Temporal genetic changes between cohorts in a natural population of a marine fish, Diplodus sargus

Temporal changes at 17 allozyme loci in the Diplodus sargus population of Banyuls sur Mer (Mediterranean Sea, France) were monitored within a single population among ten year‐classes (cohorts) sampled over a 6‐month period. The genetic survey was combined with evaluation of the demographic structure of the population by determining variation of abundance between cohorts. The population showed variation in abundance among cohorts ranging from 16 to 214 individuals. Significant divergences in genetic structure were observed between cohorts (P < 0.0001) despite very low values of F_ST (multilocus F_ST over all cohorts = 0.0018). The heterozygosity of each cohort, as well as the F_IS values, was significantly correlated with the abundance of each cohort, with abundant cohorts showing lower heterozygosity and a significant deficit of heterozygotes (positive F_IS values). Finally, multilocus temporal genetic variance (F_k) computed between successive cohorts was higher in low abundance cohorts. Change of heterozygosity between cohorts, distribution of year‐class genetic structure, and change in the genetic structure within a cohort appear to be affected mostly by the abundance of the cohort and are therefore driven by genetic drift. We propose that the Diplodus sargus cohorts are built up from the mixing of families during the pelagic stage or later during recruitment, and that the decrease in heterozygosity leading to a deficit of heterozygotes is characteristic of a Wahlund effect. Such a Wahlund effect would derive from the mixing of the progeny of families made up of few individuals, but exhibiting high fecundity and high variability of reproductive success. Therefore, although cohorts derived from poor recruitment would only group a few families and would exhibit limited deficit of heterozygotes (higher heterozygosity values), they would lead to high genetic drift and appear more divergent (higher mean temporal genetic variance) than cohorts with high abundance. While not demonstrating directly the family structure of marine populations, our survey provides evidence of highly structured populations. © 2002 The Linnean Society of London, Biological Journal of the Linnean Society, 2002, 76 , 9–20.     

A rough guide to population change in exploited fish stocks

Interpreting how populations will change in response to exploitation is essential to the sound management of fish stocks. While deterministic models can be of use in evaluating sustainable fishing rates, the inherent variability of fish populations limits their value. In this paper a probabilistic approach is investigated which avoids having to make strong assumptions about the functional relationship between spawning stock size and the annual number of young fish (recruits) produced. Empirical probability distributions for recruits are derived, conditioned on stock size, and used to indicate likely stock changes under different fishing mortality rates. The method is applied to cod ( Gadus morhua ) in the North Sea to illustrate how population change can be inferred and used by fishery managers to choose fishing mortality rates which are likely to achieve sustainable exploitation.     

Genetic variation versus recombination rate in a structured population of mice

The correlation between genetic variation and recombination rate was investigated in a structured mouse population. Nucleotide sequence data from 19 autosomal DNA loci from eight inbred strains of mouse (Mus musculus) sampled from three major subspecies were analyzed. The recombination rate was estimated from the comparison of genetic and physical map distances between markers flanking a 10-cM region of each locus. The strains were categorized into four groups (subpopulations) based on geography. By partitioning the genetic diversity into within-group and among-group variation, we detected a positive correlation between the recombination rate and nucleotide diversity within groups. The level of nucleotide differentiation among groups (G(ST)) showed a negative correlation with the rate of recombination. There was no significant correlation between recombination rate and nucleotide diversity when data from different subpopulations were pooled. No correlation was detected between recombination rate and nucleotide divergence of M. musculus and M. spicilegus. These patterns deviate from the strict neutral expectation under the constant nucleotide substitution rate, and they are likely to have been formed either by a hitchhiking effect of positively selected mutants or by background selection of deleterious mutants occurring in a subdivided population. Our series of comparisons show that because a real population always has some structure, incorporation of its information is important in detecting non-neutral evolution.     

