Environmental transition zone and rivers shape intraspecific population structure and genetic diversity of an Amazonian rain forest tree frog

Diversification processes acting across geographically continuous populations have been rarely documented in Amazonia, because of the lack of fine-scale sampling over extensive areas. We aimed to determine the geographic effects of an environmental transition zone and large rivers on the intraspecific population structure of the Manaus slender-legged tree frog (Osteocephalus taurinus) along a ~ 900 km transect of tropical rain forest. Using one mitochondrial (16S), two nuclear genes (TYR, POMC) and three microsatellites, we estimated the population structure, phylogenetic relationships and geographic variation of 262 O. taurinus and 5 O. oophagus (a close relative) along the Purus–Madeira interfluve (PMI) and opposite banks of the central Amazon and upper Madeira rivers, at central-southern Amazonia, Brazil. Six genetic clusters were identified: two corresponding to sympatric populations of O. taurinus and O. oophagus from their type locality, north of Amazon river. Within PMI, there were three distinct O. taurinus genetic clusters distributed along the geographic gradient with one main phylogeographic break found (concordant between 16S and TYR), that corresponds to a transition zone (ecotone) between dense and open rain forest ecotypes. The sixth cluster was an O. taurinus population isolated at the east bank of the upper Madeira river. In addition, restricted haplotype sharing was identified from the west to east banks at upper Madeira river. Within PMI, parapatric genetic structure is explained by a potential association of the genetic clusters to the different forest ecotypes they inhabit coupled with isolation by distance, thus supporting the gradient hypothesis for diversification. Differentiation of populations that are external to the PMI is most likely explained by the barrier effect of the Madeira and Amazon rivers. Our findings provide new evidence on diversification processes across continuous Amazonian landscapes; however, the specific mechanisms underlying the origin and maintenance of the identified phylogeographic break need to be further studied.     

Strong intraspecific variation in genetic diversity and genetic differentiation in Daphnia magna: the effects of population turnover and population size

Theory predicts that genetic diversity and genetic differentiation may strongly vary among populations of the same species depending on population turnover and local population sizes. Yet, despite the importance of these predictions for evolutionary and conservation issues, empirical studies comparing high‐turnover and low‐turnover populations of the same species are scarce. In this study, we used Daphnia magna, a freshwater crustacean, as a model organism for such a comparison. In the southern/central part of its range, D. magna inhabits medium‐sized, stable ponds, whereas in the north, it occurs in small rock pools with strong population turnover. We found that these northern populations have a significantly lower genetic diversity and higher genetic differentiation compared to the southern/central populations. Total genetic diversity across populations was only about half and average within‐population diversity only about a third of that in southern/central populations. Moreover, an average southern population contains more genetic diversity than the whole metapopulation system in the north. We based our analyses both on silent sites and microsatellites. The similarity of our results despite the contrasting mutation rates of these markers suggests that the differences are caused by contemporary rather than by historical processes. Our findings show that variation in population turnover and population size may have a major impact on the genetic diversity and differentiation of populations, and hence may lead to differences in evolutionary processes like local adaptation, hybrid vigour and breeding system evolution in different parts of a species range.     

Environmental DNA analysis shows high potential as a tool for estimating intraspecific genetic diversity in a wild fish population

Environmental DNA (eDNA) analysis has recently been used as a new tool for estimating intraspecific diversity. However, whether known haplotypes contained in a sample can be detected correctly using eDNA‐based methods has been examined only by an aquarium experiment. Here, we tested whether the haplotypes of Ayu fish (Plecoglossus altivelis altivelis) detected in a capture survey could also be detected from an eDNA sample derived from the field that contained various haplotypes with low concentrations and foreign substances. A water sample and Ayu specimens collected from a river on the same day were analysed by eDNA analysis and Sanger sequencing, respectively. The 10 L water sample was divided into 20 filters for each of which 15 PCR replications were performed. After high‐throughput sequencing, denoising was performed using two of the most widely used denoising packages, unoise3 and dada2 . Of the 42 haplotypes obtained from the Sanger sequencing of 96 specimens, 38 (unoise3 ) and 41 (dada2 ) haplotypes were detected by eDNA analysis. When dada2 was used, except for one haplotype, haplotypes owned by at least two specimens were detected from all the filter replications. Accordingly, although it is important to note that eDNA‐based method has some limitations and some risk of false positive and false negative, this study showed that the eDNA analysis for evaluating intraspecific genetic diversity provides comparable results for large‐scale capture‐based conventional methods. Our results suggest that eDNA‐based methods could become a more efficient survey method for investigating intraspecific genetic diversity in the field.     

