QTL mapping and the genetic basis of adaptation: recent developments

Quantitative trait loci (QTL) mapping has been used in a number of evolutionary studies to study the genetic basis of adaptation by mapping individual QTL that explain the differences between differentiated populations and also estimating their effects and interaction in the mapping population. This analysis can provide clues about the evolutionary history of populations and causes of the population differentiation. QTL mapping analysis methods and associated computer programs provide us tools for such an inference on the genetic basis and architecture of quantitative trait variation in a mapping population. Current methods have the capability to separate and localize multiple QTL and estimate their effects and interaction on a quantitative trait. More recent methods have been targeted to provide a comprehensive inference on the overall genetic architecture of multiple traits in a number of environments. This development is important for evolutionary studies on the genetic basis of multiple trait variation, genotype by environment interaction, host–parasite interaction, and also microarray gene expression QTL analysis.     

The application of genetic approaches for investigations of mycorrhizal symbioses

Genetic analyses of mycorrhizal symbioses have been far less common to date than molecular biological investigations. This review aims to address the problem that genetic research approaches are some of the least familiar to non specialists by providing some detailed explanations of the requirements and processes involved, including concepts of genetic variation and genetic mapping. Each section includes examples of research progress which is restricted to studies of arbuscular mycorrhizal (AM) and ectomycorrhizal (EcM) symbioses. Most such research has focussed on AM hosts or EcM fungi. For AM hosts, some early work on natural genetic variation has not been exploited yet, but new research with barley and clover will enable genetic mapping of mycorrhizal associated QTLs for the first time. EcM fungal studies have shown a genetic basis for mycorrhizal capacity and quantitative genetic differences in mycorrhizal capacity. Some recent work with EcM hosts has begun genetic mapping of QTLs associated with mycorrhizal status. Most AM genetic research has focussed on analysis of nodulation-defective mutants for their AM host status. Map-based cloning and characterisation of the first genes shown by these analyses to be essential for establishment of both nodulation and mycorrhizal symbioses are anticipated shortly. Comparisons with molecular and genetic research on plant disease resistance genes and signalling pathways may prove useful as those studies are more advanced and underlying biochemical and evolutionary relationships are likely to exist.     

CONNECTING QTLS TO THE G-MATRIX OF EVOLUTIONARY QUANTITATIVE GENETICS

Evolutionary quantitative genetics has recently advanced in two distinct streams. Many biologists address evolutionary questions by estimating phenotypic selection and genetic (co)variances ( G matrices). Simultaneously, an increasing number of studies have applied quantitative trait locus (QTL) mapping methods to dissect variation. Both conceptual and practical difficulties have isolated these two foci of quantitative genetics. A conceptual integration follows from the recognition that QTL allele frequencies are the essential variables relating the G -matrix to marker-based mapping experiments. Breeding designs initiated from randomly selected parental genotypes can be used to estimate QTL-specific genetic (co)variances. These statistics appropriately distill allelic variation and provide an explicit population context for QTL mapping estimates. Within this framework, one can parse the G -matrix into a set of mutually exclusive genomic components and ask whether these parts are similar or dissimilar in their respective features, for example the magnitude of phenotypic effects and the extent and nature of pleiotropy. As these features are critical determinants of sustained response to selection, the integration of QTL mapping methods into G -matrix estimation can provide a concrete, genetically based experimental program to investigate the evolutionary potential of natural populations.     

Natural genetic variation in Arabidopsis: tools, traits and prospects for evolutionary ecology

BACKGROUND: The model plant Arabidopsis thaliana (Arabidopsis) shows a wide range of genetic and trait variation among wild accessions. Because of its unparalleled biological and genomic resources, the potential of Arabidopsis for molecular genetic analysis of this natural variation has increased dramatically in recent years. SCOPE: Advanced genomics has accelerated molecular phylogenetic analysis and gene identification by quantitative trait loci (QTL) mapping and/or association mapping in Arabidopsis. In particular, QTL mapping utilizing natural accessions is now becoming a major strategy of gene isolation, offering an alternative to artificial mutant lines. Furthermore, the genomic information is used by researchers to uncover the signature of natural selection acting on the genes that contribute to phenotypic variation. The evolutionary significance of such genes has been evaluated in traits such as disease resistance and flowering time. However, although molecular hallmarks of selection have been found for the genes in question, a corresponding ecological scenario of adaptive evolution has been difficult to prove. Ecological strategies, including reciprocal transplant experiments and competition experiments, and utilizing near-isogenic lines of alleles of interest will be a powerful tool to measure the relative fitness of phenotypic and/or allelic variants. CONCLUSIONS: As the plant model organism, Arabidopsis provides a wealth of molecular background information for evolutionary genetics. Because genetic diversity between and within Arabidopsis populations is much higher than anticipated, combining this background information with ecological approaches might well establish Arabidopsis as a model organism for plant evolutionary ecology.     

