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

Abstract

1AbstractGenetic swamping resulting from interspecific hybridisation can increase extinction risk for threatened species. The development of high-throughput and reduced-representation genomic sequencing and analyses to generate large numbers of high resolution genomic markers has the potential to reveal introgression previously undetected using small numbers of genetic markers. However, few studies to date have implemented genomic tools to assess the impacts of interspecific hybridisation in threatened species. Here we investigate the utility of genome-wide single nucleotide polymorphisms (SNPs) to detect introgression resulting from past interspecific hybridisation in one of the world’s rarest birds. Anthropogenic impacts have resulted in hybridisation and subsequent backcrossing of the critically endangered Aotearoa New Zealand endemic kakī (black stilts; Himantopus novaezelandiae) with the non-threatened self-introduced congeneric poaka (Aotearoa New Zealand population of pied stilts, Himantopus himantopus leucocephalus), yet genetic analyses with a limited set of microsatellite markers revealed no evidence of introgression of poaka genetic material in kakī, excluding one individual. We use genomic data for ~63% of the wild adult kakī population to reassess the extent of introgression resulting from hybridisation between kakī and poaka. Consistent with previous genetic analyses, we detected no introgression from poaka into kakī. These collective results indicate that, for kakī, existing microsatellite markers provide a robust, cost-effective approach to detect cryptic hybrids. Further, for well-differentiated species, the use of genomic markers may not be required to detect admixed individuals.

Expanding the conservation genomics toolbox: Incorporating structural variants to enhance genomic studies for species of conservation concern

“…Over the past 10 years, the field of conservation genomics has largely focused on transitioning from a handful of microsatellite markers to thousands of genome‐wide single nucleotide polymorphisms (SNPs) (Allendorf et al, 2010; Mable, 2019). Whether characterized using reduced‐representation data or whole‐genome sequence (WGS) methods, SNP‐based estimates of genome‐wide variation are being used to better inform conservation by delineating species, including cryptic species (e.g., Binks et al, 2021; Quattrini et al, 2019; but see Stanton et al, 2019), detecting hybridization and introgression (Dufresnes & Dubey, 2020; Peters et al, 2016; but see Forsdick et al, 2021 preprint; Hauser et al, 2021), identifying conservation units (Liddell et al, 2020), informing conservation translocations (Dresser et al, 2017; Glassock et al, 2021), guiding conservation breeding programmes (e.g., Galla et al, ; Wright et al, 2020) and identifying the genomic basis of adaptive traits (Duntsch et al, 2020). However, SNPs constitute only one component of genome‐wide variation (Ho et al, 2020).…”

Expanding the conservation genomics toolbox: incorporating structural variants to enhance genomic studies for species of conservation concern

“…Over the past 10 years, the field of conservation genomics has largely focused on transitioning from a handful of microsatellite markers to thousands of genome-wide single nucleotide polymorphisms (SNPs) (Allendorf, Hohenlohe, & Luikart, 2010;Mable, 2019). Whether characterized using reduced-representation data or whole-genome sequence (WGS) methods, SNP-based estimates of genome-wide variation are being used to better inform conservation by delineating species, including cryptic species (e.g., Binks, Steane, & Byrne, 2021;Quattrini et al, 2019;but see Stanton et al, 2019), detecting hybridization and introgression (Dufresnes & Dubey, 2020;Peters et al, 2016; but see Forsdick et al, 2021;Hauser, Athrey, & Leberg, 2021 preprint), identifying conservation units (Liddell et al, 2020), informing conservation translocations (Dresser, Ogle, & Fitzpatrick, 2017;Glassock, Grueber, Belov, & Hogg, 2021), guiding conservation breeding programs (e.g., Galla et al, 2020;Wright et al, 2020) and identifying the genomic basis of adaptive traits (Duntsch et al, 2020). However, SNPs constitute only one component of genome-wide variation (Ho, Urban, & Mills, 2020).…”