Biology subjects

Garcia-Rodriguez, A.

Publications and source records attributed to Garcia-Rodriguez, A..

5 recordsLinked to original sources

bioRxiv2024

Global invasion patterns and dynamics of disease vector mosquitoes

Mosquitoes are regarded as the most dangerous creatures on earth, spreading deadly pathogens through their bites. Human activities are driving range expansions of many mosquito species by unintentionally introducing them beyond their native ranges. Despite the often dire consequences for human health, a global picture of the introduction trends and the resulting range expansions of mosquitoes is missing. Here, we describe the global invasion patterns of mosquitoes that are vectors of human diseases and analyze the drivers shaping them. In addition, we provide the dataset compiled for these analyses which represent the most up-to-date standardized information on first records for this taxonomic group at a regional level. Our findings reveal that a total of 45 mosquito species have hitherto been introduced into regions outside their native range worldwide, representing 24% of those known to transmit human pathogens in the wild (i.e., outside experimental conditions), with 27 species successfully established. There has been a steep increase in introductions of emerging non-native mosquito species since the mid-20th century when 28 species (62% of all introduced species) were recorded for the first time. In just the last two decades, 12 new species have been identified. The geography of introductions largely mirrors global trade and transportation flows. Initially, most introduced species were native to Africa, but over time, Asian species have become more dominant. North America, Australia and Europe have consistently been the primary recipients. Our results provide a foundation for addressing the increasing threat of non-native vector mosquitoes globally, emphasizing the need for international cooperation and comprehensive control measures to mitigate their impact on public health.

ecology↗

bioRxiv2023

baRulho: an R package to quantify degradation in animal acoustic signals

O_LIAnimal acoustic signals are shaped by selection to convey information based on their tempo, intensity, and frequency. However, sound degrades as it propagates over space and across physical obstacles (e.g., vegetation or infrastructure), which affects communication potential. Therefore, transmission experiments are designed to quantify change in signal structure in a given habitat by broadcasting and re-recording animal sounds at increasing distances. C_LIO_LIWe introduce baRulho, an R package designed to simplify the implementation of sound transmission experiments. We highlight the package features with a case study testing the effects of habitat and acoustic structure on signal transmission. Synthesized sounds that varied in frequency, duration, and frequency and amplitude modulation were broadcast and re-recorded at five increasing distances in open and closed understory at the Bosque de Tlalpan, Mexico City. With this data, we showcase baRulhos functions to prepare master sound files, annotate re-recorded test sounds, as well as to calculate and visualize measures that quantify degradation of acoustic signals in the time and frequency domain. C_LIO_LIDegradation measures in baRulho adequately quantified acoustic degradation, following predicted patterns of sound transmission in natural environments. Re-recorded signals degraded less in open habitats compared to closed habitats, with higher-frequency sounds exhibiting more degradation. Furthermore, frequency modulated sounds degraded to a greater extent than pure tones. The increased attenuation and reverberation observed in higher frequency sounds and closed habitats suggest that factors such as absorption and scattering by vegetation play significant roles in transmission patterns. C_LIO_LIThe R package baRulho provides an open-source, user-friendly suite of tools designed to facilitate analysis of animal sound degradation. Notably, it offers similar results to other sound analysis software but with significantly reduced processing time. Moreover, the package minimizes the potential for user error through automated test file annotation and verification procedures. We hope that baRulho can help enhance accessibility to transmission experiments within the research community, ultimately contributing to a deeper understanding of the ecological drivers of animal communication systems. C_LI

evolutionary biology↗

bioRxiv2019

Gut microbiome diversity detected by high-coverage 16S and shotgun sequencing of matched stool and colon biopsy samples

