Population genomic monitoring provides insight into conservation status but no correlation with demographic estimates of extinction risk in a threatened trout

Abstract

The current extinction crisis requires effective assessment and monitoring tools. Genetic approaches are appealing given the relative ease of field sampling required to estimate genetic diversity characteristics assumed related to population size, evolutionary potential, and extinction risk, and to evaluate hybridization with non‐native species simultaneously. However, linkages between population genetic metrics of diversity from survey‐style field collections and demographic estimates of population size and extinction risk are still in need of empirical examples, especially for remotely distributed species of conservation concern where the approach might be most beneficial. We capitalized on an exceptional opportunity to evaluate congruence between genetic diversity metrics and demographic‐based estimates of abundance and extinction risk from a comprehensive Multiple Population Viability Analysis (MPVA) in a threatened fish, the Lahontan cutthroat trout (LCT). We sequenced non‐native trout reference samples and recently collected and archived tissue samples of most remaining populations of LCT (N = 60) and estimated common genetic assessment metrics, predicting minimal hybridization with non‐native trout, low diversity, and declining diversity over time. We further hypothesized genetic metrics would correlate positively with MPVA‐estimated abundance and negatively with extinction probability. We uncovered several instances of hybridization that pointed to immediate management needs. After removing hybridized individuals, cautious interpretation of low effective population sizes (2–63) suggested reduced evolutionary potential for many LCT populations. Other genetic metrics did not decline over time nor correlate with MPVA‐based estimates of harmonic mean abundance or 30‐year extinction probability. Our results demonstrate benefits of genetic monitoring for efficiently detecting hybridization and, though genetic results were disconnected from demographic assessment of conservation status, they suggest reduced evolutionary potential and likely a higher conservation risk than currently recognized for this threatened fish. We emphasize that genetic information provides essential complementary insight, in addition to demographic information, for evaluating species status.

Resiliency of Apache Trout habitats in a warmer and drier climate future

“…Lack of genetic diversity within individual populations might restrict their ability to adapt in place and may warrant genetic rescue in the future (Whiteley et al 2015; Weise et al 2020). Adaptative potential should be considered in concert with the reality that many populations reside in small habitat patches (Hemstrom et al 2022). Small patch size can constrain long‐term viability and is one of the trade‐offs that comes with isolation management (Fausch et al 2009), but our identification of climate‐resilient habitats incorporated the patch size of suitable habitat as a driver of long‐term persistence (patch sizes are also known to be biased low; Dauwalter et al 2022).…”