Biology subjects

Aleixo, A.

Publications and source records attributed to Aleixo, A..

13 recordsLinked to original sources

bioRxiv2026

A chromosome-level genome of the franciscana dolphin, Pontoporia blainvillei

The franciscana dolphin (Pontoporia blainvillei) is a small coastal cetacean endemic to the southwestern Atlantic Ocean and one of the most threatened marine mammals worldwide. It faces severe threats from bycatch, habitat degradation, and pollution. Classified as "Vulnerable" by the IUCN and "Critically Endangered" in Brazil, the species restricted range, strong fidelity to shallow waters, and low reproductive rate increase its extinction risk. Here, we present the first chromosome-level genome assembly for the franciscana dolphin, generated using PacBio HiFi long-read sequencing and Hi-C chromatin conformation capture. The final assembly totaled 3.13 Gb across 22 chromosomes (1500 scaffolds), consistent with the estimated karyotype of 2n = 44, with scaffold N50 of 111.18 Mb, high BUSCO completeness (99.42%), and a consensus quality value of 65.76. This high-quality genomic resource fills an important phylogenetic gap within Cetacea, enabling comparative and conservation studies. It provides an essential foundation for population genomics research to assess genetic diversity, structure, and connectivity, thereby supporting evidence-based conservation strategies for this endangered species.

genomics↗

bioRxiv2026

Habitat specialization structures population divergence and demographic variation in Amazonian floodplain birds

Understanding how species respond to environmental change requires linking ecological traits to gene flow and demographic history across dynamic landscapes. Using population genomic data from twelve co-distributed Amazonian riverine island birds, we show that habitat specialization predicts genetic structure, divergence, and effective population size. Species specialized on dynamic sandbar scrub habitats exhibit higher gene flow, and higher genetic diversity despite smaller effective population sizes. These patterns are consistent with dispersal tracking shifting resources, which decouples genetic diversity from population size. In contrast, river-edge forest specialists show stronger spatial genetic structure and lower genetic diversity despite larger populations, consistent with long-term isolation in more stable habitats. We also detect regional variation in effective population sizes and genetic diversity across Amazonian river sub-basins, potentially reflecting historical differences in floodplain habitat availability. Overall, our results highlight how non-equilibrium dynamics shape genomic variation and emphasize habitat-driven dispersal in diversification and persistence in seasonal systems.

evolutionary biology↗

bioRxiv2026

The Vertebrate Genomes Project Phase I: A global reference genome resource

The Vertebrate Genomes Project (VGP) aims to produce complete and near-error-free reference genomes for all [~]70,000 extant vertebrate species1. Organized in four phases, it progressively targets all vertebrate orders, families, genera, and eventually all species. Here we present the completion of VGP Phase I, delivering reference genomes for [~]95% of vertebrate orders, along with additional lineages within those orders, totaling 816 species and 1.6 trillion base pairs of main haplotype sequence. These genomes were assembled and annotated over an 8-year period (2018-2026) of rapid advances in genome sequencing, assembly, and annotation methods2-4, alongside the growth of associated consortium initiatives and international collaborations5-9. They represent some of the highest-quality vertebrate genomes currently available, and most have become the primary reference for their respective species in public databases. Comparative analyses across a subset of 579 species when we reached a threshold of 85% of orders allowed us to reconstruct the genome of the last common ancestor of all vertebrates 500 million years ago, identify diverse modes of sex chromosome evolution, reveal clade-specific three-dimensional genome architecture, discover methylated epigenetic landscapes across vertebrates, and provide a framework for studying gene and pseudogene evolution, immune loci, cancer-associated genes, and other trait-associated loci. Approximately a quarter of this subset are listed as Vulnerable to Critically Endangered by the IUCN Red List of Threatened Species, and have enabled more advanced genomic investigations of extinction risk. VGP Phase I delivers a reference backbone for vertebrate genomics, enabling discoveries that would otherwise remain out of reach across evolution, conservation, and medicine. Talking pointsO_LIThe flagship paper of VGP Phase I C_LIO_LIThe highest quality collection of genomes within the eukaryotic domain of life C_LIO_LIEvolution of genome sequencing technology quality throughout VGP Phase I C_LIO_LIA driver project that has been a model for multiple large-scale, high-quality reference genome projects C_LIO_LIReleases all currently unpublished genomes in Phase I from scientific study embargoes C_LIO_LIMultiple biological discoveries across the vertebrate tree of life C_LI

genomics↗

bioRxiv2025

The genomic landscape of asymmetric introgression tracks chromosomal characteristics in tinamous (Aves: Tinamidae)

