Biology subjects

Gutierrez, A. P.

Publications and source records attributed to Gutierrez, A. P..

10 recordsLinked to original sources

bioRxiv2026

Re-invasion of the New World screwworm in Central and North America: comparative analysis of three SIT eradication efforts

In sharp contrast to biological control that seeks control of pests below economic levels, eradication programs seek total extermination of pest species. However, eradication programs are often undertaken without knowledge of the pests potential geographic distribution and relative abundance (i.e., geographic risk assessment), often leading to eradication efforts conducted across areas much greater than the potential permanent range of the target species. To demonstrate this, we review eradication efforts against the tropical New World screwworm (Cochliomyia hominivorax) in the SE USA and Mexico, the exotic sub-tropical tephritid Mediterranean fruit fly (Ceratitis capitata, medfly) in California, and the exotic tropical pink bollworm (Pectinophora gossypiella, PBW) in the SW USA. We use mechanistic physiologically based demographic models (PBDMs) that are physiologically based time varying life tables to decompose the systems and to assess risk under extant and climate change scenarios.

ecology↗

bioRxiv2025

Ex ante analyses can predict natural enemy efficacy in biological control

The success rate of biological control programs against invasive species is low because the efficacy of released natural enemies is unknown. Deconstruction of the successful biological control of the highly destructive cassava mealybug (CM) and cassava green mite (CGM) in Africa is used to show how ex ante pre-release analyses of natural enemies can increase the success rate. A meta-population tri-trophic physiologically based demographic model (PBDM) of the cassava system accurately predicted the weather-driven daily dynamics of cassava, CM, CGM, and their introduced natural enemies across the ecological zones of Africa. Marginal analyses of the simulation data enabled parsing the differing contributions of two exotic parasitoids and a fungal pathogen in the control of CM, and the contributions of two mite predators, local pathogens and rainfall mortality in the control of CGM. The contribution of each natural enemy to the [~]95% recovery of cassava yields is estimated. The results show ex ante analyses of prospective natural enemies using well parameterized PBDMs can predict natural enemy prerelease efficacy across vast geographic areas and increase the success rate of biological control programs. Ex ante analyses can also explain whether biological control is a viable option (e.g., Cure et al. 2020).

ecology↗

bioRxiv2024

Physiologically based demographic model/GIS analyses of thirteen invasive species in Africa: why the biology matters

Globally, research and policy groups often lack the expertise to develop appropriate models to analyze agroecological and invasive species problems holistically to inform management and quarantine policy development under extant and climate change over wide geographic landscapes. Off-the-shelf species distribution models (SDM) correlate weather and other variables to records of species presence and have become the mainstay for predicting the geographic distribution and favorability of invasive species (Elith 2017). However, SDM analyses lack the capacity to examine the underpinning dynamics of agroecosystems required to inform policy and develop management strategies. We propose that age-structured physiologically based demographic models (PBDMs) can solve important aspects of this challenge as they can be used to examine prospectively species dynamics locally as well as their potential geographic distribution and relative abundance across vast areas independent of presence records. PBDMs fall under the ambit of time-varying life tables (TVLTs; cf. Gilbert et al. 1976) and capture the weather driven biology, dynamics, and interactions of species, and can be used to examine the system from the perspective of any of the interacting species. Here, we use the PBDM structure to examine the dynamics across Africa of thirteen invasive species from various taxa having diverse biology and trophic interactions (see Gutierrez 1996, Gutierrez and Ponti 2013a). PBDMs are perceived to be difficult to develop, hence the raison detre is to show this is not the case and illustrate their utility invasive and endemic agricultural and medical/veterinary pest species at the local and the large geographic scale of Africa. We note that PBDMs provide a structure for continued model improvements. The development of open access software is proposed to facilitate PBDM development by non-experts emphasizing the crucial role of sound biological data on species responses to weather and to other species in a multi-trophic, interactions, and provide a guide for collecting the appropriate biological data. While the emphasis is on plant/arthropod interactions, models of diseases can be accommodated. The Supplemental Materials summarizes a large array of heritage PBDMs reported in the literature based on the methods outline herein, noting that the same model structure can be used to analyze and manage non pest species.

