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Low contemporary effective population size detected in the Critically Endangered giant sea bass, Stereolepis gigas, due to fisheries overexploitation
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... S. gigas inhabit the nearshore kelp forests and rocky reefs from Humboldt Bay, California, to Oaxaca, southern Mexico, and into the Gulf of California, with their population concentrated south of Point Conception (Crooke 1992, Domeier 2001, Hawk & Allen 2014, Ramírez-Valdez et al. 2021. Genetic evidence suggests that there is one genetically bottlenecked population throughout its range (Gaffney et al. 2007, Chabot et al. 2015. They are apex predators that consume a wide range of prey and, therefore, are anticipated to exert diverse and strong influences upon the entire food web to which they belong (Blincow et al. 2022). ...
... The International Union for the Conservation of Nature (IUCN) listed S. gigas as Critically Endangered in 1996, and the population was described as 'severely fragmented, leading to a continuing decline of mature individuals' (Cornish & Grouper & Wrasse Specialist Group 2004). Recent studies using longterm SCUBA monitoring surveys, experimental gill nets, and genetic sequencing suggest that the S. gigas population in Southern California may be increasing, likely due to the banning of inshore set gill nets in 1994, but it has not reached pre-exploitation levels (Pondella & Allen 2008, Chabot et al. 2015, House et al. 2016. However, there has never been a direct attempt to assess the population size of S. gigas off California. ...
... Gaffney et al. (2007) suggest there is only one genetically bottlenecked population of S. gigas that exists throughout its range, based on genetic sequencing and mitochondrial data obtained from tis-sue samples collected from south of Oceanside, California, to Baja California and the Gulf of California, Mexico (n = 56). Chabot et al. (2015) showed similar results from samples obtained from the Northern Channel Islands to Baja California, Mexico (n = 61). Both studies concluded that the S. gigas population has low genetic diversity and a small contemporary population size, likely due to intensive fishing, resulting in a bottlenecked population throughout their range (Gaffney et al. 2007, Chabot et al. 2015. ...
... R Core Team 2020 (hereafter GSB) were nearly extirpated in southern California during the 20th century due to fishing pressure and habitat loss (Chabot et al., 2015;Pondella & Allen, 2008). Growing up to 2.2 m (TL) and weighing 250 kg (Allen & Andrews, 2012;Domeier, 2005), GSB are considered a top predator in kelp forest and rocky reef communities. ...
... As oceanic conditions (i.e., sea surface temperature, productivity) change, aggregation cues may cause shifts in the timing and location of these aggregation events. Although recent genetic analyses have shown fish in Mexican waters may have helped US populations recover (Chabot et al., 2015;Gaffney et al., 2007;Ramírez-Valdez et al., 2021), there is no evidence to date documenting movement of fish between Mexico and the US. Currently, the only confirmed aggregation sites in U.S. waters are around Anacapa Island (Domeier, 2005), Santa Catalina Island (Clevenstine & Lowe, 2021;House et al., 2016) and La Jolla, California (Blincow, unpubl. ...
... Although a large portion (73%) of the species range is in Mexican waters, little is known of the extent of population connectivity and transboundary movement (Chabot et al., 2015;Gaffney et al., 2007;Ramírez-Valdez et al., 2021). Recent research suggests continued recovery of GSB in California waters while the species' decline may not have occurred in the southern portion of its range in Mexican waters (Clevenstine & Lowe, 2021;House et al., 2016;Ramírez-Valdez et al., 2021). ...
Site fidelity and aggregation behaviour were assessed for giant sea bass Stereolepis gigas (GSB) at Santa Barbara Island, California, USA, from 2018 to 2020. Results indicate seasonal variation in GSB presence, and network analyses revealed a preferred location in a spatially constrained pattern, indicative of aggregation behaviour. Results show GSB aggregated annually during spawning months in the same location, confirming the first known aggregation of GSB at Santa Barbara Island. Identifying and monitoring aggregation sites is vital to ensuring proper protection and ultimate recovery for this protected species in a changing climate.
... Sin embargo, todos estos estudios apuntan a la necesidad de generar información biológica básica sobre la especie que permita futuros estudios poblacionales. Información de la historia de vida, como la edad y crecimiento, relación talla y peso, estructura de tallas, edad de primera madurez sexual, proporción de machos y hembras, estadios reproductivos y hábitos alimentarios son esenciales para la evaluación de las poblaciones y su adecuado manejo (Baldwin y Keiser 2008;Pondella y Allen 2008;Chabot et al. 2015). El establecimiento de un programa de monitoreo biológico pesquero permanente es una herramienta ideal para recolectar la información biológica necesaria para cubrir los vacíos de información existente sobre el mero gigante. ...
... Las muestras de tejido de individuos de mero gigante serán utilizadas para el análisis de la estructura genética de la población utilizando herramientas moleculares. Los estudios previos en mero gigante indican que una preferencia del tejido muscular axial, seguido por hígado, branquias o aletas (Graffney et al. 2007;Chabot et al. 2015). Idealmente cada vial deberá contener dos muestras de tejido del mismo tamaño pero de diferente tejido; muscular e hígado, o muscular y aletas (Fig. 17). ...
PRESENTACIÓN
Este documento está dirigido a guiar la obtención de información a través del monitoreo biológico-pesquero del mero gigante (Stereolepis gigas) en aguas mexicanas. La información obtenida servirá para establecer la base del conocimiento biológico y ecológico de la especie. Este documento y la información obtenida pertenecen a un programa de monitoreo permanente cuyo objetivo es generar conocimiento a largo plazo y establecer diferentes líneas de estudio de la especie. El programa es el resultado de la colaboración entre instituciones académicas, Organizaciones de la Sociedad Civil y comunidades pesqueras. La información recopilada estará disponible para cualquier persona interesada que lo solicite. Más información sobre el proyecto y el acceso a los datos puede ser encontrada en la página oficial: www.merogigante.org
... Samples were sent to Laragen Inc. for purification and sequencing. Sequencing products were validated by eye and aligned in SEQUENCHER (Gene Codes Corporation; Chabot et al., 2015). Ninety-one unknown egg samples were sequenced with five known samples of Giant Sea Bass DNA. ...
... House et al. (2016) document recent temporal increases in Giant Sea Bass numbers around Santa Catalina Island though, and this has facilitated our behavioral research. Recent studies have focused on life history traits as well as the population status and vulnerability of Giant Sea Bass (Allen and Andrews, 2012;Hawk and Allen, 2014;Chabot et al., 2015). The present study attempted to increase knowledge of Giant Sea Bass by examining the different behaviors that they exhibit in the wild that are associated with reproduction, and it offers insights into the reproductive behavior of polyprionids in general. ...