The gut microbiome has a fundamental role in human health and disease. However, studying the complex structure and function of the gut microbiome using next generation sequencing is challenging and prone to reproducibility problems due to the heterogeneity of sample sets. Here, we obtained cross-sectional colon biopsies and faecal samples from nine participants in our COLSCREEN study and sequenced them in high coverage using Illumina pair-end shotgun (for faecal samples) and IonTorrent 16S (for paired feces and colon biopsies) technologies. The metagenomes consisted of between 47 and 92 million reads per sample and the targeted sequencing covered more than 300K reads per sample across seven hypervariable regions of the 16S gene. Our data is freely available and coupled with code for the presented metagenomic analysis using up-to-date bioinformatics algorithms. These results will add up to the informed insights into designing comprehensive microbiome analysis and also provide data for further testing for unambiguous gut microbiome analysis.

bioinformatics↗

bioRxiv2018

Prevalence of the fungal pathogen Batrachochytrium dendrobatidis in amphibians of Costa Rica predated first-known epizootic

Emerging infectious diseases are a growing threat to biodiversity worldwide. Outbreaks of the infectious disease chytridiomycosis, caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), have caused the decline and extinction of numerous amphibian species. In Costa Rica, a major decline event occurred in 1987, more than two decades before this pathogen was discovered. The loss of many species in Costa Rica is assumed to be due to Bd-epizootics, but there are few studies that provide data from amphibians in the time leading up to the proposed epizootics. In this study, we provide new data on Bd infection rates of amphibians collected throughout Costa Rica, in the decades prior to the epizootics. We used a quantitative PCR assay to test for Bd infection in 1016 specimens collected throughout Costa Rica. We found Bd-infected hosts collected as early as 1964, and a infection prevalence average per decade of just 4%. The infection prevalence remained relatively low and geographically constrained until the 1980s when epizootics are hypothesized to have occurred. After that time, infection prevalence increased three-fold and Bd-infected hosts we collected throughout the entire country. Our results, suggest that Bd may either have invaded Costa Rica earlier than previously known, and spread more slowly than previously reported, or that an endemic lineage of the pathogen may exists. To help visualize areas where future studies should take place, we provide a Bd habitat suitability model trained with local data. Studies that provide information on genetic lineages of Bd are needed to determine whether an endemic lineage of Bd or the Global Panzootic Lineage (identified from mass die off sites globally) was present in Costa Rica and responsible for the epizootics that caused amphibian communities to collapse.

ecology↗

bioRxiv2017

Signs of host genetic regulation in the microbiome composition in cattle

Previous studies have revealed certain genetic control by the host over the microbiome composition, although in many species the host genetic link controlling microbial composition is yet unknown. This potential association is important in livestock to study all factors and interactions that rule the effect of the microbiome in complex traits. This report aims to study whether the host genotype exerts any genetic control on the microbiome composition of the rumen in cattle. Data on 16S and 18S rRNA gene-based analysis of the rumen microbiome in 18 dairy cows from two different breeds (Holstein and Brown Swiss) were used. The effect of the genetic background of the animal (through the breed and Single Nucleotide Polymorphisms; SNP) on the relative abundance (RA) of archaea, bacteria and ciliates (with average relative abundance per breed >0.1%) was analysed using Bayesian statistics. In total, 13 genera were analysed for bacteria (5), archaea (1), and ciliates (7). All these bacteria and archaea genera showed association to the host genetic background both for breed and SNP markers, except RA for the genera Butyrivibrio and Ruminococcus that showed association with the SNP markers but not with the breed composition. Relative abundance of 57% (4/7) of ciliate analysed showed to be associated to the genetic background of the host. This host genetic link was observed in some genus of Trichostomatia family. For instance, the breed had a significant effect on Isotricha, Ophryoscolex and Polyplastron, and the SNP markers on Entodinium, Ophryoscolex and Polyplastron. In total, 77% (10/13) of microbes analysed showed to be associated to the host genetic background (either by breed or SNP genotypes). Further, the results showed a significant association between DGAT1, ACSF3, AGPAT3 and STC2 genes with the relative abundance Prevotella genus with a false discovery rate lower than 15%. The results in this study support the hypothesis and provide some evidence that there exist a host genetic component in cattle that can partially regulate the composition of the microbiome.

genomics↗