Model-based genotype and ancestry estimation for potential hybrids with mixed-ploidy

Shastry, Vivaswat; Adams, Paula E; Lindtke, Dorothea; Mandeville, Elizabeth G.; Gompert, Zachariah; Buerkle, C. Alex

doi:10.22541/au.159647051.17812698

Cited by 18 publications

(34 citation statements)

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“…Pure individuals have Q 12 = 0 because their parents contributed the same ancestry to their offspring's genome, whereas F 1 hybrids have Q 12 = 1 because their parents each contributed different ancestries. Further, F 2 hybrids have on average Q 12 = 0.5 because recombination results in a genome consisting of roughly equal parts same‐source and intersource ancestry, and previously published simulations have demonstrated that backcrossed individuals reside on lines drawn between F 1 hybrids ( Q 12 = 1.0; q = 0.5) and parental individuals ( Q 12 = 0; q = 0 or 1) (Lindtke et al, 2014; Shastry et al, 2021). The distinction between F 1 and F 2 hybrids is particularly relevant in the context of postzygotic incompatibilities in F 2 hybrids because they have recombinant genomes (i.e., chromosomes contain ancestry from both parental species), which could impose lower fitness relative to F 1 or parental individuals (Barton, 2001; Dobzhansky, 1970; Maheshwari & Barbash, 2011).…”

Section: Methodsmentioning

confidence: 99%

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Multigenerational backcrossing and introgression between two woodrat species at an abrupt ecological transition

Jahner

Matocq

2021

Molecular Ecology

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When organisms experience secondary contact after allopatric divergence, genomic regions can introgress differentially depending on their relationships with adaptation, reproductive isolation, recombination, and drift. Analyses of genome‐wide patterns of divergence and introgression could provide insight into the outcomes of hybridization and the potential relationship between allopatric divergence and reproductive isolation. Here, we generate population genetic data (26,262 SNPs; 353 individuals) using a reduced‐representation sequencing approach to quantify patterns of ancestry, differentiation, and introgression between a pair of ecologically distinct mammals—the desert woodrat (N. lepida) and Bryant's woodrat (N. bryanti)—that hybridize at a sharp ecotone in southern California. Individual ancestry estimates confirmed that hybrids were rare in this bimodal hybrid zone, and entirely consisted of a few F1 individuals and a broad range of multigenerational backcrosses. Genomic cline analyses indicated more than half of loci had elevated introgression from one genomic background into the other. However, introgression was not associated with relative or absolute measures of divergence, and loci with extreme values for both were not typically found near detoxification enzymes previously implicated in dietary specialization for woodrats. The decoupling of differentiation and introgression suggests that processes other than adaptation, such as drift, may underlie the extreme clines at this contact zone.

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Section: Methodsmentioning

confidence: 99%

“…See Figure for estimates of uncertainty. (c) Individual ancestry classes were assigned based on estimates of ancestry coefficients ( q ) and interspecific ancestry ( Q 12 ) generated with entropy (Gompert et al, 2014; Shastry et al, 2021). Pure parental N .…”

Section: Introductionmentioning

confidence: 99%

Multigenerational backcrossing and introgression between two woodrat species at an abrupt ecological transition

Jahner

Matocq

2021

Molecular Ecology

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“…We quantified population structure without a priori sample information using the Bayesian ancestry-based model entropy v1.2 56 , 57 which is based on the correlated allele frequency model of structure 58 . We used entropy to infer the number of k ancestral populations represented by the data and to estimate admixture proportions ( q ) for individuals.…”

Section: Methodsmentioning

confidence: 99%

Hierarchical genetic structure and implications for conservation of the world’s largest salmonid, Hucho taimen

Galland

Simmons

Jahner

et al. 2021

Sci Rep

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Population genetic analyses can evaluate how evolutionary processes shape diversity and inform conservation and management of imperiled species. Taimen (Hucho taimen), the world’s largest freshwater salmonid, is threatened, endangered, or extirpated across much of its range due to anthropogenic activity including overfishing and habitat degradation. We generated genetic data using high throughput sequencing of reduced representation libraries for taimen from multiple drainages in Mongolia and Russia. Nucleotide diversity estimates were within the range documented in other salmonids, suggesting moderate diversity despite widespread population declines. Similar to other recent studies, our analyses revealed pronounced differentiation among the Arctic (Selenge) and Pacific (Amur and Tugur) drainages, suggesting historical isolation among these systems. However, we found evidence for finer-scale structure within the Pacific drainages, including unexpected differentiation between tributaries and the mainstem of the Tugur River. Differentiation across the Amur and Tugur basins together with coalescent-based demographic modeling suggests the ancestors of Tugur tributary taimen likely diverged in the eastern Amur basin, prior to eventual colonization of the Tugur basin. Our results suggest the potential for differentiation of taimen at different geographic scales, and suggest more thorough geographic and genomic sampling may be needed to inform conservation and management of this iconic salmonid.

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“…We used the EM acceleration method in EMU, using 10 eigenvectors for optimization (-e 10) with a maximum of 100 optimization iterations and keeping all eigenvectors as output. We then inferred species groups using the model-based genetic clustering program entropy (Gompert et al 2014;Shastry et al 2021). Entropy infers population structure from multilocus SNP data by assigning individuals partially or completely to groups using Bayesian estimation from genotype likelihoods.…”

Section: Species Assignmentmentioning

confidence: 99%

The genetic population structure of Lake Tanganyika’sLatesspecies flock, an endemic radiation of pelagic top predators

Junker

Kimirei

et al. 2021

Preprint

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Life history traits are important factors in shaping gene flow within species, and these traits can thus be determinants of whether a species exhibits genetic homogeneity across its range, or considerable population structure. Furthermore, understanding genetic connectivity plays crucially into species conservation decisions, and genetic connectivity is an important component of modern fisheries management in fishes exploited for human consumption. In this study, we investigated the four endemic Lates species of Lake Tanganyika (Lates stappersii, L. microlepis, L. mariae and L. angustifrons), sampled along the Tanzanian shoreline, using reduced-representation genomic sequencing methods. Based on previous studies, we predicted little genetic population structure in the entirely pelagic L. stappersii and the predominantly pelagic L. microlepis. In contrast, we expected the highest genetic differentiation in populations of L. mariae, which is the most resident and for which females aggregate over spawning grounds. We predicted that L. angustifrons would show intermediate structure. We indeed find the most strongly differentiated genetic clusters in L. mariae. However, contrary to our predictions, we find evidence for genetically distinct (albeit weakly differentiated) groups within the pelagic L. stappersii and L. microlepis, and no genetic structure in L. angustifrons. We call for management approaches accounting for genetically differentiated populations of L. stappersii, L. microlepis, and L. mariae, which are commercially important species in the region.

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Model-based genotype and ancestry estimation for potential hybrids with mixed-ploidy

Cited by 18 publications

References 0 publications

Multigenerational backcrossing and introgression between two woodrat species at an abrupt ecological transition

Multigenerational backcrossing and introgression between two woodrat species at an abrupt ecological transition

Hierarchical genetic structure and implications for conservation of the world’s largest salmonid, Hucho taimen

The genetic population structure of Lake Tanganyika’sLatesspecies flock, an endemic radiation of pelagic top predators

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