Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

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

Medical genetics was revolutionized during the 1980s by the application of genetic mapping to locate the genes responsible for simple Mendelian diseases. Most diseases and traits, however, do not follow simple inheritance patterns. Geneticists have thus begun taking up the even greater challenge of the genetic dissection of complex traits. Four major approaches have been developed: linkage analysis, allele-sharing methods, association studies, and polygenic analysis of experimental crosses. This article synthesizes the current state of the genetic dissection of complex traits—describing the methods, limitations, and recent applications to biological problems.

Genetic Dissection of Complex Traits

Species distribution models predict a wholesale redistribution of trees in the next century, yet migratory responses necessary to spatially track climates far exceed maximum post-glacial rates. The extent to which populations will adapt will depend upon phenotypic variation, strength of selection, fecundity, interspecific competition, and biotic interactions. Populations of temperate and boreal trees show moderate to strong clines in phenology and growth along temperature gradients, indicating substantial local adaptation. Traits involved in local adaptation appear to be the product of small effects of many genes, and the resulting genotypic redundancy combined with high fecundity may facilitate rapid local adaptation despite high gene flow. Gene flow with preadapted alleles from warmer climates may promote adaptation and migration at the leading edge, while populations at the rear will likely face extirpation. Widespread species with large populations and high fecundity are likely to persist and adapt, but will likely suffer adaptational lag for a few generations. As all tree species will be suffering lags, interspecific competition may weaken, facilitating persistence under suboptimal conditions. Species with small populations, fragmented ranges, low fecundity, or suffering declines due to introduced insects or diseases should be candidates for facilitated migration.

/pdf/adaptation-migration-or-extirpation-climate-change-outcomes-4sp3k7vnik.pdf

Adaptation, migration or extirpation: climate change outcomes for tree populations

The plant allozyme literature was reviewed to: (1) compare genetic diversity in long-lived woody species with species representing other life forms, and (2) to investigate whether the levels and distribution of genetic diversity in woody species are related to life history and ecological characteristics. Data from 322 woody taxa were used to measure genetic diversity within species, and within and among populations of species. Woody species maintain more variation within species and within populations than species with other life forms but have less variation among populations. Woody species with large geographic ranges, outcrossing breeding systems, and wind or animal-ingested seed dispersal have more genetic diversity within species and populations but less variation among populations than woody species with other combinations of traits. Although life history and ecological traits explain a significant proportion (34%) of the variation among species for the genetic parameters measured, a large proportion of the interspecific variation is unexplained. The specific evolutionary history of each species must play an important role in determining the level and distribution of genetic diversity.

Factors influencing levels of genetic diversity in woody plant species

Adaptation to winter cold in temperate and boreal trees involves complex genetic, physiological, and developmental processes. Genecological studies demonstrate the existence of steep genetic clines...

https://www.fs.fed.us/psw/publications/neale/psw_2003_neale001_howe.pdf

From genotype to phenotype: unraveling the complexities of cold adaptation in forest trees

Genetic association is a powerful method for dissecting complex adaptive traits due to (i) fine-scale mapping resulting from historical recombination, (ii) wide coverage of phenotypic and genotypic variation within a single experiment, and (iii) the simultaneous discovery of loci and alleles. In this article, genetic association among single nucleotide polymorphisms (58 SNPs) from 20 wood- and drought-related candidate genes and an array of wood property traits with evolutionary and commercial importance, namely, earlywood and latewood specific gravity, percentage of latewood, earlywood microfibril angle, and wood chemistry (lignin and cellulose content), was tested using mixed linear models (MLMs) that account for relatedness among individuals by using a pairwise kinship matrix. Population structure, a common systematic bias in association studies, was assessed using 22 nuclear microsatellites. Different phenotype:genotype associations were found, some of them confirming previous evidence from collocation of QTL and genes in linkage maps (for example, 4cl and percentage of latewood) and two that involve nonsynonymous polymorphisms (cad SNP M28 with earlywood specific gravity and 4cl SNP M7 with percentage of latewood). The strongest genetic association found in this study was between allelic variation in α-tubulin, a gene involved in the formation of cortical microtubules, and earlywood microfibril angle. Intragenic LD decays rapidly in conifers; thus SNPs showing genetic association are likely to be located in close proximity to the causative polymorphisms. This first multigene association genetic study in forest trees has shown the feasibility of candidate gene strategies for dissecting complex adaptive traits, provided that genes belonging to key pathways and appropriate statistical tools are used. This approach is of particular utility in species such as conifers, where genomewide strategies are limited by their large genomes.

