# Genomic Evidence of Low Contemporary Effective Population Size and Southern Genetic Reservoirs in an Island Endemic Epiphytic Orchid of Taiwan

## TL;DR

This study uses genomic data to show that southern populations of a rare orchid in Taiwan have higher genetic diversity, which is important for conservation.

## Contribution

The study reveals a latitudinal genetic diversity gradient in an island endemic orchid using ddRADseq data and links it to evolutionary and conservation implications.

## Key findings

- Southern populations of Holcoglossum pumilum show higher genetic diversity compared to northern populations.
- Genome-wide data suggests a latitudinal gradient shaped by Taiwan's monsoon and mountainous landscape.
- Contemporary effective population sizes are low, with estimates mostly below 500.

## Abstract

Orchids are traded globally, where wild populations can be threatened by overharvesting, habitat loss, and climate change. Many orchid species lack ex situ protection, such as botanical gardens, making in situ genetic studies of wild populations critical to inform conservation plans. Taiwan is a center for orchid diversity and has witnessed declines in wild orchids. Holcoglossum pumilum, an island endemic epiphytic species, is popular among citizen scientists and shows potential for public engagement in biodiversity conservation. This study aims to evaluate the genetic diversity, population structure, and adaptive potential of wild Holcoglossum pumilum in Taiwan, not only to serve as an example for public outreach but also to inform conservation policy. We collected 64 plants from 18 sites across Taiwan and used ddRADseq to generate genome‐wide SNP data. We found higher genetic diversity in southern populations than in northern ones. While evidence for genetic clustering and isolation by distance was limited, we detected significant genotype–environment associations, especially with annual precipitation. Demographic reconstructions suggested a pre‐LGM expansion followed by a plateau. Contemporary Ne estimates varied by data filtering strategies but were mostly below 500. Our study demonstrates the critical role of genomic data not only in revealing the evolutionary origin of genetic diversity but also in guiding conservation plans. Specifically, we argued that the seasonal monsoon and the mountainous landscape of Taiwan may have shaped a latitudinal gradient of genetic diversity in
H. pumilum
. As a result, southern populations exhibit greater genetic diversity, which makes them priorities for conservation management.

Genome‐wide data from ddRADseq revealed a latitudinal gradient in genetic diversity in a Taiwanese endemic orchid. This study shows that genomic data not only can help us understand the evolutionary origins of genetic diversity in a species but also uncover its genetic reservoir for future conservation planning.