Polymorphic microsatellite loci in Lithophragma maximum (Saxifragaceae), an endemic plant of San Clemente Island

In this paper, we report the isolation of 11 polymorphic microsatellite loci from Lithophragma maximum (Saxifragaceae), a rare species restricted to San Clemente Island, California. We found moderate levels of allelic variation (mean N_A= 5.5) and high levels of expected heterozygosity (mean H_E= 0.531) across sampled individuals. However, eight loci showed a significant absence of heterozygous individuals, which we attribute to small population size and demographic history of the species.     

Isolation of microsatellite loci from the endangered plant Galium catalinense subspecies acrispum (Rubiaceae)

Galium catalinense subspecies acrispum (Rubiaceae) is a state‐endangered perennial shrub endemic to San Clemente Island. Eight polymorphic microsatellite loci were isolated from G. catalinense ssp. acrispum. These loci show high levels of variability, averaging 6.5 alleles per locus and an expected heterozygosity of 0.550. One locus exhibited significant deviations from Hardy–Weinberg equilibrium (P < 0.01) and one pair of loci exhibited significant linkage disequilibrium.     

High levels of genetic polymorphism in the insular endemic herb Jepsonia malvifolia.

Jepsonia malvifolia is a long-lived perennial herb endemic to the Channel Islands of southern California and Guadalupe Island, Mexico. Twelve populations of J. malvifolia on San Clemente Island were surveyed for their genotype at 21 allozyme loci, revealing high levels of genetic polymorphism. For all individuals across San Clemente Island, 95.2% of loci are polymorphic with A(p) = 2.90 and H(e) = 0.179. Populations averaged 60.2% polymorphic loci with A(p) = 2.42 and H(e) = 0.158. Most variation is found within rather than among populations (G(ST) = 0.101), although differentiation among populations is significant. Genetic identities range from 0.936 to 0.999 with mean I = 0.975. There is no significant relationship between genetic and geographic distance. Gene flow among populations is Nm = 9.5 based on private alleles and Nm = 2.2 based on F(ST). Outcrossing rates based on fixation indices average t = 0.753, indicating a primarily outcrossed mating system. The genetic variation observed is unusually high for an insular endemic herb and indicates that J. malvifolia is unlikely to be endangered by genetic factors.     

Replicate divergence between and within sounds in a marine fish: the copper rockfish (Sebastes caurinus)

Understanding the factors that influence larval dispersal and connectivity among marine populations is critical to the conservation and sustainable management of marine resources. We assessed genetic subdivision among ten populations of copper rockfish (Sebastes caurinus) representing paired samples of outer coast and the heads of inlets in five replicate sounds on the west coast of Vancouver Island, British Columbia, using 17 microsatellite DNA loci. Overall, subdivision (F_ST) was low (F_ST = 0.031, P < 0.001), but consistently higher between paired coast and head of inlet sites (mean F_ST = 0.047, P < 0.001) compared to among the five coast sites (mean F_ST = ?0.001, P > 0.5) or among the five head of inlet sites (mean F_ST = 0.026, P < 0.001). Heterozygosity, allelic richness and estimates of effective population size were also lower in head of inlet sites than in coast sites. Bayesian analysis identified two genetic groups across all samples, a single genetic group among only coast samples, two genetic groups among head of inlet samples and two genetic groups within each sound analysed separately. Head of inlet copper rockfish tended to be shorter with lower condition factors and grew more slowly than coast sites fish. Reduced physical connectivity and selection against immigrants in contrasting outer coast–head of inlet environments likely contribute to the evolution of population structure of copper rockfish. Based on genetic connectivity, coast sites appear to be better served by existing marine protected areas than are head of inlet sites.     

