Impact of reduced-representation sequencing protocols on detecting population structure in a threatened marsupial

Wright, Belinda; Grueber, Catherine E.; Lott, Matthew J.; Belov, Katherine; Johnson, Rebecca N.; Hogg, Carolyn J.

doi:10.1007/s11033-019-04966-6

Cited by 22 publications

(31 citation statements)

References 31 publications

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“…On the other hand, this in turn would have come on the expense of genomic coverage, and thus possibility to detect (any) adaptive outliers [45], and could also introduce other type of errors and biases (see e.g. [38,68,99])…”

Section: Discussionmentioning

confidence: 99%

Genome wide analysis reveals genetic divergence between Goldsinny wrasse populations

et al. 2020

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Background Marine fish populations are often characterized by high levels of gene flow and correspondingly low genetic divergence. This presents a challenge to define management units. Goldsinny wrasse (Ctenolabrus rupestris) is a heavily exploited species due to its importance as a cleaner-fish in commercial salmonid aquaculture. However, at the present, the population genetic structure of this species is still largely unresolved. Here, full-genome sequencing was used to produce the first genomic reference for this species, to study population-genomic divergence among four geographically distinct populations, and, to identify informative SNP markers for future studies. Results After construction of a de novo assembly, the genome was estimated to be highly polymorphic and of ~600Mbp in size. 33,235 SNPs were thereafter selected to assess genomic diversity and differentiation among four populations collected from Scandinavia, Scotland, and Spain. Global FST among these populations was 0.015–0.092. Approximately 4% of the investigated loci were identified as putative global outliers, and ~ 1% within Scandinavia. SNPs showing large divergence (FST > 0.15) were picked as candidate diagnostic markers for population assignment. One hundred seventy-three of the most diagnostic SNPs between the two Scandinavian populations were validated by genotyping 47 individuals from each end of the species’ Scandinavian distribution range. Sixty-nine of these SNPs were significantly (p < 0.05) differentiated (mean FST_173_loci = 0.065, FST_69_loci = 0.140). Using these validated SNPs, individuals were assigned with high probability (≥ 94%) to their populations of origin. Conclusions Goldsinny wrasse displays a highly polymorphic genome, and substantial population genomic structure. Diversifying selection likely affects population structuring globally and within Scandinavia. The diagnostic loci identified now provide a promising and cost-efficient tool to investigate goldsinny wrasse populations further.

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Section: Discussionmentioning

confidence: 99%

Genome wide analysis reveals genetic divergence between Goldsinny wrasse populations

et al. 2020

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“…Conversely, large‐scale SNP data sets can be expected to increase the resolution of downstream population analyses because of the greater abundance of genetic markers, representing broader coverage of the overall genome (Allendorf et al ). Different SNP‐calling pipelines, however, often show low concordance in derived downstream analyses (O'Rawe et al , Pfeifer , Wright et al ), requiring standardization of laboratory and bioinformatics procedures to ensure consistency in management applications. Furthermore, in the absence of an annotated reference genome for the bilby, it is currently not possible to determine whether the SNPs included in our analysis are a good representation of diversity across both neutral and functional loci.…”

Section: Discussionmentioning

confidence: 99%

“…The rate at which heterozygosity is lost from a population will be further influenced by the sex ratio of breeding individuals, interspecific variation in offspring numbers, generation times, and the mating system of the specific threatened species in question (Amos andHarwood 1998, Jamieson andLacy 2012). It is therefore important that stakeholders employ active genetic monitoring to guide and evaluate the management of genetic diversity as part of captive breeding efforts and following translocation events (Schwartz et al 2007, Hogg et al 2019).…”

