Concepts Of Population Genetics Research Articles

Remembrance of Ching Chun Li, 1912–2003

Remembrance of Ching Chun Li, 1912–2003

Habitat fragmentation effects on fitness of plant populations – a review

Habitat fragmentation threatens the survival of many species and local populations. Habitat fragmentation has two major consequences: populations become more isolated and are reduced in size. Small compared with large populations have increased extinction risks because of different types stochasticity (e.g. genetic drift) and inbreeding, which can negatively affect the fitness of individuals or populations. Habitat fragmentation may also change the abiotic conditions of the surrounding landscape, which influences biotic interactions. This review gives an introduction to the theory of the effects of habitat fragmentation on mean fitness of plant populations. It intends to help bridge the gap between conservation biologists and conservation practitioners. The paper shortly introduces basic concepts of population biology, demography and genetics and cites relevant and new literature. Special attention is given to more common plant species, which have attracted far less conservation attention than rare species.

Genetics of population isolates.

Genetic isolates, as shown empirically by the Finnish, Old Order Amish, Hutterites, Sardinian and Jewish communities among others, represent a most important and powerful tool in genetically mapping inherited disorders. The main features associated with that genetic power are the existence of multigenerational pedigrees which are mostly descended from a small number of founders a short number of generations ago, environmental and phenotypic homogeneity, restricted geographical distribution, the presence of exhaustive and detailed records correlating individuals in very well ascertained pedigrees, and inbreeding as a norm. On the other hand, the presence of a multifounder effect or admixture among divergent populations in the founder time (e.g. the Finnish and the Paisa community from Colombia) will theoretically result in increased linkage disequilibrium among adjacent loci. The present review evaluates the historical context and features of some genetic isolates with emphasis on the basic population genetic concepts of inbreeding and genetic drift, and also the state-of-the-art in mapping traits, both Mendelian and complex, on genetic isolates.

Dispersal of cereal mildews across Europe

Following the evolution and spread of the barley and the wheat mildew pathogens, ( Blumeria (Erysiphe) graminis f.sp. hordei and tritici, respectively) over a long period and a large scale in Europe brought us new insight into their population biology which appears to be much more affected by aerial dispersal than generally believed. Results on the local evolution of the number of colony forming units m −3 of air (cfu) gave us an insight into the major features of population genetics and epidemiology of the barley mildew pathogen. Firstly, the evolution of cfu demonstrates and quantifies the epidemiological significance of volunteer plants. Moreover, three or four periods of primary infections become evident per year, forcing the wind-borne pathogen spores to move from one field (or region) to the next. This makes the pathogen to be highly nomadic, and points out to be of major interest for studies across Europe. Pathogen samples were analyzed from within the geographical triangle Spain–Scotland–Byelorussia for virulence to host resistance. Most unexpectedly, virulence complexity (i.e. number of virulence genes per spore) increased by approximately one virulence per 1000 km from west to east, from Scotland and France to central and eastern Europe. It is presumably caused by the interaction of prevailing winds, pathogen spores migrating on them, and host selection. Prevailing westerly winds carry pathogen spores to the east. Along the way, they encounter barley cultivars with different genes for race-specific resistance, and selection increases virulence complexity. The increase is elucidating for basic concepts of population genetics of wind-borne species, and important for gene deployment strategies. There was ample evidence for the dispersal of genes and genotypes from the regional to the continental level and beyond. Depending on year and location, detailed analyses showed that major parts of the population in one region can be assumed to originate from neighboring or distant regions. Dispersal is reduced by distance, barriers like mountain chains, and host-free spaces. Further, mildew ‘waves’ consisting of populations highly adapted through selection in one region appear to move across Europe on the prevailing westerly winds, covering approximately 100 km/year. Another important unexpected finding relates to fundamental features of the evolution of new and dangerous pathotypes. The established way of thinking starts with the effect of (regional) mutation as the basis of variability. In contrast, our evidence stresses the importance of the extraordinary variability already present in the pathogen population due to inoculum exchange over the vast continuous areas of Europe, northern Africa and Asia where the pathogen is endemic. Though mutation will remain of importance in the end, variability through spore dispersal among regions appears to be of more immediate relevance for the rapid adaptation of cereal mildew populations. Implications of our findings for fundamental aspects of population biology and integrated pest management strategies, from the regional to the continental and intercontinental level, are outlined and discussed.