Aspects of the reproductive behavior of Giant Sea Bass, tereolepis gigas, were observed and monitored at Goat Harbor, Santa Catalina Island, California from June 2014 to August 2015. The site was visited daily during the summer months (the known spawning season); aggregations were not present during the rest of the year. Numbers of Giant Sea Bass observed at Goat Harbor ranged from 1 to 19 individuals with an average of 6. Giant Sea Bass produced booming sounds (40-80 Hz), which were often associated with aggressive behavior but may also be associated with courtship. Courtship behavior was observed during the late afternoons and was most prominent around dusk (1900-2100 h). Courtship involved sexually dimorphic, temporary color changes and displays such as circling in pairs and the nudging of the abdominal area of the presumed female by the snout of the presumed male. The courtship behaviors observed were similar to those observed for Giant Sea Bass in captivity. Although spawning was not observed directly, the available evidence suggests that spawning occurs just after dusk. Confirmation of spawning at or near the aggregation site was obtained through DNA barcoding with CO1 primers of eggs sampled from Goat Harbor near dusk. This study provides insights into courtship behavior that can be used to identify potential Giant Sea Bass spawning aggregations in the wild that are crucial for management of the species. © 2018 by the American Society of Ichthyologists and Herpetologists.
... Las poblaciones explotadas están expuestas a diferentes perturbaciones, como la sobrepesca y cambios ambientales que, en conjunto, hacen variar su abundancia (Badjeck et al. 2010, Chabot et al. 2015. Estos factores incrementan la incertidumbre en los modelos pesqueros y ocasionan retos en el manejo convencional de los recursos (monoespecífico). ...
In the scientific literature it is possible to find a series of models for both stock and ecosystem evaluation that consider environmental changes. However, in Mexico, the conventional management of exploited resources presents weaknesses by not duly considering these changes in the management proposals. Nowadays, marine ecosystems, in addition to fisheries, are exposed to the effects of climate change, so their management should consider possible changes in their structure and function. The present work aims to demonstrate the consequences of climate change on the structure and function of the ecosystem, as well as to propose an adaptive management according to these changes. The southeastern ecosystem of the Gulf of California, Mexico was used as a case study. A trophic ecosystem model developed in the Ecopath platform previously reported in the literature was used and indicators of self-organization potential (f) and degree of ecosystem order (a/c) were calculated. Temporal simulations (2006-2100) of these indicators were performed in the Ecosim platform evaluating three scenarios. The effect of climate change was induced through pdo anomalies reported in the literature. In the first scenario, f showed a trajectory of change during the period 2006-2011 towards a less orderly state, however, the indicator values are relatively high (f>0.9). The results of this work showed a moderate effect of climate change on the structure and functioning of the southeastern Gulf of California ecosystem. However, simulations of holistic ecosystem indicators suggest that this condition does not jeopardize the long-term sustainability of the ecosystem. Alternate ecosystem states were identified that could be used as benchmarks to differentially evaluate the fishery in a global context.
... and Andrews 2012; Hawk and Allen 2014;Chabot et al. 2015;House et al. 2016;Allen 2017). Like many apex predators, these fish grow slowly and were historically easily overfished. ...
The giant sea bass (GSB), Stereolepis gigas Ayres, 1859, is the largestteleost (exceeding 2 m in length and 200 kg in weight) and megacarnivore found in California kelp forest communities. Overfishing of GSB in the late 1920s crashed the population off California and in 1996 it was classified as an International Union for Conservation of Nature (IUCN) critically endangered species. Recently, three GSBwere collected off San Onofre, California and held at the Southern California Ma-rine Institute in San Pedro. Two of the three GSB were infected with Lepeophtheirus longipes Wilson, 1905 (Siphonostomatoida; Caligidae), a poorly described species of parasitic copepod previously recorded from the GSB and purportedly on other fish hosts. In this study, a detailed redescription of the female and the first description of the male of L. longipes are provided and all records of Lepeophtheirus longipes ar ereviewed. The latter revealed that L. longipesis host specific to GSB. Lepeophtheirus longipesis distinguished from its congeners by a combination of female characters that includes: (1) genital complex with prominent posterolateral lobes and is about half the length of the cephalothorax and just over two times longer than the cylindrical, indistinctly 2-segmented abdomen; (2) an antennule with a small conical processon the proximal segment; (3) maxillule with an outer conical process at the base of the dentiform process; (4) sternal furca with pointed and slightly splayed tines; (5) first exopodal segment of leg 3 with a terminal spine; and (6) third exopodal segment of leg4 with three unequal apical spines.
... Our analysis combining fishery statistics and biological monitoring of the Mexican fleet allowed us to conclude that the GSB population size could be larger than previously thought and may not meet current IUCN requirements for being classified as critically endangered throughout its distribution. Chabot et al., (2015) estimated the effective population size (Ne) of the species to be 500 individuals, including samples from California and Mexico, adding that this could be greater than 10% of the census population size (i.e., census population size <5,000). This estimate spread rapidly in the scientific community and the media and contributed to the perception of the fragile status of the GSB population (Fox, 2018;Guerra et al., 2017;Sahagun, 2018;Tallal, 2020;Wisckol, 2018). ...
Co-operation in the management of shared fish stocks is often necessary to achieve sustainability and reduce uncertainty. The United States of America (USA) and Mexico share a number of fish stocks and marine ecosystems, while there is some binational co-operation in scientific research, unilateral management decisions are generally the rule. We present a case study using the giant sea bass (Stereolepis gigas, Polyprionidae) to highlight how these management and research asymmetries can skew national perceptions of population status for a fully transboundary species. Scientific publications and annual funding related to giant sea bass are 7x and 25x higher in the USA, respectively, despite the fact that 73% of the species’ range occurs in Mexico. Conversely, annual fishery production and consumptive value of giant sea bass in Mexico are 19x and 3.5x higher than in the USA, respectively, while the non-consumptive value related to dive ecotourism is 76x higher in the USA. These asymmetries have generated a distorted view of the population status of the giant sea bass across its entire range. This and other factors related to historical fishery dynamics and policy must be accounted for when assessing population status, and subsequent appropriate management responses, across geopolitical boundaries.
