Mitochondrial Genomes Reveal Slow Rates of Molecular Evolution and the Timing of Speciation in Beavers (Castor), One of the Largest Rodent Species

Abstract

BackgroundBeavers are one of the largest and ecologically most distinct rodent species. Little is known about their evolution and even their closest phylogenetic relatives have not yet been identified with certainty. Similarly, little is known about the timing of divergence events within the genus Castor.Methodology/Principal FindingsWe sequenced complete mitochondrial genomes from both extant beaver species and used these sequences to place beavers in the phylogenetic tree of rodents and date their divergence from other rodents as well as the divergence events within the genus Castor. Our analyses support the phylogenetic position of beavers as a sister lineage to the scaly tailed squirrel Anomalurus within the mouse related clade. Molecular dating places the divergence time of the lineages leading to beavers and Anomalurus as early as around 54 million years ago (mya). The living beaver species, Castor canadensis from North America and Castor fiber from Eurasia, although similar in appearance, appear to have diverged from a common ancestor more than seven mya. This result is consistent with the hypothesis that a migration of Castor from Eurasia to North America as early as 7.5 mya could have initiated their speciation. We date the common ancestor of the extant Eurasian beaver relict populations to around 210,000 years ago, much earlier than previously thought. Finally, the substitution rate of Castor mitochondrial DNA is considerably lower than that of other rodents. We found evidence that this is correlated with the longer life span of beavers compared to other rodents.Conclusions/SignificanceA phylogenetic analysis of mitochondrial genome sequences suggests a sister-group relationship between Castor and Anomalurus, and allows molecular dating of species divergence in congruence with paleontological data. The implementation of a relaxed molecular clock enabled us to estimate mitochondrial substitution rates and to evaluate the effect of life history traits on it.

Reconstruction of karyotype evolution in core Glires. I. The genome homology revealed by comparative chromosome painting

“…The analysis of SINE distribution and the sequencing of mitochondrial genomes in rodents support the placement of Castor into the mouse-related clade (Horn et al 2011;Churakov et al 2010). Initial comparative painting investigations showed that the genome of C. fiber was extensively rearranged compared to squirrels (Graphodatsky et al 2008).…”

Chromosomal evolution in Rodentia

“…These features corroborate our suggestion that Hystricomorpha is intermediate between Anomaluromorpha and Myomorpha+Castorimorpha. Although such an arrangement contradicts the latest data based on painting with human probes, sequencing of nuclear genes and the distribution of short interspersed elements all place Hystricomorpha in a basal position to the Anomaluromorpha+Myomorpha+ Castorimorpha clade (Ferguson-Smith and Trifonov, 2007;BlangaKanfi et al, 2009;Churakov et al, 2010;Horn et al, 2011). We therefore consider the fission of HSA 14/15 and the disruption of HSA 12 onto three fragments as convergent events that took place independently in hystricomorphs, myomorphs and castorimorphs.…”

“…The latest molecular data suggest, however, that these species should be considered a separate taxon independent from Sciuromorpha (Blanga- Kanfi et al, 2009;Horn et al, 2011). According to current taxonomy, Castorimorpha includes beavers, pocket and kangaroo mice, pocket gophers-some 102 species in all.…”

Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

“…The long-range PCR strategy nevertheless remained an integral method for the majority of recent studies [e.g. (20,21)], especially to overcome many NGS platforms demand for moderate-to-high amounts of template DNA, which is of particular concern when dealing with limited material such as small invertebrates (22). However, optimizing long-range PCR can be tedious, in particular for previously uncharacterized organisms when the information required for primer design is scarce, whereas for difficult templates such as ancient DNA, long range PCR is no option at all, given the level of DNA degradation.…”