Interspersion

@article{doi1023072256726,
    author = "Elton, Charles",
    title = "Population Interspersion: An Essay on Animal Community Patterns",
    year = "1949",
    journal = "Journal of Ecology",
    url = "https://doi.org/10.2307/2256726",
    doi = "10.2307/2256726",
    openalex = "W2333326867",
    references = "doi101093aesa384602, doi101111j109636421935tb01680x, doi1023071578, doi1023071943204, doi1023071943223, doi1023071943233, doi1023071948641, doi1023072256497, doi1023073795561, doi1025919dbrbzx18"
}

@article{elton1949population1,
    author = "Elton, C. S",
    title = "Population interspersion",
    year = "1949",
    journal = "an essay on animal community patterns: Journal of Ecology, v. 37, p. 1-23",
    note = "talkorigins\_source = {true}; raw\_reference = {Elton, C. S., 1949, Population interspersion: an essay on animal community patterns: Journal of Ecology, v. 37, p. 1-23.}"
}

@article{doi1023071943519,
    author = "Whittaker, R. H.",
    title = "A Consideration of Climax Theory: The Climax as a Population and Pattern",
    year = "1953",
    journal = "Ecological Monographs",
    url = "https://doi.org/10.2307/1943519",
    doi = "10.2307/1943519",
    openalex = "W2019806387",
    references = "beauchamp1932competitive, doi101093bjpsi2134, doi101098rspb19450003, doi101111j109636421935tb01680x, doi101111j174966321948tb39854x, doi101126science111287223, doi1023071930126, doi1023071930735, doi1023071931725, doi1023071943265, doi102307211491, doi1023072256278, doi1023072256726, doi1023072479933, doi105962bhltitle56234"
}

A long‐term study was made (1947‐59) of the numbers and breeding success of the Tawny owl (Strix aluco L.) in a woodland habitat near Oxford. Parallel studies were made of the numbers and distribution of the owl's two main prey species, the Wood mouse (Apodemus sylvaticus (L.)) and the Bank vole (Clethrionomys glareolus (Schr.)). The life‐cycles of all these three interrelated species were worked out and special attention was paid to the habit of strict territoriality of the owl (on the evidence of vocalizations and of the recovery, from the regurgitated pellets of the owl, of marking rings placed on the rodents) and to the sequence of losses which occurred during the breeding of the owl. The owls' vocal defence of their territories enabled an accurate census to be made of the adult population each spring and the fact that the fledged young remained for a long time in their parents' territories made it possible to count the number of young produced each year. Investigation of the breeding habits of the owls showed that the number of fledged young produced fell far short of what was possible: some pairs of owls refrained from breeding at all, others laid eggs but failed to hatch them, yet others hatched young but failed to rear them to fledging. By and large this degree of reproductive “failure” was associated with the numbers and availability of rodent prey. At an exceptionally low density of prey no owls even attempted to breed; as densities increased, correspondingly greater numbers of fledged young were produced up to a ceiling where no more young were produced however much higher the level of abundance of the rodents rose. In spite of these wide variations in the numbers of prey and in the numbers of fledged young produced, the population of adult owls remained notably stable, increasing from a low level of 17 pairs in 1947, owing to the emergency mortality of an exceptionally hard winter, to about 30 pairs in 1955, after which the population remained stationary until the end of the study in 1959. It is clear that this stability is maintained by those young which fail to find a territory either starving or moving outside the study area, which in most cases amounts to the same thing. Thus regulation of the population studied was due to territorial intolerance acting to produce subsequent mortality, though it is not certain that this applies over a larger area.

@article{doi101111j146979981970tb01264x,
    author = "Southern, H. N.",
    title = "The natural control of a population of Tawny owls (Strix aluco)",
    year = "1970",
    journal = "Journal of Zoology",
    abstract = "A long‐term study was made (1947‐59) of the numbers and breeding success of the Tawny owl (Strix aluco L.) in a woodland habitat near Oxford. Parallel studies were made of the numbers and distribution of the owl's two main prey species, the Wood mouse (Apodemus sylvaticus (L.)) and the Bank vole (Clethrionomys glareolus (Schr.)). The life‐cycles of all these three interrelated species were worked out and special attention was paid to the habit of strict territoriality of the owl (on the evidence of vocalizations and of the recovery, from the regurgitated pellets of the owl, of marking rings placed on the rodents) and to the sequence of losses which occurred during the breeding of the owl. The owls' vocal defence of their territories enabled an accurate census to be made of the adult population each spring and the fact that the fledged young remained for a long time in their parents' territories made it possible to count the number of young produced each year. Investigation of the breeding habits of the owls showed that the number of fledged young produced fell far short of what was possible: some pairs of owls refrained from breeding at all, others laid eggs but failed to hatch them, yet others hatched young but failed to rear them to fledging. By and large this degree of reproductive “failure” was associated with the numbers and availability of rodent prey. At an exceptionally low density of prey no owls even attempted to breed; as densities increased, correspondingly greater numbers of fledged young were produced up to a ceiling where no more young were produced however much higher the level of abundance of the rodents rose. In spite of these wide variations in the numbers of prey and in the numbers of fledged young produced, the population of adult owls remained notably stable, increasing from a low level of 17 pairs in 1947, owing to the emergency mortality of an exceptionally hard winter, to about 30 pairs in 1955, after which the population remained stationary until the end of the study in 1959. It is clear that this stability is maintained by those young which fail to find a territory either starving or moving outside the study area, which in most cases amounts to the same thing. Thus regulation of the population studied was due to territorial intolerance acting to produce subsequent mortality, though it is not certain that this applies over a larger area.",
    url = "https://doi.org/10.1111/j.1469-7998.1970.tb01264.x",
    doi = "10.1111/j.1469-7998.1970.tb01264.x",
    openalex = "W2073456066",
    references = "doi1023072256726"
}

Los primates usan diferencialmente el espacio y sus tiempos para adaptarse a cambios de origen natural o antropogénicos. La especie Plecturocebus caquetensis, en estado crítico de extinción, habita en bosques fragmentados de la región Andino Amazónica al suroccidente de Colombia. La zona suroccidental de su distribución (Bota Caucana), resguarda una de las áreas prioritarias para la conectividad del hábitat, donde se hace necesario conocer la estructura de la vegetación y tendencias de uso de hábitat para informar decisiones de manejo y conservación in situ. Se analizó el uso de hábitat de un grupo de Plecturocebus caquetensis y su relación con atributos como la disponibilidad de recursos y estructura de la vegetación, en Piamonte, Cauca. El grupo de P. caquetensis sobrevive en hábitats intervenidos de tipo temporalmente inundable y no inundable. El periodo de mayor oferta de recursos durante la temporada seca en agosto y septiembre y el periodo de menor oferta de recursos es en octubre y noviembre. El grupo estuvo el 97% del tiempo en el hábitat inundable y 3% en hábitats no inundables; 49% del total de tiempo de seguimiento (134 hrs) se destinó a descanso, 24% a desplazamiento, 13% a alimentación y 15% en otras actividades. La actividad social y el desplazamiento-alimentación se vieron asociadas positivamente con la altura promedio del estrato dominante de bosque. Una alta dedicación al descanso junto a un mayor consumo de ítems vegetativos en una época de escasos recursos, sugiere una adopción de una estrategia minimizadora de energía de P. caquetensis, compartida por otros titíes y primates del viejo mundo en hábitats fragmentados. (Texto tomado de la fuente).

@article{doi101146annureves07110176000501,
    author = "Wiens, John A.",
    title = "Population Responses to Patchy Environments",
    year = "1976",
    journal = "Annual Review of Ecology and Systematics",
    abstract = "Los primates usan diferencialmente el espacio y sus tiempos para adaptarse a cambios de origen natural o antropogénicos. La especie Plecturocebus caquetensis, en estado crítico de extinción, habita en bosques fragmentados de la región Andino Amazónica al suroccidente de Colombia. La zona suroccidental de su distribución (Bota Caucana), resguarda una de las áreas prioritarias para la conectividad del hábitat, donde se hace necesario conocer la estructura de la vegetación y tendencias de uso de hábitat para informar decisiones de manejo y conservación in situ. Se analizó el uso de hábitat de un grupo de Plecturocebus caquetensis y su relación con atributos como la disponibilidad de recursos y estructura de la vegetación, en Piamonte, Cauca. El grupo de P. caquetensis sobrevive en hábitats intervenidos de tipo temporalmente inundable y no inundable. El periodo de mayor oferta de recursos durante la temporada seca en agosto y septiembre y el periodo de menor oferta de recursos es en octubre y noviembre. El grupo estuvo el 97\% del tiempo en el hábitat inundable y 3\% en hábitats no inundables; 49\% del total de tiempo de seguimiento (134 hrs) se destinó a descanso, 24\% a desplazamiento, 13\% a alimentación y 15\% en otras actividades. La actividad social y el desplazamiento-alimentación se vieron asociadas positivamente con la altura promedio del estrato dominante de bosque. Una alta dedicación al descanso junto a un mayor consumo de ítems vegetativos en una época de escasos recursos, sugiere una adopción de una estrategia minimizadora de energía de P. caquetensis, compartida por otros titíes y primates del viejo mundo en hábitats fragmentados. (Texto tomado de la fuente).",
    url = "https://doi.org/10.1146/annurev.es.07.110176.000501",
    doi = "10.1146/annurev.es.07.110176.000501",
    openalex = "W2106837814",
    references = "doi10100797814615694425, doi101086282063, doi101086282531, doi101086282907, doi101126science185414527, doi101146annureves01110170000245, doi101163156853974x00345, doi1023071936888, doi1023072256726, doi1023072406825, openalexw1484524608"
}