/pdf/association-genetics-in-pinus-taeda-l-i-wood-property-traits-4arimgqr7x.pdf

Association Genetics in Pinus taeda L. I. Wood Property Traits

Lodgepole pine (Pinuscontorta Dougl.) occupies a large and ecologically diverse range in western North America. The species is generally recognized as consisting of four subspecies, three of which are widespread and the fourth endemic to the north coast of California. Geographic isolation of subspecies is nearly complete although gene flow may occur in certain instances. Moderate heterozygosity estimates (0.10–0.14) and low standard errors of the estimate (0.02–0.04) were obtained for all populations of lodgepole pine and are comparable with other recent studies of conifers that based estimates on 20 or more loci. The distribution of allozyme variation indicates that very little population differentiation has occurred. Approximately 91% of the allozyme variability resides within populations, with 3 and 6% distributed among subspecies and among populations, respectively. The extent of population differentiation is far less than that observed for many herbaceous plants but similar to reports for other conif...

Population structure, genic diversity, and morphological variation in Pinus contorta Dougl.

The inheritance of chloroplast DNA in Douglas-fir (Pseudotsugamenziesii (Mirb.) Franco) was determined using a restriction fragment length polymorphism (RFLP) as a marker. An insertion/deletion sequence homologous to a 15.3 kilobase PstI fragment from petunia chloroplast DNA was detected in SmaI and BamHI digests of total DNAs of parent trees. Full-sib progeny (36 in total) were then assayed for this polymorphism in three sets of crosses between male and female parents with different RFLP markers. The full-sib progeny had the same restriction fragment as the male parent, with three exceptions. These data provide direct evidence for the paternal inheritance of chloroplast DNA in a gymnosperm. This result is in sharp contrast to the strict maternal and occasional biparental inheritance of chloroplast DNA observed in angiosperms. The three exceptions had restriction fragments unlike either the male or female parents of the cross, suggesting that some type of mutational or recombinational event had occurred d...

Paternal inheritance of chloroplast DNA in Douglas-fir

Chemical wood property traits were analyzed for the presence of quantitative trait loci (QTLs) in a three-generation outbred pedigree of loblolly pine (Pinus taeda L.). These traits were assayed using pyrolysis molecular beam mass spectrometry and include mass spectrum peak intensities associated with carbohydrates, α-cellulose and hemicellulose sugars, and lignin. Models for projection to latent structures (PLS) were used to also estimate the chemical composition of cell walls (i.e., α-cellulose, galactan and lignin) from mass spectrum data using multivariate regression. Both earlywood and latewood fractions from the fifth annual ring were analyzed for each trait. An interval mapping approach designed for an outbred pedigree was used to estimate the number of QTLs, the magnitude of QTL effects, and their genomic position. Eight unique QTLs influencing cell wall chemistry were detected from multiple peak intensities and/or PLS estimates using the one- and two-QTL models. Significant differences in chemical contents were observed among the populations from North Carolina vs Oklahoma, and results from QTL×environment analyses suggest that QTLs interact with environmental location. QTLs should be verified in larger experiments and in different genetic and environmental backgrounds. QTL mapping will help towards eventually identifying genes having a major effect on chemical wood properties.

Nicholas C. Wheeler

Papers

From genotype to phenotype: unraveling the complexities of cold adaptation in forest trees

Association Genetics in Pinus taeda L. I. Wood Property Traits

Population structure, genic diversity, and morphological variation in Pinus contorta Dougl.

Paternal inheritance of chloroplast DNA in Douglas-fir

Identification of QTLs influencing wood property traits in loblolly pine ( Pinus taeda L.). II. Chemical wood properties.