Biology subjects

Tseng, J.

Publications and source records attributed to Tseng, J..

8 recordsLinked to original sources

bioRxiv2026

Global adaptation to climate change in the twilight zone revealed by shared signals of selection in mesopelagic lanternfishes

Rapid accumulation of greenhouse gases threatens humanity and global diversity. The oceans absorb 30% of anthropogenic carbon emissions annually, but adaptation to climate change by the biotic components of this sink are poorly understood. Lanternfishes (Myctophiformes) are the most abundant vertebrates on the planet by biomass and the dominant mesopelagic vertebrate consumers, thus crucial components of the global carbon cycle. However, it is unknown whether lanternfishes are adapting to global warming and ocean acidification (OA). We hypothesized that warming and OA would act as major shared selective forces across diverse oceanic environments and that disparate taxa would respond in parallel through shared genetic pathways. We used whole-genome sequencing to test this hypothesis by identifying shared signals of selection across lanternfishes from multiple sites in the Atlantic and Pacific spanning three genera (Benthosema glaciale, Triphoturus mexicanus, and Diaphus theta). Across all species we found evidence of expansion from a population bottleneck possibly corresponding to the last glacial maximum and effective population sizes of only 5 million, suggesting substantial reproductive skew and spatially restricted populations. We successfully identified 34 candidate genes experiencing strong shared selection pressure across all taxa in both oceans. 81% of these candidate genes were consistent with adaptations to warming and OA, including a heat-shock protein (HSP70) and genes related to skeletal development, calcium homeostasis, and biomineralization. 14 out of 34 candidate genes are also known from experimental climate change studies to be involved in the response to hypoxia, altered pH, and thermal stress. We found significant gene ontology enrichment within these candidates for otolith morphogenesis, a major component of OA adaptation in fishes. This study provides a new approach for studying climate change adaptation at a global scale and our results imply widespread shared adaptive responses of marine species to climate change.

evolutionary biology↗

bioRxiv2025

Long-fuse evolution of carnivoran skeletal phenomes through the Cenozoic

Climatic change is hypothesized to promote phenotypic diversification. While neontological analyses are often used to test this hypothesis, extant data only captures time-averaged signals of surviving lineages. More nuanced tests require paired and longitudinal climatic and organismal data. Here, we developed the most comprehensive phenomic dataset to-date of pan-carnivorans to test hypotheses that Cenozoic climatic change influenced the evolution of the cranial, appendicular, and axial skeleton. We found support for the hypothesis that a hierarchical progression of ecological diversification across the Cenozoic significantly influenced the establishment of modern carnivorans. Specifically, extinctions during the Eocene-Oligocene Transition released crown carnivorans from a constrained adaptive zone to interfamilial skeletal diversification. Intrafamilial skeletal diversification did not occur for another 20 million years until after the Mid-Miocene Climate Transition. Our work demonstrates the essential role of macroevolutionary data from the fossil record for revealing how major global climatic events steered the evolutionary trajectories of modern skeletal phenomes.

evolutionary biology↗

bioRxiv2024

The carnivoran adaptive landscape reveals trade-offs among functional traits in the skull, appendicular, and axial skeleton

Analyses of form-function relationships are widely used to understand links between morphology, ecology, and adaptation across macroevolutionary scales. However, few have investigated functional trade-offs and covariance within and between the skull, limbs, and vertebral column simultaneously. In this study, we investigated the adaptive landscape of skeletal form and function in carnivorans to test how functional trade-offs between these skeletal regions contribute to ecological adaptations and the topology of the landscape. We found that morphological proxies of function derived from carnivoran skeletal regions exhibit trade-offs and covariation across their performance surfaces, particularly in the appendicular and axial skeletons. These functional trade-offs and covariation correspond as adaptations to different adaptive landscapes when optimized by various factors including phylogeny, dietary ecology, and, in particular, locomotor mode. Lastly, we found that the topologies of the optimized adaptive landscapes and underlying performance surfaces are largely characterized as a single gradual gradient rather than as rugged, multipeak landscapes with distinct zones. Our results suggest that carnivorans may already occupy a broad adaptive zone as part of a larger mammalian adaptive landscape that masks the form and function relationships of skeletal traits.

evolutionary biology↗

bioRxiv2023

Uncovering the mosaic evolution of carnivoran skeletal systems

The diversity of vertebrate skeletons is often attributed to adaptations to distinct ecological factors such as diet, locomotion, and sensory environment. Although the adaptive evolution of skull, appendicular skeleton, and vertebral column is well studied in vertebrates, comprehensive investigations of all skeletal components simultaneously are rarely performed. Consequently, we know little of how modes of evolution differ among skeletal components. Here, we tested if ecological and phylogenetic effects led to distinct modes of evolution among the cranial, appendicular, and vertebral regions in extant carnivoran skeletons. Using multivariate evolutionary models, we found mosaic evolution in which only the mandible, hindlimb, and posterior (i.e., last thoracic and lumbar) vertebrae showed evidence of adaptation towards ecological regimes whereas the remaining skeletal components reflect clade-specific evolutionary shifts. We hypothesize that the decoupled evolution of individual skeletal components may have led to the origination of distinct adaptive zones and morphologies among extant carnivoran families that reflect phylogenetic hierarchies. Overall, our work highlights the importance of examining multiple skeletal components simultaneously in ecomorphological analyses. Ongoing work integrating the fossil and paleoenvironmental record will further clarify deep-time drivers that govern carnivoran diversity we see today and reveal the complexity of evolutionary processes in multicomponent systems.

