Biology subjects

Meyer, R. S.

Publications and source records attributed to Meyer, R. S..

9 recordsLinked to original sources

bioRxiv2026

Genomic and phenotypic adaptation tunes an endangered California plant to the fog that climate change and wind energy will reshape

Mediterranean-climate regions support some of the most diverse and endemic-rich plant communities in the world, yet the genomic basis of plant adaptation to coastal fog, which buffers dry-season water stress in at least some of these systems, remains almost entirely uncharacterized. We investigated the population genomics of the endangered Gaviota tarplant (Deinandra increscens subsp. villosa), endemic to the fog-swept central California coastline, where a wind farm has recently been built across the largest remaining population. Using whole-genome resequencing across the fragmented range of the subspecies, we found a non-directional association between wind connectivity and genetic similarity, suggesting that the wind farm could affect gene flow among plant stands. Genome-wide association analyses identified polygenic local adaptation to fog, with GO enrichment analyses converging on the importance of cell wall remodelling, osmoregulation, developmental timing, light perception, and immunity. Herbarium specimens spanning a century reveal broader architecture and fewer disk florets in foggier, wetter sites, traits that may be underpinned by candidate genes we uncovered. Of 31 fog-associated genomic peaks, only a centromere-associated haplotype showed one of the strongest spatial associations with long-term fog and uniquely tracked germination-year fog, suggestive of early-season environmental filtering. A year of extreme drought and unusually rich fog yielded two further signals consistent with this: increased long runs of homozygosity and a smoother landscape-level allele-frequency surface. This baseline identifies candidate climate-resilient genotypes for active management and motivates experimental trials to test early-season filtering of fog-adaptive genotypes.

evolutionary biology↗

bioRxiv2026

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

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.

paleontology↗

bioRxiv2024

The reference genome of an endangered Asteraceae, Deinandra increscens subsp. villosa, endemic to the Central Coast of California

We present a high-quality reference genome of the federally endangered Gaviota tarplant, Deinandra increscens subsp. villosa (Madiinae, Asteraceae), an annual herb endemic to the Central California coast. Stewards of remaining populations have planned to apply conservation strategies informed by whole genome approaches. Generating PacBio Hifi, Oxford Nanopore Technologies, and Dovetail Omni-C data, we assembled a genome of 1.67 Gbp as 28.7 K scaffolds with a scaffold N50 of 74.9 Mb. BUSCO completeness for the final assembly was 98.1% with 15.7% duplicate copies. We annotated repeat content in 74.8% of the genome. Long terminal repeats (LTR) covered 44.0% of the genome with Copia families predominant at 22.9% followed by Gypsy at 14.2%. Both Gypsy and Copia elements were common in ancestral peaks of LTR, and the most abundant element was a Gypsy element containing nested Copia/Angela sequenced similarity, reflecting a complex evolutionary history of repeat activity. Gene annotation produced 41,039 genes and 69,563 transcripts, of which >99% were functionally annotated. BUSCO duplication rates remained very high with proteins at 50.4% complete duplicates and 46.0% single copy. Whole genome duplication (WGD) synonymous mutation rates of Gaviota tarplant and sunflower (Helianthus annuus) shared peaks that correspond to the last Asteraceae polyploidization event and subsequent divergence from a common ancestor at [~]27 mya. Tandem genes were twice as prevalent as WGD genes suggesting tandem genes could be an important strategy of environmental adaptation in this species. Article SummaryWe introduce a high-quality reference genome for the endangered Gaviota tarplant. The assembly is 1.67 Gbp with 98.1% BUSCO completeness and 41 K annotated genes. We find extensive Copia long terminal repeat sequences and tandem genes that suggest environmental adaptation strategies. Comparisons with sunflower suggest a shared polyploidization event around 27 million years ago, close to the date of the common ancestor divergence. This work underlines the importance of genomic studies in accurately understanding adaptations and conservation needs.

genomics↗

bioRxiv2022

Environmental DNA reveals invasive crayfish microbial associates and ecosystem-wide biodiversity before and after eradication

