A free lunch: microhaplotype discovery in an existing amplicon panel improves parentage assignment for the highly polymorphic Pacific oyster DOI Creative Commons
Neil F. Thompson, Ben Sutherland, Timothy J. Green

et al.

G3 Genes Genomes Genetics, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 19, 2024

Abstract Amplicon panels using genotyping by sequencing methods are now common, but have focused on characterizing SNP markers. We investigate how microhaplotype (MH) discovery within a recently developed Pacific oyster (Magallana gigas) amplicon panel could increase the statistical power for relationship assignment. Trios (offspring and two parents) from three populations in newly established breeding program were genotyped 592 locus panel. After processing, 92% of retained amplicons contained polymorphic MH variants 85% monomorphic markers variation. The increased allelic richness resulted substantially improved assignment with much lower estimated false positive rates. No substantive differences accuracy occurred between datasets, MHs separation log-likelihood values true parents highly related potential (aunts uncles). A high number Mendelian incompatibilities among trios observed, likely due to null alleles. Further development panel, including removing loci rates alleles, would enable high-throughput reducing size therefore cost research programs.

Language: Английский

Tracking the Origin of Raccoon (Procyon lotor) Translocations in Northeastern North America Using Population Genetics DOI
Matthew W. Hopken,

Brian Bjorklund,

Clara Mankowski

et al.

Northeastern Naturalist, Journal Year: 2025, Volume and Issue: 31(4)

Published: Jan. 8, 2025

Human activities have altered natural dispersal patterns of many wildlife species through intentional and accidental translocations. We used population genetics to detect recent long-distance translocations Procyon lotor (Raccoon) in northeastern North America. Three Raccoons were collected on 2 islands off the US New England coast, with suspected origins southeastern Canada. RADcapture genotype 1000 microhaplotypes assign animals source locations comparison 563 genotypes from The 3 assigned populations associated US–Canada border region. Our results add sparse scientific literature Raccoon translocations, highlighting utility for detecting movements implications disease management.

Language: Английский

Citations

0
Evaluation of contingency actions to control the spread of raccoon rabies in Ohio and Virginia DOI Creative Commons
Amy J. Davis, Richard B. Chipman,

Kathleen M. Nelson

et al.

Preventive Veterinary Medicine, Journal Year: 2024, Volume and Issue: 225, P. 106145 - 106145

Published: Feb. 9, 2024

The raccoon (Procyon lotor) variant of the rabies virus (RRV) is enzootic in eastern United States and oral vaccination (ORV) primary strategy to prevent control landscape spread. Breaches ORV management zones occasionally occur, emergency "contingency" actions may be implemented enhance local control. Contingency are an integral part landscape-scale wildlife but can very costly routinely involve enhanced surveillance (ERS) around index case. We investigated two contingency Ohio (2017-2019 2018-2021) one Virginia (2017-2019) using a dynamic, multi-method occupancy approach examine relationships between specific RRV occurrence, including whether ERS was sufficient assessed seasonally at 100-km

Language: Английский

Citations

3
Are rabid raccoons (Procyon lotor) ready for the rapture? Determining the geographic origin of rabies virus‐infected raccoons using RADcapture and microhaplotypes DOI Creative Commons
Matthew W. Hopken, Antoinette J. Piaggio, Zaid Abdo

et al.

Evolutionary Applications, Journal Year: 2023, Volume and Issue: 16(12), P. 1937 - 1955

Published: Nov. 20, 2023

North America is recognized for the exceptional richness of rabies virus (RV) wildlife reservoir species. Management RV accomplished through vaccination targeting mesocarnivore populations, such as raccoon (

Language: Английский

Citations

4
A free lunch: microhaplotype discovery in an existing amplicon panel improves parentage assignment for the highly polymorphic Pacific oyster DOI Creative Commons
Neil F. Thompson, Ben Sutherland, Timothy J. Green

et al.

G3 Genes Genomes Genetics, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 19, 2024

Abstract Amplicon panels using genotyping by sequencing methods are now common, but have focused on characterizing SNP markers. We investigate how microhaplotype (MH) discovery within a recently developed Pacific oyster (Magallana gigas) amplicon panel could increase the statistical power for relationship assignment. Trios (offspring and two parents) from three populations in newly established breeding program were genotyped 592 locus panel. After processing, 92% of retained amplicons contained polymorphic MH variants 85% monomorphic markers variation. The increased allelic richness resulted substantially improved assignment with much lower estimated false positive rates. No substantive differences accuracy occurred between datasets, MHs separation log-likelihood values true parents highly related potential (aunts uncles). A high number Mendelian incompatibilities among trios observed, likely due to null alleles. Further development panel, including removing loci rates alleles, would enable high-throughput reducing size therefore cost research programs.

Language: Английский

Citations

1