Demographic Fluctuations Research Articles

Mitochondrial DNA and nuclear microsatellites reveal high diversity and genetic structure in an avian top predator, the white-tailed sea eagle, in central Europe

We analysed 123 white-tailed sea eagles (Haliaeetus albicilla) from (primarily central) Europe with respect to variability and differentiation based on 499 bp of the mitochondrial control region and genotypes at seven unlinked nuclear microsatellites. Variability was high (overall expected heterozygosity, haplotype and nucleotide diversity being 0.70, 0.764 and 0.00698, respectively) and both marker systems showed a subdivision into two main genetic clusters (microsatellites) or haplogroups (mtDNA). In line with earlier analyses focusing on populations from northern and eastern Europe, as well as from Asia, we found a high level of admixture in Europe and no signs of a bottleneck – despite a severe decline of white-tailed sea eagle populations during the 20th century. Europe is thus a global stronghold for this species not only with respect to the number of breeding pairs but also regarding the proportion of species-wide genetic diversity. Our dense sampling revealed a possibly clinal variation within central Europe from north-west to south-east that was reflected by the distribution of mtDNA haplotypes as well as the two microsatellite-based clusters. This population differentiation in central Europe probably originated from a geographically structured postglacial colonization and was later enhanced by recent demographic fluctuations.

Climatic niche and neutral genetic diversity of the six Iberian pine species: a retrospective and prospective view

Quaternary climatic fluctuations have left contrasting historical footprints on the neutral genetic diversity patterns of existing populations of different tree species. We should expect the demography, and consequently the neutral genetic structure, of taxa less tolerant to particular climatic extremes to be more sensitive to long-term climate fluctuations. We explore this hypothesis here by sampling all six pine species found in the Iberian Peninsula (2464 individuals, 105 populations), using a common set of chloroplast microsatellite markers, and by looking at the association between neutral genetic diversity and species-specific climatic requirements. We found large variation in neutral genetic diversity and structure among Iberian pines, with cold-enduring mountain species (Pinus uncinata, P. sylvestris and P. nigra) showing substantially greater diversity than thermophilous taxa (P. pinea and P. halepensis). Within species, we observed a significant positive correlation between population genetic diversity and summer precipitation for some of the mountain pines. The observed pattern is consistent with the hypotheses that: (i) more thermophilous species have been subjected to stronger demographic fluctuations in the past, as a consequence of their maladaptation to recurrent glacial cold stages; and (ii) altitudinal migrations have allowed the maintenance of large effective population sizes and genetic variation in cold-tolerant species, especially in more humid regions. In the light of these results and hypotheses, we discuss some potential genetic consequences of impending climate change.

Genetic diversity and landscape genetic structure of otter (Lutra lutra) populations in Europe

Eurasian otter populations strongly declined and partially disappeared due to global and local causes (habitat destruction, water pollution, human persecution) in parts of their continental range. Conservation strategies, based on reintroduction projects or restoration of dispersal corridors, should rely on sound knowledge of the historical or recent consequences of population genetic structuring. Here we present the results of a survey performed on 616 samples, collected from 19 European countries, genotyped at the mtDNA control-region and 11 autosomal microsatellites. The mtDNA variability was low (nucleotide diversity = 0.0014; average number of pairwise differences = 2.25), suggesting that extant otter mtDNA lineages originated recently. A star-shaped mtDNA network did not allow outlining any phylogeographic inference. Microsatellites were only moderately variable (H o = 0.50; H e = 0.58, on average across populations), the average allele number was low (observed A o = 4.9, range 2.5–6.8; effective A e = 2.8; range 1.6–3.7), suggesting small historical effective population size. Extant otters likely originated from the expansion of a single refugial population. Bayesian clustering and landscape genetic analyses however indicate that local populations are genetically differentiated, perhaps as consequence of post-glacial demographic fluctuations and recent isolation. These results delineate a framework that should be used for implementing conservation programs in Europe, particularly if they are based on the reintroduction of wild or captive-reproduced otters.

