Fisher's sons’ effect in sexual selection: absent,intermittent or just low experimental power?

The Fisherian sexual selection paradigm has been called the null model of sexual selection. At its heart is the expectation of a genetic correlation (r_G) between female preference and male trait. However, recent meta‐analysis has shown estimated correlations are often extremely weak and not statistically significant. We show here that systematic failure of studies to reject the null hypothesis that r_G = 0 is almost certainly due to the low power of most experimental designs used. We provide an easy way to assess experimental power a priori and suggest that current data make it difficult to definitively test a key component of the Fisher effect.     

Genetic diversity of the endangered Chinese endemic herb Primulina tabacum (Gesneriaceae) revealed by amplified fragment length polymorphism (AFLP)

Primulina tabacum Hance, is a critically endangered perennial endemic to limestone area in South China. Genetic variability within and among four extant populations of this species was assessed using AFLP markers. We expected a low genetic diversity level of this narrowly distributed species, but our results revealed that a high level of genetic diversity remains, both at population level (55.5% of markers polymorphic, H _E = 0.220, I _S = 0.321), and at species level (P = 85.6% of markers polymorphic, H _E = 0.339, I _S = 0.495), probably resulting from its refugial history and/or breeding system. High levels of genetic differentiation among populations was apparent based on Nei’s genetic diversity analysis (G _st=0.350). The restricted gene flow between populations is a potential reason for the high genetic differentiation. The population genetic diversity of P. tabacum revealed here has clear implications for conservation and management. To maintain present levels of genetic diversity, in situ conservation of all populations is necessary.     

ISOLATION AND PARTIAL CHARACTERIZATION OF NITRATE ASSIMILATION MUTANTS OF DUNALIELLA TERTIOLECTA (CHLOROPHYCEAE)1

Fifteen nitrate assimilation-deficient mutants of the euryhaline green alga, Dunaliella tertiolecta Butcher were selected by their chlorate resistance. Ten mutants, unable to grow on NO₃^? but able to grow on NO₂^?, had no detectable nitrate reductase activity. Five mutants, unable to grow on either NO₃^? or NO₂^?, had depressed levels of both nitrate and nitrite reductase. A method for assaying methyl viologen-nitrate reductase in the presence of nitrite reductase is described.     

Low Levels of Genetic Diversity within Populations of Hosta clausa (Liliaceae)

Abstract Genetic diversity of Korean populations in Hosta clausa was investigated using starch gel electrophoresis. Hosta clausa is widespread, grows only along streamsides, and has both sexual and asexual reproduction. Populations of the species are small and isolated. Thirty-two percent of the loci examined were polymorphic, and mean genetic diversity within populations (He_p=0.082) was lower than mean estimates for species with very similar life history characteristics (0.131), particularly for its congener H. yingeri (0.250). The mean number of multilocus genotypes per population was 8.7, and genotypic diversity index (D_G) was 0.84. Significant differences in allele frequencies among populations were found in all seven polymorphic loci (P < 0.001). About one-fifth of the total allozyme variation was among populations (G_ST=0.192). Indirect estimate of the number of migrants per generation (Nm=0.48, calculated from mean G_ST) and nine private alleles found indicate that gene movement among populations was low. The low levels of genetic diversity within populations and the relatively high levels of genetic diversity among populations suggest that strong moist habitat preferences, clonal reproduction, low level of gene flow among populations, genetic drift, and historical events may have played roles in the genetic structuring of the species.     

Morphological differentiation following experimental bottlenecks in the butterfly Bicyclus anynana (Nymphalidae)

The consequences of population bottlenecks for morphological differentiation were investigated experimentally in the Afrotropical butterfly Bicyclus anynana (Satyrinae). A genetically variable laboratory population was used to establish daughter populations differing in the severity of the founding bottleneck (two, six, 20 and c. 300 individuals), with four to six replicate lines per treatment. Nine quantitative traits of the hind wing were measured (wing area and eight wing pattern characters) in the founders, F₁, F₂ and F₃ generations. A tenth character, egg weight, was measured in all lines in F₃. The validity of the neutral additive model was tested by regressing the observed phenotypic variance among replicate lines (V_d) at F₃ against the expected additive genetic variance among lines (2F_tV_A0, where F_t is the coefficient of inbreeding at generation t and V_A0 is the additive genetic variance in the base population). This analysis was performed for the first six principal components of the wing character set, and using two series of F_t estimates, one obtained from demographic parameters, the other from molecular markers. Overall, V_d was slightly less than expected, perhaps as a result of some characters being subject to weak stabilizing selection, but the general picture was one of close concordance with the prediction of the neutral additive model. Plots of phenotypic line means, from the parental generation through to F₃, illustrate that the observed differentiation was essentially entirely due to the initial sampling event. Egg weight showed a similar pattern of differentiation. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 89 , 107–115.     

