Biology subjects

Aguilar, A.

Publications and source records attributed to Aguilar, A..

10 recordsLinked to original sources

bioRxiv2026

Multidecadal Remote Sensing of Macrocystis Pyrifera in Argentina

The Southern Hemisphere is home to extensive forests of giant kelp (Macrocystis pyrifera), including in Argentina and the southern islands of Tierra del Fuego, which has been proposed as a potential climate refugium. This study presents the first regional time series of M. pyrifera canopy dynamics in Argentina using Landsat satellite imagery from 1985 to 2023. The forests analyzed support 247.61 km{superscript 2} of emergent canopy and are situated in the coastal waters of Argentina and a small portion of Chilean islands, with 4%, 28%, and 68% in the Chubut, Santa Cruz, and Tierra del Fuego A.e.I.A.S, respectively. The small portion of Chilean Islands are included as part of the Tierra del Fuego province analyses. Range limits were scrutinized, in part, using expert knowledge and multisatellite comparisons. Linear regression shows that between 1998 and 2023, 7.4% of kelp sites exhibited a significant trend in annual canopy area, with all observed significant trends in the positive direction. Partitioning by province boundaries, linear regression produces significant positive increases in kelp canopy area across all three provinces, although reassessment when longer temporal continuity is also warranted, where available. Observed seawater nitrate concentrations were high throughout the region (7-23 {micro}mol L-{superscript 1}), suggesting that nitrate availability was not a primary driver of canopy variability. However, positive relationships between kelp canopy and the Antarctic Oscillation suggest that regional climate variability--which alters sea surface temperature and other oceanographic conditions--may be exerting a strong influence on kelp dynamics in this region. These findings document relative stability of kelp forest area in Argentina over the most recent two and a half decades and provide preliminary evidence supporting possible increases in kelp area for the region.

ecology↗

bioRxiv2026

Transposable elements as evolutionary substrates of proteindisorder in the human proteome

Intrinsically disordered regions (IDRs) are central contributors to protein function, evolution and human disease, yet the evolutionary routes that seed new disordered segments within pre-existing proteins are still poorly understood. Sequence insertions provide a powerful mechanism for disorder expansion, but the genomic donors of inserted IDR and its long-term conformational fate remain largely unknown. Transposable elements (TEs), abundant mobile genetic elements with distinctive compositional biases, represent compelling candidates for generating disorder within proteins. Here, we systematically mapped TE-derived segments across human proteins and isoforms, and we found that these insertions are strongly enriched in intrinsic disorder. The structural consequences of their insertion are shaped by TE class and family, reflecting the sequence biases of the elements from which they originate. Recent, Primate-specific insertions preferentially generate disordered segments, whereas older insertions more frequently occupy ordered structural contexts, revealing an age-dependent transition in the conformational state of TE-derived sequences. TE-containing isoforms are expressed at lower levels than TE-free isoforms, particularly when insertions are young and disorder-rich, suggesting that intrinsic disorder may constrain the cellular tolerance of newly exonized sequences. These findings identify TEs as a major evolutionary mechanism linking genome mobility to the emergence of new disordered conformational ensembles in the human proteome.

bioinformatics↗

bioRxiv2026

Abundance-activity decoupling in sulfur-cycling bacteria reflects viral infection types in meromictic lakes

Meromictic lakes serve as analogs for redox-stratified ancient oceans with well-mixed surface waters and anoxic bottoms. Purple and green sulfur bacteria (PSB, GSB) dominate the anoxic zones where light penetrates, and their biosignatures can be used to guide interpretations of geologic records. However, PSB and GSB biosignatures do not directly reflect the microbial community composition of modern lakes, posing a challenge for their interpretation. Here, we investigate this decoupling by integrating metagenomics, metatranscriptomics, and metaHi-C virus-host linkages with the geochemical profiles of three meromictic lakes. In the phototrophic microbial plates, PSBs transcriptional activity far exceeded their abundance (73% of the total microbial community activity versus 30% of the abundance), while GSBs displayed the opposite pattern. Concurrently, PSBs were exclusively associated with temperate viruses, while GSBs were targeted by lytic infections. Sulfate-reducing bacteria (SRB) and viruses encoding genes for sulfate reduction were most active where sulfide concentration was lowest. These results reveal that viral replication strategies are associated with the decoupling between abundance and activity in anoxygenic phototrophs and sulfate reducers. These relationships could accelerate sulfur regeneration, contribute to sustaining phototrophy, and ultimately reflect in the lakes bulk biosignatures.

