Phylogeny of the genus Apodemus with a special emphasis on the subgenus Sylvaemus using the nuclear IRBP gene and two mitochondrial markers: cytochrome b and 12S rRNA

Abstract

Phylogenetic relationships among 17 extant species of Murinae, with special reference to the genus Apodemus, were investigated using sequence data from the nuclear protein-coding gene IRBP (15 species) and the two mitochondrial genes cytochrome b and 12S rRNA (17 species). The analysis of the three genes does not resolve the relationships between Mus, Apodemus, and Rattus but separates Micromys from these three genera. The analysis of the two mitochondrial regions supported an association between Apodemus and Tokudaia and indicated that these two genera are more closely related to Mus than to Rattus or Micromys. Within Apodemus, the mitochondrial data sets indicated that 8 of the 9 species analyzed can be sorted into two main groups: an Apodemus group, with A. agrarius, semotus, and peninsulae, and a Sylvaemus group, with uralensis, flavicollis, alpicola, sylvaticus, and hermonensis. The position of Apodemus mystacinus is ambiguous and might be either included in Sylvaemus or considered a distinct subgenus, Karstomys, more closely related to Sylvaemus than to Apodemus. Estimation of the divergence time for these taxa suggests a separation between 7 and 8 My ago for the three groups (mystacinus and the two subgenera Apodemus and Sylvaemus). Within each subgenus, divergence times are between 5.4 and 6 My for Apodemus and between 2.2 and 3.5 My for Sylvaemus and mystacinus. Ó

mtDNA phylogeny and evolution of laboratory mouse strains

“…Since the closest outgroup is the rather divergent Rattus norvegicus, we did not include the control region in this first tree. The maximum likelihood values were not different enough to determine which of the three most divergent groups separated first, and therefore we left this deepest slip unresolved with the following three branches diverging ( We estimated coalescence times for these branches assuming a divergence time between Mus and Rattus of 12 million yr (paleontological data from Jacobs et al 1989;Jaeger et al 1986in Michaux et al 2002Suzuki et al 2004). The results date the split between the three main groups at 371,000 ‫ע‬ 91,300 yr ago, consistent with published mtDNA data that place the divergence between Mus musculus subspecies between 0.1 Mya (based on Figure 1.…”

“…After the tree was established, and because of the difference in evolutionary scale between the divergence of wild and inbred strains, we redid the analysis including only (1) the rat; (2) the wild-derived inbred strains; (3) two common inbred strains reported to be more divergent than the others, NZB and MilP; and (4) the C57BL/6 strain, as a representative of all other common inbred strains. Assuming from paleontological data (Jacobs et al 1989;Jaeger et al 1986in Michaux et al 2002Suzuki et al 2004) that the Mus/Rattus divergence occurred 12 million yr ago, we determined substitution rates and coalescence times for all the branches in the tree. We performed a separate maximum likelihood analysis excluding the rat sequence and including all common inbred strains, but considering the whole molecule (including the control region).…”

Geography and host biogeography matter for understanding the phylogeography of a parasite

“…To discriminate between the alternative hypotheses of co-speciation versus geographic differentiation, we looked for the presence of parasites of the Heligmosomoides genus in all Apodemus species common in the western Palearctic region: A. sylvaticus, A. flavicollis Melchior1834, A. mystacinus Danford and Alston, 1877, A. uralensis (Pallas, 1811) and A. alpicola Heinrich, 1952 from the Sylvaemus subgenus, as well as A. agrarius (Pallas, 1771) from the Apodemus subgenus Michaux et al, 2002). Multiple Heligmosomoides species were described in Apodemus over continental Europe, including H. skrjarbini Schulz (1926) andH.…”

Phylogeographic history of the yellow-necked fieldmouse (Apodemus flavicollis) in Europe and in the Near and Middle East

“…The yellow-necked fieldmouse is relatively common, easy to catch and widespread all over the Western Palearctic region as well as in the Near East regions. Finally, the evolutionary history of the genus Apodemus is well known (Michaux and Pasquier, 1974;Michaux et al, 1997;Michaux et al, 2002;Serizawa et al, 2000;Suzuki et al, 2000), this genus being well represented in the fossil data. Therefore, calibration of a molecular clock is possible for this genus.…”