Login

Join for Free!
118906 members
table of contents table of contents

A report on the results of phylogenetic analyses of the endemic African …


Biology Articles » Biogeography » Phylogeny and biogeography of African Murinae based on mitochondrial and nuclear gene sequences, with a new tribal classification of the subfamily » Results

Results
- Phylogeny and biogeography of African Murinae based on mitochondrial and nuclear gene sequences, with a new tribal classification of the subfamily

Phylogenetics

The final alignments included 1140 sites and 81 taxa for cyt b, 931 sites and 62 taxa for GHR, 1233 sites and 79 taxa for IRBP, and 3304 sites for 83 taxa for the concatenated dataset. The best-fitting substitution models were TVM+G+I for the GHR and IRBP data sets, and GTR+G+I for the cyt b and combined data set (Table 1). Analysis of the combined dataset produced a single ML tree (Figure 1, lnL = - 50270.78386), the supports obtained for each node and each gene are presented in the additional files 1 (ML analysis) and 2 (Bayesian analysis). Monophyly of Murinae is strongly supported but only with inclusion of the two 'otomyine' taxa (100% BP; 1.0 PP). Ten primary lineages can be recognized within Murinae, all with strong nodal support (Figure 1, BP ≥ 97%; PP = 1.0). African murines are polyphyletic and divided among five lineages. We here describe the different lineages to highlight the relationships among the African murines.

Additional file 1. Maximum likelihood topology obtained with the combined dataset. The support values from each gene separately are indicated for the main nodes discussed in the text. The support values are indicated as follow: GHR/IRBP/cytb. A black dot indicate that the node is supported by the three dataset with a BP > 95, +: BP > 95 otherwise the BP value is indicated, ø: no data available, -: not supported by the dataset.

Format: PDF Size: 182KB Download file

Additional file 2. Bayesian topology obtained with the combined dataset. The support values from each gene separately are indicated for the main nodes discussed in the text. The support values are indicated as follow: GHR/IRBP/cytb. A black dot indicate that the node is supported by the three dataset with a BP > 95, +: BP > 95 otherwise the BP value is indicated, ø: no data available, -: not supported by the dataset.

Format: PDF Size: 310KB Download file

Table 1. Best model and estimated substitution parameter values.

Figure 1. Maximum likelihood tree for the combined dataset. A black dot indicates that BP = 100 and PP = 1.0. Otherwise values are indicated as follow: BP/PP. An "-" indicates that MrBayes results support an alternative topology. The letters refer to the main groupings discussed in the text.

The most basal lineage (Lineage 1) consists of the genera Phloeomys and Batomys, both Philippine endemics. There is very strong support (100% BP; 1.0 PP) for reciprocal monophyly of Lineage 1 and all other Murinae.

Among the remaining Murinae, the first lineage to diverge (Lineage 2, 99% BP; 1.0 PP) comprises one largely Southeast Asian clade, the Rattus group sensu lato of Verneau et al. [31], together with the Eurasian harvest mouse Micromys, again with strong support (99% BP; 1.0 PP). Within Lineage 2, Micromys is the first lineage to diverge, followed by Maxomys, then a sublineage consisting of Niviventer and Leopoldamys (100% BP; 1.0 PP), and finally, the Rattus group sensu stricto of Verneau et al. [31], comprising Rattus, Berylmys, Bandicota, Diplothrix, Bunomys and Sundamys. Almost all dichotomies within Lineage 2 are robustly supported (Figure 1).

The third lineage to diverge in the ML tree (Lineage 3, 100% BP; 1.0 PP) is a western Pacific group, divided into two well-supported sub-lineages: 1) a Philippine group (Apomys, Archboldomys, Chrotomys, and Rhynchomys: 100% BP; 1.0 PP); and 2) an Australo-Papuan group (Hydromys, Conilurus and Pseudomys: 100% BP; 1.0 PP). The relationships within Lineage 3 are mostly well resolved, save for some uncertainty over the branching order among Apomys, Chrotomys and Rhynchomys.

