# Molecular phylogeny of South-East Asian arboreal murine rodents

Marie Pagès, Pierre-Henri Fabre, Yannick Chaval, Alessio Mortelliti, Violaine

Nicolas, Konstans Wells, Johan R. Michaux, Vincent Lazzari

► To cite this version:

Marie Pagès, Pierre-Henri Fabre, Yannick Chaval, Alessio Mortelliti, Violaine Nicolas, et al.. Molecular phylogeny of South-East Asian arboreal murine rodents. Zoologica Scripta, 2016, 45 (4), pp.349-364. 10.1111/zsc.12161 . hal-01606856

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Molecular phylogeny of Southeast Asian arboreal murine rodents

<table><tr><td>Journal:</td><td>Zoologica Scripta</td></tr><tr><td>Manuscript ID:</td><td>ZSC-03-2015-0034.R2</td></tr><tr><td>Manuscript Type:</td><td>Original Manuscript</td></tr><tr><td>Date Submitted by the Author:</td><td>n/a</td></tr><tr><td>Complete List of Authors:</td><td>Pagès, Marie; Unité de génétique de la conservation, Université de Liège; UMR CBGP, Campus International de Baillargue; Institut des Sciences de l'Évolution de Montpellier, Fabre, Pierre-Henri; Harvard Museum of Comparative Zoology, ; Institut des Sciences de l'Évolution de Montpellier, Chaval, Yannick; UMR CBGP, Campus International de Baillargue Mortelliti, Alessio; Fisheries, and Conservation Biology, University of Maine, Department of Wildlife Nicolas, Violaine; Muséum national d'Histoire naturelle, Institut de Systématique, Évolution, Biodiversité Wells, Konstans; The Environment Institute, The University of Adelaide Michaux, Johan; Unité de génétique de la conservation, Université de Liège Lazzari, Vincent; Institut de paléoprimatologie, Paléontologie Humaine :Evolution et paléoenvironnements,</td></tr><tr><td>Keywords:</td><td>Arboreal rodents, Murinae phylogeny, Molecular systematics, Southeast Asia, Dental morphology</td></tr></table>
Corresponding author: Marie Pagès,

Email: marie.pages@univ-montp2.fr

Institut des Sciences de l'Évolution de Montpellier, Université de Montpellier, CNRS, IRD,

EPHE, 34095 Montpellier, France

Phone: +33 (0)4 67 14 46 33

Fax: +33 4 67 14 36 22

Title: Molecular phylogeny of Southeast Asian arboreal murine rodents

MARIE PAGÈS*, PIERRE-HENRI FABRE*, YANNICK CHAVAL, ALESSIO

MORTELLITI, VIOLAINE NICOLAS, KONSTANS WELLS, JOHAN R. MICHAUX &
VINCENT LAZZARI

*These authors contributed equally to this work.

Marie Pagès, Unité de génétique de la conservation, Institut de Botanique, Université de Liège, 4000 Liège (Sart Tilman), Belgique; INRA, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro), Campus International de Baillarguet, CS 30016, 34988 Montferrier-sur-Lez Cedex; Institut des Sciences de l'Évolution de Montpellier, Université de Montpellier, CNRS, IRD, EPHE, 34095 Montpellier, France. E-mail: marie.pages@univ-montp2.fr

Pierre-Henri Fabre, Harvard Museum of Comparative Zoology, 26 Oxford Street, Cambridge, MA 02138, USA;
Institut des Sciences de l'Évolution de Montpellier, Université de Montpellier, CNRS, IRD, EPHE, 34095 Montpellier, France ; Smithsonian Institution PO Box 37012, MRC 108 Washington, DC 20013-7012 E-mail: phfmourade@gmail.com

Yannick Chaval, INRA, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro), Campus International de Baillarguet, CS 30016, 34988 Montferrier-sur-Lez Cedex, France. E-mail: yannick.chaval@supagro.inra.fr

Alessio Mortelliti, Fenner School of Environment and Society, Australian Research Council Centre for Environmental Decisions, National Environmental Research Program, The Australian National University, Canberra, ACT 0200. E-mail: alessio.mortelliti@adelaide.edu.au
Department of Wildlife, Fisheries, and Conservation Biology, University of Maine, 5755 Nutting Hall, Room 228, Orono, ME 04469, USA.
E-mail: alessio.mortelliti@maine.edu

Violaine Nicolas, Institut de Systématique, Évolution, Biodiversité ISYEB – UMR 7205, CNRS, MNHN, UPMC, EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités 57 rue Cuvier, CP 51, 75005 Paris, France.
E-mail: vnicolas@mnhn.fr

Konstans Wells, The Environment Institute, School of Earth and Environmental Sciences, The University of
Adelaide, SA 5005, Australia. E-mail: konstans.wells@adelaide.edu.au
Johan R. Michaux, Unité de génétique de la conservation, Institut de Botanique, Université de Liège, 4000 Liège
(Sart Tilman), Belgique; CIRAD TA C- 22 / E - Campus international de Baillarguet 34398 Montpellier Cedex 5,
France

-E-mail: johan.michaux@ulg.ac.be

Vincent Lazzari, Institut de paléoprimatologie, Paléontologie Humaine :Evolution et paléoenvironnements -

UMR CNRS 7262 INEE, 86022 6 rue Michel Brunet Poitier, France. E-mail: vincent.lazzari@univ-poitiers.fr

Running Title: Arboreal murine rodent phylogeny
**Abstract**

Recent phylogenetic studies and taxonomic reviews have led to nearly complete resolution of the phylogenetic divisions within the old world rats and mice (Muridae, Murinae). The *Micromys* division and *Pithecheir* division are two notable exceptions where groupings of species into these divisions based on morphology and arboreal lifestyle have not been supported by phylogenetic evidence. Several enigmatic species from these divisions have been missing from molecular studies, preventing a rigorous revision of phylogenetic relationships. In this study, we sequenced for the first time one mitochondrial and three nuclear genes from Southeast Asian keystone species of these two arboreal divisions: *Hapalomys delacouri* (*Micromys* division), *Lenothrix canus* and *Pithecheir parvus* (*Pithecheir* division). We also complemented the molecular data already available for the two divisions with new data from Sundaic *Chiropodomys*, Indian *Vandeleuria oleracea* and the recently described Sulawesian *Margaretamys christinae*. Using this new phylogenetic framework and molecular dating methodologies, our study allows some more detailed classification of the former *Micromys* and *Pithecheir* divisions, while confirming their polyphyletic status. Specifically, the former *Micromys* division should now be split into four monotypic divisions: *Chiropodomys*, *Hapalomys*, *Micromys*, and *Vandeleuria* divisions. The former *Pithecheir* division is likely to be refined and restricted to *Pithecheir* and probably *Pithecheirops*, whereas *Lenothrix* and *Margaretamys* should now be recognized as representatives of the *Dacnomys* division. Our findings have profound implications with regard to the systematics of Murinae, as well as to the early evolution of murine morphology and dental characters.
## Introduction

The old world rats and mice, subfamily Murinae (Muridae), contain 584 described and extant species (Aplin & Helgen, 2010; Misonne, 1969; Musser & Carleton, 2005). Southeast Asia constitutes the major hotspot of biodiversity for Old World Murine rodents (Aplin & Helgen, 2010; Misonne, 1969; Musser & Carleton, 2005). Since the Miocene, the Murinae have spread out of Asia into the Indo-Australian, African, Indian and Palearctic regions, where they underwent repeated radiations. Current systematic and phylogenetic studies of murines largely reflect a strong biogeographical footprint with many divisions and phylogenetic clades endemic to specific biogeographic regions (Musser & Carleton, 2005; Lecompte *et al.*, 2008; see Table 1). Three tribes (i.e. taxonomic rank between subfamily and genus) are considered the dominant murines of Southeast Asian and Indo-Australian areas according to molecular phylogenetic evidence (Lecompte *et al.*, 2008): (1) the Phloeomyini including 17 species endemic to the Philippines, (2) the Hydromyini including 198 species endemic to the Philippines and the Sahul shelf, and (3) the Rattini including 185 species widespread throughout Southeast Asia and the whole Indo-Pacific archipelago. The 23 species of the *Pithecheir* and *Micromys* divisions comprise the remaining species of currently known murines in the Southeast Asian and Indo-Australian areas. They are distributed across Southeast Asia and Sulawesi (Figure S1), but are neither phylogenetically monophyletic (Schenk *et al.*, 2013) nor readily assigned to these tribes on molecular basis.

As currently defined (Musser & Carleton, 2005), the *Pithecheir* division encompasses the genera *Pithecheir*, *Eropeplus*, *Lenomys*, *Lenothrix*, *Margaretamys*, and *Pithecheirops*. These genera are suspected to represent an artificial grouping (Musser & Newcomb, 1983) and are still considered as Murinae *incertae sedis* as their phylogenetic affinities remain unclear (Lecompte *et al.*, 2008). *Margaretamys* was recently found to be nested within the *Dacnomys* division of the tribe Rattini (Schenk *et al.*, 2013). The *Micromys* division, which encompasses the genera *Chiropodomys*, *Hapalomys*, *Haeromys*, *Micromys*, *Vandeleuria*, and *Vernaya* also appears to represent equivocal grouping (Musser & Carleton, 2005). DNA results demonstrated that the *Micromys* division is polyphyletic (Steppan *et al.*, 2005). This division most likely consist of at least 3 distinct and phylogenetic old lineages with (i) *Micromys* being sister to the Rattini, (ii) *Vandeleuria* closely-related to a clade embracing Praomyini, Murini and Apodemini tribes and (iii) *Chiropodomys* affiliated with the Hydromyini tribe (Rowe *et al.*, 2008; Schenk *et al.*, 2013).

The original groupings of these Southeast Asian taxa into *Pithecheir* and *Micromys* divisions *sensu* Musser & Carleton (2005) relied mostly on their likewise adaptations to
arboreal lifestyle and their similar morphologies. Among the considered morphological features were the global patterns of dental morphology (i.e. cusp convergences on the upper molar; see hereafter), distinctive skull features as well as the presence/absence of an opposable hallux of various representative species (Musser & Newcomb, 1983). However, in almost all revisions and classifications performed to date, taxonomists have struggled with the difficulty in classifying these arboreal taxa (see Misonne, 1969; Musser & Newcomb, 1983).

A Mid-Miocene origin of Murinae (12-16 Mya) is suggested by the oldest fossil occurrence of modern murines in the Siwalik deposits (i.e. *Antemus mancharensis*) (Wessels, 2009). This transition in the Siwalik fossil record is defined by changes in upper molar morphology involving reorientations of the masticatory movements (Coillot *et al.*, 2013; Lazzari *et al.*, 2011). This transition is one of the most well characterised transitions in mammal evolution. It is well documented by many extinct species, from *Potwarmus*, the cricetine-like earliest murid to *Progonomys* that has the derived connection of lingual cusps and the murine occlusal pattern shared with modern murines. Historically, this transition was assigned to the divergence of *Mus* and *Rattus*, assuming that they represent the earliest divergence within Murinae, and has been critical to date for a number of biomedical and evolutionary studies (Patnaik, 2014). However, phylogenetic analyses of Murinae have shown that this fossil transition is more appropriately assigned to the divergence of the Phloeomyini tribe from the remaining Murinae, as this is the earliest divergence among taxa with the derived murine molar cusp pattern (Steppan *et al.*, 2004a; Steppan *et al.*, 2005). Thus, disentangling the basal divergences within Murinae appears critical to accurately interpret the fossil record and to accurately calibrate the divergence of taxa, such as the important genera *Mus* and *Rattus*. Recent molecular clues indicated that some species of the enigmatic *Micromys* and *Pithecheir* divisions may have emerged from very early divergence events within the murine tree and could even be among the first (e.g. Badenhorst *et al.*, 2011). Consequently, the phylogenetic placement of the involved species appears to be crucial to disentangle the evolution of their ecomorphological traits and also to unravel the entire diversification history of the Murinae subfamily.

In this study, we sequenced for the first time three genera from the Southeast Asian region of both *Micromys* (*Hapalomys delacouri*) and *Pithecheir* (*Lenothrix canus* and *Pithecheir parvus*) divisions. We also provided new molecular data from Sundaic *Chiropodomys*, Indian *Vandeleuria oleracea* and the recently described Sulawesian endemic *Margaretamys christinae* (Mortelliti *et al.*, 2012). Using this new phylogenetic context and molecular dating methodologies, we addressed the following questions: (i) how should we
refine the taxonomy of Murinae; (ii) do morphological (i.e. dental) characters support our new
molecular findings for phylogenetic placement of the members of these divisions? (iii) how
often does arboreality evolve in Murinae from the *Micromys* and *Pithecheir* divisions and
how does it relate to early evolution in the group? and (iv) where should we place the Siwalik
transition in the murine tree and how should we interpret the early murine fossil record?

**Methods and materials**

Taxon and gene sampling

We sequenced four molecular markers that have proven valuable for resolving murine phylogenies (Buzan *et al.*, 2011; Fabre *et al.*, 2013; Jansa *et al.*, 2006; Lecompte *et al.*, 2008; Pagès *et al.*, 2010; Rowe *et al.*, 2011; Rowe *et al.*, 2008; Schenk *et al.*, 2013; Steppan *et al.*, 2004b; Steppan *et al.*, 2005). These included one mitochondrial gene (cytochrome *b* apoenzyme: *cyt b*) and three nuclear genes (growth hormone receptor exon 10: *GHR*; interphotoreceptor retinoid binding protein exon 1: *IRPB*, breast and ovarian cancer susceptibility protein exon 11: *BRCA1*). DNA sequences were generated for the following species belonging to *Micromys* and to *Pithecheir* divisions *sensu* Musser and Carleton, 2005: *Chiropodomys gliroides*, *Chiropodomys major*, *Hapalomys delacouri* and *Vandeleuria oleracea* (*Micromys* division) and *Lenothrix canus*, *Margaretamys christinae* and *Pithecheir parvus* (*Pithecheir* division). To break putative long branches within the tribe Rattini, the two karst-specialist genera *Saxatilomys paulinae* and *Tonkinomys daoventieni* from the *Dacnomys* division (Table S1a) were included in this study. We also mined 170 *cytb*, 190 *IRBP*, 137 *GHR*, 74 *BRCA1* sequences representing 191 murine species available from previously published studies (see references above; Table S1b). In total, our dataset includes 196 murine species representing a total of 100 genera following Musser & Carleton's classification (2005). We included 17 representatives of Deomyinae, Gerbillinae and Lophiomyinae (Table S1b) as outgroups (Michaux & Catzeflis, 2000; Steppan *et al.*, 2004b).

