Biology subjects

Gutierrez, B.

Publications and source records attributed to Gutierrez, B..

18 recordsLinked to original sources

bioRxiv2025

A High-throughput Sequencing Screen to Identify Apomixis in Plants

In the past decade, plant biologists have made several major discoveries pertaining to the genetic basis of apomixis (clonal propagation by seed) that have shown promise in preserving high-value hybrid rice and sorghum genotypes. This progress was made possible by foundational gene discovery efforts in model species and natural apomicts, but pleiotropic obstacles still limit its broad agricultural adoption, especially in eudicots. Thus, it follows that investigations of novel apomicts will lead to the development of new molecular tools for plant breeding. The three most common ways to identify clonal seed production are cytoembryological analyses, genome sequencing to compare the DNA sequence of mother and child, and flow-cytometry seed screens. While flow-cytometry has been the dominant method for more than two decades, it requires specialized equipment, expertise, and occasional troubleshooting. Here we developed a method using short-read skim-seq at moderately low sequencing depths (3X and 6X) to screen diverse Malus genotypes maintained in a USDA germplasm collection for clonal seed production. By sequencing 55 genotypes and 1,216 of their embryos, our screening-by-sequencing method found 17 previously undescribed apomictic genotypes. Five additional apomictic genotypes were detected with flow cytometry data and using internal sequencing controls. This skim-seq embryo screening-by-sequencing method is a relatively low-cost, rapid method for detecting apomictic genotypes in diverse plant germplasm, and when used thoughtfully in conjunction with flow cytometry, provides a new way to visualize the genetic outcomes of sexual and asexual reproduction in plants.

plant biology↗

bioRxiv2025

Balancing sample sizes in parasitology: A novel experimental infection method using faecal parasite eggs and aquatic intermediate hosts.

Balancing sample sizes between infected and uninfected hosts is a common challenge in ecological parasitology, particularly when dealing with intermediate hosts involved in complex life cycles. In these life cycles, common in nature, the intermediate hosts accumulate parasites across their ontogeny, making it difficult to obtain similar numbers of naturally infected and uninfected individuals across full host body-size spectra. Here, we present a standardized and repeatable method to experimentally infect and re-infect intermediate hosts using parasite eggs derived directly from the fresh faeces of definitive hosts. We tested this methodology in a marine host-parasite system involving the acanthocephalan Profilicollis altmani, the mole crab Emerita analoga, and the grey gull Leucophaeus modestus. Crabs were raised in controlled laboratory conditions from early juvenile stages, ensuring no prior infections, and exposed to parasite eggs through filtered faecal suspensions. Larval development was tracked across two inoculation events. The first larval stage (acanthellae) appeared six days after inoculation and matured into cystacanths within the following week. After the first exposure, 55% of inoculated hosts were infected; after the second, infection prevalence reached 100%. Larger crabs acquired more parasites than smaller ones, likely due to higher filtration rates. The method closely mimics natural faecal-oral transmission while avoiding the need to isolate or handle parasite eggs directly. It also overcomes the common issue of parasite overdispersion in natural populations by enabling controlled infections across host size classes and experimental replicates. This technique is particularly useful in species with opaque cuticles, where internal parasites cannot be visually identified in vivo. Additionally, it can be extended beyond acanthocephalans to other helminth taxa (e.g., nematodes, cestodes, and digeneans) whose eggs are also shed in vertebrate faeces. Our results establish a reliable, ecologically relevant protocol for experimental parasitology in marine and freshwater systems.

ecology↗

bioRxiv2024

Genome-Wide Associations within Diverse Wild Apple Germplasm for Postharvest Blue Mold Resistance to Penicillium expansum

