Search for: All records

The close symbiotic relationships between vertebrates and their naturally-occurring bacterial microbiomes are an increasingly appreciated field of research for macro- and microbiologists alike. In many marine fish of the meso- and aphotic zones, bioluminescence is mediated by such symbioses, but the fragility, rarity, and physical inaccessibility of such taxa has prevented close analysis in the lab environment. The speciose fish genus Siphamia (Kurtiformes, Apogonidae), is an outlier among bioluminescent fish taxa in that members can be found in shallow reefs of both temperate and tropical ecoregions, making it far more accessible to research. In this study, we examine nuance in the association of Siphamia and its sole bioluminescent symbiote, the gram-negative proteobacterium Photobacterium mandapamensis. Colonies of P. mandapamensis were isolated from the ventral light organs of three different Siphamia species occupying three different climates. These bacterial isolates were screened using a PCR fingerprinting approach and unique genotypes were sequenced using Oxford Nanopore Technology. Our findings will likely shed new light on the specificity and evolution of this host-bacterium symbiosis, with temperate and tropical fish species potentially hosting different substrains of P. mandapamensis. Moreover, new substrains of P. mandapamensis - and potentially even a new species of the same genus - may be described from the light organs of previously-unexamined Siphamia species from temperate habitats. The close pairing between Siphamia and P. mandapamensis represents the first one-to-one vertebrate symbiosis to be studied extensively in the lab environment, and may soon become a model system for other vertebrate symbioses, especially in the deep ocean. 

Coral reefs are incredible hotspots of biodiversity, yet their existence is jeopardized due to drastic climatic events. Investigations of coral morphology using noninvasive approaches are crucial for taxonomic identification and resolving evolutionary relationships. The scleractinian coral genus Madracis is commonly found in Caribbean and western Atlantic reefs, where each of the six Madracis morphospecies has distinct but overlapping depth distributions. Here, we quantified phenotypic traits from macro photographs to understand how morphology varies along the depth gradient in Madracis. In total, macro photographs of 104 colonies at 5, 10, 20, or 40 meters in depth from Curaçao were analyzed for four morphospecies (M. carmbi, M. decactis, M. pharensis and M. senaria). We counted number of septa and measured intercorallite distance for 15 corallites per colony. The number of septa differed among the four Madracis morphospecies, ranging from an average of 8.66, 9.78, 9.37, and 6.60 septa for M. carmabi, M. decactis, M. pharensis and M. senaria, respectively. Average intercorallite distances were 1.09, 1.92, 1.07 and 1.2 millimeters for M. carmabi, M. decactis, M. pharensis and M. senaria, respectively. Our morphometric investigation using macro-photography is an effective method for quantifying the morphological diversity of living corals. This method allows greater sample sizes, less underwater effort and more importantly, avoids any damage to our already threatened corals. Furthermore, these data can be combined with genomic or ecological data to better understand the ecology and evolution of corals. 

Natural history collections are important resources for research and conservation. Unfortunately, sometimes certain taxa can be hard to identify to the species level or can be misidentified, impacting how those specimens and their accompanying data are used for future research and conservation. African tree frogs (Family Arthroleptidae, Genus Leptopelis) are a group of big-eyed tree frogs found across Sub-Saharan Africa. While they have morphological differences that can help tell members of the genus apart, when in the field species can look similar to each other which gives rise to them being misidentified or unidentified in collections. In particular, Leptopelis exhibit extensive intraspecific variation in coloration and pattern that makes identification based solely on morphology challenging. The goal of this project is to use DNA barcoding of the 16s mtDNA gene and morphological characteristics to update the identification of “Leptopelis sp.” specimens that are part of the California Academy of Science’s Herpetology collection to the species level. By comparing the genetic and morphological data collected to identified reference specimens in the Academy’s collection we can confirm species identification and update the Academy’s database. Having the opportunity to identify species in natural history collections using both genetic and morphological analysis helps us better understand what species are found in an area, and can reveal new localities and range expansions of poorly known species. These data serve as an important baseline for monitoring how species are adapting to global change and enable future research on these poorly known, charismatic frogs. 

Saw-scaled vipers (genus Echis) are small (up to 58 cm snout-to-vent length), venomous, eastern hemisphere snakes of the subfamily Viperinae. They are distributed across northern Africa, the Arabian Peninsula, and southwestern Asia. This group has been separated into four species complexes and twelve proposed species, however the true diversity within these groups is unclear even given numerous studies on this genus. This is partly due to uneven geographic sampling of specimens and tissue samples, overlapping distributions, and historically difficult to access species’ ranges making this genus difficult to research. Furthermore, previous studies have not used objective species delimitation approaches with either molecular or morphological data. Using recently collected tissue samples, we generate cytochrome b sequences for 24 specimens and combine these with sequences available on GenBank in order to create a time-calibrated phylogeny and estimate species level diversity using single locus species delimitation methods. We couple this with morphological analysis of specimens from the California Academy of Sciences and UC Berkeley Museum of Vertebrate Zoology collections, in order to determine if these genetically delimited species are morphologically diverged. These data can further aid in identifying specimens to species in this genus, as was demonstrated by classifying individuals to species within the Academy’s collection. 