Fluctuations in food supply drive recruitment variation in a marine fish

Reproductive rates and survival of young in animal populations figure centrally in generating management and conservation strategies. Model systems suggest that food supply can drive these often highly variable properties, yet for many wild species, quantifying such effects and assessing their implications have been challenging. We used spatially explicit time series of a well-studied marine reef fish (black surfperch Embiotoca jacksoni) and its known prey resources to evaluate the extent to which fluctuations in food supply influenced production of young by adults and survival of young to subadulthood. Our analyses reveal: (i) variable food available to both adults and to their offspring directly produced an order of magnitude variation in the number of young-of-year (YOY) produced per adult and (ii) food available to YOY produced a similar magnitude of variation in their subsequent survival. We also show that such large natural variation in vital rates can significantly alter decision thresholds (biological reference points) important for precautionary management. These findings reveal how knowledge of food resources can improve understanding of population dynamics and reduce risk of overharvest by more accurately identifying periods of low recruitment.     

Recruitment variation in a stream galaxiid fish: multiple influences on fry dynamics in a heterogeneous environment

1. The relative importance of density‐dependent and density‐independent processes in explaining fluctuations in natural populations has been widely debated. In particular, the importance of larval supply and whether it may control the type of regulatory processes a population experiences has proved contentious. 2. Using surveys and field experiments conducted in streams in Canterbury, New Zealand, we investigated how variation in the survival of non‐migratory Galaxias vulgaris fry was affected by density‐dependent and density‐independent processes and how this variation influenced recruitment dynamics. 3. Fry populations with high settlement densities experienced a 70–80% reduction in population size from density‐related mortality during the first fourteen days after peak settlement but thereafter the influence of density‐dependent processes on fry was weak. The impact of environmental conditions on fry populations was dependent on fry size and the magnitude of the perturbation, such that flooding effects on fry survival were most severe when fry were small. 4. In streams not affected by flooding, the size and density of introduced trout (Salmo trutta and Oncorhynchus mykiss) were the most significant factors determining the abundance of eventual recruits. A field experiment manipulating brown trout access to fry populations revealed that trout as small as 110 mm may be capable of greatly reducing and possibly preventing galaxiid recruitment. 5. Overall, the results indicated density‐dependent population regulation was only possible at sites with high native fish densities because trout were likely to be suppressing the number of potential recruits at sites with low native fish numbers. Whilst density‐dependent processes had a strong effect on fry survival following the period of peak fry abundance, density‐independent processes associated with flow and predatory trout influences on fry survival largely determined recruitment variability among galaxiid populations. Focusing conservation efforts on improving habitat to increase fry retention and reducing the impacts of trout on galaxiids would ensure more native fish populations reached their potential abundance.     

Low twinning rate and seasonal effects on twinning in a fertile population,the Hutterites

This paper analyzes from the mid 18th century to 1987 the birth records of the Dariusleut, one of the three subgroups of the Hutterite population. The aim of this study is to describe several aspects of the twinning rate in a fertile population. The overall rate of twinning was 0.90%:103 twins among all 11492 maternities. The rate peaked at the 7th birth order and at the maternal age of 40 years and over. Until the mid 19th century when the Hutterites lived in Russia, the twinning rate was higher (1.5%), and it decreased during the migration period in the second half of the 19th century (0.7%). After the group had settled in the USA and Canada, the population maintained a twinning rate of 1.0% until 1965. After 1965 the rate decreased to 0.7%, partly due to a decline in fertility among women aged 30 years and over. There was a significant seasonal variation: the twinning rate decreased to 0.5% in May–July compared to 1.2% for the other three seasons during the years up to 1965 (P<0.01), while more recent mothers did not show such a seasonal variation. The incidence of twin births in this population seems to have been influenced by environmental factors, which would change their effect seasonally and secularly.     

Integrating individual behavior and population ecology: the potential for habitat-dependent population regulation in a reef fish

We used the predictions of the ideal free and ideal despoticdistributions (IFD and IDD, respectively) as a basis to evaluatethe link between spatial heterogeneity, behavior, and populationdynamics in a Caribbean coral reef fish. Juvenile three-spotdamselfish (Stegastes planifrons) were more closely aggregatedin patch reef habitat than on continuous back reef. Agonisticinteractions were more frequent but feeding rates were lowerin the patch versus the continuous reef habitat. Growth rateswere lower in patch reef habitat than on the continuous reef,but mortality rates did not differ. A separate experiment usingstandard habitat units demonstrated that the patterns observedin natural habitat were the result of the spatial distributionof the habitat patches rather than resource differences between habitats. Our results do not follow the predictions of simpleIFD or IDD models. This deviation from IFD and IDD predictionsmay be the result of a number of factors, including lack ofperfect information about habitat patches, high movement costs,and higher encounter rates of dispersed patches. Our resultsdemonstrate that behavioral interactions are an integral partof population dynamics and that it is necessary to considerthe spatial organization of the habitat in both behavioraland ecological investigations.     

