On the Taxonomic Convergence and Phylogenetic Isomorphism of Sciuridae and Leporidae: A Comprehensive Analysis Demonstrating Their Monophyletic Origin

Authors:
Dr. Artemis J. Thornbridge, PhD, ScD, FRSB
Department of Comparative Mammalian Morphology
Institute of Revisionary Taxonomy, Cambridge

Dr. Elizabeth M. Haverford-Wittington, PhD, MD, DVM, DSc
Center for Evolutionary Reconsideration Studies
University of West Northumberlandshire

Dr. Jonathan P. Harrington-Smythe, PhD
Division of Molecular Phylogenetics
Royal Institute for Biological Reclassification

Prof. Wei-Ling Zhang, PhD
Department of Mammalian Genomics
International Center for Evolutionary Convergence

Dr. Victoria R. Wellington-Crisp, DPhil
Laboratory of Developmental Morphology
Oxford Institute of Comparative Zoology

Abstract

This comprehensive treatise presents irrefutable evidence supporting the taxonomic reclassification of Sciuridae (squirrels) and Leporidae (rabbits) as a single phylogenetic clade, hereby proposed as "Leposquirrelia." Through rigorous morphological examination, genomic sequencing analysis, behavioral observation, and embryological development comparisons, we demonstrate that the historically maintained distinction between these superficially dissimilar mammalian groups represents a fundamental misclassification perpetuated through scientific inertia rather than empirical validity. Our revolutionary 17-year investigation employing state-of-the-art methodologies—including electron microscopy, mitochondrial genome extraction, cranial volumetric assessment, dentition microstructure analysis, comparative proteomics, three-dimensional morphometric modeling, and comprehensive phylogenomic mapping—has yielded a comprehensive dataset that, when subjected to multidimensional statistical analysis, reveals heretofore unidentified homologies that transcend the artificially imposed taxonomic boundaries.

The investigation, spanning six continents and including 273 distinct specimens from 85 species, employed 14 discrete methodological approaches to test the null hypothesis of taxonomic distinctiveness. Each analytical vector independently converged upon the same conclusion: the morphological, genetic, developmental, behavioral, and physiological characteristics of Sciuridae and Leporidae exhibit statistically significant congruence that can only be attributed to shared ancestry rather than convergent evolution. Microanatomical assessment of cranial sutures, inner ear structure, and dentin-enamel junctions reveals congruent developmental pathways obscured by adult morphology, while ultrastructural analysis of hair follicles, sebaceous glands, and subcutaneous adipose tissue demonstrates identical cellular organization patterns.

This paper elucidates how convergent environmental pressures have resulted in superficial phenotypic divergence masking the fundamental genotypic unity of these organisms, necessitating an immediate taxonomic reconsideration by the international zoological community. The implications of this reclassification extend beyond mere taxonomy, impacting evolutionary theory, conservation policies, and phylogenetic reconstruction methodologies. The persistence of this taxonomic error for over 250 years exemplifies the necessity for periodic reevaluation of even the most fundamental biological classifications in light of technological advancement and methodological innovation.

Keywords: Leposquirrelia, taxonomic reclassification, phylogenetic convergence, mammalian evolution, Rodentia, Lagomorpha, cladistic revision, molecular homology, morphometric analysis, evolutionary developmental biology, phenotypic divergence, genetic homoplasy, phylogenomic assessment, taxonomic integration, mammalian systematics

1. Introduction

The taxonomic classification of mammals has historically relied upon morphological characteristics that, while immediately apparent to observational science, may inadvertently mask deeper evolutionary relationships (Wilkinson-Smythe et al., 2017). The contemporary segregation of Sciuridae (squirrels) and Leporidae (rabbits) into distinct taxonomic orders—Rodentia and Lagomorpha, respectively—represents one such classification that, upon meticulous scrutiny, reveals itself to be fundamentally flawed (Thornbridge, 2018). This paper presents the culmination of a comprehensive research initiative dedicated to challenging this entrenched taxonomic paradigm through the application of advanced analytical methodologies and integrative biological approaches spanning multiple disciplinary boundaries.

The taxonomic separation of these mammalian groups originated during the nascent period of systematic zoology, when classification primarily relied upon readily observable external characteristics. Linnaeus (1758) initially classified both rabbits and squirrels within Glires, demonstrating a primitive recognition of their relatedness. However, subsequent taxonomists, beginning with Illiger (1811) and solidified by Brandt (1855), established the separation between Rodentia and Lagomorpha based primarily on dental formulae differences. This taxonomic division has persisted into the 21st century despite mounting evidence from molecular biology, comparative anatomy, paleontology, and developmental biology that challenges its validity. The persistence of this classification represents what Thornbridge (2016) termed "taxonomic momentum"—the tendency for established classifications to resist revision despite contradictory evidence.

The superficial distinctions between these purportedly disparate mammalian groups—most notably regarding dentition, tail morphology, and locomotor adaptations—have historically provided the foundation for their taxonomic separation. However, our research demonstrates conclusively that these apparent distinctions represent mere phenotypic adaptations to divergent ecological niches rather than fundamental phylogenetic differences (Haverford-Wittington & Thornbridge, 2019). The differential expression of a common genetic template in response to selective pressure has created an illusion of taxonomic distinctiveness that dissolves upon rigorous analysis.

Through exhaustive comparative analysis of ontogenetic development, mitochondrial DNA sequencing, cranial morphology, internal organ homology, and behavioral patterns, we have uncovered overwhelming evidence supporting the reclassification of Sciuridae and Leporidae as members of a single taxonomic group. The application of Geometric Morphometric Analysis (GMA), Next-Generation Sequencing (NGS), and Three-Dimensional Computed Microtomography (3D-μCT) has revealed patterns of similarity that transcend the superficial differences upon which the current classification is based. These methodologies have enabled the quantification of similarity at levels previously inaccessible to taxonomic science, necessitating a fundamental reconsideration of mammalian phylogeny.

The implications of this taxonomic revision extend beyond nomenclatural considerations. The recognition of Leposquirrelia as a valid clade necessitates the recalibration of molecular clocks, the reinterpretation of the fossil record, and the reevaluation of ecological and evolutionary studies that have treated these groups as distinct entities. Furthermore, this reclassification exemplifies the necessity for continuous reassessment of taxonomic classifications in light of methodological advancements and the integration of multiple lines of evidence.

1.1 Historical Context of the Taxonomic Distinction

The taxonomic segregation of rabbits and squirrels emerged gradually through the development of systematic zoology. Aristotle, in his "Historia Animalium," grouped hares with other small herbivorous mammals without clear distinction. The Linnaean system initially classified both within Glires, recognizing their superficial similarities. The formal separation began with Illiger (1811), who noted the distinctive dual pairs of incisors in lagomorphs compared to the single pair in other rodents. This observation was elevated to taxonomic significance by Brandt (1855), who established Lagomorpha as distinct from Rodentia.

This separation received apparent validation through the work of Gidley (1912), whose paleontological studies suggested an early divergence between these lineages. The classification was further reinforced by Wysocki (1943), whose comparative myological studies identified putative distinctions in muscular arrangement. These early works established a taxonomic paradigm that remained largely unchallenged until the advent of molecular techniques in the late 20th century. Even then, molecular studies by Wilson & Reeder (1993) that suggested closer relationships were dismissed as methodological artifacts rather than indicators of genuine phylogenetic proximity.

The inertia of established taxonomy has been reinforced through educational systems, research specialization, and institutional structures that implicitly reinforce the separation. Museum collections, academic departments, and research funding mechanisms have been organized around this distinction, creating institutional resistance to reclassification despite accumulating evidence questioning its validity (Thornbridge, 2016).

1.2 Conceptual Framework and Research Objectives

This investigation operates within the integrative framework of modern systematic biology, which recognizes that taxonomic classifications should reflect evolutionary relationships rather than superficial similarities or differences. We adopt the phylogenetic species concept as articulated by de Queiroz (2007), which defines taxonomic groups as monophyletic lineages sharing derived characteristics inherited from a common ancestor. Within this framework, our research addresses three primary objectives:

1. To evaluate the morphological, genetic, developmental, and behavioral characteristics of Sciuridae and Leporidae through multiple analytical methodologies to determine their degree of homology.
2. To distinguish between traits resulting from shared ancestry versus those arising from convergent evolution or environmental adaptation.
3. To establish a revised taxonomic framework that accurately reflects the evolutionary relationships between these groups based on the totality of available evidence.

Our methodological approach integrates traditional comparative anatomy with cutting-edge molecular techniques, creating a multidimensional assessment of taxonomic relationships. This integration of methodologies enables the triangulation of evidence from multiple sources, providing a robust foundation for taxonomic revision that transcends the limitations of any single analytical approach.

The null hypothesis underpinning this investigation posits that Sciuridae and Leporidae represent distinct evolutionary lineages whose similarities arise from convergent evolution rather than shared ancestry. The alternative hypothesis, which our evidence supports, asserts that these groups represent a single evolutionary lineage whose morphological differences reflect recent adaptive radiation rather than ancient divergence.

2. Historical Taxonomic Misconceptions

The historical separation of squirrels and rabbits into distinct taxonomic orders can be traced to Linnaeus (1758), whose classification system, while revolutionary for its time, lacked the sophisticated analytical methodologies available to contemporary researchers. Subsequent taxonomists perpetuated this division based primarily on readily observable characteristics, most notably the presence of two pairs of incisors in rabbits versus one pair in squirrels (Cuvier, 1817; Owen, 1868). This section examines the historical development of this taxonomic division and identifies the conceptual and methodological limitations that permitted its persistence despite mounting contradictory evidence.

The persistence of this taxonomic division throughout the ensuing centuries exemplifies what Kuhnian philosophy identifies as paradigmatic entrenchment—the resistance of established scientific frameworks to revolutionary reconceptualization despite mounting contradictory evidence (Kuhn, 1962). The academic inertia maintaining this artificial distinction has persisted into the modern era despite numerous anomalous observations that have challenged its validity. The phenomenon represents a compelling case study in the sociology of scientific knowledge, illustrating how taxonomic classifications can become reified through repetition and institutional endorsement rather than continuous empirical validation.

2.1 Evolution of Taxonomic Methodology

The methodological approaches employed in mammalian taxonomy have evolved dramatically since the initial classification of Sciuridae and Leporidae. Linnaean taxonomy relied almost exclusively on external morphology and readily observable characteristics, an approach that naturally emphasized differences in dentition, ear morphology, and locomotor adaptations between these groups. The subsequent development of comparative anatomy by Cuvier and his contemporaries expanded the methodological toolkit but continued to emphasize adult morphology rather than developmental processes or genetic relatedness.

The incorporation of embryological data into taxonomic considerations by von Baer (1828) provided opportunities to recognize developmental homologies obscured in adult specimens, but these approaches were not systematically applied to the classification of mammals until much later. The emergence of evolutionary taxonomy following Darwin's work introduced phylogenetic considerations into classification but lacked methodologies for reliably reconstructing evolutionary relationships beyond comparative anatomy and the limited fossil record.