Mitochondrial DNA patterns in the Iberian Northern plateau: Population dynamics and substructure of the Zamora province

Several studies have shown the importance of recent events in the configuration of the genetic landscape of a specific territory. In this context, due to the phenomena of repopulation and demographic fluctuations that took place in recent centuries, the Iberian Northern plateau is a very interesting case study. The main aim of this work is to check if recent population movements together with existing boundaries (geographical and administrative) have influenced the current genetic composition of the area. To accomplish this general purpose, mitochondrial DNA variations of 214 individuals from a population located in the Western region of the Iberian Northern plateau (the province of Zamora) were analyzed. Results showed a typical Western European mitochondrial DNA haplogroup composition. However, unexpected high frequencies of U5, HV0, and L haplogroups were found in some regions. The analyses of microdifferentiation showed that there are differences between regions, but no geographic substructure organization can be noticed. It can be stated that the differences observed in the genetic pool of the sampled area at regional level results from the mixture of different populations carrying new lineages into this area at different points in history.

Characterization of microsatellite loci from a South African endemic, the Cape Dwarf Chameleon (Bradypodion pumilum)

The Cape Dwarf Chameleon (Bradypodion pumilum) is an endemic South African species that is currently threatened by habitat loss and fragmentation of its natural habitat through urbanization and agriculture. To conduct studies that will assist in understanding these anthropogenic effects on gene flow, population structure, and genetic diversity, we developed eight microsatellite loci using an enrichment protocol. Number of alleles ranged from 5 to 26 with observed heterozygosities of 0.279–0.930. Several loci did not meet HW expectations, but this may be a result of extreme demographic fluctuations that have been noted for this species. These loci will prove useful to examine the population genetics of these threatened reptiles and for providing information that will be used for generating and updating conservation assessments.

Oscillatory dynamics in rock–paper–scissors games with mutations

We study the oscillatory dynamics in the generic three-species rock–paper–scissors games with mutations. In the mean-field limit, different behaviors are found: (a) for high mutation rate, there is a stable interior fixed point with coexistence of all species; (b) for low mutation rates, there is a region of the parameter space characterized by a limit cycle resulting from a Hopf bifurcation; (c) in the absence of mutations, there is a region where heteroclinic cycles yield oscillations of large amplitude (not robust against noise). After a discussion on the main properties of the mean-field dynamics, we investigate the stochastic version of the model within an individual-based formulation. Demographic fluctuations are therefore naturally accounted and their effects are studied using a diffusion theory complemented by numerical simulations. It is thus shown that persistent erratic oscillations (quasi-cycles) of large amplitude emerge from a noise-induced resonance phenomenon. We also analytically and numerically compute the average escape time necessary to reach a (quasi-)cycle on which the system oscillates at a given amplitude.

Isolation by distance in a continuous population under stochastic demographic fluctuations

The local density of individuals is seldom uniform in space and time within natural populations. Yet, formal approaches to the process of isolation by distance in continuous populations have encountered analytical difficulties in describing genetic structuring with demographic heterogeneities, usually disregarding local correlations in the movement and reproduction of genes. We formulate exact recursions for probabilities of identity in continuous populations, from which we deduce definitions of effective dispersal () and effective density (D(e)) that generalize results relating spatial genetic structure, dispersal and density in lattice models. The latter claim is checked in simulations where estimates of effective parameters obtained from demographic information are compared with estimates derived from spatial genetic patterns in a plant population evolving in a heterogeneous and dynamic habitat. The simulations further suggest that increasing spatio-temporal correlations in local density reduce and generally decrease the product , with dispersal kurtosis influencing their sensitivity to density fluctuations. As in the lattice model, the expected relationship between the product and the genetic structure statistic a(r) holds under fluctuating density, irrespective of dispersal kurtosis. The product D sigma(2) between observed census density and the observed dispersal rate over one generation will generally be an upwardly biased (up to 400% in simulations) estimator of in populations distributed in spatially aggregated habitats.

