Integrating fish and parasite data as a holistic solution for identifying the elusive stock structure of Pacific sardines (Sardinops sagax)

There is an urgent need to clarify how different stocks, or subpopulations of fish species, are vulnerable to fishing pressure and unfavorable ocean conditions because of the increasing demand on fisheries for human consumption. For marine fishes, the potential for high gene flow increases the difficulty in determining the number of subpopulations managed in a specific fishery. Although the use of molecular data has become a common method in the past 15 years to identify fish subpopulations, no single technique or suite of techniques has been established for fish stock structure studies. We review the use of fish morphometrics, artificial tags, fish genetics, parasite genetics, and parasites as biological tags to identify subpopulations of marine fishes with a focus on the Pacific sardine (Sardinops sagax) fishery off the west coast of North America. We suggest an integration of fish- and parasite-based techniques for future stock structure studies, particularly for pelagic fish species whose stock structure can be elusive. An integration of techniques may also resolve fish stock structure over small geographic areas by increasing the number of spatial and temporal scales studied simultaneously leading to methods for successful management of marine fish species.     

Population genetic structure of three tree species in the mangrove genus Ceriops (Rhizophoraceae) from the Indo West Pacific

Ceriops is a viviparous mangrove with widespread species Ceriops decandra and C. tagal, and an endemic species C. australis. Genetic diversity of the three species was screened in 30 populations collected from 23 locations in the Indo West Pacific (IWP) using Inter-simple sequence repeats (ISSR) and sequences of partial nuclear gene (G3pdh) and chloroplast DNA (trnV-trnM). At the species level, the total gene diversity (Ht) revealed by ISSRs was 0.270, 0.118, and 0.089 in C. decandra, C. tagal, and C. australis, respectively. A total of six haplotypes of G3pdh and five haplotypes of trnV-trnM were recognized among the three species. Only C. decandra was detected containing more than one haplotype from each sequence data set (four G3pdh haplotypes and three trnV-trnM haplotypes). At the population level, genetic diversity of Ceriops was relatively low inferred from ISSRs (He = 0.028, 0.023, and 0.053 in C. decandra, C. tagal, and C. australis, respectively). No haplotype diversity within population was detected from any of the three species. Cluster analysis based on ISSRs identified three major geographical groups in correspond to the East Indian Ocean (EIO), South China Sea (SCS), and North Australia (NA) in both C. decandra and C. tagal. The cladogram from DNA sequences also detected the same three geographical groups in C. decandra. Analysis of molecular variance (AMOVA) revealed that most of the total variation was accounted for by differentiation between the three major geographical regions of both C. decandra and C. tagal. The significant genetic structure may result from the geological events in these regions during the recent Pleistocene glaciations. This study also provided insights into the phylogenetics of Ceriops. Yelin Huang and Fengxiao Tan contributed equally to this work.     

An improved method for studying the condition of fish, with an example using Pacific sardine Sardinops sagax (Jenyns)

The statistical treatment of condition used in many previous studies has been to determine a predicted weight for a fish, and to calculate a ratio of actual to predicted weight. The ratios obtained, known as condition factor K , are then further analysed using analysis of variance or other techniques to relate changes in K to other independent variables. It is suggested that condition can be studied better by using a single model to analyse the response of fish weight to a number of factors simultaneously. This approach affords benefit from the simplicity of using an integrated analysis and avoids problems with skewed distributions of ratios. An example using data on the Pacific sardine, Sardinops sagax (Jenyns), is given. Changes in condition of this fish due to monthly, yearly and temperature effects are calculated.     

Comparative population structure of three snook species (Teleostei: Centropomidae) from the eastern central Pacific

Three snook species, Centropomus viridis, Centropomus medius, and Centropomus robalito, from the eastern central Pacific, representing three of the four proposed phyletic lineages in the genus, were analyzed for genetic variability by means of allozyme and RAPD to evaluate the divergence between populations at different levels of dispersal ability and to evaluate the importance of barriers to dispersal in the population subdivision and genetic diversity. Levels of genetic diversity among species estimated by allozymes were similar and consistent with the observed levels of differentiation in marine fish species. Mean heterozygosity ranged from 0.089 for C. viridis to 0.10 for C. robalito. Genetic diversity for the snook species studied was slightly higher than the mean estimation reported in allozymes for 106 marine fish (0.055) and for anadromous fish species (0.043 to 0.057). Multilocus allele frequency homogeneity tests and population-subdivision estimates for both allozyme and RAPD markers revealed the existence of population structure in C. viridis and C. medius, in coincidence with geographic separation of samples, whereas no divergence was detected in C. robalito. This finding may be attributed to the greater population size of C. robalito, which originated by a recent population range expansion, and hence the potential for dispersal is mediated by larval drift. Fluctuations in population size and population range expansion are used to explain discrepancies between levels of genetic diversity and population structure in the studied species. Supplementary material to this paper is available in electronic format at     

