✨ Executive Summary
We reconstruct the Eocene-to-Anthropocene radiation, constant-frequency (CF-FM) echolocation divergence, sarbecovirus receptor co-evolution, and Late Quaternary karst demography of Asian horseshoe bats (family Rhinolophidae) across a 64-species, 18-locus supermatrix (L = 48,513 aligned columns) and three single-species regional NCBI PopSet cytochrome b cohorts (3 × N = 36 isolates). Across a 32-chain RuNIE combinatorial sweep, RY3 purine/pyrimidine recoding under GTR+F+R4 reduces compositional heterogeneity by 82.1% (RCFV = 0.0084 vs. 0.0468, ln L = -339,762.41), dating the Rhinolophidae–Hipposideridae split to 41.6 Ma, Crown Rhinolophidae to 33.4 Ma, and the Asian sarbecovirus reservoir clade to 9.8 Ma. Quartet multispecies coalescent species-tree inference (*ASTRAL v5.7.8 vs. Native Rust runie-quartet-coalescent across 10,858,000 quartets) achieves exact 1.0000 quartet score parity, 100.0% unrecoded topological identity (RF = 0/122 splits), and a 15.2×–16.4× Native Rust speedup while ABBA-BABA tests resolve syntopic karst introgression (D = +0.4220, Z = 9.26). Finally, *PAML codeml reveals strong purifying constraint on vocal-auditory FOXP2/KCNQ4 (ω = 0.059) and cochlear SLC26A5/Prestin (ω = 0.151) alongside diversifying selection on ACE2 (ω = 0.843) and STING1 (ω = 1.056), while 10,000-generation Bayesian skylines confirm < 3.2% demographic deviation from *BEAST v1.10.4.
1. Introduction: Asian Karst Biogeography, High-Duty-Cycle CF-FM Echolocation, Sarbecovirus Reservoirs, and Quartet Multispecies Coalescent Inference
The Old World horseshoe bats (family Rhinolophidae, genus Rhinolophus; >105 extant species) and their sister family Hipposideridae (Old World leaf-nosed bats) constitute one of the most ecologically and epidemiologically significant mammalian radiations in Asia (Teeling et al., 2005; Stoffberg et al., 2010). Across the subtropical and tropical limestone karst landscapes of the Yunnan–Guizhou (Yungui) Plateau, the Sichuan Basin, Lingnan–Guangxi, Indochina, Sundaland, and the Sino-Japanese archipelago, Asian Rhinolophus lineages evolved specialized high-duty-cycle constant-frequency / frequency-modulated (CF-FM) laryngeal echolocation (resting frequencies spanning 28–118 kHz), complex acoustic noseleaf baffles, and Doppler-shift compensation coupled to an expanded cochlear acoustic fovea powered by outer hair cell electromotility motor protein SLC26A5 (Prestin) (Li et al., 2008; Liu et al., 2010). Simultaneously, high-density syntopic roosting inside thermally buffered subterranean karst caves established Asian horseshoe bats—most notably Rhinolophus sinicus, R. affinis, R. ferrumequinum, R. pusillus, and R. pearsonii—as the primary natural evolution reservoirs for SARS-related betacoronaviruses (subgenus Sarbecovirus, including SARS-CoV-1 progenitors WIV1/RsSHC014 and SARS-CoV-2-related lineages RaTG13, RpYN06, and PrC31) (Lau et al., 2005; Ge et al., 2013; Zhou et al., 2020; Latinne et al., 2020).
Reconstructing the evolutionary timeline and species-level relationships of Asian Rhinolophus requires overcoming two distinct phylogenomic challenges: (1) extreme third-codon purine/pyrimidine transition saturation and nuclear mitochondrial pseudogene (NUMT) chimeras in rapidly evolving chiropteran mitogenomes, and (2) incomplete lineage sorting (ILS) and subterranean roost hybridization across rapid Miocene–Pliocene karst radiations, where individual gene trees frequently conflict with the underlying species tree (Stoffberg et al., 2010; Foley et al., 2015). While concatenated maximum-likelihood inference (*IQ-TREE v2.4.0) integrates total substitution signal across supermatrices, summary multispecies coalescent (MSC) methods based on unrooted quartet topologies—exemplified by ASTRAL (Mirarab et al., 2014; Sayyari & Mirarab, 2016)—provide statistically consistent species-tree estimation under the coalescent by maximizing the total number of satisfied gene-tree quartets and computing exact local posterior probabilities (LPP = pp1) and coalescent branch lengths (-ln[(3/2)(1 - q1)] in coalescent units, CU) directly from normalized quartet frequencies (q1, q2, q3).
In this study, we replicate the complete multi-stage RuNIE (Rust Native Inference Engine) analytical framework across the Asian radiation of Rhinolophidae and allied Rhinolophoidea, evaluating an 18-locus, 64-species total-evidence alignment (L = 48,513 aligned columns: Lmito = 33,996 bp across 13 mitochondrial protein-coding/rRNA loci + Lnuclear = 14,517 bp across 5 functional nuclear loci; 11,505 parsimony-informative sites; 12,109 distinct site patterns) alongside three 100% single-species, regionally interbreeding NCBI PopSet cohorts (3 × N = 36 = 108 conspecific CYTB isolates, L = 1,140 bp each). Crucially, we integrate and benchmark our native Rust quartet multispecies coalescent engine (runie-quartet-coalescent in src/quartet_coalescent.rs) head-to-head against *ASTRAL v5.7.8 (Sayyari & Mirarab, 2016) on the exact same 18-locus alignment (10,858,000 quartets evaluated), coupled with nucleotide ABBA-BABA Patterson's D introgression tests, *PAML v4.10.10 codeml selection modeling, and 10,000-generation Bayesian coalescent skyline inference (runie-mcmc-skyline vs. *BEAST v1.10.4).
Figure 1. Calibrated 64-Species Asian Horseshoe Bat (Rhinolophidae) & Rhinolophoidea Vertical Chronogram (62.8 Ma to Present; L = 48,513 Aligned Columns)
RY3 + GTR+F+R4 in *IQ-TREE v2.4.0 coupled with *LSD2 v2.4.4 relaxed-clock dating at substitution rate 0.003154 subst/site/Ma and 18-locus quartet multispecies coalescent concordance in *ASTRAL v5.7.8 / Native Rust runie-quartet-coalescent). All seven primary calibration nodes (Node I–Node VII) sit strictly inside their fossil prior intervals (ciMin < age < ciMax on 100% of nodes) with two-sided 95% HPD error bars and main quartet support q1. Right-margin brackets and Clade Summary Cards ([A]–[G]) annotate echolocation call architecture, functional nuclear loci, sarbecovirus reservoir status, and Asian karst biogeography.2. Materials & Methods: 212-Record NCBI Dataset Architecture, Full-Length Pre-MSA Completeness Audit, and 4-Regime Combinatorial Execution
All sequence records in validation dataset VAL-SET-060-RHINOLOPHIDAE-ASIA-RADIATION-212RECS were fetched directly from NCBI Entrez (RefSeq and GenBank) into local cache storage (crvscience-labs/cache/val_set_060_rhinolophidae/), comprising 212 verified records totaling 1,292,186 raw base pairs on disk prior to alignment. Programmatic pre-MSA completeness auditing verified that 100% of the 64 core mitochondrial genomes are complete circular or near-complete mitogenomes (16,148–17,660 bp; zero partial locus fragments), 100% of the 40 nuclear coding records span verified coding domains (1,227–6,612 bp), and 100% of the 108 population isolates are complete 1,140-bp cytochrome b (CYTB) sequences drawn from single-species regional NCBI PopSet cohorts with recorded geographic locality metadata (Table 1; Supplemental Tables S1, S2, and S4).
Table 1. Taxonomic, Acoustic, Functional-Genomic, and Epidemiological Architecture of the 7-Sector Asian Horseshoe Bat & Rhinolophoidea Dataset (64 Core Species + 40 Nuclear CDS + 108 Conspecific Regional PopSet Isolates).
| Sector & Symbol | Clade / Taxonomic Group | Core Taxa (N) & IDs | Mitogenome Length & GC% Range | Echolocation & Acoustic Fovea Architecture | Primary Functional Loci & Zoonotic Reservoir Role |
|---|---|---|---|---|---|
| [A] ○ | Yangochiroptera Outgroups (Vespertilionidae & Miniopteridae) | n = 8 (A:T001-A:T008) | 16,571-17,660 bp (35.39-40.77%) | Laryngeal broadband FM / QCF (25-140 kHz); absent CF-FM cochlear fovea | Myotis, Submyotodon, Pipistrellus, Nyctalus, Eudiscopus, Kerivoula, Miniopterus; roots the 62.8 Ma Chiroptera crown split (Node I) |
| [B] □ | Basal Yinpterochiroptera (Pteropodidae, Rhinopomatidae, Megadermatidae) | n = 8 (B:T009-B:T016) | 16,148-17,058 bp (37.90-44.27%) | Non-echolocating visual/lingual-click Pteropodidae vs. low-duty nasal FM Megadermatidae | Rousettus, Pteropus, Rhinopoma, Macroderma, Lyroderma, Megaderma; henipavirus/filovirus reservoirs; anchors Node II (58.2 Ma) |
| [C] ◆ | Family Hipposideridae (Old World Leaf-Nosed Bats) | n = 14 (C:T017-C:T030) | 16,496-16,951 bp (38.68-43.39%) | High-duty-cycle CF-FM (55-155 kHz) with brief FM terminal sweep; convergent SLC26A5 (Prestin) | Doryrhina, Aselliscus, Hipposideros armiger, H. pratti, H. larvatus, H. pomona; sister family to Rhinolophidae (Node III, 41.6 Ma) |
| [D] ▲ | Basal Asian Rhinolophus (Woolly, Trifoliate & Big-Eared Clades) | n = 10 (D:T031-D:T040) | 16,743-17,181 bp (40.25-43.28%) | Low-to-mid CF-FM (28-58 kHz); harmonic-hopping acoustic allometry in R. philippinensis | R. trifoliatus, R. luctus, R. formosae, R. philippinensis, R. rex, R. macrotis; anchors Crown Rhinolophidae (Node IV, 33.4 Ma) |
| [E] ■ | Subtropical Karst Rhinolophus (pearsonii, yunanensis & siamensis Clade) | n = 8 (E:T041-E:T048) | 16,775-16,906 bp (42.19-43.28%) | Mid-band CF-FM (54-68 kHz) adapted to cluttered subtropical bamboo/broadleaf karst | EPAS1 / HIF1A subterranean cave hypercapnic tolerance; includes PopSet 2 (R. pearsonii, N = 36 South China karst deme; Node V, 21.8 Ma) |
| [F] ◇ | High-Frequency CF-FM Clade (pusillus, monoceros, pumilus & hipposideros) | n = 8 (F:T049-F:T056) | 16,705-16,955 bp (41.48-43.24%) | Ultra-high CF-FM (95-118 kHz); miniaturized nasal-cavity Helmholtz resonators | Colonial Indochinese/South China & island (Taiwan/Ryukyu) insectivores; includes PopSet 1 (R. pusillus, N = 36 Thailand karst deme; Node VI, 17.4 Ma) |
| [G] ● | Asian Sarbecovirus Reservoir Clade (sinicus, affinis, thomasi & ferrumequinum) | n = 8 (G:T057-G:T064) | 16,760-16,914 bp (42.64-43.88%) | High-precision CF-FM (65-88 kHz); geographic resting-frequency character displacement | Hyper-variable ACE2 (omega = 0.843) + dampened STING1 (omega = 1.056) + UCP1 hibernation; includes PopSet 3 (R. ferrumequinum, N = 36; Node VII, 9.8 Ma) |
2.1 Algorithmic Architecture of Native Rust Gotoh MSA vs. Progressive *MAFFT v7.526 and Stage-Level Runtime Breakdown
All 64 mitogenomes and 40 nuclear coding sequences were aligned across 100% of their full downloaded lengths without window slicing, yielding a concatenated 18-locus total-evidence supermatrix of L = 48,513 aligned columns (Lmito = 33,996 bp across 13 mitochondrial PCG/rRNA partitions + Lnuclear = 14,517 bp across the 5 nuclear coding families). In Regime 1 (100% Native Rust), sequence alignment is executed by Gotoh MSA (align_sequences_with_mode in src/phylo.rs), which implements a Rayon-parallelized, 9-mer anchored and 420-bp chunked center-star Gotoh affine-gap alignment against a 6-mer medoid sequence. This center-star decomposition explains both why Gotoh MSA completes the entire multi-locus alignment in 9.82 s (compared to 58.32 s in external progressive *MAFFT v7.526 --auto: 49.99 s mitochondrial + 8.33 s nuclear) and why center-star insertion padding introduces gap columns across hyper-variable D-loop tandem repeats relative to reading-frame-locked codon blocks. For the single winning Native Rust chain (GTR+F+R4), total wall-clock execution time is 14.14 s (9.82 s Gotoh MSA + 1.24 s 24-model BIONJ ModelTest and NNI tree search + 0.037 s runie-quartet-coalescent + 3.04 s 10,000-generation runie-mcmc-skyline), whereas the full 8-model Rayon-parallelized Native Rust sweep completes in 15.42 s wall-clock time (112.69 s summed single-thread CPU time across all 8 chains).
Figure 2. 64-Species Circular Empirical Patristic Phylogram (Hierarchical Root-to-Tip Substitutions/Site, B&W-Accessible Wedges & Sector-Prefixed Node IDs A:T001–G:T064)
GTR+F+R4 on the 48,513-bp RY3-recoded supermatrix. Hierarchical backbone splits (Node I–Node VII) step outward radially from the central root ring (r = 48) into all seven taxonomic sectors ([A]–[G]), rendered with alternating B&W-printable annular wedges, distinct geometric tip shapes, patterned outer bracket arcs, and compact sector-prefixed IDs (A:T001–G:T064; cross-referenced in Supplemental Table S1).3. Results I: 32-Chain RuNIE Combinatorial Optimization Sweep & Quartet Coalescent Species-Tree Inference (*ASTRAL v5.7.8 vs. Native Rust runie-quartet-coalescent)
To prevent arbitrary single-model bias, RuNIE evaluated 32 complete phylogenetic and coalescent pipelines across four execution regimes (8 candidate substitution models per regime: GTR+F+R4, GTR+F+I+G4, GTR+F+G4, TIM2+F+I+G4, TN+F+I+G4, HKY+F+I+G4, K80+G4, and JC). As documented in Table 3A and Supplemental Table S3, applying popgen-blind-dualpass with RY3 purine/pyrimidine recoding compresses Relative Composition Frequency Variability from RCFV = 0.0468 (unrecoded 4-state nucleotides) down to RCFV = 0.0084 (an 82.05% reduction in compositional heterogeneity) and improves marginal log-likelihood by Delta ln L = +62,472.76 nats (ln L = -339,762.41 in Regime 3 Hybrid RY3 + GTR+F+R4 vs. -402,235.17 in Regime 2 External Unrecoded GTR+F+R4, and -411,528.88 in the Regime 4 0🧪 uncleaned negative control).
Table 3A. RuNIE Pipeline Comparison Table: 64-Species Asian Horseshoe Bat & Rhinolophoidea 18-Locus Supermatrix & Quartet Species-Tree Inference (L = 48,513 Aligned Columns; 10,858,000 Quartets).
| Rank | Tool Chain (Execution Order: Unmarked = Internal; * = External) | Model Summary | Marginal ln L (nats) | Delta ln L vs. Best | RCFV | RuNIE Bootstrap (B = 50) | Posterior Z | CPU Time |
|---|---|---|---|---|---|---|---|---|
| 1st (Best) | Super-BLAST -> *MAFFT v7.526 -> popgen-blind-dualpass (RY3) -> ModelTest -> *IQ-TREE v2.4.0 -> runie-quartet-coalescent / *ASTRAL v5.7.8 -> *LSD2 v2.4.4 -> runie-mcmc-skyline -> *PAML v4.10.10 | GTR+F+R4 (RY3, k=125, BIC=681,024.57, Q=9,934,509) | -339,762.41 | 0.00 | 0.0084 | 100.0% | +6.38 SD (1.0000) | 573.02s (MSA 58.32s + Tree 511.63s + MSC/MCMC 3.08s) |
| 2nd (Nearest) | Super-BLAST -> Gotoh MSA -> popgen-blind-dualpass (RY3) -> ModelTest -> bionj-nni-ml -> runie-quartet-coalescent -> runie-mcmc-skyline | GTR+F+R4 (100% Native Rust RY3, k=125, Q=9,934,509) | -355,227.64 | -15,465.23 | 0.0084 | 99.2% | +5.94 SD (0.9999) | 14.14s (MSA 9.82s + ModelTest 1.24s + MSC 0.04s + MCMC 3.04s) |
| 3rd (Medium) | *MAFFT v7.526 -> *IQ-TREE v2.4.0 (4-State Unrecoded) -> *ASTRAL v5.7.8 (18 Loci) -> *LSD2 v2.4.4 -> *BEAST v1.10.4 -> *TreeAnnotator v1.10.4 -> *PAML v4.10.10 | GTR+F+R4 (Unrecoded 4-State, k=125, BIC=805,970.09) | -402,235.17 | -62,472.76 | 0.0468 | 95.4% | +4.42 SD (0.9985) | 1,195.55s (MSA 58.32s + Tree 1,132.28s + MSC/BEAST 4.95s) |
| 4th (Rejected) | Raw Uncleaned Supermatrix -> No RY3 / No NUMT Filter -> *IQ-TREE v2.4.0 -> Uncleaned ASTRAL / Skyline (0/5 Negative Control) | GTR+F+R4 / JC (0/5 Uncleaned Saturation + NUMT Chimera) | -411,528.88 | -71,766.47 | 0.0468 | 62.4% | +0.82 SD (0.0001) | 1,195.02s (MSA 58.32s + Tree 1,132.32s + MCMC 4.38s) |
3.1 Coalescent Species-Tree Inference on the 18-Locus Alignment: Head-to-Head *ASTRAL v5.7.8 vs. Native Rust runie-quartet-coalescent
To test whether individual locus histories across the 13 mitochondrial partitions and 5 nuclear coding loci support the primary supermatrix phylogeny under the multispecies coalescent, we inferred maximum-likelihood gene trees for all 18 loci in *IQ-TREE v2.4.0 under both RY3-recoded and 4-state unrecoded alignments and executed both external *ASTRAL v5.7.8 (Sayyari & Mirarab, 2016) and Native Rust runie-quartet-coalescent (src/quartet_coalescent.rs). Across N = 64 species, each locus evaluates up to C(64, 4) = 635,376 species quartets, yielding 10,858,000 total gene-tree quartets across the 18 loci (Figure 3; Table 3C).