ecology↗

bioRxiv2023

Development of genomic markers associated to production traits in lumpfish (Cyclopterus lumpus)

Cleaner fish species have gained great importance in the control of sea lice, among them, lumpfish (Cyclopterus lumpus) has become one of the most popular. Lumpfish life cycle has been closed, and hatchery reproduction is now possible, however, current production is reliant on wild caught broodstock to meet the increasing demand. Selective breeding practices are called to play an important role in the successful breeding of most aquaculture species, including lumpfish. In this study we analysed a lumpfish population for the identification of genomic markers linked to production traits. Sequencing of RAD libraries allowed us to identify, 7,193 informative markers within the sampled individuals. Genome wide association analysis for sex, weight, condition factor and standard length was performed. One single major QTL region was identified for sex determination, while nine QTL regions were detected for weight, and three QTL regions for standard length. A total of 177 SNP markers of interest (from QTL regions) and 399 top Fst SNP markers were combined in a low-density panel, useful to obtain relevant genetic information from lumpfish populations. Moreover, a robust combined subset of 29 SNP markers (10 associated to sex, 14 to weight and 18 to standard length) provided over 90% accuracy in predicting the animals phenotype. Overall, our findings provide significant insights into the genetic control of important traits in lumpfish and deliver important genomic resources that will facilitate the establishment of selective breeding programs in lumpfish.

genomics↗

bioRxiv2020

Investigating mechanisms underlying genetic resistance to Salmon Rickettsial Syndrome in Atlantic salmon using RNA sequencing

BackgroundSalmon Rickettsial Syndrome (SRS), caused by Piscirickettsia salmonis, is one of the primary causes of morbidity and mortality in Atlantic salmon aquaculture, particularly in Chile. Host resistance is a heritable trait, and functional genomic studies have highlighted genes and pathways important in the response of salmon to the bacteria. However, the functional mechanisms underpinning genetic resistance are not yet well understood. In the current study, a large population of salmon pre-smolts were challenged with P. salmonis, with mortality levels recorded and samples taken for genotyping. In parallel, head kidney and liver samples were taken from animals of the same population with high and low genomic breeding values for resistance, and used for RNA-Sequencing to compare their transcriptome profile both pre and post infection. ResultsA significant and moderate heritability (h2 = 0.43) was shown for the trait of binary survival. Genome-wide association analyses using 38K imputed SNP genotypes across 2,251 animals highlighted that resistance is a polygenic trait. Several thousand genes were identified as differentially expressed between controls and infected samples, and enriched pathways related to the host immune response were highlighted. In addition, several networks with significant correlation with SRS resistance breeding values were identified, suggesting their involvement in mediating genetic resistance. These included apoptosis, cytoskeletal organisation, and the inflammasome. ConclusionsWhile resistance to SRS is a polygenic trait, this study has highlighted several relevant networks and genes that are likely to play a role in mediating genetic resistance. These genes may be future targets for functional studies, including genome editing, to further elucidate their role underpinning genetic variation in host resistance.

genomics↗

bioRxiv2020

A chromosome-level genome assembly for the Pacific oyster (Crassostrea gigas)