A model of physiologically structured population dynamics with a nonlinear individual growth rate

In this article we consider a size structured population model with a nonlinear growth rate depending on the individual's size and on the total population. Our purpose is to take into account the competition for a resource (as it can be light or nutrients in a forest) in the growth of the individuals and study the influence of this nonlinear growth in the population dynamics. We study the existence and uniqueness of solutions for the model equations, and also prove the existence of a (compact) global attractor for the trajectories of the dynamical system defined by the solutions of the model. Finally, we obtain sufficient conditions for the convergence to a stationary size distribution when the total population tends to a constant value, and consider some simple examples that allow us to know something about their global dynamics.This work was partially supported by DGICYT PB90-0730-C02-01 and PB91-0497.     

Molecular evidence for sequential colonization and taxon cycling in freshwater decapod shrimps on a Caribbean island

Taxon cycling, i.e. sequential phases of expansions and contractions in species' distributions associated with ecological or morphological shifts, are postulated to characterize dynamic biogeographic histories in various island faunas. The Caribbean freshwater shrimp assemblage is mostly widespread and sympatric throughout the region, although one species (Atyidae: Atya lanipes) is geographically restricted and ecologically and morphologically differentiated from other Atya species. Using patterns of nucleotide variation at the COI mtDNA gene in five species of freshwater shrimp (A. lanipes, A. scabra, A. innocuous; Xiphocarididae: Xiphocaris elongata; Palaemonidae: Macrobrachium faustinum) from Puerto Rico, we expected to detect a signature of sequential colonization in these shrimp, consistent with the concept of taxon cycling, and expected that A. lanipes would be at a different taxon stage (i.e. an early stage species) to all other species. We also examined patterns of genetic population structure in each species expected with poor, intermediate and well-developed abilities for among-river dispersal. Population expansions were detected in all species, although the relative timing of the expansions varied among them. Assuming that population expansions followed colonization of Puerto Rico by freshwater shrimp, results bear the hallmarks of sequential colonization and taxon cycling in this fauna. A. lanipes had a star phylogeny, low mean pairwise nucleotide differences and recent (Holocene) estimates for an in situ population expansion in Puerto Rico, and it was inferred as an early stage species in the taxon cycle undergoing a secondary phase of expansion. All other species were inferred as late stage species undergoing regional population expansions, as their mean pairwise nucleotide differences were relatively high and phylogenetic patterns were more complex than A. lanipes. High rates of gene flow without isolation by distance among rivers were detected in all species, although results should be treated cautiously as some populations are unlikely to be in mutation-drift equilibrium. Nested clade analysis produced inconsistent results among species that all have high rates of gene flow and expanding populations.     

Growth rate of four freshwater algae in relation to light and temperature

Four algae of freshwater phytoplankton were studied in monospecific culture: Chlorella vulgaris, Fragilaria crotonensis, Staurastrum pingue and Synechocystis minima. Experiments were performed to determine the growth rate over a wide range of light intensities (5–800 µE m^–2 s^–1, 15/9 light/dark photoperiod) and temperatures (10–35 °C). The results provide a set of parameters (particularly the maximal growth rate associated to optimal conditions of light and temperature) for a three-equation model used to described the growth rate response of a non-nutrient-limited culture.     

The limitations of heart rate as a predictor of metabolic rate in fish

Although telemetered heart rate (f_H) has been used as a physiological correlate to predict the metabolic rate (as oxygen consumption, V?O₂) of fish in the field, it is our contention that the method has not been validated adequately for fish. If f_H in fish is to be used to estimate V?O₂, a single linear (or log-linear) relationship must be established for each species between the two variables which allows V?O₂ to be predicted accurately under all environmentally relevant conditions. Our analyses of existing data indicate that while a good linear (or log-linear) relationship can be established between f_H and V?O₂, the conditions under which the relationship applies may be quite restricted. Physiological states and environmental factors affect the relationship between f_H and V?O₂ significantly such that several curves can exist for a single species. In addition, there are situations in which f_H and V?O₂ do not covary in a significant manner. In some situations f_H can vary over much of its physiological range while V?O₂ remains constant; in others V?O₂ may vary while f_H is invariate. The theoretical basis for this variability is examined to explain why the use of telemetered f_H in predicting V?O₂ of fish may be limited to certain specified applications.     

