Journal articles: 'Genetisk genealogi'

1

Uyenoyama, Marcy K. "Genealogical Structure Among Alleles Regulating Self-Incompatibility in Natural Populations of Flowering Plants." Genetics 147, no. 3 (November 1, 1997): 1389–400. http://dx.doi.org/10.1093/genetics/147.3.1389.

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A method is proposed for characterizing the structure of genealogies among alleles that regulate self-incompatibility in flowering plants. Expected distributions of ratios of divergence times among alleles, scaled by functions of allele number, were generated by numerical simulation. These distributions appeared relatively insensitive to the particular parameter values assigned in the simulations over a fourfold range in effective population size and a 100-fold range in mutation rate. Generalized least-squares estimates of the scaled indices were obtained from genealogies reconstructed from nucleotide sequences of self-incompatibility alleles from natural populations of two solanaceous species. Comparison of the observed indices to the expected distributions generated by numerical simulation indicated that the allelic genealogy of one species appeared consistent with the symmetric balancing selection generated by self-incompatibility. However, the allelic genealogy of the second species showed unusually long terminal branches, suggesting the operation of additional evolutionary processes.

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Schierup, Mikkel H., Anders M. Mikkelsen, and Jotun Hein. "Recombination, Balancing Selection and Phylogenies in MHC and Self-Incompatibility Genes." Genetics 159, no. 4 (December 1, 2001): 1833–44. http://dx.doi.org/10.1093/genetics/159.4.1833.

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AbstractUsing a coalescent model of multiallelic balancing selection with recombination, the genealogical process as a function of recombinational distance from a site under selection is investigated. We find that the shape of the phylogenetic tree is independent of the distance to the site under selection. Only the timescale changes from the value predicted by Takahata's allelic genealogy at the site under selection, converging with increasing recombination to the timescale of the neutral coalescent. However, if nucleotide sequences are simulated over a recombining region containing a site under balancing selection, a phylogenetic tree constructed while ignoring such recombination is strongly affected. This is true even for small rates of recombination. Published studies of multiallelic balancing selection, i.e., the major histocompatibility complex (MHC) of vertebrates, gametophytic and sporophytic self-incompatibility of plants, and incompatibility of fungi, all observe allelic genealogies with unexpected shapes. We conclude that small absolute levels of recombination are compatible with these observed distortions of the shape of the allelic genealogy, suggesting a possible cause of these observations. Furthermore, we illustrate that the variance in the coalescent with recombination process makes it difficult to locate sites under selection and to estimate the selection coefficient from levels of variability.

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Schierup, Mikkel H., Xavier Vekemans, and Freddy B. Christiansen. "Allelic Genealogies in Sporophytic Self-Incompatibility Systems in Plants." Genetics 150, no. 3 (November 1, 1998): 1187–98. http://dx.doi.org/10.1093/genetics/150.3.1187.

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Abstract Expectations for the time scale and structure of allelic genealogies in finite populations are formed under three models of sporophytic self-incompatibility. The models differ in the dominance interactions among the alleles that determine the self-incompatibility phenotype: In the SSIcod model, alleles act codominantly in both pollen and style, in the SSIdom model, alleles form a dominance hierarchy, and in SSIdomcod, alleles are codominant in the style and show a dominance hierarchy in the pollen. Coalescence times of alleles rarely differ more than threefold from those under gametophytic self-incompatibility, and transspecific polymorphism is therefore expected to be equally common. The previously reported directional turnover process of alleles in the SSIdomcod model results in coalescence times lower and substitution rates higher than those in the other models. The SSIdom model assumes strong asymmetries in allelic action, and the most recessive extant allele is likely to be the most recent common ancestor. Despite these asymmetries, the expected shape of the allele genealogies does not deviate markedly from the shape of a neutral gene genealogy. The application of the results to sequence surveys of alleles, including interspecific comparisons, is discussed.

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EVANS, DONALD. "WHAKAPAPA, GENEALOGY AND GENETICS." Bioethics 26, no. 4 (December 7, 2010): 182–90. http://dx.doi.org/10.1111/j.1467-8519.2010.01850.x.

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5

Slatkin, Montgomery. "Gene Genealogies Within Mutant Allelic Classes." Genetics 143, no. 1 (May 1, 1996): 579–87. http://dx.doi.org/10.1093/genetics/143.1.579.

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Abstract A coalescent theory of the gene genealogy within an allelic class that arises by a unique mutational event is developed and analyzed. To interpret this theory it was necessary to expand on existing theory for populations of varying size. Two features of the gene genealogy—the average pairwise distance and the total tree length—within the mutant class and within the nonmutant class are found. An index, I, is proposed that describes the extent to which a genealogy is similar to one from a population of constant size (for which I = 0) or to a star genealogy (for which I = 1). The value of I is positive in growing populations and is generally positive for the gene genealogy for the mutant class. The value of lis negative for a population decreasing in size and for the nonmutant class, if the mutant arose recently. The results are discussed in the context of the infinite sites model of mutation, which is appropriate for nucleotide sequence data, and the generalized stepwise mutation model, which is appropriate for microsatellite loci. The same genealogical methods are used to find the probability of at least one recombination event between a nucleotide that defines an allelic class and a marker at a nearby linked site.

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Neuhauser, Claudia, and Stephen M. Krone. "The Genealogy of Samples in Models With Selection." Genetics 145, no. 2 (February 1, 1997): 519–34. http://dx.doi.org/10.1093/genetics/145.2.519.

