Mendelian populations

Summary. Expressions (2·1), (3·1), (4·1), (5·1) are found for the composition of Mendelian populations subjected to partial self‐fertilisation, inbreeding, assortative mating, or selective fertilisation, and equations (2·2), (3·2), (4·2), (5·2) derived for the effect of selection on such populations. The effect of selection is greatly increased by inbreeding and self‐fertilisation.

@article{doi101111j1469185x1924tb00546x,
    author = "Haldane, J. B. S.",
    title = "A MATHEMATICAL THEORY OF NATURAL AND ARTIFICIAL SELECTION. PART II THE INFLUENCE OF PARTIAL SELF‐FERTILISATION, INBREEDING, ASSORTATIVE MATING, AND SELECTIVE FERTILISATION ON THE COMPOSITION OF MENDELIAN POPULATIONS, AND ON NATURAL SELECTION.",
    year = "1924",
    journal = "Biological reviews/Biological reviews of the Cambridge Philosophical Society",
    abstract = "Summary. Expressions (2·1), (3·1), (4·1), (5·1) are found for the composition of Mendelian populations subjected to partial self‐fertilisation, inbreeding, assortative mating, or selective fertilisation, and equations (2·2), (3·2), (4·2), (5·2) derived for the effect of selection on such populations. The effect of selection is greatly increased by inbreeding and self‐fertilisation.",
    url = "https://doi.org/10.1111/j.1469-185x.1924.tb00546.x",
    doi = "10.1111/j.1469-185x.1924.tb00546.x",
    openalex = "W2020102511"
}

@article{doi101007bf02459575,
    author = "Wright, S.",
    title = "Evolution in mendelian populations",
    year = "1931",
    journal = "Bulletin of Mathematical Biology",
    url = "https://www.semanticscholar.org/paper/3503eae0498c30435e10d71f96e8eda2f0df0f14",
    doi = "10.1007/BF02459575",
    is_oa = "true",
    number = "1-2",
    pages = "241-295",
    semanticscholar_citation_count = "3522",
    semanticscholar_id = "3503eae0498c30435e10d71f96e8eda2f0df0f14",
    volume = "52"
}

@article{doi101016s0092824005800114,
    author = "Wright, S.",
    title = "Evolution in Mendelian Populations.",
    year = "1931",
    journal = "Genetics",
    url = "https://www.semanticscholar.org/paper/bd91490f4639cd4066a6dc1c23c03d915b02ce4e",
    doi = "10.1016/S0092-8240(05)80011-4",
    is_oa = "true",
    number = "1-2",
    pages = "241-295",
    semanticscholar_citation_count = "6139",
    semanticscholar_id = "bd91490f4639cd4066a6dc1c23c03d915b02ce4e",
    volume = "52"
}

Page 108, last line of text, for P/P″ read P′/P″. Page 120, last line, for δ v read δ y. Page 123, line 10, for 4Nn read 4Nu. Page 125, line 1, for q read q. Page 126, line 12, for q read q. Page 135, line 5 from bottom, for y4Nsq read e4Nsq. Page 141, lines 8

@article{doi101093genetics16297,
    author = "Wright, Sewall",
    title = "EVOLUTION IN MENDELIAN POPULATIONS",
    year = "1931",
    journal = "Genetics",
    abstract = "Page 108, last line of text, for P/P″ read P′/P″. Page 120, last line, for δ v read δ y. Page 123, line 10, for 4Nn read 4Nu. Page 125, line 1, for q read q. Page 126, line 12, for q read q. Page 135, line 5 from bottom, for y4Nsq read e4Nsq. Page 141, lines 8",
    url = "https://doi.org/10.1093/genetics/16.2.97",
    doi = "10.1093/genetics/16.2.97",
    openalex = "W2171463101",
    references = "doi101017s0080456800012163, doi101017s0305004100015644, doi101086279846, doi101086279872, doi101086280193, doi101086280260, doi101111j160152231928tb02483x, doi101126science2870649, doi1023072965538, doi105962bhltitle27468"
}

for "I1 6" read "IV 6." Page 423, line 12, for "IV 13, IV 15" read "IV 14, IV 16." Page 427, line 6, for "I1 (6)" read "I1 (4)."

