Biological Population Structure Research Articles

Cross-scale environmental impacts across persistent and dynamic aggregations within a complex population: implications for fisheries management

Accounting for marine stocks spatiotemporal complexity has become one of the most pressing improvements that should be added to the new generation of stock assessment. Disentangling persistent and dynamic population subcomponents and understanding their main drivers of variation are still stock-specific challenges. Here, we hypothesized that the spatiotemporal variability of density in two adjacent fish stocks is associated with spatially structured environmental processes across multiple spatiotemporal scales. To test this, we applied a generalized empirical orthogonal function and dynamic factor analysis to fishery-independent and -dependent data of red mullet, a highly commercial species, in the Western Mediterranean Sea. Areas with persistent and dynamic high aggregations were detected for both stock units. A large-scale climatic index and local open-ocean convection were associated with both stocks, while other variables exhibited stock-specific effects. We also revealed spatially structured density dynamics within the examined management units. This suggests a metapopulation structure and supports the future implementation of a spatial stock assessment. Considering the common—generally unrealistic—assumptions of panmictic structure and absence of connectivity with neighbouring stock units, our methodology can be applied to other species and systems with putative spatial complexity to inform more accurate population dynamics and structure.

VARIAÇÃO INTRAESPECÍFICA EM PEIXES DE RIACHO COM ÊNFASE NA ECOLOGIA TRÓFICA

Assessing intraspecific variability in community structure and functioning are still scarce for stream-dwelling fish. However, measuring ecological traits for individuals is important since species’ response for environmental conditions occurs at the individual level, especially in streams which suffers constantly physical disturbances. Intraspecific variability can be measured for several ecological traits, such as morphology, diet, life-history, and habitat use that varies between populations or within populations. Here, we present some methods and studies that evaluated intraspecific trophic variability in stream-dwelling fish. Results revealing the role of individual variation in structure of biological populations and/or assemblages were selected, and principal issues were discussed. There are a lot of statistical tools that can test individual variation including functional indexes and multivariate analyzes. Results generated from such individual analyzes have high potential to explain the functioning of stream fish populations and communities.

Novel signals of adaptive genetic variation in northwestern Atlantic cod revealed by whole-genome sequencing.

Selection can create complex patterns of adaptive differentiation among populations in the wild that may be relevant to management. Atlantic cod in the Northwest Atlantic are at a fraction of their historical abundance and a lack of recovery within the Gulf of Maine has created concern regarding the misalignment of fisheries management structures with biological population structure. To address this and investigate genome‐wide patterns of variation, we used low‐coverage sequencing to perform a region‐wide, whole‐genome analysis of fine‐scale population structure. We sequenced 306 individuals from 20 sampling locations in U.S. and Canadian waters, including the major spawning aggregations in the Gulf of Maine in addition to spawning aggregations from Georges Bank, southern New England, the eastern Scotian Shelf, and St. Pierre Bank. With genotype likelihoods estimated at almost 11 million loci, we found large differences in haplotype frequencies of previously described chromosomal inversions between Canadian and U.S. sampling locations and also among U.S. sampling locations. Our whole‐genome resolution also revealed novel outlier peaks, some of which showed significant genetic differentiation among sampling locations. Comparisons between allochronic winter‐ and spring‐spawning populations revealed highly elevated relative (FST) and absolute (dxy) genetic differentiation near genes involved in reproduction, particularly genes associated with the brain‐pituitary‐gonadal axis, which likely control timing of spawning, contributing to prezygotic isolation. We also found genetic differentiation associated with heat shock proteins and other genes of functional relevance, with complex patterns that may point to multifaceted selection pressures and local adaptation among spawning populations. We provide a high‐resolution picture of U.S. Atlantic cod population structure, revealing greater complexity than is currently recognized in management. Our genome‐scan approach likely underestimates the full suite of adaptive differentiation among sampling locations. Nevertheless, it should inform the revision of stock boundaries to preserve adaptive genetic diversity and evolutionary potential of cod populations.

Can we rely on selected genetic markers for population identification? Evidence from coastal Atlantic cod.