Genetic consequences of population subdivision: the marsupial Micoureus paraguayanus (Mammalia: Didelphimorphia) as a case study

Habitat fragmentation may cause population subdivision, affecting genetic variation, leading to heterozygosity loss and increased inbreeding, and contributing to population extinction. However, some genetic models have shown that under some conditions, population subdivision can favor heterozygosity and allelic diversity, and small populations may adapt to inbreeding. Here I investigate the relationship between population subdivision and genetic diversity for the marsupial Micoureus paraguayanus (Tate, 1931) using the program Vortex. Hypothetical populations of 100 and 2000 individuals were partitioned into 1, 2, 5 or 10 populations that were linked by varying rates of dispersal and also by sex-biased dispersal. Results suggested that heterozygosity and allelic diversity declined rapidly when a population was subdivided. Genetic and demographic stochasticity diminished the effectiveness of selection against recessive lethal alleles. Dispersal partly reversed the impacts of population subdivision. However, even high rates of dispersal did not eliminate demographic fluctuations or prevent extinction. Although gene flow largely prevented genetic divergence between populations, dispersal did not prevent heterozygosity from being lost more rapidly in subdivided populations than in single populations of equivalent total size. The dynamics of small, fragmented populations were critically dependent on interactions between demographic and genetic processes. Populations of M. paraguayanus may have to be relatively large and continuous to avoid significant losses of genetic diversity.

Molecular and karyotypic phylogeography in the NeotropicalHoplias malabaricus(Erythrinidae) fish in eastern Brazil

The sedentary, predatory characin Hoplias malabaricus has one of the widest distributions of freshwater fishes in South America and is characterized by seven karyomorphs (A-G) that occur in sympatric and allopatric populations. Karyotypical patterns of variation in wild populations have been interpreted as evidence of multiple lineages within this nominal species, a possibility that may limit the validity of experimental data for particular karyomorphs. This study used the phylogeographic and genealogical concordance between cytogenetic (N = 49) and molecular (mitochondrial DNA) (N = 73) data on 17 samples, collected in 12 basins from south-eastern and north-eastern Brazil, to assess the systematic value of cytogenetic data. Cytogenetic patterns show a sex chromosome system in the 2n = 40F karyomorph. Molecular and cytogenetic data indicate a long, independent evolutionary history of karyomorphs and a coastal origin of continental populations in south-eastern Brazil. The lack of fit with molecular clock expectations of divergence between groups is likely to be due to strong demographic fluctuations during the evolution of this species complex. The results indicate that karyotypical identification provides a reliable baseline for placing experimental studies on Hoplias spp. in a phylogenetic context.

Drivers of megaherbivore demographic fluctuations: inference from elephants

AbstractEnvironmentally induced variation in survival and fecundity generates demographic fluctuations that affect population growth rate. However, a general pattern of the comparative influence of variation in fecundity and juvenile survival on elephant population dynamics has not been investigated at a broad scale. We evaluated the relative importance of conception, gestation, first year survival and subsequent survivorship for controlling demographic variation by exploring the relationship between past environmental conditions determined by integrated normalized difference vegetation index (INDVI) and the shape of age distributions at 17 sites across Africa. We showed that, generally, INDVI during gestation best explained anomalies in age structure. However, in areas with low mean annual rainfall, INDVI during the first year of life was critical. The results challenge Eberhardt's paradigm for population analysis that suggests that populations respond to limited resource availability through a sequential decrease in juvenile survival, reproductive rate and adult survival. Contrastingly, elephants appear to respond first through a reduction in reproductive rate. We conclude that this discrepancy is likely due to the evolutionary significance of extremely large body size – an adaptation that increases survival rate but decreases reproductive potential. Other megaherbivores may respond similarly to resource limitation due to similarities in population dynamics. Knowing how vital rates vary with changing environmental conditions will permit better forecasts of the trajectories of megaherbivore populations.

