Dryad Data Packages

Data from: The robustness and restoration of a network of ecological networks

Fri, 24 Feb 2012 16:11:21 GMT

Understanding species’ interactions and the robustness of interaction networks to species loss is essential to understand the effects of species’ declines and extinctions. In most studies, different types of networks (such as food webs, parasitoid webs, seed dispersal networks, and pollination networks) have been studied separately. We sampled such multiple networks simultaneously in an agroecosystem. We show that the networks varied in their robustness; networks including pollinators appeared to be particularly fragile. We show that, overall, networks did not strongly covary in their robustness, which suggests that ecological restoration (for example, through agri-environment schemes) benefitting one functional group will not inevitably benefit others. Some individual plant species were disproportionately well linked to many other species. This type of information can be used in restoration management, because it identifies the plant taxa that can potentially lead to disproportionate gains in biodiversity.

Data from: Evidence for selection at cytokine loci in a natural population of field voles (Microtus agrestis)

Tue, 13 Dec 2011 18:02:33 GMT

Individuals in natural populations are frequently exposed to a wide range of pathogens. Given the diverse profile of gene products involved in responses to different types of pathogen, this potentially results in complex pathogen-specific selection pressures acting on a broad spectrum of immune system genes in wild animals. Thus far, studies into the evolution of immune genes in natural populations have focused almost exclusively on the Major Histocompatibility Complex (MHC). However, the MHC represents only a fraction of the immune system and there is a need to broaden research in wild species to include other immune genes. Here we examine the evidence for natural selection in a range of non-MHC genes in a natural population of field voles (Microtus agrestis). We concentrate primarily on genes encoding cytokines, signaling molecules critical in eliciting and mediating immune responses, and identify signatures of natural selection acting on several of these genes. In particular, genetic diversity within Interleukin 1 beta and Interleukin 2 appears to have been maintained through balancing selection. Taken together with previous findings that polymorphism within these genes is associated with variation in resistance to multiple pathogens, this suggests that pathogen-mediated selection may be an important force driving genetic diversity at cytokine loci in voles and other natural populations. These results also suggest that, along with the MHC, preservation of genetic variation within cytokine genes should be a priority for the conservation genetics of threatened wildlife populations.

Data from: High-throughput microsatellite marker development in two sparid species and verification of their transferability in the family Sparidae

Fri, 24 Feb 2012 17:00:26 GMT

Recently 454 sequencing has emerged as a popular method for isolating microsatellites due to cost effectiveness and time saving. In this study, repeat enriched libraries from two southern African endemic sparids (Pachymetopon blochii and Lithognathus lithognathus) were 454 GS-FLX sequenced. From these, 7 370 sequences containing repeats were identified. A brief survey of 23 studies showed a significant difference between the number of sequences containing repeats (SCR) when enrichment was done first before 454 sequencing. We designed primers for 302 unique fragments containing more than five repeat units and suitable flanking regions. A fraction (<11%) of these loci were characterised with 18 polymorphic microsatellite loci (nine in each of the focal species) being described. Sanger sequencing of alleles confirmed that size variation was due to differences in the number of tandem repeats. However, a case of homoplasy and sequencing errors in the 454 sequencing were identified. These newly developed and four previously isolated loci were successfully used to identify polymorphic markers in nine other economically important species, representative of sparid diversity. The combination of newly developed markers with data from previous sparid cross-species studies showed a significant negative correlation between genetic divergence to focal species and microsatellite transferability. The high level of transferability we described (56% amplification success, 32% polymorphism) suggests that the 302 microsatellite loci identified represents an excellent resource for future studies on sparids. Microsatellite marker development should commonly include tests of transferability to reduce costs and increase feasibility of population genetics studies in non-model organisms.

Data from: Host-jump drives rapid and recent ecological speciation of the emergent fungal pathogen Colletotrichum kahawae

Fri, 24 Feb 2012 17:27:47 GMT

Ecological speciation through host-shift has been proposed as a major route for the appearance of novel fungal pathogens. The growing awareness of their negative impact on global economies and public health created an enormous interest in identifying the factors that are most likely to promote their emergence in nature. In this work, a combination of pathological, molecular and geographic data was used to investigate the recent emergence of the fungus Colletotrichum kahawae (Ck). Ck emerged as a specialist pathogen causing Coffee Berry Disease in Coffea arabica, due to its unparalleled adaptation of infecting green coffee berries. Contrary to current hypotheses, our results suggest that a recent host-jump underlay the speciation of Ck from a generalist group of fungi seemingly harmless to coffee berries. We posit that immigrant inviability and a predominantly asexual behavior could have been instrumental in driving speciation by creating pleiotropic interactions between local adaptation and reproductive patterns. Moreover, we estimate that Ck began its diversification at less than 2,200 yrs leaving a very short time frame since the divergence from its sibling lineage (∼5,600 yrs), during which a severe drop in Ck’s effective population size occurred. This further supports a scenario of recent introduction and subsequent adaptation to C. arabica. Phylogeographic data revealed low levels of genetic polymorphism but provided the first geographically consistent population structure of Ck, inferring the Angolan population as the most ancestral and the East African populations as the most recently derived. Altogether, these results highlight the significant role of host specialization and asexuality in the emergence of fungal pathogens through ecological speciation.

Data from: DNA-based analysis of regurgitates: a non-invasive approach to examine the diet of invertebrate consumers

Fri, 24 Feb 2012 17:42:39 GMT

DNA-based gut content analysis has become an important tool for unravelling feeding interactions in invertebrate communities under natural conditions. It usually implies killing of the consumer and extracting the DNA from its food, either using the whole animal or its dissected gut. This post-mortem approach, however, is not suitable for investigating the diet of rare or protected species and also prohibits tracking individual dietary preferences as each consumer can provide trophic information only once. Moreover, removing large numbers of consumers from a habitat for analysis might critically change population densities and affect species interactions. Here, we present DNA-based analysis of invertebrate regurgitates, a novel approach to overcome these limitations. Conducting feeding experiments where adult Poecilus cupreus (Coleoptera: Carabidae) were fed with larvae of Amphimallon solstitiale (Coleoptera: Scarabaeidae), we show that detection success in regurgitates compared to samples prepared from whole beetles was similar or significantly enhanced for small/medium and large prey DNA fragments, respectively. Prey DNA detection success remained high in regurgitates stored in ethanol for 21 months at room temperature prior to DNA extraction. We conclude that in those invertebrates where regurgitates can be obtained, examination of food DNA in regurgitates offers many advantages over conventional post-mortem gut content analysis.

