Why be amphidromous: expatrial dispersal and the place of source and sink population dynamics?

Amphidromous fishes are found predominantly on the tropical and subtropical islands of the globe and there are few amphidromous species on continents. I suggest that this idiosyncratic distribution relates in part to problems in self-recruitment on islands that are often young or volcanic, and which may have streams with ephemeral flows across relatively short times scales. Amphidromy provides the ability to invade new habitats as these become available either on newly emergent (often volcanic) islands, or following perturbation after stream dewatering or the impacts of volcanism on older islands as a consequence of expatrial dispersal. Source/sink population dynamics may also be involved with islands ‘downstream’ in oceanic current systems behaving as sinks, with little or no self-recruitment. Streams in steep topography seem to be favoured by amphidromous species, perhaps because they provide more rapid transport to sea of the tiny, newly hatched larvae.     

Movements and source–sink dynamics of a Masai giraffe metapopulation

Spatial variation in habitat quality and anthropogenic factors, as well as social structure, can lead to spatially structured populations of animals. Demographic approaches can be used to improve our understanding of the dynamics of spatially structured populations and help identify subpopulations critical for the long-term persistence of regional metapopulations. We provide a regional metapopulation analysis to inform conservation management for Masai giraffes (Giraffa camelopardalis tippelskirchi) in five subpopulations defined by land management designations. We used data from an individual-based mark–recapture study to estimate subpopulation sizes, subpopulation growth rates, and movement probabilities among subpopulations. We assessed the source–sink structure of the study population by calculating source–sink statistics, and we created a female-based matrix metapopulation model composed of all subpopulations to examine how variation in demographic components of survival, reproduction, and movement affected metapopulation growth rate. Movement data indicated no subpopulation was completely isolated, but movement probabilities varied among subpopulations. Source–sink statistics and net flow of individuals indicated three subpopulations were sources, while two subpopulations were sinks. We found areas with higher wildlife protection efforts and fewer anthropogenic impacts were sources, and less-protected areas were identified as sinks. Our results highlight the importance of identifying source–sink dynamics among subpopulations for effective conservation planning and emphasize how protected areas can play an important role in sustaining metapopulations.     

Does rapid evolution matter? Measuring the rate of contemporary evolution and its impacts on ecological dynamics

Rapid contemporary evolution due to natural selection is common in the wild, but it remains uncertain whether its effects are an essential component of community and ecosystem structure and function. Previously we showed how to partition change in a population, community or ecosystem property into contributions from environmental and trait change, when trait change is entirely caused by evolution (Hairston et al. 2005). However, when substantial non-heritable trait change occurs (e.g. due to phenotypic plasticity or change in population structure) that approach can mis-estimate both contributions. Here, we demonstrate how to disentangle ecological impacts of evolution vs. non-heritable trait change by combining our previous approach with the Price Equation. This yields a three-way partitioning into effects of evolution, non-heritable phenotypic change and environment. We extend the approach to cases where ecological consequences of trait change are mediated through interspecific interactions. We analyse empirical examples involving fish, birds and zooplankton, finding that the proportional contribution of rapid evolution varies widely (even among different ecological properties affected by the same trait), and that rapid evolution can be important when it acts to oppose and mitigate phenotypic effects of environmental change. Paradoxically, rapid evolution may be most important when it is least evident.     

Geographic variability of ecological niches of plant species: are competition and stress relevant?

A species’ niche position may differ strongly between geographic regions, for instance due to the effect of competitors or ecophysiological stress. However, it is unclear whether such strong geographic niche variation is the rule or the exception. We compared the niche positions of plant species between central England and eastern central Europe (as available from the literature), using phylogenetically independent contrasts. We found that most species occupied similar niche positions in both regions. More importantly, we found that niche variation was not higher in species susceptible to competitive displacement. Nor was niche variation higher in species that reach the edge of their range and thus suffer ecophysiological stress. We suggest that although these species might be easily displaced in their position along a niche axis, they may only be displaced over a short distance. Overall, ecological mechanisms that cause niche variation at the local scale may be much less relevant at the geographic scale.     

