Runs of homozygosity (ROH) occur when offspring inherit haplotypes that are identical by descent from each parent. Length distributions of ROH are informative about population history; specifically, the probability of inbreeding mediated by mating system and/or population demography. Here, we investigated whether variation in killer whale ( Orcinus orca ) demographic history is reflected in genome‐wide heterozygosity and ROH l...

Multispecies aggregations of tuna, dolphins, and seabirds are prevalent and conspicuous in the vast waters of the eastern tropical Pacific and form the basis of a commercial fishery for yellowfin tuna ( Thunnus albacares ) through setting on schools of dolphins, which is among the largest tuna fisheries in the world. Incidental dolphin mortality associated with the development and early years of the fishery was high; by 1993 i...

Reconstruction of the demographic and evolutionary history of populations assuming a consensus tree‐like relationship can mask more complex scenarios, which are prevalent in nature. An emerging genomic toolset, which has been most comprehensively harnessed in the reconstruction of human evolutionary history, enables molecular ecologists to elucidate complex population histories. Killer whales have limited extrinsic barriers to...

Estimating the number of dolphins in a group is a challenging task. To assess the accuracy and precision of dolphin group size estimates, observer estimates were compared to counts from large‐format vertical aerial photographs. During 11 research cruises, a total of 2,435 size estimates of 434 groups were made by 59 observers. Observer estimates were modeled as a function of the photo count in a hierarchical Bayesian framework...

The vaquita (Phocoena sinus) is the world's most endangered marine mammal with approximately 245 individuals remaining in 2008. This species of porpoise is endemic to the northern Gulf of California, Mexico, and historically the population has declined because of unsustainable bycatch in gillnets. An illegal gillnet fishery for an endangered fish, the totoaba (Totoaba macdonaldi) , has recently resurged throughout the vaquita'...

Reproductive parameters were estimated and compared for eastern North Pacific populations of common dolphins using specimen and photogrammetric data. Age and length data for Delphinus capensis and D. delphis specimens recovered as bycatch or strandings were used to estimate the postnatal growth rates needed to estimate age for calves measured in aerial photographs. Bayesian methods propagated uncertainty among models and revea...

Gray seals were first observed breeding in the Dutch Wadden Sea in 1985, after centuries of absence. The breeding colony there is now the largest on the European continent. We describe the changes in gray seal numbers and their geographical expansion, and estimate how these processes were influenced by immigration from other colonies. Counts of hauled out animals were carried out between 1985 and 2013, monitoring three differe...

An ecosystem approach to fisheries management is a widely recognized goal, but describing and measuring the effects of a fishery on an ecosystem is difficult. Ecological information on the entire catch (all animals removed, whether retained or discarded) of both species targeted by the fishery and nontarget species (i.e., bycatch) is required. We used data from the well‐documented purse‐seine fishery for tunas (Thunnus albacar...

Despite more than half a century of criticism, significance testing continues to be used commonly by ecologists. Significance tests are widely misused and misunderstood, and even when properly used, they are not very informative for most ecological data. Problems of misuse and misinterpretation include: (i) invalid logic; (ii) rote use; (iii) equating statistical significance with biological importance; (iv) regarding the P‐va...

Bycatch in artisanal gill nets threatens the vaquita, Phocoena sinus , with extinction. In 2008 the Mexican government announced a conservation action plan for this porpoise, with three options for a protected area closed to gill net fishing. The probability of success of each of the three options was estimated with a Bayesian population model, where success was defined as an increase in vaquita abundance after 10 yr. The mode...

A line‐transect survey for the critically endangered vaquita, Phocoena sinus , was carried out in October–November 2008, in the northern Gulf of California, Mexico. Areas with deeper water were sampled visually from a large research vessel, while shallow water areas were covered by a sailboat towing an acoustic array. Total vaquita abundance in 2008 was estimated to be 245 animals (CV = 73%, 95% CI 68–884). The 2008 estimate w...

We assessed scientists' ability to detect declines of marine mammal stocks based on recent levels of survey effort, when the actual decline is precipitous. We defined a precipitous decline as a 50% decrease in abundance in 15 yr, at which point a stock could be legally classified as “depleted” under the U.S. Marine Mammal Protection Act. We assessed stocks for three categories of cetaceans: large whales ( n = 23, most of which...

A bstract The kill of dolphins ( Stenella attenuata and S. longirostris ) in the eastern tropical Pacific tuna purse‐seine fishery has been underestimated because of unobserved deaths of nursing calves due to separation from their mothers during fishing. Based on an analysis of dolphins killed from 1973 to 1990, and depending on the length at which calves are assumed to become independent, there was a deficit of calves relativ...

A bstract A line‐transect survey specifically designed to estimate vaquita ( Phocoena sinus ) abundance over its entire range was carried out by three boats in the summer of 1997. There was a total of 125 sightings of vaquita groups, mainly due to the use of large 25 ± 150 binoculars, which were seven times more effective in detecting vaquitas than hand‐held 7 ± binoculars. Results confirmed that the range of the vaquita is re...

A bstract The abundance of the only population of vaquitas, Gulf of California harbor porpoise ( Phocoena sinus ), is estimated from four surveys conducted in Mexico between 1986 and 1993, using a variety of methods. A line‐transect approach was applied, using some parameters estimated from a related species, the harbor porpoise ( Phocoena phocoena ). Vaquita abundance is estimated as 503 (CV = 0.63) from 1986–1988 boat survey...