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Lineage Divergence and Historical Gene Flow in the Chinese Horseshoe Bat (Rhinolophus sinicus)

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Outgoing claims: the papers this work cites, builds on, or argues with.

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Conflict Among Individual Mitochondrial Proteins in Resolving the Phylogeny of Eutherian Orders
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Eco-environmental effects of the Qinghai-Tibet Plateau uplift during the Quaternary in China
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Karyotype evolution in Rhinolophus bats (Rhinolophidae, Chiroptera) illuminated by cross-species chromosome painting and G-banding comparison
inferredcites →https://doi.org/10.1007/s10592-012-0361-yopenalex-snapshot
Sibling species in South Indian populations of the rufous horse-shoe bat Rhinolophus rouxii
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TRACER version 1.1
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Hybridization as an invasion of the genome
inferredcites →https://doi.org/10.1016/j.ympev.2004.04.007openalex-snapshot
Molecular architecture of Pipistrellus pipistrellus/Pipistrellus pygmaeus complex (Chiroptera: Vespertilionidae): further cryptic species and Mediterranean origin of the divergence
inferredcites →https://doi.org/10.1016/s0169-5347(00)02026-7openalex-snapshot
Intraspecific gene genealogies: trees grafting into networks
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Adaptive protein evolution at the Adh locus in Drosophila
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TCS: a computer program to estimate gene genealogies
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The incomplete natural history of mitochondria
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distruct : a program for the graphical display of population structure
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XXXI.—On the Bats of the Rhinolophus macrotis Group, with Descriptions of Two new Forms
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A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
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A Molecular Supermatrix of the Rabbits and Hares (Leporidae) Allows for the Identification of Five Intercontinental Exchanges During the Miocene
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A New Statistical Method for Haplotype Reconstruction from Population Data
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MODELTEST: testing the model of DNA substitution.
inferredcites →https://doi.org/10.1093/bioinformatics/17.12.1246openalex-snapshot
CONSEL: for assessing the confidence of phylogenetic tree selection
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MrBayes 3: Bayesian phylogenetic inference under mixed models
inferredcites →https://doi.org/10.1093/bioinformatics/btg359openalex-snapshot
DnaSP, DNA polymorphism analyses by the coalescent and other methods
inferredcites →https://doi.org/10.1093/bioinformatics/btm233openalex-snapshot
CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure
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BEST: Bayesian estimation of species trees under the coalescent model
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Inferring population history withDIY ABC: a user-friendly approach to approximate Bayesian computation
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STATISTICAL PROPERTIES OF THE NUMBER OF RECOMBINATION EVENTS IN THE HISTORY OF A SAMPLE OF DNA SEQUENCES
inferredcites →https://doi.org/10.1093/genetics/116.1.153openalex-snapshot
A Test of Neutral Molecular Evolution Based on Nucleotide Data
inferredcites →https://doi.org/10.1093/genetics/155.2.945openalex-snapshot
Inference of Population Structure Using Multilocus Genotype Data
inferredcites →https://doi.org/10.1093/genetics/158.2.885openalex-snapshot
Distinguishing Migration From Isolation: A Markov Chain Monte Carlo Approach
inferredcites →https://doi.org/10.1093/genetics/162.4.2025openalex-snapshot
Approximate Bayesian Computation in Population Genetics
inferredcites →https://doi.org/10.1093/molbev/msq210openalex-snapshot
Testing Founder Effect Speciation: Divergence Population Genetics of the Spoonbills Platalea regia and Pl. minor (Threskiornithidae, Aves)
inferredcites →https://doi.org/10.1093/nar/25.24.4876openalex-snapshot
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools
inferredcites →https://doi.org/10.1093/oxfordjournals.jhered.a111573openalex-snapshot
GENEPOP (Version 1.2): Population Genetics Software for Exact Tests and Ecumenicism
inferredcites →https://doi.org/10.1093/oxfordjournals.jhered.a111627openalex-snapshot