Do ecological niches differ between sexual and asexual lineages of an aphid species?

According to environmental-based theories on the maintenance of sexual reproduction, sexual and asexual populations may coexist if they occupy different ecological niches. The aphid Rhopalosiphum padi offers a good opportunity to test this hypothesis since sexual and asexual lineages show local coexistence during a large part of their respective life-cycles. Because these two reproductive variants are morphologically identical but genetically distinct, we first characterized them using genetic markers in populations of R. padi in areas where sexual and asexual lineages may occur in sympatry. We then inferred the natal host plant of sexual and asexual genotypes by analysing stable isotopic ratios and showed that sexual ones mostly originated from C₃ Poaceae while asexual ones originated from C₃ and C₄ plants, although the majority came from C₄ Poaceae. These findings indicate that ecological niches of sexual and asexual lineages of R. padi differ, offering a plausible explanation for the local coexistence of the two reproductive modes in this species through habitat specialisation.     

The evolution of the α- and β-globin gene clusters in human populations

Summary DNA analysis of the - and -globin gene clusters has revealed substantial variability between individuals and populations. As well as restriction enzyme site and length polymorphisms, variation in gene copy number and type is observed. Because of this extensive polymorphism DNA analysis offers a highly informative method of studying genetic affinities between human populations. Haplotypes, consisting of a set of restriction enzyme polymorphisms distributed along the cluster, have been developed for both loci. Analysis of the molecular basis of numerous -thalassaemia alleles has revealed, in general, different sets of mutations in different populations, indicating that these postdate the racial divergence. Recent microepidemiological studies on the distribution of -thalassaemia support the hypothesis that this condition, like the {ie16-1}, has been selected because it confers protection against malaria. Population-specific DNA polymorphisms at these and other loci promise to be of considerable value to genetic anthropology.     

Deep pools of the Danube River: ecological function or turbulent sink?

Danube main channel deep pools are in-stream habitats of high ecological relevance. We used dual-frequency identification sonar to investigate seasonal and diel fish abundance in two hydrodynamically different deep pools in the main channel of the Danube River in 2008. In general, fish of different species were present in both deep pools throughout the year, irrespective of water level. High fish abundance was recorded during autumn and winter, low abundance during spring and summer. During low discharge and low temperature and particularly during low flow velocity, low kinetic energy and low shear stress, high fish abundance in densely packed aggregations were observed, a clear indication for the refuge capacity of deep pools. In contrast, during turbulent hydraulic conditions with high flow velocity, high turbulent kinetic energy and high shear stress, low fish abundance occurred, mainly consisting of single fish, small fish shoals and benthic fish specimens. Furthermore, we could reveal that calm as well as turbulent pools fulfil the requirements as refuge and feeding habitat of eurytopic, piscivorous catfish throughout the year. The application of a multiple linear model based on the hydrological parameters discharge and water temperature as well as the hydraulic parameters flow velocity, turbulent kinetic energy and shear stress provided highly significant evidence between the observed and the expected seasonal fish abundance in the deep pools (R ² = 0.77, P < 0.001). For the first time these results make clear that the main channel deep pools are important refuge and resource habitats of different species of the Danube fish community. Deep pools are key habitats for the in-stream fish community of the Danube River.     