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We introduce the genealogy of a random sample of genes taken from a large haploid population that evolves according to random reproduction with selection and mutation. Without selection, the genealogy is described by Kingman's well-known coalescent process. In the selective case, the genealogy of the sample is embedded in a graph with a coalescing and branching structure. We describe this graph, called the ancestral selection graph, and point out differences and similarities with Kingman's coalescent. We present simulations for a two-allele model with symmetric mutation in which one of the alleles has a selective advantage over the other. We find that when the allele frequencies in the population are already in equilibrium, then the genealogy does not differ much from the neutral case. This is supported by rigorous results. Furthermore, we describe the ancestral selection graph for other selective models with finitely many selection classes, such as the K-allele models, infinitely-many-alleles models, DNA sequence models, and infinitely-many-sites models, and briefly discuss the diploid case.

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Velasco Martín, Marta. "Women and Partnership Genealogies in Drosophila Population Genetics." Perspectives on Science 28, no. 2 (April 2020): 277–317. http://dx.doi.org/10.1162/posc_a_00341.

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Drosophila flies began to be used in the study of species evolution during the late 1930s. The geneticists Natasha Sivertzeva-Dobzhansky and Elizabeth Reed pioneered this work in the United States, and María Monclús conducted similar studies in Spain. The research they carried out with their husbands enabled Drosophila population genetics to take off and reveals a genealogy of women geneticists grounded in mutual inspiration. Their work also shows that women were present in population genetics from the beginning, although their contributions have previously remained unacknowledged. The similarities between their research biographies also illustrate their position in a genealogy of partnerships working on Drosophila genetics.

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Johnston, Josephine, and Mark Thomas. "Summary: The Science of Genealogy by Genetics." Developing World Bioethics 3, no. 2 (December 2003): 103–8. http://dx.doi.org/10.1046/j.1471-8731.2003.00064.x.

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Tyler, Katharine. "Ethnographic Approaches to Race, Genetics and Genealogy." Sociology Compass 2, no. 6 (November 2008): 1860–77. http://dx.doi.org/10.1111/j.1751-9020.2008.00168.x.

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10

Zhang, Kangyu, and Noah A. Rosenberg. "On the Genealogy of a Duplicated Microsatellite." Genetics 177, no. 4 (October 18, 2007): 2109–22. http://dx.doi.org/10.1534/genetics.106.063131.

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11

Achtman, Mark. "Insights from genomic comparisons of genetically monomorphic bacterial pathogens." Philosophical Transactions of the Royal Society B: Biological Sciences 367, no. 1590 (March 19, 2012): 860–67. http://dx.doi.org/10.1098/rstb.2011.0303.

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Some of the most deadly bacterial diseases, including leprosy, anthrax and plague, are caused by bacterial lineages with extremely low levels of genetic diversity, the so-called ‘genetically monomorphic bacteria’. It has only become possible to analyse the population genetics of such bacteria since the recent advent of high-throughput comparative genomics. The genomes of genetically monomorphic lineages contain very few polymorphic sites, which often reflect unambiguous clonal genealogies. Some genetically monomorphic lineages have evolved in the last decades, e.g. antibiotic-resistant Staphylococcus aureus , whereas others have evolved over several millennia, e.g. the cause of plague, Yersinia pestis . Based on recent results, it is now possible to reconstruct the sources and the history of pandemic waves of plague by a combined analysis of phylogeographic signals in Y. pestis plus polymorphisms found in ancient DNA. Different from historical accounts based exclusively on human disease, Y. pestis evolved in China, or the vicinity, and has spread globally on multiple occasions. These routes of transmission can be reconstructed from the genealogy, most precisely for the most recent pandemic that was spread from Hong Kong in multiple independent waves in 1894.

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12

Brown, K. "SCIENCE AND COMMERCE: Tangled Roots? Genetics Meets Genealogy." Science 295, no. 5560 (March 1, 2002): 1634–35. http://dx.doi.org/10.1126/science.295.5560.1634.

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13

Nielsen, Rasmus. "Mutations as Missing Data: Inferences on the Ages and Distributions of Nonsynonymous and Synonymous Mutations." Genetics 159, no. 1 (September 1, 2001): 401–11. http://dx.doi.org/10.1093/genetics/159.1.401.

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AbstractThis article describes a new Markov chain Monte Carlo (MCMC) method applicable to DNA sequence data, which treats mutations in the genealogy as missing data. The method facilitates inferences regarding the age and identity of specific mutations while taking the full complexities of the mutational process in DNA sequences into account. We demonstrate the utility of the method in three applications. First, we demonstrate how the method can be used to make inferences regarding population genetical parameters such as θ (the effective population size times the mutation rate). Second, we show how the method can be used to estimate the ages of mutations in finite sites models and for making inferences regarding the distribution and ages of nonsynonymous and synonymous mutations. The method is applied to two previously published data sets and we demonstrate that in one of the data sets the average age of nonsynonymous mutations is significantly lower than the average age of synonymous mutations, suggesting the presence of slightly deleterious mutations. Third, we demonstrate how the method in general can be used to evaluate the posterior distribution of a function of a mapping of mutations on a gene genealogy. This application is useful for evaluating the uncertainty associated with methods that rely on mapping mutations on a phylogeny or a gene genealogy.