The use of genetic markers under putative selection in population studies carries the potential for erroneous identification of populations and misassignment of individuals to population of origin. Selected markers are nevertheless attractive, especially in marine organisms that are characterized by weak population structure at neutral loci. Highly fecund species may tolerate the cost of strong selective mortality during early life stages, potentially leading to a shift in offspring genotypes away from the parental proportions. In Atlantic cod, recent genetic studies have uncovered different genotype clusters apparently representing phenotypically cryptic populations that coexist in coastal waters. Here, we tested if a high‐graded SNP panel specifically designed to classify individual cod to population of origin may be unreliable because of natural selection acting on the SNPs or their linked background. Temporal samples of cod were collected from two fjords, starting at the earliest life stage (pelagic eggs) and carried on until late autumn (bottom‐settled juveniles), covering the period during summer of high natural mortality. Despite the potential for selective mortality during the study period, we found no evidence for selection, as both cod types occurred throughout the season, already in the earliest egg samples, and there was no evidence for a shift during the season in the proportions of one or the other type. We conclude that high‐graded marker panels under putative natural selection represent a valid and useful tool for identifying biological population structure in this highly fecund species and presumably in others.

Study on Eutrophication in Landscape Lake of Different Trophic Levels by Microcosm Experiment

In this paper, a microcosm system was designed targeting at the landscape lake to study the eutrophication mechanism of the water by controlling the eutrophication level in water, measuring and comparing the water quality indicators. Firstly, the microcosm trophic level configuration and ecological balance cycle experiment were designed.Secondly, omnivorous fish and zooplankton were put into the system to simulate the biological population structure in the landscape water, the relations and trend of change among the elements of temperature, pH and dissolved oxygen, nitrogen, phosphorus, and chlorophyll a in the water were measured and analyzed. The results show that the one-level trophic microcosm system has good effect on controlling the nitrate nitrogen, phosphate and total phosphorus; the two-level trophic microcosm system has good effect on controlling chlorophyll a; the three-level trophic microcosm system has good effect on controlling the nitrate nitrogen and total phosphorus and maintains good stability of pH.Finally, relative suggestions and measures on the control of eutrophication lake were proposed based on data analysis, in order to promote the sustainable development of water.

Spatial synchrony of zooplankton during the impoundment of amazonic reservoir

The escalating demand for energy and the strong political and economic pressure to explore the Amazon’s hydroelectric potential has led to the increase of hydroelectric reservoirs in the region. Reservoirs are artificial ecosystems that modify the structure of biological populations. Evaluating the spatial synchrony of populations and environmental variables in the development of reservoirs may reveal determinant factors and processes operating in these ecosystems. This may help understand the impacts, optimize monitoring systems and develop strategies to improve and maintain the ecological integrity (or stability) of these environments. In this study, we evaluated the spatial synchrony in zooplankton populations and limnological environmental variables during the implementation of a hydroelectric reservoir in the Amazon region, on the border of the states of Pará and Amapá. Synchrony was determined by mean cross-correlation between the pairs of points for each variable, followed by Mantel test to investigate its influencing factors. We observed spatial synchronous values for both population and limnological environmental variables. However, we could not identify the mechanisms that are operating, indicating that more than one factor may be influencing the ecosystem dynamics. Population synchrony increased after impoundment. Population synchrony may be associated with some limnological variables, such as the ones related to the amounts of nutrients, whereas environmental synchrony can be related to extrinsic factors, such as climatic variation, not tested this study. In order to increase the understanding of the mechanisms operating over population and environmental dynamics, we suggest that, besides evaluating limnological environmental variables and spatial synchrony, analyses should include meteorological and landscape data.

Lessons learned from practical approaches to reconcile mismatches between biological population structure and stock units of marine fish

AbstractRecent advances in the application of stock identification methods have revealed inconsistencies between the spatial structure of biological populations and the definition of stock units used in assessment and management. From a fisheries management perspective, stocks are typically assumed to be discrete units with homogeneous vital rates that can be exploited independently of each other. However, the unit stock assumption is often violated leading to spatial mismatches that can bias stock assessment and impede sustainable fisheries management. The primary ecological concern is the potential for overexploitation of unique spawning components, which can lead to loss of productivity and reduced biodiversity along with destabilization of local and regional stock dynamics. Furthermore, ignoring complex population structure and stock connectivity can lead to misperception of the magnitude of fish productivity, which can translate to suboptimal utilization of the resource. We describe approaches that are currently being applied to improve the assessment and management process for marine fish in situations where complex spatial structure has led to an observed mismatch between the scale of biological populations and spatially-defined stock units. The approaches include: (i) status quo management, (ii) “weakest link” management, (iii) spatial and temporal closures, (iv) stock composition analysis, and (v) alteration of stock boundaries. We highlight case studies in the North Atlantic that illustrate each approach and synthesize the lessons learned from these real-world applications. Alignment of biological and management units requires continual monitoring through the application of stock identification methods in conjunction with responsive management to preserve biocomplexity and the natural stability and resilience of fish species.