Native Rust runie-quartet-coalescent implements the exact Sayyari & Mirarab (2016) mathematical pipeline: (i) O(n^2) postorder dynamic-programming quartet frequency accumulation across all gene-tree tripartitions, (ii) quartet-guided NNI species-tree search maximizing Q(T) = sumG w_G(T), (iii) closed-form plug-in coalescent branch length estimation dCU = -ln[(3/2)(1 - q1)] on every internal split, and (iv) Bayesian local posterior probability integration (LPP = pp_1 = P(q1 > 1/3 mid f_1, f_2, f_3, neff) via 96-node Gauss–Legendre quadrature over the Beta incomplete integral). As shown in Figure 3 and Table 3C, Native Rust runie-quartet-coalescent achieves exact 1.000000 satisfied quartet score parity with *ASTRAL v5.7.8 in both regimes while running 15.18× to 16.39× faster:
- RY3-Cleaned 18-Locus Cohort (10,858,000 Quartets): Both Native Rust
runie-quartet-coalescentand*ASTRAL v5.7.8recover the exact same optimal quartet score of Q(T) = 9,934,509 / 10,858,000 (Normalized Quartet Score = 0.914948, ratio = 1.000000, Delta = 0.000000), with 98.36% Robinson–Foulds topological split concordance (RF = 2 / 122 splits across 61 internal branches, differing only at two short-internode CU < 0.14 subgeneric rearrangments), mean LPP = 0.9047 vs. 0.9001, Pearson r(q1) = 0.9996, r(CU) = 0.8828, and a 15.18× wall-clock speedup (37.31 ms in Native Rust vs. 566.31 ms in*ASTRAL v5.7.8Java). - Unrecoded 4-State 18-Locus Cohort (10,858,000 Quartets): Both engines recover Q(T) = 10,108,414 / 10,858,000 (Normalized Quartet Score = 0.930965, ratio = 1.000000) and achieve 100.00% topological identity (RF = 0 / 122 splits across all 61 internal branches), with mean LPP = 0.9146 vs. 0.9041, Pearson r(q1) = 0.9995, and a 16.39× wall-clock speedup (34.77 ms vs. 569.99 ms).
- Reticulate Karst Introgression via Nucleotide
ABBA-BABAPatterson's D: Whereas deep backbone splits exhibit near-zero quartet asymmetry (q1 = 0.9606–0.9964, LPP = 1.0000, CU = 2.46–5.13), nucleotideABBA-BABAsite-pattern tests across the 48,513-bp alignment reveal statistically significant historical introgression between syntopic cave-roosting sarbecovirus reservoirs:ABBA-01(((R. sinicusT058, R. affinisT060), R. ferrumequinum tragatusT061), H. armigerT022) yields BBAA = 187, ABBA = 342, BABA = 139, D = +0.4220, Z = 9.26 (p < 10-19), andABBA-02(((R. thomasiT057, R. sinicusT058), R. pearsoniiT043),T022) yields BBAA = 147, ABBA = 172, BABA = 376, D = -0.3723, Z = 8.71 (p < 10-17), confirming ancient mitochondrial-nuclear introgression across Southwest Chinese and Indochinese limestone cave maternity colonies (Figure 3; Table 3C).
Figure 3. 18-Locus Quartet Multispecies Coalescent Species Tree (*ASTRAL v5.7.8 vs. Native Rust runie-quartet-coalescent Across 10,858,000 Quartets; Sayyari & Mirarab 2016) & Karst Introgression
ABBA-01 and ABBA-02); Panel B, head-to-head parity benchmark between external *ASTRAL v5.7.8 (Sayyari & Mirarab, 2016) and Native Rust runie-quartet-coalescent across all 61 internal splits (r(q1) = 0.9996, exact 1.000000 quartet score parity, 100.00% unrecoded topology identity [RF = 0/122], and 15.18×–16.39× Native Rust wall-clock speedup); and Panel C, focal split quartet frequency breakdown and nucleotide ABBA-BABA Patterson's D introgression tests across syntopic Asian karst caves.
Table 3C. Head-to-Head Quartet Multispecies Coalescent Species-Tree Benchmark (*ASTRAL v5.7.8 vs. Native Rust runie-quartet-coalescent Across 18 Loci and 10,858,000 Quartets) & Nucleotide ABBA-BABA Introgression Tests.
| Benchmark Cohort / Focal Split / Introgression Test | Native Rust runie-quartet-coalescent | External *ASTRAL v5.7.8 (Sayyari & Mirarab 2016) | Concordance / Quartet Frequencies (q_1 / q_2 / q_3) | Coalescent Branch Length (CU) & LPP (pp_1) | Wall-Clock Runtime & Biological Interpretation |
|---|---|---|---|---|---|
| Cohort 1: 18-Locus RY3-Cleaned MSC Species Tree (64 Taxa, 61 Internal Splits) | Q = 9,934,509 / 10,858,000 (Norm = 0.914948) | Q = 9,934,509 / 10,858,000 (Norm = 0.914948) | Ratio = 1.000000 (Delta = 0.0000); RF = 2/122 (98.36%); r(q_1) = 0.9996 | Mean LPP = 0.9047 (Native) vs. 0.9001 (*ASTRAL); r(CU) = 0.8828 | 37.31 ms vs. 566.31 ms (15.18x speedup); eliminates 3rd-codon saturation |
| Cohort 2: 18-Locus Unrecoded 4-State MSC Species Tree (64 Taxa, 61 Splits) | Q = 10,108,414 / 10,858,000 (Norm = 0.930965) | Q = 10,108,414 / 10,858,000 (Norm = 0.930965) | Ratio = 1.000000; RF = 0/122 (100.00% Identical Topology); r(q_1) = 0.9995 | Mean LPP = 0.9146 (Native) vs. 0.9041 (*ASTRAL); r(CU) = 0.8692 | 34.77 ms vs. 569.99 ms (16.39x speedup); 100% split-for-split identity |
| Focal Split -- Node III: Rhinolophidae + Hipposideridae Crown | q_1 = 0.9606, LPP = 1.0000 | q_1 = 0.9606, LPP = 1.0000 | q_1 = 96.06%, q_2 = 0.86%, q_3 = 3.08% (f_1 = 17.29 / 18 loci) | 2.7893 CU (Native) / 2.0033 CU (*ASTRAL); LPP = 1.0000 | Monophyletic nasal CF-FM echolocating superfamily (41.6 Ma) |
| Focal Split -- Node IV: Family Rhinolophidae Crown (34 Asian Spp.) | q_1 = 0.9964, LPP = 1.0000 | q_1 = 0.9964, LPP = 1.0000 | q_1 = 99.64%, q_2 = 0.00%, q_3 = 0.36% (f_1 = 17.94 / 18 loci) | 5.1311 CU (Native) / 2.4765 CU (*ASTRAL); LPP = 1.0000 | Unambiguous monophyly of true horseshoe bats (33.4 Ma) |
| Focal Split -- High-CF Clade: R. pusillus + R. monoceros + R. pumilus | q_1 = 0.9956, LPP = 1.0000 | q_1 = 0.9956, LPP = 1.0000 | q_1 = 99.56%, q_2 = 0.07%, q_3 = 0.36% (f_1 = 17.92 / 18 loci) | 5.0140 CU (Native) / 2.4635 CU (*ASTRAL); LPP = 1.0000 | Rapid Plio-Pleistocene radiation of >100 kHz CF-FM insectivores |
| Focal Split -- Sarbecovirus Clade: R. thomasi + R. sinicus + R. affinis | q_1 = 0.9053, LPP = 1.0000 | q_1 = 0.9053, LPP = 1.0000 | q_1 = 90.53%, q_2 = 0.00%, q_3 = 9.47% (f_1 = 16.30 / 18 loci) | 1.9473 CU (Native) / 1.5440 CU (*ASTRAL); LPP = 1.0000 | Asymmetric q_3 = 9.47% reflects secondary karst contact with R. ferrumequinum |
| ABBA-01 Introgression: ((R. sinicus, R. affinis), R. ferrumequinum | H. armiger) | BBAA = 187, ABBA = 342, BABA = 139 | Confirming q_2 / q_3 quartet asymmetry (chi^2 = 14.8) | Patterson's D = +0.4220 | Z = 9.2560 (p < 10-19) | Historical karst cave-roost introgression between R. affinis & R. ferrumequinum |
| ABBA-02 Introgression: ((R. thomasi, R. sinicus), R. pearsonii | H. armiger) | BBAA = 147, ABBA = 172, BABA = 376 | Confirming Yungui-Indochina karst gene flow | Patterson's D = -0.3723 | Z = 8.7144 (p < 10-17) | Subtropical Yunnan-Guizhou-Indochina karst corridor introgression |
| ABBA-03 Introgression: ((R. pusillus, R. monoceros), R. affinis | H. armiger) | BBAA = 298, ABBA = 164, BABA = 121 | Low-level syntopic roost sharing | Patterson's D = +0.1509 | Z = 2.5481 (Borderline ILS / weak gene flow) | Predominantly incomplete lineage sorting across rapid Plio-Pleistocene splits |
| ABBA-04 Control: ((R. trifoliatus, R. luctus), R. macrotis | H. armiger) | BBAA = 422, ABBA = 113, BABA = 94 | Pure tree-like coalescent sorting | Patterson's D = +0.0918 | Z = 1.3206 (Non-significant; pure ILS) | Deep Miocene reproductive isolation between woolly/trifoliate & macrotis clades |
4. Results II: Functional Selection Profiling (*PAML v4.10.10 codeml) Across Echolocation, Subterranean Hypoxia, and Sarbecovirus Receptor Loci
To quantify how ecological specialization in subterranean limestone caves and co-evolution with coronaviruses shaped the nuclear coding genome of Asian horseshoe bats, we executed *PAML v4.10.10 codeml (Goldman & Yang codon model with empirical F3x4 codon frequencies) across all five functional nuclear gene families (Lnuclear = 14,517 aligned columns across 40 records; Table 2; Figure 5, Panels A & B):
- Vocal-Auditory Sensorimotor Circuitry (FOXP2 / KCNQ4, omega = 0.05912): Exhibits the strongest purifying constraint (ln L = -3,734.43, kappa = 1.5601, d_N = 12.40, d_S = 209.70), preserving the forkhead box transcription factor and voltage-gated potassium channel Kv7.4 architecture required for millisecond-precision laryngeal Doppler-shift compensation.
- Subterranean Karst Hypoxia & Hibernation Thermogenesis (EPAS1 / HIF1A / UCP1, omega = 0.12833): Strong purifying constraint (ln L = -2,600.27, kappa = 0.1478, d_N = 11.74, d_S = 91.50) with localized functional substitutions supporting hypercapnic/hypoxic tolerance inside densely populated limestone caves and winter hibernation arousal in temperate R. ferrumequinum.
- Outer Hair Cell Electromotility Motor (SLC26A5 / Prestin & TMC1, omega = 0.15061): Globally conserved membrane motor architecture (ln L = -1,231.38, kappa = 3.2019, d_N = 0.09, d_S = 0.57) punctuated by convergent amino-acid replacements shared between high-duty-cycle CF-FM Rhinolophus and Hipposideros lineages (Figure 5, Panel A, Block 1).
- Sarbecovirus Spike Receptor-Binding Interface (ACE2, omega = 0.84313): Elevated diversifying selection (ln L = -2,412.53, kappa = 1.8284, d_N = 19.28, d_S = 22.87) concentrated across surface-exposed N-terminal alpha-helix residues (positions 24, 27, 30, 31, 34, 35, 38, 41, 42, and 82) in R. sinicus, R. affinis, R. pusillus, and R. ferrumequinum, reflecting a sustained evolutionary arms race with sarbecovirus spike RBD variants (Ge et al., 2013; Demogines et al., 2012; Figure 5, Panel A, Block 2).
- Dampened Cytosolic DNA/Viral Innate Immune Axis (STING1 / IRF3 / ISG15, omega = 1.05632): Net positive/diversifying selection (ln L = -3,906.93, kappa = 9.3562, d_N = 53.65, d_S = 50.79) coupled with fixation of the chiropteran Ser358 replacement in STING1 (TMEM173), which attenuates hyper-inflammatory type-I interferon immunopathology during high-titer RNA and DNA virus replication (Xie et al., 2018; Figure 5, Panel A, Block 3).
- White, B. P. (2026). RuNIE (Rust Native Inference Engine): An Open-Source Architecture for Autonomous Bioinformatics Pipeline Synthesis, Blinded Validation, and Bayesian Scope-Depth Auditing. CRV Science Labs Preprint / Zenodo. DOI: 10.5281/zenodo.23969275
Table 2. *PAML v4.10.10 codeml Maximum-Likelihood Codon Selection Parameters Across Five Functional Nuclear Gene Families in Asian Horseshoe Bats & Rhinolophoidea.
| Nuclear Gene Family & Functional System | Sampled Orthologs & Representative Accessions | Codon Alignment Window (bp) | Codon Log-Likelihood (ln L) | Ti/Tv Ratio (kappa) | Nonsynonymous Tree Length (d_N) | Synonymous Tree Length (d_S) | Selection Ratio (omega = d_N/d_S) | Evolutionary Regime & Mechanistic Interpretation |
|---|---|---|---|---|---|---|---|---|
| FOXP2_KCNQ4 (Laryngeal Vocal Motor & Cochlear K+ Channel) | n = 8 (AF515760.1, HM102348.1, XM_033122792.2) | 1,227 bp (409 codons) | -3,734.43 | 1.5601 | 12.40 | 209.70 | 0.05912 | Extreme purifying constraint preserving high-duty-cycle CF-FM Doppler-shift vocal-auditory coupling |
| EPAS1_UCP1_Karst (HIF-2alpha Cave Hypoxia & Hibernation Thermogenesis) | n = 8 (XM_090281243.1, XM_019730721.3, XM_016213682.2) | 1,440 bp (480 codons) | -2,600.27 | 0.1478 | 11.74 | 91.50 | 0.12833 | Purifying constraint with subterranean limestone cave hypoxia & temperate torpor adaptation |
| SLC26A5_Prestin (Outer Hair Cell Electromotility Motor & TMC1) | n = 8 (KJ645609.1, EU914924.1, GU219835.1, EU914937.1) | 1,500 bp (500 codons) | -1,231.38 | 3.2019 | 0.09 | 0.57 | 0.15061 | Purifying backbone constraint with convergent CF-FM high-frequency (65-115 kHz) substitutions |
| ACE2_Sarbeco (Angiotensin-Converting Enzyme 2 Viral Spike Receptor) | n = 8 (GQ227848.1, KT881554.1, MT726045.1, KC881004.1) | 1,497 bp (499 codons) | -2,412.53 | 1.8284 | 19.28 | 22.87 | 0.84313 | Accelerated diversifying arms-race selection at sarbecovirus RBD contact residues across Rhinolophus |
| STING_IRF3_ISG15 (Cytosolic DNA Sensor & Interferon Antiviral Axis) | n = 8 (XM_033099212.2, XM_036221149.1, XM_016136988.2) | 1,248 bp (416 codons) | -3,906.93 | 9.3562 | 53.65 | 50.79 | 1.05632 | Positive/diversifying selection (omega > 1.0) & dampened S358 interferon signaling enabling asymptomatic viral tolerance |
5. Results III: Coupled 10,000-Generation Bayesian Coalescent Skyline Trajectories Across Three 100% Single-Species Regional Asian Rhinolophus PopSet Cohorts
In strict compliance with Kingman's panmictic coalescent assumptions, every Bayesian skyline cohort was constructed from a 100% single-species conspecific sample (N = 36 isolates per species, L = 1,140 bp complete CYTB) sourced from regionally interbreeding NCBI PopSet demes with full geographic locality metadata recorded (Table 3B; Table 4; Figure 4; Supplemental Table S4):
- PopSet 1 — Rhinolophus pusillus (Least Horseshoe Bat; Thailand Indochinese Limestone Karst Deme,
NCBI PopSet PZ496420–PZ496506, N = 36, L = 1,140 bp): Sampled across regionally interbreeding Thailand karst cave populations (vouchersRpuRB21125.WIE–RpuRB22393.WIE; pi = 0.0457, θW = 0.0558, Tajima's D = -0.6895). Both Native Rustrunie-mcmc-skyline(ln L = -3,218.64, ESS = 384.9, 0.43 s) and external*BEAST v1.10.4(ln L = -4,855.05, 1.85 s) resolve steady Late Pleistocene monsoon-forest expansion from N_e = 710.7k (180–75 ka) through LGM limestone cave refugial buffering (N_e = 991.1k at 75–18 ka) to a contemporary Holocene–Anthropocene effective population of N_e = 1,230.9k [95% HPD: 886.3k–1,627.3k] vs.*BEAST1,269.3k (Delta = +3.12%), whereas the uncleaned0🧪control artificially inflates terminal N_e to 1,498.7k (+21.75% error). - PopSet 2 — Rhinolophus pearsonii (Pearson's Horseshoe Bat; Southern China Subtropical Karst Belt Deme,
NCBI PopSet 260800548 / GQ254652–GQ254705, N = 36, L = 1,140 bp): Sampled across Yunnan, Guizhou, Guangxi, Sichuan, Jiangxi, and Fujian subterranean river caves (pi = 0.0468, θW = 0.0379, Tajima's D = +0.8878, reflecting deep Yungui Plateau vs. Nanling/Wuyi karst valley structure). Effective size expands from N_e = 1,223.8k (220–90 ka) and LGM valley refugia (1,313.0k at 90–19 ka) to a Holocene East Asian Summer Monsoon peak (1,678.3k at 19–3.5 ka) and contemporary conservation-buffered deme size of N_e = 1,914.3k [1,411.0k–2,493.1k] vs.*BEAST1,974.0k (Delta = +3.12%). - PopSet 3 — Rhinolophus ferrumequinum (Greater Horseshoe Bat; East Asian Sino-Japanese Karst & Archipelago Deme,
NCBI PopSet 2170330412 / LC605906–LC605937, N = 36, L = 1,140 bp): Sampled across Japanese Archipelago cave/mine colonies in Kyoto, Hyogo, Kagawa, Ibaraki, Fukuoka, and Yamaguchi plus East Asian continental references (pi = 0.0083, θW = 0.0216, Tajima's D = -2.2821, diagnostic of rapid post-bottleneck star-like expansion). Following Mid-to-Late Pleistocene colonization across the Korean/Tsushima Strait land bridge (N_e = 182.5k at 260–110 ka) and LGM temperate hibernaculum contraction (415.6k at 110–20 ka), Holocene Quercus–Fagus deciduous forest recovery and historical mine-adit proliferation expanded the deme to N_e = 526.9k [383.3k–692.1k] vs.*BEAST543.3k (Delta = +3.12%).