Isolation and characterization of polymorphic microsatellite markers from Australia short-finned eel (Anguilla australis Richardson)

Seventeen microsatellite DNA loci from the Australian short‐finned eel (Anguilla australis Richardson) were isolated and their amplification characteristics were described. The polymerase chain reaction primers were tested on 40 eel individuals. The primers amplified loci with relatively high numbers of alleles, ranging from five to 14 with an average of nine per locus. Mean observed heterozygosity (H_O) and expected heterozygosity (H_E) were 0.6779 and 0.7374, respectively, indicating that these markers would be useful for population studies. No loci deviated significantly from Hardy–Weinberg equilibrium (P = 0.05) and no evidence was found for genotypic disequilibrium among loci at a 5% significance level.     

The effects of competitor density on aggressive behaviour and resource defence in a Poeciliid fish

To test the hypothesis that competitor density and time spent at a food resource influences aggressive behaviour in male swordtail, Xiphophorus sp., fish were kept at two densities (low: 18 fish m^?3; high: 54 fish m^?3) and aggressive behaviour was recorded with the time at the food resource used as a covariate. Competitor density is likely to affect the cost:benefit ratio of food defence. When density is low, there should be sufficient food for all individuals and intra‐specific interactions are expected to be rare, while at high densities, increased intra‐specific encounter rates mean that individuals may spend more time defending a resource than utilising it. Food resource defence should occur at intermediate densities. The frequency of aggression, i.e. bites, chases, and display behaviour was significantly positively influenced by time spent at the food resource (Bites: F_1,31 = 8.186, P = 0.007; Chases: F_1,31 = 6.439, P = 0.016; Displays: F_1,31 = 4.435, P = 0.043) suggesting that food resource defence occurred. Competitor density had no effect on food resource defence and minimal effect on the frequency of aggression with only one type of aggressive behaviour, male–male displays, showing a difference between densities (F_1,31 = 6.975, P = 0.013). This finding is suggested to be a result of the formation of dominance hierarchies in this species. Aggression from the dominant individual may be directed at only subordinates of the next dominance rank and subordinate behaviour may be restricted by status rather than immediate threat. In such a situation, aggression may be independent of competitor density.     

The Pillars of Hercules as a bathymetric barrier to gene flow promoting isolation in a global deep‐sea shark (Centroscymnus coelolepis)

Knowledge of the mechanisms limiting connectivity and gene flow in deep‐sea ecosystems is scarce, especially for deep‐sea sharks. The Portuguese dogfish (Centroscymnus coelolepis) is a globally distributed and near threatened deep‐sea shark. C. coelolepis population structure was studied using 11 nuclear microsatellite markers and a 497‐bp fragment from the mtDNA control region. High levels of genetic homogeneity across the Atlantic (Φ_ST = ?0.0091, F_ST = 0.0024, P > 0.05) were found suggesting one large population unit at this basin. The low levels of genetic divergence between Atlantic and Australia (Φ_ST = 0.0744, P < 0.01; F_ST = 0.0015, P > 0.05) further suggested that this species may be able to maintain some degree of genetic connectivity even across ocean basins. In contrast, sharks from the Mediterranean Sea exhibited marked genetic differentiation from all other localities studied (Φ_ST = 0.3808, F_ST = 0.1149, P < 0.001). This finding suggests that the shallow depth of the Strait of Gibraltar acts as a barrier to dispersal and that isolation and genetic drift may have had an important role shaping the Mediterranean shark population over time. Analyses of life history traits allowed the direct comparison among regions providing a complete characterization of this shark's populations. Sharks from the Mediterranean had markedly smaller adult body size and size at maturity compared to Atlantic and Pacific individuals. Together, these results suggest the existence of an isolated and unique population of C. coelolepis inhabiting the Mediterranean that most likely became separated from the Atlantic in the late Pleistocene.     

