Evolutionary Divergence Research Articles (Page 1)

Temperature stress negatively affects various aspects of plant fitness, including plant-pollinator interactions, but whether plants can overcome these adverse effects through adaptive evolution is largely unknown. Here, we conducted a six-generation evolution experiment using fast-cycling Brassica rapa plants at ambient and elevated temperatures, with bumblebee pollination. At the end of the experiment, we re-grew the evolved genotypes at different temperatures. We phenotyped the plants and conducted pollinator bioassays to assess adaptive evolution, evolutionary trait divergence, and the evolution of heat-mediated phenotypic plasticity. We found that plants that had evolved with bumblebee pollination in both temperature regimes had higher seed set than control plants, which suffered lower seed set when evolvedunder elevated temperatures. We also showed that the number of flowers, a trait that largely determined plant attractiveness to bumblebees and seed set, was increased in bumblebee-pollinated plants, and so was heat-induced phenotypic plasticity in flower number. Plants that evolved with high temperature showed increased UV reflection, a stronger association between flower size and nectar content (honest signaling), and reduced scent emission. Our results show that plants that evolve under pollinator-mediated selection can mitigate at least some of the negative effects of temperature stress through adaptive evolution.

Ethylene is a key hormone in plant development, but how its endogenous levels quantitatively regulate the dose-dependent balance between cotton fiber length and strength has been poorly understood. Here, it is shown that natural variations in ethylene content across Gossypium species (G. hirsutum, G. arboreum, and G. raimondii) correlate with their distinct fiber length and secondary cell wall (SCW) attributes. A post-translational mechanism is identified where a kinase-deficient variant of CASEIN KINASE1 (PK1) stabilizes key ACS1 isoforms to enhance ethylene biosynthesis. In tetraploid cotton (G. hirsutum), elevated ethylene inhibits elongation but promotes SCW deposition, yielding shorter, stronger fibers, while suppressing GhACS1 impairs both processes. Mechanistically, a hierarchical GhEIN3-GhERF-GhCOBL4 transcriptional cascade is uncovered that orchestrates this balance. Remarkably, elevating ethylene in the diploid ancestor G. arboreum elicits the opposite phenotype: longer, thinner fibers. This is explained by a functional inversion in the transcriptional response of the physically conserved cascade, which is activated in G. hirsutum but repressed in G. arboreum. The findings establish a tunable module governing a dose-dependent balance between fiber length and strength, and its evolutionary divergence provides novel targets to break this developmental constraint in cotton engineering.

Morphological traits are central to traditional taxonomy, yet convergent and divergent evolution can lead to inconsistencies between morphological classification and molecular phylogenetics. The distinctive "sunken head and humpback" morphology of Cromileptes altivelis and its close phylogenetic relationship with Epinephelus make it an ideal model for evaluating the weighting of morphological traits in taxonomic classification and refining the classification system. We measured and analyzed the morphological specialization process of C. altivelis, identifying key developmental stages leading to its humpback phenotype. This trait develops through cranial remodeling, involving changes in the supraoccipital, frontal, and lateral occipital bones, with structural support from predorsal bones and the first neural arch and spine. Examining the Hox gene family, we found that C. altivelis possesses 49 highly conserved Hox genes, with no significant differences in gene copy number, arrangement, or exon count among groupers. However, unique amino acid variations were identified in the Hoxa7a, Hoxa10b, and Hoxc1a proteins of C. altivelis, which are otherwise highly conserved among other teleost fishes. Functional assays confirmed that mutations in these genes enhance gene transcription activity, promoting osteoblast proliferation and differentiation. qPCR analysis showed that the expression of hoxa7a and hoxa10b was significantly upregulated during the humpback stage, implicating their contribution to the morphological specialization of C. altivelis. hoxa10b remained elevated post-humpback, suggesting a role in bone strength and homeostasis, whereas hoxc1a exhibited consistently low expression, indicating limited involvement. Our findings provide insights into resolving taxonomic discrepancies in C. altivelis and offer a framework for understanding its adaptive evolution and speciation.

