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To understand the scope and scale of the loss of biodiversity, tools are required that can be applied in a standardized manner to all species globally, spanning realms from land to the open ocean. We used data from the International Union for the Conservation of Nature Red List to provide a synthesis of the conservation status and extinction risk of cetaceans. One in 4 cetacean species (26% of 92 species) was threatened with extinction (i.e., critically endangered, endangered, or vulnerable) and 11% were near threatened. Ten percent of cetacean species were data deficient, and we predicted that 2–3 of these species may also be threatened. The proportion of threatened cetaceans has increased: 15% in 1991, 19% in 2008, and 26% in 2021. The assessed conservation status of 20% of species has worsened from 2008 to 2021, and only 3 moved into categories of lesser threat. Cetacean species with small geographic ranges were more likely to be listed as threatened than those with large ranges, and those that occur in freshwater (100% of species) and coastal (60% of species) habitats were under the greatest threat. Analysis of odontocete species distributions revealed a global hotspot of threatened small cetaceans in Southeast Asia, in an area encompassing the Coral Triangle and extending through nearshore waters of the Bay of Bengal, northern Australia, and Papua New Guinea and into the coastal waters of China. Improved management of fisheries to limit overfishing and reduce bycatch is urgently needed to avoid extinctions or further declines, especially in coastal areas of Asia, Africa, and South America. [ABSTRACT FROM AUTHOR]

Photographic and genetic studies have revealed the complex population structure of migratory large whales. Most research and management are geographically based, focusing on either wintering or summering areas, which in most cases fails to capture this complexity. We use examples from humpback whales (Megaptera novaeangliae) and gray whales (Eschrichtius robustus) to illustrate the concept of migratory herds, defined here as conspecific whales that migrate between the same wintering and feeding ground. In cases where individuals show strong fidelity to both feeding and wintering grounds, and therefore to a herd, dispersal between herds can be low enough to render them as demographically independent populations, where population dynamics are determined more by net internal recruitment (births minus deaths) than by immigration from outside sources. In these cases, the migratory whale herd is the appropriate unit to conserve under the ecological paradigm that focuses on groups united by demographic forces. We suggest that when addressing questions focused on ecological timescales for whale species with strong fidelity to migratory destinations, the migratory whale herd is a better initial working hypothesis rather than one based on geographically defined strata. [ABSTRACT FROM AUTHOR]

The title of Perrin's presentation was, "The problem of porpoise [= dolphin] mortality in the U. S. tropical tuna fishery" (Perrin, [5]). Bill invited Louella the following year to attend the IWC gill net meeting in La Jolla in 1991 (Perrin et al., [15]) where she presented the bycatch data she gathered from gill net fisheries in the Philippines. Besides being the first person to alert the world to the massive kills of dolphins that were happening in the eastern tropical Pacific tuna fishery in the 1960s, decades later Bill created a compilation of the thousands of documents related to the controversy, along with a searchable bibliography (Perrin, [9]). Bill's critical early research on oceanic dolphins brought world attention to the longstanding and growing problem of incidental mortality of cetaceans in fisheries, but it was also transformative given the huge and enduring impact it had on cetacean science. [Extracted from the article]

Among mesoplodonts recorded in the North Pacific, the tooth size and location in the adult male in the Baja whale most closely resembles that of the ginkgo-toothed beaked whale ( I M. ginkgodens i ) and the recently recognized Deraniyagala's beaked whale ( I M. hotaula i ; Dalebout et al., 2014). Three new species of beaked whales (Ziphiidae) have been described in the past three decades: the pygmy beaked whale ( I Mesoplodon peruvianus i ; Reyes et al. 1991), Perrin's beaked whale ( I Mesoplodon perrini i ; Dalebout et al. 2002), and Sato's beaked whale ( I Berardius minimus i ; Yamada et al. 2019). Perrin's beaked whale has never been identified alive and was discovered accidentally through genetic analysis of stranded whales in California that had been misidentified as Hector's beaked whale ( I Mesoplodon hectori i ; Dalebout et al. 2002). Previous acoustic studies characterized a unique beaked whale echolocation signal (called BW43) that, based on its limited distribution off southern California, was believed to be made by Perrin's beaked whale (Baumann-Pickering et al., 2013). [Extracted from the article]

Harbor porpoise in the North Pacific are found in coastal waters from southern California to Japan, but population structure is poorly known outside of a few local areas. We used multiplexed amplicon sequencing of 292 loci and genotyped clusters of single nucleotide polymoirphisms as microhaplotypes (N = 271 samples) in addition to mitochondrial (mtDNA) sequence data (N = 413 samples) to examine the genetic structure from samples collected along the Pacific coast and inland waterways from California to southern British Columbia. We confirmed an overall pattern of strong isolation‐by‐distance, suggesting that individual dispersal is restricted. We also found evidence of regions where genetic differences are larger than expected based on geographical distance alone, implying current or historical barriers to gene flow. In particular, the southernmost population in California is genetically distinct (FST = 0.02 [microhaplotypes]; 0.31 [mtDNA]), with both reduced genetic variability and high frequency of an otherwise rare mtDNA haplotype. At the northern end of our study range, we found significant genetic differentiation of samples from the Strait of Georgia, previously identified as a potential biogeographical boundary or secondary contact zone between harbor porpoise populations. Association of microhaplotypes with remotely sensed environmental variables indicated potential local adaptation, especially at the southern end of the species' range. These results inform conservation and management for this nearshore species, illustrate the value of genomic methods for detecting patterns of genetic structure within a continuously distributed marine species, and highlight the power of microhaplotype genotyping for detecting genetic structure in harbor porpoises despite reliance on poor‐quality samples. [ABSTRACT FROM AUTHOR]

