Biology subjects

Cornejo, O. E.

Publications and source records attributed to Cornejo, O. E..

13 recordsLinked to original sources

bioRxiv2026

Phenotype shift scores reveal the scale and phylogenetic structure of phenotypic differentiation in primates.

Continuous traits evolve unevenly across phylogenies, producing patterns of phenotypic differentiation shaped by both shared ancestry and lineage-specific change. Identifying exceptionally differentiated species pairs may therefore improve genome-phenome comparisons, but existing approaches rarely rank such contrasts across entire trees. Here we introduce the Phenotype Shift Score (PSS), a phylogenetic comparative framework integrating model-based trait divergence, observed trait range and patristic distance. Applying PSS to 153 continuous primate traits reveals trait-specific distributions of extreme differentiation across evolutionary depth. Body and brain mass show deeper-than-expected extremes under fitted Brownian motion or Ornstein-Uhlenbeck nulls, whereas body-size-adjusted brain mass localizes recent differentiation within cercopithecid lineages, complementing published branchwise reconstructions. PSS-informed groups produce more selective and more strongly enriched comparative-genomic signals than groups based on absolute phenotypic extremes. PSS is implemented in the open-source R package phyloPSS, with pairwise results available through the Primate Genome-Phenome Archive.

evolutionary biology↗

bioRxiv2026

StrataBionn: a neural network supervised classification method for microbial communities

The classification of microbial communities into discrete states or "community state types" (CSTs) is fundamental to understanding host-microbiome interactions and their clinical implications. Traditional methods, such as the nearest-neighbor approaches, often struggle with the inherent noise, high dimensionality, and non-linear signatures of taxonomic profiles. We present a novel supervised framework for microbial community classification, leveraging an Artificial Neural Network (ANN) architecture implemented in a new tool we named StrataBionn. We rigorously evaluated our approach using large-scale vaginal microbiome datasets, directly benchmarking performance against VALENCIA and a Random Forest (RF) classifier. To demonstrate the versatility of our models, we further extended the framework to oral microbiome classification, assessing its stability across diverse anatomical sites. Our supervised models consistently outperformed the nearest-neighbor approach across all evaluated datasets. In the vaginal microbiome, our method achieved an 11.6% to 13.3% increase in performance across all primary metrics, including precision, recall, accuracy, and F1-score. Furthermore, we demonstrate that this performance advantage is maintained in the oral microbiome, highlighting the generalizability of our neural network and ensemble strategies to various microbial ecosystems without the need for niche-specific algorithmic adjustments. By capturing complex feature dependencies that distance-based methods overlook, our approach provides a more robust and accurate census of microbial community structures. StrataBionns ability to learn classification schemes for any microbiome with high accuracy and explainability, through the use of provided utilities to visualize feature-space classification boundaries and perform perturbation analysis on trained classifiers, makes it ideal for broad application in microecology research. This framework offers a scalable, high-performance alternative for microbiome researchers, facilitating more precise clinical stratification and biological insights across hosts body sites.

genomics↗

bioRxiv2024

Evolutionary consequences of domestication on the selective effects of new amino acid changing mutations in canids

The domestication of wild canids led to dogs no longer living in the wild but instead residing alongside humans. Extreme changes in behavior and diet associated with domestication may have led to the relaxation of the selective pressure on traits that may be less important in the domesticated context. Thus, here we hypothesize that strongly deleterious mutations may have become less deleterious in domesticated populations. We test this hypothesis by estimating the distribution of fitness effects (DFE) for new amino acid changing mutations using whole-genome sequence data from 24 gray wolves and 61 breed dogs. We find that the DFE is strikingly similar across canids, with 26-28% of new amino acid changing mutations being neutral/nearly neutral (|s| < 1e-5), and 41-48% under strong purifying selection (|s| > 1e-2). Our results are robust to different model assumptions suggesting that the DFE is stable across short evolutionary timescales, even in the face of putative drastic changes in the selective pressure caused by artificial selection during domestication and breed formation. On par with previous works describing DFE evolution, our data indicate that the DFE of amino acid changing mutations depends more strongly on genome structure and organismal characteristics, and less so on shifting selective pressures or environmental factors. Given the constant DFE and previous data showing that genetic variants that differentiate wolf and dog populations are enriched in regulatory elements, we speculate that domestication may have had a larger impact on regulatory variation than on amino acid changing mutations. Significance StatementDomestication of dogs to live alongside humans resulted in a dramatic shift in the pressures of natural selection. Thus, comparing dogs and wolves offers a unique opportunity to assess how these shifts in selective pressures have impacted the fitness effects of individual mutations. In this project, we use patterns of genetic variation in dogs and wolves to estimate the distribution of fitness effects (DFE), or the proportions of amino acid changing mutations with varying fitness effects throughout the genome. Overall, we find that the DFE for amino acid changing mutations is similar between dogs and wolves. Even genes thought to be most affected by domestication show a similar DFE, suggesting that the DFE has remained stable over evolutionary time.