@article{doi101016s002228368280003x,
    author = "Krolewski, John J. and Bertelsen, Arthur H. and Humayun, M. Zafri and Rush, Mark G.",
    title = "Members of the Alu family of interspersed, repetitive DNA sequences are in the small circular DNA population of monkey cells grown in culture",
    year = "1982",
    journal = "Journal of Molecular Biology",
    url = "https://doi.org/10.1016/s0022-2836(82)80003-x",
    doi = "10.1016/s0022-2836(82)80003-x",
    openalex = "W2089973075",
    references = "doi1010160022283667903075, doi1010160022283672902227, doi1010160022283677900523, doi1010160022283679902614, doi1010160092867479900904, doi101016s0022283675800830, doi101093nar861201, doi101093nar92309, openalexw1546783991, openalexw2282054059"
}

A clinical and cytogenetic study of children attending schools for the educationally handicapped has been carried out in the City of Coventry. As a result of this an estimate of the population incidence of the Martin-Bell syndrome among schoolchildren has been made. Among school-boys the incidence of mental retardation due to the fra (X) was found to be 0.73 per 1000 and among schoolgirls 0.48 per 1000. The overall prevalence is 0.61 per 1000. Genetic and cytogenetic analysis of 14 families ascertained in an unbiased manner showed that the expected 50% ratio of affected to unaffected relatives was disturbed, the possible result of a segregation distortion.

@article{doi101002ajmg1320230151,
    author = "Webb, Tessa and Bundey, Sarah and Thake, A and Todd, J and Opitz, John M. and Reynolds, James F.",
    title = "Population incidence and segregation ratios in the Martin‐Bell syndrome",
    year = "1986",
    journal = "American Journal of Medical Genetics",
    abstract = "A clinical and cytogenetic study of children attending schools for the educationally handicapped has been carried out in the City of Coventry. As a result of this an estimate of the population incidence of the Martin-Bell syndrome among schoolchildren has been made. Among school-boys the incidence of mental retardation due to the fra (X) was found to be 0.73 per 1000 and among schoolgirls 0.48 per 1000. The overall prevalence is 0.61 per 1000. Genetic and cytogenetic analysis of 14 families ascertained in an unbiased manner showed that the expected 50\% ratio of affected to unaffected relatives was disturbed, the possible result of a segregation distortion.",
    url = "https://doi.org/10.1002/ajmg.1320230151",
    doi = "10.1002/ajmg.1320230151",
    openalex = "W1967089189"
}

BACKGROUND: The epidemiology of tuberculosis in urban populations is changing. Combining conventional epidemiologic techniques with DNA fingerprinting of Mycobacterium tuberculosis can improve the understanding of how tuberculosis is transmitted. METHODS: We used restriction-fragment-length polymorphism (RFLP) analysis to study M. tuberculosis isolates from all patients reported to the tuberculosis registry in San Francisco during 1991 and 1992. These results were interpreted along with clinical, demographic, and epidemiologic data. Patients infected with the same strains were identified according to their RFLP patterns, and patients with identical patterns were grouped in clusters. Risk factors for being in a cluster were analyzed. RESULTS: Of 473 patients studied, 191 appeared to have active tuberculosis as a result of recent infection. Tracing of patients' contacts with the use of conventional methods identified links among only 10 percent of these patients. DNA fingerprinting, however, identified 44 clusters, 20 of which consisted of only 2 persons and the largest of which consisted of 30 persons. In patients under 60 years of age, Hispanic ethnicity (odds ratio, 3.3; P = 0.02), black race (odds ratio, 2.3; P = 0.02), birth in the United States (odds ratio, 5.8; P < 0.001), and a diagnosis of the acquired immunodeficiency syndrome (odds ratio, 1.8; P = 0.04) were independently associated with being in a cluster. Further study of patients in clusters confirmed that poorly compliant patients with infectious tuberculosis have a substantial adverse effect on the control of this disease. CONCLUSIONS: Despite an efficient tuberculosis-control program, nearly a third of new cases of tuberculosis in San Francisco are the result of recent infection. Few of these instances of transmission are identified by conventional contact tracing.

@article{doi101056nejm199406163302402,
    author = "Small, Peter M. and Hopewell, Philip C. and Singh, Samir P. and Paz, Antonio and Parsonnet, Julie and Ruston, Delaney and Schecter, Gisela and Daley, Charles L. and Schoolnik, Gary K.",
    title = "The Epidemiology of Tuberculosis in San Francisco -- A Population-Based Study Using Conventional and Molecular Methods",
    year = "1994",
    journal = "New England Journal of Medicine",
    abstract = "BACKGROUND: The epidemiology of tuberculosis in urban populations is changing. Combining conventional epidemiologic techniques with DNA fingerprinting of Mycobacterium tuberculosis can improve the understanding of how tuberculosis is transmitted. METHODS: We used restriction-fragment-length polymorphism (RFLP) analysis to study M. tuberculosis isolates from all patients reported to the tuberculosis registry in San Francisco during 1991 and 1992. These results were interpreted along with clinical, demographic, and epidemiologic data. Patients infected with the same strains were identified according to their RFLP patterns, and patients with identical patterns were grouped in clusters. Risk factors for being in a cluster were analyzed. RESULTS: Of 473 patients studied, 191 appeared to have active tuberculosis as a result of recent infection. Tracing of patients' contacts with the use of conventional methods identified links among only 10 percent of these patients. DNA fingerprinting, however, identified 44 clusters, 20 of which consisted of only 2 persons and the largest of which consisted of 30 persons. In patients under 60 years of age, Hispanic ethnicity (odds ratio, 3.3; P = 0.02), black race (odds ratio, 2.3; P = 0.02), birth in the United States (odds ratio, 5.8; P < 0.001), and a diagnosis of the acquired immunodeficiency syndrome (odds ratio, 1.8; P = 0.04) were independently associated with being in a cluster. Further study of patients in clusters confirmed that poorly compliant patients with infectious tuberculosis have a substantial adverse effect on the control of this disease. CONCLUSIONS: Despite an efficient tuberculosis-control program, nearly a third of new cases of tuberculosis in San Francisco are the result of recent infection. Few of these instances of transmission are identified by conventional contact tracing.",
    url = "https://doi.org/10.1056/nejm199406163302402",
    doi = "10.1056/nejm199406163302402",
    openalex = "W2130462614"
}

@incollection{doi101016b9780121592707500038,
    author = "Turchin, Peter",
    title = "Population Regulation: Old Arguments and a New Synthesis",
    year = "1995",
    booktitle = "Elsevier eBooks",
    url = "https://doi.org/10.1016/b978-012159270-7/50003-8",
    doi = "10.1016/b978-012159270-7/50003-8",
    openalex = "W92537686",
    references = "doi101098rstb19900188, doi1023072256726, doi1023072937041"
}

Inter-Alu PCR is increasingly useful in human genome mapping studies. One use is the generation of alumorphs, polymorphisms resulting from the presence or absence of inter-Alu PCR products. In this study, we have increased the proportion of the genome that can be analyzed by this technique with the use of long interspersed elements (LINEs). The set of polymorphisms detected by both Alu and LINE primers are referred to as interspersed repetitive sequence variants or IRS-morphs. Since a presence-absence variant may have been the result of a recent Alu or LINE insertion, we analyzed 7 isolated IRS-morphs that were generated, in part, with a primer derived from either a consensus LINE or a young Alu subfamily specific sequence, and observed by Southern blot analysis that these variants resulted from other types of genomic alterations. The use of these primers, however, reduces background from the numerous LINEs and Alu elements in the genome, providing sharp DNA fingerprint profiles. We have demonstrated the potential usefulness of these IRS-morph profiles in human population studies. We compared 12 IRS-morphs from a single amplification reaction from five distinct population groups (Caucasian (northern European descent), Hispanic (Mexican-American), Hindu-Indian, Papua New Guinean, and Greenland Eskimo) and observed that most have variable allelic frequencies among populations. The utilization of additional IRS-morph profiles will perpetuate this technique as a tool for DNA fingerprinting and for the analysis of human populations. Key words: Alu elements, DNA fingerprint, human populations, LINEs, SINEs.