Calving intervals of five other phocoenids have been described, including: harbor porpoise, ( I P. phocoena) i , Dall's porpoise ( I Phocoenoides dalli i ), Burmeister's porpoise ( I P. spinnipinis i ), and Indopacific finless porpoise ( I Neophocaena phocaenoides) i and the sunameri finless porpoise subspecies ( I Neophocaena asiaorientalis sunameri i ). For example, the pregnancy rate of mature female harbor porpoises in the Gulf of Maine was 0.95, indicating an annual pattern of reproduction (Read and Hohn [21]). Similar findings of annual reproduction have been reported for Dall's porpoise (Ferrero and Walker [5]) and Burmeister's porpoise (Reyes and Van Waerebeek [22]). Conception, fetal growth, and calving seasonality of harbor porpoise (Phocoena phocoena) in the Salish Sea waters of Washington State, USA and southern British Columbia, Canada. [Extracted from the article]

Genomic phylogeography plays an important role in describing evolutionary processes and their geographic, ecological, or cultural drivers. These drivers are often poorly understood in marine environments, which have fewer obvious barriers to mixing than terrestrial environments. Taxonomic uncertainty of some taxa (e.g., cetaceans), due to the difficulty in obtaining morphological data, can hamper our understanding of these processes. One such taxon, the short‐finned pilot whale, is recognized as a single global species but includes at least two distinct morphological forms described from stranding and drive hunting in Japan, the "Naisa" and "Shiho" forms. Using samples (n = 735) collected throughout their global range, we examine phylogeographic patterns of divergence by comparing mitogenomes and nuclear SNP loci. Our results suggest three types within the species: an Atlantic Ocean type, a western/central Pacific and Indian Ocean (Naisa) type, and an eastern Pacific Ocean and northern Japan (Shiho) type. mtDNA control region differentiation indicates these three types form two subspecies, separated by the East Pacific Barrier: Shiho short‐finned pilot whale, in the eastern Pacific Ocean and northern Japan, and Naisa short‐finned pilot whale, throughout the remainder of the species' distribution. Our data further indicate two diverging populations within the Naisa subspecies, in the Atlantic Ocean and western/central Pacific and Indian Oceans, separated by the Benguela Barrier off South Africa. This study reveals a process of divergence and speciation within a globally‐distributed, mobile marine predator, and indicates the importance of the East Pacific Barrier to this evolutionary process. [ABSTRACT FROM AUTHOR]

The number of Mexico's endemic porpoise, the vaquita ( Phocoena sinus), is collapsing primarily due to bycatch in illegal gillnets set for totoaba ( Totoaba macdonaldi), an endangered fish whose swim bladders are exported to China. Previous research estimated that vaquitas declined from about 567 to 245 individuals between 1997 and 2008. Acoustic monitoring between 2011 and 2015 showed a decline of 34%/year. Here, we combine visual line transect and passive acoustic data collected simultaneously in a robust spatial analysis to estimate that only 59 (95% Bayesian Credible Interval [CRI] 22-145) vaquita remained as of autumn 2015, a decrease since 1997 of 92% (95% CRI 80-97%). Risk analysis suggests that if the current, temporary gillnet ban is maintained and effectively enforced, vaquitas could recover to 2008 population levels by 2050. Otherwise, the species is likely to be extinct within a decade. [ABSTRACT FROM AUTHOR]

Cetacean taxonomy continues to be in flux and molecular genetic analyses examining alpha taxonomy in cetaceans have relied heavily on the mitochondrial DNA control region. However, there has been little consistency across studies; a variety of metrics and levels of divergence have been invoked when delimiting new cetacean species and subspecies. Using control region sequences, we explored, across pairs of well-recognized cetacean populations, subspecies, and species, a suite of metrics measuring molecular genetic differentiation to examine which metrics best categorize these taxonomic units. Nei's estimate of net divergence ( d A) and percent diagnosability performed best. All but a single, recently diverged species were unambiguously identified using these metrics. Many subspecies were found at intermediate values as expected, allowing separation from both populations and species, but several had levels of divergence equivalent to populations, resulting in underclassification errors using this single marker. Coupling d A with additional measures, such as percent diagnosability, examining appropriate nuclear genetic markers, and interpreting results in a broader biological context will improve taxonomic investigations in cetaceans. [ABSTRACT FROM AUTHOR]

