The Canadian beaver (Castor canadensis) is the largest indigenous rodent in North America. We report a draft annotated assembly of the beaver genome, the first for a large rodent and the first mammalian genome assembled directly from uncorrected and moderate coverage (< 30 ×) long-reads generated by single-molecule sequencing. The genome size is 2.7 Gb estimated by k-mer analysis. We assembled the beaver genome using the new Canu assembler optimized for noisy reads. The resulting assembly was refined using Pilon supported by shortreads (80 ×) and checked for accuracy by congruency against an independent short-read assembly. We scaffolded the assembly using the exon-gene models derived from 9805 full-length open reading frames (FL-ORFs) constructed from the beaver leukocyte and muscle transcriptomes. The final assembly comprised 22,515 contigs with an N50 of 278,680 bp and an N50-scaffold of 317,558 bp. Maximum contig and scaffold lengths were 3.3 and 4.2 Mb, respectively, with a combined scaffold length representing 92% of the estimated genome size. The completeness and accuracy of the scaffold assembly was demonstrated by the complete and precise exon placement for 91.1% of the 9,805 assembled FL-ORFs and 83.1% of the BUSCO (Benchmarking Universal Single-Copy Orthologs) gene set used to assess the quality of genome assemblies. Well-represented were genes involved in dentition and enamel deposition, defining characteristics of rodents with which the beaver is well-endowed. The study provides insights for genome assembly and an important genomics resource for Castoridae and rodent evolutionary biology.
Solving problematic phylogenetic relationships often requires high quality genome data. However, for many organisms such data are still not available. Among rodents, the phylogenetic position of the beaver has always attracted special interest. The arrangement of the beaver’s masseter (jaw-closer) muscle once suggested a strong affinity to some sciurid rodents (e.g., squirrels), placing them in the Sciuromorpha suborder. Modern molecular data, however, suggested a closer relationship of beaver to the representatives of the mouse-related clade, but significant data from virtually homoplasy-free markers (for example retroposon insertions) for the exact position of the beaver have not been available. We derived a gross genome assembly from deposited genomic Illumina paired-end reads and extracted thousands of potential phylogenetically informative retroposon markers using the new bioinformatics coordinate extractor fastCOEX, enabling us to evaluate different hypotheses for the phylogenetic position of the beaver. Comparative results provided significant support for a clear relationship between beavers (Castoridae) and kangaroo rat-related species (Geomyoidea) (p < 0.0015, six markers, no conflicting data) within a significantly supported mouse-related clade (including Myodonta, Anomaluromorpha, and Castorimorpha) (p < 0.0015, six markers, no conflicting data).
The Early to Late Oligocene Propalaeocastor is the earliest known beaver genus from Eurasia. Although many species of this genus have been described, these species are defined based on very fragmentary specimens. Propalaeocastor irtyshensis from the Early Oligocene Irtysh River Formation in northwestern Xinjiang, China is one of the earliest-known members of Propalaeocastor. This species is defined on a single maxillary fragment. We revise the diagnosis of P. irtyshensis and the genus Propalaeocastor, based on newly discovered specimens from the Irtysh River Formation. The dental morphology of P. irtyshensis is very similar to other early castorids. The caudal palatine foramen of P. irtyshensis is situated in the maxillary-palatine suture. This is a feature generally accept as diagnostic character for the castorids. On the other hand, P. irtyshensis has two upper premolars, a rudimentarily developed sciuromorph-like zygomatic plate, and a relatively large protrogomorph-like infraorbital foramen. Some previous researchers suggested that Propalaeocastor is a junior synonym of Steneofiber, while other took it as a valid genus. Our morphological comparison and phylogenetic analysis suggest that Propalaeocastor differs from Steneofiber and is a valid genus. We also suggest that Agnotocastor aubekerovi, A. coloradensis, A. galushai, A. readingi, Oligotheriomys primus, and “Steneofiber aff. dehmi” should be referred to Propalaeocastor. Propalaeocastor is the earliest and most basal beaver. The origin place of Propalaeocastor and castorids is uncertain. The Early Oligocene radiation of castorids probably is propelled by the global climate change during the Eocene-Oligocene transition.
Elevated concentrations of methylmercury (MeHg) in freshwater ecosystems are of major environmental concern in large parts of the northern hemisphere. Beaver ponds have been identified as a potentially important source of MeHg. The role of beavers might be especially pronounced in large parts of Europe, where beaver populations have expanded rapidly following near-extirpation. This study evaluates the role of the age and colonization history (encompassing patterns of use and reuse) of ponds constructed by the Eurasian beaver Castor fiber in regulating MeHg concentrations in Swedish streams. In 12 beaver systems located in three regions, we quantified MeHg concentrations together with other relevant parameters on five occasions per year in 2012-2013. Five were “pioneer” systems, inundated for the first time since beaver extirpation, and seven “were recolonized”, with dams reconstructed by newly recolonizing beavers. MeHg concentrations in pioneer but not in recolonized beaver systems were up to 3.5 fold higher downstream than upstream of the ponds, and varied between seasons and years. Our results show that pioneer inundation by beavers can increase MeHg concentrations in streams, but that this effect is negligible when dams are reconstructed on previously used ponds. We therefore expect that the recovery and expansion of beavers in the boreal system will only have a transitional effect on MeHg in the environment.
A new species of demodecid mite, Demodex castoris sp. nov. (Acari: Prostigmata: Demodecidae), is described based on adult stages from the skin of the nasal region of the Eurasian beaver Castor fiber Linnaeus, 1758, collected in Poland. This is the first detection of a representative demodecid mite in rodents of the suborder Castorimorpha and also represents the first detection of a skin mite in Eurasian beavers. The new species is a small skin mite (average 173 µm in length) characterized by sexual dimorphism related to body proportions. D. castoris sp. nov. was observed in 4 out of 6 beavers examined (66.6%), with a mean intensity of 10.8 and an intensity range of 2-23 ind. host-1. This paper also contains a checklist of parasitic arthropods known from Castor spp.