Biology subjects

Valdes, P.

Publications and source records attributed to Valdes, P..

6 recordsLinked to original sources

bioRxiv2026

The genomic basis of evolutionary stasis in the 500-million-year-old red seaweed genus Ahnfeltia

The red seaweed genus Ahnfeltia is an ancient lineage that has persisted for over 500 million years with remarkably limited diversification despite a global distribution in cold-temperate intertidal habitats. Compared to the highly diverse sister lineage, Rhodymeniophycidae, Ahnfeltia provides a unique system for investigating long-term evolutionary persistence in marine macroalgae. Here, we generated chromosome-scale genomes from five populations across three species and combined population genomics with paleogeographic niche modelling. Our results reveal remarkable genomic conservation, strong geographic isolation with limited gene flow, high homozygosity, and evidence of purifying selection. Niche projections indicate long-term stability and spatial connectivity of suitable cold-temperate habitats. These findings suggest that Ahnfeltias persistence and limited diversification are linked to genomic constraints and stable ecological niches over geological timescales. This study provides new insights into the genomic basis of evolutionary stasis in ancient marine lineages and highlights potential vulnerability to ongoing climate change affecting cold-water coastal ecosystems.

evolutionary biology↗

bioRxiv2023

Early Jurassic origin of avian endothermy and thermophysiological diversity in Dinosauria

A fundamental question in dinosaur evolution is how they adapted to substantial long-term shifts in Earth System during the Mesozoic and when they developed environmentally independent, avian-style acclimatization due to the evolution of an endothermic physiology. Combining fossil occurrences with macroevolutionary and paleoclimatic models, we unveil distinct evolutionary pathways in the main dinosaur lineages: ornithischians and theropods diversified across broader climatic landscapes, trending toward cooler niches. An Early Jurassic shift to colder climates in Theropoda suggests an early adoption of endothermic thermophysiology. Conversely, sauropodomorphs exhibited prolonged climatic conservatism associated with higher thermal conditions. Paleo-biome mapping emphasizes temperature, rather than plant productivity, as the primary driver of this pattern, suggesting poikilothermic physiology with a stronger dependence on higher temperatures in sauropods since the Early Jurassic. One-Sentence SummaryDinosaur climatic evolution reveals early endothermy emergence in theropods, ornithischians but heterotherm sauropodomorphs.

paleontology↗

bioRxiv2022

Constraining the global niche suitability of the Eusuchia clade across the Cretaceous-Paleogene boundary.

The crocodiles and their close relatives, the alligators and gharials, have a compelling evolutionary history. They are a clade of great antiquity, with their most recent common ancestor emerging within the Mesozoic. However, unlike many groups of such a great age, the crocodilians have an extensive crown-group, with around two dozen extant examples. They have a limited ecomorphology, which has varied little since their inception, and their biogeography has been shown to interact closely with climate. The biogeography of crocodilians in deep time remains an outstanding question, which is complicated further by the limitations of the fossil record. The fossil record is fundamentally incomplete yet represents the most common method used to infer biogeography of organisms. The scarcity of fossil remains makes apparent absences difficult to confirm. Preservation bias will promote fossil occurrences in areas with a high sedimentation rate, which may not be the true ecological niche for a given taxon. This study uses species distribution models of extant crocodilians to infer the ecological niche of related taxa in the Maastrichtian and Danian. Models indicate a much wider latitudinal range than is observed among extant examples, and the invasion of new ecospace following the end-Cretaceous mass extinction. In addition, we find that while temperature is of significance to crocodilian biogeography, it is precipitation that is the most influential climatic variable.

paleontology↗

bioRxiv2022

Rapid ex vivo reverse genetics identifies the essential determinants of prion protein toxicity

The cellular prion protein PrPC mediates the neurotoxicity of prions and other protein aggregates through poorly understood mechanisms. Antibody-derived ligands against the globular domain of PrPC (GDL) can also initiate neurotoxicity by inducing an intramolecular R208-H140 hydrogen bond ("H-latch") between the 2-3 and {beta}2-2 loops of PrPC. Importantly, GDL that suppress the H-latch prolong the life of prion-infected mice, suggesting that GDL toxicity and prion infections exploit convergent pathways. To define the structural underpinnings of these phenomena, we transduced nineteen individual PrPC variants to PrPC-deficient cerebellar organotypic cultured slices using adenovirus-associated viral vectors (AAV). We report that GDL toxicity requires a single N-proximal cationic residue (K27 or R27) within PrPC. Alanine substitution of K27 also prevented the toxicity of PrPC mutants that induce Shmerling syndrome, a neurodegenerative disease that is suppressed by co-expression of wild-type PrPC. K27 may represent an actionable target for compounds aimed at preventing prion-related neurodegeneration.

neuroscience↗

bioRxiv2021

Climate and genetic diversity change in mammals during the Late Quaternary

Conservation decisions and future scenarios are in need of past baselines on climate change impacts in biodiversity. Although we know that climate change has contributed to diversity shifts in some mammals1,2,3,4,5,6,7, previous research often assumed that climate change is invariable across species ranges. We are therefore still ignorant of the true rates of climate change experienced by species assemblages over the last millennia, their impacts on intraspecific diversity, and how they compare to future climate change projections. Here, we use more than 9,000 Late Quaternary records, including fossils and ancient and modern DNA sequences, millennial-scale paleoclimatic reconstructions over the last 50,000 years and future climate change projections to document rates of climate change velocity and dynamics in genetic diversity experienced by an assemblage of 16 extinct and extant Holarctic mammal species. Extinct megafauna experienced velocities more than 15 times faster than the extant species, up to 15.2 km per decade. Notably, extant large-bodied grazers lost almost a 65% of their pool of genetic diversity since the Late Pleistocene, which indicates reduced ability to adapt to on-going global change. Additionally, mammal species experienced overall climate change velocities slower than that projected for the end of the 21st century but punctuated by comparable fast climate change episodes. Our results provide baselines on the impacts of ongoing and future climate change on the diversity of mammal species.

ecology↗

bioRxiv2020

Strain-dependent modifier genes determine survival in Zfp423 mice

Zfp423 encodes a transcriptional regulatory protein that interacts with canonical signaling and lineage pathways. Mutations in mouse Zfp423 or its human ortholog ZNF423 are associated with a range of developmental abnormalities reminiscent of ciliopathies, including cerebellar vermis hypoplasia and other midline brain defects. Null mice have reduced viability in most strain backgrounds. Here we show complete lethality on a C57BL/6J background, dominant rescue in backcrosses to any of 13 partner strains, with strain-dependent survival frequencies, and evidence for a BALB/c-derived survival modifier locus on chromosome 5. Survival data indicate both perinatal and postnatal periods of lethality. Anatomical data from a hypomorphic gene trap allele observed on both C57BL/6J and BALB/c congenic backgrounds shows an aggregate effect of background on sensitivity to Zfp423 loss rather than a binary effect on viability.

genetics↗