Biology subjects

Mazzoni, C.

Publications and source records attributed to Mazzoni, C..

8 recordsLinked to original sources

bioRxiv2026

IBD stress impacts gut microbiome intra-species diversity

Intra-species genomic variation results from diversity-generating processes and supplies the raw material for subsequent natural selection. Environmental stress can be regarded as the ultimate accelerator of these processes, especially for microorganisms, which can alter their DNA if presented with nutrient limitation, toxins, or pathogen attack. Chronic intestinal inflammation, as in inflammatory bowel diseases (IBD), may be regarded as prolonged environmental stress for gut commensal bacteria, bringing many enteric species down to undetectable levels. However, it remains unclear how the microbes that survive the IBD gut environment actually respond to IBD stress, and whether their stress response may leave a transient or permanent signature in their genomes. To investigate whether IBD stress induces and selects for certain genetic diversity, we performed metagenomic analyses on gut species in IBD patients and Controls. We focused on strain diversity within single individuals, which might be the result of more recent diversification processes under stress. We found measurable differences at the genome level between IBD and Controls, yet this was species-dependent. We then investigated gene-level diversity and found that certain functions were more likely to be enriched with either neutral divergence, functional divergence, or both. Functions that were enriched in IBD with both kinds of diversity were associated with motility and iron-scavenging, among others. These results may point towards functions that are under selection in the context of IBD stress, and could inform future mechanistic work, exploring previously unknown routes of bacterial diversification and adaptation to stress in the gut microbiome.

microbiology↗

bioRxiv2025

Whole-genome resequencing reveals exceptions to panmixia in the exploited top fish predator Antarctic toothfish (Dissostichus mawsoni)

Antarctic toothfish (Dissostichus mawsoni) are a critical top fish predator in the Southern Ocean for whom a changing climate and fishing pressure challenge our understanding of their population dynamics. Their complex, long-lived life history presents challenges to understanding their population dynamics that we endeavor to overcome through the use of both reduced-representation sequencing and whole-genome resequencing data from fish across different cohorts. Our unique sample set allowed us to compare genomic structure, diversity, and demographic changes between cohorts born before and after the year 2000, when changes to fisheries management practices in the Southern Ocean reduced incidences of illegal, unreported, and unregulated fishing. While our population structure analyses corroborate recent studies showing panmixia across circumpolar populations of D. mawsoni, comparisons between cohorts revealed key exceptions. A lack of admixture in fish born before 2000 contrasted with widespread admixture among post-2000 individuals, consistent with increased mixing and/or genotype influx. Concernedly, genome-wide diversity declined over time in the Ross Sea (management area 88), with the significant losses observed in heterozygosity between pre-2000 and post-2000 cohorts. Elevated levels of inbreeding in the Ross Sea, coupled with evidence for recent population contraction from positive Tajimas D values, provided potential explanations for the observed reductions in genomic diversity. Our results reconcile circumpolar panmixia with localized erosion of diversity and elevated inbreeding in the Ross Sea sector, underscoring the value of temporal monitoring and the need to prioritize future research on the interplay between fisheries pressure and environmental change in driving population dynamics and genomic structure in tootfhish.

genomics↗

bioRxiv2024

Inbreeding depression depends on the body size and environmental conditions in a threatened songbird, the aquatic warbler Acrocephalus paludicola

While inbreeding is known to affect individual fitness and thus population extinction risk, studies have under-represented non-model species of conservation concern, and rarely sought conditionality of inbreeding depression. Here, using SNPs identified with RAD-seq, we determined inbreeding depression in a threatened bird, the aquatic warbler Acrocephalus paludicola, and whether its magnitude depends on phenotypic and environmental factors. We found that the inbreeding coefficient (F) of adults with small tarsi was negatively associated with the seasonal breeding success (in males) and clutch size (in females), with the respective decrease in fitness in the most inbred relative to the least inbred individuals of ~89% and ~12%. In contrast, in adult males, for the average tarsus, wing and mass, support was low for F to be related to the long-term return rate to breeding grounds. For mean phenotypic covariates and male density, we also found low evidence that F is associated with the annual breeding success. Likewise, there was little support that mother F is related to egg hatch success and nestling survival, and - for average phenotypic traits, rainfall, temperature and nest density, and accounting for breeding peak - to clutch and fledged brood sizes. For nestlings, animal models showed that F is more negatively related to tarsus under higher temperatures and its effect varies by study year. However, for average brood size, temperature, rainfall and prey abundance, and when controlling for nestling sex, breeding peak and mother F, evidence for nestling F and tarsus association was weak. We conclude that (1) inbreeding depression on fitness components is stronger in smaller-bodied individuals, (2) considering interaction with phenotypic and environmental variables enables more accurate estimation of inbreeding depression, and (3) the inbreeding depression estimates will inform extinction risk analysis and conservation actions for the aquatic warbler.

evolutionary biology↗

bioRxiv2024

Long-read sequencing and genome assembly of natural history collection samples and challenging specimens

Museum collections harbor millions of samples, largely unutilized for long-read sequencing. Here, we use ethanol-preserved samples containing kilobase-sized DNA to show that amplification-free protocols can yield contiguous genome assemblies. Additionally, using a modified amplification-based protocol, employing an alternative polymerase to overcome PCR bias, we assembled the 3.1 Gb maned sloth genome, surpassing the previous 500 Mb protocol size limit. Our protocol also improves assemblies of other difficult-to-sequence molluscs and arthropods, including millimeter-sized organisms. By highlighting collections as valuable sample resources and facilitating genome assembly of tiny and challenging organisms, our study advances efforts to obtain reference genomes of all eukaryotes.

genomics↗

bioRxiv2023

DNA metabarcoding reveals limited consumption of livestock and black rhinoceros by spotted hyenas in a prey-rich environment