Inbreeding effects on pair fecundity and population persistence

Despite strong empirical evidence of the harmful effects of inbreeding on fecundity, spontaneous recessive deleterious mutations are generally considered as acting on survival only in evolutionary models and population viability analyses. In this study, we modelled a species with separate sexes to assess the effect of selection on fecundity in small populations on the risk of extinction. We showed that the impact of inbreeding on short-term fitness changes and that population dynamics are strongly influenced by phenotypic interactions among males and females during reproduction. In particular, population persistence was found to be highly sensitive to the level at which selection acts (i.e. individual vs. pair) and to asymmetry among sexes (in terms of mutation rates and mutational effects).  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 86 , 467–476.     

Effects on population persistence: the interaction between environmental noise colour,intraspecific competition and space

It is accepted that accurate estimation of risk of population extinction, or persistence time, requires prediction of the effect of fluctuations in the environment on population dynamics. Generally, the greater the magnitude, or variance, of environmental stochasticity, the greater the risk of population extinction. Another characteristic of environmental stochasticity, its colour, has been found to affect population persistence. This is important because real environmental variables, such as temperature, are reddened or positively temporally autocorrelated. However, recent work has disagreed about the effect of reddening environmental stochasticity. Ripa and Lundberg (1996) found increasing temporal autocorrelation (reddening) decreased the risk of extinction, whereas a simple and powerful intuitive argument (Lawton 1988) predicts increased risk of extinction with reddening. This study resolves the apparent contradiction, in two ways, first, by altering the dynamic behaviour of the population models. Overcompensatory dynamics result in persistence times increasing with increased temporal autocorrelation; undercompensatory dynamics result in persistence times decreasing with increased temporal autocorrelation. Secondly, in a spatially subdivided population, with a reasonable degree of spatial heterogeneity in patch quality, increasing temporal autocorrelation in the environment results in decreasing persistence time for both types of competition. Thus, the inclusion of coloured noise into ecological models can have subtle interactions with population dynamics.     

Environmental fluctuations,productivity, and species diversity: An experimental study

Seemingly opposing hypotheses concerning the effects of environmental fluctuations on species diversity were shown to complement one another. Studies were made on naturally occurring microbial communities growing in continuous cultures, under both low and high productivity levels. The communities consisted of species of bacteria, protozoan flagellates, and protozoan predators (sarcodinians and ciliates). Fluctuations were imposed by periodically removing a portion of the culture and refilling with sterilized medium. They were designed to mimic the effect of fluctuations periodically decreasing the demand/supply ratio of the community for the available resources. It was found that when growth rates were low (either because of low productivity levels or because of low intrinsic growth rates of the organisms concerned), fluctuations decreased species diversity, whereas when growth rates were high, fluctuations increased species diversity. It is suggested that fluctuations decrease diversity when growth rates are low because they prevent slower growing species from surviving, and increase diversity when growth rates are high because they decrease the extent of competitive domination and exclusion.     

Increasing intraspecific diversity increases predictability in population survival in the face of perturbations

It has been proposed that biodiversity can be important for ecosystem functioning and act as an insurance against perturbations and environmental fluctuations. To date, theoretical work supports this idea but direct experimental evidence is still to some extent ambiguous and debated. The main reason for this debate – and the lack of strong empirical support – is due to unavoidable experimentally and statistically inherent variance reduction effects. Here we present the results of an experimental study that circumvents earlier hidden treatments. By random draw without replacement, we collected 180 full-sibling batches of an amphipod from a large pool of possible parents. Assembled amphipod populations with diversity levels ranging from one to ten were exposed to either a single perturbation (nutrient enrichment) or two combined perturbations (nutrient enrichment and desiccation). The results show that the variance in the number of surviving individuals decreased with increasing diversity in the combined perturbations treatment. Predictability in population survival thus seemed to be higher in more diverse assemblages. Our results, together with a simple model suggest that variance-decreasing effects can be due to actual real world statistical sampling effects of increasing diversity.     