Gecko vision—visual cells,evolution, and ecological constraints

Geckos comprise both nocturnal and diurnal genera, and between these categories there are several transitions. As all geckos depend on their visual sense for prey capture, they are promising subjects for comparison of morphological modifications of visual cells adapted to very different photic environments. Retinae of 22 species belonging to 15 genera with different activity periods are examined electron microscopically. Scotopic and photopic vision in geckos is not divided between “classical” rods and cones, respectively; both are performed by one basic visual cell type. Independent of the activity periods of the individual species, the visual cells of geckos exhibit characteristics of cones at all levels of their ultrastructure. Thus, gecko retinae have to be classified as cone retinae. Only the large size and the shape of the photoreceptor outer segments in nocturnal geckos are reminiscent of rods; the outer segments are up to 60 μm in length and up to 10 μm in diameter. The visual cells of diurnal geckos have considerably smaller outer segments with lengths ranging from 6 to 12 μm and diameters ranging from 1.3 to 2.1 μm. Nocturnal and diurnal species differ in the structure of their ellipsoids. One type of visual cell in nocturnal geckos has modified mitochondria with either rudimentary cristae or no cristae at all, and one type of visual cell in diurnal geckos possesses an oil droplet. The visual cells of Phelsuma guentheri and Rhoptropus barnardi are intermediate between those of nocturnal and diurnal species.     

Colonization history, ecological shifts and diversification in the evolution of endemic Galápagos weevils

Mitochondrial DNA sequence data were obtained for eight species of flightless Galapaganus endemic weevils and one winged close relative in order to study their colonization history and modes of diversification in the Galápagos Archipelago. Contrary to most other insular radiations, the phylogeny estimates we recovered for Galapaganus do not follow the progression rule of island biogeography. The penalized likelihood age estimates of colonization of the archipelago exceed the age of the emerged islands and underscore the potential role of now sunken seamounts for the early evolution of Galapaganus . The phylogeny proposes one intra-island origin for Galapaganus endemics, but monophyly tests suggest a larger contribution of in-situ speciation on older islands. Generalist habitat preferences were reconstructed as ancestral while shifts to highland habitats were reconstructed as having evolved independently on different islands. Magnitudes and patterns of diversification rate were found to differ between older and younger islands. Our analyses reveal that the colonization sequence of islands and timing of colonization of Galapaganus could be linked with the geological and volcanic history of the islands in a rather complex scenario. Even though most islands appear to have been colonized soon after their emergence, there are notable deviations from the pattern of sequential colonization expected under the progression rule when considering only the extant emerged islands. Patterns of diversification rate variation on older and younger islands correspond to the volcanic activity or remnants of such activity, while the pattern of independent evolution of restricted habitat preferences in different islands suggests that habitat shifts could also have contributed to species diversity in Galapaganus .     

Specificity of protein — Nucleic acid interaction and the biochemical evolution

The water soluble carbodiimide mediated condensation of dipeptides of the general form Gly-X was carried out in the presence of mono- and poly-nucleotides. The observed yield of the tetrapeptide was found to be higher for peptide-nucleotide system of higher interaction specificity following mainly the anticodon-amino acid relationship (Basu, H.S. & Podder, S.K., 1981, Ind. J. Biochem. Biophys.,19, 251–253). The yield of the condensation product of L-peptide was more because of its higher interaction specificity. The extent of the racemization during the condensation of Gly-L-Phe, Gly-L-Tyr and Gly-D-Phe was found to be dependent on the specificity of the interaction —the higher the specificity, the lesser the racemization. The product formed was shown to have a catalytic effect on the condensation reaction. These data thus provide a mechanism showing how the specific interaction between amino acids/dipeptides and nucleic acids could lead to the formation of the primitive translation machinery.     

On the origin and evolution of new genes——a genomic and experimental perspective

The inherent interest on the origin of genetic novelties can be traced back to Darwin. But it was not until recently that we were allowed to investigate the fundamental process of origin of new genes by the studies on newly evolved young genes. Two indispensible steps are involved in this process:origin of new gene copies through various mutational mechanisms and evolution of novel functions, which further more leads to fixation of the new copies within populations. The theoretical framework for the former ...     

