Biology subjects

Pennington, T.

Publications and source records attributed to Pennington, T..

10 recordsLinked to original sources

bioRxiv2025

Brazil Seed Transfer Zones: Supporting Seed Sourcing for Climate-Resilient Ecosystem Restoration

O_LIEcosystem restoration is key to jointly address the biodiversity, climate, and social inequality crises. In Brazil, large-scale seed-based restoration is gaining momentum, but a national framework to match seed sources with planting sites is still lacking, undermining long-term success. C_LIO_LIWe developed the first Seed Transfer Zones (STZs) for Brazil using 25 environmental variables. We assessed restoration supply and demand within each STZ and projected the zones into the future under contrasting climate change scenarios. C_LIO_LIWe identified 48 STZs, distributed across Brazils six major vegetation regions (Amazon, Cerrado, Atlantic Forest, Caatinga, Pantanal, and Pampa). Overlaying the STZs with data on seed collection capacity and restoration opportunities revealed priority regions where seed supply is unlikely to meet demand (e.g., Cerrado). Future climate projections also indicate substantial reshaping of STZs, with 51-88% of Brazils land area expected to experience mismatches between current and future seed zones. C_LIO_LIThe creation of Brazils first STZs provides a scalable framework to guide seed sourcing for restoration, aligning supply with demand, and future-proofing projects to deliver lasting benefits for biodiversity, climate, and society. C_LI Societal Impact StatementTens of millions of hectares of degraded land in Brazil are in need of ecosystem restoration to achieve national and global biodiversity and climate goals. Sowing genetically diverse native seeds is key to restoring degraded lands to climate-resilient landscapes, but we still lack guidance on how to effectively match seed sources to restoration sites across broad geographic scales, within the context of a changing climate. We addressed this by identifying 48 Seed Transfer Zones (STZs) based on current and expected future climatic conditions. These zones will help ensure that the right seeds are used in the right places, enabling more effective and climate-smart restoration for nature and people.

ecology↗

bioRxiv2025

Thresholds of drought and terrain complexity shape biomasspatterns in South America's Caatinga

Seasonally Tropical Dry Forests (STDFs) are widespread throughout the world and store significant amounts of carbon; however, they are often overlooked in spatial assessments compared to humid tropical forests. The Caatinga, which is the largest seasonally dry tropical forest in South America, covers approximately 862,000 km{superscript 2} in northeastern Brazil and supports millions of people. Unfortunately, its carbon dynamics has not been thoroughly quantified, especially after centuries of land-use transformation and wood extraction that have significantly diminished its biomass stocks. In this study, we model the potential aboveground biomass (AGB) that Caatinga could sustain under current climatic, atmospheric, and topographic conditions. We integrated data from 301 geo-referenced plots along with high-resolution environmental predictors. The principal Component Analysis revealed two main gradients: a hydro-thermal axis dominated by precipitation, temperature, and severity of drought, and a topographic axis reflecting slope, ruggedness, and terrain position. Random Forest models, validated through both random and spatial cross-validation, explained a significant amount of variation in AGB (R{superscript 2} = 0.81, RMSE = 21 Mg ha). Our findings indicated that AGB is highly sensitive to water availability. In particular, biomass increased sharply when the maximum cumulative water deficit (MCWD) was less than -500 mm and annual rainfall exceeded approximately 1,100 mm. In contrast, elevated vapour pressure deficit (VPD) and potential evapotranspiration (PET) were associated with reduced carbon storage. Topographic heterogeneity further influenced AGB, with rugged and concave terrains supporting potential biomass levels more than twice as high as those found in flat, convex areas. Our predictive map reveals a mosaic of low-biomass cores and localized high-biomass refugia, highlighting the dual influence of hydroclimatic and topographic factors. These findings reposition Caatinga as a heterogeneous and dynamic potential carbon reservoir - historically degraded by changes in land-use but still capable of storing substantial carbon. This research offers critical insights for the restoration, conservation and mitigation efforts for climate change in tropical drylands worldwide.

ecology↗

bioRxiv2025

A Non-canonical Role for Hepatocyte MLKL in Promoting Mitochondrial Dysfunction and Senescence in the Aging Liver