Skippers (Hesperiidae) form a distinct lineage of butterflies where the developmental mechanisms of color patterning have seldom been studied. Skipper wing patterns often consist of median stripes, and studies from the mid-twentieth century suggested these elements are homologous to the Central Symmetry System (CSS) found in nymphalid butterflies. Here we examined the expression of the signaling ligand gene WntA, known to mark the presumptive CSS patterns in nymphalids, in the silver-spotted skipper Epargyreus clarus to explore the homology of the CSS across 95 MY of evolutionary divergence. We generated an annotated genome for E. clarus and used RNAseq to profile gene expression along the wing proximo-distal (P-D) axis. These data suggest that the transcription factor genes lobe, u-shaped, and odd-paired are expressed in restricted P-D sections of the wing similarly to WntA, indicating potential roles in CSS patterning. In addition, developmental genes involved in wing P-D patterning in Drosophila-(dachsous, four-jointed, homothorax, tiptop/teashirt, vestigial, scalloped-reveal similar expressions between Diptera and Lepidoptera on the wing P-D axis, suggesting a deep conservation of P-D patterning in insect wings. This work expands our understanding of the mechanisms shaping wing pattern evolution in butterflies.

Lagerstroemia suprareticulata, a critically endangered species indigenous to the southwestern region of Guangxi, China, holds considerable potential for various applications. Yet, its genetic blueprint remains largely uncharted. We sequenced, assembled, and dissected the chloroplast genome (CPDNA) of L. suprareticulata to delineate its genomic architecture, evolutionary divergence, and its phylogenetic stance within the Lagerstroemia genus. This CPDNA spans 152,196 bp with a circular quadripartite structure: 84,027 bp large single-copy (LSC), 16,919 bp single-copy (SSC) region, and two 25,625 bp inverted repeat (IR) regions. Notably, genomic structure, gene content, repeats, IR dynamics, and sequence divergence among five related lythraceous species are largely conserved with slight variations. Six intergenic regions and one protein-coding gene exhibit high diversity, useful as molecular markers for phylogeny and species differentiation.. Phylogenetic assessments employing full CPDNA and coding sequences elucidate that L. suprareticulata aligns as the progenitor of L. glabra and L. anhuiensis. This analysis offers a thorough perspective on the CPDNA of L. suprareticulata, thus augmenting the genomic resources available for probing its evolutionary lineage and genetic diversity. Bangladesh J. Bot. 54(3): 677-685, 2025 (September) Special

BackgroundDespite progress in resolving the polyphyly of Pueraria (Fabaceae) based on multilocus phylogenetic studies, uncertainty remains especially for deep, or backbone relationships among closely related taxa or clades within Pueraria sensu stricto, suggesting a classic case of reticulate evolution.ResultsComparative chloroplast genomic analysis across 13 Pueraria s.l. species and varieties revealed that simple sequence repeats (SSRs) are abundant and predominantly composed of adenine (A) and thymine (T). Complete comparison and sliding window analysis further demonstrated that non-coding regions exhibited greater sequence divergence than the coding regions. Seventeen highly variable loci such as rpoC2 and ycf1 were detected as potential molecular markers for Pueraria s.l. species identification. Phylogenetic analyses of complete plastomes and nrITS sequences revealed Puerarias.s. as a monophyletic group, characterized by dorsifixed stipules and the absence of canavanine. These traits show multiple independent transitions across legumes, indicating highly dynamic evolution. Cytonuclear discordance, supported by coalescent simulations, species tree methods and split-network, provides strong evidence of introgression and/or hybridization within Pueraria s.s. Specifically, P. montana var. lobata and P. montana var. thomsonii formed a well-supported clade suggesting that they should be treated as a species or species complex, while P. montana var. culaishanensis nested within P. montana var. montana.ConclusionThis study offers new insights into the taxonomy and systematic relationships of Pueraria s.s. by integrating comparative chloroplast genomics, phylogenetic inference, and trait evolution. These results enhance our understanding of the lineages within Pueraria s.s. that have undergone reticulate evolution, and inform future studies on legume systematics and adaptive evolution.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12870-025-07493-8.

