henhaobio
Sign in

bioRxivPaleontologyPreprint

First Plant sedaDNA assemblage from California reveals ecological stability throughout 10,000 years of human presence at Lake Elsinore

Madeline SlimpiD, Lisa N. MartineziD, Joshua D. KappiD, Matthew E. KirbyiD, Glen M. Sproul Dit MacDonaldiD, Don L. HankinsiD, Sebastian Melrose, Matthew G. JohnsoniD, Beth ShapiroiD, Rachel Sarah MeyeriD

PDFDOICodeData
In-depth full-text digest available · Jump to digest ↓

Abstract

As we face the sixth mass extinction, understanding how ecosystems have persisted--or collapsed--through millennia of changing climates and human activity is critical for preventing biodiversity loss. We bolstered the past 24,000 years of plant and mammal records using targeted capture of ancient sedimentary DNA (sedaDNA) from Southern Californias Lake Elsinore, a cultural center for the Payomkawichum (Luiseno), Cahuilla, and other Peoples. Our sedaDNA approach generated a diverse dataset that included 18 plant orders not previously documented from Lake Elsinore. We paired these records with local measurements and paleo evidence of fire regimes, climate, demographic history, and ethnobotanical knowledge. We find that ecological stability persisted for 10,000 years of continuous human presence, reflecting ecosystem resilience through major climatic shifts, altered fire regimes, and varying intensities of Indigenous land use. SedaDNA revealed increased availability of food, medicinal, and utilitarian plant taxa during this period of botanical stability, shedding light on ancient fire-environment-human interactions that can inform contemporary management strategies.

In-depth summary

Claude Opus 5.5 · xhigh effort · 8 Nov 2026 · from the full text of version 1 (16 Jun 2026) · CC BY 4.0

Angiosperms353 capture of Lake Elsinore sedimentary DNA recovers 50 land-plant orders across 24,000 years, with a fire-linked community shift preceding a persistent Holocene chaparral assemblage.

SedaDNA had not been applied to California's past plant communities, where warm conditions speed DNA decay, and existing pollen, archaeological and ethnographic records lack a concurrent Holocene record linking vegetation to people. This work tests whether a commercial universal capture kit can recover such assemblages and co-analyzes them with fire, paleoclimate, demographic and ethnobotanical evidence.

Key results

  1. ShownAngiosperms353 hybridization capture yielded a broader land-plant record than shotgun libraries and than pollen, macrofossil and ethnobotanical sources, and it also recovered some non-angiosperm orders off-target.

    50 Streptophyta orders retained (13 non-angiosperm); 32 shared with traditional records and 18 additional; 59 orders in capture vs 47 in shotgun libraries; plant-mapped relative reads doubled and angiosperm read proportion rose 2.4 fold vs shotgun; orders missed were untargeted ferns, gymnosperms and a lycopod order. · Lake Elsinore sedaDNA recovery of broad…; Tables

  2. ShownPlant community composition shifted after the intense-fire transition that began 13,200 ybp. Chaparral-rich orders rose and an aquatic order declined in the Holocene high-fire period, which settled into a new persistent assemblage.

    Kruskal-Wallis/Dunn (Bonferroni, alpha 0.05): Crossosomatales, Fagales, Myrtales, Solanales, Rosales, Lamiales higher in high-fire period; Alismatales higher in low-fire period; Gentianales dipped then recovered; Poales, Caryophyllales, Brassicales, Malvales n.s. Jaccard ordination: chaparral community took ∼5,500 years to form, stable ∼4,500 years. · Vegetation shift with fire; Ecological change at Lake Elsinore; Tables

  3. SuggestedWithin the Holocene, human cultural phases coincided with significant change in only two culturally important orders. Most phase differences separated the low-population phases before 10,550 ybp from later Holocene phases, which the authors attribute mainly to climate.

    6 human-activity phases; within the Holocene only Solanales (Early to Late Holocene) and Fagales (Early to Middle Holocene) rose significantly; Fagales peaked 7,200-3,440 ybp, when mortars and pestles appear archaeologically; Pre-archaeological Evidence and European Arrival bins showed no differences, attributed to small samples. · Vegetation shift with human activity; Human legacy at Lake Elsinore; Analyses Methods

  4. ShownDeglacial climate periods, especially the Bølling-Allerød Interstadial, separated several orders, and a few orders tracked proxies for runoff or lake productivity.

    Bølling-Allerød (14,700-12,900 ybp): Caryophyllales lower than Holocene and LGM; Crossosomatales lower than Holocene; Alismatales and Malvales higher than Holocene and LGM. Only Myrtales rose with percent sand; with LOI at 550°C, Asparagales increased and Crossosomatales decreased. · Vegetation shift with paleoclimate; Figure legends

  5. ShownPlant reads showed ancient DNA signatures (short fragments and damage at read ends), and the younger core gave better recovery.

    Mapped plant reads were mostly 30 bp; mapDamage showed weak to moderate end-elevated misincorporation in Poales, Caryophyllales, Asparagales, Alismatales and Fabales (Crossosomatales lacked a reference genome); the Holocene core gave a 3.15:1 ratio of mapped plant reads vs the older core. · Abundance of ancient plant reads; Verification of Ancient Reads

Methods, data and reproducibility

DNA from 88 sediment samples across two Lake Elsinore cores was built into single-stranded libraries, enriched with Angiosperms353 and mammal mitochondrial baits, mapped with BWA aln to OneKP and NCBI references, collapsed to plant orders, and compared across fire, paleoclimate and human-activity bins using Kruskal-Wallis/Dunn tests and Jaccard ordination.

