing the frequency of lethal drought nonlinearly; and (6) mortality happens rapidly relative to growth intervals needed for forest recovery. These high-confidence drivers, in concert with research supporting greater vulnerability perspectives, support an overall viewpoint of greater forest vulnerability globally. We surmise that mortality vulnerability is being discounted in part due to difficulties in predicting threshold responses to extreme climate events. Given the profound ecological and societal implications of underestimating global vulnerability to hotter drought, we highlight urgent challenges for research, management, and policy-making communities.

/pdf/on-underestimation-of-global-vulnerability-to-tree-mortality-1w5zrntf70.pdf

On underestimation of global vulnerability to tree mortality and forest die‐off from hotter drought in the Anthropocene

Variation in xylem anatomy among selected populations of lodgepole pine (Pinus contorta Dougl. ex Loud. var. latifolia Engelm.) was examined using digital image analysis based on an annual growth ring (age 10) per tree. Four subpopulations were selected using the following criteria for height growth and wood density: (i) fast growth and high density; (ii) slow growth and high density; (iii) fast growth and low density; and (iv) slow growth and low den- sity. Significant differences were found among subpopulations for several anatomical parameters including tracheid den - sity, lumen size, and cell wall thickness that may affect the economic value and utilization of wood. Principal component analysis indicate that the first four principal components (PCs) were associated with ( i) ring area (PC1), (ii) earlywood density (PC2), (iii) latewood density (PC3), and (iv) lumen shape in earlywood (PC4), suggesting that these aspects of wood properties and growth are controlled by different sets of genes. Relative contributions of total number of tracheids, tracheid lumen size, and cell wall thickness to ring area and correlations between cell wall area proportion and X-ray density are discussed.

Variation in xylem anatomy of selected populations of lodgepole pine

LTR retrotransposons (LTR-RTs) are ubiquitous and represent the dominant repeat element in plant genomes, playing important roles in functional variation, genome plasticity and evolution. With the advent of new sequencing technologies, a growing number of whole-genome sequences have been made publicly available, making it possible to carry out systematic analyses of LTR-RTs. However, a comprehensive and unified annotation of LTR-RTs in plant groups is still lacking. Here, we constructed a plant intact LTR-RTs dataset, which is designed to classify and annotate intact LTR-RTs with a standardized procedure. The dataset currently comprises a total of 2,593,685 intact LTR-RTs from genomes of 300 plant species representing 93 families of 46 orders. The dataset is accompanied by sequence, diverse structural and functional annotation, age determination and classification information associated with the LTR-RTs. This dataset will contribute valuable resources for investigating the evolutionary dynamics and functional implications of LTR-RTs in plant genomes.

/pdf/a-comprehensive-annotation-dataset-of-intact-ltr-51beedxh2j.pdf

A comprehensive annotation dataset of intact LTR retrotransposons of 300 plant genomes

Ginkgo (Ginkgo biloba L.) is an excellent landscape species. Its yellow-green leaf mutants are ideal materials for research on pigment synthesis, but the regulatory mechanism of leaf coloration in these ginkgo mutants remains unclear. We compared the metabolomes and transcriptomes of green and mutant yellow leaves of ginkgo over the same period in this study. The results showed that the chlorophyll content of normal green leaves was significantly higher than that of mutant yellow leaves of ginkgo. We obtained 931.52M clean reads from different color leaves of ginkgo. A total of 283 substances in the metabolic profiles were finally detected, including 50 significantly differentially expressed metabolites (DEMs). We identified these DEMs and 1361 differentially expressed genes (DEGs), with 37, 4, 3 and 13 DEGs involved in the photosynthesis, chlorophyll, carotenoid, and flavonoid biosynthesis pathways, respectively. Moreover, integrative analysis of the metabolomes and transcriptomes revealed that the flavonoid pathway contained the upregulated DEM (−)-epicatechin. Fourteen DEGs from the photosynthesis pathway were positively or negatively correlated with the DEMs. Our findings suggest a complex metabolic network in mutant yellow leaves. This study will provide a basis for studies of leaf color variation and regulation.

/pdf/metabolomic-and-transcriptomic-analyses-of-mutant-yellow-84lfytsfzu.pdf

Metabolomic and transcriptomic analyses of mutant yellow leaves provide insights into pigment synthesis and metabolism in Ginkgo biloba

Ginkgo biloba microRNA profiling reveals new insight into leaf color mutation

https://ir.library.oregonstate.edu/downloads/j96021192

Tongli Wang

Papers

Variation in xylem anatomy of selected populations of lodgepole pine

A comprehensive annotation dataset of intact LTR retrotransposons of 300 plant genomes

Metabolomic and transcriptomic analyses of mutant yellow leaves provide insights into pigment synthesis and metabolism in Ginkgo biloba

Ginkgo biloba microRNA profiling reveals new insight into leaf color mutation

Climate effects on red alder growth in the Pacific Northwest of North America