Biology subjects

Posada, D.

Publications and source records attributed to Posada, D..

At least 19 recordsLinked to original sources

bioRxiv2025

Single-cell phylodynamics reveal rapid late-stage colorectal cancer expansions

Single-cell whole-genome sequencing of 335 cells from seven colorectal cancers, coupled with Bayesian phylodynamic modeling, revealed tumors often originate decades before diagnosis, remain indolent, and expand rapidly within two years. Strong spatial structuring with minimal interregional mixing was observed, while substitution rates varied widely and were decoupled from growth. Our findings highlight extended evolutionary stasis and sudden expansion, informing strategies for early detection and intervention.

evolutionary biology↗

bioRxiv2025

Taxonomic Diversity of Ants (Formicidae) in Forest Fragments of Tropical Dry Forest in Atlantico, Colombia

This study provides the first taxonomic diversity analysis of ants in the department of Atlantico, Colombia, documenting 6.75% of the countrys known ant species, 29.5% of its genera, and 63.3% of its subfamilies. We report the first record of Leptogenys volcanica in the Colombian Caribbean and expand the known distribution of 19 species within Atlantico. Our results show marked differences in species composition among forest fragments. El Morro exhibited the highest taxonomic distinctness (TD), supporting a community composed of more distantly related species. In contrast, Uninorte, an isolated urban fragment, had the lowest TD value, suggesting a more taxonomically clustered community and potentially acting as a diversity sink. Nesting values indicate that El Morro functions as a biodiversity reservoir, while the species composition of Los Charcones appears shaped by past land-use changes. The dominance of Myrmicinae and Formicinae aligns with patterns observed in other tropical dry forests. Although fragmentation was not directly assessed, patterns of alpha, beta, and taxonomic distinctness suggest that isolation and land use may influence community composition. El Morro emerges as a key fragment for regional conservation. Enhancing habitat connectivity could help mitigate biodiversity loss in these fragmented landscapes. This study provides a critical baseline for future research on ant ecology and conservation in the Caribbean region of Colombia.

ecology↗

bioRxiv2025

Intraline genomic heterogeneity of the triple-negative breast cancer MDA-MB-231 cell line

Cancer cell lines are valuable models for studying tumor biology, yet their genomic evolution during culture can compromise experimental reproducibility. We conducted a detailed genomic analysis of the triple-negative breast cancer cell line MDA-MB-231, examining sublines obtained from different sources, at various time points, and across distinct passages. We introduce the concept of intraline heterogeneity (ILH) to highlight the genomic variability observed among these sublines. Our analyses revealed extensive genomic diversity, including differences in single nucleotide variants (SNVs) and copy number alterations (CNAs). In particular, CNAs exhibited remarkable heterogeneity, with pronounced chromosomal gains and losses between sublines, underscoring the impact of genomic instability on ILH. These findings suggest that ILH may influence experimental outcomes, emphasizing the importance of considering passage-specific genomic characterization to ensure consistency and reliability in cancer research.

genomics↗

bioRxiv2024

Unraveling the phylogenetic signal of gene expression from single-cell RNA-seq data

Single-cell RNA sequencing (scRNA-seq) has transformed our understanding of phenotypic heterogeneity. Although the predominant focus of scRNA-seq analyses has been assessing gene expression changes, several approaches have been proposed in recent years to identify changes at the DNA level from scRNA-seq data. In this study, we evaluated the relative performance of six strategies for calling single-nucleotide variants from scRNA-seq data using 381 single-cell transcriptomes from five cancer patients. Specifically, we focused on the quality of the inferred genotypes and the resulting single-cell phylogenies. We found that scAllele, Monopogen, and Monovar consistently returned phylogenetically informative genotype calls, providing more precise signals of discrimination between tumor and normal cells within heterogeneous samples and among distinct subclonal lineages in longitudinal samples. In addition, we evaluated the evolution of gene expression along the cell phylogenies. While most transcriptomic variation was very plastic and did not correlate with the cell phylogeny, a group of genes associated with cell cycle processes showed a strong phylogenetic signal in one of the patients, underscoring a potential link between gene expression patterns and lineage-specific traits in the context of cancer progression. In summary, our study highlights the potential of scRNA-seq data for inferring cell phylogenies to decipher the evolutionary dynamics of cell populations.

genomics↗

bioRxiv2023

DelSIEVE: joint inference of single-nucleotide variants, somatic deletions, and cell phylogeny from single-cell DNA sequencing data