microbiology↗

bioRxiv2026

Convergent reduction in skeletal density during benthic to pelagic transitions in Baikal sculpins

Habitat transitions are a major driver of morphological evolution. Teleost fishes have repeatedly transitioned from benthic to pelagic habitats, often evolving predictable changes in body shape that enhance hydrodynamic efficiency. While freshwater sculpins (Cottidae, Perciformes) are usually benthic, two genera in Lake Baikal, Comephorus and Cottocomephorus, have independently evolved into midwater niches. As sculpins lack a swim bladder, these lineages instead improved buoyancy through reduced skeletal density and increased lipid stores. Using micro-computed tomography and two-dimensional morphometrics, we characterized skeletal evolution across the Baikal sculpin radiation. We found that parallel changes in bone mineral density and microstructure independently evolved in the two pelagic clades. Density reductions occurred throughout the skull in pelagic species. The basibranchials and neurocranium exhibited the lowest overall bone density across all cranial elements. While the jaws maintained the highest absolute density values among the bones we measured, they also showed the greatest proportional reduction in density associated with pelagic habitat use, with a 56.86% decrease in percentage hydroxyapatite and a 21.39% increase in porosity. Morphometric analyses further identified convergence toward an elongate body shape, reduced and posteriorly shifted eyes, and elevated fin insertion in pelagic taxa. These results demonstrate a repeated skeletal lightening and body shape changes accompanying benthic-to-pelagic transitions. This pattern mirrors other benthic-to-pelagic transitions in teleosts that lack swim bladders, highlighting shared biomechanical and microstructural solutions to life in the open water.

evolutionary biology↗

bioRxiv2025

Small uncultured viral-like entities redraw the origin of viruses and cellular compartments

The HK97-fold is an ancient, conserved protein structure that forms protein shells. It is the building block of capsids that protect the genome of viruses in the Duplodnaviria realm, infecting organisms across all domains of life. It is also the building block of encapsulins, compartments that confine biochemical reactions in prokaryotes. Recent genomic studies have hypothesized that encapsulins evolved from HK97-fold viruses. However, this evolutionary pathway is challenging to justify biophysically because HK97-fold viruses form larger and more complex protein shells than encapsulins. We addressed this paradox by searching for smaller and simpler HK97-fold viral capsids across ecosystems. The investigation yielded a well-defined group of viral entities, which encode HK97-fold proteins displaying molecular similarities with encapsulins and lacking portal and tail genes. The structural phylogenetic analysis of HK97-fold entities revealed bidirectional evolutionary transitions between encapsulins and HK97-fold viruses. An evolutionary mechanism responsible for such transitions was proposed based on the presence of lysogeny-associated genes in the viral entities and the structural and molecular parallels between encapsulins and procapsids, the immature state of viral capsids before genome packaging. We concluded that procapsids are akin to the common HK97-fold protein shell ancestor and might still facilitate transitions between modern viruses and encapsulins. The potential genomic and biochemical functions of HK97-fold procapsids make them an ideal candidate model for the early evolution of life and might require a revision of the role of viral capsids in the biosphere.

bioinformatics↗

bioRxiv2023

Behavioral Thermoregulation in Captive Fish: Molecular, Physiological, and Welfare Implications