genetics↗

bioRxiv2024

Phylogenetic signal in primate tooth enamel proteins and its relevance for paleoproteomics

Ancient tooth enamel, and to some extent dentin and bone, contain characteristic peptides that persist for long periods of time. In particular, peptides from the enamel proteome (enamelome) have been used to reconstruct the phylogenetic relationships of fossil specimens and to estimate divergence times. However, the enamelome is based on only about 10 genes, whose protein products undergo fragmentation post mortem. Moreover, some of the enamelome genes are paralogous or may coevolve. This raises the question as to whether the enamelome provides enough information for reliable phylogenetic inference. We address these considerations on a selection of enamel-associated proteins that has been computationally predicted from genomic data from 232 primate species. We created multiple sequence alignments (MSAs) for each protein and estimated the evolutionary rate for each site and examined which sites overlap with the parts of the protein sequences that are typically isolated from fossils. Based on this, we simulated ancient data with different degrees of sequence fragmentation, followed by phylogenetic analysis. We compared these trees to a reference species tree. Up to a degree of fragmentation that is similar to that of fossil samples from 1-2 million years ago, the phylogenetic placements of most nodes at family level are consistent with the reference species tree. We found that the composition of the proteome influences the phylogenetic placement of Tarsiiformes. For the inference of molecular phylogenies based on paleoproteomic data, we recommend characterizing the evolution of the proteomes from the closest extant relatives to maximize the reliability of phylogenetic inference.

evolutionary biology↗

bioRxiv2022

Ghost admixture in eastern gorillas

Archaic admixture has had a significant impact on human evolution with multiple events across different clades, including from extinct hominins such as Neanderthals and Denisovans into modern humans. Within the great apes archaic admixture has been identified in chimpanzees and bonobos, but the possibility of such events has not been explored in other species. Here, we address this question using high-coverage whole genome sequences from all four extant gorilla subspecies, including six newly sequenced eastern gorillas from previously unsampled geographic regions. Using Approximate Bayesian Computation (ABC) with neural networks to model the demographic history of gorillas, we find a signature of admixture from an archaic ghost lineage into the common ancestor of eastern gorillas, but not western gorillas. We infer that up to 3% of the genome of these individuals is introgressed from an archaic lineage that diverged more than 3 million years ago from the common ancestor of all extant gorillas. This introgression event took place before the split of mountain and eastern lowland gorillas, likely more than 40 thousand years ago, and may have influenced perception of bitter taste in eastern gorillas. When comparing the introgression landscapes of gorillas, humans and bonobos, we find a consistent depletion of introgressed fragments on the X chromosome across these species. However, depletion in protein-coding content is not detectable in eastern gorillas, possibly as a consequence of stronger genetic drift in this species.

evolutionary biology↗

bioRxiv2021

PRDM9 directs recombination hotspots to prevent competition with meiotic transcription

PRDM9 drives recombination hotspots in some mammals, including mice and apes. Non-functional orthologs of PRDM9 are present in a wide variety of vertebrates, but why it is functionally maintained in some lineages is not clear. One possible explanation is that PRDM9 plays a role in ensuring that meiosis is successful. During meiosis, available DNA may be a limiting resource given the tight packaging of chromosomes and could lead to competition between two key processes: meiotic transcription and recombination. Here we explore this potential competition and the role that PRDM9 might play in their interaction. Leveraging existing mouse genomic data, we use resampling schemes that simulate shuffled features along the genome and models that account for the rarity of features in the genome, to test if PRDM9 influences interactions between recombination hotspots and meiotic transcription in a whole genome framework. We also explored possible DNA sequence motifs associated to clusters of hotspots not tied to transcription or PRDM9. We find evidence of competition between meiotic transcription and recombination, with PRDM9 appearing to relocate recombination to avoid said conflict. We also find that retrotransposons may be playing a role in directing hotspots in the absence of other factors.

genomics↗

bioRxiv2021

Evolutionary implications of recombination differences across diverging populations of Anopheles

