Genomic sequencing confirms absence of introgression despite past hybridisation between a critically endangered bird and its common congener

Forsdick, Natalie; Martini, Denise; Brown, Liz; Cross, Hugh; Maloney, Richard F.; Steeves, Tammy E.; Knapp, Michael

doi:10.1016/j.gecco.2021.e01681

Cited by 13 publications

(12 citation statements)

References 105 publications

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“…Given the strong population genetic structure observed above, we used 0.95 as a conservative threshold for admixture. Thus, individuals with assignment probabilities <0.95 to a single cluster were considered admixed (Forsdick et al, 2021; Senn & Pemberton, 2009). PCA also supported regional population genetic structure identified by STRUCTURE (Figure 5).…”

Section: Resultsmentioning

confidence: 99%

Weaving place‐based knowledge for culturally significant species in the age of genomics: Looking to the past to navigate the future

Rayne

Blair²,

Dale³

et al. 2022

Evolutionary Applications

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Relationships with place provide critical context for characterizing biocultural diversity. Yet, genetic and genomic studies are rarely informed by Indigenous or local knowledge, processes, and practices, including the movement of culturally significant species. Here, we show how place-based knowledge can better reveal the biocultural complexities of genetic or genomic data derived from culturally significant species.As a case study, we focus on culturally significant southern freshwater kōura (crayfish) in Aotearoa me Te Waipounamu (New Zealand, herein Aotearoa NZ). Our results, based on genotyping-by-sequencing markers, reveal strong population genetic structure along with signatures of population admixture in 19 genetically depauperate populations across the east coast of Te Waipounamu. Environment association and differentiation analyses for local adaptation also indicate a role for hydroclimatic variables-including temperature, precipitation, and water flow regimes-in shaping local adaptation in kōura. Through trusted partnerships between community and researchers, weaving genomic markers with place-based knowledge has both provided

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Section: Resultsmentioning

confidence: 99%

Weaving place‐based knowledge for culturally significant species in the age of genomics: Looking to the past to navigate the future

Rayne

Blair²,

Dale³

et al. 2022

Evolutionary Applications

Self Cite

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“…Human activities through urbanisation, habitat destruction, predator control and poaching directly contribute to interspecies hybridisation (Germain et al, 2008). In some cases, interspecific hybridisation can increase extinction risk for threatened species (Forsdick et al, 2021). As backcrossing progresses, the morphological differences between the parent species and the backcrosses decrease, making it increasingly difficult to detect backcrossing using only phenotypic traits (McFarlane and Pemberton, 2019).…”

Section: Interspecies Hybridisationmentioning

confidence: 99%

“…Another example of the effective use of the GBS method was the assessment of hybridisation, especially the degree of introgression to date between the species of two closely related birds -one of which is critically endangered with extinction (Forsdick et al, 2021). The black stilt (BS) (Himantopus novaezelandiae) is one of the rarest birds on earth and, unfortunately, capable of hybridising with the fairly common species of the white-headed stilt (WHS) (H. himantopus leucocephalus).…”

Section: Birdsmentioning

confidence: 99%

Genotyping-by-sequencing (GBS) as a tool for interspecies hybrid detection

Podbielska

Piórkowska

2022

Annals of Animal Science

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Genotyping-by-sequencing (GBS) is an extremely useful, modern and relatively inexpensive approach to discovering high-quality single-nucleotide polymorphisms (SNPs), which seem to be the most promising markers for identifying hybrid individuals between different species, especially those that can create backcrosses. In addition, GBS could become an invaluable tool in finding backcrosses, even several generations back. Its potential for the use of restriction enzymes and species is almost unlimited. It can also be successfully applied to species for which a reference genome is not established. In this paper, we describe the GBS technique, its main advantages and disadvantages, and the research carried out using this method concerning interspecies hybridisation and the identification of fertile hybrids. We also present future approaches that could be of interest in the context of the GBS method.

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“…This generates genome-wide high-throughput sequencing data, making it a suitable genotyping method for obtaining individual-level genotype information that can be compared across individuals and populations. Consequently, RADseq has been used in numerous ecological, evolutionary, and conservation genomic studies to address varied questions (Andrews et al 2016 ), such as describing population structure and connectivity, detecting hybrids, resolving phylogenies, and identifying genome regions under selection (Near et al 2018 ; Ewart et al 2019 ; Hofmeister et al 2021 ; Stuart et al 2021 ; Forsdick et al 2021 ). Although RADseq does not require a reference genome (Baird et al 2008 ; Peterson et al 2012 ), the use of a reference genome typically improves the reliability of genotype calls and downstream inferences (Shafer et al 2017 ).…”

Section: Introductionmentioning

confidence: 99%

Tracing the introduction of the invasive common myna using population genomics

et al. 2023

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The common myna (Acridotheres tristis) is one of the most invasive bird species in the world, yet its colonisation history is only partly understood. We identified the introduction history and population structure, and quantified the genetic diversity of myna populations from the native range in India and introduced populations in New Zealand, Australia, Fiji, Hawaii, and South Africa, based on thousands of single nucleotide polymorphism markers in 814 individuals. We were able to identify the source population of mynas in several invasive locations: mynas from Fiji and Melbourne, Australia, were likely founded by individuals from a subpopulation in Maharashtra, India, while mynas in Hawaii and South Africa were likely independently founded by individuals from other localities in India. Our findings suggest that New Zealand mynas were founded by individuals from Melbourne, which, in turn, were founded by individuals from Maharashtra. We identified two genetic clusters among New Zealand mynas, divided by New Zealand’s North Island’s axial mountain ranges, confirming previous observations that mountains and thick forests may form barriers to myna dispersal. Our study provides a foundation for other population and invasion genomic studies and provides useful information for the management of this invasive species.

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Genomic sequencing confirms absence of introgression despite past hybridisation between a critically endangered bird and its common congener

Cited by 13 publications

References 105 publications

Weaving place‐based knowledge for culturally significant species in the age of genomics: Looking to the past to navigate the future

Weaving place‐based knowledge for culturally significant species in the age of genomics: Looking to the past to navigate the future

Genotyping-by-sequencing (GBS) as a tool for interspecies hybrid detection

Tracing the introduction of the invasive common myna using population genomics

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