Environmental fluctuations and the maintenance of genetic diversity in age or stage-structured populations

The ability of random fluctuations in selection to maintain genetic diversity is greatly increased when generations overlap. This result has been derived previously using genetic models with very special assumptions about the population age structure. Here we explore its robustness in more realistic population models, with very general age structure or physiological structure. For a range of genetic models (haploid, diploid, single and multilocus) we find that the condition for maintaining genetic diversity generalizes almost without change. Genetic diversity is maintained by selection if a product of the form (generation overlap)×(selection intensity)×(variability in the selection regime) is sufficiently large, where the generation overlap is measured in units of Fisher's reproductive value. This conclusion is based on a local evolutionary stability analysis, which differs from the standard “protected polymorphism” criterion for the maintenance of genetic diversity. Simulation results match the predictions from the local stability analysis, but not those from the protected polymorphism criterion. The condition obtained here for maintaining genetic diversity requires fitness fluctuations that are substantial but well within the range observed in many studies of natural populations.     

Low intraspecific diversity in a polynucleobacter subcluster population numerically dominating bacterioplankton of a freshwater pond

Cultivation-dependent and -independent methods were combined to investigate the microdiversity of a Polynucleobacter subcluster population (Betaproteobacteria) numerically dominating the bacterioplankton of a small, humic freshwater pond. Complete coverage of the population by cultivation allowed the analysis of microdiversity beyond the phylogenetic resolution of ribosomal markers. Fluorescent in situ hybridization with two probes specific for the narrow subcluster C (PnecC bacteria) of the Polynucleobacter cluster revealed that this population contributed up to 60% to the total number of bacterioplankton cells. Microdiversity was investigated for a date at which the highest relative numbers of PnecC were observed. A clone library of fragments of the ribosomal operon (16S rRNA genes, complete 16S-23S internal transcribed spacer 1 [ITS1], partial 23S rRNA genes) amplified with universal bacterial primers was constructed. The library was stepwise screened for fragments from PnecC bacteria and for different ITS genotypes of PnecC bacteria. The isolated PnecC strains were characterized by sequencing of the 16S rRNA genes and the ITS1. Both the clone library and the established culture collection contained only the same three ITS genotypes, and one of them contributed 46% to the entire number of clones. Genomic fingerprinting of the isolates with several methods always resulted in the detection of only one fingerprint per ITS genotype. We conclude that a Polynucleobacter population with an extremely low intraspecific diversity and an uneven structure numerically dominated the bacterioplankton community in the investigated habitat. This low intraspecific diversity is in strong contrast to the high intraspecific diversities found in marine bacterial populations.     

Quantitative evaluation of intraspecific genetic diversity in a natural fish population using environmental DNA analysis

Recent advances in environmental DNA (eDNA) analysis using high‐throughput sequencing (HTS) enable evaluation of intraspecific genetic diversity in a population. As the intraspecific genetic diversity provides invaluable information for wildlife conservation and management, there is an increasing demand to apply eDNA analysis to population genetics and the phylogeography by quantitative evaluation of intraspecific diversity. However, quantitative evaluations of intraspecific genetic diversity using eDNA is not straightforward because the number of eDNA sequence reads obtained by HTS may not be an index of the quantity of eDNA. In this study, to quantitatively evaluate genetic diversity using eDNA analysis, we applied a quantitative eDNA metabarcoding method using the internal standard DNAs. We targeted Ayu (Plecoglossus altivelis altivelis) and added internal standard DNAs with known copy numbers to each eDNA sample obtained from three rivers during the library preparation process. The sequence reads of each Ayu haplotype were successfully converted to DNA copy numbers based on the relationship between the copy numbers and sequence reads of the internal standard DNAs. In all rivers, the calculated copy number of each haplotype showed a significant positive correlation with the haplotype frequency estimated by a capture‐based survey. Furthermore, estimates of genetic indicators such as nucleotide diversity based on the eDNA copy numbers were comparable with those estimated based on a capture‐based study. Our results demonstrate that eDNA analysis with internal standard DNAs enables reasonable quantification of intraspecific genetic diversity, and this method could thus be a promising tool in the field of population genetics and phylogeography.     

Landscape effects on temporal and spatial properties of vole population fluctuations