Population genetics and its implications for conservation of rare and endangered plants

Population genetics is of great value in the study on the conservtion of rare and endangered plants.The authors introduced some important concepts in population genetics, including effective population size, inbreeding, genetic drift and gene flow, and then proposed some areas in which population genetics can be usedfor the conservation of rare and endangered plants.

A Population Genetic Analysis of the Potential for a Crude Oil Spill to Induce Heritable Mutations and Impact Natural Populations

The primary environmental impact following an oil spill typically is acute toxicity to fish and wildlife. However, multigenerational effects through toxicant-induced heritable mutations might also occur. Some polycyclic aromatic hydrocarbon (PAH) components of crude oil are potentially mutagenic, although specific components and doses that induce mutations are poorly known. We applied population genetics concepts to assess the extent of mortality and the persistence of deleterious heritable mutations resulting from exposure to potential mutagens, such as crude oil. If lethal mutations are induced, the population will experience some mortality, but the mutations are quickly removed or reduced to low frequency by natural selection. This occurs within one or a few generations when mutations are dominant or partially recessive. Totally recessive alleles persist in low frequency for many generations, but result in relatively little impact on the population, depending on the number of mutated loci. We also applied population genetics concepts to assess the potential for heritable mutations induced by the Exxon Valdez oil spill in Prince William Sound, Alaska, to affect pink salmon populations. We stress that breeding units (e.g., streams with distinct spawning populations of salmon) must be considered individually to assess heritable genetic effects. For several streams impacted by the oil spill, there is inconsistency between observed egg mortality and that expected if lethal heritable mutations had been induced by exposure to crude oil. Observed mortality was either higher or lower than expected depending on the spawning population, year, and cohort considered. Any potential subtle effect of lethal mutations induced by the Exxon Valdez oil spill is overridden by natural environmental variation among spawning areas. We discuss the need to focus on population-level effects in toxicological assessments because fish and wildlife management focuses on populations, not individuals.

Bacteria gone native vs. bacteria gone awry?: plasmidic transfer and bacterial evolution.

Despite the importance, abundance, and diversity of bacteria, we are just beginning to understand their evolutionary biology. Sex, understood as genetic exchange, is one of the keystone issues in bacterial evolution. Most bacteria reproduce by binary fission, and genetic exchange is independent of reproduction (1). If there is little or no genetic exchange among clones, each strain evolves as an independent lineage, and standard population genetics concepts, such as allelic frequencies and changes of these frequencies in populations, are not applicable (2). On the other hand, if recombination is common among related bacterial lineages (i.e., within bacterial species), we may analyze bacterial populations like most other organisms using standard population genetics methods (2). Recently, Maynard-Smith et al. (3), using detailed analyses based on multilocus linkage disequilibrium, have shown that there is a wide range of bacterial sexualities, ranging from lineages with little or no recombination (like Salmonella ) to others that are almost panmictic (like Neisseria gonorrhoeae ), and some with intermediate (and more complicated) sexualities: localized recombination among closely related strains ( Rhizobium meliloti ) or apparently very clonal populations, due to few very successful strains, have a structure called “epidemic” (e.g., Neisseria meningitidis ) (3). These analyses are mainly based on multilocus enzyme electrophoresis data from chromosomal genes. But bacteria have a fascinating complication; they usually present accessory genes, in the form of smaller chromosomes, known as plasmids (4, 5). Plasmids usually encode specific functions, such as conjugation, antibiotic resistance, sugar utilization, colicin activity, and nitrogen fixation (5–8). Some plasmids are small and cryptic (i.e, without any known function, if any), whereas others are large and more complex (5, 9). Plasmidic genes are not only dynamic, due to rearrangements and duplications within and among them (9, 10), they are also capable of moving among strains, among related bacterial …