On the origin and evolution of new genes——a genomic and experimental perspective

The inherent interest on the origin of genetic novelties can be traced back to Darwin, But it was not until recently that we were allowed to investigate the fundamental process of origin of new genes by the studies on newly evolved young genes. Two indispensible steps are involved in this process: origin of new gene copies through various mutational mechanisms and evolution of novel functions, which fur-ther more leads to fixation of the new copies within populations. The theoretical framework for the former step formed in 1970s. Ohno proposed gene duplication as the most important mechanism producing new gene copies. He also believed that the most common fate for new gene copies is to become pseudogenes. This classical view was validated and was also challenged by the characterization of the first functional young gene jingwei in Drosophila. Recent genome-wide comparison on young genes of Drosophila has elucidated a compre-hensive picture addressing remarkable roles of various mechanisms besides gene duplication during origin of new genes. Case surveys revealed it is not rare that new genes would evolve novel structures and functions to contribute to the adaptive evolution of organisms.Here, we review recent advances in understanding how new genes originated and evolved on the basis of genome-wide results and ex-perimental efforts on cases, We would finally discuss the future directions of this fast-growing research field in the context of functional genomics era.     

Leaf gas exchange,source–sink relationship,and growth response of cotton to the interactive effects of nitrogen rate and planting density

Nitrogen (N) rate and plant density (PD) are important factors for sustainable cotton production. The objective of this study is to examine the effects of nitrogen rate and plant density on plant growth, source–sink relationship, and cotton yield. A split-plot arrangement was used in the field experiment with the main plots assigned to N rate (120 and 180 kg/ha), and the sub-plots assigned to plant density (8, 10, and 12 plants/m²). Results showed significant N and PD interaction on plant growth, leaf gas exchange, and yield. Higher plant growth and cotton yield were noted under low nitrogen rate and high planting density than other treatment combinations. Leaf photosynthesis, stomatal conductance, intercellular CO₂, transpiration rate, and water use efficiency were considerably influenced by planting density and nitrogen rate. Maximum values of these traits were obtained under low nitrogen rate with high planting density or high nitrogen rate with medium planting density, while the least values were under low nitrogen rate with low planting density. Correlation analysis revealed highly significant and positive relation between leaf gas exchange and cotton yield.     

The effects of gene flow and population isolation on the genetic structure of␣reintroduced wild turkey populations: Are genetic signatures of source populations retained?

To counter losses of genetic diversity in reintroduced populations, species sometimes are reintroduced into networks of populations with the potential to exchange individuals. In reintroduced populations connected by gene flow, patterns of genetic structure initiated by the founding event may become obscured, and populations may eventually follow an isolation-by-distance model of genetic differentiation. Taking advantage of well-documented reintroduction histories of wild turkey populations in Indiana, we assessed the degree to which gene flow among reintroduced populations has obscured genetic signatures left by the founding events. Using a suite of nuclear microsatellite loci and sequence data from the mitochondrial control region, we characterized the level of genetic diversity and degree of genetic structure within and among: (1) reintroduced populations in isolated northern Indiana Fish and Wildlife Areas, (2) reintroduced populations in southern Indiana Fish and Wildlife Areas, where the distribution of populations is more continuous, and (3) source populations used for these reintroductions. We also utilized individual-based assignment tests to determine the relative contribution of source populations to the current distribution of alleles in reintroduced populations. Our results indicate that wild turkey reintroductions in Indiana have left distinct genetic signatures on populations that are detectable even after several decades. Although we found some case-specific evidence for gene flow, particularly in regions where populations are in close proximity, our data indicate on overall paucity of gene flow at a regional scale. Such post-reintroduction genetic monitoring has immediate implications for the design of optimal strategies to reintroduce wildlife for conservation and management.     

Demography in relation to population density in two herbivorous marsupials: testing for source–sink dynamics versus independent regulation of population size

