Biology subjects

Pease, J. B.

Publications and source records attributed to Pease, J. B..

6 recordsLinked to original sources

bioRxiv2025

Repeated evolutionary turnover of vertebrate skeletal muscle myosins

Myosin heavy chain proteins are essential for muscle contraction and nearly every physiological function in animals, but their diversity and evolution outside mammals is largely unknown. We comprehensively model the evolutionary history of over 1100 heavy-chain myosins. We find that skeletal muscle myosins are located in a conserved tandem gene array in all vertebrate species, but repeated gene duplication-loss turnover has surprisingly led to an independently evolved set of core skeletal muscle myosins in each major vertebrate group. Despite these separate derivations of these myosin subfamilies, each major vertebrate group exhibits consistent tissue-specific patterns of subfamily expression and specialized myosin subfamily expression in extreme muscles. Our results show that muscle evolution across vertebrates is not based in conserved orthologous motor myosins, as might be expected for such a core structural protein family. Instead, we find that skeletal muscle myosins have evolved as a shifting cluster of genes that is constantly changing and diversifying to balance the need to maintain core physiology, while innovating new physiological possibilities.

genomics↗

bioRxiv2025

Upslope diversification and gene flow among congeneric Andean trees

O_LIHybridization and introgression are increasingly recognized as important in plant evolution, yet their prevalence and consequences remain poorly understood in tropical Andean trees, where species coexist at low densities and turn over rapidly across elevation gradients. C_LIO_LIHere, we investigate whether species boundaries are maintained among congeneric Andean Prunus distributed across the Andes-Amazon elevational gradient by reconstructing phylogenetic relationships, divergence times, and patterns of historical and recent gene flow. C_LIO_LIWe find that Andean Prunus diversified during the Miocene, likely in response to novel habitat opportunities resulting from mountain uplift, combined with allopatric processes. Despite this evolutionary divergence, these species show extensive ancient introgression and recent admixture, indicating that species boundaries remain permeable across both ecological and phylogenetic distance. C_LIO_LITogether, these results suggest that Andean Prunus comprise distinct but evolutionarily connected lineages that retain morphological identity while potentially functioning as a long-lived syngameon, with implications for understanding the origin and maintenance of tropical tree diversity and future response to global change. C_LI

evolutionary biology↗

bioRxiv2025

Longevity in plants impacts phylogenetic and population dynamics

Many long-lived plant species exhibit notable patterns in phylogenies, such as short molecular branch lengths and high gene-tree conflict. However, it is not clear what biological properties of long-lived plant species or concomitant processes acting within these lineages generate these patterns. To explore this mystery, we implemented an agent-based model and conducted simulations to investigate how longevity affects molecular evolution and population dynamics. Through these simulations, we demonstrated that the patterns exhibited in empirical datasets for long-lived species can be explained by their lifespan and overlapping generations. We also show that somatic mutations can exacerbate these patterns, although evidence for substantive rates in empirical systems high enough to impact phylogenetic patterns is scarce. We discuss several empirical datasets containing life history shifts that exhibit diverse phylogenomic patterns. The variation produced through different parameterizations of our simulations reflects the diversity of patterns found in empirical datasets. Our results have broad implications for phylogenomic patterns and population genetics in general, as well as for specifically explaining patterns of evolution in long-lived lineages.

evolutionary biology↗

bioRxiv2024

Enhanced pollen tube performance at high temperature contributes to thermotolerant fruit production in tomato.

