Tan Vuong

Tamás Tu

Gabor Görföl

Satoru Csorba

Fuka Arai

Dai Kikuchi

Daisuke Fukui

Neil Koyabu

Saw Furey

Bawm

San Kyaw

Lin

Vuong Tan

Tamás Görföl

Gábor Csorba

Satoru Arai

Fuka Kikuchi

Daisuke Koyabu

Neil M Furey

Saw Bawm

Phillip Alviola

Chu Thi Hang

Nguyen Truong

Tran Anh Tuan

Alexandre Hassanin

Integrative taxonomy and biogeography of Asian yellow house bats (Vespertilionidae: Scotophilus) in the Indomalayan Region

Keywords: integrative taxonomy, comparative phylogeography, multiple datasets, sympatric species, Scotophilus

des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

Introduction

Species constitute one of the fundamental units of study in many fields of biology.

However, the multiplicity of species concepts and criteria used to delineate species boundaries have led to considerable taxonomic confusion and numerous controversies [START_REF] Aldhebiani | Species concept and speciation[END_REF][START_REF] De Queiroz | Ernst Mayr and the modern concept of species[END_REF][START_REF] De Queiroz | Species concepts and species delimitation[END_REF]. A typical example of such confusion concerns the systematics of the genus Scotophilus Leach, 1821 (family Vespertilionidae), which comprises yellow house bats that are widely distributed in the Old World tropics.

Until the third edition of Mammal Species of the World [START_REF] Wilson | Mammal Species of the World: A Taxonomic and Geographic Reference[END_REF], most mammalogists adopted the Biological Species Concept [START_REF] Mayr | Systematics and the origin of species from the viewpoint of a zoologist[END_REF]. As such, they usually regarded morphological and ecological variation and/or geographical isolation as indicative of reproductive isolation among sister species and considered that the systematics of mammals were relatively complete and accurate [START_REF] Baker | Speciation in mammals and the genetic species concept[END_REF]. Following taxonomic reviews in the 20 th century, [START_REF] Simmons | Order Chiroptera[END_REF] recognised 12 valid species in the genus Scotophilus, most of which were polytypic and widely distributed in the Old World tropics. Since this time, exploration of poorly studied regions and development of analytical approaches that integrate morphological, molecular and acoustic data have altered taxonomic opinions regarding the utility of different species concepts and associated criteria for delineating species boundaries, including within Scotophilus spp. [START_REF] Baker | Speciation in mammals and the genetic species concept[END_REF][START_REF] Demos | Hidden diversity of African yellow house bats (Vespertilionidae, Scotophilus): Insights from multilocus phylogenetics and lineage delimitation[END_REF][START_REF] Francis | The role of DNA barcodes in understanding and conservation of mammal diversity in Southeast Asia[END_REF][START_REF] Trujillo | Molecular phylogenetics of the bat genus Scotophilus (Chiroptera: Vespertilionidae): Perspectives from paternally and maternally inherited genomes[END_REF][START_REF] Vallo | Advances in taxonomy of African House Bats (Scotophilus, Vespertilionidae)[END_REF]. For instance, recent integrative studies have revealed that certain traditionally accepted and polytypic species of Scotophilus in Africa actually comprise several distinct species which were previously unrecognized or subsumed as subspecies due to their morphological similarities. As a consequence, the number of valid African Scotophilus species has increased from eight [START_REF] Simmons | Order Chiroptera[END_REF] to 18 and will likely continue to grow as further cryptic forms of widespread taxa are found [START_REF] Demos | Hidden diversity of African yellow house bats (Vespertilionidae, Scotophilus): Insights from multilocus phylogenetics and lineage delimitation[END_REF][START_REF] Trujillo | Molecular phylogenetics of the bat genus Scotophilus (Chiroptera: Vespertilionidae): Perspectives from paternally and maternally inherited genomes[END_REF][START_REF] Vallo | Resurrection of an East African house bat species Scotophilus altilis Allen, 1914 (Chiroptera: Vespertilionidae)[END_REF][START_REF] Vallo | Advances in taxonomy of African House Bats (Scotophilus, Vespertilionidae)[END_REF].

Prior to 1940, Asian Scotophilus included 17 distinct taxa (species and subspecies) (Figure 1; Table S1). Between 1940 and[START_REF] Avise | Phylogeography: The history and formation of species[END_REF], several studies addressed the taxonomic status of Scotophilus spp. in Asia on the basis of their morphology (Table 1). These led to consensus among early bat taxonomists that two sizes of yellow house bats, small and large, co-occur in many parts of the Indomalayan Region [START_REF] Corbet | The mammals of the Indomalayan Region: A systematic review[END_REF][START_REF] Hill | Bats from Thailand and Cambodia[END_REF][START_REF] Shamel | A collection of bats from Thailand (Siam)[END_REF][START_REF] Siddiqi | Notes on the status of bats of the genus Scotophilus from Southern Asia with key to the recognized forms[END_REF][START_REF] Tate | Review of the vespertilionine bats, with special attention to genera and species of the Archbold collections[END_REF]. However, these studies frequently employed differing criteria to interpret morphological variation in their specimen material and consequently applied different taxonomic approaches to the same geographical populations. A typical example of this is apparent in the differences in the systematics of the two yellow house bats present in the Sunda Islands (e.g. Java, Bali, Belitung and Borneo).

Within the Sunda Islands, [START_REF] Tate | Review of the vespertilionine bats, with special attention to genera and species of the Archbold collections[END_REF] included all specimens of yellow house bats collected on Java and nearby islands in three subspecies of S. temminckii Horsfield, 1824 (=S. kuhlii [START_REF] Leach | The characters of three new genera of bats without foliaceous appendages to the nose[END_REF]; see [START_REF] Hill | Bats from Thailand and Cambodia[END_REF]: S. t. temminckii, S. t. collinus Sody, 1936and S. t. solutatus Sody, 1936. In contrast, Shamel (1942) classified the small and large yellow house bats on Java into two distinct species, Pachyotus (=Scotophilus) temminckii and P. solutatus, respectively. The taxonomic situation became more complex when Siddiqi (1960) also classified Javanese yellow house bats into two species, the smaller S. t. temminckii and the larger S. heathii Horsfield, 1831. However, specimens of the larger species and females of the smaller taxon recognized by Siddiqui (1960) were morphologically comparable to those of P. solutatus (sensu Shamel, 1940). Likewise, [START_REF] Corbet | The mammals of the Indomalayan Region: A systematic review[END_REF] allocated Asian Scotophilus into just two polytypic species, namely (1) S. kuhlii, including subspecies/synonyms occurring widely in the Indomalayan Region: castaneus Horsfield, 1851, collinus, consobrinus Allen, 1906, fulvus Gray, 1843, gairdneri Kloss, 1917, panayensis Sody, 1928, solutatus, swinhoei Blyth, 1860, temminckii, and wroughtoni Thomas, 1897;and (2) S. heathii, including the synonyms belangeri Geoffroy I., 1834, flaveolus [START_REF] Horsfield | A catalogue of the Mammalia in the Museum of the Hon[END_REF], insularis Allen, 1906, luteus Blyth, 1851and watkinsi Sanborn 1952 which were restricted to mainland Asia, plus celebensis Sody, 1928 endemic to Sulawesi. This view ignored the treatments of [START_REF] Shamel | A collection of bats from Thailand (Siam)[END_REF] and [START_REF] Siddiqi | Notes on the status of bats of the genus Scotophilus from Southern Asia with key to the recognized forms[END_REF] in considering all yellow house bats on Java and nearby islands as representatives of S. kuhlii sensu lato (s.l.) and created extensive overlap in the morphology of bats of this taxon (i.e. FA: 45-59 mm) and those of S. heathii s.l. (i.e. FA ≥55 mm) (Figure 1; Table 1).

Contrary to earlier treatments [START_REF] Corbet | The mammals of the Indomalayan Region: A systematic review[END_REF][START_REF] Shamel | A collection of bats from Thailand (Siam)[END_REF][START_REF] Siddiqi | Notes on the status of bats of the genus Scotophilus from Southern Asia with key to the recognized forms[END_REF][START_REF] Tate | Review of the vespertilionine bats, with special attention to genera and species of the Archbold collections[END_REF], [START_REF] Kitchener | Morphological variation among populations of Scophilus kuhlii (sensu lato) Leach, 1821 (Chiroptera: Vespertilionidae) from the Greater and Lesser Sunda Islands, Indonesia[END_REF] argued that smaller Scotophilus with a FA of less than 54 mm on the Greater (Java and Borneo) and Lesser Sunda Islands were readily identifiable as two distinct species, namely the smaller S. collinus (i.e. mean FA values for males and females: 49.1 and 50.9 respectively) and the larger S. kuhlii (i.e. mean FA values for males and females are 51.8 and 52.5, respectively). Both of these species were further divided into two morphological forms, but only those of the larger species, S. kuhlii s.l. were regarded as two subspecies, namely S. k. temminckii inhabiting West and East Java and its relatively smaller sister S. k. solutatus, occurring on East Java and Bali. On East Java, two subspecies of S. kuhlii were recognised in adjacent mountain ranges separated by the Bondoyudo River plains, and the authors even suggested that they might be distinct species.

In light of the above, the taxonomic status of several subspecies or races of two polytypic species, S. kuhlii s.l. and S. heathii s.l. (sensu [START_REF] Corbet | The mammals of the Indomalayan Region: A systematic review[END_REF]) is likely inaccurate. Many of these taxa were originally described as distinct species or subspecies that were individually distinguished by certain morphological variation (pelage colour or body size) and/or geographical hiatus (Figure 1; Table S1). Nonetheless, [START_REF] Simmons | Order Chiroptera[END_REF] and subsequent authors [START_REF] Hutson | Scotophilus celebensis[END_REF][START_REF] Moratelli | Family Vespertilionidae (Vesper Bats)[END_REF][START_REF] Sinaga | Scotophilus collinus[END_REF]Srinivasulu & Srinivasulu, 2019a[START_REF] Srinivasulu | Scotophilus kuhlii[END_REF] recognised only four distinct species of Asian Scotophilus: (1) S. kuhlii, found widely in the Indomalayan Region;

(2) S. collinus, occurring sporadically in the Greater and Lesser Sunda Islands; (3) S. heathii, found in mainland Asia, except for the southern Indochinese subregion; and (4) S. celebensis, endemic to Sulawesi (Figure 1). Among these, the separation of S. celebensis from S. heathii was regarded as provisional [START_REF] Simmons | Order Chiroptera[END_REF] because it was based solely on the disjunct distributions of the two taxa [START_REF] Corbet | The mammals of the Indomalayan Region: A systematic review[END_REF][START_REF] Tate | Review of the vespertilionine bats, with special attention to genera and species of the Archbold collections[END_REF].

