# Five Hidden Species in a Widespread European Vertebrate: Disentangling the Alpine Newt Cryptic Species Complex Through Genomic Phylogeography

## TL;DR

Genomic analysis reveals five hidden species within the alpine newt, reshaping our understanding of its biodiversity and evolutionary history.

## Contribution

The study identifies five distinct cryptic species within the alpine newt using genomic phylogeography and reveals mito-nuclear discordance.

## Key findings

- Genomic data reveals five distinct species within the alpine newt complex.
- A previously considered 'ghost lineage' mtDNA is shown to represent a distinct species.
- Mito-nuclear discordance and range fragmentation are linked to historical glaciation and habitat decline.

## Abstract

Through genomic phylogeography, previously unrecognised biodiversity can be revealed. The alpine newt serves as a case in point: this taxon carries highly distinct mtDNA clades and has a severely fragmented range. We obtain genome‐wide data with target enrichment by sequence capture to delineate cryptic species and disentangle their phylogenetic relationships. Furthermore, we explore potential niche divergence and glaciation‐driven distribution dynamics. On the basis of the uncovered genetic structure, we distinguish five main groups that we propose should be treated as distinct species. Limited interspecific genetic admixture often occurs away from current contact zones between these species, in line with a scenario of current range reduction, compared to the Last Glacial Maximum. A decline in suitable habitat also explains the fragmented nature of current species ranges. We uncover pronounced mito‐nuclear discordance. We show that an ancient mtDNA lineage endemic to the Vlasina Plateau on the border between Serbia and Bulgaria, previously interpreted to be a ‘ghost lineage’, in fact represents a distinct species. However, it is nested considerably deeper inside the alpine newt species complex than mtDNA suggests. Our study illustrates how genomic phylogeography allows intricate evolutionary histories to be untangled.