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AN ASSESSMENT OF THE SYSTEMATICS OF THE GENUS DESMOMYS THOMAS, 1910 (RODENTIA: MURIDAE) USING MITOCHONDRIAL DNA SEQUENCES Leonid A. Lavrenchenko1 and Erik Verheyen2 1 2

Severtsov Institute of Ecology and Evolution RAS, Leninsky pr., 33, Moscow, 119071 Russia Royal Belgian Institute of Natural Sciences, Vautierstraat 29, 1000 Brussels, Belgium

Abstract:

We analyzed two mitochondrial gene fragments to assess genetic divergence within the genus Desmomys endemic to Ethiopia and its phylogenetic relationships with related genera. The phylogenetic analysis supported the monophyly of the Arvicanthini-Otomyini group and revealed that Stochomys is clearly a member of Arvicanthini. Our study demonstrated that D. harringtoni and D. yaldeni belong to remarkably different mitochondrial lineages, the estimated divergence time between them is 4.10-5.38 Myr. Such early splitting of specialized forest dweller, D. yaldeni, from its sole congener supposes a more ancient formation of some elements of Ethiopian forest rodent fauna than is assumed today.

Key words:

Rodentia; Muridae; Desmomys; Ethiopia; phylogeny; evolution; mitochondrial DNA

1.

INTRODUCTION

For a long time Desmomys has been treated as a subgenus of Pelomys (Ellerman, 1941; Corbet and Hill, 1991); presently, based on unique dental patterns, the generic status of the former taxon (including the single species, D. harringtoni, endemic to Ethiopia) was confirmed (Musser and Carleton, 1993). A recent phylogenetic study based on sequencing of mitochondrial DNA (Ducroz et al., 2001) revealed that Desmomys is a sister group to Rhabdomys and, hence, is a member of arvicanthines. Moreover, it was 363 B.A. Huber et al. (eds.), African Biodiversity, 363–369. © 2005 Springer. Printed in the Netherlands.

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Leonid A. Lavrenchenko and Erik Verheyen

suggested that arvicanthine rodents (Arvicanthis, Mylomys, Pelomys, Lemniscomys, Desmomys and Rhabdomys) are part of tribe Arvicanthini that also comprises Aethomys, Dasymys, Grammomys, and Hybomys. The systematic position of other African genera considered by Misonne (1969) as members of the Arvicanthis “Division” still remains unclear. Recently, a second Desmomys species, D. yaldeni, was described from Ethiopia (Lavrenchenko, 2003). The aim of this paper is to enhance our knowledge on arvicanthine rodents by adding new data and to focus particularly on the phylogenetic relationships of the two Desmomys species.

2.

MATERIALS AND METHODS

Specimens of D. harringtoni and D. yaldeni were collected in the course of the Joint Ethiopian-Russian Biological Expedition (for localities, field and museum numbers see Lavrenchenko, 2003). DNA was extracted from 96% alcohol preserved tissue samples by the standard phenol-chloroform method, PCR amplification and sequencing of segments of 16S rRNA (16S) and cytochrome-b (cyt-b) genes were carried out using primers and protocols described previously for Lophuromys by Lavrenchenko et al. (2004). We also used sequence data on relevant African murines from the database of the Royal Belgian Institute of Natural Sciences. Additional sequences for 16S and cyt-b genes were retrieved from GenBank: Otomys irroratus (AF141253; AF141222), O. sloggetti (AF141254; AF141223), Aethomys namaquensis (AF141246; AF141215), Grammomys sp. (AF141249; AF141218), Hybomys univittatus (AF141250; AF141219), Dasymys rufulus (AF141247; AF141216), D. incomtus (AF141248; AF141217), Lemniscomys rosalia (AF141238; AF141209), L. zebra (AF141235; AF141207), L. macculus (AF141237; AF141208), L. bellieri (AF141236; AF004586), L. striatus (AF141240; AF141211; AF141239; AF141210), Arvicanthis sp. (AF141230; AF004584; AF141231; AF141205; AF141232; AF004576), A. abyssinicus (AF141227; AF004566), A. niloticus (AF141228; AF004569), Pelomys campanae (AF141242; AF141213), Mylomys dybowskii (AF141241; AF141212), Desmomys harringtoni (AF141233; AF141206), and Rhabdomys pumilio (AF141244; AF141214). Phylogenetic relationships were analysed by maximum-parsimony (MP), neighbour-joining (NJ) and maximum-likelihood (ML) methods. The phylogenetic analyses were conducted using PAUP* v.4.0b4a (Swofford, 2000). ModelTest 3.06 (Posada and Crandall, 1998) was employed for the choice of the best model of sequence evolution for the NJ and ML analyses. This was the general time reversible model (GTR+G+I, alpha=0.695, pin=0.447). Simpler analyses were also carried out using the Tamura-Nei (TrN) and the Kimura’s two-parameter (K2P) models. The relative stability

Molecular Systematics of Desmomys

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of the NJ-MP and ML trees was assessed by bootstrapping with 10000 and 100 replicates, respectively. The estimates of divergence times were obtained on the basis of transversional changes in both 16S sequences and third codon positions of the cyt-b sequences. Traditionally accepted divergence time of 12 Myr for the dichotomy Mus/Rattus (Jaeger et al., 1986) was used as the calibration point. Relative-rate tests were conducted with Mega 2.1 program (Kumar et al., 2001).

3.

