New Software for the Fast Estimation of Population Recombination Rates (FastEPRR) in the Genomic Era

Recombination has essential roles in increasing genetic variability within a population and in ensuring successful meiotic events. The objective of this study is to (i) infer the population scaled recombination rate (ρ), and (ii) identify and characterize localities of increased recombination rate for the domestic cat, Felis silvestris catus. SNPs (n = 701) were genotyped in twenty-two cats of Eastern random bred origin. The SNPs covered ten different chromosomal regions (A1, A2, B3, C2, D1, D2, D4, E2, F2, X) with an average region size of 850 Kb and an average SNP density of 70 SNPs/region. The Bayesian method in the program inferRho was used to infer regional population recombination rates and hotspots localities. The regions exhibited variable population recombination rates and four decisive recombination hotspots were identified on cat chromosome A2, D1, and E2 regions. No correlation was detected between the GC content and the locality of recombination spots. The hotspots enclosed L2 LINE elements and MIR and tRNA-Lys SINE elements in agreement with hotspots found in other mammals.

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Corrigendum to: Fast Estimation of Recombination Rates Using Topological Data Analysis

Genetics ◽

10.1093/genetics/iyab194 ◽

2021 ◽

Author(s):

Devon P Humphreys ◽

Melissa R McGuirl ◽

Miriam Miyagi ◽

Andrew J Blumberg

Keyword(s):

Data Analysis ◽

Topological Data Analysis ◽

Recombination Rates ◽

Fast Estimation ◽

Topological Data

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Fast Estimation of Recombination Rates Using Topological Data Analysis

Genetics ◽

10.1534/genetics.118.301565 ◽

2019 ◽

Vol 211 (4) ◽

pp. 1191-1204 ◽

Cited By ~ 6

Author(s):

Devon P. Humphreys ◽

Melissa R. McGuirl ◽

Michael Miyagi ◽

Andrew J. Blumberg

Keyword(s):

Data Analysis ◽

Topological Data Analysis ◽

Recombination Rates ◽

Fast Estimation ◽

Topological Data

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A Comparison of Linkage Disequilibrium Patterns and Estimated Population Recombination Rates across Multiple Populations

The American Journal of Human Genetics ◽

10.1086/429274 ◽

2005 ◽

Vol 76 (4) ◽

pp. 681-687 ◽

Cited By ~ 78

Author(s):

David M. Evans ◽

Lon R. Cardon

Keyword(s):

Linkage Disequilibrium ◽

Recombination Rates ◽

Multiple Populations ◽

Population Recombination

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Recombination and the power of statistical tests of neutrality

Genetics Research ◽

10.1017/s0016672399003870 ◽

1999 ◽

Vol 74 (1) ◽

pp. 65-79 ◽

Cited By ~ 134

Author(s):

JEFFREY D. WALL

Keyword(s):

Balancing Selection ◽

Statistical Tests ◽

Neutral Theory ◽

Population Subdivision ◽

Test Statistics ◽

Recombination Rates ◽

Tests Of Neutrality ◽

Power Studies ◽

New Statistics ◽

Population Recombination

Two new test statistics were constructed to detect departures from the equilibrium neutral theory that tend to produce genealogies with longer internal branches (e.g. population subdivision or balancing selection). The new statistics are based on a measure of linkage disequilibrium between adjacent pairs of segregating sites. Simulations were run to determine the power of these and previously proposed test statistics to reject an island model of geographic subdivision. Unlike previous power studies, this one uses a coalescent model with recombination. It is found that recombination rates on the order of the mutation rate substantially reduce the power of most test statistics, and that one of the new test statistics is generally more powerful than the others. Two suggestions are made for increasing the power of the statistical tests examined here. First, they can be made more powerful if critical values are obtained from simulations that condition on a lower bound for the population recombination rate. Secondly, for the same total length sequenced, power is increased if independent loci are considered instead of a single contiguous stretch.

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