Biology subjects

Moore, D. G.

Publications and source records attributed to Moore, D. G..

4 recordsLinked to original sources

bioRxiv2026

Genome-wide divergence in a desert plant in the Baja California Peninsula driven by glacial cycles and adaptation to different climatic conditions

The processes that generate distinct patterns of population subdivision (i.e., phylogeographic breaks) and facilitate local adaptations continue to be a focal point of evolutionary research. Here, we used whole-genome sequencing, demographic modeling, ecological niche modeling, and genotype-environment association analysis paired with outlier tests to understand patterns and drivers of diversification of the desert shrub Encelia farinosa in the Baja California Peninsula. We found that E. farinosa was represented by three moderately differentiated (0.027 < Fst < 0.068) genetically distinct groups, distributed across the North, Central and Southern regions of the Peninsula. Demographic analyses revealed fluctuations in the effective population sizes and two lineage divergence events, which coincided with the onset of recent glacial cycles. The ecological niche modeling recovered concordant southward shifts and decrease in the suitable habitat for all E. farinosa groups during the Last Glacial period. Analyses of associations between putative adaptive loci and environmental variables suggested that climate has been an important driver of adaptive genetic variation, with regional differentiation primarily associated with solar irradiation, temperature, and precipitation seasonality. We demonstrate that local adaptations in E. farinosa involve multiple genes associated with immune response, stress response, and morphological adaptations associated with arid climate such as leaf pubescence. Our findings indicate that current levels of differentiation and genetic variation in E. farinosa can be explained by the interplay of processes acting at multiple temporal scales, including isolation by distance, glaciation-mediated demographic processes, and recent natural selection shaping specific adaptations for each geographical group.

evolutionary biology↗

bioRxiv2025

Behavioral and phenotypic constraint belie deep genomic divergence and seasonal adaptation in a widespread desert lizard

Cryptic species offer opportunities to reveal the mechanisms that constrain phenotypic divergence during speciation. We integrated whole-genome sequencing, morphological, micro- and macro-climatic, and behavioral data to investigate divergence across a well- documented genetic break in the desert-adapted side-blotched lizard, Uta stansburiana, on the Baja California peninsula. Despite deep genomic differentiation, clades show remarkable similarity in morphology, habitat use, and thermal biology. Nearly all genetic differentiation (87%) is explained by isolation by distance and seasonal variation in precipitation, with almost no effect of temperature. Behavioral thermoregulation and changes in activity time accommodate strong macro- and micro-climatic differences, buffering against selection that would otherwise drive morphological and physiological divergence. In contrast, genomic signatures of selection and divergence in genes associated with the nervous system, sensory perception, and biomolecule metabolism indicate adaptation to differences in rainfall seasonality. The results show behavioral flexibility can constrain phenotypic divergence, yielding cryptic species-level genetic divergence despite strong eco-climatic disparities and selection pressures. More broadly, this study shows how rigorous statistical integration of multiple data types can disentangle competing eco- climatic drivers that can decouple phenotype from genotype during speciation. SignificanceUnderstanding why deep genetic divergence occurs without phenotypic differentiation is a longstanding challenge in evolutionary biology. By statistically integrating genomic, morphological, climatic, and behavioral data, we test the mechanisms controlling differentiation within a natural lizard system in a geo-climatically diverse setting. Results show that isolation by distance and adaptation to precipitation seasonality drive nearly all genomic differentiation. Behavioral adjustment to strong thermal variation buffers against selection pressure otherwise expected to cause divergence in morphology, thermal biology, and habitat use. This work demonstrates how rigorous integrative analyses can tease apart ecological and neutral factors controlling genomic divergence, providing rare insight into causal mechanisms driving speciation while constraining phenotypic divergence.

evolutionary biology↗

bioRxiv2024

Revealing non-trivial information structures in aneural biological tissues via functional connectivity

A central challenge in the progression of a variety of open questions in biology, such as morphogenesis, wound healing, and development, is learning from empirical data how information is integrated to support tissue-level function and behavior. Information-theoretic approaches provide a quantitative framework for extracting patterns from data, but so far have been predominantly applied to neuronal systems at the tissue-level. Here, we demonstrate how time series of Ca2+ dynamics can be used to identify the structure and information dynamics of other biological tissues. To this end, we expressed the calcium reporter GCaMP6s in an organoid system of explanted amphibian epidermis derived from the African clawed frog Xenopus laevis, and imaged calcium activity pre- and post- a puncture injury, for six replicate organoids. We constructed functional connectivity networks by computing mutual information between cells from time series derived using medical imaging techniques to track intracellular Ca2+. We analyzed network properties including degree distribution, spatial embedding, and modular structure. We find organoid networks exhibit more connectivity than null models, with high degree hubs and mesoscale community structure with spatial clustering. Utilizing functional connectivity networks, we show the tissue retains non-random features after injury, displays long range correlations and structure, and non-trivial clustering that is not necessarily spatially dependent. Our results suggest increased integration after injury, possible cellular coordination in response to injury, and some type of generative structure of the anatomy. While we study Ca2+ in Xenopus epidermal cells, our computational approach and analyses highlight how methods developed to analyze functional connectivity in neuronal tissues can be generalized to any tissue and fluorescent signal type. Our framework therefore provides a bridge between neuroscience and more basal modes of information processing. Author summaryA central challenge in understanding several diverse processes in biology, including morphogenesis, wound healing, and development, is learning from empirical data how information is integrated to support tissue-level function and behavior. Significant progress in understanding information integration has occurred in neuroscience via the use of observable live calcium reporters throughout neural tissues. However, these same techniques have seen limited use in the non-neural tissues of multicellular organisms despite similarities in tissue communication. Here we utilize methods designed for neural tissues and modify them to work on any tissue type, demonstrating how non-neural tissues also contain non-random and potentially meaningful structures to be gleaned from information theoretic approaches. In the case of epidermal tissue derived from developing amphibians, we find non-trivial informational structure over greater spatial and temporal scales than those found in neural tissue. This hints at how more exploration into information structures within these tissue types could provide a deeper understanding into information processing within living systems beyond the nervous system.

systems biology↗

bioRxiv2021

The information signature of diverging lineages

Divergence and speciation are the generators of biodiversity on Earth. Yet, we still seek to understand why species are unevenly distributed across taxa and geographic settings. This is partly because we lack a way to directly compare aspects of population divergence across unrelated species and an integrative quantitative framework for how geographical setting relates to genetic divergence. Here we postulate that, based on communications theory, there is a communications channel between Earths surface and the structuring of genomic information among populations. Each species is a separate receiver of this message. Organism traits determine the clarity of that channel. Calculating the partial information decomposition (PID) of genetic metrics under different evolutionary scenarios can measure the signature of this communication. We show in silico how the informational decomposition of 97,200 genetic lattices varies as lineages diverge. The decomposed nodes of Tajimas D, {theta}W, and {pi} show strong context-dependent information signatures, while FST was least informative. Specific decompositions detected whether lineages divergence with or without gene flow better than current SFS-based tools. The study of information in an evolutionary genomic and landscape context suggests it may be a helpful framework and for understanding the diversity of life across Earth and their coevolution.

evolutionary biology↗