The fourth lineage consists of the genus Mus (Lineage 4, 100% BP; 1.0 PP), represented by all four subgenera including the African Nannomys. The relationships among the four Mus subgenera remain unresolved as the position of Mus (Nannomys) minutoides and Mus (Coelomys) crociduroides is unstable between ML and BI analyses [see additional files 1 and 2].

The fifth murine lineage is a diverse and robustly supported African assemblage (Lineage 5, 100% BP; 1.0 PP) that corresponds to the 'Praomys group' of Lecompte et al. [13]. The monophyly of Lineage 5 is further supported by a shared insertion of 6 bp (TTGCCT) at position 893 of the GHR gene alignment. Although the basal nodes within Lineage 5 are poorly supported, it appears likely that Mastomys and Myomyscus are both paraphyletic. The order of branching between sublineages is unresolved and incongruent between ML and BI analyses [see additional files 1 and 2]. However, several terminal groups have strong support: 1) Myomyscus verreauxii + Colomys + Zelotomys (100% BP; 1.0 PP); 2) Mastomys (apart from M. pernanus) (100% BP; 1.0 PP); and 3) Praomys (apart from P. verschureni) (82% BP; 1.0 PP).

The sixth lineage (Lineage 6, 100% BP; 1.0 PP) consists of the genus Malacomys, the African swamp rats, here represented by two of the two recognized species.

The seventh murine lineage (Lineage 7, 99% BP; 1.0 PP) comprises the Eurasian genus Apodemus and the Ryukyu Island endemic genus Tokudaia.

The eighth lineage (Lineage 8, 97% BP; 1.0 PP) consists of the Indian genera Cremnomys and Millardia, the latter represented by two species.

The ninth murine lineage (Lineage 9, 100% BP; 1.0 PP) consists of the African 'otomyines' Parotomys and Otomys. As noted earlier, Musser and Carleton [8] included these taxa in a separate subfamily – Otomyinae.

The last murine lineage (Lineage 10, 90% BP; 1.0 PP) is very diverse and unites a large African assemblage of 'arvicanthines' (sensu Ducroz et al. [12]). Nodal support for 'arvicanthine' monophyly is moderately strong (90% BP; 1.0 PP). Branching order within this group is less well defined, with numerous distinct lineages apparent. The Indian bush rat genus Golunda occupies a basal position with moderate support (81% BP; 0.85 PP). Other near-basal lineages include Oenomys, Stochomys + Hybomys, Micaelamys, Grammomys, Aethomys, Dasymys and a well supported (100% BP; 1.0 PP) sublineage which diversified later, consisting of Arvicanthis, Lemniscomys, Mylomys, Desmomys, Rhabdomys and Pelomys.

Relationships among the ten lineages are partially resolved under each of ML and BI but nodal support values are only moderate to strong. The best support is observed for a diverse Afro-Asian large group comprising Lineages 4 to 7, which we here call Clade A (93% BP; 1.0 PP). Monophyly of Clade A is further supported by an insertion of 6 bp (YGGAYG) at position 86 of the GHR alignment. Within this group, Lineages 6 and 7 are identified as sister lineages but with only moderate support (77% BP; 0.68 PP); and Lineages 4 and 5 form a second sister pair, also with only moderate support (77% BP; 0.69 PP). Lineages 8, 9 and 10, also representing a mix of both African and Asian taxa, are united on the ML tree with moderate to strong support (87% BP, 1.00 PP) in what is named Clade B. Lineages 9 and 10 are sister taxa, with a very strong nodal support (100% BP; 1.0 PP).

Clades A and B are identified as sister lineages on the ML tree, and build up what we refer to Clade C, albeit with very low support (51% BP). This clade C includes all the African murines. A different topology was obtained under BI [see additional file 2] in which Lineage 3 (Philippine and Australo-Papuan groups) forms the sister group of Clade B, once again with low support (0.60 PP). This was the only discrepancy in branching order among the primary lineages of Murinae observed between the two methods.