... Giant Sea Bass are often found in kelp forests on rocky reefs as adults, while juveniles are found at sandy bottom areas (Domeier, 2001). These large, demersal teleosts reach lengths greater than 2 m, weights greater than 200 kg, ages of up to 76 years, and are apex predators (Horn and Ferry-Graham, 2006;Allen and Andrews, 2012;Hawk and Allen, 2014;Chabot et al., 2015;House et al., 2016;Allen, 2017). ...
This study provided a first detailed description of the acoustic calls and the possible sound production mechanism in the Giant Sea Bass (Stereolepis gigas). Passive acoustic (hydrophone) recordings of Giant Sea Bass sounds were made of three mature individuals (40-45 kg) held in a circular 17,000 l seawater tank isolated from other fish species. Four basic sounds plus combinations were identified from the tank recordings when fish were present and were encountered on numerous occasions throughout the study. We classified the basic sounds as two types of pulses (A and B), short bursts, and long bursts, and combinations of short and long bursts. Mean peak frequencies of the four sound types were less than 39 Hz, while mean durations ranged from 67 ms to 545 ms, depending on sound type. We also obtained and dissected two mature, adult Giant Sea Bass to describe the morphology of a putative sound production mechanism. Five putative sonic muscles were discovered between each of the first six pleural ribs of the male examined. These five massive muscles (¼obliquus superioris?) unite ribs 3 to 9 and were found at the level of the deep hypaxial musculature. The identification of these sounds and accompanying sonic mechanism marks the first occurrence of sound production in the family of wreckfishes (Polyprionidae). This knowledge of the acoustic characteristics increases our ability to document the presence, activity, and possibly the abundance of this critically endangered species at spawning sites.
... This species is truly a giant among reef fishes reaching lengths of 2.3 m (7 ft.) and weights exceeding 260 kg (560 lbs.). Giants were over-exploited by their fishery in the early 1900s, and depressed populations had prevented much research into their biology until recently (Hawk and Allen 2014, Chabot et al. 2015, House et al. 2016, Allen 2017. Although it remains red-listed by the IUCN, the population of Giants now appears to be mounting a comeback due to a moratorium on catch in 1982 and more significantly the nearshore gill net ban in the coastal waters of southern California in 1994 (Pondella and Allen 2008). ...
One of the age-old mysteries surrounding the Giant Sea Bass (Stereolepis gigas) has been "where are the baby giants?" For almost a century, we have known that their young-of-the-year (= YOY or baby) do not look anything like the adults (Figure 1). However, where the YOY recruits could be found remained largely unknown until now. That mystery has now been solved courtesy of our three-year study on the distribution and ecology of their young-of-the-year (YOY) off southern California. The main goal of that study was to determine the distribution and general ecology of the YOY of this rare, elusive, and endangered species through extensive SCUBA surveys (Benseman and Allen 2018). This article is protected by copyright. All rights reserved.
... While the GSB population remains protected but depressed, the population appears to be recovering slowly (Pondella and Allen, 2008;House et al., 2016). Estimates of their effective population size remain around 500 (Chabot et al., 2015). They have been observed more frequently in the last 15 years (Pondella and Allen, 2008), with juveniles continuously being caught and released in the recreational fisheries (Baldwin and Keiser, 2008). ...
This study identified nursery habitat, recruitment patterns, the planktonic larval duration (PLD), size and age at settlement, and growth rate of the young-of-the-year (YOY) Giant Sea Bass (GSB), Stereolepis gigas, off Southern California. A total of 160 YOY GSB were sighted on 150 transects over a three-year period. Young-of-the-year GSB were relatively rare (maximum density of 40/ha) and recruitment was limited to a few areas. In 2014-2015, densities of YOY GSB were significantly higher at six locations off sandy beaches nearest the heads of submarine canyons off Redondo Beach, Newport Beach, and La Jolla, California. The vast majority of occurrences of YOY (73%) were within 500 m of the heads of submarine canyons. Three color phases of YOY were discovered ranging (smallest to largest individuals) from black to brown to orange. Recruitment occurred from July through February with peak abundances occurring in the late summer months from August through October. YOY occurred at depths from 2 m to nearly 10 m. Overall, size of YOY GSB increased with depth in the shallow sand riffle zone. YOY grew rapidly at 1.23 mm/day (n = 23) with collected individuals ranging from 31 to 84 d old based on daily ring increments in otoliths. The planktonic larval duration was estimated to be about one lunar month (26.8±2.4 d) based on the presence of the first settlement check and size of earliest settlers. Size at settlement was estimated to be 14.4±3.0 mm TL (10.6±2.5 mm standard length [SL]). This information adds substantially to our knowledge of early developmental processes and recruitment patterns of Giant Sea Bass that are crucial to our understanding of their life history and to making informed decisions regarding fisheries management policies and conservation efforts. © 2018 by the American Society of Ichthyologists and Herpetologists.
... Giant sea bass were severely overfished in the twentieth century leading to local extinctions. Restrictions on harvest off California have led to at least a mild resurgence in the population (Pondella and Allen 2008;House et al. 2016) and, based on a genetics study, an effective population size of perhaps 500 individuals off southern California and northern Baja California (Chabot et al. 2015). However, there has been no direct assessment of their numbers off California. ...
... Based on the calculations in this study, the average annual number of landed incidentally caught S. gigas could represent somewhere between 2% and 19% of current local population estimates for this species (Chabot, Hawk, & Allen, 2015). Given uncertainties surrounding the fate of any S. gigas that may be lethally captured in gill and trammel nets above the allowable take of one fish per day, it may be prudent to view these as minimum estimates of popula- (Figure 4a) generates no revenue to gill and trammel net fishers for target species in the month of July, when S. gigas CPUE is highest. ...
Although the economic value of wildlife historically has been attributed to its consumptive use, the global growth of ecotourism has expanded wildlife valuation to include non‐consumptive uses. In California, the critically endangered giant sea bass ( Stereolepis gigas ) is paradoxically both a flagship species in the recreational dive industry and regularly sold in California's commercial fisheries when incidentally caught. The differences in the economic value of S. gigas to these two key stakeholders – commercial fishers and recreational scuba divers – were explored.
The average annual landing value of S. gigas was US2.3 million per year. The non‐consumptive use value was calculated by approximating the annual number of recreational charter boat divers and determining divers' willingness‐to‐pay for a S. gigas sighting.