Recombination is one of the main evolutionary mechanisms responsible for changing the genomic architecture of populations; and in essence, it is the main mechanism by which novel combinations of alleles, haplotypes, are formed. A clear picture that has emerged across study systems is that recombination is highly variable, even among closely related species. However, it is only until very recently that we have started to understand how recombination variation between populations of the same species impact genetic diversity and divergence. Here, we used whole-genome sequence data to build fine-scale recombination maps for nine populations within two species of Anopheles, Anopheles gambiae and Anopheles coluzzii. The genome-wide recombination averages were on the same order of magnitude for all populations except one. Yet, we identified significant differences in fine-scale recombination rates among all population comparisons. We report that effective population sizes, and presence of a chromosomal inversion has major contribution to recombination rate variation along the genome and across populations. We identified over 400 highly variable recombination hotspots across all populations, where only 9.6% are shared between two or more populations. Additionally, our results are consistent with recombination hotspots contributing to both genetic diversity and absolute divergence (dxy) between populations and species of Anopheles. However, we also show that recombination has a small impact on population genetic differentiation as estimated with FST. The minimal impact that recombination has on genetic differentiation across populations represents the first empirical evidence against recent theoretical work suggesting that variation in recombination along the genome can mask or impair our ability to detect signatures of selection. Our findings add new understanding to how recombination rates vary within species, and how this major evolutionary mechanism can maintain and contribute to genetic variation and divergence within a prominent malaria vector.

evolutionary biology↗

bioRxiv2020

Comparative transcriptomic analysis reveals key components controlling spathe color in Anthurium andraeanum (Hort.)

Anthurium andraeanum (Hort.) is an important ornamental in the tropical cut-flower industry. However, there is currently not enough information to establish a clear connection between the genetic model(s) proposed and the putative genes involved in the differentiation between colors. In this study, 18 cDNA libraries related to the spathe color and developmental stages of A. andraeanum cut-flowers were characterized by transcriptome sequencing technology. For the de novo transcriptome, a total of 114,334,082 primary sequence reads were obtained from the Illumina sequencer and were assembled into 151,652 unigenes. Approximately 58,476 transcripts were generated and used for comparative transcriptome analysis between three varieties that differ in spathe color ( Sasha (white), Honduras (red), and Rapido (purple)). A large number of differentially expressed genes (8,324) that were potentially involved in multiple biological and metabolic pathways were identified, including the flavonoid and anthocyanin biosynthetic pathways. Our results showed that chalcone synthase (CHS) and flavonoid 3-hydroxylase (F3H) were the main genes differentially expressed in the white/red/purple comparison. We also identified a differentially expressed cytochrome P450 in the late developmental stage of the purple spathe that appeared to determine the difference between the red- and purple-colored spathes. Additionally, putative MYB-domain protein candidates that could be responsible for the control of the biosynthetic pathway were identified. The results provided basic sequence information for future research on spathe color, which have important implications for breeding strategies in this ornamental. Core ideasO_LIRNA-seq was performed on three anthurium varieties. C_LIO_LIGene expression was compared for developmental stage and spathe color. C_LIO_LIDifferentially expressed unigenes were identified. C_LIO_LIPutative MYB-domain protein candidates of the anthocyanin biosynthetic pathway were identified. C_LI

genomics↗

bioRxiv2019

COMICS: A pipeline for the composite identification of selection across multiple genomic scans using Invariant Coordinate Selection in R

Identifying loci that are under selection versus those that are evolving neutrally is a common challenge in evolutionary genetics. Moreover, with the increase in sequence data, genomic studies have begun to incorporate the use of multiple methods to identify candidate loci under selection. Composite methods are usually implemented to transform the data into a multi-dimensional scatter where outliers are identified using a distance metric, the most common being Mahalanobis distance. However, studies have shown that the power of Mahalanobis distance reduces as the number of dimensions increases. Because the number of methods for detecting selection continue to grow, this is an undesirable feature of Mahalanobis distance. Other composite methods such as invariant coordinate selection (ICS) have proven to be a robust method for identifying outliers in multi-dimensional space; though, this method has not been implemented for genomic data. Here we use simulated genomic data to test the performance of ICS in identifying outlier loci from multiple selection scans and compare the results to the performance of Mahalanobis distances. We show that the ICS outperformed Mahalanobis distance in all aspects including false positives, false negatives, and recall. Furthermore, ICS also performed better when identifying loci with weaker selection coefficients. We also introduce a pipeline in a R-Shiny smart wrapper environment that implements the ICS on multiple scans of selection. Importantly, we show that the ICS is a robust method for identifying outliers in multi-dimensional space and recommend its use for studies aimed at identifying loci under selection in the genome.

bioinformatics↗

bioRxiv2018

Genetic differentiation and intrinsic genomic features explain variation in recombination hotspots among cocoa tree populations