FSTAT (Version 1.2): A Computer Program to Calculate F-Statistics
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026201openalex-snapshot
Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic Inference
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Phylogenetic Analysis in the Anomaly Zone
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Genetic consequences of climatic oscillations in the Quaternary
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PHYLOGEOGRAPHIC HISTORY OF THE LAND SNAIL CANDIDULA UNIFASCIATA (HELICELLINAE, STYLOMMATOPHORA): FRAGMENTATION, CORRIDOR MIGRATION, AND SECONDARY CONTACT
inferredcites →https://doi.org/10.1111/j.0014-3820.2004.tb01577.xopenalex-snapshot
DOES GENE FLOW CONSTRAIN ADAPTIVE DIVERGENCE OR VICE VERSA? A TEST USING ECOMORPHOLOGY AND SEXUAL ISOLATION IN TIMEMA CRISTINAE WALKING-STICKS
inferredcites →https://doi.org/10.1111/j.1095-8312.2007.00942.xopenalex-snapshot
Molecular phylogeny of New World sheath-tailed bats (Emballonuridae: Diclidurini) based on loci from the four genetic transmission systems in mammals
inferredcites →https://doi.org/10.1111/j.1365-294x.2005.02553.xopenalex-snapshot
Detecting the number of clusters of individuals using the software structure : a simulation study
inferredcites →https://doi.org/10.1111/j.1365-294x.2008.03750.xopenalex-snapshot
Recent divergence with gene flow in Tennessee cave salamanders (Plethodontidae:Gyrinophilus) inferred from gene genealogies
inferredcites →https://doi.org/10.1111/j.1365-294x.2008.03946.xopenalex-snapshot
Divergent selection and heterogeneous genomic divergence
inferredcites →https://doi.org/10.1111/j.1365-294x.2008.04021.xopenalex-snapshot
Phylogeography of the greater horseshoe bat,Rhinolophus ferrumequinum: contrasting results from mitochondrial and microsatellite data
inferredcites →https://doi.org/10.1111/j.1365-294x.2008.04035.xopenalex-snapshot
Variable responses of skinks to a common history of rainforest fluctuation: concordance between phylogeography and palaeo‐distribution models
inferredcites →https://doi.org/10.1111/j.1365-294x.2010.04560.xopenalex-snapshot
Historical male‐mediated introgression in horseshoe bats revealed by multilocus DNA sequence data
inferredcites →https://doi.org/10.1111/j.1365-294x.2010.04704.xopenalex-snapshot
Pleistocene climatic cycling drives intra‐specific diversification in the intermediate horseshoe bat (Rhinolophus affinis) in Southern China
inferredcites →https://doi.org/10.1111/j.1471-8286.2004.00684.xopenalex-snapshot
micro ‐ checker : software for identifying and correcting genotyping errors in microsatellite data
inferredcites →https://doi.org/10.1111/j.1471-8286.2005.01031.xopenalex-snapshot
G eneland : a computer package for landscape genetics
inferredcites →https://doi.org/10.1111/j.1471-8286.2007.01769.xopenalex-snapshot
Bayesian clustering algorithms ascertaining spatial population structure: a new computer program and a comparison study
inferredcites →https://doi.org/10.1111/j.1558-5646.2008.00345.xopenalex-snapshot
COALESCENT ANALYSES OF MULTIPLE LOCI SUPPORT A NEW ROUTE TO SPECIATION IN BIRDS
inferredcites →https://doi.org/10.1111/j.1755-0998.2008.02434.xopenalex-snapshot
Development and characterization of novel microsatellite markers from the Chinese rufous horseshoe bat (Rhinolophus sinicus) with cross‐species amplification in closely related taxa
inferredcites →https://doi.org/10.1126/science.3576198openalex-snapshot
Gene Flow and the Geographic Structure of Natural Populations
inferredcites →https://doi.org/10.1146/annurev.ecolsys.34.011802.132421openalex-snapshot
Species-Level Paraphyly and Polyphyly: Frequency, Causes, and Consequences, with Insights from Animal Mitochondrial DNA
inferredcites →https://doi.org/10.1146/annurev.es.16.110185.000553openalex-snapshot
Analysis of Hybrid Zones
inferredcites →https://doi.org/10.1186/1471-2105-11-401openalex-snapshot
Inference on population history and model checking using DNA sequence and microsatellite data with the software DIYABC (v1.0)
inferredcites →https://doi.org/10.1186/1471-2148-10-208openalex-snapshot
Pleistocene glacial cycle effects on the phylogeography of the Chinese endemic bat species, Myotis davidii
inferredcites →https://doi.org/10.1186/1471-2148-7-214openalex-snapshot
BEAST: Bayesian evolutionary analysis by sampling trees
inferredcites →https://doi.org/10.1186/1471-2148-8-21openalex-snapshot
Phylogeography and Demographic History of Chinese Black-Spotted Frog Populations (Pelophylax nigromaculata): Evidence for Independent Refugia Expansion and Secondary Contact
inferredcites →https://doi.org/10.14601/phytopathol_mediterr-14998u1.29openalex-snapshot
