Biology subjects

Hoeppner, M. P.

Publications and source records attributed to Hoeppner, M. P..

7 recordsLinked to original sources

bioRxiv2026

Parallel phenotypes underpinned by different genes in the visual system of two trans-isthmian coral reef fish species pairs

Understanding the genetic basis of adaptation in natural populations to changing environmental conditions is challenging. The relatively simple genotype-to-phenotype relationship between opsin genes and visual pigments offers a particularly informative model to explore the molecular mechanisms underpinning adaptive phenotypic change in natural populations. Here we leveraged the natural experiment provided by the tectonic closure of the Central American seaway that created allopatric, sister taxa in multiple, independent lineages of marine organisms and exposed them to distinct underwater light environments: either the more turbid Tropical Eastern Pacific (TEP), or the spectrally broader Caribbean Sea. Using two species pairs of planktivorous teleosts, the Azurina multilineata/A. atrilobata damselfish and the Cephalopholis (Paranthias) furcifer/C. colonus groupers, we explore to what extent visual sensitivity converged to similar adaptations in response to similar foraging strategies and shared underwater light in each marine basin. We found that the compression of the underwater light field towards the central portion of the spectrum from Caribbean to TEP waters is reflected in similar shifts towards the centre of the light spectrum in overall single and double cone sensitivities in both families. Both TEP species have single (short-wavelength) cone sensitivities shifted to longer wavelengths and double (long-wavelength) cone sensitivities shifted to shorter wavelengths, compared to their Caribbean counterparts. These parallel shifts in visual sensitivities observed in response to shared underwater light environments are accomplished by different underlying opsin gene toolsets in the two lineages. Similarly, expression changes in pathways associated with the visual system revealed limited parallelism at the molecular level.

evolutionary biology↗

bioRxiv2025

Comparative genomic analyses of trans-ithmanian reef fishes reveals different molecular targets of environmental adaptation in different families.

The extent to which selection acts upon the same molecular targets when faced with the same environmental changes has important implications for our understanding of the repeatability and predictability of evolutionary processes. Replicated natural experiments are well positioned to provide insight, however often these involve closely related species or populations of the same species. Given that the similarity of genetic background makes the same molecular change more likely, it is essential to evaluate the extent to which molecular parallelism occurs in more distantly related species. The rise of the Isthmus of Panama presents an ideal natural experiment to investigate the prevalence of parallel molecular changes in distantly related lineages exposed to the same environmental regimes of temperature, salinity and primary productivity in the two newly formed oceans. Here, we generate high-quality reference genomes for two replicate pairs of geminate reef fishes, one in the family Pomacentridae and one in the Serranidae. Comparative analyses of positive selection in protein-coding genes and of gene family evolution revealed multiple signals of potentially adaptive divergence between geminate species in response to environmental regime. Common targets of selection between families included MAPK signalling (MAP3K10), solute transport (SLC46A2) and reproduction (ZPL3L), as well as expansions in immune and MAPK related gene families. Overall, however, we found minimal evidence of parallelism between families either at the gene level or when considering higher functional categories. Our findings suggest that phylogenetic constraints may limit the levels of molecular parallelism in distant lineages even when faced with comparable selective pressures. Significance StatementUnderstanding the extent to which species exposed to similar environmental conditions may adapt using similar genetic solutions has important implications for our understanding of evolutionary processes and how we may expect species to adapt in the future. However, systems where multiple, independent lineages are faced with the same shift in conditions are rare. The rise of the Isthmus of Panama provides a unique, natural experiment where multiple marine species have been divided and exposed to radically different environmental conditions. Here, we generate genomes for separated species in two distantly related families of reef fishes and compare genome-wide patterns of divergence. Our analyses identified signals of selection in protein-coding genes and shifts in gene family size consistent with adaptation to the distinct environments, however the specific genes and pathways involved predominantly differed between the families, revealing that, even under shared selective pressures, molecular mechanisms may differ across more distant lineages.