@article{doi101139g96087,
    author = "Kass, David H. and Batzer, Mark A. and Deininger, Prescott L.",
    title = "Characterization and population diversity of interspersed repeat sequence variants (IRS-morphs)",
    year = "1996",
    journal = "Genome",
    abstract = "Inter-Alu PCR is increasingly useful in human genome mapping studies. One use is the generation of alumorphs, polymorphisms resulting from the presence or absence of inter-Alu PCR products. In this study, we have increased the proportion of the genome that can be analyzed by this technique with the use of long interspersed elements (LINEs). The set of polymorphisms detected by both Alu and LINE primers are referred to as interspersed repetitive sequence variants or IRS-morphs. Since a presence-absence variant may have been the result of a recent Alu or LINE insertion, we analyzed 7 isolated IRS-morphs that were generated, in part, with a primer derived from either a consensus LINE or a young Alu subfamily specific sequence, and observed by Southern blot analysis that these variants resulted from other types of genomic alterations. The use of these primers, however, reduces background from the numerous LINEs and Alu elements in the genome, providing sharp DNA fingerprint profiles. We have demonstrated the potential usefulness of these IRS-morph profiles in human population studies. We compared 12 IRS-morphs from a single amplification reaction from five distinct population groups (Caucasian (northern European descent), Hispanic (Mexican-American), Hindu-Indian, Papua New Guinean, and Greenland Eskimo) and observed that most have variable allelic frequencies among populations. The utilization of additional IRS-morph profiles will perpetuate this technique as a tool for DNA fingerprinting and for the analysis of human populations. Key words: Alu elements, DNA fingerprint, human populations, LINEs, SINEs.",
    url = "https://doi.org/10.1139/g96-087",
    doi = "10.1139/g96-087",
    openalex = "W2045651608",
    references = "doi1010160003269783904189, doi1010160022283681902199, doi1010160092867487900791, doi1010160092867488901596, doi1010160888754387900036, doi101038332164a0, doi101073pnas74125463, doi101073pnas86176686, doi101073pnas892110065, doi101073pnas912512288"
}

The AGG interspersion pattern and flanking microsatellite markers and their association with instability of the FMR1 (CGG)(n) repeat, involved in the fragile X syndrome, were analyzed in DNA from filter-paper blood spots randomly collected from the Danish newborn population. Comparison of DXS548-FRAXAC1 haplotype frequencies in the normal population and among fragile X patients suggested strong linkage disequilibrium between normal alleles and haplotype 7-3 and between fragile X alleles and haplotype 2-1 and 6-4. Comparison of the AGG interspersion pattern in 143 alleles, ranging in size from 34-62 CGG, and their associated haplotypes indicates the existence of at least three mutational pathways from normal alleles toward fragile X alleles in the Danish population. Two subgroups of normal alleles, with internal sequences of (CGG)(10)AGG(CGG)(19) and (CGG)(9)AGG(CGG)(12) AGG(CGG)(9), possibly predisposed for expansion, were identified in the data set. When alleles larger than 34 CGG were investigated, comparing the length of 3' uninterrupted CGG triplets (uCGG), we found that alleles associated with haplotype 2-1 and 6-4 contain significantly longer stretches of uCGG than alleles associated with haplotype 7-3. Thus, the data support that (CGG)(n) instability is correlated to the length of uCGG.

@article{doi101002109686282000071793299aidajmg430co2w,
    author = "Larsen, Lars Allan and Armstrong, Judith S.M. and Gr�nskov, Karen and Hjalgrim, Helle and Macpherson, James and Br�ndum-Nielsen, Karen and Hasholt, Lis and N�rgaard-Pedersen, Bent and Vuust, Jens",
    title = "Haplotype and AGG-interspersion analysis ofFMR1 (CGG)n alleles in the Danish population: Implications for multiple mutational pathways towards fragile X alleles",
    year = "2000",
    journal = "American Journal of Medical Genetics",
    abstract = "The AGG interspersion pattern and flanking microsatellite markers and their association with instability of the FMR1 (CGG)(n) repeat, involved in the fragile X syndrome, were analyzed in DNA from filter-paper blood spots randomly collected from the Danish newborn population. Comparison of DXS548-FRAXAC1 haplotype frequencies in the normal population and among fragile X patients suggested strong linkage disequilibrium between normal alleles and haplotype 7-3 and between fragile X alleles and haplotype 2-1 and 6-4. Comparison of the AGG interspersion pattern in 143 alleles, ranging in size from 34-62 CGG, and their associated haplotypes indicates the existence of at least three mutational pathways from normal alleles toward fragile X alleles in the Danish population. Two subgroups of normal alleles, with internal sequences of (CGG)(10)AGG(CGG)(19) and (CGG)(9)AGG(CGG)(12) AGG(CGG)(9), possibly predisposed for expansion, were identified in the data set. When alleles larger than 34 CGG were investigated, comparing the length of 3' uninterrupted CGG triplets (uCGG), we found that alleles associated with haplotype 2-1 and 6-4 contain significantly longer stretches of uCGG than alleles associated with haplotype 7-3. Thus, the data support that (CGG)(n) instability is correlated to the length of uCGG.",
    url = "https://doi.org/10.1002/1096-8628(20000717)93:2<99::aid-ajmg4>3.0.co;2-w",
    doi = "10.1002/1096-8628(20000717)93:2<99::aid-ajmg4>3.0.co;2-w",
    openalex = "W2169238082",
    references = "doi1010160092867491902835, doi101016009286749190397h, doi1010160092867494901341, doi101038ng099488, doi101086301869, doi101126science1675488, doi101126science25250091097, doi101126science25250091179, openalexw1545516169, openalexw1568074043"
}

We previously reported a 1:259 prevalence of female carriers of FMR1 premutation-size alleles (greater than 54 triplet repeats) in the general population. We now have screened 10 572 independent males from the same population for similar alleles using high-throughput Southern blotting. We identified 13 male carriers of an allele with more than 54 repeats. This corresponds to a prevalence of 1:813 males (95% confidence interval 1:527 to 1:1781). Haplotype analysis of four markers flanking the triplet array revealed that the prevalence of the major fragile X mutation-associated haplotype was increased among FMR1 alleles of 40-54 repeats. Although sequencing of highly unstable premutation alleles from fragile X families revealed only pure CGG tracts, this was not the case for alleles of similar size that were identified in males from the general population. Forty-eight out of forty-nine alleles of 40 or more triplets had one or two AGG interruptions. This observation, combined with the observation of the enrichment of major fragile X syndrome haplotypes in all alleles of this size, is evidence that the loss of an AGG interruption in the triplet repeat array is not necessary for expansion of normal alleles of 29-30 triplets to intermediate size. The loss of AGG interruptions thus appears to be a late event that leads to greatly increased instability and may be related to the haplotype background of specific FMR1 alleles.

@article{doi101093hmg114371,
    author = "Dombrowski, Christian",
    title = "Premutation and intermediate-size FMR1 alleles in 10 572 males from the general population: loss of an AGG interruption is a late event in the generation of fragile X syndrome alleles",
    year = "2002",
    journal = "Human Molecular Genetics",
    abstract = "We previously reported a 1:259 prevalence of female carriers of FMR1 premutation-size alleles (greater than 54 triplet repeats) in the general population. We now have screened 10 572 independent males from the same population for similar alleles using high-throughput Southern blotting. We identified 13 male carriers of an allele with more than 54 repeats. This corresponds to a prevalence of 1:813 males (95\% confidence interval 1:527 to 1:1781). Haplotype analysis of four markers flanking the triplet array revealed that the prevalence of the major fragile X mutation-associated haplotype was increased among FMR1 alleles of 40-54 repeats. Although sequencing of highly unstable premutation alleles from fragile X families revealed only pure CGG tracts, this was not the case for alleles of similar size that were identified in males from the general population. Forty-eight out of forty-nine alleles of 40 or more triplets had one or two AGG interruptions. This observation, combined with the observation of the enrichment of major fragile X syndrome haplotypes in all alleles of this size, is evidence that the loss of an AGG interruption in the triplet repeat array is not necessary for expansion of normal alleles of 29-30 triplets to intermediate size. The loss of AGG interruptions thus appears to be a late event that leads to greatly increased instability and may be related to the haplotype background of specific FMR1 alleles.",
    url = "https://doi.org/10.1093/hmg/11.4.371",
    doi = "10.1093/hmg/11.4.371",
    openalex = "W2166567981",
    references = "openalexw1545516169"
}

Although LINE-1 (long interspersed nucleotide element-1, L1) retrotransposons comprise 17% of the human genome, an exhaustive search of the December 2001 "freeze" of the haploid human genome working draft sequence (95% complete) yielded only 90 L1s with intact ORFs. We demonstrate that 38 of 86 (44%) L1s are polymorphic as to their presence in human populations. We cloned 82 (91%) of the 90 L1s and found that 40 of the 82 (49%) are active in a cultured cell retrotransposition assay. From these data, we predict that there are 80-100 retrotransposition-competent L1s in an average human being. Remarkably, 84% of assayed retrotransposition capability was present in six highly active L1s (hot L1s). By comparison, four of five full-length L1s involved in recent human insertions had retrotransposition activity comparable to the six hot L1s in the human genome working draft sequence. Thus, our data indicate that most L1 retrotransposition in the human population stems from hot L1s, with the remaining elements playing a lesser role in genome plasticity.

