Pedigree reconstruction in wild cichlid fish populations

It is common practice to use microsatellites to detect parents and their offspring in wild and captive populations, in order to reconstruct a pedigree. However, correct inference is often constrained by a number of factors, including the absence of demographic data and ignorance regarding the completeness of parental sampling. Here we present a new Bayesian estimator that simultaneously estimates the pedigree and the size of the unsampled population. The method is robust to genotyping error, and can estimate pedigrees in the absence of demographic data. Using a large-scale microsatellite assay in four wild cichlid fish populations of Lake Tanganyika (1000 individuals in total), we assess the performance of the Bayesian estimator against the most popular assignment program, Cervus. We found small but significant pedigrees in each of the tested populations using the Bayesian procedure, but Cervus had very high type I error rates when the size of the unsampled population was assumed to be lower than what it was. The need of pedigree relationships to infer adaptive processes in natural populations places strong constraints on sampling design and identification of multigenerational pedigrees in natural populations.     

Evidence of melanoma in wild marine fish populations

The increase in reports of novel diseases in a wide range of ecosystems, both terrestrial and marine, has been linked to many factors including exposure to novel pathogens and changes in the global climate. Prevalence of skin cancer in particular has been found to be increasing in humans, but has not been reported in wild fish before. Here we report extensive melanosis and melanoma (skin cancer) in wild populations of an iconic, commercially-important marine fish, the coral trout Plectropomus leopardus. The syndrome reported here has strong similarities to previous studies associated with UV induced melanomas in the well-established laboratory fish model Xiphophorus. Relatively high prevalence rates of this syndrome (15%) were recorded at two offshore sites in the Great Barrier Reef Marine Park (GBRMP). In the absence of microbial pathogens and given the strong similarities to the UV-induced melanomas, we conclude that the likely cause was environmental exposure to UV radiation. Further studies are needed to establish the large scale distribution of the syndrome and confirm that the lesions reported here are the same as the melanoma in Xiphophorus, by assessing mutation of the EGFR gene, Xmrk. Furthermore, research on the potential links of this syndrome to increases in UV radiation from stratospheric ozone depletion needs to be completed.     

Disease interaction between farmed and wild fish populations

This paper reviews the literature on disease interaction between wild and farmed fish and recommends strategies to reduce the disease risks to both populations. Most, if not all, diseases of farmed fish originate in wild populations. The close contact between farmed and wild fish readily leads to pathogens exchange. Aquaculture creates conditions ( e.g. high stocking levels) conducive to pathogen transmission and disease; hence pathogens can overspill back, resulting in high levels of challenge to wild populations. This is exemplified by sea lice infections in farmed Atlantic salmon. Stocking with hatchery reared fish or aquaculture escapees can affect disease dynamics in wild populations. Whirling disease has been spread to many wild rainbow trout populations in the US with the release of hatchery reared stock. The greatest impact of aquaculture on disease in wild populations has resulted from the movement of fish for cultivation. Examples of exotic disease introduction following movement of live fish for aquaculture with serious consequences for wild populations are reviewed. The salmon parasite, Gyrodactylus salaris, has destroyed wild salmon populations in 44 Norwegian rivers. Crayfish plague has wiped out European crayfish over much of Europe. Eels numbers have declined in Europe and infection with the swimbladder nematode Anguillicola crassus has in part been blamed. The impact of disease in farmed fish on wild populations can mitigated. Risk analysis methods need to be refined and applied to live fish movement and new aquacultural developments. Appropriate biosecurity strategies, based on risk assessments, should be developed to reduce pathogen exchange and mitigate the consequences.     

The use of tumors in wild populations of fish to assess ecosystem health

Evidence has linked toxicants in aquatic systems with cancer in fish and population level effects on species. Thus some types of tumors may be useful monitors of ecosystem health, at least as affected by genotoxins and promoters. However, tumors caused by purely genetic mechanisms or by virus would not be good indicators. Only neoplasms which have chemicals as a portion of their etiology (either as initiators or promoters) would be useful in assessing ecosystem health. Lesions which may fit these criteria include liver neoplasms (both biliary and hepatic) and skin lesions in a variety of primarily benthic fishes, and neural lesions in various drum species and in butterfly fish species. Two studies purporting to demonstrate a lack of tumors in fish from polluted areas have been reexamined and found either to have insufficient data on vulnerable species or to actually support a tumor-pollution linkage. Thus certain lesions in vulnerable species or species groups may serve as a mechanism to assess one facet of ecosystem health.     