Liver aging is characterized by chronic inflammation and metabolic dysfunction that contributes to the progression of metabolic dysfunction-associated steatotic liver disease (MASLD). Necroptosis, a form of inflammatory cell death, is activated in aging livers, and genetic (Ripk3-/-or Mlkl-/- mice) or pharmacological (RIPK1 inhibitor necrostatin-1s) inhibition of necroptosis attenuates liver inflammation and pathology. However, the cell type-specific role of necroptosis in liver aging remains unclear. Given that MLKL is expressed in hepatocytes, and its expression increases with age, we generated hepatocyte-specific MLKL-overexpressing mice (MLKLHepOE) to determine its role in liver aging. Unexpectedly, MLKL overexpression in hepatocytes did not induce necroptosis, but instead upregulated markers of cellular senescence (cell cycle arrest genes and SASP factors), increased macrophage infiltration, and elevated M1 macrophage marker expression. Electron microscopy and mitochondrial analyses revealed abnormal mitochondrial morphology, elevated oxidative stress, and disrupted mitochondrial dynamics, while lipidomics demonstrated alterations in hepatic lipid metabolites. In agreement with our observations in MLKLHepOE mice, MLKL overexpression in AML12 hepatocytes impaired mitochondrial respiration, increased proinflammatory extracellular vesicle (EV) release, and induced senescence markers, without triggering cell death. Together, these findings reveal a non-lethal, non-necroptotic role for MLKL in promoting hepatocyte senescence and metabolic dysfunction via mitochondrial impairment and EV-mediated inflammation. Our study highlights MLKL as a novel driver of liver inflammaging and a potential therapeutic target for age-related liver disease.

cell biology↗

bioRxiv2025

Fis1 is required for the development of the dendritic mitochondrial network in pyramidal cortical neurons

Mitochondrial ATP production and calcium buffering are critical for metabolic regulation and neurotransmission making the formation and maintenance of the mitochondrial network a critical component of neuronal health. Cortical pyramidal neurons contain compartment-specific mitochondrial morphologies that result from distinct axonal and dendritic mitochondrial fission and fusion profiles. We previously showed that axonal mitochondria are maintained at a small size as a result of high axonal mitochondrial fission factor (Mff) activity. However, loss of Mff activity had little effect on cortical dendritic mitochondria, raising the question of how fission/fusion balance is controlled in the dendrites. Thus, we sought to investigate the role of another fission factor, fission 1 (Fis1), on mitochondrial morphology, dynamics and function in cortical neurons. We knocked down Fis1 in cortical neurons both in primary culture and in vivo, and unexpectedly found that Fis1 depletion decreased mitochondrial length in the dendrites, without affecting mitochondrial size in the axon. Further, loss of Fis1 activity resulted in both increased mitochondrial motility and dynamics in the dendrites. These results argue Fis1 exhibits dendrite selectivity and plays a more complex role in neuronal mitochondrial dynamics than previously reported. Functionally, Fis1 loss resulted in reduced mitochondrial membrane potential, increased sensitivity to complex III blockade, and decreased mitochondrial calcium uptake during neuronal activity. The altered mitochondrial network culminated in elevated resting calcium levels that increased dendritic branching but reduced spine density. We conclude that Fis1 regulates morphological and functional mitochondrial characteristics that influence dendritic tree arborization and connectivity.

cell biology↗

bioRxiv2023

Do Reticulate Relationships Between Tropical Trees Drive Diversification? Insights from Inga (Fabaceae)

Evolutionary radiations underlie much of the species diversity of life on Earth, particularly within the worlds most species-rich tree flora - that of the Amazon rainforest. Hybridisation occurs in many radiations, with effects ranging from homogenisation of species to generation of genetic and phenotypic novelty that fuels speciation, but the influence of hybridisation on Amazonian tree radiations has been little studied. We address this using the ubiquitous, species-rich, neotropical tree genus Inga, which typifies rapid radiations of rainforest trees. We assess patterns of gene tree incongruence to ascertain whether hybridisation was associated with rapid radiation in Inga. Given the importance of insect herbivory in structuring rainforest tree communities (and hence the potential for hybridisation to promote adaptation through admixture of defence traits), we also test whether introgression of loci underlying chemical defences against herbivory occurred during the radiation of Inga. Our phylogenomic analyses of 189/288 Inga species using >1300 target capture loci showed widespread introgression in Inga. Specifically, we found widespread phylogenetic incongruence explained by introgression, with phylogenetic networks recovering multiple introgression events across Inga and up to 20% of shared, likely introgressed, genetic variation between some species. In addition, most defence chemistry loci showed evidence of positive selection and marginally higher levels of introgression. Overall, our results suggest that introgression has occurred widely over the course of Ingas history, likely facilitated by extensive dispersal across Amazonia, and that in some cases introgression of chemical defence loci may influence adaptation in Inga.