@article{doi101073pnas0831042100,
    author = "Brouha, Brook and Schustak, Joshua and Badge, Richard M. and Lutz, Sheila and Farley, Alexander H. and Moran, John V. and Kazazian, Haig H.",
    title = "Hot L1s account for the bulk of retrotransposition in the human population",
    year = "2003",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = {Although LINE-1 (long interspersed nucleotide element-1, L1) retrotransposons comprise 17\% of the human genome, an exhaustive search of the December 2001 "freeze" of the haploid human genome working draft sequence (95\% complete) yielded only 90 L1s with intact ORFs. We demonstrate that 38 of 86 (44\%) L1s are polymorphic as to their presence in human populations. We cloned 82 (91\%) of the 90 L1s and found that 40 of the 82 (49\%) are active in a cultured cell retrotransposition assay. From these data, we predict that there are 80-100 retrotransposition-competent L1s in an average human being. Remarkably, 84\% of assayed retrotransposition capability was present in six highly active L1s (hot L1s). By comparison, four of five full-length L1s involved in recent human insertions had retrotransposition activity comparable to the six hot L1s in the human genome working draft sequence. Thus, our data indicate that most L1 retrotransposition in the human population stems from hot L1s, with the remaining elements playing a lesser role in genome plasticity.},
    url = "https://doi.org/10.1073/pnas.0831042100",
    doi = "10.1073/pnas.0831042100",
    openalex = "W2091279754",
    references = "doi101007bf01731581, doi1010160092867493900785, doi101016s0022283605803602, doi101016s0092867400819972, doi101016s0092867400819984, doi10103835057062, doi10103874184, doi101093oxfordjournalsmolbeva040454, doi101128mcb214142914392001, doi101146annurevgenet35102401091032"
}

CONTEXT: Premutation expansions (55-200 CGG repeats) of the fragile X mental retardation 1 (FMR1) gene are frequent in the general population, with estimated prevalences of 1 per 259 females and 1 per 813 males. Several articles have recently described the presence of late-onset neurological symptoms in male carriers of premutation (FMR1) alleles. The main clinical features described in this newly identified syndrome are cerebellar ataxia and intention tremor. Additional documented symptoms include short-term memory loss, executive functional deficits, cognitive decline, parkinsonism, peripheral neuropathy, lower-limb proximal muscle weakness, and autonomic dysfunction. OBJECTIVE: To study the penetrance of the fragile X-associated tremor/ataxia syndrome (FXTAS) among premutation carriers. DESIGN, SETTING, AND PARTICIPANTS: Family-based study of 192 individuals (premutation carriers and controls) whose families belong to the Northern or Southern California Fragile X Associations. Data were collected (March 2002-April 2003) through a survey and a standardized neurological examination, which was videotaped and subsequently scored in a blinded fashion. MAIN OUTCOME MEASURES: Penetrance of intention tremor and ataxia among adult carriers (aged > or =50 years) of premutation expansions of the FMR1 gene. RESULTS: Data from the survey of 192 individuals demonstrated an age-related penetrance of the combination of reported intention tremor and gait ataxia in male carriers (17%, 38%, 47%, and 75% [lower-bound estimates] for participants aged 50-59, 60-69, 70-79, and > or =80 years, respectively). The male carrier group had an age-adjusted 13-fold increased risk (95% confidence interval, 3.9-25.4; P =.003) of combined intention tremor and gait ataxia when compared with male controls. The clinical examination data from 93 individuals demonstrated that male carriers experienced more difficulties on each of 3 standardized neurological rating scales compared with controls (P<.05). Female carrier scores were also higher than those of female controls (P<.05) on 2 of the 3 neurological rating scales, but no participant was identified with probable or definite FXTAS. CONCLUSIONS: The study demonstrates that older male carriers of premutation alleles of the FMR1 gene are at high risk of developing FXTAS. Since male premutation carriers are relatively common in the general population, older men with ataxia and intention tremor should be screened for the FMR1 mutation, especially if these signs are accompanied by parkinsonism, autonomic dysfunction, or cognitive decline, regardless of family history.

@article{doi101001jama2914460,
    author = "Jacquemont, Sébastien",
    title = "Penetrance of the Fragile X–Associated Tremor/Ataxia Syndrome in a Premutation Carrier Population",
    year = "2004",
    journal = "JAMA",
    abstract = "CONTEXT: Premutation expansions (55-200 CGG repeats) of the fragile X mental retardation 1 (FMR1) gene are frequent in the general population, with estimated prevalences of 1 per 259 females and 1 per 813 males. Several articles have recently described the presence of late-onset neurological symptoms in male carriers of premutation (FMR1) alleles. The main clinical features described in this newly identified syndrome are cerebellar ataxia and intention tremor. Additional documented symptoms include short-term memory loss, executive functional deficits, cognitive decline, parkinsonism, peripheral neuropathy, lower-limb proximal muscle weakness, and autonomic dysfunction. OBJECTIVE: To study the penetrance of the fragile X-associated tremor/ataxia syndrome (FXTAS) among premutation carriers. DESIGN, SETTING, AND PARTICIPANTS: Family-based study of 192 individuals (premutation carriers and controls) whose families belong to the Northern or Southern California Fragile X Associations. Data were collected (March 2002-April 2003) through a survey and a standardized neurological examination, which was videotaped and subsequently scored in a blinded fashion. MAIN OUTCOME MEASURES: Penetrance of intention tremor and ataxia among adult carriers (aged > or =50 years) of premutation expansions of the FMR1 gene. RESULTS: Data from the survey of 192 individuals demonstrated an age-related penetrance of the combination of reported intention tremor and gait ataxia in male carriers (17\%, 38\%, 47\%, and 75\% [lower-bound estimates] for participants aged 50-59, 60-69, 70-79, and > or =80 years, respectively). The male carrier group had an age-adjusted 13-fold increased risk (95\% confidence interval, 3.9-25.4; P =.003) of combined intention tremor and gait ataxia when compared with male controls. The clinical examination data from 93 individuals demonstrated that male carriers experienced more difficulties on each of 3 standardized neurological rating scales compared with controls (P<.05). Female carrier scores were also higher than those of female controls (P<.05) on 2 of the 3 neurological rating scales, but no participant was identified with probable or definite FXTAS. CONCLUSIONS: The study demonstrates that older male carriers of premutation alleles of the FMR1 gene are at high risk of developing FXTAS. Since male premutation carriers are relatively common in the general population, older men with ataxia and intention tremor should be screened for the FMR1 mutation, especially if these signs are accompanied by parkinsonism, autonomic dysfunction, or cognitive decline, regardless of family history.",
    url = "https://doi.org/10.1001/jama.291.4.460",
    doi = "10.1001/jama.291.4.460",
    openalex = "W2144550671"
}

An optimized set of 24 mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) loci, including a discriminatory subset of 15 loci, has recently been defined for the typing of Mycobacterium tuberculosis. Here, we evaluated the performances of this MIRU-VNTR typing system in combination with spoligotyping for the detection of transmission chains in a population-based study comprising 91% of culture-confirmed tuberculosis patients reported in 2003 in Hamburg, Germany. Of the 154 isolates investigated, more than 90% had high IS6110 copy numbers (>/=6). IS6110 restriction fragment length polymorphism (RFLP) typing resulted in 13 clusters, 5 of which had a confirmed epidemiological link. All five, as well as six of the eight IS6110 clusters with no identified epidemiological link, were perfectly matched by MIRU-VNTR typing with the 24 loci. Two IS6110 clusters were split by differences into 6 to 12 MIRU-VNTR loci, clearly supporting the absence of a link, as judged by contact tracing data. In contrast, only one MIRU-VNTR cluster, grouping what were probably epidemiologically unlinked isolates, was split by IS6110 RFLP. However, these isolates were also distinguished by spoligotyping. Both the optimized 24-locus and 15-locus sets thus showed a comparable to slightly better predictive value, especially when combined with spoligotyping, than the current gold standard IS6110 RFLP for the study of tuberculosis transmission in Hamburg. Because the epidemiological characteristics of this setting are similar to those of many developed countries, these results support the wide applicability of this real-time genotyping approach for population-based studies of M. tuberculosis transmission.