Strong nonlinear selection against fluctuating asymmetry in wild populations of a marine fish

Theoretical links between fluctuating asymmetry (FA) and fitness have led many to use FA as a proxy for average fitness. However, studies examining whether asymmetry actually correlates with individual fitness in wild populations are relatively rare and often use simple measures of association (e.g., correlation coefficients). Consequently, the pattern of selection on asymmetry in the wild is seldom clear. We examined selection on FA of pectoral fin morphology in two wild populations of a marine fish (the kelp perch; Brachyistius frenatus). As expected, variance in signed FA in each initial sample was significantly greater than that found in the surviving population, indicating selection against FA. Our estimate of the fitness surface confirmed perfect symmetry as the phenotypic optimum and indicated strong, nonlinear selection against asymmetry. No difference in the form of selection was detected between populations. However, the level of FA in the initial samples varied among populations, leading to an overall difference in the level of selective mortality. Our results suggest that selection on asymmetry in wild populations may be strongly nonlinear, and indicate that the demographic costs of asymmetry may play a substantial role in the dynamics of populations.     

A review of methods for estimating mortality due to parasites in wild fish populations

Six methods are described for detecting mortality due to parasitic infections in natural fish populations. They are: (a) through autopsies; (b) by determining the frequency of infections known to be eventually lethal; (c) by observing a decrease in the prevalence of a long-lived parasite (or permanent scar from a parasite) with host age; (d) by observing a decrease in the variance/mean ratio for the parasites with host age; (e) by comparing the observed frequency of a combination of two independent events with the calculated probability of their occurrence; and finally (f) by comparing the observed frequency distribution of the parasite, with a projected frequency based on data from lightly infected fish. In this technique, negative binomials are fitted to the data and truncated at various points. Some advantages and disadvantages of the different methods are given, together with examples. The methods do not necessarily provide definitive answers, but they are indicative of whether or not significant parasite-related mortality may be occurring, and in some cases provide an estimate of its probable magnitude in terms of the total host mortality rate.     

Predicting infestation parameters and impacts of caligid copepods in wild and cultured fish populations

Summary

The intensity and timing of infestation events of caligid copepods in wild or cultured fish populations may be predicted from previous local production of nauplius I of the parasite. However, this relationship is not well established, the spatial scales over which it operates are unclear, and the role of host reactions to the invading copepodid is unknown. Rate of development (and population structure), generation time and rate and actual reproductive output are temperature-dependent. In Ireland between five and seven generations of Lepeophtheirus salmonis (Krøyer) can develop annually and generation time varies from over 120 days in winter to 23 days in summer. Host reactions may affect the rate of development of the parasite but are less important than temperature. Host reactions may also cause parasite mortality, but this effect is specific for individual host parasite associations. The distribution of L. salmonis in cultured host populations is typically normal but is very over-dispersed in wild populations with heavy infestations. Parasiteinduced morphological damage to the host is correlated with physiological impacts. Physiological effects are present even when morphological damage is slight and so intermittent chemotherapeutic control of infestations cannot prevent some parasite impact from occurring.     

Diagnostic methodology is critical for accurately determining the prevalence of Ichthyophonus infections in wild fish populations

Several different techniques have been employed to detect and identify Ichthyophonus spp. in infected fish hosts; these include macroscopic observation, microscopic examination of tissue squashes, histological evaluation, in vitro culture, and molecular techniques. Examination of the peer-reviewed literature revealed that when more than 1 diagnostic method is used, they often result in significantly different results; for example, when in vitro culture was used to identify infected trout in an experimentally exposed population, 98.7% of infected trout were detected, but when standard histology was used to confirm known infected tissues from wild salmon, it detected ~50% of low-intensity infections and ~85% of high-intensity infections. Other studies on different species reported similar differences. When we examined a possible mechanism to explain the disparity between different diagnostic techniques, we observed non-random distribution of the parasite in 3-dimensionally visualized tissue sections from infected hosts, thus providing a possible explanation for the different sensitivities of commonly used diagnostic techniques. Based on experimental evidence and a review of the peer-reviewed literature, we have concluded that in vitro culture is currently the most accurate diagnostic technique for determining infection prevalence of Ichthyophonus , particularly when the exposure history of the population is not known.     