Stated landings volumes of S. gigas appear to represent a minimum annual extraction of 2% to 19% of the S. gigas population. Using self‐reported fishery catch location data, S. gigas bycatch hotspots were identified and used to inform suggestions for strategic spatial and temporal closures.
Overall, these results highlight the value of giant sea bass beyond fisheries and underscore the importance of incorporating non‐consumptive values when developing harvest policies and marine management plans.
... Ultimately, we had 61 samples covering the primary range of the Giant Sea Bass from southern and Baja California, Mexico. Working with Holly Hawk and my postdoc, Chris Chabot, we carried out standard population genetics assays including the mitochondrial control region and microsatellite analysis of nuclear DNA (Chabot et al., 2015). The findings were surprising. ...
Marine fishes have been intensively studied, and some of the fundamental ideas in the science of marine ecology have emerged from the body of knowledge derived from this diverse group of organisms. This unique, authoritative, and accessible reference, compiled by 35 luminary ecologists, evolutionary biologists, and ichthyologists, provides a synthesis and interpretation of the large, often daunting, body of information on the ecology of marine fishes. The focus is on the fauna of the eastern Pacific, especially the fishes of the California coast, a group among the most diverse and best studied of all marine ecosystems. A generously illustrated and comprehensive source of information, this volume will also be an important launching pad for future research and will shed new light on the study of marine fish ecology worldwide. The contributors touch on many fields in biology, including physiology, development, genetics, behavior, ecology, and evolution. The book includes sections on the history of research, both published and unpublished data, sections on collecting techniques, and references to important earlier studies.
The giant sea bass, Stereolepis gigas, is the largest bony fish that inhabits California shallow rocky reef communities and is listed by IUCN as a critically endangered species, yet little is known about its life history. To address questions of growth and longevity, 64 samples were obtained through collaborative efforts with commercial fish markets and scientific gillnetting. Sagittae (otoliths) were cross-sectioned and analyzed with digital microscopy. Age estimates indicate that S. gigas is a long-lived species attaining at least 76 years of age. Over 90% of the variation between age (years) and standard length (mm) was accounted for in the von Bertalanffy growth model (R2 = 0.911). The calculated von Bertalanffy growth function parameters (K = 0.044, t0 = -0.339, L∞= 2026.2 mm SL) for S. gigas were characteristic of a large, slow-growing, apex predator.
The composition of the present-day California marine fish fauna is largely a reflection of trophic interactions. This chapter first organizes the subject of food and feeding in fishes into three parts and variously draws examples from members of the California marine fish fauna. It discusses factors that determine diet including body shape and feeding behavior, identifies types of food capture, and describes several kinds of feeding mechanisms. Second, it describes some of the major types of food items consumed by representative taxa of the California fauna and associate these taxa with standard trophic level designations. Third, it uses generalized profiles of trophic relationships to portray the main feeding interactions among fishes occupying bay-estuarine, inner and outer shelf, rocky intertidal, rocky reef and kelp bed, epipelagic, and deep midwater habitats.
NeEstimator v2 is a completely revised and updated implementation of software that produces estimates of contemporary effective population size, using several different methods and a single input file. NeEstimator v2 includes three single-sample estimators (updated versions of the linkage disequilibrium and heterozygote-excess methods, and a new method based on molecular coancestry), as well as the two-sample (moment-based temporal) method. New features include the following: (i) an improved method for accounting for missing data; (ii) options for screening out rare alleles; (iii) confidence intervals for all methods; (iv) the ability to analyse data sets with large numbers of genetic markers (10 000 or more); (v) options for batch processing large numbers of different data sets, which will facilitate cross-method comparisons using simulated data; and (vi) correction for temporal estimates when individuals sampled are not removed from the population (Plan I sampling). The user is given considerable control over input data and composition, and format of output files. The freely available software has a new JAVA interface and runs under MacOS, Linux and Windows.
A new Bayesian method that uses individual multilocus genotypes to estimate rates of recent immigration (over the last several generations) among populations is presented. The method also estimates the posterior probability distributions of individual immigrant ancestries, population allele frequencies, population inbreeding coefficients, and other parameters of potential interest. The method is implemented in a computer program that relies on Markov chain Monte Carlo techniques to carry out the estimation of posterior probabilities. The program can be used with allozyme, microsatellite, RFLP, SNP, and other kinds of genotype data. We relax several assumptions of early methods for detecting recent immigrants, using genotype data; most significantly, we allow genotype frequencies to deviate from Hardy-Weinberg equilibrium proportions within populations. The program is demonstrated by applying it to two recently published microsatellite data sets for populations of the plant species Centaurea corymbosa and the gray wolf species Canis lupus. A computer simulation study suggests that the program can provide highly accurate estimates of migration rates and individual migrant ancestries, given sufficient genetic differentiation among populations and sufficient numbers of marker loci.
The tope shark, Galeorhinus galeus, is a commercially important member of the Triakidae that has been exploited globally for the past 80 years. Here we describe
13 microsatellite loci for G. galeus discovered by next-generation sequencing (Roche 454 pyrosequencing) and their utility for eastern Pacific smooth-hound sharks
(Mustelus). These loci were polymorphic (3–12 alleles) with observed heterozygosity between 0.11 and 0.86 and expected heterozygosity
between 0.24 and 0.87. Several loci (7 of 13) amplified consistently for Mustelus californicus and M. henlei. These loci are the first to be characterized explicitly for G. galeus and should be useful in the investigation of population structure of this vulnerable elasmobranch.
The brown smooth-hound shark, Mustelus henlei (Triakidae), is an endemic member of the eastern Pacific shark assemblage considered both commercially and recreationally
important. Here, microsatellite loci for M. henlei discovered by next-generation sequencing (Roche 454 pyrosequencing) are described. All loci were polymorphic (3–10 alleles)
with observed heterozygosities between 0.24 and 0.89 and expected heterozygosities between 0.23 and 0.86. These loci are the
first to be characterized explicitly for M. henlei and should be useful for the investigation of population structure and gene flow in this species and for other members of
the Triakidae.
growth and late maturity Severe population declines have been documented for several snappers and groupers (Lutjanidae, Serranidae) in the Atlantic and the Gulf of California, several rockfishes (Sebastinae) in the Pacific, and some sharks (Selachei), skates (Rajidae), and sawfishes (Pristidae). Regulatory agencies should be apprised that these groups are extraordinarily vulnerable, and priority management should be given to these species, The greatest threat to many long-lived marine species may be bycatch (including regulatory dis- card) in fisheries,tar geting other, often more-productive species. Regulatory,agencies must monitor bycatch of long-lived species and move to implement conservation actions if population declines are recorded. The most effective management strategy for some species taken as bycatch and for tar- geted species such as deeper-water groupers and Pacific rockfishes, may be establishment of large, protected marine reserves to supplement traditional management practices outside of the protected areas. The AFS supports the development, use, and evaluation of large marine reserves or Marine Protected Areas to protect and rebuild vulnerable populations. These reserves must have clearly defined goals, include a wide variety of environmental conditions, be of sufficient number to pro- tect marine ecosystems within each region, allow adaptive management, and be large enough to be self-sustaining. The AFS encourages its members to become involved by providing technical infor- mation needed for protection of at-risk marine stocks to international , federal, state, and provincial policy makers, so decisions are made on a scientific, rather than emotional or political, basis.