BIOEDIT: A USER-FRIENDLY BIOLOGICAL SEQUENCE ALIGNMENT EDITOR AND ANALYSIS PROGRAM FOR WINDOWS 95/98/ NT
inferredcites →https://doi.org/10.1534/genetics.103.024182openalex-snapshot
Multilocus Methods for Estimating Population Sizes, Migration Rates and Divergence Time, With Applications to the Divergence of Drosophila pseudoobscura and D. persimilis
inferredcites →https://doi.org/10.1534/genetics.107.081810openalex-snapshot
Population Genetics of Speciation in Two Closely Related Wild Tomatoes (Solanum Section Lycopersicon)
inferredcites →https://doi.org/10.1554/0014-3820(2001)055[0859:pngcfm]2.0.co;2openalex-snapshot
PREDICTING NUCLEAR GENE COALESCENCE FROM MITOCHONDRIAL DATA: THE THREE-TIMES RULE
inferredcites →https://doi.org/10.1644/05-mamm-a-395r2.1openalex-snapshot
PHYLOGENETICS OF SMALL HORSESHOE BATS FROM EAST ASIA BASED ON MITOCHONDRIAL DNA SEQUENCE VARIATION
inferredcites →https://doi.org/10.5281/zenodo.13414956openalex-snapshot
On the bats of the Rhinolophus macrotis group with descriptions of two new forms

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Bats of the Vietnamese Mekong Delta: A revised checklist with significant new records
inferred← citeshttps://doi.org/10.5852/ejt.2017.274zenodo-depositor-declared
Comparative phylogeography of bamboo bats of the genus Tylonycteris (Chiroptera, Vespertilionidae) in Southeast Asia
inferred← citeshttps://doi.org/10.1002/ece3.73087openalex-snapshot
Hibernation Shifts in Gut Microbiota Composition and Metabolic Function in the Chinese Horseshoe Bat ( Rhinolophus sinicus )
inferred← citeshttps://doi.org/10.1002/mbo3.670openalex-snapshot
Gut microbial diversity in two insectivorous bats: Insights into the effect of different sampling sources
inferred← citeshttps://doi.org/10.1007/s10709-014-9794-1openalex-snapshot
Introgression of mitochondrial DNA promoted by natural selection in the Japanese pipistrelle bat (Pipistrellus abramus)
inferred← citeshttps://doi.org/10.1016/j.biocon.2019.108269openalex-snapshot
Automatic standardized processing and identification of tropical bat calls using deep learning approaches
inferred← citeshttps://doi.org/10.1016/j.virol.2021.05.008openalex-snapshot
Analysis of codon usage of Horseshoe Bat Hepatitis B virus and its host
inferred← citeshttps://doi.org/10.1016/j.ympev.2019.106544openalex-snapshot
Species delimitation and evolutionary reconstruction within an integrative taxonomic framework: A case study on Rhinolophus macrotis complex (Chiroptera: Rhinolophidae)
inferred← citeshttps://doi.org/10.1016/j.ympev.2019.106551openalex-snapshot
Resolving evolutionary relationships among six closely related taxa of the horseshoe bats (Rhinolophus) with targeted resequencing data
inferred← citeshttps://doi.org/10.1093/biolinnean/blx017openalex-snapshot
Genomics of introgression in the Chinese horseshoe bat (Rhinolophus sinicus) revealed by transcriptome sequencing
inferred← citeshttps://doi.org/10.1093/ve/veab007openalex-snapshot
The evolutionary history of ACE2 usage within the coronavirus subgenus Sarbecovirus
inferred← citeshttps://doi.org/10.1093/zoolinnean/zlaf199openalex-snapshot
Whole-genome sequencing uncovers genomic divergence and gene flow in closely related virus-harbouring horseshoe bats ( Rhinolophus )
inferred← citeshttps://doi.org/10.1101/2020.07.31.20166090openalex-snapshot
Land Use Change and Coronavirus Emergence Risk
inferred← citeshttps://doi.org/10.1111/bij.12138openalex-snapshot
Multiple cases of asymmetric introgression among horseshoe bats detected by phylogenetic conflicts across loci
inferred← citeshttps://doi.org/10.1111/bij.12620openalex-snapshot
The use of museum samples for large-scale sequence capture: a study of congeneric horseshoe bats (family Rhinolophidae)
inferred← citeshttps://doi.org/10.1111/eth.12627openalex-snapshot
The effects of cultural drift on geographic variation in echolocation calls of the Chinese rufous horseshoe bat (Rhinolophus sinicus)
inferred← citeshttps://doi.org/10.1111/jzs.12169openalex-snapshot
Integrative taxonomy of theRhinolophus macrotiscomplex (Chiroptera, Rhinolophidae) in Vietnam and nearby regions
inferred← citeshttps://doi.org/10.1111/mec.13425openalex-snapshot
Speciation processes in putative island endemic sister bat species: false impressions from mitochondrial DNA and microsatellite data
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Lack of genetic isolation by distance, similar genetic structuring but different demographic histories in a fig‐pollinating wasp mutualism
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Phylogeography of horseshoe bat sarbecoviruses in Vietnam and neighbouring countries. Implications for the origins of SARS ‐ CoV and SARS ‐ CoV ‐2