Testing the ‘Laacher See hypothesis’: tephra as dental abrasive

In a series of recent studies, changes in material culture and settlement pattern in the Late Glacial of Northern Europe have been linked to the eruption of the Laacher See volcano. This eruption occurred c. 13,000 years ago towards the end of the Allerød chronozone. It is argued that the tephra fall-out from this eruption set in motion significant demographic fluctuations along the northern periphery of Late Glacial human settlement and that these led to a number of material culture transformations. In particular, the emergence of the regionally distinct techno-complexes with large tanged points – the Bromme culture in southern Scandinavia and the Perstunian culture in northeastern Europe – and the temporary abandonment of central European regions are thought to relate to this eruption. While numerous archaeological datasets are in accord with this ‘Laacher See hypothesis’, the forcing mechanism or mechanisms that brought about these archaeologically visible changes have remained largely unexplored. A particular challenge is to explain how some of the culture-historical effects of the Laacher See eruption seem to change or become more pronounced with distance from the eruptive centre. We here investigate one potential middle-range link between the Laacher See eruption and Late Glacial fauna and foragers: tephra as dental abrasive. We use instrumented nanoindentation to quantitatively investigate tephra from a number of sites covering the medial and distal fall-out zones as well as the dental enamel of Homo sapiens and key prey species of Late Glacial foragers. Our results show that the Laacher See tephra contained particles roughly twice as hard as even the hardest portions of any of the teeth investigated. We also suggest that fluoride-induced weakening of dental enamel may have further aggravated tooth wear. These mechanisms may have acted in concert to produce elevated levels of, in particular, animal mortality, which in turn may have led to an abandonment of the affected landscapes.

Measuring Time, Population, and Residential Mobility from the Surface at San Marcos Pueblo, North Central New Mexico

To understand the effects of European contact on the organization, size, and mobility of Pueblo populations in the Southwest requires detailed knowledge of the occupational histories of the aggregated settlements that typify the late prehistoric and early historic record. Unfortunately, such understanding is generally lacking because the methods used to document occupational histories of settlements tend to either obscure fine-grained temporal distinctions or necessitate costly, and politically objectionable, large-scale excavations. To overcome these difficulties, we use surface expressions to analyze the occupational and population history of San Marcos Pueblo (LA98), an aggregated, late prehistoric site in the Galisteo Basin of New Mexico that persisted to the Pueblo Revolt of 1680. Field methods include detailed mapping of the settlement and systematic surface collections of middens. Frequency seriation, correspondence analysis, and mean ceramic dates of decorated ceramic rims comprise our principal analytic methods and demonstrate that the pueblo was abandoned four times before 1680. Causes of abandonment are discussed. Relative scale measures of population show demographic fluctuations with maximum aggregation during the fifteenth century. Despite demographic pulses, the pueblo remained vital until the terminal abandonment.

Life style and genetic variation in teleosts: the case of pelagic (Aphia minuta) and benthic (Gobius niger) gobies (Perciformes: Gobiidae)

The pattern of genetic variability of two species of Mediterranean gobiids was compared, with reference to their different life history traits (Aphia minuta paedomorphic and pelagic; Gobiusniger metamorphosed and benthic). The aim was to evaluate how different life histories can affect the genetic structure in these marine teleosts. The study was carried out on populations of both species sampled in the western Mediterranean and in the Adriatic Sea. Seven restriction endonucleases were used for the RFLP analysis of a mitochondrial DNA segment comprising the NADH dehydrogenase subunits 3, 4L and 4. The results highlighted two different patterns of genetic variation, a weak genetic structure in A. minuta and population subdivision in G. niger. These observations may be explained not only in terms of the different dispersal capabilities of these species, but also considering that A. minuta is an abbreviate iteroparous spawner while G. niger is a protracted iteroparous spawner. Because abbreviate iteroparity is a reproductive strategy selected in stable environments with high resource availability, Pliocene and Pleistocene climate oscillations may have represented factors that negatively influenced the reproductive success of A. minuta, producing demographic fluctuations and bottlenecks, as suggested by the mismatch distribution analysis. The weak genetic structure of A. minuta populations seems to be therefore due to a more recent re-colonization of the Mediterranean basin after a severe population decline, rather than to the high vagility of this pelagic goby.