@article{doi101093genetics163290,
    author = "Wright, Sewall",
    title = "EVOLUTION IN MENDELIAN POPULATIONS",
    year = "1931",
    journal = "Genetics",
    abstract = {for "I1 6" read "IV 6." Page 423, line 12, for "IV 13, IV 15" read "IV 14, IV 16." Page 427, line 6, for "I1 (6)" read "I1 (4)."},
    url = "https://doi.org/10.1093/genetics/16.3.290",
    doi = "10.1093/genetics/16.3.290",
    openalex = "W4251848466"
}

@misc{wright1931evolution1,
    author = "Wright, S",
    title = "Evolution in Mendelian populations",
    year = "1931",
    howpublished = "Genetics, v. 16, p. 97- 159",
    note = "talkorigins\_source = {true}; raw\_reference = {Wright, S., 1931, Evolution in Mendelian populations: Genetics, v. 16, p. 97- 159.}"
}

@article{dobzhansky1950mendelian,
    author = "Dobzhansky, Theodosius",
    title = "Mendelian Populations and Their Evolution",
    year = "1950",
    journal = "The American Naturalist",
    url = "https://doi.org/10.1086/281638",
    doi = "10.1086/281638",
    number = "819",
    openalex = "W2012665350",
    pages = "401-418",
    volume = "84"
}

@article{doi101086281638,
    author = "Dobzhansky, Theodosius",
    title = "Mendelian Populations and Their Evolution",
    year = "1950",
    journal = "The American Naturalist",
    url = "https://doi.org/10.1086/281638",
    doi = "10.1086/281638",
    openalex = "W2012665350"
}

A method is presented by which the gene diversity (heterozygosity) of a subdivided population can be analyzed into its components, i.e., the gene diversities within and between subpopulations. This method is applicable to any population without regard to the number of alleles per locus, the pattern of evolutionary forces such as mutation, selection, and migration, and the reproductive method of the organism used. Measures of the absolute and relative magnitudes of gene differentiation among subpopulations are also proposed.

@article{doi101073pnas70123321,
    author = "Nei, Masatoshi",
    title = "Analysis of Gene Diversity in Subdivided Populations",
    year = "1973",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "A method is presented by which the gene diversity (heterozygosity) of a subdivided population can be analyzed into its components, i.e., the gene diversities within and between subpopulations. This method is applicable to any population without regard to the number of alleles per locus, the pattern of evolutionary forces such as mutation, selection, and migration, and the reproductive method of the organism used. Measures of the absolute and relative magnitudes of gene differentiation among subpopulations are also proposed.",
    url = "https://doi.org/10.1073/pnas.70.12.3321",
    doi = "10.1073/pnas.70.12.3321",
    openalex = "W1988182864"
}

Transposable elements are DNA sequences, found throughout eukaryotes, that transpose replicatively and cause numerous genetic and developmental effects on their hosts. A model of the evolution of transposable elements in Mendelian populations is proposed. From its analysis, formulas for the mean copy number and frequency spectrum are obtained.

@article{doi101093genetics1043457,
    author = "Langley, C. and Brookfield, J. and Kaplan, N.",
    title = "Transposable elements in mendelian populations. I. A theory.",
    year = "1983",
    journal = "Genetics",
    abstract = "Transposable elements are DNA sequences, found throughout eukaryotes, that transpose replicatively and cause numerous genetic and developmental effects on their hosts. A model of the evolution of transposable elements in Mendelian populations is proposed. From its analysis, formulas for the mean copy number and frequency spectrum are obtained.",
    url = "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1202088",
    doi = "10.1093/genetics/104.3.457",
    is_oa = "true",
    number = "3",
    pages = "457-471",
    semanticscholar_citation_count = "123",
    semanticscholar_id = "4217c8cc4b1e0a99451d53a184f7ecbb40599e13",
    volume = "104"
}

Methods are proposed for estimating the parameters in the frequency spectrum derived from the model of Langley, Brookfield and Kaplan for the evolution of a transposable element in a finite Mendelian population. Statistical properties of these estimates are studied, and the results are supported with simulation data. The effects on the estimates caused by possible insensitivities of the experimental technique are also discussed. To illustrate the proposed methodology, the data of Montgomery and Langley are analyzed.