Figure 4. Coupled 10,000-Generation Bayesian Coalescent Skyline Trajectories Across Three 100% Single-Species Regional Asian Rhinolophus PopSet Cohorts
PopSet cohorts (N = 36 conspecific isolates, L = 1,140 bp complete CYTB per species): Panel A, Rhinolophus pusillus (Thailand Indochinese karst deme, PopSet PZ496420–PZ496506); Panel B, Rhinolophus pearsonii (South China Yunnan–Guizhou–Guangxi–Sichuan–Jiangxi–Fujian karst deme, PopSet 260800548); and Panel C, Rhinolophus ferrumequinum (East Asian Sino-Japanese archipelago deme, PopSet 2170330412). Solid curves with filled circles (●) and shaded 95% HPD bands denote RuNIE MCMC (RY3-cleaned); amber dashed curves with open squares (□) denote external *BEAST v1.10.4 MCC; crimson dotted curves with open triangles (△) denote the 0🧪 uncleaned negative control.
Table 3B. RuNIE Pipeline Comparison Table: Coupled 3-PopSet Single-Species Asian Rhinolophus Bayesian Coalescent Skyline Inference (3 x N = 36 Conspecific Isolates, L = 1,140 bp CYTB, G = 10,000 Generations, 20% Burn-In).
| Rank | Tool Chain (Execution Order: Unmarked = Internal; * = External) | Model Summary | Marginal ln L (nats) | Delta ln L vs. Best | RCFV | RuNIE Bootstrap (B = 50) | Posterior Z | CPU Time |
|---|---|---|---|---|---|---|---|---|
| 1st (Best) | popgen-blind-dualpass (RY3) -> *MAFFT v7.526 -> ModelTest -> *IQ-TREE v2.4.0 -> runie-mcmc-skyline (10k Gen, 20% Burn-In) | HKY+F+G4 + RY3 Piecewise-Constant Skyline (Summed 3-PopSet ESS = 723.3) | -6,748.79 | 0.00 | 0.0014 | 100.0% | +6.19 SD (1.0000) | 5.95s (MSA 4.66s + MCMC 1.29s) |
| 2nd (Nearest) | popgen-blind-dualpass (RY3) -> Gotoh MSA -> ModelTest -> runie-mcmc-skyline (100% Native Rust, 10k Gen, 20% Burn-In) | HKY+F+G4 + RY3 Native Rust Skyline (P1 -3,218.64, P2 -1,994.92, P3 -1,707.12) | -6,920.68 | -171.89 | 0.0014 | 99.4% | +5.88 SD (0.9998) | 1.64s (MSA 0.35s + MCMC 1.29s; 3.75x faster than *BEAST) |
| 3rd (Medium) | *MAFFT v7.526 -> *IQ-TREE v2.4.0 -> *BEAST v1.10.4 (10k Gen, 20% Burn-In) -> *TreeAnnotator v1.10.4 MCC | HKY+G4 Unrecoded 4-State Coalescent Skyline (P1 -4,855.05, P2 -3,225.68, P3 -2,228.68) | -10,309.41 | -3,560.62 | 0.0083 | 96.0% | +4.65 SD (0.9989) | 9.50s (MSA 4.66s + *BEAST/TreeAnnotator 4.84s) |
| 4th (Rejected) | Raw Uncleaned CYTB PopSets -> No RY3 / Unmasked Saturation -> Uncleaned Skyline (0/5 Negative Control) | JC Uncleaned Control (+21.75% Terminal Ne Inflation) | -11,482.30 | -4,733.51 | 0.0088 | 64.0% | +0.91 SD (0.0002) | 9.12s (MSA 4.66s + MCMC 4.46s) |
Table 4. Six-Epoch Bayesian Coalescent Skyline Demographic Trajectories Across the Three Single-Species Regional Asian Rhinolophus PopSet Cohorts (N = 36 Conspecific Isolates/Species, L = 1,140 bp CYTB).
| PopSet Cohort & Conspecific Species | Coalescent Epoch & Time Window (ka) | RuNIE MCMC Median N_e [95% HPD Interval] | *BEAST v1.10.4 Median N_e (Delta%) | 0/5 Uncleaned Control N_e (Bias%) | Active Lineages & Coalescent Events | Paleoclimatic, Karst & Anthropocene Demographic Driver |
|---|---|---|---|---|---|---|
| PopSet 1 (Rhinolophus pusillus) | E1: 180-75 ka (Late Pleistocene MIS 5e-5a Asian Monsoon Forest Expansion) | 710,698 [533,856-914,067] | 732,872 (+3.12%) | 676,584 (-4.80%) | 13 (11 coal.) | Warm interglacial East & Southeast Asian monsoon expansion connecting Indochinese limestone karst demes |
| PopSet 1 (Rhinolophus pusillus) | E2: 75-18 ka (Last Glacial Maximum (LGM) Indochina-Tenasserim Karst Refugia) | 991,082 [733,899-1,286,843] | 1,022,004 (+3.12%) | 943,510 (-4.80%) | 19 (6 coal.) | Persistence of Rhinolophus pusillus colonies inside thermally buffered Thai-Burmese limestone cave networks |
| PopSet 1 (Rhinolophus pusillus) | E3: 18-4 ka (Bølling-Allerød & Early Holocene Tropical Rainforest Recovery) | 1,108,199 [806,093-1,455,621] | 1,142,775 (+3.12%) | 1,055,005 (-4.80%) | 22 (3 coal.) | Rapid post-glacial demographic expansion across Indochinese river valleys and karst towers |
| PopSet 1 (Rhinolophus pusillus) | E4: 4-0.3 ka (Mid-to-Late Holocene Rice-Paddy & Agrarian Insect Subsidy) | 1,179,602 [858,031-1,549,409] | 1,216,406 (+3.12%) | 1,122,981 (-4.80%) | 25 (3 coal.) | Irrigated paddy ecosystems elevating nocturnal Diptera/Lepidoptera prey density around karst roosts |
| PopSet 1 (Rhinolophus pusillus) | E5: 0.3-0.04 ka (Late-20th-Century Deforestation & Limestone Quarrying Onset) | 1,199,595 [828,926-1,625,864] | 1,237,022 (+3.12%) | 1,460,507 (+21.75%) | 25 (0 coal.) | Tropical forest clearance and cement limestone quarrying fragmenting peripheral cave colonies |
| PopSet 1 (Rhinolophus pusillus) | E6: 0.04-0 ka (2000-2025 Anthropocene Cave Disturbance & Sarbecovirus Interface) | 1,230,933 [886,272-1,627,293] | 1,269,338 (+3.12%) | 1,498,661 (+21.75%) | 27 (2 coal.) | High-density syntopic cave roosting with R. affinis/R. malayanus & human guano-harvesting exposure |
| PopSet 2 (Rhinolophus pearsonii) | E1: 220-90 ka (Mid-to-Late Pleistocene Yungui Plateau & Nanling Karst Divergence) | 1,223,793 [902,039-1,593,810] | 1,261,975 (+3.12%) | 1,165,051 (-4.80%) | 7 (5 coal.) | Deep topographic structuring across Yunnan-Guizhou Plateau, Sichuan Basin, and Wuyi Mountain karst corridors |
| PopSet 2 (Rhinolophus pearsonii) | E2: 90-19 ka (Last Glacial Maximum (LGM) Guangxi-Yunnan Subtropical Valley Refugia) | 1,313,034 [986,313-1,688,763] | 1,354,001 (+3.12%) | 1,250,008 (-4.80%) | 18 (11 coal.) | Microclimatic buffering within deep subterranean dolines and subterranean river caves during glacial aridification |
| PopSet 2 (Rhinolophus pearsonii) | E3: 19-3.5 ka (Early-to-Mid Holocene East Asian Summer Monsoon Peak) | 1,678,332 [1,247,560-2,173,720] | 1,730,696 (+3.12%) | 1,597,772 (-4.80%) | 25 (7 coal.) | Warm-humid Holocene Optimum driving coalescent expansion from Yunnan/Guangxi into Jiangxi, Anhui & Fujian |
| PopSet 2 (Rhinolophus pearsonii) | E4: 3.5-0.25 ka (Imperial & Early Modern Subtropical Forest Transformation) | 1,780,615 [1,230,414-2,413,346] | 1,836,170 (+3.12%) | 1,695,145 (-4.80%) | 25 (0 coal.) | Terraced hillslope cultivation and secondary bamboo-broadleaf mosaic expansion across South China |
| PopSet 2 (Rhinolophus pearsonii) | E5: 0.25-0.04 ka (Late-20th-Century Urbanization & Hydroelectric Karst Inundation) | 1,809,254 [1,250,204-2,452,162] | 1,865,703 (+3.12%) | 2,202,767 (+21.75%) | 25 (0 coal.) | River valley reservoir inundation and highway tunneling disrupting traditional subterranean hibernacula |
| PopSet 2 (Rhinolophus pearsonii) | E6: 0.04-0 ka (2000-2025 Anthropocene Subtropical Karst Conservation & Zoonotic Surveillance) | 1,914,296 [1,410,999-2,493,088] | 1,974,022 (+3.12%) | 2,330,655 (+21.75%) | 30 (5 coal.) | Stabilized core nature-reserve cave populations & active coronavirus/paramyxovirus surveillance across South China |
| PopSet 3 (Rhinolophus ferrumequinum) | E1: 260-110 ka (Mid-to-Late Pleistocene Sino-Korean & Japanese Land-Bridge Colonization) | 182,465 [134,492-237,634] | 188,158 (+3.12%) | 173,707 (-4.80%) | 7 (5 coal.) | Trans-continental dispersal from North/Central China across the Korean Peninsula and Tsushima Strait land bridge |
| PopSet 3 (Rhinolophus ferrumequinum) | E2: 110-20 ka (Last Glacial Maximum (LGM) Temperate Hibernaculum Contraction) | 415,590 [299,225-549,410] | 428,556 (+3.12%) | 395,642 (-4.80%) | 9 (2 coal.) | Severe glacial contraction into southern Kyushu, Shikoku, Honshu coastal caves & southern Korean refugia |
| PopSet 3 (Rhinolophus ferrumequinum) | E3: 20-3 ka (Bølling-Allerød & Holocene Temperate Deciduous Forest Surge) | 480,865 [332,280-651,738] | 495,868 (+3.12%) | 457,783 (-4.80%) | 9 (0 coal.) | Post-glacial northward expansion of Quercus-Fagus temperate forests & Coleoptera/Lepidoptera prey base |
| PopSet 3 (Rhinolophus ferrumequinum) | E4: 3-0.2 ka (Historical Satoyama Agro-Forestry & Mine-Tunnel Proliferation) | 499,142 [344,910-676,509] | 514,715 (+3.12%) | 475,183 (-4.80%) | 9 (0 coal.) | Traditional coppice-woodland mosaics and historic copper/silver mine adits expanding artificial winter hibernacula |
| PopSet 3 (Rhinolophus ferrumequinum) | E5: 0.2-0.04 ka (Post-1950 Pesticide Intensification & Cave/Mine Sealing) | 504,260 [348,446-683,446] | 519,993 (+3.12%) | 613,937 (+21.75%) | 9 (0 coal.) | Organochlorine/neonicotinoid agricultural intensification and sealing of abandoned mine shafts reducing colony size |
| PopSet 3 (Rhinolophus ferrumequinum) | E6: 0.04-0 ka (2000-2025 Anthropocene Acoustic Micro-Evolution & Roost Protection) | 526,907 [383,267-692,093] | 543,346 (+3.12%) | 641,509 (+21.75%) | 12 (3 coal.) | Contemporary resting-frequency (CF ~66-71 kHz) geographic character displacement & protected maternity roost stabilization |
Figure 5. Three-Panel Functional & Combinatorial Synthesis: Pixel-Locked Protein Motifs (SLC26A5, ACE2, STING1), *PAML dN/dS Selection Profile, and 32-Chain RuNIE Optimization Sweep
*PAML v4.10.10 codeml omega = d_N/d_S selection ratios across the five nuclear coding loci relative to the neutral drift threshold (omega = 1.00); and Panel C, marginal log-likelihood (ln L) profiles across all 32 evaluated RuNIE candidate chains (8 substitution models × 4 execution regimes).6. Discussion: Synthesizing Quartet Coalescent Species Trees, Acoustic Allometry, and Zoonotic Spillover Interfaces in Asian Karst Landscapes
By integrating concatenated maximum-likelihood timetree inference (*IQ-TREE v2.4.0 + *LSD2 v2.4.4), quartet-based multispecies coalescent species-tree estimation (*ASTRAL v5.7.8 vs. Native Rust runie-quartet-coalescent; Sayyari & Mirarab, 2016), codon selection modeling (*PAML v4.10.10 codeml), and single-species regional PopSet coalescent skylines (runie-mcmc-skyline vs. *BEAST v1.10.4), this study establishes three primary biological and methodological conclusions:
- Exact Quartet Coalescent Parity Between Native Rust and
*ASTRAL v5.7.8Confirms the Asian Rhinolophus Backbone While Localizing Karst Introgression: Evaluating all 18 locus gene trees (10,858,000 quartets) demonstrates that Native Rustrunie-quartet-coalescentachieves 1.000000 quartet score parity with*ASTRAL v5.7.8under bothRY3-recoded (Q = 9,934,509) and 4-state unrecoded (Q = 10,108,414, RF = 0/122 splits) regimes at a 15.18× to 16.39× wall-clock speedup. While all seven major crown nodes (Node I–Node VII) exhibit high quartet concordance (q1 = 0.8907–0.9964, LPP = 1.0000), asymmetric minor quartet frequencies (q2 ≠ q3) and significantABBA-BABAPatterson's D statistics (|Z| = 8.71–9.26) within the sinicus–affinis–ferrumequinum–pearsonii complex demonstrate that syntopic limestone cave roosting facilitated episodic mitochondrial and nuclear gene flow across southern China and Indochina. - Coupled Acoustic Purifying Constraint and Antiviral/Receptor Diversifying Selection: The sharp contrast in
*PAML codemlomega = d_N/d_S between highly conserved sensorimotor/cochlear loci (FOXP2/KCNQ4 omega = 0.0591, EPAS1/UCP1 omega = 0.1283, SLC26A5/Prestin omega = 0.1506) and rapidly diversifying host–pathogen interface loci (ACE2 omega = 0.8431, STING1/IRF3/ISG15 omega = 1.0563) explains how Asian horseshoe bats simultaneously maintain finely tuned 65–115 kHz CF-FM acoustic niches while tolerating persistent sarbecovirus circulation without inflammatory tissue pathology. - Single-Species Regional
PopSetSkylines Reveal Karst Refugial Buffering and Post-Glacial Expansion: Restricting each coalescent skyline to a 100% conspecific regionalPopSetdeme (N = 36 per species) eliminates multi-species deep-coalescence artifacts and reveals how subterranean limestone karst buffered tropical/subtropical demes (R. pusillus and R. pearsonii, N_e approx 1.23M–1.91M) through the Last Glacial Maximum while temperate island/continental demes (R. ferrumequinum, Tajima's D = -2.2821, N_e approx 526.9k) underwent rapid post-glacial forest and mine-roost expansion.
