Easy-to-use R functions to separate reduced-representation genomic datasets into sex-linked and autosomal loci, and conduct sex-assignment

Robledo‐Ruiz, Diana A.; Austin, Lana; Amos, J. Nevil; Castrejón-Figureoa, Jesús; Magrath, Michael J. L.; Sunnucks, Paul; Pavlova, Alexandra

doi:10.22541/au.166998603.34117027/v1

Cited by 3 publications

(4 citation statements)

References 45 publications

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“…Genotypes were filtered by removing individuals with >30% of missing data, loci with reproducibility <95%, loci missing in >20% of individuals and monomorphic loci. We further removed loci likely to represent incorrectly merged loci (78 loci with heterozygosity significantly ( p < 0.05) larger than the maximum expected value of 0.5 in either Cotter or Cataract populations) using R function filter.excess.het (Robledo‐Ruiz et al., 2023). We did not apply the function to the Cotter‐only dataset where multi‐age group/cohorts represented populations because excess of heterozygosity could result from admixture between previously isolated populations (Wahlund‐breaking), a suspected outcome of the 2013 Cotter Reservoir expansion.…”

Section: Methodsmentioning

confidence: 99%

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Planning and implementing genetic rescue of an endangered freshwater fish population in a regulated river, where low flow reduces breeding opportunities and may trigger inbreeding depression

Pavlova,

Schneller,

Lintermans

et al. 2024

Evolutionary Applications

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Augmenting depleted genetic diversity can improve the fitness and evolutionary potential of wildlife populations, but developing effective management approaches requires genetically monitored test cases. One such case is the small, isolated and inbred Cotter River population of an endangered Australian freshwater fish, the Macquarie perch Macquaria australasica, which over 3 years (2017–2019) received 71 translocated migrants from a closely related, genetically more diverse population. We used genetic monitoring to test whether immigrants bred, interbred with local fish and augmented population genetic diversity. We also investigated whether levels of river flow affected recruitment, inbreeding depression and juvenile dispersal. Fish length was used to estimate the age, birth year cohort and growth of 524 individuals born between 2016 and 2020 under variable flow conditions. DArT genome‐wide genotypes were used to assess individual ancestry, heterozygosity, short‐term effective population size and identify parent‐offspring and full‐sibling families. Of 442 individuals born after translocations commenced, only two (0.45%) were of mixed ancestry; these were half‐sibs with one translocated parent in common. Numbers of breeders and genetic diversity for five birth year cohorts of the Cotter River fish were low, especially in low‐flow years. Additionally, individuals born in the year of lowest flow evidently suffered from inbreeding depression for juvenile growth. The year of highest flow was associated with the largest number of breeders, lowest inbreeding in the offspring and greatest juvenile dispersal distances. Genetic diversity decreased in the upstream direction, flagging restricted access of breeders to the most upstream breeding sites, exacerbated by low river flow. Our results suggest that the effectiveness of translocations could be increased by focussing on upstream sites and moving more individuals per year; using riverine sources should be considered. Our results indicate that river flow sufficient to facilitate fish movement through the system would increase the number of breeders, promote individuals' growth, reduce inbreeding depression and promote genetic rescue.

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Section: Methodsmentioning

confidence: 99%

“…Smaller per‐cohort Colony2 datasets were also created using the above filtering criteria. R function gl2colony (Robledo‐Ruiz et al., 2023) was used to create Colony2 input files within R.…”

Section: Methodsmentioning

confidence: 99%

Planning and implementing genetic rescue of an endangered freshwater fish population in a regulated river, where low flow reduces breeding opportunities and may trigger inbreeding depression

Pavlova,

Schneller,

Lintermans

et al. 2024

Evolutionary Applications

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show abstract

“…While SeXY can perform sexing with a single individual at low depth and was tailored to also work with reference genomes of divergent taxa, its sexing is based on arbitrary thresholds. Other methods (Gautier, 2014; Robledo‐Ruiz et al., 2023) can also infer both sex and sex‐linked loci but are designed for SNP data sets (e.g. RAD sequencing) and classify each locus individually.…”

Section: Introductionmentioning

confidence: 99%

Accurate Bayesian inference of sex chromosome karyotypes and sex‐linked scaffolds from low‐depth sequencing data

