Biology subjects

Lizano, E.

Publications and source records attributed to Lizano, E..

18 recordsLinked to original sources

bioRxiv2026

A sample-to-identification workflow to monitor animal and plant biodiversity using metabarcoding and real time analysis

Environmental DNA (eDNA) has emerged as a transformative tool for biodiversity monitoring, offering a non-invasive means to detect and identify species across various ecosystems. However, despite its potential, current eDNA methodologies have significant limitations, including limited sensitivity, restriction to a specific taxonomic group, lengthy processing times, the need for specialized laboratory conditions and equipment, as well as computational bottlenecks in equipment, connectivity, and algorithms. Overcoming these limitations is crucial for the real-time monitoring of a high number of taxa in field-based scenarios. Here we present an integrated eDNA workflow from extraction to data analysis that mitigates several of these challenges through several technical innovations. Our approach adapts the Tagsteady protocol to Nanopore sequencing, integrates multiplex PCR for simultaneous plant and animal detection, and introduces RTBioScan, a real-time analysis pipeline employing hierarchical basecalling and OTU-level consensus generation to achieve high-accuracy taxonomic assignments during sequencing. Using a single set of universal primers, we integrate metabarcoding and barcoding into a cohesive protocol, utilizing universal markers for both animals and plants (cytochrome oxidase 1 region, COI, and Internal Transcribed Spacer 2, ITS2). This comprehensive approach can detect and identify a broad spectrum of species, from individual organisms to entire communities in a single workflow.

ecology↗

bioRxiv2026

Targeted Chromosomal Sequencing of Wild Bonobos Identifies a Genetically Distinct Subpopulation East of the Lomami River

Bonobos (Pan paniscus), an endangered species, have for decades been genetically understudied, partly due to difficulties in obtaining high-quality samples. The study of their genome is important not only for understanding their evolution, but also for improving conservation efforts, including population management, diversity and inbreeding assessment, and tracking rescued individuals to combat illegal wildlife trafficking. Here, we use chromosome 21 target capture data from 156 non-invasively collected faecal samples from wild bonobos to perform a comprehensive analysis of their population structure. We confirm the existence of three previously suggested subpopulations identified here as Western, Central and Eastern bonobos which are defined by natural barriers of gene flow such as the Lomami River. By estimating levels of inbreeding, diversity and differentiation, we find support for isolation of mainly Western and Eastern populations and add information on the dispersal routes of their ancestors. We infer split times and separation of these populations and apply a genetic framework to geolocalize samples of unknown origin, showing that locations of their potential origin can be estimated with a precision of up to a median of [~]50 km. Our study provides valuable insight into the evolution and population structure of bonobos and reveals how rivers act as strong barriers between populations. It also offers resources for conservation efforts and highlights the need to monitor bonobo populations more closely, in particular isolated ones. ImpactBonobos have been difficult to study genetically due to their remote forest habitat and endangered status. Here we used non-invasive sampling and chromosome 21 target capture sequencing to perform the most detailed analysis to date of their population structure. We find three main subpopulations and genetic differentiation influenced by river barriers, especially with populations found on the Eastern side of the Lomami river. This data will be useful for identifying the geographic origin of confiscated samples and thus aid bonobo conservation efforts.

