# Conservation hints for Pinna nobilis from a century-old genetic time capsule

## TL;DR

This study uses ancient DNA to uncover the evolutionary history of the noble pen shell and its resilience to environmental challenges over the past century.

## Contribution

The study standardizes a protocol for extracting DNA from ancient byssus samples and reveals the genetic origins of Pinna nobilis.

## Key findings

- Two main genetic lineages were identified, originating 2.5 mya and 1.5 mya.
- The species showed resilience to human overexploitation, pollution, and environmental changes.
- Pleistocene genetic traits persist due to high effective population size.

## Abstract

The noble pen shell, Pinna nobilis, is an iconic marine bivalve endemic to the Mediterranean Sea, playing a key role as an ecosystem engineer. Over the past century, it has faced severe threats from overharvesting, pollution, and catastrophic mass mortality events. This study analysed 119 mitochondrial COI gene sequences from historical (1700s, 1920s, 1970s, 1990s) and modern (2000s) samples, including survivors of recent mass mortality crises. We standardised a protocol to extract DNA from ancient byssus samples over a century old and dated the emergence of the mitochondrial lineages of Pinna nobilis, uncovering its evolutionary history in unprecedented detail. Our findings suggest two main temporal origins for the species’ genetic variation: (i) a group of modern lineages directly descended from Pinna nobilis early ancestors originating 2.5 mya, and (ii) a large group derived from the first Pleistocene radiation of the species, approximately 1.5 mya. Importantly, our research depicts the evolutionary response of Pinna nobilis to three major challenges in the last century: human overexploitation, pollution, and environmental changes. Our results highlight the species’ remarkable resilience, likely mediated by Pleistocene genetic traits, whose persistence over time mainly depends on the maintaining of a high effective population size to ensure successful recruitment.

The online version contains supplementary material available at 10.1038/s41598-025-21574-6.