Markov chains for Monte Carlo tests of genetic equilibrium in multidimensional contingency tables

Hardy-Weinberg equilibrium and linkage equilibrium are fundamental concepts in population genetics. In practice, testing linkage equilibrium in haplotype data is equivalent to testing independence in a large, sparse, multidimensional contingency table. Testing Hardy-Weinberg and linkage equilibrium simultaneously on multilocus genotype data introduces the additional complications of missing information and symmetry constraints on marginal probabilities. To avoid unreliable large-sample approximations for sparse contingency tables, one can use exact tests like Fisher's classical test that condition on observed marginal totals. Unfortunately, computing p-values for exact tests is often infeasible because of the large number of tables consistent with the marginal totals of an observed table. We develop here Markov chains for sampling from the appropriate conditional distributions for testing genetic equilibrium. These chains compare favorably with a parallel, independent-sampling method that we present. For n haplotype observations on J loci, the Markov chains converge to their stationary distributions in $[(J - 1)n 1n n]/2 + O(n)$ steps and can be an efficient tool for estimating p-values. Our theoretical treatment of these results involves strong stationary stopping times, order statistics, large deviations and the embedding of Poisson processes. We include some general results on the application of strong stationary times to bounding the precision and bias of sample average estimators.

Genetically complex cardiovascular traits. Origins, problems, and potential solutions.

Modern molecular genetic analysis tools are making it possible for researchers to investigate, and in many cases actually disclose, mutations and other genetic factors that contribute to disease susceptibility. However, the ease with which these factors can be identified is dictated by not only the number of factors underlying or influencing the trait, but also by the manner in which these factors interact. Traits that are influenced by multiple genetic and nongenetic factors are termed "complex" genetic traits and are receiving a great deal of attention in the current medical literature. Hypertension and blood pressure regulation are considered paradigmatic complex traits. In this paper, the origin, nature, and dilemmas associated with the analysis of complex traits are considered. Basic biochemical and physiological determinants of blood pressure are described in an effort to show how genetic complexity could arise within an individual, and fundamental concepts in population genetics and evolutionary theory are discussed to expose the reasons certain forms of genetic complexity can emerge and be sustained in the population at large. Methods for approaching the genetic dissection of complex traits and diseases are also enumerated, with simple descriptions of the scientific motivation offered for each. Problems plaguing these approaches are also discussed. Finally, areas for future research are outlined with the hope of sparking further debate on the subject.

Divergence and speciation as viewed from an insect hybrid zone

Hybridism is examined both from Darwin's point of view and in light of current views on the species concept. It seems that many of the relevant concepts of population genetics and speciation are inherent in primitive molecular evolution and may be useful in explaining divergent evolution from the earliest life forms. When divergent genomes meet they may hybridize and, in many cases, form a hybrid zone. Work on insect hybrid zones is used to exemplify the factors and processes involved. Many such zones are the result of postglacial secondary contact and involve some form of hybrid unfitness. They usually comprise multigenic differences and each gene may have different properties. Two grasshoppers, Podisma pedestris and Chorthippus parallelus, are used as case studies. In the case of P. pedestris, as a result of vegetation analysis, it is possible to be fairly sure that the zone is not environmentally determined but rather the result of heterozygous disadvantage at many loci. In the other species, in which two divergent mate recognition systems meet, there is no evidence of their reinforcement toward speciation, despite the F1 hybrids showing severe testis dysfunction and providing another example of Haldane's rule. A scenario for the postglacial contact and hybridization is proferred in an attempt to explain differences between disjunct sections of the zone. It is argued that gene flow occurs over only very small distances in hybrid zones and that the zones themselves will not move far because they fall in low density traps. Compound hybrid zones may be formed by cycles of range contraction and expansion and the substructure of a species will be determined by its life style. Hybrid zones provide a demonstration that divergence occurs in various characters at different rates and divergence brings with it hybrid disadvantage and frequency dependence. Speciation is seen as some way down this path, but occasional transfers of genetic material may still occur.