Post-harvest disease caused by the blue mold fungus, Penicillium expansum, accounts for a substantial proportion of economic losses in United States apple industry. Multiple modes of entry in the apple supply chain, plus emerging fungicide resistance, limit the current and long-term viability of using chemical controls alone. Previous phenotypic screens of Malus accessions in the USDA-ARS apple germplasm have identified varying levels of blue mold disease resistance in some wild apple accessions and hybrids. These wild apple species contain reservoirs of genetic resistance that can be integrated into apple breeding programs to complement the previously identified qM-Pe3.1 marker from M. sieversii. We sought to identify these novel loci by combining historical phenotypes of the USDA-ARS wild apple germplasm with low-pass genomic sequencing to perform association mapping. Multi-locus mixed models identified five single nucleotide polymorphisms (SNPs) significantly associated with reduction of post-harvest rot under high concentration of P. expansum inoculum, and one SNP associated under low inoculum concentration. Within a 25,000 base pair window of these SNPs, we found candidate genes encoding proteins with known pathogen immune response and defense roles, such as a Cobra-like 7, flavin monooxygenase, LRR receptors, PR5-like receptor kinase, and a putative resistance protein RGA3. We present these loci as targets for identifying accessions with beneficial alleles that can be targeted for fine mapping and use in Malus breeding programs to achieve M. domestica lines with natural post-harvest rot resistance.

genetics↗

bioRxiv2024

Notch is Required for Neural Progenitor Proliferation During Embryonic Eye Regrowth

The ability of an organism to regrow tissues is regulated by various signaling pathways. One such pathway that has been studied widely both in the context of regeneration and development is the Notch signaling pathway. Notch signaling is required for development of the eye and regeneration of tissues in multiple organisms but it is unknown if Notch plays a role in the regulation of Xenopus laevis embryonic eye regrowth. We found that Notch1 is required for eye regrowth and regulates retinal progenitor cell proliferation. Chemical and molecular inhibition of Notch1 significantly decreased eye regrowth through reducing retinal progenitor cell proliferation without affecting retinal differentiation. Temporal inhibition studies showed that Notch function is required during the first day of regrowth. Interestingly, Notch1 loss-of-function phenocopied the effects of the inhibition of the proton pump, V-ATPase, where retinal proliferation but not differentiation was blocked during eye regrowth. Overexpression of a form of activated Notch1, the Notch intracellular domain (NICD) was sufficient to rescue loss of eye regrowth due to V-ATPase inhibition, suggesting that Notch acts downstream of V-ATPase. These findings highlight the importance of the Notch signaling pathway in eye regeneration and its role in inducing retinal progenitor cell proliferation in response to injury.

developmental biology↗

bioRxiv2023

Genome of the North American wild apple species Malus angustifolia

Apple (Malus x domestica Borkh.) production faces many challenges stemming from abiotic and biotic stresses. Abiotic stressors, such as extreme temperatures, droughts, and spring frosts, can lead to diminished yields and tree loss, while biotic stresses like fire blight and pest infestations further reduce tree health and fruit quality. To lessen the threat of these challenges, plant breeders aim to introduce resistance and resilience genes into cultivated varieties. However, high-relatedness among cultivated varieties and breeding lines, coupled with the long juvenility and generation times in apples, hinder the breeding process. The introduction of resistance traits from wild relatives is also constrained by these factors, as well as the lack of genomic resources that could assist in accelerating the introgression process. Herein, we report the assembly and annotation of Malus angustifolia, the Southern Crabapple, one of Eastern North Americas native species. Using a combination of Pacific Biosciences High Fidelity reads, Next-generation short read sequencing, as well as chromatin conformation capture sequencing, we achieve an extremely contiguous haplotype-resolved assembly. We perform comparative haplotypic analyses to identify SNPs and large structural variants, shedding light on the genomic landscape of M. angustifolia. Finally, we explore the phylogenetic and syntenic relationships between Eurasian Malus progenitors and the recently sequenced North American species, contributing valuable insights to the broader understanding of apple evolution and potential breeding strategies.