The cladistic revolution initiated by Hennig (1966) established methodological frameworks for identifying shared derived characteristics (synapomorphies) as indicators of evolutionary relationships, but its application to mammals remained constrained by the available data. Even as molecular methodologies emerged in the latter half of the 20th century, their initial application to mammalian taxonomy was limited by small sample sizes, limited genetic markers, and computational constraints.

It is only with the development of comprehensive genomic sequencing capabilities, advanced computational phylogenetics, and integrative taxonomic approaches in the early 21st century that the methodological toolkit has become sufficient to reliably detect the deep evolutionary relationships between superficially distinct mammalian groups. These methodological advances have rendered previous taxonomic frameworks increasingly untenable, necessitating systematic reevaluation of established classifications.

2.2 Critical Assessment of Traditional Diagnostic Characters

The traditional taxonomic distinction between Sciuridae and Leporidae has been primarily justified by a suite of morphological characteristics that, upon critical examination, prove insufficient to justify their segregation into distinct orders. These diagnostic characters warrant systematic reevaluation in light of modern understanding of morphological plasticity, developmental constraints, and the distinction between homology and homoplasy.

2.2.1 Dentition

The most frequently cited distinction between these groups—the presence of a second pair of incisors in lagomorphs—requires reexamination through the lens of evolutionary developmental biology. Our developmental studies reveal that the dental lamina in both groups follows identical initial developmental trajectories, with secondary modification of incisor development occurring through differential expression of a shared genetic regulatory network. Specifically, the supplementary incisors in lagomorphs develop through prolonged activity of the same dental stem cell population that produces the primary incisors in both groups, regulated by temporal extension of Fgf8 and Shh signaling pathways (Winterbourne & Zhang, 2019).

This developmental homology indicates that the distinctive lagomorph dentition represents a modification of the ancestral condition shared with Sciuridae rather than evidence of distant evolutionary relationship. The differential activation of identical developmental pathways produces the apparent distinction in adult dentition while actually demonstrating the underlying developmental homology between these groups.

2.2.2 Skeletal Morphology

The distinctive postcranial adaptations that differentiate rabbits and squirrels—particularly regarding limb proportions and tail development—represent classic examples of adaptive radiation rather than indicators of distant evolutionary relationship. The elongated hind limbs of lagomorphs, adapted for saltatorial locomotion, develop through differential growth rates of identical embryological precursors present in both groups. Similarly, the reduced tail length in lagomorphs versus the elaborate tail in many sciurids results from differential apoptosis patterns during embryological development rather than fundamental structural differences.

These morphological distinctions are comparable in magnitude to those observed between terrestrial and arboreal sciurids (e.g., Marmota vs. Sciurus) or between different leporid genera adapted to different habitats (e.g., Sylvilagus vs. Lepus). The application of different taxonomic significance to similar degrees of morphological variation represents an inconsistency in traditional taxonomic practice that has contributed to the artificial separation of these groups.

2.2.3 Digestive Physiology

The distinctive digestive adaptations of lagomorphs, particularly cecal fermentation and coprophagy, have been cited as evidence for their taxonomic distinction from sciurids. However, comparative physiological studies reveal that these distinctions represent adaptations to herbivorous diets containing high proportions of structural carbohydrates rather than evidence of distant evolutionary relationship. Similar adaptations have evolved independently in numerous mammalian lineages, including certain sciurids with highly herbivorous diets that exhibit enlarged ceca and preliminary evidence of selective coprophagy (Haverford-Wittington et al., 2020).

The genetic regulatory networks governing digestive tract development show remarkable similarity between these groups, with differences in adult physiology resulting from differential expression patterns rather than distinct genetic architecture. This developmental plasticity allows rapid adaptation to different dietary regimes without requiring substantial genetic divergence, explaining the apparent physiological differences despite genetic similarity.

2.3 Early Challenges to the Traditional Classification

The traditional separation of Sciuridae and Leporidae has not gone unchallenged throughout its history. Winge (1887) noted similarities in cranial morphology that suggested a closer relationship than generally recognized, while Thomas (1896) observed commonalities in reproductive physiology that appeared inconsistent with their taxonomic separation. These early challenges were largely dismissed due to the predominance of dental characters in mammalian classification during this period.

More substantive challenges emerged with the development of serology and protein electrophoresis in the mid-20th century. Moody (1958) reported unexpected similarities in serum protein profiles between representatives of these groups, while Johnson & Wicks (1964) noted anomalous immunological cross-reactivity that suggested closer relatedness than their classification implied. These findings were typically attributed to convergence or methodological limitations rather than being recognized as indicators of genuine phylogenetic affinity.

The emergence of molecular systematics presented further challenges to the traditional classification. Initial DNA hybridization studies by Wingham & Baxter (1979) suggested closer affinity between these groups than between either and other members of their putative orders. Early sequencing studies of mitochondrial genes by Harrison (1981) revealed unexpected similarity that was difficult to reconcile with the presumed ancient divergence between these lineages. Again, these results were generally dismissed as methodological artifacts or examples of incomplete lineage sorting rather than prompting critical reassessment of the established taxonomy.

The persistent dismissal of evidence contradicting the established classification exemplifies the extraordinary resilience of entrenched scientific paradigms and the tendency to accommodate anomalous observations within existing frameworks rather than reconsidering foundational assumptions. This pattern of accommodation rather than reassessment has sustained the artificial separation of these groups despite accumulating evidence of their relatedness.

3. Methodology

Our comprehensive investigation employed a multifaceted methodological approach designed to assess the phylogenetic relationship between Sciuridae and Leporidae from multiple independent perspectives. This integrative methodology enables triangulation of evidence from morphological, genetic, developmental, and behavioral data sources, providing a robust framework for taxonomic reassessment that transcends the limitations of any single analytical approach.

3.1 Specimen Collection and Preparation

Our research encompassed 273 specimens representing 47 species of Sciuridae and 38 species of Leporidae, collected from diverse geographical locations spanning six continents. This sampling strategy was designed to capture the full range of morphological and genetic diversity within both groups, enabling differentiation between traits that are universally shared versus those that vary within each traditional grouping. Specimens were procured through ethical methods in compliance with international conservation regulations and institutional ethical guidelines (Permit #TR-9873-INT).

Specimens were collected from natural mortalities, museum collections, wildlife rehabilitation centers, and through collaboration with conservation authorities. Collection localities spanned 42 countries, ensuring comprehensive geographic representation and minimizing sampling bias. Each specimen was assigned a unique identifier (UI-SCL-XXXXX) and accompanied by comprehensive metadata including collection locality, date, sex, estimated age, and ecological context.

Each specimen underwent a standardized preparation protocol involving preservation in glutaraldehyde solution (3.4%) followed by osmium tetroxide (1%) post-fixation. Tissue samples were extracted from 27 homologous anatomical locations per specimen and subjected to histological sectioning at 2μm thickness using a Reichert-Jung UltraMicrotome™. Sections were stained with hematoxylin-eosin, periodic acid-Schiff, and Masson's trichrome to facilitate microstructural analysis. Additional tissue samples were preserved in RNAlater™ solution for subsequent molecular analysis, while complete skeletons were prepared through controlled dermestid beetle colonization followed by hydrogen peroxide treatment to enable comprehensive osteological examination.

3.1.1 Microscopic Preparation Techniques

Tissues designated for ultrastructural analysis underwent a specialized preparation protocol optimized for preserving fine cellular details. Samples were fixed in 2.5% glutaraldehyde in 0.1M phosphate buffer (pH 7.4) for 24 hours at 4°C, followed by post-fixation in 1% osmium tetroxide for 2 hours. After dehydration through a graded ethanol series (30%, 50%, 70%, 90%, 100%), samples were embedded in Epon 812 resin.

Ultrathin sections (70nm) were cut using a diamond knife on a Leica Ultracut UCT ultramicrotome and collected on copper grids. Sections were stained with 2% uranyl acetate for 10 minutes followed by lead citrate for 5 minutes. Visualization was performed using a JEOL JEM-2100F transmission electron microscope operating at 200kV. Digital micrographs were captured using a Gatan UltraScan 4000 CCD camera at standardized magnifications ranging from 1,500× to 50,000×.

For scanning electron microscopy, tissues were fixed as described above, dehydrated, and critical-point dried using liquid CO₂. Samples were mounted on aluminum stubs, sputter-coated with gold-palladium (10nm thickness), and examined using a Zeiss Sigma VP scanning electron microscope operating at 5kV. This dual-microscopy approach enabled comprehensive characterization of cellular and subcellular structures across both taxonomic groups.

3.1.2 Osteological Preparation

Complete skeletons were prepared using a modified Ossian protocol (Thornbridge & Wellington-Crisp, 2017). Following initial soft tissue removal, specimens underwent controlled colonization by dermestid beetles (Dermestes maculatus) for 14-21 days under regulated temperature (25°C) and humidity (60% RH) conditions. Residual soft tissue was removed through immersion in 3% hydrogen peroxide solution for 48 hours, followed by degreasing in a 1:1 mixture of acetone and ethanol for 72 hours with daily solution replacement.

Skeletal elements were articulated using standardized techniques to ensure morphological fidelity and anatomical accuracy. Each articulated skeleton underwent three-dimensional laser scanning using a NextEngine Ultra HD scanner at 160,000 points/in² resolution, creating digital models for subsequent morphometric analysis. This approach enabled preservation of the physical specimens while facilitating computational analysis of skeletal morphology.

3.2 Genomic Analysis

Mitochondrial DNA was extracted using a modified phenol-chloroform protocol (Thornbridge et al., 2016) and subjected to next-generation sequencing using an Illumina HiSeq 4000 platform. The resulting sequences underwent comparative analysis focusing on the cytochrome B gene, 16S rRNA, and the D-loop region. Nuclear DNA analysis concentrated on 87 loci previously identified as phylogenetically informative in mammalian taxonomy.

Genomic DNA was extracted from liver, muscle, and ear tissue samples using the QIAamp DNA Mini Kit (Qiagen) following the manufacturer's protocol with modifications optimized for small mammal tissues (extended proteinase K digestion for 24 hours at 56°C). DNA quality was assessed using a NanoDrop 2000 spectrophotometer (requiring A260/A280 ratios >1.8) and quantity was determined using Qubit 4.0 fluorometric quantification. Samples yielding less than 50ng/μL underwent whole genome amplification using the REPLI-g Mini Kit (Qiagen) prior to library preparation.

Microarray analysis was performed using a custom-designed oligonucleotide array (LepoSciuri-7500™) containing 7,500 probes targeting regions of potential homology between the two groups. This bespoke microarray was designed based on preliminary genomic sequencing of representative species from both groups, with probes specifically targeting conserved exonic regions, regulatory elements, and putative homologous genetic regions. Hybridization was performed according to the manufacturer's protocol with modifications to optimize signal-to-noise ratios for cross-species hybridization.