Embryo ecology: Developmental synchrony and asynchrony in the embryonic development of wild annual fish populations

Embryo–environment interactions are of paramount importance during the development of all organisms, and impacts during this period can echo far into later stages of ontogeny. African annual fish of the genus Nothobranchius live in temporary pools and their eggs survive the dry season in the dry bottom substrate of the pools by entering a facultative developmental arrest termed diapause. Uniquely among animals, the embryos (encased in eggs) may enter diapause at three different developmental stages. Such a system allows for the potential to employ different regulation mechanisms for each diapause. We sampled multiple Nothobranchius embryo banks across the progressing season, species, and populations. We present important baseline field data and examine the role of environmental regulation in the embryonic development of this unique system. We describe the course of embryo development in the wild and find it to be very different from the typical development under laboratory conditions. Development across the embryo banks was synchronized within and across the sampled populations with all embryos entering diapause I during the rainy season and diapause II during the dry season. Asynchrony occurred at transient phases of the habitat, during the process of habitat desiccation, and at the end of the dry season. Our findings reveal the significance of environmental conditions in the serial character of the annual fish diapauses.     

Reconstructing sibling relationships in wild populations

Reconstruction of sibling relationships from genetic data is an important component of many biological applications. In particular, the growing application of molecular markers (microsatellites) to study wild populations of plant and animals has created the need for new computational methods of establishing pedigree relationships, such as sibgroups, among individuals in these populations. Most current methods for sibship reconstruction from microsatellite data use statistical and heuristic techniques that rely on a priori knowledge about various parameter distributions. Moreover, these methods are designed for data with large number of sampled loci and small family groups, both of which typically do not hold for wild populations. We present a deterministic technique that parsimoniously reconstructs sibling groups using only Mendelian laws of inheritance. We validate our approach using both simulated and real biological data and compare it to other methods. Our method is highly accurate on real data and compares favorably with other methods on simulated data with few loci and large family groups. It is the only method that does not rely on a priori knowledge about the population under study. Thus, our method is particularly appropriate for reconstructing sibling groups in wild populations.     

Female fecundity traits in wild populations of African annual fish: the role of the aridity gradient

The evolution of life history is shaped by life expectancy. Life‐history traits coevolve, and optimal states for particular traits are constrained by trade‐offs with other life‐history traits. Life histories contrast among species, but may also diverge intraspecifically, at the level of populations. We studied the evolution of female reproductive allocation strategy, using natural populations of two sympatric species of African annual fishes, Nothobranchius furzeri and Nothobranchius orthonotus. These species inhabit pools in the Mozambican savanna that are formed in the rainy season and persist for only 2–10 months. Using 207 female N. furzeri from 11 populations and 243 female N. orthonotus from 14 populations, we tested the effects of genetic background (intraspecific lineage) and life expectancy (position on the aridity gradient determining maximum duration of their temporary habitat) on female fecundity traits. First, we found that variation in female body mass was small within populations, but varied considerably among populations. Second, we found that fecundity was largely defined by female body mass and that females spawned most of their eggs in the morning. Third, we found that the trade‐off between egg size and egg number varied among lineages of N. furzeri and this outcome has been confirmed by data from two separate years. Overall, we demonstrate that local conditions were important determinants for Nothobranchius growth and fecundity and that eggs size in arid region was less limited by female fecundity than in humid region.     

Spatial patterns of diversity at the putative recognition domain of resistance gene candidates in wild bean populations

Leucine Rich Repeats (LRR) domains have been identified on most known plant resistance genes and appear to be involved in the specific recognition of pathogen strains. Here we explore the processes which may drive the evolution of this putative recognition domain. We developed AFLP markers specifically situated in the LRR domain of members of the PRLJ1 complex Resistance Gene Candidate (RGC) family identified in common bean (Phaseolus vulgaris). Diversity for these markers was assessed in ten wild populations of P. vulgaris and compared to locally co-occurring pathogen populations of Colletotrichum lindemuthianum. Nine PRLJ1 LRR specific markers were obtained. Marker sequences revealed that RGC diversity at PRLJ1 is similar to that at other complex R-loci. Wild bean populations showed contrasting levels of PRLJ1 LRR diversity and were all significantly differentiated. We could not detect an effect of local C. lindemuthianum population diversity on the spatial distribution of P. vulgaris PRLJ1 diversity. However, host populations have been previously assessed for neutral (RAPD) markers and for resistance phenotypes to six strains of C. lindemuthianum isolated from cultivated bean fields. A comparative analysis of PRLJ1 LRR diversity and host diversity for resistance phenotypes indicated that evolutionary processes related to the antagonistic C. lindemuthianum/P. vulgaris interaction are likely to have shaped molecular diversity of the putative recognition domains of the PRLJ1 RGC family members.     