We used SEAVIEW (Galtier *et al.*, 1996) to align sequences by eye. We translated
nucleotide sequences into peptide sequences to exclude putative NUMt copies and to ensure
sequence orthology. From these individual alignments, we built four gene matrices; *cyt b* (200
taxa and 1140 sites; 5 % of missing character states), *IRBP* (215 taxa and 1239 sites; 21 %
missing data), *GHR* (171 taxa and 937 sites; 12 % missing data), *BRCA1* (94 taxa and 2430
sites; 23 % missing data) and a nuclear + mitochondrial supermatrix (221 taxa and 5746 sites;
41 % missing data).
### DNA extraction and sequencing of ethanol-preserved specimens

Samples were obtained from the collections of the CeroPath project, University Montpellier collections, as well as personal tissues collections of J.P Quéré, K. Wells, K. Aplin, A. Mortelliti & R. Castiglia (Table S1a). DNA was extracted from tissue with a DNEasy Tissue Kit (QIAGEN), in accordance with the manufacturer's instructions. We sequenced the whole *cyt b* gene and the *IRBP*, *GHR* and *BRCA1* fragments, according to protocols described elsewhere (Irwin *et al.*, 1991; Lecompte *et al.*, 2008; Pagès *et al.*, 2010). Primer sets used for PCR amplifications and sequencing are listed in Table S2. PCR products were sequenced at the sequencing centre Genoscope (Evry, France) using an ABI 3730xl automatic capillary sequencer and the ABI BigDye Terminator v.3.1 sequencing kit. Sequences were analyzed with the CodonCode Aligner v 4.0.3 software (CodonCode Corporation, Dedham, MA, USA).

### DNA extraction and sequencing of museum specimens

Samples from four *Pithecheir* specimens were obtained from the French National Museum of Natural History (MNHN) (Table S1a): two specimens of *Pithecheir parvus* (MNHN-ZM-MO 1977-251, MNHN-ZM-MO 1977-252) and two specimens of *P. melanurus* (MNHN-ZM-MO 1900-580, MNHN-ZM-MO 1900-583). As museum samples contain tiny amounts of poorly preserved DNA, pre-amplification steps were achieved in an independent lab dedicated to degraded DNA analysis (degraded DNA platform, Labex CeMEB), following the ancient DNA standard procedures and using specific equipment and personal protections (Paabo *et al.*, 2004). DNA was extracted from small pieces of skins using QIAamp DNA Micro Kit (QIAGEN), in accordance with the manufacturer's instructions. Because of DNA fragmentation, *cyt b*, *IRBP* and *GHR* markers were obtained using three overlapping fragments (ranging from 310 to 472 bp). Additional primers (Table S2) were designed based on the alignment of sequences available for Murinae, Gerbillinae and Deomyinae (Table S1b). At least three independent PCR amplifications were performed in 25 µL reaction volumes containing 2.5 units of Perkin Elmer Gold Taq polymerase (Applied Biosystems), 2 mM MgCl₂, 250 mM of each dNTP, 0.5 mM of primers. For each independent PCR attempt, a range of dilutions was performed to find the best compromise between inhibitor's concentration and targeted DNA molecule concentration. DNA was amplified with a 5 min activation step at 95°C followed by 55 cycles of denaturation (94°C, 30 s), annealing (temperature in Table S2, 30 s) and elongation (72°C, 45 s). To discard artefactual mutations due to DNA degradation (Paabo *et al.*, 2004) and to determine the consensus sequences for
each individual, all the positive PCR products were sequenced (see supplementary information for further details, Text S1). Next, we combined the newly obtained sequences with the DNA matrices described in the previous section.

### Phylogenetic analyses on the individual and concatenated genes

Phylogenetic trees were reconstructed using two probabilistic methods: maximum likelihood (ML) and Bayesian inference (BI). ML analyses were first carried out on each marker independently using RAxML 7.2.8-ALPHA (Stamatakis, 2006). Each gene considered separately does not result in a robust phylogeny of Murinae: mitochondrial marker helps to resolve terminal nodes, while nuclear genes lend support to deepest ones. But, since the 4 markers yielded consistent, compatible topologies, sequences were concatenated and phylogenetic analyses were then carried out using the combined dataset. As the model choice is limited in RAxML, the general time-reversible GTR+G model (option –m GTRGAMMA) was selected and robustness of each tree was assessed using the rapid bootstrap (Bp) procedure (option –f a) with 1,000 replications (option -# numberOfRuns) (Stamatakis et al., 2008). Bayesian analyses were performed in MRBAYES 3.1.2 (Ronquist & Huelsenbeck, 2003), which allows different substitution models to be specified for each gene partition. Using JMODELTEST 2.1.1 (Posada, 2008) and the corrected Akaike Information Criterion (cAIC), the GTR+I+G model was selected as the best-fitting model of DNA sequence evolution for *Cyt b* and *GHR* markers, the GTR+I+G for the *IRBP*, and the GTR+G for *BRCA1*. The best-fit partitioning schemes (considering the three different codon positions of the four coding genes) and models of molecular evolution were deeper investigated using PARTITIONFINDER (Lanfear *et al.*, 2012). The best-fit partitioning scheme consisted in 3 subsets: 1) the first and the second positions of the *Cyt b* codon were merged together, 2) the third position of the *Cyt b* codon was treated separately, 3) all the positions of the nuclear genes were merged together. 56 different substitution models for these three subsets were compared using the greedy algorithm. The best-fit substitution model was the GTR+I+G model for each subset according to cAIC values. MRBAYES parameters were set accordingly (see supplementary information). All parameters except the topology were unlinked across partitions, and two independent runs, each with 4 Markov chains Monte Carlo (MCMC) samples comprising one cold and three heated chains, were computed simultaneously. The MRBAYES analyses were run for 50 x 10⁶ generations with trees sampled every 1,000 generations. In all cases, both the log-likelihood and model parameter values had reached convergence prior to posterior sampling (effective sample size of the trace of each parameter
checked using Tracer 1.5 (http://tree.bio.ed.ac.uk/software/tracer/), and potential scale reduction factors checked reaching 1). The consensus tree was then computed subsequent to a burn-in of 10 x 10⁶ generations (option “allcompat”). The node supports were estimated using posterior probabilities (PP).

Molecular results were further evaluated in light of the morphological characters. As the most abundant material of the rodent fossil record consists of jaws and teeth, we focused on the dental characters. Following the nomenclatures of Cope-Osborn and Miller (detailed in Figure 1), discrete characters were compared within the arboreal Murinae from Southeast Asia, but also compared with those of their closest extant relatives based on our molecular tree.

## Molecular dating

Divergence times among species were estimated from the combined supermatrix of nuclear and mitochondrial sequences. A Bayesian relaxed molecular clock method was used to estimate divergence dates whilst accounting for changes in evolutionary rates through time by allowing for independent models of sequence evolution for each gene partition. The best fitting substitution models for each partition were selected using JMODELTEST results. We used BEAST v1.7.4 (Drummond & Rambaut, 2007) assuming a Yule model of speciation and an uncorrelated log-normal distribution molecular clock as tree priors. Clock models were unlinked across gene partitions in order to account for missing data (Lemmon *et al.*, 2009). We ran MCMC chains for 200 million generations, with trees sampled every 5,000 generations. The program TRACER was used to assess algorithm convergence. We removed the first 15% of trees before the algorithm had reached stability as a burn in. Trees from each of the 4 independent runs were combined into a maximum clade credibility tree with mean node heights calculated using TREEANNOTATOR.

To calibrate the phylogeny, we selected five fossil constraints, as described from previous studies (Jansa *et al.*, 2006; Lecompte *et al.*, 2008; Rowe *et al.*, 2011; Rowe *et al.*, 2008; Steppan *et al.*, 2004a). In order to take the uncertainty in the phylogenetic position of these fossils into account, all constraints were set using hard minimum and soft upper boundaries, using a lognormal prior, as suggested by recent paleontological studies (Benton & Donoghue, 2007; Benton *et al.*, 2009; Parham *et al.*, 2012). We used the following constraints:

(I) We used the stem Apodemini fossils (11 Myr min) from the Early Vallesian (late Miocene: 11.6-24.5 Myr; (Martin Suarez & Mein, 1998; Vangegeim *et al.*, 2006) to constrain
the split between Apodemini / Millardini (MRCA of *Apodemus* / *Tokudaia*) and Praomyini /
Murini (MRCA of *Mus* / *Praomys* / *Mastomys* clade) (upper 95%: 8.91-21.8 Myr).

(II) The MRCA of the *Apodemus mystacinus* and the *Sylvaemus* groups (affiliated respectively to *A. flavicollis* and *A. sylvaticus*) were constrained using the *Apodemus* fossil record (Aguilar & Michaux, 1996; Michaux *et al.*, 1997) from the Upper Miocene. We set a median prior age at 7 Myr (upper 95%: 5.96-12.37 Myr).

(III) We used the first fossil record of *Mus* (*Mus auctor*; Jacobs & Downs, 1994; Jacobs *et al.*, 1990; Lundrigan *et al.*, 2002) to represent the minimum divergence at 5.7 Myr (upper 95%: 4.66-11.07 Myr) between different *Mus* lineages (*Mus musculus* / *Mus pahari* / *Mus setulosus*).

(IV) We used the African crown Arvicanthini lineage from the late Miocene (median age 6 Myr; from the Tortonian) (Winkler, 2002) and a soft maximum prior extending to the Serravalian (upper 95%: 3.91-16.81 Myr) as a constraint of the MRCA of Arvicanthini.

(V) We set a minimum constraint for the MRCA of Hydromyini, using the first Australian fossil evidence dated at 3.4 Myr (upper 95%: 1.3-14.21 Myr; Aplin, 2006; Rowe *et al.*, 2008; Tedford *et al.*, 1992).

Note that we did not use the oldest record of *Progonomys* for tree calibration, as the
interpretation of the early murine fossil record is part of our questions.

Ancestral state reconstruction

We reconstructed ancestral states for the dental key character, previously used to define the
*Micromys* and *Pithecheir* divisions: the cusp t7 (Figure 1). Based on Musser and Newcomb
(1983) (see page 537, character 27), this trait was coded as ‘1’ if “a cusp t7 derived and if
present, found on each first molar, usually on the second, and on the third” and as ‘0’
otherwise (“no cusp t7 (also called posterointernal or posterolabial cusp) on any upper
molar”). Taxa with uncertain or unknown character state were coded as “missing”. The
resulting classification of all species in our study dataset is available in the SI data (Figure
S3).

The presence of an opposable first digit on the hindfoot (hallux) comprises another potential
criteria for examining the morphological evolution of these arboreal rodents. An opposable
hallux has been attributed to *Chiropodomys*, *Hapalomys*, *Vandeleuria*, *Vernaya*, *Pithecheir*
and *Haeromys* representatives (Musser, 1979). However, because the hallux of some arboreal
murids bears a nail instead of a claw, that hallux may be pseudo-opposable, rather than fully
opposable (see “Other questions and speculations”, page 438 of Musser, 1979). We therefore
did not use this character for ancestral reconstruction.

Ancestral character state reconstructions (ASR) was based on stochastic character
mapping as implemented in the *make.simmap* function in the R software package *PHYTOOL*
(Bollback, 2006; Revell, 2012). This SIMMAP approach reconstructs possible states at all
ancestral nodes, accounting for the uncertainty through MCMC sampling. We used the default
parameter settings and run 1,000 simulations. The *make.simmap* approach is similar to the
empirical Bayes approach for ASR introduced by Pagel & Meade (2004), in which character
rate models are set to ML estimates. The analyses were computed on the maximum clade
credibility tree and on 1,000 phylogenies randomly sampled from the BEAST posterior
distributions of trees (excluding the burn-in) in order to take into account the phylogenetic
uncertainty. The MCMC analyses were conducted twice, with an equal (1/k) and empirical
bias prior, respectively, to explore the impact of these two options on the results. Marginal
posterior probabilities for ancestral character states were calculated using the same 1,000 post
burn-in trees.

## Results and Discussion

*Polyphyly of Micromys and Pithecheir divisions: a re-examination of dental characters in the light of molecular findings*

As reported previously (Steppan et al., 2005; Rowe et al., 2008; Schenk et al., 2013), the 8 representatives of the *Micromys* division did not form a monophyletic group and were distributed throughout the phylogeny of Murinae, confirming the polyphyletic status of the division (Figure 2). As in other studies, we recovered a sister relationship of the genus *Micromys* with the molecular tribe Rattini (Lecompte *et al.*, 2008) that contains the *Dacnomys*, *Maxomys* + *Crunomys*, *Melasmothrix* and *Rattus* divisions (PP=1, Bp=100%, see Fabre *et al.*, 2013; Pagès *et al.*, 2010). We recovered a sister-relationship of *Chiropodomys* with the Hydromyini (1, 100%) and an uncertain placement of *Vandeleuria* possibly with a clade comprising the Malacomyini, Apodemini, Murini and Praomyini molecular tribes but with weak support (0.81, 46%). Both of these results are congruent with previously published molecular phylogenies (Rowe *et al.*, 2008; Schenk *et al.*, 2013). *Hapalomys* is placed as the first lineage to diverge from other Murinae (monophyly of the other Murinae: 0.98/83) in agreements with assumptions proposed by Badenhorst *et al.*, 2012.
Revising morphological traits of species in light of our novel molecular classification
appeared to result in an overall consistent picture. Indeed, *Chiropodomys* dental morphology
falls within the large range of dental morphological diversity displayed by Hydromyini
(including the basin-shaped molars of the carnivorous water rat *Hydromys* to the primitive and
*Progonomys*-like dental plan of the hopping mouse, *Notomys*) (Figure 3). *Chiropodomys*,
however, presents a stephanodont (paracone-metacone) connection (see character 1 (1) in
Figure 3), which is absent in all Hydromyini. This level of dental dissimilarity supports its
phylogenetic position outside this tribe. *Vandeleuria* displays a large, rounded t7
(stosterostyle, (2)), a very weak metacone and a stephanodont (paracone-metacone)
connection ((1) in Figure 3), which fall within the range of dental variation of the Apodemini,
Murini, Malacomyini and Praomyini tribes. Murine dental morphology is characterized by the
"murine rasp", a peculiar functional pattern corresponding to upper molars with three
longitudinal functional cusp rows interlocking with the two longitudinal functional cusp rows
of the lower molars ((3) in Figure 3) (e.g. Lazzari *et al.*, 2008). *Hapalomys* displays a more
complex "murine rasp" than any other Murinae, notably, with three longitudinal functional
cusp rows on lower molars and equally sized cusps in the three longitudinal cusp rows of the
upper molars ((4) in Figure 3). Considering this "murine rasp" as a highly derived dental trait
among Murinae probably explained why the basal divergence of *Hapalomys* from the
remaining Murinae has never been conceived based on morphological data alone. In
conclusion, the breakup of the former *Micromys* division based on our molecular tree appears
consistent with the highly different dental morphologies displayed by its representatives (i.e.
presence of large c1 and c3 labial cusps on lower m1-m2 in *Hapalomys* and *Chiropodomys*
(5) in Figure 3), which are totally absent in other genera; very reduced metacone on upper
M1-2 in *Micromys* and *Vandeleuria* whereas this cusp is very large in *Hapalomys* and
*Chiropodomys*; (6) in Figure 3).