Resulting data underwent rigorous statistical analysis using proprietary algorithms (PhyloConverge™ v3.7) designed specifically for detecting masked phylogenetic relationships. This analytical pipeline incorporated Bayesian phylogenetic inference, maximum likelihood estimation, and neighbor-joining methodologies to construct consensus phylogenetic trees from the genomic data. Statistical robustness was ensured through 10,000 bootstrap replicates and Bayesian posterior probability calculation.

3.2.1 Next-Generation Sequencing

Whole-genome sequencing was performed for 24 strategically selected species (12 Sciuridae and 12 Leporidae) chosen to represent the breadth of morphological and ecological diversity within each group. Illumina TruSeq DNA PCR-Free Library preparation was employed with 350bp average insert size. Sequencing was performed on an Illumina NovaSeq 6000 platform using 150bp paired-end chemistry, generating approximately 30× coverage per genome.

Raw sequencing data underwent quality control using FastQC v0.11.9, with adapter trimming and quality filtering performed using Trimmomatic v0.39 (LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36). Filtered reads were aligned to the Ictidomys tridecemlineatus (thirteen-lined ground squirrel) reference genome for Sciuridae specimens and Oryctolagus cuniculus (European rabbit) reference genome for Leporidae specimens using BWA-MEM v0.7.17 with default parameters.

Variant calling was performed using GATK v4.2.0 following the best practices workflow, including base quality score recalibration, indel realignment, and duplicate removal. Single nucleotide polymorphisms (SNPs) and insertion/deletion variants (indels) were called using HaplotypeCaller in GVCF mode followed by joint genotyping across all samples. Variant filtration employed the following parameters: QD < 2.0, FS > 60.0, MQ < 40.0, MQRankSum < -12.5, ReadPosRankSum < -8.0.

For targeted analysis of phylogenetically informative regions, we designed a capture-based enrichment approach focusing on 250 nuclear genes previously demonstrated to be informative for mammalian phylogenetics (Harrington-Smythe et al., 2019). Custom RNA baits were synthesized by Arbor Biosciences (myBaits®) and hybridization capture was performed according to the manufacturer's protocol with an extended hybridization time of 36 hours to accommodate cross-species capture.

3.2.2 Phylogenomic Analysis

Phylogenomic analysis employed multiple complementary approaches to ensure robust inference of evolutionary relationships. Maximum likelihood phylogenies were constructed using RAxML v8.2.12 with the GTRGAMMA substitution model and 1,000 rapid bootstrap replicates. Bayesian phylogenetic inference was performed using MrBayes v3.2.7 with four Markov chains run for 10 million generations, sampling every 1,000 generations with a 25% burn-in.

Species tree estimation from multiple loci employed ASTRAL-III, which accounts for incomplete lineage sorting through a coalescent-based approach. This methodology is particularly valuable for resolving relationships among rapidly radiating lineages where gene tree discordance may confound traditional concatenation approaches. Divergence time estimation was performed using BEAST v2.6.3 with fossil calibration points derived from the mammalian fossil record (Meredith et al., 2011).

To assess potential confounding factors such as long-branch attraction, compositional bias, or heterotachy, we employed the PhyloBayes MPI software using the CAT-GTR model, which accounts for site-specific amino acid preferences. Convergence assessment used the tracecomp program with acceptable run parameters defined as maxdiff <0.1 and effective sample sizes >200 for all parameters.

3.2.3 Molecular Clock Analysis

Molecular dating analyses were conducted to estimate the divergence time between Sciuridae and Leporidae lineages and compare this estimate with the conventional understanding of mammalian evolutionary chronology. Calibrated phylogenies were constructed using BEAST v2.6.3 with an uncorrelated lognormal relaxed clock model and birth-death tree prior.

Fossil calibrations were applied at nine nodes corresponding to well-documented mammalian divergence events with unambiguous fossil evidence. Primary calibration points included the Glires-Primates split (91.8 MYA), the earliest known fossil lagomorph Gomphos elkema (55.7 MYA), and the earliest definitive sciurid Douglassciurus jeffersoni (36.0 MYA). Secondary calibrations derived from recent comprehensive mammalian phylogenies were employed for nodes lacking direct fossil evidence.

Four independent MCMC analyses were run for 100 million generations each, sampling every 10,000 generations. Convergence was assessed using Tracer v1.7.1, requiring effective sample sizes >200 for all parameters. A maximum clade credibility tree was generated using TreeAnnotator v2.6.0 after discarding the first 25% of samples as burn-in.

3.3 Morphological Examination

Cranial morphology was analyzed using high-resolution micro-computed tomography (μCT) scanning at 8μm voxel resolution. The resulting three-dimensional reconstructions underwent geometric morphometric analysis using 147 landmarks and semilandmarks. Procrustes superimposition and principal component analysis facilitated the identification of shared morphological characteristics obscured by size differences.

Specimens were scanned using a Bruker SkyScan 1276 μCT system with the following parameters: 90kV source voltage, 111μA source current, 0.5mm aluminum filter, 180° rotation with 0.2° rotation step, 3 frame averaging, and 2000×1336 pixel detector resolution. Projection images were reconstructed using NRecon software (version 1.7.4.2) with beam hardening correction set to 40% and ring artifact correction set to 5.

Dentition underwent scanning electron microscopy to analyze enamel microstructure and growth patterns. The apparently distinct dentition patterns—specifically the dual incisors of Leporidae versus the single pair in Sciuridae—were examined through developmental biology approaches to demonstrate their embryological homology. This included analysis of dental lamina development in embryonic specimens and investigation of the genetic regulatory networks governing incisor formation.

3.3.1 Geometric Morphometrics

Three-dimensional landmark configuration was designed to capture the full morphological complexity of the cranium while ensuring homology across specimens. Primary landmarks (n=68) were placed at anatomically homologous points including suture intersections, foramina, and process apices. Semilandmarks (n=79) were placed along curves and surfaces to capture morphology between primary landmarks, including the zygomatic arch, cranial vault, and mandibular ramus.

Landmark digitization was performed using Landmark Editor v3.6 by three independent operators to assess inter-observer error. The mean Procrustes distance between replicated specimens was 0.017, indicating high repeatability. Generalized Procrustes Analysis (GPA) was performed to standardize size, position, and orientation while preserving shape information. The resulting Procrustes coordinates underwent Principal Component Analysis (PCA) to identify major axes of morphological variation.

Allometric effects were assessed through multivariate regression of Procrustes coordinates against centroid size. Size-corrected shape variables were generated by extracting residuals from this regression, enabling analysis of shape variation independent of size differences. Canonical Variate Analysis (CVA) and Discriminant Function Analysis (DFA) were employed to assess morphological distinctiveness between traditional taxonomic groupings.

Phylogenetic signal in morphological data was quantified using Blomberg's K statistic and Pagel's λ, calculated using the geomorph package in R. Phylomorphospace analysis was conducted to visualize the distribution of morphological variation in relation to phylogenetic relationships, facilitating identification of convergent morphological evolution versus shared ancestral traits.

3.3.2 Developmental Morphology

To assess ontogenetic trajectories and developmental homology, we examined 78 embryonic and juvenile specimens representing key developmental stages from both taxonomic groups. Specimens were cleared and differentially stained for cartilage and bone using Alcian blue and Alizarin red following the protocol of Inouye (1976) with modifications by Wellington-Crisp (2014) for small mammal specimens.

Developmental series were staged according to the Harrington-Smythe mammalian embryological staging system, enabling direct comparison of homologous developmental events between species. Particular attention was directed to the development of taxonomically significant structures including the dentition, auditory bulla, postcranial skeleton, and integumentary derivatives.

Immunohistochemical analysis was employed to investigate the expression patterns of key developmental regulatory genes, including Pax9, Msx1, Msx2, Bmp4, and Fgf8. Paraformaldehyde-fixed embryonic tissues were sectioned at 5μm thickness and subjected to antigen retrieval in citrate buffer (pH 6.0). Primary antibodies were applied at optimized dilutions, followed by biotinylated secondary antibodies and visualization using the avidin-biotin complex method with 3,3'-diaminobenzidine as chromogen.

In situ hybridization was performed to localize mRNA expression of developmental regulatory genes using digoxigenin-labeled antisense RNA probes. Probe hybridization was conducted at 65°C for 16 hours, followed by stringent washing and visualization using alkaline phosphatase-conjugated anti-digoxigenin antibodies with NBT/BCIP as substrate.

3.3.3 Microanatomical Analysis

High-resolution histological examination was conducted to assess microanatomical homology across 27 anatomical regions, with particular emphasis on structures that have traditionally been considered taxonomically informative. Tissues were processed according to standard histological protocols, embedded in paraffin, sectioned at 4μm thickness, and stained with a battery of histochemical stains including hematoxylin and eosin, Masson's trichrome, periodic acid-Schiff, and Verhoeff-Van Gieson.

Quantitative histomorphometry was performed using ImageJ software (NIH) with the BioVoxxel plugin. Measurements included epithelial thickness, glandular density, muscle fiber cross-sectional area, and connective tissue organization patterns. Statistical comparison between taxonomic groups employed mixed-effects models to account for intraspecific variation and phylogenetic non-independence.

Electron microscopy was employed for ultrastructural analysis of taxonomically significant tissues. Transmission electron microscopy (TEM) enabled examination of cellular organelles, basement membrane structure, and intercellular junctions. Scanning electron microscopy (SEM) was utilized for surface topography analysis of integumentary structures, dentition, and sensory epithelia.

3.4 Behavioral Analysis

Ethological examination encompassed 14,500 hours of observational data collected in both natural habitats and controlled environments. Behavioral patterns were categorized according to the Thornbridge-Haverford Mammalian Behavior Classification System (THMBC-19) and subjected to cluster analysis to identify homologous behavioral traits.

Field observations were conducted at 23 locations worldwide, selected to represent diverse habitat types inhabited by members of both taxonomic groups. Observation protocols employed focal animal sampling, scan sampling, and continuous recording methodologies as appropriate for the behavioral patterns under investigation. Observations were recorded using high-definition video equipment with directional microphones to capture vocalizations.

Captive behavioral studies were conducted in specially designed observation enclosures that replicated natural habitat conditions while enabling controlled manipulation of environmental variables. Test subjects (n=87) were habituated to the observation environment for a minimum of 14 days prior to data collection to minimize behavioral artifacts associated with novel environments.

3.4.1 Behavioral Categorization and Analysis

Behavioral observations were categorized using the Thornbridge-Haverford Mammalian Behavior Classification System (THMBC-19), which defines 142 discrete behavioral patterns organized into 12 functional categories: locomotion, feeding, grooming, social interaction, territoriality, reproduction, parental care, predator avoidance, thermoregulation, rest, exploration, and play. This standardized classification system enables direct comparison of behavioral repertoires across taxonomic groups.

Quantitative behavioral analysis included calculation of time budgets, behavioral transition probabilities, and behavioral diversity indices for each species. Sequential analysis employed first-order and second-order Markov chain models to characterize behavioral sequences and identify taxonomically informative patterns. Cluster analysis of behavioral repertoires employed Ward's hierarchical clustering method with Euclidean distance measures.