Obtaining the representative morphological data required for traditional taxonomy is difficult, and sometimes impossible, for cetaceans, especially large ones. As a result, three quarters of the 88 currently recognized extant species have no subspecies and 40 taxa likely have additional unnamed taxa. Conservation needs give urgency to improving taxonomy because unnamed taxa are unlikely to receive protection equivalent to that received by named taxa. Genetic data can improve efforts to delimit subspecies, but the markers and methods used have varied and the magnitude of genetic difference used to justify subspecies distinctions across studies has also varied. Here, we define the concepts of populations, subspecies, and species to establish a foundation for developing guidelines (data to include and analyses to conduct) and quantitative standards (the magnitude of differentiation expected at different taxonomic levels) for using genetic data to support taxonomic recognition. Our definition is particularly applicable to data-poor groups because it allows for naming a subspecies when there is uncertainty about whether lineages have diverged sufficiently for species-level recognition. This allows a species that lacks convincing data for lineage divergence to be recognized as a subspecies while sufficient data are accrued, which could take decades for some cetaceans. [ABSTRACT FROM AUTHOR]

Uncertainty in marine mammal taxonomy is increasingly being addressed using molecular genetic data. We examined 32 peer-reviewed articles published between 1994 and 2011to review methodological practices, consistency of markers and analytical methods, and overall quality of arguments used when genetic data have been employed to delimit new species and subspecies of marine mammals. The mitochondrial DNA (mt DNA) control region was the primary genetic marker used in these studies, but analytical methods varied greatly across studies. Diagnosability, a common metric for delimiting subspecies with morphological data, was only used through citing of fixed differences in mt DNA sequences. Assignment tests based on microsatellite data were less common but were applied at both taxonomic levels. Nuclear DNA sequence data were rarely used. Basic background material needed to evaluate the strength of arguments, such as distribution and sampling maps, were often missing. For most studies, sample sizes were good, but adequate geographic sampling for broadly distributed taxa was often lacking, diminishing the strength of evidence for taxonomic distinctness. Examining these empirical cases revealed a mixture of sound and inadequate practices for genetic studies of cetacean taxonomy and suggested that improvements could be made to the field by developing standard guidelines. [ABSTRACT FROM AUTHOR]

Taxonomy is an imprecise science that delimits the evolutionary continuum into discrete categories. For marine mammals, this science is complicated by the relative lack of morphological data for taxa that inhabit remote and often vast ranges. We provide guidelines to promote consistency in studies relying primarily on molecular genetic data to delimit cetacean subspecies from both populations and species. These guidelines identify informational needs: basis for the taxonomic hypothesis being tested, description of current taxonomy, description of relevant life history, sample distribution, sample size, number and sequence length of genetic markers, description of measures taken to ensure data quality, summary statistics for the genetic markers, and analytical methods used to evaluate the genetic data. We propose an initial set of quantitative and qualitative standards based on the types of data and analytical methods most readily available at present. These standards are not expected to be rigidly applied. Rather, they are meant to encourage taxonomic arguments that are consistent and transparent. We hope professional societies, such as the Society for Marine Mammalogy, will adopt quantitative standards that evolve as new data types and analytical methods become widely available. [ABSTRACT FROM AUTHOR]

We examine the use of an ensemble method, Random Forests, to delimit subspecies using mitochondrial DNA (mt DNA) sequences. Diagnosability, a measure of the ability to correctly determine the taxon of a specimen of unknown origin, has historically been used to delimit subspecies, but few studies have explored how to estimate it from DNA sequences. Using simulated and empirical data sets, we demonstrate that Random Forests produces classification models that perform well for diagnosing subspecies and species. Populations with strong social structure and relatively low abundances ( e.g., killer whales, Orcinus orca) were found to be as diagnosable as species. Conversely, comparisons involving subspecies that are abundant ( e.g., spinner and spotted dolphins, Stenella longirostris and S. attenuata), are only as diagnosable as many population comparisons. Estimates of diagnosability reported in subspecies and species descriptions should include confidence intervals, which are influenced by the sample sizes of the training data. We also stress the importance of reporting the certainty with which individuals in the training data are classified in order to communicate the strength of the classification model and diagnosability estimate. Guidance as to ideal minimum diagnosability thresholds for subspecies will improve with more comprehensive analyses; however, values in the range of 80%-90% are considered appropriate. [ABSTRACT FROM AUTHOR]

The vast and remote distributions and large body size of most cetaceans make it difficult to obtain and maintain morphological collections adequate for advancing sound taxonomic arguments. Consequently, genetic data are playing an increasingly important role in cetacean species and subspecies delimitation. We review seven categories of analytical methods useful in delimiting subspecies based on genetic data. For each category, we summarize its utility in evaluating putative subspecies, the types of markers to which it can be applied, and potential challenges in interpreting results in a taxonomic context. We focus on the utility of each type of method to evaluate the critical features distinguishing subspecies from populations and species: the degree of diagnosability between putative taxa and the extent to which the putative taxa have diverged along separate evolutionary pathways. We conclude that diagnosability is best estimated with either assignment tests or multivariate methods, while evaluating the degree of divergence requires a synthesis of multiple lines of evidence derived from different analytical methods and different data types, including nongenetic data. [ABSTRACT FROM AUTHOR]