bioinformatics↗

bioRxiv2025

Palaeoproteomic insights into the deep roots of the cave bear lineage in Europe

Palaeoproteomics has emerged as a powerful tool for reconstructing the evolutionary history of extinct species, particularly when ancient DNA is poorly preserved or beyond recovery. Here, we present the first large-scale enamel proteomic study focused on the cave bear, spanning specimens from the Early to Late Pleistocene. A primary objective was to determine whether the ursid population from level TD4 of Gran Dolina (Sierra de Atapuerca, Spain) belongs to the cave or the brown bear lineage, a long-standing taxonomic debate. We analyzed specimens from the Atapuerca sites, alongside comparative material from other southwestern European localities. Using LC-MS/MS and an acid demineralization protocol without enzymatic digestion, we successfully recovered enamel proteomes from all fossil samples, including the oldest specimens. Protein profiles were obtained for each extinct ursid, enabling the identification of taxonomically informative peptides across multiple individuals per taxon. Notably, two novel single amino acid polymorphisms (SAPs), found in ameloblastin (AMBN) and alpha-1 antitrypsin (SERPINA1), were restricted to Middle and Late Pleistocene cave bears and may represent new phylogenetic markers for this clade. This study provides the first molecular phylogenetic placement of Ursus dolinensis, supporting its basal position within the speloid lineage, consistent with its proposed ancestral status. Our results highlight the strong phylogenetic signal preserved in dental enamel and the exceptional biomolecular preservation at Atapuerca, providing a robust framework for reconstructing the evolutionary history of Ursidae. Moreover, the consistent recovery of systemic proteins, such as serpins, underscores the potential of enamel proteomes to capture not only evolutionary relationships but also physiological signals relevant to extinct ursids. SignificanceThe phylogenetic position of Ursus dolinensis within the Ursidae family has been a subject of long-standing debate. While some authors place it within the speloid lineage, others suggest affinities with arctoid bears. Here, we analyze the bear population from level TD4 of Gran Dolina (Sierra de Atapuerca, Spain) using palaeoproteomic methods for the first time. Molecular evidence supports the inclusion of U. dolinensis within the speloid lineage, in a basal position, supporting its potential ancestral position. These findings extend the evolutionary depth of the speloid clade in Europe and demonstrate the power of enamel palaeoproteomics to resolve deep-time relationships beyond the limits of ancient DNA, revealing the deep evolutionary roots of the lineage.

evolutionary biology↗

bioRxiv2025

ProteoParc: A tool to generate protein reference databases for ancient and non-model organisms

Over the last few years, the increasing interest in analysing the proteome of extinct and non-model organisms has generated a new field of research expanding the scope of proteomics. The lack of curated databases and/or molecular data from these organisms forces researchers to manually search in different public repositories for related protein sequences, either for MS/MS peptide identification or ZooMS marker annotation. This can lead to format incongruences and hinder reproducibility between studies. To address this issue, we introduce ProteoParc, a user-friendly software that generates reference databases by systematically downloading and processing protein sequences from the most widely used public repositories. The pipelines output is a non-redundant protein database, formatted to be interpreted by typical peptide identification software. Moreover, the user can adjust the database dimension and composition by applying different criteria to include only a certain number of genes or species. Thus, ProteoParc is an easy and fast, custom-made bioinformatic tool useful for future paleoproteomics analysis in ancient samples related to understudied organisms.

bioinformatics↗

bioRxiv2025

The genomic landscape of spider monkeys and northern muriquis from a conservation perspective

BackgroundMost populations of spider monkeys (Ateles) and muriquis (Brachyteles), two Neotropical primate genera, are under severe anthropogenic threats. Yet, taxon-wide population-level studies leveraging their degree of endangerment linked to their genetic diversity patterns and demographic history are lacking. To properly address this, there is a need to expand from morphological and genetic marker-based studies. ResultsWe generated high-coverage genome sequencing for 58 individuals sampled across 8 Atelidae species, in the first population-wide study of all extant spider monkey species, in the wild and captivity, alongside northern muriquis (Brachyteles hypoxanthus). Additionally, we present a high-contiguity reference genome for Ateles hybridus. Here, we observe the overall levels of genetic diversity and genetic load of the analyzed populations do not align to their IUCN endangerment category. Moreover, we show that in the wild, genetic load is overall higher compared to the captive populations analyzed. Then, we depict two main trans and cis-Andean sister clades in Ateles, and further structure and dynamics outlined by the Madeira River in the latter clade. Lastly, we find that genes in highly divergent regions between Ateles and B. hypoxanthus are involved in central nervous system development and photorreception. ConclusionsOur study shows i) the lack of concordance between the genetic diversity levels and extinction risk of these populations, suggestive of recent and strong external drivers; ii) increased genetic load in the wild in contrast to effective captive management, indicating mostly past demographic events; iii) structure and dynamics in spider monkeys that agrees with common biogeographical patterns and iv) genetic divergence between Ateles and Brachyteles potentially linked to distinct environmental light levels.

