Biology subjects

Knowlton, N.

Publications and source records attributed to Knowlton, N..

6 recordsLinked to original sources

bioRxiv2026

The impacts of light and location on reproductive timing in the Orbicella species complex

Coral spawning events rely on tight synchronicity of gamete release to increase fertilization success by increasing gamete density in the water. Differences in spawning time can cause temporal reproductive isolation and minimize hybridization with closely related coral species. Sexual reproductive success is important as it generates the genetic diversity necessary for corals to survive large scale environmental stressors such as heat waves and bleaching events. The coordination of coral spawning events within a population maintains species boundaries and increases ecosystem-wide genetic diversity. Here we generate a database of spawning events in conjunction with depth and geographic location of the three species in the Orbicella species complex to assess variability in reproductive timing. The dataset, gathered from published papers, restoration practitioners, scientist throughout the Caribbean, contains almost three decades of data and includes 265 reproductive events. Our findings indicate that some aspects of each spawning season (month and day after the full moon) are influenced by latitude whereas others, such as spawning time in relation to local sunset, may exhibit variation based on geographic location. Combined, our results suggest that the reproductive timeframe of Orbicella spp. is triggered by factors associated with latitudinal gradients, such as the amount of energy from the sun, but the specific time of gamete release may be connected to other environmental factors that occur at a local scale or vary year-to-year.

ecology↗

bioRxiv2024

Dietary resilience of coral reef fishes to habitat degradation

The ability of consumers to adjust their diet in response to resource shifts is a key mechanism allowing the persistence of populations and underlying species adaptive capacity. Yet on coral reefs, one of the marine habitats most vulnerable to global change, the extent to which species alter their diet remains poorly understood. Here, we integrated DNA-based gut content analyses (metabarcoding), otolith analysis, body condition, and field surveys to test how diet can mediate effects of habitat degradation on two invertivorous fishes: Chaetodon capistratus, a browser, and Hypoplectrus puella, an active predator. Metabarcoding revealed significant dietary variation in both species across a habitat gradient. However, the response was more pronounced in the browser, whose diet was anthozoan-dominated on healthy reefs, whereas annelid-dominated on degraded reefs. We found reduced growth and body condition on degraded reefs in the browser but not the active predator. Our results reveal that dietary versatility can serve as a mechanism to cope with degraded environments, but that species differ as to whether these changes are sufficient to buffer from changes in habitat. We detected intraspecific dietary variation across sites that suggests food webs and energy flow differ at relatively small scales between healthy and degraded reefs.

ecology↗

bioRxiv2021

Linking photoacclimation responses and microbiome shifts between depth-segregated sibling species of reef corals

Metazoans host complex communities of microorganisms that include dinoflagellates, fungi, bacteria, archaea, and viruses. Interactions among members of these complex assemblages allow hosts to adjust their physiology and metabolism to cope with environmental variation and occupy different habitats. Here, using reciprocal transplantation across depths, we studied adaptive divergence in the Caribbean corals Orbicella annularis and O. franksi. When transplanted from deep to shallow, O. franksi experienced fast photoacclimation, low mortality, and maintained a consistent bacterial community. In contrast, O. annularis experienced higher mortality, and limited photoacclimation when transplanted from shallow to deep. The photophysiological collapse of O. annularis in the deep environment was associated with an increased microbiome variability and reduction of some bacterial taxa. Differences in the symbiotic algal community were more pronounced between coral species than between depths. Our study suggests that these sibling species are adapted to distinctive light environments partially driven by the algae photoacclimation capacity and the microbiome robustness, highlighting the importance of niche specialization in symbiotic corals for the maintenance of species diversity. Our findings have implications for the management of these threatened Caribbean corals and the effectiveness of coral reef restoration efforts.

microbiology↗

bioRxiv2020

Base-substitution mutation rate across the nuclear genome of Alpheus snapping shrimp and the timing of isolation by the Isthmus of Panama