GENE TREES AND ORGANISMAL HISTORIES: A PHYLOGENETIC APPROACH TO POPULATION BIOLOGY.

A "gene tree" is the phylogeny of alleles or haplotypes for any specified stretch of DNA. Gene trees are components of population trees or species trees; their analysis entails a shift in perspective from many of the familiar models and concepts of population genetics, which typically deal with frequencies of phylogenetically unordered alleles. Molecular surveys of haplotype diversity in mitochondrial DNA (mtDNA) have provided the first extensive empirical data suitable for estimation of gene trees on a microevolutionary (intraspecific) scale. The relationship between phylogeny and geographic distribution constitutes the phylogeographic pattern for any species. Observed phylogeographic trees can be interpreted in terms of historical demography by comparison to predictions derived from models of gene lineage sorting, such as inbreeding theory and branching-process theory. Results of such analyses for more than 20 vertebrate species strongly suggest that the demographies of populations have been remarkably dynamic and unsettled over space and recent evolutionary time. This conclusion is consistent with ecological observations documenting dramatic population-size fluctuations and range shifts in many contemporary species. By adding an historical perspective to population biology, the gene-lineage approach can help forge links between the disciplines of phylogenetic systematics (and macroevolutionary study) and population genetics (microevolution). Preliminary extensions of the "gene tree" methodology to haplotypes of nuclear genes (such as Adh in Drosophila melanogaster) demonstrate that the phylogenetic perspective can also help to illuminate molecular-genetic processes (such as recombination or gene conversion), as well as contribute to knowledge of the origin, age, and molecular basis of particular adaptations.

The Population Biology of Host-Pathogen Interactions

Plant pathology literature provides ample evidence of growing knowledge of the biochemical, physiological, and genetic nature of host-pathogen interactions. Equally important, but less often studied, aspects of host-pathogen interactions are the complementary genetic changes that occur in the coevolution of host and pathogen populations. It is widely accepted that this coevolution of plants and their pathogens can be understood best in the context of integrated host-pathogen systems (e.g. 60). Pathogen population studies have been limited by a shortage of genetically well-defined host-pathogen systems based on easily scored genetic markers. Such markers are necessary to make use of the concepts of population genetics in improving our knowledge of host-pathogen population interactions. In particular, understanding the processes that drive genetic change in pathogen populations is essential to develop adequate and proper methods of disease control. Incorporating princi-

POPULATION GENETICS AND EVOLUTION

These lecture notes introduce key concepts of mathematical population genetics within the most elementary setting and describe a few recent applications to microbial evolution experiments. Pointers to the literature for further reading are provided, and some of the derivations are left as exercises for the reader.

Reviews

Book reviewed in this article: Basic Concepts in Population, Quantitative and Evolutionary Genetics. By J. F. Crow Population Genetics and Molecular Evolution. Edited by T. Ohta and K. Aoki Cancer Cytogenetics. By S. Heim and F. Mitelman

Using the domestic cat in the teaching of genetics

The domestic cat has the potential to enrich the learning experiences of students of genetics. Not only is it an animal that is very familiar to students, it also displays genetic polymorphism that is expressed in the readily visible variations in coat colour, coat pattern, and coat composition. The domestic cat can provide exemplars to illustrate many of the concepts of transmission genetics, including dominance, incomplete dominance, multiple allelism, X-linkage, and lethality. The cat can also be used to illustrate other relevant concepts, including X-inactivation and effect of environment on the phenotype, as well as concepts of population genetics. Use of the domestic cat, then, can be a valuable complement to the use of the organisms that have traditionally been the objects of study in genetics. While the cat is not a suitable animal for actual breeding experiments, the use of computer simulations or discussions with cat breeders can substitute for this activity. The paper provides examples based on...