@article{doi101128jcm0139306,
    author = "Oelemann, Mara Cardoso and Diel, Roland and Vatin, Vincent and Haas, Walter and Rüsch–Gerdes, Sabine and Locht, Camille and Niemann, Stefan and Supply, Philip",
    title = "Assessment of an Optimized Mycobacterial Interspersed Repetitive- Unit-Variable-Number Tandem-Repeat Typing System Combined with Spoligotyping for Population-Based Molecular Epidemiology Studies of Tuberculosis",
    year = "2006",
    journal = "Journal of Clinical Microbiology",
    abstract = "An optimized set of 24 mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) loci, including a discriminatory subset of 15 loci, has recently been defined for the typing of Mycobacterium tuberculosis. Here, we evaluated the performances of this MIRU-VNTR typing system in combination with spoligotyping for the detection of transmission chains in a population-based study comprising 91\% of culture-confirmed tuberculosis patients reported in 2003 in Hamburg, Germany. Of the 154 isolates investigated, more than 90\% had high IS6110 copy numbers (>/=6). IS6110 restriction fragment length polymorphism (RFLP) typing resulted in 13 clusters, 5 of which had a confirmed epidemiological link. All five, as well as six of the eight IS6110 clusters with no identified epidemiological link, were perfectly matched by MIRU-VNTR typing with the 24 loci. Two IS6110 clusters were split by differences into 6 to 12 MIRU-VNTR loci, clearly supporting the absence of a link, as judged by contact tracing data. In contrast, only one MIRU-VNTR cluster, grouping what were probably epidemiologically unlinked isolates, was split by IS6110 RFLP. However, these isolates were also distinguished by spoligotyping. Both the optimized 24-locus and 15-locus sets thus showed a comparable to slightly better predictive value, especially when combined with spoligotyping, than the current gold standard IS6110 RFLP for the study of tuberculosis transmission in Hamburg. Because the epidemiological characteristics of this setting are similar to those of many developed countries, these results support the wide applicability of this real-time genotyping approach for population-based studies of M. tuberculosis transmission.",
    url = "https://doi.org/10.1128/jcm.01393-06",
    doi = "10.1128/jcm.01393-06",
    openalex = "W2148496884",
    references = "doi101046j1365295819976361999x, doi101046j13652958200001905x, doi101056nejm199406163302402, doi101073pnas9841901, doi1010990022128714451189, doi101128jcm0139206, doi101128jcm3124064091993, doi101128jcm3549079141997, doi101128jcm3910356335712001, doi101128jcm4326886952005"
}

BACKGROUND: The Direct Repeat locus of the Mycobacterium tuberculosis complex (MTC) is a member of the CRISPR (Clustered regularly interspaced short palindromic repeats) sequences family. Spoligotyping is the widely used PCR-based reverse-hybridization blotting technique that assays the genetic diversity of this locus and is useful both for clinical laboratory, molecular epidemiology, evolutionary and population genetics. It is easy, robust, cheap, and produces highly diverse portable numerical results, as the result of the combination of (1) Unique Events Polymorphism (UEP) (2) Insertion-Sequence-mediated genetic recombination. Genetic convergence, although rare, was also previously demonstrated. Three previous international spoligotype databases had partly revealed the global and local geographical structures of MTC bacilli populations, however, there was a need for the release of a new, more representative and extended, international spoligotyping database. RESULTS: The fourth international spoligotyping database, SpolDB4, describes 1939 shared-types (STs) representative of a total of 39,295 strains from 122 countries, which are tentatively classified into 62 clades/lineages using a mixed expert-based and bioinformatical approach. The SpolDB4 update adds 26 new potentially phylogeographically-specific MTC genotype families. It provides a clearer picture of the current MTC genomes diversity as well as on the relationships between the genetic attributes investigated (spoligotypes) and the infra-species classification and evolutionary history of the species. Indeed, an independent Naïve-Bayes mixture-model analysis has validated main of the previous supervised SpolDB3 classification results, confirming the usefulness of both supervised and unsupervised models as an approach to understand MTC population structure. Updated results on the epidemiological status of spoligotypes, as well as genetic prevalence maps on six main lineages are also shown. Our results suggests the existence of fine geographical genetic clines within MTC populations, that could mirror the passed and present Homo sapiens sapiens demographical and mycobacterial co-evolutionary history whose structure could be further reconstructed and modelled, thereby providing a large-scale conceptual framework of the global TB Epidemiologic Network. CONCLUSION: Our results broaden the knowledge of the global phylogeography of the MTC complex. SpolDB4 should be a very useful tool to better define the identity of a given MTC clinical isolate, and to better analyze the links between its current spreading and previous evolutionary history. The building and mining of extended MTC polymorphic genetic databases is in progress.

@article{doi10118614712180623,
    author = "Brudey, Karine and Driscoll, Jeffrey and Rigouts, Leen and Prodinger, Wolfgang M. and Gori, Andrea and Al‐Hajoj, Sahal and Allix, Caroline and Aristimuño, Liselotte and Arora, Jyoti and Baumanis, Viesturs and Binder, Lothar and Cafrune, Patrícia Izquierdo and Cataldi, Angel and Cheong, Soonfatt and Diel, Roland and Ellermeier, C and Evans, Jason T. and Fauville‐Dufaux, Maryse and Ferdinand, Séverine and de Viedma, Darı́o Garcı́a and Garzelli, Carlo and Gazzola, Lidia and Gomes, Harrison Magdinier and Guttierez, M Cristina and Hawkey, Peter M. and van Helden, Paul D. and Kadival, Gurujaj V and Kreiswirth, Barry N. and Kremer, Kristin and Kubín, Milan and Kulkarni, Savita P and Liens, Benjamin and Lillebæk, Troels and Ly, Ho Minh and Martı́n, Carlos and Martin, Christian and Mokrousov, Igor and Нарвская, О. В. and Ngeow, Yun Fong and Naumann, Ludmilla and Niemann, Stefan and Parwati, Ida and Rahim, Zeaur and Rasolofo-Razanamparany, Voahangy and Rasolonavalona, T and Rossetti, Maria Lúcia Rosa and Rüsch–Gerdes, Sabine and Sajduda, Anna and Samper, Sofía and Shemyakin, I. G. and Singh, Urvashi B. and Somoskövi, Ákos and Skuce, Robin and van Soolingen, Dick and Streicher, Elizabeth M. and Suffys, Philip Noël and Tortoli, Enrico and Tračevska, Tatjana and Vincent, Véronique and Victor, Tommie C. and Warren, Robin M. and Yap, Sook Fan and Zaman, Khadiza and Portaels, Françoise and Rastogi, Nalin and Sola, Christophe",
    title = "Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology",
    year = "2006",
    journal = "BMC Microbiology",
    abstract = "BACKGROUND: The Direct Repeat locus of the Mycobacterium tuberculosis complex (MTC) is a member of the CRISPR (Clustered regularly interspaced short palindromic repeats) sequences family. Spoligotyping is the widely used PCR-based reverse-hybridization blotting technique that assays the genetic diversity of this locus and is useful both for clinical laboratory, molecular epidemiology, evolutionary and population genetics. It is easy, robust, cheap, and produces highly diverse portable numerical results, as the result of the combination of (1) Unique Events Polymorphism (UEP) (2) Insertion-Sequence-mediated genetic recombination. Genetic convergence, although rare, was also previously demonstrated. Three previous international spoligotype databases had partly revealed the global and local geographical structures of MTC bacilli populations, however, there was a need for the release of a new, more representative and extended, international spoligotyping database. RESULTS: The fourth international spoligotyping database, SpolDB4, describes 1939 shared-types (STs) representative of a total of 39,295 strains from 122 countries, which are tentatively classified into 62 clades/lineages using a mixed expert-based and bioinformatical approach. The SpolDB4 update adds 26 new potentially phylogeographically-specific MTC genotype families. It provides a clearer picture of the current MTC genomes diversity as well as on the relationships between the genetic attributes investigated (spoligotypes) and the infra-species classification and evolutionary history of the species. Indeed, an independent Naïve-Bayes mixture-model analysis has validated main of the previous supervised SpolDB3 classification results, confirming the usefulness of both supervised and unsupervised models as an approach to understand MTC population structure. Updated results on the epidemiological status of spoligotypes, as well as genetic prevalence maps on six main lineages are also shown. Our results suggests the existence of fine geographical genetic clines within MTC populations, that could mirror the passed and present Homo sapiens sapiens demographical and mycobacterial co-evolutionary history whose structure could be further reconstructed and modelled, thereby providing a large-scale conceptual framework of the global TB Epidemiologic Network. CONCLUSION: Our results broaden the knowledge of the global phylogeography of the MTC complex. SpolDB4 should be a very useful tool to better define the identity of a given MTC clinical isolate, and to better analyze the links between its current spreading and previous evolutionary history. The building and mining of extended MTC polymorphic genetic databases is in progress.",
    url = "https://doi.org/10.1186/1471-2180-6-23",
    doi = "10.1186/1471-2180-6-23",
    openalex = "W2096162460"
}

Standardized mycobacterial interspersed repetitive-unit-variable-number tandem repeat (MIRU-VNTR) typing based on 15 and 24 loci recently has been proposed for Mycobacterium tuberculosis genotyping. So far, this optimized system has been assessed in a single, 1-year population-based study performed in Germany (M. C. Oelemann, R. Diel, V. Vatin, W. Haas, S. Rusch-Gerdes, C. Locht, S. Niemann, and P. Supply, J. Clin. Microbiol. 45:691-697, 2007). Here, we evaluated these optimized formats in a much larger population-based study conducted during 39 months in the Brussels capital region of Belgium. Isolates from 807 patients were genotyped. The resolution power, cluster, and lineage identification by the standardized MIRU-VNTR sets were compared to those obtained using standardized IS6110-restriction fragment length polymorphism (RFLP), spoligotyping, and a previous 12-MIRU-VNTR-locus set. On a subset representing 77% of the cases during a 16-month period, a high concordance was observed between unique isolates or strain clusters as defined by standardized MIRU-VNTR and IS6110-RFLP (i.e., more than five IS6110 bands). When extended to the entire population-based collection, the discriminatory subset of 15 loci decreased the strain-clustering rate by almost twofold compared to that of the old 12-locus set. The addition of the nine ancillary MIRU-VNTR loci and/or spoligotyping only slightly further decreased this strain-clustering rate. Familial, social, and/or geographic proximity links were found in 48% of the clusters identified, and well-known risk factors for tuberculosis transmission were identified. Finally, an excellent correspondence was determined between our MIRU-VNTR-spoligotyping strain identifications and external reference strain lineages included in the MIRU-VNTRplus database and identified by, e.g., large sequence polymorphisms. Our results reinforce the proposal of standardized MIRU-VNTR typing as a new reference genotyping method for the epidemiological and phylogenetic screening of M. tuberculosis strains.