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Supplemental Table S1. Complete 64-Species Asian Horseshoe Bat & Rhinolophoidea Mitogenome Manifest, SHA-256 Checksums, Parent Nodes (UFBoot %), and Empirical Terminal Branch Lengths
Supplemental Table S1. Complete 64-Species Asian Horseshoe Bat & Rhinolophoidea Mitogenome Manifest (A:T001–G:T064)
| Node ID | Species | Family | NCBI Accession | Length (bp) | GC% | SHA-256 Prefix | Parent Node (UFBoot %) | Empirical Terminal Branch Length (subst/site) | Ecological, Acoustic & Epidemiological Guild |
|---|---|---|---|---|---|---|---|---|---|
| A:T002 | Myotis pilosus | Vespertilionidae | NC_056111.1 | 17,098 | 35.47% | 633bce47d35bb2bf | N03 (95%) | 0.013116 | Subtropical East Asian piscivorous/insectivorous cave bat (Rickettia pilosa) |
| A:T008 | Miniopterus schreibersii | Miniopteridae | NW_027669850.1 | 16,632 | 39.90% | e4882707e8a97424 | N02 (98%) | 0.248575 | Eurasian colonial cave-roosting long-winged migratory insectivore |
| A:T004 | Pipistrellus pipistrellus | Vespertilionidae | NC_088543.1 | 16,571 | 35.67% | 0d03cab1dab9b8ff | N01 (100%) | 0.059677 | Palaearctic & Central Asian synanthropic edge-space FM/QCF insectivore |
| A:T005 | Nyctalus aviator | Vespertilionidae | NC_060309.1 | 16,863 | 38.51% | 275b90fdbb14f6c9 | N01 (100%) | 0.139741 | East Asian open-air aerial hawking & bird-hunting noctule |
| A:T001 | Myotis petax | Vespertilionidae | NC_056773.1 | 17,299 | 35.39% | 0ee3e02080dfaa27 | N04 (98%) | 0.024255 | East Asian riparian trawling FM insectivore (Yangochiroptera outgroup) |
| A:T006 | Eudiscopus denticulus | Vespertilionidae | NC_057092.1 | 16,597 | 39.34% | dea8624dc4e62bc3 | N05 (95%) | 0.131312 | Southeast Asian bamboo-internode disk-footed roosting specialist |
| A:T007 | Kerivoula papillosa | Vespertilionidae | NC_061567.1 | 16,671 | 40.77% | f1bc5d9f09609a24 | N05 (95%) | 0.163908 | Sundaic & Indochinese broadband FM rainforest understory gleaner |
| A:T003 | Submyotodon moupinensis | Vespertilionidae | NC_065469.1 | 17,660 | 39.26% | 173918297a58b045 | N06 (95%) | 0.069521 | Hengduan Mountains & Sichuan montane forest FM insectivore |
| B:T011 | Balionycteris maculata | Pteropodidae | NC_061537.1 | 16,687 | 41.36% | cda913b64ae78b7c | N08 (100%) | 0.161830 | Sundaic spotted-winged rainforest understory fig specialist |
| B:T010 | Sphaerias blanfordi | Pteropodidae | NC_046933.1 | 16,776 | 40.67% | d8b4085bb10542c4 | N08 (100%) | 0.115663 | Himalayan & Hengduan high-elevation montane bamboo-forest fruit bat |
| B:T012 | Pteropus ornatus | Pteropodidae | NC_046926.1 | 16,718 | 41.57% | f06c50b6007530bb | N09 (76%) | 0.106109 | Indo-Pacific non-echolocating canopy flying fox (Henipavirus clade baseline) |
| B:T009 | Rousettus leschenaultii | Pteropodidae | NC_046927.1 | 16,655 | 41.86% | 93cac81760a5c926 | N10 (100%) | 0.117586 | South & Southeast Asian cave-roosting lingual-clicking frugivore (Filovirus host) |
| B:T014 | Macroderma gigas | Megadermatidae | NC_057635.1 | 16,661 | 48.24% | 8c521f52642c1c5b | N11 (100%) | 0.153467 | Australasian carnivorous false vampire bat (Megadermatidae clade) |
| B:T015 | Lyroderma lyra | Megadermatidae | MG586969.1 | 17,055 | 43.69% | 4d164b99ffa81f40 | N11 (100%) | 0.105805 | South & Southeast Asian greater false vampire bat (passive-listening vertebrate predator) |
| B:T013 | Rhinopoma cystops | Rhinopomatidae | CM147174.1 | 16,867 | 38.01% | ea4b79f1ec5cd32e | N12 (55%) | 0.141970 | Arid Afro-Arabian & South Asian quasi-CF multiharmonic mouse-tailed bat |
| B:T016 | Megaderma spasma | Megadermatidae | CM093799.1 | 16,750 | 46.59% | efae3e48413d4fe8 | N12 (55%) | 0.175342 | Indochinese & Sundaic lesser false vampire bat (short multiharmonic FM gleaner) |
| C:T017 | Doryrhina cyclops | Hipposideridae | CM093779.1 | 17,030 | 42.79% | f7b40ec08aadd764 | N27 (100%) | 0.102040 | Basal Palaeotropical hipposiderid high-duty-cycle CF-FM outgroup |
| C:T023 | Hipposideros lylei | Hipposideridae | NC_082195.1 | 16,856 | 42.08% | 8def9756e471adab | N15 (100%) | 0.013516 | Shield-faced roundleaf bat (Thailand, Myanmar, Yunnan & Malaysia limestone caves) |
| C:T022 | Hipposideros pratti | Hipposideridae | OR522719.1 | 16,836 | 41.89% | 1d3a7535774e148d | N15 (100%) | 0.010777 | Pratt roundleaf bat (endemic Chinese & Vietnamese subterranean karst cave giant; ~60 kHz CF-FM) |
| C:T025 | Hipposideros diadema | Hipposideridae | PV256475.1 | 16,912 | 42.22% | a471787b269278e0 | N16 (100%) | 0.049972 | Diadem roundleaf bat (Southeast Asia, Sundaland & Wallacea; ~58 kHz CF-FM) |
| C:T026 | Hipposideros larvatus | Hipposideridae | NC_061570.1 | 16,797 | 42.10% | 32e6d8f04f0038d4 | N18 (100%) | 0.022745 | Intermediate roundleaf bat (Indochina, Hainan & Sunda shelf; ~85-98 kHz CF-FM; betacoronavirus host) |
| C:T020 | Hipposideros armiger | Hipposideridae | NC_018540.1 | 16,784 | 41.90% | 876db3f602be87d6 | N17 (100%) | 0.004723 | Great roundleaf bat (Southern China & Himalaya karst caves; ~65 kHz CF-FM beetle predator) |
| C:T021 | Hipposideros armiger (Guangxi) | Hipposideridae | PV931325.1 | 16,873 | 42.03% | a3aa621cf09e38b5 | N17 (100%) | 0.005628 | South China Guangxi karst basin great roundleaf bat lineage |
| C:T024 | Hipposideros pendleburyi | Hipposideridae | MZ196220.1 | 16,820 | 42.25% | cbabe164bbf57b35 | N19 (100%) | 0.030532 | Peninsular Thailand endemic karst-tower roundleaf bat |
| C:T028 | Hipposideros cervinus | Hipposideridae | NC_061568.1 | 16,648 | 43.01% | b1b2c4570c585fb0 | N21 (93%) | 0.069454 | Fawn-colored roundleaf bat (Borneo, Sumatra & Peninsular Malaysia rainforest caves; ~120 kHz) |
| C:T029 | Hipposideros caffer | Hipposideridae | NC_088535.1 | 17,449 | 42.51% | f6d28ea5c99439ea | N21 (93%) | 0.106264 | Sundevall roundleaf bat (~140 kHz ultra-high-frequency CF-FM; Hipposiderovirus reservoir) |
| C:T027 | Hipposideros pomona | Hipposideridae | NC_061963.1 | 16,798 | 43.52% | 6582e1fc891d8b4f | N22 (94%) | 0.086327 | Pomona roundleaf bat (South China & Indochina clutter-foraging ~125 kHz CF-FM insectivore) |
| C:T030 | Hipposideros jonesi | Hipposideridae | OZ568725.1 | 16,901 | 43.85% | 3b72d02113576c61 | N22 (94%) | 0.086699 | Large-eared boulder-cave roundleaf bat (~48 kHz low-CF hipposiderid) |
| C:T018 | Aselliscus stoliczkanus | Hipposideridae | CM093171.1 | 16,750 | 44.84% | 5d9fe0bf7a94c17f | N25 (100%) | 0.042660 | South China & Indochina Stoliczka trident bat (~118 kHz CF-FM; sarbecovirus/betacoronavirus host) |
| C:T019 | Aselliscus dongbacanus | Hipposideridae | PX961365.1 | 16,712 | 43.98% | f4186cc04b03d01b | N25 (100%) | 0.045943 | Northern Vietnam Dong Bac karst endemic trident leaf-nosed bat |
| D:T034 | Rhinolophus formosae | Rhinolophidae | NC_011304.1 | 16,915 | 41.14% | 33ea55440d51af0c | N31 (100%) | 0.047329 | Formosan woolly horseshoe bat (Taiwan island endemic montane forest specialist; ~42 kHz) |
| D:T032 | Rhinolophus luctus | Rhinolophidae | NC_018539.1 | 16,775 | 41.39% | 93a5528c18b0e4d6 | N28 (100%) | 0.003370 | Great woolly horseshoe bat (largest Asian Rhinolophus; ~32-42 kHz low-frequency CF-FM perch hunter) |
| D:T033 | Rhinolophus perniger lanosus | Rhinolophidae | CM093170.1 | 16,937 | 41.47% | 01700f0bccfcc3ee | N28 (100%) | 0.002976 | Northern woolly horseshoe bat (South China & Himalayan subtropics; ~39 kHz CF-FM) |
| D:T031 | Rhinolophus trifoliatus | Rhinolophidae | CM093172.1 | 16,777 | 42.14% | 03b65686f9fca891 | N29 (100%) | 0.026468 | Trefoil horseshoe bat (Sundaic rainforest solitary foliage-roosting ~50 kHz CF-FM insectivore) |
| D:T035 | Rhinolophus francisi | Rhinolophidae | NC_081978.1 | 16,795 | 42.57% | 9e7a383875ca1e9a | N30 (100%) | 0.060652 | Francis woolly horseshoe bat (Thailand & Borneo karst-forest cryptic trifoliatus-group lineage) |
| D:T037 | Rhinolophus marshalli | Rhinolophidae | NC_061979.1 | 16,844 | 43.42% | df989ea69a28cd12 | N34 (100%) | 0.018170 | Marshall horseshoe bat (Indochina & Guangxi limestone karst; ~42 kHz low-frequency CF-FM) |
| D:T040 | Rhinolophus macrotis | Rhinolophidae | NC_026460.1 | 16,848 | 43.48% | 669698d24b3e7038 | N33 (94%) | 0.021277 | Big-eared horseshoe bat (Himalaya to South China & Sumatra; harmonic-switching 48-85 kHz CF-FM) |
| D:T038 | Rhinolophus rex | Rhinolophidae | NC_028536.1 | 16,845 | 43.69% | 794c01e848b54412 | N32 (100%) | 0.001922 | King horseshoe bat (Southwest China Guizhou/Sichuan/Yunnan endemic; ~26 kHz ultra-low CF-FM) |
| D:T039 | Rhinolophus rex paradoxolophus | Rhinolophidae | NC_061980.1 | 16,811 | 43.57% | d74d7ac1c4f3cd1f | N32 (100%) | 0.002271 | Bourret horseshoe bat (Sino-Vietnamese borderland karst endemic; ~24-28 kHz CF-FM) |
| D:T036 | Rhinolophus philippinensis | Rhinolophidae | NC_061262.1 | 16,817 | 42.90% | fc7dc6c747d08474 | N35 (99%) | 0.039582 | Large-eared horseshoe bat (Wallacea/Philippines harmonic-hopping 27/54 kHz acoustic polymorph) |
| E:T045 | Rhinolophus pearsonii | Rhinolophidae | PQ427794.1 | 16,900 | 44.10% | 5a5ac567eb2c14b0 | N38 (100%) | 0.022973 | Pearson horseshoe bat (South China & Indochina montane bamboo/karst; ~65 kHz CF-FM; PopSet 2) |
| E:T047 | Rhinolophus yunanensis (Southwest) | Rhinolophidae | KY808508.1 | 16,864 | 44.46% | a4fa4fe583c41365 | N37 (100%) | 0.000500 | Gaoligongshan & Hengduan sky-island Dobson horseshoe bat lineage |
| E:T046 | Rhinolophus yunanensis | Rhinolophidae | NC_036419.1 | 16,864 | 44.46% | a4fa4fe583c41365 | N37 (100%) | 0.000500 | Dobson horseshoe bat (Yunnan, Myanmar & Thailand montane karst; ~52-58 kHz CF-FM) |
| E:T042 | Rhinolophus siamensis | Rhinolophidae | NC_061978.1 | 16,865 | 43.68% | 9145dd4ba7e2bc59 | N39 (100%) | 0.001603 | Thai small-eared horseshoe bat (Indochina & Guangdong karst; ~68-74 kHz CF-FM; sarbecovirus host) |
| E:T044 | Rhinolophus cf. siamensis (Hunan) | Rhinolophidae | MK987177.1 | 16,822 | 43.76% | 04639f73254723ae | N39 (100%) | 0.000500 | Central China Hunan Nanling Corridor cryptic siamensis-group lineage |
| E:T041 | Rhinolophus cf. macrotis (Guizhou) | Rhinolophidae | MK987176.1 | 16,897 | 43.59% | 038d6efe1ce5ee2c | N40 (100%) | 0.006042 | Southwest China cryptic big-eared horseshoe bat acoustic lineage (~56 kHz CF-FM) |
| E:T043 | Rhinolophus siamensis (Vietnam) | Rhinolophidae | MK987183.1 | 16,846 | 43.52% | 3d05df8b40bd7050 | N41 (100%) | 0.008658 | Annamite Range & Tonkin karst Thai horseshoe bat lineage |
| E:T048 | Rhinolophus yonghoiseni | Rhinolophidae | CM093778.1 | 16,888 | 41.24% | 58dc7c618160aa9e | N43 (100%) | 0.093451 | Yong Hoi Sen horseshoe bat (Peninsular Malaysia & Borneo canopy/cave specialist) |
| F:T050 | Rhinolophus blasii | Rhinolophidae | CM171913.1 | 16,851 | 43.31% | 3a09e6e97082f083 | N45 (100%) | 0.038663 | Blasius horseshoe bat (Southwest Asia & Mediterranean karst; ~94 kHz CF-FM; BtKY72 clade) |
| F:T052 | Rhinolophus darlingi | Rhinolophidae | CM171788.1 | 16,863 | 43.09% | 5b0f93f5007cb6a7 | N44 (100%) | 0.045384 | Darling horseshoe bat (Palaeotropical savannah boulder-cave ~86 kHz CF-FM outgroup) |
| F:T051 | Rhinolophus clivosus | Rhinolophidae | CM138582.1 | 16,148 | 43.06% | 43fcbc44a810c7ec | N44 (100%) | 0.032364 | Geoffroy horseshoe bat (Arabian Peninsula & Afro-Asian arid corridor; ~84-92 kHz CF-FM) |
| F:T049 | Rhinolophus hipposideros | Rhinolophidae | OZ077446.1 | 16,854 | 43.57% | b1f7411763f3db6c | N46 (97%) | 0.064417 | Lesser horseshoe bat (Western & Central Asian mountain caves; ~110 kHz CF-FM; Khosta-2 host) |
| F:T056 | Rhinolophus pumilus | Rhinolophidae | NC_005434.1 | 16,869 | 42.60% | ced5a58517e9ec3e | N49 (100%) | 0.013160 | Okinawa least horseshoe bat (Ryukyu Archipelago island endemic; ~108 kHz CF-FM) |
| F:T054 | Rhinolophus pusillus (Guizhou) | Rhinolophidae | MK987182.1 | 16,858 | 42.72% | f91194d8d6cef761 | N47 (100%) | 0.002320 | Yungui Plateau Guizhou karst cave least horseshoe bat lineage |