@article{doi101093genetics1043485,
    author = "Kaplan, N. and Brookfield, J.",
    title = "Transposable Elements in Mendelian Populations. III. Statistical Results.",
    year = "1983",
    journal = "Genetics",
    abstract = "Methods are proposed for estimating the parameters in the frequency spectrum derived from the model of Langley, Brookfield and Kaplan for the evolution of a transposable element in a finite Mendelian population. Statistical properties of these estimates are studied, and the results are supported with simulation data. The effects on the estimates caused by possible insensitivities of the experimental technique are also discussed. To illustrate the proposed methodology, the data of Montgomery and Langley are analyzed.",
    url = "https://doi.org/10.1093/genetics/104.3.485",
    doi = "10.1093/genetics/104.3.485",
    is_oa = "true",
    number = "3",
    pages = "485-495",
    semanticscholar_citation_count = "44",
    semanticscholar_id = "03183764c7f99b266004292b2debfa9e3278afd5",
    volume = "104"
}

A model of the evolution of a transposable element family in a Mendelian host population is proposed that incorporates heritable phenotypic mutations in the elements. The temporal behavior of the numbers of mutant and wild-type elements is studied, and the expected extinction time of the transposable element family is examined. Our results indicate that, if the mutant can be transposed equally well in the presence of the wild type, then it can be expected to be found in preponderance, whereas elements, such as retroviruses, where the transposing genome and its phenotypic expression are coupled, may be characterized by a low mutant frequency.

@article{doi101093genetics1092459,
    author = "Kaplan, Norman and Darden, Tom and Langley, Charles H.",
    title = "EVOLUTION AND EXTINCTION OF TRANSPOSABLE ELEMENTS IN MENDELIAN POPULATIONS",
    year = "1985",
    journal = "Genetics",
    abstract = "A model of the evolution of a transposable element family in a Mendelian host population is proposed that incorporates heritable phenotypic mutations in the elements. The temporal behavior of the numbers of mutant and wild-type elements is studied, and the expected extinction time of the transposable element family is examined. Our results indicate that, if the mutant can be transposed equally well in the presence of the wild type, then it can be expected to be found in preponderance, whereas elements, such as retroviruses, where the transposing genome and its phenotypic expression are coupled, may be characterized by a low mutant frequency.",
    url = "https://doi.org/10.1093/genetics/109.2.459",
    doi = "10.1093/genetics/109.2.459",
    openalex = "W1959616200",
    references = "doi1010160022283682904703, doi1010160092867482904627, doi1010160092867482904639, doi1010160092867483901332, doi101038295025a0, doi101038302119a0, doi101093genetics1043473, doi101093nar8246113, doi101146annurevge15120181001251, doi101146annurevge17120183001531"
}

A model of the evolution of a transposable element family in a Mendelian host population is proposed that incorporates heritable phenotypic mutations in the elements. The temporal behavior of the numbers of mutant and wild-type elements is studied, and the expected extinction time of the transposable element family is examined. Our results indicate that, if the mutant can be transposed equally well in the presence of the wild type, then it can be expected to be found in preponderance, whereas elements, such as retroviruses, where the transposing genome and its phenotypic expression are coupled, may be characterized by a low mutant frequency.

@article{s261fc62d3d7d6b3f15635b277ce3b707355a1a32e,
    author = "Kaplan, N. and Darden, T. and Langley, C.",
    title = "Evolution and extinction of transposable elements in Mendelian populations.",
    year = "1985",
    journal = "Genetics",
    abstract = "A model of the evolution of a transposable element family in a Mendelian host population is proposed that incorporates heritable phenotypic mutations in the elements. The temporal behavior of the numbers of mutant and wild-type elements is studied, and the expected extinction time of the transposable element family is examined. Our results indicate that, if the mutant can be transposed equally well in the presence of the wild type, then it can be expected to be found in preponderance, whereas elements, such as retroviruses, where the transposing genome and its phenotypic expression are coupled, may be characterized by a low mutant frequency.",
    url = "https://www.semanticscholar.org/paper/61fc62d3d7d6b3f15635b277ce3b707355a1a32e",
    doi = "10.1093/genetics/109.2.459",
    is_oa = "true",
    number = "2",
    pages = "459-480",
    semanticscholar_citation_count = "126",
    semanticscholar_id = "61fc62d3d7d6b3f15635b277ce3b707355a1a32e",
    volume = "109"
}

@article{doi101111j155856461987tb05876x,
    author = "Wilson, D. S.",
    title = "ALTRUISM IN MENDELIAN POPULATIONS DERIVED FROM SIBLING GROUPS: THE HAYSTACK MODEL REVISITED",
    year = "1987",
    journal = "Evolution",
    url = "https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/j.1558-5646.1987.tb05876.x",
    doi = "10.1111/j.1558-5646.1987.tb05876.x",
    is_oa = "true",
    number = "5",
    pages = "1059-1070",
    semanticscholar_citation_count = "136",
    semanticscholar_id = "0e1b47b104865ed5d5845acf022f5e72f531b724",
    volume = "41"
}