Population genetics of Howellia aquatilis (Campanulaceae) in disjunct locations throughout the Pacific Northwest

Howellia aquatilis A.Gray (water howellia) is a federally-listed threatened aquatic plant species with limited distribution in four states: California, Idaho, Montana, and Washington. Previous studies have shown a lack of genetic variation within the species; these studies, however, have excluded samples from one or more states. There have been no published studies on the population biology or genetics of the six known California populations or their evolutionary relationship to the other Pacific Northwest populations. We used Amplified Fragment Length Polymorphisms to identify genetic variation within and among the California populations, and to compare the California populations to the Idaho, Montana, and Washington populations. Analysis of molecular variance of 92 individuals from the six California populations show that 83.8% of genetic variation is found within populations and 16.2% among populations (P < 0.001). All sampled populations from all states provide 83.7% variation within and 16.3% variation among populations (P < 0.001). A UPGMA analysis confirms there is no clear clustering of Howellia aquatilis populations within California, that the Montana populations cluster within the California populations, and, although with limited population sample sizes, the Idaho and Washington populations are distantly related to all other populations. Waterfowl migration patterns support a hypothesis for avian dispersal as a primary factor in gene flow in Howellia aquatilis.     

Population structure of Anisakis simplex (Nematoda) in harbor porpoises Phocoena phocoena off Denmark

The population structure and habitat selection of Anisakis simplex in 35 harbor porpoises off Denmark are described. The nematodes were collected from the stomach and duodenal ampulla and were categorized as third-stage larvae, fourth-stage larvae, subadults, and adults. The porpoises harbored 8,043 specimens of A. simplex. The proportion of adults and subadults increased with infrapopulation size. The number of development stages across infrapopulations covaried significantly (Kendall's test of concordance). Concordance was higher in hosts with the highest intensities than in those with low and medium intensities. All stages occurred mainly in the forestomach, but this trend was stronger for the adults. Adult and subadult sex ratios did not depart significantly from 1:1. Our data suggested that recruitment and duration of each stage were the main factors accounting for infrapopulation structure. The preference of A. simplex for the forestomach conformed with previous studies, but the narrower distribution of adults relative to other stages might indicate a strategy to enhance mating opportunities. Information on sex ratios of A. simplex is scarce and contradictory. We suggest that the discrepancies might partly reflect differences in categorization criteria and statistical methods.     

Population genetic structure of the catadromous Australian bass from throughout its range

One hatchery-derived impoundment and nine wild riverine populations of the catadromous percoid Australian bass Macquaria novemaculeata were examined at six polymorphic allozyme loci to reveal population genetic structure. Subtle genetic differences among many populations indicated that fish did not interact as a panmictic unit, but rather conformed to an isolation by distance pattern of population structure. The hatchery-derived Glenbawn Dam sample differed from the riverine populations in both average heterozygosity and number of polymorphic loci, demonstrating the need for caution in supplementation programs to rehabilitate wild riverine populations.     

Population genetic structure of three pond-inhabiting Daphnia species on a regional scale (Flanders, Belgium)

1. Only a few studies have compared patterns of genetic variation among populations of different Daphnia species on a regional scale. The present study addresses this gap and examines the relationship between diversity as revealed by allozyme variation and habitat size for populations of Daphnia pulex, D. obtusa and D. curvirostris in Flanders (Belgium). In addition, we examined whether patterns of isolation‐by‐distance could be observed in each of these three Daphnia species. 2. The relationship between genetic diversity and habitat size varied among Daphnia species that occur in the same region. In D. pulex and D. obtusa populations, a positive relationship between local genetic diversity and habitat size was found, whereas the relationship was negative in D. curvirostris populations. 3. Regional genetic diversity was lower than expected from patterns of local genetic diversity in D. pulex and D. obtusa populations in Flanders. This suggests that the subdivision of local Daphnia populations in a region did not obviously increase genetic diversity. 4. Genetic differentiation among populations of these three species in Flanders was moderate and comparable with values observed in other Daphnia species. Patterns of isolation‐by‐distance could be observed, but the scatter was high (D. pulex) or the slope was very low (D. obtusa).     

