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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 article informs that marine conservation biologist working for the U.S. National Marine Fisheries Service specializing in marine mammals. Topics include led the marine mammal genetics program at the Southwest Fisheries Science Center, chaired the Society for Marine Mammalogy's Conservation Committee; and served on the U.S. delegation to the International Whaling Commission, and continue to serve as the International Union for Conservation of Nature's (IUCN) Cetacean Specialist Group.

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]

The article reports that Barbara Taylor has been researching marine mammals, and led the marine mammal genetics program at the Southwest Fisheries Science Center in La Jolla, California. It mentions that the group identifies Units to Conserve using genetic data and has promoted developing guidelines and standards to facilitate naming new taxa of cetaceans using primarily genetic data.

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.

In many organisms, especially those of conservation concern, traditional lines of evidence for taxonomic delineation, such as morphological data, are often difficult to obtain. In these cases, genetic data are often the only source of information available for taxonomic studies. In particular, population surveys of mitochondrial genomes offer increased resolution and precision in support of taxonomic decisions relative to conventional use of the control region or other gene fragments of the mitochondrial genome. To improve quantitative guidelines for taxonomic decisions in cetaceans, we build on a previous effort targeting the control region and evaluate, for whole mitogenome sequences, a suite of divergence and diagnosability estimates for pairs of recognized cetacean populations, subspecies, and species. From this overview, we recommend new guidelines based on complete mitogenomes, combined with other types of evidence for isolation and divergence, which will improve resolution for taxonomic decisions, especially in the face of small sample sizes or low levels of genetic diversity. We further use simulated data to assist interpretations of divergence in the context of varying forms of historical demography, culture, and ecology. [ABSTRACT FROM AUTHOR]

In cases of severe wildlife population decline, a key question is whether recovery efforts will be impeded by genetic factors, such as inbreeding depression. Decades of excess mortality from gillnet fishing have driven Mexico’s vaquita porpoise (Phocoena sinus) to ~10 remaining individuals. We analyzed whole-genome sequences from 20 vaquitas and integrated genomic and demographic information into stochastic, individual-based simulations to quantify the species’ recovery potential. Our analysis suggests that the vaquita’s historical rarity has resulted in a low burden of segregating deleterious variation, reducing the risk of inbreeding depression. Similarly, genome-informed simulations suggest that the vaquita can recover if bycatch mortality is immediately halted. This study provides hope for vaquitas and other naturally rare endangered species and highlights the utility of genomics in predicting extinction risk. [ABSTRACT FROM AUTHOR]

The article discusses a research study on the simulation-based approach for population structure evaluation of non-equilibrial generic dynamics called Generational Gene Shift (GGS) of species such as the bowhead whales or Balaena mysticetus. Researchers created an individual-based model of generic and population dynamics of bowhead whales using the R package rmetasim that recreates various aspects including demography, whaling history and sex matched with datasets from simulated populations for genetic analyses. Results of empirical data indicated that of the 33 loci, nine were out of the Hardy-Weinberg equilibrium (HWE) while the age-stratified cohorts showed that four out of the 60 tests have significant genetic differentiation.

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]

The Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis) is endemic to the middle and lower reaches of the Yangtze River, China. It is the only freshwater population of porpoises in the world and is currently listed as Endangered by IUCN. In November and December 2006 we used two boats and line transect methods to survey the entire current range of the population, except for two lakes (Poyang and Dongting). Sighting results were similar for both boats, so we pooled all data and analyzed them using two line transect models and a strip transect model. All models produced similar estimates of abundance (1111, 1225 and 1000). We then added independent estimates of the number of porpoises from the two lakes for a total estimate of approximately 1800 porpoises. Our findings indicate that the population continues to decline and that its distribution is becoming more fragmented. Our current estimate in the main river is slightly less than half the estimate from surveys between 1984 and 1991 (which was probably an underestimate). We also found an apparent gap in the distribution of porpoises between Yueyang and Shishou (∼150km), where sightings had previously been common. Continued threats to Yangtze finless porpoises include bycatch in unregulated and unselective fishing, habitat degradation through dredging, pollution and noise, vessel strikes and water development. Immediate protective measures are urgently needed to ensure the persistence of finless porpoises in the Yangtze River. The survey design and analytical methods developed in this study might be appropriate for surveys of cetaceans in other river systems. [Copyright &y& Elsevier]