Social networks in fish

Social network theory underwent rapid development in the 1970s by sociologists and was recently further refined by physicists. Network theory has been applied to systems consisting of interconnected components as different as that of actors in Hollywood, the neural network of the nematode worm Caenorhabditis elegans, and the US national power grid. Network theory has great potential as a conceptual tool, for example, it can be used to provide quantitative predictions regarding information transmission, spreading of diseases, and the potential for establishing reciprocal altruistic relationships. Conventionally behavioural studies have been restricted to the analysis of social interactions between isolated pairs or small groups of individuals. Here we built up, however, from pair‐wise interactions, the social network of an entire population of guppies (Poecilia reticulata) in Trinidad. We show that guppies have highly structured social networks with significant repeated interactions between male–male, female–female and male–female pairs. Furthermore, sexual segregation within the network is positively correlated with the strength of the social interactions. Finally, individuals were observed to be more variable in their inter‐sexual interactions than their intra‐sexual ones.     

Calcium regulation in wild populations of a freshwater cartilaginous fish, the lake sturgeon Acipenser fulvescens

Lake sturgeon, Acipenser fulvescens, are one of a few species of cartilaginous fishes that complete their life cycle entirely in freshwater. Sturgeons maintain very low concentrations of circulating calcium (Ca²⁺) compared with other vertebrates, and therefore, face unique challenges in regard to Ca²⁺ regulation, which are likely to be magnified during vitellogenic stages of the reproductive cycle. In the present study, Ca²⁺ concentrations and associated hormones of female and male lake sturgeon were examined in two wild populations, and were related to reproductive stage. In both populations, free, bound and total Ca²⁺ were low, peaking in mid-late vitellogenic females. Internal Ca²⁺ and phosphate (PO₄³⁻) concentrations were inversely related to environmental concentrations, suggesting that these ions are preferentially retained and that mechanisms for mobilization are up-regulated under diminished environmental concentrations. Plasma 17β-estradiol, 11-ketotestosterone and testosterone, peaked in mid-late vitellogenic females, while the androgens peaked in spawning males. Urine Ca²⁺ was more tightly regulated than other divalent ions and decreased in spawning fish. Therefore, the increases in free plasma Ca²⁺, the very low circulating concentrations of free and total Ca²⁺, and the increase in PO₄³⁻ and bound Ca²⁺ in low Ca²⁺ environments indicate unique adaptations to Ca²⁺ regulation in the lake sturgeon.     

Multiple paternity in wild populations of invasive

Multiple paternity within litters has been recorded among a variety of small mammal species, including some species of rodents. Although multiple mating has been observed in wild Rattus populations, whether such mating results in litters with multiple paternities has not been established previously. For studies involving invasive species, awareness is useful of the level of genetic diversity a single pregnant invader can bring to a population. Multiple paternity is a means of providing additional genetic diversity to founding populations of rats on islands, which might improve population fitness. We used a genetic approach to confirm that multiple paternity occurs in wild populations of two rat species (Rattus norvegicus and R. rattus) in New?Zealand. This was accomplished by genotyping litters of embryos in pregnant females, and subtracting the known maternal alleles to find the number of paternal alleles necessary to form the litter. The number of paternal contributors cannot be overestimated by this method, befitting a conservative approach to the detection of multiple paternity, but can be underestimated. We used simulations to investigate the level of underestimation likely under two possible scenarios involving multiple paternity.     

Selection against immigrants in wild seabird populations

Immigration is a major demographic parameter shaping population dynamics and is an important driver of eco‐evolutionary patterns, but the fitness consequences for individuals following their settlement to a new population (immigrants) remain poorly tested in wild animal populations, particularly among long‐lived species. Here we show that immigrants have a lower fitness than residents in three wild seabird populations (wandering albatross Diomedea exulans, southern fulmar Fulmarus glacialoides, snow petrel Pagodroma nivea). Across all species and during a 32‐year period, immigrants made on average ?9 to 29% fewer breeding attempts, had 5–31% fewer fledglings, had 2–16% lower breeding success and produced 6–46% fewer recruits. Female immigration and male residency were also favored through differences in breeding performance. We provide evidence for selection against immigrants in wild populations of long‐lived species and our results are consistent with female‐biased dispersal in birds being driven by asymmetric limiting resources and the competitive ability of dispersers vs. non‐dispersers.