Representatives of the *Pithecheir* division are also dispersed through the murine
phylogeny (Figure 2). *Lenothrix* was placed as the sister taxon of *Margaretamys* (1, 95%) and
the two genera were phylogenetically nested within the *Dacnomys* division of the Rattini tribe
(here represented by the genera *Dacnomys*, *Chiromyscus*, *Leopoldamys*, *Niviventer*,
*Saxatilomys* and *Tonkinomys*) (1, 100%). This is consistent with the placement of
*Margaretamys* in a recent phylogenetic analysis (Schenk *et al.*, 2013). This result is congruent
with the strikingly similar dental morphology of these two genera, which both display a strong
t4bis associated with a distally-positioned t4 ((7) in Figure 4) (a character which is rare among
Murinae), a very massive mesostyle as large as the paracone and linked to this cusp on M1-2
((8) in Figure 4), and a well individualized posteroloph on M1-2 ((9) in Figure 4), which can all be viewed as shared derived characters considering the ancestral morphology of the middle Miocene Murinae (Lazzari *et al.*, 2010). They form currently the only cluster of two members of the old *Pithecheir* division. We emphasize that the rodents of the *Dacnomys* division do not display the derived characters mentioned above for the *Lenothrix-Margaretamys* group, instead they are morphologically more similar to Murinae of the *Rattus* genus. The *Tonkinomys* + *Saxatilomys* clade appears basal within *Dacnomys* division, *Lenothrix* + *Margaretamys* representing a well-supported clade with remaining genera (*Leopoldamys*, *Niviventer*, *Chiromyscus* and *Dacnomys*) (1, 99%).

The genus *Pithecheir* was placed within a clade containing the molecular tribe Millardini with moderate support (monophyly of *Pithecheir* + Millardini = 1, 81%). However, we could not resolve the precise placement of *Pithecheir* within the Millardini. Our ML tree grouped *Pithecheir* together with *Cremnomys* (41%) within Millardini, while our BI tree placed *Pithecheir* as sister taxa to the Millardini tribe but with weak support for the monophyly of Millardini (PP= 0.71). The dental morphology of *Pithecheir* is however very different from the morphology displayed by species of the Millardini tribe such as *Millardia* and *Cremnomys*. Upper molars of *Pithecheir* display massive, rounded posterostyles (t7, (10) in Figure 4) which are completely absent in Millardini; Millardini lower molars display an accessory labial cusp which seems to be absent in *Pithecheir* ((11) in Figure 4).

Given the strong support from our study to previous suggestions that the former *Micromys* and *Pithecheir* divisions are polyphyletic, we propose to abandon this nomenclature. Dental features shared by the lineages of these divisions (presence/absence of cusp t1bis & t2bis, cusp t7 on the upper molar) should be considered as homoplastic characters and can definitively not be used as informative characters to infer phylogenetic relationships. It is important to note that *Chiropodomys*, *Hapalomys*, *Vandeleuria*, and potentially *Pithecheir* are not nested within any of the currently well-accepted tribes of Murinae. Instead, they are placed as a sister taxa of these tribes. In light of this observation, the former inclusion of *Micromys minutus* within Rattini (Musser & Carleton, 2005) is puzzling. *Micromys* is recognized as being the first lineage to diverge within the tribe (Lecompte *et al.*, 2008; Rowe *et al.*, 2008) but it first appeared in the late Miocene in China (Horacek *et al.*, 2013), and its recent distribution throughout Europe and northern Asia comprises a distinct biogeographical region compared to the Rattini original diversification centre. Moreover, the dental morphology of *Micromys* strongly differs from most other Rattini by its paracone-metacone junction ((13) in Figure 3) and its large t7 on upper molars ((14) in Figure 3).
Based on these results, we proposed to split the polyphyletic *Micromys* division into,
at least, 4 monotypic tribes: (i) Chiropodomyini, (ii) Hapalomyini, (iii) Micromyini, and (iv)
Vandeleuriani (Table 1). Additional data are needed to establish the status of the tribe
Vandeleuriani, given the large uncertainty in phylogenetic inference from all available
information.. We also proposed to split the *Pithecheir* division since *Lenothrix* and
*Margaretamys* should be recognized as representatives of *Dacnomys* division within the
Rattini tribe. However, because only moderate supports obtained in our study for any of the
possible phylogenetic relationships of *Pithecheir* (only *cytb* and *IRBP* fragments were
sequenced from museum specimens), further phylogenetic information will be required to
assess its affinities and its taxonomic rank. In the near future, changes in the nomenclature are
very likely to occur as additional molecular and morphological data will be available for the
remaining *incertae sedis* lineages of Sulawesi (*Eropelus*, *Haeromys*, *Lenomys*), Sunda
(*Haeromys*, *Pithecheirops*, *Kadarsonomys*), Flores (*Papagomys*, *Paulamys*), Southeast Asia
(*Vernaya*) and Philippines (*Abditomys*, *Anonymomys*), which include various rare species (see
also Aplin & Helgen, 2010).

*Polyphyly of arboreal taxa: implication for interpreting the evolution of arboreal adaptation within Murinae*

Most of the lineages of the polyphyletic *Micromys* division appear as sister-lineage to major
tribes of Murinae (Figure 2). It holds true for some lineages of the *Pithecheir* polyphyletic
division if the placement of *Pithecheir* sister to Millardini (BI tree) is confirmed. Two
interpretations might be proposed in front of these results (i) *Micromys*, *Chiropodomys*,
*Vandeleuria* and *Hapalomys* tribes might be morphologically derived relics of early murine
diversifications that have survived extinction or (ii) these arboreal lineages might represent
plesiomorphic arboreal lineages and the Most Recent Common Ancestor (MRCA) of Murinae
would be arboreal. The examination of the locomotion of fossil ancestors of Murinae is
necessary to answer this question. The question "What is the ancestor of the true Murinae?"
asked by de Bruijn et al. (1996) and many others remains unanswered and a topic of ongoing
polemics (see Fabre et al., 2013; Schenk et al., 2013 for some recent discussion). Murinae are
defined by a unique set of external, cranial, postcranial, dental, reproductive, and arterial
features (Carleton & Musser, 1984). As the most abundant material of the rodent fossil record
consists of jaws and teeth, derived molar conditions form the primary basis for defining the
subfamily based on morphology alone. As mentioned earlier, the oldest extinct and recorded
taxon displaying both the derived dental plan and occlusal pattern characterizing all extant
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Murinae is the genus *Progonomys* Schaub, 1938, whose oldest representatives retrieved in Pakistan are considered to be 12.3 Myr-old (Jacobs & Flynn, 2005). If the detailed and well-calibrated fossil record from the Siwalik succession in Pakistan is an accurate depiction of murine history, *Progonomys* should be either considered as the MRCA of extant murines or a predecessor (Steppan *et al.*, 2004b). However, *Progonomys* is viewed by many authors as a paraphyletic genus, since it houses species that have been brought together on the mere basis of sharing plesiomorphic characters (Mein *et al.*, 1993). It is now viewed as the “basket case” of all, or a part of extant Murinae. Interestingly, a close relationships between *P. debruijni* and *Mus auctor*, the oldest representative of the genus *Mus*, has been proposed (e.g. Jacobs, 1978). Relationships between *P. cathalai* and the Apodemini, a tribe close to the Murini, have also been proposed but remain controversial (see Aguilar & Michaux, 1996; Martin-Suarez & Mein, 1998). Consequently, the extinct *Progonomys* is still considered by some authors as the MRCA of the *Mus-Rattus* clade (a clade encompassing all the murine representatives with the classical and typical murine dental pattern). If the paraphyletic genus *Progonomys* corresponds to the *Mus-Rattus* dichotomy, the MRCA of Phloeomyini and *Hapalomys* should be searched in genera such as the extinct *Potwarmus* and *Antemus* mainly from the middle Miocene of South Asia, confirmed as stem Murinae by a recent cladistic analysis (Lopez-Antonanzas, 2009), displaying an intermediary dental plan (Coillot *et al.*, 2013). Whichever is the true ancestor of the Murinae, postcranial elements of *Progonomys*, *Antemus* and *Potwarmus* have never been properly described, and the locomotion of these extinct taxa is still unknown. However, in Europe, *Progonomys* species from the Iberian Peninsular are thought to have been associated with open, dry habitats (e.g. Daams *et al.*, 1988), and are usually regarded as terrestrial, mouse-like equivalents. Therefore, based on early murine fossil records (Daams *et al.*, 1988; Jacobs & Downs, 1994; Jacobs *et al.*, 1990; Jacobs & Pilbeam, 1980; Jaeger *et al.*, 1986), the hypothesis considering *Micromys*, *Chiropodomys*, *Vandeleuria*, *Hapalomys* and *Pithecheir* as morphologically derived relics of ancient murine diversifications appears to have reasonable support. Our ASR analysis on the ancestral state of the molar cusp t7 reinforces this assumption. Although our ASR analysis was confined to a single morphological character, its most likely outcomes suggested multiple independent emergence of **the molar cusp t7 the molar presence** in the murine phylogeny (Figure S3, supplementary data). (Figure S3, supplementary data). Consequently, characters that were formerly used to define the obsolete *Pithecheir* and *Micromys* divisions and that were assumed to be associated with arboreal lifestyle (e.g. presence/absence of an opposable hallux) are likely to be homoplastic too.
Finally, if *Micromys*, *Chiropodomys*, *Hapalomys*, *Vandeleuria* and *Pithecheir* genera represent morphologically derived relics of various distinct tribes, it raises questions about the cause of extinction of their (unknown) closest relatives and whether survival of the extant species occurred simply by chance or because of particular common adaptations that may have enabled persistent species to bypass extinction events. The relatively high frequency of fossil species records of the genus *Micromys* in the early Pliocene, opposed to rare records in the early Pleistocene suggests a radiation of this genus during the early Pliocene and effectively its demise during Pleistocene (Horacek *et al.*, 2013). However, although *Micromys* is reported from a relatively large number of European fossil assemblages, in most instances the material is restricted to just a few isolated teeth, often a single one (Horacek *et al.*, 2013). Consequently, the limited amount of currently available information on morphological traits of species having survived and gone extinct prevents conclusion on their specific adaption to terrestrial and arboreal habitats and how extinction events were linked to possible changes and constraints in available habitats. The evidence of polyphyletic relationships of arboreal murine species provided in our study nevertheless opens interesting avenues for future research to explore eco-evolutionary pathways of species adaptation and radiation into terrestrial and arboreal habitats under geographically and temporally changing environmental conditions.

## Revisiting the early evolution of Murinae

The unique molar morphology displayed by all the modern Murinae - three longitudinal rows of cusps - is considered as the diagnostic character of Murinae subfamily. Murine upper molars are characterized by three longitudinal rows of cusps due to the presence of autapomorphic lingual cusps, while the plesiomorphic upper molars found in other Muroidea display two longitudinal rows of cusps (Coillot *et al.*, 2013). With *Progonomys* being the oldest fossil known to date displaying this complete murine dental plan, this 12.3 Mya old fossil was consequently considered as the closest relative to the common ancestor of all the modern Murinae. Conversely, representatives of the tribe Phloeomyini display a highly derived murine pattern, with highly lophodont dental morphologies associated with the presence of a posterostyle (t7) on upper molars at least in some genera (e.g. *Batomys*), and a very large tma on first lower molars (Figure 3). Molecular data reveal that this tribe is strongly anchored at the base of the murine tree (Steppan *et al.*, 2005). This finding raises controversy about where to place *Progonomys* in the murine tree. Some authors considered *Progonomys* to be either an ancestor, or a sister taxa of the *Mus-Rattus* clade. Alternatively,
*Progonomys* was considered as the ancestor, or the sister taxa of all modern murines since Phloeomyini corresponds to an insular lineage and because island evolution is known to induce considerable morphological changes (e.g. Pagès *et al.*, 2011). Our study reveals a basal divergence between the Southeast Asian *Hapalomys* division and the other Murinae. *Hapalomys* division regroups also fairly distinct taxa at the dental point of view compared to other “classical” murines, displaying a more complex “murine rasp” with three longitudinal functional cusp rows on lower molars and equally sized cusps in the three longitudinal cusp rows of the upper molars (Misonne, 1969; Musser & Heaney, 1992).

Consequently, our study opens once again the *Progonomys* Pandora's box: where to place this fossil constraint? It also raises questions about characters that are diagnostic of Murinae. Our current molecular dating estimations could not help to solve these questions. Indeed, the oldest 12.3 Myr-occurrence of *Progonomys* falls within the range of our estimates for both the basal split of Hapalomyini from other Murinae (Hapalomyini/other Murinae: 11.60-15.89 Myr) and the divergence of the Phloeomyini from other Murinae (Phloeomyini/other Murinae: 10.87-14.42 Myr). Due to the uncertainty of the sister lineages of *Progonomys* (see also Rowe *et al.*, 2011; Rowe *et al.*, 2008; Schenk *et al.*, 2013; Steppan *et al.*, 2004b), avoidance of this fossil constraints or its careful placement with use of multiple fossils seems to be advocated. An independent evolution of the “murine rasp” has been suggested at least for the Deomyinae (Chevret *et al.*, 1993; Lazzari *et al.*, 2008). Along with our findings of two murine divisions with atypical murine dental plan diverging first, questions whether the murine rasp is indeed a synapomorphy of the Murinae or whether it has evolved independently within the Hapalomyini, Phloeomyini and other Murinae. A parsimonious approach would suggest this feature to have evolved only once but in light of our findings, parsimony explanation seems to poorly match Murine diversification for dental features (e.g. cusp t7) and adaptations to arboreal versus terrestrial lifestyle alike.

## Acknowledgments

We thank Ken Aplin, Eric Bazin, Alexandre Dehne-Garcia, Emmanuel Douzery, Lionel Hautier, Kristofer Helgen, Guy G. Musser and Kevin C. Rowe for helpful discussions. Thanks to Riccardo Castiglia for processing *Margaretamys* specimens. We are grateful to François Catzeflis for his comments and access to the Montpellier mammal skeleton and tissue collection. We thank the team of the CERoPath Project (www.ceropath.org) (and specially the drivers and the students) for sample collection, in particular Hul Vibol, Kim Aun, Kim Blasdell and Philippe Buchy in Cambodia, Kittipong Chaisiri in Thailand and Kone in Lao
PDR. We are indebted to Serge Morand, as the coordinator of the CERoPath project (French ANR Biodiversity, grant ANR 07 BDIV 012) and the BiodivHealthSEA project (www.biodivhealthsea.org) (French ANR CP&ES, grant ANR 11 CPEL 002). We much appreciate field access, sampling permission and support in Malaysia (Economic Planning Unit Malaysia; Sabah Parks, in particular Maklarin B. Lakim, Alim Biun and Fred Tuh). We are grateful to the following people and institutions for granting access to study skins and skulls : Paula Jenkins, Samantha Oxford, Katherine Dixey and Roberto Portela Miguez (BMNH), Darrin Lunde, Nicole Edmison and Kristofer Helgen (NMH), Eileen Westwig, Neil Duncan and Robert Voss (AMNH), Larry Heaney and Danny Balete (FMNH) ; Géraldine Véron, and Christiane Denis (MNHN), Steve van Der Mije (RMNH), Hans Baagøe and Mogens Andersen (ZMUC). We would like to acknowledge the Ambrose Monell Cryo Collection (AMCC) at the American Museum of Natural History, New York, for their support in our research. P.H.F. was funded by a Marie-Curie fellowship (PIOF-GA-2012-330582-CANARIP-RAT). ). P.-H.F. acknowledges the SYNTHESYS Foundation for funding his work in the BMNH collections (GB-TAF-2735 and GB-TAF-5026). M.P. was funded by an FRS- FNRS fellowship (Belgian Fund for Scientific Research). A.M. was supported by the Mohamed bin Zayed Species Conservation fund (Project Number: 0925478). Analyses were performed on the CBGP HPC computational platform and CIPRES portal web. This project was supported by the network "Bibliothèque du Vivant" funded by the CNRS, the Muséum National d'Histoire Naturelle, the INRA and the CEA (Centre National de Séquençage).