Genetic effective size,Ne, tracks density in a small freshwater cyprinid,Pecos bluntnose shiner (Notropis simus pecosensis)

Genetic monitoring tracks changes in measures of diversity including allelic richness, heterozygosity and genetic effective size over time, and has emerged as an important tool for understanding evolutionary consequences of population management. One proposed application of genetic monitoring has been to estimate abundance and its trajectory through time. Here, genetic monitoring was conducted across five consecutive year for the Pecos bluntnose shiner, a federally threatened minnow. Temporal changes in allele frequencies at seven microsatellite DNA loci were used to estimate variance effective size (N_eV) across adjacent years in the time series. Likewise, effective size was computed using the linkage disequilibrium method (N_eD) for each sample. Estimates of N_e were then compared to estimates of adult fish density obtained from traditional demographic monitoring. For Pecos bluntnose shiner, density (catch‐per‐unit‐effort), N_eV and N_eD were positively associated across this time series. Results for Pecos bluntnose shiner were compared to a related and ecologically similar species, the Rio Grande silvery minnow. In this species, density and N_eV were negatively associated, which suggested decoupling of abundance and effective size trajectories. Conversely, density and N_eD were positively associated. For Rio Grande silvery minnow, discrepancies among estimates of N_e and their relationships with adult fish density could be related to effects of high variance in reproductive success in the wild and/or effects of supplementation of the wild population with captive‐bred and reared fish. The efficacy of N_e as a predictor of density and abundance may depend on intrinsic population dynamics of the species and how these dynamics are influenced by the landscape features, management protocols and other factors.     

genodive version 3.0: Easy‐to‐use software for the analysis of genetic data of diploids and polyploids

genodive version 3.0 is a user‐friendly program for the analysis of population genetic data. This version presents a major update from the previous version and now offers a wide spectrum of different types of analyses. genodive has an intuitive graphical user interface that allows direct manipulation of the data through transformation, imputation of missing data, and exclusion and inclusion of individuals, population and/or loci. Furthermore, genodive seamlessly supports 15 different file formats for importing or exporting data from or to other programs. One major feature of genodive is that it supports both diploid and polyploid data, up to octaploidy (2n = 8x) for some analyses, but up to hexadecaploidy (2n = 16x) for other analyses. The different types of analyses offered by genodive include multiple statistics for estimating population differentiation (φ_ST, F_ST, F?_ST, G_ST, G?_ST, G??_ST, D_est, R_ST, ρ), analysis of molecular variance‐based K‐means clustering, Hardy–Weinberg equilibrium, hybrid index, population assignment, clone assignment, Mantel test, Spatial Autocorrelation, 23 ways of calculating genetic distances, and both principal components and principal coordinates analyses. A unique feature of genodive is that it can also open data sets with nongenetic variables, for example environmental data or geographical coordinates that can be included in the analysis. In addition, genodive makes it possible to run several external programs (lfmm , structure , instruct and vegan ) directly from its own user interface, avoiding the need for data reformatting and use of the command line. genodive is available for computers running Mac OS X 10.7 or higher and can be downloaded freely from: http://www.patrickmeirmans.com/software .     

Genetic variation in low elevation Douglas-fir of British Columbia and its relevance to gene conservation

Patterns of variation were studied at 20 isozyme loci in 49 coastal, low-elevation Douglas-fir populations in SW British Columbia and NW Washington State. Several components of variation were estimated for each population including the number of alleles per locus N _a, number of alleles per polymorphic locus N _a(95), inbreeding F, heterozygosity H, and population divergence D. F was near zero indicating nearly complete outcrossing within populations. H was quite high (16%) and in aecord with previous studies of Douglas-fir. D values were low (equivalent to Wrights F _ST of 0.08) indicating levels of gene flow sufficient to largely homogenize populations. The parameters of diversity N _a, N _a(95), H, and D showed little intercorrelation across populations. A homogenous pattern of genetic relationship among populations was shown by the clustering of populations based on their inferred relationship, and by the principal components of the matrix of inferred genetic relationship. Because of the complex nature of gene diversity and the continuous nature of population differentiation in Douglas-fir, it is difficult with isozyme markers to identify specific populations of value for genetic conservation in this species.This paper is dedicated to J.C. Heaman on the occasion of his retirement.     