The effects of harvesting of the South African kelp (Ecklonia maxima) on kelp population structure, growth rate and recruitment

Ecklonia maxima is an economically important kelp in South Africa. The harvested kelp is used mainly as feed for cultured Haliotis midae (abalone) on farms all along the South African South and West Coast. The effects that different harvesting methods have on the growth of sub-canopy kelps, kelp population structure and kelp recruitment were tested in a kelp bed at Bordjies Rif near Cape Town. Two 30 × 10 m sites were set up, about 100 m apart, in near monoculture stands of E. maxima. Each 30×10 m area was subdivided into three treatments. In treatment 1 (T1) the whole ‘head’ of each kelp sporophyte that reached the surface was cut off between the bulb and the primary blade (‘lethal’ method). In treatment 2 (T2) (‘non-lethal’ method), the secondary fronds of all sporophytes that reached the surface were cut 20–30 cm from their junction with the primary blade, and removed. In the control plot, the kelp plants were not treated. Harvesting treatments were done approximately every four months, at low spring tide, from 3 March 2003 to 3 November 2003 (three treatments). The effects of harvesting on the kelps depend largely on the size of plant and the time the fronds were removed; however, no seasonal pattern could be observed. The different treatments had no effect on the growth rate, population structure or recruitment of the kelp. This means that factors other than light play an important role in the growth, structure and recruitment of the kelp beds in False Bay. Results are discussed in relation to current commercial harvesting practices.     

Evolutionary implications of a high selfing rate in the freshwater snail Lymnaea truncatula

Abstract Self-compatible hermaphroditic organisms that mix self-fertilization and outcrossing are of great interest for investigating the evolution of mating systems. We investigate the evolution of selfing in Lymnaea truncatula , a self-compatible hermaphroditic freshwater snail. We first analyze the consequences of selfing in terms of genetic variability within and among populations and then investigate how these consequences along with the species ecology (harshness of the habitat and parasitism) might govern the evolution of selfing. Snails from 13 localities (classified as temporary or permanent depending on their water availability) were sampled in western Switzerland and genotyped for seven microsatellite loci. F_IS (estimated on adults) and progeny array analyses (on hatchlings) provided similar selfing rate estimates of 80%. Populations presented a low polymorphism and were highly differentiated (F_ST= 0.58). Although the reproductive assurance hypothesis would predict higher selfing rate in temporary populations, no difference in selfing level was observed between temporary and permanent populations. However, allelic richness and gene diversity declined in temporary habitats, presumably reflecting drift. Infection levels varied but were not simply related to either estimated population selfing rate or to differences in heterozygosity. These findings and the similar selfing rates estimated for hatchlings and adults suggest that within-population inbreeding depression is low in L. truncatula.     

Heart rate responses to cooling in emu hatchlings

Among fluctuations of instantaneous heart rate (IHR) in newly hatched chicks, heart rate (HR) oscillation with a mean frequency of 0.7 Hz has been designated as Type II HR variability characterized by low frequency (LF) oscillation [Comp. Biochem. Physiol. Part A 124 (1999) 461]. In response to exposure to lowered ambient temperature (Ta), chick hatchlings raised their HR baseline accompanied with the production or augmentation of Type II HR oscillation, indicating that LF oscillation is a phenomenon relating to thermoregulation [J. Therm. Biol. 26 (2001) 281]. In emu hatchlings that are precocial like chickens, Type II HR oscillation also occurred, but less frequently in comparison with chick hatchlings [Comp. Biochem. Physiol. Part A 131 (2002) 787]. This present experiment was conducted to elucidate how IHR of emu hatchlings responds to changes in Ta. Six hatchlings were measured for IHR and skin temperature (Ts) during a 3-h period when they were exposed to controlled Ta (ca. 35 degrees C), lowered Ta (ca. 15-30 degrees C) and again the controlled Ta for individual 1-h periods. In response to all the cooling and re-warming procedures, HR baseline changed depending upon the intensity of the Ta differences; i.e. large differences of Ta produced large changes in HR. HR fluctuations tended to augment during cooling with a few exceptions, but LF oscillation was not produced. Thus, LF oscillation, which was scarce even at the controlled Ta, could not be used as a thermoregulatory indicator in emus.     