牛、绵羊角的遗传定位及遗传机制研究进展

角属于动物颅骨附属物,为反刍动物所特有。牛(Bos taurus)、绵羊(Ovis aries)角的表型包括野生型两角表型、人工驯化的无角表型、畸形角等多种。牛和绵羊是阐明角的质量性状和数量性状之间的关系以及质量性状的多基因调控机制等方面的理想动物模型。近年来,对角性状研究不断深入,在阐明新器官起源进化、自然选择、性别选择和人工选择对角表型的影响等方面取得了一系列进展。本文详细介绍了角的研究概况、多角表型遗传定位、无角位点基因遗传定位和畸形角等,并对目前牛和绵羊角的遗传机制及存在的问题进行了分析,以期为反刍动物角性状和其他特异性性状遗传机制研究提供参考。     

High-density detection of restriction-site-associated DNA markers for rapid mapping of mutated loci in Neurospora

The wealth of sequence information available for Neurospora crassa and other fungi has greatly facilitated evolutionary and molecular analyses of this group. Although "reverse" genetics, in which genes are first identified by their sequence rather than by their mutant phenotypes, serves as a valuable new approach for elucidating biological processes, classical "forward" genetic analysis is still extremely useful. Unfortunately, mapping mutations and identifying the corresponding genes has typically been slow and laborious. To facilitate forward genetics in Neurospora, we have adapted microarray-based restriction-site-associated DNA (RAD) mapping for use with N. crassa oligonucleotide microarrays. This technique was used to simultaneously detect an unprecedented number of genomewide restriction site polymorphisms from two N. crassa strains: Mauriceville and Oak Ridge. Furthermore, RAD mapping was used to quickly map a previously unknown gene, defective in methylation-7 (dim-7).     

Towards identifying genes underlying ecologically relevant traits in Arabidopsis thaliana

A major challenge in evolutionary biology and plant breeding is to identify the genetic basis of complex quantitative traits, including those that contribute to adaptive variation. Here we review the development of new methods and resources to fine-map intraspecific genetic variation that underlies natural phenotypic variation in plants. In particular, the analysis of 107 quantitative traits reported in the first genome-wide association mapping study in Arabidopsis thaliana sets the stage for an exciting time in our understanding of plant adaptation. We also argue for the need to place phenotype-genotype association studies in an ecological context if one is to predict the evolutionary trajectories of plant species.     

Fundamentals of fungal molecular population genetic analyses

The last two decades have seen tremendous growth in the development and application of molecular methods in the analyses of fungal species and populations. In this paper, I provide an overview of the molecular techniques and the basic analytical tools used to address various fundamental population and evolutionary genetic questions in fungi. With increasing availability and decreasing cost, DNA sequencing is becoming a mainstream data acquisition method in fungal evolutionary genetic studies. However, other methods, especially those based on the polymerase chain reaction, remain powerful in addressing specific questions for certain groups of taxa. These developments are bringing fungal population and evolutionary genetics into mainstream ecology and evolutionary biology.     

Molecular genetic bases of adaptation processes and approaches to their analysis

Great interest in studying the molecular genetic bases of the adaptation processes is explained by their importance in understanding evolutionary changes, in the development of intraspecific and interspecific genetic diversity, and in the creation of approaches and programs for maintaining and restoring populations. The article examines the sources and conditions for generating adaptive genetic variability and contribution of neutral and adaptive genetic variability to the population structure of species; methods for identifying the adaptive genetic variability on the genome level are also described. Considerable attention is paid to the potential of new technologies of genome analysis, including next-generation sequencing and some accompanying methods. In conclusion, the important role of the joint use of genomics and proteomics approaches in understanding the molecular genetic bases of adaptation is emphasized.     

Gene mapping in the wild with SNPs: guidelines and future directions

One of the biggest challenges facing evolutionary biologists is to identify and understand loci that explain fitness variation in natural populations. This review describes how genetic (linkage) mapping with single nucleotide polymorphism (SNP) markers can lead to great progress in this area. Strategies for SNP discovery and SNP genotyping are described and an overview of how to model SNP genotype information in mapping studies is presented. Finally, the opportunity afforded by new generation sequencing and typing technologies to map fitness genes by genome-wide association studies is discussed.     

