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Protocols

NewHybrids specifications

Information


Unique identifier OMICS_20132
Name NewHybrids
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 1.1
Stability Beta
Requirements
GFMCMC library
Source code URL http://ib.berkeley.edu/labs/slatkin/eriq/software/EricCode.tgz
Maintained Yes

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Documentation


Maintainer


  • person_outline Eric C. Anderson

Publication for NewHybrids

NewHybrids citations

 (140)
call_split

Hybridization and differential introgression associated with environmental shifts in a mistletoe species complex

2018
Sci Rep
PMCID: 5882953
PMID: 29615778
DOI: 10.1038/s41598-018-23707-6
call_split See protocol

[…] lated and performed ten replicates with 100 000 MCMC after 50 000 burning period. The outputs of each replicate were combined in CLUMPP for visualization.We then used the Bayesian model-based program NEWHYBRIDS to calculate the posterior probability of individuals belonging to one of six categories: (1) pure CALY, (2) pure SCHI, (3) first generation hybrids, (4) second generation hybrids, (5) CALY […]

call_split

Introgression among three rockfish species (Sebastes spp.) in the Salish Sea, northeast Pacific Ocean

2018
PLoS One
PMCID: 5864001
PMID: 29566070
DOI: 10.1371/journal.pone.0194068
call_split See protocol

[…] ates are similar among species.Hybrids in coastal and Salish Sea populations of S. auriculatus, S. caurinus, and S. maliger were identified with Structure version 2.3.3 [, ]. We evaluated the program NewHybrids [] to identify hybrids as well, but power was low due to the limited number of loci, and the hybrid class distinctions would not further objectives. Sequence data were formatted using xmfa2 […]

call_split

Cleaner fish escape salmon farms and hybridize with local wrasse populations

2018
R Soc Open Sci
PMCID: 5882703
PMID: 29657779
DOI: 10.1098/rsos.171752
call_split See protocol

[…] ased on the genotype frequencies from the 200 loci in the western (PureA = Austevoll and Stavanger) and southern (PureB = Kristiansand, Strömstad and Kungsbacka) samples. Simulations were analysed in NEWHYBRIDS v. 1.1 [] which estimates the posterior probability of each individual to belong to one of the six hybrid classes. The analysis was done using the uniform prior option and default genotype […]

call_split

Population genetic structure, introgression, and hybridization in the genus Rhizophora along the Brazilian coast

2018
Ecol Evol
PMCID: 5869270
PMID: 29607041
DOI: 10.1002/ece3.3900
call_split See protocol

[…] ore function to balance discrimination power and overfitting.To identify and classify eventual two‐generation hybrids as F1s, F2s or backcrosses, we used a different model‐based method implemented in NewHybrids 1.1 (Anderson & Thompson, ). We performed 10 independent MCMC runs with 500,000 steps following a burn‐in period of 100,000 iterations for different prior distribution combinations. We perf […]

call_split

Single nucleotide polymorphisms in native South American Atlantic coast populations of smooth shelled mussels: hybridization with invasive European Mytilus galloprovincialis

2018
PMCID: 5824471
PMID: 29471805
DOI: 10.1186/s12711-018-0376-z
call_split See protocol

[…] than any other assignment probability to any other group.Following preliminary analyses that indicated that the Argentinian population of Puerto Madryn (PMD) contained possible hybrids, the software NewHybrids v1 [] was used to estimate the posterior probability that individuals from PMD fell into each of the six genotypic categories (or classes corresponding to hybrid categories): native M. plat […]

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Cryptic genetic diversity in the mottled rabbitfish Siganus fuscescens with mitochondrial introgression at a contact zone in the South China Sea

2018
PLoS One
PMCID: 5821360
PMID: 29466431
DOI: 10.1371/journal.pone.0193220

[…] (0.1 < q < 0.9) and potential hybrid ancestry for 13 individuals. The majority (N = 10) of the putative hybrids were in the HKG sample, with 1 and 2 putative hybrids in SNF and MOR, respectively. The NEWHYBRIDS algorithm however identified only 7 of the 13 individuals having mixed ancestry in STRUCTURE as putative hybrids. All 7 individuals (marked in ) were categorized as F2 hybrids: 4 from sampl […]


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NewHybrids institution(s)
Department of Statistics, University of Washington, Seattle, WA, USA
NewHybrids funding source(s)
National Science Foundation grant BIR-9807747

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