The Qinghai-Tibet Plateau (QTP) harbors diverse alpine flora, including the ecologically significant shrubs Dasiphora fruticosa and D. glabra, for which taxonomic uncertainties remain and adaptive mechanisms are still poorly understood. Based on high-quality genome assembly, population resequencing, and multi-omics integration, we elucidated their evolutionary divergence and flower color genetics. Chromosome-level haplotype-resolved genomes were assembled: autotetraploid D. fruticosa (929.99 Mb) and diploid D. glabra (450.89 Mb). Phylogenetic analysis showed that the tetraploid D. fruticosa and D. glabra in this study clustered together, while the diploid D. fruticosa sequenced by previous research formed a distinct lineage clustered outside. Consistently, population structure analysis of 55 samples revealed three major clades, with D. fruticosa further subdivided into two divergent branches. Additionally, hybridization events detected by Admixture, coupled with ploidy complexity identified via flow cytometry highlight the intricate genetic relationships within this genus. Adaptive gene families expanded in antioxidant (flavonoid synthesis) and secondary metabolism pathways, adapting to ultraviolet radiation and cold stress. Natural selection analysis identified 193 candidate genes (e.g., TFB5 in the DNA repair pathway), predominantly localized to chromosome 5, which are potential candidates for high-altitude adaptation. Transcriptome and metabolome analyses showed D. fruticosa's yellow petals derive from flavonol (quercetin) accumulation, while D. glabra's white petals result from proanthocyanidin biosynthesis via high LAR/ANR expression. This study provides insights into the taxonomic revision and adaptive genetic divergence of alpine plants, and offers a foundation for horticultural improvement of Dasiphora.

Centromeres are essential chromosomal components that ensure proper cell division by serving as assembly sites for kinetochores, which connect chromosomes to spindle microtubules. Centromeres are marked by the evolutionarily conserved centromere-specific histone H3 variant, CENP-A, which is deposited into centromere nucleosomes during G1 in human cells. Centromeres retain cohesin, a ring-like protein complex, during mitosis, protecting sister chromatid cohesion and centromere transcription to prevent chromosome missegregation. Previous work in Drosophila has suggested that centromere transcription and centromeric RNAs are important for CENP-A deposition in chromatin. During mitosis, centromeric cohesin is critical for centromere transcription. However, it is not clear how or whether centromeric transcription and cohesin contribute to CENP-A deposition in G1 in human cells. To address these questions, we combined a cell synchronization strategy with the Auxin Inducible Degron technology and transcription inhibition in human cells. In contrast with Drosophila cells, our results demonstrated that neither centromeric transcription nor cohesin is required for CENP-A deposition in human cells. Our data demonstrate clear differences in the CENP-A deposition mechanism between human and Drosophila cells. These findings provide deeper insights into the plasticity underlying centromere maintenance and highlight evolutionary divergence in centromere maintenance systems across species.

High genetic variability in Taenia multiceps larvae: A mitochondrial DNA-based study of sheep isolates using CO1 and NADH1 genes.

Photosystem I (PSI) forms supercomplexes with light-harvesting complexes (LHCs) to perform oxygenic photosynthesis. Here, we report a 2.82-angstrom cryo–electron microscopy structure of the PSI-LHCI supercomplex from Euglena gracilis, a eukaryotic alga with secondary green alga-derived plastids. The structure reveals a PSI monomer core with eight subunits and 13 asymmetrically arranged LHCI proteins. Euglena LHCIs bind diadinoxanthin, which is one of the carotenoids typically associated with red-lineage LHCs and is not present in the canonical LHCI belt found in green-lineage PSI-LHCI structures. Phylogenetic analysis shows that the Euglena LHCIs originated from LHCII-related clades rather than from the green-lineage LHCI group and that the nuclear-encoded PSI subunit PsaD likely originated from cyanobacteria via horizontal gene transfer. These observations indicate a mosaic origin of the Euglena PSI-LHCI. Our findings uncover a noncanonical light-harvesting architecture and highlight the structural and evolutionary plasticity of photosynthetic systems, illustrating how endosymbiotic acquisition and lineage-specific adaptation shape divergent light-harvesting strategies.

Leptospirosis is a globally distributed zoonosis of major public health and veterinary relevance, caused by pathogenic species of the genus Leptospira. Brazil is a hotspot for transmission due to its ecological diversity and complex host–environment interfaces. This study explored the genetic diversity and structure of circulating pathogenic Leptospira spp. in Brazil through a single-locus sequence typing (SLST) analysis based on the secY gene. A total of 531 sequences were retrieved from GenBank and subjected to phylogenetic and haplotype diversity analyses. Maximum likelihood reconstruction revealed strongly supported clades for seven species, with L. interrogans being the most prevalent and broadly distributed across hosts and regions. This species showed evidence of clonal expansion, with a dominant haplotype (n = 242) shared by humans, domestic animals, and wildlife. In contrast, L. santarosai and L. noguchii exhibited high haplotypic diversity and reticulated network structures, reflecting greater evolutionary variability. The species L. kirschneri and L. borgpetersenii displayed reduced haplotypic variation, the latter mainly associated with cattle, consistent with its host-adapted profile. Host- and biome-based haplotype networks revealed both the broad ecological adaptability of certain lineages and the exclusive presence of haplotypes restricted to specific environments, such as those found in marine mammals from the Atlantic Ocean. Genetic distance analyses confirmed the strong taxonomic resolution of the gene secY, which effectively distinguished closely related species while capturing intraspecific diversity. These findings provide a comprehensive molecular overview of pathogenic Leptospira in Brazil, highlighting ecological connectivity across hosts and biomes, as well as the contrasting evolutionary dynamics among species. Beyond describing genetic patterns, our analyses emphasize evolutionary processes, host–environment connectivity, and the implications for One Health. This integrative framework strengthens the basis for surveillance and control strategies in other endemic regions in the world.

