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

Biological activities and distribution of plant saponins.

Experiments suggest that biomass-derived black carbon (biochar) affects microbial populations and soil biogeochemistry. Both biochar and mycor- rhizal associations, ubiquitous symbioses in terrestrial ecosystems, are potentially important in various ecosystem services provided by soils, contributing to sustainable plant production, ecosystem restoration, and soil carbon sequestration and hence mitigation of global climate change. As both biochar and mycor- rhizal associations are subject to management, under- standing and exploiting interactions between them could be advantageous. Here we focus on biochar effects on mycorrhizal associations. After reviewing the experimental evidence for such effects, we critically examine hypotheses pertaining to four mechanisms by which biochar could influence mycorrhizal abundance and/or functioning. These mechanisms are (in decreas- ing order of currently available evidence supporting them): (a) alteration of soil physico-chemical proper- ties; (b) indirect effects on mycorrhizae through effects on other soil microbes; (c) plant-fungus signaling interference and detoxification of allelochemicals on biochar; and (d) provision of refugia from fungal grazers. We provide a roadmap for research aimed at testing these mechanistic hypotheses.

http://www.css.cornell.edu/faculty/lehmann/publ/PlantSoil%20300,%209-20,%202007,%20Warnock.pdf

Mycorrhizal responses to biochar in soil – concepts and mechanisms

Biochar application to soils is being considered as a means to sequester carbon (C) while concurrently improving soil functions. The main focus of this report is providing a critical scientific review of the current state of knowledge regarding the effects of biochar application to soils on soil properties and functions. Wider issues, including atmospheric emissions and occupational health and safety associated to biochar production and handling, are put into context. The aim of this review is to provide a sound scientific basis for policy development, to identify gaps in current knowledge, and to recommend further research relating to biochar application to soils. See Table 1 for an overview of the key findings from this report. Biochar research is in its relative infancy and as such substantially more data are required before robust predictions can be made regarding the effects of biochar application to soils, across a range of soil, climatic and land management factors. Definition In this report, biochar is defined as: “charcoal (biomass that has been pyrolysed in a zero or low oxygen environment) for which, owing to its inherent properties, scientific consensus exists that application to soil at a specific site is expected to sustainably sequester carbon and concurrently improve soil functions (under current and future management), while avoiding shortand long-term detrimental effects to the wider environment as well as human and animal health." Biochar as a material is defined as: "charcoal for application to soils". It should be noted that the term 'biochar' is generally associated with other co-produced end products of pyrolysis such as 'syngas'. However, these are not usually applied to soil and as such are only discussed in brief in the report. Biochar properties Biochar is an organic material produced via the pyrolysis of C-based feedstocks (biomass) and is best described as a ‘soil conditioner’. Despite many different materials having been proposed as biomass feedstock for biochar (including wood, crop residues and manures), the suitability of each feedstock for such an application is dependent on a number of chemical, physical, environmental, as well as economic and logistical factors. Evidence suggests that components of the carbon in biochar are highly recalcitrant in soils, with reported residence times for wood biochar being in the range of 100s to 1,000s of years, i.e. approximately 101,000 times longer than residence times of most soil organic matter. Therefore, biochar addition to soil can provide a potential sink for C. It is important to note, however, that there is a paucity of data concerning biochar produced from feedstocks other than wood, but the information that is available is discussed in the report. Owing to the current interest in climate change mitigation, and the irreversibility of biochar application to soil, an effective evaluation of biochar stability in the environment and its effects on soil processes and functioning is paramount. The current state of knowledge concerning these factors is discussed throughout this report.

Biochar Application to Soils - A Critical Scientific Review of Effects on Soil Properties, Processes and Functions