genomics↗

bioRxiv2023

First whole genome sequence and assembly of the Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps), a critically endangered species, using Oxford Nanopore Technologies

The Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps) is currently considered one of the most endangered primates in the world and is classified as critically endangered (IUCN). It faces multiple threats, the most significant one being habitat loss due to deforestation in western Ecuador. Genomic tools are key for the management of endangered species, but this requires a reference genome which until now was unavailable for A. f. fusciceps. The present study reports the first whole genome sequence and assembly of A. f. fusciceps generated using Oxford Nanopore long reads. DNA was extracted from a subadult male and libraries were prepared for sequencing following the Ligation Sequencing Kit SQK-LSK112 workflow. Sequencing was performed using a MinION Mk1C sequencer. The sequencing reads were processed to generate a genome assembly. Two different assemblers were used to obtain draft genomes using raw reads, of which the Flye assembly was found to be superior. The final assembly has a total length of 2.63 Gb and contains 3,861 contigs, with an N50 of 7,560,531 bp. The assembly was analyzed for annotation completeness based on primate ortholog prediction using a high-resolution database, and was found to be 84.3% complete, with a low number of duplicated genes indicating a precise assembly. The annotation of the assembly predicted 31,417 protein-coding genes, comparable to other mammal assemblies. A reference genome for this critically endangered species will allow researchers to gain insight into the genetics of its populations and thus aid conservation and management efforts of this vulnerable species.

genomics↗

bioRxiv2023

USING SMALL MOLECULES TO TURN AN RNA APTAMER INTO SENSORS FOR INORGANIC TARGETS WITHOUT IN VITRO SELECTION

Fluorescent light-up aptamer (FLAP) systems are promising biosensing platforms that can be genetically encoded. Here, we describe how a single FLAP that works with specific organic ligands can detect multiple, structurally unique, non-fluorogenic, and reactive inorganic targets. We developed 4-O-functionalized benzylidene imidazolinones as pre-ligands with suppressed fluorescent binding interactions with the RNA aptamer Baby Spinach. Inorganic targets, hydrogen sulfide (H2S) or hydrogen peroxide (H2O2), can specifically convert these pre-ligands into the native benzylidene imidazolinones, and thus be detected with Baby Spinach. Adaptation of this approach to live cells opened a new opportunity for top-down construction of whole-cell sensors: Escherichia coli transformed with a Baby Spinach-encoding plasmid and incubated with pre-ligands generated fluorescence in response to exogenous H2S or H2O2. Our approach eliminates the requirement of in vitro selection of a new aptamer sequence for molecular target detection, allows for the detection of short-lived targets, thereby advancing FLAP systems beyond their current capabilities. Leveraging the functional group reactivity of small molecules can lead to cell-based sensors for inorganic molecular targets, exploiting a new synergism between synthetic organic chemistry and synthetic biology.

biochemistry↗

bioRxiv2023

A haplotype resolved chromosome-scale assembly of North American wild apple Malus fusca and comparative genomics of the fire blight Mfu10 locus.

The Pacific crabapple (Malus fusca) is a wild relative of the commercial apple (Malus x domestica). With a range extending from Alaska to Northern California, M. fusca is extremely hardy and disease resistant. The species represents an untapped genetic resource for development of new apple cultivars with enhanced stress resistance. However, gene discovery and utilization of M. fusca has been hampered by the lack of genomic resources. Here, we present a high-quality, haplotype-resolved, chromosome-scale genome assembly and annotation for M. fusca. The genome was assembled using high-fidelity long-reads and scaffolded using genetic maps and high-throughput chromatin conformation capture sequencing, resulting in one of the most contiguous apple genomes to date. We annotated the genome using public transcriptomic data from the same species taken from diverse plant structures and developmental stages. Using this assembly, we explored haplotypic structural variation within the genome of M. fusca, identifying thousands of large variants. We further showed high sequence co-linearity with other domesticated and wild Malus species. Finally, we resolve a known quantitative trait locus associated with resistance to fire blight (Erwinia amylovora). Insights gained from the assembly of a reference-quality genome of this hardy wild apple relative will be invaluable as a tool to facilitate DNA-informed introgression breeding.