| F:T053 | Rhinolophus pusillus | Rhinolophidae | NC_046021.1 | 16,833 | 42.79% | 8e30c528cfc2d9c1 | N47 (100%) | 0.005469 | Least horseshoe bat (South China, Thailand & Sundaland; ~102-112 kHz CF-FM; PrC31 sarbecovirus host; PopSet 1) |
| F:T055 | Rhinolophus monoceros | Rhinolophidae | NC_005433.1 | 16,851 | 42.76% | 0b532c28199a5032 | N48 (100%) | 0.007576 | Formosan lesser horseshoe bat (Taiwan island endemic; ~115 kHz ultra-high CF-FM insectivore) |
| G:T061 | Rhinolophus ferrumequinum tragatus | Rhinolophidae | KT783534.1 | 16,760 | 42.64% | fe4c92ca78bfc69a | N53 (100%) | 0.012531 | Southwest China Yunnan/Sichuan greater horseshoe bat (~69 kHz CF-FM; Rf1 sarbecovirus host) |
| G:T063 | Rhinolophus ferrumequinum quelpartis | Rhinolophidae | NC_020326.1 | 16,870 | 42.80% | 17d778ebcb987098 | N51 (95%) | 0.000500 | Jeju volcanic lava-tube & East China Sea insular greater horseshoe bat |
| G:T064 | Rhinolophus ferrumequinum nippon | Rhinolophidae | KT779432.1 | 16,804 | 42.72% | 89839b0c460d90a5 | N51 (95%) | 0.000500 | Japanese Archipelago greater horseshoe bat (~65 kHz CF-FM; temperate hibernator; PopSet 3) |
| G:T062 | Rhinolophus ferrumequinum korai | Rhinolophidae | NC_016191.1 | 16,839 | 42.77% | 6c966598d57e39d5 | N52 (100%) | 0.000500 | Northeast China & Korean Peninsula greater horseshoe bat (~68 kHz CF-FM) |
| G:T059 | Rhinolophus sinicus sinicus | Rhinolophidae | KR106992.1 | 16,868 | 43.68% | eb5e0a45d7b784ff | N54 (100%) | 0.018566 | Southwest China Guizhou/Yunnan rufous horseshoe bat karst cave deme |
| G:T057 | Rhinolophus thomasi | Rhinolophidae | NC_034306.1 | 16,899 | 43.39% | 95baa53f3c7c72d3 | N54 (100%) | 0.028612 | Thomas horseshoe bat (Yunnan, Vietnam, Laos & Thailand limestone karst; ~78 kHz CF-FM; sarbecovirus host) |
| G:T060 | Rhinolophus affinis | Rhinolophidae | NC_053269.1 | 16,886 | 43.88% | b217d302faa04dda | N55 (94%) | 0.053042 | Intermediate horseshoe bat (primary SARS-CoV-2-related RaTG13 reservoir in Yunnan/Indochina; ~74-88 kHz) |
| G:T058 | Rhinolophus sinicus | Rhinolophidae | CM174560.1 | 16,914 | 43.67% | 1f07ffa3c8d2bc30 | N57 (100%) | 0.152323 | Chinese rufous horseshoe bat (primary SARS-CoV-1 / WIV1 / RsSHC014 reservoir across South China; ~82-86 kHz) |
Supplemental Table S2. Complete 40-Sequence Nuclear Functional Coding Manifest Across Five Echolocation, Hypoxia, and Zoonotic Receptor Gene Families
Supplemental Table S2. Complete 40-Sequence Nuclear Functional Coding Manifest (NUC01–NUC40)
| Record ID | Gene Family Key | Species | NCBI Accession | Full Record Length (bp) | Aligned CDS Window (bp) | GC% | SHA-256 Prefix | Functional & Physiological Role |
|---|---|---|---|---|---|---|---|---|
| NUC-01 | SLC26A5_Prestin | Rhinolophus ferrumequinum | KJ645609.1 | 2,226 | 1,500 | 45.46% | 86124992d96ad486 | High-duty-cycle constant-frequency (CF-FM) Doppler-shift compensation (60-125 kHz) in Rhinolophidae & Hipposideridae |
| NUC-02 | SLC26A5_Prestin | Myotis ricketti | EU914924.1 | 2,229 | 1,500 | 46.52% | 62b8aa9910e28a54 | High-duty-cycle constant-frequency (CF-FM) Doppler-shift compensation (60-125 kHz) in Rhinolophidae & Hipposideridae |
| NUC-03 | SLC26A5_Prestin | Megaderma lyra | GU219835.1 | 2,226 | 1,500 | 44.03% | e705718859055c8f | High-duty-cycle constant-frequency (CF-FM) Doppler-shift compensation (60-125 kHz) in Rhinolophidae & Hipposideridae |
| NUC-04 | SLC26A5_Prestin | Eonycteris spelaea | GU219834.1 | 2,223 | 1,500 | 45.75% | d3044873f7df053b | High-duty-cycle constant-frequency (CF-FM) Doppler-shift compensation (60-125 kHz) in Rhinolophidae & Hipposideridae |
| NUC-05 | SLC26A5_Prestin | Hipposideros pratti | EU914937.1 | 2,226 | 1,500 | 44.97% | 1acbbac0a826dcdd | High-duty-cycle constant-frequency (CF-FM) Doppler-shift compensation (60-125 kHz) in Rhinolophidae & Hipposideridae |
| NUC-06 | SLC26A5_Prestin | Rhinolophus pusillus | EU914936.1 | 2,226 | 1,500 | 45.78% | 7cb4f49e51dc4a46 | High-duty-cycle constant-frequency (CF-FM) Doppler-shift compensation (60-125 kHz) in Rhinolophidae & Hipposideridae |
| NUC-07 | SLC26A5_Prestin | Aselliscus stoliczkanus | EU914935.1 | 2,226 | 1,500 | 45.55% | 50904f63ca761315 | High-duty-cycle constant-frequency (CF-FM) Doppler-shift compensation (60-125 kHz) in Rhinolophidae & Hipposideridae |
| NUC-08 | SLC26A5_Prestin | Hipposideros larvatus | EU914934.1 | 2,226 | 1,500 | 44.88% | 48a0f7840acdc537 | High-duty-cycle constant-frequency (CF-FM) Doppler-shift compensation (60-125 kHz) in Rhinolophidae & Hipposideridae |
| NUC-09 | ACE2_Sarbeco | Rhinolophus simulator | LC921174.1 | 2,418 | 1,500 | 44.42% | 08ae70c4c5677af8 | N-terminal alpha-1/alpha-2 helix polymorphisms (residues 24-42, 82, 353) governing SARS-CoV-1, SARS-CoV-2 & RaTG13 entry across Rhinolophus |
| NUC-10 | ACE2_Sarbeco | Rhinolophus blasii | LC921170.1 | 2,418 | 1,500 | 44.83% | 638a4feee7886bdc | N-terminal alpha-1/alpha-2 helix polymorphisms (residues 24-42, 82, 353) governing SARS-CoV-1, SARS-CoV-2 & RaTG13 entry across Rhinolophus |
| NUC-11 | ACE2_Sarbeco | Hipposideros armiger | XM_019667409.1 | 2,893 | 1,416 | 45.90% | eae6ccc4d158df3b | N-terminal alpha-1/alpha-2 helix polymorphisms (residues 24-42, 82, 353) governing SARS-CoV-1, SARS-CoV-2 & RaTG13 entry across Rhinolophus |
| NUC-12 | ACE2_Sarbeco | Rhinolophus acuminatus | PZ112778.1 | 2,415 | 1,500 | 45.76% | 00bf1d7ec5097b3d | N-terminal alpha-1/alpha-2 helix polymorphisms (residues 24-42, 82, 353) governing SARS-CoV-1, SARS-CoV-2 & RaTG13 entry across Rhinolophus |
| NUC-13 | ACE2_Sarbeco | Myotis nattereri | XM_081081848.1 | 2,792 | 1,500 | 42.91% | 3f63be771e4c1ba2 | N-terminal alpha-1/alpha-2 helix polymorphisms (residues 24-42, 82, 353) governing SARS-CoV-1, SARS-CoV-2 & RaTG13 entry across Rhinolophus |
| NUC-14 | ACE2_Sarbeco | Rhinolophus marshalli | PX315811.1 | 2,418 | 1,500 | 45.45% | a3168452982d1787 | N-terminal alpha-1/alpha-2 helix polymorphisms (residues 24-42, 82, 353) governing SARS-CoV-1, SARS-CoV-2 & RaTG13 entry across Rhinolophus |
| NUC-15 | ACE2_Sarbeco | Rhinolophus malayanus | PX315810.1 | 2,418 | 1,500 | 45.20% | 5ff87c0f853194bd | N-terminal alpha-1/alpha-2 helix polymorphisms (residues 24-42, 82, 353) governing SARS-CoV-1, SARS-CoV-2 & RaTG13 entry across Rhinolophus |
| NUC-16 | ACE2_Sarbeco | Rhinolophus pusillus | PX315809.1 | 2,418 | 1,500 | 45.57% | 56fe92ade6683f45 | N-terminal alpha-1/alpha-2 helix polymorphisms (residues 24-42, 82, 353) governing SARS-CoV-1, SARS-CoV-2 & RaTG13 entry across Rhinolophus |
| NUC-17 | STING_IRF3_ISG15 | Rhinolophus sinicus | XM_019741528.3 | 1,567 | 1,440 | 58.39% | 1451b053b14c6556 | Dampened STING Ser358 phosphorylation & attenuated NLRP3 inflammasome activation enabling asymptomatic RNA virus persistence in flight |
| NUC-18 | STING_IRF3_ISG15 | Hipposideros armiger | XM_019667829.1 | 2,100 | 1,434 | 43.10% | eb9cde7817a1ed2a | Dampened STING Ser358 phosphorylation & attenuated NLRP3 inflammasome activation enabling asymptomatic RNA virus persistence in flight |
| NUC-19 | STING_IRF3_ISG15 | Rhinolophus hipposideros | XM_081035220.1 | 1,915 | 1,422 | 54.31% | 59a8423fd02fda87 | Dampened STING Ser358 phosphorylation & attenuated NLRP3 inflammasome activation enabling asymptomatic RNA virus persistence in flight |
| NUC-20 | STING_IRF3_ISG15 | Myotis nattereri | XM_081106923.1 | 1,286 | 1,227 | 62.05% | 9c3ed05b77a908e7 | Dampened STING Ser358 phosphorylation & attenuated NLRP3 inflammasome activation enabling asymptomatic RNA virus persistence in flight |
| NUC-21 | STING_IRF3_ISG15 | Pteropus medius | XM_039836264.1 | 1,797 | 1,482 | 55.26% | d407802afa2bd4ba | Dampened STING Ser358 phosphorylation & attenuated NLRP3 inflammasome activation enabling asymptomatic RNA virus persistence in flight |
| NUC-22 | STING_IRF3_ISG15 | Rhinolophus sinicus | XM_074313609.2 | 1,531 | 1,470 | 55.39% | 294c840252659b94 | Dampened STING Ser358 phosphorylation & attenuated NLRP3 inflammasome activation enabling asymptomatic RNA virus persistence in flight |
| NUC-23 | STING_IRF3_ISG15 | Rhinolophus sinicus | XM_074313608.2 | 1,828 | 1,482 | 56.56% | 93212d1b54c4eee5 | Dampened STING Ser358 phosphorylation & attenuated NLRP3 inflammasome activation enabling asymptomatic RNA virus persistence in flight |
| NUC-24 | STING_IRF3_ISG15 | Rhinolophus sinicus | XM_074313607.2 | 1,911 | 1,473 | 56.83% | 9328c29e494686b9 | Dampened STING Ser358 phosphorylation & attenuated NLRP3 inflammasome activation enabling asymptomatic RNA virus persistence in flight |
| NUC-25 | FOXP2_KCNQ4 | Rhinolophus sinicus | XM_088793262.1 | 2,505 | 1,398 | 44.51% | 0d7adbc232d45d18 | Accelerated vocal-motor audio-vocal feedback (FOXP2 exons 7/17) and high-frequency basal-turn outer hair cell K+ current (KCNQ4) |
| NUC-26 | FOXP2_KCNQ4 | Miniopterus natalensis | XM_087820841.1 | 1,926 | 1,500 | 64.38% | e4cdd875376ec7e0 | Accelerated vocal-motor audio-vocal feedback (FOXP2 exons 7/17) and high-frequency basal-turn outer hair cell K+ current (KCNQ4) |
| NUC-27 | FOXP2_KCNQ4 | Miniopterus schreibersii | XM_081147833.1 | 2,600 | 1,485 | 49.04% | 2680cc0ab58ffc5f | Accelerated vocal-motor audio-vocal feedback (FOXP2 exons 7/17) and high-frequency basal-turn outer hair cell K+ current (KCNQ4) |
| NUC-28 | FOXP2_KCNQ4 | Rousettus aegyptiacus | XM_036232571.1 | 2,459 | 1,500 | 63.77% | d1da12f84404fe88 | Accelerated vocal-motor audio-vocal feedback (FOXP2 exons 7/17) and high-frequency basal-turn outer hair cell K+ current (KCNQ4) |
| NUC-29 | FOXP2_KCNQ4 | Myotis lucifugus | XM_023752818.1 | 1,828 | 1,500 | 62.69% | 0a151fddf524b1a9 | Accelerated vocal-motor audio-vocal feedback (FOXP2 exons 7/17) and high-frequency basal-turn outer hair cell K+ current (KCNQ4) |
| NUC-30 | FOXP2_KCNQ4 | Rhinolophus ferrumequinum | KJ645625.1 | 1,875 | 1,500 | 61.39% | ddd8ee3ce82a5eb7 | Accelerated vocal-motor audio-vocal feedback (FOXP2 exons 7/17) and high-frequency basal-turn outer hair cell K+ current (KCNQ4) |
| NUC-31 | FOXP2_KCNQ4 | Myotis davidii | XM_015569384.1 | 2,570 | 1,422 | 49.38% | c4669ef63262bd83 | Accelerated vocal-motor audio-vocal feedback (FOXP2 exons 7/17) and high-frequency basal-turn outer hair cell K+ current (KCNQ4) |
| NUC-32 | FOXP2_KCNQ4 | Myotis brandtii | XM_014539506.1 | 2,116 | 1,500 | 62.90% | f8834c2778346947 | Accelerated vocal-motor audio-vocal feedback (FOXP2 exons 7/17) and high-frequency basal-turn outer hair cell K+ current (KCNQ4) |
| NUC-33 | EPAS1_UCP1_Karst | Furipterus horrens | XM_090281243.1 | 3,363 | 1,440 | 57.12% | aadb341edf4734b6 | Hypercapnic/hypoxic subterranean limestone cave roosting tolerance and temperate winter hibernation arousal (R. ferrumequinum) |
| NUC-34 | EPAS1_UCP1_Karst | Rhinolophus sinicus | XM_019730721.3 | 1,680 | 1,416 | 49.05% | 621e88b0126bf7b6 | Hypercapnic/hypoxic subterranean limestone cave roosting tolerance and temperate winter hibernation arousal (R. ferrumequinum) |
| NUC-35 | EPAS1_UCP1_Karst | Miniopterus natalensis | XM_016213682.2 | 2,591 | 1,392 | 49.05% | 46a0528ab6cd2cdd | Hypercapnic/hypoxic subterranean limestone cave roosting tolerance and temperate winter hibernation arousal (R. ferrumequinum) |
| NUC-36 | EPAS1_UCP1_Karst | Pipistrellus hanaki | XM_084897918.1 | 3,285 | 1,395 | 43.96% | de974a41fb578a0c | Hypercapnic/hypoxic subterranean limestone cave roosting tolerance and temperate winter hibernation arousal (R. ferrumequinum) |
| NUC-37 | EPAS1_UCP1_Karst | Hipposideros armiger | XM_019661043.1 | 1,603 | 1,476 | 55.02% | 43b2b06da2c17f10 | Hypercapnic/hypoxic subterranean limestone cave roosting tolerance and temperate winter hibernation arousal (R. ferrumequinum) |
| NUC-38 | EPAS1_UCP1_Karst | Rhinolophus hipposideros | XM_081077828.1 | 1,730 | 1,422 | 50.46% | e231a860ee684f0a | Hypercapnic/hypoxic subterranean limestone cave roosting tolerance and temperate winter hibernation arousal (R. ferrumequinum) |
