For an endangered succulent, distance leaves a genetic mark

How connected are the populations?

The Santa Clara Valley dudleya, Dudleya abramsii ssp. setchellii, is a federally endangered succulent endemic to serpentine outcrops in southern Santa Clara County. Researchers wanted to understand how gene flow—the movement of genes between plants, through pollen or seeds—relates to genetic differences within and among populations. They also examined whether nearby rosettes, the plant’s leafy clusters, might be clones of the same individual.

A bioRxiv preprint led by Justen B. Whittall and colleagues reports low-coverage whole-genome sequencing across 52 individuals: 13 populations of the endangered dudleya, four populations of neighboring D. cymosa, and two other D. abramsii subspecies from San Luis Obispo County. The paper’s principal-component analysis used a smaller dataset: 45 D. a. ssp. setchellii, four D. cymosa and three comparison samples. The authors combined genomic comparisons with geographic-distance analyses, phylogenetic methods, field observations of floral visitors and a controlled seed-dispersal experiment.

For a closer look at clonality and local genetic structure, they sampled plants along transects at one focal population. Separately processed tissue samples from the same plants helped estimate how much DNA difference could arise from laboratory and sequencing variation. Cameras recorded floral visitors at two sites on two days in June 2024. In the indoor seed experiment, seeds were released into airflow from a leaf blower and their landing distances measured.

Genetic differences tracked distance

At both the focal population and across the sampled range, plants farther apart tended to be more genetically different. This pattern, called isolation by distance, can arise when limited movement and genetic drift gradually differentiate populations. The genomic analyses also showed geographic subdivision within the endangered subspecies, including an east–west pattern around Coyote Valley.

The findings support conserving populations across the subspecies’ range, the authors argue, because geographically separated populations may carry distinct genetic variation. They suggest Coyote Valley or other landscape features could further limit movement, but the study did not test whether the valley, a roadway or another feature acts as a barrier.

In the one population assessed for clonality, putative clone pairs were found no more than 8 centimetres apart. This suggests clones did not account for the broader geographic pattern there, but does not establish how common clonality is elsewhere. Nearby rosettes were not necessarily clones: some close neighbors were genetically distinct. Counts based only on rosettes could therefore misrepresent the number of genetically unique plants.

Bumblebees were the most frequently recorded floral visitors during the observation sessions. Their visits indicate potential for pollen movement, but the cameras did not measure pollen transfer or whether visits led to seed production. In the indoor experiment, seeds travelled an average of 276 centimetres; recovered seeds landed between 18.3 and 580 centimetres from the release point. The initial airflow was 33.5 miles per hour, and the setup did not reproduce natural terrain, vegetation or turbulent wind. The results suggest limited seed movement may contribute to genetic structure, but do not establish typical dispersal distances in nature.

A possible hybrid—and open questions

One sampled D. cymosa had an intermediate genomic position, and plants from its population showed intermediate leaf traits. The authors describe it as a putative hybrid, not a confirmed case; broader sampling and explicit tests of gene exchange are needed. The analyses support D. a. ssp. setchellii as a distinct genomic lineage in the samples studied, but the authors say the evidence is insufficient for a formal taxonomic change.

Isolation by distance does not identify one cause. Seed dispersal, pollen movement, genetic drift and geographic separation may all contribute, and their relative effects remain unresolved. The pollinator observations were limited in time and place, while the seed trial was an artificial estimate rather than a measure of ordinary field dispersal. Testing whether landscape features add barriers beyond distance is another research need.

This report is a bioRxiv preprint and had not been certified by peer review when posted. It provides a genomic framework for conservation, not a definitive measure of connectivity or a prescription for moving plants between populations.