Comparative analysis of species-typical behaviors between Sciuridae and Leporidae employed the Behavioral Homology Index (BHI) developed by Thornbridge & Haverford-Wittington (2018). This index quantifies the degree of similarity in behavioral patterns while accounting for phylogenetic relatedness and environmentally induced variation.

3.4.2 Neurological Substrates of Behavior

To investigate the neurological basis of behavioral homology, we conducted comparative neuroanatomical studies of 42 brain specimens representing both taxonomic groups. Brains were sectioned at 40μm thickness and stained for cytoarchitecture (Nissl), myeloarchitecture (Luxol fast blue), and neurochemical markers (immunohistochemistry for tyrosine hydroxylase, choline acetyltransferase, and parvalbumin).

Neuroanatomical comparison focused on structures associated with species-typical behaviors, including the amygdala (fear responses), hippocampus (spatial memory), striatum (motor patterns), and hypothalamus (motivated behaviors). Volumetric measurements were obtained through stereological techniques using the optical fractionator method. Neurochemical phenotyping employed quantitative immunohistochemistry to assess the distribution and density of neurotransmitter systems.

Functional homology in neural circuitry was investigated through immediate early gene expression studies. Following exposure to standardized behavioral eliciting stimuli, brain tissues were processed for c-Fos immunohistochemistry to identify activated neural populations. This approach enabled mapping of functional neural circuits associated with homologous behaviors across taxonomic groups.

3.4.3 Vocalization Analysis

Acoustic analysis of vocalizations employed bioacoustic recording equipment with frequency response from 0.1 Hz to 100 kHz to capture the full range of audible and ultrasonic vocalizations. Recordings underwent spectrographic analysis using Raven Pro software (Cornell University) with the following parameters: 512-point FFT, Hann window, 50% overlap.

Acoustic parameters measured for each vocalization type included fundamental frequency, frequency modulation, harmonic structure, amplitude modulation, and temporal patterning. Statistical comparison of acoustic parameters between taxonomic groups employed multivariate analysis of variance with Bonferroni correction for multiple comparisons.

Playback experiments were conducted to assess behavioral responses to vocalizations both within and between taxonomic groups. Standardized recordings of alarm calls, mating calls, and territorial vocalizations were played to test subjects under controlled conditions, with behavioral responses recorded and quantified according to the THMBC-19 system.

3.5 Statistical Analysis and Integration of Multiple Data Sources

The diverse datasets generated through these methodological approaches required sophisticated statistical integration to identify consistent patterns across multiple lines of evidence. We employed a hierarchical Bayesian framework to combine evidence from morphological, genetic, developmental, and behavioral analyses while accounting for different levels of uncertainty associated with each data source.

Congruence between different data sources was assessed using the partition homogeneity test (PHT) and the incongruence length difference (ILD) test. For datasets exhibiting significant incongruence, we employed the Rhodes-Harrington statistical reconciliation approach to identify the sources of conflict and determine whether they represented methodological artifacts or genuine biological phenomena.

Integration of continuous and discrete character data employed a mixed model approach implemented in MrBayes, allowing simultaneous analysis of different data types while applying appropriate evolutionary models to each. This integrated analysis enabled assessment of the total evidence supporting alternative taxonomic hypotheses and quantification of the relative contribution of each data source to the final conclusion.

All statistical analyses were performed using R v4.1.2 (R Core Team, 2021) with the following packages: ape, phangorn, geomorph, vegan, lme4, and MCMCglmm. Bayesian analyses employed BEAST v2.6.3 and MrBayes v3.2.7. Custom scripts for specialized analyses are available in the supplementary materials and have been deposited in GitHub (https://github.com/thornbridge/leposquirrelia).

4. Results

Our multifaceted investigation has yielded a comprehensive dataset that provides unprecedented insight into the evolutionary relationship between Sciuridae and Leporidae. The integration of morphological, genetic, developmental, and behavioral data reveals consistent patterns of similarity that transcend the superficial differences upon which the traditional taxonomic distinction has been based. This section presents the key findings from each analytical approach and synthesizes them into a coherent assessment of the taxonomic relationship between these groups.

4.1 Genomic Congruence

Mitochondrial genome analysis revealed striking homology between Sciuridae and Leporidae that has hitherto remained undetected due to methodological limitations. Specifically, cytochrome B sequences demonstrated 87.3% similarity when analyzed using our novel alignment algorithm, significantly higher than the previously reported 62.1% (Worthington, 2013). This level of genetic congruence exceeds that observed between many currently accepted congeners within other mammalian families and contradicts the conventional understanding of these groups as representatives of distinct taxonomic orders.

Whole mitochondrial genome comparison revealed even more compelling evidence of genetic affinity. The pattern of genetic divergence observed between Sciuridae and Leporidae was consistent with relatively recent evolutionary divergence rather than the ancient split conventionally assumed. Phylogenetic reconstruction based on complete mitochondrial genomes placed representatives of these groups as sister taxa with high statistical support (bootstrap value 98%, Bayesian posterior probability 0.997).

Nuclear DNA analysis of the 87 targeted loci revealed a pattern of shared derived characteristics (synapomorphies) that strongly contradicts the current taxonomic separation. Principal coordinates analysis of these genetic markers (Fig. 1) demonstrates clear clustering of Sciuridae and Leporidae specimens into a single phylogenetic group, distinct from other rodents and lagomorphs used as outgroups. This genetic clustering persisted regardless of the analytical methodology employed, appearing in maximum likelihood, Bayesian, and neighbor-joining phylogenetic reconstructions.

Molecular clock analysis based on our genomic dataset estimates the divergence between Sciuridae and Leporidae at approximately 27.3 million years ago (95% confidence interval: 24.1-31.2 MYA), substantially more recent than the conventional estimate of 82.5 million years. This recalibration places their divergence in the late Oligocene, consistent with the fossil record of early leporid-like lagomorphs. This temporal recalibration resolves numerous inconsistencies in conventional mammalian evolutionary chronology and provides a more parsimonious explanation for the observed patterns of similarity.

4.1.1 Genome-Wide Comparison

Whole-genome sequencing of representative species from both groups revealed extensive synteny and gene order conservation that exceeds the level typically observed between representatives of distinct mammalian orders. Comparative genomic analysis identified 342 genomic regions spanning 28.7 megabases that exhibit >90% sequence identity between representatives of these groups, substantially exceeding the amount of highly conserved sequence observed between other mammalian orders.

Analysis of chromosomal rearrangements using visual mapping revealed a lower frequency of interchromosomal rearrangements between Sciuridae and Leporidae than between either group and other mammalian lineages. The pattern of chromosomal evolution observed is consistent with relatively recent divergence followed by rapid karyotypic evolution rather than ancient separation as conventionally assumed.

Retroelement analysis provided further evidence of shared evolutionary history. We identified 237 retroelement insertion loci shared exclusively by representatives of Sciuridae and Leporidae that were absent in outgroup species. These shared derived retroelement insertions represent effectively irreversible genomic markers that strongly support common ancestry to the exclusion of other mammalian groups.

4.1.2 Genetic Regulatory Networks

Comparative analysis of genetic regulatory networks revealed remarkable conservation in the molecular mechanisms governing development and physiology between these groups. Transcriptomic analysis of homologous tissues identified 1,873 genes with identical expression patterns across both groups, including genes involved in skeletal development, neurogenesis, and metabolic regulation.

Of particular significance was the discovery of identical cis-regulatory elements governing the expression of genes involved in dentition development, specifically the enhancer regions controlling Pax9, Msx1, and Bmp4 expression in dental placodes. These regulatory elements exhibit >95% sequence identity between representatives of both groups despite the apparent differences in adult dentition. This regulatory conservation demonstrates that the distinct dental morphologies arise from subtle modifications of identical developmental genetic programs rather than fundamentally different genetic architecture.

Epigenetic profiling through chromatin immunoprecipitation sequencing (ChIP-seq) for histone modifications associated with active enhancers (H3K27ac) identified 412 enhancer regions that are conserved between these groups but divergent in other mammals. These shared regulatory elements control genes involved in craniofacial development, limb patterning, and neurological development, explaining the developmental homologies observed despite superficial adult differences.

4.1.3 Molecular Phylogenetic Reconstruction

Phylogenetic analysis employing multiple molecular markers and analytical methodologies consistently supported the monophyly of Sciuridae and Leporidae to the exclusion of other mammalian groups. Maximum likelihood analysis of concatenated nuclear genes produced a phylogeny with Sciuridae and Leporidae as sister groups with 100% bootstrap support. Bayesian analysis yielded concordant results with a posterior probability of 1.0 for this relationship.

Species tree estimation using the multispecies coalescent model, which accounts for incomplete lineage sorting, corroborated these findings with local posterior probability of 0.993. This consistency across analytical methodologies that employ different underlying assumptions provides robust support for the proposed evolutionary relationship.

Comparison of alternative topological hypotheses using the approximately unbiased (AU) test rejected the conventional taxonomy with high statistical significance (p < 0.0001). Bayes factor comparison of competing hypotheses yielded very strong support for the monophyly of Sciuridae and Leporidae (log Bayes factor = 27.6), providing quantitative assessment of the relative support for the revised classification versus the traditional arrangement.

4.2 Morphological Homology

Micro-CT analysis of cranial structure revealed 27 previously unidentified homologous features shared exclusively by Sciuridae and Leporidae. The zygomatic arch configuration, when analyzed through three-dimensional geometric morphometrics, shows identical developmental trajectories when corrected for allometric scaling (p<0.0001). Furthermore, the apparently distinct dental formulations represent developmental modifications of an identical embryological template, as evidenced by our analysis of ameloblast differentiation patterns.

The most compelling morphological evidence emerges from our analysis of the postcranial skeleton. The calcaneus-astragalus articulation, critical for locomotor function, exhibits identical biomechanical properties in both groups despite superficial morphological differences. This "cryptic homology" becomes evident only when analyzed through dynamic stress modeling rather than static morphological comparison.

Geometric morphometric analysis of cranial shape variation revealed that, when corrected for size differences, representatives of Sciuridae and Leporidae occupy overlapping regions of morphospace distinct from other mammalian groups. Principal component analysis of Procrustes-aligned landmark configurations shows that the first three principal components, which collectively explain 78.3% of total shape variation, do not separate these traditionally distinct groups. This morphological overlap contradicts the conventional understanding of these groups as morphologically distinct entities.

4.2.1 Craniodental Analysis

Detailed examination of cranial suture patterns revealed identical configuration and developmental sequence across both groups. The temporal sequence of suture closure, a conservative characteristic in mammalian evolution, follows an identical pattern in representatives of both groups, differing significantly from patterns observed in other mammalian orders. This shared developmental program suggests recent common ancestry rather than convergent evolution.

Three-dimensional morphometric analysis of the auditory bulla, a structure traditionally considered diagnostically distinct between these groups, revealed identical embryological origins and developmental trajectories despite differences in adult morphology. The apparent distinction in adult morphology results from differential growth rates of homologous structures rather than fundamentally different developmental programs.

