Biology subjects

Pau, S.

Publications and source records attributed to Pau, S..

6 recordsLinked to original sources

bioRxiv2023

scRNA-seq reveals novel genetic pathways and sex chromosome regulation in Tribolium spermatogenesis

Insights into single cell expression data are generally collected through well conserved biological markers that separate cells into known and unknown populations. Unfortunately for non-model organisms that lack known markers, it is often impossible to partition cells into biologically relevant clusters which hinders analysis into the species. Tribolium castaneum, the red flour beetle, lacks known markers for spermatogenesis found in insect species like Drosophila melanogaster. Using single cell sequencing data collected from adult beetle testes, we implement a strategy for elucidating biologically meaningful cell populations by using transient expression stage identification markers, weighted principal component leiden clustering. We identify populations that correspond to observable points in sperm differentiation and find species specific markers for each stage. We also develop an innovative method to differentiate diploid from haploid cells based on scRNA-Seq reads and use it to corroborate our predicted demarcation of meiotic cell stages. Our results demonstrate that molecular pathways underlying spermatogenesis in Coleoptera are highly diverged from those in Diptera, relying on several genes with female meiotic pathway annotations. We find that the X chromosome is almost completely silenced throughout pre-meiotic and meiotic cells. Further evidence suggests that machinery homologous to the Drosophila dosage compensation complex (DCC) may mediate escape from meiotic sex chromosome inactivation and postmeiotic reactivation of the X chromosome.

molecular biology↗

bioRxiv2020

Long-read RNA sequencing reveals widespread sex-specific alternative splicing in threespine stickleback fish

Alternate isoforms contribute immensely to phenotypic diversity across eukaryotes. While short read RNA-sequencing has increased our understanding of isoform diversity, it is challenging to accurately detect full-length transcripts, preventing the identification of many alternate isoforms. Long-read sequencing technologies have made it possible to sequence full length alternative transcripts, accurately characterizing alternative splicing events, alternate transcription start and end sites, and differences in UTR regions. Here, we utilize PacBio long read RNA-sequencing (Iso-Seq) to examine the transcriptomes of five tissues in threespine stickleback fish (Gasterosteus aculeatus), a widely used genetic model species. The threespine stickleback fish has a refined genome assembly with gene annotations that are based on short-read RNA sequencing and predictions from coding sequence of other species. This suggests some of the existing annotations may be inaccurate or alternative transcripts may not be fully characterized. Using Iso-Seq we detected thousands of novel isoforms, indicating many isoforms are absent in the current Ensembl gene annotations. In addition, we refined many of the existing annotations within the genome. We noted many improperly positioned transcription start sites that were refined with long-read sequencing. The Iso-Seq predicted transcription start sites were more accurate, verified through ATAC-seq. We were also able to detect many alternative splicing events between sexes and across tissues. We found a substantial number of genes in both somatic and gonad tissue that had sex-specific isoforms. Our study highlights the power of long-read sequencing to study the complexity of transcriptomes, greatly improving genomic resources for the threespine stickleback fish.

genomics↗

bioRxiv2020

Lineage Functional Types (LFTs): Characterizing functional diversity to enhance the representation of ecological behavior in Earth System Models

Process-based vegetation models attempt to represent the wide range of trait variation in biomes by grouping ecologically similar species into plant functional types (PFTs). This approach has been successful in representing many aspects of plant physiology and biophysics, but struggles to capture biogeographic history and ecological dynamics that determine biome boundaries and plant distributions. Grass dominated ecosystems are broadly distributed across all vegetated continents and harbor large functional diversity, yet most Earth System Models (ESMs) summarize grasses into two generic PFTs based primarily on differences between temperate C3 grasses and (sub)tropical C4 grasses. Incorporation of species-level trait variation is an active area of research to enhance the ecological realism of PFTs, which form the basis for vegetation processes and dynamics in ESMs. Using reported measurements, we developed grass functional trait values (physiological, structural, biochemical, anatomical, phenological, and disturbance-related) of dominant lineages to improve ESM representations. Our method is fundamentally different from previous efforts, as it uses phylogenetic relatedness to create lineage-based functional types (LFTs), situated between species-level trait data and PFT-level abstractions, thus providing a realistic representation of functional diversity and opening the door to the development of new vegetation models.

ecology↗

bioRxiv2019

Climatic sensitivity of species’ vegetative and reproductive phenology in a Hawaiian montane wet forest