There is abundant geographic variation in both morphology and gene frequency in most species. The extent of geographic variation results from a balance of forces tending to produce local genetic differentiation and forces tending to produce genetic homogeneity. Mutation, genetic drift due to finite population size, and natural selection favoring adaptations to local environmental conditions will all lead to the genetic differentiation of local populations, and the movement of gametes, individuals, and even entire populations--collectively called gene flow--will oppose that differentiation. Gene flow may either constrain evolution by preventing adaptation to local conditions or promote evolution by spreading new genes and combinations of genes throughout a species' range. Several methods are available for estimating the amount of gene flow. Direct methods monitor ongoing gene flow, and indirect methods use spatial distributions of gene frequencies to infer past gene flow. Applications of these methods show that species differ widely in the gene flow that they experience. Of particular interest are those species for which direct methods indicate little current gene flow but indirect methods indicate much higher levels of gene flow in the recent past. Such species probably have undergone large-scale demographic changes relatively frequently.

@article{doi101126science3576198,
    author = "Slatkin, Montgomery",
    title = "Gene Flow and the Geographic Structure of Natural Populations",
    year = "1987",
    journal = "Science",
    abstract = "There is abundant geographic variation in both morphology and gene frequency in most species. The extent of geographic variation results from a balance of forces tending to produce local genetic differentiation and forces tending to produce genetic homogeneity. Mutation, genetic drift due to finite population size, and natural selection favoring adaptations to local environmental conditions will all lead to the genetic differentiation of local populations, and the movement of gametes, individuals, and even entire populations--collectively called gene flow--will oppose that differentiation. Gene flow may either constrain evolution by preventing adaptation to local conditions or promote evolution by spreading new genes and combinations of genes throughout a species' range. Several methods are available for estimating the amount of gene flow. Direct methods monitor ongoing gene flow, and indirect methods use spatial distributions of gene frequencies to infer past gene flow. Applications of these methods show that species differ widely in the gene flow that they experience. Of particular interest are those species for which direct methods indicate little current gene flow but indirect methods indicate much higher levels of gene flow in the recent past. Such species probably have undergone large-scale demographic changes relatively frequently.",
    url = "https://doi.org/10.1126/science.3576198",
    doi = "10.1126/science.3576198",
    openalex = "W2066362596",
    references = "doi1010079783642686351, doi1010160040580977900454, doi1010382011145a0, doi101086410450, doi101093genetics16297, doi101098rspb19830075, doi101111j146918091949tb02451x, doi101111j155856461981tb04864x, doi101111j155856461984tb05657x, doi101111j155856461985tb04079x, doi101146annureves16110185002141, doi101722611310, doi104159harvard9780674865327, doi105962bhltitle27468, openalexw1593551567, openalexw1606400913"
}

@article{s24c673a97833c84983ffb64be47bd646861e8c848,
    author = "Wright, S.",
    title = "Evolution in Mendelian populations. 1931.",
    year = "1990",
    journal = "Bulletin of mathematical biology",
    url = "https://www.semanticscholar.org/paper/4c673a97833c84983ffb64be47bd646861e8c848",
    doi = "10.1007/BF02459575",
    is_oa = "true",
    pmid = "2185860",
    semanticscholar_citation_count = "37",
    semanticscholar_id = "4c673a97833c84983ffb64be47bd646861e8c848"
}

The proposal that all mitochondrial DNA (mtDNA) types in contemporary humans stem from a common ancestor present in an African population some 200,000 years ago has attracted much attention. To study this proposal further, two hypervariable segments of mtDNA were sequenced from 189 people of diverse geographic origin, including 121 native Africans. Geographic specificity was observed in that identical mtDNA types are shared within but not between populations. A tree relating these mtDNA sequences to one another and to a chimpanzee sequence has many deep branches leading exclusively to African mtDNAs. An African origin for human mtDNA is supported by two statistical tests. With the use of the chimpanzee and human sequences to calibrate the rate of mtDNA evolution, the age of the common human mtDNA ancestor is placed between 166,000 and 249,000 years. These results thus support and extend the African origin hypothesis of human mtDNA evolution.