The Pacific oyster (Crassostrea gigas) is a marine bivalve species with vital roles in coastal ecosystems and aquaculture globally. While extensive genomic tools are available for C. gigas, highly contiguous reference genomes are required to support both fundamental and applied research. In the current study, high coverage long and short read sequence data generated on Pacific Biosciences and Illumina platforms from a single female individual specimen was used to generate an initial assembly, which was then scaffolded into 10 pseudo chromosomes using both Hi-C sequencing and a high density SNP linkage map. The final assembly has a scaffold N50 of 58.4 Mb and a contig N50 of 1.8 Mb, representing a step advance on the previously published C. gigas assembly. The new assembly was annotated using Pacific Biosciences Iso-Seq and Illumina RNA-Seq data, identifying 30K putative protein coding genes, with an average of 3.9 transcripts per gene. Annotation of putative repeat elements highlighted an inverse relationship with gene density, and identified putative centromeres of the metacentric chromosomes. An enrichment of Helitron rolling circle transponsable elements was observed, suggesting their potential role in shaping the evolution of the C. gigas genome. This new chromosome-level assembly will be an enabling resource for genetics and genomics studies to support fundamental insight into bivalve biology, as well as for genetic improvement of C. gigas in aquaculture breeding programmes.

genomics↗

bioRxiv2019

Potential of genomic selection for improvement of resistance to Ostreid Herpes virus in Pacific oyster (Crassostrea gigas)

In genomic selection (GS), genome-wide SNP markers are used to generate genomic estimated breeding values (gEBVs) for selection candidates. The application of GS in shellfish looks promising and has the potential to help in dealing with one of the main issues currently affecting Pacific oyster production worldwide, which is the \"summer mortality syndrome\". This causes periodic mass mortality in farms worldwide and has mainly been attributed to a specific variant of the Ostreid herpesvirus (OsHV-1-var). In the current study, we evaluated the potential of genomic selection for host resistance OsHV in Pacific oysters, and compared it to pedigree-based approaches. An OsHV-1 disease challenge was performed using an immersion-based virus exposure treatment for oysters for seven days. 768 samples were genotyped using the medium density SNP array for oysters. GWAS was performed for the survival trait using a GBLUP approach in BLUPF90 software. Heritability ranged from 0.25{+/-}0.05 to 0.37{+/-}0.05 (mean{+/-}s.e) based on pedigree and genomic information, respectively. Genomic prediction was more accurate than pedigree prediction, and SNP density reduction had little impact on prediction accuracy until marker densities dropped below [~]500 SNPs. This demonstrates the potential for GS in Pacific oyster breeding programs and importantly, demonstrates that a low number of SNPs might suffice to obtain accurate gEBVs, thus potentially making the implementation of GS more cost effective.

genomics↗

bioRxiv2018

Discovery and functional annotation of quantitative trait loci affecting resistance to sea lice in Atlantic salmon

Sea lice (Caligus rogercresseyi) are ectoparasitic copepods which have a large negative economic and welfare impact in Atlantic salmon (Salmo salar) aquaculture, particularly in Chile. A multi-faceted prevention and control strategy is required to tackle lice, and selective breeding contributes via cumulative improvement of host resistance to the parasite. While host resistance has been shown to be heritable, little is yet known about the individual loci that contribute to this resistance, the potential underlying genes, and their mechanisms of action. In this study we took a multifaceted approach to identify and characterise quantitative trait loci (QTL) affecting hose resistance in a population of 2,688 Caligus-challenged Atlantic salmon post-smolts from a commercial breeding programme. We used low and medium density genotyping to collect genome-wide SNP marker data for all animals. Moderate heritablility estimates of 0.28 and 0.24 were obtained for lice density (as a measure of host resistance) and growth during infestation respectively. Three QTL explaining between 7 and 13 % of the genetic variation in resistance to sea lice (as represented by the traits of lice density) were detected on chromosomes 3, 18 and 21. Characterisation of these QTL regions was undertaken using RNA sequencing and pooled whole genome sequencing data. This resulted in the identification of a shortlist of potential underlying causative genes, and candidate functional mutations for further study. For example, candidates within the chromosome 3 QTL include a putative premature stop mutation in TOB1 (an anti-proliferative transcription factor involved in T cell regulation) and an uncharacterized protein which showed significant differential allelic expression (implying the existence of a cis-acting regulatory mutation). While host resistance to sea lice is polygenic in nature, the results of this study highlight significant QTL regions together explaining a moderate proportion of the heritability of the trait. Future investigation of these QTL may enable improved knowledge of the functional mechanisms of host resistance to sea lice, and incorporation of functional variants to improve genomic selection accuracy.