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14

Takahata, Naoyuki, and Masatoshi Nei. "GENE GENEALOGY AND VARIANCE OF INTERPOPULATIONAL NUCLEOTIDE DIFFERENCES." Genetics 110, no. 2 (June 1, 1985): 325–44. http://dx.doi.org/10.1093/genetics/110.2.325.

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ABSTRACT A mathematical theory is developed for computing the probability that m genes sampled from one population (species) and n genes sampled from another are derived from l genes that existed at the time of population splitting. The expected time of divergence between the two most closely related genes sampled from two different populations and the time of divergence (coalescence) of all genes sampled are studied by using this theory. It is shown that the time of divergence between the two most closely related genes can be used as an approximate estimate of the time of population splitting (T) only when T ≡ t/(2 N) is small, where t and N are the number of generations and the effective population size, respectively. The variance of Nei and Li's estimate (d) of the number of net nucleotide differences between two populations is also studied. It is shown that the standard error (sd) of d is larger than the mean when T is small (T << 1). In this case, sd is reduced considerably by increasing sample size. When T is large (T > 1), however, a large proportion of the variance of d is caused by stochastic factors, and increase in the sample size does not help to reduce sd. To reduce the stochastic variance of d, one must use data from many independent unlinked gene loci.

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15

Pfaffelhuber, P., B. Haubold, and A. Wakolbinger. "Approximate Genealogies Under Genetic Hitchhiking." Genetics 174, no. 4 (December 2006): 1995–2008. http://dx.doi.org/10.1534/genetics.106.061887.

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16

Wakeley, John, and Nicolas Aliacar. "Gene Genealogies in a Metapopulation." Genetics 159, no. 2 (October 1, 2001): 893–905. http://dx.doi.org/10.1093/genetics/159.2.893.

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Abstract A simple genealogical process is found for samples from a metapopulation, which is a population that is subdivided into a large number of demes, each of which is subject to extinction and recolonization and receives migrants from other demes. As in the migration-only models studied previously, the genealogy of any sample includes two phases: a brief sample-size adjustment followed by a coalescent process that dominates the history. This result will hold for metapopulations that are composed of a large number of demes. It is robust to the details of population structure, as long as the number of possible source demes of migrants and colonists for each deme is large. Analytic predictions about levels of genetic variation are possible, and results for average numbers of pairwise differences within and between demes are given. Further analysis of the expected number of segregating sites in a sample from a single deme illustrates some previously known differences between migration and extinction/recolonization. The ancestral process is also amenable to computer simulation. Simulation results show that migration and extinction/recolonization have very different effects on the site-frequency distribution in a sample from a single deme. Migration can cause a U-shaped site-frequency distribution, which is qualitatively similar to the pattern reported recently for positive selection. Extinction and recolonization, in contrast, can produce a mode in the site-frequency distribution at intermediate frequencies, even in a sample from a single deme.

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Tiffin, Peter, and Brandon S. Gaut. "Sequence Diversity in the Tetraploid Zea perennis and the Closely Related Diploid Z. diploperennis: Insights From Four Nuclear Loci." Genetics 158, no. 1 (May 1, 2001): 401–12. http://dx.doi.org/10.1093/genetics/158.1.401.

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Abstract Polyploidy has been an extremely common phenomenon in the evolutionary history of angiosperms. Despite this there are few data available to evaluate the effects of polyploidy on genetic diversity and to compare the relative effects of drift and selection in polyploids and related diploids. We investigated DNA sequence diversity at four nuclear loci (adh1, glb1, c1, and waxy) from the tetraploid Zea perennis and the closely related diploid Z. diploperennis. Contrary to expectations, we detected no strong evidence for greater genetic diversity in the tetraploid, or for consistent differences in the effects of either drift or selection between the tetraploid and the diploid. Our failure to find greater genetic diversity in Z. perennis may result from its relatively recent origin or demographic factors associated with its origin. In addition to comparing genetic diversity in the two species, we constructed genealogies to infer the evolutionary origin of Z. perennis. Although these genealogies are equivocal regarding the mode of origin, several aspects of these genealogies support an autotetraploid origin. Consistent with previous molecular data the genealogies do not, however, support the division of Zea into two sections, the section Zea and the section Luxuriantes.

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Speidel, Leo, Lara Cassidy, Robert W. Davies, Garrett Hellenthal, Pontus Skoglund, and Simon R. Myers. "Inferring Population Histories for Ancient Genomes Using Genome-Wide Genealogies." Molecular Biology and Evolution 38, no. 9 (June 15, 2021): 3497–511. http://dx.doi.org/10.1093/molbev/msab174.

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Abstract Ancient genomes anchor genealogies in directly observed historical genetic variation and contextualize ancestral lineages with archaeological insights into their geography and cultural associations. However, the majority of ancient genomes are of lower coverage and cannot be directly built into genealogies. Here, we present a fast and scalable method, Colate, the first approach for inferring ancestral relationships through time between low-coverage genomes without requiring phasing or imputation. Our approach leverages sharing patterns of mutations dated using a genealogy to infer coalescence rates. For deeply sequenced ancient genomes, we additionally introduce an extension of the Relate algorithm for joint inference of genealogies incorporating such genomes. Application to 278 present-day and 430 ancient DNA samples of >0.5x mean coverage allows us to identify dynamic population structure and directional gene flow between early farmer and European hunter-gatherer groups. We further show that the previously reported, but still unexplained, increase in the TCC/TTC mutation rate, which is strongest in West Eurasia today, was already present at similar strength and widespread in the Late Glacial Period ~10k−15k years ago, but is not observed in samples >30k years old. It is strongest in Neolithic farmers, and highly correlated with recent coalescence rates between other genomes and a 10,000-year-old Anatolian hunter-gatherer. This suggests gene-flow among ancient peoples postdating the last glacial maximum as widespread and localizes the driver of this mutational signal in both time and geography in that region. Our approach should be widely applicable in future for addressing other evolutionary questions, and in other species.

