Statistical methods for identifying hybrids and groups

Anderson, Eric C.; Bertorelle, Giorgio; Bruford, Michael William; Hauffe, Heidi C.; Rizzoli, Annapaola; Vernesi, Cristiano

doi:10.1017/cbo9780511626920.003

Cited by 9 publications

(9 citation statements)

References 8 publications

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“…Because the power of detection of late hybrid generations is limited3435 we did not attempted to distinguish those different classes and treated them in this study as a single group of late-hybrids36. A considerable amount of genetic data is required to distinguish genealogical classes and it is very difficult to accurately resolve further genealogical classes or second-backcrossed hybrids with NEWHYBRIDS or any other Bayesian Program37. NEWHYBRIDS analyses were based on the same computational parameters as those conducted in STRUCTURE using a threshold of q = 0.90.…”

Section: Methodsmentioning

confidence: 99%

Past climate changes facilitated homoploid speciation in three mountain spiny fescues (Festuca, Poaceae)

Marques

Draper²,

López-Herránz

et al. 2016

Sci Rep

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Apart from the overwhelming cases of allopolyploidization, the impact of speciation through homoploid hybridization is becoming more relevant than previously thought. Much less is known, however, about the impact of climate changes as a driven factor of speciation. To investigate these issues, we selected Festuca picoeuropeana, an hypothetical natural hybrid between the diploid species F. eskia and F. gautieri that occurs in two different mountain ranges (Cantabrian Mountains and Pyrenees) separated by more than 400 km. To unravel the outcomes of this mode of speciation and the impact of climate during speciation we used a multidisciplinary approach combining genome size and chromosome counts, data from an extensive nuclear genotypic analysis, plastid sequences and ecological niche models (ENM). Our results show that the same homoploid hybrid was originated independently in the two mountain ranges, being currently isolated from both parents and producing viable seeds. Parental species had the opportunity to contact as early as 21000 years ago although niche divergence occurs nowadays as result of a climate-driven shift. A high degree of niche divergence was observed between the hybrid and its parents and no recent introgression or backcrossed hybrids were detected, supporting the current presence of reproductive isolation barriers between these species.

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Section: Methodsmentioning

confidence: 99%

Past climate changes facilitated homoploid speciation in three mountain spiny fescues (Festuca, Poaceae)

Marques

Draper²,

López-Herránz

et al. 2016

Sci Rep

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Section: Introductionmentioning

confidence: 99%

“…The identification of hybrids and the ability to determine the presence, types and numbers of individuals of different hybrid classes can provide crucial information on the presence, magnitude and timescale over which introgression is occurring. While several statistical approaches [reviewed by (Anderson 2009;Payseur & Rieseberg 2016)] and software programs exist [e.g. STRUCTURE (Hubisz et al 2009); NEWHYBRIDS (Anderson & Thompson 2002); BAYESASS (Wilson & Rannala 2003); GENODIVE (Meirmans & Van Tienderen 2004), which uses the maximum-likelihood method of (Buerkle 2005)] to identify hybrids, most do not assign to hybrid class, thus losing potentially important information.…”

Section: Introductionmentioning

confidence: 99%

parallelnewhybrid: an R package for the parallelization of hybrid detection using newhybrids