Populations of northern small rodents have previously been observed to fluctuate in spatial synchrony over distances ranging from tens to hundreds of kilometers between sites. It has been suggested that this phenomenon is caused by common environmental perturbations, mobile predators or dispersal movements. However, very little focus has been given to how the physical properties of the geographic area over which synchrony occurs, such as landscape composition and climate, affect spatial population dynamics. This study reports on the spatial and temporal properties of vole population fluctuations in two areas of western Finland: one composed of large interconnected areas of agricultural farmland interspersed by forests and the other highly dominated by forest areas, containing more isolated patches of agricultural land. Furthermore, the more agricultural area exhibits somewhat milder winters with less snow than the forested area. We found the amplitude of vole cycles to be essentially the same in the two areas, suggesting that the relative amount of predation on small rodents by generalist versus specialist predators is similar in both areas. No seasonal differences in the timing of synchronization were observable for Microtus voles, whereas bank vole populations in field habitats appeared to become synchronized primarily during winter. Microtus populations in field habitats exhibited smaller spatial variation and a higher degree of synchrony in the more continuous agricultural landscape than in the forest-dominated landscape. We suggest that this inter-areal difference is due to differences in the degree of inter-patch connectivity, with predators and dispersal acting as the primary synchronizing agents. Bank vole populations in field habitats were more synchronized within the forest-dominated landscape, most likely reflecting the suitability of the inter-patch matrix and the possibility of dispersal. Our study clearly indicates that landscape composition needs to be taken into account when describing the spatial properties of small rodent population dynamics.     

Black noise and population persistence

Biological populations are susceptible to random variation in environmental influences such as temperature and moisture. This variability (or noise) can determine population size and, ultimately, cause extinctions. Extinction risk depends on noise colour or the amount of short- and long-term variation. Most environmental noise is reddened: the variation is dominated by long-term fluctuations. Recent modelling has shown that moderately reddened noise affects populations differently from the white noise used in earlier studies. However, some geophysical phenomena, such as temperature and river height, can have deeply reddened ''brown'' or even ''black'' spectra. We find that, compared to environments characterized by red noise, very long population persistence times are more likely for black noise. Unlike previous work incorporating a simple autoregressive model of reddened noise, our model suggests that the large variation associated with persistence in a red-noise environment limits our ability to predict the fate of particular populations subject to this noise colour. Thus, we identify the colour of noise experienced by a population (red or black) as a crucial factor in any attempt to manage or conserve that population.     

Global Salmonidae introductions reveal stronger ecological effects of changing intraspecific compared to interspecific diversity

The introduction of organisms within the native range of wild conspecifics is a widespread phenomenon and locally modifies patterns in intraspecific diversity. However, our knowledge of the resulting ecological effects, as opposed to those caused by invasion‐induced changes in interspecific diversity, is still limited. Here, we investigated the ecological effects of native and non‐native invaders across levels of biological organisations and recipient organisms using the global and long history introductions of salmonids. Our meta‐analysis demonstrated that the global effects of native species introductions exceeded those induced by non‐native invaders. The impacts of native invaders were primarily manifested at the individual level on wild conspecifics, but remained largely unexplored on other native organisms and at the community and ecosystem levels. Overlooked and poorly appreciated, quantifying the impacts of native invaders has important implications because human‐assisted introductions of domesticated organisms are ubiquitous and likely to proliferate in the future.     

Small rodent population fluctuations: The effects of age structure and seasonality

Despite more than 50 years of effort, the causes and mechanisms of small rodent population fluctuations remain unknown. The two major questions are as follows: (1) what is the cause of population decline and (2) what is the cause of cyclicity and its geographical variation? At present, no hypothesis can provide answers to both these questions. Recently, progress has been made by Boonstra (1994), who proposed the senescence hypothesis to explain the cause of cyclic decline in population numbers. Here, we tested the main prediction that voles in decline are older than in other phases of the cycle, by analysing changes in age structure in a fluctuating population of the bank vole (Clethrionomys glareolus). The results generally support this prediction; however, the differences in absolute age seem to be too small to explain the occurrence of senescent animals exclusively in declines. We propose a new model to explain changes in age structure and the mechanisms behind the decline and geographic variation in cyclicity. It is based on the idea that voles are oldest in declines, developed independently of Boonstra. However, it differs in three respects: (1) it is more general and thereby applicable to the whole cycle; (2) density-dependent changes in age structure are based on the bimodality in a female's age at first reproduction; and (3) it stresses developmental rather than physiological changes in the quality of decline of animals as being relevant to the rate of senescence. We propose that seasonality of the environment is a principal candidate to explain geographical variation in cyclicity. We present substantial theoretical and empirical evidence to indicate that in more seasonal environments with shortened vegetation periods, population dynamics is inevitably less stable due to increased variation in two critical parameters – age at first reproduction and the length of the breeding season – which determine population growth rates. Any external perturbation may then easily destabilize population numbers. The general applicability of the seasonality-senescence hypothesis to other mammalian species decreases with declining r and increasing life span. The hypothesis is falsifiable, and testable predictions are provided.     