genomics↗

bioRxiv2022

Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico

Over 200 different SARS-CoV-2 lineages have been observed in Mexico by November 2021. To investigate lineage replacement dynamics, we applied a phylodynamic approach and explored the evolutionary trajectories of five dominant lineages that circulated during the first year of local transmission. For most lineages, peaks in sampling frequencies coincided with different epidemiological waves of infection in Mexico. Lineages B.1.1.222 and B.1.1.519 exhibited similar dynamics, constituting clades that likely originated in Mexico and persisted for >12 months. Lineages B.1.1.7, P.1 and B.1.617.2 also displayed similar dynamics, characterized by multiple introduction events leading to a few successful extended local transmission chains that persisted for several months. For the largest B.1.617.2 clades, we further explored viral lineage movements across Mexico. Many clades were located within the south region of the country, suggesting that this area played a key role in the spread of SARS-CoV-2 in Mexico.

evolutionary biology↗

bioRxiv2022

Activity-Based Imaging of Lipid Environments Targeted by Peroxynitrite in Biomimetic Vesicles and Live Cells

Lipid environments can be chemically impacted by peroxynitrite (ONOO-), a reactive species generated under nitrative stress. Molecular tools used for investigating ONOO- reactivity in biological membranes remain underdeveloped, available probes lack the ability of subcellular localization, and the standard methods for detecting ONOO- in vivo are indirect. Here we investigated ONOO- in diverse lipid environments (biomimetic giant vesicles, live mammalian cells, and within the lung lining) using a biocompatible and membrane-localized phospholipid named DPPC-TC-ONOO-. This designer lipid and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine self-assemble to giant vesicles that respond to ONOO- by generating fluorescence. These vesicles remain intact after sensing ONOO- and exhibit excellent selectivity against other redox species. We delivered DPPC-TC-ONOO- into live HeLa and RAW cells via lipid nanoparticles (LNPs). Cytokine-induced nitrative stress led to enhanced fluorescence of the lipid clusters, primarily in the endoplasmic reticulum. These LNPs allowed the detection of ONOO- reactivity and nitrative stress around bronchioles within precision cut lung slices in response to acute lung injury (ALI). Furthermore, the use of the LNPs allowed for the detection of pulmonary macrophages from bronchoalveolar lavage following ALI in C57BL6/J but not in Nos2-/- mice. These investigations revealed significant advantages of DPPC-TC-ONOO- over its non-amphiphilic analog. Our work presents (i) an unprecedented function for biomimetic membranes, (ii) the potential of LNPs for delivering designer lipids into cells and tissues, (iii) real-time imaging of endogenous ONOO- at the organelle level in mammalian cells, and (iv) a direct method of studying nitrative stress due to ALI ex vivo and in vivo.

biochemistry↗

bioRxiv2021

Identification of site-specific evolutionary trajectories shared across human betacoronaviruses

Comparing the evolution of distantly related viruses can provide insights into common adaptive processes related to shared ecological niches. Phylogenetic approaches, coupled with other molecular evolution tools, can help identify mutations informative on adaptation, whilst the structural contextualization of these to functional sites of proteins may help gain insight into their biological properties. Two zoonotic betacoronaviruses capable of sustained human-to-human transmission have caused pandemics in recent times (SARS-CoV-1 and SARS-CoV-2), whilst a third virus (MERS-CoV) is responsible for sporadic outbreaks linked to animal infections. Moreover, two other betacoronaviruses have circulated endemically in humans for decades (HKU1 and OC43). To search for evidence of adaptive convergence between established and emerging betacoronaviruses capable of sustained human-to-human transmission (HKU1, OC43, SARS-CoV-1 and SARS-CoV-2), we developed a methodological pipeline to classify shared non-synonymous mutations as putatively denoting homoplasy (repeated mutations that do not share direct common ancestry) or stepwise evolution (sequential mutations leading towards a novel genotype). In parallel, we look for evidence of positive selection, and draw upon protein structure data to identify potential biological implications. We find 30 mutations, with four of these [codon sites 18121 (nsp14/residue 28), 21623 (spike/21), 21635 (spike/25) and 23948 (spike/796); SARS-CoV-2 genome numbering] displaying evolution under positive selection and proximity to functional protein regions. Our findings shed light on potential mechanisms underlying betacoronavirus adaptation to the human host and pinpoint common mutational pathways that may occur during establishment of human endemicity.