Data from: Why do so few patients with heart failure participate in cardiac rehabilitation? A cross-sectional survey from England, Wales and Northern Ireland

Fri, 24 Feb 2012 18:00:32 GMT

OBJECTIVES: To determine why so few patients with chronic heart failure in England, Wales, and Northern Ireland take part in cardiac rehabilitation. DESIGN: Two-stage, postal questionnaire-based, national survey. PARTICIPANTS AND SETTING: Stage 1: 277 cardiac rehabilitation centres in England, Wales, and Northern Ireland registered on the National Audit of Cardiac Rehabilitation register in 2009–10. Stage 2: 35 centres that indicated in stage 1 that they provide a separate cardiac rehabilitation programme for patients with heart failure. RESULTS: Full data were available for 224/277 (81%) cardiac rehabilitation centres. Only 90/224 (40%) routinely offered phase 3 cardiac rehabilitation to patients with heart failure. Of these 90 centres that offered rehabilitation, 43% did so only when heart failure was secondary to myocardial infarction or revascularisation. Less than half (39%) had a specific rehabilitation programme for heart failure. Of those not providing for patients with heart failure, 134/224 (60%) considered a lack of resources and 89/224 (40%) exclusion from commissioning contracts as the reason for not recruiting patients with heart failure. Overall, only 35/224 (16%) centres provided a separate rehabilitation programme for people with heart failure. CONCLUSION: Patients with heart failure as a primary diagnosis are excluded from most cardiac rehabilitation programmes in England, Wales, and Northern Ireland. A lack of resources and direct exclusion from local commissioning agreements are the main barriers for not offering rehabilitation to patients with heart failure.

Data from: Species and phylogenetic nomenclature

Fri, 24 Feb 2012 21:48:29 GMT

The motivation for the development of phylogenetic nomenclature (originally called “phylogenetic taxonomy”) was to allow biological classification (or “systematization”) to represent phylogenetic relationships, and to embody important principles such as “the untenability of paraphyletic groups” (de Queiroz and Gauthier 1990). From this starting point de Queiroz and Gauthier developed a creative new basis for systematization in which the entities are not ranked taxa but clades (de Queiroz and Gauthier 1990, 1992, 1994; de Queiroz 1992, 1994). Instead of attaching names to taxa by reference to a type and a rank, as in traditional biological nomenclature, phylogenetic nomenclature labels taxa by the use of multiple “specifiers” – specimens or apomorphic traits that unambiguously refer to a particular monophyletic taxon. The subsequent development of phylogenetic nomenclature included formation of a scholarly society, the International Society for Phylogenetic Nomenclature, and development of a formal Code, the PhyloCode (http://www.phylocode.org), that is now in final preparation for publication at University of California Press. The hope for many phylogenetic systematists was for a new system of nomenclature that would firmly connect taxonomy to phylogeny and would allow for more stable ways to name the many significant clades that make up the Tree of Life. However, a major challenge for the development of the PhyloCode has been the treatment of species. We argue in this paper that the approach taken to species in the PhyloCode is at odds with the motivations that drove many to support phylogenetic nomenclature and that these problems should be fixed before the PhyloCode is published and officially implemented.

Data from: Life history change in response to fishing and an introduced predator in the East African cyprinid Rastrineobola argentea

Thu, 12 Jan 2012 16:19:42 GMT

Fishing and introduced species are among the most important stressors affecting freshwaters, and can be important selective agents. We examined the combined effects of commercial fishing and an introduced predator (Nile perch, Lates niloticus) on life history traits in an African cyprinid fish (Rastrineobola argentea) native to the Lake Victoria basin in East Africa. To understand whether these two stressors have driven shifts in life history traits of R. argentea, we tested for associations between life history phenotypes and the presence/absence of stressors both spatially (across 10 Ugandan lakes) and temporally (over 4 decades in Lake Victoria). Overall, introduced Nile perch and fishing tended to be associated with a suite of life history responses in R. argentea, including: decreased body size, maturation at smaller sizes, and increased reproductive effort (larger eggs; and higher relative fecundity, clutch volume, and ovary weight). This is one of the first well-documented examples of fisheries-induced phenotypic change in a tropical, freshwater stock; the magnitude of which raises some concerns for the long-term sustainability of this fishery, now the most important (by mass) in Lake Victoria.

Data from: Evolutionary dynamics of separate and combined exposure of Pseudomonas fluorescens SBW25 to antibiotics and bacteriophage

Fri, 20 Jan 2012 15:48:00 GMT

The use of bacteriophages against pathogenic bacteria in health care and in the food industry is now being advocated as an alternative to the use of antibiotics. But what is the evolutionary response for a bacterial population if both antibiotics and phages are used in combination? We employ an experimental evolution approach to address these questions and exposed Pseudomonas fluorescens SBW25 and a related hypermutator strain (mutS-) to the action of the antibiotic rifampicin and the lytic bacteriophage SBW25φ2. We then compared the densities, growth rates, and the mutations at the rpoB locus leading to rifampicin resistance of the evolved bacterial populations. We observed that the evolutionary response of populations under different treatments varied depending on the order in which the antimicrobials were added and whether the bacterium was a hypermutator. We found that wild type rifampicin-resistant populations involved in biofilm formation often reverted to rifampicin sensitivity when stresses were added sequentially. In contrast, when the mortality agents were added simultaneously, phage populations frequently went extinct and the bacteria evolved antibiotic resistance. Finally, populations of the hypermutator mutS- converged to a single genotype at the rpoB locus. Future investigation on other bacteria and using different antibiotics and bacteriophage are needed to evaluate the generality of our findings.

Data from: Genetic signature of adaptive peak shift in threespine stickleback

Thu, 23 Feb 2012 20:39:50 GMT

Transition of an evolving population to a new adaptive optimum is predicted to leave a signature in the distribution of effect sizes of fixed mutations. If they affect many traits (are pleiotropic), large effect mutations should contribute more when a population evolves to a farther adaptive peak than to a nearer peak. We tested this prediction in wild threespine stickleback fish (Gasterosteus aculeatus) by comparing the estimated frequency of large effect genetic changes underlying evolution as the same ancestor adapted to two lake types since the end of the ice age. A higher frequency of large effect genetic changes (quantitative trait loci) contributed to adaptive evolution in populations that adapted to lakes representing a more distant optimum than to lakes in which the optimum phenotype was nearer to the ancestral state. Our results also indicate that pleiotropy, not just optimum overshoot, contributes to this difference. These results suggest that a series of adaptive improvements to a new environment leaves a detectable mark in the genome of wild populations. Although not all assumptions of the theory are likely met in natural systems, the prediction may be robust enough to the complexities of natural environments to be useful when forecasting adaptive responses to large environmental changes.