Does natural selection alter genetic architecture? An evaluation of quantitative genetic variation among populations of Allonemobiussocius and A. fasciatus

To make long-term predictions using present quantitative genetic theory it is necessary to assume that the genetic variance–covariance matrix ( G ) remains constant or at least changes by a constant fraction. In this paper we examine the stability of the genetic architecture of two traits known to be subject to natural selection; femur length and ovipositor length in two species of the cricket Allonemobius. Previous studies have shown that in A. fasciatus and A. socius natural selection favours an increased body size southwards but a decreased ovipositor length. Such countergradient selection should tend to favour a change in G . In the total sample of eight populations of A. socius and one of A. fasciatus we show that there is significant variation in all genetic covariance components, i.e. V_A for body size, V_A for ovipositor length, and Cov_A. This variation results entirely from an increase in the covariances of A. fasciatus. However, although larger, these components are approximately proportionally increased, thereby leading to no statistically significant change in the genetic correlation. A proportional increase in the covariance components is consistent with changes resulting from genetic drift. On the other hand, the genetic covariance components are significantly correlated with the length of the growing season suggesting that the change in the genetic architecture is the result of selection and drift.     

Genomewide patterns of variation in genetic diversity are shared among populations,species and higher‐order taxa

Genomewide screens of genetic variation within and between populations can reveal signatures of selection implicated in adaptation and speciation. Genomic regions with low genetic diversity and elevated differentiation reflective of locally reduced effective population sizes (N_e) are candidates for barrier loci contributing to population divergence. Yet, such candidate genomic regions need not arise as a result of selection promoting adaptation or advancing reproductive isolation. Linked selection unrelated to lineage‐specific adaptation or population divergence can generate comparable signatures. It is challenging to distinguish between these processes, particularly when diverging populations share ancestral genetic variation. In this study, we took a comparative approach using population assemblages from distant clades assessing genomic parallelism of variation in N_e. Utilizing population‐level polymorphism data from 444 resequenced genomes of three avian clades spanning 50 million years of evolution, we tested whether population genetic summary statistics reflecting genomewide variation in N_e would covary among populations within clades, and importantly, also among clades where lineage sorting has been completed. All statistics including population‐scaled recombination rate (ρ), nucleotide diversity (π) and measures of genetic differentiation between populations (F_ST, PBS, d_xy) were significantly correlated across all phylogenetic distances. Moreover, genomic regions with elevated levels of genetic differentiation were associated with inferred pericentromeric and subtelomeric regions. The phylogenetic stability of diversity landscapes and stable association with genomic features support a role of linked selection not necessarily associated with adaptation and speciation in shaping patterns of genomewide heterogeneity in genetic diversity.     

The number of breeders explains genetic connectivity in an endangered bird

Connectivity is central to ecology and evolution as it focuses on the movement of individuals or genes across landscapes. Genetic connectivity approaches aim to understand gene flow but often estimate it indirectly based on metrics of genetic differentiation, which can also be affected by other evolutionary forces such as genetic drift. Gene flow and genetic drift are driven by separate ecological mechanisms with potentially differing effects on genetic differentiation and interpretations of genetic connectivity. The ecological mechanisms contributing to gene flow and genetic drift are primarily effective dispersal, or movement followed by successful reproduction, and the number of breeders in a local population, N_b, respectively. Yet, rarely are these ecological mechanisms and genetic connectivity measured simultaneously across landscapes. We examine the roles of effective dispersal and N_b on genetic connectivity across the entire range of the endangered snail kite (Rostrhamus sociabilis plumbeus), between 2006–2015. We find that both N_b and effective dispersal are important predictors of genetic connectivity across this landscape, but that N_b has a 3 × stronger effect on genetic connectivity. Furthermore, N_b is positively correlated with heterozygosity and allelic richness within patches, suggesting a potentially important role of genetic drift, in addition to gene flow, on genetic connectivity. These results emphasize that conservation efforts should focus on not only between‐patch processes of movement but also within‐patch processes regarding habitat quality and local population size for increasing genetic connectivity.     