Wringe

Stanley

Jeffery

et al. 2016

Molecular Ecology Resources

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Hybridization among populations and species is a central theme in many areas of biology, and the study of hybridization has direct applicability to testing hypotheses about evolution, speciation and genetic recombination, as well as having conservation, legal and regulatory implications. Yet, despite being a topic of considerable interest, the identification of hybrid individuals, and quantification of the (un)certainty surrounding the identifications, remains difficult. Unlike other programs that exist to identify hybrids based on genotypic information, newhybrids is able to assign individuals to specific hybrid classes (e.g. F , F ) because it makes use of patterns of gene inheritance within each locus, rather than just the proportions of gene inheritance within each individual. For each comparison and set of markers, multiple independent runs of each data set should be used to develop an estimate of the hybrid class assignment accuracy. The necessity of analysing multiple simulated data sets, constructed from large genomewide data sets, presents significant computational challenges. To address these challenges, we present parallelnewhybrid, an r package designed to decrease user burden when undertaking multiple newhybrids analyses. parallelnewhybrid does so by taking advantage of the parallel computational capabilities inherent in modern computers to efficiently and automatically execute separate newhybrids runs in parallel. We show that parallelization of analyses using this package affords users several-fold reductions in time over a traditional serial analysis. parallelnewhybrid consists of an example data set, a readme and three operating system-specific functions to execute parallel newhybrids analyses on each of a computer's c cores. parallelnewhybrid is freely available on the long-term software hosting site github (www.github.com/bwringe/parallelnewhybrid).

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“…The model-based approach described by Anderson and Thompson (2002) and Anderson (2009) and implemented in the program NEWHYBRIDS was used to assign each individual to one of the two parental classes (tule or URB) or to one of several hybrid classes (F 1 , F 2 , or backcross) based on their microsatellite genotypes. This model is similar to other clustering algorithms but also takes into account known patterns of Mendelian inheritance to assign posterior probabilities that each individual in a data set belongs to each potential class.…”

Section: Hybrid Detectionmentioning

confidence: 99%

“…This model is similar to other clustering algorithms but also takes into account known patterns of Mendelian inheritance to assign posterior probabilities that each individual in a data set belongs to each potential class. This model does not require fixed allelic differences between parental classes (Anderson and Thompson 2002); however, analysis of simulated data has been advocated as a means of evaluating assignment accuracy for any given study (Anderson 2009).…”

Section: Hybrid Detectionmentioning

confidence: 99%

Persistent Reproductive Isolation between Sympatric Lineages of Fall Chinook Salmon in White Salmon River, Washington

Smith

Engle

2011

Trans Am Fish Soc

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Populations of fall Chinook salmon Oncorhynchus tshawytscha in the Columbia River are divided among two evolutionarily significant units: lower Columbia River fall Chinook salmon (or “tules”) in the lower portion of the river and upriver “brights” (URBs) in the upper portion. The two lineages migrate together through portions of the lower Columbia River but spawn allopatrically. Little White Salmon National Fish Hatchery has been releasing URBs adjacent to what was historically exclusively tule spawning habitat in the White Salmon River for approximately 22 years. Tules and URBs now spawn in sympatry in the adjacent White Salmon River, and potential introgression between these two lineages has been identified as a genetic risk of the hatchery program. To assess the extent of introgression, we analyzed 13 microsatellite loci in juveniles taken from the White Salmon River in three consecutive years. Assignment tests revealed that juveniles leaving the White Salmon River from March to early May resembled tules, while those leaving from late May to June resembled URBs. Model‐based hybrid detection revealed that between 4.3% and 15.0% of the juveniles in each year were tule × URB hybrids. No hybrid adults were detected in any of the collections examined. The divergence between the tule and URB populations in the White Salmon River was comparable to that between allopatric populations representing the two lineages. Although hybrid juveniles are produced in the wild, we found no evidence that they survive to return as adults or successfully cross back into the parental populations. The separation between the two fall Chinook salmon lineages thus appears to be based on intrinsic as well as extrinsic factors.

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Statistical methods for identifying hybrids and groups

Cited by 9 publications

References 8 publications

Past climate changes facilitated homoploid speciation in three mountain spiny fescues (Festuca, Poaceae)

Past climate changes facilitated homoploid speciation in three mountain spiny fescues (Festuca, Poaceae)

parallelnewhybrid: an R package for the parallelization of hybrid detection using newhybrids

Persistent Reproductive Isolation between Sympatric Lineages of Fall Chinook Salmon in White Salmon River, Washington

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