Previous research supports the idea that all sea pens anchor to soft sediment using a long, basal, peduncle. The discovery of several pennatulacean sea pen species (rockpens) with an adaptation to bind to rocky substrata alters this understanding. The evolutionary history of octocorals, including these sea pens, has long been poorly understood due to a slow rate of mitochondrial gene evolution and a consequent lack of phylogenetically informative molecular markers to distinguish species. The objective of this project is to analyze three species of rockpens (Calibelemnon francei, Anthoptilum gowlettholmesae, Anthoptilum sp. Alaska) and other octocorals to construct a phylogeny to better understand the evolutionary relationships between these taxa. Using preserved specimens from the California Academy of Sciences' Department of Invertebrate Zoology, the genes of ten octocoral species were analyzed. This project sequenced three protein-coding mitochondrial genes, ND2, ND6, and msh1, and phylogenetic tree construction and analysis were done using Geneious and R Studio. Additionally, SEM photographs of the sclerites were used to morphologically characterize the taxa. We hypothesize that all rockpens actually belong to the genus Anthoptilum and form a monophyletic clade with other species of the genus that do not inhabit rocky substrata. Future research will require investigating how other non-rock inhabiting species in the genus Anthoptilum are phylogenetically related to the rockpens. 

Science comics have become an increasingly popular medium for science communication. Reputable institutions and publications such as the WHO, NASA, Nature Journal and MacMillan Publishers have published science comics to explain complex scientific and medical phenomena to the public. However, science comics that center the stories of underrepresented scientists and the ways in which their intersectional identities are transforming science have yet to be created. Concerningly, people of color, women, and LGBTQIA+ identifying continue to be underrepresented in STEMM. Studies have shown students who report feeling positive STEMM identity and ability in high school declared undergraduate STEMM majors at greater proportions. Therefore, identifying ways to foster a sense of belonging and personal interest in STEMM among secondary school students is crucial. Utilizing art and narrative storytelling, The Field Scientist challenges perceptions of what science looks like and who does science to make science more accessible, exciting and inclusive for underrepresented secondary school students.. The series follows the real biographical narratives of a diverse cohort of scientists as they recount their most memorable field experiences. The Field Scientist will be available digitally via the platform issuu.com and disseminated to secondary school students. Online surveys will be utilized to elicit audience response, assess feelings of belonging and determine the effectiveness of science comics in challenging perceptions of exclusionary scientific culture and community. Ultimately, The Field Scientist aspires to encourage adolescent audiences to view themselves as scientists and contemplate how their identities can further transform the shifting landscape of science. 

The California floristic province is home to more than 30% of all Castilleja species across the North American wildflower genus (family Orobanchaceae). While some of the approximately 200 species are distinct morphologically, the five species composing the coastal California Castilleja species complex exhibit overlapping morphologies and geographic ranges, which poses particular challenges for species identification. To determine species, current keys employ a combination of geography, leaves, and reproductive structures. The sepals, known collectively as the calyx, are modified leaves that protect the flower and have historically been one of several important traits for diagnosing species in the complex. In this project, we utilized geometric morphometrics to quantify and describe calyx shape for three calyces per individual of five individuals across seven species, including two outgroups (n = 84). While traditional morphometrics only capture linear variation, geometric morphometrics translate more complex elements of shape. Calyx outlines were created from field scans and analyzed with Procrustes-based geometric morphometrics using three landmarks, followed by elliptic Fourier analysis. The first principal component axis across all samples explained 43.8% of variation and emphasized the depths of the calyx clefts relative to each other. Several species overlap in the morphospace while others remain distinct, which suggests limited morphological differentiation of the calyx across species and may allow for variation in successful pollination. Future analyses will quantify morphological variation in other floral organs observed both within individuals and within species to comprehensively assess morphological variation in the complex. 

Webs play many essential roles in spider biology, including communication, prey capture, locomotion, and reproduction. One interesting morphological feature of many spiders is the cribellum, a plate located near the silk-producing structures called spinnerets, and used to create a special type of matted silk that captures prey mechanically, instead of with glue droplets used by many orb-weaving spiders. The cribellum is hypothesized to have been present in the ancestor of all araneomorph spiders, but lost multiple times over the course of spider evolution. One group of spiders, the ‘marronoids’, shows a pattern of repeated loss and gain of this structure, placing them at a transitional position in the evolution of spider webs, with further implications for the web capture strategy, and other ecological conditions such as water-associated habitat. Studying the timing of the loss of the cribellum may yield insight to the cryptic ecology and morphology of the marranoid clade, and more broadly, araneomorph spiders. We use comparative phylogenetic methods to identify ancestral states of morphological and behavioral characters, and examine divergence dates with fossil calibrations. To do this, 98 representative spiders from the marronoid clade were coded by zoogeographic region, distribution proximity to a body of water and type, web type, and observed aquatic behavior. The morphology of the cribellum and spinnerets was assessed using 42 characters with multiple states. We identified patterns of evolution of the cribellum and aquatic habitat associations in the context of phylogeny, and geologic time. 

Scientific collections hold value in a wide range of fields, from conservation to species-restoration. However, many are unaware of collections’ direct contributions to scientific discovery. Collections are a key source of data, but may not be emphasized to emerging scientists as such. While institutions make collections more accessible, preserved specimens may be misunderstood as nothing more than static, dead creatures in cabinets. To combat this, I created a StoryMap on the history of specimen collections and how they have changed, with case-studies and interviews from the California Academy of Sciences that illuminate collections’ roles in modern conservation. StoryMaps are interactive multimedia pieces that present information in novel, highly engaging ways. This more-accessible medium allows for an easily digestible story encompassing 100 years of specimen-collection. Participants between the ages of 18-25 will answer questions before and after reading the StoryMap to gauge how perceptions of the value of scientific collections have changed. Ultimately, this project endeavors to leave young adults with a deeper appreciation for specimen collections and thus contribute to them centering specimens in future decision-making. Young adults are a key generation that is shaping the future of science. Thus, comprehending the value of specimen collections is paramount to ensuring collections are adequately supported in the future, and that research in species conservation continues. As technology rapidly advances, the value of specimen collections grows, and supporting their stewardship ensures access to historical data as new research questions emerge.