The relevance of pedigrees in the conservation genomics era

Abstract

Over the past 50 years conservation genetics has developed a substantive toolbox to inform species management. One of the most long‐standing tools available to manage genetics—the pedigree—has been widely used to characterize diversity and maximize evolutionary potential in threatened populations. Now, with the ability to use high throughput sequencing to estimate relatedness, inbreeding, and genome‐wide functional diversity, some have asked whether it is warranted for conservation biologists to continue collecting and collating pedigrees for species management. In this perspective, we argue that pedigrees remain a relevant tool, and when combined with genomic data, create an invaluable resource for conservation genomic management. Genomic data can address pedigree pitfalls (e.g., founder relatedness, missing data, uncertainty), and in return robust pedigrees allow for more nuanced research design, including well‐informed sampling strategies and quantitative analyses (e.g., heritability, linkage) to better inform genomic inquiry. We further contend that building and maintaining pedigrees provides an opportunity to strengthen trusted relationships among conservation researchers, practitioners, Indigenous Peoples, and Local Communities.

Reduced representation sequencing to understand the evolutionary history of Torrey pine (Pinus torreyana parry) with implications for rare species conservation

“…This study demonstrates that genomic data can provide substantial resolution in estimates of genetic diversity for rare species and is needed to understand the evolutionary processes underlying population persistence. In addition, relatedness among individuals approximated with such data can contribute knowledge necessary to designing, complementing, or completing pedigrees of wild or captive populations of endangered species (Galla et al, 2022). We also show that using genome-wide data to both model demographic changes over space and time and to tease apart evolutionary processes contributing to population structure can help prioritize ex situ collections and identify candidate populations for assisted gene flow.…”

Genetic management on the brink of extinction: sequencing microsatellites does not improve estimates of inbreeding in wild and captive Vancouver Island marmots (Marmota vancouverensis)

“…However, our studbook greatly benefitted from prior behavioural observations to help estimate relatedness among founders. This approach is highly recommended as it can improve the reliability of kinship and inbreeding estimates, and minimize unknown relationships among founders (Russell et al 1994, Kennedy et al 2014, Taylor 2015, Frankham et al 2017, Hogg et al 2019, Galla et al 2021. In this sense, our studbook is likely more accurate in estimating relatedness compared to studies that did not have any prior information during inception.…”

“…However, new wild marmots have recently been recruited into the captive breeding program but are lacking pedigree data to estimate how they might be related to captive individuals. This presents a drawback to relying on the studbook alone, suggesting a hybrid approach of both behavioural and molecular data sets is likely ideal (Galla et al 2020, Galla et al 2021.…”

Comparing genome‐based estimates of relatedness for use in pedigree‐based conservation management

“…intensively managed wild or semi-wild populations (i.e., in situ or "sorta situ"; Galla et al, 2022;Wildt et al, 2019;Wolfe et al, 2012).…”

“…Pedigrees continue to provide high precision estimates of inbreeding and relatedness when pedigrees are robust (i.e., many generations deep with relatively low missing data; Putnam & Ivy, 2014;Robinson et al, 2013). However, there are several limitations common in pedigrees for small populations that can hinder their utility for genetic management (Galla et al, 2022). One is that the individuals forming the initial captive population (hereafter, founders) are often of unknown relationships and assumed to be equally unrelated (Ballou, 1983;Hogg et al, 2019).…”