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Many international, national, state, and local organizations prioritize the ranking of threatened and endangered species to help direct conservation efforts. For example, the International Union for Conservation of Nature (IUCN) assesses the Green Status of species and publishes the influential Red List of threatened species. Unfortunately, such conservation yardsticks do not explicitly consider genetic or genomic diversity (GD), even though GD is positively associated with contemporary evolutionary fitness, individual viability, and with future evolutionary potential. To test whether populations of genome sequences could help improve conservation assessments, we estimated GD metrics from 82 publicly available mammalian datasets and examined their statistical association with attributes related to conservation. We also considered intrinsic biological factors, including trophic level and body mass, that could impact GD and quantified their relative influences. Our results identify key population GD metrics that are both reflective and predictive of IUCN conservation categories. Specifically, our analyses revealed that Watterson's theta (the population mutation rate) and autozygosity (a product of inbreeding) are associated with the current Red List categorization, likely because demographic declines that lead to "listing" decisions also reduce levels of standing genetic variation. We argue that by virtue of this relationship, conservation organizations like IUCN could leverage emerging genome sequence data to help categorize Red List threat rankings (especially in otherwise data‐deficient species) and/or enhance Green Status assessments to establish a baseline for future population monitoring. Thus, our paper (1) outlines the theoretical and empirical justification for a new GD‐based assessment criterion, (2) provides a bioinformatic pipeline for estimating GD from population genomic data, and (3) suggests an analytical framework that can be used to measure baseline GD while providing quantitative GD context for consideration by conservation authorities. [ABSTRACT FROM AUTHOR]

The North American river otter Lontra canadensis was once widespread in North America but became extinct in the State of Indiana owing to habitat losses and unregulated trapping. However, following reintroduction, the population has expanded markedly since 1995, representing a notable conservation success story.The recent population growth has led to conflict with recreational angling groups who perceive otters as competitors. To investigate the extent of this competition, a DNA‐based study was conducted to determine whether material from the stomachs of trapper‐harvested otters could be used to identify fish prey species they had eaten.Representative specimens from 33 wild fish species were used as positive controls for DNA assays of otter prey. Mitochondrial DNA barcoding sequences generated from each fish species were used to develop a piscine barcoding assay to identify otter prey species.Fourteen otter carcasses were dissected, and multiple independent DNA extractions and mitochondrial sequencing reactions were performed on the prey bolus from each stomach. The sequences were analysed bioinformatically for taxonomic assignment to prey species.DNA evidence of nearly two dozen fish species, including species of recreational (e.g. bass) or conservation interest (darters) was found in the stomach material.This approach could help to determine the presence of prey species in otter diets, including those fish of conservation concern. That, in turn, would help to determine the best management options for conserving both otters and fish. [ABSTRACT FROM AUTHOR]

Fish species have diverse breeding behaviors that make them valuable for testing theories on genetic mating systems and reproductive tactics. Here we review genetic appraisals of paternity and maternity in wild fish populations. Behavioral phenomena quantified by genetic markers in various species include patterns of multiple mating by both sexes; frequent cuckoldry by males and rare cuckoldry by females in nest-tending species; additional routes to surrogate parentage via nest piracy and egg-thievery; egg mimicry by nest-tending males; brood parasitism by helper males in cooperative breeders; clutch mixing in oral brooders; kinship in schooling fry of broadcast spawners; sperm storage by dams in female-pregnant species; and sex-role reversal, polyandry, and strong sexual selection on females in some male-pregnant species. Additional phenomena addressed by genetic parentage analyses in fishes include clustered mutations, filial cannibalism, and local population size. All results are discussed in the context of relevant behavioral and evolutionary theory.

Statistical methods for estimating genetic parentage are increasingly applied to accommodate limited marker polymorphism and the incomplete sampling of individuals. Neff et al. (2000a, Mol. Ecol. 9, 515-528; 2000b, Mol. Ecol. 9, 529-539) published a method (Pat) that estimates the proportion of next-generation individuals sired by a focal male, taking into account that the male may be genetically compatible, by random chance, with offspring that are not his own. Here we employ this method to reestimate paternity of 68 nest-guarding males from several fish species. The difference between the conventional exclusion-based estimate and Pat was >0.05 in only four of the 68 (5.9%) fish nests analyzed. An analytical formula shows that the difference between the two estimates is expected to be negligible if the focal male is consistent with a large proportion of the genotyped offspring, or if marker polymorphism is high. In addition, computer simulations illustrate how numbers of marker loci and their levels of genetic polymorphism, as well as the mating system of the organism under study, can influence estimates of paternity derived from exclusion-based estimates and Pat. Finally, we discuss various applications of these estimators including cases where additional biological information is present in the form of behavioral observations on parental care.