Recent genetic studies have improved our understanding of the taxonomy and biogeography of Asian yellow house bats [START_REF] Francis | The role of DNA barcodes in understanding and conservation of mammal diversity in Southeast Asia[END_REF][START_REF] Hisheh | Implications of contrasting patterns of genetic variability in two vespertilionid bats from the Indonesian archipelago[END_REF][START_REF] Trujillo | Molecular phylogenetics of the bat genus Scotophilus (Chiroptera: Vespertilionidae): Perspectives from paternally and maternally inherited genomes[END_REF][START_REF] Yu | Phylogeographic relationships of Scotophilus kuhlii between Hainan island and mainland China[END_REF]. In relation to morphological taxonomy, the separation of the two differently sized species, S. kuhlii and S. heathii, has been highly supported by genetic analyses [START_REF] Francis | The role of DNA barcodes in understanding and conservation of mammal diversity in Southeast Asia[END_REF][START_REF] Trujillo | Molecular phylogenetics of the bat genus Scotophilus (Chiroptera: Vespertilionidae): Perspectives from paternally and maternally inherited genomes[END_REF]. Within S. kuhlii s.l., all recent studies have found little genetic differences between geographically distant populations in the Lesser Sunda Islands [START_REF] Hisheh | Implications of contrasting patterns of genetic variability in two vespertilionid bats from the Indonesian archipelago[END_REF], from Vietnam, Peninsular Malaysia and the Philippines [START_REF] Trujillo | Molecular phylogenetics of the bat genus Scotophilus (Chiroptera: Vespertilionidae): Perspectives from paternally and maternally inherited genomes[END_REF], from northern and southern Indochina (Laos and Vietnam) [START_REF] Francis | The role of DNA barcodes in understanding and conservation of mammal diversity in Southeast Asia[END_REF] and from Hainan Island and mainland China [START_REF] Yu | Phylogeographic relationships of Scotophilus kuhlii between Hainan island and mainland China[END_REF]. These data indicate that gene flow across the studied populations of S. kuhlii has not been limited by geographical distance or sea-barriers [START_REF] Hisheh | Implications of contrasting patterns of genetic variability in two vespertilionid bats from the Indonesian archipelago[END_REF][START_REF] Yu | Phylogeographic relationships of Scotophilus kuhlii between Hainan island and mainland China[END_REF]. While comparable morphological data are still lacking due to inadequate or disparate sampling, it is very likely that S. kuhlii represents a monotypic species. For this reason, research is needed to confirm the taxonomic validity of species or subspecies that were subsumed into or distinguished from S. kuhlii on the basis of morphology alone.

Compared to S. kuhlii s.l., S. heathii s.l. has similar eco-ethological preferences.

However, the latter species may have a greater dispersal ability due to its higher wing loading and aspect ratio e.g. 15 vs 11.6 and 8.0 vs 6.96, respectively [START_REF] Francis | A field guide to the mammals of South-East Asia[END_REF][START_REF] Luo | Wing morphology predicts geographic range size in vespertilionid bats[END_REF][START_REF] Norberg | Ecological morphology and flight in bats (Mammalia; Chiroptera): Wing adaptations, flight performance, foraging strategy and echolocation[END_REF][START_REF] Zhu | Morphology, echolocation calls and diet of Scotophilus kuhlii (Chiroptera: Vespertilionidae) on Hainan island, South China[END_REF]. If so, this would suggest that S. heathii s.l. could also maintain a strong gene flow between its geographically distant populations. This inference is supported by [START_REF] Trujillo | Molecular phylogenetics of the bat genus Scotophilus (Chiroptera: Vespertilionidae): Perspectives from paternally and maternally inherited genomes[END_REF] who analysed genetic divergences in mtDNA (Cytb) and nuDNA (zinc finger Yzfy gene) sequences between S. heathii from Yunnan (China) and northern and southern Vietnam and suggested that these represent the same species. Conversely, [START_REF] Francis | The role of DNA barcodes in understanding and conservation of mammal diversity in Southeast Asia[END_REF] found that S. heathii bats from northern Indochina (northern Vietnam and Laos) and southern Indochina (southern Vietnam) constituted two highly divergent clusters of COI gene sequences. Because comparable COI divergence exist between many closely related species in the Vespertilioninae, [START_REF] Francis | The role of DNA barcodes in understanding and conservation of mammal diversity in Southeast Asia[END_REF] suggested that Indochinese S. heathii may represent a complex of different species.

However, since mitochondrial data are maternally inherited, they should not be solely used to draw taxonomic conclusions [START_REF] Dool | Nuclear introns outperform mitochondrial DNA in inter-specific phylogenetic reconstruction: Lessons from horseshoe bats (Rhinolophidae: Chiroptera)[END_REF]Hassanin, An, Ropiquet, Nguyen, & Couloux, 2013;[START_REF] Nesi | DNA barcoding of African fruit bats (Mammalia, Pteropodidae). The mitochondrial genome does not provide a reliable discrimination between Epomophorus gambianus and Micropteropus pusillus[END_REF][START_REF] Tu | Comparative phylogeography of bamboo bats of the genus Tylonycteris (Chiroptera, Vespertilionidae) in Southeast Asia[END_REF][START_REF] Tu | Four species in one: Multigene analyses reveal phylogenetic patterns within Hardwicke's woolly bat, Kerivoula hardwickii-complex (Chiroptera, Vespertilionidae) in Asia. Hystrix[END_REF]. For a more integrative approach, the hypothesis of [START_REF] Francis | The role of DNA barcodes in understanding and conservation of mammal diversity in Southeast Asia[END_REF] requires further testing with biparental genetic markers, geographically denser sampling and additional morphological data.

This paper presents a phylogeographic study of Asian Scotophilus based on new specimens obtained from different areas in the Indomalayan Region. To this end, we integrate genetic and morphological analyses to (1) address taxonomic uncertainties (e.g. misidentifications or potential cryptic diversity) regarding Asian yellow house bats; (2) evaluate patterns in the demographic and evolutionary histories of species recognized by this study; and (3) consider the roles of ecological factors in shaping the current distributions, population genetic structures and morphological variation of the species. Our overall aim was to improve understanding of the taxonomy and biogeography of Asian yellow house bats.

Materials and Methods

Taxonomic sampling

In this study, we examined 106 bats of S. kuhlii s.l. (n=76) and S. heathii s.l. (n=30) collected from different parts in the Indomalayan Region (Figure 1 S2) to explore their phylogeographic and phylogenetic relationships. We further sequenced two nuclear genes including intron 9 of TUFM (elongation factor Tu, mitochondrial precursor) and intron 6 of ZFYVE27 (zinc finger, FYVE domain containing 27) for six selected specimens of S. kuhlii (n=2) and S. heathii (n=4) to test any incongruence between mitochondrial and nuclear DNA phylogenies. Based on previous studies [START_REF] Roehrs | Tribal phylogenetic relationships within Vespertilioninae (Chiroptera: Vespertilionidae) based on mitochondrial and nuclear sequence data[END_REF][START_REF] Trujillo | Molecular phylogenetics of the bat genus Scotophilus (Chiroptera: Vespertilionidae): Perspectives from paternally and maternally inherited genomes[END_REF], Murina cyclotis Dobson, 1872 of the subfamily Murininae and Eptesicus pachyomus Dobson, 1871 of the subfamily Vespertilioninae were chosen as outgroups in phylogenetic analyses. Genetic sequences available for these outgroup species in GenBank are indicated in Table S2.

Genetic analyses

DNA extraction, amplification, sequencing

Total DNA was extracted from tissue samples using the QIAGEN DNAeasy Tissue Kit (Qiagen, Hilden, Germany) according to the manufacturer's protocol. Primer sets used for PCR amplification of Cytb were Mt-14724F/Cyb-15915R (Irwin, Kocher, & Wilson, 1991), Cyb-14726F/Cyb-15909R (Arai et al., 2016) and for COI were UTyrLA/C1L705 [START_REF] Hassanin | Pattern and timing of diversification of Cetartiodactyla (Mammalia, Laurasiatheria), as revealed by a comprehensive analysis of mitochondrial genomes[END_REF] or MammMt-5533F/MammMt-7159R (Arai et al., 2019) and for TUFM and ZFYVE27 were TUFM-EX9U/TUFM-EX10L and ZFYVE27-EX6U/ZFYVE27-EX7L, respectively (Hassanin et al. 2013) (See Table S3 for more details).

Amplifications were done in a volume of 20 μl including 3 μl of Buffer 10X with MgCl2, 2 μl of dNTP (6.6 mM), 0.12 μl of Taq DNA polymerase (2.5 U, Qiagen, Hilden, Germany) and 0.5-1 μl of the two primers at 10 μM. The standard PCR conditions were as follows: 4 min at 95ºC; 5 cycles of denaturation/annealing/extension with 45 s at 95ºC, 1 min at 60ºC and 1 min at 72ºC, followed by 30 cycles of 30 s at 95ºC, 45 s at 55ºC, and 1 min at 72ºC, followed by 10 min at 72ºC. PCR products were resolved by electrophoresis on a 1.5% agarose gel stained with ethidium bromide and visualized under UV light.

Both strands of PCR products were sequenced using Sanger sequencing on an ABI 3730 automatic sequencer at the Centre National de Séquençage (Genoscope) in Evry (France) and ABI 3730xl DNA Analyzer at the Infectious Disease Surveillance Center, Japan.

The sequences were edited and assembled using CodonCode Aligner Version 3.7.1 (CodonCode Corporation) and Genetyx v11 software (Genetyx Corporation, Japan).

Heterozygous positions (double peaks) of nuclear gene sequences were scored using the IUPAC ambiguity codes. Sequences generated for this study were deposited in the EMBL/DDBJ/GenBank database under the accession numbers MT820574-MT820611, MT820613-MT820624, MT820574-MT820611 (Appendix 1).

Phylogeographic analyses using mtDNA sequences

The number of haplotypes, haplotype diversity (h), and nucleotide diversity (π) for the two nominal species, S. kuhlii s.l. and S. heathii s.l., were calculated from the alignments of 82 COI (576 bp) and 58 Cytb (1140 bp) sequences (Alignments S1 and S2) using DNASP v5.10 [START_REF] Librado | DnaSP v5: A software for comprehensive analysis of DNA polymorphism data[END_REF]. Maximum parsimony haplotype networks were reconstructed using the TCS algorithm in PopArt [START_REF] Leigh | POPART: Full-feature software for haplotype network construction[END_REF]. Following this, a hierarchical analysis of molecular variation (AMOVA) [START_REF] Excoffier | Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction data[END_REF] was performed with 1,000 permutations in Genodive v.3.0 [START_REF] Meirmans | GENOTYPE and GENODIVE: Two programs for the analysis of genetic diversity of asexual organisms[END_REF] to quantify the genetic variation within and among groups in the TCS network.

Phylogenetic reconstruction

Phylogenetic trees of Asian Scotophilus spp. were reconstructed from DNA alignments (Alignments S3-S7) using Bayesian Inference (BI) and Maximum-Likelihood (ML) methods. DNA sequences were aligned with Aliview v. 1.25 [START_REF] Larsson | AliView: A fast and lightweight alignment viewer and editor for large datasets[END_REF]. No gaps and stop codons were found in the alignments of the mitochondrial COI and Cytb proteincoding genes. In contrast, a few gaps were included in the alignments of the nuclear genes, but their positions were not ambiguous. The indels (insertion or deletion) shared by at least two taxa in the alignments of each nuclear gene were coded as additional characters ("1": insertion; "0": deletion) and analysed as a separate partition in the Bayesian analyses. The models of nucleotide evolution were selected under jModelTest V. 2. 1.7 (Posada, 2008) using the Akaike Information Criterion (AIC): GTR+G for COI dataset, GTR+I for Cytb dataset, and HKY model for TUFM and ZFYVE27 datasets. The BI analyses were conducted with MrBayes v. 3.2.5 [START_REF] Ronquist | MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space[END_REF] using five separate datasets: ( 1) COI (48 sequences; 657 bp), ( 2) Cytb (39 sequences; 1140 bp), (3) TUFM (642 bp and 10 indels; 8 sequences), ZFYVE27 (734 bp and 7 indel; 8 sequences) and ( 5) nuDNA (combining two nuclear genes; 1376 bp and 17 indels, 8 sequences) (Alignments S3-S7). The posterior probabilities (PP) were calculated using four independent Markov chains run for 10 7 Metropolis-coupled MCMC generations, with trees sampled every 1000 generations and a burn-in of 25%. The ML analyses of COI, Cytb, and nuDNA datasets (Alignments S3, S4, and S7) were conducted with W-IQ-TREE tool available online (http://iqtree.cibiv.univie.ac.at/) [START_REF] Hoang | UFBoot2: Improving the Ultrafast Bootstrap Approximation[END_REF][START_REF] Nguyen | IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies[END_REF][START_REF] Trifinopoulos | W-IQ-TREE: A fast online phylogenetic tool for maximum likelihood analysis[END_REF] with 1,000 ultrafast bootstrap replicates.