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Barton, N. H., and A. M. Etheridge. "The Effect of Selection on Genealogies." Genetics 166, no. 2 (February 2004): 1115–31. http://dx.doi.org/10.1534/genetics.166.2.1115.

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Barton, N. H., and A. M. Etheridge. "The Effect of Selection on Genealogies." Genetics 166, no. 2 (February 1, 2004): 1115–31. http://dx.doi.org/10.1093/genetics/166.2.1115.

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Abstract The coalescent process can describe the effects of selection at linked loci only if selection is so strong that genotype frequencies evolve deterministically. Here, we develop methods proposed by Kaplan, Darden, and Hudson to find the effects of weak selection. We show that the overall effect is given by an extension to Price’s equation: the change in properties such as moments of coalescence times is equal to the covariance between those properties and the fitness of the sample of genes. The distribution of coalescence times differs substantially between allelic classes, even in the absence of selection. However, the average coalescence time between randomly chosen genes is insensitive to the current allele frequency and is affected significantly by purifying selection only if deleterious mutations are common and selection is strong (i.e., the product of population size and selection coefficient, Ns > 3). Balancing selection increases mean coalescence times, but the effect becomes large only when mutation rates between allelic classes are low and when selection is extremely strong. Our analysis supports previous simulations that show that selection has surprisingly little effect on genealogies. Moreover, small fluctuations in allele frequency due to random drift can greatly reduce any such effects. This will make it difficult to detect the action of selection from neutral variation alone.

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Epperson, Bryan K. "Gene Genealogies in Geographically Structured Populations." Genetics 152, no. 2 (June 1, 1999): 797–806. http://dx.doi.org/10.1093/genetics/152.2.797.

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Abstract Population genetics theory has dealt only with the spatial or geographic pattern of degrees of relatedness or genetic similarity separately for each point in time. However, a frequent goal of experimental studies is to infer migration patterns that occurred in the past or over extended periods of time. To fully understand how a present geographic pattern of genetic variation reflects one in the past, it is necessary to build genealogy models that directly relate the two. For the first time, space-time probabilities of identity by descent and coalescence probabilities are formulated and characterized in this article. Formulations for general migration processes are developed and applied to specific types of systems. The results can be used to determine the level of certainty that genes found in present populations are descended from ancient genes in the same population or nearby populations vs. geographically distant populations. Some parameter combinations result in past populations that are quite distant geographically being essentially as likely to contain ancestors of genes at a given population as the past population located at the same place. This has implications for the geographic point of origin of ancestral, “Eve,” genes. The results also form the first model for emerging “space-time” molecular genetic data.

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Nordborg, Magnus, and Hideki Innan. "The Genealogy of Sequences Containing Multiple Sites Subject to Strong Selection in a Subdivided Population." Genetics 163, no. 3 (March 1, 2003): 1201–13. http://dx.doi.org/10.1093/genetics/163.3.1201.

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Abstract A stochastic model for the genealogy of a sample of recombining sequences containing one or more sites subject to selection in a subdivided population is described. Selection is incorporated by dividing the population into allelic classes and then conditioning on the past sizes of these classes. The past allele frequencies at the selected sites are thus treated as parameters rather than as random variables. The purpose of the model is not to investigate the dynamics of selection, but to investigate effects of linkage to the selected sites on the genealogy of the surrounding chromosomal region. This approach is useful for modeling strong selection, when it is natural to parameterize the past allele frequencies at the selected sites. Several models of strong balancing selection are used as examples, and the effects on the pattern of neutral polymorphism in the chromosomal region are discussed. We focus in particular on the statistical power to detect balancing selection when it is present.

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23

Felsenstein, Joseph. "Estimating effective population size from samples of sequences: inefficiency of pairwise and segregating sites as compared to phylogenetic estimates." Genetical Research 59, no. 2 (April 1992): 139–47. http://dx.doi.org/10.1017/s0016672300030354.

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SummaryIt is known that under neutral mutation at a known mutation rate a sample of nucleotide sequences, within which there is assumed to be no recombination, allows estimation of the effective size of an isolated population. This paper investigates the case of very long sequences, where each pair of sequences allows a precise estimate of the divergence time of those two gene copies. The average divergence time of all pairs of copies estimates twice the effective population number and an estimate can also be derived from the number of segregating sites. One can alternatively estimate the genealogy of the copies. This paper shows how a maximum likelihood estimate of the effective population number can be derived from such a genealogical tree. The pairwise and the segregating sites estimates are shown to be much less efficient than this maximum likelihood estimate, and this is verified by computer simulation. The result implies that there is much to gain by explicitly taking the tree structure of these genealogies into account.

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Gan, Han L., Adrian Röllin, and Nathan Ross. "Dirichlet approximation of equilibrium distributions in Cannings models with mutation." Advances in Applied Probability 49, no. 3 (September 2017): 927–59. http://dx.doi.org/10.1017/apr.2017.27.