Data from: On-farm dynamic management of genetic diversity: the impact of seed diffusions and seed saving practices on a population-variety of bread wheat

Thu, 23 Feb 2012 20:50:25 GMT

Since the domestication of crop species, humans have derived specific varieties for particular uses, and shaped the genetic diversity of these varieties. Here, using an interdisciplinary approach combining ethnobotany and population genetics, we document the within-variety genetic structure of a population-variety of bread wheat (Triticum aestivum L.) in relation to farmers practices to decipher their contribution to crop species evolution. Using 19 microsatellites markers, we conducted two complementary graph theory-based methods to analyze population structure and gene flow among 19 sub-populations of a single population-variety (Rouge de Bordeaux, RDB). The ethnobotany approach allowed us to determine the RDB history including diffusion and reproduction events. We found that the complex genetic structure among the RDB sub-populations is highly consistent with the structure of the seed diffusion and reproduction network drawn based on the ethnobotanical study. This structure highlighted the key role of the farmer-led seed diffusion through founder effects, selection and genetic drift due to human practices. An important result is that the genetic diversity conserved on farm is complementary to that found in the genebank indicating that both systems are required for a more efficient crop diversity conservation..

Data from: Chromosome number evolves independently of genome size in a clade with non-localized centromeres (Carex: Cyperaceae)

Thu, 23 Feb 2012 21:02:30 GMT

The effects of chromosome rearrangement on genome size are poorly understood. While chromosome duplications and deletions have predictable effects on genome size, chromosome fusion, fission, and translocation do not. In this study, we investigate genome size and chromosome number evolution in 87 species of Carex, one of the most species-rich genera of flowering plants and one that has undergone an exceptionally high rate of chromosome rearrangement. Using phylogenetic generalized least squares regression, we find that the correlation between chromosome number and genome size in the genus grades from flat or weakly positive at fine phylogenetic scales to weakly negative at deeper phylogenetic scales. The rate of chromosome evolution exhibits a significant increase near the crown of a species-rich clade that arose approximately 5 million years ago. Genome size evolution, however, demonstrates a nearly constant rate across the entire tree. We hypothesize that this decoupling of genome size from chromosome number helps explain the high lability of chromosome number in the genus, as it reduces indirect selection on chromosome number.

Data from: Decoupling of genetic and phenotypic divergence in a headwater landscape

Wed, 22 Feb 2012 18:02:48 GMT

In stream organisms, the landscape affecting intraspecific genetic and phenotypic divergence is comprised of two fundamental components: the stream network and terrestrial matrix. These components are known to differentially influence genetic structure in stream species, but, to our knowledge, no study has compared their effects on genetic and phenotypic divergence. We examined how the stream network and terrestrial matrix affect genetic and phenotypic divergence in two stream salamanders, Gyrinophilus porphyriticus and Eurycea bislineata, in the Hubbard Brook Watershed, New Hampshire, USA. Based on previous findings and differences in adult terrestriality, we predicted that genetic divergence and phenotypic divergence in body morphology would be correlated in both species, but structured primarily by distance along the stream network in G. porphyriticus, and by overland distance in E. bislineata. Surprisingly, spatial patterns of genetic and phenotypic divergence were not strongly correlated. Genetic divergence, based on AFLPs, increased with absolute geographic distance between sites. Phenotypic divergence was unrelated to absolute geographic distance, but related to relative stream vs. overland distances. In G. porphyriticus, phenotypic divergence was low when sites were close by stream distance alone and high when sites were close by overland distance alone. The opposite was true for E. bislineata. These results show that small differences in life history can produce large differences in patterns of intraspecific divergence, and the limitations of landscape genetic data for inferring phenotypic divergence. Our results also underscore the importance of explicitly comparing how terrestrial and aquatic conditions affect spatial patterns of divergence in species with biphasic life cycles.

Data from: Comparative analysis of encephalization in mammals reveals relaxed constraints on anthropoid primate and cetacean brain scaling

Wed, 22 Feb 2012 18:23:06 GMT

There is a well-established allometric relationship between brain and body mass in mammals. Deviation of relatively increased brain size from this pattern appears to coincide with enhanced cognitive abilities. To examine whether there is a phylogenetic structure to such episodes of changes in encephaliazation across mammals we used phylogenetic techniques to analyze brain mass, body mass, and encephalization quotient (EQ) among 630 extant mammalian species. Among all mammals, anthropoid primates and odontocete cetaceans have significantly greater variance in EQ, suggesting that evolutionary constraints that result in a strict correlation between brain and body mass have independently become relaxed. Moreover, ancestral state reconstructions of absolute brain mass, body mass, and EQ revealed patterns of increase and decrease in EQ within anthropoid primates and cetaceans. We propose both neutral drift and selective factors may have played a role in the evolution of brain:body allometry.

Data from: Genetic effects on mating success and partner choice in a social mammal

Wed, 22 Feb 2012 19:03:45 GMT

Mating behavior has profound consequences for two phenomena - individual reproductive success and the maintenance of species boundaries - that contribute to evolutionary processes. Studies of mating behavior in relation to individual reproductive success are common in many species, but studies of mating behavior in relation to genetic variation and species boundaries are less commonly conducted in socially complex species. Here, we leveraged extensive observations of a wild yellow baboon (Papio cynocephalus) population that has experienced recent gene flow from a close sister taxon, the anubis baboon (Papio anubis), to examine how admixture-related genetic background affects mating behavior. We identified novel effects of genetic background on mating patterns, including an advantage accruing to anubis-like males and assortative mating among both yellow-like and anubis-like pairs. These genetic effects acted alongside social dominance rank, inbreeding avoidance, and age to produce highly nonrandom mating patterns. Our results suggest that this population may be undergoing admixture-related evolutionary change, driven in part by nonrandom mating. However, the strength of the genetic effects is mediated by behavioral plasticity and social interactions, emphasizing the strong influence of social context on mating behavior in socially complex species.

Data from: Evolutionary ecology of Early Paleocene planktonic foraminifera: size, depth habitat and symbiosis

Wed, 22 Feb 2012 19:37:34 GMT

The carbon stable isotope (13C) composition of the calcitic tests of planktonic foraminifera has an important role as a geochemical tracer of ocean carbon system changes associated with the Cretaceous/Paleogene (K/Pg) mass extinction event and its aftermath. Questions remain, however, about the extent of 13C isotopic disequilibrium effects and the impact of depth habitat evolution on test calcite 13C among rapidly evolving Paleocene species, and the influence this has on reconstructed surface-to-deep ocean dissolved inorganic carbon (DIC) gradients. A synthesis of new and existing multispecies data, on the relationship between 13C and 18O and test size, sheds light on these issues. Results suggest that early Paleocene species quickly radiated into a range of depths habitats in a thermally stratified water column. Negative 18O gradients with increasing test size in some species of Praemurica suggest either ontogenetic or ecotypic dependence on calcification temperature that may reflect depth/light controlled variability in symbiont photosynthetic activity. The pattern of positive 13C test-size correlations allows us to (1) identify metabolic disequilibrium 13C effects in small foraminifera tests, as occur in the immediate aftermath of the K/Pg event, (2) constrain the timing of evolution of foraminiferal photosymbiosis to 63.5 Ma, ~0.9 Myr earlier than previously suggested, and (3) identify the apparent loss of symbiosis in a late-ranging morphotype of Praemurica. These findings have implications for interpreting 13C DIC gradients at a resolution appropriate for incoming highly resolved K/Pg core records.