@article{doi101126science1840702,
    author = "Vigilant, Linda and Stoneking, Mark and Harpending, Henry and Hawkes, Kristen and Wilson, Allan C.",
    title = "African Populations and the Evolution of Human Mitochondrial DNA",
    year = "1991",
    journal = "Science",
    abstract = "The proposal that all mitochondrial DNA (mtDNA) types in contemporary humans stem from a common ancestor present in an African population some 200,000 years ago has attracted much attention. To study this proposal further, two hypervariable segments of mtDNA were sequenced from 189 people of diverse geographic origin, including 121 native Africans. Geographic specificity was observed in that identical mtDNA types are shared within but not between populations. A tree relating these mtDNA sequences to one another and to a chimpanzee sequence has many deep branches leading exclusively to African mtDNAs. An African origin for human mtDNA is supported by two statistical tests. With the use of the chimpanzee and human sequences to calibrate the rate of mtDNA evolution, the age of the common human mtDNA ancestor is placed between 166,000 and 249,000 years. These results thus support and extend the African origin hypothesis of human mtDNA evolution.",
    url = "https://doi.org/10.1126/science.1840702",
    doi = "10.1126/science.1840702",
    openalex = "W2072889251",
    references = "doi101007bf01734101, doi101038325031a0, doi101038scientificamerican117998, doi101073pnas7641967, doi101073pnas77116715, doi101073pnas85166002, doi101126science147365368, doi101126science3125610, doi101146annurevge22120188002513, doi102307530156"
}

▪ Abstract Inbreeding depression critically influences both mating system evolution and the persistence of small populations prone to accumulate mutations. Under some circumstances, however, inbreeding will tend to purge populations of enough deleterious recessive mutations to reduce inbreeding depression (ID). The extent of purging depends on many population and genetic factors, making it impossible to make universal predictions. We review 52 studies that compare levels of ID among species, populations, and lineages inferred to differ in inbreeding history. Fourteen of 34 studies comparing ID among populations and species found significant evidence for purging. Within populations, many studies report among-family variation in ID, and 6 of 18 studies found evidence for purging among lineages. Regression analyses suggest that purging is most likely to ameliorate ID for early traits (6 studies), but these declines are typically modest (5–10%). Meta-analyses of results from 45 populations in 11 studies reveal no significant overall evidence for purging, but rather the opposite tendency, for more selfing populations to experience higher ID for early traits. The likelihood of finding purging does not vary systematically with experimental design or whether early or late traits are considered. Perennials are somewhat less likely to show purging than annuals (2 of 10 vs. 7 of 14). We conclude that although these results doubtless reflect variation in population and genetic parameters, they also suggest that purging is an inconsistent force within populations. Such results also imply that attempts to deliberately reduce the load via inbreeding in captive rearing programs may be misguided. Future studies should examine male and female fitness traits over the entire life cycle, estimate mating histories at all levels (i.e. population and families within populations), report data necessary for meta-analysis, and statistically test for purging of genetic loads.

@article{doi101146annurevecolsys301479,
    author = "Byers, Diane L. and Waller, Donald M.",
    title = "Do Plant Populations Purge Their Genetic Load? Effects of Population Size and Mating History on Inbreeding Depression",
    year = "1999",
    journal = "Annual Review of Ecology and Systematics",
    abstract = "▪ Abstract Inbreeding depression critically influences both mating system evolution and the persistence of small populations prone to accumulate mutations. Under some circumstances, however, inbreeding will tend to purge populations of enough deleterious recessive mutations to reduce inbreeding depression (ID). The extent of purging depends on many population and genetic factors, making it impossible to make universal predictions. We review 52 studies that compare levels of ID among species, populations, and lineages inferred to differ in inbreeding history. Fourteen of 34 studies comparing ID among populations and species found significant evidence for purging. Within populations, many studies report among-family variation in ID, and 6 of 18 studies found evidence for purging among lineages. Regression analyses suggest that purging is most likely to ameliorate ID for early traits (6 studies), but these declines are typically modest (5–10\%). Meta-analyses of results from 45 populations in 11 studies reveal no significant overall evidence for purging, but rather the opposite tendency, for more selfing populations to experience higher ID for early traits. The likelihood of finding purging does not vary systematically with experimental design or whether early or late traits are considered. Perennials are somewhat less likely to show purging than annuals (2 of 10 vs. 7 of 14). We conclude that although these results doubtless reflect variation in population and genetic parameters, they also suggest that purging is an inconsistent force within populations. Such results also imply that attempts to deliberately reduce the load via inbreeding in captive rearing programs may be misguided. Future studies should examine male and female fitness traits over the entire life cycle, estimate mating histories at all levels (i.e. population and families within populations), report data necessary for meta-analysis, and statistically test for purging of genetic loads.",
    url = "https://doi.org/10.1146/annurev.ecolsys.30.1.479",
    doi = "10.1146/annurev.ecolsys.30.1.479",
    openalex = "W2139787612",
    references = "doi101093genetics25466, doi101093oxfordjournalsjhereda023085"
}

