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F_ST between archaic and present-day samples.

ABSTRACT: The increasing abundance of DNA sequences obtained from fossils calls for new population genetics theory that takes account of both the temporal and spatial separation of samples. Here, we exploit the relationship between Wright's F_ST and average coalescence times to develop an analytic theory describing how F_ST depends on both the distance and time separating pairs of sampled genomes. We apply this theory to several simple models of population history. If there is a time series of samples, partial population replacement creates a discontinuity in pairwise F_ST values. The magnitude of the discontinuity depends on the extent of replacement. In stepping-stone models, pairwise F_ST values between archaic and present-day samples reflect both the spatial and temporal separation. At long distances, an isolation by distance pattern dominates. At short distances, the time separation dominates. Analytic predictions fit patterns generated by simulations. We illustrate our results with applications to archaic samples from European human populations. We compare present-day samples with a pair of archaic samples taken before and after a replacement event.

SUBMITTER: Ortega-Del Vecchyo D

PROVIDER: S-EPMC6781139 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature

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FST between archaic and present-day samples.

Ortega-Del Vecchyo Diego D Slatkin Montgomery M

Heredity 20181211 6

The increasing abundance of DNA sequences obtained from fossils calls for new population genetics theory that takes account of both the temporal and spatial separation of samples. Here, we exploit the relationship between Wright's FST and average coalescence times to develop an analytic theory describing how FST depends on both the distance and time separating pairs of sampled genomes. We apply this theory to several simple models of population history. If there is a time s ...[more]

PMID: 30538303

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Project description:PurposeRedlining was a discriminatory housing policy in the United States that began in 1933 and denoted neighborhoods with high proportions of Black individuals as "undesirable" and a high risk for lending, which therefore excluded people from obtaining traditional insured mortgages to purchase a home. Simultaneously, realtors discouraged Black individuals from purchasing homes in predominantly non-Black neighborhoods. This resulted in decreased home ownership and wealth accumulation among Black individuals and neighborhoods with high proportions of Black individuals. This study investigated rates of visual impairment and blindness (VIB) in neighborhoods that at one time were graded for redlining.DesignSecondary data analysis of American Community Survey data and historical grades for redlining.ParticipantsUnited States census tracts (CTs) from 2010 with historical grades for redlining.MethodsOne-way analysis of variance, Kruskal-Wallis test, chi-square test, and logistic regression modeling.Main outcome measuresThe main outcome was CT percentage of residents reporting VIB and the association with historical grades for redlining. Grades were converted to numeric values (1 to 4, with higher values indicating worse grade) and aggregated over a CT based on the distribution of grades within to obtain a redlining score. Logistic regression was used to model the effect of redlining on the probability of having VIB.ResultsEleven thousand six hundred sixty-eight CTs were analyzed. Logistic regression found that a 1-unit increase in average redlining score was associated with a 13.4% increased odds of VIB after controlling for CT measures of age, sex, people of color (any non-White race), state, and population size (odds ratio [OR], 1.134; 95% confidence interval [CI], 1.131-1.138; P < 0.001). Similar results were observed for an additional model that adjusted for the estimated percentage of Black residents within a CT (OR, 1.180; 95% CI, 1.177-1.183; P < 0.001).ConclusionsHistorical government-sanctioned residential segregation through redlining was found to be associated with higher proportions of people living with VIB in these neighborhoods today. Understanding how neighborhood segregation impacts eye health is important for planning improved mechanisms of eye care delivery to mitigate health disparities.Financial disclosure(s)Proprietary or commercial disclosure may be found after the references.

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F_ST between archaic and present-day samples.

Publications

F<sub>ST</sub> between archaic and present-day samples.

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