Data from: MHC diversity, malaria and lifetime reproductive success in collared flycatchers

Wed, 22 Feb 2012 19:58:32 GMT

Major Histocompatibility Complex (MHC) genes encode proteins involved in the recognition of parasite-derived antigens. Their extreme polymorphism is presumed to be driven by coevolution with parasites. Host-parasite coevolution was also hypothesised to optimize within-individual MHC diversity at the intermediate level. Here, we use unique data on lifetime reproductive success (LRS) of female collared flycatchers to test whether LRS is associated with within-individual MHC class II diversity. We also examined the association between MHC and infection with avian malaria. Using 454 sequencing, we found that individual flycatchers carry between 3 and 23 functional MHC class II B alleles. Predictions of the optimality hypothesis were not confirmed by our data as the prevalence of blood parasites decreased with functional MHC diversity. Furthermore, we did not find evidence for an association between MHC diversity and LRS.

Data from: The effect of cost surface parameterization on landscape resistance estimates

Fri, 20 Jan 2012 16:00:31 GMT

A cost or resistance surface is a representation of a landscape’s permeability to animal movement or gene flow and is a tool for measuring functional connectivity in landscape ecology and genetics studies. Parameterizing cost surfaces by assigning weights to different landscape elements has been challenging however, because true costs are rarely known; thus, expert opinion is often used to derive relative weights. Assigning weights would be made easier if the sensitivity of different landscape resistance estimates to relative costs was known. We carried out a sensitivity analysis of three methods to parameterize a cost surface and two models of landscape permeability: least cost path and effective resistance. We found two qualitatively different responses to varying cost weights: linear and asymptotic changes. The most sensitive models (i.e. those leading to linear change) were accumulated least cost and effective resistance estimates on a surface coded as resistance (i.e. where high-quality elements were held constant at a low-value, and low-quality elements were varied at higher values). All other cost surface scenarios led to asymptotic change. Developing a cost surface that produces a linear response of landscape resistance estimates to cost weight variation will improve the accuracy of functional connectivity estimates, especially when cost weights are selected through statistical model fitting procedures. On the other hand, for studies where cost weights are unknown and model selection is not being used, methods where resistance estimates vary asymptotically with cost weights may be more appropriate, because of their relative insensitivity to parameterization.

Data from: Do different disparity proxies converge on a common signal? Insights from the cranial morphometrics and evolutionary history of Pterosauria (Diapsida: Archosauria)

Tue, 07 Feb 2012 17:24:05 GMT

Disparity, or morphological diversity, is often quantified by evolutionary biologists investigating the macroevolutionary history of clades over geological timescales. Disparity is typically quantified using proxies for morphology, such as measurements, discrete anatomical characters, or geometric morphometrics. If different proxies produce differing results, then the accurate quantification of disparity in deep time may be problematic. However, despite this, few studies have attempted to examine disparity of a single clade using multiple morphological proxies. Here, as a case study for this question, we examine the disparity of the volant Mesozoic fossil reptile clade Pterosauria, an intensively studied group that achieved substantial morphological, ecological, and taxonomic diversity during their 145+ million year evolutionary history. We characterise broadscale patterns of cranial morphological disparity for pterosaurs for the first time using landmark-based geometric morphometrics, and make comparisons to calculations of pterosaur disparity based on alternative metrics. Landmark-based disparity calculations suggest that monofenestratan pterosaurs were more diverse cranially than basal non-monofenestratan pterosaurs (at least when the aberrant anurognathids are excluded), and that peak cranial disparity may have occurred in the Early Cretaceous, relatively late in pterosaur evolution. Significantly, our cranial disparity results are broadly congruent with those based on whole skeleton discrete character and limb proportion datasets, indicating that these divergent approaches document a consistent pattern of pterosaur morphological evolution. Therefore, pterosaurs provide an exemplar case demonstrating that different proxies for morphological form can converge on the same disparity signal, which is encouraging because often only one such proxy is available for extinct clades represented by fossils. Furthermore, mapping phylogeny into cranial morphospace demonstrates that pterosaur cranial morphology is significantly correlated with, and potentially constrained by, phylogenetic relationships.

Data from: Genetic and phenotypic variation in juvenile development in relation to temperature and developmental pathway in a geometrid moth

Thu, 26 Jan 2012 18:51:01 GMT

Life histories show genetic population-level variation due to spatial variation in selection pressures. Phenotypic plasticity in life histories is also common, facilitating fine-tuning of the phenotype in relation to the prevailing selection regime. In multivoltine (≥ 2 generations / year) insects, individuals following alternative developmental pathways (diapause / direct development) experience different selection regimes. We studied the genetic and phenotypic components of juvenile development in Cabera exanthemata (Lepidoptera: Geometridae) in a factorial split-brood experiment. F2 offspring of individuals originating from populations in northern and central Finland were divided among manipulations defined by temperature (14ºC / 20ºC) and day length (24h / 15h). Short day length invariably induced diapause, whereas continuous light almost invariably induced direct development in both regions, although northern populations are strictly univoltine in the wild. Individuals from northern Finland had higher growth rates, shorter development times and higher pupal masses than individuals from central Finland across the conditions, indicating genetic differences between regions. Individuals that developed directly into adults tended to have higher growth rates, shorter development times and higher pupal masses than those entering diapause, indicating phenotypic plasticity. Temperature-induced plasticity was substantial; growth rate was much higher, development time much shorter and pupal mass higher at 20ºC than at 14ºC. The degree of plasticity in relation to developmental pathway was pronounced at 20ºC in growth rate and development time and at 14ºC in pupal mass, emphasizing multidimensionality of reaction norms. The observed genetic variation and developmental plasticity seem adaptive in relation to time-stress due to seasonality.

Data from: Genetic variation underlying the expression of a polyphenism

Wed, 18 Jan 2012 18:19:53 GMT

Polyphenic traits are widespread, and represent a conditional strategy sensitive to environmental cues. The environmentally cued threshold (ET) model considers the switchpoint between alternative phenotypes as a polygenic quantitative trait with normally distributed variation. However, the genetic variation for switchpoints has rarely been explored empirically. Here we used inbred lines to investigate the genetic variation for the switchpoint in the mite Rhizoglyphus echinopus, in which males are either fighters or scramblers. The conditionality of male dimorphism varied among inbred lines, indicating that there was genetic variation for switchpoints in the base population, as predicted by the ET model. Our results also suggest a mixture between canalised and conditional strategists in R. echinopus. We propose that major genes that canalise morph expression and affect the extent to which a trait can be conditionally expressed could be a feature of the genetic architecture of threshold traits in other taxa.