橙腹田鼠中延缓性密度依赖效应和种群波动

检验了延迟的密度依赖对橙腹田鼠 (Microtusochrogaster)一个波动种群的生存和生殖的影响 ,研究持续了 63个月 ,取样间隔为 3 5天。在研究期间 ,该种群的密度经历了 4次波动 ,每次波动的高峰都在 11月至次年 1月 ,种群数量在冬季下降。生存和生殖都有负面的密度依赖效应 ,最大效应具有 2个月的时滞。种群存活率增长对种群密度最大的正面效应具有 2个月的时滞 ,而对与增加生殖则有 3个月的时滞。内部因素和冬季都可能推延对生殖的密度依赖效应 ,但是本文未能检验这些内部因素的影响。季节性影响看来与对生存的延缓性密度依赖效应无关。负面的延缓性密度依赖效应对生存和生殖的净作用可能在于减少、而不是阻止橙腹田鼠种群波动的幅度     

Stochastic density effects on adult fish survival and implications for population fluctuations

The degree to which population fluctuations arise from variable adult survival relative to variable recruitment has been debated widely for marine organisms. Disentangling these effects remains challenging because data generally are not sufficient to evaluate if and how adult survival rates are regulated by stochasticity and/or population density. Using unique time series for a largely unexploited reef fish, we found both population density and stochastic food supply impacted adult survival. The estimated effect of variable survival on adult abundance (both mean and variability) rivalled that of variable recruitment. Moreover, we show density‐dependent adult survival can dampen impacts of stochastic recruitment. Thus, food variability may alter population fluctuations by simultaneously regulating recruitment and compensatory adult survival. These results provide an additional mechanism for why intensified density‐independent mortality (via harvest or other means) amplifies population fluctuations and emphasises need for research evaluating the causes and consequences of variability in adult survival.     

Climate effects on population fluctuations of the white-throated dipper Cinclus cinclus

1. Climate change may have profound consequences for many organisms. We have studied fluctuations in a population of the white-throated dipper Cinclus cinclus during 31 years (1978-2008) in a river system in southern Norway in relation to both large-scale and local weather conditions occurring during the non-breeding season. 2. Multiple regression and partial least squares regression were used to model the growth rate of the population, accounting for population size in the previous year. 3. Population growth was influenced by North Atlantic Oscillation (NAO), mean winter temperature, precipitation and timing of ice formation on the main lake in the river system in autumn. These variables explained 84% of the variation in population growth over the 31-year study period. 4. Local winter conditions played a prominent role in explaining the population fluctuations, which is plausible because the dipper depends on open water for foraging. In the study area, winters can be harsh and rivers and lakes may freeze and severely affect the subsequent population size of the dipper in spring. 5. The breeding population of the dipper does not seem yet to have reached a level where all possible territories in the area have been occupied, even after mild winters, and the estimated carrying capacity is also decidedly lower (66 breeding pairs) than the number of available territories. If the trend of milder winters continues, the population might increase in the future. However, strong climate variation is expected to continue in the future, and hence periods of rapid growth of the dipper population will probably be followed by severe declines.     

Lysophosphatidic acid receptor-dependent secondary effects via astrocytes promote neuronal differentiation

Lysophosphatidic acid (LPA) is a simple phospholipid derived from cell membranes that has extracellular signaling properties mediated by at least five G protein-coupled receptors referred to as LPA(1)-LPA(5). In the nervous system, receptor-mediated LPA signaling has been demonstrated to influence a range of cellular processes; however, an unaddressed aspect of LPA signaling is its potential to produce specific secondary effects, whereby LPA receptor-expressing cells exposed to, or "primed," by LPA may then act on other cells via distinct, yet LPA-initiated, mechanisms. In the present study, we examined cerebral cortical astrocytes as possible indirect mediators of the effects of LPA on developing cortical neurons. Cultured astrocytes express at least four LPA receptor subtypes, known as LPA(1)-LPA(4). Cerebral cortical astrocytes primed by LPA exposure were found to increase neuronal differentiation of cortical progenitor cells. Treatment of unprimed astrocyte-progenitor cocultures with conditioned medium derived from LPA-primed astrocytes yielded similar results, suggesting the involvement of an astrocyte-derived soluble factor induced by LPA. At least two LPA receptor subtypes are involved in LPA priming, since the priming effect was lost in astrocytes derived from LPA receptor double-null mice (LPA(1)((-/-))/LPA(2)((-/-))). Moreover, the loss of LPA-dependent differentiation in receptor double-null astrocytes could be rescued by retrovirally transduced expression of a single deleted receptor. These data demonstrate that receptor-mediated LPA signaling in astrocytes can induce LPA-dependent, indirect effects on neuronal differentiation.