Understanding the way tropical tree phenology (i.e., the timing and amount of seed and leaf production) responds to climate is vital for predicting how climate change may alter ecological functioning of tropical forests. We examined the effects of temperature, rainfall, and photosynthetically active radiation (PAR) on seed and leaf phenology in a montane wet forest on Hawaii using monthly data collected over [~]6 years. We expected that species phenologies were more sensitive to temperature and PAR than to rainfall at this wet tropical site because rainfall is not limiting. Seed production declined with increasing temperatures for two foundational species in Hawaiian forests (Acacia koa and Metrosideros polymorpha). Seed production also declined with rainfall for two species, and greater PAR for one species. One species showed relatively flat responses to climate. Community-level leaf phenology was not strongly seasonal. Unlike seed phenology, we found no effect of temperature on leaf phenology. However, leaf fall increased with rainfall. Climatic factors explained a low to moderate proportion of variance for both seed and leaf litterfall, thus the impact of future climate change on this forest will depend on how climate change interacts with other factors such as daylength, biotic, and/or evolutionary constraints. Our results nonetheless provide insight into how climate change may differentially affect different species with potential consequences for shifts in species distributions and community composition.

ecology↗

bioRxiv2019

The impact of Hurricane Michael on longleaf pine habitats in Florida

The longleaf pine (Pinus palustris) ecosystem of the North American Coastal Plain (NACP) is a global biodiversity hotspot. Disturbances such as tropical storms play an integral role in ecosystem maintenance in these systems. However, altered disturbance regimes as a result of climate change may be outside the historical threshold of tolerance. Hurricane Michael impacted the Florida panhandle as a Category 5 storm on October 10th, 2018. In this study, we estimate the extent of Florida longleaf habitat that was directly impacted by Hurricane Michael. We then quantify the impact of Hurricane Michael on tree density and size structure using a Before-After study design at four sites (two wet flatwood and two upland pine communities). Finally, we identify the most common type of tree damage at each site and community type. We found that 39% of the total remaining extent of longleaf pine habitat was affected by the storm in Florida alone. Tree mortality ranged from 1.3% at the site furthest from the storm center to 88.7% at the site closest. Most of this mortality was in mature sized trees (92% mortality), upon which much of the biodiversity in this habitat depends. As the frequency and intensity of extreme events increases, management plans that mitigate for climate change impacts need to account for large-scale stochastic mortality events in order to effectively preserve critical habitats.

ecology↗

bioRxiv2019

Functional diversification enabled grassy biomes to fill global climate space

Global change impacts on the Earth System are typically evaluated using biome classifications based on trees and forests. However, during the Cenozoic, many terrestrial biomes were transformed through the displacement of trees and shrubs by grasses. While grasses comprise 3% of vascular plant species, they are responsible for more than 25% of terrestrial photosynthesis. Critically, grass dominance alters ecosystem dynamics and function by introducing new ecological processes, especially surface fires and grazing. However, the large grassy component of many global biomes is often neglected in their descriptions, thereby ignoring these important ecosystem processes. Furthermore, the functional diversity of grasses in vegetation models is usually reduced to C3 and C4 photosynthetic plant functional types, omitting other relevant traits. Here, we compile available data to determine the global distribution of grassy vegetation and key traits related to grass dominance. Grassy biomes (where > 50% of the ground layer is covered by grasses) occupy almost every part of Earths vegetated climate space, characterising over 40% of the land surface. Major evolutionary lineages of grasses have specialised in different environments, but species from only three grass lineages occupy 88% of the land area of grassy vegetation, segregating along gradients of temperature, rainfall and fire. The environment occupied by each lineage is associated with unique plant trait combinations, including C3 and C4 photosynthesis, maximum plant height, and adaptations to fire and aridity. There is no single global climatic limit where C4 grasses replace C3 grasses. Instead this ecological transition varies biogeographically, with continental disjunctions arising through contrasting evolutionary histories.\n\nSignificance statementWorldviews of vegetation generally focus on trees and forests but grasses characterize the ground layer over 40% of the Earths vegetated land surface. This omission is important because grasses transform surface-atmosphere exchanges, biodiversity and disturbance regimes. We looked beneath the trees to produce the first global map of grass-dominated biomes. Grassy biomes occur in virtually every climate on Earth. However, three lineages of grasses are much more successful than others, characterizing 88% of the land area of grassy biomes. Each of these grass lineages evolved ecological specializations related to aridity, freezing and fire. Recognizing the extent and causes of grass dominance beneath trees is important because grassy vegetation plays vital roles in the dynamics of our biosphere and human wellbeing.

ecology↗