This initiative was supported by grants to AFS and the Virginia Institute of Marine Science by the Pew Charitable Trusts, NMFS Office of Protected Resources, National Fish and Wildlife Foundation, The Munson Foundation and the Homeland Foundation, J.A. Musick, Principal investigator.
In January 2010, a massive giant sea bass (500 lbs, 227 kg; near maximum reported size of 557 lbs, 253 kg) was captured off Santa Cruz Island by commercial gill-netters. This specimen presented a unique opportunity to estimate and validate of the potential longevity of the largest nearshore teleost of the northeastern Pacific. A transverse section of the sagittal otolith produced consistent counts of 62 opaque annuli along two different axes of the ventral sulcus region, translating into an estimated birth year of 1948. This age estimate was supported by measurements of radiocarbon (14 C) in the other sagittal otolith core (within the first year of growth), relative to D 14 C reference records used for bomb radiocarbon dating. Two otolith core samples produced D 14 C values that were classified as pre-bomb (prior to ,1958–59), indicating a minimum lifespan of 51 years. It is likely that giant sea bass can live more than 60 or 70 years based on growth zone counts, but there is no evidence in the literature or this study to support longevity of 100 years.
Use of genetic methods to estimate effective population size (Ne) is rapidly increasing, but all approaches make simplifying assumptions unlikely to be met in real populations. In particular, all assume a single, unstructured population, and none has been evaluated for use with continuously distributed species. We simulated continuous populations with local mating structure, as envisioned by Wright's concept of neighborhood size (NS), and evaluated performance of a single-sample estimator based on linkage disequilibrium (LD), which provides an estimate of the effective number of parents that produced the sample (Nb). Results illustrate the interacting effects of two phenomena, drift and mixture, that contribute to LD. Samples from areas equal to or smaller than a breeding window produced estimates close to the NS. As the sampling window increased in size to encompass multiple genetic neighborhoods, mixture LD from a two-locus Wahlund effect overwhelmed the reduction in drift LD from incorporating offspring from more parents. As a consequence, never approached the global Ne, even when the geographic scale of sampling was large. Results indicate that caution is needed in applying standard methods for estimating effective size to continuously distributed populations.Heredity advance online publication, 8 May 2013; doi:10.1038/hdy.2013.37.
The 1992 Convention on Biological Diversity has established an international framework for broader conservation objectives for the management of ocean use activities (cf. Sainsbury and Sumaila, 2003). The Convention calls for preservation of biological diversity, including genetic, species and ecosystem diversity, thereby creating a demand for developing management forms that can cope with this issue. A number of initiatives have been developed to address this and other related international agreements. Notably, Ecosystem-Based Fishery Management (EBFM; cf. Brodziak and Link, 2002; Sainsbury and Sumaila, 2003) has emerged as a holistic approach to maintaining ecosystems and sustainable fisheries. EBFM should incorporate all levels of diversity, but in practice has focused on species and ecosystem diversity (e.g., Brodziak and Link, 2002). The application of EBFM must be broadened to include conservation of genetic diversity, including intraspecific diversity, which are not necessarily protected by maintaining diversity at higher levels (cf. Kenchington, 2003).
Scientific justification for conserving genetic diversity stems from several sources including: (1) maintaining adaptability of natural populations; (2) the future utility of genetic resources for medical and other purposes; and (3) changes in life history traits and behaviour that influence the dynamics of fish populations, energy flows in the ecosystem, and ultimately, sustainable yield. The challenge is to formulate appropriate management actions for the preservation of genetic diversity (e.g., Sainsbury and Sumaila, 2003). This will require consensus on what it is we are trying to preserve (e.g., alleles, traits, population structure) and some means of assessing genetic status. This paper endeavours to outline a process to develop management advice for marine genetic diversity. We challenge fish conservation geneticists to consider their work in a more applied context so that management actions can be developed to preserve genetic resources.
Summary: GenAlEx: Genetic Analysis in Excel is a cross-platform package for population genetic analyses that runs within Microsoft Excel. GenAlEx offers analysis of diploid codominant, haploid and binary genetic loci and DNA sequences. Both frequency-based (F-statistics, heterozygosity, HWE, population assignment, relatedness) and distance-based (AMOVA, PCoA, Mantel tests, multivariate spatial autocorrelation) analyses are provided. New features include calculation of new estimators of population structure: G′ST, G′′ST, Jost’s Dest and F′ST through AMOVA, Shannon Information analysis, linkage disequilibrium analysis for biallelic data and novel heterogeneity tests for spatial autocorrelation analysis. Export to more than 30 other data formats is provided. Teaching tutorials and expanded step-by-step output options are included. The comprehensive guide has been fully revised.Availability and implementation: GenAlEx is written in VBA and provided as a Microsoft Excel Add-in (compatible with Excel 2003, 2007, 2010 on PC; Excel 2004, 2011 on Macintosh). GenAlEx, and supporting documentation and tutorials are freely available at: http://biology.anu.edu.au/GenAlEx.Contact:
rod.peakall@anu.edu.au
What to do about fisheries collapse and the decline of large fishes in marine ecosystems is a critical debate on a global
scale. To address one aspect of this debate, a major fisheries management action, the removal of gill nets in 1994 from the
nearshore arena in the Southern California Bight (34°26′30″N, 120°27′09″W to 33°32′03″N, 117°07′28″W) was analyzed. First,
the impetus for the gill net ban was the crash of the commercial fishery for white seabass (Atractoscion nobilis; Sciaenidae) in the early 1980s. From 1982 to 1997 catch remained at a historically low level (47.8±3.0mt) when compared
to landings from 1936–1981, but increased significantly from 1995–2004 (r=0.89, P<0.01) to within the 95% confidence limit of the historic California landings. After the white seabass fishery crashed in
the early 1980s, landings of soupfin (Galeorhinus galeus; Triakidae) and leopard shark (Triakis semifasciata; Triakidae) also significantly declined (r=0.95, P<0.01 and r=0.91, P<0.01, respectively) until the gill net closure. After the closure both soupfin and leopard shark significantly increased
in CPUE (r=0.72, P=0.02 and r=0.87, P<0.01, respectively). Finally, giant sea bass (Stereolepis gigas; Polyprionidae) the apex predatory fish in this ecosystem, which was protected from commercial and recreational fishing in
1981, were not observed in a quarterly scientific SCUBA monitoring program from 1974 to 2001 but reappeared in 2002–2004.