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confidence: 99%

Genetic Management of Captive and Reintroduced Bilby Populations

et al. 2019

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Captive breeding and translocation, whereby selected individuals are used to supplement or re‐establish failing populations, are powerful tools for conserving threatened fauna. These tools, however, are rarely successful at establishing self‐sustaining populations that can survive without ongoing human assistance. The maintenance of genetic diversity and demographic security in captivity, or following wildlife translocation events, is important for improving the long‐term effectiveness of threatened species recovery efforts around the world. Routine population monitoring using hypervariable genetic markers represents a promising technique for evaluating the effect of established management practices on population structure and genetic diversity across various spatial and temporal scales. In this study, we employed a data set of 1,068 single nucleotide polymorphisms to conduct a comprehensive survey of population structure and genetic diversity in greater bilbies (Macrotis lagotis) held at 13 zoos and wildlife sanctuaries across Australia between August 1996 and December 2016. We observed significant genetic structuring across the study sites, consistent with the limited exchange of animals between independently managed facilities. The majority of variation, however, still occurred at the level of individual bilbies (75%, P < 0.001). We also uncovered evidence for an ongoing loss of genetic diversity in some conservation‐fenced populations, despite a slight excess of heterozygosity across the sampling sites as a whole. Maintaining the genetic health of bilbies in captivity or following translocation will therefore require stakeholders to focus on reducing individual mortality, and maintaining genetic connectivity across all existing populations through the regular exchange of selected individuals. As such, admixture is expected to play an increasingly important role in future conservation programs. © 2019 The Authors. Journal of Wildlife Management published by Wiley Periodicals, Inc. on behalf of The Wildlife Society.

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“…On the other hand, this in turn would have come on the expense of genomic coverage, and thus possibility to detect (any) adaptive outliers (Hoban et al 2016), and could also introduce other type of errors and biases (see e.g. Maroso et al 2018;Wright et al 2019;Graham et al 2020).…”

Section: Frankham 1996; Allendorf and Ryman 2014)mentioning

confidence: 99%

Genome wide analysis reveals genetic divergence between Goldsinny wrasse populations

Jansson¹,

Besnier²,

Malde³

et al. 2020

Preprint

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Background: Marine fish populations are often characterized by high levels of gene flow and correspondingly low genetic divergence. This presents a challenge to define management units. Goldsinny wrasse (Ctenolabrus rupestris) is a heavily exploited species due to its importance as a cleaner-fish in commercial salmonid aquaculture. However, at the present, the population genetic structure of this species is still largely unresolved. Here, full-genome sequencing was used to produce the first genomic reference for this species, to study population-genomic divergence among four geographically distinct populations, and, to identify informative SNP markers for future studies. Results: After construction of a de novo assembly, the genome was estimated to be highly polymorphic and of ~600Mbp in size. 33 235 SNPs were thereafter selected to assess genomic diversity and differentiation among four populations collected from Scandinavia, Scotland, and Spain. Global FST among these populations was 0.015–0.092. Approximately 4% of the investigated loci were identified as putative global outliers, and ~1% within Scandinavia. SNPs showing large divergence (FST>0.15) were picked as candidate diagnostic markers for population assignment. 173 of the most diagnostic SNPs between the two Scandinavian populations were validated by genotyping 47 individuals from each end of the species’ Scandinavian distribution range. 69 of these SNPs were significantly (p<0.05) differentiated (mean FST_173_loci=0.065, FST_69_loci=0.140). Using these validated SNPs, individuals were assigned with high probability (≥ 94%) to their populations of origin.Conclusions: Goldsinny wrasse displays a highly polymorphic genome, and substantial population genomic structure. Diversifying selection likely affects population structuring globally and within Scandinavia. The diagnostic loci identified now provide a promising and cost-efficient tool to investigate goldsinny wrasse populations further.

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Impact of reduced-representation sequencing protocols on detecting population structure in a threatened marsupial

Cited by 22 publications

References 31 publications

Genome wide analysis reveals genetic divergence between Goldsinny wrasse populations

Genome wide analysis reveals genetic divergence between Goldsinny wrasse populations

Genetic Management of Captive and Reintroduced Bilby Populations

Genome wide analysis reveals genetic divergence between Goldsinny wrasse populations

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