Genetic polymorphism of Microbotryum violaceum s. I. isolates collected from different plant species on the territory of Russia

The present-day studies in the field of systematics and phylogeny of microorganisms, fungi, in particular, are characterized by a wide use of new approaches and methods of molecular biology. The use of a diversity of genetic markers permits a distinct differentiation of closely related species into individual evolutionary independent lines. It is shown in this work that all Microbotryum violaceum s. l. isolates studied by us are divided into five evolutionary groups according to the host plant.     

The molecular genetic mapping of cereal crops

The application of modern methods of genetic mapping using RFLP and PCR technologies allowed to advance essentially in construction of rye genome genetic maps and mapping of some morphological and breeding-valuable genes. Genetic mapping of cereal genomes, such as rye, wheat, maize and rice using common set of DNA-probes permitted to reveal considerable evolutionary conservation in gene organization and localization. This allows to use more effectively method of comparative mapping for fast localization and tagging of genes in genomes of less investigated species.     

Evolutionary hotspots in the middle and lower reaches of the Yangtze River Basin

Geographic areas that contain high genetic divergence among populations may be regions of evolutionary potential and conservation importance. Following the methods for mapping patterns of genetic divergence and diversity in a Geographic Information Systems (GIS) framework, we combined genetic landscapes across nineteen co-distributed species in the middle and lower reaches of the Yangtze River Basin (MLYRB) to identify important regions of evolutionary potential and assess whether these hotspots have high conservation importance. Diversity hotspots were mainly distributed in the Tai Lake sub-basin of the MLYRB. Several areas of high genetic divergence were located in the Dongting Lake, Hanshui and other lower mainstream sub-basins. Additionally, two areas of low divergence (coolspots) were identified in the lower mainstream sub-basin. In total, our results identified 14 evolutionary hotspots in the MLYRB. Our study provides a first assessment of the diversity and divergence patterns across a wide variety of species in the habitats of the MLYRB and, therefore, a working hypothesis for determining geographical areas of high evolutionary potential and conservation importance in the MLYRB.     

Impact of genetic architecture on the relative rates of X versus autosomal adaptive substitution

Molecular evolutionary theory predicts that the ratio of autosomal to X-linked adaptive substitution (K(A)/K(x)) is primarily determined by the average dominance coefficient of beneficial mutations. Although this theory has profoundly influenced analysis and interpretation of comparative genomic data, its predictions are based upon two unverified assumptions about the genetic basis of adaptation. The theory assumes that 1) the rate of adaptively driven molecular evolution is limited by the availability of beneficial mutations, and 2) the scaling of evolutionary parameters between the X and the autosomes (e.g., the beneficial mutation rate, and the fitness effect distribution of beneficial alleles, per X-linked versus autosomal locus) is constant across molecular evolutionary timescales. Here, we show that the genetic architecture underlying bouts of adaptive substitution can influence both assumptions, and consequently, the theoretical relationship between K(A)/K(x) and mean dominance. Quantitative predictions of prior theory apply when 1) many genomically dispersed genes potentially contribute beneficial substitutions during individual steps of adaptive walks, and 2) the population beneficial mutation rate, summed across the set of potentially contributing genes, is sufficiently small to ensure that adaptive substitutions are drawn from new mutations rather than standing genetic variation. Current research into the genetic basis of adaptation suggests that both assumptions are plausibly violated. We find that the qualitative positive relationship between mean dominance and K(A)/K(x) is relatively robust to the specific conditions underlying adaptive substitution, yet the quantitative relationship between dominance and K(A)/K(x) is quite flexible and context dependent. This flexibility may partially account for the puzzlingly variable X versus autosome substitution patterns reported in the empirical evolutionary genomics literature. The new theory unites the previously separate analysis of adaptation using new mutations versus standing genetic variation and makes several useful predictions about the interaction between genetic architecture, evolutionary genetic constraints, and effective population size in determining the ratio of adaptive substitution between autosomal and X-linked genes.     

Molecular ecological approaches to studying the evolutionary impact of selective harvesting in wildlife