Pairwise genetic distances between divergent phylogenetic lineages or TCS clusters were calculated with PAUP* v. 4b10 [START_REF] Swofford | PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods)[END_REF] using the uncorrected p-distance.

Isolation by distance (IBD)

Geographic distances (km) between geographic haplogroups of S. kuhlii s.l. and S. heathii s.l. were generated using Geographic Distance Matrix Generator v. 1.2.3 (Ersts, 2020).

We tested for correlations between pairwise mtDNA distances (minimum p-distance) and geographic distances with the Mantel test [START_REF] Mantel | The Detection of Disease Clustering and a Generalized Regression Approach[END_REF] using the generalized linear model in PAST 3.07 [START_REF] Hammer | PAST: Paleontological statistics software package for education and data analysis[END_REF]. We also tested for correlations between pairwise genetic distance (FST/(1-FST) and geographic distance (ln km) for three geographic haplogroups of S. heathii identified in the COI network.

Historical demography

The dynamics of effective female population size within S. kuhlii s.l. and S. heathii s.l.

were estimated from the Bayesian skyline plot (BSP) method in BEAST v.2.5.2 [START_REF] Bouckaert | BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis[END_REF] using COI datasets (Alignment S1). As no calibration point (fossil record or biogeographic event) was available for Scotophilus, we used a mutation rate of 2×10 -8 per site per million years for the COI gene based on previous studies (i.e. [START_REF] Tu | Comparative phylogeography of bamboo bats of the genus Tylonycteris (Chiroptera, Vespertilionidae) in Southeast Asia[END_REF][START_REF] Mao | Pleistocene climatic cycling drives intra-specific diversification in the intermediate horseshoe bat (Rhinolophus affinis) in Southern China[END_REF]. The model of evolution of COI dataset was selected by jModelTest. We ran a MCMC chain of 20 million generations, sampled every 1000 generations and a burn-in of 10% with uncorrelated lognormal relaxed molecular clock. Tracer v.1.6 (available in the BEAST package) was used to assess the adequacy of chain mixing and MCMC chain convergence using ESS values of >200 and to visualize the Bayesian skyline plots.

Morphological analyses

Morphological comparison

Ninety-seven Scotophilus specimens listed in the Appendix 1 were included in our morphological analyses. All of the specimens examined were adults, as confirmed by the presence of fully ossified metacarpal-phalangeal joints.

External measurements were taken to the nearest 0.1 mm from alcohol-preserved specimens. These included: FA-length of forearm, Tib-tibia length, from the knee joint to the ankle. Craniodental measurements were taken to the nearest 0.01 mm using digital calipers under a stereomicroscope. These included: GSL-total length of skull, from the most anterior part of the upper incisors to the occiput; SL-greatest length of skull, the anterior rim of the alveolus of the 1 st upper incisor to the most posteriorly projecting point of the occipital region; CBL-condylobasal length, from the occipital condyles to the anterior of the alveolus of the 1 st upper incisor; CCL-condylo-canine length, from the exoccipital condyle to the most anterior part of the canine; ZB-greatest width of the skull across the zygomatic arches; C 1 C 1 -greatest width across the upper canines between their buccal borders; M 3 M 3 -greatest width across the crowns of the last upper molars; CM 3 -maxillary toothrow length, from the anterior of the upper canine to the posterior of the crown of the 3 rd upper molar; ML-length of mandible, from the anterior rim of the alveolus of the first lower incisor to the most posterior part of the condyle; and CM3-mandibular toothrow length, from the anterior of the lower canine to the posterior of the crown of the 3 rd lower molar.

In this study, we initially assigned our study specimens to different groups based on molecular data. Specimens lacking genetic information were classified into molecular groups according to their geographic origin (Figure 1). As specimens examined within these groups lacked sexual dimorphism in all external and craniodental measurements (T-test, p> 0.05), the phenetic affinity of the identified taxa with both sexes combined was inferred through univariate and multivariate analyses of their morphometrics. Principal Component Analysis (PCA) of study specimens was undertaken in PAST 3.07 [START_REF] Hammer | PAST: Paleontological statistics software package for education and data analysis[END_REF] using 10 logtransformed craniodental measurements. Equalities of mean values of morphometrics and PC scores among different taxa were tested using a one-way analysis of variance (ANOVA), followed by a post-hoc Tukey HSD multiple comparison test for unequal sample sizes (Tukey-Kramer) [START_REF] Zar | Biostatistical Analysis[END_REF].

RESULTS

Genetic analyses 3.1.1. Phylogeographic patterns of Asian Scotophilus inferred from mtDNA sequences

In the COI alignment (576 bp), 22 haplotypes were identified among 43 individuals of S. kuhlii s.l., and 18 haplotypes among 39 individuals of S. heathii s.l.. In the Cytb alignment (1,140 bp), 27 haplotypes were identified among 46 bats of S. kuhlii s.l. and seven among 12 bats of S. heathii s.l. (Figure 1; Appendix 1; Table S2). Haplotype (Hd) and nucleotide diversities (π) calculated from COI and Cytb alignments for the entire populations of each taxon were high i.e. >0.86 and >0.01, respectively (Table S4). In both species, most individuals examined, even those from the same locations, carried unique COI or Cytb haplotypes.

The COI and Cytb networks reconstructed for S. kuhlii s.l. and S. heathii s.l. have a "bush-like" shape without ancestral haplotype (Figure 1). However, mtDNA haplotypes derived from geographically distant populations of S. kuhlii s.l. were found to be intermixed or identical, whereas those of S. heathii s.l. displayed geographical patterns. For instance, the COI TCS network shows the separation of three clusters of haplotypes derived from individuals of S. heathii s.l. collected in: (1) Indian Subcontinent, including those collected from locations 1-3 in Pakistan and location 4 in India;

(2) southern Indochina, including those found from locations 16-21; and (3) northern Indochina, including samples found from locations 9-12. AMOVA analyses revealed that pairwise genetic distances (Fst) among these three clusters were between 0.11-0.433 and significant (Table S5). Likewise, in the Cytb TCS network, the private haplotypes found in three geographic areas (Yunnan (China), northern and southern Vietnam (or Indochina) were also separated (Figure 1).

Consistent with the observed divergences in phylogeographic patterns between the two species, Mantel tests (Figure S1A) showed a lack of statistically significant correlations between pairwise mtDNA and geographic distances in S. kuhlii s.l. (correlation R 2 <0.3) and the opposite in S. heathii s.l. (R 2 ≥0.66) (Figure S1A). Similarly, the genetic differentiation among three geographic haplotype clusters of the latter taxon obtained from COI network analysis largely resulted from IBD effects (Table S5; Figure S1B).

Phylogeny of the Asian Scotophilus inferred from mtDNA sequences

The phylogenetic trees reconstructed from the alignments of mtDNA genes (COI and 2a) and the other containing haplotypes from southern Vietnam (=lineage A; Figure 2a ) (PP/BP=1/97-100). The range of p-distances calculated from Cytb sequences between these three lineages was 3.7-4.2%, whereas those within populations in northern and southern

Vietnam were ≤1% (Table 2). the TUFM and ZFYVE27 sequence alignments, all Scotophilus bats examined shared a total of 8 and 3 indels respectively, whereas S. kuhlii and S. heathii were diagnosed by several indels (Figure 2c). Likewise, and inconsistent with mtDNA trees, the substructure of geographical populations in S. heathii were not recovered in our analyses of separated or combined nuDNA sequences (Figures 2c andS2). The genetic distances calculated from concatenation of the two nuclear introns (i.e. the p-distances) between S. kuhlii and S. heathii ranged between 1.4 and 1.6%, whereas the nuDNA sequences of selected bats of both species from different geographical units were identical (p-distances <0.1%) (Table 2).

Phylogeny of Indochinese

Historical demography

Our Bayesian skyline plot (BSP) analyses indicated that populations of both S. kuhlii and S. heathii have maintained their long-term stability since the Mid-Late Pleistocene (ca.

1.5-0.5 million years ago (Mya) and experienced rapid expansion since ca. 0.3 Mya (Late Pleistocene). However, since 0.1 Mya of the late Pleistocene, the total effective population size of S. kuhlii was always larger than S. heathii (Figure S4).

Morphological analyses

Asian Scotophilus are relatively large vespertilionids which share similar morphological characteristics: i.e. moderately-sized ears; tragus very long and narrow, tapering slightly towards tip and curving forwards; skulls thick and heavily-built, with just one pair of large, well-developed upper incisors; dental formula I1/3, C1/1, P1/2, M3/3 (Figures 3 and4) [START_REF] Corbet | The mammals of the Indomalayan Region: A systematic review[END_REF][START_REF] Dobson | On the genus Scotophilus, with description of a new genus and species allied thereto[END_REF][START_REF] Tate | Review of the vespertilionine bats, with special attention to genera and species of the Archbold collections[END_REF].

Both univariate and multivariate analyses of morphological characters revealed a large individual originally identified as S. kuhlii from Java (Indonesia) (HNHM 2869.22) as an extreme outlier, distantly related to other specimens of S. kuhlii sensu stricto (s.s.) but resembled our specimens of S. heathii s.s. (Figure 5; Table 3). As genetic data were not available and its external and craniodental characters matched those of S. ? solutatus s.s.

(sensu [START_REF] Tate | Review of the vespertilionine bats, with special attention to genera and species of the Archbold collections[END_REF][START_REF] Shamel | A collection of bats from Thailand (Siam)[END_REF], this Javanese specimen was treated as a separate taxon in subsequent analyses. Accordingly, S. kuhlii s.s. differs from S. heathii s.s. in its smaller body and skull size: i.e. FA: 45.7-53.1 vs 54.3-66.0 mm and GSL: 18.30-20.18 vs 20.85-25.20 mm (Table 3; Figure 5; Table S6). Aside from the presence of a well-developed occipital helmet in S. heathii s.s., the skull morphology of both species is similar (Figure 4; Table 3).

As shown in Figure 3, species identification of Asian yellow house bats based solely on pelage colour should be cautiously interpreted due to geographical variation. Although pelage colour is useful for distinguishing taxa living in sympatry, the reliability of this trait seems doubtful for comparing specimens from different countries, and it is entirely inaccurate for museum specimens due to fading of colour during preservation.

Within S. kuhlii s.s., specimens from mainland Asia (India, Myanmar, Indochina, Peninsular Malaysia) and the Philippines overlapped significantly in body and skull size (Figure 5; Table 3). Likewise, within S. heathii s.s., separation between specimens initially allocated to different mtDNA lineages was lacking, although local differentiations were recovered in phenotypes among bats of pairwise geographic populations, even at fine scales (Figure 5; Table 3). For instance, bats of S. heathii s.s. in southern Indochina appeared in three different morphological subgroups according to body and skull size i.e. with a FA of 54.3 to 66.0 mm or a GSL of 20.85 to 25.20 mm, respectively (ANOVA, p≤0.05; Table S7):

(1) smaller bats in south-central Vietnam (location No. 21 and adjacent area, Figure 1); (2) intermediate bats in north-eastern Cambodia (location No. 18, Figure 1); and (3) larger bats in the central highlands of Vietnam (location No. 19, Figure 1) (Figure 5). Similarly, in the PCA of craniodental characters (Figure 5), S. heathii s.s. bats in the Indian Subcontinent and southern Indochina were separated by PC2 which is significantly correlated with the greatest width across the upper canines (C 1 C 1 ) (Table S6).

Discussion

Cryptic diversity or inadequate taxonomy?