The diet of large carnivores is of great interest to conservation managers, as it can reveal the extent of human-carnivore conflict and the impact of carnivores on species of high conservation priority. Metabarcoding of environmental DNA can identify species and is often more reliable in doing so than observational or morphological methods. Metabarcoding is particularly powerful at detecting elusive and rare species and has therefore become a widely applied tool in biodiversity research. Here, we used DNA metabarcoding of fecal samples to determine the diet of spotted hyenas in the Ngorongoro Crater, a protected area in Northern Tanzania surrounded by areas co-inhabited by pastoralists. We assessed which species hyenas preferably consumed over a 24-year period and how frequently they consumed pastoralist livestock and black rhinoceros, a species of high economic value and conservation priority. We further estimated the effects of three key socio-demographic variables - age, social rank, and sex - on the propensity of hyenas to consume livestock. We detected DNA from 20 species in 371 hyena feces. Hyenas preferably consumed blue wildebeest and Grants gazelle. Among the detected species were five domestic species and one wild species that lived in the pastoralist-inhabited areas but not the Crater. This shows that resident Crater hyenas undertake foraging trips to areas surrounding the Crater. DNA of domestic species however was rarely detected (4.1% of 434 detections), and predominantly in feces of old hyenas. This suggests that Crater hyenas rarely consume livestock and that livestock is mostly consumed by hyenas less capable of hunting fleet-footed and powerful wild prey. No DNA of black rhinoceros was detected in any of the samples, suggesting that Crater hyenas do not frequently consume rhinoceros. Our findings suggest that the impact of Crater hyenas on livestock and wildlife of high conservation priority is limited. Our study highlights the potential of DNA metabarcoding to assess the extent of human-carnivore conflict and to guide evidence-based conservation efforts to promote coexistence of carnivores, humans and species of high conservation priority.

animal behavior and cognition↗

bioRxiv2023

GENI: a web server to identify gene set enrichments in tumor samples

The Cancer Genome Atlas (TCGA) and other projects provide informative tumor-associated genomic data for the broad research community. Hence, several useful web-based tools have been generated to ease non-expert users with the analysis and characterization of a specific gene behavior in selected tumors. However, none of the existing tools offer the user the means to evaluate the expression profile of a given gene in the context of the whole transcriptome. Currently, such analyses require prior bioinformatic knowledge and expertise. Therefore, we developed GENI (Gene ENrichment Identifier) as a fast, user-friendly tool to analyze the TCGA expression data for gene set enrichments. GENI analyzes large-scale tumor-associated gene expression datasets and evaluates biological relevance, thus offering researchers a simplified means to analyze cancer patient-derived data. Availability and implementationGENI is a freely available fast web-based tool developed using the R programming language. It is accessible via the URL: https://yoavshaul-lab.shinyapps.io/gsea-geni/. The complete script can be found at https://github.com/ArataHayashi/GENI-Gene-ENrichment-Identifier.

bioinformatics↗

bioRxiv2022

Evidence of backcross inviability and mitochondrial DNA paternal leakage in sea turtle hybrids

Hybridization is known to be part of many species evolutionary history. Sea turtles have a fascinating hybridization system in which species separated by as much as 43 million years are still capable of hybridizing. Indeed, the largest nesting populations in Brazil of loggerheads (Caretta caretta) and hawksbills (Eretmochelys imbricata) have a high incidence of hybrids between these two species. A third species, olive ridleys (Lepidochelys olivacea), is also known to hybridize although at a smaller scale. Here we used restriction site-associated DNA sequencing (RAD-Seq) markers, mitogenomes, and satellite-telemetry to investigate the patterns of hybridization and introgression in the Brazilian sea turtle population and their relationship with the migratory behaviors between feeding and nesting aggregations. We also explicitly test if the mixing of two divergent genomes in sea turtle hybrids causes mitochondrial paternal leakage. We developed a new species-specific PCR-assay capable of detecting mitochondrial DNA (mtDNA) inheritance from both parental species and performed ultra-deep sequencing to estimate the abundance of each mtDNA type. Our results show that all adult hybrids are first generation (F1) and most display a loggerhead migratory behavior. We detected paternal leakage in F1 hybrids and different proportions of mitochondria from maternal and paternal species. Although previous studies showed no significant fitness decrease in hatchlings, our results support genetically-related hybrid breakdown possibly caused by cytonuclear incompatibility. Further research on hybrids from other populations besides Brazil and between different species will show if backcross inviability and mitochondrial paternal leakage is observed across sea turtle species.

evolutionary biology↗

bioRxiv2017

Demography and selection shape transcriptomic divergence in field crickets

Gene flow, demography, and selection can result in similar patterns of genomic variation and disentangling their effects is key to understanding speciation. Here, we assess transcriptomic variation to unravel the evolutionary history of Gryllus rubens and Gryllus texensis, cryptic field cricket species with highly divergent mating behavior. We infer their demographic history and screen their transcriptomes for footprints of selection in the context of the inferred demography. We find strong support for a long history of bidirectional gene flow, which ceased during the late Pleistocene, and a bottleneck in G. rubens consistent with a peripatric origin of this species. Importantly, the demographic history has likely strongly shaped patterns of neutral genetic differentiation (empirical FST distribution). Concordantly, FST based selection detection uncovers a large number of outliers, likely comprising many false positives, echoing recent theoretical insights. Alternative genetic signatures of positive selection, informed by the demographic history of the sibling species, highlighted a smaller set of loci; many of these are candidates for controlling variation in mating behavior. Our results underscore the importance of demography in shaping overall patterns of genetic divergence and highlight that examining both demography and selection facilitates a more complete understanding of genetic divergence during speciation.

evolutionary biology↗