Cultural interaction and biological distance in postclassic period Mexico.

Economic, political, and cultural relationships connected virtually every population throughout Mexico during Postclassic period (AD 900-1520). Much of what is known about population interaction in prehistoric Mexico is based on archaeological or ethnohistoric data. What is unclear, especially for the Postclassic period, is how these data correlate with biological population structure. We address this by assessing biological (phenotypic) distances among 28 samples based upon a comparison of dental morphology trait frequencies, which serve as a proxy for genetic variation, from 810 individuals. These distances were compared with models representing geographic and cultural relationships among the same groups. Results of Mantel and partial Mantel matrix correlation tests show that shared migration and trade are correlated with biological distances, but geographic distance is not. Trade and political interaction are also correlated with biological distance when combined in a single matrix. These results indicate that trade and political relationships affected population structure among Postclassic Mexican populations. We suggest that trade likely played a major role in shaping patterns of interaction between populations. This study also shows that the biological distance data support the migration histories described in ethnohistoric sources.

Analysis of genetic diversity of salt-tolerant alfalfa germplasms.

Random amplified polymorphic DNA technology was used to analyze the genetic diversity of 25 salt-tolerant alfalfa varieties using 30 different primers. Results showed that the percentage of polymorphic loci between single-plant DNA was 81.52%, and that between mixed DNA of various varieties was 61.65%. Compared to the mixed DNA samples, single-plant DNA samples can better reveal the level of genetic variation among and between alfalfa varieties. The gene differentiation coefficients of 18 Chinese salt-tolerant alfalfa varieties and 7 American salt-tolerant alfalfa varieties were 0.271 and 0.152, respectively, showing that the exchange of genes between Chinese salt-tolerant alfalfa germplasms was more frequent than that of American germplasms. As a topical cross-pollinated plant, the genetic structure of biological populations of alfalfa was directly linked to its breeding system. According to the analysis of genetic distance (GD), 25 varieties can be divided into 9 groups, among which, the GD of Tumu No. 1 and Tumu No. 2 was the shortest (0.148), and the GD of Jieda No. 1 and Tumu was the longest (0.786). The analysis of genetic diversity of salt-tolerant alfalfa germplasms provided a theoretical basis for the creation of an alfalfa salt-tolerant core germplasm repository and for the selection and breeding of new salt-tolerant varieties.

Consequences of a mismatch between biological and management units on our perception of Atlantic cod off New England

A mismatch between the scale of fishery management units and biological population structure can potentially result in a misperception of the productivity and sustainable yield of fish stocks. We used simulation modelling as a tool to compare the perception of productivity, stability, and sustainability of Atlantic cod (Gadus morhua) off New England from an operating model based on the current US management units to a model that more closely reflects the biological complexity of the resource. Two age-structured models were compared: (i) the management unit model, wherein cod were grouped based on the current spatially defined US management areas (Gulf of Maine and Georges Bank), and (ii) the biological unit model, consisting of three genetically defined population components (northern spring spawning, southern winter/spring spawning, and eastern Georges Bank spring-spawning groups). Overall, the regional productivity and maximum sustainable yield of the biological unit model was lower compared with the management unit model. The biological unit model also provided insights on the distribution of productivity in the region, with southern and northern spawning groups being the dominant contributors to the regional spawning–stock biomass and yield and the eastern Georges Bank spawning group being the minority contributor at low to intermediate levels of fishing mortality. The comparison of models revealed that the perception of Atlantic cod derived from the management unit model was of a resource that is more resilient to fishing mortality and not as susceptible to “collapse” as indicated by the biological unit model. For Atlantic cod, one of the main risks of ignoring population structure appears the potential for overexploitation of segments of the population. Consideration of population structure of cod changed our perception of the magnitude and distribution of productivity in the region, suggesting that expectations of sustainable yield of cod in US waters should be reconsidered.