We compared demography of populations along gradients of population density in two medium-sized herbivorous marsupials, the common brushtail possum Trichosurus vulpecula and the rufous bettong Aepyprymnus rufescens, to test for net dispersal from high density populations (acting as sources) to low density populations (sinks). In both species, population density was positively related to soil fertility, and variation in soil fertility produced large differences in population density of contiguous populations. We predicted that if source–sink dynamics were operating over this density gradient, we should find higher immigration rates in low-density populations, and positive relationships of measures of individual fitness—body condition, reproductive output, juvenile growth rates and survivorship—to population density. This was predicted because under source–sink dynamics, immigration from high-density sites would hold population density above carrying capacity in low-density sites. The study included 13 populations of these two species, representing a more than 50-fold range of density for each species, but we found that individual fitness, immigration rates and population turnover were similar in all populations. We conclude that net dispersal from high to low density populations had little influence on population dynamics in these species; rather, all populations appeared to be independently regulated at carrying capacity, with a balanced exchange of dispersers among populations. These two species have suffered recent reductions in range, and they are ecologically similar to other species that have declined to extinction in inland Australia. It has been argued that part of the cause of the vulnerability of species like these is that they exhibit source–sink dynamics, and disturbance to source habitats can therefore cause large-scale population collapses. The results of our study argue against this interpretation.     

Molecular regulation of sink–source transition in rice leaf sheaths during the heading period

The upper leaf sheath of rice (Oryza sativa L.) serves as a temporary starch sink before heading, subsequently becoming a carbon source tissue to the growing panicle at the post-heading stage. The time of sink–source transition in upper leaf sheaths is highly correlated to the panicle exsertion. Here, we found that the expression profiles of starch synthesis genes such as ADP-glucose pyrophosphorylase large subunit 2, granule-bound starch synthase II, soluble starch synthase I, starch branching enzyme (SBE) I, SBEIII, and SBEIV were highly correlated with starch content changes during the heading period in the second leaf sheath below the flag leaf. In addition, the α-amylase2A and β-amylase were considered as major genes that were in charge of starch degradation at the post-heading period. Of the five sucrose transporter (OsSUT) genes, OsSUT1 and OsSUT4 appeared to play an important role in sucrose loading into the phloem of source leaf sheaths. Moreover, the microarray-based data implied that the dominant processes associated with functional leaf sheath transition from sink to source were carbohydrate metabolism and the translocation of the carbon and nitrogen sources and inorganic phosphate.     

Characterization of the effects of inter-tree competition on source–sink balance in Chinese pine trees with the GreenLab model

We investigate the characteristics of individual tree response to competition on source–sink balance through the functional–structural plant model GreenLab. Four Chinese pine (Pinus tabulaeformis Carr.) trees were destructively sampled and were divided into two groups: high-density group and low-density group. First, the effects of density on organ dimensions and on organ relative mass were analysed based on experimental measurements. These were primary indicators of the plant response to competition. Second, the hidden parameters of the GreenLab model, as well as a tree-specific characteristic surface, were estimated using the data of total tree biomass for needle and wood compartments, for each of the four trees in parallel. The quality of the fitting is finally validated using data of individual organ mass at shoot level for the sampled branches. The Mann–Whitney Student’s t test showed that there were significant differences between the shoot attributes of the two groups for shoot diameter, shoot biomass and needle biomass. No significant difference was found for current year shoot lengths of the two groups. The parametric identification of the model allowed estimating and comparing the amount of biomass that was allocated to primary growth and to secondary growth in the two density conditions. It showed that biomass allocated to secondary growth (ring compartment) was the most strongly affected by density, and that the organ demand satisfaction ratio profiles of each of these trees were a relevant, integrated indicator of the tree state.     

Refuge evolution and the population dynamics of coupled host—parasitoid associations