The formation of the Isthmus of Panama and final closure of the Central American Seaway (CAS) provides an independent calibration point for examining the rate of DNA substitutions. This vicariant event has been widely used to estimate the substitution rate across mitochondrial genomes and to date evolutionary events in other taxonomic groups. Nuclear sequence data is increasingly being used to complement mitochondrial datasets for phylogenetic and evolutionary investigations; these studies would benefit from information regarding the rate and pattern of DNA substitutions derived from the nuclear genome. To estimate this genomewide neutral mutation rate (), genotype-by-sequencing (GBS) datasets were generated for three transisthmian species pairs in Alpheus snapping shrimp. Using a Bayesian coalescent approach (G-PhoCS) applied to 44,960 GBS loci, we estimated to be 2.64E-9 substitutions/site/year, when calibrated with the closure of the CAS at 3 Ma. This estimate is remarkably similar to experimentally derived mutation rates in model arthropod systems, strengthening the argument for a recent closure of the CAS. To our knowledge this is the first use of transisthmian species pairs to calibrate the rate of molecular evolution from GBS data.

evolutionary biology↗

bioRxiv2019

Environmental DNA survey captures patterns of fish and invertebrate diversity across a tropical seascape

Accurate, rapid, and comprehensive biodiversity assessments are critical for investigating ecological processes and supporting conservation efforts. Environmental DNA (eDNA) surveys show promise as a way to effectively characterize fine-scale patterns of community composition, but most studies to date have evaluated its effectiveness in single habitats and for conspicuous taxonomic groups in temperate ecosystems. We tested whether a single PCR survey of eDNA in seawater using a broad metazoan primer could identify differences in community composition between five adjacent habitats at 19 sites across a tropical Caribbean bay in Panama. We paired this effort with visual fish surveys to compare methods for a conspicuous taxonomic group. eDNA revealed a tremendous diversity of animals (8,586 operational taxonomic units), including many small taxa that would be undetected in traditional in situ surveys. Fish comprised only 0.07% of the taxa detected by a broad COI primer, yet included 43 species not observed in the visual survey. eDNA revealed significant differences in fish and invertebrate community composition across adjacent habitats and areas of the bay driven in part by taxa known to be habitat-specialists or tolerant to wave action. Our results demonstrate the ability of broad eDNA surveys to identify biodiversity patterns in the ocean.

ecology↗

bioRxiv2017

Recurrent loss of heterozygosity correlates with clinical outcome in pancreatic neuroendocrine cancer

Pancreatic neuroendocrine tumors (pNETs) are uncommon cancers arising from pancreatic islet cells. Analysis of gene mutation, copy number and RNA expression of 57 sporadic pNETs showed that pNET genomes are dominated by aneuploidy. Remarkably, ~25% of pNETs had genomes characterized by recurrent loss of heterozygosity (LoH) of the same 10 chromosomes, accompanied by bi-allelic MEN1 inactivation, and these cases had generally poor clinical outcome. Another ~25% of all pNETs had chromosome 11 LoH and bi-allelic MEN1 inactivation, lacking the recurrent LoH pattern - these had universally good clinical outcome. Some level of aneuploidy was common, and overall ~80% of pNETs had LoH of [≥]1 chromosome. This aneuploidy led to changes in RNA expression at the level of whole chromosomes and allowed pathogenic germline variants (e.g. ATM) to be expressed unopposed, inactivating downstream tumor suppressor pathways. Some pNETs appear to utilize VHL gene methylation or mutation to activate pseudo-hypoxia. Contrary to expectation neither tumor morphology within well-differentiated pNETs nor single gene mutation had significant associations with clinical outcome, nor did expression of RNAs reflecting the activity of immune, differentiation, proliferative or tumor suppressor pathways. MEN1 was the only statistically significant recurrently mutated driver gene in pNETs. Only one pNET had clearly oncogenic and actionable SNVs (in PTEN and FLCN) confirmed by corroborating RNA expression changes. The two distinct patterns of aneuploidy described here, associated with markedly poor and good clinical outcome respectively, define a novel oncogenic mechanism and the first route to genomic precision oncology for this tumor type.

cancer biology↗