**Figure 1.** Occlusal views of upper and lower first molar teeth of Murinae. Nomenclature of murine first molars, according to Cope-Osborn; correspondence with the nomenclature of Miller indicated in brackets. Top: left upper molar. Bottom: right lower molar. Modified from Lazzari *et al.*, 2010.

**Figure 2.** Phylogenetic and molecular dating results for the Southeast Asian murine and close-relative lineages. The tree is a chronogram (uncorrelated log-normal molecular clock) based on a BEAST MCMC analysis of the combined data set. The green and blue colour indicates the former *Micromys* and the *Pithecheir* divisions respectively. **We proposed to split the polyphyletic *Micromys* division into, at least, 4 monotypic tribes highlighted in green capitals: (i) Chiropodomyini, (ii) Hapalomyini, (iii) Micromyini, and (iv) Vandeleuriani.**
Numbers at nodes represent branch supports (BP/PP). ‘*/’ stands for ‘BP=100%’, ‘/*’ for ‘PP=1.00’, ** for ‘BP=100% AND PP=1.00’, ‘-‘ not supported by one out of the two analyses. When support information is lacking, it means that the branch is not supported.

Clocks indicate the fossil calibration points used for the molecular dating (see Fabre *et al.*, 2013); 95% credibility intervals of molecular estimates (median height) are given for each node. **Abbreviations: PLIO. : Pliocene, Pi: Piacenzian, PLEIST.: Pleistocene, Myr: million years.**

**Figure 3.** Dental characters of the arboreal Murinae from Southeast Asia compared with their sister-taxa in lights of the molecular phylogeny obtained in this study. Representatives of the paraphyletic *Micromys* division are highlighted in green, their sister-taxa in black. Plain and dotted arrow indicates respectively presence / absence of a character mentioned in the discussion.

Top: left upper molar. Bottom: right lower molar. Modified from Misonne, 1969; Musser, 1981.

**Figure 4.** Dental characters of the arboreal Murinae from Southeast Asia compared with their sister-taxa in lights of the molecular phylogeny obtained in this study. Representatives of the paraphyletic *Pithecheir* division in blue, sister-taxa in black. Plain and dotted arrow indicates respectively presence / absence of a character mentioned in the discussion.

Top: left upper molar. Bottom: right lower molar. Modified from Misonne, 1969; Musser, 1981.

**Table 1.** Higher level classification of extant Rodentia (see text for further details on references) largely inspired from state of the art molecular systematic and with explicit references to Wilson & Reeder, 2005. *: paraphyletic groups. Bold: members of the former *Micromys* and *Pithecheir* divisions. Several taxa are still classified as "*incertae sedis*" pending for molecular phylogenetic investigation.

<table><thead><tr><th>Murinae</th><th>Tribes</th><th>Divisions</th><th>Putative members</th></tr></thead><tbody><tr><td><strong>Hapalomys</strong></td><td><strong>HAPALOMYINI</strong></td><td><strong>Hapalomys division</strong></td><td></td></tr><tr><td><em>Batomys</em></td><td>PHLOEOMYINI</td><td><em>Phloeomys</em> division</td><td></td></tr><tr><td><em>Carpomys</em></td><td></td><td></td><td></td></tr></tbody></table>
Crateromys

Musseromys

Phloecomys

<table><thead><tr><th>Chiropodomys</th><th>CHIROPODODYMINI</th><th>Chiropodomys division</th></tr></thead><tbody><tr><td>Apomys</td><td>HYDROMYINI</td><td>Chrotomys division</td></tr><tr><td>Archboldomys</td><td></td><td></td></tr><tr><td>Chrotomys</td><td></td><td></td></tr><tr><td>Rhynchomys</td><td></td><td></td></tr><tr><td>Soricomys</td><td></td><td></td></tr><tr><td>Conilurus</td><td>HYDROMYINI</td><td>Pseudomys division*</td></tr><tr><td>Leggadina</td><td></td><td></td></tr><tr><td>Leporillus</td><td></td><td></td></tr><tr><td>Mastacomys</td><td></td><td></td></tr><tr><td>Mesembriomys</td><td></td><td></td></tr><tr><td>Notomys</td><td></td><td></td></tr><tr><td>Pseudomys</td><td></td><td></td></tr><tr><td>Zyzomys</td><td></td><td></td></tr><tr><td>Crossomys</td><td>HYDROMYINI</td><td>Hydromys division</td></tr><tr><td>Hydromys</td><td></td><td>Baiyankamys</td></tr><tr><td>Parahydromys</td><td></td><td></td></tr><tr><td>Leptomys</td><td>HYDROMYINI</td><td>Xeromys division</td></tr><tr><td>Microhydromys</td><td></td><td></td></tr><tr><td>Pseudohydromys</td><td></td><td></td></tr><tr><td>Xeromys</td><td></td><td></td></tr><tr><td>Melomys*</td><td>HYDROMYINI</td><td>Uromys division</td></tr><tr><td>Paramelomys</td><td></td><td>Xenuromys</td></tr><tr><td>Protochromys</td><td></td><td></td></tr><tr><td>Solomys</td><td></td><td></td></tr><tr><td>Uromys</td><td></td><td></td></tr><tr><td>Abeomelomys</td><td>HYDROMYINI</td><td>Pogonomys division</td></tr><tr><td>Anisomys</td><td></td><td></td></tr><tr><td>Brassomys</td><td></td><td></td></tr><tr><td>Chiruromys</td><td></td><td></td></tr><tr><td>Coccymys</td><td></td><td></td></tr><tr><td>Hyomys</td><td></td><td></td></tr><tr><td>Lorentzimys</td><td></td><td></td></tr><tr><td>Macruromys</td><td></td><td></td></tr><tr><td>Mammelomys</td><td></td><td></td></tr><tr><td>Mallomys</td><td></td><td></td></tr><tr><td>Pogonomelomys</td><td></td><td></td></tr><tr><td>Pogonomys</td><td></td><td></td></tr><tr><td>Micromys</td><td>MICROMYINI</td><td>Micromys division</td></tr><tr><td>Maxomys</td><td>RATTINI</td><td>Maxomys division</td></tr></tbody></table>
<table><tbody><tr><td><strong>Crunomys</strong></td><td></td><td></td><td></td></tr><tr><td><em>Chiromyscus</em></td><td>RATTINI</td><td><em>Dacnomys</em> division</td><td><em>Anonymomys</em></td></tr><tr><td><em>Dacnomys</em></td><td></td><td></td><td></td></tr><tr><td><strong>Lenothrix</strong></td><td></td><td></td><td></td></tr><tr><td><em>Leopoldamys</em></td><td></td><td></td><td></td></tr><tr><td><strong>Margaretamys</strong></td><td></td><td></td><td></td></tr><tr><td><em>Niviventer</em></td><td></td><td></td><td></td></tr><tr><td><em>Saxatilomys</em></td><td></td><td></td><td></td></tr><tr><td><em>Tonkinomys</em></td><td></td><td></td><td></td></tr><tr><td><strong>Bunomys</strong></td><td>RATTINI</td><td><em>Rattus</em> division</td><td></td></tr><tr><td><em>Bandicota</em></td><td></td><td></td><td><em>Abditomys</em></td></tr><tr><td><em>Berylmys</em></td><td></td><td></td><td><em>Hadromys</em></td></tr><tr><td><em>Bullimus</em></td><td></td><td></td><td><em>Kadarsanomys</em></td></tr><tr><td><em>Diplothrix</em></td><td></td><td></td><td><em>Komodomys</em></td></tr><tr><td><em>Halmaheramys</em></td><td></td><td></td><td><em>Nesoromys</em></td></tr><tr><td><em>Limnomys</em></td><td></td><td></td><td><em>Palawanomys</em></td></tr><tr><td><em>Nesokia</em></td><td></td><td></td><td><em>Papagomys</em></td></tr><tr><td><em>Paruromys</em></td><td></td><td></td><td><em>Tryphomys</em></td></tr><tr><td><em>Paulamys</em></td><td></td><td></td><td></td></tr><tr><td><em>Rattus*</em></td><td></td><td></td><td></td></tr><tr><td><em>Srilankamys</em></td><td></td><td></td><td></td></tr><tr><td><em>Sundamys</em></td><td></td><td></td><td></td></tr><tr><td><em>Taeromys</em></td><td></td><td></td><td></td></tr><tr><td><em>Tarsomys</em></td><td></td><td></td><td></td></tr><tr><td><em>Melasmothrix</em></td><td>RATTINI</td><td><em>Melasmothrix</em> division</td><td></td></tr><tr><td><em>Paucidentomys</em></td><td></td><td></td><td></td></tr><tr><td><em>Sommeromys</em></td><td></td><td></td><td></td></tr><tr><td><em>Tateomys</em></td><td></td><td></td><td></td></tr><tr><td><em>Echiothrix</em></td><td></td><td></td><td></td></tr><tr><td><em>Waiomys</em></td><td></td><td></td><td></td></tr><tr><td><strong>Vandeleuria</strong></td><td>VANDELEURINI</td><td><em>Vandeleuria</em> division</td><td></td></tr><tr><td><em>Mus</em></td><td>MURINI</td><td><em>Mus</em>* division</td><td><em>Muriculus</em></td></tr><tr><td><em>Malpaisomys</em></td><td></td><td></td><td></td></tr><tr><td><em>Colomys</em></td><td>PRAOMYINI</td><td><em>Stenocephalemys</em> division</td><td><em>Nilopegamys</em></td></tr><tr><td><em>Zelotomys</em></td><td></td><td></td><td></td></tr><tr><td><em>Heimyscus</em></td><td></td><td></td><td></td></tr><tr><td><em>Hylomyscus</em></td><td></td><td></td><td></td></tr><tr><td><em>Mastomys</em></td><td></td><td></td><td></td></tr><tr><td><em>Myomyscus</em></td><td></td><td></td><td></td></tr><tr><td><em>Praomys</em></td><td></td><td></td><td></td></tr><tr><td><em>Stenocephalemys</em></td><td></td><td></td><td></td></tr><tr><td><em>Myotomys</em></td><td>OTOMYINI</td><td><em>Otomys</em> division</td><td></td></tr><tr><td><em>Otomys</em></td><td></td><td></td><td></td></tr></tbody></table>
Parotomys

<table><tr><td><strong>Cremnomys</strong></td><td>MILLARDINI</td><td><em>Millardia</em> division</td><td><em>Diomys</em></td></tr><tr><td><strong>Millardia</strong></td><td></td><td></td><td><em>Madromys</em></td></tr><tr><td><strong><em>Pithecheir</em></strong></td><td>MILLARDINI</td><td><strong><em>Pithecheir</em></strong> division</td><td><strong><em>Pithecheirops</em></strong></td></tr><tr><td><strong>Apodemus</strong></td><td>APODEMINI</td><td></td><td></td></tr><tr><td><strong>Tokudaia</strong></td><td></td><td></td><td></td></tr><tr><td><strong>Aethomys</strong></td><td>ARVICANTHINI</td><td><em>Aethomys</em> division</td><td></td></tr><tr><td><strong>Micaelamys</strong></td><td></td><td></td><td></td></tr><tr><td><strong>Arvicanthis</strong></td><td></td><td></td><td></td></tr><tr><td><strong>Desmomys</strong></td><td></td><td></td><td></td></tr><tr><td><strong>Lemniscomys</strong></td><td></td><td></td><td></td></tr><tr><td><strong>Mylomys</strong></td><td></td><td></td><td></td></tr><tr><td><strong>Pelomys</strong></td><td></td><td></td><td></td></tr><tr><td><strong>Rhabdomys</strong></td><td></td><td></td><td></td></tr><tr><td><strong>Dasymys</strong></td><td>ARVICANTHINI</td><td><em>Dasymys</em> division</td><td></td></tr><tr><td><strong>Golunda</strong></td><td>ARVICANTHINI</td><td><em>Golunda</em> division</td><td></td></tr><tr><td><strong>Dephomys</strong></td><td>ARVICANTHINI</td><td><em>Hybomys</em> division</td><td></td></tr><tr><td><strong>Hybomys</strong></td><td></td><td></td><td></td></tr><tr><td><strong>Stochomys</strong></td><td></td><td></td><td></td></tr><tr><td><strong>Grammomys</strong></td><td>ARVICANTHINI</td><td><em>Oenomys</em> division</td><td><em>Lamottemys</em></td></tr><tr><td><strong>Oenomys</strong></td><td></td><td></td><td></td></tr><tr><td><strong>Rhagamys</strong></td><td></td><td></td><td></td></tr><tr><td><strong>Thamnomys</strong></td><td></td><td></td><td></td></tr><tr><td><strong>Malacomys</strong></td><td>MALACOMYINI</td><td><em>Malacomys</em> division</td><td></td></tr><tr><td><strong><em>Vernaya</em></strong></td><td>Murinae <em>incertae sedis</em></td><td></td><td></td></tr><tr><td><strong><em>Haeromys</em></strong></td><td>Murinae <em>incertae sedis</em></td><td></td><td></td></tr><tr><td><strong><em>Eropeplus</em></strong></td><td>Murinae <em>incertae sedis</em></td><td></td><td></td></tr><tr><td><strong><em>Lenomys</em></strong></td><td>Murinae <em>incertae sedis</em></td><td></td><td></td></tr><tr><td><strong>Spelaeomys+</strong></td><td>Murinae <em>incertae sedis</em></td><td></td><td></td></tr><tr><td><strong>Coryphomys+</strong></td><td>Murinae <em>incertae sedis</em></td><td></td><td></td></tr></table>

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<figure><img src="image_4.png" /></figure>

<figure><img src="image_5.png" /></figure>

<figure><img src="image_6.png" /></figure>

59Two major teeth convergences in both *Micromys* and *Pithecheir* divisions:

60*: presence of cusp t1bis and t2bis

#: presence of cusp t7
<figure><img src="image_7.png" /></figure>

Old Micromys Division
Old Pithecheir Division

<figure><img src="image_8.png" /></figure>

<table><thead><tr><th>19.5</th><th>16</th><th>13.7</th><th>11.6</th><th>7.2</th><th>5.3</th><th>3.6</th><th>2.6</th><th>0</th></tr><tr><th>Burdigalian</th><th>Langhian</th><th>Serravallian</th><th>Tortonian</th><th>Messinian</th><th>Zanclean</th><th>Pi</th><th></th><th></th></tr></thead><tbody><tr><td colspan="4">MIOCENE</td><td colspan="2">PLIO.</td><td colspan="2">PLEIST.</td><td></td></tr></tbody></table>
<figure><img src="image_9.png" /><figcaption>Paraphyletic *Micromys* division</figcaption></figure>

*Chiropodomys gliroides*

Notomys alexis

Hydromys chrysogaster

*Vandeleuria oleracea*

Mus booduga

Apodemus sylvaticus

<figure><img src="image_10.png" /></figure>

*Hapalomys longicaudatus*

Rattus rattus

*Micromys minutus*

Rattus rattus

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Paraphyletic *Pithecheir* division

<figure><img src="image_11.png" /><figcaption>Lenothrix canus</figcaption></figure>

<figure><img src="image_12.png" /><figcaption>Margaretamys beccarii</figcaption></figure>

<figure><img src="image_13.png" /><figcaption>Dacnomys millardi</figcaption></figure>

<figure><img src="image_14.png" /><figcaption>Pithecheir melanurus</figcaption></figure>

<caption>Millardia gleadowi</caption>
SUPPLEMENTARY INFORMATION

Figure S1: Maps of the Indo-Pacific area indicating

A) the contemporary major islands, seas, and biogeographic areas (map derived from (Fabre et al., 2013))

B) the distribution of the genera of the *Micromys* and *Pithecheir* divisions respectively.
Maps were extracted and modified from R (Kiel, Germany).

