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Nunez, R.

Publications and source records attributed to Nunez, R..

5 recordsLinked to original sources

Mixture Models Unveil the Origin of the Enigmatic Satyrine Butterfly Genera Calisto and Llorenteana (Lepidoptera, Nymphalidae, Satyrinae).

We provide the first comprehensive analysis of the origin of two enigmatic Satyrinae genera of uncertain affinities. Calisto, the only Satyrinae genus from the West Indies and endemic to these islands, has resisted numerous attempts at phylogenetic placement, regardless of the data type or methods used. Llorenteana, a monotypic genus from northwestern Mexico, has never been included in a molecular phylogenetic study, and past authors have placed it in five different genera and subtribes. We used mostly published genomic data, but also newly sequenced whole genome data from museum specimens and old DNA extracts, extracted BUSCO genes and prepared several datasets. These datasets differed in the degree of heterogeneity and saturation, the number of nucleotide positions used (all positions or only the first two), and were analyzed as nucleotides or as amino acids. We employed several methods for phylogenetic reconstruction using both partitioned and mixture models, as well as ASTRAL, and we inferred divergence times and ancestral areas of origin for Calisto and Llorenteana. The phylogenetic placement of Calisto varied among datasets when we used partitioned models and ASTRAL; however, most datasets resulted in the same relationships under mixture models. Our results suggest that Calisto is part of a clade of Old World origin that colonized the New World from north to south, thus sharing ancestry with Nearctic taxa. Llorenteana constitutes one of the earliest splits within the Euptychiina, a subtribe of Neotropical origin, but descending together with the Pronophilina from Nearctic ancestors. We propose the recognition of Erebiina stat. rev. as the only subtribe comprising the former Calistina syn. nov., Callerebiina syn. nov, Maniolina syn. nov., and Ypthimina syn. nov.

evolutionary biology↗

Environmental Variation Promotes Convergent Evolution and Rapid Diversification of Wing Shape and Color in Skipper Butterflies

Predation is a key driver of speciation and phenotypic diversification, yet how antipredator traits evolve and persist over evolutionary time remains poorly understood. We generated target sequence capture and whole-genome sequencing data for the skipper butterfly subfamily Eudaminae (Hesperiidae) to test whether antipredator defenses, in interaction with environmental variation, promote diversification. We focus on two antipredation wing traits: hindwing tails, which deflect predator attacks, and blue-green coloration, which may enhance motion dazzle and be used as warning coloration. Applying phylogenomics, morphometrics, and comparative methods, we model trait evolution in relation to diel activity and geographic distribution and find that hindwing tails repeatedly evolved at least seven times and blue-green coloration at least fifteen times. Both traits are associated with elevated speciation rates, but evolutionary transitions toward tailless wings and non-iridescent coloration occurred more frequently than trait gains, indicating high evolutionary lability of these antipredator defenses. Trait loss, particularly pronounced in tropical diurnal species, may reflect trade-offs in flight performance, shifts in predation guilds, or the evolution of alternative defensive traits. Our findings highlight rampant convergent evolution of wing traits that are under strong predator-mediated selection. By identifying how antipredator defenses and environmental contexts influence phenotypic and species diversification, this study provides new insights into the ecological and evolutionary processes underlying insect diversity.

evolutionary biology↗

The effect of Sinorhizobium meliloti volatilomes and synthetic long-chain methylketones on soil and Medicago truncatula microbiomes