1. High elevation treelines 1.1 The task 1.2 Previous works 2. Definitions and conventions 2.1 The life form 'tree' 2.2 Lines and transitions 2.3 Limitation, stress and disturbance 2.4 Altitude-related and other environmental drivers 2.5 Treeline nomenclature 3. Treeline patterns 3.1 Treeline taxa 3.2 The summit syndrome and other treeline depressions 3.3 Mass elevation effect 3.4 Treeline elevation 3.5 Time matters 3.6 Forest structure near treeline 4. Treeline climate 4.1 Specific aspects of treeline climatology 4.2 Criteria to define temperature regimes at treeline 4.3 Treeline temperatures in different bioclimatic regions 4.4 Seedbed and branch temperatures 4.5 Whole forest temperatures 5. Global mountain statistics based on treeline elevation 5.1 Mountain geostatistics 5.2 Elevational belts 5.3 Global treeline ecotones 6. Structure and stature of treeline trees 6.1 Foliage properties 6.2 Wood properties 6.3 Bark properties 6.4 Root traits 6.5 Tree stature 6.6 Dry matter allocation in treeline trees 7. Growth and development 7.1 Tree growth near treeline 7.2 Xylogenesis at treeline 7.3 Apical growth dynamics 7.4 Root growth 7.5 Phenology at treeline 8. Evolutionary adjustments to life at treeline 8.1 Phylogenetic selection 8.2 Genotypic responses of growth and development 8.3 Genotypic responses of physiological traits 9. Reproduction, early life stages and tree demography 9.1 Amount and quality of seeds at high elevation 9.2 Germination, seedling and sapling stage 9.3 Tree demography at treeline 10. Freezing and other forms of stress 10.1 Stress at treeline in a fitness context 10.2 Mechanisms and principles of freezing resistance 10.3 Freezing resistance in treeline trees 10.4 Other forms of stress at treeline 11. Water, nutrient and carbon relations 11.1 Tree water relations during the growing season 11.2 Nutrient relations 11.3 Carbon relations 12. Treeline formation - currently, in the past and in the future 12.1 Causes of current treelines 12.2 Treelines in the recent past 12.3. Treelines in the distant past (Holocene) 12.4 Future treelines References Taxonomic index Subject index

Alpine treelines : functional ecology of the global high elevation tree limits

The use of in vitro shoot cultures to evaluate osmotic and salt tolerance and the effects of salt and mannitol in the medium on proline and sugar accumulation were investigated in two poplar species, P. euphratica and P. alba cv. Pyramidalis × P. tomentosa. Shoot length, leaf number, whole plant dry weight, and the accumulation of proline and total soluble sugars in leaves were quantified after 2 weeks. All P.
 euphratica plantlets survived at all levels of mannitol and NaCl, while the mortality of P. alba cv. Pyramidalis × P. tomentosa increased both at the mannitol and the NaCl treatments. A significant increase in proline accumulation was observed in both young and mature P. euphratica leaves at 200 mM mannitol and above, and at 150 mM NaCl and above. The total soluble sugar content increased in young P. euphratica leaves at 250 mM NaCl; however, it decreased in the mature leaves. Similar increases of the total soluble sugar content were not seen in P. alba cv. Pyramidalis × P. tomentosa plants in response to either mannitol or NaCl treatment. Our results suggest that accumulated proline and sugars promote osmotic and salt tolerance. The effects of accumulated proline and total soluble sugars on leaves are discussed in relation to growth and osmotic adjustment.

Effects of saline and osmotic stress on proline and sugar accumulation in Populus euphratica in vitro.

Aim To understand global patterns of genetic variation in plant species on mountains and to consider the significance of mountains for the genetic structure and evolution of plant species. Location Global. Methods We review published studies. Results Genetic diversity within populations can vary along altitudinal gradients in one of four patterns. Eleven of 42 cited studies (26% of the total) found that populations at intermediate altitudes have greater diversity than populations at lower and higher altitudes. This is because the geographically central populations are under optimal environmental conditions, whereas the peripheral populations are in suboptimal situations. The second pattern, indicating that higher populations have less diversity than lower populations, was found in eight studies (19%). The third pattern, indicating that lower populations have lower diversity than higher populations, was found in 10 studies (24%). In 12 studies (29%), the intrapopulation genetic variation was found to be unaffected by altitude. Evidence of altitudinal differentiation was found in more than half of these studies, based on measurements of a range of variables including genome size, number of chromosomes or a range of loci using molecular markers. Furthermore, great variation has been found in phenotypes among populations at different altitudes in situ and in common garden experiments, even in cases where there was no associated variation in molecular composition. Mountains can be genetic barriers for species that are distributed at low elevations, but they can also provide pathways for species that occupy high-elevation habitats. [Correction added after publication 9 October 2007: ‘less diversity’ changed to ‘greater diversity’ in the second sentence of the Results section of the Abstract]. Main conclusions Genetic diversity within populations can vary along altitudinal gradients as a result of several factors. The results highlight the importance of phenotypic examinations in detecting altitudinal differences. The influence of mountain ridges on genetic differentiation varies depending, inter alia , on the elevation at which the species occurs. Based on these findings, zoning by altitudes or ridges would be helpful for the conservation of tree populations with the onset of global warming.