genomics↗

bioRxiv2024

Local genetic adaptation to habitat in wild chimpanzees

How populations adapt to their environment is a fundamental question in biology. Yet we know surprisingly little about this process, especially for endangered species such as non-human great apes. Chimpanzees, our closest living relatives, are particularly interesting because they inhabit diverse habitats, from rainforest to woodland-savannah. Whether genetic adaptation facilitates such habitat diversity remains unknown, despite having wide implications for evolutionary biology and conservation. Using 828 newly generated exomes from wild chimpanzees, we find evidence of fine-scale genetic adaptation to habitat. Notably, adaptation to malaria in forest chimpanzees is mediated by the same genes underlying adaptation to malaria in humans. This work demonstrates the power of non-invasive samples to reveal genetic adaptations in endangered populations and highlights the importance of adaptive genetic diversity for chimpanzees. One-Sentence SummaryChimpanzees show evidence of local genetic adaptation to habitat, particularly to pathogens, such as malaria, in forests.

evolutionary biology↗

bioRxiv2024

Screening great ape museum specimens for DNA viruses

Natural history museum collections harbour a record of wild species from the past centuries, providing a unique opportunity to study animals as well as their infectious agents. Thousands of great ape specimens are kept in these collections, and could become an important resource for studying the evolution of DNA viruses. Their genetic material is likely to be preserved in dry museum specimens, as reported previously for monkeypox virus genomes from historical orangutan specimens. Here, we screened 209 great ape museum specimens for 99 different DNA viruses, using hybridization capture coupled with short-read high-throughput sequencing. We determined the presence of multiple viruses within this dataset from historical specimens and obtained several near-complete viral genomes. In particular, we report high-coverage (>18-fold) hepatitis B virus genomes from one gorilla and two chimpanzee individuals, which are phylogenetically placed within clades infecting the respective host species.

genomics↗

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↗

bioRxiv2023

Whole genome approach to the structure and dynamics of Cacajao wild populations

Despite showing the greatest primate diversity on the planet, genomic studies on Amazonian primates show very little representation in the literature. With 48 geolocalized high coverage whole genomes from wild uakari monkeys, we present the first population-level study on platyrrhines using whole genome data. In a very restricted range of the Amazon rainforest, eight uakari species (Cacajao genus) have been described and categorized into bald and black uakaris, based on phenotypic and ecological differences. Despite a slight habitat overlap, we show that posterior to their split 0.92 Mya, bald and black uakaris have remained independent, without gene flow. Nowadays, these two groups present distinct genetic diversity and group-specific variation linked to pathogens. We propose differing hydrology patterns and effectiveness of geographic barriers have modulated the intra-group connectivity and structure of uakari populations. Beyond increasing their representation, with this work we explored the effects of the Amazon rainforests dynamism on platyrrhine species.

evolutionary biology↗

bioRxiv2023

Enamel proteins reveal biological sex and genetic variability within southern African Paranthropus