Genetic parameters widely used to monitor genetic variation in conservation programmes, such as effective number of founders, founder genome equivalents and effective population size, are interrelated in terms of coancestries and variances of contributions from ancestors to descendants. A new parameter, the effective number of non-founders, is introduced to describe the relation between effective number of founders and founder genome equivalents. Practical recommendations for the maintenance of genetic variation in small captive populations are discussed. To maintain genetic diversity, minimum coancestry among individuals should be sought. This minimizes the variances of contributions from ancestors to descendants in all previous generations. The method of choice of parents and the system of mating should be independent of each other because a clear-cut recommendation cannot be given on the latter.

@article{doi101017s0016672399004449,
    author = "Caballero, Armando and Toro, M. Á.",
    title = "Interrelations between effective population size and other pedigree tools for the management of conserved populations",
    year = "2000",
    journal = "Genetics Research",
    abstract = "Genetic parameters widely used to monitor genetic variation in conservation programmes, such as effective number of founders, founder genome equivalents and effective population size, are interrelated in terms of coancestries and variances of contributions from ancestors to descendants. A new parameter, the effective number of non-founders, is introduced to describe the relation between effective number of founders and founder genome equivalents. Practical recommendations for the maintenance of genetic variation in small captive populations are discussed. To maintain genetic diversity, minimum coancestry among individuals should be sought. This minimizes the variances of contributions from ancestors to descendants in all previous generations. The method of choice of parents and the system of mating should be independent of each other because a clear-cut recommendation cannot be given on the latter.",
    url = "https://doi.org/10.1017/s0016672399004449",
    doi = "10.1017/s0016672399004449",
    openalex = "W2047578253",
    references = "doi101093genetics163290"
}

@misc{s272efbcfd0f91184c48056f26841a2286a4a85d8d,
    author = "Wright, S.",
    title = "EVOLUTION I N MENDELIAN POPULATIONS",
    year = "2001",
    url = "https://www.semanticscholar.org/paper/72efbcfd0f91184c48056f26841a2286a4a85d8d",
    is_oa = "true",
    semanticscholar_citation_count = "1",
    semanticscholar_id = "72efbcfd0f91184c48056f26841a2286a4a85d8d"
}

Gene identity by descent (IBD) is a fundamental concept that underlies genetically mediated similarities among relatives. Gene IBD is traced through ancestral meioses and is defined relative to founders of a pedigree, or to some time point or mutational origin in the coalescent of a set of extant genes in a population. The random process underlying changes in the patterns of IBD across the genome is recombination, so the natural context for defining IBD is the ancestral recombination graph (ARG), which specifies the complete ancestry of a collection of chromosomes. The ARG determines both the sequence of coalescent ancestries across the chromosome and the extant segments of DNA descending unbroken by recombination from their most recent common ancestor (MRCA). DNA segments IBD from a recent common ancestor have high probability of being of the same allelic type. Non-IBD DNA is modeled as of independent allelic type, but the population frame of reference for defining allelic independence can vary. Whether of IBD, allelic similarity, or phenotypic covariance, comparisons may be made to other genomic regions of the same gametes, or to the same genomic regions in other sets of gametes or diploid individuals. In this review, I present IBD as the framework connecting evolutionary and coalescent theory with the analysis of genetic data observed on individuals. I focus on the high variance of the processes that determine IBD, its changes across the genome, and its impact on observable data.

