Biology subjects

Beraut, E.

Publications and source records attributed to Beraut, E..

5 recordsLinked to original sources

bioRxiv2025

A chromosome-level genome assembly of a vernal pool specialist amphibian, the Western Spadefoot, Spea hammondii

We assembled and annotated a chromosome-level reference genome for the Western Spadefoot, Spea hammondii (Anura, Scaphiopodidae) representing one of only three amphibians included in the California Conservation Genomics Project (CCGP). Spea hammondii is a vernal pool breeding anuran native to California and northwestern Baja California which has undergone both range contractions and local extirpations across its distribution, primarily due to habitat loss and degradation and drought. The species is recognized by the state of California as a Species of Special Concern and is proposed for listing under the United States Endangered Species Act. Using the established CCGP pipeline, this S. hammondii genome was produced using Pacific Biosciences HiFi long-reads and Omni-C proximity ligation, resulting in a de novo genome assembly 1.14 Gb in length, distributed across 479 scaffolds (scaffold N50 = 120.8 Mb; largest scaffold = 183.6 Mb) with a BUSCO completeness score of 90.9% using a conserved tetrapod ortholog set. Our assembly shows high base accuracy (QV = 63.7) and low frameshift error in coding regions (QV 50.42). Annotation of this genome yielded 20,434 genes with a BUSCO completeness score of 94.7%. This reference genome, in combination with range-wide resequencing data from CCGP, will facilitate statewide population genomic assessments to delineate conservation units, quantify inbreeding and genomic load, and test for adaptive variation associated with vernal pool hydrology and drought tolerance, all of which are important considerations in the proposed federal listing.

genomics↗

bioRxiv2024

A highly contiguous genome assembly for the Yellow Warbler (Setophaga petechia)

The Yellow Warbler (Setophaga petechia) is a small songbird in the New World Warbler family (Parulidae) that exhibits phenotypic and ecological differences across a widespread distribution and is important to Californias riparian habitat conservation. Here, we present a high-quality de novo genome assembly of a vouchered female Yellow Warbler from southern California. Using HiFi long-read and Omni-C proximity sequencing technologies, we generated a 1.22 Gb assembly including 687 scaffolds with a contig N50 of 6.80 Mb, scaffold N50 of 21.18 Mb, and a BUSCO completeness score of 96.0%. This highly contiguous genome assembly provides an essential resource for understanding the history of gene flow, divergence, and local adaptation and can inform conservation management of this charismatic bird species.

evolutionary biology↗

bioRxiv2023

Remarkably high repeat content in the genomes of sparrows: the importance of genome assembly completeness for transposable element discovery.

Transposable elements (TE) play critical roles in shaping genome evolution. However, the highly repetitive sequence content of TEs is a major source of assembly gaps. This makes it difficult to decipher the impact of these elements on the dynamics of genome evolution. The increased capacity of long-read sequencing technologies to span highly repetitive regions of the genome should provide novel insights into patterns of TE diversity. Here we report the generation of highly contiguous reference genomes using PacBio long read and Omni-C technologies for three species of sparrows in the family Passerellidae. To assess the influence of sequencing technology on TE annotation, we compared these assemblies to three chromosome-level sparrow assemblies recently generated by the Vertebrate Genomes Project and nine other sparrow species generated using a variety of short- and long-read technologies. All long-read based assemblies were longer in length (range: 1.12-1.41 Gb) than short-read assemblies (0.91-1.08 Gb). Assembly length was strongly correlated with the amount of repeat content, with longer genomes showing much higher levels of repeat content than typically reported for the avian order Passeriformes. Repeat content for the Bells sparrow (31.2% of genome) was the highest level reported to date for a songbird genome assembly and was more in line with woodpecker (order Piciformes) genomes. CR1 LINE elements retained from an expansion that occurred 25-30 million years ago were the most abundant TEs in the song sparrow genome. Although the other five sparrow species also exhibit evidence for a spike in CR1 LINE activity at 25-30 million years ago, LTR elements stemming from more recent expansions were the most abundant elements in these species. LTRs were uniquely abundant in the Bells sparrow genome deriving from two recent peaks of activity. Higher levels of repeat content (79.2-93.7%) were found on the W chromosome relative to the Z (20.7-26.5) or autosomes (16.1-30.9%). These patterns support a dynamic model of transposable element expansion and contraction underpinning the seemingly constrained and small sized genomes of birds. Our work highlights how the resolution of difficult-to-assemble regions of the genome with new sequencing technologies promises to transform our understanding of avian genome evolution.

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↗

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↗