inferred← citeshttps://doi.org/10.1128/mbio.01197-24openalex-snapshot
Diversity and spillover risk of swine acute diarrhea syndrome and related coronaviruses in China and Southeast Asia
inferred← citeshttps://doi.org/10.1186/s12862-018-1289-8openalex-snapshot
Coexistence of two sympatric cryptic bat species in French Guiana: insights from genetic, acoustic and ecological data
inferred← citeshttps://doi.org/10.1371/journal.pone.0098035openalex-snapshot
Heteroplasmy and Ancient Translocation of Mitochondrial DNA to the Nucleus in the Chinese Horseshoe Bat (Rhinolophus sinicus) Complex
inferred← citeshttps://doi.org/10.2174/2666796701999201211205557openalex-snapshot
Coronavirus Pandemic: Role of Bats And Zoonotic Transmission in Humans
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Evidencia de introgresión genética entre Pteronotus fulvus y Pteronotus gymnonotus (Chiroptera: Mormoopidae)
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The complete mitochondrial genome of a Chinese rufous horseshoe bat subspecies, Rhinolophus sinicus sinicus (Chiroptera: Rhinolophidae)
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Characterization of the complete mitochondrial genome of the Rhinolophus sinicus sinicus (Chiroptera: Rhinolophidae) from Central China
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A Taxonomic Revision of the Kerivoula hardwickii Complex (Chiroptera: Vespertilionidae) with the Description of a New Species
inferred← citeshttps://doi.org/10.3390/ani11030733openalex-snapshot
Effects of Colonization, Geography and Environment on Genetic Divergence in the Intermediate Leaf-Nosed Bat, Hipposideros larvatus
inferred← citeshttps://doi.org/10.3390/ani14081177openalex-snapshot
Sex Differences in Cochlear Transcriptomes in Horseshoe Bats
inferred← citeshttps://doi.org/10.3390/ani16172669openalex-snapshot
Evolutionary History of the Rhinolophus pusillus Species Complex Reveals Phylogeographic Diversification Across the East Asian Mainland–Island System
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Genetic Introgression and Morphological Variation in Naked-Back Bats (Chiroptera: Mormoopidae: Pteronotus Species) along Their Contact Zone in Central America
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Characterization of Novel Rhabdoviruses in Chinese Bats
inferred← citeshttps://doi.org/10.7287/peerj.15231v0.1/reviews/1openalex-snapshot
Peer Review #1 of "Sex differences in gene expression and alternative splicing in the Chinese horseshoe bat (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.15231v0.1/reviews/2openalex-snapshot
Peer Review #2 of "Sex differences in gene expression and alternative splicing in the Chinese horseshoe bat (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.15231v0.1/reviews/3openalex-snapshot
Peer Review #3 of "Sex differences in gene expression and alternative splicing in the Chinese horseshoe bat (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.15231v0.1/reviews/4openalex-snapshot
Peer Review #4 of "Sex differences in gene expression and alternative splicing in the Chinese horseshoe bat (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.15231v0.2/reviews/2openalex-snapshot
Peer Review #2 of "Sex differences in gene expression and alternative splicing in the Chinese horseshoe bat (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj.15231v0.2/reviews/3openalex-snapshot
Peer Review #3 of "Sex differences in gene expression and alternative splicing in the Chinese horseshoe bat (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj.15231v0.2/reviews/4openalex-snapshot
Peer Review #4 of "Sex differences in gene expression and alternative splicing in the Chinese horseshoe bat (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj.15231v0.2/reviews/5openalex-snapshot
Peer Review #5 of "Sex differences in gene expression and alternative splicing in the Chinese horseshoe bat (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj.15231v0.3/reviews/2openalex-snapshot
Peer Review #2 of "Sex differences in gene expression and alternative splicing in the Chinese horseshoe bat (v0.3)"
inferred← citeshttps://doi.org/10.7287/peerj.15231v0.3/reviews/3openalex-snapshot
Peer Review #3 of "Sex differences in gene expression and alternative splicing in the Chinese horseshoe bat (v0.3)"
inferred← citeshttps://doi.org/10.7287/peerj.15231v0.3/reviews/5openalex-snapshot
Peer Review #5 of "Sex differences in gene expression and alternative splicing in the Chinese horseshoe bat (v0.3)"
inferred← citeshttps://doi.org/10.7717/peerj.15231openalex-snapshot
Sex differences in gene expression and alternative splicing in the Chinese horseshoe bat
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