Biodiversity monitoring in conservation projects is essential to understand environmental status and recovery. However, traditional field surveys can be expensive, time-consuming, biased towards visual detection, and focused on measuring a limited set of taxa. Environmental DNA (eDNA) methods provide a new approach to biodiversity monitoring that has the potential to sample a taxonomically broader set of organisms with similar effort, but many of these approaches are still in the early stages of development and testing. Here, we use multilocus eDNA metabarcoding to understand how the removal of invasive red swamp crayfish impacts local biodiversity of a desert oasis ecosystem, as well as to detect crayfish both directly and indirectly. We tracked crayfish DNA signatures, microbial DNA associated with crayfish, and biodiversity of plant, fungal, animal, and bacterial communities through time. We were unsuccessful in detecting crayfish directly in either control tanks or oases using targeted metabarcoding primers for invertebrates and eukaryotes, similar to previous studies which have shown variable levels of success in detecting crayfish from environmental samples. However, we were successful in discerning a suite of 90 crayfish-associated taxa to serve as candidate bioindicators of invasive presence using 16S and Fungal ITS2 metabarcoding. Ranking these 90 taxa by their geographic distribution in eDNA surveys and by evidence of crayfish-associations in the literature, we support 9 taxa to be high-ranking, and suggest they be prioritized in future biomonitoring. Biodiversity analyses from five metabarcode loci including plants, animals, and both prokaryotic and eukaryotic microbes showed that communities differed but that species richness remained relatively similar between oases through time. Our results reveal that, while there are limitations of eDNA approaches to detect crayfish and other invasive species, microbial bioindicators offer a largely untapped biomonitoring opportunity for invasive species management, adding a valuable resource to a conservation managers toolkit.

ecology↗

bioRxiv2021

From zero to infinity: minimum to maximum diversity of the planet by spatio-parametric Rao's quadratic entropy

AimThe majority of work done to gather information on Earth diversity has been carried out by in-situ data, with known issues related to epistemology (e.g., species determination and taxonomy), spatial uncertainty, logistics (time and costs), among others. An alternative way to gather information about spatial ecosystem variability is the use of satellite remote sensing. It works as a powerful tool for attaining rapid and standardized information. Several metrics used to calculate remotely sensed diversity of ecosystems are based on Shannons Information Theory, namely on the differences in relative abundance of pixel reflectances in a certain area. Additional metrics like the Raos quadratic entropy allow the use of spectral distance beside abundance, but they are point descriptors of diversity, namely they can account only for a part of the whole diversity continuum. The aim of this paper is thus to generalize the Raos quadratic entropy by proposing its parameterization for the first time. InnovationThe parametric Raos quadratic entropy, coded in R, i) allows to represent the whole continuum of potential diversity indices in one formula, and ii) starting from the Raos quadratic entropy, allows to explicitly make use of distances among pixel reflectance values, together with relative abundances. Main conclusionsThe proposed unifying measure is an integration between abundance- and distance-based algorithms to map the continuum of diversity given a satellite image at any spatial scale.

ecology↗

bioRxiv2020

A Biodiversity Composition Map of California Derived from Environmental DNA Metabarcoding and Earth Observation

Unique ecosystems globally are under threat from ongoing anthropogenic environmental change. Effective conservation management requires more thorough biodiversity surveys that can reveal system-level patterns and that can be applied rapidly across space and time. We offer a way to use environmental DNA, community science and remote sensing together as methods to reduce the discrepancy between the magnitude of change and historical approaches to measure it. Taking advantages of modern ecological models, we integrate environmental DNA and Earth observations to evaluate regional biodiversity patterns for a snapshot of time, and provide critical community-level characterization. We collected 278 samples in Spring 2017 from coastal, shrub and lowland forest sites in California, a large-scale biodiversity hotspot. We applied gradient forest to model 915 family occurrences and community composition together with environmental variables and multi-scalar habitat classifications to produce a statewide biodiversity-based map. 16,118 taxonomic entries recovered were associated with environmental variables to test their predictive strength on alpha, beta, and zeta diversity. Local habitat classification was diagnostic of community composition, illuminating a characteristic of biodiversity hotspots. Using gradient forest models, environmental variables predicted 35% of the variance in eDNA patterns at the family level, with elevation, sand percentage, and greenness (NDVI32) as the top predictors. This predictive power was higher than we found in published literature at global scale. In addition to this indication of substantial environmental filtering, we also found a positive relationship between environmentally predicted families and their numbers of biotic interactions. In aggregate, these analyses showed that strong eDNA community-environment correlation is a general characteristic of temperate ecosystems, and may explain why communities easily destabilize under disturbances. Our study provides the first example of integrating citizen science based eDNA with biodiversity mapping across the tree of life, with promises to produce large scale, high resolution assessments that promote a more comprehensive and predictive understanding of the factors that influence biodiversity and enhance its maintenance.

ecology↗

bioRxiv2019

Beach environmental DNA fills gaps in photographic biomonitoring to track spatiotemporal community turnover across 82 phyla