The evolutionary relationships among extinct African hominin taxa are highly debated and largely unresolved, due in part to a lack of molecular data. Even within taxa, it is not always clear, based on morphology alone, whether ranges of variation are due to sexual dimorphism versus potentially undescribed taxonomic diversity. For Paranthropus robustus, a Pleistocene hominin found only in South Africa, both phylogenetic relationships to other taxa 1,2 and the nature of intraspecific variation 3-6 are still disputed. Here we report the mass spectrometric (MS) sequencing of enamel proteomes from four ca. 2 million year (Ma) old dental specimens attributed morphologically to P. robustus, from the site of Swartkrans. The identification of AMELY-specific peptides and semi-quantitative MS data analysis enabled us to determine the biological sex of all the specimens. Our combined molecular and morphometric data also provide compelling evidence of a significant degree of variation within southern African Paranthropus, as previously suggested based on morphology alone 6. Finally, the molecular data also confirm the taxonomic placement of Paranthropus within the hominin clade. This study demonstrates the feasibility of recovering informative Early Pleistocene hominin enamel proteins from Africa. Crucially, it also shows how the analysis of these proteins can contribute to understanding whether hominin morphological variation is due to sexual dimorphism or to taxonomic differences. We anticipate that this approach can be widely applied to geologically-comparable sites within South Africa, and possibly more broadly across the continent.

evolutionary biology↗

bioRxiv2022

Y chromosome sequence and epigenomic reconstruction across human populations

Recent advances in long-read sequencing technologies have allowed the generation and curation of more complete genome assemblies, enabling the analysis of traditionally neglected chromosomes, such as the human Y chromosome (chrY). Native DNA was sequenced on a MinION Oxford Nanopore Technologies sequencing device to generate genome assemblies for 7 major chrY human haplogroups. We analyzed and compared the chrY enrichment of sequencing data obtained using two different selective sequencing approaches: adaptive sampling and flow cytometry chromosome sorting. We show that adaptive sampling can produce data to create assemblies comparable to chromosome sorting while being a less expensive and time-consuming technique. We also assessed haplogroup-specific structural variants, which would be otherwise difficult to study using short-read sequencing data only. Finally, we took advantage of this technology to detect and profile epigenetic modifications amongst the considered haplogroups. Altogether, we provide a framework to study complex genomic regions with a simple, fast, and affordable methodology that could be applied to larger population genomics datasets.

genomics↗

bioRxiv2021

Transcriptome innovations in primates revealed by single-molecule long-read sequencing

Transcriptomic diversity greatly contributes to the fundamentals of disease, lineage-specific biology, and environmental adaptation. However, much of the actual isoform repertoire contributing to shaping primate evolution remains unknown. Here, we combined deep long- and short-read sequencing complemented with mass spectrometry proteomics in a panel of lymphoblastoid cell lines (LCLs) from human, three other great apes, and rhesus macaque, producing the largest full-length isoform catalog in primates to date. Our transcriptomes reveal thousands of novel transcripts, some of them under active translation, expanding and completing the repertoire of primate gene models. Our comparative analyses unveil hundreds of transcriptomic innovations and isoform usage changes related to immune function and immunological disorders. The confluence of these innovations with signals of positive selection and their limited impact in the proteome points to changes in alternative splicing in genes involved in immune response as an important target of recent regulatory divergence in primates.

evolutionary biology↗

bioRxiv2021

Whole-genomes from the extinct Xerces Blue butterfly reveal low diversity and long-term population decline

The Xerces Blue (Glaucopsyche xerces) is considered to be the first butterfly to become extinct at global scale in historical times. It was notable for its chalky lavender wings with conspicuous white spots on the ventral wings. The last individuals were collected in their restricted habitat, in the dunes near the Presidio military base in San Francisco, in 1941. We sequenced the genomes of four 80 to 100-year-old Xerces Blue, and seven historical and one modern specimens of its closest relative, the Silvery Blue (G. lygdamus). We compared these to a novel annotated genome of the Green-Underside Blue (G. alexis). Phylogenetic relationships inferred from complete mitochondrial genomes indicate that Xerces Blue was a distinct species that diverged from the Silvery Blue lineage at least 850,000 years ago. Using nuclear genomes, both species experienced population growth during the Eemian interglacial period, but the Xerces Blue decreased to a very low effective population size subsequently, a trend opposite to that observed in the Silvery Blue. Runs of homozygosity and deleterious load in the Xerces Blue were significantly greater than in the Silvery Blue, suggesting a higher incidence of inbreeding. These signals of population decline observed in Xerces Blue could be used to identify and monitor other insects threatened by human activities, whose extinction patterns are still not well known.