With rapid advancements in single-cell DNA sequencing (scDNA-seq), various computational methods have been developed to study evolution and call variants on single-cell level. However, modeling deletions remains challenging because they affect total coverage in ways that are difficult to distinguish from technical artifacts. We present DelSIEVE, a statistical method that infers cell phylogeny and single-nucleotide variants, accounting for deletions, from scDNA-seq data. DelSIEVE distinguishes deletions from mutations and artifacts, detecting more evolutionary events than previous methods. Simulations show high performance, and application to cancer samples reveals varying amounts of deletions and double mutants in different tumors.

bioinformatics↗

bioRxiv2022

Single-cell phylogenies reveal deviations from clock-like, neutral evolution in cancer and healthy tissues

How tumors evolve affects cancer progression, therapy response, and relapse. However, whether tumor evolution is driven primarily by selectively advantageous or neutral mutations remains under debate. Resolving this controversy has so far been limited by the use of bulk sequencing data. Here, we leverage the high resolution of single-cell DNA sequencing (scDNA-seq) to test for clock-like, neutral evolution. Under neutrality, different cell lineages evolve at a similar rate, accumulating mutations according to a molecular clock. We developed and benchmarked a test of the somatic clock based on single-cell phylogenies and applied it to 22 scDNA-seq datasets. We rejected the clock in 10/13 cancer and 5/9 healthy datasets. The clock rejection in seven cancer datasets could be related to known driver mutations. Our findings demonstrate the power of scDNA-seq for studying somatic evolution and suggest that some cancer and healthy cell populations are driven by selection while others seem to evolve under neutrality.

evolutionary biology↗

bioRxiv2022

The evolution of two transmissible leukaemias colonizing the coasts of Europe

Transmissible cancers are malignant cell clones that spread among individuals through transfer of living cancer cells. Several such cancers, collectively known as bivalve transmissible neoplasia (BTN), are known to infect and cause leukaemia in marine bivalve molluscs. This is the case of BTN clones affecting the common cockle, Cerastoderma edule, which inhabits the Atlantic coasts of Europe and north-west Africa. To investigate the origin and evolution of contagious cancers in common cockles, we collected 6,854 C. edule specimens and diagnosed 390 cases of BTN. We then generated a reference genome for the species and assessed genomic variation in the genomes of 61 BTN tumours. Analysis of tumour-specific variants confirmed the existence of two cockle BTN lineages with independent clonal origins, and gene expression patterns supported their status as haemocyte-derived marine leukaemias. Examination of mitochondrial DNA sequences revealed several mitochondrial capture events in BTN, as well as co-infection of cockles by different tumour lineages. Mutational analyses identified two lineage-specific mutational signatures, one of which resembles a signature associated with DNA alkylation. Karyotypic and copy number analyses uncovered genomes marked by pervasive instability and polyploidy. Whole-genome duplication, amplification of oncogenes CCND3 and MDM2, and deletion of the DNA alkylation repair gene MGMT, are likely drivers of BTN evolution. Characterization of satellite DNA identified elements with vast expansions in the cockle germ line, yet absent from BTN tumours, suggesting ancient clonal origins. Our study illuminates the evolution of contagious cancers under the sea, and reveals long-term tolerance of extreme instability in neoplastic genomes.

evolutionary biology↗

bioRxiv2022

Transcriptome landscape of kleptoplastic sea slug Elysia viridis

Certain sacoglossan sea slugs can sequester and maintain photosynthetically active chloroplasts through algae feeding, a phenomenon called kleptoplasty. The period while these plastids remain active inside the slugs body is species- and environment-dependent and can span from a few days to more than three weeks. Here we report for the first time the transcriptome of sea slug Elysia viridis (Montagu, 1804), which can maintain kleptoplasts for more than two weeks and is distributed along all the Atlantic European coastline. The obtained transcriptome of E. viridis comprised 12,884 protein-coding sequences (CDS). The shortest one was 261bp, and the longest 8,766bp; the whole transcriptome has a total length of 9.3Mb (Table S4 and Fig. S2). Analysing these CDS, we identified 9,422 different proteins, with best hits mainly from two genera: Elysia (87.2%), and Plakobranchus (11.0%) (Fig. S2); the other 2.3% corresponded to multiple genera of sea slugs and snails (Tectipleura) (Kano et al., 2016). We got the functional annotation (Gene Ontologies, GO) corresponding to 9,333 CDS: 4,755 CDS associated with 2,583 Biological Process (BP); 5,466 CDS linked to 683 Cellular Components (CC); and 6,693 related to 1,606 Molecular Functions (MF). We identified 201 CDS related to response to stress (GO:0006950) and 10 CDS associated with the regulation of response to stress (GO:0080134). Focussing on the ROS-quenching toolkit, we found 24 CDS related to oxidoreductase complex (GO:1990204) and 560 annotated with oxidoreductase activity (GO:0016491) acting in a large number of donors, e.g., CH-OH, CH=O, C=O, CH and CH2. In addition, we found 39 CDS with antioxidant activity (GO:00162099) and other CDS with ROS-quenching function: superoxide dismutase (GO:0004784), peroxidase (GO:0004601), glutathione oxidoreductase (GO:0097573) and peroxidase (GO:0004602); and thioredoxin peroxidase (GO:0008379) activity. Furthermore, we found 8 CDS related to the symbiont response (GO:0140546) and nine related to the pattern recognition receptor signalling pathway (GO:0002221).

