Who are you? A framework to identify and report genetic sample mix‐ups

Duntsch, Laura; Brekke, Patricia; Ewen, John G.; Santure, Anna W.

doi:10.1111/1755-0998.13575

Cited by 3 publications

(3 citation statements)

References 66 publications

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“…All fledglings are banded before they leave the nest, survival is surveyed twice a year, and all reproductive attempts across the island are monitored over an individual's lifetime (Low & Part, 2009). This study originally included confirmed genotype data for 480 hihi from Tiritiri Mātangi (Duntsch et al, 2022). However, although there is no natural migration between hihi sites, 98 of the initial sample pool were translocated from Tiritiri Mātangi to other sanctuaries throughout their lives.…”

Section: Methodsmentioning

confidence: 99%

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Genomic signatures of inbreeding depression for a threatened Aotearoa New Zealand passerine

et al. 2023

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For small and isolated populations, the increased chance of mating between related individuals can result in a substantial reduction in individual and population fitness. Despite the increasing availability of genomic data to measure inbreeding accurately across the genome, inbreeding depression studies for threatened species are still scarce due to the difficulty of measuring fitness in the wild. Here, we investigate inbreeding and inbreeding depression for the extensively monitored Tiritiri Mātangi island population of a threatened Aotearoa New Zealand passerine, the hihi (Notiomystis cincta). First, using a custom 45 k single nucleotide polymorphism (SNP) array, we explore genomic inbreeding patterns by inferring homozygous segments across the genome. Although all individuals have similar levels of ancient inbreeding, highly inbred individuals are affected by recent inbreeding, which can probably be explained by bottleneck effects such as habitat loss after European arrival and their translocation to the island in the 1990s. Second, we investigate genomic inbreeding effects on fitness, measured as lifetime reproductive success, and its three components, juvenile survival, adult annual survival and annual reproductive success, in 363 hihi. We find that global inbreeding significantly affects juvenile survival but none of the remaining fitness traits. Finally, we employ a genome‐wide association approach to test the locus‐specific effects of inbreeding on fitness, and identify 13 SNPs significantly associated with lifetime reproductive success. Our findings suggest that inbreeding depression does impact hihi, but at different genomic scales for different traits, and that purging has therefore failed to remove all variants with deleterious effects from this population of conservation concern.

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Section: Methodsmentioning

confidence: 99%

“…This study originally included confirmed genotype data for 480 hihi from Tiritiri Mātangi (Duntsch et al, 2022). However, although there is no natural migration between hihi sites, 98 of the initial sample pool were translocated from Tiritiri Mātangi to other sanctuaries throughout their lives.…”

Section: Hihi Population Monitoring and Samplingmentioning

confidence: 99%

Genomic signatures of inbreeding depression for a threatened Aotearoa New Zealand passerine

et al. 2023

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“…We assessed relatedness among the samples using the KING‐robust estimator (Manichaikul et al., 2010) implemented with NGSRelate v2 (Hanghøj et al., 2019) to confirm repeatability of positive controls and detect sample mix‐ups (following Duntsch et al., 2022). All within‐ and between‐plate positive controls revealed high relatedness (KING >0.48, where KING kinship coefficients of 0.354–0.5 correspond to duplicates; Manichaikul et al., 2010).…”

Section: Methodsmentioning

confidence: 99%

The genetic legacy of the first successful reintroduction of a mammal to Britain: Founder events and attempted genetic rescue in Scotland's beaver population

Taylor,

Costanzi,

Dicks

et al. 2023

Evolutionary Applications

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Conservation translocations often inherently involve a risk of genetic diversity loss, and thus loss of adaptive potential, but this risk is rarely quantified or monitored through time. The reintroduction of beavers to Scotland, via the Scottish Beaver Trial in Knapdale, is an example of a translocation that took place in the absence of genetic data for the founder individuals and resulted in a small and suspected to be genetically depauperate population. In this study we use a high‐density SNP panel to assess the genetic impact of that initial translocation and the effect of subsequent reinforcement translocations using animals from a different genetic source to the original founders. We demonstrate that the initial translocation did, indeed, lead to low genetic diversity (Ho = 0.052) and high mean kinship (KING‐robust = 0.159) in the Knapdale population compared to other beaver populations. We also show that the reinforcement translocations have succeeded in increasing genetic diversity (Ho = 0.196) and reducing kinship (KING robust = 0.028) in Knapdale. As yet, there is no evidence of admixture between the two genetic lineages that are now present in Knapdale and such admixture is necessary to realise the full genetic benefits of the reinforcement and for genetic reinforcement and then rescue to occur; future genetic monitoring will be required to assess whether this has happened. We note that, should admixture occur, the Knapdale population will harbour combinations of genetic diversity not currently seen elsewhere in Eurasian beavers, posing important considerations for the future management of this population. We consider our results in the wider context of beaver conservation throughout Scotland and the rest of Britain, and advocate for more proactive genetic sampling of all founders to allow the full integration of genetic data into translocation planning in general.

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A high-density linkage map reveals broad- and fine-scale sex differences in recombination in the hihi (stitchbird; Notiomystis cincta)

Tan,

Scherer,

Stuart

et al. 2024

Heredity

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Recombination, the process of DNA exchange between homologous chromosomes during meiosis, plays a major role in genomic diversity and evolutionary change. Variation in recombination rate is widespread despite recombination often being essential for progression of meiosis. One such variation is heterochiasmy, where recombination rates differ between sexes. Heterochiasmy has been observed across broad taxonomic groups, yet it remains an evolutionary enigma. We used Lep-MAP3, a pedigree-based software that is efficient in handling large datasets, to generate linkage maps for the hihi or stitchbird (Notiomystis cincta), utilising information from >36 K SNPs and 36 families. We constructed 29 linkage maps, including for the previously unscaffolded Z chromosome. The hihi is an endangered passerine endemic to Aotearoa New Zealand that is sexually dimorphic and exhibits high levels of sexual conflict, including sperm competition. Patterns in recombination in the hihi are consistent with those in other birds, including higher recombination rates in micro-chromosomes. Heterochiasmy in the hihi is male-biased, in line with predictions of the Haldane-Huxley rule, with the male linkage map being 15% longer. Micro-chromosomes exhibit heterochiasmy to a greater extent, contrary to that reported in other birds. At the intra-chromosomal level, heterochiasmy is higher nearer to chromosome ends and in gene-rich regions. Regions of extreme heterochiasmy are enriched for genes implicated in cell structure. This study adds an important contribution in assessing evolutionary theories of heterochiasmy and provides a framework for future studies investigating fine-scale heterochiasmy.

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Who are you? A framework to identify and report genetic sample mix‐ups

Cited by 3 publications

References 66 publications

Genomic signatures of inbreeding depression for a threatened Aotearoa New Zealand passerine

Genomic signatures of inbreeding depression for a threatened Aotearoa New Zealand passerine

The genetic legacy of the first successful reintroduction of a mammal to Britain: Founder events and attempted genetic rescue in Scotland's beaver population

A high-density linkage map reveals broad- and fine-scale sex differences in recombination in the hihi (stitchbird; Notiomystis cincta)

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