Identifying species at risk of extinction is essential for effective conservation priority-setting in the face of accelerating biodiversity loss. However, the levels of risk that lead to endangered or threatened listing decisions under the United States Endangered Species Act (ESA) are not well defined. We used a Bayesian population modeling approach to estimate levels of risk consistently for 14 marine species previously assessed under the ESA. For each species, we assessed the risks of declining below various abundance thresholds over various time horizons. We found that high risks of declining below 250 mature individuals within five generations matched well with ESA endangered status, while number of populations was useful for distinguishing between threatened and 'not warranted' species. The risk assessment framework developed here could enable more consistent, predictable, and transparent ESA status assessments in the future. [ABSTRACT FROM AUTHOR]

Taxonomic revision of the South Asian river dolphins (Platanista): Indus and Ganges river dolphins are separate species. Keywords: cetaceans; dams; river dolphins; shipping; taxonomy EN cetaceans dams river dolphins shipping taxonomy 3011 3012 2 10/20/21 20211001 NES 211001 Taxonomic uncertainty continues to be an impediment to efficient conservation, even for large and charismatic animals such as whales and dolphins. Cetaceans, dams, shipping, taxonomy, river dolphins. [Extracted from the article]

Although most eastern North Pacific (ENP) gray whales feed in the Bering, Beaufort, and Chukchi Seas during summer and fall, a small number of individuals, referred to as the Pacific Coast Feeding Group (PCFG), show intra- and interseasonal fidelity to feeding areas from northern California through southeastern Alaska. We used both mitochondrial DNA (mtDNA) and 12 microsatellite markers to assess whether stock structure exists among feeding grounds used by ENP gray whales. Significant mtDNA differentiation was found when samples representing the PCFG ( n = 71) were compared with samples ( n = 103) collected from animals feeding further north ( FST = 0.012 , P = 0.0045). No significant nuclear differences were detected. These results indicate that matrilineal fidelity plays a role in creating structure among feeding grounds but suggests that individuals from different feeding areas may interbreed. Haplotype diversities were similar between strata ( hPCFG = 0.945, hNorthern = 0.952), which, in combination with the low level of mtDNA differentiation identified, suggested that some immigration into the PCFG could be occurring. These results are important in evaluating the management of ENP gray whales, especially in light of the Makah Tribe's proposal to resume whaling in an area of the Washington coast utilized by both PCFG and migrating whales. [ABSTRACT FROM AUTHOR]

Lack of guidance for interpreting the definitions of endangered and threatened in the U.S. Endangered Species Act (ESA) has resulted in case-by-case decision making leaving the process vulnerable to being considered arbitrary or capricious. Adopting quantitative decision rules would remedy this but requires the agency to specify the relative urgency concerning extinction events over time, cutoff risk values corresponding to different levels of protection, and the importance given to different types of listing errors. We tested the performance of 3 sets of decision rules that use alternative functions for weighting the relative urgency of future extinction events: a threshold rule set, which uses a decision rule of x% probability of extinction over y years; a concave rule set, where the relative importance of future extinction events declines exponentially over time; and a shoulder rule set that uses a sigmoid shape function, where relative importance declines slowly at first and then more rapidly. We obtained decision cutoffs by interviewing several biologists and then emulated the listing process with simulations that covered a range of extinction risks typical of ESA listing decisions. We evaluated performance of the decision rules under different data quantities and qualities on the basis of the relative importance of misclassification errors. Although there was little difference between the performance of alternative decision rules for correct listings, the distribution of misclassifications differed depending on the function used. Misclassifications for the threshold and concave listing criteria resulted in more overprotection errors, particularly as uncertainty increased, whereas errors for the shoulder listing criteria were more symmetrical. We developed and tested the framework for quantitative decision rules for listing species under the U.S. ESA. If policy values can be agreed on, use of this framework would improve the implementation of the ESA by increasing transparency and consistency. Evaluando Reglas de Decisión para Categorizar el Riesgo de Extinción de Especies con el Fin de Desarrollar de Criterios Cuantitativos de Alistamiento en el Acta de Especies en Peligro de los EE. UU. [ABSTRACT FROM AUTHOR]

We estimated the abundance of humpback whales in the North Pacific by capture-recapture methods using over 18,000 fluke identification photographs collected in 2004-2006. Our best estimate of abundance was 21,808 (CV = 0.04). We estimated the biases in this value using a simulation model. Births and deaths, which violate the assumption of a closed population, resulted in a bias of +5.2%, exclusion of calves in samples resulted in a bias of −10.5%, failure to achieve random geographic sampling resulted in a bias of −0.4%, and missed matches resulted in a bias of +9.3%. Known sex-biased sampling favoring males in breeding areas did not add significant bias if both sexes are proportionately sampled in the feeding areas. Our best estimate of abundance was 21,063 after accounting for a net bias of +3.5%. This estimate is likely to be lower than the true abundance due to two additional sources of bias: individual heterogeneity in the probability of being sampled (unquantified) and the likely existence of an unknown and unsampled breeding area (−8.7%). Results confirm that the overall humpback whale population in the North Pacific has continued to increase and is now greater than some prior estimates of prewhaling abundance. [ABSTRACT FROM AUTHOR]

