# Canonical Discriminant Mapping of Origins in Andalusian Black Cattle: Inbreeding and Coancestry Decomposition via Mendelian Sampling Variances and Nodal Ancestor Contributions

## TL;DR

This study explores the genetic structure and conservation needs of the Andalusian Black Cattle breed, emphasizing the importance of preserving genetic diversity through traditional practices like transhumance.

## Contribution

The study introduces a novel approach to analyzing inbreeding and coancestry using Mendelian sampling variances and nodal ancestor contributions in a culturally significant cattle breed.

## Key findings

- Córdoba is identified as the principal genetic nucleus with the highest number of ancestors and moderate inbreeding.
- Canonical discriminant analysis shows that the first discriminant function explains most of the variation among groups.
- Historical transhumance practices are found to preserve genetic diversity despite signs of inbreeding.

## Abstract

The Negra Andaluza is a traditional Andalusian cattle breed with deep cultural and historical roots in southern Spain. Although once essential for agricultural labor and timber transport, today, it faces genetic erosion due to declining population size and changes in land use. Our findings show that regions with limited connectivity exhibit signs of genetic isolation, while areas historically linked by transhumant routes retain greater diversity. These patterns highlight the urgent need for targeted conservation strategies that prioritize the protection of genetically rich nuclei, such as those in Córdoba, and reinforce gene flow through controlled breeding programs. Revitalizing traditional livestock practices like transhumance is not only culturally valuable but also essential for maintaining the breed’s genetic variability, adaptability, and long-term survival.

The Andalusian Black Cattle (Negra Andaluza) represents a genetic lineage linked to the ancient Eurasian aurochs, shaped by domestication events in the Near East and later introgressions from Italian and North African wild cattle. This study investigates the breed’s anthropological and historical origins, geographical distribution, and genetic structure. Key influences include historical use as draft animals, regional breeding preferences, and gene flow via transhumant routes. The genetic analysis reveals that Córdoba is the principal nucleus, accounting for 448 identified ancestors, compared to 252 in Huelva and 193 in Seville. In Córdoba, contributions of nodal ancestors through inbreeding loops reached a maximum of 0.0447, while mean inbreeding (F¯) was 0.000949 and mean coancestry (C¯) was 0.000475, indicating moderate but geographically structured genetic drift. In contrast, areas with better connectivity showed higher heterogeneity and lower inbreeding contributions. Canonical discriminant analysis (CDA) revealed that the first discriminant function (F1) explained 79.72% of the variation among groups, primarily driven by nodal ancestors and inbreeding loops. Despite these signs of inbreeding, historical transhumance has helped preserve overall genetic diversity. These findings offer essential insights for conservation programs aimed at maintaining both the genetic integrity and adaptive potential of this historically and culturally important breed.