  • Lake Elsinore sediment cores LEDC10-1 and LEGC03-3 (archived at 4 °C, collected 2010 and 2003), 1cm plugs spanning 24,000 years; shotgun and target-capture libraries · environmental DNA (land plants, algae, mammals, other taxa) · n = 88 sediment samples; 8 extraction blanks · PRJNA1465454 (NCBI SRA BioProject)
  • OneKP plant transcriptome reference, supplemented with NCBI RefSeq data for 9 families, plus NCBI eukaryote and prokaryote mitochondrial and nuclear genomes · multiple (green plants, eukaryotes, prokaryotes) · n = over 1,400 green plants (OneKP)
  • NCBI reference genomes for mapDamage authenticity checks: Juncus effusus, Cereus fernanbucensis, Platanthera zijinensis, Triglochin maritima, Trifolium repens · plants (one species per tested order) · n = five orders tested · GCA_027726005.1; GCA_024363205.1; GCA_039513925.1; GCA_001185155.1; GCA_030408175.1
  • Human reference genome used to remove human-derived reads before SRA submission · human · GRCh38.p13
  • Published Lake Elsinore proxies: charcoal counts (Martinez 2020; O'Keefe 2023), percent sand (Kirby 2010, 2018), LOI organic matter, pollen, and MAAT (Feakins 2019)
  • Archaeological, demographic and ethnographic chronology (Grenda 1997; Daisy Cave 18,670 cal BP; Arlington Man 13,000 ybp) used to define human-activity phases · n = 6 phases
  • CalFlora native-species records used to discard non-California plant orders and list native genera for Riverside County · plants (California flora) · n = 12 orders removed
Methods & tools
Angiosperms353 target capture baits (MyBaits v3 protocol, Arbor Biosciences), Megamammals capture baits (72 mammal mitochondria), Single-stranded library preparation (Kapp et al. 2021), Illumina NextSeq 550, FastP (v0.23.1; v.0.23.4), BWA aln (v0.7.17), BBMap / BBMask (v38.00), samtools (v1.13), Bowtie2 (v2.4.4), Picard Tools (v3.0), mapDamage (v. 2.3.0), BLASTn, R (v.4.4.0): stats Kruskal-Wallis, dunn.test, mgcv GAM, phyloseq (v1.41.1), vegan (v2.6.8), ranacapa (v0.1.0), ggplot2 (v3.5.1)
Data & accessions
https://calflora.org/
Software & environment
FastP v0.23.1/v.0.23.4, BWA aln v0.7.17, BBMask v38.00, samtools v1.13, Bowtie2 v2.4.4, Picard v3.0, mapDamage v. 2.3.0, R v.4.4.0 (phyloseq v1.41.1, vegan v2.6.8, ranacapa v0.1.0, ggplot2 v3.5.1, mgcv v1.9.1); no container specified.
Reproducibility gaps
Raw reads are in NCBI SRA BioProject PRJNA1465454 (no URL printed), with primate reads removed to respect Tribal sovereignty; test statistics and the filtered data frame sit in Supplementary Documents of unstated hosting; no container or lockfile.
Limitations (6)
  • Taxa were resolved only to order owing to read degradation and missing references (32 California plant families unrepresented); Angiosperms353 did not target fern, gymnosperm or lycopod orders, so woodland gymnosperms such as Juniperus and Pinus were not recovered. · stated by the authors
  • Warm-climate preservation produced sparse, short reads and weaker recovery than pollen for some taxa such as oaks; primate reads made up 35% of quality-filtered reads, and the cores lacked enough reliable mammal sedaDNA to test against fire, climate or demography. · stated by the authors
  • Sampling at ∼272-year intervals (vs ∼43 years in the prior charcoal study) limits detection of immediate post-fire vegetation responses, and the Pre-archaeological Evidence and European Arrival bins were likely too small to show significant differences. · stated by the authors
  • Fire, climate and human activity are intertwined drivers at the Pleistocene-Holocene transition and remain difficult to separate; linking Holocene Fagales and Solanales shifts to Indigenous use is acknowledged as speculative, and green algae reads were not validated. · stated by the authors
  • Period definitions and results are reported inconsistently: the intense-fire transition is 13,200-10,200 ybp in Results but 13,250-10,000 ybp in Methods, and the Solanales rise is Early-to-Late Holocene in Results but Middle-to-Late in the Discussion. · noted in this summary
  • Order-level relative read abundance after bait capture may reflect uneven bait affinity and reference coverage rather than plant biomass, and the text reports only directions of Dunn contrasts without test statistics, p-values or per-bin sample sizes. · noted in this summary

Read this if you work with ancient sedimentary DNA from warm or Mediterranean-type settings, or want to combine target-capture plant records with fire, paleoclimate and Indigenous ethnobotanical evidence.

Citations
0

Reproducibility ledger

Nobody has reported trying to reproduce this paper yet. Did you replicate an experiment or run the code? Your report saves the next lab a week.

Sign in to file a reproducibility report.

Related papers

Similarity Map
SelectedSame fieldCross-field
THISBaker '25Tonno '20Murchie '19Beaulieu '26Madrigal-Tr '21Kjær '25
61% semantic matchEcology
Dorothy Nevé Baker, Darren J. Larsen, Emily Fairfax+3 more·Ecosphere·Oct 1, 2025