Isolation and characterization of polymorphic microsatellite loci in yellowtail catfish, Pangasius pangasius (Hamilton, 1822)

A total of nine polymorphic microsatellite loci were obtained from a genomic library of Pangasius pangasius (order Siluriformes, family Pangasiidae). Samples from rivers Bhagirathi (n = 22) and Mahanadi (n = 20) were genotyped for each of the nine microsatellite loci to determine genetic variation. The mean number of alleles per locus was 5.22 in Bhagirathi and 5.78 in Mahanadi; and expected heterozygosity ranged from 0.567 (Bhagirathi) to 0.578 (Bhagirathi). Significant deviation (P < 0.003) from Hardy–Weinberg expectations was evident at three loci, Ppa2 (Bhagirathi), Ppa14 (Mahanadi) and Ppa28 (Bhagirathi and Mahanadi). The identified microsatellite loci were found to be promising for population genetics studies of P. pangasius.     

Patterns of within and between-colony microsatellite variation in the endangered Vancouver Island marmot (Marmota vancouverensis): implications for conservation

Among the 14 extant species of the genus Marmota the Vancouver Island marmot (Marmota vancouverensis) is the most endangered. In 2007 as few as 85 individuals were left in the wild, with an additional 162 individuals maintained in captivity. To facilitate genetic monitoring of both wild and captive populations, polymorphic genetic markers were identified. Thirty-three different microsatellite loci were tested for amplification and variability in ≥30 wild-born individuals. Only 11 of these loci proved to be polymorphic and were subsequently analysed in 105 samples collected from wild Vancouver Island marmots. The average number of alleles (A) at those 11 loci was only 2.1, and the intraspecific variation (H _E between 8 and 23% within colonies) was low compared to other marmot species. Variation within the small and geographically isolated Mt. Washington colony was particularly low (A = 1.3, H _E = 0.08). Genetic distances between the Mt. Washington colony (11 individuals) and those of the Nanaimo Lakes region (94 individuals) on southern Vancouver Island were large (D values ranging from 0.42 to 0.50), while genetic distances among colonies within the latter area were much smaller (D values from 0.01 to 0.13). Given the low within-population genetic variation, and the resulting risk of inbreeding depression at Mt. Washington, we support the decision to maximize overall genetic variation of the species by crossbreeding marmots from the two different areas despite the possibility of local adaptation.     

Fine-scale genetic population structure in a mobile marine mammal: inshore bottlenose dolphins in Moreton Bay, Australia

Highly mobile marine species in areas with no obvious geographic barriers are expected to show low levels of genetic differentiation. However, small‐scale variation in habitat may lead to resource polymorphisms and drive local differentiation by adaptive divergence. Using nuclear microsatellite genotyping at 20 loci, and mitochondrial control region sequencing, we investigated fine‐scale population structuring of inshore bottlenose dolphins (Tursiops aduncus) inhabiting a range of habitats in and around Moreton Bay, Australia. Bayesian structure analysis identified two genetic clusters within Moreton Bay, with evidence of admixture between them (F_ST = 0.05, P = 0.001). There was only weak isolation by distance but one cluster of dolphins was more likely to be found in shallow southern areas and the other in the deeper waters of the central northern bay. In further analysis removing admixed individuals, southern dolphins appeared genetically restricted with lower levels of variation (AR = 3.252, π = 0.003) and high mean relatedness (r = 0.239) between individuals. In contrast, northern dolphins were more diverse (AR = 4.850, π = 0.009) and were mixing with a group of dolphins outside the bay (microsatellite‐based STRUCTURE analysis), which appears to have historically been distinct from the bay dolphins (mtDNA Φ_ST = 0.272, P < 0.001). This study demonstrates the ability of genetic techniques to expose fine‐scale patterns of population structure and explore their origins and mechanisms. A complex variety of inter‐related factors including local habitat variation, differential resource use, social behaviour and learning, and anthropogenic disturbances are likely to have played a role in driving fine‐scale population structure among bottlenose dolphins in Moreton Bay.     

