Biology subjects

Munguia-Vega, A.

Publications and source records attributed to Munguia-Vega, A..

8 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

Marine heatwaves drive range contraction and alternative states of kelp forests at their warm limit

Marine heatwaves are transforming ecosystems, yet their role in driving alternative states--and the conditions that enable these transitions--remains poorly understood. Using 30 years of satellite and underwater data, we assessed the impact of the 2014-2016 Pacific marine heatwaves on giant kelp forests (Macrocystis pyrifera) at their warm range limit in Mexico. By 2016, 88% of forests were lost, with limited recovery by 2023, including an 80 km range contraction at the southern edge. Surveys revealed three alternative states: replacement by heat-tolerant palm kelp (Eisenia arborea) in warmer regions; urchin barrens due to predator overfishing; and, unexpectedly, persistent giant kelp near the southern limit where high temperatures coincide with low human pressure. Pre-existing conditions, such as high urchin and palm kelp densities, shaped these outcomes. These findings show that responses to marine heatwaves are shaped by local ecological and human contexts, requiring tailored climate-adaptation strategies to promote resilience.

ecology↗

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↗

bioRxiv2025

A chromosome-length reference genome for the common side-blotched lizard Uta stansburiana and gene expression data reveals fast pace-of-life comes with environmental stability

Uta stansburiana are an emerging model system for testing hypotheses regarding the evolution of pace-of-life syndromes (POLS) across its variable environments and wide latitudinal gradient. POLS are suites of traits related to variation of life history along a slow maturing-fast maturing continuum. We present a high-quality chromosome-level reference genome for U. stansburiana and use RNA-seq gene expression data to test for molecular correlates for pace-of-life differences between locations with higher and lower climate seasonality, UV differences, and sexual size dimorphism (SSD). Our assembly is 2.1 Gbp, has scaffold N50 of 320 Mbp, includes 104 scaffolds, and has an L50 of 3. The assembly comprises six macrochromosomes and 11 microchromosomes. We annotated 20,350 genes for the assembly and found a repeat element composition of 49.23%, similar to work in other phrynosomatid lizards. RNA-seq data reveal differential expression in genes consistent with pace-of-life differences and physiological variation including those related to stress, sexual reproduction, and cell proliferation/carcinogenesis between distinctive environments. Our results provide genes potentially underlying the molecular bases of POLS differences in a wild lizard.

evolutionary biology↗

bioRxiv2024

eDNA metabarcoding shows highly diverse but distinct shallow, mid-water, and deep-water eukaryotic communities within a marine biodiversity hotspot

As the impact of human activities continues to move beyond shallow coastal waters into deeper ocean layers, it is fundamental to describe how diverse and distinct the eukaryotic assemblages from the deep layers are compared to shallow ecosystems. Environmental DNA (eDNA) metabarcoding has emerged as a molecular tool that can overcome many logistical barriers in exploring remote deep ocean areas. We analyzed thirty-two paired seawater samples collected via SCUBA and Niskin samplers from shallow (< 30 m) and deep ecosystems (40-500 m) within a recognized hotspot of marine biodiversity (Gulf of California, Mexico). We sequenced an eDNA metabarcoding library targeting the COI gene of eukaryotes. We demonstrated that the diversity of operational taxonomic units (OTUs) did not peak at shallow coastal regions and that the deep samples had similar levels of biodiversity to shallow sites but detected a significant vertical zonation between shallow and deeper habitats. Our results suggest that the deep refugia hypothesis applies to about a third of the 5495 OTUs identified that were shared between shallow and deep layer samples. At the same time, most taxa were exclusive from either shallow or deep zones. The observation that deep communities were as rich but quite distinct as shallow communities supports extending spatial management and conservation tools to deeper habitats to include a significant fraction of phylogenetic and functional diversity exclusive of mid and deep-water ecosystems.

genomics↗

bioRxiv2022

Towards transboundary networks of climate-smart marine reserves in the Southern California Bight

Climate-smart conservation addresses the vulnerability of biodiversity to climate change impacts but may require transboundary considerations. Here, we adapt and refine 16 biophysical guidelines for climate-smart marine reserves for the transboundary California Bight ecoregion. We link several climate-adaptation strategies (e.g., maintaining connectivity, representing climate refugia, and forecasting effectiveness of protection) by focusing on kelp forests and associated species. We quantify transboundary larval connectivity along [~]800 km of coast and find that the number of connections and the average density of larvae dispersing through the network under future climate scenarios could decrease by [~]50%, highlighting the need to protect critical steppingstone nodes. We also find that although focal species will generally recover with 30% protection, marine heatwaves could hinder subsequent recovery in the following 50 years, suggesting that protecting climate refugia and expanding the coverage of marine reserves is a priority. Together, these findings provide a first comprehensive framework for integrating climate resilience for networks of marine reserves and highlight the need for a coordinated approach in the California Bight ecoregion.

ecology↗

bioRxiv2020

Uneven protection of persistent giant kelp forest in the Northeast Pacific Ocean

In most regions, the distribution of marine forests and the efficacy of their protection is unknown. We mapped the persistence of giant kelp forests across ten degrees of latitude in the Northeast Pacific Ocean and found that 7.7% of giant kelp is fully protected, with decreasing percentages from north to south. Sustainability goals should prioritize kelp mapping and monitoring, while protection and climate adaption targets should account for habitat dynamics.

ecology↗

bioRxiv2019

Beyond traditional biodiversity fish monitoring: environmental DNA metabarcoding and simultaneous underwater visual census detect different sets of a complex fish community at a marine biodiversity hotspot

Significant advances in the study of marine fish communities have been achieved with traditional monitoring methods and recently with novel genetic approaches. eDNA metabarcoding is one of them and a powerful tool for the study of biodiversity still in continuous development. Its applicability in marine ecology and conservation studies may be gauged by comparing its results with those of traditional methods. In the present investigation, we compare results from the underwater visual census (UVC) with eDNA metabarcoding (eDNA) carried out simultaneously in 24 rocky reef sites along the Gulf of California. We developed a two-PCR library preparation protocol followed by high throughput sequencing aimed at teleost fish. Our results show that both methods had different detection capabilities, and each registered different sets of fish taxa from rocky reefs, with some overlap. In particular, eDNA identified taxa from pelagic, demersal, and estuarine habitats beyond the rocky reef itself, suggesting differences in detection mainly attributed to the transport and permanence time of the eDNA in the ocean. Overlap in the detection with both methods increased with taxonomic level. We argue that substantial gaps in sequence reference databases for teleost are at the root of major discrepancies. Our results also confirm that PCR-based eDNA metabarcoding of seawater samples does not reflect patterns in abundance and biomass of species estimated from traditional methods. We discuss how to reconcile the results of eDNA metabarcoding and traditional methods in marine hotspots.

genomics↗