evolutionary biology↗

bioRxiv2022

SIEVE: joint inference of single-nucleotide variants and cell phylogeny from single-cell DNA sequencing data

Single-cell DNA sequencing (scDNA-seq) has enabled the identification of single nucleotide somatic variants and the reconstruction of cell phylogenies. However, statistical phylogenetic models for cell phylogeny reconstruction from raw sequencing data are still in their infancy. Here we present SIEVE (SIngle-cell EVolution Explorer), a statistical method for the joint inference of somatic variants and cell phylogeny under the finite-sites assumption from scDNA-seq reads. SIEVE leverages raw read counts for all nucleotides at candidate variant sites, and corrects the acquisition bias of branch lengths. In our simulations, SIEVE outperforms other methods both in phylogenetic accuracy and variant calling accuracy. We apply SIEVE to three scDNA-seq datasets, for colorectal (CRC) and triple-negative breast cancer (TNBC), one of them generated by us. On simulated data, SIEVE reliably infers homo-and heterozygous somatic variants. The analysis of real data uncovers that double mutant genotypes are rare in CRC but unexpectedly frequent in TNBC samples.

bioinformatics↗

bioRxiv2022

Phylovar: Towards scalable phylogeny-aware inference of single-nucleotide variations from single-cell DNA sequencing data

Single-nucleotide variants (SNVs) are the most common variations in the human genome. Recently developed methods for SNV detection from single-cell DNA sequencing (scDNAseq) data, such as SCI{Phi} and scVILP, leverage the evolutionary history of the cells to overcome the technical errors associated with single-cell sequencing protocols. Despite being accurate, these methods are not scalable to the extensive genomic breadth of single-cell whole-genome (scWGS) and whole-exome sequencing (scWES) data. Here we report on a new scalable method, Phylovar, which extends the phylogeny-guided variant calling approach to sequencing datasets containing millions of loci. Through benchmarking on simulated datasets under different settings, we show that, Phylovar outperforms SCI{Phi} in terms of running time while being more accurate than Monovar (which is not phylogeny-aware) in terms of SNV detection. Furthermore, we applied Phylovar to two real biological datasets: an scWES triple-negative breast cancer data consisting of 32 cells and 3375 loci as well as an scWGS data of neuron cells from a normal human brain containing 16 cells and approximately 2.5 million loci. For the cancer data, Phylovar detected somatic SNVs with high or moderate functional impact that were also supported by bulk sequencing dataset and for the neuron dataset, Phylovar identified 5745 SNVs with non-synonymous effects some of which were associated with neurodegenerative diseases. We implemented Phylovar and made it publicly available at https://github.com/mae6/Phylovar.git.

cancer biology↗

bioRxiv2021

Interpreting dN/dS under different selective regimes in cancer evolution

The standard relationship between the dN/dS statistic and the selection coefficient is contingent upon the computation of the rate of fixation of non-synonymous and synonymous mutations among divergent lineages (substitutions). In cancer genomics, however, dN/dS is typically calculated by including mutations that are still segregating in the cell population. The interpretation of dN/dS within sexual populations has been shown to be problematic. Here we used a simple model of somatic evolution to study the relationship between dN/dS and the selection coefficient in the presence of deleterious, neutral, and beneficial mutations in cancer. We found that dN/dS can be used to distinguish cancer genes under positive or negative selection, but it is not always informative about the magnitude of the selection coefficient. In particular, under the asexual scenario simulated, dN/dS is insensitive to negative selection strength. Furthermore, the relationship between dN/dS and the positive selection coefficient depends on the mutation detection threshold, and, in particular scenarios, it can become non-linear. Our results warn about the necessary caution when interpreting the results drawn from dN/dS estimates in cancer.

evolutionary biology↗

bioRxiv2021

Mitochondrial genome sequencing of marine leukemias reveals cancer contagion between clam species in the Seas of Southern Europe