evolutionary biology↗

bioRxiv2025

Comparative Genomics of Transisthmian Damselfishes (Abudefduf saxatilis and A. troschelii)

The uplift of the Central American Isthmus (CAI) represents a natural laboratory for the study of allopatric speciation in marine organisms. Several geminate species pairs of both vertebrates and invertebrates formed following the uplift of the CAI, including damselfishes of the Pomacentridae family. However, to date no studies have explored the genomic differences among geminate species in the Pacific and Atlantic Oceans. In this study we present genome assemblies for the transisthmian species pair consisting of the Sergeant Major Abudefduf saxatilis (Tropical Atlantic) and the Panamic Sergeant Major Abudefduf troschelii (Tropical Eastern Pacific) derived from PacBio long-read sequencing. The new genomes are near-chromosome level, and among the highest-quality genomes currently available for coral reef fishes. We show that large structural variants distinguish the two species, including a 9 megabase inversion in linkage group (putative chromosome) 6. Additionally, we show through an analysis of demographic history that alleles within the two genomes have different coalescence time distributions, which may be due to different effective population sizes, population structures, and/or selection regimes in the two oceans. Finally, we highlight gene families that were significantly expanded or contracted between A. troschelii and A. saxatilis. Some of these are related to the environmental conditions that differ between the two oceans, such as gamma crystallin M (crygm), which is linked to vision, and vitellogenin (vtg), which is associated with egg provisioning. These genomes set the stage for comparative analyses of genetic structure and selection on the marine organisms that originated with the formation of the CAI. Significance StatementUnderstanding speciation in oceans has represented a historical challenge, given the high rates of dispersal during larval stages for most marine groups. There are few geologic events that have propelled marine biodiversity while completely blocking the genetic exchange during the speciation process. The final closure of the Central American Isthmus (CAI), 2.8 million years ago, is one of these few examples where marine populations from the tropical Pacific and Atlantic oceans have been completely isolated, providing the opportunity to study how genomes diverge in the absence of gene flow. Here, we present the first comparative genomics study of marine organisms separated by the CAI, showing that genomes on the two sides of the CAI differ structurally. We also identify contractions and expansions of various gene families between the two species, which are potentially associated with adaptations to the different environmental conditions in the two oceans. This represents a relevant first step for comparative genomics of geminate species isolated by a major geologic event.

genomics↗

bioRxiv2023

Mutational and transcriptional landscape of pediatric B-cell precursor lymphoblastic lymphoma

Pediatric B-cell precursor (BCP) lymphoblastic malignancies are neoplasms with manifestation either in bone marrow/blood (BCP acute lymphoblastic leukemia, BCP-ALL) or less common in extramedullary tissue (BCP lymphoblastic lymphoma, BCP-LBL). Although both presentations are similar in morphology and immunophenotype molecular studies are virtually restricted to BCP-ALL so far. The lack of molecular studies on BCP-LBL is probably due to its rarity and the restriction to tiny, mostly formalin-fixed paraffin embedded (FFPE) tissues. Here we present the first comprehensive mutational and transcriptional analysis of what we consider the largest BCP-LBL cohort described to date (n=97). Whole exome sequencing indicates a mutational spectrum of BCP-LBL strikingly similar to that found in BCP-ALL. However, epigenetic modifiers were more frequently mutated in BCP-LBL, whereas BCP-ALL was more frequently affected by mutation in genes involved in B-cell development. Integrating copy number alterations, somatic mutations and gene expression by RNA-sequencing revealed virtually all molecular subtypes originally defined in BCP-ALL to be present in BCP-LBL too, with only 7% of lymphomas that were not assigned to a subtype. Therefore, the results here described may pave the way for molecular risk adapted treatment protocols for BCP-LBL patients. KeypointsComprehensive molecular characterization of B-cell precursor lymphoblastic lymphoma allows molecular subtyping analogous to leukemias Compared to leukemias, lymphomas show more alterations in epigenetic modifiers and less in B-cell development genes