Our study investigates the possible drivers of recombination hotspots in Theobroma cacao using ten genetically differentiated populations. By comparing recombination patterns between multiple populations, we obtain a novel view of recombination at the population-divergence timescale. For each population, a fine-scale recombination map was generated using the coalescent with a standard method based on linkage disequilibrium (LD). These maps revealed higher recombination rates in a domesticated population and a population that has undergone a recent bottleneck. We inferred hotspots of recombination for each population and find that the genomic locations of hotspots correlate with genetic differentiation between populations (FST). We used randomization approaches to generate appropriate null models to understand the association between hotspots of recombination and both DNA sequence motifs and genomic features. We found that hotspot regions contained fewer known retroelement sequences than expected and were overrepresented near transcription start and termination sites. Our findings indicate that recombination hotspots are evolving in a way that is consistent with genetic differentiation but are also preferentially driven to near coding regions. We illustrate that, consistent with predictions in plant domestication, the recombination rate of the domesticated population is orders of magnitude higher than that of other populations. More importantly, we find two fixed mutations in the domesticated populations FIGL1 protein. FIGL1 has been shown to increase recombination rates in Arabidopsis by several orders of magnitude, suggesting a possible mechanism for the observed increased recombination rate in the domesticated population.

genomics↗

bioRxiv2018

Ancestry informative alleles captured with reduced representation library sequencing in Theobroma cacao

As the source of chocolate, cacao has become one of the most important crops in the world. The identification of molecular markers to understand the demographic history, genetic diversity and population structure plays a pivotal role in cacao breeding programs. Here, we report the use of a modified genotyping-by-sequencing (GBS) approach for large-scale single nucleotide polymorphism (SNP) discovery and allele ancestry mapping. We identified 12,357 bi-allelic SNPs after filtering, of which, 7,009 variants were ancestry informative. The GBS approach proved to be rapid, cost-effective, and highly informative for ancestry assignment in this species.

genomics↗

bioRxiv2017

Genomic insights into the domestication of the chocolate tree, Theobroma cacao L.

Domestication has had a strong impact on the development of modern societies. We sequenced 200 genomes of the chocolate plant Theobroma cacao L. to show for the first time that a single population underwent strong domestication approximately 3,600 years (95% CI: 2481 - 10,903 years ago) ago, the Criollo population. We also show that during the process of domestication, there was strong selection for genes involved in the metabolism of the colored protectants anthocyanins and the stimulant theobromine, as well as disease resistance genes. Our analyses show that domesticated populations of T. cacao (Criollo) maintain a higher proportion of high frequency deleterious mutations. We also show for the first time the negative consequences the increase accumulation of deleterious mutations during domestication on the fitness of individuals (significant negative correlation between Criollo ancestry and Kg of beans per hectare per year, P = 0.000425).

genomics↗

bioRxiv2017

Tripolar mitosis drives the association between maternal genotypes of PLK4 and aneuploidy in human preimplantation embryos

Aneuploidy is prevalent in human preimplantation embryos and is the leading cause of pregnancy loss. Many aneuploidies arise during oogenesis, increasing in frequency with maternal age. Superimposed on these meiotic aneuploidies are a range of errors occurring during early mitotic divisions of the embryo, contributing to widespread chromosomal mosaicism. Here we reanalyzed a published dataset comprising preimplantation genetic testing for aneuploidy in 24,653 blastomere biopsies from day-3 cleavage-stage embryos, as well as 17,051 trophectoderm biopsies from day-5 blastocysts. We focused on complex abnormalities that affected multiple chromosomes simultaneously, seeking to quantify their incidences and gain insight into their mechanisms of formation. In addition to well-described patterns such as triploidy and haploidy, we identified 4.7% of day-3 blastomeres possessing karyotypes suggestive of tripolar mitosis in normally-fertilized diploid zygotes or descendant diploid cells. We further supported this hypothesis using time-lapse data from an intersecting set of 77 cleavage-stage embryos. The diploid tripolar signature was rare among day-5 blastocyst biopsies (0.5%), suggesting that complex aneuploidy generated by tripolar mitosis impairs cellular and/or early embryonic survival. Strikingly, we found that the tripolar mitosis mechanism is responsible for the previously described association with common maternal genetic variants spanning PLK4. Our findings are consistent with the role of PLK4 as the master regulator of centriole duplication with a known capacity to induce tripolar mitosis when mutated or mis-expressed. Taken together, we propose that tripolar mitosis is a key mechanism generating karyotype-wide aneuploidy in cleavage-stage embryos and implicate PLK4-mediated centrosome abnormality as a factor influencing its occurrence.

genetics↗