Clonally transmissible cancers are tumour lineages that are transmitted between individuals via the transfer of living cancer cells. In marine bivalves, leukemia-like transmissible cancers, called hemic neoplasia, have demonstrated the ability to infect individuals from different species. We performed whole-genome sequencing in eight warty venus clams that were diagnosed with hemic neoplasia, from two sampling points located more than 1,000 nautical miles away in the Atlantic Ocean and the Mediterranean Sea Coasts of Spain. Mitochondrial genome sequencing analysis in tumour tissues from neoplastic animals revealed the coexistence of haplotypes from two different clam species. Phylogenies estimated from mitochondrial and nuclear markers confirmed this leukemia originated in striped venus clams and later transmitted to clams of the species warty venus, in which it survives as a contagious cancer. The analysis of mitochondrial and nuclear gene sequences supports all studied tumours belong to a single neoplastic lineage that spreads in the Seas of Southern Europe.

genomics↗

bioRxiv2021

Phylogenomic Analyses Of 2,786 Genes In 158 Lineages Support a Root of The Eukaryotic Tree of Life Between Opisthokonts (Animals, Fungi and Their Microbial Relatives) and All Other Lineages

Advances in phylogenetics and high-throughput sequencing have allowed the reconstruction of deep phylogenetic relationships in the evolution of eukaryotes. Yet, the root of the eukaryotic tree of life remains elusive. The most popular hypothesis in textbooks and reviews is a root between Unikonta (Opisthokonta + Amoebozoa) and Bikonta (all other eukaryotes), which emerged from analyses of a single gene fusion. Subsequent highly-cited studies based on concatenation of genes supported this hypothesis with some variations or proposed a root within Excavata. However, concatenation of genes neither considers phylogenetically-informative events (i.e. gene duplications and losses), nor provides an estimate of the root. A more recent study using gene tree-species tree reconciliation methods suggested the root lies between Opisthokonta and all other eukaryotes, but only including 59 taxa and 20 genes. Here we apply a gene tree - species tree reconciliation approach to a gene-rich and taxon-rich dataset (i.e. 2,786 gene families from two sets of ~158 diverse eukaryotic lineages) to assess the root, and we iterate each analysis 100 times to quantify tree space uncertainty. We estimate a root between Fungi and all other eukaryotes, or between Opisthokonta and all other eukaryotes, and reject alternative roots from the literature. Based on further analysis of genome size we propose Opisthokonta + others as the most likely root. Impact summaryFinding the root of the eukaryotic tree of life is critical for the field of comparative biology as it allows us to understand the timing and mode of evolution of characters across the evolutionary history of eukaryotes. But this is one of the most challenging questions in evolutionary biology because the age (~1.8 billion years), diversity and complexity of eukaryotes challenge phylogenomic methods. This study evaluates the root using reconciliation of gene trees and species trees instead of the more common approach of analyzing concatenated genes. The dataset used in this study is bigger and more taxonomically inclusive than the dataset of any previous study about the eukaryotic root, and supports a root at or within Opisthokonta (e.g. animals and fungi). Finally, we explicitly test alternative hypotheses from the literature, and again find support for an Opisthokonta root.

evolutionary biology↗

bioRxiv2020

CellPhy: accurate and fast probabilistic inference of single-cell phylogenies from scDNA-seq data

We introduce a maximum likelihood framework called CellPhy for inferring phylogenetic trees from single-cell DNA sequencing (scDNA-seq) data. CellPhy leverages a finite-site Markov genotype substitution model with 16 diploid states, akin to those typically used in statistical phylogenetics. It includes a dedicated error function for single cells that incorporates amplification/sequencing error and allelic dropout (ADO). Moreover, it can explicitly consider the uncertainty of the variant calling process by using genotype likelihoods as input. We implemented CellPhy in a widely used open-source phylogenetic inference package (RAxML-NG) that provides statistical confidence measurements on the estimated tree and scales particularly well on large scDNA-seq datasets with hundreds or thousands of cells. To benchmark CellPhy, we carried out 19,400 coalescent simulations of cell samples from exponentially-growing tumors for which the true phylogeny was known. We evolved single-cell diploid DNA genotypes along the simulated genealogies under different scenarios, including infinite- and finite-sites nucleotide mutation models, trinucleotide mutational signatures, sequencing, and amplification errors, allele dropouts, and cell doublets. Our simulations suggest that CellPhy is robust to amplification/sequencing errors and ADO and outperforms state-of-the-art methods under realistic scDNA-seq scenarios both in terms of accuracy and speed. Also, we sequenced 24 single-cell whole-genomes from a colorectal tumor. Together with three published scDNA-seq data sets, we analyzed these empirical data to illustrate how CellPhy can provide more reliable biological insights than most competing methods. CellPhy is freely available at https://github.com/amkozlov/cellphy.

