# Integrating Morphology and Chloroplast Genomics: A New East Asian Species of Aletris (Nartheciaceae) With Insights Into Regional Phylogeny and Evolution

## TL;DR

A new plant species, Aletris medogensis, was discovered in the Himalayas using a combination of physical traits and chloroplast DNA analysis, helping clarify plant evolution in the region.

## Contribution

The discovery of a new Aletris species and the integration of morphology with chloroplast genomics to resolve taxonomic and evolutionary questions.

## Key findings

- Aletris medogensis is a new species characterized by unique morphological and chloroplast genomic traits.
- Phylogenomic analysis shows A. medogensis is closely related to A. alpestris and has distinct chloroplast genome variations.
- Positive selection in genes ccsA, cemA, and rps12 suggests adaptive evolution in the new species.

## Abstract

The genus Aletris L. (Nartheciaceae) encompasses approximately 21–24 species distributed in East Asia and North America, yet taxonomic ambiguity persists due to overlapping morphological traits among closely related species. During fieldwork in southeastern Xizang, China, a morphologically distinct candidate species, Aletris medogensis, was discovered. To validate its taxonomic status and explore evolutionary relationships within East Asian Aletris, we integrated detailed morphological observation with comparative chloroplast phylogenomics. The newly proposed species is characterized by creeping stolons, narrow leaves, and glandular‐pubescent inflorescences. Comparative analysis of 14 East Asian Aletris complete chloroplast genomes revealed a conserved quadripartite structure with species‐specific variations, including pseudogenization of ycf1, loss of rrn4.5, and shifts in IR boundaries. Phylogenomic analyses strongly supported
A. medogensis
as a distinct species closely related to
A. alpestris
. We identified 18 hypervariable regions as potential molecular markers and detected signals of positive selection in genes
ccsA
,
cemA
, and rps12, suggesting adaptive evolution. This study confirms the recognition of
A. medogensis
as a new species endemic to the eastern Himalayas and demonstrates the utility of chloroplast genomics in resolving taxonomic complexity and understanding evolutionary mechanisms in Aletris.

Based on morphological and chloroplast phylogenomic analyses, we describe Aletris medogensis as a new species endemic to the eastern Himalayas. Comparative genomics revealed structural variations, hypervariable markers, and signatures of positive selection in key genes, providing robust evidence for species delimitation and insights into the evolutionary mechanisms of Aletris. This study highlights the power of integrating traditional and molecular approaches in plant systematics.