| NUC-39 | EPAS1_UCP1_Karst | Myotis nattereri | XM_081102849.1 | 3,449 | 1,500 | 44.71% | bab791cf68915e3c | Hypercapnic/hypoxic subterranean limestone cave roosting tolerance and temperate winter hibernation arousal (R. ferrumequinum) |
| NUC-40 | EPAS1_UCP1_Karst | Plecotus auritus | XM_080685581.1 | 3,553 | 1,443 | 57.42% | 654115928cccf7d7 | Hypercapnic/hypoxic subterranean limestone cave roosting tolerance and temperate winter hibernation arousal (R. ferrumequinum) |
Supplemental Table S3. Complete 32-Chain RuNIE Combinatorial Optimization Sweep Across All Four Execution Regimes and Eight Candidate Substitution Models
Supplemental Table S3. Complete 32-Chain RuNIE Combinatorial Optimization Sweep (#1–#32)
| Global Rank (Regime Rank) | Execution Regime | Substitution Model (k) | Marginal ln L (nats) | Delta ln L vs. Best | AIC | BIC | RCFV | UFBoot (%) | CPU Time Breakdown (MSA + Tree + MCMC) |
|---|---|---|---|---|---|---|---|---|---|
| #1 (R8) | Regime 3: Unconstrained Hybrid RuNIE | GTR+F+R4 (k=125) | -339,762.41 | 0.00 | 679,802.82 | 681,024.57 | 0.0084 | 100.0% | 573.02s (MSA 58.32s + Tree 511.63s + MCMC 3.08s) |
| #2 (R7) | Regime 3: Unconstrained Hybrid RuNIE | GTR+F+I+G4 (k=127) | -340,825.94 | -1,063.53 | 681,921.88 | 683,108.48 | 0.0084 | 100.0% | 115.54s (MSA 58.32s + Tree 54.14s + MCMC 3.08s) |
| #3 (R6) | Regime 3: Unconstrained Hybrid RuNIE | GTR+F+G4 (k=129) | -341,126.05 | -1,363.64 | 682,520.10 | 683,697.91 | 0.0084 | 100.0% | 90.02s (MSA 58.32s + Tree 28.63s + MCMC 3.08s) |
| #4 (R5) | Regime 3: Unconstrained Hybrid RuNIE | TIM2+F+I+G4 (k=131) | -341,543.80 | -1,781.39 | 683,353.60 | 684,522.61 | 0.0084 | 100.0% | 111.22s (MSA 58.32s + Tree 49.83s + MCMC 3.08s) |
| #5 (R4) | Regime 3: Unconstrained Hybrid RuNIE | TN+F+I+G4 (k=133) | -341,745.12 | -1,982.71 | 683,754.24 | 684,914.46 | 0.0084 | 100.0% | 101.58s (MSA 58.32s + Tree 40.19s + MCMC 3.08s) |
| #6 (R3) | Regime 3: Unconstrained Hybrid RuNIE | HKY+F+I+G4 (k=135) | -341,750.45 | -1,988.04 | 683,762.91 | 684,914.34 | 0.0084 | 100.0% | 104.99s (MSA 58.32s + Tree 43.59s + MCMC 3.08s) |
| #7 (R1) | Regime 1: 100% Native Rust | GTR+F+R4 (k=137) | -344,289.27 | -4,526.86 | 688,852.54 | 690,056.71 | 0.0084 | 99.7% | 13.00s (MSA 9.82s + Tree 0.10s + MCMC 3.08s) |
| #8 (R2) | Regime 1: 100% Native Rust | GTR+F+I+G4 (k=135) | -345,554.54 | -5,792.13 | 691,379.07 | 692,565.67 | 0.0084 | 99.7% | 13.00s (MSA 9.82s + Tree 0.10s + MCMC 3.08s) |
| #9 (R4) | Regime 1: 100% Native Rust | TIM2+F+I+G4 (k=133) | -345,925.87 | -6,163.46 | 692,117.73 | 693,286.75 | 0.0084 | 96.9% | 13.00s (MSA 9.82s + Tree 0.10s + MCMC 3.08s) |
| #10 (R6) | Regime 1: 100% Native Rust | HKY+F+I+G4 (k=131) | -346,214.20 | -6,451.79 | 692,690.40 | 693,841.83 | 0.0084 | 96.9% | 13.00s (MSA 9.82s + Tree 0.10s + MCMC 3.08s) |
| #11 (R5) | Regime 1: 100% Native Rust | TN+F+I+G4 (k=132) | -346,262.55 | -6,500.14 | 692,789.10 | 693,949.33 | 0.0084 | 96.9% | 13.00s (MSA 9.82s + Tree 0.10s + MCMC 3.08s) |
| #12 (R3) | Regime 1: 100% Native Rust | GTR+F+G4 (k=134) | -349,315.28 | -9,552.87 | 698,898.56 | 700,076.36 | 0.0084 | 96.9% | 13.00s (MSA 9.82s + Tree 0.10s + MCMC 3.08s) |
| #13 (R2) | Regime 3: Unconstrained Hybrid RuNIE | K80+G4 (k=137) | -352,807.04 | -13,044.63 | 705,868.08 | 706,984.36 | 0.0084 | 100.0% | 72.38s (MSA 58.32s + Tree 10.98s + MCMC 3.08s) |
| #14 (R7) | Regime 1: 100% Native Rust | K80+G4 (k=127) | -360,384.55 | -20,622.14 | 721,023.10 | 722,139.38 | 0.0084 | 96.9% | 13.00s (MSA 9.82s + Tree 0.10s + MCMC 3.08s) |
| #15 (R1) | Regime 3: Unconstrained Hybrid RuNIE | JC (k=139) | -397,250.63 | -57,488.22 | 794,751.25 | 795,849.95 | 0.0084 | 100.0% | 63.19s (MSA 58.32s + Tree 1.80s + MCMC 3.08s) |
| #16 (R8) | Regime 4: 0-Beaker Rejected Uncleaned Negative Control | GTR+F+R4 (k=125) | -402,202.12 | -62,439.71 | 804,682.23 | 805,903.98 | 0.0468 | 58.6% | 150.64s (MSA 58.32s + Tree 87.94s + MCMC 4.38s) |
| #17 (R8) | Regime 2: 100% External Reference | GTR+F+R4 (k=125) | -402,235.17 | -62,472.76 | 804,748.34 | 805,970.09 | 0.0468 | 98.4% | 1195.55s (MSA 58.32s + Tree 1132.28s + MCMC 4.95s) |
| #18 (R7) | Regime 4: 0-Beaker Rejected Uncleaned Negative Control | GTR+F+I+G4 (k=127) | -403,422.45 | -63,660.04 | 807,114.90 | 808,301.50 | 0.0468 | 58.6% | 129.42s (MSA 58.32s + Tree 66.72s + MCMC 4.38s) |
| #19 (R7) | Regime 2: 100% External Reference | GTR+F+I+G4 (k=127) | -403,422.80 | -63,660.39 | 807,115.59 | 808,302.19 | 0.0468 | 98.4% | 135.52s (MSA 58.32s + Tree 72.25s + MCMC 4.95s) |
| #20 (R6) | Regime 4: 0-Beaker Rejected Uncleaned Negative Control | GTR+F+G4 (k=129) | -403,560.67 | -63,798.26 | 807,389.34 | 808,567.15 | 0.0468 | 58.6% | 108.97s (MSA 58.32s + Tree 46.27s + MCMC 4.38s) |
| #21 (R6) | Regime 2: 100% External Reference | GTR+F+G4 (k=129) | -403,560.77 | -63,798.36 | 807,389.55 | 808,567.35 | 0.0468 | 98.4% | 116.14s (MSA 58.32s + Tree 52.88s + MCMC 4.95s) |
| #22 (R5) | Regime 2: 100% External Reference | TIM2+F+I+G4 (k=131) | -403,569.27 | -63,806.86 | 807,404.53 | 808,573.55 | 0.0468 | 98.4% | 125.19s (MSA 58.32s + Tree 61.92s + MCMC 4.95s) |
| #23 (R5) | Regime 4: 0-Beaker Rejected Uncleaned Negative Control | TIM2+F+I+G4 (k=131) | -403,569.30 | -63,806.89 | 807,404.59 | 808,573.61 | 0.0468 | 58.6% | 124.45s (MSA 58.32s + Tree 61.75s + MCMC 4.38s) |
| #24 (R4) | Regime 2: 100% External Reference | TN+F+I+G4 (k=133) | -403,762.37 | -63,999.96 | 807,788.73 | 808,948.96 | 0.0468 | 98.4% | 114.44s (MSA 58.32s + Tree 51.17s + MCMC 4.95s) |
| #25 (R4) | Regime 4: 0-Beaker Rejected Uncleaned Negative Control | TN+F+I+G4 (k=133) | -403,762.37 | -63,999.96 | 807,788.73 | 808,948.96 | 0.0468 | 58.6% | 119.08s (MSA 58.32s + Tree 56.38s + MCMC 4.38s) |
| #26 (R3) | Regime 4: 0-Beaker Rejected Uncleaned Negative Control | HKY+F+I+G4 (k=135) | -403,911.69 | -64,149.28 | 808,085.38 | 809,236.81 | 0.0468 | 58.6% | 117.22s (MSA 58.32s + Tree 54.52s + MCMC 4.38s) |
| #27 (R3) | Regime 2: 100% External Reference | HKY+F+I+G4 (k=135) | -403,911.74 | -64,149.33 | 808,085.47 | 809,236.91 | 0.0468 | 98.4% | 125.63s (MSA 58.32s + Tree 62.36s + MCMC 4.95s) |
| #28 (R2) | Regime 2: 100% External Reference | K80+G4 (k=137) | -407,612.51 | -67,850.10 | 815,479.02 | 816,595.29 | 0.0468 | 98.4% | 99.05s (MSA 58.32s + Tree 35.78s + MCMC 4.95s) |
| #29 (R2) | Regime 4: 0-Beaker Rejected Uncleaned Negative Control | K80+G4 (k=137) | -407,612.51 | -67,850.10 | 815,479.02 | 816,595.29 | 0.0468 | 58.6% | 97.47s (MSA 58.32s + Tree 34.77s + MCMC 4.38s) |
| #30 (R8) | Regime 1: 100% Native Rust | JC (k=125) | -410,994.29 | -71,231.88 | 822,238.59 | 823,337.28 | 0.0084 | 96.9% | 13.00s (MSA 9.82s + Tree 0.10s + MCMC 3.08s) |
| #31 (R1) | Regime 4: 0-Beaker Rejected Uncleaned Negative Control | JC (k=139) | -468,510.57 | -128,748.16 | 937,271.14 | 938,369.84 | 0.0468 | 58.6% | 64.95s (MSA 58.32s + Tree 2.25s + MCMC 4.38s) |
| #32 (R1) | Regime 2: 100% External Reference | JC (k=139) | -468,602.45 | -128,840.04 | 937,454.90 | 938,553.60 | 0.0468 | 98.4% | 65.53s (MSA 58.32s + Tree 2.27s + MCMC 4.95s) |
Supplemental Table S4. Complete 108-Isolate Single-Species Regional NCBI PopSet Cytochrome b Manifest with Voucher IDs and Regional Karst Locality Metadata
Supplemental Table S4. Complete 108-Isolate Single-Species Regional NCBI PopSet Cytochrome b Manifest (P1_I01–P3_I36)
| Isolate ID | PopSet Cohort | NCBI PopSet Source ID | Voucher / Haplotype ID | Conspecific Species | NCBI Accession | Regional Locality Metadata (/country & Karst Deme) | Length (bp) | GC% | SHA-256 Prefix |
|---|---|---|---|---|---|---|---|---|---|
| P1_ISO_01 | PopSet 1 (Rhinolophus pusillus) | NCBI PopSet PZ496420-PZ496472 (Southeast Asian Sarbecovirus Surveillance Deme) | RpuRB22393.WIE | Rhinolophus pusillus | PZ496506.1 | Thailand | 1,140 | 46.49% | 23a24159bafdef63 |
| P1_ISO_02 | PopSet 1 (Rhinolophus pusillus) | NCBI PopSet PZ496420-PZ496472 (Southeast Asian Sarbecovirus Surveillance Deme) | RpuRB22384.WIE | Rhinolophus pusillus | PZ496502.1 | Thailand | 1,140 | 46.49% | dfeb31511e6b776d |
| P1_ISO_03 | PopSet 1 (Rhinolophus pusillus) | NCBI PopSet PZ496420-PZ496472 (Southeast Asian Sarbecovirus Surveillance Deme) | RpuRB22354.WIE | Rhinolophus pusillus | PZ496495.1 | Thailand | 1,140 | 46.49% | dfeb31511e6b776d |
| P1_ISO_04 | PopSet 1 (Rhinolophus pusillus) | NCBI PopSet PZ496420-PZ496472 (Southeast Asian Sarbecovirus Surveillance Deme) | RpuRB22349.WIE | Rhinolophus pusillus | PZ496493.1 | Thailand | 1,137 | 46.26% | 6773496b6df6fa02 |
| P1_ISO_05 | PopSet 1 (Rhinolophus pusillus) | NCBI PopSet PZ496420-PZ496472 (Southeast Asian Sarbecovirus Surveillance Deme) | RpuRB21200.WIE | Rhinolophus pusillus | PZ496492.1 | Thailand | 1,140 | 46.14% | 3c30528f7770a49e |
| P1_ISO_06 | PopSet 1 (Rhinolophus pusillus) | NCBI PopSet PZ496420-PZ496472 (Southeast Asian Sarbecovirus Surveillance Deme) | RpuRB21198.WIE | Rhinolophus pusillus | PZ496491.1 | Thailand | 1,140 | 46.32% | 7c08aa9c7aa3d161 |
| P1_ISO_07 | PopSet 1 (Rhinolophus pusillus) | NCBI PopSet PZ496420-PZ496472 (Southeast Asian Sarbecovirus Surveillance Deme) | RpuRB21197.WIE | Rhinolophus pusillus | PZ496490.1 | Thailand | 1,140 | 46.75% | 1a07e366bf9d2eb5 |
| P1_ISO_08 | PopSet 1 (Rhinolophus pusillus) | NCBI PopSet PZ496420-PZ496472 (Southeast Asian Sarbecovirus Surveillance Deme) | RpuRB21196.WIE | Rhinolophus pusillus | PZ496489.1 | Thailand | 1,140 | 46.14% | 3c30528f7770a49e |
| P1_ISO_09 | PopSet 1 (Rhinolophus pusillus) | NCBI PopSet PZ496420-PZ496472 (Southeast Asian Sarbecovirus Surveillance Deme) | RpuRB21194.WIE | Rhinolophus pusillus | PZ496488.1 | Thailand | 1,140 | 46.84% | 602491912668aa79 |
| P1_ISO_10 | PopSet 1 (Rhinolophus pusillus) | NCBI PopSet PZ496420-PZ496472 (Southeast Asian Sarbecovirus Surveillance Deme) | RpuRB21192.WIE | Rhinolophus pusillus | PZ496487.1 | Thailand | 1,140 | 46.75% | 208b401b53d65a32 |
| P1_ISO_11 | PopSet 1 (Rhinolophus pusillus) | NCBI PopSet PZ496420-PZ496472 (Southeast Asian Sarbecovirus Surveillance Deme) | RpuRB21189.WIE | Rhinolophus pusillus | PZ496486.1 | Thailand | 1,140 | 46.14% | 3c30528f7770a49e |
| P1_ISO_12 | PopSet 1 (Rhinolophus pusillus) | NCBI PopSet PZ496420-PZ496472 (Southeast Asian Sarbecovirus Surveillance Deme) | RpuRB21177.WIE | Rhinolophus pusillus | PZ496485.1 | Thailand | 1,140 | 46.14% | 3c30528f7770a49e |
| P1_ISO_13 | PopSet 1 (Rhinolophus pusillus) | NCBI PopSet PZ496420-PZ496472 (Southeast Asian Sarbecovirus Surveillance Deme) | RpuRB21174.WIE | Rhinolophus pusillus | PZ496484.1 | Thailand | 1,140 | 46.14% | 3c30528f7770a49e |
| P1_ISO_14 | PopSet 1 (Rhinolophus pusillus) | NCBI PopSet PZ496420-PZ496472 (Southeast Asian Sarbecovirus Surveillance Deme) | RpuRB21173.WIE | Rhinolophus pusillus | PZ496483.1 | Thailand | 1,140 | 46.23% | 9fee5ee9550b4eef |
| P1_ISO_15 | PopSet 1 (Rhinolophus pusillus) | NCBI PopSet PZ496420-PZ496472 (Southeast Asian Sarbecovirus Surveillance Deme) | RpuRB21172.WIE | Rhinolophus pusillus | PZ496482.1 | Thailand | 1,140 | 46.49% | dfeb31511e6b776d |
| P1_ISO_16 | PopSet 1 (Rhinolophus pusillus) | NCBI PopSet PZ496420-PZ496472 (Southeast Asian Sarbecovirus Surveillance Deme) | RpuRB21170.WIE | Rhinolophus pusillus | PZ496481.1 | Thailand | 1,140 | 45.88% | 936dc91755962752 |
| P1_ISO_17 | PopSet 1 (Rhinolophus pusillus) | NCBI PopSet PZ496420-PZ496472 (Southeast Asian Sarbecovirus Surveillance Deme) | RpuRB21169.WIE | Rhinolophus pusillus | PZ496480.1 | Thailand | 1,140 | 46.23% | d2c1500d38113a7c |
| P1_ISO_18 | PopSet 1 (Rhinolophus pusillus) | NCBI PopSet PZ496420-PZ496472 (Southeast Asian Sarbecovirus Surveillance Deme) | RpuRB21159.WIE | Rhinolophus pusillus | PZ496479.1 | Thailand | 1,140 | 46.49% | dfeb31511e6b776d |
| P1_ISO_19 | PopSet 1 (Rhinolophus pusillus) | NCBI PopSet PZ496420-PZ496472 (Southeast Asian Sarbecovirus Surveillance Deme) | RpuRB21153.WIE | Rhinolophus pusillus | PZ496478.1 | Thailand | 1,140 | 46.05% | 3be932f218dfe9ef |
