Multifaceted framework for defining conservation units: An example from Atlantic salmon (Salmo salar) in Canada

Abstract

Conservation units represent important components of intraspecific diversity that can aid in prioritizing and protecting at‐risk populations, while also safeguarding unique diversity that can contribute to species resilience. In Canada, identification and assessments of conservation units is done by the Committee on the Status of Endangered Wildlife in Canada (COSEWIC). COSEWIC can recognize conservation units below the species level (termed “designatable units”; DUs) if the unit has attributes that make it both discrete and evolutionarily significant. There are various ways in which a DU can meet criteria of discreteness and significance, and increasing access to “big data” is providing unprecedented information that can directly inform both criteria. Specifically, the incorporation of genomic data for an increasing number of non‐model species is informing more COSEWIC assessments; thus, a repeatable, robust framework is needed for integrating these data into DU characterization. Here, we develop a framework that uses a multifaceted, weight of evidence approach to incorporate multiple data types, including genetic and genomic data, to inform COSEWIC DUs. We apply this framework to delineate DUs of Atlantic salmon (Salmo salar, L.), an economically, culturally, and ecologically significant species, that is also characterized by complex hierarchical population structure. Specifically, we focus on an in‐depth example of how our approach was applied to a previously data limited region of northern Canada that was defined by a single large DU. Application of our framework with newly available genetic and genomic data led to subdividing this DU into three new DUs. Although our approach was developed to meet criteria of COSEWIC, it is widely applicable given similarities in the definitions of a conservation unit.

Variable parallelism in the genomic basis of age at maturity across spatial scales in Atlantic Salmon

“…We selected K = 5, based on PCA results, and inspection of cross-entropy criteria which showed highest rates of reduction in cross-entropy until K = 5 (Figure S1). However, we acknowledge additional changes in percent variation explained and cross-entropy values past K = 5, and alternative values of K are likely also valid using this approach (Lawson et al, 2018) especially given known hierarchical population structure in Atlantic Salmon (Bradbury et al, 2014;Lehnert et al, 2023). We focus on these first five primary ancestry sources, as our goal here is to characterize the main potential sources of broad-scale population structure that may be associated with 1SW proportion.…”

Living in a post‐industrial landscape: repeated patterns of genetic divergence in brown trout (Salmo trutta L.) across the British Isles

“…In anadromous fishes this has particular relevance where there is commercial exploitation through a mixed-stock fishery at sea harvesting genetically distinct populations of differing natal origin and risk status; evidence of capture from such vulnerable populations should inform fishing effort and restrictions (e.g. Bradbury et al, 2016;Gilbey et al, 2021;King et al, 2016;Koljonen et al, 2014;Lehnert et al, 2023;Shaklee et al, 1999). Conversely, the study of genetic diversity and population structure may sometimes highlight how recognised taxonomic units lack evolutionary significance, as in the case of the phenotypically described and the critically-endangered Balearic shearwater (Puffinus mauretanicus), which has been shown to exhibit no significant evidence of genetic distinction from the less threatened Yelkouan present.…”

Hierarchical population genetic structure and signatures of adaptation inLates calcarifer

“…We follow with an approach to identify units of BP through both isolation, that is discreteness of higher-level groups, and testing for evolutionary significant differences between genetic groupings (i.e. adaptive genetic loci) (Lehnert et al, 2023).…”

“…Conservation of both species-level and intraspecific variation can serve to promote ecological, cultural and economic functions of organisms, resilience and genetic variation for future adaptive potential e.g. (Layton et al, 2021; Lehnert et al, 2023; Schindler et al, 2010). Identification of both specific and intraspecific variation can be considered both through isolation and adaptation (Waples, 1991).…”