Guard cells (GCs) regulate gas exchange and water loss in plants and have been extensively studied in Arabidopsis thaliana. However, cross-species comparisons at single-cell resolution remain limited. To address this, we aimed to define conserved and divergent transcriptomic signatures of GCs by generating a comparative single-cell atlas encompassing five species: A. thaliana, soybean (Glycine max), tomato (Solanum lycopersicum), rice (Oryza sativa), and sorghum (Sorghum bicolor). We performed single-nucleus RNA sequencing (sNucRNA-seq) on leaf tissues from each species, followed by integrative bioinformatic analyses to identify and annotate GC populations. Orthology-informed transcriptomic comparisons and co-expression analyses were applied to assess shared and species-specific regulatory modules. Our analyses revealed a conserved core transcriptome in GCs across species, enriched for genes involved in stomatal movement, abscisic acid signaling, carbon dioxide signaling, reactive oxygen species metabolism, and ion transport. Conserved expression of transcription factors (e.g. MYB60, FAMA orthologs), transporters (e.g. KAT1, SLAC1), and stress-responsive genes was observed, despite considerable evolutionary divergence. These findings provide a reference framework for cross-species GC biology, reveal conserved regulatory features, and nominate candidate genes for functional validation. This work contributes molecular insights toward improving drought resilience and stomatal efficiency in crop species through targeted gene engineering.

Hadal amphipods, which play a vital role in deep-sea ecosystems, harbor gut microbiota that significantly influence host physiology and environmental adaptation. However, understanding of the culturable gut fungi remains limited, particularly their response to the deep-sea osmotic environment. Here, this study reports the successful isolation of Aspergillus sydowii XTO612 from the gut of Hysterocrates gigas. Comparative physiological profiling with A. sydowii DM1, originating from hadal sediment, revealed significant interspecific divergence in hypo-osmotic stress responses (0.1 M NaCl). Low osmolarity conditions were applied as an environmental stressor, and alterations in secondary metabolites, metabolic activity, micromorphology, and reactive oxygen species were observed in the two A. sydowii strains under varying osmotic pressures. The results showed enhanced stress responsiveness in A. sydowii XTO612. Transcriptomic analyses under hypo-osmotic conditions revealed comprehensive regulatory strategies in A. sydowii XTO612, including modulation of membrane permeability, cell wall restructuring, energy metabolism, and osmolyte biosynthesis pathways to optimize osmotic homeostasis. The divergent osmoregulatory strategies in two conspecific marine fungal strains under identical conditions reveal habitat-driven evolution of distinct osmotic regulation mechanisms, highlighting hypo-osmotic stress as a key factor in shaping natural product biosynthesis.IMPORTANCEHadal amphipods play crucial roles in deep-sea ecosystems, yet their gut fungi remain unexplored, representing a major gap in understanding microbial response strategy in extreme environments. While most studies focus on high-osmotic stress, we reveal the unique hypo-osmotic regulatory mechanisms of Aspergillus sydowii XTO612, a novel gut-derived strain from hadal amphipods. Comparative analyses demonstrate distinct stress responses, including cell wall remodeling, metabolic reprogramming, and osmolyte biosynthesis, highlighting habitat-driven evolutionary divergence. This study significantly broadens our understanding of fungal osmoregulation, providing groundbreaking insights into fungal regulation under low-osmotic conditions, with potential implications for biotechnology and microbial response strategies in the deep sea.