genetics↗

bioRxiv2017

Gene expression response to sea lice in Atlantic salmon skin: an RNA-Seq comparison between resistant and susceptible animals

BackgroundSea lice are parasitic copepods that cause large economic losses to salmon aquaculture worldwide. Frequent chemotherapeutic treatments are typically required to control this parasite, and alternative measures such as breeding for improved host resistance are desirable. Insight into the host-parasite interaction and mechanisms of host resistance can lead to improvements in selective breeding, and potentially novel treatment targets. In this study, RNA sequencing was used to study the skin transcriptome of Atlantic salmon parasitized with sea lice (C. rogercresseyi). The overall aims were to compare the transcriptomic profile of skin at louse attachment sites and healthy skin, and to assess differences between animals with varying levels of resistance to the parasite.\n\nResultsAtlantic salmon were challenged with C. rogercresseyi, growth and lice count measurements were taken for each fish. 21 animals were selected and RNA-Seq was performed on skin from a louse attachment site, and skin distal to attachment sites for each animal. These animals were classified into family-balanced groups according to the traits of resistance (high vs low lice count), and growth during infestation (an indication of tolerance). Overall comparison of skin from louse attachment sites versus healthy skin showed that 4,355 genes were differentially expressed, indicating local up-regulation of several immune pathways and activation of tissue repair mechanisms. Comparison between resistant and susceptible animals highlighted expression differences in several immune response and pattern recognition genes, and also myogenic and iron availability factors. Genomic regions showing signs of differentiation between resistant and susceptible fish were identified using an Fst analysis.\n\nConclusionsComparison of the skin transcriptome between louse attachment sites and healthy skin has yielded a detailed profile of genes and pathways with putative roles in the local host immune response to C. rogercresseyi. The difference in skin gene expression profile between resistant and susceptible animals led to the identification of several immune and myogenic pathways potentially involved in host resistance. Components of these pathways may be targets for studies aimed at improved or novel treatment strategies, or to prioritise candidate functional polymorphisms to enhance genomic selection for host resistance in commercial salmon farming.

genetics↗

bioRxiv2017

Characterization Of Amylase And Protease Activities In The Digestive System Of Concholepas concholepas (Gastropoda, muricidae)

Concholepas concholepas (loco) is a carnivorous gastropod that inhabits the coast of Chile and Peru. Its fisheries showed a great importance in the past decades, however, now mainly relies on artisanal management of wild stocks. Feeding is one of the important factors that have restrained the establishment of large scale field rearing of loco. C. concholepas food preferences consist of mytilids and cirripeds, however its digestive physiology has not been studied and its digestive enzymes have not been yet characterized. The purification of amylase and protease from the digestive gland and the gland of Leiblein of C. concholepas were performed by ionic exchange chromatography (DEAE-cellulose), and substrate-PAGE indicated the presence of the amylase and protease in the fractions collected from the column. Amylase enzymatic assays showed its maximum activity at pH 7.0 and 50{degrees}C in the digestive gland. Protease on the other hand showed a great acidic activity, specifically at pH 3.0 in both organs, also at 50{degrees}C. Inhibition of the amylolytic activity was observed in the presence of EDTA, and metal ions like MnCl2, MgCl2, ZnSO4, while it was enhanced in the presence of CaCl2, NaCl, KCl. Protease inhibition assays were also performed evidencing mainly the presence of aspartic proteases and a low but not inexistent presence of serine proteases. Our results provide evidence of important proteolytic but also amylolytic activities present in the digestive system of loco, providing evidence that this mollusc has wider digestive capabilities than initially though, which could potentially lead to the development of alternative food diets.

biochemistry↗