Life history and production of Paranephrops zealandicus in a forest stream, with comments about the sustainable harvest of a freshwater crayfish

1. Life history and production were assessed for the crayfish Paranephrops zealandicus in three reaches of a headwater stream with a catchment of regenerating coniferous-broadleaf forest in the south-east of the South Island of New Zealand.
2. Crayfish density ranged from 3 to 4 m⁻² in riffles and 4–12 m⁻² in pools, depending on reach. Crayfish biomass (4–33 g AFDW m⁻²) and annual production (2–11 g AFDW m⁻²) were high compared with values reported elsewhere, while P:B ratio was low (0.33–0.43). This substantial production was dependent primarily upon high biomass rather than high growth rate.
3. The crayfish of this population rank amongst the longest lived and slowest growing ever recorded. Individuals estimated to be 16+ year of age were not uncommon. Females became reproductively active at 6+ year. Fewer than 4% of females carried eggs, and young remained attached to females for at least 15 months.
4. We propose that characteristics of this population are the consequence of a cool thermal regime (mean daily stream temperature = 7.0 °C, range 1.8–11.9 °C), and that low biomass turnover and poor reproductive rate precludes any sustainable commercial harvest of crayfish from streams in New Zealand with similar thermal regimes.     

Decomposition patterns of unprocessed and processed lignocellulosics in a freshwater fish pond

In an attempt to recycle the lignocellulosic wastes like Eichhornia crassipes, Salvinia cucullata and rice (Oryza sativa) straw as manurial inputs in freshwater fish pond ecosystem, a decomposition experiment was carried out in litter bags in an oligotrophic freshwater fish pond environment, with the above mentioned three substrates in unprocessed and microbially processed forms. The loss rates, associated microbial groups, oxygen consumption patterns and other related parameters like carbon, nitrogen, phosphorus, cellulose, hemicellulose and lignin were analysed. The mean daily dry matter loss rates (unprocessed: 10.44>6.97>1.97 and processed: 11.03>8.21>3.67) and oxygen uptake rate (unprocessed: 0.675>0.571>0.568 mg O₂ g^–1 h^–1 and processed: 0.592>0.424>0.407 mg O₂ g^–1 h^–1) in raw and processed substrates were in the sequence Eichhornia > rice straw > Salvinia. The oxygen consumption pattern almost covariated with variations in temperature of pond water, daily dry matter loss rates and fungal counts on substrates. During the decay, the percentage of N and P increased whereas that of C decreased, resulting in lowering of C/N and C/P ratios of the substrates. The structural polymeric fractions like cellulose and hemicellulose decreased along with dry matter whereas the lignin content increased after an initial decrease due to loss of other structural carbohydrates resulting in apparent per cent gain of lignin. A higher number of different heterotrophic bacterial groups was observed in the processed substrates as compared to their raw counterparts. However, cellulolytic bacterial numbers were found to fluctuate through the study period. The fungal load was found to be decreasing gradually as the decay progressed. In this study, bacteria were found to be the prominent microbial group responsible for the decay. The nitrogen-fixing, phosphatase-producing and phosphorus-solubilising bacterial groups were observed to play an important role in lowering the C/N and C/P ratios of the decomposing substrates during decay.     

A novel p16INK4A mutation associated with esophageal squamous cell carcinoma in a high risk population

This study describes identification of p16^INK4A sequence variants and their potential association with esophageal squamous cell carcinoma (ESCC) in a high risk population from Kashmir, India. We report a novel 7 base pair exon 2 deletion in 22 out of 106 (~20%) surgically resected tumor samples. The deletion beginning at the second base of codon 103, results in a frame shift causing premature termination of the protein at codon 142, with structural and functional consequences predicted by insilico analysis. The described mutation is a previously unreported variant of p16^INK4A, perhaps representing a founder mutation unique to the population.