Biology subjects

Glass, J. R.

Publications and source records attributed to Glass, J. R..

7 recordsLinked to original sources

bioRxiv2026

Mean temperature determines whether winter variability accelerates or buffers energy loss

Winter survival in dormant animals depends on conserving finite energy reserves, yet winter temperatures fluctuate around shifting means. In ectotherms, metabolic rate increases exponentially with temperature, so thermal variability is expected to accelerate energy loss, with important consequences for overwinter survival and population persistence under climate change. However, it remains unclear whether dormant ectotherms can compensate physiologically for thermal variability. We overwintered Bombus impatiens queens under constant (2, 3, 4{degrees}C) or variable (2 {+/-} 6{degrees}C or 4 {+/-} 6{degrees}C) regimes for six weeks, then measured metabolic rates across a range of temperatures. The temperature dependence of metabolic rate shifted in response to thermal experience, but the direction of compensation depended on mean temperature: variability centered on 2{degrees}C elevated metabolic rate and increased thermal sensitivity relative to all other conditions, whereas variability centered on 4{degrees}C reduced metabolic rate and dampened thermal sensitivity relative to constant 4{degrees}C. We used these metabolic responses to simulate rates of lipid depletion and found that survival trajectories echoed physiological shifts: experiencing variability around 2{degrees}C would reduce subsequent survival time, whereas experiencing variability around 4{degrees}C would preserve subsequent survival even under variable future conditions. Thus, identical thermal variance produced opposite energetic outcomes depending on the mean temperature around which fluctuations occurred. Integrating both temperature means and variability is, therefore, essential for predicting overwintering survival in a changing world.

physiology↗

bioRxiv2026

A chromosome-level reference genome for Pacific herring (Clupea pallasii) from the Bering Sea

Pacific herring (Clupea pallasii) serve as a critical trophic link between plankton and many marine species targeted by fisheries. With a broad distribution throughout the North Pacific Ocean, from the Arctic to temperate latitudes, herring hold ecological, economic, and cultural importance. Despite this importance, genomic resources for this species, such as reference genome sequences, have only recently become available. To date, only one scaffold-level reference genome, representing a specimen from the Gulf of Alaska (Vancouver; 1,379 scaffolds), has been published to NCBI. Addressing this data gap, we produced a high quality 795Mb genome sequence organized into 26 chromosomes combining long read sequencing with short read sequencing of proximity ligation libraries. Our assembly is highly complete (BUSCO score of 97.7%) and contiguous (922 contigs, N50 = 7,338,470, L50 = 38; 26 scaffolds, N50 = 31,494,017; L50 = 12). Pacific herring south of the Aleutian Islands and the Alaska Peninsula are genetically differentiated from those in the Bering Sea, making a reference genome from the eastern Bering Sea an important addition to the Pacific herrings genomic toolbox.

genomics↗

bioRxiv2025

Cryptic diversity arises from glacial cycles in Pacific herring, a critical forage fish

Forage fishes are biological drivers throughout the Pacific Ocean, from the Arctic to nearly subtropical latitudes. As a critical trophic link, the health and stability of Pacific herring (Clupea pallasii) populations have implications for other marine species, including several targeted by large, productive fisheries. Previous research has indicated marked divergence between Pacific herring in the Bering Sea and the Gulf of Alaska. Seeking to localize this biogeographic break, we generated low coverage whole genome resequencing data for 120 Pacific herring from seven sites across the northern Gulf of Alaska and the eastern Bering Sea and Aleutian Islands. Single nucleotide polymorphisms across the mitogenome (267) and nuclear genome ([~]5.6 million) corroborate a biogeographic break in Pacific herring along the Alaska Peninsula and Aleutian Islands, as far west as Unalaska. We identified two distinct populations: one exists along the northern coasts of the Aleutian Islands and in the eastern Bering Sea; the other occupies the southern edge of the Aleutians and the Gulf of Alaska. Two mitochondrial haplogroups co-occurring at collection sites across the Gulf of Alaska suggest secondary contact between two populations, likely representing glacial refugia. Our results underscore the importance of geological events to contextualize the diversification of forage fish species.

genomics↗

bioRxiv2022

Widespread sympatry in a species-rich clade of marine fishes (Carangoidei)

The patterns of speciation in marine fishes are largely unknown, in part due to the deficiency of species-level phylogenies and information on species distributions, and partly due to conflicting relationships between species dispersal, range size, and patterns of co- occurrence. Most research on global patterns of marine fish speciation has focused on coral reef or pelagic species. Carangoidei is a clade of marine fishes including the trevallies, remoras, and dolphinfishes that utilize both coral reef and pelagic environments, spanning the ecologies of coral reef obligate and open-ocean species. We used sequence capture of 1314 ultraconserved elements (UCEs) from 154 taxa to generate a phylogeny of Carangoidei and its parent clade, Carangiformes. Age-range correlation analyses of the geographic distributions and divergence times of sister species pairs reveal widespread sympatry, with 73% of sister species pairs exhibiting a sympatric geographic distribution, regardless of node age, and most species pairs co-existing across large portions of their ranges. We also observe greater disparity in body size and water column depth utilization between sympatric than allopatric sister species. These and other ecological or behavioral attributes likely facilitate sympatry among the most closely related carangoid species, which exhibit sympatry at a larger taxonomic scale than has previously been described in marine fishes.