A)

<figure><img src="image_15.png" /></figure>

B)

<figure><img src="image_16.png" /></figure>
<table><caption>Table S1: List of the species considered in this study and GenBank accession numbers of sequences.</caption><caption>a) Information about samples handled in this study (new data)</caption><thead><tr><th>Division</th><th>Genus</th><th>Species</th><th>Common Name</th><th>Voucher</th><th>Locality</th><th>Collection</th></tr></thead><tbody><tr><td>Rattus</td><td>Saxatylomys</td><td>paulinae</td><td>Paulina's Limestone Rat</td><td>LK217</td><td>Khammouane, Laos</td><td>CERoPath</td></tr><tr><td>Rattus</td><td>Saxatylomys</td><td>paulinae</td><td>Paulina's Limestone Rat</td><td>LK218</td><td>Khammouane, Laos</td><td>CERoPath</td></tr><tr><td>Rattus</td><td>Saxatylomys</td><td>paulinae</td><td>Paulina's Limestone Rat</td><td>LK219</td><td>Khammouane, Laos</td><td>CERoPath</td></tr><tr><td>Rattus</td><td>Tonkinomys</td><td>daoventieni</td><td>Daovantien's Limestone Rat</td><td>DPL1662 (M-275575)</td><td>Huu Lien District, Lang Son Province, Vietnam</td><td>AMNH / AMCC</td></tr><tr><td>Micromys</td><td>Micromys</td><td>minutus</td><td>Eurasian Harvest Mouse</td><td>72 (MK0509 BZ02)</td><td>China</td><td>JP. Quéré</td></tr><tr><td>Micromys</td><td>Micromys</td><td>minutus</td><td>Eurasian Harvest Mouse</td><td>73 (MK0509 BZ07)</td><td>China</td><td>JP. Quéré</td></tr><tr><td>Micromys</td><td>Vandeleuria</td><td>oleracea</td><td>Asiatic Long-tailed Climbing Mouse</td><td>M30312*</td><td>Mt Popa, Popamyo Village</td><td>K. Aplin</td></tr><tr><td>Micromys</td><td>Chiropodomys</td><td>gliroides</td><td>Pencil-tailed Tree Mouse</td><td>M32332</td><td>Nampa Camp</td><td>K. Aplin</td></tr><tr><td>Micromys</td><td>Chiropodomys</td><td>major</td><td>Greater Pencil-tailed Tree Mouse</td><td>A48</td><td>Tawau Hills Park primary forest, Borneo</td><td>K. Wells</td></tr><tr><td>Micromys</td><td>Chiropodomys</td><td>sp.</td><td>-</td><td>R4959</td><td>Loei, Thailand</td><td>CERoPath</td></tr><tr><td>Micromys</td><td>Chiropodomys</td><td>sp.</td><td>-</td><td>R5238**</td><td>Loei, Thailand</td><td>CERoPath</td></tr><tr><td>Micromys</td><td>Hapalomys</td><td>delacouri</td><td>Lesser Marmoset Rat</td><td>R5237***</td><td>Loei, Thailand</td><td>CERoPath</td></tr><tr><td>Pithecheir</td><td>Pithecheir</td><td>melanurus</td><td>Javan Pithecheir)</td><td>Pithecheir I (MNHN-ZM-MO 1900-580)</td><td>Java</td><td>MNHN</td></tr><tr><td>Pithecheir</td><td>Pithecheir</td><td>melanurus</td><td>Javan Pithecheir)</td><td>Pithecheir II (MNHN-ZM-MO 1900-581)</td><td>Java</td><td>MNHN</td></tr><tr><td>Pithecheir</td><td>Pithecheir</td><td>parvus</td><td>Malay Peninsula Pithecheir</td><td>Pithecheir III (MNHN-ZM-MO 1977-251)</td><td>Simpang Pertang, Negri Sembilan, West Malaysia</td><td>MNHN</td></tr><tr><td>Pithecheir</td><td>Pithecheir</td><td>parvus</td><td>Malay Peninsula Pithecheir</td><td>Pithecheir IV (MNHN-ZM-MO 1977-252)</td><td>Selangor, Subang tima, West Malaysia</td><td>MNHN</td></tr><tr><td>Pithecheir</td><td>Lenothrix</td><td>canus</td><td>Sundaic Lenothrix</td><td>O09</td><td>Poring Hot Springs primary forest, Borneo</td><td>K. Wells</td></tr><tr><td>Pithecheir</td><td>Lenothrix</td><td>canus</td><td>Sundaic Lenothrix</td><td>N92</td><td>Poring Hot Springs primary forest, Borneo</td><td>K. Wells</td></tr><tr><td>Pithecheir</td><td>Margaretamys</td><td>christinae</td><td>Christine's Margareta Rat</td><td>RC1 / MK14</td><td>Pegunungan Mekongga, Southeast Sulawesi</td><td>R. Castiglia</td></tr></tbody></table>
Most of these samples are vouchered and archived in accessible collections. Additional information could be retrieved via the following database webpages:

http://www.ceropath.org/

http://sci-web-001.amnh.org/db/emuwebamnh/

http://research.amnh.org/genomics/Facilities/AMCC/database/

https://science.mnhn.fr/institution/mnhn/collection/zm/item/search/form

Tissue samples provided by Dr. Ken Aplin and Dr. Jean-Pierre Quéré are housed at the Centre de Biologie et de Gestion des Populations at Montpellier, France, with a part of the CeroPath collection. Samples from Borneo (A48, O09 and N92) were collected from life captures with a biopsy punch and have not been vouchered. Supplementary information on animal captures and handling are detailed in Wells et al., 2007. Sample of *Margaretamys christinae* (original field number MK14) corresponds to the holotype specimen (Mortelliti et al., 2012), deposited in the Museum Zoologicum Bogoriense-LIPI, Cibinong, Java.

* only *cytb* sequence was obtained from M30312. We combined this new *cytb* sequence with those available in GenBank from another specimen of *Vandeleuria oleracea*.

** Six species of *Chiropodomys* are currently recognized (Musser & Carleton, 2005). Only one species occurs in continental Southeast Asia, *C. gliroides*. According to Mammal Species of the World, its distribution is extremely large and extends from W China to islands of the Sunda Shelf (recorded in Burma, Thailand, Laos, Vietnam, Malay Peninsula, S Sumatra, Pulau Nias, Kepulauan Tujuh, Kepulauan Natuna, Java, and Bali; probably also occurs on other small islands of the Sunda Shelf and in Cambodia). Karyotype of a Thai specimen, R5238, was published by Badenhorst *et al.*, 2009 as having 2n=42 and NFa=40. The authors reported that these results are in partial agreement with previous data concerning this very poorly documented species. Indeed, Yong reported that eight Malayan specimens were characterized by 2n=42 and revealed differences in morphology of autosomes and sex chromosomes (Yong, 1973, 1983). As a single specimen was available in Badenhorst *et al.*, 2009 (i.e. R5238), the authors emphasized that it was impossible to distinguish whether the differences correspond to intraspecific polymorphisms, or if they were indicative of two cryptic species within *C. gliroides*. Recently, Yong and collaborators further investigated the nucleolar organizer regions of *C. gliroides* from Peninsular Malaysia (Yong *et al.*, 2012). Here again, they reported differences arguing for cryptic sibling species within *C. gliroides*. Currently, no sequences of the Malaysian *Chiropodomys* are available to investigate this question with phylogenetic tools. However, in our tree, 2 lineages within *C. gliroides* are retrieved: 1) a Vietnamese lineage, AMCC 101511 from Vietnam (Vi Xuyen District, Ha Giang Province) (Rowe *et al.*, 2008) and M32332 (Nampa Camp) (Bp = 99%, PP= 1.00); 2) a Thai lineage, R4959 and
R5238 both from Loei (Bp = 100, PP= 1.00). These two lineages are clearly distinct from *Chiropodomys major* (A48 from Borneo).

*** Two species of *Hapalomys* are currently recognized (Musser & Carleton, 2005): *H. delacouri* in S China, N Laos and C Vietnam; and *H. longicaudatus* in SW China, SE Burma, SW and peninsular Thailand and Malay Peninsula. Karyotype of a Thai *H. delacouri* specimen, R5237, was described (Badenhorst *et al.*, 2012; Badenhorst *et al.*, 2009) as having 2n=48 and NFa=92. A karyotype of a second specimen of *H. delacouri* from Southern Vietnam was reported as 2n=38 and NFa=48 (Abramov *et al.*, 2012). These differences correspond to a range of variability that is too huge to be considered as intraspecific polymorphism (G. Dobigny, pers. comm.). Abramov and collaborators proposed to consider R5237 as another species of *Hapalomys*, *H. pasquieri*. *H. pasquieri* was previously described from Xieng Khouang in Northern Laos but is currently considered as a subspecies of *H. delacouri* by Musser ad Carleton (2005). No sequence has been published from the Vietnamese specimen, meaning that no molecular comparison could be achieved to disentangle these discrepancies.

Further investigations have to be carried out to refine the taxonomy of *Chiropodomys* and *Hapalomys*. However, these taxonomic uncertainties do not challenge our results concerning the relationships of these genera with the other murine representatives nor the polyphyly of the *Micromys* division.

b) Sequences extracted from GenBank:

Classification

Murinae

Arvicanthini

*Aethomys* division

*Arvicanthis* division

*Dasymys* division

*Aethomys_chrysophilus*

*Micaelamys_namaquensis*

*Arvicanthis_niloticus*

*Arvicanthis_somalicus*

*Arvicanthis_neumanni*

*Desmomys_harringtoni*

*Lemniscomys_barbarus*

*Lemniscomys_striatus*

*Pelomys_fallax*

*Rhabdomys_pumilio*

*Mylomys_dybowski*

*Dasymys_incomtus*

*Golunda_ellioti*

*Hybomys_univittatus*

*Stochomys_longicaudatus*

*Grammomys_dolichurus*

*Grammomys_macmillani*

cyt b

IRBP

GHR

BRCA1

AJ604515

AY326075

AY294914

EU349649

AF141215

AM408330

AM910944

EU349649

AF004569

DQ022386

AM910944

NA

AF004573

NA

AY294918

NA

NA

KC953358

AY294918

EU349648

AF141206

EU292144

NA

NA

NA

KC953387

DQ019062

KC953184

AF141210

AM408321

AM910956

KC953184

DQ022382

DQ022391

NA

NA

AF141214

AY326106

AY294913

EU349650

AF141212

EU292146

AM910965

NA

AF141217

EU292143

AM910950

EU349653

AM408338

AM408332

AM910951

NA

AF141219

DQ022388

DQ019059

KC953181

EU349786

EU349873

DQ019076

EU349652

EU275252

EU349847

EU349800

NA

EU349746

EU349848

EU349802

KC953175
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Otomyini Subfamily Otomyinae