Summary We have investigated the theoretical consequences of character evolution for the population dynamics of a host—parasitoid interaction, assuming a monophagous parasitoid. In the purely ecological model it is assumed that hosts can escape parasitism by being in absolute refuges. A striking property of this model is a threshold effect in control of the host by the parasitoid, when host density dependence is weak. The approximate criteria for the parasitoid to regulate the host to low densities are (1) that the parasitoid's maximum population growth rate should exceed the host's and (2) that the maximum growth rate of the host in the refuge should be less than unity. We then use this ecological framework as a basis for a model which considers evolutionary changes in quantitative characters influencing the size of the absolute refuge. For each species, an increase in its refuge-determining character comes at a cost to maximum population growth rate. We show that refuge evolution can substantially alter the population dynamics of the purely ecological model, resulting in a number of emergent and sometimes counter-intuitive properties. In general, when the host has a high carrying capacity, systems are polarized either with low or minor refuge and top-down control of the host by the parasitoid or with a refuge and bottom-up control of the host by a combination of its own density dependence and the parasitoid. A particularly tantalizing result is that co-evolutionary dynamics can modify ecologically unstable systems into ones which are either stable or quasi-stable (with bouts of unstable dynamics, punctuating long-term periods of quasi-stable behaviour). We present five quantitative criteria which must all be met for the parasitoid to be the agent responsible for control of the host at a co-evolutionary equilibrium. The apparent stringency of this full set of requirements supports the empirically-based suggestion that monophagous parasitoid-driven systems should be less common in nature than those driven by multiple forms of density dependence. Further, we apply our theory to the question of whether exploiters may harvest their victims at maximum sustainable yields and to the evolutionary stability of biological control. Finally, we present a series of testable predictions of our theory and methods useful for testing them.     

Endemic and introduced haplotypes of Batrachochytrium dendrobatidis in Japanese amphibians: sink or source?

The global emergence of the amphibian chytrid pathogen Batrachochytrium dendrobatidis (Bd) is one of the most compelling, and troubling, examples of a panzootic. Only discovered in 1998, Bd is now recognized as a proximate driver of global declines in amphibian diversity and is now widely acknowledged as a key threatening process for this ancient class of vertebrates. Moreover, Bd has become a member of a small group of highly virulent multihost pathogens that are known to have had effects on entire vertebrate communities and the ecosystem‐level effects of Bd‐driven amphibian declines are starting to emerge as a consequence of regional decreases in amphibian diversity. Despite the speed at which this species of aquatic chytrid has become a focus of research efforts, major questions still exist about where Bd originated, how it spreads, where it occurs and what are Bd’s effects on populations and species inhabiting different regions and biomes. In this issue, Goka et al. (2009 ) make an important contribution by publishing the first nationwide surveillance for Bd in Asia. Although previous data had suggested that amphibians in Asia are largely uninfected by Bd, these surveys were limited in their extent and few firm conclusions could be drawn about the true extent of infection. Goka et al. herein describe a systematic surveillance of Japan for both native and exotic species in the wild, as well as amphibians housed in captivity, using a Bd‐specific nested PCR reaction on a sample of over 2600 amphibians. Their results show that Bd is widely prevalent in native species across Japan in at least three of the islands that make up the archipelago, proving for the first time that Asia harbours Bd.     

The North Sea: source or sink for nitrogen and phosphorus to the Atlantic Ocean?

Annual nitrogen and phosphorus budgets for the whole North Sea taking into account the most recent data available were established. The area considered has a total surface of approximately 700,000km² and corresponds to the definition by OSPARCOM (Oslo and Paris Commission) with the exclusion of the Skagerrak and Kattegat areas. Input and output fluxes were determined at the marine, atmospheric, sediment and continental boundaries, and riverine inputs based on river flows and nutrient concentrations at the river–estuary interface were corrected for possible estuarine retention. The results showed that the North Sea is an extremely complex system subjected to large inter-annual variability of marine water circulation and freshwater land run-off. Consequently, resulting total N (TN) and P (TP) fluxes are extremely variable from 1 year to another and this has an important influence on the budget of these elements. Total inputs to the North Sea are 8870±4860kTNyear^–1 and 494±279kTPyear^–1. Denitrification is responsible for the loss of 23±7% of the TN inputs while sediment burial is responsible for the retention of only of 2±2% of the TP input. For TN, due to the large variability on marine and estuarine fluxes, and to the uncertainty related to the denitrification rate, it was concluded that the North Sea could either be a source (1930kTNyear^–1) or a sink (1700kTNyear^–1) for the waters of the North Atlantic Ocean. For TP it was concluded that the North Sea is mostly a source (–4 to 52kTPyear^–1) for the waters of the North Atlantic Ocean.