@article{doi101128jcm0208907,
    author = "Allix‐Béguec, Caroline and Fauville‐Dufaux, Maryse and Supply, Philip",
    title = "Three-Year Population-Based Evaluation of Standardized Mycobacterial Interspersed Repetitive-Unit-Variable-Number Tandem-Repeat Typing of Mycobacterium tuberculosis",
    year = "2008",
    journal = "Journal of Clinical Microbiology",
    abstract = "Standardized mycobacterial interspersed repetitive-unit-variable-number tandem repeat (MIRU-VNTR) typing based on 15 and 24 loci recently has been proposed for Mycobacterium tuberculosis genotyping. So far, this optimized system has been assessed in a single, 1-year population-based study performed in Germany (M. C. Oelemann, R. Diel, V. Vatin, W. Haas, S. Rusch-Gerdes, C. Locht, S. Niemann, and P. Supply, J. Clin. Microbiol. 45:691-697, 2007). Here, we evaluated these optimized formats in a much larger population-based study conducted during 39 months in the Brussels capital region of Belgium. Isolates from 807 patients were genotyped. The resolution power, cluster, and lineage identification by the standardized MIRU-VNTR sets were compared to those obtained using standardized IS6110-restriction fragment length polymorphism (RFLP), spoligotyping, and a previous 12-MIRU-VNTR-locus set. On a subset representing 77\% of the cases during a 16-month period, a high concordance was observed between unique isolates or strain clusters as defined by standardized MIRU-VNTR and IS6110-RFLP (i.e., more than five IS6110 bands). When extended to the entire population-based collection, the discriminatory subset of 15 loci decreased the strain-clustering rate by almost twofold compared to that of the old 12-locus set. The addition of the nine ancillary MIRU-VNTR loci and/or spoligotyping only slightly further decreased this strain-clustering rate. Familial, social, and/or geographic proximity links were found in 48\% of the clusters identified, and well-known risk factors for tuberculosis transmission were identified. Finally, an excellent correspondence was determined between our MIRU-VNTR-spoligotyping strain identifications and external reference strain lineages included in the MIRU-VNTRplus database and identified by, e.g., large sequence polymorphisms. Our results reinforce the proposal of standardized MIRU-VNTR typing as a new reference genotyping method for the epidemiological and phylogenetic screening of M. tuberculosis strains.",
    url = "https://doi.org/10.1128/jcm.02089-07",
    doi = "10.1128/jcm.02089-07",
    openalex = "W2166379983",
    references = "doi101016s1473309907701081, doi101056nejm199406163302402, doi101056nejm199406163302403, doi101073pnas0511240103, doi101073pnas94189869, doi101128jcm0139206, doi101128jcm0139306, doi101128jcm3124064091993, doi101128jcm3549079141997, doi10118614712180623, doi101371journalppat0010005"
}

@article{doi102353jmoldx2009080173,
    author = "Fernández-Carvajal, Isabel and Walichiewicz, Paulina and Xiaosen, Xie and Pan, Ruiqin and Hagerman, Paul J. and Tassone, Flora",
    title = "Screening for Expanded Alleles of the FMR1 Gene in Blood Spots from Newborn Males in a Spanish Population",
    year = "2009",
    journal = "Journal of Molecular Diagnostics",
    url = "https://doi.org/10.2353/jmoldx.2009.080173",
    doi = "10.2353/jmoldx.2009.080173",
    openalex = "W2032687048"
}

The identification of population bottlenecks is critical in conservation because populations that have experienced significant reductions in abundance are subject to a variety of genetic and demographic processes that can hasten extinction. Genetic bottleneck tests constitute an appealing and popular approach for determining if a population decline has occurred because they only require sampling at a single point in time, yet reflect demographic history over multiple generations. However, a review of the published literature indicates that, as typically applied, microsatellite-based bottleneck tests often do not detect bottlenecks in vertebrate populations known to have experienced declines. This observation was supported by simulations that revealed that bottleneck tests can have limited statistical power to detect bottlenecks largely as a result of limited sample sizes typically used in published studies. Moreover, commonly assumed values for mutation model parameters do not appear to encompass variation in microsatellite evolution observed in vertebrates and, on average, the proportion of multi-step mutations is underestimated by a factor of approximately two. As a result, bottleneck tests can have a higher probability of 'detecting' bottlenecks in stable populations than expected based on the nominal significance level. We provide recommendations that could add rigor to inferences drawn from future bottleneck tests and highlight new directions for the characterization of demographic history.

@article{doi101111j1365294x201205635x,
    author = "Peery, M. Zachariah and Kirby, Rebecca and Reid, Brendan N. and Stoelting, Ricka E. and Doucet‐Bëer, Elena and Robinson, Stacie J. and Vásquez‐Carrillo, Catalina and Pauli, Jonathan N. and Palsbøll, Per J.",
    title = "Reliability of genetic bottleneck tests for detecting recent population declines",
    year = "2012",
    journal = "Molecular Ecology",
    abstract = "The identification of population bottlenecks is critical in conservation because populations that have experienced significant reductions in abundance are subject to a variety of genetic and demographic processes that can hasten extinction. Genetic bottleneck tests constitute an appealing and popular approach for determining if a population decline has occurred because they only require sampling at a single point in time, yet reflect demographic history over multiple generations. However, a review of the published literature indicates that, as typically applied, microsatellite-based bottleneck tests often do not detect bottlenecks in vertebrate populations known to have experienced declines. This observation was supported by simulations that revealed that bottleneck tests can have limited statistical power to detect bottlenecks largely as a result of limited sample sizes typically used in published studies. Moreover, commonly assumed values for mutation model parameters do not appear to encompass variation in microsatellite evolution observed in vertebrates and, on average, the proportion of multi-step mutations is underestimated by a factor of approximately two. As a result, bottleneck tests can have a higher probability of 'detecting' bottlenecks in stable populations than expected based on the nominal significance level. We provide recommendations that could add rigor to inferences drawn from future bottleneck tests and highlight new directions for the characterization of demographic history.",
    url = "https://doi.org/10.1111/j.1365-294x.2012.05635.x",
    doi = "10.1111/j.1365-294x.2012.05635.x",
    openalex = "W2127249590",
    references = "doi101038nrg1348, doi101086301869, doi101111j1365294x200502683x"
}

As DNA profiling systems become more complex, advancements to a relatively simple technique are presented that promote greater accessibility and usefulness for a variety of applications. In contrast, other simple tools commonly used to teach students about forensics and human populations have notable drawbacks. Two Alutetraplex systems, utilizing four Alu presence/absence variants in a single reaction were therefore developed to provide a simple methodology to generate complex profiles. A third Alutetraplex system is presented, escalating the number of possible genotypes to 531,441, with all alleles of the 12 dimorphic markers being relatively common. Reproducible results were attained even with the use of crude DNA preparations stored frozen for several years with multiple freeze thaws. The incorporation of GelRed DNA stain instead of the highly toxic ethidium bromide promotes greater accessibility, particularly in a classroom setting. This study demonstrates the effectiveness of this profiling system as a simple but informative methodology to analyze paternity, genetic mapping of human traits, and provides data to illustrate its potential in assessing ancestry or geographic origins of an individual.