Phylogeography of the Bluegill Sunfish,Lepomis macrochirus, in the Mississippi River Basin

The Mississippi River Basin supports the richest fish fauna in eastern North America and has played a key role in the maintenance of fish biodiversity, especially as a refuge for freshwater fishes during glaciations. In this study, we investigated the phylogeography of the bluegill sunfish, Lepomis macrochirus, in eastern North America, using complete sequence of the mitochondrial ND1 gene from 369 samples collected at 15 sites. Phylogenetic analysis revealed two major lineages (northern and southern clades) in a parsimony network. A sympatric distribution of the lineages was widely observed in the Mississippi Basin. Sequence diversity in the two lineages was significantly lower in glaciated regions around the Great Lakes than in unglaciated regions. The two lineages were estimated to have diverged in the Kansan glaciation, and refugia for both existed around the Ouachita Highlands. The southern clade dispersed during the Yasmouth Interglacial, prior to the dispersal of the northern clade during the Sangamon Interglacial. In the northern clade, low genetic diversity and population fragmentation inferred by nested clade analysis (NCA) were considered due to bottleneck events in the Wisconsin glaciation, while the southern clade showed isolation by distance in a Mantel test. A difference in demographic fluctuation suggests that sympatry of the two lineages has resulted from recent secondary admixture through the range expansion of the northern clade in the post-Pleistocene. Large-scale admixture of multiple mtDNA lineages in L. macrochirus, which has not been recorded in other fishes in the Mississippi River Basin, may result from their high vagility.

Demographic factors and genetic variation influence population persistence under environmental change

Population persistence has been studied in a conservation context to predict the fate of small or declining populations. Persistence models have explored effects on extinction of random demographic and environmental fluctuations, but in the face of directional environmental change they should also integrate factors affecting whether a population can adapt. Here, we examine the population-size dependence of demographic and genetic factors and their likely contributions to extinction time under scenarios of environmental change. Parameter estimates were derived from experimental populations of the rainforest species, Drosophila birchii, held in the lab for 10 generations at census sizes of 20, 100 and 1000, and later exposed to five generations of heat-knockdown selection. Under a model of directional change in the thermal environment, rapid extinction of populations of size 20 was caused by a combination of low growth rate (r) and high stochasticity in r. Populations of 100 had significantly higher reproductive output, lower stochasticity in r and more additive genetic variance (V(A)) than populations of 20, but they were predicted to persist less well than the largest size class. Even populations of 1000 persisted only a few hundred generations under realistic estimates of environmental change because of low V(A) for heat-knockdown resistance. The experimental results document population-size dependence of demographic and adaptability factors. The simulations illustrate a threshold influence of demographic factors on population persistence, while genetic variance has a more elastic impact on persistence under environmental change.

The effects of stochastic population dynamics on food web structure

We develop a stochastic, individual-based model for food web simulation which in the large-population limit reduces to the well-studied Webworld model, which has been used to successfully construct model food webs with several realistic features. We demonstrate that an almost exact match is found between the population dynamics in fixed food webs, and that the demographic fluctuations have systematic effects when the new model is used to construct food webs due to the presence of species with small populations.

Testing the ‘Laacher See hypothesis’: a health hazard perspective

It has recently been suggested that the Laacher See volcanic eruption, which occurred around 13,000 years ago, initiated significant demographic fluctuations along the northern periphery of Late Glacial human settlement and that these led to a number of material culture transformations. The origins of the Southern Scandinavian Bromme culture and the northeastern European Perstunian culture as well as the temporary abandonment of Central European regions have been linked to this eruption. However, it remains unclear precisely which aspects of the eruption stimulated Late Glacial foragers to abandon their traditional ways of life. Paradoxically, the culture–historical impact of the eruption appears greater further away from the eruptive centre. Here, we investigate one potential middle-range link between the Laacher See eruption and Late Glacial fauna and foragers: tephra as a health hazard. We use laser-diffraction particle-size analysis to quantitatively investigate tephra from one site with a secure Late Glacial archaeological deposit. In addition, we use values previously reported in the literature and a predictive model to calculate the hazard potential along a transect of two of the three major Laacher See tephra fans. Our results show that the Laacher See tephra may have posed a potential health hazard and that its hazard potential may have increased with distance from the vent. To our knowledge this is the only study that attempts to quantify the changing grain-size composition of tephra fall-out longitudinally in this way, at least with regard to a prehistoric eruption. We close by discussing, more speculatively, other possible health-pertinent effects of the Laacher See eruption and suggest ways in which future work can further evaluate the impact of this eruption on Late Glacial populations.

