Phylogenomics from Whole Genome Sequences Using aTRAM.

Novel sequencing technologies are rapidly expanding the size of data sets that can be applied to phylogenetic studies. Currently the most commonly used phylogenomic approaches involve some form of genome reduction. While these approaches make assembling phylogenomic data sets more economical for organisms with large genomes, they reduce the genomic coverage and thereby the long-term utility of the data. Currently, for organisms with moderate to small genomes ($<$1000 Mbp) it is feasible to sequence the entire genome at modest coverage ($10-30\times$). Computational challenges for handling these large data sets can be alleviated by assembling targeted reads, rather than assembling the entire genome, to produce a phylogenomic data matrix. Here we demonstrate the use of automated Target Restricted Assembly Method (aTRAM) to assemble 1107 single-copy ortholog genes from whole genome sequencing of sucking lice (Anoplura) and out-groups. We developed a pipeline to extract exon sequences from the aTRAM assemblies by annotating them with respect to the original target protein. We aligned these protein sequences with the inferred amino acids and then performed phylogenetic analyses on both the concatenated matrix of genes and on each gene separately in a coalescent analysis. Finally, we tested the limits of successful assembly in aTRAM by assembling 100 genes from close- to distantly related taxa at high to low levels of coverage.Both the concatenated analysis and the coalescent-based analysis produced the same tree topology, which was consistent with previously published results and resolved weakly supported nodes. These results demonstrate that this approach is successful at developing phylogenomic data sets from raw genome sequencing reads. Further, we found that with coverages above $5-10\times$, aTRAM was successful at assembling 80-90% of the contigs for both close and distantly related taxa. As sequencing costs continue to decline, we expect full genome sequencing will become more feasible for a wider array of organisms, and aTRAM will enable mining of these genomic data sets for an extensive variety of applications, including phylogenomics. [aTRAM; gene assembly; genome sequencing; phylogenomics.].

Redescription of Antarctophthirus microchir (Anoplura: Echinophthiriidae) from the South American sea lion, Otaria flavescens, from Patagonia, Argentina.

Antarctophthirus microchir was originally described from Phocarctos hookeri on the basis of 1 female and 1 male only. We redescribe adults and describe, for the first time, the 3 nymphal stages from specimens collected from Otaria flavescens from Patagonia, using light and scanning electron microscopy. The present material can be distinguished from other Antarctophthirus species by the presence of a fringe of setae on the back of the head, only present in Antarctophthirus trichechi and Antarctophthirus callorhini. However, A. trichechi also possess a prominent proboscis with large hooks, and A. callorhini presents less abundant and nonuniform abdominal scales in shape and size. Other differential features of A. microchir are the pattern of ovoid and uniform scales and longitudinal grooves in the surface of spines. Nymphal stage 1 differs from 2 and 3 mainly by the absence of scales and thorax without ventral spines or hairs. Nymphal stages 2 and 3 may be distinguished by the disposition of the occipital apophyses. Antarctophthirus microchir has been reported from 5 sea lion species from both hemispheres. Considering the conservative morphology, and ecological and evolutionary features of sucking lice, we raise the question of whether A. microchir from different sea lion hosts may represent a complex of cryptic species.