Biology subjects

Brewer, M. S.

Publications and source records attributed to Brewer, M. S..

8 recordsLinked to original sources

bioRxiv2025

Evolutionary diversity and function of odorant receptors in birds

Abstract: Odorant receptors (ORs) form among the largest gene families in vertebrates; most mammals have hundreds of intact OR genes. Although birds display diverse behavior and ecology, they were long thought to rely minimally on olfaction. We reexamine this idea by using genomic data to uncover diverse and variable OR repertoires in birds, including the nocturnal kiwi (Apteryx mantelli), which possesses the largest number of ORs known (3,750). We reveal that widespread gene conversion is shaping the evolution of bird ORs, reflecting a novel mechanism for generating functional diversity. We show that ORs are expressed in avian olfactory sensory neurons and show responses to defined, ecologically relevant odorants. Our results demonstrate the importance and functional mechanisms underlying olfaction in birds.

evolutionary biology↗

bioRxiv2023

The effects of social experience on host gut microbiome in male zebrafish (Danio rerio)

Although the gut and the brain vastly differ in physiological function, they have been interlinked in a variety of different neurological and behavioral disorders. The bacteria that comprise the gut microbiome communicate and influence the function of various physiological processes within the body including nervous system function. However, the effects of social experience in the context of dominance and chronic stress on gut microbiome remain poorly understood. Here, we examined whether social experience impacts the host zebrafish (Danio rerio) gut microbiome. We studied how social dominance during the first two weeks of social interactions changed the composition of zebrafish gut microbiome by comparing gut bacterial composition, diversity and relative abundance among socially dominant, submissive, social isolates, and control group-housed communal fish. Using amplicon sequencing of the 16S rRNA gene, we report that social dominance significantly affects host gut bacterial community composition but not bacterial diversity. At the genus-level, Aeromonas and unclassified Enterobacteriaceae relative abundance decreased in dominant individuals while commensal bacteria (e.g., Exiguobacterium and Cetobacterium) increased in relative abundance. Conversely, the relative abundance of Psychrobacter and Acinetobacter was increased in subordinates, isolates, and communal fish compared to dominant fish. The shift in commensal and pathogenic bacteria highlights the impact of social experience and the accompanying stress on gut microbiome with potentially similar effects in other social organisms. IMPORTANCEDisruptions in the gut microbiome negatively impact various systems in the body. Recently, the gut microbiome has been associated with neurological deficits in both behavioral and neurodegenerative disorders. Given the increasing prevalence in diagnosis of both neurological disease and behavioral disorders, researching the link between social behaviors and the gut microbiome is critical to better understand how the gut and the brain communicate during healthy and diseased states. Our research findings demonstrate the effects of social dominance and chronic stress on host gut microbiome composition. By identifying variations in bacterial relative abundance based on social experience and associated stress, a broader understanding of pathogenic (e.g., Enterobacteriaceae, Aeromonas) versus commensal communities (e.g., Exiguobacterium, Cetobacterium) and related host physiology can be inferred.

microbiology↗

bioRxiv2021

Killer Knots: Molecular evolution of Inhibitor Cystine Knot toxins in wandering spiders (Araneae: Ctenidae)

Venom expressed by the nearly 50,000 species of spiders on Earth largely remains an untapped reservoir of a diverse array of biomolecules with potential for pharmacological and agricultural applications. A large fraction of the noxious components of spider venoms are a functionally diverse family of structurally related polypeptides with an inhibitor cystine knot (ICK) motif. The cysteine-rich nature of these toxins makes structural elucidation difficult, and most studies have focused on venom components from the small handful of medically relevant spider species such as the highly aggressive Brazilian wandering spider Phoneutria nigriventer. To alleviate difficulties associated with the study of ICK toxins in spiders, we devised a comprehensive approach to explore the evolutionary patterns that have shaped ICK functional diversification using venom gland transcriptomes and proteomes from phylogenetically distinct lineages of wandering spiders and their close relatives. We identified 626 unique ICK toxins belonging to seven topological elaborations. Phylogenetic tests of episodic diversification revealed distinct regions between cysteine residues that demonstrated differential evidence of positive or negative selection, which may have structural implications towards the specificity and efficacy of these toxins. Increased taxon sampling and whole genome sequencing will provide invaluable insights to further understand the evolutionary processes that have given rise to this diverse class of toxins.

evolutionary biology↗

bioRxiv2020

Ultraconserved elements help resolve the phylogeny of an ancient radiation of venomous flies (Diptera: Asilidae)

Robber flies or assassin flies (Diptera: Asilidae) are a diverse family of venomous predators. The most recent classification organizes Asilidae into 14 subfamilies based on a comprehensive morphological phylogeny, but many of these have not been supported in a subsequent molecular study using traditional molecular markers. To address questions of monophyly in Asilidae, we leveraged the recently developed Diptera-wide UCE baitset to compile seven datasets comprising 151 robber flies and 146 - 2,508 loci, varying in the extent of missing data. We also studied the behavior of different nodal support metrics, as the non-parametric bootstrap is known to perform poorly with large genomic datasets. Our ML phylogeny was fully resolved and well-supported, but partially incongruent with the coalescent phylogeny. Further examination of the datasets suggested the possibility that GC bias had influenced gene tree inference and subsequent species tree analysis. The subfamilies Brachyrhopalinae, Dasypogoninae, Dioctriinae, Stenopogoninae, Tillobromatinae, Trigonomiminae, and Willistonininae were not recovered as monophyletic in either analysis, consistent with a previous molecular study. The inter-subfamily relationships are summarized as follows: Laphriinae and Dioctriinae (in part) are successively sister to the remaining subfamilies, which form two clades; the first consists of a grade of Stenopogoninae (in part), Willistonininae (in part), Bathypogoninae+Phellinae, Stichopogoninae, Leptogastrinae, Ommatiinae, and Asilinae; the second clade consists of a thoroughly paraphyletic assemblage of genera from Dioctriinae (in part), Trigonomiminae, Stenopogoninae (in part), Tillobromatinae, Brachyrhopalinae, and Dasypogoninae. We find that nodal support does not significantly vary with missing data. Furthermore, the bootstrap appears to overestimate nodal support, as has been reported from many recent studies. Gene concordance and site concordance factors seem to perform better, but may actually underestimate support. We instead recommend quartet concordance as a more appropriate estimator of nodal support. Our comprehensive phylogeny demonstrates that the higher classification of Asilidae is far from settled, and it will provide a much-needed foundation for a thorough revision of the subfamily classification.

