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The Beaver's Phylogenetic Lineage Illuminated by Retroposon Reads

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The Beaver's Phylogenetic Lineage Illuminated by Retroposon Reads

Liliya Doronina et al. Sci Rep.

Abstract

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).

Conflict of interest statement

The authors declare no competing financial interests.

Figures

Figure 1
Figure 1. Snapshot of retroposon presence/absence analysis from Illumina paired-end reads (PE-RAD).
(a) Library construction: genomic SbfI digestion, P1 adapter ligation, random sharing (further shown for a selected single read), and size selection of 350–750 nt followed by the P2 adapter ligation and amplification steps. (b) Paired-end Illumina sequencing: the P1 and P2 sequencing primers generate shifted and partially overlapped ~100-nt reads. (c) The described PE-RAD sequences were taken from Senn et al. to build a gross genome assembly including ~134,000 fasta contigs >200 nt. (d) RepeatMasking revealed ~88,000 repeats and ~4,000 rodent-specific SINE loci. These loci were extracted from the fasta assembly using the coordinate extractor tool fastCOEX described in Materials and Methods. For control, the 11 phylogenetically informative loci were PCR-amplified/sequenced in beaver and comparatively sequenced in additional rodents. (e) Informative SINEs (black balls) are shared by beaver and kangaroo rat (6) or all species of the mouse-related clade (5 plus 1 additional previously published marker is denoted by *), indicating their close relationship. The in this study performed analyses are shown in white boxes. The rodent paintings were provided by Jón Baldur Hlíðberg.
Figure 2
Figure 2. Reconstruction of the rodent phylogenetic relationships based on a gross beaver genome assembly and retroposon presence/absence screening (highlighted in blue).
3,780 potential phylogenetically informative retroposons were extracted from the beaver reference assembly and projected onto sequence information of other rodent genomes and onto PCR-amplified orthologs from Anomaluromorpha. These newly revealed markers are shown as enlarged red balls. Previously identified phylogenetically diagnostic retroposon markers are indicated by black and two conflicting yellow balls. The two screening strategies and the resulting diagnostic presence/absence patterns are indicated for Castorimorpha and also the mouse-related clade. The myomorphous, sciurimorphous, and hystricomorphous zygomasseteric systems are illustrated to the right (blue and red lines show anterior parts of medial and lateral masseter, respectively; for details of zygomasseteric systems in rodents see Potapova27). The mandible types are noted: sciurognathous and hystricognathous. For the squirrel-related clade, only the zygomasseteric system of Sciuridae is presented. The rodent paintings were provided by Jón Baldur Hlíðberg.

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