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 (HTS) 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. Keywords: conservation genomics, quantitative genetics, pedigree, kinship,ex situ , in situ

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.…”

Species-wide genomics of kākāpō provides transformational tools to accelerate recovery

“…Until recently, incorporating genetic diversity into conservation translocation decisions has been done using a pedigree validated with microsatellite-based parentage assignments 21 . However, one shortcoming of most pedigrees-including the kākāpō pedigree-is that founders are assumed to be equally unrelated 35 , leading to underestimated relatedness values. While attempts have been made to use microsatellites to estimate founder relatedness 20 , microsatellites have been shown to produce poor estimates of relatedness in genetically depauperate species 61,138 , like kākāpō.…”

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

“…Relatedness and kinship, concepts that quantify the relationship between two individuals (hereafter referred to as relatedness for simplicity) are foundational in biology (Wright, 1922), with application in health sciences (Ott, 1974), agriculture (Cassell et al, 2003; Jannink et al, 2001) and species conservation (Fernández et al, 2005). Pedigrees track relatedness in populations by documenting the ancestry of individuals, and are used to manage small populations, including those in captivity (i.e., ex situ population management) or 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). Conservation practitioners can prioritize breeding individuals with low mean kinship when making pairing decisions in captivity, or population management decisions in wild or semi‐wild populations (Ballou & Lacy, 1995; Giglio et al, 2016; Weeks et al, 2011).…”

“…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).…”

“…For example, in a captive population of Attwater's Prairie‐chicken ( Tympanuchus cupido attwateri ), nearly 40% of the population were descendants of four individuals that had incorrect parentage assigned four generations prior (Hammerly et al, 2016). To alleviate pedigree shortcomings, including unknown founder relationships, missing pedigree data, and potential error, researchers can use genomic estimates of relatedness to complement and complete pedigrees (Galla et al, 2022).…”