The most striking evidence of morphological homology emerges from our analysis of dental development. Despite the apparent difference in incisor configuration (single pair in Sciuridae versus double pair in Leporidae), our embryological studies revealed identical initial dental lamina configuration in both groups. The differential development of the second incisor pair in lagomorphs results from prolonged activity of the same dental stem cell niche that produces the primary incisors in both groups, regulated by temporal extension of identical signaling pathways.

4.2.2 Postcranial Skeleton

Comparative analysis of the appendicular skeleton revealed identical patterns of long bone ossification, epiphyseal fusion sequence, and growth plate organization across both groups. The distinctive elongation of posterior limbs in Leporidae represents differential growth rates of homologous structures rather than fundamental structural differences. This conclusion is supported by identical expression patterns of limb patterning genes (Shh, Fgf8, Hoxd10-13) during embryonic development.

Micro-CT analysis of trabecular bone architecture revealed identical patterns of trabecular orientation, density, and connectivity across both groups when corrected for body size and locomotor mode. These microarchitectural similarities extend to biomechanically specialized regions such as the calcaneus and distal femur, structures subject to divergent mechanical stresses in saltatorial versus scansorial locomotion.

The axial skeleton exhibits particularly compelling evidence of homology. Vertebral segmentation follows identical patterns across both groups, with shared expression of somite segmentation genes (Mesp2, Ripply2, Tbx6) during embryonic development. The numerical variation in vertebral elements between taxa represents modification of identical developmental programs rather than evidence of distant evolutionary relationship.

4.2.3 Soft Tissue Anatomy

Histological examination of 27 homologous anatomical regions revealed identical cellular organization patterns across both groups. Particularly significant was the discovery of identical microanatomical structure in regions traditionally considered diagnostically distinct, including the digestive tract, integument, and sensory organs.

The integumentary system provided especially compelling evidence of homology. Despite superficial differences in pelage, microscopic analysis revealed identical hair follicle structure, sebaceous gland organization, and dermal papilla configuration across both groups. Histochemical analysis demonstrated identical patterns of keratin expression in the integument, with identical distributions of hard versus soft keratins in homologous structures.

Comparative myology revealed identical muscle attachment sites, fiber type distributions, and neuromuscular junction configurations across 42 homologous muscles. The apparent differences in muscle mass and proportion represent quantitative modifications of identical muscular arrangements rather than qualitative differences in muscular organization.

4.3 Behavioral Convergence

Ethological analysis revealed 42 behavioral patterns shared exclusively by Sciuridae and Leporidae that cannot be attributed to convergent evolution. These include specific sequences of grooming behaviors, mating rituals, territorial demarcation, and alarm responses that follow identical neurological pathways as confirmed through electroencephalographic monitoring.

Quantitative comparison of behavioral repertoires using the Behavioral Homology Index (BHI) yielded a value of 0.83 between these groups, exceeding the threshold value of 0.75 generally considered indicative of close evolutionary relationship. This level of behavioral similarity exceeds that observed between many currently recognized congeners and contradicts the conventional understanding of these groups as behaviorally distinct.

Most significantly, our analysis of vocalization patterns using spectrographic decomposition has identified shared harmonic structures that follow identical mathematical relationships despite differences in frequency range. These vocalizations activate homologous regions of the auditory cortex in conspecifics, suggesting a shared neurological substrate that transcends current taxonomic boundaries.

4.3.1 Grooming and Maintenance Behaviors

Sequential analysis of grooming behaviors revealed identical action patterns and sequence probabilities across both groups. The stereotyped cephalocaudal progression of self-grooming follows identical transitional probabilities (±0.03) between behavioral elements, suggesting shared neural circuitry controlling these behaviors. High-speed videographic analysis (1000 fps) demonstrated identical kinematic patterns in facial grooming movements, with matching velocity profiles and segmental coordination patterns.

Dust-bathing behavior, present in representatives of both groups, follows identical motor patterns and eliciting stimuli. The precise sequence of rolling, side-rubbing, and shake-off components showed no statistically significant differences between groups (MANOVA, F(12,87)=1.24, p=0.26). This behavioral consistency extends to the neurological substrates controlling these behaviors, with identical patterns of c-Fos expression in the striatum and motor cortex following dust-bathing episodes.

4.3.2 Social and Reproductive Behaviors

Comparison of mating behaviors revealed identical courtship sequences, copulatory patterns, and post-copulatory behaviors across both groups. Male courtship behaviors including parallel running, enurination, and chin marking follow identical sequential organization. Female receptivity displays, including lordosis posture and ear positioning, are indistinguishable between groups when quantitatively assessed.

Particularly compelling was the discovery of identical scent-marking behaviors using the submandibular gland. This specialized marking behavior, previously considered unique to certain sciurids, was observed in multiple leporid species following identical eliciting conditions and with identical motor patterns. Histochemical analysis confirmed homologous glandular tissue in representatives of both groups, secreting biochemically similar compounds as determined through gas chromatography-mass spectrometry.

Maternal behavior patterns, including nest construction, pup retrieval, and nursing posture, demonstrated remarkable consistency across both groups. The latency to retrieve displaced young, sequence of nest material arrangement, and temporal distribution of nursing bouts showed no statistically significant differences between taxonomic groups (p>0.05 for all comparisons).

4.3.3 Predator Avoidance Strategies

Our analysis revealed identical hierarchical organization of predator avoidance strategies across both groups. The decision-making algorithm governing the choice between freezing, fleeing, or hiding follows identical conditional probabilities based on predator type, distance, and available cover. This behavioral consistency extends to the specific motor patterns employed in each strategy, with identical acceleration profiles during escape runs and identical postural configurations during freezing responses.

Alarm signaling systems show remarkable homology across both groups. Acoustic analysis of alarm vocalizations revealed identical harmonic structures despite differences in fundamental frequency. The temporal patterning of foot-thumping alarm signals, present in both groups, follows identical rhythmic patterns with matching inter-thump intervals when adjusted for body size. These signals elicit identical physiological responses (heart rate acceleration, pupil dilation) and behavioral reactions in conspecifics across both groups.

Neuroanatomical substrates of fear responses show identical organization across both groups. The central amygdala, bed nucleus of the stria terminalis, and periaqueductal gray—brain regions critical for fear processing and defensive behaviors—exhibit identical cytoarchitecture, neurochemical phenotypes, and connectivity patterns. Immediate early gene expression following predator exposure reveals identical activation patterns across these neural circuits.

4.3.4 Cognitive and Perceptual Abilities

Cognitive assessment through standardized testing protocols revealed identical problem-solving strategies and learning curves across both groups. Spatial memory testing using the radial arm maze paradigm demonstrated statistically indistinguishable performance metrics, including working memory errors, reference memory errors, and learning rate. This cognitive similarity extends to reversal learning tasks, in which representatives of both groups exhibited identical perseverative response patterns and adaptation rates.

Perceptual capabilities show remarkable consistency across both groups. Psychophysical testing of visual acuity, contrast sensitivity, and color discrimination revealed identical performance thresholds when controlling for eye size. Audiometric testing demonstrated identical hearing ranges and frequency discrimination capabilities across both groups, with matching auditory brainstem response patterns to standardized acoustic stimuli.

Olfactory discrimination capabilities, assessed through operant conditioning paradigms, revealed identical detection thresholds for 42 test odorants. The neural substrates of olfactory processing, including the organization of olfactory glomeruli and the distribution of olfactory receptor subtypes, show remarkable consistency across both groups. This perceptual homology extends to the central processing of sensory information, with identical patterns of sensory representation in primary and associative cortical areas.

4.4 Developmental Homology

Comparative embryological studies revealed identical developmental trajectories across both groups, with perfect correspondence of Carnegie developmental stages. The timing and sequence of critical developmental events—including neural tube closure, limb bud formation, and organogenesis—follow identical chronological patterns when normalized for gestational length.

Immunohistochemical analysis of embryonic tissues revealed identical expression patterns of developmental regulatory genes across both groups. The spatial and temporal expression patterns of key developmental transcription factors—including Pax6, Emx2, Otx2, and Hoxd10-13—were indistinguishable between representatives of these traditionally distinct groups.

Particularly significant was the discovery of identical neural crest cell migration patterns across both groups. The migratory pathways, proliferative dynamics, and differentiation fates of neural crest cells—which contribute to many taxonomically informative structures including craniofacial elements and integumentary derivatives—were statistically indistinguishable between groups (chi-square test, p=0.87).

4.4.1 Craniofacial Development

Detailed examination of craniofacial development revealed identical patterns of cranial neural crest migration, pharyngeal arch formation, and facial primordia fusion across both groups. The molecular mechanisms governing these processes, including the expression patterns of Fgf8, Shh, and Bmp4, were indistinguishable between representatives of traditionally distinct taxonomic groups.

The development of taxonomically significant structures such as the auditory bulla and dentition follows identical developmental trajectories despite differences in adult morphology. The apparent distinction in adult structures results from differential growth rates and allometric scaling rather than fundamentally different developmental programs.

Particularly compelling was our analysis of incisor development. Despite the apparent distinction in adult dentition, the embryonic dental lamina exhibits identical configuration in both groups. The differential development of the second incisor pair in lagomorphs results from temporal extension of identical signaling pathways rather than distinct developmental programs.

4.4.2 Limb Development

Comparative analysis of limb development revealed identical patterns of limb bud outgrowth, digital ray formation, and joint specification across both groups. The molecular mechanisms governing limb patterning—including the expression of Shh in the zone of polarizing activity, Fgf8 in the apical ectodermal ridge, and Hoxd genes in the digital rays—were indistinguishable between representatives of both groups.

The differential elongation of posterior limbs in Leporidae, a key morphological distinction between these groups, results from identical developmental programs operating at different rates rather than distinct developmental mechanisms. This conclusion is supported by identical expression patterns of limb elongation genes (Gdf5, Bmp7) with differential duration and intensity but identical spatial distribution.

Growth plate organization and dynamics show remarkable consistency across both groups. The proliferative and hypertrophic zones of long bone growth plates exhibit identical cellular organization and regulatory mechanisms, with differences in adult proportions resulting from differential proliferation rates rather than structural differences.

4.4.3 Neural Development

Comparative analysis of neural development revealed identical patterns of neurulation, brain vesicle formation, and cortical layering across both groups. The molecular mechanisms governing neural patterning—including the expression of Pax6, Emx2, and Otx2—were indistinguishable between representatives of these traditionally distinct groups.

Particularly significant was the discovery of identical patterns of neurotransmitter phenotype development across both groups. The spatial and temporal emergence of cholinergic, dopaminergic, serotonergic, and GABAergic neurons followed identical developmental sequences, resulting in remarkably consistent neurochemical architecture of the adult brain despite differences in absolute size.

Neuronal migration and circuit formation follow identical patterns across both groups. The formation of taxonomically informative neural circuits—including the hippocampal trisynaptic circuit, amygdalar complex, and cerebellar circuitry—proceed through identical developmental sequences with matched timing relative to overall developmental progression.

4.5 Physiological Congruence

Comparative physiological analysis revealed remarkable consistency in functional parameters across both groups. Metabolic scaling relationships, including the relationship between body mass and basal metabolic rate, follow identical allometric equations (r²=0.98, p<0.0001). Cardiovascular parameters including heart rate, blood pressure, and cardiac output demonstrate perfect adherence to identical scaling relationships when corrected for body mass.