evolutionary biology↗

bioRxiv2022

A switch in jaw form-function coupling during the evolution of mammals

The evolutionary shift from a single-element ear, multi-element jaw to a multi-element ear, single-element jaw during the transition to crown mammals marks one of the most dramatic structural transformations in vertebrates. Research on this transformation has focused on mammalian middle-ear evolution, but a mandible comprised of only the dentary is equally emblematic of this evolutionary radiation. Here we show that the remarkably diverse jaw shapes of crown mammals are coupled with surprisingly stereotyped jaw stiffness. This strength-based morphofunctional regime has a genetic basis and allowed mammalian jaws to effectively resist deformation as they radiated into highly disparate forms with markedly distinct diets. The main functional consequences for the mandible of decoupling hearing and mastication were a trade-off between higher jaw stiffness versus decreased mechanical efficiency and speed compared to non-mammals. This fundamental and consequential shift in jaw form-function underpins the ecological and taxonomic diversification of crown mammals.

evolutionary biology↗

bioRxiv2022

Endogenous Rab38 regulates LRRK2's membrane recruitment and substrate Rab phosphorylation in melanocytes

Point mutations in LRRK2 cause Parkinsons Disease and augment LRRK2s kinase activity. However, cellular pathways that enhance LRRK2 kinase function have not been identified. While overexpressed Rab29 draws LRRK2 to Golgi membranes to increase LRRK2 kinase activity, there is little evidence that endogenous Rab29 performs this function under physiological conditions. Here we identify Rab38 as a novel physiological regulator of LRRK2. In mouse melanocytes, which express high levels of Rab38, Rab32, and Rab29, knockdown of Rab38 but not Rab32 or Rab29 decreases phosphorylation of multiple LRRK2 substrates, including Rab10 and Rab12, by both exogenous and endogenous LRRK2. In B16-F10 mouse melanoma cells, Rab38 drives LRRK2 membrane association, and overexpressed kinase-active but not kinase-inactive LRRK2 shows striking pericentriolar recruitment, which is dependent on the presence of endogenous Rab38 but not Rab32 or Rab29. Deletion or mutation of LRRK2 at the Rab38 binding site in the N-terminal armadillo domain decreases LRRK2 membrane association, pericentriolar recruitment, and ability to phosphorylate Rab10. Consistently, overexpression of LRRK2350-550, a fragment that encompasses the Rab38 binding site, blocks endogenous LRRK2s phosphorylation of Thr73-Rab10. Finally, disruption of BLOC-3, the guanine nucleotide exchange factor for Rab38 and 32, inhibits Rab38s regulation of LRRK2. In sum, our data identify Rab38 as a physiologic regulator of LRRK2 function and lend support to a model in which LRRK2 plays a central role in Rab GTPase coordination of vesicular trafficking.

cell biology↗

bioRxiv2021

The Human Tumor Atlas Network (HTAN) Breast PreCancer Atlas: A multi-omic integrative analysis of ductal carcinoma in situ with clinical outcomes

Ductal carcinoma in situ (DCIS) is the most common precursor of invasive breast cancer (IBC), with variable propensity for progression. We have performed the first multiscale, integrated profiling of DCIS with clinical outcomes by analyzing 677 DCIS samples from 481 patients with 7.1 years median follow-up from the Translational Breast Cancer Research Consortium (TBCRC) 038 study and the Resource of Archival Breast Tissue (RAHBT) cohorts. We identified 812 genes associated with ipsilateral recurrence within 5 years from treatment and developed a classifier that was predictive of DCIS or IBC recurrence in both cohorts. Pathways associated with recurrence include proliferation, immune response, and metabolism. Distinct stromal expression patterns and immune cell compositions were identified. Our multiscale approach employed in situ methods to generate a spatially resolved atlas of breast precancers, where complementary modalities can be directly compared and correlated with conventional pathology findings, disease states, and clinical outcome. HIGHLIGHTS Development of a new classifier for DCIS recurrence or progression Outcome associated pathways identified across multiple data types and compartments Four stroma-specific signatures identified CNAs characterize DCIS subgroups associated with high risk invasive cancers

cancer biology↗

bioRxiv2019

Brain meta-state transitions demarcate spontaneous thoughts in movie-viewing and resting cognition

Using new methods to capture streams of neural meta-state transitions in single participants, we characterize the psychological meaning of these regular neural events. Similar to past group-average-based analyses, participants individual transition streams aligned to meaningful events during movie-viewing. However, our individual-based approach also afforded observation of participants idiosyncratic transition timing at rest. Across these two dramatically different task contexts, transitions featured similar trait-like frequency, concurrence with activation of regions associated with spontaneous thought, and suppression by attention regions. Based on this generalization, as well as the centrality of semantics to thought, we argue transitions serve as a general, implicit neurobiological marker of new thoughts, and that their frequency therefore approximates participants mentation rate. Finally, to contribute convergent validity and illustrate the utility of our approach for thought dynamics, we regressed resting transition rate and movie-viewing group temporal conformity against trait neuroticism, yielding a first neural confirmation of the \"mental noise\" theory.

neuroscience↗