EVOLUTION OF INCOMPATIBILITY-INDUCING MICROBES IN SUBDIVIDED HOST POPULATIONS

Many insects, other arthropods, and nematodes harbor maternally inherited bacteria inducing "cytoplasmic incompatibility" (CI), reduced egg hatch when infected males mate with uninfected females. Although CI drives the spread of these microbes, selection on alternative, mutually compatible strains in panmictic host populations does not act directly on CI intensity but favors higher "effective fecundity," the number of infected progeny an infected female produces. We analyze the consequences of host population subdivision using deterministic and stochastic models. In subdivided populations, effective fecundity remains the primary target of selection. For strains of equal effective fecundity, if population density is regulated locally (i.e., "soft selection"), variation among patches in infection frequencies may induce change in the relative frequencies of the strains. However, whether this change favors stronger incompatibility depends on initial frequencies. Demographic fluctuations maintain frequency variation that tends to favor stronger incompatibility. However, this effect is weak; even with small patches, minute increases in effective fecundity can offset substantial decreases in CI intensity. These results are insensitive to many details of host life cycle and migration and to systematic outbreeding or inbreeding within patches. Selection acting through transfer between host species may be required to explain the prevalence of CI.

Large bottleneck size in Cauliflower Mosaic Virus populations during host plant colonization.

The effective size of populations (Ne) determines whether selection or genetic drift is the predominant force shaping their genetic structure and evolution. Despite their high mutation rate and rapid evolution, this parameter is poorly documented experimentally in viruses, particularly plant viruses. All available studies, however, have demonstrated the existence of huge within-host demographic fluctuations, drastically reducing Ne upon systemic invasion of different organs and tissues. Notably, extreme bottlenecks have been detected at the stage of systemic leaf colonization in all plant viral species investigated so far, sustaining the general idea that some unknown obstacle(s) imposes a barrier on the development of all plant viruses. This idea has important implications, as it appoints genetic drift as a constant major force in plant virus evolution. By co-inoculating several genetic variants of Cauliflower mosaic virus into a large number of replicate host plants, and by monitoring their relative frequency within the viral population over the course of the host systemic infection, only minute stochastic variations were detected. This allowed the estimation of the CaMV Ne during colonization of successive leaves at several hundreds of viral genomes, a value about 100-fold higher than that reported for any other plant virus investigated so far, and indicated the very limited role played by genetic drift during plant systemic infection by this virus. These results suggest that the barriers that generate bottlenecks in some plant virus species might well not exist, or can be surmounted by other viruses, implying that severe bottlenecks during host colonization do not necessarily apply to all plant-infecting viruses.

How limit cycles and quasi-cycles are related in systems with intrinsic noise

Fluctuations and noise may alter the behaviour of dynamical systems considerably. Forexample, oscillations may be sustained by demographic fluctuations in biologicalsystems where a stable fixed point is found in the absence of noise. We here extendthe theoretical analysis of such stochastic effects to models which have a limitcycle for some range of the model parameters. We formulate a description offluctuations about the periodic orbit which allows the relation between the stochasticoscillations in the fixed-point phase and the oscillations in the limit cycle phase tobe elucidated. In the case of the limit cycle, a suitable transformation into aco-moving frame allows fluctuations transverse and longitudinal with respect tothe limit cycle to be effectively decoupled. While longitudinal fluctuations areof a diffusive nature, those in the transverse direction follow a stochastic pathmore akin to that of an Ornstein–Uhlenbeck process. Their power spectrum iscomputed analytically within a van Kampen expansion in the inverse system size. Thesubsequent comparison with numerical simulations, carried out in two differentways, illustrates the effects that can occur due to diffusion in the longitudinaldirection.