Early taxonomists differed considerably in how they delineated species boundaries between taxa allocated to S. kuhlii s.l. and S. heathii s.l. (sensu [START_REF] Corbet | The mammals of the Indomalayan Region: A systematic review[END_REF] in the Indomalayan Region, especially those found on the Sunda Islands (Table 1). According to our integrated analyses, S. kuhlii s.s. and S. heathii s.s. are genetically and morphologically distinct species. The former species is monotypic whereas the latter one is likely polytypic. In particular, FA -a standard measurement with low variation among bat researchers-appears to be reliable for differentiating the two species, as indicated by our PCAs on craniodental traits (Figures 5 andS5). Pairwise comparisons of FA data in different studies (Figure 6)

show that apart from some larger individuals in Java and nearby islands (Belitung and Borneo), all other bats assigned to S. kuhlii s.l. in the Indomalayan Region are morphologically comparable to our S. kuhlii s.s. (i.e. FA ≤53.1 mm). This includes S. collinus (sensu [START_REF] Kitchener | Morphological variation among populations of Scophilus kuhlii (sensu lato) Leach, 1821 (Chiroptera: Vespertilionidae) from the Greater and Lesser Sunda Islands, Indonesia[END_REF] which we regarded as a member of S. kuhlii in agreement with previous authors (e.g. [START_REF] Corbet | The mammals of the Indomalayan Region: A systematic review[END_REF][START_REF] Shamel | A collection of bats from Thailand (Siam)[END_REF][START_REF] Tate | Review of the vespertilionine bats, with special attention to genera and species of the Archbold collections[END_REF]. Regarding the larger specimens of S. kuhlii s.l. (i.e. FA ≥53.4 mm) from Java, Belitung and Borneo, some were identified as S. k. temminckii in past studies [START_REF] Kitchener | Morphological variation among populations of Scophilus kuhlii (sensu lato) Leach, 1821 (Chiroptera: Vespertilionidae) from the Greater and Lesser Sunda Islands, Indonesia[END_REF][START_REF] Siddiqi | Notes on the status of bats of the genus Scotophilus from Southern Asia with key to the recognized forms[END_REF]Sody, 1928Sody, , 1936)), whereas others were identified as S. k. collinus and S. k. solutatus (Sody, 1936;[START_REF] Tate | Review of the vespertilionine bats, with special attention to genera and species of the Archbold collections[END_REF]. These controversial specimens and those of S. heathii s.l. in mainland Asia and Java [START_REF] Shamel | A collection of bats from Thailand (Siam)[END_REF][START_REF] Siddiqi | Notes on the status of bats of the genus Scotophilus from Southern Asia with key to the recognized forms[END_REF][START_REF] Tate | Review of the vespertilionine bats, with special attention to genera and species of the Archbold collections[END_REF], S. ? celebensis in Sulawesi (Sody, 1928;[START_REF] Tate | Review of the vespertilionine bats, with special attention to genera and species of the Archbold collections[END_REF], and P. solutatus (=S. solutatus) in Java (Indonesia) [START_REF] Shamel | A collection of bats from Thailand (Siam)[END_REF] are comparable to our specimens of S. ? solutatus s.s. and S. heathii s.s. (Figure 6; Tables 1 and3). The new evidence from our study suggests that the current taxonomy of Asian Scotophilus spp. (i.e. [START_REF] Moratelli | Family Vespertilionidae (Vesper Bats)[END_REF][START_REF] Simmons | Order Chiroptera[END_REF] is inaccurate. [START_REF] Kitchener | Morphological variation among populations of Scophilus kuhlii (sensu lato) Leach, 1821 (Chiroptera: Vespertilionidae) from the Greater and Lesser Sunda Islands, Indonesia[END_REF] assigned yellow house bats with forearm lengths of ≤ 54 mm from the Sunda Islands to either S. collinus s.s. or S. kuhlii s.s. depending on body size i.e. the mean FA values for males / females of each taxon were 49.1 / 50.9 and 51.8 / 52.5, respectively. Their a priori species identifications were then checked by multiple regressions and discriminant function analyses (DFAs) of morphological characters. However, certain issues render the classification of [START_REF] Kitchener | Morphological variation among populations of Scophilus kuhlii (sensu lato) Leach, 1821 (Chiroptera: Vespertilionidae) from the Greater and Lesser Sunda Islands, Indonesia[END_REF] unconvincing. For instance, our pairwise comparison of FA values among the taxa recognised by different authors (Figure 6) reveals that their assumption of the upper limit in forearm length for S. kuhlii s.l. was unjustified and that their study materials may have contained misidentified individuals of a larger form (or S. heathii s.s / S. ? solutatus). Our study and previous taxonomic works (i.e. [START_REF] Hill | Bats from Thailand and Cambodia[END_REF][START_REF] Shamel | A collection of bats from Thailand (Siam)[END_REF][START_REF] Tate | Review of the vespertilionine bats, with special attention to genera and species of the Archbold collections[END_REF] have also confirmed the existence of individual variation in size and pelage among bats of the same Scotophilus species found in either sympatry or allopatry. As a consequence, the initial species identification of specimens by [START_REF] Kitchener | Morphological variation among populations of Scophilus kuhlii (sensu lato) Leach, 1821 (Chiroptera: Vespertilionidae) from the Greater and Lesser Sunda Islands, Indonesia[END_REF] was uncertain particularly when considering the extensive overlap in all morphometrics given for their recognised taxa with pooled geographic populations i.e.

the range of FA values for males / females of each taxon were 44.6-51.9 / 45.2-52.8 and 50.5-54.0 / 50.3-53.7, respectively. In addition to potential misidentification of specimens assigned a priori, the sample sizes of these taxa were heavily skewed in the two DFAs of [START_REF] Kitchener | Morphological variation among populations of Scophilus kuhlii (sensu lato) Leach, 1821 (Chiroptera: Vespertilionidae) from the Greater and Lesser Sunda Islands, Indonesia[END_REF] which set apart two putative taxa (i.e. the datasets for males and females of S. collinus / S. kuhlii were 82 / 10 and 124 / 8, respectively). As such imbalanced datasets tend to produce unsatisfactory classifiers, the classification of a priori taxa in these DFAs should be considered doubtful, even if statistically significant [START_REF] López | An insight into classification with imbalanced data: Empirical results and current trends on using data intrinsic characteristics[END_REF]. Consistent with this, separation between the two a priori taxa was not recovered in their DFA of skull characters of both sexes combined (as there is no sexually dimorphic effects on size) using another simulated dataset for S. collinus / S. kuhlii (i.e. 178 / 19 respectively). In particular, [START_REF] Hisheh | Implications of contrasting patterns of genetic variability in two vespertilionid bats from the Indonesian archipelago[END_REF] considered that S. kuhlii s.l. bats throughout the Lesser Sunda Islands can be treated as a panmictic unit. According to [START_REF] Kitchener | Morphological variation among populations of Scophilus kuhlii (sensu lato) Leach, 1821 (Chiroptera: Vespertilionidae) from the Greater and Lesser Sunda Islands, Indonesia[END_REF], the study area of [START_REF] Hisheh | Implications of contrasting patterns of genetic variability in two vespertilionid bats from the Indonesian archipelago[END_REF] encompasses two sister species which overlap in size, S. k. solutatus and S. collinus, i.e. FA values (in mm) of their males / females are 50.3-52.4 / 50.5-52.9 and 44.6-51.9 / 46.4-52.8, respectively. This evidence suggests that the classification of different cryptic species within S. kuhlii s.l. in the Sunda Islands by [START_REF] Kitchener | Morphological variation among populations of Scophilus kuhlii (sensu lato) Leach, 1821 (Chiroptera: Vespertilionidae) from the Greater and Lesser Sunda Islands, Indonesia[END_REF] reflected only artificial groups of a single species which resemble our S. kuhlii s.s.. The latter taxonomic inference is supported by the high overlap in FA values between different putative species determined by [START_REF] Kitchener | Morphological variation among populations of Scophilus kuhlii (sensu lato) Leach, 1821 (Chiroptera: Vespertilionidae) from the Greater and Lesser Sunda Islands, Indonesia[END_REF] and our S. kuhlii s.s. (Figure 6). Moreover, from a biogeographical viewpoint, geographical distance and/or marine straits between the Lesser Sunda Islands (=study areas of [START_REF] Hisheh | Implications of contrasting patterns of genetic variability in two vespertilionid bats from the Indonesian archipelago[END_REF])

and other parts in the Indomalayan Region (our study) (Figure 1) cannot be considered as a reliable barrier to long-range dispersal and associated gene flow within this species [START_REF] Hisheh | Implications of contrasting patterns of genetic variability in two vespertilionid bats from the Indonesian archipelago[END_REF][START_REF] Yu | Phylogeographic relationships of Scotophilus kuhlii between Hainan island and mainland China[END_REF] this study).

Based on COI distances of >2%, [START_REF] Francis | The role of DNA barcodes in understanding and conservation of mammal diversity in Southeast Asia[END_REF] suggested that two cryptic species may be recognized in S. heathii, one from northern Indochina (haplotype C-h7 in Figure 2a) and the other from southern Indochina (haplotypes A-h11, h14, h15, and h17 in Figure 2a). Our phylogeographic analyses of COI sequences from a wider taxonomic sampling (including specimens from Cambodia and Vietnam) do not support this view. For instance, our haplotypes from Indochina fall into three lineages (i.e. A, B and C) (Figures 2a andS2). However, the pairwise p-distances calculated from COI sequences between these lineages ranged between 1.1-4.0% and overlapped with their intraspecific variation (i.e.

lineages A: 0-1.6%) (Table 2). In particular, the interspecific divergences between our Indochinese lineages (A, B and C) were not supported by either nuDNA or morphological analyses (Figures 2c, S2 and 5; Table 2). This is consistent with the results of [START_REF] Trujillo | Molecular phylogenetics of the bat genus Scotophilus (Chiroptera: Vespertilionidae): Perspectives from paternally and maternally inherited genomes[END_REF], in which S. heathii bats from Yunnan (southern China), northern Vietnam and southern Vietnam have identical zfy gene sequences, whereas they belong to three divergent Cytb haplogroups (p-distances: 3.7-4.2%) (Figures 2b andS2; Table 2). Indeed, the absence of structured signals in nuclear datasets may be a consequence of low mutation rates or incomplete lineage sorting of these loci (i.e. Hassanin et al. 2013). However, the mito-nuclear discordance of S. heathii may be best explained by female philopatry and male biased dispersers [START_REF] Arnold | Female natal philopatry and gene flow between divergent clades of Pallid bats (Antrozous pallidus)[END_REF][START_REF] Rivers | Genetic population structure of Natterer's bats explained by mating at swarming sites and philopatry[END_REF][START_REF] Tu | Comparative phylogeography of bamboo bats of the genus Tylonycteris (Chiroptera, Vespertilionidae) in Southeast Asia[END_REF].

As such, the hypothesis of potential cryptic diversity within Indochinese S. heathii s.l. can be ruled out. Similarly, the relatively higher genetic divergence of COI sequences among two morphologically overlapping populations of S. heathii s.l. in spatially distant subregions (Indochina lineages A, B, and C and the Indian Subcontinent lineage D (5.1-7.6% pdistances) (Figures 1-3 and S2; Table 2)) might also be attributable to their potential sex-biased gene flow followed by IBD effects (Figure S1). Thus, while further analyses of samples from the intervening zones [START_REF] Nabhan | The impact of taxon sampling on phylogenetic inference: A review of two decades of controversy[END_REF][START_REF] Zwickl | Increased taxon sampling greatly reduces phylogenetic error[END_REF] and/or nuclear markers are needed, the possibility that allopatric speciation events have occurred without morphological changes in the above populations of S. heathii s.s. [START_REF] Bickford | Cryptic species as a window on diversity and conservation[END_REF][START_REF] Tu | Comparative phylogeography of bamboo bats of the genus Tylonycteris (Chiroptera, Vespertilionidae) in Southeast Asia[END_REF][START_REF] Tu | Four species in one: Multigene analyses reveal phylogenetic patterns within Hardwicke's woolly bat, Kerivoula hardwickii-complex (Chiroptera, Vespertilionidae) in Asia. Hystrix[END_REF] would seem very unlikely.