Cannibalism is widespread in natural populations of fishes, where the stomachs of adults frequently contain conspecific juveniles. Furthermore, field observations suggest that guardian males routinely eat offspring from their own nests. However, recent genetic paternity analyses have shown that fish nests often contain embryos not sired by the nest-tending male (because of cuckoldry events, egg thievery, or nest piracy). Such findings, coupled with the fact that several fish species have known capabilities for distinguishing kin from nonkin, raise the possibility that cannibalism by guardian males is directed primarily or exclusively toward unrelated embryos in their nests. Here, we test this hypothesis by collecting freshly cannibalized embryos from the stomachs of several nest-tending darter and sunfish males in nature and determining their genetic parentage by using polymorphic microsatellite markers. Our molecular results clearly indicate that guardian males do indeed consume their own genetic offspring, even when unrelated (foster) embryos are present within the nest. These data provide genetic documentation of filial cannibalism in nature. Furthermore, they suggest that the phenomenon may result, at least in part, from an inability of guardians to differentiate between kin and nonkin within their own nests.

Breeding, male North American sunfish (Centrarchidae), are often brightly coloured and promiscuous. However, the largemouth bass (Micropterus salmoides) is sexually monomorphic in appearance and socially monogamous. Unlike some other nest-tending centrarchids in the genus Lepomis, largemouth bass have also been reported to provide biparental care to eggs and fry. Here we use microsatellite markers in order to test whether social monogamy predicts genetic monogamy in the largemouth bass. Offspring were collected from 26 nests each usually guarded by a pair of adults, many of which were also captured. Twenty-three of these progeny cohorts (88%) proved to be composed almost exclusively of full-sibs and were thus the product of monogamous matings. Cuckoldry by males was rare. The genetic data also revealed that some nests contain juveniles that were not the progeny of the guardian female, a finding that can be thought of as low-level 'female cuckoldry'. Overall, however, the data provide what may be the first genetic documentation of near-monogamy and biparental care in a vertebrate with external fertilization.

Nearly all of the 906 embryos from a male-tended nest of the sand goby (Pomatoschistus minutus) were genotyped at two hypervariable microsatellite loci to document conclusively the number of mothers and their relative genetic contributions to the nest. The true number of mothers determined by this nearly exhaustive genetic appraisal was compared to computer simulation treatments based on allele frequencies in the population, assumptions about reproductive skew, and statistical sampling strategies of progeny subsets. The "ground-truthed" appraisal and the theoretical estimates showed good agreement, indicating that for this nest a random sample of approximately 20 offspring would have sufficed for assessing the true number of biological parents (but not necessarily their relative genetic contributions). Also, a general dilocus matrix procedure is suggested for organizing and interpreting otherwise cumbersome data sets when extremely large numbers of full-sib and half-sib embryos from a nest are genotyped at two or more hypervariable loci.

We address various statistical aspects of biological parentage in multi-offspring broods that arise via multiple paternity or multiple maternity and, hence, consist of mixtures of full- and half-sibs. Conditioned on population genetic parameters, computer simulations described herein permit estimation of: (1) the mean number of offspring needed to detect all parental gametes in a brood and (2) the relationship between the number of distinct parental gametes found in a brood and the number of parents. Results are relevant to the design of empirical studies employing molecular markers to assess genetic parentage in polygynous or polyandrous species with large broods, such as are found in many fishes, amphibians, insects, plants and other groups. The utility of this approach is illustrated using two empirical data sets.

Small populations are vulnerable to increased genetic load and drift that can lead to reductions in fitness and adaptive potential. By analyzing 66 individual whole genomes of Montezuma Quail (Cyrtonyx montezumae) from multiple populations, we illustrate how genetic load is dynamic over evolutionary time. We show that Montezuma Quail are evolving like a ring species, where the terminal extant populations from Arizona and Texas have been separated for ~16,500 years. The Texas populations have remained small but stable since the separation, whereas the Arizona population is much larger today but has been contracting for thousands of years. Most deleterious mutations across the genome are young and segregating privately in each population and a greater number of deleterious alleles are present in the larger population. Our data indicate that ancestral load is purged during strong bottlenecks, but the reduced efficiency of selection in small populations means that segregating deleterious mutations are more likely to rise in frequency over time. Forward-time simulations indicate that severe population declines in historically large populations is more detrimental to individual fitness, whereas long-term small populations are more at risk for reduced adaptive potential and population-level fitness. Our study highlights the intimate connections among evolutionary history, historical demography, genetic load, and evolutionary potential in wild populations. [ABSTRACT FROM AUTHOR]