Data from: Complex patterns of multivariate selection on the ejaculate of a broadcast spawning marine invertebrate

Tue, 21 Feb 2012 17:35:31 GMT

Assessing how selection operates on several, potentially interacting, components of the ejaculate is a challenging endeavour. Ejaculates can be subject to natural and/or sexual selection, which can impose both linear (directional) and nonlinear (stabilizing, disruptive and correlational) selection on different ejaculate components. Most previous studies have examined linear selection of ejaculate components and, consequently, we know very little about patterns of nonlinear selection on the ejaculate. Even less is known about how selection acts on the ejaculate as a functionally integrated unit, despite evidence of covariance among ejaculate components. Here we assess how selection acts on multiple ejaculate components simultaneously in the broadcast spawning sessile invertebrate Mytilus galloprovincialis using the statistical tools of multivariate selection analyses. Our analyses of relative fertilization rates revealed complex patterns of selection on sperm velocity, motility and morphology. Interestingly, the most successful ejaculates were made up of slower-swimming sperm with relatively low percentages of motile cells, and sperm with smaller head volumes that swam in highly pronounced curved swimming trajectories. These results are consistent with an emerging body of literature on fertilization kinetics in broadcast spawners, and shed light on the fundamental nature of selection acting on the ejaculate as a functionally integrated unit.

Data from: A significant component of ageing (DNA damage) is reflected in fading breeding colors: an experimental test using innate antioxidant mimetics in painted dragon lizards

Tue, 21 Feb 2012 17:49:57 GMT

A decade ahead of their time, von Schantz and coworkers united sexual selection and free radical biology by identifying causal links between deep-rooted physiological processes that dictate resistance to toxic waste from oxidative metabolism (reactive oxygen species), and phenotypic traits, such as ornaments. Ten years later, these ideas have still only been tested with indirect estimates of free radical levels (oxidative stress) subsequent to the action of innate and dietary antioxidants. Here we measure net superoxide (a selection pressure for antioxidant production) and experimentally manipulate superoxide antioxidation using a synthetic mimetic of superoxide dismutase, Eukarion 134 (EUK). We then measure the toxic effect of superoxide in terms of DNA erosion and concomitant loss of male breeding coloration in the lizard, Ctenophorus pictus. Control males suffered more DNA damage than EUK-males. Spectroradiometry showed that male coloration is lost in relation to superoxide and covaries with DNA erosion; in control males these variables explained 72 % of color loss, whereas in EUK males, the fading of coloration was unaffected by superoxide and unrelated to DNA damage. Thus, EUK’s powerful antioxidation removes the erosion effect of superoxide on coloration and experimentally verifies the prediction that colors reflect innate capacity for antioxidation.

Data from: The relation between the neutrality index for mitochondrial genes and the distribution of mutational effects on fitness

Tue, 21 Feb 2012 17:59:04 GMT

We explore factors affecting patterns of polymorphism and divergence (as captured by the neutrality index) at mammalian mitochondrial loci. To do this, we develop a population genetic model that incorporates a fraction of neutral amino acid sites, mutational bias, and a probability distribution of selection coefficients against new nonsynonymous mutations. We confirm, by reanalyzing publicly available data sets, that the mitochondrial cyt-b gene shows a broad range of neutrality indices across mammalian taxa, and explore the biological factors that can explain this observation. We find that observed patterns of differences in the neutrality index, polymorphism and divergence are not caused by differences in mutational bias. They can, however, be explained by a combination of a small fraction of neutral amino acid sites, weak selection acting on most amino acid mutations, and differences in effective population size among taxa.

Data from: Divergence and biogeography of the recently evolved Macaronesian red Festuca (Gramineae) species inferred from coalescence-based analyses

Wed, 04 Jan 2012 20:06:47 GMT

Studying the biogeography and the phylogeography of the endemic Macaronesian red Festuca species (Loliinae, Poaceae) is of prime interest in understanding the speciation and colonization patterns of recently evolved groups in oceanic archipelagos. Coalescence-based analyses of plastid trnLF sequences were employed to estimate evolutionary parameters and to test different species-history scenarios that model the pattern of species divergence. Bayesian IM estimates of species divergence times suggested that ancestral lineages of diploid Macaronesian and Iberian red fescues could have diverged between 1.2 to 1.57 Ma. When empirical data was compared to the expected distributions of discordance and p-distance statistics, two species-history models were supported in which the first branching lineage derived in Canarian F. agustinii. Its sister lineage involved a recent polytomy, following the Canarian model, or the sequential branching of lineages leading to Madeiran F. jubata and finally to the sister clades of the continental F. rivularis and the Azorean F. francoi and F. petraea, following the Sequential model. Nested Clade Phylogeographic Analysis (NCPA) and a first-proposed host-parasite co-evolutionary ParaFit method were used to detect the phylogeographic signal. NCPA inferred long distance colonizations for the entire diploid red Festuca complex, but allopatric fragmentation and isolation by distance (IBD) patterns were inferred within archipelagos. In addition, the ParaFit method suggested a generalized pattern of a Stepping Stone Model at all hierarchical levels. Maximum likelihood - based Dispersal-Extinction-Colonization (DEC) models were superimposed on the Sequential species tree. The three-independent-colonization (3IC) model was the best supported biogeographic scenario, concurring with previous analysis based on multilocus AFLP data.

Data from: Contemporary evolution of sea urchin gamete-recognition proteins: experimental evidence of density-dependent gamete performance predicts shifts in allele frequencies over time

Tue, 14 Feb 2012 18:52:37 GMT

Species whose reproductive strategies evolved at one density regime might be poorly adapted to other regimes. Field and laboratory experiments on the sea urchin Strongylocentrotus franciscanus examined the influences of the two most common sperm bindin alleles, which differ at two amino acid sites, on fertilization success. In the field experiment, the Arginine/Glycine (RG) genotype performed best at low densities and the Glycine/Arginine (GR) genotype at high densities. In the lab experiment, the RG genotype had a higher affinity with available eggs, whereas the GR genotype was less likely to induce polyspermy. These sea urchins can reach 200 years of age. The RG allele dominates in old sea urchins, whereas younger sea urchins have near equal RG and GR allele frequencies. A latitudinal cline in RG and GR genotypes is consistent with longer survival of sea urchins in the north and with predominance of RG genotypes in older individuals. The oldest sea urchins were likely conceived at low densities, before sea-urchin predators, like sea otters, were overharvested and sea urchin densities exploded off the west coast. Contemporary evolution of gamete-recognition proteins might allow species to adapt to shifts in abundances and reduces the risk of reproductive failure in altered populations.