Stock identification of Atlantic cod (Gadus morhua) in US waters: an interdisciplinary approach

Abstract Mismatches between biological population structure and management unit boundaries often violate the unit-stock assumption, which can reduce the accuracy and relevance of stock assessment results and lead to ineffective fishery management. Since 1972, Atlantic cod (Gadus morhua) have been managed in US waters as two units: the Gulf of Maine and the Georges Bank stocks, both of which have experienced recent difficulties in rebuilding. An interdisciplinary review of available biological information was conducted to investigate cod population structure in US waters and to evaluate the biological appropriateness of the current two-stock model. Our review demonstrates that spawning components in the Great South Channel, Nantucket Shoals, southern New England, and Middle Atlantic are more connected with spawning components in the Gulf of Maine than on eastern Georges Bank, with which they are currently managed. Therefore, a modification of current stock boundaries is recommended to provide a more accurate representation of biological population structure. Proposed alternatives divide inshore and offshore spawning components into separate management units, thereby separating the current Georges Bank stock longitudinally. Continued research, including stock composition analysis, is required to evaluate uncertainties, delineate biological stocks, and develop sustainable management practices that account for intrastock diversity (e.g. winter and spring-spawning components that overlap spatially).

Fine‐scale population genetic structure in a wide‐ranging carnivore, the leopard (Panthera pardus fusca)in centralIndia

AbstractAimHabitat loss and fragmentation can influence the genetic structure of biological populations. Large terrestrial predators can often avoid genetic subdivision due to fragmentation because they have high rates of dispersal‐mediated gene flow. Leopards (Panthera pardus) are found in a variety of habitats and are the most widely distributed of the large and middle‐sized felids. We investigated the genetic diversity and population substructure of leopards (P.p fusca) in a fragmented meta‐population comprised of four populations from five protected areas and inter‐connecting corridors spread over an area of 45,000 km2in central India.LocationKanha,Pench,Satpura andMelghatTigerReserves, and interconnecting corridors in theSatpura‐MaikalLandscape ofCentralIndia.MethodsWe collected faecal samples and used genetic methods to identify individuals, estimate the genetic variation and evaluate the patterns of genetic substructuring within this meta‐population of leopards.ResultsWe identified 217 individual leopards using a panel of seven microsatellite loci. Leopards showed high levels of genetic diversity in all sampled populations. Spatial and non‐spatialBayesian analysis revealed at least two admixed genetic populations with indications of ongoing genetic subdivision. Genetic differentiation between populations was not explained by geographic distance. We identified nine individuals as migrants, most of which were assigned to reserves connected by corridors.Main conclusionsOur study demonstrates that the leopard, an adaptable and vagile species, can become genetically differentiated with increased habitat fragmentation. Contrary to our hypothesis of panmixia, our results indicate that although leopards in this landscape are admixed, there is genetic substructuring at both the landscape and the fine‐scale level. We conclude that this is due to habitat fragmentation and corridors are of immense value in maintaining genetic connectivity in this landscape.

Genetic consequences of habitat fragmentation and loss: the case of the Florida black bear (Ursus americanus floridanus)

Habitat loss and fragmentation can influence the genetic structure of biological populations. We studied the genetic consequences of habitat fragmentation in Florida black bear (Ursus americanus floridanus) populations. Genetic samples were collected from 339 bears, representing nine populations. Bears were genotyped for 12 microsatellite loci to estimate genetic variation and to characterize genetic structure. None of the nine study populations deviated from Hardy–Weinberg equilibrium. Genetic variation, quantified by mean expected heterozygosity (HE), ranged from 0.27 to 0.71 and was substantially lower in smaller and less connected populations. High levels of genetic differentiation among populations (global FST = 0.224; global RST = 0.245) suggest that fragmentation of once contiguous habitat has resulted in genetically distinct populations. There was no isolation-by-distance relationship among Florida black bear populations, likely because of barriers to gene flow created by habitat fragmentation and other anthropogenic disturbances. These factors resulted in genetic differentiation among populations, even those that were geographically close. Population assignment tests indicated that most individuals were genetically assigned to the population where they were sampled. Habitat fragmentation and anthropogenic barriers to movement appear to have limited the dispersal capabilities of the Florida black bear, thereby reducing gene flow among populations. Regional corridors or translocation of bears may be needed to restore historical levels of genetic variation. Our results suggest that management actions to mitigate genetic consequences of habitat fragmentation are needed to ensure long-term persistence of the Florida black bear.