AbstractEnvironmental DNA (eDNA) metabarcoding is emerging as a biomonitoring tool available to the citizen science community that promises to augment or replace photographic observation. However, eDNA results and photographic observations have rarely been compared to document their individual or combined power. Here, we use eDNA multilocus metabarcoding, a method deployed by the CALeDNA Program, to inventory and evaluate biodiversity variation along the Pillar Point headland near Half Moon Bay, California. We describe variation in presence of 13,000 taxa spanning 82 phyla, analyze spatiotemporal patterns of beta diversity, and identify metacommunities. Inventory and measures of turnover across space and time from eDNA analysis are compared to the same measures from Global Biodiversity Information Facility (GBIF) data, which contain information largely contributed by iNaturalist photographic observations. We find eDNA depicts local signals with high seasonal turnover, especially in prokaryotes. We find a diverse community dense with pathogens and parasites in the embayment, and a State Marine Conservation Area (SMCA) with lower species richness than the rest of the beach peninsula, but with beta diversity signals showing resemblance to adjacent unprotected tidepools. The SMCA differs in observation density, with higher density of protozoans, and animals in Ascidiacea, Echinoidea, and Polycladida. Local contributions to beta diversity are elevated in a section of East-facing beach. GBIF observations are mostly from outside the SMCA, limiting some spatial comparisons. However, our findings suggest eDNA samples can link the SMCA sites to sites with better GBIF inventory, which may be useful for imputing species from one site given observations from another. Results additionally support >3800 largely novel biological interactions. This research, and accompanying interactive website support eDNA as a gap-filling tool to measure biodiversity that is available to community and citizen scientists.

ecology↗

bioRxiv2019

Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with Nanopore sequencing

BackgroundLong-read sequencing facilitates assembly of complex genomic regions. In plants, loci containing nucleotide-binding, leucine-rich repeat (NLR) disease resistance genes are an important example of such regions. NLR genes make up one of the largest gene families in plants and are often clustered, evolving via duplication, contraction, and transposition. We recently mapped the Xo1 locus for resistance to bacterial blight and bacterial leaf streak, found in the American heirloom rice variety Carolina Gold Select, to a region that in the Nipponbare reference genome is rich in NLR genes.\n\nResultsToward identification of the Xo1 gene, we combined Nanopore and Illumina reads to generate a high-quality genome assembly for Carolina Gold Select. We identified 529 full or partial NLR genes and discovered, relative to the reference, an expansion of NLR genes at the Xo1 locus. One NLR gene at Xo1 has high sequence similarity to the cloned, functionally similar Xa1 gene. Both harbor an integrated zfBED domain and near-identical, tandem, C-terminal repeats. Across diverse Oryzeae, we identified two sub-clades of such NLR genes, varying in the presence of the zfBED domain and the number of repeats.\n\nConclusionsWhole genome sequencing combining Nanopore and Illumina reads effectively resolves NLR gene loci, providing context as well as content. Our identification of an Xo1 candidate is an important step toward mechanistic characterization, including the role(s) of the zfBED domain. Further, the Carolina Gold Select genome assembly will facilitate identification and exploitation of other useful traits in this historically important rice variety.

plant biology↗

bioRxiv2018

Anacapa Toolkit: an environmental DNA toolkit for processing multilocus metabarcode datasets

1. Environmental DNA (eDNA) metabarcoding is a promising method to monitor species and community diversity that is rapid, affordable, and non-invasive. Longstanding needs of the eDNA community are modular informatics tools, comprehensive and customizable reference databases, flexibility across high-throughput sequencing platforms, fast multilocus metabarcode processing, and accurate taxonomic assignment. As bioinformatics tools continue to improve, addressing each of these demands within a single bioinformatics toolkit is becoming a reality.\n\n2. We present the modular metabarcode sequence toolkit Anacapa (https://github.com/limey-bean/Anacapa/), which addresses the above needs, allowing users to build comprehensive reference databases and assign taxonomy to raw multilocus metabarcode sequence data A novel aspect of Anacapa is our database building module, Creating Reference libraries Using eXisting tools (CRUX), which generates comprehensive reference databases for specific user-defined metabarcode loci. The Quality Control and Dereplication module sorts and processes multiple metabarcode loci and processes merged, unmerged and unpaired reads maximizing recovered diversity. Followed by amplicon sequence variants (ASVs) detection using DADA2. The Anacapa Classifier module aligns these ASVs to CRUX-generated reference databases using Bowtie2. Taxonomy is assigned to ASVs with confidence scores using a Bayesian Lowest Common Ancestor (BLCA) method. The Anacapa Toolkit also includes an R package, ranacapa, for automated results exploration through standard biodiversity statistical analysis.\n\n3. We performed a series of benchmarking tests to verify that the Anacapa Toolkit generates comprehensive reference databases that capture wide taxonomic diversity and that it can assign high-quality taxonomy to both MiSeq-length and Hi-Seq length sequence data. We demonstrate the value of the Anacapa Toolkit to assigning taxonomy to eDNA sequences from seawater samples from southern California including capability of this tool kit to process multilocus metabarcoding data.\n\n4. The Anacapa Toolkit broadens the exploration of eDNA and assists in biodiversity assessment and management by generating metabarcode specific databases, processing multilocus data, retaining all read types, and expanding non-traditional eDNA targets. Anacapa software and source code are open and available in a virtual container to ease installation.

bioinformatics↗