@article{doi104172215771451000200,
    author = "Kass, David H.",
    title = "A Simple Method of Generating Complex DNA Profiles Utilizing Alu-based Markers with Applications in Forensics, Paternity, Genetic Mapping, Population Studies and Ancestry",
    year = "2013",
    journal = "Journal of Forensic Research",
    abstract = "As DNA profiling systems become more complex, advancements to a relatively simple technique are presented that promote greater accessibility and usefulness for a variety of applications. In contrast, other simple tools commonly used to teach students about forensics and human populations have notable drawbacks. Two Alutetraplex systems, utilizing four Alu presence/absence variants in a single reaction were therefore developed to provide a simple methodology to generate complex profiles. A third Alutetraplex system is presented, escalating the number of possible genotypes to 531,441, with all alleles of the 12 dimorphic markers being relatively common. Reproducible results were attained even with the use of crude DNA preparations stored frozen for several years with multiple freeze thaws. The incorporation of GelRed DNA stain instead of the highly toxic ethidium bromide promotes greater accessibility, particularly in a classroom setting. This study demonstrates the effectiveness of this profiling system as a simple but informative methodology to analyze paternity, genetic mapping of human traits, and provides data to illustrate its potential in assessing ancestry or geographic origins of an individual.",
    url = "https://doi.org/10.4172/2157-7145.1000200",
    doi = "10.4172/2157-7145.1000200",
    openalex = "W2334684287",
    references = "doi101139g96087"
}

Coilia nasus is found in the Yangtze River and the coastal waters of China, Korea, and Japan. Two ecotypes (anadromous and freshwater-resident populations) are distributed throughout the Yangtze River basin based on their ecology and behavior, but relatively little is known about the population structure of this species. Analysis of short interspersed element (SINE) insertions, which vary among individuals, has been acknowledged to provide a unique way to study population divergence. SINEs isolated from C. nasus were characterized, and this enabled analysis of the SINE insertion pattern in six populations distributed throughout the Yangtze River basin. In all populations, four SINE loci displayed individual polymorphism, and two SINE loci showed a stochastic loss in all individuals of two resident populations. The correlation between genetic and geographic populations indicated a degree of genetic isolation in this species. In contrast with Coilia grayii and Coilia mystus, two SINE loci appeared only in C. nasus. Sequencing analysis indicated that the high insertion variability of SINEs was attributed mainly to the tails, which contained various repeat copies. The results in this study will be useful for sustainable management of fishery resources and conservation of this species.

@article{doi101016jbse201312022,
    author = "Liu, Dong and Li, Yingying and Tang, Wenqiao and Yang, Jin-Quan and Guo, Hongyi and Zhu, Guoli and Li, Hui‐Hua",
    title = "Population structure of Coilia nasus in the Yangtze River revealed by insertion of short interspersed elements",
    year = "2014",
    journal = "Biochemical Systematics and Ecology",
    abstract = "Coilia nasus is found in the Yangtze River and the coastal waters of China, Korea, and Japan. Two ecotypes (anadromous and freshwater-resident populations) are distributed throughout the Yangtze River basin based on their ecology and behavior, but relatively little is known about the population structure of this species. Analysis of short interspersed element (SINE) insertions, which vary among individuals, has been acknowledged to provide a unique way to study population divergence. SINEs isolated from C. nasus were characterized, and this enabled analysis of the SINE insertion pattern in six populations distributed throughout the Yangtze River basin. In all populations, four SINE loci displayed individual polymorphism, and two SINE loci showed a stochastic loss in all individuals of two resident populations. The correlation between genetic and geographic populations indicated a degree of genetic isolation in this species. In contrast with Coilia grayii and Coilia mystus, two SINE loci appeared only in C. nasus. Sequencing analysis indicated that the high insertion variability of SINEs was attributed mainly to the tails, which contained various repeat copies. The results in this study will be useful for sustainable management of fishery resources and conservation of this species.",
    url = "https://doi.org/10.1016/j.bse.2013.12.022",
    doi = "10.1016/j.bse.2013.12.022",
    openalex = "W2061710597",
    references = "doi101002sici15211878200002222148aidbies630co2z, doi101007s004380100563, doi101016jympev200410023, doi101016s0092867402010413, doi101089152791600459894, doi101093nargkg500, doi101093oxfordjournalsmolbeva003747, doi101111j1365294x200603104x, doi101146annurevgenet40110405090448, doi103390ijms13033085"
}

AIM: Aberrant global DNA methylation is involved in the development of several diseases, including cardiovascular disease (CVD). We investigated whether the methylation of long interspersed nuclear element-1 (LINE-1) in leukocytes is associated with dyslipidemia, a major risk factor for CVD, in the Japanese general population. METHODS: We conducted a cross-sectional study consisting of 420 Japanese subjects (187 men and 233 women) without a clinical history of cancer, stroke, or ischemic heart disease. LINE-1 DNA methylation levels in leukocytes were measured using a pyrosequencing method. RESULTS: Significantly higher odds ratios (ORs) for hypermethylation were observed in the high LDL cholesterol and high LDL/HDL ratio groups than the corresponding normal group (high LDLC group: OR, 1.88; 95% confidence interval [CI], 1.20-2.96, high LDL/HDL ratio group: OR, 1.90; 95% CI, 1.20-3.01). Subjects with 2 or more lipid abnormalities had significantly higher ORs for hypermethylation than those with no lipid abnormality (OR, 2.31; 95% CI, 1.11-4.82). CONCLUSION: LINE-1 DNA hypermethylation in leukocytes was associated with CVD risk profiles: high LDLC, high LDL/HDL ratio, and the degree of abnormal lipid metabolism.

@article{doi105551jat43570,
    author = "Tsuboi, Yoshiki and Yamada, Hiroya and Munetsuna, Eiji and Yamazaki, Mirai and Mizuno, Genki and Murase, Yuri and Ohashi, Koji and Ishikawa, Hiroaki and Kondo, Mari and Inoue, Takashi and Hashimoto, Shuji and Hamajima, Nobuyuki and Suzuki, Koji",
    title = "Relationship between Long Interspersed Nuclear Element-1 DNA Methylation in Leukocytes and Dyslipidemia in the Japanese General Population",
    year = "2018",
    journal = "Journal of Atherosclerosis and Thrombosis",
    abstract = "AIM: Aberrant global DNA methylation is involved in the development of several diseases, including cardiovascular disease (CVD). We investigated whether the methylation of long interspersed nuclear element-1 (LINE-1) in leukocytes is associated with dyslipidemia, a major risk factor for CVD, in the Japanese general population. METHODS: We conducted a cross-sectional study consisting of 420 Japanese subjects (187 men and 233 women) without a clinical history of cancer, stroke, or ischemic heart disease. LINE-1 DNA methylation levels in leukocytes were measured using a pyrosequencing method. RESULTS: Significantly higher odds ratios (ORs) for hypermethylation were observed in the high LDL cholesterol and high LDL/HDL ratio groups than the corresponding normal group (high LDLC group: OR, 1.88; 95\% confidence interval [CI], 1.20-2.96, high LDL/HDL ratio group: OR, 1.90; 95\% CI, 1.20-3.01). Subjects with 2 or more lipid abnormalities had significantly higher ORs for hypermethylation than those with no lipid abnormality (OR, 2.31; 95\% CI, 1.11-4.82). CONCLUSION: LINE-1 DNA hypermethylation in leukocytes was associated with CVD risk profiles: high LDLC, high LDL/HDL ratio, and the degree of abnormal lipid metabolism.",
    url = "https://doi.org/10.5551/jat.43570",
    doi = "10.5551/jat.43570",
    openalex = "W2795766622",
    references = "doi101016b9780123808660600022, doi101016jmad200812003, doi10103835057062, doi101038nature05919, doi101038ng1089, doi101093nargki987, doi101093nargnh032, doi10116101res0000267856007130a, doi105551jat15792, openalexw2435745310"
}

@article{doi101016jfishres201901012,
    author = "Xue, Dong‐Xiu and Yang, Qiao-Li and Li, Yulong and Zong, Shaobing and Gao, Tianxiang and Liu, Jinxian",
    title = "Comprehensive assessment of population genetic structure of the overexploited Japanese grenadier anchovy (Coilia nasus): Implications for fisheries management and conservation",
    year = "2019",
    journal = "Fisheries Research",
    url = "https://doi.org/10.1016/j.fishres.2019.01.012",
    doi = "10.1016/j.fishres.2019.01.012",
    openalex = "W2913374103",
    references = "doi101016jbse201312022"
}

BACKGROUND: Seasonal migration is one of the most spectacular events in nature; however, the molecular mechanisms related to this phenomenon have not been investigated in detail. The Chinese tapertail, or Japanese grenadier anchovy, Coilia nasus, is a valuable migratory fish of high economic importance and special migratory dimorphism (with certain individuals as non-migratory residents). RESULTS: In this study, an 870.0-Mb high-quality genome was assembled by the combination of Illumina and Pacific Biosciences sequencing. Approximately 812.1 Mb of scaffolds were linked to 24 chromosomes using a high-density genetic map from a family of 104 full siblings and their parents. In addition, population sequencing of 96 representative individuals from diverse areas along the putative migration path identified 150 candidate genes, which are mainly enriched in 3 Ca2+-related pathways. Based on integrative genomic and transcriptomic analyses, we determined that the 3 Ca2+-related pathways are critical for promotion of migratory adaption. A large number of molecular markers were also identified, which distinguished migratory individuals and non-migratory freshwater residents. CONCLUSIONS: We assembled a chromosome-level genome for the Chinese tapertail anchovy. The genome provided a valuable genetic resource for understanding of migratory adaption and population genetics and will benefit the aquaculture and management of this economically important fish.