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AbstractConsider a haploid population of fixed finite size with a finite number of allele types and having Cannings exchangeable genealogy with neutral mutation. The stationary distribution of the Markov chain of allele counts in each generation is an important quantity in population genetics but has no tractable description in general. We provide upper bounds on the distributional distance between the Dirichlet distribution and this finite-population stationary distribution for the Wright–Fisher genealogy with general mutation structure and the Cannings exchangeable genealogy with parent independent mutation structure. In the first case, the bound is small if the population is large and the mutations do not depend too much on parent type; 'too much' is naturally quantified by our bound. In the second case, the bound is small if the population is large and the chance of three-mergers in the Cannings genealogy is small relative to the chance of two-mergers; this is the same condition to ensure convergence of the genealogy to Kingman's coalescent. These results follow from a new development of Stein's method for the Dirichlet distribution based on Barbour's generator approach and a probabilistic description of the semigroup of the Wright–Fisher diffusion due to Griffiths and Li (1983) and Tavaré (1984).

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Mortimer, Robert K., and John R. Johnston. "GENEALOGY OF PRINCIPAL STRAINS OF THE YEAST GENETIC STOCK CENTER." Genetics 113, no. 1 (May 1, 1986): 35–43. http://dx.doi.org/10.1093/genetics/113.1.35.

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ABSTRACT We have constructed a genealogy of strain S288C, from which many of the mutant and segregant strains currently used in studies on the genetics and molecular biology of Saccharomyces cerevisiae have been derived. We have determined that its six progenitor strains were EM93, EM126, NRRL YB-210 and the three baking strains Yeast Foam, FLD and LK. We have estimated that approximately 88% of the gene pool of S288C is contributed by strain EM93. The principal ancestral genotypes were those of segregant strains EM93-1C and EM93-3B, initially distributed by C. C. Lindegren to several laboratories. We have analyzed an isolate of a lyophilized culture of strain EM93 and determined its genotype as MAT a/MAT? SUC2/SUC2 GAL2/gal2 MAL/MAL mel/mel CUP1/cup1 FLO1/flo1. Strain EM93 is therefore the probable origin of genes SUC2, gal2, CUP1 and flo1 of S288C. We give details of the current availability of several of the progenitor strains and propose that this genealogy should be of assistance in elucidating the origins of several types of genetic and molecular heterogeneities in Saccharomyces.

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Fu, Y. X., and W. H. Li. "Statistical tests of neutrality of mutations." Genetics 133, no. 3 (March 1, 1993): 693–709. http://dx.doi.org/10.1093/genetics/133.3.693.

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Abstract Mutations in the genealogy of the sequences in a random sample from a population can be classified as external and internal. External mutations are mutations that occurred in the external branches and internal mutations are mutations that occurred in the internal branches of the genealogy. Under the assumption of selective neutrality, the expected number of external mutations is equal to theta = 4Ne mu, where Ne is the effective population size and mu is the rate of mutation per gene per generation. Interestingly, this expectation is independent of the sample size. The number of external mutations is likely to deviate from its neutral expectation when there is selection while the number of internal mutations is less affected by the presence of selection. Statistical properties of the numbers of external mutations and of internal mutations are studied and their relationships to two commonly used estimates of theta are derived. From these properties, several new statistical tests based on a random sample of DNA sequences from the population are developed for testing the hypothesis that all mutations at a locus are neutral.

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Drummond, Alexei J., Geoff K. Nicholls, Allen G. Rodrigo, and Wiremu Solomon. "Estimating Mutation Parameters, Population History and Genealogy Simultaneously From Temporally Spaced Sequence Data." Genetics 161, no. 3 (July 1, 2002): 1307–20. http://dx.doi.org/10.1093/genetics/161.3.1307.

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Abstract Molecular sequences obtained at different sampling times from populations of rapidly evolving pathogens and from ancient subfossil and fossil sources are increasingly available with modern sequencing technology. Here, we present a Bayesian statistical inference approach to the joint estimation of mutation rate and population size that incorporates the uncertainty in the genealogy of such temporally spaced sequences by using Markov chain Monte Carlo (MCMC) integration. The Kingman coalescent model is used to describe the time structure of the ancestral tree. We recover information about the unknown true ancestral coalescent tree, population size, and the overall mutation rate from temporally spaced data, that is, from nucleotide sequences gathered at different times, from different individuals, in an evolving haploid population. We briefly discuss the methodological implications and show what can be inferred, in various practically relevant states of prior knowledge. We develop extensions for exponentially growing population size and joint estimation of substitution model parameters. We illustrate some of the important features of this approach on a genealogy of HIV-1 envelope (env) partial sequences.

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Cohen, Bernard L. "Genetics and Molecular Systematics of Brachiopods." Paleontological Society Papers 7 (November 2001): 53–68. http://dx.doi.org/10.1017/s1089332600000899.

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When Charles Darwin wrote that “Our classifications will come to be, as far as they may be so made, genealogies…we have to discover and trace the many diverging lines of descent in our natural genealogies by characters…which have long been inherited” (Darwin, 1859), he presciently laid down aims and objectives of systematics that have become attainable only since the development of genetics and of molecular approaches to systematics. Genetics elucidates the heredity of characters; molecular systematics measures the degrees of relationship between diverging lineages (Griffiths et al., 1993; Page and Holmes, 1998; Graur and Li, 2000). This article attempts to review these essential aids to the art and science of brachiopod classification as they stand today. Every step so far taken to promote molecular approaches to brachiopod systematics has yielded new, unexpected, and valuable information, but there remains massive scope for new work and new workers.

