With our increasing ability for generating whole-genome sequences, comparative analysis of whole genomes has become a powerful tool for understanding the structure, function, and evolutionary history of human and other vertebrate genomes. By virtue of their position basal to bony vertebrates, cartilaginous fishes (class Chondrichthyes) are a valuable outgroup in comparative studies of vertebrates. Recently, a holocephalan cartilaginous fish, the elephant shark, Callorhinchus milii (Subclass Holocephali: Order Chimaeriformes), has been proposed as a model genome, and low-coverage sequence of its genome has been generated. Despite such an increasing interest, the evolutionary history of the modern holocephalans-a previously successful and diverse group but represented by only 39 extant species-and their relationship with elasmobranchs and other jawed vertebrates has been poorly documented largely owing to a lack of well-preserved fossil materials after the end-Permian about 250 Ma. In this study, we assembled the whole mitogenome sequences for eight representatives from all the three families of the modern holocephalans and investigated their phylogenetic relationships and evolutionary history. Unambiguously aligned sequences from these holocephalans together with 17 other vertebrates (9,409 nt positions excluding entire third codon positions) were subjected to partitioned maximum likelihood analysis. The resulting tree strongly supported a single origin of the modern holocephalans and their sister-group relationship with elasmobranchs. The mitogenomic tree recovered the most basal callorhinchids within the chimaeriforms, which is sister to a clade comprising the remaining two families (rhinochimaerids and chimaerids). The timetree derived from a relaxed molecular clock Bayesian method suggests that the holocephalans originated in the Silurian about 420 Ma, having survived from the end-Permian (250 Ma) mass extinction and undergoing familial diversifications during the late Jurassic to early Cretaceous (170-120 Ma). This postulated evolutionary scenario agrees well with that based on the paleontological observations.

Global marine wild‐capture landings have remained relatively stable for >20 years; however, there is a lack of credible fishing capacity and effort information required to assess the sustainability and efficiency of the global fleet. As such, we estimated global fishing capacity and effort from 1950 to 2012 using a relatively comprehensive database developed by the FAO, supplemented by other data sources. Using random sampling techniques, we estimated the uncertainty surrounding many of our estimates enabling the identification of deficiencies and limitations. Global fishing capacity and effort increased rapidly from the late 1970s through to around 2010 before stabilizing. The Asian fleet is more than an order of magnitude larger than any other region in both capacity and effort, and continues to increase. Most other regions have stabilized, and there have been considerable declines in Europe and, to a lesser extent, in North America. Developed nations, as a whole, have decreased in both measures in the recent years and are responsible for the stabilization of the global trend. Developing and undeveloped countries are still increasing with the former having the largest fleet and showing the greatest relative increase with the socioeconomic impacts of reversing these trends likely to be high. The efficiency of the global fleet, in terms of watt days of fishing effort per tonnage of wild marine catch, is now less than in 1950 despite the considerable technological advances, and expansion throughout the world's oceans, that has occurred during this period of time.

No abstract

Chondrichthyans possess endoskeletal appendages called branchial rays that extend laterally from their hyoid and gill-bearing (branchial) arches. Branchial ray outgrowth, like tetrapod limb outgrowth, is maintained by Sonic hedgehog (Shh) signaling. In limbs, distal endoskeletal elements fail to form in the absence of normal Shh signaling, whereas shortened duration of Shh expression correlates with distal endoskeletal reduction in naturally variable populations. Chondrichthyans also exhibit natural variation with respect to branchial ray distribution-elasmobranchs (sharks and batoids) possess a series of ray-supported septa on their hyoid and gill arches, whereas holocephalans (chimaeras) possess a single hyoid arch raysupported operculum. Here we show that the elongate hyoid rays of the holocephalan Callorhinchus milii grow in association with sustained Shh expression within an opercular epithelial fold, whereas Shh is only transiently expressed in the gill arches. Coincident with this transient Shh expression, branchial ray outgrowth is initiated in C. milii but is not maintained, yielding previously unrecognized vestigial gill arch branchial rays. This is in contrast to the condition seen in sharks, where sustained Shh expression corresponds to the presence of fully formed branchial rays on the hyoid and gill arches. Considered in light of current hypotheses of chondrichthyan phylogeny, our data suggest that the holocephalan operculum evolved in concert with gill arch appendage reduction by attenuation of Shhmediated branchial ray outgrowth, and that chondrichthyan branchial rays and tetrapod limbs exhibit parallel developmental mechanisms of evolutionary reduction.

We develop a potentially widely applicable framework for analysing the vulnerability, resilience risk and exposure of chondrichthyan species to all types of anthropogenic stressors in the marine environment. The approach combines the three components of widely applied vulnerability analysis (exposure, sensitivity and adaptability) (ESA) with three components (exposure, susceptibility and productivity) (ESP) of our adaptation of productivity–susceptibility analysis (PSA). We apply our 12‐step ESA‒ESP analysis to evaluate the vulnerability (risk of a marked reduction of the population) of each of 132 chondrichthyan species in the Exclusive Economic Zone of southern Australia. The vulnerability relates to a species’ resilience to a spatial (or suitability) reduction of its habitats from exposure to up to eight climate change stressors. Vulnerability also relates to anthropogenic mortality added to natural mortality from exposure to the stressors of five types of fishing and seven other types of anthropogenic hazards. We use biological attributes as risk factors to evaluate risk related to resilience at the species or higher taxonomic level. We evaluate each species’ exposure to anthropogenic stressors by assigning it to one of six ecological groups based on its lifestyle (demersal versus pelagic) and habitat, defined by bathymetric range and substrates. We evaluate vulnerability for 11 scenarios: 2000–2006 when fishing effort peaked; 2018 following a decade of fisheries management reforms; low, medium and high standard future carbon dioxide equivalent emissions scenarios; and their six possible climate–fishing combinations. Our results demonstrate the value of refugia from fishing and how climate change exacerbates the risks from fishing.