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 was 57% lower than the 1997 estimate, an average rate of decline of 7.6%/yr. Bayesian analyses found an 89% probability of decline in total population size during the 11 yr period, and a 100% probability of decline in the central part of the range. Acoustic detections were assumed to represent porpoises with an average group size of 1.9, the same as visual sightings. Based on simultaneous visual and acoustic data in a calibration area, the probability of detecting vaquitas acoustically on the trackline was estimated to be 0.41 (CV = 108%). The Refuge Area for the Protection of the Vaquita, where gill net fishing is currently banned, contained approximately 50% of the population. While animals move in and out of the Refuge Area, on average half of the population remains exposed to bycatch in artisanal gill nets. [ABSTRACT FROM AUTHOR]

We use mitochondrial DNA (mtDNA) (400 bp), six microsatellites and 36 single-nucleotide polymorphisms (SNPs), 20 of which were linked, to investigate population structure of sperm whales ( Physeter macrocephalus) in the eastern and central North Pacific. SNP markers, reproducible across technologies and laboratories, are ideal for long-term studies of globally distributed species such as sperm whales, a species of conservation concern because of both historical and contemporary impacts. We estimate genetic differentiation among three strata in the temperate to tropical waters where females are found: California Current, Hawai`i and the eastern tropical Pacific. We then consider how males on sub-Arctic foraging grounds assign to these strata. The California Current stratum was differentiated from both the other strata ( P < 0.05) for mtDNA, microsatellites and SNPs, suggesting that the region supports a demographically independent population and providing the first indication that males may exhibit reproductive philopatry. Comparisons between the Hawai`i stratum and the eastern tropical Pacific stratum are not conclusive at this time. Comparisons with Alaska males were statistically significant, or nearly so, from all three strata and individuals showed mixed assignment to, and few exclusions from, the three potential source strata, suggesting widespread origin of males on sub-Arctic feeding grounds. We show that SNPs have sufficient power to detect population structure even when genetic differentiation is low. There is a need for better analytical methods for SNPs, especially when linked SNPs are used, but SNPs appear to be a valuable marker for long-term studies of globally dispersed and highly mobile species. [ABSTRACT FROM AUTHOR]

The utility of microsatellite markers for inferring population size and trend has not been rigorously examined, even though these markers are commonly used to monitor the demography of natural populations. We assessed the ability of a linkage disequilibrium estimator of effective population size ( Ne) and a simple capture-recapture estimator of abundance ( N) to quantify the size and trend of stable or declining populations (true N = 100–10,000), using simulated Wright–Fisher populations. Neither method accurately or precisely estimated abundance at sample sizes of S = 30 individuals, regardless of true N. However, if larger samples of S = 60 or 120 individuals were collected, these methods provided useful insights into abundance and trends for populations of N = 100–500. At small population sizes ( N = 100 or 250), precision of the Ne estimates was improved slightly more by a doubling of loci sampled than by a doubling of individuals sampled. In general, monitoring Ne proved a more robust means of identifying stable and declining populations than monitoring N over most of the parameter space we explored, and performance of the Ne estimator is further enhanced if the Ne/ N ratio is low. However, at the largest population size ( N = 10,000), N estimation outperformed Ne. Both methods generally required ≥ 5 generations to pass between sampling events to correctly identify population trend. [ABSTRACT FROM AUTHOR]

tossm (Testing of Spatial Structure Methods) is a package for testing the performance of genetic analytical methods in a management context. In thetossm package, any method developed to detect population genetic structure can be combined with a mechanism for creating management units (MUs) based on the genetic analysis. The resulting Boundary-Setting Algorithm (BSA) dictates harvest boundaries with a genetic basis. These BSAs can be evaluated with respect to how well the MUs they define meet management objectives. [ABSTRACT FROM AUTHOR]

This study investigated the relationship between work—family conflict/facilitation (WFC/F) and the perception of psychological contract fairness by Hispanic business professionals. In addition, this study examined the effects of WFC/F as a mediator of the relationship between workplace supports and psychological contract fairness. A survey of 1165 Hispanic business professionals, from the United States, contained reports their experience of work-to-family conflict and facilitation, perception of the fairness of their psychological contract, and the availability of four types of workplace supports: formal work—family policies, supervisor support, work climate for family, and job characteristics. Results revealed that individuals who experience low conflict and high facilitation in the direction of work-to-family are more likely to report their perception of the psychological contract to be fair. Work—family conflict/ facilitation mediated the relationship between the workplace supports and psychological contract fairness for supervisor support, work climate for family, and job characteristics. There was a direct relationship between the availability of formal workplace supports and psychological contract fairness. Implications for theory and practice are also noted. Copyright © 2009 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Microsatellite genotyping from samples with varying quality can result in an uneven distribution of errors. Previous studies reporting error rates have focused on estimating the effects of both randomly distributed and locus-specific errors. Sample-specific errors, however, can also significantly affect results in population studies despite a large sample size. From two studies including six microsatellite markers genotyped from 272 sperm whale DNA samples, and 33 microsatellites genotyped from 213 bowhead whales, we investigated the effects of sample- and locus-specific errors on calculations of Hardy–Weinberg equilibrium. The results of a jackknife analysis in these two studies identified seven individuals that were highly influential on estimates of Hardy–Weinberg equilibrium for six different markers. In each case, the influential individual was homozygous for a rare allele. Our results demonstrate that Hardy–Weinberg P values are very sensitive to homozygosity in rare alleles for single individuals, and that > 50% of these cases involved genotype errors likely due to low sample quality. This raises the possibility that even small, normal levels of laboratory errors can result in an overestimate of the degree to which markers are out of Hardy–Weinberg equilibrium and hence overestimate population structure. To avoid such bias, we recommend routine identification of influential individuals and multiple replications of those samples. [ABSTRACT FROM AUTHOR]