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]

Three subspecies of fin whales (Balaenoptera physalus) are currently recognized, including the northern fin whale (B. p. physalus), the southern fin whale (B. p. quoyi), and the pygmy fin whale (B. p. patachonica). The Northern Hemisphere subspecies encompasses fin whales in both the North Atlantic and North Pacific oceans. A recent analysis of 154 mitogenome sequences of fin whales from these two ocean basins and the Southern Hemisphere suggested that the North Pacific and North Atlantic populations should be treated as different subspecies. Using these mitogenome sequences, in this study, we conduct analyses on a larger mtDNA control region data set, and on 23 single-nucleotide polymorphisms (SNPs) from 144 of the 154 samples in the mitogenome data set. Our results reveal that North Pacific and North Atlantic fin whales can be correctly assigned to their ocean basin with 99% accuracy. Results of the SNP analysis indicate a correct classification rate of 95%, very low rates of gene flow among ocean basins, and that distinct mitogenome matrilines in the North Pacific are interbreeding. These results indicate that North Pacific fin whales should be recognized as a separate subspecies, with the name B. p. velifera Cope in Scammon 1869 as the oldest available name. [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 article offers information on the marine species condition at Upper Gulf of California. Topics discussed include concern for extinction of vaquita porpoise, most endangered marine mammal of Mexico; reduction of freshwater flow into the Upper Gulf of California (UGC) due to damming and diversion of the Colorado River, cause decline in vaquita; and collaborative efforts required among fishermen, the seafood supply chain, and environmental and fisheries agencies for conservative solution.

There are three described subspecies of fin whales (Balaenoptera physalus): B. p. physalus Linnaeus, 1758 in the Northern Hemisphere, B. p. quoyi Fischer, 1829 in the Southern Hemisphere, and a recently described pygmy form, B. p. patachonica Burmeister, 1865. The discrete distribution in the North Pacific and North Atlantic raises the question of whether a single Northern Hemisphere subspecies is valid. We assess phylogenetic patterns using ∼16 K base pairs of the complete mitogenome for 154 fin whales from the North Pacific, North Atlantic - including the Mediterranean Sea - and Southern Hemisphere. A Bayesian tree of the resulting 136 haplotypes revealed several well-supported clades representing each ocean basin, with no haplotypes shared among ocean basins. The North Atlantic haplotypes (n = 12) form a sister clade to those from the Southern Hemisphere (n = 42). The estimated time to most recent common ancestor (TMRCA) for this Atlantic/Southern Hemisphere clade and 81 of the 97 samples from the North Pacific was approximately 2 Ma. 14 of the remaining North Pacific samples formed a well-supported clade within the Southern Hemisphere. The TMRCA for this node suggests that at least one female from the Southern Hemisphere immigrated to the North Pacific approximately 0.37 Ma. These results provide strong evidence that North Pacific and North Atlantic fin whales should not be considered the same subspecies, and suggest the need for revision of the global taxonomy of the 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]

Genetic data are often critical for defining populations for management purposes (e.g., identifying geographic boundaries or diagnostic characters for genetically discrete subunits) but can be called into question by both scientific and legal review. This can result in reversed or delayed implementation of management actions. We discuss methods for data quality control and quality analysis and describe examples of steps applied to 2 of the most common types of genetic data, mitochondrial DNA sequences, and microsatellite genotypes. These steps can serve both as guides to conservation geneticists and as an initial protocol for managers to determine whether genetic data will hold up against legal and scientific challenges. In addition, we suggest types of data and quality measures that should be reported as supplementary materials to published reports. These supplementary data serve to reduce the occurrence of legal and conservation controversies and improve reproducibility over time in population genetics studies where genetic monitoring is likely to play an increasing role. [ABSTRACT FROM PUBLISHER]