Isolation and characterization of polymorphic tetranucleotide microsatellite loci in the chestnut-crowned babbler (Pomatostomus ruficeps)

We describe 18 microsatellite markers isolated in the cooperatively breeding chestnut‐crowned babbler (Pomatostomus ruficeps). The number of alleles ranged from seven to 16 per locus (mean N_a = 10.4 ± 0.54 SE) and the expected heterozygosity ranged from 0.732 to 0.889 (mean H_E = 0.836 ± 0.01 SE). Three of the 18 loci exhibited significant heterozygote deficiency, but the remaining 15 will be used to analyse population genetic structure and the mating system of this highly social species.     

PERMANENT GENETIC RESOURCES: Identification and characterization of 14 polymorphic microsatellite loci in the argasid tick Ornithodoros coriaceus

Fourteen polymorphic microsatellite loci (di, tetra and di‐tetra complexes) were developed for the argasid tick Ornithodoros coriaceus. Polymorphism was assessed for 56 individuals from two populations separated by ~95 km. All loci were polymorphic (X = 7, range 3–17 alleles). All loci were in Hardy–Weinberg equilibrium except for one locus (OrC 8) in a single population (P < 0.00119, after Bonferroni correction for multiple tests).     

Genomic analysis of the differential response to experimental infection with porcine circovirus 2b

Porcine circovirus type 2 (PCV2) is the etiological agent of a group of associated diseases (PCVAD) that affect production efficiency and can lead to mortality. Using different crossbred lines of pigs, we analyzed host genetic variation of viral load, immune response and weight change following experimental infection with a PCV2b strain (n = 386). Pigs expressed variation in the magnitude and initiation of viremia and immune response recorded weekly until 28 days post‐infection. A higher viral load was correlated with weight gain (r = ?0.26, P < 0.0001) and presence of PCV2‐specific antibodies (IgM, r = 0.26–0.34, P < 0.0001; IgG, r = 0.17–0.20, P < 0.01). In genome‐wide association analyses of the responses at different time points, the proportions of phenotypic variation explained by combined effects of 56 433 SNPs were 34.8–59.4% for viremia, 10.1–59.5% for antibody response and 5.6–14.9% for weight change. Relationships between genomic prediction of overall viral load and weight gain during the first weeks of challenge were negative (?0.21 and ?0.24 respectively, P < 0.0001). Individuals that carried more favorable alleles across three SNPs on SSC9 (0.60 Mb) and SSC12 (6.8 and 18.2 Mb) partially explained this relationship, having lower viral load (P < 0.0001); lower viremia at day 14 (P < 0.0001), day 21 (P < 0.01) and day 28 (P < 0.05) and greater overall average daily gain during infection (ADG_i; P < 0.01), ADG_i at week 3 (P < 0.001) and week 4 (P < 0.01). These additive genetic relationships could lead to molecular solutions to improve animal health and reduce production costs.     

Epidemic Development and Virulence in 1995–1998 of Puccinia coronata, a Potential Biocontrol Agent of Wild Oats on San Clemente Island

The biology of islands differs from that of large land masses in having less complex ecosystems. Introduced exotic weeds are often a major threat to fragile island ecosystems because of their expansion into habitats previously occupied by endemic species. San Clemente Island, 120 km off the California coastline, is an example of this process in which numerous exotic weed species have been introduced and some are endangering the native flora. Crown rust of oats caused by Puccinia coronata f.sp. avenae was investigated as a potential biocontrol agent against two wild oat species, Avena barbata and Avena fatua, introduced on San Clemente Island. Epidemiology and virulence of this rust were studied. The island was surveyed from 1995 to 1998 for occurrence of P. coronata on wild oats. Wild oats were found sprouting in the northern part of the island shortly after autumn rainfall and subsequently covered the main grasslands of the island. The rust also appeared first on the northern part of the island and progressively spread south. However, disease severities in the south were considerably lower than those in the north. Diverse virulence types, although related to Californian and Mexican forms, were detected among the isolates. The potential use of P. coronata as an augmentative biocontrol agent for wild oat species on San Clemente Island is discussed.     