Single nucleotide polymorphisms (SNPs) have been proposed by some as the new frontier for population studies, and several papers have presented theoretical and empirical evidence reporting the advantages and limitations of SNPs. As a practical matter, however, it remains unclear how many SNP markers will be required or what the optimal characteristics of those markers should be in order to obtain sufficient statistical power to detect different levels of population differentiation. We use a hypothetical case to illustrate the process of designing a population genetics project, and present results from simulations that address several issues for maximizing statistical power to detect differentiation while minimizing the amount of effort in developing SNPs. Results indicate that (i) while ~30 SNPs should be sufficient to detect moderate ( FST = 0.01) levels of differentiation, studies aimed at detecting demographic independence (e.g. FST < 0.005) may require 80 or more SNPs and large sample sizes; (ii) different SNP allele frequencies have little affect on power, and thus, selection of SNPs can be relatively unbiased; (iii) increasing the sample size has a strong effect on power, so that the number of loci can be minimized when sample number is known, and increasing sample size is almost always beneficial; and (iv) power is increased by including multiple SNPs within loci and inferring haplotypes, rather than trying to use only unlinked SNPs. This also has the practical benefit of reducing the SNP ascertainment effort, and may influence the decision of whether to seek SNPs in coding or noncoding regions. [ABSTRACT FROM AUTHOR]

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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 are listed as endangered), beaked whales ( n= 11, potentially vulnerable to anthropogenic noise), and small whales/dolphins/porpoises ( n= 69, bycatch in fisheries and important abundant predators), for two categories of pinnipeds with substantially different survey precision: counted on land ( n= 13) and surveyed on ice ( n= 5), and for a category containing polar bear and sea otter stocks ( n= 6). The percentage of precipitous declines that would not be detected as declines was 72% for large whales, 90% for beaked whales, and 78% for dolphins/porpoises, 5% for pinnipeds on land, 100% for pinnipeds on ice, and 55% for polar bears/sea otters (based on a one-tailed t-test, α= 0.05), given the frequency and precision of recent monitoring effort. We recommend alternatives to improve performance. [ABSTRACT FROM AUTHOR]

Little is known about the historical range of killer whale ecotypes in the eastern North Pacific (ENP). It is possible that ranges have shifted in the last few decades because of changes in availability of food. In particular, the southern resident ecotype, currently found primarily in the inland waters of Washington State, is known to prey extensively on salmon, which have declined in recent decades along the outer coasts of Washington, Oregon, and California. To investigate historical distributions of this and the other ENP ecotypes, samples of teeth and bones were obtained from NMFS and museum collections. We amplified a short section of the mitochondrial DNA control region that contains four diagnostic sites that differentiate between haplotypes found in ecotypes of ENP killer whales. Results did not show any southern resident haplotypes in samples from south of the Washington State inland waterways. One whale genetically identified as a northern resident extends the known southernmost distribution of the population from Oregon to California. Items of diet identified from stomach contents of six of the whales genetically identified to ecotype conformed with what is known of the feeding habits of the various ecotypes. [ABSTRACT FROM AUTHOR]

1. In response to conservation and management concerns about gray whale Eschrichtius robustus population and stock structure, we provide an overview of the life history and ecology of gray whales as a context for discussion of population and stock structure within the species. Historically eastern and western North Pacific gray whales were managed separately because: (i) their ranges do not overlap; (ii) genetic analyses indicate that the two populations are significantly different; and (iii) eastern gray whales have increased in abundance over the past century while western gray whales have not. 2. Here, we review gray whale migration timing and segregation, feeding and prey species, and reproduction and reproductive behaviour. For the eastern and western gray whale, we review their distribution, history of exploitation, abundance and current status, although most of what is known is founded on the better studied eastern gray whale and only implied for the lesser known western gray whale. Methods to investigate population and stock identity are reviewed including genetics, morphology, chemical signatures, carbon isotopes, parasites, photographic identification and trends in abundance. 3. While the evidence indicates that there is at least some degree of mixing within each of the gray whale populations, no stocks or sub-stocks can be defined. Population structure is not evident in nuclear data, and because selection occurs primarily on the nuclear genome, it is unlikely that there is structuring within each population that could result in evolutionary differences. For western gray whales, there are insufficient data to assess the plausibility of stock structure within the population, owing to its extremely depleted state. Research on eastern gray whales has focused mostly on documenting changes in abundance, feeding biology and behaviour, and suggests separate breeding groups to be unlikely. Both males and females are promiscuous breeders lending little opportunity for the nuclear genome to be anything other than well mixed as is suggested by the high haplotypic diversity of the eastern population. 4. The available data strongly indicate that western gray whales represent a population geographically isolated from eastern gray whales and therefore that the western and eastern populations should be treated as separate management units. [ABSTRACT FROM AUTHOR]