evolutionary biology↗

bioRxiv2021

Variation in predicted COVID-19 risk among lemurs and lorises

The novel coronavirus SARS-CoV-2, which in humans leads to the disease COVID-19, has caused global disruption and more than 1.5 million fatalities since it first emerged in late 2019. As we write, infection rates are currently at their highest point globally and are rising extremely rapidly in some areas due to more infectious variants. The primary viral target is the cellular receptor angiotensin-converting enzyme-2 (ACE2). Recent sequence analyses of the ACE2 gene predicts that many nonhuman primates are also likely to be highly susceptible to infection. However, the anticipated risk is not equal across the Order. Furthermore, some taxonomic groups show high ACE2 amino acid conservation, while others exhibit high variability at this locus. As an example of the latter, analyses of strepsirrhine primate ACE2 sequences to date indicate large variation among lemurs and lorises compared to other primate clades despite low sampling effort. Here, we report ACE2 gene and protein sequences for 71 individual strepsirrhines, spanning 51 species and 19 genera. Our study reinforces previous results and finds additional variability in other strepsirrhine species, and suggests several clades of lemurs have high potential susceptibility to SARS-CoV-2 infection. Troublingly, some species, including the rare and Endangered aye-aye (Daubentonia madagascariensis), as well as those in the genera Avahi and Propithecus, may be at high risk. Given that lemurs are endemic to Madagascar and among the primates at highest risk of extinction globally, further understanding of the potential threat of COVID-19 to their health should be a conservation priority. All feasible actions should be taken to limit their exposure to SARS-CoV-2.

genetics↗

bioRxiv2020

Comprehensive identification of somatic nucleotide variants in human brain tissue

Post-zygotic mutations incurred during DNA replication, DNA repair, and other cellular processes lead to somatic mosaicism. Somatic mosaicism is an established cause of various diseases, including cancers. However, detecting mosaic variants in DNA from non-cancerous somatic tissues poses significant challenges, particularly if the variants only are present in a small fraction of cells. Here, the Brain Somatic Mosaicism Network conducted a coordinated, multi-institutional study to: (i) examine the ability of existing methods to detect simulated somatic single nucleotide variants (SNVs) in DNA mixing experiments; (ii) generate multiple replicates of whole genome sequencing data from the dorsolateral prefrontal cortex, other brain regions, dura mater, and dural fibroblasts of a single neurotypical individual; (iii) devise strategies to discover somatic SNVs; and (iv) apply various approaches to validate somatic SNVs. These efforts led to the identification of 43 bona fide somatic SNVs that ranged in variant allele fractions from ~0.005 to ~0.28. Guided by these results, we devised best practices for calling mosaic SNVs from 250X whole genome sequencing data in the accessible portion of the human genome that achieve 90% specificity and sensitivity. Finally, we demonstrated that analysis of multiple bulk DNA samples from a single individual allows the reconstruction of early developmental cell lineage trees. Thus, this study provides a unified set of best practices to detect somatic SNVs in non-cancerous tissues. The data and methods are freely available to the scientific community and should serve as a guide to assess the contributions of somatic SNVs to neuropsychiatric diseases.

genomics↗

bioRxiv2019

Metagenomic analysis of a blood stain from the French revolutionary Jean-Paul Marat (1743-1793)

