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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]

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]

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 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]

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]

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]

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.

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]

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]

Uncertainties about biological data and human effects often delay decisions on management of endangered species. Some decision makers argue that uncertainty about the risk posed to a species should lead to precautionary decisions, whereas others argue for delaying protective measures until there is strong evidence that a human activity is having a serious effect on the species. We have developed a method that incorporates uncertainty into the estimate of risk so that delays in action can be reduced or eliminated. We illustrate our method with an actual situation of a deadlock over how to manage Hector's dolphin (Cephalorhychus hectori). The management question is whether sufficient risk is posed to the dolphins by mortalities in gillnets to warrant regulating the fisheries. In our quantitative risk assessment, we use a population model that incorporates both demographic ( between-individual) and environmental ( between-year) stochasticity. We incorporate uncertainty in estimates of model parameters by repeatedly running the model for different combinations of survival and reproductive rates. Each value is selected at random from a probability distribution that represents the uncertainty in estimating that parameter. Before drawing conclusions, we perform sensitivity analyses to see whether model assumptions alter conclusions and to recommend priorities for future research. In this example, uncertainty did not alter the conclusion that there is a high risk of population decline if current levels of gillnet mortality continue. Sensitivity analyses revealed this to be a robust conclusion. Thus, our analysis removes uncertainty in the scientific data as an excuse for inaction. [ABSTRACT FROM AUTHOR]

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]

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]

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]

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]

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]

Under the U.S. Endangered Species Act (ESA), a species can be listed if it is at risk “in all or a significant portion of its range,” but the ESA provides no guidance on how to interpret this key phrase. We propose a simple test to determine whether the areas of a species' range in which it is currently at risk amount to a significant portion: If the species were to become extirpated from these areas, at that point would the entire species be at risk? If so, then these areas represent a significant portion of the species' range. By establishing the species itself as the point of reference for determining significance, this test directs attention to biological risk factors and avoids difficulties inherent in subjective evaluations of importance to humans. For broadly distributed species this framework could provide ESA protection due to cumulative risks before the entire species met the criteria to be considered threatened or endangered. This framework also allows a somewhat broader concept of range to include major components of diversity necessary for long-term persistence. The concept of a historical template (i.e., conditions under which the species was known to be viable) is important in providing a fixed reference point for evaluating viability. Empirical examples illustrate how these concepts have been applied in recent ESA listing determinations. Most ESA-listed units of Pacific salmon (Oncorhynchus spp.) can be divided into multiple strata that differ in terms of ecology, geology, or life-history traits of the component populations. The goal of ESA recovery planning is to restore viable populations in enough strata that the listed unit as a whole is no longer threatened or endangered in all or a significant portion of its range. In a recent review of Pacific herring (Clupea pallasii ) in Puget Sound, current status (some populations increasing and others declining) was evaluated in the context of the historical template, and it was concluded that current patterns of distribution and abundance do not depart substantially from what would be expected at any point in time under natural conditions in a large metapopulation. The Canadian lynx (Lynx canadensis ) is ESA listed in the contiguous United States, where it occurs in four geographic areas. Populations in one region, the Northern Rockies/Cascades, have always been the most important for long-term persistence of the species in the United States. Because the other regions never contained more than limited amounts of good-quality lynx habitat, those areas are not considered to represent a significant portion of the species' range. [ABSTRACT FROM AUTHOR]

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.

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.