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McVean, Gilean A. T., and Niall J. Cardin. "Approximating the coalescent with recombination." Philosophical Transactions of the Royal Society B: Biological Sciences 360, no. 1459 (July 7, 2005): 1387–93. http://dx.doi.org/10.1098/rstb.2005.1673.

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The coalescent with recombination describes the distribution of genealogical histories and resulting patterns of genetic variation in samples of DNA sequences from natural populations. However, using the model as the basis for inference is currently severely restricted by the computational challenge of estimating the likelihood. We discuss why the coalescent with recombination is so challenging to work with and explore whether simpler models, under which inference is more tractable, may prove useful for genealogy-based inference. We introduce a simplification of the coalescent process in which coalescence between lineages with no overlapping ancestral material is banned. The resulting process has a simple Markovian structure when generating genealogies sequentially along a sequence, yet has very similar properties to the full model, both in terms of describing patterns of genetic variation and as the basis for statistical inference.

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Kim, Jaehee, Noah A. Rosenberg, and Julia A. Palacios. "Distance metrics for ranked evolutionary trees." Proceedings of the National Academy of Sciences 117, no. 46 (November 2, 2020): 28876–86. http://dx.doi.org/10.1073/pnas.1922851117.

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Genealogical tree modeling is essential for estimating evolutionary parameters in population genetics and phylogenetics. Recent mathematical results concerning ranked genealogies without leaf labels unlock opportunities in the analysis of evolutionary trees. In particular, comparisons between ranked genealogies facilitate the study of evolutionary processes of different organisms sampled at multiple time periods. We propose metrics on ranked tree shapes and ranked genealogies for lineages isochronously and heterochronously sampled. Our proposed tree metrics make it possible to conduct statistical analyses of ranked tree shapes and timed ranked tree shapes or ranked genealogies. Such analyses allow us to assess differences in tree distributions, quantify estimation uncertainty, and summarize tree distributions. We show the utility of our metrics via simulations and an application in infectious diseases.

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31

Lynch, John. "Geography, Genealogy and Genetics: Dialectical Substance in Newspaper Coverage of Research on Race and Genetics." Western Journal of Communication 72, no. 3 (August 25, 2008): 259–79. http://dx.doi.org/10.1080/10570310802210130.

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32

Sano, Akinori, and Hidenori Tachida. "Gene Genealogy and Properties of Test Statistics of Neutrality Under Population Growth." Genetics 169, no. 3 (November 15, 2004): 1687–97. http://dx.doi.org/10.1534/genetics.104.032797.

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Kuhner, M. K., J. Yamato, and J. Felsenstein. "Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling." Genetics 140, no. 4 (August 1, 1995): 1421–30. http://dx.doi.org/10.1093/genetics/140.4.1421.

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Abstract We present a new way to make a maximum likelihood estimate of the parameter 4N mu (effective population size times mutation rate per site, or theta) based on a population sample of molecular sequences. We use a Metropolis-Hastings Markov chain Monte Carlo method to sample genealogies in proportion to the product of their likelihood with respect to the data and their prior probability with respect to a coalescent distribution. A specific value of theta must be chosen to generate the coalescent distribution, but the resulting trees can be used to evaluate the likelihood at other values of theta, generating a likelihood curve. This procedure concentrates sampling on those genealogies that contribute most of the likelihood, allowing estimation of meaningful likelihood curves based on relatively small samples. The method can potentially be extended to cases involving varying population size, recombination, and migration.

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Nicolaisen, Lauren E., and Michael M. Desai. "Distortions in Genealogies due to Purifying Selection and Recombination." Genetics 195, no. 1 (July 2, 2013): 221–30. http://dx.doi.org/10.1534/genetics.113.152983.

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35

Nicoglou, Antonine. "The evolution of phenotypic plasticity: Genealogy of a debate in genetics." Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 50 (April 2015): 67–76. http://dx.doi.org/10.1016/j.shpsc.2015.01.003.

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Takahata, N. "Gene genealogy in three related populations: consistency probability between gene and population trees." Genetics 122, no. 4 (August 1, 1989): 957–66. http://dx.doi.org/10.1093/genetics/122.4.957.

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Abstract A genealogical relationship among genes at a locus (gene tree) sampled from three related populations was examined with special reference to population relatedness (population tree). A phylogenetically informative event in a gene tree constructed from nucleotide differences consists of interspecific coalescences of genes in each of which two genes sampled from different populations are descended from a common ancestor. The consistency probability between gene and population trees in which they are topologically identical was formulated in terms of interspecific coalescences. It was found that the consistency probability thus derived substantially increases as the sample size of genes increases, unless the divergence time of populations is very long compared to population sizes. Hence, there are cases where large samples at a locus are very useful in inferring a population tree.

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Slatkin, M. "Linkage disequilibrium in growing and stable populations." Genetics 137, no. 1 (May 1, 1994): 331–36. http://dx.doi.org/10.1093/genetics/137.1.331.