Bacterial volatile compounds play important roles in intra- and interkingdom interactions but very little is known about their effects on soil and plant microbiomes. The legume symbiont Sinorhizobium meliloti (Sm) releases volatile methylketones (MKs), one of which acts as an infochemical in bacteria and hampers plant-bacteria interactions. MK production in Sm is modestly increased in the absence of the long-chain-fatty-acyl-coenzyme-A (CoA) synthetase FadD. To explore further the ecological role of MKs on soil and plant bacterial communities, we aimed at obtaining an MK-overproducer Sm strain by deleting the 3-oxo-acyl-CoA-thiolase-encoding fadA gene. Analyses of the Sm wild type (wt), and fad mutant volatilomes identified seventeen compounds consisting mostly of MKs and fatty acid methyl esters (FAMEs) and revealed that the fadA mutant produced more MKs than the fadD mutant and much more than the wt, while in the fadD mutant FAME emission was increased. When natural soil or the rhizosphere of Medicago truncatula were exposed to wt and fadA volatilomes or synthetic MKs, bacterial alpha- or beta-diversity were not strongly affected but specific genera were identified which responded differentially to each condition. Interestingly, Sm volatilomes had a significant effect on root endosphere Ensifer/Sinorhizobium populations by maintaining their abundance over time in contrast to control conditions or exposure to synthetic MKs. This study provides new insights on the synthesis of rhizobial volatile compounds and represents the first exploration of the effects of bacterial volatilomes on plant bacterial communities, contributing to increase our knowledge on the complex molecular bases underlying plant-bacteria interactions.

microbiology↗

Immune and malignant cell phenotypes of ovarian cancer are determined by distinct mutational processes

High-grade serous ovarian cancer (HGSOC) is an archetypal cancer of genomic instability patterned by distinct mutational processes, intratumoral heterogeneity and intraperitoneal spread. We investigated determinants of immune recognition and evasion in HGSOC to elucidate co- evolutionary processes underlying malignant progression and tumor immunity. Mutational processes and anatomic sites of tumor foci were key determinants of tumor microenvironment cellular phenotypes, inferred from whole genome sequencing, single-cell RNA sequencing, digital histopathology and multiplexed immunofluorescence of 160 tumor sites from 42 treatment-naive HGSOC patients. Homologous recombination-deficient (HRD)-Dup (BRCA1 mutant-like) and HRD- Del (BRCA2 mutant-like) tumors harbored increased neoantigen burden, inflammatory signaling and ongoing immunoediting, reflected in loss of HLA diversity and tumor infiltration with highly- differentiated dysfunctional CD8+ T cells. Foldback inversion (FBI, non-HRD) tumors exhibited elevated TGF{beta} signaling and immune exclusion, with predominantly naive/stem-like and memory T cells. Our findings implicate distinct immune resistance mechanisms across HGSOC subtypes which can inform future immunotherapeutic strategies. HIGHLIGHTSO_LIMulti-region, multi-modal profiling of malignant and immune cell phenotypes in ovarian cancer C_LIO_LIAnatomic site specificity is a determinant of cancer cell and intratumoral immune phenotypes C_LIO_LITumor mutational processes impact mechanisms of immune control and immune evasion C_LIO_LISpatial topology of HR-deficient tumors is defined by immune interactions absent from immune inert HR-proficient subtypes C_LI

cancer biology↗

Identification and quantification of Lyme pathogen strains by deep sequencing of outer surface protein C (ospC) amplicons

Mixed infection of a single tick or host by Lyme disease spirochetes is common and a unique challenge for diagnosis, treatment, and surveillance of Lyme disease. Here we describe a novel protocol for differentiating Lyme strains based on deep sequencing of the hypervariable outer-surface protein C locus (ospC). Improving upon the traditional DNA-DNA hybridization method, the next-generation sequencing-based protocol is high-throughput, quantitative, and able to detect new pathogen strains. We applied the method to over one hundred infected Ixodes scapularis ticks collected from New York State, USA in 2015 and 2016. Analysis of strain distributions within individual ticks suggests an overabundance of multiple infections by five or more strains, inhibitory interactions among co-infecting strains, and presence of a new strain closely related to Borreliella bissettiae. A supporting bioinformatics pipeline has been developed. With the newly designed pair of universal ospC primers targeting intergenic sequences conserved among all known Lyme pathogens, the protocol could be used for culture-free identification and quantification of Lyme pathogens in wildlife and clinical specimens across the globe.

microbiology↗