@article{doi101534genetics112148825,
    author = "Thompson, E. A.",
    title = "Identity by Descent: Variation in Meiosis, Across Genomes, and in Populations",
    year = "2013",
    journal = "Genetics",
    abstract = "Gene identity by descent (IBD) is a fundamental concept that underlies genetically mediated similarities among relatives. Gene IBD is traced through ancestral meioses and is defined relative to founders of a pedigree, or to some time point or mutational origin in the coalescent of a set of extant genes in a population. The random process underlying changes in the patterns of IBD across the genome is recombination, so the natural context for defining IBD is the ancestral recombination graph (ARG), which specifies the complete ancestry of a collection of chromosomes. The ARG determines both the sequence of coalescent ancestries across the chromosome and the extant segments of DNA descending unbroken by recombination from their most recent common ancestor (MRCA). DNA segments IBD from a recent common ancestor have high probability of being of the same allelic type. Non-IBD DNA is modeled as of independent allelic type, but the population frame of reference for defining allelic independence can vary. Whether of IBD, allelic similarity, or phenotypic covariance, comparisons may be made to other genomic regions of the same gametes, or to the same genomic regions in other sets of gametes or diploid individuals. In this review, I present IBD as the framework connecting evolutionary and coalescent theory with the analysis of genetic data observed on individuals. I focus on the high variance of the processes that determine IBD, its changes across the genome, and its impact on observable data.",
    url = "https://doi.org/10.1534/genetics.112.148825",
    doi = "10.1534/genetics.112.148825",
    openalex = "W2113697014",
    references = "doi101017s0370164600023993"
}

Identifying genomic regions targeted by positive selection has been a long-standing interest of evolutionary biologists. This objective was difficult to achieve until the recent emergence of next-generation sequencing, which is fostering the development of large-scale catalogues of genetic variation for increasing number of species. Several statistical methods have been recently developed to analyse these rich data sets, but there is still a poor understanding of the conditions under which these methods produce reliable results. This study aims at filling this gap by assessing the performance of genome-scan methods that consider explicitly the physical linkage among SNPs surrounding a selected variant. Our study compares the performance of seven recent methods for the detection of selective sweeps (iHS, nSL, EHHST, xp-EHH, XP-EHHST, XPCLR and hapFLK). We use an individual-based simulation approach to investigate the power and accuracy of these methods under a wide range of population models under both hard and soft sweeps. Our results indicate that XPCLR and hapFLK perform best and can detect soft sweeps under simple population structure scenarios if migration rate is low. All methods perform poorly with moderate-to-high migration rates, or with weak selection and very poorly under a hierarchical population structure. Finally, no single method is able to detect both starting and nearly completed selective sweeps. However, combining several methods (XPCLR or hapFLK with iHS or nSL) can greatly increase the power to pinpoint the selected region.

@article{doi101111mec13360,
    author = "Vatsiou, Alexandra and Bazin, Éric and Gaggiotti, Oscar E.",
    title = "Detection of selective sweeps in structured populations: a comparison of recent methods",
    year = "2015",
    journal = "Molecular Ecology",
    abstract = "Identifying genomic regions targeted by positive selection has been a long-standing interest of evolutionary biologists. This objective was difficult to achieve until the recent emergence of next-generation sequencing, which is fostering the development of large-scale catalogues of genetic variation for increasing number of species. Several statistical methods have been recently developed to analyse these rich data sets, but there is still a poor understanding of the conditions under which these methods produce reliable results. This study aims at filling this gap by assessing the performance of genome-scan methods that consider explicitly the physical linkage among SNPs surrounding a selected variant. Our study compares the performance of seven recent methods for the detection of selective sweeps (iHS, nSL, EHHST, xp-EHH, XP-EHHST, XPCLR and hapFLK). We use an individual-based simulation approach to investigate the power and accuracy of these methods under a wide range of population models under both hard and soft sweeps. Our results indicate that XPCLR and hapFLK perform best and can detect soft sweeps under simple population structure scenarios if migration rate is low. All methods perform poorly with moderate-to-high migration rates, or with weak selection and very poorly under a hierarchical population structure. Finally, no single method is able to detect both starting and nearly completed selective sweeps. However, combining several methods (XPCLR or hapFLK with iHS or nSL) can greatly increase the power to pinpoint the selected region.",
    url = "https://doi.org/10.1111/mec.13360",
    doi = "10.1111/mec.13360",
    openalex = "W2131888512",
    references = "doi101016s0092824005800114, doi101017s0016672300014634, doi101038nature01140, doi101038nature06250, doi101038nbt1486, doi101093bioinformaticsbti623, doi101093genetics15531405, doi101093molbevmsi237, doi101098rspb19960237, doi101371journalpbio0040072, doi101534genetics108092221"
}