evolutionary biology↗

bioRxiv2020

Pick Your Poison: Molecular Evolution of Venom Proteins in Asilidae (Insecta: Diptera)

Robber flies are an understudied family of venomous, predatory Diptera. With the recent characterization of venom from three asilid species, it is possible for the first time to study the molecular evolution of venom genes in this unique lineage. To accomplish this, a novel whole-body transcriptome of Eudioctria media was combined with 10 other publicly available asiloid thoracic or salivary gland transcriptomes to identify putative venom gene families and assess evidence of pervasive positive selection. A total of 348 gene families of sufficient size were analyzed, and 33 of these were predicted to contain venom genes. We recovered 151 families containing homologs to previously described venoms, and 40 of these were uniquely gained in Asilidae. Our gene family clustering suggests that many asilidin venom gene families are not natural groupings as originally delimited. Additionally, robber-fly venoms have relatively few sites under positive selection, consistent with the hypothesis that the venom of older lineages are dominated by negative selection acting to maintain toxic function.

evolutionary biology↗

bioRxiv2019

Environmental Niche Adaptation Revealed Through Fine Scale Phenological Niche Modeling

AimPhenology, the temporal response of a population to its climate, is a crucial behavioral trait shared across life on earth. How species adapt their phenologies to climate change is poorly understood but critical in understanding how species will respond to future change. We use a group of flies (Rhaphiomidas) endemic to the North American deserts to understand how species adapt to changing climatic conditions. Here we explore a novel approach for taxa with constrained phenologies aimed to accurately model their environmental niche and relate this to phenological and morphological adaptations in a phylogenetic context. TaxonInsecta, Diptera, Mydidae, Rhaphiomidas LocationNorth America, Mojave, Sonoran and Chihuahuan Deserts. MethodsWe gathered geographical and phenological occurrence data for the entire genus Rhaphiomidas, and, estimated a time calibrated phylogeny. We compared Daymet derived temperature values for a species adult occurrence period (phenology) with those derived from WorldClim data that is partitioned by month or quarter to examine what effect using more precise data has on capturing a species environmental niche. We then examined to what extent phylogenetic signal in phenological traits, climate tolerance and morphology can inform us about how species adapt to different environmental regimes. ResultsWe found that the Bioclim temperature data, which are averages across monthly intervals, poorly represent the climate windows to which adult flies are actually adapted. Using temporally-relevant climate data, we show that many species use a combination of morphological and phenological changes to adapt to different climate regimes. There are also instances where species changed only phenology to track a climate type or only morphology to adapt to different environments. Main ConclusionsWithout using a fine-scale phenological data approach, identifying environmental adaptations could be misleading because the data do not represent the conditions the animals are actually experiencing. We find that fine-scale phenological niche models are needed when assessing taxa that have a discrete phenological window that is key to their survival, accurately linking environment to morphology and phenology. Using this approach, we show that Rhaphiomidas use a combination of niche tracking and adaptation to persist in new niches. Modeling the effect of phenology on such species niches will be critical for better predictions of how these species might respond to future climate change.

evolutionary biology↗

bioRxiv2019

Diversity and function of fungi associated with the fungivorous millipede, Brachycybe lecontii

Fungivorous millipedes (subterclass Colobognatha) likely represent some of the earliest known mycophagous terrestrial arthropods, yet their fungal partners remain elusive. Here we describe relationships between fungi and the fungivorous millipede, Brachycybe lecontii. Their fungal community is surprisingly diverse with 176 genera, 39 orders, and four phyla and includes several undescribed species. Of particular interest are twelve genera conserved across wood substrates and millipede clades that comprise the core fungal community of B. lecontii. Wood decay fungi, long speculated to serve as the primary food source for Brachycybe species, were absent from this core assemblage and proved lethal to millipedes in pathogenicity assays while entomopathogenic Hypocreales were more common in the core but had little effect on millipede health. This study represents the first survey of fungal communities associated with any colobognath millipede, and these results offer a glimpse into the complexity of millipede fungal communities.

microbiology↗

bioRxiv2017

FUSTr: a tool to find gene Families Under Selection in Transcriptomes

FUSTr is a tool for finding genes in transcriptomic datasets under strong positive selection that automatically detects isoform designation patterns in transcriptome assemblies to maximize phylogenetic independence in downstream analysis. When applied to previously studied spider toxin families as well as simulated data, FUSTr successfully grouped coding sequences into proper gene families as well as correctly identified those under strong positive selection. FUSTr provides a tool capable of utilizing multi-processor high-performance computational facilities and is scalable for large transcriptomic biodiversity datasets.\n\nAvailabilityFUSTr is freely available under a GNU license and can be downloaded at https://github.com/tijeco/FUSTr.\n\nContactcoleti16@students.ecu.edu

bioinformatics↗