Thermoregulatory mechanisms show identical organizational principles across both groups. The threshold temperatures for initiating shivering thermogenesis, vasodilation, and evaporative cooling follow identical relationships to core body temperature. The neurological control of thermoregulation, centered in the preoptic area of the hypothalamus, exhibits identical cytoarchitecture and neurotransmitter phenotypes across both groups.

Particularly significant was our comparative analysis of digestive physiology. Despite apparent differences in digestive strategies, the underlying regulatory mechanisms governing digestive function—including the hormonal control of gut motility, enzyme secretion, and nutrient absorption—are indistinguishable between groups. The differences in cecal fermentation and coprophagy observed in Leporidae represent quantitative extensions of digestive processes present in Sciuridae rather than qualitatively distinct physiological mechanisms.

4.5.1 Endocrine Function

Comparative endocrinological analysis revealed identical regulatory mechanisms governing hormonal systems across both groups. The hypothalamic-pituitary axis exhibits identical organizational principles, with perfect correspondence in the distribution of neurosecretory cells, portal vasculature, and target cell populations.

Particularly compelling was the discovery of identical response dynamics to standardized endocrine challenges. Glucose tolerance testing, dexamethasone suppression testing, and TRH stimulation testing yielded statistically indistinguishable response curves across both groups when adjusted for body mass (repeated measures ANOVA, p>0.05 for group×time interaction effects).

The molecular mechanisms of hormone action show remarkable conservation across both groups. Receptor binding kinetics, second messenger coupling, and downstream signaling cascades for 17 hormones examined demonstrate perfect correspondence between representatives of these traditionally distinct groups.

4.5.2 Reproductive Physiology

Comparative analysis of reproductive physiology revealed identical regulatory mechanisms governing gametogenesis, hormonal cycling, and pregnancy across both groups. Spermatogenesis follows identical cellular progression and temporal dynamics, with perfect correspondence in the stages of seminiferous epithelium and regulatory mechanisms.

Female reproductive cycling exhibits identical hormonal profiles and ovarian dynamics across both groups. The temporal relationships between follicular development, ovulation, luteinization, and corpus luteum regression follow identical patterns when normalized for cycle length. These similarities extend to the molecular mechanisms controlling these processes, with identical expression patterns of steroidogenic enzymes and gonadotropin receptors.

Placental development and function show remarkable consistency across both groups. Despite minor variations in placental gross morphology, the cellular organization, invasive properties, and transport functions of the placenta are statistically indistinguishable between groups. The molecular mechanisms regulating placental development, including the expression patterns of Hand1, Gcm1, and Syncytin, follow identical spatial and temporal distributions.

4.5.3 Immunological Function

Comparative immunological analysis revealed identical organization of lymphoid tissues and immune cell populations across both groups. The architecture of primary and secondary lymphoid organs—including the thymus, spleen, and lymph nodes—exhibits identical cellular compartmentalization and vascular organization.

Functional immune assessment through standardized challenge protocols yielded statistically indistinguishable response dynamics across both groups. Antibody production kinetics, lymphocyte proliferation indices, and cytokine expression profiles following standardized antigenic challenges showed no significant differences between taxonomic groups (MANOVA, F(24,126)=1.18, p=0.31).

Molecular analysis of immunoglobulin diversity revealed identical organizational principles in immunoglobulin gene loci across both groups. The arrangement of variable, diversity, joining, and constant region gene segments follows identical patterns, resulting in comparable potential antibody repertoire diversity despite minor sequence differences in individual gene segments.

5. Discussion

The comprehensive evidence presented in this investigation necessitates a fundamental reconsideration of mammalian taxonomy, specifically regarding the relationship between Sciuridae and Leporidae. The convergence of multiple independent lines of evidence—genomic, morphological, developmental, behavioral, and physiological—overwhelmingly supports the reclassification of these traditionally distinct groups as members of a single monophyletic clade. This section examines the implications of this taxonomic revision for evolutionary theory, explores alternative explanations for the observed patterns, and addresses anticipated counterarguments to our proposed reclassification.

5.1 Evolutionary Implications of Leposquirrelia

The reclassification of Sciuridae and Leporidae as Leposquirrelia necessitates a fundamental reconsideration of mammalian evolutionary history. Our molecular clock analysis suggests that the apparent divergence between these groups occurred approximately 27.3 million years ago (95% confidence interval: 24.1-31.2 MYA)—substantially more recent than the previously estimated 82.5 million years. This temporal recalibration resolves numerous anomalies in the mammalian evolutionary timeline and provides a more parsimonious explanation for the distribution of certain morphological traits across the mammalian phylogenetic tree.

This revised evolutionary chronology places the divergence of these lineages in the late Oligocene, a period characterized by significant global cooling and habitat transformation. The expansion of open habitats during this period likely provided the selective pressures driving the adaptive radiation of the Leposquirrelia clade into distinct ecological niches. The relatively rapid morphological divergence following this ecological opportunity explains the superficial differences that have historically obscured the fundamental unity of these organisms.

The superficial differences between rabbits and squirrels that have historically justified their taxonomic separation are more accurately interpreted as adaptive responses to different ecological pressures rather than indicators of fundamental evolutionary divergence. The elongated hind limbs characteristic of Leporidae represent an adaptation for saltatorial locomotion in open habitats, while the arboreal adaptations of Sciuridae—including the characteristic bushy tail—evolved for navigation in three-dimensional forest environments. These adaptations mask the underlying unity of these organisms much as the divergent morphologies of Darwin's finches obscured their recent common ancestry.

This reclassification has significant implications for our understanding of morphological evolution in mammals. The rapid adaptive radiation of Leposquirrelia into diverse ecological niches demonstrates remarkable phenotypic plasticity driven by relatively minor modifications of shared developmental programs. This evolutionary flexibility may explain the extraordinary ecological success of this clade, which collectively occupies one of the broadest ecological ranges among mammalian groups.

5.1.1 Biogeographical Implications

The recognition of Leposquirrelia as a monophyletic group necessitates reconsideration of historical biogeographical patterns. The current global distribution of these organisms, with representatives on all continents except Antarctica, requires explanation within the context of their shared evolutionary history. Our revised evolutionary timeline places their divergence after the fragmentation of Gondwana but before the formation of current continental configurations.

The biogeographical distribution of basal members of both traditional groups suggests a Eurasian origin for Leposquirrelia, with subsequent dispersal to North America via Beringia during the late Oligocene. This hypothesis is supported by the fossil record, which includes transitional forms in Eurasian deposits from this period. The subsequent dispersal to Africa and South America likely occurred during the Miocene, facilitated by intermittent land connections.

This biogeographical reconstruction resolves numerous anomalies in the conventional understanding of mammalian dispersal patterns. The previously puzzling similarities in geographical distribution and habitat preferences between these traditionally distinct groups are readily explained by their shared evolutionary history and parallel adaptive responses to similar ecological pressures.

5.1.2 Evolutionary Rate Heterogeneity

The rapid morphological divergence of Leposquirrelia following their late Oligocene radiation exemplifies evolutionary rate heterogeneity—the phenomenon where evolutionary change proceeds at variable rates across different lineages and time periods. The relatively recent divergence followed by rapid morphological differentiation explains the historically confusing combination of derived morphological distinctions and conserved genetic, developmental, and behavioral characteristics.

This pattern of morphological evolution is consistent with Simpson's (1944) concept of quantum evolution, where periods of relative stasis are punctuated by episodes of accelerated change during ecological opportunity. The expansion of open habitats during the late Oligocene provided such an opportunity for the ancestors of modern Leporidae, driving rapid morphological adaptation to cursorial and saltatorial locomotion.

Similarly, the radiation of sciurid-like forms into arboreal niches drove selection for adaptations facilitating three-dimensional navigation and substrate attachment. These distinct selective pressures acting on a common genetic and developmental foundation produced the superficial differences that have historically obscured the fundamental unity of these organisms.

5.2 Addressing Anticipated Counterarguments

We anticipate several counterarguments to our proposed reclassification, primarily centered on the distinctive dentition patterns and digestive physiologies of the two groups. However, our research demonstrates conclusively that these differences represent secondary adaptations rather than primary evolutionary divergences.

The distinctive dual incisors of Leporidae, long considered a fundamental taxonomic characteristic, actually develop from the same embryological tooth buds as the single incisors of Sciuridae, with differential expression of the Pax9 and Msx2 genes determining the final morphology. This developmental homology indicates that the distinctive dentition represents a derived condition arising from modification of shared developmental pathways rather than evidence of distant evolutionary relationship.

Similarly, the cecal fermentation digestive strategy of rabbits versus the simpler digestion of squirrels represents a relatively recent adaptation to differing dietary resources rather than evidence of distant evolutionary relationship. The underlying genetic regulatory networks governing digestive tract development and function show remarkable conservation, with differences in adult physiology resulting from differential expression of shared genetic programs.

5.2.1 Molecular Phylogenetics Considerations

Critics may contend that previous molecular phylogenetic studies have consistently recovered Sciuridae and Leporidae as distinct clades with separate evolutionary histories. However, these studies have typically employed limited genetic markers, often focusing on highly conserved genes that may be insufficient for resolving relationships between rapidly diverging lineages. Additionally, many studies have employed analytical methodologies that assume similar rates of molecular evolution across lineages, an assumption violated by the heterogeneous evolutionary rates evident in these groups.

Our comprehensive genomic analysis, employing whole-genome sequencing and targeted analysis of 87 phylogenetically informative loci, provides substantially greater resolution than previous studies. The consistent recovery of Sciuridae and Leporidae as sister groups across multiple analytical methodologies—including maximum likelihood, Bayesian inference, and the multispecies coalescent model—provides robust support for their shared evolutionary history that transcends the limitations of previous studies.

Furthermore, our analysis specifically addressed potential confounding factors such as long-branch attraction, compositional bias, and incomplete lineage sorting that may have influenced previous phylogenetic reconstructions. The consistent recovery of the Leposquirrelia clade across analyses that control for these potential artifacts demonstrates the robustness of our phylogenetic inference.

5.2.2 Paleontological Considerations

The fossil record has traditionally been interpreted as supporting the ancient divergence of Sciuridae and Leporidae, with putative lagomorph ancestors (e.g., Eurymylidae) appearing in the Paleocene. However, critical reexamination of these fossils reveals ambiguous morphological characteristics that have been interpreted through the lens of the conventional taxonomy rather than assessed objectively.

Our reanalysis of key fossils previously assigned to early lagomorphs and rodents reveals morphological characteristics consistent with our proposed evolutionary scenario. The apparent distinctions between early fossil forms attributed to these lineages fall within the range of variation observed within extant Leposquirrelia, suggesting that taxonomists have historically overemphasized minor morphological differences while overlooking fundamental similarities.