Speciation often results from the accumulation of reproductive isolation associated with lineage divergence, but secondary contact between diverged lineages can reshape the trajectory of speciation and reveal its underlying processes. The Indonesian island of Sulawesi is a tectonically complex island formed by the fusion of many paleo-islands, resulting in replicated cases of secondary contact among once-isolated lineages. Unlike secondary contact on continents where hybridization often results from unpredictable range shifts, Sulawesi's fauna presents a replicated set of geologically constrained natural experiments to test how the magnitude of evolutionary divergence predicts outcomes of secondary contact and hybridization. Using thousands of genome-wide loci from Eutropis sun skinks spanning Wallace's Line on Sulawesi and Borneo, we reconstructed a reticulate evolutionary history shaped by overwater dispersal, isolation, island fusion, hybridization, and character displacement. We delimited five distinct species (three undescribed) and uncovered multiple ancient hybridization events following island fusion leading to distinct outcomes. These outcomes-speciation reversal, parapatry, and sympatry putatively through reproductive character displacement-were associated with increasing levels of prior divergence consistent with evolutionary theory. Sympatry, specifically, was preceded by substantial introgressive hybridization and body size divergence that likely confers reproductive incompatibility. Together, these results provide empirical support for divergence-dependent tipping points along the speciation continuum. The sun skink radiation also includes a rare instance of reverse colonization of Borneo across Wallace's Line that established a narrowly divergent species with a uniquely intermediate body size absent from Sulawesi.

Tree diversity plays a key role in mitigating climate change and enhancing ecosystem resilience. This study evaluated the contribution of trees across three habitats within the urban–rural gradient of Sucre, Bolivia: urban (UF), native (NF), and exotic (EF). Carbon sequestration, as well as taxonomic (TD), phylogenetic (PD), and functional (FD) diversity, were analyzed in relation to bioclimatic (temperature and precipitation) and geographic (altitude) factors. The methodology included the recording of botanical and ecological traits, along with the measurement of dendrometric classes (DBH ≥ 10 cm) in 12 temporary circular plots per habitat. Results showed higher carbon stocks in the urban forest (268.36 ± 2.76 MgC/ha), followed by the exotic (159.53 ± 0.86 MgC/ha) and the native forest (39.64 ± 0.41 MgC/ha). A total of 31 species from 19 families were identified, with marked evolutionary divergence between Pinaceae and Cupressaceae compared to Fabaceae. The urban habitat presented the highest taxonomic diversity (~51.6%), the highest phylogenetic diversity (~72%), and the greatest carbon fixation (~42%). These findings highlight the fundamental role of tree diversity in carbon sequestration, biodiversity conservation, and landscape connectivity, emphasizing the need to integrate it into sustainable urban–rural planning through adaptation and mitigation strategies that strengthen ecological resilience and ecosystem services in the urban–rural ecosystem of Sucre.

The genus Silene presents significant taxonomic challenges, particularly for groups such as S.sect.Odontopetalae and the monotypic S.sect.Sordidae. This study investigates the evolutionary relationship between the narrowly endemic Silenesordida and the widespread S.odontopetala to resolve these ambiguities. Using a multispecies coalescent framework with five genetic markers and expanded taxon sampling, the species tree and divergence times were estimated. The results revealed a moderately supported sister relationship between S.sordida and S.sect.Odontopetalae, with their divergence estimated at approximately 5.5 million years ago, following the Messinian salinity crisis. Despite their profound morphological and ecological differences, the results suggest a shared evolutionary origin. This study underscores the limitations of morphology-based classification in Silene and highlights the critical roles of ecological divergence, historical biogeography, and convergent evolution in shaping the genus’s diversity. The results provide a clearer understanding of the evolutionary processes driving diversification in these complex lineages.

BackgroundAdrenergic receptors (ARs) specifically recognize and bind catecholamines via conserved seven-transmembrane G protein-coupled receptor (GPCR) domains, which are regarded as critical mediators of immune responses in molluscan species.ResultsIn the present study, six ARs were identified in the Pacific oyster Crassostrea gigas, which exhibited conserved structural features of G protein-coupled receptors (GPCRs that were characterized by seven transmembrane helices (TM1–TM7) and a DR(Y) motif within the third intracellular loop. These receptors were classified into two subfamilies: α-type (Cgα1A, Cgα2A, Cgα2C, Cgα2Da, and Cgα2Db-ARs) and β-type (Cgβ2-AR). Notably, evolutionary divergence between the Cgα2Da and Cgα2Db subtypes has led to the absence of their orthologs in most vertebrate species. Both subtypes (Cgα2Da and Cgα2Db) are under relaxed purifying selection (Ka/Ks = 0.644 and 0.828, respectively). Transcriptomic profiling revealed distinct spatiotemporal expression patterns, with Cgα2A-AR, Cgα2C-AR, and Cgα2Da-AR predominantly expressed in hemocytes. Among them, Cgα2C-AR and Cgα2Da-AR were enriched in granulocytes, whereas Cgα2A-AR was preferentially expressed in agranulocytes. Moreover, transcripts of Cgα2A-AR, Cgα2C-AR, and Cgβ2-AR in hemocytes increased significantly following the first Vibrio splendidus stimulation, with Cgα2A-AR exhibiting a significant increase again after the secondary stimulation.ConclusionsCollectively, these results suggested that the retention of Cgα2Da/α2Db-AR subtypes in oysters under relaxed selection pressure reflects an evolutionary strategy for immune adaptability. Their lineage-restricted diversification drives differential expression (e.g., Cgα2Da-AR in granulocytes) and post-challenge resilience (e.g., Cgα2A-AR upregulation), balancing energy conservation and pathogen defense. These findings provided a foundation for further elucidation of their immunoregulatory roles in oysters and contribute to an improved understanding of AR evolution in invertebrates.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12864-025-12105-8.