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]

Historical variation in food resources is expected to be a major driver of cetacean evolution, especially for the smallest species like porpoises. Despite major conservation issues among porpoise species (e.g., vaquita and finless), their evolutionary history remains understudied. Here, we reconstructed their evolutionary history across the speciation continuum. Phylogenetic analyses of 63 mitochondrial genomes suggest that porpoises radiated during the deep environmental changes of the Pliocene. However, all intra-specific subdivisions were shaped during the Quaternary glaciations. We observed analogous evolutionary patterns in both hemispheres associated with convergent evolution to coastal versus oceanic environments. This suggests that similar mechanisms are driving species diversification in northern (harbor and Dall's) and southern species (spectacled and Burmeister's). In contrast to previous studies, spectacled and Burmeister's porpoises shared a more recent common ancestor than with the vaquita that diverged from southern species during the Pliocene. The low genetic diversity observed in the vaquita carried signatures of a very low population size since the last 5,000 years. Cryptic lineages within Dall's, spectacled and Pacific harbor porpoises suggest a richer evolutionary history than previously suspected. These results provide a new perspective on the mechanisms driving diversification in porpoises and an evolutionary framework for their conservation. [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.

In an open letter published in 2002 in the "New York Times", 21 distinguished scientists criticized Japan's program of scientific research whaling, noting its poor design and unjustified reliance upon lethal sampling. In a Forum article in "BioScience," Aron, Burke, and Freeman castigate the letter's signers and accuse them of meddling in political issues without sufficient knowledge of the science involved in those issues. As members of the Scientific Committee (SC) of the International Whaling Commission (IWC), we can attest that the signers of the open letter correctly summarized criticisms made by researchers very familiar with Japanese scientific whaling. One such critique was presented and discussed last year at a meeting of the SC. It was authored by SC members representing a broad range of countries, yet mention of this paper and others like it was absent from Aron and his colleagues' commentary, betraying a selectiveness that pervades their article. The authors quote lines from SC reports to support their contention that the IWC regards scientific whaling as valuable, but they fail to acknowledge many other sections that are highly critical of the Japanese program. Japan's scientific whaling program in the North Pacific (JARPN) was originally described as a feasibility study, but it included no performance measures by which to judge its success or failure. Fundamental problems of the JARPN II study include a lack of testable hypotheses or performance measures; inappropriate use of ecosystem models and failure to include sensitivity analyses and key data on other ecosystem components; selective or inappropriate use of data or methods in estimating whale abundance; unnecessary reliance on lethal sampling; inappropriate geographic sampling for population structure analysis; and unrealistic assessments of the effect of the proposed catches on the populations concerned.

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.

False killer whales (Pseudorca crassidens) are large delphinids typically found in deep water far offshore. However, in the Hawaiian Archipelago, there are 2 resident island-associated populations of false killer whales, one in the waters around the main Hawaiian Islands (MHI) and one in the waters around the Northwestern Hawaiian Islands (NWHI). We use mitochondrial DNA (mtDNA) control region sequences and genotypes from 16 nuclear DNA (nucDNA) microsatellite loci from 206 individuals to examine levels of differentiation among the 2 island-associated populations and offshore animals from the central and eastern North Pacific. Both mtDNA and nucDNA exhibit highly significant differentiation between populations, confirming limited gene flow in both sexes. The mtDNA haplotypes exhibit a strong pattern of phylogeographic concordance, with island-associated populations sharing 3 closely related haplotypes not found elsewhere in the Pacific. However, nucDNA data suggest that NWHI animals are at least as differentiated from MHI animals as they are from offshore animals. The patterns of differentiation revealed by the 2 marker types suggest that the island-associated false killer whale populations likely share a common colonization history, but have limited contemporary gene flow. [ABSTRACT FROM PUBLISHER]