In addition, CPUE of giant seabass increased significantly from 1995 to 2004 (r=0.82, P<0.01) in the gill net monitoring program. The trends in abundance of these fishes return were not correlated with sea surface
temperature (SST), the Pacific Decadal Oscillation (PDO) or the El Niño/Southern Oscillation (ENSO). All four species increased
significantly in either commercial catch, CPUE, or in the SCUBA monitoring program after the 1994 gill net closure, whereas
they had declined significantly, crashed, or were absent prior to this action. This suggests that removing gill nets from
coastal ecosystems has a positive impact on large marine fishes.
We present STRUCTURE HARVESTER (available at http://taylor0.biology.ucla.edu/structureHarvester/), a web-based program for collating results generated by the program STRUCTURE. The program provides a fast way to assess
and visualize likelihood values across multiple values of K and hundreds of iterations for easier detection of the number of genetic groups that best fit the data. In addition, STRUCTURE
HARVESTER will reformat data for use in downstream programs, such as CLUMPP.
KeywordsStructure–Population structure–Population genetics–Evanno method–Visualization–Clustering
The sandbar shark, Carcharhinus plumbeus, is a long-lived species with low lifetime fecundity that is heavily fished in the western North Atlantic. Inshore nursery
grounds increase survivorship of sandbar shark pups and the principal nurseries are in the mid-Atlantic region. We calculated
effective number of breeders (Nb) and effective population size (Ne) for adults utilizing the nursery grounds of the Delaware Bay and the Eastern Shore of Virginia by genotyping 902 animals
across five cohorts at eight microsatellite loci. Estimates of Nb and Ne were compared to estimates of census size (Nc) of cohorts obtained from Delaware Bay. The estimated Ne/Nc and Nb/Nc ratios were 0.45 or higher whether the Delaware Bay cohorts were considered as distinct year classes or combined. This is
in contrast to estimated Ne/Nc ratios in other exploited marine fishes, which are several orders of magnitude smaller. Instead, the Ne/Nc ratio of sandbar sharks is similar to that found in marine and terrestrial mammals.
We examined population structure in the wreckfish, Polyprion americanus, by assaying six microsatellite loci in 422 individuals collected throughout the geographic range. Eighteen hapuku, P. oxygeneios, were assayed at the same loci for use as an outgroup. Expected heterozygosities ranged from 0.49 to 0.88 and averaged 0.66.
Allele-frequency distributions at those loci indicated that samples from the eastern North Atlantic, western North Atlantic
and the Mediterranean were genetically similar, confirming the pattern seen in a previous analysis of mitochondrial DNA (mtDNA)
restriction fragment length polymorphisms (RFLPs). Both mtDNA and microsatellite studies differentiated northern and southern
wreckfish stocks. However, in contrast to the mtDNA studies, allelic variation at microsatellite loci clearly differentiated
wreckfish from two Southern Hemisphere locations, Brazil and the South Pacific. Far more genetic variation was observed at
microsatellite loci than with mtDNA RFLPs (haplotype diversity averaged 0.01), and we saw more evidence of population structure
with the microsatellite loci. The differentiation between southern and northern wreckfish supports the distribution records,
which indicate that wreckfish do not occur in the tropics. Temperature profiles and current patterns throughout the southern
oceans apparently also prevent significant gene flow between the South Pacific and Brazilian samples.
This note summarizes developments of the genepop software since its first description in 1995, and in particular those new to version 4.0: an extended input format, several estimators of neighbourhood size under isolation by distance, new estimators and confidence intervals for null allele frequency, and less important extensions to previous options. genepop now runs under Linux as well as under Windows, and can be entirely controlled by batch calls.
Note that an updated reference for Genepop is Rousset (2008) genepop’007: a complete re-implementation of the genepop software for Windows and Linux (DOI: 10.1111/j.1471-8286.2007.01931.x)
We describe extensions to the method of Pritchard et al. for inferring population structure from multilocus genotype data. Most importantly, we develop methods that allow for linkage between loci. The new model accounts for the correlations between linked loci that arise in admixed populations (“admixture linkage disequilibium”). This modification has several advantages, allowing (1) detection of admixture events farther back into the past, (2) inference of the population of origin of chromosomal regions, and (3) more accurate estimates of statistical uncertainty when linked loci are used. It is also of potential use for admixture mapping. In addition, we describe a new prior model for the allele frequencies within each population, which allows identification of subtle population subdivisions that were not detectable using the existing method. We present results applying the new methods to study admixture in African-Americans, recombination in Helicobacter pylori, and drift in populations of Drosophila melanogaster. The methods are implemented in a program, structure, version 2.0, which is available at http://pritch.bsd.uchicago.edu.
Expected values of Wright'sF-statistics are functions of probabilities of identity in state. These values may be quite different under an infinite allele model and under stepwise mutation processes such as those occurring at microsatellite loci. However, a relationship between the probability of identity in state in stepwise mutation models and the distribution of coalescence times can be deduced from the relationship between probabilities of identity by descent and the distribution of coalescence times. The values of FIS and FST can be computed using this property. Examination of the conditional probability of identity in state given some coalescence time and of the distribution of coalescence times are also useful for explaining the properties of FIS and FST at high mutation rate loci, as shown here in an island model of population structure.