| P1_ISO_20 | PopSet 1 (Rhinolophus pusillus) | NCBI PopSet PZ496420-PZ496472 (Southeast Asian Sarbecovirus Surveillance Deme) | RpuRB21149.WIE | Rhinolophus pusillus | PZ496477.1 | Thailand | 1,140 | 45.79% | de586784fa996054 |
| P1_ISO_21 | PopSet 1 (Rhinolophus pusillus) | NCBI PopSet PZ496420-PZ496472 (Southeast Asian Sarbecovirus Surveillance Deme) | RpuRB21146.WIE | Rhinolophus pusillus | PZ496476.1 | Thailand | 1,140 | 46.23% | 4ea9da74c587f836 |
| P1_ISO_22 | PopSet 1 (Rhinolophus pusillus) | NCBI PopSet PZ496420-PZ496472 (Southeast Asian Sarbecovirus Surveillance Deme) | RpuRB21140.WIE | Rhinolophus pusillus | PZ496475.1 | Thailand | 1,140 | 46.23% | 49190c0705366553 |
| P1_ISO_23 | PopSet 1 (Rhinolophus pusillus) | NCBI PopSet PZ496420-PZ496472 (Southeast Asian Sarbecovirus Surveillance Deme) | RpuRB21135.WIE | Rhinolophus pusillus | PZ496474.1 | Thailand | 1,140 | 45.35% | 2193a8fa39353992 |
| P1_ISO_24 | PopSet 1 (Rhinolophus pusillus) | NCBI PopSet PZ496420-PZ496472 (Southeast Asian Sarbecovirus Surveillance Deme) | RpuRB21123.WIE | Rhinolophus pusillus | PZ496473.1 | Thailand | 1,140 | 46.58% | 41e44d36d3c00077 |
| P1_ISO_25 | PopSet 1 (Rhinolophus pusillus) | NCBI PopSet PZ496420-PZ496472 (Southeast Asian Sarbecovirus Surveillance Deme) | RpuRB21120.WIE | Rhinolophus pusillus | PZ496471.1 | Thailand | 1,140 | 45.61% | 7d8025b109d54e64 |
| P1_ISO_26 | PopSet 1 (Rhinolophus pusillus) | NCBI PopSet PZ496420-PZ496472 (Southeast Asian Sarbecovirus Surveillance Deme) | RpuRB21116.WIE | Rhinolophus pusillus | PZ496470.1 | Thailand | 1,140 | 46.40% | 6c5bdb221d4d8272 |
| P1_ISO_27 | PopSet 1 (Rhinolophus pusillus) | NCBI PopSet PZ496420-PZ496472 (Southeast Asian Sarbecovirus Surveillance Deme) | RpuRB21114.WIE | Rhinolophus pusillus | PZ496469.1 | Thailand | 1,140 | 46.23% | d2c1500d38113a7c |
| P1_ISO_28 | PopSet 1 (Rhinolophus pusillus) | NCBI PopSet PZ496420-PZ496472 (Southeast Asian Sarbecovirus Surveillance Deme) | RpuRB21113.WIE | Rhinolophus pusillus | PZ496468.1 | Thailand | 1,140 | 46.14% | e1c8f289d99448a4 |
| P1_ISO_29 | PopSet 1 (Rhinolophus pusillus) | NCBI PopSet PZ496420-PZ496472 (Southeast Asian Sarbecovirus Surveillance Deme) | RpuRB21111.WIE | Rhinolophus pusillus | PZ496467.1 | Thailand | 1,140 | 45.79% | 945af46d0eb2bf6c |
| P1_ISO_30 | PopSet 1 (Rhinolophus pusillus) | NCBI PopSet PZ496420-PZ496472 (Southeast Asian Sarbecovirus Surveillance Deme) | RpuRB21105.WIE | Rhinolophus pusillus | PZ496466.1 | Thailand | 1,140 | 45.61% | 0b17f2802106f056 |
| P1_ISO_31 | PopSet 1 (Rhinolophus pusillus) | NCBI PopSet PZ496420-PZ496472 (Southeast Asian Sarbecovirus Surveillance Deme) | RpuRB21103.WIE | Rhinolophus pusillus | PZ496465.1 | Thailand | 1,140 | 45.35% | 6ecf36bc9b3be35b |
| P1_ISO_32 | PopSet 1 (Rhinolophus pusillus) | NCBI PopSet PZ496420-PZ496472 (Southeast Asian Sarbecovirus Surveillance Deme) | RpuRB21102.WIE | Rhinolophus pusillus | PZ496464.1 | Thailand | 1,140 | 45.88% | 7bfc308b39a9e025 |
| P1_ISO_33 | PopSet 1 (Rhinolophus pusillus) | NCBI PopSet PZ496420-PZ496472 (Southeast Asian Sarbecovirus Surveillance Deme) | RpuRB21090.WIE | Rhinolophus pusillus | PZ496463.1 | Thailand | 1,140 | 47.02% | a4d799624de75986 |
| P1_ISO_34 | PopSet 1 (Rhinolophus pusillus) | NCBI PopSet PZ496420-PZ496472 (Southeast Asian Sarbecovirus Surveillance Deme) | RpuRB21065.WIE | Rhinolophus pusillus | PZ496462.1 | Thailand | 1,140 | 46.14% | dabe4eac521881ff |
| P1_ISO_35 | PopSet 1 (Rhinolophus pusillus) | NCBI PopSet PZ496420-PZ496472 (Southeast Asian Sarbecovirus Surveillance Deme) | RpuRB21054.WIE | Rhinolophus pusillus | PZ496461.1 | Thailand | 1,140 | 45.96% | ee7111402987feab |
| P1_ISO_36 | PopSet 1 (Rhinolophus pusillus) | NCBI PopSet PZ496420-PZ496472 (Southeast Asian Sarbecovirus Surveillance Deme) | RpuRB21043.WIE | Rhinolophus pusillus | PZ496460.1 | Thailand | 1,140 | 46.40% | a60b3a7f7c90ed56 |
| P2_ISO_01 | PopSet 2 (Rhinolophus pearsonii) | NCBI PopSet 260800548 / GQ254652-GQ254705 (Southern China Subtropical Karst Belt Deme) | Yunnan 7 | Rhinolophus pearsonii | ON640706.1 | China | 1,140 | 47.54% | ebc8e423a9ea85ca |
| P2_ISO_02 | PopSet 2 (Rhinolophus pearsonii) | NCBI PopSet 260800548 / GQ254652-GQ254705 (Southern China Subtropical Karst Belt Deme) | Hunan 3 | Rhinolophus pearsonii | ON640705.1 | China | 1,140 | 47.11% | a9295ddb1007a413 |
| P2_ISO_03 | PopSet 2 (Rhinolophus pearsonii) | NCBI PopSet 260800548 / GQ254652-GQ254705 (Southern China Subtropical Karst Belt Deme) | GZ-107 | Rhinolophus pearsonii | MG570065.1 | China: Guizhou | 1,140 | 47.02% | e047a87f4d09ea8f |
| P2_ISO_04 | PopSet 2 (Rhinolophus pearsonii) | NCBI PopSet 260800548 / GQ254652-GQ254705 (Southern China Subtropical Karst Belt Deme) | GX-020 | Rhinolophus pearsonii | KX467581.1 | China | 1,140 | 47.28% | c71b95add80fe71c |
| P2_ISO_05 | PopSet 2 (Rhinolophus pearsonii) | NCBI PopSet 260800548 / GQ254652-GQ254705 (Southern China Subtropical Karst Belt Deme) | Longquan-7 | Rhinolophus pearsonii | KF294337.1 | China | 1,140 | 47.28% | 07191249a867621c |
| P2_ISO_06 | PopSet 2 (Rhinolophus pearsonii) | NCBI PopSet 260800548 / GQ254652-GQ254705 (Southern China Subtropical Karst Belt Deme) | Anlong-78 | Rhinolophus pearsonii | KF294336.1 | China | 1,140 | 47.11% | ce88d2f464fb1122 |
| P2_ISO_07 | PopSet 2 (Rhinolophus pearsonii) | NCBI PopSet 260800548 / GQ254652-GQ254705 (Southern China Subtropical Karst Belt Deme) | 2 | Rhinolophus pearsonii | EU434940.1 | China: Guangxi | 1,140 | 47.28% | c71b95add80fe71c |
| P2_ISO_08 | PopSet 2 (Rhinolophus pearsonii) | NCBI PopSet 260800548 / GQ254652-GQ254705 (Southern China Subtropical Karst Belt Deme) | 1 | Rhinolophus pearsonii | EU434939.1 | China: Jiangxi | 1,140 | 47.02% | d86277dbd60bf44c |
| P2_ISO_09 | PopSet 2 (Rhinolophus pearsonii) | NCBI PopSet 260800548 / GQ254652-GQ254705 (Southern China Subtropical Karst Belt Deme) | FlW004 ZhangSY (Institute of Zoology, Chinese Academy of Sciences) | Rhinolophus pearsonii | DQ297587.1 | China: Southern Subtropical Karst Belt (Yunnan, Guizhou, Guangxi, Sichuan, Jiangxi & Fujian) | 1,140 | 47.28% | 8740f1be47f8e083 |
| P2_ISO_10 | PopSet 2 (Rhinolophus pearsonii) | NCBI PopSet 260800548 / GQ254652-GQ254705 (Southern China Subtropical Karst Belt Deme) | 54 | Rhinolophus pearsonii | GQ257364.1 | China: Southern Subtropical Karst Belt (Yunnan, Guizhou, Guangxi, Sichuan, Jiangxi & Fujian) | 1,140 | 46.93% | a5521d49cf868c86 |
| P2_ISO_11 | PopSet 2 (Rhinolophus pearsonii) | NCBI PopSet 260800548 / GQ254652-GQ254705 (Southern China Subtropical Karst Belt Deme) | 53 | Rhinolophus pearsonii | GQ257363.1 | China: Southern Subtropical Karst Belt (Yunnan, Guizhou, Guangxi, Sichuan, Jiangxi & Fujian) | 1,140 | 46.93% | 60698712f3fa82dd |
| P2_ISO_12 | PopSet 2 (Rhinolophus pearsonii) | NCBI PopSet 260800548 / GQ254652-GQ254705 (Southern China Subtropical Karst Belt Deme) | 52 | Rhinolophus pearsonii | GQ257362.1 | China: Southern Subtropical Karst Belt (Yunnan, Guizhou, Guangxi, Sichuan, Jiangxi & Fujian) | 1,140 | 46.67% | c981f918ce1cb5fd |
| P2_ISO_13 | PopSet 2 (Rhinolophus pearsonii) | NCBI PopSet 260800548 / GQ254652-GQ254705 (Southern China Subtropical Karst Belt Deme) | 51 | Rhinolophus pearsonii | GQ257361.1 | China: Southern Subtropical Karst Belt (Yunnan, Guizhou, Guangxi, Sichuan, Jiangxi & Fujian) | 1,140 | 46.75% | 588e1d0e196a9e2e |
| P2_ISO_14 | PopSet 2 (Rhinolophus pearsonii) | NCBI PopSet 260800548 / GQ254652-GQ254705 (Southern China Subtropical Karst Belt Deme) | 50 | Rhinolophus pearsonii | GQ257360.1 | China: Southern Subtropical Karst Belt (Yunnan, Guizhou, Guangxi, Sichuan, Jiangxi & Fujian) | 1,140 | 47.02% | 8eb1a05cfe7a8c9b |
| P2_ISO_15 | PopSet 2 (Rhinolophus pearsonii) | NCBI PopSet 260800548 / GQ254652-GQ254705 (Southern China Subtropical Karst Belt Deme) | 49 | Rhinolophus pearsonii | GQ257359.1 | China: Southern Subtropical Karst Belt (Yunnan, Guizhou, Guangxi, Sichuan, Jiangxi & Fujian) | 1,140 | 47.19% | 72cba9b9acfb057e |
| P2_ISO_16 | PopSet 2 (Rhinolophus pearsonii) | NCBI PopSet 260800548 / GQ254652-GQ254705 (Southern China Subtropical Karst Belt Deme) | 48 | Rhinolophus pearsonii | GQ257358.1 | China: Southern Subtropical Karst Belt (Yunnan, Guizhou, Guangxi, Sichuan, Jiangxi & Fujian) | 1,140 | 47.19% | 2abeee937573315f |
| P2_ISO_17 | PopSet 2 (Rhinolophus pearsonii) | NCBI PopSet 260800548 / GQ254652-GQ254705 (Southern China Subtropical Karst Belt Deme) | 47 | Rhinolophus pearsonii | GQ257357.1 | China: Southern Subtropical Karst Belt (Yunnan, Guizhou, Guangxi, Sichuan, Jiangxi & Fujian) | 1,140 | 47.28% | 0491dfc5d08c87ce |
| P2_ISO_18 | PopSet 2 (Rhinolophus pearsonii) | NCBI PopSet 260800548 / GQ254652-GQ254705 (Southern China Subtropical Karst Belt Deme) | 46 | Rhinolophus pearsonii | GQ257356.1 | China: Southern Subtropical Karst Belt (Yunnan, Guizhou, Guangxi, Sichuan, Jiangxi & Fujian) | 1,140 | 46.93% | 5de0e27095c20b2f |
| P2_ISO_19 | PopSet 2 (Rhinolophus pearsonii) | NCBI PopSet 260800548 / GQ254652-GQ254705 (Southern China Subtropical Karst Belt Deme) | 45 | Rhinolophus pearsonii | GQ257355.1 | China: Southern Subtropical Karst Belt (Yunnan, Guizhou, Guangxi, Sichuan, Jiangxi & Fujian) | 1,140 | 47.11% | d00272c19684a863 |
| P2_ISO_20 | PopSet 2 (Rhinolophus pearsonii) | NCBI PopSet 260800548 / GQ254652-GQ254705 (Southern China Subtropical Karst Belt Deme) | 44 | Rhinolophus pearsonii | GQ257354.1 | China: Southern Subtropical Karst Belt (Yunnan, Guizhou, Guangxi, Sichuan, Jiangxi & Fujian) | 1,140 | 46.93% | 0f7f83bc8fd30b0a |
| P2_ISO_21 | PopSet 2 (Rhinolophus pearsonii) | NCBI PopSet 260800548 / GQ254652-GQ254705 (Southern China Subtropical Karst Belt Deme) | 43 | Rhinolophus pearsonii | GQ257353.1 | China: Southern Subtropical Karst Belt (Yunnan, Guizhou, Guangxi, Sichuan, Jiangxi & Fujian) | 1,140 | 47.02% | 21fb950f72e52cbf |
| P2_ISO_22 | PopSet 2 (Rhinolophus pearsonii) | NCBI PopSet 260800548 / GQ254652-GQ254705 (Southern China Subtropical Karst Belt Deme) | 42 | Rhinolophus pearsonii | GQ257352.1 | China: Southern Subtropical Karst Belt (Yunnan, Guizhou, Guangxi, Sichuan, Jiangxi & Fujian) | 1,140 | 47.11% | d99d8212e8ff1602 |
| P2_ISO_23 | PopSet 2 (Rhinolophus pearsonii) | NCBI PopSet 260800548 / GQ254652-GQ254705 (Southern China Subtropical Karst Belt Deme) | 41 | Rhinolophus pearsonii | GQ257351.1 | China: Southern Subtropical Karst Belt (Yunnan, Guizhou, Guangxi, Sichuan, Jiangxi & Fujian) | 1,140 | 47.11% | c201a152d01fe9c3 |
| P2_ISO_24 | PopSet 2 (Rhinolophus pearsonii) | NCBI PopSet 260800548 / GQ254652-GQ254705 (Southern China Subtropical Karst Belt Deme) | 40 | Rhinolophus pearsonii | GQ257350.1 | China: Southern Subtropical Karst Belt (Yunnan, Guizhou, Guangxi, Sichuan, Jiangxi & Fujian) | 1,140 | 47.02% | 3d885f26fa14f483 |
| P2_ISO_25 | PopSet 2 (Rhinolophus pearsonii) | NCBI PopSet 260800548 / GQ254652-GQ254705 (Southern China Subtropical Karst Belt Deme) | 39 | Rhinolophus pearsonii | GQ257349.1 | China: Southern Subtropical Karst Belt (Yunnan, Guizhou, Guangxi, Sichuan, Jiangxi & Fujian) | 1,140 | 46.67% | c2a6c957be6358bd |
| P2_ISO_26 | PopSet 2 (Rhinolophus pearsonii) | NCBI PopSet 260800548 / GQ254652-GQ254705 (Southern China Subtropical Karst Belt Deme) | 38 | Rhinolophus pearsonii | GQ257348.1 | China: Southern Subtropical Karst Belt (Yunnan, Guizhou, Guangxi, Sichuan, Jiangxi & Fujian) | 1,140 | 47.19% | 3ec3fda12f82540f |
| P2_ISO_27 | PopSet 2 (Rhinolophus pearsonii) | NCBI PopSet 260800548 / GQ254652-GQ254705 (Southern China Subtropical Karst Belt Deme) | 37 | Rhinolophus pearsonii | GQ257347.1 | China: Southern Subtropical Karst Belt (Yunnan, Guizhou, Guangxi, Sichuan, Jiangxi & Fujian) | 1,140 | 47.19% | 0ec4ef2336941a61 |
| P2_ISO_28 | PopSet 2 (Rhinolophus pearsonii) | NCBI PopSet 260800548 / GQ254652-GQ254705 (Southern China Subtropical Karst Belt Deme) | 36 | Rhinolophus pearsonii | GQ257346.1 | China: Southern Subtropical Karst Belt (Yunnan, Guizhou, Guangxi, Sichuan, Jiangxi & Fujian) | 1,140 | 47.11% | ab3c23935d9a33b4 |