Population genetic structure of three freshwater mussel (Unionidae) species within a small stream system: significant variation at local spatial scales

1. Unionid mussels are highly threatened, but little is known about genetic structure in populations of these organisms. We used allozyme electrophoresis to examine partitioning of genetic variation in three locally abundant and widely distributed species of mussels from a catchment in Ohio. 2. Within‐population variation was similar to that previously reported for freshwater mussels, but genotype frequencies exhibited heterozygote deficiencies in many instances. All three species exhibited significant among‐population variation. Evidence of isolation‐by‐distance was found in Elliptio dilatata and Ptychobranchus fasciolaris, while Lampsilis siliquoidea showed no geographical pattern of among‐population variation. 3. Our results suggest that the isolating effects of genetic drift were greater in L. siliquoidea than in the other species. Differentiation of populations occurred at a much smaller spatial scale than has previously been found in freshwater mussels. Differences among species may reflect differences in the dispersal abilities of fishes that serve as hosts for the glochidia larvae of mussels. 4. Based on our results, we hypothesise that species of mussels that are common to large rivers exhibit relatively large amounts of within‐population genetic variation and little differentiation over large geographical distances. Conversely, species typical of small streams show lower within‐population genetic variation and populations will be more isolated. If this hypothesis can be supported, it may prove useful in the design of conservation strategies that maintain the genetic structure of target species.     

Some species of the genus Phyllodoce (Polychaeta) from Southern California

Five species of the genus Phyllodoce from Southern California are reviewed. A new subgenus (Aponaitides) is proposed and a new species, Phyllodoce cuspidata , is described. A key to the Southern California species is included.     

Population genetic structure of the tropical tree species Aegiphila sellowiana (Lamiaceae)

The Tibagi River, located in southern Brazil, is associated with a significant degree of environmental heterogeneity, along its 550 km extension. There is concern about the integrity of this river's ecosystem, as human interference has been increasing. Aegiphila sellowiana (Lamiaceae) is an important pioneer tree species, commonly found near rivers; the fruit is consumed by avifauna. We studied this species along three ecological gradients, comprising the upper, middle, and lower regions of the Tibagi River basin. The genetic structure of nine subpopulations of A. sellowiana distributed along these gradients was investigated using RAPDs. Moderate levels of gene diversity (ranging from 0.091 to 0.132) were identified, inferred by a traditional approach and a Bayesian model-based method. The F-statistic, G(ST) parameters and molecular variance analysis showed high genetic differentiation among the three regions (39.5 to 50.26%). Analysis of molecular variance revealed high levels of genetic variation between populations (50.26%), while lower values of genetic variation (ranging from 9.56 to 16.35%) were seen between subpopulations within the upper, middle, and lower regions of the Tibagi River basin. The validity of these results was confirmed by principal coordinate analysis. Linear regression analysis showed significant correlations (r = 0.621, P = 0.0001) between the genetic and geographical distances. The differences observed in genetic variation between regions are probably due to habitat fragmentation; for conservation purposes, we recommend that at least one subpopulation from each region of the Tibagi River should be maintained.     

Population genetic structure of the South American species Hypochaeris lutea (Asteraceae)

The genus Hypochaeris has a recent evolutionary history caused by long‐distance dispersal in conjunction with adaptive radiation in the South American continent. Hypochaeris lutea is a perennial herb that grows mostly at altitudes of around 1000 m in cold swamps of the southern regions of Brazil. We investigated the amplified fragment length polymorphism (AFLP) in 270 individuals representing 11 Brazilian populations of H. lutea to elucidate the population genetic structure of this species. The frequencies of polymorphic loci and gene diversity ranged from 83.42% to 91.66% and from 0.26 to 0.34, respectively. Analysis of molecular variance revealed that most of the genetic variability was found within (76.67%) rather than among (23.3%) populations, agreeing with the pattern of genetic distribution within and among populations observed in other allogamous species of Hypochaeris. A Mantel test showed no correlation between genetic and geographic distances when all populations were considered. Simulations performed using a Bayesian approach consistently identified two clusters with different admixture proportions of individuals, as also revealed by a UPGMA dendrogram of populations. The pattern of genetic structure observed in H. lutea is consistent with a process of successive colonization events by long‐distance dispersal resembling the rapid and recent radiation that has been proposed to explain the origin of the South American species of Hypochaeris.     