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Abstract Nonrandom associations between alleles at different loci can be tested for using Fisher's exact test. Extensive simulations show that there is a substantial probability of obtaining significant nonrandom associations between closely or completely linked polymorphic neutral loci in a population of constant size at equilibrium under mutation and genetic drift. In a rapidly growing population, however, there will be little chance of finding significant nonrandom associations even between completely linked loci if the growth has been sufficiently rapid. This result is illustrated by the analysis of mitochondrial DNA sequence data from humans. In comparing all pairs of informative sites, fewer than 5% of the pairs show significant disequilibrium in Sardinians, which have apparently undergone rapid population growth, while 20% to 30% in !Kung and Pygmies, which apparently have not undergone rapid growth, show significance. The extent of linkage disequilibrium in a population is closely related to the gene genealogies of the loci examined, with "star-like" genealogies making significant linkage disequilibrium unlikely.

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38

Faerge, I., A. Egeskov-Madsen, and P. Holm. "295 THE SHAPE OF PORCINE NEURAL PROGENITOR CELL CELLULAR GENEALOGIES REVEALED BY TIME-LAPSE IMAGING." Reproduction, Fertility and Development 23, no. 1 (2011): 245. http://dx.doi.org/10.1071/rdv23n1ab295.

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Porcine neural progenitor cells (pNPC) derived from embryonic stem cells are capable of self-renewal and differentiation into neural and glia lineages, rendering them promising candidates for cell-based therapy of neurodegenerative diseases in a large animal biomedical model. A prerequisite for the successful future therapeutic use of pNPC is a comprehensive characterisation and understanding of the neurogenic process. This is important for learning how to direct cell fates into required proportions of the cell type wanted for the specific brain disease to be treated, and it is crucial for avoiding uncontrolled cell proliferation leading to fatal tumour formations. Time-lapse analysis is a powerful tool to obtain live cell characterisation by analysing individual cell fate. Information on cellular development, division, and differentiation can be composed into a pedigree-like structure denoted as cellular genealogy giving an overview of the proliferation profile of a cell culture and the duration of each cell cycle (Al-Kofani et al. 2006). The aim of the study was to construct cellular genealogies of pNPC and differentiated neural lineages, respectively, by time-lapse imaging to evaluate the effect of external variables observed by changes in the topology of the cellular genealogy. Porcine NPC were derived from epiblast cells isolated from day-9 porcine blastocysts and cultured in DMEM/12, Pen/strep, B27 and N2 with basic fibroblast growth factor and epidermal growth factor, and differentiation was obtained by withdrawal of basic fibroblast growth factor and epidermal growth factor. The state of cellular development of undifferentiated and differentiated pNPC was verified immunohistochemically by the presence of SOX2, NESTIN, TUJI, and GFAB (Rasmussen et al. 2010). The time-lapse images were captured by a Nikon Biostation with a 10× resolution under phase contrast in a humidified chamber at 38°C with 5% CO2, 5% O2, and 90% N2. For each sequence, images were captured at intervals of 10 min in 16 frames. Sequences 1, 2, and 3 constituted passage 15 pNPC, passage 4 pNPC, and presumably differentiated cells, respectively. For each sequence, cell cycle length was calculated after manual tracking of selected cells. The cell cycle length of pNPC is shown in Table 1. Based on these data, cellular genealogies characteristic of each individual cell type have been constructed. Table 1.Cell cycle length of porcine neutral progenitor cells (pNPC) before and after differentiation

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39

Rasmuson, Marianne. "Genealogy and gene trees." Hereditas 145, no. 1 (April 25, 2008): 20–27. http://dx.doi.org/10.1111/j.0018-0661.2008.2041.x.

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40

Tëtushkin, E. Ya. "Genetic genealogy: History and methodology." Russian Journal of Genetics 47, no. 5 (May 2011): 507–20. http://dx.doi.org/10.1134/s1022795411040132.

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41

Palacios, Julia A., John Wakeley, and Sohini Ramachandran. "Bayesian Nonparametric Inference of Population Size Changes from Sequential Genealogies." Genetics 201, no. 1 (July 28, 2015): 281–304. http://dx.doi.org/10.1534/genetics.115.177980.

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42

Vekemans, X., and M. Slatkin. "Gene and allelic genealogies at a gametophytic self-incompatibility locus." Genetics 137, no. 4 (August 1, 1994): 1157–65. http://dx.doi.org/10.1093/genetics/137.4.1157.

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Abstract The properties of gene and allelic genealogies at a gametophytic self-incompatibility locus in plants have been investigated analytically and checked against extensive numerical simulations. It is found that, as with overdominant loci, there are two genealogical processes with markedly different time scales. First, functionally distinct allelic lines diverge on an extremely long time scale which is inversely related to the mutation rate to new alleles. These alleles show a genealogical structure which is similar, after an appropriate rescaling of time, to that described by the coalescent process for genes at a neutral locus. Second, gene copies sampled within the same functional allelic line show genealogical relationships similar to neutral gene genealogies but on a much shorter time scale, which is on the same order of magnitude as the harmonic mean of the number of gene copies within an allelic line. These results are discussed in relation to data showing trans-specific polymorphisms for alleles at the gametophytic self-incompatibility locus in the Solanaceae. It is shown that population sizes on the order of 4 x 10(5) and a mutation rate per locus per generation as high as 10(-6) could account for estimated allelic divergence times in this family.

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43

Hey, J. "The structure of genealogies and the distribution of fixed differences between DNA sequence samples from natural populations." Genetics 128, no. 4 (August 1, 1991): 831–40. http://dx.doi.org/10.1093/genetics/128.4.831.