We use single genomes from seven tinamou species (Palaeognathae: Tinamidae) and apply a genome-architecture-aware phylogenomic approach to (1) quantify the landscape of introgression, (2) discriminate among conflicting genealogical signals in the genome, and (3) reconstruct evolutionary history. Using summary statistics and full likelihood, we detect pervasive asymmetric introgression between two sympatric Amazonian species clouding phylogenetic relationships in this group. However, these introgression results are sensitive to the assumed species tree. When assuming the Z-chromosome phylogeny as the species tree, the landscape of introgression is non-random; introgression is negatively associated with chromosome length, elevated at macrochromosome ends, and near zero for the Z-chromosome (the avian sex chromosome). A pseudo-autosomal region on the Z-chromosome, which recombines homologously with that of the W-chromosome, shows elevated introgression comparable to that of autosomes. Our results resolve the species tree of tinamous and imply a history of linked selection purging migrant alleles that are deleterious in the hybrid genome. This selection is countered in regions of the genome expected to experience elevated recombination, allowing introgressed alleles to accumulate across >20% of the genome. This work demonstrates a genome-architecture-aware approach to resolving the species tree in the face of introgression. As chromosome-level reference genomes spanning the tree of life become increasingly available, phylogenomic studies would benefit from the adoption of genome-architecture-aware approaches like ours. This is because the genomic landscapes of introgression and genealogy are largely predicted by chromosomal characteristics.

genomics↗

bioRxiv2025

Geographical variation in mitogenomes of the largetooth sawfish Pristis pristis: challenges and perspectives for conservation efforts

Sawfishes (Pristidae) have been severely impacted by coastal development and unregulated fisheries and are considered Critically Endangered by the IUCN Red List. Environmental DNA (eDNA) analyses have shown potential for monitoring elasmobranch species, with various studies focusing on using species-specific approaches to detect Pristis species. However positive detection using existing probes has not been confirmed in some geographic regions where they would be expected. Here, we aimed to test whether mutations at key sites have been detrimental to species-specific detection of P. pristis (Linnaeus, 1758) using the existing probe set. To test this hypothesis mitogenomes were assembled that were found to follow the typical pattern of vertebrate mitogenomic organization. Phylogenetic trees showed similar topologies and confirmed geographic mitochondrial variation in P. pristis. Mismatches for the published 12S species-specific probe set for P. pristis were identified that prevent amplification of positive control samples from Brazil. However, ddPCR detection of the positive control was possible using a newly designed species-specific probe set. This study highlights how geographical variation can severely impact the success of generally applying species-specific detection systems developed based on data from only one geographical region. The new mitogenomes and species-specific probe set developed here may also contribute to improving the potential to map and monitor these Critically Endangered species across the globe. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/639618v1_ufig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@1fb30fborg.highwire.dtl.DTLVardef@4cd3a8org.highwire.dtl.DTLVardef@1dbd985org.highwire.dtl.DTLVardef@a5d7d3_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO C_FIG

ecology↗

bioRxiv2024

Pipeasm: a tool for automated large chromosome-scale genome assembly and evaluation

MotivationWith increasing initiatives to study biodiversity through high-quality reference genomes and the growing capacity of sequencing a wide range of organisms, there is a pressing need for an accessible, reproducible, and user-friendly tool that incorporates state-of-the-art methodologies for large genome assembly. ResultsWe introduce Pipeasm, a Snakemake pipeline designed for assembling vertebrate genomes using HiFi PacBio, ONT, and HiC data. By setting a configuration file with input information and suggested parameters, Pipeasm was able to assemble multiple-sized diploid genomes ready for manual curation. Availability and ImplementationPipeasm requires an environment with Snakemake and Singularity and is available at https://github.com/itvgenomics/pipeasm.

bioinformatics↗

bioRxiv2024

Whole-genome phylogenomics of the tinamous (Aves: Tinamidae): comparing gene tree estimation error between BUSCOs and UCEs illuminates rapid divergence with introgression