evolutionary biology↗

bioRxiv2022

Spinophilin limits metabotropic glutamate receptor 5 scaffolding to the postsynaptic density and cell type-specifically mediates excessive grooming

BackgroundConstitutive knockout of the obsessive-compulsive disorder-associated protein, disks large associated protein 3 (SAPAP3), results in repetitive motor dysfunction, such as excessive grooming, caused by increased metabotropic glutamate receptor 5 (mGluR5) activity in striatal direct- and indirect pathway medium spiny neurons (dMSNs and iMSNs, respectively). However, MSN subtype-specific signaling mechanisms that mediate mGluR5-dependent adaptations underlying excessive grooming are not fully understood. Here, we investigate the MSN subtype-specific roles of the striatal signaling hub protein, spinophilin, in mediating repetitive motor dysfunction associated with mGluR5 function. MethodsQuantitative proteomics and immunoblotting were utilized to identify how spinophilin impacts mGluR5 phosphorylation and protein interaction changes. Plasticity and repetitive motor dysfunction associated with mGluR5 action was measured using our novel conditional spinophilin mouse model that had spinophilin knocked out from striatal dMSNs or/and iMSNs. ResultsLoss of spinophilin only in iMSNs decreased performance of a novel motor repertoire, but loss of spinophilin in either MSN subtype abrogated striatal plasticity associated with mGluR5 function and prevented excessive grooming caused by SAPAP3 knockout mice and treatment with the mGluR5-specific positive allosteric modulator (VU0360172) without impacting locomotion-relevant behavior. Biochemically, we determined spinophilins protein interaction correlates with grooming behavior and loss of spinophilin shifts mGluR5 interactions from lipid-raft associated proteins toward postsynaptic density (PSD) proteins implicated in psychiatric disorders. ConclusionsThese results identify spinophilin as a novel striatal signaling hub molecule in MSNs that cell subtype-specifically mediates behavioral, functional, and molecular adaptations associated with repetitive motor dysfunction in psychiatric disorders.

neuroscience↗

bioRxiv2022

Anterior insular cortex inputs to the dorsolateral striatum govern the maintenance of binge alcohol drinking

How does binge drinking alcohol change synaptic function, and do these changes maintain binge consumption? The anterior insular cortex (AIC) and dorsolateral striatum (DLS) are brain regions implicated in alcohol use disorder. In mice, we found that binge drinking alcohol produced glutamatergic synaptic adaptations selective to AIC inputs within the DLS. Photoexciting AIC[->]DLS circuitry during binge drinking decreased alcohol, but not water consumption and altered alcohol drinking mechanics. Further, drinking mechanics alone from drinking session data predicted alcohol-related circuit changes. AIC[->]DLS manipulation did not alter operant, valence, or anxiety-related behaviors. These findings suggest that alcohol-mediated changes at AIC inputs govern behavioral sequences that maintain binge drinking and may serve as a circuit-based biomarker for the development of alcohol use disorder.

neuroscience↗

bioRxiv2019

Introgression in Brownea suggests that reticulate evolution contributes to Amazonian tree diversity