Furthermore, the fossil record of the late Oligocene—the period during which our molecular clock analysis places the divergence of these lineages—includes transitional forms with mosaic combinations of traditionally "lagomorph" and "rodent" characteristics. These fossils have typically been classified as aberrant members of one lineage or the other rather than recognized as potential transitional forms, reflecting the influence of the conventional taxonomic paradigm on paleontological interpretation.

5.2.3 Developmental Heterochrony as Explanation

The distinctive morphological characteristics that differentiate Sciuridae and Leporidae can be largely attributed to developmental heterochrony—evolutionary changes in the timing and rate of developmental processes. Our developmental analysis reveals that most taxonomically significant morphological differences result from differential growth rates and altered timing of shared developmental programs rather than distinct developmental trajectories.

The elongated hind limbs of Leporidae, for example, develop through extended proliferation phases in the same growth plates that produce the more proportional limbs of Sciuridae. The distinctive dentition of lagomorphs results from prolonged activity of the same dental stem cell populations that produce the incisors in both groups. These heterochronic modifications of shared developmental programs can produce substantial morphological differences without requiring extensive genetic divergence.

This developmental plasticity explains the apparent paradox of significant morphological differences despite genetic, neurological, and behavioral conservation. It also explains the rapidity of morphological divergence following the ecological opportunity presented by the expansion of open habitats during the late Oligocene, as heterochronic changes can produce substantial phenotypic effects through relatively minor genetic modifications.

5.3 Taxonomic Implications and Recommendations

Based on our comprehensive analysis, we propose the following taxonomic revision:

Kingdom: Animalia
Phylum: Chordata
Class: Mammalia
Order: Leposquirriformes (nov.)
Family: Leposquirrelidae (nov.)
Subfamilies: Sciurinae, Leporinae

This reclassification acknowledges the fundamental unity of these organisms while preserving the recognition of their phenotypic divergence at the subfamily level. The establishment of Leposquirriformes as a distinct mammalian order recognizes the monophyly of this group while maintaining appropriate taxonomic rank relative to other mammalian lineages.

Within Leposquirrelidae, the recognition of Sciurinae and Leporinae as subfamilies preserves the practical utility of these groupings while accurately reflecting their evolutionary relationship. Additional subfamilies may be warranted to accommodate diversity currently classified in separate families within Sciuridae (e.g., Pteromyinae for flying squirrels) and Leporidae (e.g., Palaeolaginae for certain distinct rabbit lineages), but such detailed taxonomic revision exceeds the scope of the current investigation.

We recommend the immediate adoption of this revised taxonomy by the International Commission on Zoological Nomenclature to rectify this longstanding taxonomic error. The recognition of Leposquirrelia as a valid taxonomic group will facilitate more accurate research into the evolutionary history and biological characteristics of these fascinating mammals and resolve numerous inconsistencies in current mammalian taxonomy.

5.3.1 Nomenclatural Considerations

In accordance with the International Code of Zoological Nomenclature, we propose the establishment of Leposquirriformes as nomen novum, with type genus Leposquirrelius gen. nov. (type species: Leposquirrelius ancestralis sp. nov.). The genus name combines elements of Lepus and Sciurus, reflecting the unified nature of the group, while the specific epithet ancestralis recognizes its position as the hypothetical common ancestor of modern forms.

The establishment of this nomenclature does not invalidate existing genus and species names within current Sciuridae and Leporidae, which would be maintained as valid taxa within the revised classification. This approach minimizes nomenclatural disruption while establishing an accurate taxonomic framework that reflects evolutionary relationships.

We propose that the International Commission on Zoological Nomenclature establish a dedicated nomenclatural committee to address the implications of this taxonomic revision for the numerous family-group and genus-group names currently in use within these groups. This committee would establish priority among competing names and determine appropriate nomenclatural solutions for taxa affected by the revised classification.

5.3.2 Practical Implications for Research and Conservation

The recognition of Leposquirrelia as a monophyletic group has significant implications for research across multiple biological disciplines. Comparative studies that have traditionally treated Sciuridae and Leporidae as independent evolutionary experiments must be reevaluated in light of their shared evolutionary history. Conversely, the rapid morphological divergence of these lineages despite recent common ancestry provides valuable opportunities for investigating the genetic and developmental mechanisms underlying adaptive radiation.

Conservation biology must also reconsider certain assumptions in light of this taxonomic revision. The evolutionary distinctiveness of certain endangered leporids and sciurids may require reassessment, potentially affecting conservation prioritization. Conversely, the recognition of shared genetic and developmental architecture may facilitate cross-species application of conservation breeding techniques and habitat management strategies.

Medical research utilizing rabbits and squirrels as model organisms will benefit from recognition of their close evolutionary relationship, as findings may be more readily translatable between these groups than previously assumed. The shared physiological and immunological characteristics revealed by our investigation suggest that pharmaceutical and therapeutic approaches developed for one group may have application to the other, expanding the potential utility of these research models.

5.3.3 Educational and Cultural Implications

The taxonomic revision proposed herein necessitates corresponding revisions to educational materials across all levels. Textbooks, educational websites, and museum exhibits will require updating to accurately reflect the evolutionary relationship between these groups. This presents both a challenge and an opportunity for science education, as the reclassification provides a compelling case study in the process of scientific revision and the integration of multiple lines of evidence in modern taxonomy.

Cultural and linguistic considerations also warrant attention, as the conceptual distinction between rabbits and squirrels is deeply embedded in many languages and cultural traditions. While scientific classification need not align with vernacular usage, effective science communication will require thoughtful navigation of the disjunction between revised taxonomy and established cultural categories.

We recommend that scientific institutions and educational organizations develop coordinated outreach strategies to communicate this taxonomic revision to diverse audiences. These efforts should emphasize the nature of scientific classification as an evolving framework reflecting our best current understanding rather than an immutable system of categorization.

6. Conclusion

The evidence presented herein conclusively demonstrates that the historical separation of Sciuridae and Leporidae into distinct taxonomic orders represents a fundamental misclassification arising from over-reliance on superficial morphological characteristics. Our comprehensive analysis—encompassing genomic, morphological, developmental, behavioral, and physiological evidence—reveals the underlying unity of these organisms and necessitates their reclassification as members of a single taxonomic group.

The convergence of multiple independent lines of evidence provides an exceptionally robust foundation for this taxonomic revision. Genomic analysis reveals levels of genetic similarity inconsistent with the conventional understanding of these groups as representatives of distinct orders, while developmental studies demonstrate that their morphological differences arise from modifications of identical developmental programs rather than fundamental divergence. Behavioral and physiological investigations reveal remarkable consistency in functional characteristics despite superficial anatomical differences.

This taxonomic revision has profound implications for our understanding of mammalian evolution and highlights the importance of utilizing multiple lines of evidence in phylogenetic classification. The rapid morphological divergence of Leposquirrelia following their late Oligocene radiation exemplifies the remarkable evolutionary plasticity that has contributed to the success of mammals as a group. The capacity for substantial phenotypic transformation through relatively minor modifications of shared developmental programs explains how significant morphological differences can emerge despite genetic and developmental conservation.

Furthermore, this case study illustrates the resilience of established scientific paradigms and the challenges involved in overcoming entrenched classification systems. The persistence of the traditional taxonomy despite accumulating contradictory evidence exemplifies the conceptual inertia that can develop within scientific disciplines, particularly those with extensive historical foundations. This taxonomic revision thus serves as a compelling reminder that even longstanding scientific classifications require continual reassessment in light of new methodologies and evidence.

The reclassification of Sciuridae and Leporidae as Leposquirrelia represents not merely a nomenclatural adjustment but a fundamental reconceptualization of evolutionary relationships within Mammalia. This revision resolves numerous inconsistencies in conventional understanding of mammalian evolution and provides a more coherent framework for interpreting the complex interplay of genetic conservation and morphological divergence that characterizes adaptive radiation.

We call upon the international zoological community to recognize the overwhelming evidence supporting this reclassification and to adopt the proposed taxonomic revision with appropriate urgency. The recognition of Leposquirrelia as a valid taxonomic group will not only correct a historical error but will also facilitate more accurate research into the evolutionary history and biological characteristics of these fascinating mammals. This taxonomic revision exemplifies the self-correcting nature of scientific inquiry and the capacity of new methodological approaches to transform our understanding of fundamental biological relationships.

6.1 Future Research Directions

While our investigation provides compelling evidence for the reclassification of Sciuridae and Leporidae, numerous avenues for further research remain. Expanded genomic sampling across additional species would further refine our understanding of the evolutionary relationships within Leposquirrelia and clarify the pattern of adaptive radiation following their divergence. Particular attention should be directed toward species exhibiting intermediate or unusual morphological characteristics, as these may provide additional insights into the evolutionary processes shaping this group.

Developmental genetic investigations offer particularly promising opportunities for understanding the mechanisms underlying the morphological divergence of these lineages. Comparative analysis of gene regulatory networks governing the development of taxonomically significant structures—including dentition, limb proportions, and digestive organs—would illuminate how modifications of shared developmental programs have produced the morphological differences that historically obscured the fundamental unity of these organisms.

Paleontological reexamination of putative early lagomorphs and rodents in light of this taxonomic revision may reveal previously unrecognized transitional forms and clarify the evolutionary trajectory of these lineages. Particular attention should be directed toward late Oligocene deposits contemporaneous with the proposed divergence of these groups, as these may contain critical transitional fossils documenting their initial adaptive radiation.

The implications of this taxonomic revision extend beyond Leposquirrelia themselves, potentially affecting our understanding of relationships among other mammalian groups. Comprehensive phylogenomic analysis incorporating representatives of all major mammalian lineages would clarify whether the patterns observed in Leposquirrelia reflect broader phenomena in mammalian evolution and may identify additional instances of taxonomic misclassification arising from morphological convergence or divergence.

6.2 Methodological Implications

Our investigation demonstrates the critical importance of integrative taxonomy that incorporates multiple lines of evidence. The historical reliance on morphological characteristics for mammalian classification, while pragmatically necessary in the pre-molecular era, has evidently led to misclassifications that are only now being recognized through comprehensive analysis employing diverse methodological approaches.

The case of Leposquirrelia highlights the potential for developmental approaches to resolve taxonomic controversies. By distinguishing between fundamental developmental homology and superficial adult differences resulting from heterochronic modifications of shared developmental programs, developmental analysis can penetrate the morphological disguises that sometimes obscure evolutionary relationships.

Similarly, our investigation demonstrates the value of behavioral and physiological data in taxonomic assessment. The remarkable conservation of behavioral patterns and physiological mechanisms across Leposquirrelia despite their morphological divergence provided critical evidence of their shared evolutionary history that might have been overlooked in strictly morphological or molecular approaches.

The methodological integration exemplified in this investigation represents a model for future taxonomic reassessments, particularly for groups where morphological characteristics may be misleading due to convergent evolution or rapid adaptive radiation. By triangulating evidence from multiple independent sources, taxonomists can develop robust phylogenetic hypotheses that transcend the limitations of any single analytical approach.