Data from: Fisher's geometrical model of fitness landscape and variance in fitness within a changing environment

Tue, 07 Feb 2012 17:37:37 GMT

The fitness of an individual can be simply defined as the number of its offspring in the next generation. However, it is not well understood how selection on the phenotype determines fitness. In accordance with Fisher’s fundamental theorem, fitness should have no or very little genetic variance, whereas empirical data suggest that is not the case. To bridge these knowledge gaps, we follow Fisher’s geometrical model and assume that fitness is determined by multivariate stabilizing selection towards an optimum that may vary among generations. We assume random mating, free recombination, additive genes, and uncorrelated stabilizing selection and mutational effects on traits. In a constant environment, we find that genetic variance in fitness under mutation-selection balance is a U-shaped function of the number of traits (i.e. of the so-called “organismal complexity”). Because the variance can be high if the organism is of either low or high complexity, this suggests that complexity has little direct costs. Under a temporally varying optimum, genetic variance increases relative to a constant optimum and increasingly so when the mutation rate is small. Therefore mutation and changing environment together can maintain high genetic variance. These results therefore lend support to Fisher’s geometric model of a fitness landscape.

Data from: Response to selection on cold tolerance is constrained by inbreeding

Thu, 02 Feb 2012 18:28:46 GMT

The evolutionary potential of any given population is of fundamental importance for its longer-term prospects. Modern land-use practices often result in small and isolated populations, increasing extinction risk through reduced genetic diversity caused by inbreeding or drift. Concomitant genetic erosion may further interfere with a population’s evolutionary potential. In this study we investigate the consequences of inbreeding on evolutionary potential (the ability to increase cold resistance) in the tropical butterfly Bicyclus anynana. We applied artificial selection to chill-coma recovery time, starting from three levels of inbreeding (outbred control, one or two full-sib matings). Ten generations of selection produced highly divergent phenotypes, with the lines selected for increased cold tolerance showing by ca. 28% shorter recovery times after cold exposure relative to unselected controls. Correlated responses to selection in 10 life history and stress resistance traits were essentially absent. Inbred lines showed a weaker response to selection, thus indicating a reduced evolutionary potential. Inbreeding depression was still measurable in some traits after the course of selection. Traits more closely related to fitness showed a clear fitness rebound, suggesting a trait-specific impact of purging. Our findings have important implications for the longer-term survival of small populations in fragmented landscapes.

Data from: Patterns of reproductive isolation in Nolana (Chilean Bellflower)

Tue, 07 Feb 2012 16:49:31 GMT

We examined reproductive isolating barriers at four postmating stages among 11 species from the morphologically diverse genus Nolana (Solanaceae). At least one stage was positively correlated with both genetic and geographic distance between species. Postzygotic isolation was generally stronger and faster evolving than postmating prezygotic isolation. In addition, there was no evidence for mechanical isolation or for reproductive character displacement in floral traits that can influence pollinator isolation. In general, among the potential isolating stages examined here, postzygotic barriers appear to be more effective contributors to reducing gene flow, including between sympatric species.

Data from: Costs and constraints conspire to produce honest signalling: insights from an ant queen pheromone

Wed, 08 Feb 2012 16:12:01 GMT

Signal costs and evolutionary constraints have both been proposed as ultimate explanations for the ubiquity of honest signalling, but the interface between these two factors is unclear. Here, I propose a pluralistic interpretation, and use game theory to demonstrate that evolutionary constraints determine whether signals evolve to be costly or cheap. Specifically, when the costs or benefits of signalling are strongly influenced by the sender’s quality, low-cost signals evolve. The model reaffirms that cheap and costly signals can both be honest, and predicts that expensive signals should have more positive allometric slopes than cheap ones. The new framework is applied to an experimental study of an ant queen pheromone that honestly signals fecundity. Juvenile hormone was found to have opposing, dose-dependent effects on pheromone production and fecundity and was fatal at high doses, indicating that endocrine-mediated trade-offs preclude dishonesty. Several lines of evidence suggest that the realised cost of pheromone production may be non-trivial, and the antagonistic effects of juvenile hormone indicate the presence of significant evolutionary constraints. I conclude that the honesty of queen pheromones and other signals is likely enforced by both the cost of dishonesty and a suite of evolutionary constraints.

Data from: Sex roles and mutual mate choice matters during mate sampling

Mon, 20 Feb 2012 16:43:45 GMT

The roles of females and males in mating competition and mate choice have lately proven more variable, between and within species, than previously thought. In nature, mating competition occurs during mate search, and is expected to be regulated by the numbers of potential mates and same-sex competitors. Here, we present the first study to test how a temporal change in sex roles affects mating competition and mate choice during mate sampling. Our model system (the marine fish Gobiusculus flavescens) is uniquely suitable because of its change in sex roles, from conventional to reversed, over the breeding season. As predicted from sex role theory, courtship was typically initiated by males and terminated by females early in the breeding season. The opposite pattern was observed late in the season, at which time several females often simultaneously courted the same male. Mate-searching females visited more males early than late in the breeding season. Our study shows that mutual mate choice and mating competition can have profound effects on female and male behavior. Future work needs to consider the dynamical nature of mating competition and mate choice if we aim to fully understand sexual selection in the wild.

Data from: Is your phylogeny informative? Measuring the power of comparative methods

Thu, 02 Feb 2012 15:15:08 GMT

Phylogenetic comparative methods may fail to produce meaningful results when either the underlying model is inappropriate or the data contain insufficient information to inform the inference. The ability to measure the statistical power of these methods has become crucial to ensure that data quantity keeps pace with growing model complexity. Through simulations, we show that commonly applied model choice methods based on information criteria can have remarkably high error rates; this can be a problem because methods to estimate the uncertainty or power are not widely known or applied. Furthermore, the power of comparative methods can depend significantly on the structure of the data. We describe a Monte Carlo based method which addresses both of these challenges, and show how this approach both quantifies and substantially reduces errors relative to information criteria. The method also produces meaningful confidence intervals for model parameters. We illustrate how the power to distinguish different models, such as varying levels of selection, varies both with number of taxa and structure of the phylogeny. We provide an open-source implementation in the pmc (“Phylogenetic Monte Carlo”) package for the R programming language. We hope such power analysis becomes a routine part of model comparison in comparative methods.

Data from: Effective population size in eusocial Hymenoptera with worker-produced males

Fri, 17 Feb 2012 16:31:58 GMT

In many eusocial Hymenoptera, a proportion of males are produced by workers. To assess the effect of male production by workers on the effective population size Ne, a general expression of Ne in Hymenoptera with worker-produced males is derived on the basis of the genetic drift in the frequency of a neutral allele. Stochastic simulation verifies that the obtained expression gives a good prediction of Ne under a wide range of conditions. Numerical computation with the expression indicates that worker reproduction generally reduces Ne. The reduction can be serious in populations with a unity or female biased breeding sex ratio. Worker reproduction may increase Ne in populations with a male biased breeding sex ratio, only if each laying worker produce a small number of males and the difference of male progeny number among workers is not large. Worker reproduction could be an important cause of the generally lower genetic variation found in Hymenoptera, through its effect on Ne.