@article{barton2016sewall,
    author = "Barton, Nicholas H",
    title = "Sewall Wright on Evolution in Mendelian Populations and the “Shifting Balance”",
    year = "2016",
    journal = "Genetics",
    url = "https://doi.org/10.1534/genetics.115.184796",
    doi = "10.1534/genetics.115.184796",
    number = "1",
    openalex = "W2225028202",
    pages = "3-4",
    volume = "202",
    references = "doi101093genetics16297, doi101093genetics196506, doi101093genetics244538, doi101093genetics282114, doi101093genetics282139, doi101093genetics284304, doi101093genetics31139, doi101093genetics62111, doi101111j155856461997tb03650x, doi1023071981923"
}

@incollection{crossref2019part,
    title = "PART THREE. EVOLUTION IN MENDELIAN POPULATIONS: TELEOLOGY GETS MATHEMATICAL",
    year = "2019",
    booktitle = "Not by Design",
    url = "https://doi.org/10.1525/9780520944404-004",
    doi = "10.1525/9780520944404-004",
    openalex = "W4256520976",
    pages = "151-254"
}

An interesting evolutionary question that still remains open is the connectivity between marine populations. Marine currents can favour the dispersal of larvae or adults, but they can also produce eddies and gyres generating oceanographic fronts, thus limiting gene flow. To address this subject, we selected the Atlantic-Mediterranean transition, where several fronts are located: Gibraltar Strait (GS), Almeria-Oran Front (AOF) and Ibiza Channel (IC). Seven populations of the marine crab Liocarcinus depurator (Cadiz, West and East Alboran, Alacant, Valencia, Ebro Delta and North Catalonia) located along this transition were analysed in six consecutive years (2014-2019) using a fragment of the COI (Cytochrome Oxidase subunit I) gene. All sequences (966) belonged to two well defined haplogroups: ATL (most abundant in Atlantic waters) and MED (predominant in Mediterranean waters). Following a geographic variation, the frequency of ATL decreased significantly from Cadiz to North Catalonia. However, this variation presented steps due to the effect of oceanographic restrictions/fronts. Significant effects were recorded for GS (2015, 2017, 2018 and 2019), AOF (all years except 2018) and IC (2016). The intensity and precise location of these fronts changed over time. Multivariate analyses distinguished three main population groups: Cadiz, Alboran Sea and the remaining Mediterranean populations. These findings could be relevant to properly define Marine Protected Areas and for conservation and fisheries policies.

@article{doi101038s41598022139414,
    author = "Ojeda, Víctor Pedro Cuadros and Serra, Bruna and Lagares, Clàudia and Rojo-Francàs, Eva and Sellés, Maria and Marco‐Herrero, Elena and García, Encarnación and Farré, Marc and Arenas, C. and Abelló, Pere and Mestres, Francesc",
    title = "Interannual fluctuations in connectivity among crab populations (Liocarcinus depurator) along the Atlantic-Mediterranean transition",
    year = "2022",
    journal = "Scientific Reports",
    abstract = "An interesting evolutionary question that still remains open is the connectivity between marine populations. Marine currents can favour the dispersal of larvae or adults, but they can also produce eddies and gyres generating oceanographic fronts, thus limiting gene flow. To address this subject, we selected the Atlantic-Mediterranean transition, where several fronts are located: Gibraltar Strait (GS), Almeria-Oran Front (AOF) and Ibiza Channel (IC). Seven populations of the marine crab Liocarcinus depurator (Cadiz, West and East Alboran, Alacant, Valencia, Ebro Delta and North Catalonia) located along this transition were analysed in six consecutive years (2014-2019) using a fragment of the COI (Cytochrome Oxidase subunit I) gene. All sequences (966) belonged to two well defined haplogroups: ATL (most abundant in Atlantic waters) and MED (predominant in Mediterranean waters). Following a geographic variation, the frequency of ATL decreased significantly from Cadiz to North Catalonia. However, this variation presented steps due to the effect of oceanographic restrictions/fronts. Significant effects were recorded for GS (2015, 2017, 2018 and 2019), AOF (all years except 2018) and IC (2016). The intensity and precise location of these fronts changed over time. Multivariate analyses distinguished three main population groups: Cadiz, Alboran Sea and the remaining Mediterranean populations. These findings could be relevant to properly define Marine Protected Areas and for conservation and fisheries policies.",
    url = "https://doi.org/10.1038/s41598-022-13941-4",
    doi = "10.1038/s41598-022-13941-4",
    openalex = "W4282581500",
    references = "doi103934dcdsb201419883"
}