Teaching the principles of genetics with the aid of the herediscope

The herediscope is discussed as a useful, simply constructed, tool for teaching the concepts of inheritance. Qualitative inheritance is readily taught through use of the herediscope. Sex inheritance may be used as an example, and various modes of gene action may be utilized, including epistasis between loci. A gradual progression to the concepts of quantitative inheritance may be made, using multiple modifying loci for a qualitative trait as an intermediate stage. The concepts of population genetics and the normal distribution may also be introduced with its aid.

Genetic diversity in California sea otters: Theoretical considerations and management implications

The California sea otter population was reduced to a small number of animals by fur hunters in the 18th and 19th centuries. The population has partially recovered but is still threatened, largely because of its vulnerability in the event of a major oil spill. The translocation of enough animals to establish a second colony outside the present range has been suggested as a means of reducing the vulnerability of the population. Any population that has been reduced to a small number and then allowed to increase may have lost some of its original genetic diversity. The loss of genetic diversity often results in deleterious effects, such as increased juvenile mortality and reduced fertility. It is therefore of interest to determine the degree of genetic diversity which the California sea otter population should have theoretically lost during its population ‘bottleneck’ and the number of otters which should be translocated in order to avoid substantial loss of genetic diversity in the new colony. Application of some of the concepts of population genetics to the California sea otter indicates that the current population should theoretically retain a large proportion (77%) of whatever genetic diversity existed in the original population and that a new colony resulting from the successful translocation of 50 breeding otters would retain much of the present genetic diversity after 40 years.

Mating systems and population structure in two closely related species of the wheat group I. Variation between and within populations

Samples of seven wild populations of the predominantly selfing species Triticum longissimum were compared with samples of five populations of the closely related, but predominantly outcrossing species, T. speltoides. For most of the 36 quantitative characters which were examined, the differences between populations, the total variances of the populations and the mean within-family variances, were greater in the selfer than in the outbreeder. Theoretical models were analysed in an attempt to explain these results, using concepts of classical population genetics.

Genetic Effects of Radiation

This short book reviews the effects of radiation on hereditary material and the consequence for the genetic structure of populations. The author limits his discussion to biological problems and studiously avoids the moral, ethical, or economic considerations of radiation mutation in man. The unemotional presentation of observations and hypotheses permits the intelligent reader to formulate his own conclusions regarding the hazards of radiation exposure. The basic concepts of radiation physics, the principles of heredity, the concepts of gene actions, and methods employed for the study of mutation in experimental organisms are introduced in the early chapters. The effects of radiation dosage, radiation intensity, energy levels, secondary radiochemical effects, and the differential sensitivities of developing germ cells are then discussed in detail. Then follows an excellent review of the concepts of population genetics, with particular emphasis upon the balance of mutation and selection in maintaining genetic equilibrium in populations. The last

Plant breeding systems

New concepts in population genetics call for reappraisal of plant breeding procedures; this commentary evaluates certain breeding procedures according to their probable effectiveness in promoting maximum gene recombinations and achieving maximum fitness. Breeding is viewed as an accelerated evolutionary process where appropriate design and control substitute for long duration of complex interactions of genotype with environment in the wild state. Crossing selected sibs in early generations is a means of re-assembling adaptive genes capable of functioning in a balanced polygenic system. The probability that any one individual in early generations after a cross would carry all or most of the potentially co-adaptive genes is very remote; hence strict inbreeding or pure line selection from early generations will not produce the best balanced genotypes. The recombination of two or more partly balanced genotypes by sib crossing magnifies the chance that a maximum number of harmoniously functioning genes will be assembled and through subsequent inbreeding emerge as stable and widely adapted varieties. Breeding procedures are viewed in perspective as they proceed from maximum inbreeding to maximum interbreeding or from pure line selection to bulk selection with natural or enforced sib-crossing.