evolutionary biology↗

bioRxiv2021

Genome of a Giant (Trevally): Caranx ignobilis

Caranx ignobilis, commonly known as the kingfish or giant trevally, is a large, reef-associated apex predator. It is a prized sportfish, targeted heavily throughout its tropical and subtropical range in the Indian and Pacific Oceans, and it has drawn significant interest in aquaculture due to an unusual tolerance for freshwater. In this study, we present a high-quality nuclear genome assembly of a C. ignobilis individual from Hawaiian waters, which have recently been shown to host a genetically distinct population. The assembly has a contig NG50 of 7.3Mbp and scaffold NG50 of 46.3Mbp. Twenty-five of the 203 scaffolds contain 90% of the genome. We also present the raw Pacific Biosciences continuous long-reads from which the assembly was created. A Hi-C dataset (Dovetail Genomics Omni-C) and Illumina-based RNA-seq from eight tissues are also presented; the latter of which can be particularly useful for annotation and studies of freshwater tolerance. Overall, this genome assembly and supporting data is a valuable tool for ecological and comparative genomics studies of kingfish and other carangoid fishes.

genomics↗

bioRxiv2021

Genome Assembly of the Roundjaw Bonefish (Albula glossodonta), a Vulnerable Circumtropical Sportfish

BackgroundBonefishes are cryptic species indiscriminately targeted by subsistence and recreational fisheries worldwide. The roundjaw bonefish, Albula glossodonta is the most widespread bonefish species in the Indo-Pacific and is listed as vulnerable to extinction by the IUCNs Red List due to anthropogenic activities. Whole-genome datasets allow for improved population and species delimitation, which - prior to this study - were lacking for Albula species. ResultsWe generated a high-quality genome assembly of an A. glossodonta individual from Hawai i, USA. The assembled contigs had an NG50 of 4.75 Mbp and a maximum length of 28.2 Mbp. Scaffolding yielded an NG50 of 14.49 Mbp, with the longest scaffold reaching 42.29 Mbp. Half the genome was contained in 20 scaffolds. The genome was annotated with 28.3 K protein-coding genes. We then analyzed 66 A. glossodonta individuals and 38,355 SNP loci to evaluate population genetic connectivity between six atolls in Seychelles and Mauritius in the Western Indian Ocean. We observed genetic homogeneity between atolls in Seychelles and evidence of reduced gene flow between Seychelles and Mauritius. The South Equatorial Current could be one mechanism limiting gene flow of A. glossodonta populations between Seychelles and Mauritius. ConclusionsQuantifying the spatial population structure of widespread fishery species such as bonefishes is necessary for effective transboundary management and conservation. This population genomic dataset mapped to a high-quality genome assembly allowed us to discern shallow population structure in a widespread species in the Western Indian Ocean. The genome assembly will be useful for addressing the taxonomic uncertainties of bonefishes globally.

genomics↗

bioRxiv2021

Prolonged morphological expansion of spiny-rayed fishes following the end-Cretaceous

Spiny-rayed fishes (Acanthomorpha) dominate modern marine habitats and comprise more than a quarter of all living vertebrate species1-3. It is believed that this dominance resulted from explosive lineage and phenotypic diversification coincident with the Cretaceous-Paleogene (K-Pg) mass-extinction event4. It remains unclear, however, if living acanthomorph diversity is the result of a punctuated burst or gradual accumulation of diversity following the K-Pg. We assess these hypotheses with a time-calibrated phylogeny inferred using ultraconserved elements from a sampling of species that represent over 91% of all acanthomorph families, as well as an extensive body shape dataset of extant species. Our results indicate that several million years after the end-Cretaceous, acanthomorphs underwent a prolonged and significant expansion of morphological disparity primarily driven by changes in body elongation, and that acanthomorph lineages containing the bulk of the living species diversity originated throughout the Cenozoic. These acanthomorph lineages radiated into distinct regions of morphospace and retained their iconic phenotypes, including a large group of laterally compressed reef fishes, fast-swimming open-ocean predators, bottom-dwelling flatfishes, seahorses, and pufferfishes. The evolutionary success of spiny-rayed fishes is the culmination of a post K-Pg adaptive radiation in which rates of lineage diversification were decoupled from periods of high phenotypic disparity.

evolutionary biology↗