Rising temperature extremes during critical reproductive periods threaten the yield of major grain and fruit crops. Flowering plant reproduction depends on development of sufficient numbers of pollen grains and on their ability to generate a cellular extension, the pollen tube, which elongates through the pistil to deliver sperm cells to female gametes for double fertilization. These critical phases of the life cycle are sensitive to temperature and limit productivity under high temperature (HT). Previous studies have investigated the effects of HT on pollen development, but little is known about how HT applied during the pollen tube growth phase affects fertility. Here, we used tomato as a model fruit crop to determine how HT affects the pollen tube growth phase, taking advantage of cultivars noted for fruit production in exceptionally hot growing seasons. We found that exposure to HT solely during the pollen tube growth phase limits fruit biomass and seed set more significantly in thermosensitive cultivars than in thermotolerant cultivars. Importantly, we found that pollen tubes from the thermotolerant Tamaulipas cultivar have enhanced growth in vivo and in vitro under HT. Analysis of the pollen tube transcriptomes response to HT allowed us to develop hypotheses for the molecular basis of cellular thermotolerance in the pollen tube and we define two response modes (enhanced induction of stress responses, and higher basal levels of growth pathways repressed by heat stress) associated with reproductive thermotolerance. Importantly, we define key components of the pollen tube stress response identifying enhanced ROS homeostasis and pollen tube callose synthesis and deposition as important components of reproductive thermotolerance in Tamaulipas. Our work identifies the pollen tube growth phase as a viable target to enhance reproductive thermotolerance and delineates key pathways that are altered in crop varieties capable of fruiting under HT conditions. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=95 SRC="FIGDIR/small/606234v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@25e5acorg.highwire.dtl.DTLVardef@98fb1org.highwire.dtl.DTLVardef@1b8b9cborg.highwire.dtl.DTLVardef@adcca4_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

bioRxiv2023

Flavonols improve thermotolerance in tomato pollen during germination and tube elongation by maintaining ROS homeostasis

Elevated temperatures impair pollen performance and reproductive success, resulting in lower crop yields. The Solanum lycopersicum anthocyanin reduced (are) mutant has a FLAVANONE 3 HYDROXYLASE (F3H) gene mutation resulting in impaired synthesis of flavonol antioxidants. The are mutant has reduced pollen performance and seed set relative to the VF36 parental line, which is accentuated at elevated temperatures. Transformation of are with the wild-type F3H gene, or chemical complementation with flavonols, prevented temperature-dependent ROS accumulation in pollen and reversed ares reduced viability, germination, and tube elongation to VF36 levels. VF36 transformed with an F3H overexpression construct prevented temperature driven ROS increases and impaired pollen performance, revealing thermotolerance results from elevated flavonol synthesis. Although stigmas of are had reduced flavonols and elevated ROS, the growth of are pollen tubes were similarly impaired in both are and VF36 pistils. RNA-Seq was performed at optimal and stress temperatures in are, VF36, and the VF36 F3H overexpression line at multiple timepoints across pollen tube elongation. Differentially expressed gene numbers increased with duration of elevated temperature in all genotypes, with the largest number in are. These findings suggest potential agricultural interventions to combat the negative effects of heat-induced ROS in pollen that leads to reproductive failure. One sentence summaryFlavonol antioxidants reduce the negative impacts of elevated temperatures on pollen performance by reducing levels of heat induced reactive oxygen species and modulation of heat-induced changes in the pollen transcriptome.

plant biology↗

bioRxiv2017

Quartet Sampling distinguishes lack of support from conflicting support \newline in the plant tree of life

Premise of the StudyPhylogenetic support has been difficult to evaluate within the plant tree of life partly due to the difficulty of distinguishing conflicted versus poorly informed branches. As datasets continue to expand in both breadth and depth, new support measures are needed that are more efficient and informative.\n\nMethodsWe describe the Quartet Sampling (QS) method, a quartet-based evaluation system that synthesizes several phylogenetic and genomic analytical approaches. QS characterizes discordance in large-sparse and genome-wide datasets, overcoming issues of alignment sparsity and distinguishing strong conflict from weak support. We test QS with simulations and recent plant phylogenies inferred from variously sized datasets.\n\nKey ResultsQS scores demonstrate convergence with increasing replicates and are not strongly affected by branch depth. Patterns of QS support from different phylogenies leads to a coherent understanding of ancestral branches defining key disagreements, including the relationships of Ginkgo to cycads, magnoliids to monocots and eudicots, and mosses to liverworts. The relationships of ANA grade angiosperms, major monocot groups, bryophytes, and fern families are likely highly discordant in their evolutionary histories, rather than poorly informed. QS can also detect discordance due to introgression in phylogenomic data.\n\nConclusionsThe QS method represents an efficient and effective synthesis of phylogenetic tests that offer more comprehensive and specific information on branch support than conventional measures. The QS method corroborates growing evidence that phylogenomic investigations that incorporate discordance testing are warranted to reconstruct the complex evolutionary histories surrounding in particular ANA grade angiosperms, monocots, and non-vascular plants.

evolutionary biology↗