@article{doi101093gigasciencegiz157,
    author = "Xu, Gangchun and Bian, Chao and Nie, Zhijuan and Li, Jia and Wang, Yuyu and Xu, Dongpo and You, Xinxin and Liu, Hongbo and Gao, Jiancao and Li, Hongxia and Liu, Kai and Yang, Jian and Li, Quanjie and Shao, Nailin and Zhuang, Yanbing and Fang, Di‐An and Jiang, Tao and Lv, Yunyun and Huang, Yu and Gu, Ruobo and Xu, Junmin and Ge, Wei and Shi, Qiong and Xu, Pao",
    title = "Genome and population sequencing of a chromosome-level genome assembly of the Chinese tapertail anchovy (Coilia nasus) provides novel insights into migratory adaptation",
    year = "2020",
    journal = "GigaScience",
    abstract = "BACKGROUND: Seasonal migration is one of the most spectacular events in nature; however, the molecular mechanisms related to this phenomenon have not been investigated in detail. The Chinese tapertail, or Japanese grenadier anchovy, Coilia nasus, is a valuable migratory fish of high economic importance and special migratory dimorphism (with certain individuals as non-migratory residents). RESULTS: In this study, an 870.0-Mb high-quality genome was assembled by the combination of Illumina and Pacific Biosciences sequencing. Approximately 812.1 Mb of scaffolds were linked to 24 chromosomes using a high-density genetic map from a family of 104 full siblings and their parents. In addition, population sequencing of 96 representative individuals from diverse areas along the putative migration path identified 150 candidate genes, which are mainly enriched in 3 Ca2+-related pathways. Based on integrative genomic and transcriptomic analyses, we determined that the 3 Ca2+-related pathways are critical for promotion of migratory adaption. A large number of molecular markers were also identified, which distinguished migratory individuals and non-migratory freshwater residents. CONCLUSIONS: We assembled a chromosome-level genome for the Chinese tapertail anchovy. The genome provided a valuable genetic resource for understanding of migratory adaption and population genetics and will benefit the aquaculture and management of this economically important fish.",
    url = "https://doi.org/10.1093/gigascience/giz157",
    doi = "10.1093/gigascience/giz157",
    openalex = "W2997721182",
    references = "doi101016jbse201312022"
}

Metabolic syndrome (MetS) is cluster of metabolic diseases, including abdominal obesity, hyperglycemia, high blood pressure, and dyslipidemia, that directly escalate the risk of type 2 diabetes, heart disease, and stroke. Thioredoxin-interacting protein (TXNIP) is a binding protein for thioredoxin, a molecule that is a key inhibitor of cellular oxidation, and thus regulates the cellular redox state. Epigenetic alteration of the TXNIP-encoding locus has been associated with components of MetS. In the present study, we sought to determine whether the level of TXNIP methylation in blood is associated with MetS in the general Japanese population. DNA was extracted from the peripheral blood cells of 37 subjects with and 392 subjects without MetS. The level of TXNIP methylation at cg19693031 was assessed by the bisulfite-pyrosequencing method. We observed that TXNIP methylation levels were lower in MetS subjects (median 74.9%, range 71.7-78.4%) than in non-MetS subjects (median 77.7%, range 74.4-80.5%; p = 0.0024). Calculation of the confounding factor-adjusted odds ratios (ORs) and 95% confidence intervals (CIs) for hypomethylation revealed that subjects with MetS exhibited significantly higher ORs for hypomethylation than did those without MetS (OR, 2.92; 95% CI, 1.33-6.62; p = 0.009). Our findings indicated that lower levels of TXNIP methylation are associated with MetS in the general Japanese population. Altered levels of DNA methylation in TXNIP at cg19693031 might play an important role in the pathogenesis of MetS.

@article{doi101507endocrjej210339,
    author = "Yamazaki, Mirai and Yamada, Hiroya and Munetsuna, Eiji and Maeda, Keisuke and Ando, Yoshitaka and Mizuno, Genki and Fujii, Ryosuke and Tsuboi, Yoshiki and Ohashi, Koji and Ishikawa, Hiroaki and Hashimoto, Shuji and Hamajima, Nobuyuki and Suzuki, Koji",
    title = "DNA methylation level of the gene encoding thioredoxin-interacting protein in peripheral blood cells is associated with metabolic syndrome in the Japanese general population",
    year = "2021",
    journal = "Endocrine Journal",
    abstract = "Metabolic syndrome (MetS) is cluster of metabolic diseases, including abdominal obesity, hyperglycemia, high blood pressure, and dyslipidemia, that directly escalate the risk of type 2 diabetes, heart disease, and stroke. Thioredoxin-interacting protein (TXNIP) is a binding protein for thioredoxin, a molecule that is a key inhibitor of cellular oxidation, and thus regulates the cellular redox state. Epigenetic alteration of the TXNIP-encoding locus has been associated with components of MetS. In the present study, we sought to determine whether the level of TXNIP methylation in blood is associated with MetS in the general Japanese population. DNA was extracted from the peripheral blood cells of 37 subjects with and 392 subjects without MetS. The level of TXNIP methylation at cg19693031 was assessed by the bisulfite-pyrosequencing method. We observed that TXNIP methylation levels were lower in MetS subjects (median 74.9\%, range 71.7-78.4\%) than in non-MetS subjects (median 77.7\%, range 74.4-80.5\%; p = 0.0024). Calculation of the confounding factor-adjusted odds ratios (ORs) and 95\% confidence intervals (CIs) for hypomethylation revealed that subjects with MetS exhibited significantly higher ORs for hypomethylation than did those without MetS (OR, 2.92; 95\% CI, 1.33-6.62; p = 0.009). Our findings indicated that lower levels of TXNIP methylation are associated with MetS in the general Japanese population. Altered levels of DNA methylation in TXNIP at cg19693031 might play an important role in the pathogenesis of MetS.",
    url = "https://doi.org/10.1507/endocrj.ej21-0339",
    doi = "10.1507/endocrj.ej21-0339",
    openalex = "W3207480321",
    references = "doi105551jat43570"
}

Muskrat (Ondatra zibethicus) populations have been declining in North America for decades. The precise cause of these widespread declines has not yet been identified. Over a similar timeframe, wetlands across large regions of North America have been experiencing an invasion of hybrid cattail Typha x glauca. This invasion is associated with many negative consequences for wetlands, including a reduction in biodiversity, open water habitat, and interspersion of water and vegetation. Muskrats are strongly tied to wetlands, especially where there is a high degree of interspersion of water and emergent vegetation. Therefore, a widespread reduction in interspersion caused by T. x glauca invasions may be contributing to widespread muskrat population declines. We sought to better understand the impact of marsh interspersion on fine-scale muskrat habitat use in light of widespread invasions of T. x glauca. We measured intensity of habitat use by muskrats in a large, Typha-dominated marsh in south-central Ontario using camera traps, stratifying camera placement along a gradient of interspersion. We found no correlation between interspersion and intensity of use. The ubiquity of T. x glauca and low overall interspersion at our study site may have prevented a robust test of our hypothesis. Further research is needed to determine precisely how interspersion affects muskrat habitat use at a fine scale, and how potential changes in habitat quality and use may be contributing to widespread muskrat population declines.

@article{doi101002ece373155,
    author = "Melvin, Gregory P and Bowman, Jeff",
    title = "Marsh Interspersion and Muskrat (Ondatra zibethicus) Habitat Use.",
    year = "2026",
    journal = "Ecology and evolution",
    abstract = "Muskrat (Ondatra zibethicus) populations have been declining in North America for decades. The precise cause of these widespread declines has not yet been identified. Over a similar timeframe, wetlands across large regions of North America have been experiencing an invasion of hybrid cattail Typha x glauca. This invasion is associated with many negative consequences for wetlands, including a reduction in biodiversity, open water habitat, and interspersion of water and vegetation. Muskrats are strongly tied to wetlands, especially where there is a high degree of interspersion of water and emergent vegetation. Therefore, a widespread reduction in interspersion caused by T. x glauca invasions may be contributing to widespread muskrat population declines. We sought to better understand the impact of marsh interspersion on fine-scale muskrat habitat use in light of widespread invasions of T. x glauca. We measured intensity of habitat use by muskrats in a large, Typha-dominated marsh in south-central Ontario using camera traps, stratifying camera placement along a gradient of interspersion. We found no correlation between interspersion and intensity of use. The ubiquity of T. x glauca and low overall interspersion at our study site may have prevented a robust test of our hypothesis. Further research is needed to determine precisely how interspersion affects muskrat habitat use at a fine scale, and how potential changes in habitat quality and use may be contributing to widespread muskrat population declines.",
    url = "https://pmc.ncbi.nlm.nih.gov/articles/PMC12952997/",
    doi = "10.1002/ece3.73155",
    openalex = "W7133550852",
    pmcid = "PMC12952997",
    pmid = "41783353"
}