Environmental Enrichment (EE) serves as a cornerstone in the attempt to emulate natural habitats for captive organisms. While substantial strides have been made in this field, current methodologies still grapple with discrepancies between recreated habitats and the innate conditions vital for maintaining biological homeostasis in captive species. Our study highlights the pivotal role of behavioral thermoregulation in modulating molecular and physiological outcomes in captive fish. Collective evidence suggests that enabling fish to autonomously regulate temperature confers numerous beneficial cellular and systemic effects. Specifically, introducing a thermal gradient within the EE paradigm correlated with increased survival metrics, enhanced physiological parameters, and improved welfare indices, establishing the criticality of thermoregulation in captivity. In contrast, the lack of a thermoregulatory framework resulted in the emergence of transient free radicals, a clear marker of temperature-induced oxidative stress. Persistent disruptions in free radical equilibrium, especially in uniform temperature settings, were linked to DNA damage, heightened cellular apoptosis, tissue anomalies, and metabolic deviations. In conclusion, this research underscores the significance of behavioral thermoregulation as an integral feature of EE, especially related to fish in controlled environments. Our data present key biomarkers valuable for optimizing fish welfare and highlight the necessity for sustained research into their adaptability and survival benchmarks. Such insights aim to enhance EE protocols, fortifying their efficacy in mirroring natural habitats and, in turn, advancing the welfare benchmarks of captive organisms.

physiology↗

bioRxiv2022

Speciation genomics and the role of depth in the divergence of rockfishes (Sebastes) revealed through Pool-seq analysis of enriched sequences

Speciation in the marine environment is challenged by the wide geographic distribution of many taxa and potential for high rates of gene flow through larval dispersal mechanisms. Depth has recently been proposed as a potential driver of ecological divergence in fishes and yet it is unclear how adaptation along these gradients shapes genomic divergence. The genus Sebastes contains numerous species pairs that are depth segregated and can provide a better understanding of the mode and tempo of genomic diversification. Here we present exome data on two species pairs of rockfishes that are depth segregated and have different degrees of divergence: S. chlorostictus-S. rosenblatti and S. crocotulus-S. miniatus. We were able to reliably identify islands of divergence in the species pair with more recent divergence (S. chlorostictus-S. rosenblatti) and discovered a number of genes associated with neurosensory function, suggesting a role for this pathway in the early speciation process. We also reconstructed demographic histories of divergence and found the best supported model was isolation followed by asymmetric secondary contact for both species pairs. These results suggest past ecological/geographic isolation followed by asymmetric secondary contact of deep to shallow species. Our results provide another example of using rockfish as a model for studying speciation and support the role of depth as an important mechanism for diversification in the marine environment.

evolutionary biology↗

bioRxiv2021

The antique genetic plight of the Mediterranean monk seal (Monachus monachus)

Disentangling the impact of Late Quaternary climate change from human activities can have crucial implications on the conservation of endangered species. We investigated the population genetics and demography of the Mediterranean monk seal (Monachus monachus), one of the worlds most endangered marine mammals, through an unprecedented dataset encompassing historical (extinct) and extant populations from the eastern North Atlantic to the entire Mediterranean Basin. We show that Cabo Blanco (Western Sahara/Mauritania), Madeira, Western Mediterranean (historical range), and Eastern Mediterranean regions segregate into four populations. This structure is likely the consequence of recent drift, combined with long-term isolation by distance (R2 = 0.7), resulting from prevailing short-distance (< 500 km) and infrequent long-distance dispersal (< 1,500 km). All populations (Madeira especially), show high levels of inbreeding and low levels of genetic diversity, seemingly declining since historical time, but surprisingly not being impacted by the 1997 massive die-off in Cabo Blanco. Approximate Bayesian Computation analyses support scenarios combining local extinctions and a major effective population size decline in all populations during Antiquity. Our results suggest that the early densification of human populations around the Mediterranean Basin coupled with the development of seafaring techniques were the main drivers of the decline of Mediterranean monk seals.

genetics↗

bioRxiv2019

Evolutionary history of the porpoises (Phocoenidae) across the speciation continuum: a mitogenome phylogeographic perspective

