A target enrichment bait set for studying relationships among ostariophysan fishes

SummaryTarget enrichment of conserved nuclear loci has helped reconstruct evolutionary relationships among a wide variety of species. While there are preexisting bait sets to enrich a few hundred loci across all fishes or a thousand loci from acanthomorph fishes, no bait set exists to enrich large numbers (>1000 loci) of ultraconserved nuclear loci from ostariophysans, the second largest actinopterygian superorder.In this manuscript, we describe how we designed a bait set to enrich 2,708 ultraconserved nuclear loci from ostariophysan fishes by combining an existing genome assembly with low coverage sequence data collected from two ostariophysan lineages.We perform a series of enrichment experiments using this bait set across the ostariophysan Tree of Life, from the deepest splits among the major groups (>150 MYA) to more recent divergence events that have occured during the last 50 million years.Our results demonstrate that the bait set we designed is useful for addressing phylogenetic questions from the origin of crown ostariophysans to more recent divergence events, and our in silico results suggest that this bait set may be useful for addressing evolutionary questions in closely related groups of fishes, like Clupeiformes.

Behavioral responses of sea lamprey (Petromyzon marinus) to a putative alarm cue derived from conspecific and heterospecific sources

The sea lamprey, Petromyzon marinus, exhibits a spectacular alarm response to the odor emitted from decayed conspecifics that may differ substantially in function from the well-characterized system in ostariophysan fishes. Here, we report a series of three laboratory experiments designed to characterize the behavioral responses of migratory-phase lampreys to a set of odors derived from conspecific and heterospecific tissues, determine whether sex or sexual maturation alters these responses, and ascertain if the putative alarm substance derives from a particular region of the body. A number of the findings were consistent with the prevailing predator-avoidance paradigm for fish alarm substances released from the skin after predator attack in that: (1) dilute odors derived from freshly ground skin were highly repellent; (2) the substance is contained in the organism early in life; (3) the odor derived from a close relative was avoided whereas those of a distant relative were not; and (4) upon sexual maturity female response to the alarm substance was attenuated. Two interesting patterns arose that differed substantially from the prevailing paradigm: (1) conspecific odors remained repellent after 96 h of aerobic decay; and (2) the cue was emitted from multiple areas of the body, not just the skin, and the repellency of the odor derived from any tissue increased in accordance with its mass. A persistent cue emitted from several sources suggests a broader ecological function than the detection and avoidance of a predator.