Research

Ligia occidentalis, known as the sea slater, is a common isopod found scuttling on the rocky intertidal along the US and Mexican Pacific coast, unable to cross water or travel far. Molecular phylogeographic studies of L. occidentalis across much of its range demonstrated extensive genetic diversity and deep divergences, however these populations are morphologically indistinguishable. Advances in statistical and molecular applications to systematics have resulted in robust novel species descriptions based on molecular characters alone, including within Ligia. We leveraged 235 publicly available sequences from GenBank and BOLD, along with 26 specimens from the Los Angeles Natural History Museum, representing 262 localities from Oregon to Guerrero, Mexico, to assess whether distinct species of Ligia could be identified. We analyzed 16S and COI sequence data using distance- and tree-based methods to investigate genetic divergence among Ligia populations in the Los Angeles Harbor region. We conducted phylogenetic analyses and used four molecular species delimitation approaches, including Automatic Barcode Gap Discovery and Assemble Species by Automatic Partitioning, to test whether these populations represent independent evolutionary lineages. By integrating macroevolutionary and population genetic analyses comparing Los Angeles populations with other coastal populations, we identify and distinguish a novel, previously unrecognized species.

Cowcod (Sebastes levis) is a long-lived species of rockfish known for its distinctive coloration and large size, making them a popular target for recreational and commercial fisheries, leading to severe overfishing. As a result, Cowcod populations declined dramatically, reducing their unfished biomass to an estimated 7% of historical stocks. This has prompted the establishment of Cowcod Conservation Areas to allow the species to recover.  Previous studies suggested the existence of three distinct genetic lineages, one north and two south of Point Conception, California. This project will use a genome assembly coupled with low coverage whole genome sequencing to assess variation and population structure across the species’ geographic range through genome-wide diversity (θ) admixture analysis, principal component analysis (PCA), and pairwise population differentiation (FST). Preliminary analysis produced a contiguous genome with elevated BUSCO scores for Cowcod. Additionally, genome-wide SNPs revealed two lineages with a genome-wide FST of 0.13, a value similar to what is found in other distinct species.  Genome-wide diversity (θ) was lower in Cowcod compared to other species, which could be due to recent overfishing or historical events. This preliminary work will be expanded with additional data to determine the geographical extent of the different lineages and if there is mixture amongst the groups, potentially contributing to the development of future fisheries management.

Type specimens are a vital component of scientific understanding and biodiversity research. A type is an exemplary specimen of a taxon that serves to establish uniform features of that particular species. They anchor species descriptions and are critical for taxonomists working on revisions or new descriptions, and are the most valuable specimens in a natural history collection. The Marine Biodiversity Center at the Natural History Museum of Los Angeles County is currently digitizing 200+ glass slides containing crustacean type material. These slides include small species (<5mm) and their numerous dissected body parts. Here we present the workflow developed to efficiently stabilize, curate, digitize, and mobilize these specimens. The digitization pipeline begins with a full specimen inventory and condition assessment to determine curation needs. Each slide then proceeds through a standardized sequence of curation, digitization, and label imaging. Significant challenges include slides in poor condition with missing coverslips, cracked slides, and non-archival grade materials as well as incomplete taxonomic data requiring archival backtracking and additional taxonomic research. We offer solutions to address these issues without sacrificing efficiency. Stabilizing and maintaining these physical objects in perpetuity is essential to understanding our natural world. Making their data freely available is invaluable to protecting our world’s biodiversity.

Sphaeromatidae is a family of nearly 700 species of small, mostly shallow marine isopods. Its members demonstrate high morphological variability, which has contributed to a long and often conflicted taxonomic history. Previous attempts to construct molecular phylogenies have confirmed monophyly of the family and identified distinct supra-generic groupings, but were unable to resolve many deeper relationships due to extremely variable expansion regions in the otherwise slowly evolving 18S rDNA gene. Because hydrogen-bonded stem regions of the ribosomal RNA are more strongly conserved than the unbonded loop regions, sections of these variable insertions can be aligned with high confidence and preserve phylogenetic signal. With specimens at the Natural History Museum of Los Angeles, we produce more accurate alignments for 16S and 18S rDNA, by accounting for the evolutionary constraints of RNA secondary structure, and combine them with COI sequences for better resolution of a multi-locus sphaeromatid phylogeny. Hundreds of sequences are already published for these three loci, including for difficult to sample species, so re-analysis which leverages existing data is a practical way to resolve phylogenetic relationships. We also add representatives of previously unsequenced genera, improving taxonomic coverage. Our phylogeny sets the stage for exploring the biogeography, morphological innovations, reproductive systems, and diversification of this abundant, widespread isopod family.

