The complete mitochondrial genome of Aegialites californicus (Motchoulsky, 1845) (insecta: coleoptera: salpingidae).

The flightless intertidal beetle genus Aegialites (family Salpingidae) is distributed along the Northern Pacific coasts, from California to Alaska and from Northern Japan to Kamchatka. Systematics of Aegialites and its phylogenetic relationships to other members of Salpingidae are unclear, and little genetic information is available. We here present the first complete mitochondrial genome of this genus, represented by Aegialites californicus (Motchoulsky, 1845) from Sonoma County, California, U.S.A. The complete mitochondrial genome of A. californicus is 15,899 bp long and comprises 13 protein-coding (PCG), two ribosomal RNA (rRNA) and 22 transfer RNA (tRNA) genes. The phylogenetic analysis places A.californicus as sister to other members of family Salpingidae. The mitochondrial genome sequence of A. californicus will contribute to future phylogenetic and taxonomic studies of genus Aegialites, family Salpingidae and superfamily Tenebrionoidea.

Scoutknife: A naïve, whole genome informed phylogenetic robusticity metric.

Background: The phylogenetic bootstrap, first proposed by Felsenstein in 1985, is a critically important statistical method in assessing the robusticity of phylogenetic datasets. Core to its concept was the use of pseudo sampling - assessing the data by generating new replicates derived from the initial dataset that was used to generate the phylogeny. In this way, phylogenetic support metrics could overcome the lack of perfect, infinite data. With infinite data, however, it is possible to sample smaller replicates directly from the data to obtain both the phylogeny and its statistical robusticity in the same analysis. Due to the growth of whole genome sequencing, the depth and breadth of our datasets have greatly expanded and are set to only expand further. With genome-scale datasets comprising thousands of genes, we can now obtain a proxy for infinite data. Accordingly, we can potentially abandon the notion of pseudo sampling and instead randomly sample small subsets of genes from the thousands of genes in our analyses. Methods: We introduce Scoutknife, a jackknife-style subsampling implementation that generates 100 datasets by randomly sampling a small number of genes from an initial large-gene dataset to jointly establish both a phylogenetic hypothesis and assess its robusticity. We assess its effectiveness by using 18 previously published datasets and 100 simulation studies. Results: We show that Scoutknife is conservative and informative as to conflicts and incongruence across the whole genome, without the need for subsampling based on traditional model selection criteria. Conclusions: Scoutknife reliably achieves comparable results to selecting the best genes on both real and simulation datasets, while being resistant to the potential biases caused by selecting for model fit. As the amount of genome data grows, it becomes an even more exciting option to assess the robusticity of phylogenetic hypotheses.

The evolution of annelids reveals two adaptive routes to the interstitial realm.

Many animals permanently inhabit the marine interstitium, the space between sand grains [1, 2]. Different evolutionary scenarios may explain the existence of interstitial animals [3, 4]. These scenarios include (1) that the interstitial realm is the ancestral habitat of bilaterians [5, 6], (2) that interstitial taxa evolved from larger ancestors by miniaturization, or (3) progenesis [3]. The first view mirrors the former hypothesis that interstitial annelids, called archiannelids, were at the base of the annelid radiation [7]. Based on morphological data, however, progenesis is generally favored for interstitial annelids today [3, 4, 8]. Herein, our phylogenomic approach revealed that interstitial archiannelids are robustly placed into two groups nested within the annelid tree. Evolution of the first group comprising among others Dinophilidae is best explained by progenesis. In contrast, the second group comprising Protodrilida and Polygordiidae appears to have evolved by stepwise miniaturization adapting from coarser to finer sediments. Thus, in addition to progenesis [3, 4], miniaturization, thought to be too slow for an adaptation to the interstitium [3], is an important second route allowing adaptation to interstitial environments. Both progenesis and miniaturization should be considered when investigating evolution of interstitial taxa [1, 3].