Harvesting of wildlife populations by humans is usually targeted by sex, age or phenotypic criteria, and is therefore selective. Selective harvesting has the potential to elicit a genetic response from the target populations in several ways. First, selective harvesting may affect population demographic structure (age structure, sex ratio), which in turn may have consequences for effective population size and hence genetic diversity. Second, wildlife-harvesting regimes that use selective criteria based on phenotypic characteristics (e.g. minimum body size, horn length or antler size) have the potential to impose artificial selection on harvested populations. If there is heritable genetic variation for the target characteristic and harvesting occurs before the age of maturity, then an evolutionary response over time may ensue. Molecular ecological techniques offer ways to predict and detect genetic change in harvested populations, and therefore have great utility for effective wildlife management. Molecular markers can be used to assess the genetic structure of wildlife populations, and thereby assist in the prediction of genetic impacts by delineating evolutionarily meaningful management units. Genetic markers can be used for monitoring genetic diversity and changes in effective population size and breeding systems. Tracking evolutionary change at the phenotypic level in the wild through quantitative genetic analysis can be made possible by genetically determined pedigrees. Finally, advances in genome sequencing and bioinformatics offer the opportunity to study the molecular basis of phenotypic variation through trait mapping and candidate gene approaches. With this understanding, it could be possible to monitor the selective impacts of harvesting at a molecular level in the future. Effective wildlife management practice needs to consider more than the direct impact of harvesting on population dynamics. Programs that utilize molecular genetic tools will be better positioned to assess the long-term evolutionary impact of artificial selection on the evolutionary trajectory and viability of harvested populations.     

A review of the application of molecular genetics for fisheries management and conservation of sharks and rays

Since the first investigation 25 years ago, the application of genetic tools to address ecological and evolutionary questions in elasmobranch studies has greatly expanded. Major developments in genetic theory as well as in the availability, cost effectiveness and resolution of genetic markers were instrumental for particularly rapid progress over the last 10 years. Genetic studies of elasmobranchs are of direct importance and have application to fisheries management and conservation issues such as the definition of management units and identification of species from fins. In the future, increased application of the most recent and emerging technologies will enable accelerated genetic data production and the development of new markers at reduced costs, paving the way for a paradigm shift from gene to genome-scale research, and more focus on adaptive rather than just neutral variation. Current literature is reviewed in six fields of elasmobranch molecular genetics relevant to fisheries and conservation management (species identification, phylogeography, philopatry, genetic effective population size, molecular evolutionary rate and emerging methods). Where possible, examples from the Indo-Pacific region, which has been underrepresented in previous reviews, are emphasized within a global perspective.     

Phylin 2.0: Extending the phylogeographical interpolation method to include uncertainty and user‐defined distance metrics

Estimating geographical ranges of intra‐specific evolutionary lineages is crucial to the fields of biogeography, evolution, and biodiversity conservation. Models of isolation mechanisms often consider multiple distances in order to explain genetic divergence. Yet, the available methods to estimate the geographical ranges of lineages are based on direct geographical distances, neglecting other distance metrics that can better explain the spatial genetic structure. We extended the phylogeographical interpolation method (phylin ) in order to accommodate user‐defined distance metrics and to incorporate the uncertainty associated with genetic distance calculation. These new features were tested with simulated and empirical data sets. Multiple distance matrices were generated including geographical, resistance, and environmental distances to derive maps of lineage occurrence. The new additions to this method improved the ability to predict lineage occurrence, even with low sample size. We used a regression framework to quantify the relationship between the genetic divergence and competing distance matrices representing potential isolation processes that are subsequently used in the interpolation process. Including uncertainty in tree topology and the different distance matrices improved the robustness of the variograms, allowing a better fit of the theoretical model of spatial dependence. The improvements to the method increase its potential application in other fields. Accurately mapping genetic divergence can help to locate potential contact zones between lineages as well as barriers to gene flow, which has a broad interest in biogeographical and evolutionary studies. Additionally, conservation efforts could benefit from the integration of genetic variation and landscape features in a spatially explicit framework.     

生态基因组学研究进展

生态基因组学是一个整合生态学、分子遗传学和进化基因组学的新兴交叉学科。生态基因组学将基因组学的研究手段和方法引入生态学领域,通过将群体基因组学、转录组学、蛋白质组学等手段与方法将个体、种群及群落、生态系统不同层次的生态学相互作用整合起来,确定在生态学响应及相互作用中具有重要意义的关键的基因和遗传途径,阐明这些基因及遗传途径变异的程度及其生态和进化后果的特征,从基因水平探索有机体响应天然环境(包括生物与非生物的环境因子)的遗传学机制。生态基因组学的研究对象可以分为模式生物与非模式生物两大类。拟南芥、酿酒酵母等模式生物在生态基因组学领域发挥了重要作用。随着越来越多基因组学技术的开发与完善,越来越多的非模式生物生态基因组学的研究将为生态学的发展提供重要的理论与实践依据。生态基因组学最核心的方法包括寻找序列变异、研究基因差异表达和分析基因功能等方法。生态基因组学已广泛渗透到生态学的相关领域中,将会在生物对环境的响应、物种间的相互作用、进化生态学、全球变化生态学、入侵生态学、群落生态学等研究领域发挥更大的作用。