Global patterns of genetic variation in plant species along vertical and horizontal gradients on mountains

Betula maximowicziana is a long-lived pioneer tree species in Japanese cool temperate forests that plays an important role in maintenance of the forest ecosystem and has high economic value. Here we assess the wide-range genetic structure of 23 natural populations of B. maximowicziana using 11 simple sequence repeat (SSR) loci. Genetic diversity within populations was relatively low in all populations (mean H(E), 0.361; mean allelic richness, 2.80; mean rare allelic richness, 1.02). The population differentiation was also relatively low (F(ST), 0.062). Genetic distance-based and Bayesian clustering analysis revealed that the populations examined here could be divided into a southern group and a northern group. Analysis of rare allelic richness and Bayesian clustering revealed evidence for both southern and northern refugia during the last glacial period. Furthermore, a comparison of regional genetic diversity revealed significant clines in allelic richness. In spatial genetic structure evaluation, significant isolation by distance (IBD) was detected among the 23 populations, but not within regions. Moreover, significant population bottlenecks were found in all populations under infinite allele model (IAM) assumptions. These unusual, significant bottlenecks might be because of the processes of postglacial colonization and the species' characters and/or life history as a long-lived pioneer tree species. The wide-range, regional genetic structure found in this study provides an important baseline for conservation and forest management, including the identification of evolutionarily significant units (ESUs) and/or management units (MUs) of B. maximowicziana.

Wide-range analysis of genetic structure of Betula maximowicziana, a long-lived pioneer tree species and noble hardwood in the cool temperate zone of Japan.

Conservation of the local genetic variation and evolutionary integrity of economically and ecologically important trees is a key aspect of studies involving forest genetics, and a population demographic history of the target species provides valuable information for this purpose. Here, the genetic structure of 48 populations of Betula maximowicziana was assessed using 12 expressed sequence tag-simple sequence repeat (EST-SSR) markers. Genetic diversity was lower in northern populations than southern ones and structure analysis revealed three groups: northern and southern clusters and an admixed group. Eleven more genomic-SSR loci were added and the demographic history of these three groups was inferred by approximate Bayesian computation (ABC). The ABC revealed that a simple split scenario was much more likely than isolation with admixture, suggesting that the admixture-like structure detected in this species was due to ancestral polymorphisms. The ABC analysis suggested that the population growth and divergence of the three groups occurred 96 800 (95% CI, 20 500-599 000) and 28 300 (95% CI, 8700-98 400) years ago, respectively. We need to be aware of several sources of uncertainty in the inference such as assumptions about the generation time, overlapping of generations, confidence intervals of the estimated parameters and the assumed model in the ABC. However, the results of the ABC together with the model-based maps of reconstructed past species distribution and palaeoecological data suggested that the modern genetic structure of B. maximowicziana originated prior to the last glacial maximum (LGM) and that some populations survived in the northern range even during the LGM.

The population demography of Betula maximowicziana, a cool-temperate tree species in Japan, in relation to the last glacial period: its admixture-like genetic structure is the result of simple population splitting not admixing.

http://webpages.icav.up.pt/PTDC/AAC-CLI/110755/papers/Hu_etal_2008_Ann_Botany.pdf

Nuclear DNA Microsatellites Reveal Genetic Variation but a Lack of Phylogeographical Structure in an Endangered Species, Fraxinus mandshurica, Across North-east China

Yuji Ide

Papers

Effects of saline and osmotic stress on proline and sugar accumulation in Populus euphratica in vitro.

Global patterns of genetic variation in plant species along vertical and horizontal gradients on mountains

Wide-range analysis of genetic structure of Betula maximowicziana, a long-lived pioneer tree species and noble hardwood in the cool temperate zone of Japan.

The population demography of Betula maximowicziana, a cool-temperate tree species in Japan, in relation to the last glacial period: its admixture-like genetic structure is the result of simple population splitting not admixing.

Nuclear DNA Microsatellites Reveal Genetic Variation but a Lack of Phylogeographical Structure in an Endangered Species, Fraxinus mandshurica, Across North-east China