Cymothoid isopods are well-known fish parasites, with members of Ceratothoa commonly found in the buccal cavity. Despite a high incidence of infection, we document a previously-unreported host-parasite relationship on Zebra Perch (Kyphosus azureus), an herbivorous fish in the shallow marine waters off Southern California. We observe the presence of a potentially undescribed Ceratothoa that exhibits an atypical attachment pattern. Infamously most congeners attach to the tongue, but these female isopods are primarily located on the roof of the fish’s mouth. Micro-computer tomography (μCT scanning) on both male and female specimens provides insight to the internal isopod reproductive anatomy. Due to their lifestyle as sequential hermaphrodites and limited swimming ability as adults, their mating dynamics are a mystery.  Observations of females revealing various stages of brood development allow for this unexplored isopod system to be a model for paternity testing, since multiple males can be associated with a single female within Cymothoidae. Our findings thus far provide a foundation for determining whether this represents a new species or reveals a much larger range for a member of Ceratothoa than previously known, as comprehensive mapping and molecular research has been limited. By integrating morphological data with high-resolution imaging, our findings pave the way for a formal description of this unique population and its ecological role in the Eastern Pacific. 

Formalin preservation is an invaluable tool for preserving morphology in marine invertebrate specimens across museum collections. These specimens have long been deemed unusable for molecular analysis due to the various damages that formalin induces in DNA. Current DNA extraction protocols for formalin preserved specimens rely widely on commercial kits and/or hazardous methods, such as phenol-chloroform or highly alkaline reagents. To counter these challenges, we developed a low-cost DNA extraction workflow without using commercial kits. A slightly alkaline, SDS-based lysis buffer was used in overnight digestion of formalin-preserved samples (>10 years) that had later been moved to ethanol, followed by extraction with in-house buffers. One sample lot (n=20 extractions) from each of the following crustacean species was used: Caprella mutica, Phronima sedentaria, and Porcelio scaber americanus. Internal tissue from the lower extremity of a Bathynomus giganteus individual was also used (n=10 extractions). DNA was recovered from all samples and all species amplified for the 16S marker. Successful reactions were sequenced using Nanopore, and sequences from 3 of the 4 species (with the exception of P. sedentaria) aligned with their taxonomically identification using BLAST. This workflow produced a low-cost, accessible approach to generating genetic support for taxonomic identification, making predominantly older and formalin preserved natural history collections available for study. 

Phreatoicidea is a suborder of isopods (Crustacea, Peracarida) that first appear in the fossil record and become widely distributed in marine habitats during the Carboniferous period 300–325 MYA. Today, there are 114 described extant species in 6 families that are restricted to freshwater systems, including subterranean aquifers, groundwater-fed springs, seepages, and even muddy road ruts. These extant members are restricted to geographic regions that comprised Gondwanaland in the early Jurassic (200 MYA). Although morphological phylogenies supported a basal relationship to all other isopods, some recent molecular phylogenies instead nest Phreatoicidea with other Isopoda. Despite their importance in understanding deeper phylogenies of Isopoda, relationships within the suborder Phreatoicidea have not been addressed with molecular data. For instance, one morphological phylogeny proposed that Pilbarophreatoicus in northwestern Australia is more closely related to two Indian genera than to many other Australian Phreatoicidea. Currently, no molecular data is available to test this claim. This project combines publicly available sequences with new 18S rRNA, 16S rRNA, and Cytochrome Oxidase 1 data from extant species to construct the most robust molecular phylogeny to date, shedding light on the origins of the current distribution. This effort provides a molecular backbone for the suborder, the first step toward understanding the isolation and radiation of a once ubiquitous taxon.