RESULTS

Sequence data from 907 bp of combined 16S (535 bp) and cyt-b (372 bp) genes were used for the phylogenetic analyses. The combined sequences among ingroup haplotypes show 370 variable sites of which 269 are informative under parsimony. With a few exceptions, NJ, MP and ML results are quite consistent with each other. The results suggest the basal position of the lineage Rattus-Mus-Nannomys within the ingroup. Traditional association between Mus and Nannomys is supported with low bootstrap value in the MP and ML analyses (results not shown) although based on the NJ tree Nannomys is more closely related to Rattus (Fig. 1). All three reconstruction methods reveal that the “African lineage” (sensu Ducroz et al., 2001), including Arvicanthini and Otomyini, is the sister clade to the Praomys group s. lat. (represented here by Praomys s. str., Mastomys, Hylomyscus, Colomys and Malacomys). With all these methods, the “African lineage” is well supported, however, the monophyly of the tribe Arvicanthini was not unequivocally confirmed. Moreover, in the NJ (GTR+G+I), MP and ML analyses, Otomys appears to be nested within the clade containing the Arvicanthini genera. Only NJ analyses using simpler models (K2P and TrN) indicated the basal position of the Otomys clade relative to all studied Arvicanthini genera (again without any statistical support) (Fig. 1). Stochomys longicaudatus always appears as a member of Arvicanthini, although its affiliations with other representatives of the tribe remain unresolved. All analyses indicate the monophyly of the arvicanthine genera (although only NJ results support this association with relatively weak bootstrap value) and suggest that Desmomys is the sister group to Rhabdomys (this association was constantly supported by higher bootstrap values). The relationships between other arvicanthine genera remain uncertain: only NJ analyses indicate the basal position of the DesmomysRhabdomys clade relative to the rest of the group with relatively weak bootstrap support. Our study revealed that D. harringtoni and D. yaldeni form a monophyletic group, but also that they belong to deeply diverged

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Figure 1. NJ tree constructed from TrN distances. Values above and below branches indicate percentage bootstrap support (>50%) for the NJ and MP trees, respectively (10,000 replicates). Acomys spinosissimus, Lophuromys nudicaudus, and L. flavopunctatus are used as outgroups.

mitochondrial lineages. The proportion of mismatches between these two haplotypes is 6.4% for 16S and 11.7% for cyt-b. These values lie well within the range typical for well-differentiated congeneric species or even related genera in Muroidea (e.g. Fadda et al., 2001; Lecompte et al., 2002). The results of the Tajima’s relative-rate test demonstrate no significant variation of evolution rate. The estimated divergence times between the two Desmomys species are similar for both genes: 5.38 Myr (95% CI = 2.55-8.21 Myr) for 16S and 4.10 Myr (95% CI = 1.75-6.45 Myr) for cyt-b. At the same


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time, these results should be treated with caution because of the limited amount of data. Nevertheless, it seems reasonable to conclude that the diversification within the genus Desmomys might have started in the beginning of the Pliocene.

4.

DISCUSSION

The results of our phylogenetic analysis are largely consistent with those in a previous study on arvicanthine rodents (Ducroz et al., 2001). The monophyly of the so-called “African lineage” (Arvicanthini + Otomyini) was confirmed. However, it is noteworthy that the position of tribe Otomyini still remains uncertain. Further study based on analyses of other mithohondrial and nuclear genes is necessary to find out whether this clade is the sister group to Arvicanthini or nests within the latter. Our analysis revealed that Stochomys is clearly a member of Arvicanthini. Additional studies should test the inclusion of other putative members (Dephomys, Lamottemys, Oenomys, Thallomys, and Thamnomys) in this tribe. Clustering of Desmomys and Rhabdomys was constantly supported by significant bootstrap values in all analyses. Contrary to the previous phylogenetic analysis of arvicanthines (Ducroz et al., 2001) we have found no evidence for faster evolution in these two lineages. Given this result, it seems unlikely that the Desmomys – Rhabdomys grouping is an artifact of long branch attraction as supposed by Ducroz et al. (2001). The fact that Desmomys clusters with the predominantly South African taxon Rhabdomys suggests that there may have been an ancient association between faunas of the Ethiopian Plateau and South Africa. Furthermore, the results of our study support the distinctness of the recently described D. yaldeni. As both known Desmomys species are endemic to Ethiopia, we can assume that the genus has evolved mostly, or even exclusively on the Ethiopian Plateau. Molecular clock estimates of divergence times suggest early diversification within Desmomys (4.10-5.38 Myr) relative to other Ethiopian endemic species assemblages studied so far: Praomys albipes / Stenocephalemys complex (1.34-2.24 Myr – Fadda et al., 2001; 1.9-2.4 Myr – Lecompte et al., 2002) and Ethiopian Lophuromys flavopunctatus species complex (0.70-0.88 Myr – Lavrenchenko et al., 2004). Desmomys yaldeni inhabits humid afromontane forests and possesses some morphological characteristics that can be interpreted as adaptations to ecological specialization uncommon for arvicanthine rodents: a supposedly climbing life style and a diet that mainly consists of invertebrates and/or fruits and berries. Previously, we regarded D. yaldeni as an additional line of evidence supporting our hypothesis that the Ethiopian forest rodent fauna originated recently from native ancestors (Lavrenchenko, 2003). However,

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the inferred early split of this specialized forest dweller from its sole congener suggests that D. yaldeni may be older (presumably originated at the beginning of the Pliocene) than other elements of this forest fauna.

ACKNOWLEDGEMENTS We wish to thank the Ethiopian Science and Technology Commission for support in the field work organisation. Dr. A.A. Darkov has coordinated field operations. Mr. A.A. Warshavsky has assisted in collecting specimens for this study. Two anonymous referees made helpful comments on the manuscript. The work of L.A.L. in the Royal Belgian Institute of Natural Sciences (Brussels) was supported by a Research Fellowship from the DWTC and a NATO Research Fellowship. This research was supported by the DWTC project 31.64 and the RFBR project 03-04-48924. Participation of the senior author at the Symposium was supported by the DFG.

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