Although highly variable loci, such as microsatellite loci, are revolutionizing both evolutionary and conservation biology, data from these loci need to be carefully evaluated. First, because these loci often have very high within-population heterozygosity, the magnitude of differentiation measures may be quite small. For example, maximum GST values for populations with no common alleles at highly variable loci may be small and are at maximum less than the average within-population homozygosity. As a result, measures that are variation independent are recommended for highly variable loci. Second, bottlenecks or a reduction in population size can generate large genetic distances in a short time for these loci. In this case, the genetic distance may be corrected for low variation in a population and tests to detect bottlenecks are advised. Third, statistically significant differences may not reflect biologically meaningful differences both because the patterns of adaptive loci may not be correlated with highly variable loci and statistical power with these markers is so high. As an example of this latter effect, the statistical power to detect a one-generation bottleneck of different sizes for different numbers of highly variable loci is discussed. All of these concerns need to be incorporated in the utilization and interpretation of patterns of highly variable loci for both evolutionary and conservation biology.
We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci—e.g., seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/~pritch/home.html.
Microsatellite markers are routinely used to investigate the genetic structuring of natural populations. The knowledge of how genetic variation is partitioned among populations may have important implications not only in evolutionary biology and ecology, but also in conservation biology. Hence, reliable estimates of population differentiation are crucial to understand the connectivity among populations and represent important tools to develop conservation strategies. The estimation of differentiation is c from Wright's FST and/or Slatkin's RST, an FST -analogue assuming a stepwise mutation model. Both these statistics have their drawbacks. Furthermore, there is no clear consensus over their relative accuracy. In this review, we first discuss the consequences of different temporal and spatial sampling strategies on differentiation estimation. Then, we move to statistical problems directly associated with the estimation of population structuring itself, with particular emphasis on the effects of high mutation rates and mutation patterns of microsatellite loci. Finally, we discuss the biological interpretation of population structuring estimates.
Although highly variable loci, such as microsatellite loci, are revolutionizing both evolutionary and conservation biology, data from these loci need to be carefully evaluated. First, because these loci often have very high within-population heterozygosity, the magnitude of differentiation measures may be quite small. For example, maximum GST values for populations with no common alleles at highly variable loci may be small and are at maximum less than the average within-population homozygosity. As a result, measures that are variation independent are recommended for highly variable loci. Second, bottlenecks or a reduction in population size can generate large genetic distances in a short time for these loci. In this case, the genetic distance may be corrected for low variation in a population and tests to detect bottlenecks are advised. Third, statistically significant differences may not reflect biologically meaningful differences both because the patterns of adaptive loci may not be correlated with highly variable loci and statistical power with these markers is so high. As an example of this latter effect, the statistical power to detect a one-generation bottleneck of different sizes for different numbers of highly variable loci is discussed. All of these concerns need to be incorporated in the utilization and interpretation of patterns of highly variable loci for both evolutionary and conservation biology.
Genetic variation among three species of Trachurus (T. trachurus, T. mediterraneus and T. picturatus) from Turkey was investigated by phylogenetic analysis of the entire mtDNA control region (CR) (862 bp, n ¼ 182) and partial cytochrome (cyt) b (239 bp, n ¼ 174) sequences. Individuals were collected at nine stations in four geographic locations: North-eastern Mediterranean Sea, Aegean Sea, Sea of Marmara and Black Sea. Polymerase chain reaction-direct sequencing of the CR and the partial cyt b genes produced 28 and 131 distinct haplotypes, respectively. Maximum likelihood, neighbour-joining and maximum parsimony methods pro-duced similar tree topologies. The results of both CR and cyt b sequence analyses revealed the existence of several species-specific nucleotide sites that can be used to discriminate between the three species.
Maintaining genetic variation for future evolutionary change is an important issue for conservation biology. However, there is controversy over the effective population size (Ne) required for endangered species to retain their evolutionary potential, with proposed sizes ranging from 500 to 5000. The highest estimate is based on the assumption that 90% of mutations are deleterious. We review the arguments for an effective size of 5000 and conclude that it assumes effective mutation rates that are too low, and heritabilities that are, in general, very high. We conclude that an Ne of 500-1000 is appropriate at this time.
The 50/500 rule has been used as a guiding principle in conservation for assessing minimum viable effective population size (N(e)). There is much confusion in the recent literature about how the 500 value should be applied to assess extinction risk and set priorities in conservation biology. Here, we argue that the confusion arises when the genetic basis for a short-term N(e) of 50 to avoid inbreeding depression is used to justify a long-term N(e) of 500 to maintain evolutionary potential. This confusion can result in misleading conclusions about how genetic arguments alone are sufficient to set minimum viable population (MVP) thresholds for assessing the extinction risk of threatened species, especially those that emphasize that MVPs should be in the thousands to maintain evolutionary potential.
Reproductive mode of the two widespread species Polyprion americanus (Bloch and Schneider, 1801) and P. oxygeneios (Schneider in Bloch and Schneider, 1801) was investigated in specimens from New Zealand waters. Analysis of sex ratios, length frequencies and gonad morphology indicates that both species are primary gonochorists. Published suggestions that Polyprion species are hermaphroditic and undergo sex change are rejected.
Sequence variation in nuclear and mitochondrial genes of the giant sea bass Stereolepis gigas collected from the Pacific coast and the northern Sea of Cortez was examined. Restriction fragment length polymorphism analysis and direct sequencing showed extremely low mtDNA sequence diversity (13 closely related haplotypes with no evidence of geographical population subdivision). The mitochondrial haplotype mismatch distribution is consistent with a population expansion following the Last Pleistocene glaciation. Differences in single nucleotide polymorphism frequencies between Pacific and Sea of Cortez populations were detected at two of four nuclear loci, which may reflect natural selection or genetic drift in populations with low effective numbers of males. Although Pacific coast and Sea of Cortez populations of giant sea bass do not exhibit the mitochondrial phylogenetic break characteristic of many species with disjunct Pacific and Gulf populations, the possibility of genetic differentiation at nuclear loci suggests that a cautious approach to broodstock selection for captive breeding and restoration programmes be exercised.
Knowledge of statistical power is essential for sampling design and data evaluation when testing for genetic differentiation. Yet, such information is typically missing in studies of conservation and evolutionary genetics, most likely because of complex interactions between the many factors that affect power. powsim is a 32-bit Windows/DOS simulation-based computer program that estimates power (and α error) for chi-square and Fisher's exact tests when evaluating the hypothesis of genetic homogeneity. Optional combinations include the number of samples, sample sizes, number of loci and alleles, allele frequencies, and degree of differentiation (quantified as FST). powsim is available at http://www.zoologi.su.se/~ryman.