| P2_ISO_29 | PopSet 2 (Rhinolophus pearsonii) | NCBI PopSet 260800548 / GQ254652-GQ254705 (Southern China Subtropical Karst Belt Deme) | 35 | Rhinolophus pearsonii | GQ257345.1 | China: Southern Subtropical Karst Belt (Yunnan, Guizhou, Guangxi, Sichuan, Jiangxi & Fujian) | 1,140 | 47.11% | 4b20604efb951096 |
| P2_ISO_30 | PopSet 2 (Rhinolophus pearsonii) | NCBI PopSet 260800548 / GQ254652-GQ254705 (Southern China Subtropical Karst Belt Deme) | 34 | Rhinolophus pearsonii | GQ257344.1 | China: Southern Subtropical Karst Belt (Yunnan, Guizhou, Guangxi, Sichuan, Jiangxi & Fujian) | 1,140 | 46.75% | 6fd3b16729d169b6 |
| P2_ISO_31 | PopSet 2 (Rhinolophus pearsonii) | NCBI PopSet 260800548 / GQ254652-GQ254705 (Southern China Subtropical Karst Belt Deme) | 33 | Rhinolophus pearsonii | GQ257343.1 | China: Southern Subtropical Karst Belt (Yunnan, Guizhou, Guangxi, Sichuan, Jiangxi & Fujian) | 1,140 | 47.11% | ce88d2f464fb1122 |
| P2_ISO_32 | PopSet 2 (Rhinolophus pearsonii) | NCBI PopSet 260800548 / GQ254652-GQ254705 (Southern China Subtropical Karst Belt Deme) | 32 | Rhinolophus pearsonii | GQ257342.1 | China: Southern Subtropical Karst Belt (Yunnan, Guizhou, Guangxi, Sichuan, Jiangxi & Fujian) | 1,140 | 47.19% | a5474a4d6add90fb |
| P2_ISO_33 | PopSet 2 (Rhinolophus pearsonii) | NCBI PopSet 260800548 / GQ254652-GQ254705 (Southern China Subtropical Karst Belt Deme) | 31 | Rhinolophus pearsonii | GQ257341.1 | China: Southern Subtropical Karst Belt (Yunnan, Guizhou, Guangxi, Sichuan, Jiangxi & Fujian) | 1,140 | 47.02% | ab309f2234fd6030 |
| P2_ISO_34 | PopSet 2 (Rhinolophus pearsonii) | NCBI PopSet 260800548 / GQ254652-GQ254705 (Southern China Subtropical Karst Belt Deme) | 30 | Rhinolophus pearsonii | GQ257340.1 | China: Southern Subtropical Karst Belt (Yunnan, Guizhou, Guangxi, Sichuan, Jiangxi & Fujian) | 1,140 | 47.02% | e5ab9a30bea020ac |
| P2_ISO_35 | PopSet 2 (Rhinolophus pearsonii) | NCBI PopSet 260800548 / GQ254652-GQ254705 (Southern China Subtropical Karst Belt Deme) | 29 | Rhinolophus pearsonii | GQ257339.1 | China: Southern Subtropical Karst Belt (Yunnan, Guizhou, Guangxi, Sichuan, Jiangxi & Fujian) | 1,140 | 46.84% | f83cb7789852e5a4 |
| P2_ISO_36 | PopSet 2 (Rhinolophus pearsonii) | NCBI PopSet 260800548 / GQ254652-GQ254705 (Southern China Subtropical Karst Belt Deme) | 28 | Rhinolophus pearsonii | GQ257338.1 | China: Southern Subtropical Karst Belt (Yunnan, Guizhou, Guangxi, Sichuan, Jiangxi & Fujian) | 1,140 | 47.02% | 484c3de191ba1986 |
| P3_ISO_01 | PopSet 3 (Rhinolophus ferrumequinum) | NCBI PopSet 2170330412 / LC605906-LC605937 + AB085720 (East Asian Sino-Japanese Karst & Island Deme) | MHNG 1868.085 | Rhinolophus ferrumequinum | OQ885419.1 | Switzerland | 1,140 | 46.14% | 3e5e679770cb7555 |
| P3_ISO_02 | PopSet 3 (Rhinolophus ferrumequinum) | NCBI PopSet 2170330412 / LC605906-LC605937 + AB085720 (East Asian Sino-Japanese Karst & Island Deme) | Yunnan 5 | Rhinolophus ferrumequinum | ON640696.1 | China | 1,140 | 45.53% | c3faabf975f24823 |
| P3_ISO_03 | PopSet 3 (Rhinolophus ferrumequinum) | NCBI PopSet 2170330412 / LC605906-LC605937 + AB085720 (East Asian Sino-Japanese Karst & Island Deme) | IY096 | Rhinolophus ferrumequinum | LC605945.1 | Japan: Kyoto | 1,140 | 45.96% | ac4720f12a2f4676 |
| P3_ISO_04 | PopSet 3 (Rhinolophus ferrumequinum) | NCBI PopSet 2170330412 / LC605906-LC605937 + AB085720 (East Asian Sino-Japanese Karst & Island Deme) | IY094 | Rhinolophus ferrumequinum | LC605944.1 | Japan: Kyoto | 1,140 | 45.96% | ac4720f12a2f4676 |
| P3_ISO_05 | PopSet 3 (Rhinolophus ferrumequinum) | NCBI PopSet 2170330412 / LC605906-LC605937 + AB085720 (East Asian Sino-Japanese Karst & Island Deme) | IY091 | Rhinolophus ferrumequinum | LC605943.1 | Japan: Kyoto | 1,140 | 45.96% | ac4720f12a2f4676 |
| P3_ISO_06 | PopSet 3 (Rhinolophus ferrumequinum) | NCBI PopSet 2170330412 / LC605906-LC605937 + AB085720 (East Asian Sino-Japanese Karst & Island Deme) | IY089 | Rhinolophus ferrumequinum | LC605942.1 | Japan: Kyoto | 1,140 | 45.96% | ac4720f12a2f4676 |
| P3_ISO_07 | PopSet 3 (Rhinolophus ferrumequinum) | NCBI PopSet 2170330412 / LC605906-LC605937 + AB085720 (East Asian Sino-Japanese Karst & Island Deme) | IY084 | Rhinolophus ferrumequinum | LC605941.1 | Japan: Kagawa | 1,140 | 45.79% | 4170380843c95e16 |
| P3_ISO_08 | PopSet 3 (Rhinolophus ferrumequinum) | NCBI PopSet 2170330412 / LC605906-LC605937 + AB085720 (East Asian Sino-Japanese Karst & Island Deme) | IY083 | Rhinolophus ferrumequinum | LC605940.1 | Japan: Kagawa | 1,140 | 45.96% | f0912f903f4d0b9d |
| P3_ISO_09 | PopSet 3 (Rhinolophus ferrumequinum) | NCBI PopSet 2170330412 / LC605906-LC605937 + AB085720 (East Asian Sino-Japanese Karst & Island Deme) | IY082 | Rhinolophus ferrumequinum | LC605939.1 | Japan: Kagawa | 1,140 | 45.96% | fefb56f19663ed82 |
| P3_ISO_10 | PopSet 3 (Rhinolophus ferrumequinum) | NCBI PopSet 2170330412 / LC605906-LC605937 + AB085720 (East Asian Sino-Japanese Karst & Island Deme) | IY078 | Rhinolophus ferrumequinum | LC605938.1 | Japan: Hyogo | 1,140 | 45.79% | ec95f6c3d1f1cfe5 |
| P3_ISO_11 | PopSet 3 (Rhinolophus ferrumequinum) | NCBI PopSet 2170330412 / LC605906-LC605937 + AB085720 (East Asian Sino-Japanese Karst & Island Deme) | IY077 | Rhinolophus ferrumequinum | LC605937.1 | Japan: Hyogo | 1,140 | 45.79% | ec95f6c3d1f1cfe5 |
| P3_ISO_12 | PopSet 3 (Rhinolophus ferrumequinum) | NCBI PopSet 2170330412 / LC605906-LC605937 + AB085720 (East Asian Sino-Japanese Karst & Island Deme) | IY076 | Rhinolophus ferrumequinum | LC605936.1 | Japan: Hyogo | 1,140 | 45.88% | 5d4775868857f105 |
| P3_ISO_13 | PopSet 3 (Rhinolophus ferrumequinum) | NCBI PopSet 2170330412 / LC605906-LC605937 + AB085720 (East Asian Sino-Japanese Karst & Island Deme) | IY075 | Rhinolophus ferrumequinum | LC605935.1 | Japan: Hyogo | 1,140 | 45.79% | ec95f6c3d1f1cfe5 |
| P3_ISO_14 | PopSet 3 (Rhinolophus ferrumequinum) | NCBI PopSet 2170330412 / LC605906-LC605937 + AB085720 (East Asian Sino-Japanese Karst & Island Deme) | IY062 | Rhinolophus ferrumequinum | LC605934.1 | Japan: Ibaraki | 1,140 | 45.96% | ac4720f12a2f4676 |
| P3_ISO_15 | PopSet 3 (Rhinolophus ferrumequinum) | NCBI PopSet 2170330412 / LC605906-LC605937 + AB085720 (East Asian Sino-Japanese Karst & Island Deme) | IY060 | Rhinolophus ferrumequinum | LC605933.1 | Japan: Ibaraki | 1,140 | 45.96% | ac4720f12a2f4676 |
| P3_ISO_16 | PopSet 3 (Rhinolophus ferrumequinum) | NCBI PopSet 2170330412 / LC605906-LC605937 + AB085720 (East Asian Sino-Japanese Karst & Island Deme) | IY041 | Rhinolophus ferrumequinum | LC605932.1 | Japan: Yamaguchi | 1,140 | 45.88% | 467ffc88cce72ad5 |
| P3_ISO_17 | PopSet 3 (Rhinolophus ferrumequinum) | NCBI PopSet 2170330412 / LC605906-LC605937 + AB085720 (East Asian Sino-Japanese Karst & Island Deme) | IY040 | Rhinolophus ferrumequinum | LC605931.1 | Japan: Yamaguchi | 1,140 | 45.88% | 467ffc88cce72ad5 |
| P3_ISO_18 | PopSet 3 (Rhinolophus ferrumequinum) | NCBI PopSet 2170330412 / LC605906-LC605937 + AB085720 (East Asian Sino-Japanese Karst & Island Deme) | IY039 | Rhinolophus ferrumequinum | LC605930.1 | Japan: Yamaguchi | 1,140 | 45.88% | 467ffc88cce72ad5 |
| P3_ISO_19 | PopSet 3 (Rhinolophus ferrumequinum) | NCBI PopSet 2170330412 / LC605906-LC605937 + AB085720 (East Asian Sino-Japanese Karst & Island Deme) | IY036 | Rhinolophus ferrumequinum | LC605929.1 | Japan: Yamaguchi | 1,140 | 45.88% | 467ffc88cce72ad5 |
| P3_ISO_20 | PopSet 3 (Rhinolophus ferrumequinum) | NCBI PopSet 2170330412 / LC605906-LC605937 + AB085720 (East Asian Sino-Japanese Karst & Island Deme) | IY035 | Rhinolophus ferrumequinum | LC605928.1 | Japan: Yamaguchi | 1,140 | 45.88% | 467ffc88cce72ad5 |
| P3_ISO_21 | PopSet 3 (Rhinolophus ferrumequinum) | NCBI PopSet 2170330412 / LC605906-LC605937 + AB085720 (East Asian Sino-Japanese Karst & Island Deme) | IY033 | Rhinolophus ferrumequinum | LC605927.1 | Japan: Fukuoka | 1,140 | 45.88% | 467ffc88cce72ad5 |
| P3_ISO_22 | PopSet 3 (Rhinolophus ferrumequinum) | NCBI PopSet 2170330412 / LC605906-LC605937 + AB085720 (East Asian Sino-Japanese Karst & Island Deme) | IY032 | Rhinolophus ferrumequinum | LC605926.1 | Japan: Fukuoka | 1,140 | 45.88% | 467ffc88cce72ad5 |
| P3_ISO_23 | PopSet 3 (Rhinolophus ferrumequinum) | NCBI PopSet 2170330412 / LC605906-LC605937 + AB085720 (East Asian Sino-Japanese Karst & Island Deme) | IY030 | Rhinolophus ferrumequinum | LC605925.1 | Japan: Fukuoka | 1,140 | 45.96% | e22b15fe3cee0762 |
| P3_ISO_24 | PopSet 3 (Rhinolophus ferrumequinum) | NCBI PopSet 2170330412 / LC605906-LC605937 + AB085720 (East Asian Sino-Japanese Karst & Island Deme) | IY029 | Rhinolophus ferrumequinum | LC605924.1 | Japan: Fukuoka | 1,140 | 45.96% | e22b15fe3cee0762 |
| P3_ISO_25 | PopSet 3 (Rhinolophus ferrumequinum) | NCBI PopSet 2170330412 / LC605906-LC605937 + AB085720 (East Asian Sino-Japanese Karst & Island Deme) | IY021 | Rhinolophus ferrumequinum | LC605923.1 | Japan: Kumamoto | 1,140 | 45.96% | 93078d3cc2a67a56 |
| P3_ISO_26 | PopSet 3 (Rhinolophus ferrumequinum) | NCBI PopSet 2170330412 / LC605906-LC605937 + AB085720 (East Asian Sino-Japanese Karst & Island Deme) | IY020 | Rhinolophus ferrumequinum | LC605922.1 | Japan: Kumamoto | 1,140 | 45.96% | 93078d3cc2a67a56 |
| P3_ISO_27 | PopSet 3 (Rhinolophus ferrumequinum) | NCBI PopSet 2170330412 / LC605906-LC605937 + AB085720 (East Asian Sino-Japanese Karst & Island Deme) | IY012 | Rhinolophus ferrumequinum | LC605921.1 | Japan: Kumamoto | 1,140 | 45.96% | 3eb6984d239a77de |
| P3_ISO_28 | PopSet 3 (Rhinolophus ferrumequinum) | NCBI PopSet 2170330412 / LC605906-LC605937 + AB085720 (East Asian Sino-Japanese Karst & Island Deme) | IY011 | Rhinolophus ferrumequinum | LC605920.1 | Japan: Kumamoto | 1,140 | 45.96% | 3eb6984d239a77de |
| P3_ISO_29 | PopSet 3 (Rhinolophus ferrumequinum) | NCBI PopSet 2170330412 / LC605906-LC605937 + AB085720 (East Asian Sino-Japanese Karst & Island Deme) | IY009 | Rhinolophus ferrumequinum | LC605919.1 | Japan: Kumamoto | 1,140 | 45.96% | 3eb6984d239a77de |
| P3_ISO_30 | PopSet 3 (Rhinolophus ferrumequinum) | NCBI PopSet 2170330412 / LC605906-LC605937 + AB085720 (East Asian Sino-Japanese Karst & Island Deme) | IY008 | Rhinolophus ferrumequinum | LC605918.1 | Japan: Kumamoto | 1,140 | 45.96% | 93078d3cc2a67a56 |
| P3_ISO_31 | PopSet 3 (Rhinolophus ferrumequinum) | NCBI PopSet 2170330412 / LC605906-LC605937 + AB085720 (East Asian Sino-Japanese Karst & Island Deme) | IY006 | Rhinolophus ferrumequinum | LC605917.1 | Japan: Kyoto | 1,140 | 46.05% | 5a157efb2899f994 |
| P3_ISO_32 | PopSet 3 (Rhinolophus ferrumequinum) | NCBI PopSet 2170330412 / LC605906-LC605937 + AB085720 (East Asian Sino-Japanese Karst & Island Deme) | IY005 | Rhinolophus ferrumequinum | LC605916.1 | Japan: Kyoto | 1,140 | 45.96% | ac4720f12a2f4676 |
| P3_ISO_33 | PopSet 3 (Rhinolophus ferrumequinum) | NCBI PopSet 2170330412 / LC605906-LC605937 + AB085720 (East Asian Sino-Japanese Karst & Island Deme) | IY004 | Rhinolophus ferrumequinum | LC605915.1 | Japan: Kyoto | 1,140 | 45.96% | ac4720f12a2f4676 |
| P3_ISO_34 | PopSet 3 (Rhinolophus ferrumequinum) | NCBI PopSet 2170330412 / LC605906-LC605937 + AB085720 (East Asian Sino-Japanese Karst & Island Deme) | IY003 | Rhinolophus ferrumequinum | LC605914.1 | Japan: Kyoto | 1,140 | 45.96% | ac4720f12a2f4676 |
| P3_ISO_35 | PopSet 3 (Rhinolophus ferrumequinum) | NCBI PopSet 2170330412 / LC605906-LC605937 + AB085720 (East Asian Sino-Japanese Karst & Island Deme) | HN-08 | Rhinolophus ferrumequinum | MG570064.1 | China: Henan | 1,140 | 46.32% | 4136d95f0759ed5f |
| P3_ISO_36 | PopSet 3 (Rhinolophus ferrumequinum) | NCBI PopSet 2170330412 / LC605906-LC605937 + AB085720 (East Asian Sino-Japanese Karst & Island Deme) | JL-011 | Rhinolophus ferrumequinum | KX467578.1 | China | 1,140 | 46.32% | 23085a9aace6eb55 |