As an old group that has diversified in South America over millions of years, the tinamous (Palaeognathae: Tinamidae) are of high interest for understanding the evolution of birds and the assembly of the Neotropical biota. However, there are currently no complete species-level phylogenies of this group. Most prior work has been based on either morphological data or a small number of molecular markers, each of which has limited capability for reconstructing the tinamou phylogeny. Therefore, the interrelationships of most tinamou species are uncertain. We analyzed 80 whole-genomes from a mix of historical study skins and frozen tissues, including all 46 recognized species of tinamous to (1) reconstruct their interrelationships, (2) estimate the timeframe of tinamou evolution, and (3) examine for the effects of incomplete lineage sorting (ILS) and ancestral introgression on genome evolution. We compared results for coding (BUSCO) and ultraconserved element (UCE) loci, as well as sex-linked and autosomal markers, and used fossil-calibrated tip-dating to estimate divergence times. Tinamous diverged from their sister-group, the extinct Moas, 50-60 mya, and their crown divergence occurred roughly 30-40 mya, followed by constant diversification rates until the present. Phylogenetic reconstructions were largely robust across methods and datasets. Only one clade in the genus Crypturellus displayed substantial species-tree discordance across the different data sets. To investigate the impacts of introgression on this discordance, we quantified introgression for 100kb non-overlapping windows across the genome, and identified pervasive genome-wide introgression. The distribution of this introgression across the genome was dependent on the assumed phylogeny applied to the f-branch model. When assuming one of these topologies in the f-branch model, patterns of introgression matched theoretical predictions about genome architecture. Overall, we present the most complete phylogeny for tinamous to date, identify an unrecognized species, and provide a case study for species-level phylogenomic analysis using whole-genomes.

genomics↗

bioRxiv2021

Genomic architecture controls spatial structuring in Amazonian birds

Large rivers are ubiquitously invoked to explain the distributional limits and speciation of the Amazon Basins mega-diversity. However, inferences on the spatial and temporal origins of Amazonian species have narrowly focused on evolutionary neutral models, ignoring the potential role of natural selection and intrinsic genomic processes known to produce heterogeneity in differentiation across the genome. To test how genomic architecture impacts our ability to reconstruct patterns of spatial diversification across multiple taxa, we sequenced whole genomes for populations of bird species that co-occur in southeastern Amazonian. We found that phylogenetic relationships within species and demographic parameters varied across the genome in predictable ways. Genetic diversity was positively associated with recombination rate and negatively associated with the species tree topology weight. Gene flow was less pervasive in regions of low recombination, making these windows more likely to retain patterns of population structuring that matched the species tree. We further found that approximately a third of the genome showed evidence of selective sweeps and linked selection skewing genome-wide estimates of effective population sizes and gene flow between populations towards lower values. In sum, we showed that the effects of intrinsic genomic characteristics and selection can be disentangled from the neutral processes to elucidate how speciation hypotheses and biogeographic patterns are sensitive to genomic architecture.

genomics↗

bioRxiv2021

River network rearrangements promote speciation in lowland Amazonian birds

Large Amazonian rivers impede dispersal for many species, but lowland river networks frequently rearrange, thereby altering the location and effectiveness of river-barriers through time. These rearrangements may promote biotic diversification by facilitating episodic allopatry and secondary contact among populations. We sequenced genome-wide markers to evaluate histories of divergence and introgression in six Amazonian avian species-complexes. We first tested the assumption that rivers are barriers for these taxa and found that even relatively small rivers facilitate divergence. We then tested whether species diverged with gene flow and recovered reticulate histories for all species, including one potential case of hybrid speciation. Our results support the hypothesis that river dynamics promote speciation and reveal that many rainforest taxa are micro-endemic, unrecognized and thus threatened with imminent extinction. We propose that Amazonian hyper-diversity originates in part from fine-scale barrier displacement processes -including river dynamics- which allow small populations to differentiate and disperse into secondary contact.

evolutionary biology↗

bioRxiv2021

Population dynamics of Amazonian floodplain forest species support spatial variation on genetic diversity but not range expansions through time

AimWe tested if historical demographic changes of populations occurring on the floodplains of a major Amazon Basin tributary could be associated with range expansions from upper and middle sections of the river, following the establishment of widespread river-created environments during the Late Pleistocene and Holocene. LocationSolimoes River, Western Amazon, South America TaxonMyrmoborus lugubris, Thamnophilus cryptoleucus and Myrmotherula assimilis Methods: We analyzed thousands of UltraConserved Elements to explore spatial patterns of genetic diversity and connectivity between individuals. Range expansions were tested with alternative methods. We quantified habitat preference for the analyzed species in order to test if the occupation of dynamic habitats could predict spatial patterns of genetic diversity. ResultsOur study did not support shared population range expansions related to historical regionalized changes in habitat availability. We found considerable variation in the spatial distribution of the genetic diversity between studied taxa, and that species with higher levels of specialization to dynamic environments have a more heterogeneous distribution of genetic diversity and reduced levels of gene flow across space. Main conclusionsOur results suggest that demographic expansions along the Solimoes River might be linked to geographic homogeneous oscillation in the distribution of floodplain environments, promoting effective population size changes but not range expansion. We found that habitat specificity might be a good predictor of population connectivity along the Amazonian floodplains.

evolutionary biology↗

bioRxiv2018

Species delimitation and biogeography of the gnatcatchers and gnatwrens (Aves: Polioptilidae)