Data from: Dietary hardness, loading behavior, and the evolution of skull form in bats

Fri, 17 Feb 2012 16:55:51 GMT

The morphology and biomechanics of the vertebrate skull reflect the physical properties of diet and behaviors used in food acquisition and processing. We use phyllostomid bats, the most diverse mammalian dietary radiation, to investigate if and how changes in dietary hardness and loading behaviors during feeding shaped the evolution of skull morphology and biomechanics. When selective regimes of food hardness are modeled, we found that species consuming harder foods have evolved skull shapes that allow for more efficient bite force production. These species have shorter skulls and a greater reliance on the temporalis muscle, both of which contribute to a higher mechanical advantage at an intermediate gape angle. The evolution of cranial morphology and biomechanics also appears to be related to loading behaviors. Evolutionary changes in skull shape and the relative role of the temporalis and masseter in generating bite force are correlated with changes in the use of torsional and bending loading behaviors. Functional equivalence appears to have evolved independently among three lineages of species that feed on liquids and are not obviously morphologically similar. These trends in cranial morphology and biomechanics provide insights into behavioral and ecological factors shaping the skull of a trophically diverse clade of mammals.

Data from: Forecasting changes in population genetic structure of Alpine plants in response to global warming

Fri, 17 Feb 2012 19:34:25 GMT

Species range shifts in response to climate and land use change are commonly forecasted with species distribution models based on species occurrence or abundance data. Although appealing, these models ignore the genetic structure of species, and the fact that different populations might respond in different ways due to adaptation to their environment. Here, we introduced ancestry distribution models, i.e., statistical models of the spatial distribution of ancestry proportions, for forecasting intra-specific changes based on genetic admixture instead of species occurrence data. Using multi-locus genotypes and extensive geographic coverage of distribution data across the European Alps, we applied this approach to 20 alpine plant species considering a global increase in temperature from 0.25°C to 4°C. We forecasted the magnitudes of displacement of contact zones between plant populations potentially adapted to warmer environments and other populations. While a global trend of movement in a northeast direction was predicted, the magnitude of displacement was species-specific. For a temperature increase of 2°C, contact zones were predicted to move by 92 km on average (minimum of 5 km, maximum of 212 km), and by 188 km for an increase of 4°C (minimum of 11 km, maximum of 393 km). Intra-specific turnover – measuring the extent of change in global population genetic structure – was generally found to be moderate for 2°C of temperature warming. For 4°C of warming, however, the models indicated substantial intra-specific turnover for ten species. These results illustrate that, in spite of unavoidable simplifications, ancestry distribution models open new perspectives to forecast population genetic changes within species, and complement more traditional distribution-based approaches.

Data from: Herbivores modify selection on plant functional traits in a temperate rainforest understory

Fri, 17 Feb 2012 19:43:18 GMT

There is limited evidence regarding the adaptive value of plant functional traits in contrasting light environments. It has been suggested that changes in these traits in response to light availability can increase herbivore susceptibility. We tested the adaptive value of plant functional traits linked with carbon gain in contrasting light environments, and also evaluated whether herbivores can modify selection on these traits in each light environment. In a temperate rainforest, we examined phenotypic selection on functional traits in seedlings of the pioneer tree Aristotelia chilensis growing in sun (canopy gap) and shade (forest understory), and subjected to either natural herbivory or herbivore exclusion. We found differential selection on functional traits depending on light environment. In sun, there was positive directional selection on photosynthetic rate and relative growth rate (RGR), indicating that selection favors competitive ability in a high-resource environment. Seedlings with high specific leaf area (SLA) and intermediate RGR were selected in shade, suggesting that light capture and a conservative resource-use are favored in the understory. Herbivores reduced the strength of positive directional selection acting on SLA in shade. We provide the first demonstration that natural herbivory rates can change the strength of selection on plant ecophysiological traits, i.e., attributes whose main function is resource uptake. Research addressing the evolution of shade tolerance should incorporate the selective role of herbivores.

Data from: De novo characterization of the Timema cristinae transcriptome facilitates marker discovery and inference of genetic divergence.

Wed, 04 Jan 2012 17:54:12 GMT

Adaptation to different ecological environments can promote speciation. Although numerous examples of such ‘ecological speciation’ exist, the genomic basis of the process, and the role of gene flow in it, remains less understood. This is, at least in part, because systems that are well characterized in terms of their ecology often lack genomic resources. In this study we characterize the transcriptome of Timema cristinae stick insects, a system that has been researched intensively in terms of ecological speciation, but for which genomic resources have not been previously developed. Specifically, we obtained >1 million 454 sequencing reads that assembled into 84,937 contigs representing approximately 18,282 unique genes and tens of thousands of potential molecular markers. Second, as an illustration of their utility, we used these genomic resources to assess multi-locus genetic divergence within both an ecotype pair and a species pair of Timema stick insects. The results suggest variable levels of genetic divergence and gene flow among taxon pairs and genes and illustrate a first step towards future genomic work in Timema.

Data from: Divergent natural selection with gene flow along major environmental gradients in Amazonia: insights from genome scans, population genetics and phylogeography of the characin fish Triportheus albus

Thu, 16 Feb 2012 19:10:58 GMT

The unparalleled diversity of tropical ecosystems like the Amazon Basin has been traditionally explained using spatial models within the context of climatic and geological history. Yet, it is adaptive genetic diversity that defines how species evolve and interact within an ecosystem. Here we combine genome scans, population genetics and sequenced-based phylogeographic analyses to examine spatial and ecological arrangements of selected and neutrally evolving regions of the genome of an Amazonian fish, Triportheus albus. Using a sampling design encompassing five major Amazonian rivers, three hydrochemical settings, and 352 nuclear markers and two mitochondrial DNA genes, we assess the influence of environmental gradients as biodiversity drivers in Amazonia. We identify strong divergent natural selection with gene flow and isolation by environment across craton (black and clear color) and Andean (white colour) derived water types. Furthermore, we find that heightened selection and population genetic structure present at the interface of these water types appears more powerful in generating diversity than the spatial arrangement of river systems and vicariant biogeographic history. The results from our study challenge assumptions about the origin and distribution of adaptive and neutral genetic diversity in tropical ecosystems. In addition, they have important implications for measures of biodiversity and evolutionary potential in one of the world’s most diverse and iconic ecosystems.

Data from: Rapid evolution of an adaptive cyanogenesis cline in introduced North American white clover (Trifolium repens L.)