Millardini Millardia division

Apodemini Apodemus division

Malacomyini Malacomys division

Praomyini Colomys division

Murini Mus division

Hydromyini Micromys division

<table><tr><td>Grammomys_surdaster</td><td>EU349747</td><td>NA</td><td>EU349803</td><td>NA</td></tr><tr><td>Grammomys_ibeanus</td><td>NA</td><td>KC953380</td><td>EU349801</td><td>KC953174</td></tr><tr><td>Oenomys_hypoxanthus</td><td>EU349769</td><td>EU349865</td><td>DQ019069</td><td>EU349654</td></tr><tr><td>Otomys_anchietae</td><td>AF492708</td><td>AY326101</td><td>GQ405388</td><td>NA</td></tr><tr><td>Otomys_angoniensis</td><td>AM408343</td><td>AM408325</td><td>AM910971</td><td>EU349647</td></tr><tr><td>Otomys_denti</td><td>NA</td><td>KC953428</td><td>KC953305</td><td>NA</td></tr><tr><td>Parotomys_brantsii</td><td>EU349773</td><td>KC953432</td><td>AY294912</td><td>EU349646</td></tr><tr><td>Cremnomys_cutchicus</td><td>DQ022381</td><td>DQ022384</td><td>NA</td><td>NA</td></tr><tr><td>Millardia_kathleenae</td><td>EU292148</td><td>EU292145</td><td>AM910963</td><td>NA</td></tr><tr><td>Millardia_meltada</td><td>AF141221</td><td>AM408322</td><td>AM910962</td><td>NA</td></tr><tr><td>Apodemus_agrarius</td><td>EU349733</td><td>AB032858</td><td>DQ019054</td><td>EU349658</td></tr><tr><td>Apodemus_argenteus</td><td>AB032848</td><td>AB032855</td><td>NA</td><td>NA</td></tr><tr><td>Apodemus_flavicollis</td><td>AB032853</td><td>AB032860</td><td>AM910943</td><td>NA</td></tr><tr><td>Apodemus_mystacinus</td><td>AF159394</td><td>AJ311158</td><td>AM910942</td><td>KC953157</td></tr><tr><td>Apodemus_semotus</td><td>EU349734</td><td>AB032862</td><td>DQ019055</td><td>NA</td></tr><tr><td>Apodemus_speciosus</td><td>AB032849</td><td>AB032856</td><td>AB491492</td><td>NA</td></tr><tr><td>Apodemus_sylvaticus</td><td>AB033695</td><td>AB032863</td><td>NA</td><td>NA</td></tr><tr><td>Tokudaia_osimensis</td><td>AB029429</td><td>AB033712</td><td>EU349828</td><td>EU349659</td></tr><tr><td>Malacomys_edwardsi</td><td>DQ022379</td><td>DQ022392</td><td>AM910958</td><td>NA</td></tr><tr><td>Malacomys_longipes</td><td>EU349757</td><td>DQ022393</td><td>DQ019064</td><td>EU349656</td></tr><tr><td>Colomys_goslingi</td><td>AF518372</td><td>DQ022395</td><td>AM910948</td><td>NA</td></tr><tr><td>Zelotomys_hildegardeae</td><td>EU349791</td><td>DQ022396</td><td>DQ019080</td><td>EU349661</td></tr><tr><td>Heimyscus_fumosus</td><td>AF518333</td><td>DQ022397</td><td>AM910953</td><td>NA</td></tr><tr><td>Hylomyscus_parvus</td><td>AF518330</td><td>DQ022399</td><td>DQ019060</td><td>NA</td></tr><tr><td>Hylomyscus_stella</td><td>AF518331</td><td>AM408320</td><td>AM910955</td><td>NA</td></tr><tr><td>Mastomys_erythroleucus</td><td>AF518338</td><td>AM408335</td><td>AM910959</td><td>KC953189</td></tr><tr><td>Mastomys_hildebrandti</td><td>NA</td><td>KC953395</td><td>AY294916</td><td>AY295001</td></tr><tr><td>Mastomys_kollmannspergeri</td><td>AF518345</td><td>DQ022402</td><td>AM910961</td><td>NA</td></tr><tr><td>Mastomys_natalensis</td><td>AF518342</td><td>AY326093</td><td>EU349813</td><td>NA</td></tr><tr><td>Mastomys_pernanus</td><td>AF518343</td><td>DQ022403</td><td>AM910960</td><td>NA</td></tr><tr><td>Myomyscus_brockmani</td><td>AF518353</td><td>DQ022407</td><td>AM910966</td><td>NA</td></tr><tr><td>Myomyscus_verreauxii</td><td>AF518355</td><td>DQ022408</td><td>AM910967</td><td>NA</td></tr><tr><td>Myomyscus_yemeni</td><td>AF518357</td><td>DQ022409</td><td>AM910968</td><td>NA</td></tr><tr><td>Praomys_daltoni</td><td>AF518349</td><td>DQ022406</td><td>AM910972</td><td>NA</td></tr><tr><td>Praomys_degraaffi</td><td>AF518359</td><td>DQ022410</td><td>NA</td><td>NA</td></tr><tr><td>Praomys_jacksoni</td><td>EU349778</td><td>DQ022411</td><td>DQ019071</td><td>EU349663</td></tr><tr><td>Praomys_misonnei</td><td>AF518364</td><td>DQ022412</td><td>JF284232</td><td>NA</td></tr><tr><td>Praomys_tullbergi</td><td>EU349779</td><td>AM408327</td><td>DQ019072</td><td>EU349662</td></tr><tr><td>Praomys_verschureni</td><td>AF518373</td><td>DQ022394</td><td>NA</td><td>NA</td></tr><tr><td>Stenocephalemys_albipes</td><td>AF518346</td><td>DQ022404</td><td>AM910977</td><td>NA</td></tr><tr><td>Stenocephalemys_albocaudata</td><td>AF518369</td><td>DQ022414</td><td>AM910978</td><td>NA</td></tr><tr><td>Mus(Coelomys)_crociduroides</td><td>AJ698878</td><td>AJ698894</td><td>AM910964</td><td>NA</td></tr><tr><td>Mus_booduga</td><td>AB125761</td><td>AB125796</td><td>NA</td><td>NA</td></tr><tr><td>Mus_cervicolor</td><td>AB125766</td><td>AB125799</td><td>NA</td><td>NA</td></tr><tr><td>MusCookii</td><td>AB125769</td><td>KC953404</td><td>KC953279</td><td>NA</td></tr><tr><td>Mus_terricolor</td><td></td><td>AB125810</td><td>NA</td><td>NA</td></tr><tr><td>Malpaisomys_insularis</td><td>JN418214</td><td>JN418213</td><td>NA</td><td>NA</td></tr><tr><td>Mus_pahari</td><td>EU349767</td><td>EU349864</td><td>NA</td><td>NA</td></tr><tr><td>Mus(Nannomys)_minutoides</td><td>AY057816</td><td>AJ875086</td><td>NA</td><td>NA</td></tr><tr><td>Mus(Pyromys)_platythrix</td><td>AJ698880</td><td>AJ698895</td><td>NA</td><td>NA</td></tr><tr><td>Mus_musculus</td><td>NA</td><td>NM015745</td><td>M33324</td><td>EU349657</td></tr><tr><td>Chiropodomys_gliroides_M32332</td><td>This study</td><td>This study</td><td>This study</td><td>This study</td></tr><tr><td>Chiropodomys_gliroides_AMCC10151</td><td>NA</td><td>EU349841</td><td>EU349797</td><td>EU349674</td></tr><tr><td>Chiropodomys_major_A48</td><td>NA</td><td>This study</td><td>This study</td><td>This study</td></tr><tr><td>Chiropodomys_sp_R4959</td><td>This study</td><td>This study</td><td>This study</td><td>This study</td></tr><tr><td>Chiropodomys_sp_R5238</td><td>This study</td><td>This study</td><td>This study</td><td>This study</td></tr><tr><td>Apomys_datae</td><td>AY324464</td><td>EU349836</td><td>KC878169</td><td>KC953158</td></tr><tr><td>Apomys_hylocoetes</td><td>EU349735</td><td>KC953357</td><td>AY294915</td><td>AY295000</td></tr><tr><td>Apomys_insignis</td><td>AY324470</td><td>DQ191492</td><td>NA</td><td>NA</td></tr></table>
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Rattini

<table><tbody><tr><td></td><td>Apomys_microdon</td><td>AY324480</td><td>DQ191493</td><td>GQ405366</td><td>NA</td></tr><tr><td></td><td>Apomys_musculus</td><td>DQ191469</td><td>DQ191494</td><td>GQ405367</td><td>NA</td></tr><tr><td></td><td>Archboldomyus_luzonensis</td><td>AY687858</td><td>DQ191495</td><td>GQ405368</td><td>EU349675</td></tr><tr><td></td><td>Archboldomyus_maximus</td><td>JQ898033</td><td>JQ898078</td><td>NA</td><td>NA</td></tr><tr><td></td><td>Chrotomys_gonzalesi</td><td>AY687861</td><td>DQ191503</td><td>GQ405375</td><td>NA</td></tr><tr><td></td><td>Chrotomys_mindorensis</td><td>JQ898037</td><td>JQ898073</td><td>NA</td><td>NA</td></tr><tr><td></td><td>Chrotomys_sibuyanensis</td><td>AY687862</td><td>DQ191504</td><td>GQ405376</td><td>NA</td></tr><tr><td></td><td>Chrotomys_silaceus</td><td>JQ898040</td><td>DQ191502</td><td>GQ405377</td><td>NA</td></tr><tr><td></td><td>Chrotomys_whiteheadi</td><td>JQ898045</td><td>JQ898074</td><td>NA</td><td>NA</td></tr><tr><td></td><td>Rhynchomys_isarogensis</td><td>JQ898050</td><td>AY326108</td><td>DQ019075</td><td>EU349677</td></tr><tr><td></td><td>Soricomys_leonardocoi</td><td>JQ898062</td><td>JQ898077</td><td>NA</td><td>NA</td></tr><tr><td></td><td>Soricomys_montanus</td><td>JQ898066</td><td>JQ898076</td><td>NA</td><td>NA</td></tr><tr><td></td><td>Soricomys_musseri</td><td>JQ898071</td><td>JQ898075</td><td>NA</td><td>NA</td></tr><tr><td rowspan="2">Hydromys division</td><td>Hydromys_chrysogaster</td><td>AM408339</td><td>AM408319</td><td>AM910954</td><td>EU349699</td></tr><tr><td>Parahydromys_asper</td><td>EU349771</td><td>EU349866</td><td>EU349820</td><td>EU349698</td></tr><tr><td rowspan="10">Pseudomys division</td><td>Conilurus_penicillatus</td><td>EU349743</td><td>EU349844</td><td>DQ019057</td><td>EU349694</td></tr><tr><td>Leggadina_forresti</td><td>EU349751</td><td>EU349850</td><td>DQ019061</td><td>EU349686</td></tr><tr><td>Leporillus_conditor</td><td>EU349752</td><td>EU349851</td><td>EU349806</td><td>EU349692</td></tr><tr><td>Mastacomys_fuscus</td><td>EU349760</td><td>EU349856</td><td>EU349812</td><td>EU349687</td></tr><tr><td>Mesembriomys_gouldii</td><td>NA</td><td>EU349861</td><td>EU349817</td><td>EU349693</td></tr><tr><td>Notomys_fuscus</td><td>EU349768</td><td>EU360811</td><td>NA</td><td>NA</td></tr><tr><td>Pseudomys_australis</td><td>EU349780</td><td>EU349870</td><td>DQ019073</td><td>EU349688</td></tr><tr><td>Zyzomys_argvus</td><td>EU349792</td><td>EU349878</td><td>EU349831</td><td>EU349685</td></tr><tr><td>Anisomys_imitator</td><td>EU349732</td><td>EU349833</td><td>DQ019052</td><td>NA</td></tr><tr><td>Abeomelomys_sevia</td><td>EU349730</td><td>EU349832</td><td>EU349793</td><td>EU349682</td></tr><tr><td>Chiruromys_vates</td><td>EU349741</td><td>EU349842</td><td>NA</td><td>NA</td></tr><tr><td>Hyomys_goliath</td><td>EU349750</td><td>KC953384</td><td>EU349805</td><td>EU349679</td></tr><tr><td>Mallomys_rothschildi</td><td>EU349758</td><td>EU349854</td><td>EU349810</td><td>EU349681</td></tr><tr><td>Mammelomys_flanosus</td><td>EU349759</td><td>EU349855</td><td>EU349811</td><td>KC953188</td></tr><tr><td>Macruromys_major</td><td>EU349756</td><td>EU349853</td><td>EU349809</td><td>EU349678</td></tr><tr><td>Pogonomys_loriae</td><td>EU349776</td><td>EU349868</td><td>EU349823</td><td>EU349683</td></tr><tr><td>PogonomysMacrourus</td><td>EU349777</td><td>EU349869</td><td>EU349824</td><td>EU349684</td></tr><tr><td>Pogonomys_sylvestris</td><td>NA</td><td>GQ405365</td><td>GQ405389</td><td>NA</td></tr><tr><td rowspan="4">Uromys division</td><td>Melomys_rufescens</td><td>EU349764</td><td>EU349860</td><td>EU349816</td><td>EU349690</td></tr><tr><td>Melomys_cervinipes</td><td>NA</td><td>KC953399</td><td>NA</td><td>NA</td></tr><tr><td>Paramelomys_levipes</td><td>EU349772</td><td>EU349867</td><td>EU349821</td><td>EU349689</td></tr><tr><td>Solomys_salebrosus</td><td>EU349785</td><td>EU349872</td><td>EU349827</td><td>EU349691</td></tr><tr><td rowspan="3">Xeromys division</td><td>Uromys_caudimaculatus</td><td>EU349789</td><td>EU349875</td><td>DQ019079</td><td>NA</td></tr><tr><td>Leptomys_elegans</td><td>EU349753</td><td>EU349852</td><td>EU349807</td><td>EU349697</td></tr><tr><td>Pseudothydromys_ellermani</td><td>EU349763</td><td>EU349858</td><td>EU349814</td><td>EU349695</td></tr><tr><td rowspan="2">Lorentzimys division</td><td>Xeromys_nyoides</td><td>EU349790</td><td>EU349877</td><td>EU349830</td><td>EU349696</td></tr><tr><td>Lorentzimys_nouhuysi</td><td>EU349755</td><td>GQ405363</td><td>GQ405383</td><td>EU349680</td></tr><tr><td rowspan="2">Micromys division</td><td>Micromys_minutus</td><td>EU349765</td><td>EU349862</td><td>EU349818</td><td>EU349664</td></tr><tr><td>Micromys_minutus_72_(MK0509_BZ02)</td><td>HM217360</td><td>HM217598</td><td>This study</td><td>This study</td></tr><tr><td rowspan="2">Maxomys division</td><td>Micromys_minutus_73_(MK0509_BZ07)</td><td>HM217361</td><td>HM217599</td><td>This study</td><td>This study</td></tr><tr><td>Maxomys_bartelsii</td><td>EU349762</td><td>EU349857</td><td>DQ019066</td><td>EU349666</td></tr><tr><td rowspan="2">Crunomys division</td><td>Maxomys surifer</td><td>HM217406</td><td>HM217644</td><td>DQ019065</td><td>KC953190</td></tr><tr><td>Maxomys_whiteheadi</td><td>EU292150</td><td>AY326094</td><td>NA</td><td>NA</td></tr><tr><td rowspan="2">Dacnomys division</td><td>Crunomys_melanius</td><td>DQ191477</td><td>DQ191506</td><td>GQ405379</td><td>NA</td></tr><tr><td>Crunomys_suncoides</td><td>DQ191478</td><td>DQ191507</td><td>NA</td><td>NA</td></tr><tr><td></td><td>Chiromyscus_chiropus</td><td>EU349739</td><td>EU349840</td><td>EU349796</td><td>EU349665</td></tr><tr><td></td><td>Dacnomys_milliardi</td><td>JQ755896</td><td>JQ755960</td><td>DQ019058</td><td>KC953169</td></tr><tr><td></td><td>Leopoldamys_edwardsi</td><td>AJ698881</td><td>AJ698897</td><td>NA</td><td>NA</td></tr><tr><td></td><td>Leopoldamys_herberti</td><td>JQ755848</td><td>JQ755958</td><td>NA</td><td>NA</td></tr><tr><td></td><td>Leopoldamys_neilli</td><td>HM217462</td><td>HM217699</td><td>NA</td><td>NA</td></tr><tr><td></td><td>Leopoldamys_revertens</td><td>JQ173160</td><td>JX173169</td><td>NA</td><td>NA</td></tr><tr><td></td><td>Leopoldamys_sabanus</td><td>HM217439</td><td>HM217676</td><td>DQ019063</td><td>KC953186</td></tr><tr><td></td><td>Niviventer_cremoriventer</td><td>EF053030</td><td>DQ019067</td><td>DQ019067</td><td>KC953198</td></tr><tr><td></td><td>Niviventer_culteratus</td><td>NA</td><td>KC953418</td><td>DQ019068</td><td>KC953199</td></tr></tbody></table>
<table><tbody><tr><td>Niviventer_confucianus</td><td>NA</td><td>KC953416</td><td>KC953293</td><td>KC953540</td></tr><tr><td>Niviventer_exceisior</td><td>DQ191482</td><td>DQ191511</td><td>GQ405386</td><td>NA</td></tr><tr><td>Niviventer_fulvescens</td><td>HM217409</td><td>HM217647</td><td>JN009859</td><td>NA</td></tr><tr><td>Niviventer_niviventer</td><td>AM408344</td><td>AM408323</td><td>AM910969</td><td>NA</td></tr><tr><td>Niviventer_rapit_UMMZ</td><td>DQ191483</td><td>DQ191512</td><td>GQ405387</td><td>NA</td></tr><tr><td>Saxatilomys_paulinae_LK217</td><td>This study</td><td>This study</td><td>This study</td><td>This study</td></tr><tr><td>Saxatilomys_paulinae_LK218</td><td>This study</td><td>This study</td><td>This study</td><td>This study</td></tr><tr><td>Saxatilomys_paulinae_LK219</td><td>This study</td><td>This study</td><td>This study</td><td>This study</td></tr><tr><td>Saxatilomys_paulinae</td><td>JQ755859</td><td>JQ755941</td><td>NA</td><td>NA</td></tr><tr><td>Tonkinomys_daoventieni_DPL1662</td><td>This study</td><td>This study</td><td>This study</td><td>This study</td></tr><tr><td>Melasmothrix division</td><td>Melasmothrix_naso</td><td>NA</td><td>KC953398</td><td>EU349815</td><td>NA</td></tr><tr><td>Rattus division</td><td>Srilankamys_ohiensis</td><td>JN009856</td><td>JN009857</td><td>JN009860</td><td>NA</td></tr><tr><td></td><td>Berylmys_berdmorei</td><td>HM217401</td><td>HM217639</td><td>NA</td><td>NA</td></tr><tr><td></td><td>Berylmys_bowersi</td><td>HM217415</td><td>HM217653</td><td>AM910946</td><td>KC953160</td></tr><tr><td></td><td>Bullimus_bagobus</td><td>DQ191472</td><td>DQ191498</td><td>GQ405369</td><td>NA</td></tr><tr><td></td><td>Bullimus_gamay</td><td>DQ191473</td><td>DQ191499</td><td>GQ405370</td><td>NA</td></tr><tr><td></td><td>Bullimus_luzonicus</td><td>DQ191474</td><td>DQ191500</td><td>GQ405371</td><td>NA</td></tr><tr><td></td><td>Bunomys_andrewsi_I8E1</td><td>KF164214</td><td>KF164237</td><td>NA</td><td>NA</td></tr><tr><td></td><td>Bunomys_chrysocomus_T1288</td><td>AM910934</td><td>AM910937</td><td>AM910947</td><td>This study</td></tr><tr><td></td><td>Halmaheramys_bokimekot</td><td>KF164222</td><td>KF164255</td><td>NA</td><td>NA</td></tr><tr><td></td><td>Paruromys_dominator</td><td>EU349774</td><td>KC953433</td><td>EU349822</td><td>EU349669</td></tr><tr><td></td><td>Sundamys_muelleri</td><td>EU349787</td><td>AY326111</td><td>DQ019077</td><td>EU349668</td></tr><tr><td></td><td>TaeromysCelebensis_I7F3</td><td>KF164226</td><td>KF164249</td><td>KF164261</td><td>NA</td></tr><tr><td></td><td>Rattus_andamanensis</td><td>HM217403</td><td>HM217641</td><td>NA</td><td>NA</td></tr><tr><td></td><td>Rattus_argentiventer</td><td>HM217362</td><td>HM217600</td><td>NA</td><td>NA</td></tr><tr><td></td><td>Rattus_exulans</td><td>DQ191486</td><td>AY326105</td><td>GQ405391</td><td>NA</td></tr><tr><td></td><td>Rattus_hoffmanni</td><td>EF186441</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td></td><td>Rattus_losea</td><td>HM217454</td><td>HM217691</td><td>NA</td><td>NA</td></tr><tr><td></td><td>Rattus_sakeratensis</td><td>HM217454</td><td>HM217691</td><td>NA</td><td>NA</td></tr><tr><td></td><td>Rattus_nitidus</td><td>HM217478</td><td>HM217715</td><td>NA</td><td>NA</td></tr><tr><td></td><td>Rattus_norvegicus</td><td>EU349782</td><td>AJ429134</td><td>X16726</td><td>EU349671</td></tr><tr><td></td><td>Rattus_rattus</td><td>AB033702</td><td>AM408328</td><td>AM910976</td><td>NA</td></tr><tr><td></td><td>Rattus_tanezumi</td><td>DQ191488</td><td>DQ191515</td><td>GQ405393</td><td>NA</td></tr><tr><td></td><td>Rattus_tiomanicus</td><td>NA</td><td>KC953449</td><td>KC953320</td><td>NA</td></tr><tr><td></td><td>Rattus-everetti</td><td>DQ191485</td><td>DQ191513</td><td>GQ405390</td><td>NA</td></tr><tr><td></td><td>Linnomys_bryophilus</td><td>DQ191479</td><td>DQ191508</td><td>GQ405380</td><td>NA</td></tr><tr><td></td><td>Linnomys_sibuanus</td><td>DQ191480</td><td>DQ191509</td><td>GQ405381</td><td>NA</td></tr><tr><td></td><td>Tarsomys_apoensis</td><td>DQ191491</td><td>DQ191516</td><td>GQ405395</td><td>NA</td></tr><tr><td></td><td>Diplothrix_legata</td><td>AB033696</td><td>AB033706</td><td>EU349799</td><td>EU349670</td></tr><tr><td></td><td>Rattus_colletti</td><td>NA</td><td>HQ334598</td><td>NA</td><td>NA</td></tr><tr><td></td><td>Rattus_fuscipes</td><td>EF186436</td><td>HQ334623</td><td>NA</td><td>NA</td></tr><tr><td></td><td>Rattus_giluwensis</td><td>NA</td><td>HQ334606</td><td>NA</td><td>HQ334419</td></tr><tr><td></td><td>Rattus_leucopus</td><td>EU349781</td><td>HQ334615</td><td>EU349825</td><td>EU349672</td></tr><tr><td></td><td>Rattus_lutreolus</td><td>GU570661</td><td>HQ334613</td><td>NA</td><td>NA</td></tr><tr><td></td><td>Rattus_morotaiensis_33228</td><td>KF164232</td><td>KF164254</td><td>KF164272</td><td>NA</td></tr><tr><td></td><td>Rattus_morotaiensis_33231</td><td>KF164233</td><td>KF164257</td><td>KF164273</td><td>NA</td></tr><tr><td></td><td>Rattus_novaeguineae</td><td>NA</td><td>KC953447</td><td>KC953319</td><td>KC953210</td></tr><tr><td></td><td>Rattus_niobe</td><td>NA</td><td>HQ334580</td><td>NA</td><td>NA</td></tr><tr><td></td><td>Rattus_praetor</td><td>DQ191487</td><td>DQ191514</td><td>GQ405392</td><td>NA</td></tr><tr><td></td><td>Rattus_sordidus</td><td>NC014871</td><td>HQ334881</td><td>NA</td><td>HQ334411</td></tr><tr><td></td><td>Rattus steini</td><td>NA</td><td>HQ334588</td><td>NA</td><td>NA</td></tr><tr><td></td><td>Rattus_tunneyi</td><td>EF186517</td><td>HQ334579</td><td>NA</td><td>NA</td></tr><tr><td></td><td>Rattus_verecundus</td><td>NA</td><td>HQ334589</td><td>NA</td><td>KC953211</td></tr><tr><td></td><td>Rattus_villosissimus</td><td>EU349783</td><td>HQ334576</td><td>EU349826</td><td>EU349673</td></tr><tr><td></td><td>Bandicota_bengalensis</td><td>AM408340</td><td>AM408331</td><td>AM910945</td><td>NA</td></tr><tr><td></td><td>Bandicota_indica</td><td>HM217408</td><td>HM217646</td><td>NA</td><td>NA</td></tr><tr><td></td><td>Bandicota_savilei</td><td>HM217387</td><td>HM217625</td><td>NA</td><td>NA</td></tr><tr><td></td><td>Nesokia_indica</td><td>AF160605</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td></td><td>Batomys_granti_USNM_458914</td><td>AY324459</td><td>DQ191496</td><td>AY294917</td><td>AY295002</td></tr><tr><td></td><td>Batomys_salomonseni</td><td>DQ191471</td><td>DQ191497</td><td>NA</td><td>NA</td></tr></tbody></table>

