Many important model organisms for biomedical and evolutionary research have sequenced genomes, but occupy a phylogenetically isolated position, evolutionarily distant from other sequenced genomes. This phylogenetic isolation is exemplified for zebrafish, a vertebrate model for cis-regulation, development and human disease, whose evolutionary distance to all other currently sequenced fish exceeds the distance between human and chicken. Such large distances make it difficult to align genomes and use them for comparative analysis beyond gene-focused questions. In particular, detecting conserved non-genic elements (CNEs) as promising cis-regulatory elements with biological importance is challenging. Here, we develop a general comparative genomics framework to align isolated genomes and to comprehensively detect CNEs. Our approach integrates highly sensitive and quality-controlled local alignments and uses alignment transitivity and ancestral reconstruction to bridge large evolutionary distances. We apply our framework to zebrafish and demonstrate substantially improved CNE detection and quality compared with previous sets. Our zebrafish CNE set comprises 54 533 CNEs, of which 11 792 (22%) are conserved to human or mouse. Our zebrafish CNEs (http://zebrafish.stanford.edu) are highly enriched in known enhancers and extend existing experimental (ChIP-Seq) sets. The same framework can now be applied to the isolated genomes of frog, amphioxus, Caenorhabditis elegans and many others.

Measuring 802.15.4 reception in three testbeds, we find that most intermediate links are bursty: they shift between poor and good delivery. We present a metric to measure this link burstiness and name it β. We find that link burstiness affects protocol performance and that β can predict the effects. We show that measuring β allows us to reason about how long a protocol should pause after encountering a packet failure to reduce its transmission cost. We find that using β as a guide to setting a single constant in a standard sensor network data collection protocol reduces its average transmission cost by 15%. In addition to data from 802.15.4 testbeds, we examine traces from 802.11b networks and find β has a broader relevance in the wireless domain.