The New World avian family Polioptilidae (gnatcatchers and gnatwrens) is distributed from Argentina to Canada and includes 15 species and more than 60 subspecies. No study to date has evaluated phylogenetic relationships within this family and the historical pattern of diversification within the group remains unknown. Moreover, species limits, particularly in widespread taxa that show geographic variation, remain unclear. In this study, we delimited species and estimated phylogenetic relationships using multilocus data for the entire family. We then used the inferred diversity along with alternative taxonomic classification schemes to evaluate how lumping and splitting of both taxa and geographical areas influenced biogeographic inference. Species-tree analyses grouped Polioptilidae into four main clades: Microbates, Ramphocaenus, a Polioptila guianensis complex, and the remaining members of Polioptila. Ramphocaenus melanurus was sister to the clade containing M. cinereiventris and M. collaris, which formed a clade sister to all species within Polioptila. Polioptila was composed of two clades, the first of which included the P. guianensis complex; the other contained all remaining species in the genus. Using multispecies coalescent modeling, we inferred a more than 3-fold increase in species diversity, of which 87% represent currently recognized species or subspecies. Much of this diversity corresponded to subspecies that occur in the Neotropics. We identified three polyphyletic species, and delimited 4-6 previously undescribed candidate taxa. Probabilistic modeling of geographic ranges on the species tree indicated that the family likely had an ancestral origin in South America, with all three genera independently colonizing North America. Support for this hypothesis, however, was sensitive to the taxonomic classification scheme used and the number of geographical areas allowed. Our study proposes the first phylogenetic hypothesis for Polioptilidae and provides genealogical support for the reclassification of species limits. Species limits and the resolution of geographical areas that taxa inhabit influence the inferred spatial diversification history.

evolutionary biology↗

bioRxiv2018

Allele Phasing Greatly Improves the Phylogenetic Utility of Ultraconserved Elements

Advances in high-throughput sequencing techniques now allow relatively easy and affordable sequencing of large portions of the genome, even for non-model organisms. Many phylogenetic studies reduce costs by focusing their sequencing efforts on a selected set of targeted loci, commonly enriched using sequence capture. The advantage of this approach is that it recovers a consistent set of loci, each with high sequencing depth, which leads to more confidence in the assembly of target sequences. High sequencing depth can also be used to identify phylogenetically informative allelic variation within sequenced individuals, but allele sequences are infrequently assembled in phylogenetic studies.\n\nInstead, many scientists perform their phylogenetic analyses using contig sequences which result from the de novo assembly of sequencing reads into contigs containing only canonical nucleobases, and this may reduce both statistical power and phylogenetic accuracy. Here, we develop an easy-to-use pipeline to recover allele sequences from sequence capture data, and we use simulated and empirical data to demonstrate the utility of integrating these allele sequences to analyses performed under the Multispecies Coalescent (MSC) model. Our empirical analyses of Ultraconserved Element (UCE) locus data collected from the South American hummingbird genus Topaza demonstrate that phased allele sequences carry sufficient phylogenetic information to infer the genetic structure, lineage divergence, and biogeographic history of a genus that diversified during the last three million years. The phylogenetic results support the recognition of two species, and suggest a high rate of gene flow across large distances of rainforest habitats but rare admixture across the Amazon River. Our simulations provide evidence that analyzing allele sequences leads to more accurate estimates of tree topology and divergence times than the more common approach of using contig sequences.

evolutionary biology↗

bioRxiv2016

Habitat preference predicts genetic diversity and population divergence in Amazonian birds

The ecological traits of organisms may predict important evolutionary parameters such as genetic diversity, population genetic structure, and demographic history. Making these ecological-evolutionary links is difficult because robust, comparable genetic estimates are required from many species with differing ecologies. In Amazonian birds, differences in habitat preference are an important component of ecological diversity. A subset of Amazonian birds is restricted to forest edge and open forest along floodplains, whereas another subset occurs only in the interior of tall, upland forest. Here, we examine the link between habitat and evolutionary metrics using 20 pairs of closely related and co-distributed bird species in which one member of the pair occurs primarily in forest edge and floodplains, and the other occurs in upland forest interior. We use standardized geographic sampling and genomic data from the same set of 2,416 independent markers to estimate genetic diversity, population structure, and demographic history in each species. We find that species of upland forest have higher genetic diversity, greater divergence across the landscape, more genetically distinct populations, and deeper gene histories than floodplain species. Our results reveal that species ecology in the form of habitat preference is an important predictor of genetic diversity and divergence and suggest that floodplain and upland avifaunas in the Amazon may be on separate evolutionary trajectories and require different conservation strategies.

evolutionary biology↗