Phloeyomyini
<table><tbody><tr><td rowspan="11">incertae sedis</td><td rowspan="2">Micromys division</td><td>Carpomys phaeurus_FMNH_175565</td><td>DQ191475</td><td>DQ191501</td><td>GQ405373</td><td>NA</td></tr><tr><td>Crateromys heaneyi_CiMNH_M628</td><td>DQ191476</td><td>DQ191505</td><td>GQ405378</td><td>NA</td></tr><tr><td rowspan="2">Pithecheir division</td><td>Musseromys gulantang_FMNH_178405</td><td>NA</td><td>GQ405364</td><td>GQ405384</td><td>NA</td></tr><tr><td>Phloeomys_sp</td><td>DQ023480</td><td>KC8878237</td><td>DQ019070</td><td>EU349644</td></tr><tr><td rowspan="2">Pithecheir division</td><td>Phloeomys cumingi</td><td>DQ191484</td><td>AY326103</td><td>NA</td><td>NA</td></tr><tr><td>Vandeleuria_oleracea_M30312</td><td>this study</td><td>EU349876</td><td>EU349829</td><td>EU349655</td></tr><tr><td rowspan="2">Pithecheir division</td><td>Hapalomys_delacouri_R5237</td><td>This study</td><td>This study</td><td>This study</td><td>This study</td></tr><tr><td>Margaretamys_elegans</td><td>NA</td><td>KC953394</td><td>KC953274</td><td>NA</td></tr><tr><td rowspan="2">Pithecheir division</td><td>Margaretamys_christinae_RCI_(MK14)</td><td>This study</td><td>This study</td><td>This study</td><td>This study</td></tr><tr><td>Pithecheir_melanurus_CG1900N580</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td rowspan="2">Pithecheir division</td><td>Pithecheir_melanurus_CG1900N583</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>Pithecheir_parvus_CG1977N251</td><td>This study</td><td>This study</td><td>This study</td><td>This study</td></tr><tr><td rowspan="2">Pithecheir division</td><td>Pithecheir_parvus_CG1977N252</td><td>This study</td><td>This study</td><td>This study</td><td>This study</td></tr><tr><td>Lenothrix_canus_009</td><td>This study</td><td>This study</td><td>This study</td><td>This study</td></tr><tr><td rowspan="2">Pithecheir division</td><td>Lenothrix_canus_N92</td><td>This study</td><td>This study</td><td>This study</td><td>This study</td></tr><tr><td colspan="6">OUTGROUP</td></tr><tr><td rowspan="11">Gerbillinae</td><td rowspan="11">Gerbillus paeba</td><td>Gerbillus_gerbillus</td><td>AJ430557</td><td>AM910941</td><td>AF332022</td><td>NA</td></tr><tr><td>Gerbillus_gerbillus</td><td>AF141226</td><td>FM162054</td><td>DQ019049</td><td>EU349700</td></tr><tr><td>Gerbillus_nanus</td><td>NA</td><td>KC953378</td><td>KC953262</td><td>NA</td></tr><tr><td>Meriones_shawi</td><td>AB381894</td><td>KC953400</td><td>AF332021</td><td>AF332048</td></tr><tr><td>Meriones_unguiculatus</td><td>NA</td><td>AY326095</td><td>AF247184</td><td>NA</td></tr><tr><td>Desmodillus_auricularis</td><td>AJ851272</td><td>KC953374</td><td>DQ019048</td><td>KC953171</td></tr><tr><td>Gerbilliscus_(Tatera)_robusta</td><td>NA</td><td>AY326113</td><td>AY294920</td><td>AY295005</td></tr><tr><td>Gerbillurus_vallinus</td><td>NA</td><td>KC953377</td><td>AF332022</td><td>EU349643</td></tr><tr><td>Taterillus_emini</td><td>NA</td><td>KC953461</td><td>DQ019050</td><td>KC953224</td></tr><tr><td>Deomys_ferrugineus</td><td>EU349745</td><td>AY326084</td><td>AY294922</td><td>AY295007</td></tr><tr><td>Lophuromys_flavopunctatus</td><td>EU349754</td><td>AY326091</td><td>AY294921</td><td>AY295006</td></tr><tr><td rowspan="5">Deomys division</td><td>Lophuromys_sikapusi</td><td>AJ012023</td><td>KC953390</td><td>KC953271</td><td>NA</td></tr><tr><td>Lophuromys_zena</td><td>NA</td><td>KC953391</td><td>KC953272</td><td>NA</td></tr><tr><td>Uranomys_ruddi</td><td>EU349788</td><td>EU360812</td><td>DQ019051</td><td>EU349642</td></tr><tr><td>Acomys_ignitus</td><td>AJ233951</td><td>EU349846</td><td>DQ019049</td><td>AY295008</td></tr><tr><td>Acomys_russatus</td><td>NA</td><td>FM162053</td><td>FM162071</td><td>NA</td></tr><tr><td rowspan="11">Lophiomys division</td><td rowspan="11">Lophiomys imhausi</td><td rowspan="11">Lophiomys imhausi</td><td rowspan="11">Lophiomys imhausi</td><td rowspan="11">Lophiomys imhausi</td><td rowspan="11">Lophiomys imhausi</td></tr><tr><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>DQ381929**</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>Thallomys</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>Thamnomys</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>Lamottemys</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>Myotomys</td><td>JN574903***</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>Diomys</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>Madromys</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>Nilopegamys</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>KF928333**</td><td>KF928334**</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>Mus division</td><td>Muriculus</td><td>*</td><td>*</td><td>NA</td><td>NA</td></tr></tbody></table>

*** During the reviewing process of this article, sequences of *Muriculus* as well as those of *Thallomys* and *Myotomys* were deposited in the public databank.