Temperature preferences and oxygen consumption of three species of sculpin (Cottus) from the Pit River drainage,California

Synopsis I examined the temperature preferences and routine metabolic rates of Pit sculpin, Cottius pitensis, marbled sculpin, C. klamathensis macrops, and rough sculpin, C. asperrimus, of the Pit River drainage of California to determine if the distributional patterns of these species can be explained on the basis of physiological or behavioral responses to temperature. The routine metabolic rates of these species did not increase significantly between 10 and 15°C, indicating an area of thermal compensation. Metabolic rates then rapidly increased between 15 and 20°C (Q₁₀ values>4.0) followed by little increase between 20 and 25°C (Q₁₀ values >2.0), indicating another area of thermal compensation. The final temperature preferenda of Pit, marbled and rough sculpin were 11.2, 12.1 and 13.5°C, respectively. Marbled and rough sculpin appear to be more stenothermal than Pit sculpin. At acclimation temperatures of 10, 15 and 20°C the acute preferred temperatures of marbled and rough sculpin ranged from 11.1 to 14.7° C and 13.3 to 14.4°C, respectively. Values for Pit sculpin ranged from 9.9 to 16.4°C at acclimation temperatures of 10, 15 and 20°C. The distributions of marbled and rough sculpin are consistent with their behavioral and metabolic responses to temperature. The widespread distribution of Pit sculpin is consistent with its greater tolerance of high temperatures and eurythermal behavior, but the absence of Pit sculpin from habitats dominated by marbled and rough sculpin is not consistent with a temperature related explanation.     

Three new species of galium (rubiaceae) from Baja California

The species described as new are apparently narrow endemics, all belonging to that section ofGalium having fruits with long straight specialized hairs.Galium wigginsii andG. moranii are of the widespreadG. wrightii-G. parishii complex, whereasG. carterae is most like the rarely collectedG. oresbium Greenman of northeastern Mexico.     

A new species of Minuartia (Caryophyllaceae) from Northwest California

Minuartia decumbens, a serpentine endemic resembling the members of theMinuartia nuttallii-M. rosei complex, is described, illustrated and contrasted with the complex.     

Anisakis simplex: CO(2)-fixing enzymes and development throughout the in vitro cultivation from third larval stage to adult

We studied the effect of CO(2) on the in vitro cultivation of Anisakis simplex, an aquatic parasitic nematode of cetaceans (final hosts) and fish, squid, crustaceans and other invertebrates (intermediate/paratenic hosts), and, occasionally, of man (accidental host). The results showed that a high pCO(2), at a suitable temperature, is vital for the optimum development of these nematodes, at least from the third larval stage (L3) to adult. After 30 days cultivation in air, molting to L4 (fourth larval stage) was reduced to 1/3, while survival was about 1/3 of that when cultivated in air + 5% CO(2). The activity of the CO(2)-fixing enzymes, PEPCK and PEPC, was also studied. Throughout the development of the worms studied, PEPCK activity was much higher than that of PEPC (e.g., 305 vs. 6.8 nmol/min.mg protein, respectively, in L3 collected from the host fish). The activity of these enzymes in the worms cultivated in air + 5% CO(2) was highest during M3, and was also generally higher than that of those cultivated in air only, especially during molting from L3 to L4 (e.g., in recently molted L4, PEPCK activity was 3.7 times greater than that of PEPC 2.9 times greater than when cultivated in air).     

An overlooked new species of Smilax (Smilacaceae) from Northern California

Smilax jamesii, a new species from northern California is described and illustrated. Its distribution and its distinction from the other species of the area, 5.californica (A. DC.) A. Gray, are discussed, as is its relationship to the other species of the sectionCoprosmanthus.     

Population structure and dynamics of sympatric Apodemus species (Rodentia: Muridae)

This paper describes the population biology of sympatric populations of Apodemus sylvaticus and A. flavicollis in western England. Annual changes in population siie closely resembled those seen in allopatric populations such that simultaneous peaks in number occurred only in autumn and early winter. Numbers of A. sylvaticus were low and stable in early summer increasing rapidly in late summer and autumn and remaining high throughout winter before a sharp decline in spring. Numbers of A. flavicollis increased after the start of reproduction and continued to rise throughout summer and autumn. The period of major decline of this species was during early winter. Densities of A. sylvaticus and A. flavicollis were comparable with those cited in allopatric studies. Spring populations of both species consisted of cohorts first appearing in the late summer and autumn of the previous year. Few individuals present in spring survived the summer. Reproduction of A. flavicollis commenced four to six weeks before that of A. sylvaticus . Seasonal variation in mean weight of adult males and females also indicates that those changes, due to the acquisition of secondary sex characteristics and reproductive maturity, occur earlier in A. flavicollis than in A. sylvaticus . Data presented contain no evidence of interspecific competition and it is concluded that interspecific differences, chiefly asynchrony in reproduction and annual population cycles, contribute to their stable coexistence.