All larger forms of yellow house bats on Java and nearby islands (i.e. FA values of ≥53.4 mm and GSL ≥20.5 mm) were previously referred to as S. kuhlii [START_REF] Corbet | The mammals of the Indomalayan Region: A systematic review[END_REF][START_REF] Simmons | Order Chiroptera[END_REF]. However, their taxonomic identity was an issue of debate for many years (Figure 6; Table 1). Having examined one of these controversial specimens from Java (HNHM 2869.22), our results suggest that it resembles S. heathii s.s. more than S. kuhlii s.s.

(Figures 456; Table 3). This specimen was collected by the Novara Expedition (1857-1859)

and its identity was determined by the British zoologist, Oldfield Thomas (1858Thomas ( -1929)). It should be noted that before [START_REF] Hill | Bats from Thailand and Cambodia[END_REF] confirmed that S. kuhlii should replace S. temminckii as the correct name for smaller Asian yellow house bats, S. kuhlii was used for larger bats by several taxonomists (Allen, 1906;[START_REF] Osgood | Mammals of the Kelley-Roosevelts and Delacour Asiatic expedition[END_REF][START_REF] Shamel | A collection of bats from Thailand (Siam)[END_REF]Thomas, 1897) instead of S. heathii which other authors used [START_REF] Siddiqi | Notes on the status of bats of the genus Scotophilus from Southern Asia with key to the recognized forms[END_REF][START_REF] Tate | Review of the vespertilionine bats, with special attention to genera and species of the Archbold collections[END_REF] (Table 1). This suggests that the previous allocation of our examined specimen (and S. ? solutatus s.s.) and the larger Scotophilus from Java and nearby islands (i.e. Borneo) as S.

kuhlii s.l. (sensu [START_REF] Corbet | The mammals of the Indomalayan Region: A systematic review[END_REF][START_REF] Simmons | Order Chiroptera[END_REF][START_REF] Kitchener | Morphological variation among populations of Scophilus kuhlii (sensu lato) Leach, 1821 (Chiroptera: Vespertilionidae) from the Greater and Lesser Sunda Islands, Indonesia[END_REF][START_REF] Tate | Review of the vespertilionine bats, with special attention to genera and species of the Archbold collections[END_REF] was misguided. In addition, while research on Asian bats has intensified in recent years, most survey effort has focused on habitats such as tropical forests which support high bat diversity [START_REF] Kingston | Research priorities for bat conservation in Southeast Asia: A consensus approach[END_REF], whereas bats that live commensally with humans are comparatively neglected [START_REF] Jung | Urbanisation and its effects on bats-A global metaanalysis[END_REF]. Scotophilus spp. are one of the most common bats in urban-rural habitats but roost in high shelters (e.g. roofs of houses) and forage in open spaces above the effective range of ground-based live-traps (i.e. mist-nets and harp traps) [START_REF] Bates | Bats of the Indian Subcontinent[END_REF][START_REF] Francis | A field guide to the mammals of South-East Asia[END_REF][START_REF] Hisheh | Implications of contrasting patterns of genetic variability in two vespertilionid bats from the Indonesian archipelago[END_REF]. As such, they are likely under-surveyed in many regions of Southeast Asia (Figure 1). Consequently, the disjunct distribution of large yellow house bats between mainland Asia (or S. heathii s.s.) and Sulawesi (S. celebensis s.s.)

(Figure 1) determined by previous authors (e.g. [START_REF] Corbet | The mammals of the Indomalayan Region: A systematic review[END_REF][START_REF] Simmons | Order Chiroptera[END_REF][START_REF] Tate | Review of the vespertilionine bats, with special attention to genera and species of the Archbold collections[END_REF] may be due to erroneous naming of voucher specimens and gaps in survey coverage.

Alternatively, the separation of S. celebensis from S. heathii by [START_REF] Simmons | Order Chiroptera[END_REF] could be regarded as unsubstantiated. Thus, until additional analyses further elucidate their phylogenetic relationships, all large yellow house bats (i.e. FA ≥53.4 mm and GSL ≥20.5 mm (Figure 6; Tables 1 and3) occurring in mainland Asia (S. heathii s.s.), Java and nearby islands (S. ? solutatus), and Sulawesi (S. celebensis s.s.) should be regarded as representatives of a single species: S. heathii.

Comparative phylogeography of Asian Scotophilus spp.

The absence of star-like TCS haplotype networks (Figure 1) and results of BSP analyses (Figure S4) in our study indicate that both S. kuhlii and S. heathii have maintained a constant or expanding effective population size through time since the Mid-Pleistocene. The distribution and lack of bottlenecks in the evolutionary history of Asian yellow house bats in the Indomalayan Region thus differs strikingly from other co-distributed bat species i.e.

bamboo bats (Tylonycteris spp.) [START_REF] Tu | Comparative phylogeography of bamboo bats of the genus Tylonycteris (Chiroptera, Vespertilionidae) in Southeast Asia[END_REF], woolly bats (Kerivoula spp.) [START_REF] Khan | Systematics of Malaysian woolly bats (Vespertilionidae: Kerivoula) inferred from mitochondrial, nuclear, karyotypic, and morphological data[END_REF][START_REF] Tu | Four species in one: Multigene analyses reveal phylogenetic patterns within Hardwicke's woolly bat, Kerivoula hardwickii-complex (Chiroptera, Vespertilionidae) in Asia. Hystrix[END_REF], horseshoe bats (Rhinolophus spp.) [START_REF] Mao | Pleistocene climatic cycling drives intra-specific diversification in the intermediate horseshoe bat (Rhinolophus affinis) in Southern China[END_REF]. This may be attributable to eco-ethological differences [START_REF] Avise | Phylogeography: The history and formation of species[END_REF][START_REF] Hassanin | Comparative phylogeography of African fruit bats (Chiroptera, Pteropodidae) provide new insights into the outbreak of Ebola virus disease in West Africa, 2014-2016[END_REF][START_REF] Moussy | Migration and dispersal patterns of bats and their influence on genetic structure: Bat movements and genetic structure[END_REF]. For example, Asian yellow house bats are strong dispersers and aerial-hawking, open space foragers [START_REF] Bates | Bats of the Indian Subcontinent[END_REF][START_REF] Francis | A field guide to the mammals of South-East Asia[END_REF][START_REF] Norberg | Ecological morphology and flight in bats (Mammalia; Chiroptera): Wing adaptations, flight performance, foraging strategy and echolocation[END_REF], whereas

Tylonycteris, Kerivoula and Rhinolophus spp. have a much weaker dispersal ability because they are mostly forest-dwelling taxa [START_REF] Khan | Systematics of Malaysian woolly bats (Vespertilionidae: Kerivoula) inferred from mitochondrial, nuclear, karyotypic, and morphological data[END_REF][START_REF] Mao | Pleistocene climatic cycling drives intra-specific diversification in the intermediate horseshoe bat (Rhinolophus affinis) in Southern China[END_REF][START_REF] Tu | Comparative phylogeography of bamboo bats of the genus Tylonycteris (Chiroptera, Vespertilionidae) in Southeast Asia[END_REF][START_REF] Aldhebiani | Species concept and speciation[END_REF]. Thus, unlike forest-dependent species, the dispersal and associated gene flow among geographic populations of Asian Scotophilus might be less restricted by physical and ecological barriers [START_REF] Hisheh | Implications of contrasting patterns of genetic variability in two vespertilionid bats from the Indonesian archipelago[END_REF][START_REF] Yu | Phylogeographic relationships of Scotophilus kuhlii between Hainan island and mainland China[END_REF]. In addition, while the population structure and dynamics of species with low dispersal capacities were strongly influenced by the past compression and expansion of forests during glacial and interglacial periods in the Pleistocene [START_REF] Khan | Systematics of Malaysian woolly bats (Vespertilionidae: Kerivoula) inferred from mitochondrial, nuclear, karyotypic, and morphological data[END_REF][START_REF] Mao | Pleistocene climatic cycling drives intra-specific diversification in the intermediate horseshoe bat (Rhinolophus affinis) in Southern China[END_REF][START_REF] Tu | Comparative phylogeography of bamboo bats of the genus Tylonycteris (Chiroptera, Vespertilionidae) in Southeast Asia[END_REF][START_REF] Aldhebiani | Species concept and speciation[END_REF] and by current patterns of deforestation [START_REF] Kingston | Research priorities for bat conservation in Southeast Asia: A consensus approach[END_REF], Asian Scotophilus spp. may have been less affected by such changes.

Our comparative phylogeographic analyses show that geographically distant populations of S. kuhlii in the Indomalayan Region possess very low genetic and morphological variation, whereas those of S. heathii in mainland Asia display divergent mtDNA sequences and phenotypes (see section 4.1 for more detail). As discussed above, the incongruences in phylogeographic patterns of mtDNA genetic diversity between the two sympatric species may be attributable to sex-biased gene flows [START_REF] Avise | Phylogeography: The history and formation of species[END_REF][START_REF] Slatkin | Gene flow and the geographic structure of natural populations[END_REF].

More specifically, the phylogenetic signals in our mtDNA and nuDNA datasets for S. heathii may be consistent with female philopatry and male-biased dispersal whereas those for S.

kuhlii do not exhibit sex-biased dispersal [START_REF] Arnold | Female natal philopatry and gene flow between divergent clades of Pallid bats (Antrozous pallidus)[END_REF][START_REF] Rivers | Genetic population structure of Natterer's bats explained by mating at swarming sites and philopatry[END_REF][START_REF] Tu | Comparative phylogeography of bamboo bats of the genus Tylonycteris (Chiroptera, Vespertilionidae) in Southeast Asia[END_REF]. As both species may have maintained gene flows among their populations, the geographic variation observed in external and craniodental traits might reflect their phenotypic plasticity to adapt to selective forces imposed by environmental variability, as well as interspecific competition for common resources in areas of sympatry [START_REF] Chevin | Adaptation, plasticity, and extinction in a changing environment: Towards a predictive theory[END_REF][START_REF] Ghalambor | Adaptive versus non-adaptive phenotypic plasticity and the potential for contemporary adaptation in new environments[END_REF][START_REF] Lande | Evolution of phenotypic plasticity and environmental tolerance of a labile quantitative character in a fluctuating environment[END_REF][START_REF] Spaeth | Morphological convergence and coexistence in three sympatric North American species of Microtus (Rodentia: Arvicolinae)[END_REF][START_REF] Tienderen | Generalists, specialists, and the evolution of phenotypic plasticity in sympatric populations of distinct Species[END_REF][START_REF] Zamudio | Phenotypes in phylogeography: Species' traits, environmental variation, and vertebrate diversification[END_REF].