The French revolutionary Jean-Paul Marat (1743-1793) was assassinated in 1793 in his bathtub, where he was trying to find relief from the debilitating skin disease he was suffering from. At the time of his death, Marat was annotating newspapers, which got stained with his blood and were subsequently preserved by his sister. We extracted and sequenced DNA from the blood stain and also from another section of the newspaper, which we used for comparison. Results from the human DNA sequence analyses were compatible with a heterogeneous ancestry of Marat, with his mother being of French origin and his father born in Sardinia. Metagenomic analyses of the non-human reads uncovered the presence of fungal, bacterial and low levels of viral DNA. Relying on the presence/absence of microbial species in the samples, we could cast doubt on several putative infectious agents that have been previously hypothesised as the cause of his condition but for which we detect not a single sequencing read. Conversely, some of the species we detect are uncommon as environmental contaminants and may represent plausible infective agents. Based on all the available evidence, we hypothesize that Marat may have suffered from a fungal infection (seborrheic dermatitis), possibly superinfected with bacterial opportunistic pathogens.

genetics↗

bioRxiv2018

Unbiased whole genomes from mammalian feces using fluorescence-activated cell sorting

Ecological flexibility, extended lifespans, and large brains, have long intrigued evolutionary biologists, and comparative genomics offers an efficient and effective tool for generating new insights into the evolution of such traits. Studies of capuchin monkeys are particularly well situated to shed light on the selective pressures and genetic underpinnings of local adaptation to diverse habitats, longevity, and brain development. Distributed widely across Central and South America, they are inventive and extractive foragers, known for their sensorimotor intelligence. Capuchins have the largest relative brain size of any monkey and a lifespan that exceeds 50 years, despite their small (3-5 kg) body size. We assemble a de novo reference genome for Cebus imitator and provide the first genome annotation of a capuchin monkey. Through high-depth sequencing of DNA derived from blood, various tissues and feces via fluorescence activated cell sorting (fecalFACS) to isolate monkey epithelial cells, we compared genomes of capuchin populations from tropical dry forests and lowland rainforests and identified population divergence in genes involved in water balance, kidney function, and metabolism. Through a comparative genomics approach spanning a wide diversity of mammals, we identified genes under positive selection associated with longevity and brain development. Additionally, we provide a technological advancement in the use of non-invasive genomics for studies of free-ranging mammals. Our intra- and interspecific comparative study of capuchin genomics provides new insights into processes underlying local adaptation to diverse and physiologically challenging environments, as well as the molecular basis of brain evolution and longevity. SIGNIFICANCESurviving challenging environments, living long lives, and engaging in complex cognitive processes are hallmark characteristics of human evolution. Similar traits have evolved in parallel in capuchin monkeys, but their genetic underpinnings remain unexplored. We developed and annotated a reference assembly for white-faced capuchin monkeys to explore the evolution of these phenotypes. By comparing populations of capuchins inhabiting rainforest versus dry forests with seasonal droughts, we detected selection in genes associated with kidney function, muscular wasting, and metabolism, suggesting adaptation to periodic resource scarcity. When comparing capuchins to other mammals, we identified evidence of selection in multiple genes implicated in longevity and brain development. Our research was facilitated by our new method to generate high- and low-coverage genomes from non-invasive biomaterials.

genomics↗

bioRxiv2018

Selective single molecule sequencing and assembly of a human Y chromosome of African origin

Mammalian Y chromosomes are often neglected from genomic analysis. Due to their inherent assembly difficulties, high repeat content, and large ampliconic regions1, only a handful of species have their Y chromosome properly characterized. To date, just a single human reference quality Y chromosome, of European ancestry, is available due to a lack of accessible methodology2-5. To facilitate the assembly of such complicated genomic territory, we developed a novel strategy to sequence native, unamplified flow sorted DNA on a MinION nanopore sequencing device. Our approach yields a highly continuous and complete assembly of the first human Y chromosome of African origin. It constitutes a significant improvement over comparable previous methods, increasing continuity by more than 800%6, thus allowing a chromosome scale analysis of human Y chromosomes. Sequencing native DNA also allows to take advantage of the nanopore signal data to detect epigenetic modifications in situ7. This approach is in theory generalizable to any species simplifying the assembly of extremely large and repetitive genomes.

genomics↗