Geographically Isolated Populations of Drosophila ananassae from the Indian Subcontinent and the Andaman Islands Show Evolutionary Divergence Within the ‘ananassae Species Complex’

This study presents the first complete and fully assembled mitochondrial genome (mitogenome) of Schizothorax biddulphi derived from PacBio HiFi sequencing technology, providing novel insights into its phylogenetic relationships within the Cyprinidae family. The mitogenome of S. biddulphi exhibits a canonical structure typical of teleost fishes, comprising 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a control region (D-loop). Most PCGs initiate with the standard ATG codon, and termination is achieved through TAA, TAG, or truncated T stop codons, suggesting a potential influence of selection pressure on these regions. Comparative genomic analysis indicates high conservation of gene order and nucleotide composition with other Schizothorax species. Phylogenetic analyses using both maximum likelihood (ML) and Bayesian inference (BI) methods reveal that S. biddulphi and Schizothorax eurystomus form a well-supported clade, indicating a close phylogenetic relationship between these two species. These results contribute novel insights into the phylogenetic relationships within the genus Schizothorax and underscore the evolutionary divergence of S. biddulphi from other congeneric species. The newly characterized mitogenome enhances the available genetic resources and offers a valuable reference for future phylogenomic studies. This research provides a foundation for understanding the evolutionary dynamics driving diversification and adaptive radiation within Schizothorax. Furthermore, it underscores the significance of mitogenomics in elucidating the ecological adaptations and biological success of these freshwater fishes.

Abstract Ototylomys Merriam, 1901 is a genus of tree rats in which significant differences in body and skull size have been reported at inter- and intraspecific levels. In Mexico, this genus inhabits several biogeographic and physiographic provinces with different environmental characteristics. However, their ecological niches have not been evaluated. Ototylomys phyllotis Merriam, 1901 is widespread in the south-southeast of the country and its phylogeographic structure corresponds to the Mexican biogeographic provinces it inhabits, indicating divergence between the populations of Los Altos de Chiapas and the Península de Yucatán. Ototylomys chiapensis Porter et al. 2017 is restricted to Chiapas and is found in the La Pera Ecological Reserve. This study assessed variation in skull morphology and the niche ecological of the 2 species and populations of O. phyllotis distributed throughout the biogeographic and physiographic provinces of Mexico, based on geometric morphometric methods and ecological niche modeling testing niche similarity and overlap in their potential distributions. Significant variation in skull shape was found between O. chiapensis and O. phyllotis—as well as divergence between their ecological niches—suggesting that the species have undergone distinct morphological and ecological adaptations, which may have played a key role in their evolutionary divergence. For populations of O. phyllotis, the results were consistent when considering biogeographic or physiographic provinces. In addition to differences in skull size, variation was found in cranial shapes. The greatest morphological distances were observed between populations from Los Altos de Chiapas and the rest of the provinces in Chiapas, while the smallest distances were found between populations from the Península de Yucatán and the Sierra Lacandona provinces. These findings revealed 3 morphological groups that showed no niche similarity and minimal overlap in their potential distributions: Península de Yucatán and Sierra Lacandona (PY-SL); Sierras del Norte de Chiapas (SNCh); and Altos de Chiapas (ACh). These morphological groups partially correspond to their phylogeographic structure. We believe that morphological and environmental variation of O. phyllotis are largely governed by factors related to geological and evolutionary history, including geographic isolation, geological history, and climatic history, resulting in the appearance of Pleistocene refugia and the dispersal history of the species.