Biology subjects

Hoke, K. L.

Publications and source records attributed to Hoke, K. L..

4 recordsLinked to original sources

bioRxiv2025

The effect of environmental enrichment on whole-brain gene expression in an imperiled fish

When hatchery-reared fish are used to augment wild populations, phenotypic mismatch caused by differences between hatchery and wild environments can limit efforts to conserve fish species at risk of extinction. Some phenotypes adapted to or induced by hatchery environments are thought to be maladapted for life in the wild. Thus, enriching the hatchery environment (abiotically and biotically) to make it more similar to the wild may induce phenotypes, including gene expression profiles, that are better suited to the environments fish will experience after release. Here, we took a molecular approach (TagSeq) to elucidate how abiotic and biotic (predator training) enrichment impacts the whole-brain gene expression of a species of conservation concern, the Arkansas darter (Etheostoma cragini), comparing the effects in two hatchery populations to a wild reference population. While we found no effect of biotic enrichment, we found that numerous genes were differentially expressed between populations and abiotic enrichment treatments. Notably, we found that expression profiles of hatchery fish more closely resembled those of wild fish when reared with abiotic enrichment. Functional analysis revealed that many differentially expressed genes were related to feeding behavior, development, and reproduction. These results have implications for conservation, supporting the management of darters at the level of the population and the use of abiotic enrichment to reduce phenotypic mismatch between hatchery and wild fish.

molecular biology↗

bioRxiv2024

Flexibility in Gene Coexpression at Developmental and Evolutionary Timescales

The explosion of next-generation sequencing technologies has allowed researchers to move from studying single genes to thousands of genes, and thereby to also consider the relationships within gene networks. Like others, we are interested in understanding how developmental and evolutionary forces shape the expression of individual genes, as well as the interactions among genes. In pursuing these questions, we confronted the central challenge that standard approaches fail to control the Type I error and/or have low power in the presence of high dimensionality (i.e., large number of genes) and small sample size, as in many gene expression studies. To overcome these challenges, we used random projection tests and correlation network comparisons to characterize differences in network connectivity and density. We detail central challenges, discuss sample size guidelines, and provide rigorous statistical approaches for exploring coexpression differences with small sample sizes. We apply these approaches in a species known for rapid adaptation - the Trinidadian guppy (Poecilia reticulata). Our findings provide evidence for coexpression network differences at developmental and evolutionary timescales and suggest that flexibility in gene coexpression relationships could promote evolvability.

evolutionary biology↗

bioRxiv2019

Non-parallel transcriptional divergence during parallel adaptation

How underlying mechanisms bias evolution toward predictable outcomes remains an area of active debate. In this study, we leveraged phenotypic plasticity and parallel adaptation across independent lineages of Trinidadian guppies (Poecilia reticulata) to assess the predictability of gene expression evolution during parallel adaptation. Trinidadian guppies have repeatedly and independently adapted to high- and low-predation environments in the wild. We combined this natural experiment with a laboratory breeding design to attribute transcriptional variation to the genetic influences of population of origin and developmental plasticity in response to rearing with or without predators. We observed substantial gene expression plasticity as well as the evolution of expression plasticity itself across populations. Genes exhibiting expression plasticity within populations were more likely to also differ in expression between populations, with the direction of population differences more likely to be opposite those of plasticity. While we found more overlap than expected by chance in genes differentially expressed between high- and low-predation populations from distinct evolutionary lineages, the majority of differentially expressed genes were not shared between lineages. Our data suggest alternative transcriptional configurations associated with shared phenotypes, highlighting a role for transcriptional flexibility in the parallel phenotypic evolution of a species known for rapid adaptation.

evolutionary biology↗

bioRxiv2018

Differences In Neural Activity, But Not Behavior, Across Social Contexts In Guppies, Poecilia reticulata

Animals are continually faced with the challenge of producing context-appropriate social behaviors. In many instances, animals produce unrelated behaviors across contexts. However, in some instances the same behaviors are produced across different social contexts, albeit in response to distinct stimuli and with distinct purposes. We took advantage of behavioral similarities across mating and aggression contexts in guppies, Poecilia reticulata, to understand how patterns of neural induction differ across social contexts when behaviors are nonetheless shared across contexts. While these is growing interest in understanding behavioral mechanisms in guppies, resources are sparse. As part of this study, we developed a neuroanatomical atlas of the guppy brain as a research community resource. Using this atlas, we found that neural activity in the preoptic area reflected social context, whereas individual differences in behavioral motivation paralleled activity in the posterior tuberculum and ventral telencephalon (teleost homologs of the ventral tegmental area and lateral septum, respectively). Our findings suggest independent coding of social salience versus behavioral motivation when behavioral repertoires are shared across social contexts.\n\nSummary statementActivity in distinct brain regions reflects behavioral context versus social motivation in a in which behavioral repertoires are shared across social contexts (Trinidadian guppies, Poecilia reticulata).

animal behavior and cognition↗