Hybridization of cultivated Vitis vinifera with wild V. californica and V. girdiana in California

Hybridization of introduced domesticates and closely related natives is well documented in annual crops. The widespread introduction of the domesticated grapevine, Vitis vinifera, into California where it overlaps with two native congenerics, with which it is interfertile, provides opportunity to investigate hybridization between woody perennials. Although geographically widespread, the introduction over the past two centuries has been limited to a few elite clonal cultivars, providing a unique opportunity to study the effects of hybridization on the native species. The amount of hybridization with V. vinifera and the genetic diversity of wild‐growing Vitis californica and Vitis girdiana were examined using nineteen microsatellite markers. STRUCTURE analysis was used to define hybrid and introgressed individuals and to analyze genetic structure of the native species. FAMOZ software was used to identify which V. vinifera cultivars served as parents of F₁ hybrids. The three species were clearly distinguished by STRUCTURE analysis. Thirty percent of 119 V. californica vines were hybrids. The domesticated parent was identified for 16 F₁ hybrid vines; the original California cultivar, ‘Mission’, was the parent of eight. Backcrosses were also found, showing introgression into subsequent generations. Similar results were obtained for a small sample of V. girdiana. Removing hybrids greatly reduced the genetic variation of the presumed pure species, among which there was essentially no genetic structure. Limited genetic variability indicates the California natives may be threatened by genetic erosion. The discovery of F₁ hybrids of ‘Mission’, a cultivar not grown in the areas for ~100 years, suggests long generation times for wild vines that, often, grow into expansive liana and propagate by layering, all factors that limit recruitment in populations already disjunct by habitat lose. Hermaphroditic flowers and fruit that is more attractive to birds may favor the production of backcross seed and establishment of introgressed individuals.     

Plastic and genetic responses of a common sedge to warming have contrasting effects on carbon cycle processes

Climate warming affects plant physiology through genetic adaptation and phenotypic plasticity, but little is known about how these mechanisms influence ecosystem processes. We used three elevation gradients and a reciprocal transplant experiment to show that temperature causes genetic change in the sedge Eriophorum vaginatum. We demonstrate that plants originating from warmer climate produce fewer secondary compounds, grow faster and accelerate carbon dioxide (CO₂) release to the atmosphere. However, warmer climate also caused plasticity in E. vaginatum, inhibiting nitrogen metabolism, photosynthesis and growth and slowing CO₂ release into the atmosphere. Genetic differentiation and plasticity in E. vaginatum thus had opposing effects on CO₂ fluxes, suggesting that warming over many generations may buffer, or reverse, the short‐term influence of this species over carbon cycle processes. Our findings demonstrate the capacity for plant evolution to impact ecosystem processes, and reveal a further mechanism through which plants will shape ecosystem responses to climate change.     

On the Probabilities of Obtaining Negative Estimates of Genetic Variance Components

This paper derives the probabilities of obtaining negative estimates of additive and dominance genetic variances when one uses the traditional weighted least square method for estimating genetic variances as given in MATHER and JINKS (1971). The model considered involves P₁, P₂, F₂, B₁ (Backcross to P₁) and B₂ (Backcross to P₂). The results are derived under the ordinary assumptions as made in the genetic literatures. It is shown that unless the genetic effects are very large and environmental effects small, the probabilities of obtaining negative estimates of additive and dominance variances are in general quite large.     

INCREASED PROBABILITY OF EXTINCTION DUE TO DECREASED GENETIC EFFECTIVE POPULATION SIZE: EXPERIMENTAL POPULATIONS OF CLARKIA PULCHELLA

We established replicated experimental populations of the annual plant Clarkia pulchella to evaluate the existence of a causal relationship between loss of genetic variation and population survival probability. Two treatments differing in the relatedness of the founders, and thus in the genetic effective population size (N_e), were maintained as isolated populations in a natural environment. After three generations, the low N_e treatment had significantly lower germination and survival rates than did the high N_e treatment. These lower germination and survival rates led to decreased mean fitness in the low N_e populations: estimated mean fitness in the low N_e populations was only 21% of the estimated mean fitness in the high N_e populations. This inbreeding depression led to a reduction in population survival: at the conclusion of the experiment, 75% of the high N_e populations were still extant, whereas only 31% of the low N_e populations had survived. Decreased genetic effective population size, which leads to both inbreeding and the loss of alleles by genetic drift, increased the probability of population extinction over that expected from demographic and environmental stochasticity alone. This demonstrates that the genetic effective population size can strongly affect the probability of population persistence.     