The low morphological variation of S. kuhlii specimens throughout the Indomalayan Region suggests that the species has maintained a generalist phenotype suited to a variety of environments. By contrast, the morphological variability of S. heathii indicates that its geographic populations, even those at small scales, may have evolved plastic phenotypes that suit the particular habitats they inhabit [START_REF] Chevin | Adaptation, plasticity, and extinction in a changing environment: Towards a predictive theory[END_REF][START_REF] Lande | Evolution of phenotypic plasticity and environmental tolerance of a labile quantitative character in a fluctuating environment[END_REF][START_REF] Spaeth | Morphological convergence and coexistence in three sympatric North American species of Microtus (Rodentia: Arvicolinae)[END_REF][START_REF] Tienderen | Generalists, specialists, and the evolution of phenotypic plasticity in sympatric populations of distinct Species[END_REF][START_REF] Zamudio | Phenotypes in phylogeography: Species' traits, environmental variation, and vertebrate diversification[END_REF]. As such, the generalist populations of S.kuhlii may have experienced fewer adverse effects from climate and associated habitat changes than S.

heathii. They may also have had more advantages than S. heathii when colonizing and adapting to new habitats [START_REF] Bonte | Costs of dispersal[END_REF][START_REF] Ghalambor | Adaptive versus non-adaptive phenotypic plasticity and the potential for contemporary adaptation in new environments[END_REF][START_REF] Hollander | Dispersal and phenotypic plasticity[END_REF][START_REF] Kelly | Phenotypic plasticity: Molecular mechanisms and adaptive significance[END_REF][START_REF] Lande | Evolution of phenotypic plasticity and environmental tolerance of a labile quantitative character in a fluctuating environment[END_REF][START_REF] Moussy | Migration and dispersal patterns of bats and their influence on genetic structure: Bat movements and genetic structure[END_REF]. These inferences suggest that S. heathii bats may be more philopatric to their native areas compared to S. kuhlii. If so, this would explain how S. kuhlii can occupy a wider geographic range in the Indomalayan Region relative to S. heathii (Figure 1), even though S.

heathii would be expected to have greater dispersal ability based on its wing morphology.

It should be noted that bats of S. kuhlii and S. heathii found either in sympatry or allopatry do not overlap in most morphological traits (i.e. FA; Figures 3456). As discussed above, it is very likely that S. kuhlii and S. heathii have co-existed for a long time. Both species are also known to share similar eco-ethological preferences and feeding guilds [START_REF] Bates | Bats of the Indian Subcontinent[END_REF][START_REF] Francis | A field guide to the mammals of South-East Asia[END_REF][START_REF] Norberg | Ecological morphology and flight in bats (Mammalia; Chiroptera): Wing adaptations, flight performance, foraging strategy and echolocation[END_REF]. Because prey density usually decreases from cluttered to open habitats, strong interspecific competition likely occurred in areas of sympatry during their evolutionary history [START_REF] Grether | The evolutionary consequences of interspecific aggression: Aggression between species[END_REF][START_REF] Müller | Aggregative response in bats: Prey abundance versus habitat[END_REF][START_REF] Roeleke | How bats escape the competitive exclusion principle-Seasonal shift from intraspecific to interspecific competition drives space use in a bat ensemble[END_REF]. To reduce niche overlap, co-existing related species typically evolve mechanisms for resource partitioning [START_REF] Chevin | Adaptation, plasticity, and extinction in a changing environment: Towards a predictive theory[END_REF][START_REF] Lande | Evolution of phenotypic plasticity and environmental tolerance of a labile quantitative character in a fluctuating environment[END_REF][START_REF] Tienderen | Generalists, specialists, and the evolution of phenotypic plasticity in sympatric populations of distinct Species[END_REF] that result in detectable differences in morphology or echolocation call parameters [START_REF] Kingston | Acoustic divergence in two cryptic Hipposideros species: A role for social selection[END_REF][START_REF] Zhang | Morphology, echolocation and foraging behaviour in two sympatric sibling species of bat (Tylonycteris pachypus and Tylonycteris robustula) (Chiroptera: Vespertilionidae)[END_REF]. This would be consistent with the morphological differences between the two species. a -Sody, 1928;b -Tate, 1942;c -Shamel, 1942;d -Siddiqi, 1960;[START_REF] Corbet | The mammals of the Indomalayan Region: A systematic review[END_REF]f -Kitchener et al. (1997); g -this study; and h -desired ranges for S. kuhiii and S. heathii.

  ; Appendix 1). Of which, 97 voucher specimens are held in the Institute of Ecology and Biological Resources (IEBR, Hanoi, Vietnam), the Hungarian Natural History Museum (HNHM, Budapest, Hungary), the Centre for Biodiversity Conservation (CBC, Royal University of Phnom Penh, Cambodia), the University of Tokyo Hokkaido Forest (UTHF, Furano, Hokkaido, Japan), and the University of the Philippines Los Banos Museum of Natural History (UPLB-MNH, Laguna, Philippines) (See Appendix 1). Tissue samples were collected from the chest muscles of voucher specimens or from the patagium (biopsy punches; 3 mm diameter) of released individuals and preserved in 95% ethanol and stored at -20°C. We generated 38 Cytb (complete cytochrome b; 1,140 bp) and 43 COI (fragment of cytochrome c oxidase subunit I; 705-1554 bp) sequences from 49 examined individuals encountered during field surveys undertaken by the authors between 2008 and 2019 (30 specimens were sequenced for both mitochondrial genes) (Appendix 1). These newly generated sequences were compared to the 20 Cytb and 41 COI sequences available in GenBank for Asian Scotophilus spp. collected from other localities in the Indomalayan Region by other authors (Figure 1; Table

  Scotophilus based on nuDNA sequence analysesBayesian trees reconstructed from three nuDNA datasets i.e. TUFM, ZFYVE27 and concatenation of the two nuDNA introns from selected individuals of S. kuhlii and S. heathii from the northern and southern Indochinese geographical units, as revealed by analyses of mtDNA sequences, are presented in Figures2c, S2 and S3, respectively. Consistent with mtDNA trees, the nuDNA trees supported the monophyly of Scotophilus and the two nominal species, S. kuhlii and S. heathii, with maximum robustness (PP/BP=1). More specifically, in

FiguresFigure 1 .-Figure 2 .

 12 Figures

Figure 3 .Figure 4 .

 34 Figure 3. Live and wet specimens (not to scale) of Scotophilus heathii and S. kuhlii collected in sympatry in two different regions of Vietnam. Northern Vietnam (Location 10): a -S. heathii / c -S. kuhlii. South-Central Vietnam (Location 21): b -S. heathii / d -S. kuhlii

Figure 5 .

 5 Figure 5. Scatter plots from morphological analyses of Asian Scotophilus spp. a and b: Variation in external (FA vs. Tib) and skull traits (GSL vs. ZB) among specimens of Scotophilus spp., respectively. Boxplots (with an interquartile range) to find outliers in the datasets were embedded; c: Plot of PC 1 against PC 2 from PCA on log-transformed craniodental measurements. The legends of symbols follow Figure 1. Bats of S. heathii found in three spatially isolated locations(18, 19, and 21) in Southern Indochina (Figure1) appear as three relatively separated subpopulations.

Figure 6 .

 6 Figure 6. Pairwise comparison of FA ranges (min-max) for Asian Scotophilus spp. recognized in present and previous studies.

  Figure 2. Values in diagonal in bold show the maximum intraspecific distances within each taxon calculated from the respective datasets; NA -not available.

  Figure S1: Mantel tests for isolation by distance effects on pairwise genetic divergences among geographic populations of studied Scotophilus spp.

Figure S4 .

 S4 Figure S4. Bayesian skyline plot representing historical demographic trends in S. kuhlii (above) and S. heathii (below). The X-axis presents time as years before present. The Y-axis represents the effective female population size (Ne). Mean estimated Ne represents as the solid line, whereas solid intervals refer the 95% highest probability density.

Figure S5 .

 S5 Figure S5. Correlation between mean values of PC1's scores obtained from PCA of skull characters and FA values of Asian Scotophilus spp.

  Cytb) are depicted in Figures2 and S2. The genus Scotophilus and the two species S. kuhlii s.l. and S. heathii s.l. were monophyletic in all phylogenetic analyses with maximal support (PP/BP=1/100). Interspecific distances (uncorrected p-distance) calculated from COI and Cytb datasets between these nominal species were ≥13.9% and ≥14.5% respectively (Table2). S. heathii s.l., our COI trees (Figures2a and S2) recovered four lineages, A, B, C, and D. Haplotypes from southern Indochina appeared in lineages A (comprising those collected from locationsNo. 16, 17, 19, 20 and 21 in Figure1) and B (those collected from location No. 18 in Figure1), whereas haplotypes from northern Indochina and the Indian

	Within Subcontinental (India and Pakistan) formed two sister lineages, C and D respectively. The
	range of pairwise p-distances estimated from COI sequences between lineages A and B were
	1.1-2.3%, 2.6-4.0% between C and A+B, 5.1-7.1% between C and D, and 5.2-7.6% between
	A+B and D. The maximum intraspecific variation within these lineages (i.e. lineage A) was
	≤1.6% (Table 2). Likewise, in our Cytb tree (Figures 2b and S2), a single individual from
	Yunnan (China) occupied a basal position to a clade (PP/BP=1/93) united by two well-
	supported sister lineages, one containing haplotypes in northern Vietnam (=lineage C; Figure
	Within S. kuhlii s.l., all COI and Cytb trees included bats from different geographic
	areas or subunits of the Indomalayan Region i.e. (1) India and Myanmar, (2) Indochina
	(Cambodia, Laos, Vietnam) and southern China, (3) Peninsular Malaysia, and (4) the

Philippines intertwined with a maximum intraspecific genetic divergence (p-distance) calculated from COI and Cytb sequences of ≤2.3% (Figures

2a-b and S2

; Table

2

).

Table 2 : Range (min-max) of uncorrected p-distances (%) between Asian Scotophilus spp. and selected outgroups, based on COI (Cytb) (below the diagonal) and nuDNA (above the diagonal) datasets.

 2

	Taxon	1	2	3	A	B	4	C	D
	1. M. cyclotis		9.5	11.3-11.7	11.3-11.3	NA		11.6-11.6	NA
	2. E. pachyomus	20.1 (19.6)		6.8-7.0	6.8-6.9	NA		6.8-6.9	NA
	3. S. kuhlii	21.1 -22.7 (19.7-20.3)	20.9-21.8 (21.1-21.7)	0.0 2.3(2.2)	1.4-1.6	NA		1.5-1.7	NA

Table 3 : External and craniodental measurements (in mm) of Asian Scotophilus spp

 3 . Values are given as mean ± SD, n; min-max. 1105Acronyms and definitions for measurements are given in the Materials and Methods section. 1106

	S. kuhlii s.l.
	Character

Table S7 . Pairwise comparisons (ANOVA-tests) of morphometrics among geographical populations of S. heathii s.l. in Indochina.

 S7 Acronyms and definitions for measurements are given in the Materials and Methods.

	Character	North VN		Highland Central VN	South Central VN
	Highland Central VN	South Central	Cambodia	South Central	Cambodia	Cambodia
	(Location: 18)	(Location: 21 and nearby)	(Location: 19)	(Location: 21 and nearby)	(Location: 19)	(Location: 19)

* -This specimen resembles S. ?. solutatus[START_REF] Shamel | A collection of bats from Thailand (Siam)[END_REF][START_REF] Tate | Review of the vespertilionine bats, with special attention to genera and species of the Archbold collections[END_REF]

Acknowledgements

We would like to thank numerous agencies and individuals for their research permits and assistance during our study: In Vietnam, the Vietnam Administration of Forestry (MONRE), Nguyen Van Sinh, Le Xuan Canh and Nguyen Quang Truong of the IEBR (Hanoi); in Cambodia, the Centre for Biodiversity Conservation at the Royal University of Phnom Penh and Fauna & Flora International; in Myanmar, the Ministry of Livestock, Fisheries and Rural Development; in Philippines, Juan Carlos T. Gonzalez and Edison A. Cosico of UPLB MNH.