evolutionary biology↗

bioRxiv2020

Characterizing the genetic diversity of the Andean blueberry (Vaccinium floribundum Kunth.) across the Ecuadorian Highlands

The Ecuadorian paramo, a high altitude tundra-like ecosystem, is a unique source of various ecosystem services and distinct biodiversity. Anthropogenic activities are associated with its fragmentation, which alters ecological factors and directly threatens resident species. Vaccinium floribundum Kunth., commonly known as Andean blueberry or mortino, is a wild shrub endemic to the Andean region and highly valued in Ecuador for its berries, which are widely used in food preparations and hold an important cultural value. Since it is a wild species, mortino could be vulnerable to environmental changes, resulting in a reduction of the size and distribution of its populations. To evaluate the extent of these effects on the mortino populations, we assessed the genetic diversity and population structure of the species along the Ecuadorian highlands. We designed and developed a set of 30 homologous SSR markers and used 16 of these to characterize 100 mortino individuals from 27 collection sites. Our results revealed a high degree of genetic diversity (HE=0.73) for the Ecuadorian mortino, and a population structure analyses suggested the existence of distinct genetic clusters present in the northern, central and southern highlands. A fourth, clearly differentiated cluster was also found and included individuals from locations at higher elevations. We suggest that the population structure of the species could be explained by an isolation-by-distance model and can be associated to the geological history of the Andean region. Our results suggest that elevation could also be a key factor in the differentiation of mortino populations. This study provides an extensive overview of the species across its distribution range in Ecuador, contributing to a better understanding of its conservation status. These results can assist the development of conservation programs for this valuable biological and cultural resource and for the paramo ecosystems as a whole.

genetics↗

bioRxiv2020

Understanding the genetic diversity of the guayabillo (Psidium galapageium), an endemic plant of the Galapagos Islands

Oceanic archipelagos are known to host a variety of endemic plant species. The genetic diversity and structure of these species is an important indicator of their evolutionary history and can inform appropriate conservation strategies that mitigate the risks to which theyre exposed, including invasive species and environmental disturbances. A comprehensive consideration of the role of their natural history, as well as the landscape features and the geological history of the islands themselves is required to adequately understand any emerging patterns. Such is the case for the guayabillo (Psidium galapageium), an understudied endemic plant from the Galapagos Islands with important ecological and economic roles. In this study we designed and evaluated 13 informative SSR markers and used them to investigate the genetic diversity, population structure and connectivity of the guayabillo populations from San Cristobal, Isabela and Santa Cruz islands. A total of 208 guayabillo individuals were analyzed, revealing a strong population structure between islands and two distinct genetic lineages for the Santa Cruz population. Overall, the guayabillo genetic diversity is relatively high, an unusual pattern for an insular endemic species which is possibly explained by its polyploidy and the geographical features of the islands. These include their broad altitudinal ranges and habitat heterogeneity. For populations displaying a lower genetic diversity such as San Cristobal, the history of human disturbance could be an important factor explaining these observations. Some similarities between individuals in Santa Cruz and the San Cristobal population could be explained by population differentiation or distinct natural histories of separate lineages. Our findings highlight the complex population dynamics that shape the genetic diversity of species like the guayabillo and emphasize the need to explore the currently unresolved questions about this Galapagos endemic plant.