<Emphasis Type="Italic">n</Emphasis>-Alkane assimilation and <Emphasis Type="Italic">tert</Emphasis>-butyl alcohol (TBA) oxidation capacity in <Emphasis Type="Italic">Mycobacterium austroafricanum</Emphasis> strains

Mycobacterium austroafricanum IFP 2012, which grows on methyl tert-butyl ether (MTBE) and on tert-butyl alcohol (TBA), the main intermediate of MTBE degradation, also grows on a broad range of n-alkanes (C₂ to C₁₆). A single alkB gene copy, encoding a non-heme alkane monooxygenase, was partially amplified from the genome of this bacterium. Its expression was induced after growth on n-propane, n-hexane, n-hexadecane and on TBA but not after growth on LB. The capacity of other fast-growing mycobacteria to grow on n-alkanes (C₁ to C₁₆) and to degrade TBA after growth on n-alkanes was compared to that of M. austroafricanum IFP 2012. We studied M. austroafricanum IFP 2012 and IFP 2015 able to grow on MTBE, M. austroafricanum IFP 2173 able to grow on isooctane, Mycobacterium sp. IFP 2009 able to grow on ethyl tert-butyl ether (ETBE), M. vaccae JOB5 (M. austroaafricanum ATCC 29678) able to degrade MTBE and TBA and M. smegmatis mc2 155 with no known degradation capacity towards fuel oxygenates. The M. austroafricanum strains grew on a broad range of n-alkanes and three were able to degrade TBA after growth on propane, hexane and hexadecane. An alkB gene was partially amplified from the genome of all mycobacteria and a sequence comparison demonstrated a close relationship among the M. austroafricanum strains. This is the first report suggesting the involvement of an alkane hydroxylase in TBA oxidation, a key step during MTBE metabolism.     

An Experimental Study on the Food Chain Among Bacteria,Paramecium and Daphnia

A quantitative study is made of the feeding of Paramecium caudatum on bacteria and of the feeding of Daphnia pulex on Paramecium and bacteria. The growth yield of P. caudatum on a diet of an unidentified yellow-colored bacterium was about 55% on a dry weight basis. Paramecium would not grow if the concentration of bacteria is less than 1 . 10₇ cells ml. Several other bacterial species were tested. Paramecium could not grow successfully on all of them, but could on Rhodopseudomonas spheroides. Adults of Daphnia pulex could grow and reproduce on a diet of P. caudatum alone, but young grew successfully only when bacteria were present.     

Respiratory inhibitors of a magnetic bacterium Magnetospirillum sp. AMB-1 capable of growing aerobically

Respiratory inhibitors of a magnetic bacterium Magnetospirillum sp. AMB-1, which is able to grow aerobically, were investigated using a microbial electrode system. The respiration of strain AMB-1 was inhibited by 2-heptyl-4-hydroxyquinoline N-oxide (HQNO), KCN and dicumarol. Strain AMB-1 cannot grow in the presence of these inhibitors under aerobic conditions. On the other hand, strain AMB-1 can grow and form magnetite (Fe₃O₄) particles with HQNO and KCN under anaerobic conditions. Growth and magnetite formation of strain AMB-1 were reduced by dicumarol, which also inhibited iron reduction under anaerobic conditions, whereas iron reduction was not inhibited by HQNO and KCN.     

Genetic diversity, gene flow and drift in Bavarian red deer populations (Cervus elaphus)

The red deer (Cervus elaphus) populationof Bavaria in Southern Germany was severelyreduced during the 19th century due toover-hunting. The species has since recoveredwithin designated areas. Subsequent habitatfragmentation presumably has changed thegenetic structure of Bavarian red deer.In order to assess the genetic diversity, weanalysed samples obtained from nine differentBavarian and two adjacent (Thueringen andCzech-Republic) red deer populations,genotyping 19 microsatellite loci. Our analysesrevealed moderate and significant differencesin diversity. Referring to assignment tests,the genetic differentiation of Bavarian reddeer was sufficient to assign an individual'sorigin to the correct population at an averageof 91.6%. The correlation of genetic andgeographic distance matrices revealed noevidence for isolation by distance. Thecoalescent model analysis suggests that thegenetic structure used to be characterized by adrift–gene flow equilibrium and is nowinfluenced by drift and disruption of the geneflow. Only three of the examined populationsshowed a probability of less than 10% that twogenes within these populations share a commonancestor (F _IS-value). Twopopulations had high F _IS values,indicating the influence of drift.Additionally, the intrapopulation indicesrevealed a low variability in thesepopulations. The estimated effective populationsizes (N _e) were generally in thesame range as the actual population sizes. Theinbreeding rates, based on the estimated N _e, and the inbreeding coefficientssuggested that the Bavarian red deerpopulations are in a stable state.