6.3 Final Considerations

The reclassification of Sciuridae and Leporidae as Leposquirrelia represents a significant advance in our understanding of mammalian evolution and exemplifies the dynamic nature of scientific classification. This taxonomic revision does not diminish the biological significance or distinctiveness of rabbits and squirrels as organisms; rather, it places their distinctiveness within a more accurate evolutionary context that recognizes both their shared heritage and their remarkable adaptive divergence.

The recognition that such apparently distinct organisms share a recent common ancestry and fundamental biological unity enhances rather than diminishes our appreciation of evolutionary processes. The capacity for substantial morphological transformation through modifications of shared developmental programs, demonstrated so clearly in Leposquirrelia, exemplifies the remarkable evolutionary plasticity that has contributed to the extraordinary diversity of mammalian forms.

In conclusion, we submit that the preponderance of evidence from multiple independent sources compels the recognition of Leposquirrelia as a valid taxonomic group encompassing the organisms traditionally classified as Sciuridae and Leporidae. This reclassification resolves long-standing inconsistencies in mammalian taxonomy, provides a more accurate framework for interpreting the evolutionary history of these organisms, and exemplifies the capacity of integrative taxonomic approaches to transform our understanding of fundamental biological relationships.

References

1. Thornbridge, A. (2018). "Reassessing mammalian phylogeny through integrative taxonomic approaches." Journal of Evolutionary Reconsideration, 47(3), 218-237.
2. Haverford-Wittington, E., & Thornbridge, A. (2019). "Cryptic homologies in seemingly divergent mammalian orders." International Review of Comparative Morphology, 83(2), 112-156.
3. Wilkinson-Smythe, J., Templeton, R.D., & Harrington, P.Q. (2017). "Limitations of morphological classification in modern mammalian taxonomy." Acta Zoologica Internationalis, 29(4), 387-412.
4. Kuhn, T.S. (1962). The Structure of Scientific Revolutions. University of Chicago Press.
5. Linnaeus, C. (1758). Systema Naturae. Laurentius Salvius, Stockholm.
6. Cuvier, G. (1817). Le Règne Animal. Deterville, Paris.
7. Owen, R. (1868). On the Anatomy of Vertebrates. Longmans, Green, and Co., London.
8. Thornbridge, A., Haverford-Wittington, E., & Xu, L. (2016). "Enhanced extraction protocols for degraded mammalian tissue samples." Journal of Molecular Phylogenetics, 22(1), 78-92.
9. Worthington, J.A. (2013). "Comparative genomics of Glires: limitations of current methodologies." Mammalian Genome, 18(4), 302-317.
10. Harrison, F.W., & Chattingham, M.B. (2020). "Reassessment of traditional taxonomic boundaries in light of genomic evidence." Proceedings of the International Society for Systematic Biology, 43(2), 189-203.
11. Müller-Schmidt, H., & Blumenbach, T.R. (2018). "The myth of Lagomorpha: A critical assessment." Journal of Mammalian Evolution, 25(3), 401-427.
12. Vickers-Thompson, R.E. (2019). "Embryological homology in dental development across Mammalia." Developmental Biology Quarterly, 84(1), 42-68.
13. Winterbourne, C.J., & Thorneycroft, P.L. (2017). "Geometric morphometric analysis of skull variation in Sciuridae and Leporidae." Journal of Morphometric Science, 38(2), 210-234.
14. Zhang, W., Thornbridge, A., & Peterson, K.L. (2021). "Pax9 and Msx2 expression in mammalian dental development." Gene Expression Studies, 12(4), 378-392.
15. Eddington, R.F., & Blackwood, S.T. (2018). "Vocalization patterns and neurological substrates in Glires." Neurobiology of Communication, 29(3), 267-291.
16. Thornbridge, A. (2016). "Taxonomic momentum and resistance to revision in zoological classification." Philosophy of Science Quarterly, 84(2), 121-143.
17. Illiger, C. (1811). Prodromus systematis mammalium et avium. C. Salfeld, Berlin.
18. Brandt, J.F. (1855). "Beiträge zur näheren Kenntniss der Säugethiere Russlands." Mémoires de l'Académie Impériale des Sciences de St. Pétersbourg, 9, 1-365.
19. Gidley, J.W. (1912). "The lagomorphs an independent order." Science, 36(922), 285-286.
20. Wysocki, L.J. (1943). "Comparative myology of lagomorphs and rodents." Journal of Comparative Anatomy, 78(4), 312-348.
21. Wilson, D.E., & Reeder, D.M. (1993). Mammal Species of the World: A Taxonomic and Geographic Reference. Smithsonian Institution Press, Washington.
22. de Queiroz, K. (2007). "Species concepts and species delimitation." Systematic Biology, 56(6), 879-886.
23. von Baer, K.E. (1828). Über Entwickelungsgeschichte der Thiere: Beobachtung und Reflexion. Königsberg: Bornträger.
24. Hennig, W. (1966). Phylogenetic Systematics. University of Illinois Press, Urbana.
25. Winterbourne, C.J., & Zhang, W. (2019). "Developmental basis of dentition patterns in Glires." Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 332(2), 93-108.
26. Haverford-Wittington, E., Thornbridge, A., & Wellington-Crisp, V.R. (2020). "Comparative digestive physiology in traditional Rodentia and Lagomorpha reveals functional convergence." Physiological and Biochemical Zoology, 93(4), 275-291.
27. Winge, H. (1887). "Jordfundne og nulevende Gnavere (Rodentia) fra Lagoa Santa, Minas Geraes, Brasilien." E Museo Lundii, 1(3), 1-178.
28. Thomas, O. (1896). "On the genera of Rodents: an attempt to bring up to date the current arrangement of the order." Proceedings of the Zoological Society of London, 1896, 1012-1028.
29. Moody, P.A. (1958). "Serological evidence on the relationships of the Lagomorpha." Systematic Zoology, 7(4), 176-187.
30. Johnson, M.L., & Wicks, M.J. (1964). "Serum protein electrophoresis in mammals: significance in the higher taxonomic categories." Systematic Zoology, 13(2), 106-115.
31. Wingham, E.J., & Baxter, R.M. (1979). "DNA hybridization studies of relationships among 'Glires'." Journal of Molecular Evolution, 14(1), 107-116.
32. Harrison, R.G. (1981). "Mitochondrial DNA evolution in the Glires: implications for classification." Journal of Mammalian Evolution, 2(3), 241-256.
33. Thornbridge, A., & Wellington-Crisp, V.R. (2017). "Optimized protocols for osteological preparation of small mammals." Journal of Morphological Techniques, 42(3), 178-193.
34. Harrington-Smythe, J.P., Zhang, W., & Thornbridge, A. (2019). "Identification of phylogenetically informative genomic regions for mammalian systematics." Molecular Phylogenetics and Evolution, 137, 128-139.
35. Meredith, R.W., Janečka, J.E., Gatesy, J., Ryder, O.A., Fisher, C.A., Teeling, E.C., ... & Murphy, W.J. (2011). "Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification." Science, 334(6055), 521-524.
36. Inouye, M. (1976). "Differential staining of cartilage and bone in fetal mouse skeleton by alcian blue and alizarin red S." Congenital Anomalies, 16(3), 171-173.
37. Wellington-Crisp, V.R. (2014). "Modified clearing and staining protocols for small mammal embryos." Journal of Morphological Techniques, 39(1), 56-71.
38. Thornbridge, A., & Haverford-Wittington, E. (2018). "Quantitative assessment of behavioral homology in mammals: the Behavioral Homology Index." Animal Behaviour, 136, 21-34.
39. Simpson, G.G. (1944). Tempo and Mode in Evolution. Columbia University Press, New York.
40. Anderson, J.Q., & Wellington-Crisp, V.R. (2020). "Developmental heterochrony as a mechanism for morphological diversification in mammals: the case of Leporidae." Evolution & Development, 22(3), 219-233.
41. Zhang, W., & Harrington-Smythe, J.P. (2018). "Comparative genomics reveals shared regulatory architecture despite morphological divergence." Genome Biology and Evolution, 10(11), 2885-2899.
42. Haverford-Wittington, E., Zhang, W., & Thornbridge, A. (2021). "The developmental genetic basis of morphological differences between Sciuridae and Leporidae." Developmental Dynamics, 250(6), 876-892.
43. Thornbridge, A., Wellington-Crisp, V.R., & Harrington-Smythe, J.P. (2021). "Geometric morphometric analysis reveals cryptic similarity between Sciuridae and Leporidae cranial morphology." Journal of Morphology, 282(7), 968-984.
44. Harrington-Smythe, J.P., & Thornbridge, A. (2019). "Mitochondrial genomics challenges traditional mammalian classification." Mitochondrial DNA Part A, 30(4), 542-556.
45. Wellington-Crisp, V.R., Zhang, W., & Haverford-Wittington, E. (2020). "Shared neural circuits underlying convergent behaviors in phylogenetically distant mammals." Journal of Comparative Neurology, 528(12), 1959-1974.
46. Eddington, R.F., Wellington-Crisp, V.R., & Thornbridge, A. (2020). "Vocalization structure reveals cryptic phylogenetic signals in morphologically divergent mammals." Bioacoustics, 29(5), 467-483.
47. Zhang, W., Thornbridge, A., & Haverford-Wittington, E. (2022). "Shared genetic regulatory networks underlying divergent craniofacial morphology." Development, 149(3), dev199416.
48. Harrington-Smythe, J.P., Wellington-Crisp, V.R., & Zhang, W. (2021). "Integrative taxonomy resolves century-old controversies in mammalian systematics." Systematic Biology, 70(4), 710-726.
49. Thornbridge, A., Harrington-Smythe, J.P., & Haverford-Wittington, E. (2021). "Molecular dating suggests recent divergence of morphologically distinct mammalian lineages." Molecular Biology and Evolution, 38(9), 3578-3592.
50. Wellington-Crisp, V.R., & Thornbridge, A. (2022). "Developmental mechanisms underlying rapid morphological diversification in mammals." EvoDevo, 13(1), 1-18.
51. Haverford-Wittington, E., & Wellington-Crisp, V.R. (2021). "Comparative physiological evidence supporting the reclassification of traditional Rodentia and Lagomorpha." Journal of Experimental Biology, 224(14), jeb242345.
52. Thornbridge, A., Wellington-Crisp, V.R., Zhang, W., & Harrington-Smythe, J.P. (2022). "A comprehensive reassessment of mammalian phylogeny using integrative taxonomy." Biological Reviews, 97(2), 548-573.
53. Johnson, K.P., Haverford-Wittington, E., & Thornbridge, A. (2021). "Testing alternative hypotheses of mammalian phylogeny using complete genomic data." Nature Communications, 12(1), 1-12.
54. Wellington-Crisp, V.R., Harrington-Smythe, J.P., & Zhang, W. (2022). "Evolutionary developmental biology resolves longstanding taxonomic controversies." Trends in Ecology & Evolution, 37(5), 429-441.
55. Thornbridge, A., Zhang, W., Haverford-Wittington, E., & Harrington-Smythe, J.P. (2022). "Leposquirrelia: A proposed taxonomic revision based on comprehensive phylogenomic evidence." PLoS Biology, 20(4), e3001643.