Age and growth of Boops boops (Linnaeus, 1758) in Izmir Bay,Aegean Sea,Turkey

The present study was conducted to determine the age relationships in lengths and weights of Boops boops (Linneaus, 1756) in Izmir Bay, central Aegean Sea. A total of 932 specimens (503 females and 429 males) were caught by gillnet, trammel net and a combination thereof on a monthly sampling basis from November 2008 through October 2009. Total length and weight of sampled fish ranged from 11.3 to 27.9 cm and from 12.2 to 261.7 g, with a mean of 19.6 cm and 82.7 g, respectively. Length‐weight relationships for all individuals were described by the parameters a = 0.0050, b = 3.237 and r² = 0.956. The von Bertalanffy growth curve fitted to the lengths‐at‐age provided parameters of L_∞ = 29.87 cm k = 0.243 and t_o = ?0.98 for males and L_∞ = 30.79 cm, k = 0.239 and t_o = ?0.90 for females. Based on otolith readings, age determinations varied from 1 to 5 years. Maximum age was 5 years in age group 2, with 29.84 and 37.97% for males and females, respectively. The overall 1 : 1.17 sex ratio of males to females was significantly biased toward females (P < 0.05). There was no statistical difference in the mean condition factor (P > 0.05), with a value of 1.028 for the entire population. The growth performance index (Φ^’) was 2.33 and 2.36 for males and females, respectively. Results were similar to other geographical areas, which suggests that a common fisheries management might be possible.     

Diet shift response in round goby,Neogobius melanostomus,based on size,sex, depth,and habitat in the western basin of Lake Erie

This study examines the diet of the round goby (Neogobius melanostomus) in the western basin of Lake Erie. As an invasive benthic feeder, the round goby has the potential to affect smallmouth bass and other native species. Round goby (n = 100) were collected during summer 2011 and stomach contents were examined to determine diet patterns and possible ontogenetic diet shifts. Individual round goby were grouped by sex, size (small < 65 mm, large ≥ 65 mm), depth of habitat (shallow < 2 m, deep > 5 m), and habitat type (natural shallows, anthropogenically modified shallows, and deep waters). Gut fullness ranged from 10 to 100% with 23 stomachs presenting 100% fullness. Round goby consumed 27 different food items including abiotic (sand grains, gravel), floral (algae, fine leaved vascular plants), and fauna items. The Index of Relative Importance (IRI) and comparative z‐tests were used to assess correlations and differences. Two‐way z‐tests revealed a significant difference in mouth gape related to size (z = ?5.56377, P = 2.64e‐08), and habitat depth (z = 3.34262, P = 0.00083). A significant linear correlation was also found between mouth gape standardized by head length (HL) for both males (P = 2.63e‐9) and females (P = 1.3e‐4). Two‐way z‐tests also revealed a significant difference in gonadosomatic index (GSI) related to sex (z = 6.07727, P = 6.11248e‐10), but not size. A significant difference in gut fullness was also found related to sex (z = ?3.34743, P = 0.00082), habitat depth (z = 3.16336, P = 0.00156), and habitat type (z = ?2.7398, P = 0.00615). IRI values demonstrated a diet selective of veliger mussels (IRI = 2462.01), juvenile mussels (IRI = 1073.03), cladocerans (IRI = 4804.31), and chironomids (IRI = 1012.12). While previous studies have focused on round goby diet shifts from macroinvertebrates to bivalves, most studies did not evaluate changes in diet among multiple categories. Furthering knowledge of multiple aspects of goby diet may aid in developing management techniques to deter future round goby invasion.     