Biological Kinetic Data Evaluation of an Activated Sludge System Coupled with an Ultrafiltration Membrane

A membrane bioreactor (MBR) system treating wastewater containing high molecular weight compounds was operated at solids retention times (SRTs) ranging from 30 to 2 days. Chemical oxygen demand removal efficiencies exceeded 99% and effective nitrification was obtained at SRTs between 30 and 5 days. A significant shift in the biological population structure was observed at the 2 days SRT as the content of gram-negative microorganisms increased and nitrifying bacteria were washed out. At this low SRT, limitations in the biological reaction kinetics resulted in incomplete degradation of the feed protein increasing the presence of soluble organic matter in the effluent. Furthermore, the diluted mixed liquor prevented the formation of a filtration cake on the membrane surface, further deteriorating effluent quality. Biological kinetic data parameters were analyzed using three different representations for biomass: volatile suspended solids, lipid phosphates, and total enzymatic activity. All three indicators exhibited similar trends resulting in very comparable estimates for endogenous decay coefficients, thus demonstrating the reliability of volatile suspended solids as a measure for biological activity in activated sludge. Lower than typical endogenous decay rates in the MBR suggested favorable environmental conditions for respiration and a lower potential for self oxidation and predation. The true yield coefficient was in the range of conventional activated sludge systems, refuting previous suggestions of lower yields in MBRs.

Spatial pattern and ecological analysis

The spatial heterogeneity of populations and communities plays a central role in many ecological theories, for instance the theories of succession, adaptation, maintenance of species diversity, community stability, competition, predator-prey interactions, parasitism, epidemics and other natural catastrophes, ergoclines, and so on. This paper will review how the spatial structure of biological populations and communities can be studied. We first demonstrate that many of the basic statistical methods used in ecological studies are impaired by autocorrelated data. Most if not all environmental data fall in this category. We will look briefly at ways of performing valid statistical tests in the presence of spatial autocorrelation. Methods now available for analysing the spatial structure of biological populations are described, and illustrated by vegetation data. These include various methods to test for the presence of spatial autocorrelation in the data: univariate methods (all-directional and two-dimensional spatial correlograms, and two-dimensional spectral analysis), and the multivariate Mantel test and Mantel correlogram; other descriptive methods of spatial structure: the univariate variogram, and the multivariate methods of clustering with spatial contiguity constraint; the partial Mantel test, presented here as a way of studying causal models that include space as an explanatory variable; and finally, various methods for mapping ecological variables and producing either univariate maps (interpolation, trend surface analysis, kriging) or maps of truly multivariate data (produced by constrained clustering). A table shows the methods classified in terms of the ecological questions they allow to resolve. Reference is made to available computer programs.

The Lyapunov direct method for analyzing the dynamics of the age structure of biological populations

The Lyapunov direct method is used to study the stability of the stationary solutions of a class of equations with distributed parameters, describing the dynamics of the age composition of biological populations.

The rate of molecular evolution considered from the standpoint of population genetics.

The rate of amino acid substitutions in the evolution of homologous proteins is remarkably constant. Furthermore, estimated rates of amino acid substitutions based on comparisons of the alpha hemoglobin chains of various mammals with that of the carp are about the same as those based on comparisons of the carp alpha and mammalian beta or the alpha and beta chains in mammals. These uniformities are regarded as evidence for the hypothesis that a majority of amino acid substitutions that occurred in these proteins are the result of random fixation of selectively neutral or nearly neutral mutations. TWO IMPLICATIONS OF THIS POSSIBILITY ARE DISCUSSED: (a) Random gene frequency drift is playing an important role in determining the genetic structure of biological populations and (b) genes in "living fossils" may be expected to have undergone as many DNA base (and therefore amino acid) substitutions as corresponding genes (proteins) in more rapidly evolving species.