The wreckfish Polyprion americanus, a large [>1 m total length (LT)] demersal teleost, is distributed globally in temperate waters, including both sides of the North and South Atlantic Oceans, the Mediterranean, the western South Pacific, and the southern Indian Ocean. Wreckfish spawn off the south-eastern U.S. on an area of the Blake Plateau (the Charleston Bump) characterized by an extensive ridge having approximately 100 m relief, in 450–600 m depths. Juvenile wreckfish (<60 cm LT) are pelagic and, in the North Atlantic, are not reported from the Blake Plateau fishing area, but occur in by-catch and fishery landings in the eastern Atlantic. Analysis of nine restriction fragment length profiles from a PCR-amplified fragment (∼1.5 kb) of the ND1 mitochondrial gene indicated no stock separation between eastern North Atlantic (Azores, Majorca, Madeira), and western North Atlantic (Blake Plateau) wreckfish. Restriction site differences separate western South Atlantic wreckfish from the North Atlantic; however, South Atlantic wreckfish share restriction-site similarities with western Pacific wreckfish that are not shared with North Atlantic wreckfish. North Atlantic circulation provides a mechanism for a long-lived pelagic stage to be dispersed from Blake Plateau spawning grounds to the eastern North Atlantic. Global circulation patterns may explain both the dispersal of mtDNA haplotypes and the disjunct distribution of wreckfish body lengths in a temperate, deep-water vagile species with an extended pelagic juvenile stage such as wreckfish.
This paper describes simulation tests to compare methods for detecting recent bottlenecks using microsatellite data. This
study considers both type I error (detecting a bottleneck when there wasn’t one) and type II error (failing to detect a bottleneck
when there was one) under a variety of scenarios. The two most promising methods were the range in allele size conditioned
on the number of alleles, M
k
, and heterozygosity given the number of alleles, H
k
, under a two-phase mutation model; in most of the simulations one of these two methods had the lowest type I and type II
error relative to other methods. M
k
was the method most likely to correctly identify a bottleneck when a bottleneck lasted several generations, the population
had made a demographic recovery, and mutation rates were high or pre-bottleneck population sizes were large. On the other
hand H
k
was most likely to correctly identify a bottleneck when a bottleneck was more recent and less severe and when mutation rates
were low or pre-bottleneck population sizes were small. Both methods were prone to type I errors when assumptions of the model
were violated, but it may be easier to design a conservative heterozygosity test than a conservative ratio test.
GENALEX is a user-friendly cross-platform package that runs within Microsoft Excel, enabling population genetic analyses of codominant, haploid and binary data. Allele frequency-based analyses include heterozygosity, F statistics, Nei's genetic distance, population assignment, probabilities of identity and pairwise relatedness. Distance-based calculations include AMOVA, principal coordinates analysis (PCA), Mantel tests, multivariate and 2D spatial autocorrelation and TWOGENER. More than 20 different graphs summarize data and aid exploration. Sequence and genotype data can be imported from automated sequencers, and exported to other software. Initially designed as tool for teaching, GENALEX 6 now offers features for researchers as well. Documentation and the program are available at http://www.anu.edu.au/BoZo/GenAlEx/
DNA degradation, low DNA concentrations and primer-site mutations may result in the incorrect assignment of microsatellite genotypes, potentially biasing population genetic analyses. MICRO-CHECKER is WINDOWS(R)-based software that tests the genotyping of microsatellites from diploid populations. The program aids identification of genotyping errors due to nonamplified alleles (null alleles), short allele dominance (large allele dropout) and the scoring of stutter peaks, and also detects typographic errors. MICRO-CHECKER estimates the frequency of null alleles and, importantly, can adjust the allele and genotype frequencies of the amplified alleles, permitting their use in further population genetic analysis.
The bottleneck of the state-of-the-art algorithms for geometric Steiner problems is usually the concatenation phase, where the prevailing approach treats the generated full Steiner trees as edges of a hypergraph and uses an LP-relaxation of the minimum spanning tree in hypergraph (MSTH) problem. We study this original and some new equivalent relaxations of this problem and clarify their relations to all classical relaxations of the Steiner problem. In an experimental study, an algorithm of ours which is designed for general graphs turns out to be an efficient alternative to the MSTH approach.
msatcommander is a platform‐independent program designed to search for microsatellite arrays, design primers, and tag primers using an automated routine. msatcommander accepts as input DNA sequence data in single‐sequence or concatenated, fasta ‐formatted files. Search data and locus‐specific primers are written to comma‐separated value files for subsequent use in spreadsheet or database programs. Binary versions of the graphical interface for msatcommander are available for Apple OS X and Windows XP. Users of other operating systems may run the graphical interface version using the available source code, provided their environment supports at least Python 2.4, Biopython 1.43, and wxPython 2.8.
msatcommander is available from http://code.google.com/p/msatcommander/ .
We present here a new version of the Arlequin program available under three different forms: a Windows graphical version (Winarl35), a console version of Arlequin (arlecore), and a specific console version to compute summary statistics (arlsumstat). The command-line versions run under both Linux and Windows. The main innovations of the new version include enhanced outputs in XML format, the possibility to embed graphics displaying computation results directly into output files, and the implementation of a new method to detect loci under selection from genome scans. Command-line versions are designed to handle large series of files, and arlsumstat can be used to generate summary statistics from simulated data sets within an Approximate Bayesian Computation framework.
Although F(ST) is widely used as a measure of population structure, it has been criticized recently because of its dependency on within-population diversity. This dependency can lead to difficulties in interpretation and in the comparison of estimates among species or among loci and has led to the development of two replacement statistics, F'(ST) and D. F'(ST) is the normal F(ST) standardized by the maximum value it can obtain, given the observed within-population diversity. D uses a multiplicative partitioning of diversity, based on the effective number of alleles rather than on the expected heterozygosity. In this study, we review the relationships between the three classes of statistics (F(ST), F'(ST) and D), their estimation and their properties. We illustrate the relationships between the statistics using a data set of estimates from 84 species taken from the last 4 years of Molecular Ecology. As with F(ST), unbiased estimators are available for the two new statistics D and F'(ST). Here, we develop a new unbiased F'(ST) estimator based on G(ST), which we call G''(ST). However, F'(ST) can be calculated using any F(ST) estimator for which the maximum value can be obtained. As all three statistics have their advantages and their drawbacks, we recommend continued use of F(ST) in combination with either F'(ST) or D. In most cases, F'(ST) would be the best choice among the latter two as it is most suited for inferences of the influence of demographic processes such as genetic drift and migration on genetic population structure.