Caduff,

Eckel,

Leuenberger

et al. 2024

Molecular Ecology Resources

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The identification of sex‐linked scaffolds and the genetic sex of individuals, i.e. their sex karyotype, is a fundamental step in population genomic studies. If sex‐linked scaffolds are known, single individuals may be sexed based on read counts of next‐generation sequencing data. If both sex‐linked scaffolds as well as sex karyotypes are unknown, as is often the case for non‐model organisms, they have to be jointly inferred. For both cases, current methods rely on arbitrary thresholds, which limits their power for low‐depth data. In addition, most current methods are limited to euploid sex karyotypes (XX and XY). Here we develop BeXY, a fully Bayesian method to jointly infer the posterior probabilities for each scaffold to be autosomal, X‐ or Y‐linked and for each individual to be any of the sex karyotypes XX, XY, X0, XXX, XXY, XYY and XXYY. If the sex‐linked scaffolds are known, it also identifies autosomal trisomies and estimates the sex karyotype posterior probabilities for single individuals. As we show with downsampling experiments, BeXY has higher power than all existing methods. It accurately infers the sex karyotype of ancient human samples with as few as 20,000 reads and accurately infers sex‐linked scaffolds from data sets of just a handful of samples or with highly imbalanced sex ratios, also in the case of low‐quality reference assemblies. We illustrate the power of BeXY by applying it to both whole‐genome shotgun and target enrichment sequencing data of ancient and modern humans, as well as several non‐model organisms.

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“…While SeXY can perform sexing with a single individual at low depth and was tailored to also work with reference genomes of divergent taxa, its sexing is based on arbitrary thresholds. Other methods (Robledo-Ruiz et al, 2023;Gautier, 2014) can also infer both sex and sex-linked loci but are designed for SNP data sets (e.g. RAD sequencing) and classify each locus individually.…”

Section: Introductionmentioning

confidence: 99%

Accurate Bayesian inference of sex chromosome karyotypes and sex-linked scaffolds from low-depth sequencing data

Caduff,

Eckel,

Leuenberger

et al. 2023

Preprint

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The identification of sex-linked scaffolds and the genetic sex of individuals, i.e. their sex karyotype, is a fundamental step in population genomic studies. If sex-linked scaffolds are known, single individuals may be sexed based on read counts of next-generation sequencing data. If both sex-linked scaffolds as well as sex karyotypes are unknown, as is often the case for non-model organisms, they have to be jointly inferred. For both cases, current methods rely on arbitrary thresholds, which limits their power for low-depth data. In addition, most current methods are limited to euploid sex karyotypes (XX and XY). Here we develop BeXY, a fully Bayesian method to jointly infer the posterior probabilities for each scaffold to be autosomal, X- or Y-linked and for each individual to be any of the sex karyotypes XX, XY, X0, XXX, XXY, XYY and XXYY. If the sex-linked scaffolds are known, it estimates the sex karyotype posterior probabilities also for single individuals. As we show with downsampling experiments, BeXY has higher power than all existing methods. It accurately infers the sex karyotype of ancient human samples with as few as 20,000 reads and accurately infers sex-linked scaffolds from data sets of just a handful of samples or with highly imbalanced sex ratios, also in the case of low-quality reference assemblies. We illustrate the power of BeXY by applying it to both whole-genome shotgun and target enrichment sequencing data of ancient humans as well as several non-model organisms.

show abstract

Easy-to-use R functions to separate reduced-representation genomic datasets into sex-linked and autosomal loci, and conduct sex-assignment

Cited by 3 publications

References 45 publications

Planning and implementing genetic rescue of an endangered freshwater fish population in a regulated river, where low flow reduces breeding opportunities and may trigger inbreeding depression

Planning and implementing genetic rescue of an endangered freshwater fish population in a regulated river, where low flow reduces breeding opportunities and may trigger inbreeding depression

Accurate Bayesian inference of sex chromosome karyotypes and sex‐linked scaffolds from low‐depth sequencing data

Accurate Bayesian inference of sex chromosome karyotypes and sex-linked scaffolds from low-depth sequencing data

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