cancer biology↗

bioRxiv2023

Host and microbiome jointly contribute to adaptation to a complex environment

Most animals and plants have associated microorganisms, collectively referred to as their microbiomes, which can provide essential functions. Given their importance, host-associated microbiomes have the potential to contribute substantially to adaptation of the host-microbiome assemblage (the "metaorganism"). Microbiomes may be especially important for rapid adaptation to novel environments because microbiomes can change more rapidly than host genomes. However, it is not well understood how hosts and microbiomes jointly contribute to metaorganism adaptation. We developed a model system with which to disentangle the contributions of hosts and microbiomes to metaorganism adaptation. We established replicate mesocosms containing the nematode Caenorhabditis elegans co-cultured with microorganisms in a novel complex environment (laboratory compost). After approximately 30 nematode generations (100 days), we harvested worm populations and associated microbiomes, and subjected them to a common garden experiment designed to unravel the impacts of microbiome composition and host genetics on metaorganism adaptation. We observed that adaptation took different trajectories in different mesocosm replicates, with some increasing in fitness and others decreasing, and that interactions between host and microbiome played an important role in these contrasting evolutionary paths. We chose two exemplary mesocosms (one with a fitness increase and one with a decrease) for detailed study. For each example, we identified specific changes in both microbiome composition (for both bacteria and fungi) and nematode gene expression associated with each change in fitness. Our study provides experimental evidence that adaptation to a novel environment can be jointly influenced by host and microbiome.

evolutionary biology↗

bioRxiv2019

DNA methylation facilitates local adaptation and adaptive transgenerational plasticity

While environmentally inducible epigenetic marks are discussed as one mechanism of transgenerational plasticity, environmentally stable epigenetic marks emerge randomly. When resulting in variable phenotypes, stable marks can be targets of natural selection analogous to DNA sequence-based adaptation processes. We studied both postulated pathways in natural populations of three-spined sticklebacks (Gasterosteus aculeatus) and sequenced their methylomes and genomes across a salinity cline. Consistent with local adaptation, populations showed differential methylation (pop-DMS) at genes enriched for osmoregulatory processes. In a two-generation experiment, 62% of these pop-DMS were insensitive to salinity manipulation, suggesting that they could be stable targets for natural selection. Two-thirds of the remaining inducible pop-DMS became more similar to patterns detected in wild populations from the corresponding salinity, and this pattern accentuated over consecutive generations, indicating a mechanism of adaptive transgenerational plasticity. Natural DNA methylation patterns can thus be attributed to two epigenetic pathways underlying the rapid emergence of adaptive phenotypes in the face of environmental change.

evolutionary biology↗

bioRxiv2019

The functional repertoire encoded within the native microbiome of the model nematode Caenorhabditis elegans

The microbiome is generally assumed to have a substantial influence on the biology of multicellular organisms. The exact functional contributions of the microbes are often unclear and cannot be inferred easily from 16S rRNA genotyping, which is commonly used for taxonomic characterization of the bacterial associates. In order to bridge this knowledge gap, we here analyzed the metabolic competences of the native microbiome of the model nematode Caenorhabditis elegans. We integrated whole genome sequences of 77 bacterial microbiome members with metabolic modelling and experimental characterization of bacterial physiology. We found that, as a community, the microbiome can synthesize all essential nutrients for C. elegans. Both metabolic models and experimental analyses further revealed that nutrient context can influence how bacteria interact within the microbiome. We identified key bacterial traits that are likely to influence the microbes ability to colonize C. elegans (e.g., pyruvate fermentation to acetoin) and the resulting effects on nematode fitness (e.g., hydroxyproline degradation). Considering that the microbiome is usually neglected in the comprehensive research on this nematode, the resource presented here will help our understanding of C. elegans biology in a more natural context. Our integrative approach moreover provides a novel, general framework to dissect microbiome-mediated functions.

microbiology↗