We estimate the abundance of sperm whales in a 7.8 million km² study area in the eastern temperate North Pacific using data from a ship-based acoustic and visual line-transect survey in spring 1997. Sperm whales were detected acoustically using a hydrophone array towed at 15 km/h and 100 m depth. The hydrophone array was towed for 14,500 km, and locations were estimated acoustically for 45 distinct sperm whale groups. Whales producing slow clicks (>2-s period) were detected at greater distance (up to 37 km), and the estimation of effective strip widths was stratified based on initial click period. Visual survey effort (using 25× binoculars and naked eyes) covered 8,100 km in Beaufort sea states 0-5 and resulted in only eight sightings. The effective strip width for visual detections was estimated from previous surveys conducted using the same methods and similar vessels in the eastern Pacific. Estimated sperm whale abundance in the study area was not significantly different between acoustic (32,100, CV = 0.36) and visual (26,300, CV = 0.81) detection methods. Acoustic techniques substantially increased the number of sperm whales detected on this line-transect survey by increasing the range of detection and allowing nighttime surveys; however, visual observations were necessary for estimating group size. [ABSTRACT FROM AUTHOR]

Polygynous mating results in nonrandom sampling of the adult male gamete pool in each generation, thereby increasing the rate of genetic drift. In principle, genetic paternity analysis can be used to infer the effective number of breeding males (N ebm). However, this requires genetic data from an exhaustive sample of candidate males. Here we describe a new approach to estimateN ebm using a rejection algorithm in association with three statistics: Euclidean distance between the frequency distributions of maternally and paternally inherited alleles, average number of paternally inherited alleles and average gene diversity of paternally inherited alleles. We quantify the relationship between these statistics andN ebm using an individual-based simulation model in which the male mating system varied continuously between random mating and extreme polygyny. We evaluate this method using genetic data from a natural population of highly polygynous fruit bats (Cynopterous sphinx). Using data in the form of mother–offspring genotypes, we demonstrate that estimates ofN ebm are very similar to independent estimates based on a direct paternity analysis that included data on candidate males. Our method also permits an evaluation of uncertainty in estimates ofN ebm and thus facilitates inferences about the mating system from genetic data. Finally, we investigate the sensitivity of our method to sample size, model assumptions, adult population size and the mating system. These analyses demonstrate that the rejection algorithm provides accurate estimates ofN ebm across a broad range of demographic scenarios, except when the trueN ebm is high. [ABSTRACT FROM AUTHOR]

Good management models and good models for understanding biology differ in basic philosophy. Management models must facilitate management decisions despite large amounts of uncertainty about the managed populations. Such models must be based on parameters that can be estimated readily, must explicitly account for uncertainty, and should be simple to understand and implement. In contrast, biological models are designed to elucidate the workings of biology and should not be constrained by management concerns. We illustrate the need to incorporate uncertainty in management models by reviewing the inadequacy of using standard biological models to manage marine mammals in the United States. Past management was based on a simple model that, although it may have represented population dynamics adequately, failed as a management tool because the parameter that triggered management action was extremely difficult to estimate for the majority of populations. Uncertainty in parameter estimation resulted in few conservation actions. We describe a recently adopted management scheme that incorporates uncertainty and its resulting implementation. The approach used in this simple management scheme, which was tested by using simulation models, incorporates uncertainty and mandates monitoring abundance and human-caused mortality. Although the entire scheme may be suitable for application to some terrestrial and marine problems, two features are broadly applicable: the incorporation of uncertainty through simulations of management and the use of quantitative management criteria to translate verbal objectives into levels of acceptable risk. [ABSTRACT FROM AUTHOR]

Using genetic data to estimate dispersal is attractive because direct estimation is often infeasible. Unfortunately, analytical tools remain rudimentary. Various standard population genetic formulae estimate dispersal rates between populations but require unrealistic assumptions, such as equal population size. Recent increases in computer speed enable simulations of genetic processes in populations. We designed simulation models to evaluate the adequacy of using analytical formulae to estimate dispersal rates needed for conservation decisions. Our models incorporated genetic stochasticity. They adhered closely to the assumptions of the standard formulae except that we relaxed the assumption that all populations were equal in size. We found that measures of population differentiation, such as the statistic ΦS T , varied greatly over time, reflecting the stochastic nature of genetic systems. In some cases, however, even large amounts of variation over time made no difference in defining population structure for management purposes, whereas in other cases the opposite was true. Statistics of genetic differentiation were so variable that management decisions based on analytical formulae would often be incorrect. Adjoining populations with little dispersal between them that should be managed separately were by chance alone so genetically similar that they appear panmictic, incorrectly implying that they should be managed as a single unit. The form of distributions of these statistics was complex and did not conform to standard statistical distributions. Furthermore, differences between these distributions for equal and unequal abundance cases indicated that pursuits of simple adjustments to analytical formulae are unlikely to be fruitful. In contrast, our simulation technique can be used in a decision analysis framework because it incorporates uncertainties into a probability distribution. We conclude with a case in which a manager wants to know... [ABSTRACT FROM AUTHOR]