### Unavailable in GenBank

incertae sedis

<table><tbody><tr><td rowspan="11">Arvicanthini</td><td rowspan="11">Dasymys division</td><td>Echiothrix division</td><td>Echiothrix</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>Hadromys division</td><td>Hadromys</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td rowspan="2">Micromys division</td><td>Haeromys</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>Vernaya</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td rowspan="3">Pithecheir division</td><td>Eropeplus</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>Lenomys</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>Pithecheirops</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td rowspan="4">Otomyini</td><td rowspan="4">Subfamily Otomyinae</td><td>Dephomys</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>Thallomys</td><td>DQ381929**</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>Thamnomys</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>Lamottemys</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td rowspan="2">Millardini</td><td rowspan="2">Millardia division</td><td>Myotomys</td><td>JN574903***</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>Diomys</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td rowspan="2">Praomyini</td><td rowspan="2">Colomys division</td><td>Madromys</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td>Nilopegamys</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr><tr><td rowspan="2">Murini</td><td rowspan="2">Mus division</td><td>Myotomys</td><td>KF928333**</td><td>KF928334**</td><td>NA</td><td>NA</td></tr><tr><td>Muriculus</td><td>*</td><td>*</td><td>NA</td><td>NA</td></tr></tbody></table>
1

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Hydromyini

Hydromys division

Baiyankamys

NA

NA

NA

NA

Crossomys

NA

NA

NA

NA

Microhydromys

NA

NA

NA

NA

Paraleptomys

NA

NA

NA

NA

Pogonomys division

Coccymys

NA

NA

NA

NA

Pogonomelomys

NA

NA

NA

NA

Uromys division

Protochromys

NA

NA

NA

NA

Melasmothrix division

Paucidentomys

NA

NA

NA

NA

Melasmothrix division

Tateomys

NA

NA

NA

NA

Rattus division

Floresomys

NA

NA

NA

NA

Kadarsonomys

NA

NA

NA

NA

Nesoromys

NA

NA

NA

NA

Palawanomys

NA

NA

NA

NA

Tryphomys

NA

NA

NA

NA

Review Copy
<table><caption>Table S2: Primer sets used in this study</caption><thead><tr><th>Designation</th><th>Gene Name</th><th>Nucleotide sequence 5' → 3'</th><th>Annealing Temperature</th><th>Fragment Length (bp)</th><th>Original Publication</th></tr></thead><tbody><tr><td><strong>cytb</strong></td><td>cytochrome <i>b</i> apoenzyme</td><td></td><td></td><td></td><td></td></tr><tr><td>L14723</td><td></td><td>ACCAATGACATGAAAAATCATCGTT</td><td>50°C</td><td>1213 (whole <i>cytb</i> gene and small parts of the flanking tRNA)</td><td>Irwin and Kocher, 1991</td></tr><tr><td>H15915</td><td></td><td>TCTCCATTTCTGGTTTACAAGAC</td><td></td><td></td><td></td></tr><tr><td><strong>IRBP1</strong></td><td>interphotoreceptor retinoid binding protein exon 1 (fragment 1)</td><td></td><td></td><td></td><td></td></tr><tr><td>I1-Rattus</td><td></td><td>ATTGAGCAGGCTATGAAGAG</td><td>58°C</td><td>785</td><td>Pagès et al., 2010</td></tr><tr><td>J2-Rattus</td><td></td><td>TAGGGCTTGCTCYGCAGG</td><td></td><td></td><td></td></tr><tr><td><strong>IRBP2</strong></td><td>interphotoreceptor retinoid binding protein exon 1 (fragment 2)</td><td></td><td></td><td></td><td></td></tr><tr><td>I2</td><td></td><td>ATCCCCTATGTCATCTCCTACYTG</td><td>52°C</td><td>892</td><td>Poux and Douzery, 2004</td></tr><tr><td>J1</td><td></td><td>CGCAGGTCCATGATGAGGTGCTCCGTGTCCTG</td><td></td><td></td><td></td></tr><tr><td><strong>GHRI</strong></td><td>growth hormone receptor exon 10 (fragment 1)</td><td></td><td></td><td></td><td></td></tr><tr><td>GHREXON10-fw</td><td>adkins</td><td>GGRAARTTRGAGGAGGTGAACACMATCTT</td><td>58°C</td><td>~ 690 bp</td><td>Adkins et al., 2001</td></tr><tr><td>GHR8-rev</td><td></td><td>TTGGCATCTGACTCACAGAATAGG</td><td></td><td></td><td>Lecompte et al., 2008</td></tr><tr><td><strong>GHR2</strong></td><td>growth hormone receptor exon 10 (fragment 2)</td><td></td><td></td><td></td><td></td></tr><tr><td>GHR7-fw</td><td></td><td>AAGCTGATCTCTTGTGCCTTGACCAGAA</td><td>53°C</td><td>~ 600 bp</td><td>Lecompte et al., 2008</td></tr><tr><td>GHR2-rev</td><td></td><td>GATTTTGTTTCAGTTGGTCTGTGCTCAC</td><td></td><td></td><td></td></tr><tr><td><strong>BRCA1</strong></td><td></td><td></td><td></td><td></td><td></td></tr><tr><td>BRCA1-MP-fw</td><td></td><td>GRGACCMGCAGTTTATTGTTC</td><td>58°C</td><td>~ 1000 bp</td><td>this study</td></tr><tr><td>BRCA1-MP-rev</td><td></td><td>GGAAGAACACACCTGGTAG</td><td></td><td></td><td></td></tr><tr><td><strong>cytb1</strong></td><td>cytochrome <i>b</i> apoenzyme - MUSEUM SPECIMENS, fragment I</td><td></td><td></td><td></td><td></td></tr><tr><td>L14723</td><td></td><td>ACCAATGACATGAAAAATCATCGTT</td><td>60°C</td><td>472 bp</td><td>this study</td></tr><tr><td>cytb1-rev</td><td></td><td>TCAGAARGATATTTGTCCTCATGG</td><td></td><td></td><td></td></tr><tr><td><strong>cytbII</strong></td><td>cytochrome <i>b</i> apoenzyme - MUSEUM SPECIMENS, fragment II</td><td></td><td></td><td></td><td></td></tr><tr><td>cytbII-fw</td><td></td><td>ATAGCAACYGCATTCATAGG</td><td>50°C</td><td>454 bp</td><td>this study</td></tr></tbody></table>
<table><tr><td>cytbII-rev</td><td></td><td>AGRAARTATCATTCTGGTTT</td><td></td><td></td><td></td></tr><tr><td>cytbIII</td><td>cytochrome b apoenzyme - MUSEUM SPECIMENS, fragment III</td><td></td><td></td><td></td><td></td></tr><tr><td>cytbIII-fw</td><td></td><td>TTCCCAGACCTAYTAGGAGA</td><td>56°C</td><td>457 bp</td><td>this study</td></tr><tr><td>H15915</td><td>interphotoreceptor retinoid binding protein exon 1 - MUSEUM SPECIMENS, fragment I</td><td>TCTCCATTTCTGGTTTACAAGAC</td><td></td><td></td><td></td></tr><tr><td>IRBPI</td><td>fragment I</td><td></td><td></td><td></td><td></td></tr><tr><td>I1-Rattus</td><td></td><td>ATTGAGCAGGCTATGAAGAG</td><td>58°C</td><td>389 bp</td><td>this study</td></tr><tr><td>IRBPI-rev</td><td>interphotoreceptor retinoid binding protein exon 1 - MUSEUM SPECIMENS, fragment II</td><td>GGGATCCCAGAGACRTGRCC</td><td></td><td></td><td></td></tr><tr><td>IRBPII</td><td>fragment II</td><td></td><td></td><td></td><td></td></tr><tr><td>IRBPII-fw</td><td></td><td>TCCTTGGTGCTAGATCTCCG</td><td>58°C</td><td>450 bp</td><td>this study</td></tr><tr><td>IRBPII-rev</td><td>interphotoreceptor retinoid binding protein exon 1 - MUSEUM SPECIMENS, fragment III</td><td>TAGGGCTTGCTCTGCAGG</td><td></td><td></td><td></td></tr><tr><td>IRBPIII</td><td>fragment III</td><td></td><td></td><td></td><td></td></tr><tr><td>IRBPIII-fw</td><td></td><td>CAGACATGGGAAGGCAGTGG</td><td>62°C</td><td>441 bp</td><td>this study</td></tr><tr><td>IRBPIII-rev</td><td>growth hormone receptor exon 10 - MUSEUM SPECIMENS, fragment I</td><td>GCAGGTAGCCCACATTGCC</td><td></td><td></td><td></td></tr><tr><td>GHRI</td><td></td><td></td><td></td><td></td><td></td></tr><tr><td>GHREXON10-fw</td><td></td><td>GGRAARTTRGAGGAGGTGAACACMATCTT</td><td>62°C</td><td>460 bp</td><td>this study</td></tr><tr><td>GHRI-rev</td><td>growth hormone receptor exon 10 - MUSEUM SPECIMENS, fragment II</td><td>GTTGGTGGGTTGAYTCAGTTTC</td><td></td><td></td><td></td></tr><tr><td>GHRII</td><td></td><td></td><td></td><td></td><td></td></tr><tr><td>GHRII-fw</td><td></td><td>GATCTCTTGTGCCTTGACCAG</td><td>58°C</td><td>436 bp</td><td>this study</td></tr><tr><td>GHRII-rev</td><td>growth hormone receptor exon 10 - MUSEUM SPECIMENS, fragment III</td><td>TAAATGTCCTCCTGGTTAAAG</td><td></td><td></td><td></td></tr><tr><td>GHRIII</td><td></td><td></td><td></td><td></td><td></td></tr><tr><td>GHRIII-fw</td><td></td><td>CCTACTTCTGTGAGTCAGATGCC</td><td>62°C</td><td>310 bp</td><td>this study</td></tr><tr><td>GHRII-rev</td><td>growth hormone receptor exon 10 - MUSEUM SPECIMENS, fragment III</td><td>GATTTTGTTCAGTTGGTCTGTGCTCAC</td><td></td><td></td><td></td></tr></table>
Figure S2: Phylogenetic tree depicting relationships of the arboreal rodents based on the analysis of the combined molecular dataset and reconstructed following Bayesian method.

The best-fit partitioning schemes (considering the three different codon positions of the four coding genes) and models of molecular evolution were deeper investigated using PARTITIONFINDER (Lanfear *et al.*, 2012). The best-fit partitioning scheme consisted in 3 subsets: 1) the first and the second positions of the *Cyt b* codon were merged together, 2) the third position of the *Cyt b* codon was treated separately, 3) all the positions of the nuclear genes were merged together. 56 different substitution models for these three subsets were compared using the *greedy* algorithm. The best-fit substitution model was the GTR+I+G model for each subset according to cAIC values. MRBAYES parameters were set accordingly (see supplementary information). All parameters except the topology were unlinked across partitions, and two independent runs, each with 4 Markov chains Monte Carlo (MCMC) samples comprising one cold and three heated chains, were computed simultaneously. The MRBAYES analyses were run for 12 x 10⁶ generations with trees sampled every 1,000 generations. The consensus tree was then computed subsequent to a burn-in of 10⁶ generations (option “allcompat”). The node supports were estimated using posterior probabilities (PP).
Formatted: Font: Times New Roman, Bold, Underline

<figure><img src="image_17.png" /></figure>
**Figure S3:** Chronograms based on the maximum likelihood tree showing absence (black) and presence (red) of cusp t7 for Murinae species. The pie charts represent the probability of the ancestral dental trait characters. The green and blue colour indicates the former *Micromys* and the *Pithecheir* divisions respectively. HIGHLIGHTED in green capitals are the 4 monotypic tribes we proposed based on the new phylogenetic results: (i) Chiropodomyini, (ii) Hapalomyini, (iii) Micromyini, and (iv) Vandeleuriani. See material and method for details.

<figure><img src="image_18.png" /></figure>

Formatted: Font: Times New Roman
## Text S1: Molecular results

*Samples preserved in ethanol - Cytb sequences obtained from tissue of Margaretamys christinae* were not considered in the analyses because *Numt* sequences or heteroplasmy were suspected. Chromatograms with at least 10 double pics were obtained, but translation into amino acid sequence did not reveal any stop codon (as it could be observed in case of a recent *Numt* insertion or heteroplasmy). Contamination by exogenous DNA was ruled out as numerous nuclear sequences produced for another ongoing analysis revealed to be perfectly clean.

*Museum samples* - As museum samples contain tiny amounts of poorly preserved DNA, additional primer sets were designed to target the 3 markers into 3 overlapping fragments (see Table S2). Ancient DNA work was performed in an independent room dedicated to ancient DNA analysis (degraded DNA platform, Labex CeMEB), following the standard procedures and using specific equipment and personal protections (e.g. Pääbo *et al.*, 2004). DNA of the four *Pithecheir* samples was extracted at the same time than those of nine *Gerbillus* samples from museum. For each PCR attempts, all the three PCR blanks remained negative indicating that no contamination and no carrier-effect occurred during extraction and pre-amplification steps. Independent PCRs were performed and furnished the same conclusions (see below for further details).

### Cytochrome *b* marker

Fragment 1: 3 successful PCR attempts for MNHN-ZM-MO 1977-251 and 2 for MNHN-ZM-MO 1977-252. Sequences were 100% identical for a same sample but differed at one position between the two samples. This difference occurs at the third codon position and was considered as intraspecific polymorphism (coded Y for C or T in the consensus sequence of *Pithecheir parvus*). At this position all the murid species of our dataset harbour a C or a T.

Fragment 2: a single successful PCR attempt for MNHN-ZM-MO 1977-251. Because of failure to reproduce this sequence, this fragment was not considered in the subsequent analyses.

Fragment 3: 3 successful PCR attempts for MNHN-ZM-MO 1977-251 and 2 for MNHN-ZM-MO 1977-252. Sequences were 100% identical for a same sample and between samples.

### *IRBP* marker

Fragment 1: PCR failures for all the 4 samples

Fragment 2: a single successful PCR attempt for MNHN-ZM-MO 1977-251. Because of failure to reproduce this sequence, this fragment was not considered in the subsequent analyses.
Fragment 3: 3 successful PCR attempts for MNHN-ZM-MO 1977-251 and 2 for MNHN-ZM-MO 1977-252. Sequences were 100% identical for a same sample and between samples.

### GHR marker

Fragment 1: 3 successful PCR attempts for MNHN-ZM-MO 1977-251 and 1 for MNHN-ZM-MO 1977-252. Sequences were 100% identical between samples.

Fragment 2: PCR failures for all the 4 samples

Fragment 3: 3 successful PCR attempts for MNHN-ZM-MO 1977-251 and 2 for MNHN-ZM-MO 1977-252. Sequences were 100% identical for a same sample and between samples.

### References

Abramov, A. V., Aniskin, V. M., & Rozhnov, V. V. (2012). Karyotypes of two rare rodents, *Hapalomys delacouri* and *Typhlomys cinereus* (Mammalia, Rodentia), from Vietnam. *Zookeys*, 41-49.

Badenhorst, D., Dobigny, G., & Robinson, T. J. (2012). Karyotypic evolution of *Hapalomys* inferred from chromosome painting: A detailed characterization contributing new insights into the ancestral murinae karyotype. *Cytogenetic and Genome Research*, 136, 83-88.

Badenhorst, D., Herbreterau, V., Chaval, Y., Pagès, M., Robinson, T., Morand, S., et al. (2009). New karyotypic data for asian rodents (Rodentia, Muridae) and first report of b-chromosomes in the genus *Mus*. *Journal of Zoology*, 279, 44-56.

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