Molecular Phylogenetics of Rodentia

Rodentia represents the largest order of mammals, encompassing over 2,000 species distributed across diverse ecosystems. Molecular phylogenetics has revolutionised our understanding of rodent evolution by integrating sequence data from mitochondrial and nuclear loci, advanced phylogenomic approaches and calibrated molecular clocks. Recent analyses have reconciled divergence time estimates with the fossil record, placing the crown-group origin shortly after the Cretaceous–Palaeogene boundary and a rapid intraordinal radiation in the early Palaeogene. High-throughput sequencing has resolved deep splits among major clades—Myomorpha, Sciuromorpha and Hystricognathi—while multi-gene datasets have refined relationships within speciose families. Phylogeographic studies, leveraging complete mitogenomes and nuclear markers, have illuminated the impact of climatic oscillations on range fragmentation and secondary contact in both widespread and endemic lineages. Collectively, these molecular frameworks provide a robust backbone for taxonomy, biogeography and the study of adaptive diversification, with implications for conservation strategies and the use of rodents as biomedical models.

Research from Nature Portfolio

Recent studies have employed a combination of mitochondrial and nuclear markers to revisit relationships within the jerboa subfamily Allactaginae. By analysing sequences from fifteen nuclear genes alongside cytochrome b, researchers have clarified intergeneric and interspecific relationships, confirming the species status of several taxa and revealing previously underappreciated diversity within genera such as Orientallactaga, Allactaga and Pygeretmus. Species distribution modelling projected onto palaeoenvironmental reconstructions has traced speciation events to periods of range fragmentation, highlighting niche conservatism in arid belt ecosystems. These approaches have refined divergence time estimates and produced hypotheses regarding the timing and locale of major cladogenetic events.

Molecular Phylogenetics of Rodentia publication trend

The graph below shows the total number of articles in molecular phylogenetics of rodentia across all publications each year (not limited to Nature Index journals).

Technical terms

Molecular clock: A method for estimating divergence times by relating genetic mutation rates to elapsed evolutionary time.

Mitochondrial genome (mitogenome): The complete set of mitochondrial DNA, commonly used in phylogenetic analysis due to its maternal inheritance and rapid mutation rate.

Nuclear gene: A gene located in the cell nucleus that provides independent phylogenetic signal complementary to mitochondrial data.

Phylogeography: The study of the historical processes that shape the geographic distributions of lineages.

Fossil calibration: The incorporation of dating information from well-dated fossils to constrain molecular clock analyses.

References

1. Molecular and Paleontological Evidence for a Post-Cretaceous Origin of Rodents. PLOS ONE (2012).
2. Molecular systematics of the Sicista tianschanica species complex: a contribution from historical DNA analysis. PeerJ (2021).
3. Whole mitochondrial genome sequence and phylogenetic relationships of Williams’s jerboa (Scarturus williamsi) from Turkey. PeerJ (2020).
4. Phylogenetic relations and range history of jerboas of the Allactaginae subfamily (Dipodidae, Rodentia). Scientific Reports (2022).