We are also grateful to Victor van Cakenberghe (UA, Belgium), Lincoln H. Schmitt (UWA, Australia), and Ibnu Maryanto (LIPI, Indonesia) for their kind help. We also thank the three anonymous reviewers for their helpful comments on the manuscript. This research was supported by the "ATM Barcode" funded by the MNHN, the network "Bibliothèque du Vivant" funded by the CNRS, the MNHN, the INRA, the CEA (Genoscope) to A.H and V.T.T; the Hungarian Scientific Research Fund -OTKA K112440, the National Research, Development and Innovation Fund of Hungary -NKFIH KH130360, and the SYNTHESYS Project, financed by the European Community Research Infrastructure Action under the FP7 "Capacities" Program to TG and GC; the NTP-NFTÖ-17 project funded by the Hungarian Ministry of Human Capacities to TG; a grant-in-aid on Research Program on Emerging and Re-emerging Infectious Diseases, Japan Agency for Medical Research and Development (AMED) (JP15fk0108005, JP16fk0108117, JP17fk0108217, JP18fk0108017, JP19fk0108097, and JP20fk0108097), a grant-in-aid from the Japan Society for the Promotion of Science 24405045 to S.A, K.K., and D.F.; the KAKENHI (18H04816, 18H02492, 18K19359, 18KK0207) and JRPs-LEAD with DFG to D.K.; the project TN18/T07 funded by the Vietnam Academy of Science and Technology (VAST) to T.A.T and N.T.S.; and the Rufford Foundation (UK).

Data Availability Statement

The authors confirm that the data supporting the findings of this study are available within the article and/or its supplementary materials.

Tables

 Table 1:Synopsis of taxonomic studies on Asian Scotophilus between 1940-2000 ( †) .

Author

Reference materials Taxonomic treatment [1] India, Hainan, Taiwan (Formosa), Malacca, Java, Bali, Luzon S. kuhlii (forearm length (FA, in mm): 41, immature holotype) S. temminckii (=fulvus) (FA £ 51) includes consobrinus, castaneus, wroughtoni, panayensis, collinus, and gairdneri as similar sized races/ synonyms and a larger sized Javanese one, solutatus (FA: 55-55). India: Kashmir, Myanmar (Burma), Hainan, Sri Lanka (Ceylon) S. heathii (FA ³ 54) with belangeri (=luteus=flaveolus), insularis, and celebensis as races/synonyms [2] Java, Singapore, Thailand, French Indochina

Pachyotis temminckii (FA: 48.2-52.5) includes temminckii=castaneus, consobrinus, wroughtoni, panayensis, collinus, and gairdneri as synonyms/ races West Java, Depok, Pelabuhan P. solutatus (FA: 53.8-58.9) ( †) Prior to the mid-20 th century, Asian Scotophilus included 17 taxa (species and subspecies) described as new to science (detailed in Figure 1; Table S1). Authors: 1 -Tate, 1942;2 -Shamel, 1942;3 -Sanborn, 1952;4 -Siddiqui, 1960;5 -Hill & Thonglongya, 1972;6 -Corbet & Hill, 1992;7 -Kitchener et al., 1997 Appendix 1. Asian Scotophilus specimens were collected and/or examined directly by the authors in this study.

See Material and Methods for acronyms of museums and genetic markers. ( †) -tissue samples only. ( ‡) -Localities for specimens included in Alignment S5. Alignment of TuFM sequences included in the phylogenetic analyses.

Alignment S6. Alignment of ZFYVE27 sequences included in the phylogenetic analyses.

Alignment S7. Alignment of nuDNA sequences (combining TuFM and ZFYVE27 genes) included in the phylogenetic analyses. Table S1. List of species and subspecies of the Asian Scotophilus described as new to science prior to the mid-20 th century.

List of Tables

Table S2. Genetic sequences of Asian Scotophilus spp. and outgroups in GenBank included in molecular analyses in the present study.

Table S3. Primers used to amplify and sequence DNA in the present study.

Table S4. mtDNA divergence within Asian Scotophilus spp.

Table S5. COI genetic variation in three clusters of geographic populations of S. heathii s.l.. Table S6. Factor loading for two first PCs obtained from PCA of cranial characters.

Table S7. Pairwise comparisons (ANOVA-tests) of morphometrics among geographical populations of S. heathii s.l. in Indochina. Table S2. Genetic sequences of Asian Scotophilus spp. and outgroups in GenBank included in molecular analyses in the present study.

List of Figures

( †) -Locations of specimens included in molecular analyses are indicated by numbers (after colon) as representing in Figure 1. Country codes include: IN -India, KH -Cambodia; LA -Laos; and VN -Vietnam. ( ‡) -Numbers (in parentheses) after Genbank accession numbers for Cytb and COI sequences of studied Scotophilus specimens are respective haplotypes representing in Figures 1 and2. Reference ( §) : 1 -Francis et al., 2010;2 -Ikram et al., unpublished;3 -Kruskop et al., unpublished;4 -Rahman & Choudhury, unpublished;5 -Srinivasulu et al., unpublished;6 -Tan et al., 2020;7 -Trujillo et al., 2009;8 -Tu et al., 2014;9 -Tu et al., 2017;and 10 -Tu et al., 2018.


Brice Chardin

Emmanuel Coquery

Marie Pailloux

Jean-Marc Petit

RQL: An SQL-like Query Language for Discovering Meaningful Rules

The Rule Query Language (RQL) is an SQL-like pattern mining language that extends and generalizes functional dependencies to new and unexpected rules. It brings to the data analysts' desktop a convenient tool to discover logical implications between attributes of the database. Such implications may reveal data quality problems or surprising correlations between attributes over some part of the database. The computation of RQL queries is based on a query rewriting technique that pushes as much processing as possible to the underlying DBMS. This contribution is an attempt to bridge the gap between pattern mining and databases and facilitates the use of data mining techniques by SQL-aware analysts and students.

I. INTRODUCTION

Pattern mining can be seen as an automated part of data exploration. For instance, functional dependencies or conditional functional dependencies are definitely useful to understand the data and to identify data quality problems [START_REF] Bohannon | Conditional functional dependencies for data cleaning[END_REF]. However, pattern mining techniques are rarely usable directly by data analysts. Most of the time, they have to perform some data preprocessing between different systems and formats. The pattern mining codes themselves often require to be compiled from some specific programming languages. All these steps are out of reach of many data analysts, rending round-trip engineering into a nightmare. Automated rule generation can also flood the analyst with huge amounts of patterns, and make it difficult to extract useful information. Other techniques have to be provided to interact with the data and give useful feedback to the analysts.

Demo contribution

To improve pattern mining usability for data exploration, we introduce a Rule Query Language (RQL) that allows SQL-aware analysts to use pattern mining techniques with an interactive, user-friendly interface. In this demonstration, we show the usability of this web interface from the point of view of a data analyst. We focus on the expressive power of RQL through various examples, showing how easy it is to devise new and surprising rules with a very simple language derived from SQL. We also introduce how the data analysts can interact with the system through RQL queries and counterexamples taken from the database. During the demo, participants will be invited to formulate their own queries on predefined databases to discover attribute relationships through generated rules and counterexamples.

Figure 1 gives a preview of the web interface for RQL, made available 1 for research and educational purposes. This interface provides a unified access to the user's data and pattern mining techniques using declarative languages: SQL and RQL.

From previous works [START_REF] Agier | On Armstrong-compliant logical query languages[END_REF], [START_REF] Agier | Unifying framework for rule semantics: Application to gene expression data[END_REF], [START_REF] Chardin | Query Rewriting for Rule Mining in Databases[END_REF], RQL is compliant with Armstrong's axioms, i.e. the language generalizes functional dependencies to a new class of dependencies based on logical implications (if ... then statements). To the best of our knowledge, this class of dependencies has not been studied before. We have proven that these dependencies can be efficiently computed from a database using a two step technique. First, a non trivial SQL subquery is generated to compute a base of the associated closure system -a base is also called a context in formal concept analysis terminology [START_REF] Ganter | Formal Concept Analysis[END_REF]. Then, a state of the art algorithm [START_REF] Murakami | Efficient algorithms for dualizing large-scale hypergraphs[END_REF] is used to generate a canonical cover of rules from this base. This approach allows RQL to benefit from DBMSs' query optimization to access the data, and keep the data where they are.

Figure 2 gives an overview of this architecture with respect to RQL query processing. As for SQL queries, the application simply forwards them to the underlying DBMS, which makes the transition between SQL and RQL transparent to the user. The ultimate goal of this work is to integrate pattern mining techniques into core DBMS technologies [START_REF] Netz | Integration of data mining with database technology[END_REF].

Related works Defining specific languages for pattern mining is a long standing goal [START_REF] Blockeel | A practical comparative study of data mining query languages[END_REF], for example using constraint programming techniques [START_REF] Guns | Itemset mining: A constraint programming perspective[END_REF]. Nevertheless, we argue that pattern mining languages should benefit from direct extensions of the SQL language, since data are often stored in DBMSs. Several other practical propositions follow this principle and interact more directly with DBMSs query engines [START_REF] Fang | Splash: ad-hoc querying of data and statistical models[END_REF], [START_REF] Ordonez | One-pass data mining algorithms in a DBMS with UDFs[END_REF], [START_REF] Blockeel | An inductive database system based on virtual mining views[END_REF]. To make things concrete, let us consider the running example given in Figure 3 with the EMP table. The attribute Educlevel represents the number of years of formal education, Sal the yearly salary, Bonus the yearly bonus and Comm the yearly commission. The meaning of other attributes is straightforward.

To begin with, let us extract functional dependencies (FD) from the relation Emp. Recall that a FD X → Y holds in r if for all tuples t1, t2 ∈ r, and for all attribute A ∈ X such that t1 The FINDRULES keyword identifies a RQL query, which generates rules of the form X → Y with X and Y disjoint attribute sets taken from the OVER clause. The SCOPE clause defines tuple-variables over some tables obtained by classical SQL queries. An optional WHERE clause defines relationships between tuple-variables, similar to the SQL WHERE clause. The CONDITION ON $A clause defines the predicate to be Note that the difference between Q 1 and Q 2 naturally lies on the predicate to be evaluated, but also on the number of tuple variables required. The predicate of Q 1 is evaluated on pairs of tuples, while Q 2 considers a single tuple.

[A] = t2[A] then for all A ∈ Y , t1[A] = t2[A]. With
Example 3. The following query Q 1 restricts the scope of Q 1 , leading to the notion of conditional functional dependencies [START_REF] Bohannon | Conditional functional dependencies for data cleaning[END_REF]. For example, we consider only employees with a level of qualification above 16. In that case, Sal → Comm holds, meaning that employees earning similar salaries receive similar commissions.

Q 1 : FINDRULES OVER Empno,
We have shown so far query examples related to implications (in formal Concept Analysis) and functional dependencies (in databases). Nevertheless, RQL is not restricted to these types of queries at all and can express many more rules.

Example 5. Assume we are interested in a kind of sequential dependencies [START_REF] Golab | Sequential dependencies[END_REF], i.e. dependencies showing similar behavior of attribute values. Q 3 discovers numerical attributes that vary together (i.e., X → Y means that if X increases then Y also increases).

Q 3 : FINDRULES OVER Educlevel, Sal, Bonus, Comm SCOPE t1, t2 Emp CONDITION ON $A IS t1.$A > t2.$A
Sal → Comm and Comm → Sal hold in Emp, which means that a higher salary is equivalent to a higher commission. Example 6. Continuing the previous example, assume now the analyst wants to focus on male employees (see also Figure 1).

Q 3 : FINDRULES OVER Educlevel, Sal, Bonus, Comm SCOPE t1, t2 (SELECT * FROM Emp WHERE Sex='M') CONDITION ON $A IS t1.$A > t2.$A
In that case, Educlevel → Bonus also holds, which means that male employees with higher education levels receive higher bonuses.

Example 7. Instead of narrowing the scope of a query, userdefined conditions can bind different tuple variables together with a custom relationship specified in the WHERE clause of the RQL query. For example, Q 4 finds disparities between managers and managees, i.e. rules on attributes for which managers have values greater than or equal to their managees.

