# A Dominant Founder Lineage Has Possible Fitness Costs for the Endangered Mexican Grey Wolf

## TL;DR

The Mexican grey wolf population faces genetic challenges due to inbreeding, but interbreeding strategies have helped reduce these issues and improve genetic diversity.

## Contribution

The study provides genomic insights into inbreeding and lineage contributions in the Mexican grey wolf ex situ breeding program.

## Key findings

- Inbreeding levels decreased after inter-lineage pairings, possibly due to fitness costs of inbreeding depression.
- Higher inbreeding and autozygosity were linked to reduced lifespan and reproductive performance.
- Ghost Ranch and Aragón lineages helped reduce inbreeding in the genetically distinct McBride lineage.

## Abstract

The Mexican grey wolf (
Canis lupus baileyi
) is an endangered and genetically distinct subspecies of grey wolf adapted to the warm climates of the southwestern United States and Mexico. Following centuries of eradication efforts, Mexican grey wolves were protected under the Endangered Species Act in 1976, prompting an international ex situ breeding program to preserve their genetic legacy. Seven remnant wolves founded the three distinct lineages of this program: McBride, Ghost Ranch, and Aragón. However, concerns of rising inbreeding levels motivated the implementation of inter‐lineage pairings to decelerate genetic erosion. To evaluate the genetic health of the ex situ managed population, we analysed genome‐wide variation across several generations of breeding wolves and their descendants (n = 179). Despite ongoing conservation interventions, we found a sharp decline in effective population size over the past 50 generations. However, estimates of inbreeding diminished over time following the inter‐lineage pairings, reflecting efficient pedigree management or potential fitness costs of inbreeding depression, as higher levels of inbreeding and autozygosity were associated with reduced lifespan and reproductive performance. Increasing contributions of Ghost Ranch and Aragón ancestry also aided in reducing levels of inbreeding observed in the more genetically distinct McBride lineage. These findings highlight the challenges of maintaining genetic diversity in bottlenecked populations, reveal fine‐scale patterns of inbreeding within the pedigree and underscore the urgent need to preserve genetic contributions from all founder lineages. Genomic insights from this study can guide breeding strategies to reduce kinship, balance ancestry and mitigate inbreeding depression, safeguarding the evolutionary legacy and the long‐term persistence of the Mexican grey wolf.