Historical changes affecting food resources are a major driver of cetacean evolution. Small cetaceans like porpoises (Phocoenidae) are among the most metabolically challenged marine mammals and are particularly sensitive to changes in their food resources. The seven species of this family inhabit mostly temperate waters and constitute a textbook example of antitropical distribution. Yet, their evolutionary history remains poorly known despite major conservation issues threatening the survival of some porpoises (e.g., vaquita and Yangzte finless porpoises). Here, we reconstructed their evolutionary history across the speciation continuum, from intraspecific subdivisions to species divergence. Phylogenetic analyses of 63 mitochondrial genomes suggest that, like other toothed whales, porpoises radiated during the Pliocene in response to deep environmental changes. However, all intra-specific phylogeographic patterns were shaped during the Quaternary Glaciations. We observed analogous evolutionary patterns in both hemispheres associated with convergent adaptations to coastal versus oceanic environments. This result suggests that the mechanism(s) driving species diversification in the relatively well-known species from the northern hemisphere may apply also to the poorly-known southern species. In contrast to previous studies, we showed that the spectacled and Burmeisters porpoises share a more recent common ancestor than with the vaquita that diverged from southern species during the Pliocene. The low genetic diversity observed in the vaquita carried signatures of a very low population size throughout at least the last 5,000 years, leaving one single relict mitochondrial lineage. Finally, we observed unreported subspecies level divergence within Dalls, spectacled and Pacific harbor porpoises, suggesting a richer evolutionary history than previously suspected. These results provide a new perspective on the mechanism driving the adaptation and speciation processes involved in the diversification of cetacean species. This knowledge can illuminate their demographic trends and provide an evolutionary framework for their conservation.

evolutionary biology↗

bioRxiv2018

Fin whale (Balaenoptera physalus) mitogenomics: A cautionary tale of defining sub-species from mitochondrial sequence monophyly

HighlightsO_LIMitochondrial monophyly is commonly employed to define evolutionary significant units.\nC_LIO_LIMonophyly may be caused by insufficient sampling or a recent common ancestor.\nC_LIO_LIMitogenomic studies are generally based on few samples and prone to sampling issues.\nC_LIO_LIExpanded mitogenome sampling negates previous monophyly in fin whales.\nC_LI\n\nAbstractThe advent of massive parallel sequencing technologies has resulted in an increase of studies based upon complete mitochondrial genome DNA sequences that revisit the taxonomic status within and among species. Spatially distinct monophyly in mitogenomic genealogies, i.e., the sharing of a recent common ancestor among con-specific samples collected in the same region has been viewed as evidence for subspecies. Several recent studies in cetaceans have employed this criterion to suggest subsequent intraspecific taxonomic revisions. We reason that employing intra-specific, spatially distinct monophyly at non-recombining, clonally inherited genomes is an unsatisfactory criterion for defining subspecies based upon theoretical (genetic drift) and practical (sampling effort) arguments. This point is illustrated by a re-analysis of a global mitogenomic assessment of fin whales, Balaenoptera physalus spp., published by Archer et al. (2013) which proposed to further subdivide the Northern Hemisphere fin whale subspecies, B. p. physalus. The proposed revision was based upon the detection of spatially distinct monophyly among North Atlantic and North Pacific fin whales in a genealogy based upon complete mitochondrial genome DNA sequences. The extended analysis conducted in this study (1,676 mitochondrial control region, 162 complete mitochondrial genome DNA sequences and 20 microsatellite loci genotyped in 358 samples) revealed that the apparent monophyly among North Atlantic fin whales reported by Archer et al. (2013) to be due to low sample sizes. In conclusion, defining sub-species from monophyly (i.e., the absence of para-or polyphyly) can lead to erroneous conclusions due to relatively \"trivial\" aspects, such as sampling. Basic population genetic processes (i.e., genetic drift and migration) also affect the time to most recent common ancestor and hence the probability that individuals in a sample are monophyletic.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=195 SRC=\"FIGDIR/small/488130v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (28K):\norg.highwire.dtl.DTLVardef@1e38e54org.highwire.dtl.DTLVardef@9533eborg.highwire.dtl.DTLVardef@183b5b5org.highwire.dtl.DTLVardef@eae09_HPS_FORMAT_FIGEXP M_FIG C_FIG

evolutionary biology↗