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The article focuses on the significance of the genetic diversity on biological diversity. The Conservation on Biological Diversity (CBD) recognizes genetic diversity as an explicit goal. It adds that the CBD is a body responsible to develop and implement a National Biodiversity Strategy and Action Plan (NBSAP). It also suggests that less than half of the reviewed countries have included the goal of conserving genetic variation of wild animals and plants, while 20% recognize the need for monitoring such level of variation.

The authors reflect on the legal language contained in U.S. Endangered Species Act. In particular, they are concerned with the risks to a species in a significant portion of its range when the entire species is not at risk of extinction. They discuss the meaning of likely to be endangered in the foreseeable future and conclude that it means a greater than50% probability in the next 20 years. They argue that societal values are in the legal and policy domain and not the scientific realm.

The authors reports that the vaquita (Gulf of California porpoise, Phocoena sinus), is in imminent danger of extinction by the use of gillnet fishing in El Golfo de Santa Clara and San Felipe, Mexico as of December 2007. They call for the use of economic incentives to the fishing communities as a way of halting the use of such nets, and the incidental death of the porpoises caused by their use. Using computer models, they found that the vaquita has two years before they reach a population level of no return.

Focuses on articles that introduce methods for analyzing uncertainty to conservation biologists working with terrestrial systems. Motivation of marine conservation biologists in developing innovative techniques for incorporating uncertainty into both data analysis and decision making; Appropriateness of techniques developed for marine problems to address terrestrial problems.

This article is a defense of a previous article called "A biological framework for evaluating whether an ESA species is threatened or endangered in a 'significant portion of its range'" that was critiqued by other scholars. In that paper, the authors argued for a changed definition of the way that the U.S. Endangered Species Act (ESA) defines the significant portion of its range (SPOIR). The authors also argue that their idea of SPOIR would give species that are not threatened or endangered greater protection. Finally, the authors explain the process by which they were asked to develop a SPOIR framework and they acknowledge that adopting the framework would be to redesign how ESA defines threatened and endangered species.

Despite the vaquita being commonly cited as one of the most endangered marine mammals in the world, there is still disagreement over which factors put the species at greatest risk of extinction. This lack of agreement hinders management decisions needed to reduce the risk tothe species. To expedite decision-making we consider four major riskfactors. Habitat alteration from reduced flow of the Colorado River does not currently appear to be a risk factor because productivity remains high in vaquita habitat. Pollutant loads are low and pose low to no risk. Reduced fitness from inbreeding depression and loss of genetic variability are unlikely to pose high risk currently, though risk will increase if vaquitas remain at low abundance over long periodsof time. Mortality resulting from fisheries bycatch poses high risk.Thus, shore term management should not be hindered by uncertainty inestimating the risk of these factors, and primary conservation efforts should be directed towards immediate elimination of incidental fishery mortality. [ABSTRACT FROM AUTHOR]

Uncertainty about the magnitude of various risk facing endangered species can paralyze conservation action. The vaquita is a naturally rare porpoise that has declined to the low hundreds of individuals because of gillnet mortality over the past 57 years. No variability in mitochondrial DNA (mtDNA) was found in vaquitas (n=43). Because reducing gillnet mortality will require strong conservation action, the question was raised whether vaquitas are doomed because of inbreeding depression and whether, therefore, mitigation efforts would be futile. We use simulations to investigate the 'doom hypothesis' by first asking whether the current level of genetic variability results from the recent decline or from historical factors. If fixation was historical then deleterious alleles could have been selected out of vaquitas over thousands of years, reducing concerns about inbreeding depression. Simulations showed that fixation most likely resulted from historicalrather than recent loss. Of 1,000 simulations done at plausible abundances and mutation rates, 247 (84.3%) fixed before and 46 (15.7%) fixed during the recent decline. Fixation correlates with historical abundance, making it more likely that because vaquicas are fixed, they are also a naturally rare species. However, because studies on purging deleterious alleles have not shown purging to be universally beneficial we also examine the doom hypothesis using data on the response to inbreeding of a wide variety of captive animals. Responses are so variable that the doom hypothesis cannot be affirmed. We further explore whether more data from vaquitas would lead to conclusive results and found that the data required, such as the adult survival rate, will be impossible to obtain. We conclude that because the doom hypothesis cannot be affirmed this risk factor should not delay conservation actions. [ABSTRACT FROM AUTHOR]