Q 4 : FINDRULES OVER Educlevel, Sal, Bonus, Comm SCOPE t1, t2 Emp WHERE t1.Empno = t2.Mgrno CONDITION ON $A IS t1.$A >= t2.$A
In this example, ∅ → Bonus holds in Emp, which means that managers always earn a bonus greater than or equal to their managees'.

III. FEEDBACK THROUGH COUNTEREXAMPLES

Given a RQL query, the data analyst may also interact with the system to know whether or not a given rule holds. She can provide a rule to the system and two cases arise: either the rule holds and the analyst is notified that the rule is indeed valid; or the rule does not hold which means that at least one counterexample exists and one of them is provided by the system. This notion of counterexample is well known for functional dependencies, and provides very good feedback to the data analyst with her own data.We strongly believe that counterexamples are a great tool to help the analyst understand why a particular rule does not hold, and refine if necessary her analysis in an iterative process.

To illustrate counterexamples, suppose that a data analyst wants to explore her hypothesis that higher salaries and higher education levels yield higher bonuses (Salary, Educlevel → Bonus), using Q 3 . Figure 4 gives an overview of what RQL provides as a counterexample for this rule, that is, two tuples among which one (employee No. 10) has a higher Salary and Educlevel than the other (employee No. 50), but not a higher Bonus.

With this counterexample as a starting point, and especially the SQL query generated to extract it from the database, the data analyst can quickly switch to SQL to get an idea of why this rule is not verified. For instance, employees that are either female or have a finance job are easily pointed out as having a higher salary and education level, but lower bonuses than others. The data analyst can then refine her RQL query, for example by narrowing the scope of the data, such as in Q 3 where a higher Educlevel by itself implies a higher Bonus.

The number of tuples required to provide a counterexample depends on the number of tuple variables. Q 3 or FDs need at least two tuples. But with Q 2 , one tuple (for instance employee No. 30) is enough to prove that the rule Workdept → Mgrno does not hold.

Rule verification:

The

IV. IMPLEMENTATION AND APPLICATION

The RQL web application has been implemented in Java with the Play Framework [START_REF]Play framework[END_REF]. External tools have been used for the most expensive part of the rule generation process, i.e. the enumeration of minimal transversal of hypergraphs [START_REF] Murakami | Efficient algorithms for dualizing large-scale hypergraphs[END_REF]. The chosen DBMS is Oracle 11g Release 2.

Importantly, the web interface discloses the SQL code generated by the system to help the user build her own queries. For instance, the query used to retrieve an arbitrary counterexample from the database can be extended so that the analyst identifies more insightful ones.

RQL can be interacted with in two modes: (i) a Sample DB is provided with selected examples to offer a quick way into RQL (ii) a Sandbox allows users to upload and query their own data (currently limited to 3 tables and 200 kB). RQL has been used by 120 undergraduate students to play with functional dependencies and other constraints in a database course at INSA Lyon. Not surprisingly, the notion of counterexamples has been widely used by students. RQL has been appreciated for its ability to bridge the gap between the SQL language and functional dependencies in database design by providing a unified interface for both SQL and RQL queries.

Previous works [START_REF] Chardin | Query Rewriting for Rule Mining in Databases[END_REF] have highlighted the efficiency of RQL as a two step process, even on large databases.

V. CONCLUSION

RQL is introduced as a web interface to discover rule patterns over relational databases. RQL subsumes SQL statements by providing the opportunity to specify and get results as a set of rules or some counterexamples. The rule mining problem is seen as a query processing problem, for which we have proposed a query rewriting technique allowing the delegation of as much processing as possible to the underlying DBMS engine [START_REF] Chardin | Query Rewriting for Rule Mining in Databases[END_REF]. RQL allows SQL developers to extract precise information without any specific knowledge in data mining.

Fig. 1 .

 1 Fig. 1. Web interface for RQL

  satisfied by each attribute $A occurring in the left-and righthand sides of the rule. To illustrate the expressiveness of RQL queries, we now provide several examples. Example 2. Let us consider null values known to be common in real-life databases. With RQL, the data analyst has the opportunity to discover rules between attributes with respect to null values as shown with query Q 2 . Q 2 : FINDRULES OVER Empno, Lastname, Workdept, Job, Sex, Bonus, Mgrno SCOPE t1 Emp CONDITION ON $A IS t1.$A IS NULL The rule Mgrno → Workdept holds in Emp since each time the attribute Mgrno is null in a tuple, then Workdept is also null for the same tuple (only employee No. 20 in this example).

3 . 1 Fig. 4 .

 314 Fig. 4. Counterexample with RQL

TABLES VIEWS Submit your RQL or SQL query:

  FINDRULES OVER Educlevel, Sal, Bonus, Comm SCOPE t1, t2 (SELECT * FROM Emp WHERE Sex = 'M') CONDITION ON A IS t1.A > t2.A

	Query Query	Help Help	Log out Log out	About About
					SQL examples:
					SQL 1 SQL 1	Content of Emp
					SQL 2 SQL 2	Schema of Emp
					RQL examples:
					RQL 1 RQL 1	Null values in Emp
					RQL 2 RQL 2	Functional dependencies on Emp
					RQL 3 RQL 3	Functional dependencies on a subset of Emp
					RQL 4 RQL 4	Approximate functional dependencies on Emp
				Submit Query Submit Query	RQL 5 RQL 5	Sequential dependencies on Emp

EMP

DEPT

EMP_WITH_DEPTNAME

EMP_SUBSET

Sample DB Sample DB user@rql.insa-lyon.fr user@rql.insa-lyon.fr

  RQL, FDs are expressed in a similar way.Example 1. Q 1 discovers FDs from Emp over a subset of attributes.Note how the CONDITION clause matches the previous logical implication. We have also restricted FDs discovery to a subset of seven attributes in the OVER clause. In this example, a canonical cover of FDs that hold in Emp is generated (composed of twenty-four FDs), including FDs such as Empno → Lastname or Workdept → Job.

	Q 1 : FINDRULES
	OVER Empno, Lastname, Workdept, Job,
	Sex, Bonus, Mgrno
	SCOPE t1, t2 Emp
	CONDITION ON $A IS t1.$A = t2.$A
	Overall, a RQL query has the following general form:
	FINDRULES
	OVER [set of attributes: A 1 , ..., A n ]
	SCOPE [tuple variables: t 1 , ..., t n ]
	WHERE [condition on (t 1 , ..., t n )]
	CONDITION ON [attribute variable: $A]
	IS [condition on ($A, t 1 , ..., t n )]

  Example 4. Query Q 1 is an approximation of Q 1 for numeric values similar to Metric Functional Dependencies[START_REF] Koudas | Metric functional dependencies[END_REF], where strict equality is discarded to take into account variations under 10%. For instance, salaries 41250 and 38250 are considered

	EMP Empno Lastname Workdept	Job	Educlevel Sex	Sal	Bonus Comm Mgrno
	10	SPEN	C01	FINANCE	18	F	52750	500	4220	20
	20	THOMP	-	MANAGER	18	M	41250	800	3300	-
	30	KWAN	-	FINANCE	20	F	38250	500	3060	10
	50	GEYER	-	MANAGER	16	M	40175	700	3214	20
	60	STERN	D21	SALE	14	M	32250	500	2580	30
	70	PULASKI	D21	SALE	16	F	36170	700	2893	100
	90	HENDER	D21	SALE	17	F	29750	500	2380	10
	100	SPEN	C01	FINANCE	18	M	26150	800	2092	20
	Fig. 3. Running example
	close (7.5% difference), but not salaries 41250 and 36170
	(13.1% difference).
	Q 1 : FINDRULES
	OVER Educlevel, Sal, Bonus, Comm
	SCOPE t1, t2 Emp
	CONDITION ON $A IS
	2 * ABS(t1.$A-t2.$A)/(t1.$A+t2.$A)<0.1
							Lastname, Workdept, Job,
						Sex, Bonus
					SCOPE t1, t2 (SELECT * FROM Emp
						WHERE Educlevel > 16)
					CONDITION ON $A IS t1.$A = t2.$A
					Interestingly, Sex → Bonus holds with this restriction,
					meaning that above a certain level of qualification (16), the
					gender determines the bonus.

rule Sal Educlevel bonus is false Counter-example:

	EMPNO	LASTNAME	WORKDEPT	JOB	EDUCLEVEL	SEX	SAL	BONUS	COMM	MGRNO
	10		SPEN	C01	FINANCE	18	F	52750	500	4220	20
	50		GEYER	null	MANAGER	16	M	40175	700	3214	20
	Generated query:
	1.	SELECT SELECT t1 t1.*, .*, t2 t2.* .*
	2.	FROM FROM Emp t1 Emp t1, , Emp t2 Emp t2


External Stakeholders Oriented Governance: Yes, why not, but what for? The Wine Co-operatives Case

Agricultural cooperatives have an original organizational structure in which their democratic governance is directed towards the community in every sense. In this context, we have examined to what extent a stronger partnership with external actors would create value for the cooperatives. We surveyed a representative sample of winemaking cooperatives in Languedoc-Roussillon and analyzed their partnership governance methods, their size, their performance and the effects of the first two points on the third one using structural equation modelling. It was found that frequent and extensive interaction between the winemaking cooperatives and their external stakeholders was a source of additional performance in the long term, an effect which is added to that of the size.

Introduction

Facing globalization and market volatility issues, agricultural co-ops have to adapt in their management and governance practices. In this context, our study deals with the in uence of a more external stakeholders oriented governance, and so a more participative decision-making process, on wine co-ops performance.

Theoretical framework and methodology

We focused on stakeholders theory [START_REF] Freeman | Strategic management: a stakeholder approach[END_REF][START_REF] Freeman | Stakeholder theory: The state of the art[END_REF] to study the intimate mechanisms of cooperatives governance and more precisely the impact of external actors on them [START_REF] Cornforth | The governance of cooperatives and mutual associations: a paradox perspective[END_REF][START_REF] Charreaux | Gouvernance des entreprises : valeur partenariale contre valeur actionnariale[END_REF]. Furthermore, we looked at the links between partnership governance and firm performance [START_REF] Jensen | Value Maximisation, Stakeholder Theory, and the Corporate Objective Function[END_REF] which are rather under studied, especially as far as co-ops are concerned.

We designed a specific model (agricultural sector) that attempts to explain these complex relationships, also including the effect of cooperative size, and we tested it on wine co-ops in the South of France (Languedoc-Roussillon). Our sample was made of 87 co-ops, representing 50% of the economic weight of wine cooperation in this area. We used a structural equation modelling and 16 indicators to run our empirical study (figure 1).

Results

We first found that the partnership dimension of agricultural co-ops and especially wine ones is a fact and that external stakeholders (customers, suppliers, auditors, agricultural professional organisations, etc…) play an important role inside the "black box" of co-ops.

Our second finding was that an increasing level of wine co-ops external partnership governance and a higher size imply a more important level of global long run performance (figure 1). The model has a very good validity (high GoF), relationships between concepts are positive and highly significant.

Our third and last finding consisted on showing that external partnership governance is multi-faced and has contrasted effects on co-ops long-term performance. For example, the degree of openness of internal governance has a positive effect on financial performance (figure 2), whereas external interactions of BoD limit vines loss (figure 3).

Conclusion

We can say that this survey underlined the crucial importance of external stakeholders on agricultural co-ops governance and economic performance. Their influence, mixed with more classical determinants (size of the firm), lead to higher long-term value creation.

These results represent a significant advance in the study of cooperative governance and allow us to develop organizational improvements for winemaking cooperatives. Some future researches could go further on this topic with a larger sample of wine and other agricultural co-ops, with more frequent governance variables measurement and a more dynamic approach.