plant biology↗

bioRxiv2019

Thetaburst TMS to the posterior superior temporal sulcus decreases resting-state fMRI connectivity across the face processing network

Humans process faces using a network of face-selective regions distributed across the brain. Neuropsychological patient studies demonstrate that focal damage to nodes in this network can impair face recognition, but such patients are rare. We approximated the effects of damage to the face network in neurologically normal human participants using thetaburst transcranial magnetic stimulation (TBS). Multi-echo functional magnetic resonance imaging (fMRI) resting-state data were collected pre- and post-TBS delivery over the face-selective right superior temporal sulcus (rpSTS), or a control site in the right motor cortex. Results showed that TBS delivered over the rpSTS reduced resting-state connectivity across the extended face-processing network. This connectivity reduction was observed not only between the rpSTS and other face-selective areas, but also between non-stimulated face-selective areas across the ventral, medial and lateral brain surfaces (e.g. between the right amygdala and bilateral fusiform face areas and occipital face areas). TBS delivered over the motor cortex did not produce significant changes in resting-state connectivity across the face-processing network. These results demonstrate that, even without task-induced fMRI signal changes, disrupting a single node in a brain network can decrease the functional connectivity between nodes in that network that have not been directly stimulated. Author SummaryHuman behavior is dependent on brain networks that perform different cognitive functions. We combined thetaburst transcranial magnetic stimulation (TBS) with resting-state fMRI to study the face processing network. Disruption of the face-selective right posterior superior temporal sulcus (rpSTS) reduced fMRI connectivity across the face network. This impairment in connectivity was observed not only between the rpSTS and other face-selective areas, but also between non-stimulated face-selective areas on the ventral and medial brain surfaces (e.g. between the right amygdala and bilateral fusiform face areas and occipital face areas). Thus, combined TBS/fMRI can be used to approximate and measure the effects of focal brain damage on brain networks, and suggests such an approach may be useful for mapping intrinsic network organization. Technical TermsO_ST_ABSTBS vs TMSC_ST_ABSTranscranial magnetic stimulation (TMS) is a method that induces current in neural tissue by using a rapidly changing magnetic field. The pattern of magnetic field changes can vary. Thetaburst TMS (TBS) is a type of TMS where the same stimulation pattern fluctuates at around a 5Hz cycle. Multi-echo fMRIDuring typical fMRI, protons are excited and there is a delay, the echo time, before data are collected. That delay is typically designed to result in a high contrast for blood oxygenation differences. In multi-echo fMRI, data are collected at several echo times each time protons are excited. This results in data that have different levels of contrast for blood oxygenation differences. This added information can be used to empirically decrease noise. Face networkA group of brain regions that show significant activity changes in response to visual face stimuli. While these regions have been defined using univariate analyses with task-based fMRI, they often significantly correlate with each other at rest. In this manuscript, the following regions were a priori defined as part of the face network: posterior superior temporal sulcus (pSTS), amygdala, fusiform face area (FFA), and occipital face area (OFA). Matrix based analysis (MBA)A recent approach that uses a Bayesian multilevel modeling framework to identify pairs of ROIs where a decrease in correlation magnitude was larger than expected along with a measure of statistical evidence. With this approach, correlations between all pairs of ROIs are assessed as part of a single model rather than many independent statistical tests.

neuroscience↗

bioRxiv2019

Oropouche virus cases identified in Ecuador using an optimised rRT-PCR informed by metagenomic sequencing