Molecular divergence estimates

Estimated divergence times are indicated on the ML topology in Figure 2. A detailed chronogram is provided in the additional file 3. The standard deviations of all estimates fall between 0.5 to 0.7 Million years (My); this error value is implied in all divergence estimates indicated below. Divergence time estimations, standard deviations and credibility intervals calculated by multidivtime for the main nodes are indicated in the additional file 4, both for the combined dataset and for each gene separately. There is good congruence between the various estimations but with larger standard deviations for the ones based on one gene than for the values obtained with the combined dataset.

Additional file 3. Chronogram showing the posterior divergence ages within Murinae. The topology corresponds with the ML tree in Figure 1. Divergence times have been estimated from the concatenated Cytochrome b, IRBP and GHR sequences by a Bayesian relaxed molecular clock method with two fossil calibration time constraints (nodes indicated by a star).

Format: PDF Size: 179KB Download file


Additional file 4. Estimated dates of divergence (Mya), standard deviation (SD) and 95% credibility intervals (CD) for selected nodes in Figure 2 and additional file 3 based on Bayesian approximation from the concatenation of the three genes and for each gene separately.

Format: DOC Size: 54KB Download file


Figure 2. Simplified chronogram with the main murine groups. For each group the oldest fossil is indicated by an arrow according to [51,52,65,66,71,73,76,104,105,108,134-136]. Black area represents African taxa, light grey the Australasian taxa, and dark grey the Eurasian ones.

The earliest cladogenic event (to Lineage 1) is dated to 12.3 Mya. Emergence of the Clade C containing all African taxa as well as many Eurasian lineages is dated 11.1 Mya. Cladogenesis of the Afro-Asian Clades A and B is dated to 11 Mya. Divergences between each of Lineages 4 + 5, 6 + 7 and Clade B all fall within the interval 10.1–10.3 Mya. However, while these lineages originated more or less simultaneously, their subsequent diversification was unbalanced and asynchronous. Five of the seven lineages comprise only one or two genera (Lineages 4, 6, 7, 8 and 9), while the two most diverse and well-sampled lineages, corresponding to the main part of the African diversity, radiated somewhat at different times, at about 8.4 Mya (Lineage 10: 'arvicanthines') and 7.6 Mya (Lineage 5: 'Praomys group'), respectively. As we have a good sampling within these African groups (14 of 18 genera in the 'arvicanthines' and 8 of 9 genera in the Praomys group), we are confident that our results accurately reflect the diversification histories of these lineages.

The phylogeny shows strong geographic structure (shown Figure 2) with most primary lineages restricted to a single biogeographic area. Notable exceptions are the genus Mus (Lineage 4), which includes both Eurasian and African sub-lineages, Lineages 9+10 which are predominantly African ('otomyines' and 'arvicanthines') but also includes the Asian genus Golunda, and the African Praomys group (Lineage 5) which also includes the Arabian species Myomyscus yemeni.

Three near-basal cladogenic events within Murinae correspond to separations between 'mostly Asian' and 'mostly African' lineages. The first of these, dated to 10.22 Mya, separates the Praomys group (Lineage 5) from the predominantly Asian genus Mus. The second, dated to 10.20 Mya, separates the African 'arvicanthines+otomyines' (Lineages 9+10) from the Asian Millardia/Cremnomys (Lineage 8). The third one, dated to 10.16 Mya, separates Malacomys from Apodemus/Tokudaia.

Within Lineage 10, there is a younger separation, dated to around 8.4 Mya, between the African 'arvicanthines' and Golunda, a genus currently found only in Asia. Within Mus, divergence of the African subgenus Nannomys from various Eurasian subgenera is dated to 6.6 Mya.


rating: 1.00 from 1 votes | updated on: 23 Oct 2008 | views: 10666 |

Rate article:







excellent!bad…