Hybridization has the potential to generate or homogenize biodiversity and is a particularly common phenomenon in plants, with an estimated 25% of species undergoing inter-specific gene flow. However, hybridization in Amazonias megadiverse tree flora was assumed to be extremely rare despite extensive sympatry between closely related species, and its role in diversification remains enigmatic because it has not yet been examined empirically. Using members of a dominant Amazonian tree family (Brownea, Fabaceae) as a model to address this knowledge gap, our study recovered extensive evidence of hybridization among multiple lineages across phylogenetic scales. More specifically, our results uncovered several historical introgression events between Brownea lineages and indicated that gene tree incongruence in Brownea is best explained by introgression, rather than solely by incomplete lineage sorting. Furthermore, investigation of recent hybridization using [~]19,000 ddRAD loci recovered a high degree of shared variation between two Brownea species which co-occur in the Ecuadorian Amazon. Our analyses also showed that these sympatric lineages exhibit homogeneous rates of introgression among loci relative to the genome-wide average, implying a lack of selection against hybrid genotypes and a persistence of hybridization over time. Our results demonstrate that gene flow between multiple Amazonian tree species has occurred across temporal scales, and contrasts with the prevailing view of hybridizations rarity in Amazonia. Overall, our results provide novel evidence that reticulate evolution influenced diversification in part of the Amazonian tree flora, which is the most diverse on Earth.

evolutionary biology↗

bioRxiv2019

Freezing and water availability structure the evolutionary diversity of trees across the Americas

The historical course of evolutionary diversification shapes the current distribution of biodiversity, but the main forces constraining diversification are unclear. We unveil the evolutionary structure of tree species diversity across the Americas to assess whether an inability to move (dispersal limitation) or to evolve (niche conservatism) is the predominant constraint in plant diversification and biogeography. We find a fundamental divide in tree lineage composition between tropical and extratropical environments, defined by the absence versus presence of freezing temperatures. Within the Neotropics, we uncover a further evolutionary split between moist and dry forests. Our results demonstrate that American tree lineages, though broadly distributed geographically, tend to retain their ancestral environmental relationships and that phylogenetic niche conservatism is the primary force structuring the distribution of tree biodiversity.

ecology↗

bioRxiv2019

The Origin and Early Evolution of the Legumes are a Complex Paleopolyploid Phylogenomic Tangle closely associated with the Cretaceous-Paleogene (K-Pg) Boundary

The consequences of the Cretaceous-Paleogene (K-Pg) boundary (KPB) mass extinction for the evolution of plant diversity are poorly understood, even although evolutionary turnover of plant lineages at the KPB is central to understanding the assembly of the Cenozoic biota. One aspect that has received considerable attention is the apparent concentration of whole genome duplication (WGD) events around the KPB, which may have played a role in survival and subsequent diversification of plant lineages. In order to gain new insights into the origins of Cenozoic biodiversity, we examine the origin and early evolution of the legume family, one of the most important angiosperm clades that rose to prominence after the KPB and for which multiple WGD events are found to have occurred early in its evolution. The legume family (Leguminosae or Fabaceae), with c. 20.000 species, is the third largest family of Angiospermae, and is globally widespread and second only to the grasses (Poaceae) in economic importance. Accordingly, it has been intensively studied in botanical, systematic and agronomic research, but a robust phylogenetic framework and timescale for legume evolution based on large-scale genomic sequence data is lacking, and key questions about the origin and early evolution of the family remain unresolved. We extend previous phylogenetic knowledge to gain insights into the early evolution of the family, analysing an alignment of 72 protein-coding chloroplast genes and a large set of nuclear genomic sequence data, sampling thousands of genes. We use a concatenation approach with heterogeneous models of sequence evolution to minimize inference artefacts, and evaluate support and conflict among individual nuclear gene trees with internode certainty calculations, a multi-species coalescent method, and phylogenetic supernetwork reconstruction. Using a set of 20 fossil calibrations we estimate a revised timeline of legume evolution based on a selection of genes that are both informative and evolving in an approximately clock-like fashion. We find that the root of the family is particularly difficult to resolve, with strong conflict among gene trees suggesting incomplete lineage sorting and/or reticulation. Mapping of duplications in gene family trees suggest that a WGD event occurred along the stem of the family and is shared by all legumes, with additional nested WGDs subtending subfamilies Papilionoideae and Detarioideae. We propose that the difficulty of resolving the root of the family is caused by a combination of ancient polyploidy and an alternation of long and very short internodes, shaped respectively by extinction and rapid divergence. Our results show that the crown age of the legumes dates back to the Maastrichtian or Paleocene and suggests that it is most likely close to the KPB. We conclude that the origin and early evolution of the legumes followed a complex history, in which multiple nested polyploidy events coupled with rapid diversification are associated with the mass extinction event at the KPB, ultimately underpinning the evolutionary success of the Leguminosae in the Cenozoic.

evolutionary biology↗