Oropouche virus (OROV) is responsible for outbreaks of Oropouche fever in parts of South America. We recently identified and isolated OROV from a febrile Ecuadorian patient, however, a previously published rRT-PCR assay did not detect OROV in the patient sample. A primer mismatch to the Ecuadorian OROV lineage was identified from metagenomic sequencing data. We report the optimisation of an rRT-PCR assay for the Ecuadorian OROV lineage, which subsequently identified a further five cases in a cohort of 196 febrile patients. We isolated OROV via cell culture and developed an algorithmically-designed primer set for whole-genome amplification of the virus. Metagenomic sequencing of the patient samples provided OROV genome coverage ranging from 68 - 99%. The additional cases formed a single phylogenetic cluster together with the initial case. OROV should be considered as a differential diagnosis for Ecuadorian patients with febrile illness to avoid mis-diagnosis with other circulating pathogens.

genomics↗

bioRxiv2019

The evolutionary dynamics of Oropouche Virus (OROV) in South America

The Amazon basin is host to numerous arthropod-borne viral pathogens that cause febrile disease in humans. Among these, Oropouche orthobunyavirus (OROV) is a relatively understudied member of the Peribunyavirales that causes periodic outbreaks in human populations in Brazil and other South American countries. Although several studies have described the genetic diversity of the virus, the evolutionary processes that shape the viral genome remain poorly understood. Here we present a comprehensive study of the genomic dynamics of OROV that encompasses phylogenetic analysis, evolutionary rate estimates, inference of natural selective pressures, recombination and reassortment, and structural analysis of OROV variants. Our study includes all available published sequences, as well as a set of new OROV genomes sequences obtained from patients in Ecuador, representing the first set of viral genomes from this country. Our results show that differing evolutionary processes on the three segments that encompass the viral genome lead to variable evolutionary rates and TMRCAs that could be explained by cryptic reassortment. We also present the discovery of previously unobserved putative N-linked glycosylation sites, and codons which evolve under positive selection on the viral surface proteins, and discuss the potential role of these features in the evolution of the virus through a combined phylogenetic and structural approach.

evolutionary biology↗

bioRxiv2018

Psidium guajava in the Galapagos Islands: population genetics and history of an invasive species

The threat of invasive plant species in island populations prompts the need to better understand their population genetics and dynamics. In the Galapagos islands, this is exemplified by the introduced guava (Psidium guajava), considered one of the greatest threats to the local biodiversity due to its effective spread in the archipelago and its ability to outcompete endemic species. To better understand its history and genetics, we analyzed individuals from three inhabited islands in the Galapagos archipelago with 11 SSR markers. Our results reveal similar genetic diversity between islands, suggestive of gene flow between them. Populations appear to be distinct between the islands of San Cristobal and Isabela, with the population of Santa Cruz being composed as a mixture from both. Additional evidence for genetic bottlenecks and the inference of introduction events suggests an original introduction of the species in San Cristobal, from where it was later introduced to Isabela, and finally into Santa Cruz. Alternatively, an independent introduction event for Isabela is also possible. These results are contrasted with the historical record, providing a first overview of the history of P. guajava in the Galapagos islands and its current population dynamics.

evolutionary biology↗

bioRxiv2018

Parallel Evolution and the Emergence of Highly Pathogenic Avian Influenza A Viruses

Parallel molecular evolution and adaptation are important phenomena commonly observed in viruses. Here we exploit parallel molecular evolution to understand virulence evolution in avian influenza viruses (AIV). Highly-pathogenic AIVs independently evolve from low-pathogenic ancestors via acquisition of a polybasic cleavage sites (pCS). Why some AIV lineages but not others evolve in this way is unknown. We hypothesise that the parallel emergence of highly-pathogenic AIV may be facilitated by permissive or compensatory mutations occurring across the AIV genome. We combined phylogenetic, statistical and structural approaches to discover parallel mutations in AIV genomes associated with the highly-pathogenic phenotype. Parallel mutations were screened using a new statistical test of mutation-phenotype association and further evaluated in the contexts of positive selection and protein function. The mutational panel we present reveals new links between virulence evolution and other viral traits and raises the possibility of predicting aspects of AIV evolution.

evolutionary biology↗