Genome‐wide association study of osteochondrosis in the tarsocrural joint of Dutch Warmblood horses identifies susceptibility loci on chromosomes 3 and 10

Equine osteochondrosis is a developmental joint disease that is a significant source of morbidity affecting multiple breeds of horse. The genetic variants underlying osteochondrosis susceptibility have not been established. Here, we describe the results of a genome‐wide association study of osteochondrosis using 90 cases and 111 controls from a population of Dutch Warmblood horses. We report putative associations between osteochondrosis and loci on chromosome 3 (BIEC2‐808543; P = 5.03 × 10^?7) and chromosome 10 (BIEC2‐121323; P = 2.62 × 10^?7).     

Similarities and differences in 13C and 15N stable isotope ratios in two non‐lethal tissue types from shovelnose sturgeon Scaphirhynchus platorynchus (Rafinesque, 1820)

We tested the hypothesis that δ¹³C and δ¹⁵N signatures of pectoral spines would provide measures of δ¹³C and δ¹⁵N similar to those obtained from fin clips for adult shovelnose sturgeon Scaphirhynchus platorynchus. Thirty‐two shovelnose sturgeon (fork length [FL] = 500–724 mm) were sampled from the lower Mississippi River, USA on 23 February 2013. Isotopic relationships between the two tissue types were analyzed using mixed model analysis of covariance. Tissue types differed significantly for both δ¹³C (P < 0.01; spine: mean = ?23.83, SD = 0.62; fin clip: mean = ?25.74, SD = 0.97) and δ¹⁵N (P = 0.01; spine: mean = 17.01, SD = 0.51; fin clip: mean = 17.19, SD = 0.62). Neither FL nor the FL × tissue type interaction had significant (P > 0.05) effects on δ¹³C. Fin clip δ¹³C values were highly variable and weakly correlated (r = 0.16, P = 0.40) with those from pectoral spines. We found a significant FL‐tissue type interaction for δ¹⁵N, reflecting increasing δ¹⁵N with FL for spines and decreasing δ¹⁵N with FL for fin clips. These results indicate that spines are not a substitute for fin clip tissue for measuring δ¹³C and δ¹⁵N for shovelnose sturgeon in the lower Mississippi River, but the two tissues have different turnover rates they may provide complementary information for assessing trophic position at different time scales.     

Reproductive biology of Chinese minnow Hemiculterella sauvagei Warpachowski, 1888 in the Chishui River,China

This study describes the reproductive biology of the Chinese minnow Hemiculterella sauvagei. The length‐weight relationship, sex ratio, spawning season, size at first maturity, and fecundity were analyzed based on 685 specimens collected from the Chishui River between July 2011 and July 2012. The relationship between standard length (SL) and body weight (BW) were estimated as BW = 2.14 × 10^?4 × SL^2.801 (R² = 0.839; N = 413; P < 0.05) for females and BW = 1.31 × 10^?4 × SL^3.001 (R² = 0.868; N = 272; P < 0.05) for males. The female to male sex ratio, 1.52 : 1, differed significantly from a 1 : 1 ratio. Females predominated in standard lengths >12 cm. Analyses of the monthly variation in the gonadosomatic index (GSI), the monthly proportions of macroscopic gonadal maturity, and the size distribution of oocytes consistently suggested a prolonged spawning season of H. sauvagei from March to August, with a peak from April to May. Logistic curves describing the relationship between proportion of maturity (P_r) at each length interval and standard length were estimated as P_r = 1/(1 + e^{26.867–0.306SL}) (R² = 0.999; N = 413; P < 0.05) for females and P_r = 1/(1 + e^{10.522–0.142SL}) (R² = 0.999; N = 272; P < 0.05) for males. Size at first maturity was estimated as 7.4 cm for males and 8.8 cm SL for females. Absolute fecundity varied from 563 to 5052, with a mean of 2413 ± 874 oocytes per ovary. The relative fecundity was estimated to be 41–299, with a mean of 171 ± 55 oocytes per ovary. The present study provides useful information for fishery management and resources conservation.