bioinformatics↗

bioRxiv2020

Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission

The COVID-19 pandemic has sparked an urgent need to uncover the underlying biology of this devastating disease. Though RNA viruses mutate more rapidly than DNA viruses, there are a relatively small number of single nucleotide polymorphisms (SNPs) that differentiate the main SARS-CoV-2 clades that have spread throughout the world. In this study, we investigated over 7,000 SARS-CoV-2 datasets to unveil both intrahost and interhost diversity. Our intrahost and interhost diversity analyses yielded three major observations. First, the mutational profile of SARS-CoV-2 highlights iSNV and SNP similarity, albeit with high variability in C>T changes. Second, iSNV and SNP patterns in SARS-CoV-2 are more similar to MERS-CoV than SARS-CoV-1. Third, a significant fraction of small indels fuel the genetic diversity of SARS-CoV-2. Altogether, our findings provide insight into SARS-CoV-2 genomic diversity, inform the design of detection tests, and highlight the potential of iSNVs for tracking the transmission of SARS-CoV-2.

genomics↗

bioRxiv2019

Massive gene presence/absence variation in the mussel genome as an adaptive strategy: first evidence of a pan-genome in Metazoa

Mussels are ecologically and economically relevant edible marine bivalves, highly invasive and resilient to biotic and abiotic stressors causing recurrent massive mortalities in other species. Here we show that the Mediterranean mussel Mytilus galloprovincialis has a complex pan-genomic architecture, which includes a core set of 45,000 genes shared by all individuals plus a surprisingly high number of dispensable genes ([~]15,000). The latter are subject to presence/absence variation (PAV), i.e., they may be entirely missing in a given individual and, when present, they are frequently found as a single copy. The enrichment of dispensable genes in survival functions suggests an adaptive value for PAV, which might be the key to explain the extraordinary capabilities of adaptation and invasiveness of this species. Our study underpins a unique metazoan pan-genome architecture only previously described in prokaryotes and in a few non-metazoan eukaryotes, but that might also characterize other marine invertebrates.\n\nSignificance statementIn animals, intraspecific genomic diversity is generally thought to derive from relatively small-scale variants, such as single nucleotide polymorphisms, small indels, duplications, inversions and translocations. On the other hand, large-scale structural variations which involve the loss of genomic regions encoding protein-coding genes in some individuals (i.e. presence/absence variation, PAV) have been so far only described in bacteria and, occasionally, in plants and fungi. Here we report the first evidence of a pan-genome in the animal kingdom, revealing that 25% of the genes of the Mediterranean mussel are subject to PAV. We show that this unique feature might have an adaptive value, due to the involvement of dispensable genes in functions related with defense and survival.

genetics↗

bioRxiv2019

Accuracy of somatic variant detection in multiregional tumor sequencing data

Multiregional bulk sequencing data is necessary to characterize intratumor genetic heterogeneity. Novel somatic variant calling approaches aim to address the particular characteristics of multiregional data, but it remains unclear to which extent they improve compared to single-sample strategies. Here we compared the performance of 16 single-nucleotide variant calling approaches on multiregional sequencing data under different scenarios with in-silico and real sequencing reads, including varying sequencing coverage and increasing levels of spatial clonal admixture. Under the conditions simulated, methods that use information across multiple samples do not necessarily perform better than some of the standard calling methods that work sample by sample. Nonetheless, our results indicate that under difficult conditions, Mutect2 in multisample mode, in combination with a correction step, seems to perform best. Our analysis provides data-driven guidance for users and developers of somatic variant calling tools.

bioinformatics↗

bioRxiv2019

Rapid evolution and biogeographic spread in a colorectal cancer

How and when tumoral clones start spreading to surrounding and distant tissues is currently unclear. Here, we leveraged a model-based evolutionary framework to investigate the demographic and biogeographic history of a colorectal cancer. Our analyses strongly support an early monoclonal metastatic colonization, followed by a rapid population expansion at both primary and secondary sites. Moreover, we infer a hematogenous metastatic spread seemingly under positive selection, plus the return of some tumoral cells from the liver back to the colon lymph nodes. This study illustrates how sophisticated techniques typical of organismal evolution can provide a detailed picture of the complex tumoral dynamics over time and space.

cancer biology↗