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Abstract When two samples of DNA sequences are compared, one way in which they may differ is in the presence of fixed differences, which are defined as sites at which all of the sequences in one sample are different from all of the sequences in a second sample. The probability distribution of the number of fixed differences is developed. The theory employs Wright-Fisher genealogies and the infinite sites mutation model. For the case when both samples are drawn randomly from the same population it is found that genealogies permitting fixed differences are very unlikely. Thus the mere presence of fixed differences between samples is statistically significant, even for small samples. The theory is extended to samples from populations that have been separated for some time. The relationship between a simple Poisson distribution of mutations and the distribution of fixed differences is described as a function of the time since populations have been isolated. It is shown how these results may contribute to improved tests of recent balancing or directional selection.

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44

Donnelly, Peter, and Simon Tavaré. "The ages of alleles and a coalescent." Advances in Applied Probability 18, no. 01 (March 1986): 1–19. http://dx.doi.org/10.1017/s0001867800015573.

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A new coalescent is introduced to study the genealogy of a sample from the infinite-alleles model of population genetics. This coalescent also records the age ordering of alleles in the sample. The distribution of this process is found explicitly for the Moran model, and is shown to be robust for a wide class of reproductive schemes.Properties of the ages themselves and the relationship between ages and class sizes then follow readily.

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45

Donnelly, Peter, and Simon Tavaré. "The ages of alleles and a coalescent." Advances in Applied Probability 18, no. 1 (March 1986): 1–19. http://dx.doi.org/10.2307/1427237.

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A new coalescent is introduced to study the genealogy of a sample from the infinite-alleles model of population genetics. This coalescent also records the age ordering of alleles in the sample. The distribution of this process is found explicitly for the Moran model, and is shown to be robust for a wide class of reproductive schemes.Properties of the ages themselves and the relationship between ages and class sizes then follow readily.

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46

Raquin, Anne-Laure, Frantz Depaulis, Amaury Lambert, Nathalie Galic, Philippe Brabant, and Isabelle Goldringer. "Experimental Estimation of Mutation Rates in a Wheat Population With a Gene Genealogy Approach." Genetics 179, no. 4 (August 2008): 2195–211. http://dx.doi.org/10.1534/genetics.107.071332.

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47

Takahata, N. "Genealogy of neutral genes and spreading of selected mutations in a geographically structured population." Genetics 129, no. 2 (October 1, 1991): 585–95. http://dx.doi.org/10.1093/genetics/129.2.585.

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Abstract In a geographically structured population, the interplay among gene migration, genetic drift and natural selection raises intriguing evolutionary problems, but the rigorous mathematical treatment is often very difficult. Therefore several approximate formulas were developed concerning the coalescence process of neutral genes and the fixation process of selected mutations in an island model, and their accuracy was examined by computer simulation. When migration is limited, the coalescence (or divergence) time for sampled neutral genes can be described by the convolution of exponential functions, as in a panmictic population, but it is determined mainly by migration rate and the number of demes from which the sample is taken. This time can be much longer than that in a panmictic population with the same number of breeding individuals. For a selected mutation, the spreading over the entire population was formulated as a birth and death process, in which the fixation probability within a deme plays a key role. With limited amounts of migration, even advantageous mutations take a large number of generations to spread. Furthermore, it is likely that these mutations which are temporarily fixed in some demes may be swamped out again by non-mutant immigrants from other demes unless selection is strong enough. These results are potentially useful for testing quantitatively various hypotheses that have been proposed for the origin of modern human populations.

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48

Wolinsky, Howard. "Genetic genealogy goes global." EMBO reports 7, no. 11 (October 20, 2006): 1072–74. http://dx.doi.org/10.1038/sj.embor.7400843.

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Wu, Yufeng. "Inference of population admixture network from local gene genealogies: a coalescent-based maximum likelihood approach." Bioinformatics 36, Supplement_1 (July 1, 2020): i326—i334. http://dx.doi.org/10.1093/bioinformatics/btaa465.

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Abstract Motivation Population admixture is an important subject in population genetics. Inferring population demographic history with admixture under the so-called admixture network model from population genetic data is an established problem in genetics. Existing admixture network inference approaches work with single genetic polymorphisms. While these methods are usually very fast, they do not fully utilize the information [e.g. linkage disequilibrium (LD)] contained in population genetic data. Results In this article, we develop a new admixture network inference method called GTmix. Different from existing methods, GTmix works with local gene genealogies that can be inferred from population haplotypes. Local gene genealogies represent the evolutionary history of sampled haplotypes and contain the LD information. GTmix performs coalescent-based maximum likelihood inference of admixture networks with inferred local genealogies based on the well-known multispecies coalescent (MSC) model. GTmix utilizes various techniques to speed up the likelihood computation on the MSC model and the optimal network search. Our simulations show that GTmix can infer more accurate admixture networks with much smaller data than existing methods, even when these existing methods are given much larger data. GTmix is reasonably efficient and can analyze population genetic datasets of current interests. Availability and implementation The program GTmix is available for download at: https://github.com/yufengwudcs/GTmix. Supplementary information Supplementary data are available at Bioinformatics online.

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Tyler, Katharine. "Teaching and Learning Guide for: Ethnographic approaches to race, genetics and genealogy." Sociology Compass 3, no. 5 (July 20, 2009): 847–52. http://dx.doi.org/10.1111/j.1751-9020.2009.00231.x.

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Journal articles on the topic 'Genetisk genealogi'

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