Sat, 26 Nov 2011 03:09:40 GMT

White clover is polymorphic for cyanogenesis (HCN production after tissue damage), and this herbivore defense polymorphism has served as a classic model for studying adaptive variation. The cyanogenic phenotype requires two interacting biochemical components; the presence/absence of each component is controlled by a simple Mendelian gene (Ac/ac and Li/li). Climate-associated cyanogenesis clines occur in both native (Eurasian) and introduced populations worldwide, with cyanogenic plants predominating in warmer locations. Moreover, previous studies have suggested that epistatic selection may act within populations to maintain cyanogenic (AcLi) plants and acyanogenic plants that lack both components (acli plants) at the expense of plants possessing a single component (Acli and acLi plants). Here we examine the roles of selection, gene flow, and demography in the evolution of a latitudinal cyanogenesis cline in introduced North American populations. Using 1,200 plants sampled across a 1,650 km transect, we determine the distribution of cyanogenesis variation across the central U.S. and investigate whether clinal variation is adaptive or an artifact of population introduction history. We also test for evidence of epistatic selection. We detect a clear latitudinal cline, with cyanogenesis frequencies increasing from 11% to 86% across the transect. Population structure analysis using nine microsatellite loci indicates that the cline is adaptive and not a byproduct of demographic history. However, we find no evidence for epistatic selection within populations. Our results provide strong evidence for rapid adaptive evolution in these introduced populations, and they further suggest that the mechanisms maintaining adaptive variation may vary among populations of a species.

Data from: Building genetic networks using relatedness information: a novel approach for the estimation of dispersal and characterization of group structure in social animals

Thu, 05 Jan 2012 17:40:38 GMT

Natal dispersal is an important life history trait driving variation in individual fitness and, therefore, a proper understanding of the factors underlying dispersal behaviour is critical to many fields including population dynamics, behavioural ecology and conservation biology. However, individual dispersal patterns remain difficult to quantify despite many years of research using direct and indirect methods. Here, we quantify dispersal in a single intensively-studied population of the cooperatively breeding chestnut-crowned babbler (Pomatostomus ruficeps) using genetic networks created from the combination of pairwise relatedness data and social networking methods and compare this to dispersal estimates from re-sighting data. Not only does this novel approach identify movements between social groups within our study sites but also provides an estimation of immigration rates of individuals originating outside the study site. Both genetic and re-sighting data indicated that dispersal was strongly female-biased, but the magnitude of dispersal estimates was much greater using genetic data. This suggests that many previous studies relying on mark-recapture data may have significantly underestimated dispersal. An analysis of spatial genetic structure within the sampled population also supports the idea that females are more dispersive, with females having no structure beyond the bounds of their own social group while male genetic structure expands for 750 meters from their social group. Although the genetic network approach we have used is an excellent tool for visualising the social and genetic microstructure of social animals and identifying dispersers, our results also indicate the importance of applying them in parallel with behavioural and life history data.

Data from: Evidence of inbreeding depression but not inbreeding avoidance in a natural house sparrow population

Tue, 13 Dec 2011 19:46:13 GMT

Inbreeding is common in small and threatened populations, and often has a negative effect on individual fitness and genetic diversity. Thus, inbreeding can be an important factor affecting the persistence of small populations. In this study we investigated the effects of inbreeding on fitness in a small, wild population of house sparrows (Passer domesticus) on the island of Aldra, Norway. The population was founded in 1998 by four individuals (one female and three males). After the founding event the adult population rapidly increased to about 30 individuals in 2001. At the same time the mean inbreeding coefficient among adults increased from 0 to 0.04 in 2001, and thereafter fluctuated between 0.06 and 0.10, indicating a highly inbred population. We found a negative effect of inbreeding on lifetime reproductive success which seemed to be mainly due to an effect of inbreeding on annual reproductive success. This resulted in selection against inbred females. However, the negative effect of inbreeding was less strong in males, suggesting that selection against inbred individuals is at least partly sex-specific. To examine whether individuals avoided breeding with close relatives we compared observed inbreeding and kinship coefficients in the population with those obtained from simulations of random mating. We found no significant differences between the two, indicating weak or absent inbreeding avoidance. We conclude that there was inbreeding depression in our population. Despite this, birds did not seem to actively avoid mating with close relatives, perhaps as a consequence of constraints on mating possibilities in such a small population.

Data from: Gene flow and pathogen transmission among bobcats (Lynx rufus) in a fragmented urban landscape

Tue, 10 Jan 2012 20:47:11 GMT

Urbanization can result in the fragmentation of once contiguous natural landscapes into a patchy habitat interspersed within a growing urban matrix. Animals living in fragmented landscapes often have reduced movement among habitat patches due to avoidance of intervening human development, which potentially leads to both reduced gene flow and pathogen transmission between patches. Mammalian carnivores with large home ranges, such as bobcats (Lynx rufus), may be particularly sensitive to habitat fragmentation. We performed genetic analyses on bobcats and their directly transmitted viral pathogen, feline immunodeficiency virus (FIV), to investigate the effects of urbanization on bobcat movement. We predicted that urban development, including major freeways, would limit bobcat movement and result in genetically structured host and pathogen populations. We analyzed molecular markers from 106 bobcats and 19 FIV isolates from seropositive animals in urban southern California. Our findings indicate that reduced gene flow between two primary habitat patches has resulted in genetically distinct bobcat subpopulations separated by urban development including a major highway. However, the distribution of genetic diversity among FIV isolates determined through phylogenic analyses indicates that pathogen genotypes are less spatially structured – exhibiting a more even distribution between habitat fragments. We conclude that the types of movement and contact sufficient for disease transmission occur with enough frequency to preclude structuring among the viral population, but that the bobcat population is structured due to low levels of effective bobcat migration resulting in gene flow. We illustrate the utility in using multiple molecular markers that differentially detect movement and gene flow between subpopulations when assessing connectivity.

Data from: Are there indirect fitness benefits of female extra-pair reproduction? Lifetime reproductive success of within-pair and extra-pair offspring

Wed, 15 Feb 2012 17:07:50 GMT

The forces driving extra-pair reproduction by socially monogamous females, and the resulting genetic polyandry, remain unclear. A testable prediction of the hypothesis that extra-pair reproduction partly reflects indirect selection on females is that extra-pair young (EPY) will be fitter than their within-pair young (WPY) maternal half-siblings. This prediction has not been comprehensively tested in a wild population, requiring data on the lifetime reproductive success (LRS) of maternal half-sib EPY and WPY. We used 17 years of genetic parentage data from song sparrows, Melospiza melodia, to compare the LRS of hatched EPY and WPY maternal half-siblings measured as their lifetime number of hatched offspring, recruited offspring and hatched grandoffspring. EPY hatchlings were not significantly fitter than WPY hatchlings for any of three measures of LRS. Furthermore, opposite to prediction, EPY hatchlings tended to have lower LRS than their maternal half-sibling WPY hatchlings on average. EPY also tended to be less likely to survive to hatch than their maternal half-sibling WPY. Taken together, these results fail to support one key hypothesis explaining the evolution of genetic polyandry by socially monogamous females and suggest there may be weak indirect selection against female extra-pair reproduction in song sparrows.

Data from: Effect of habitat fragmentation on the genetic diversity of peripheral populations of beech in Central Italy

Wed, 15 Feb 2012 17:19:46 GMT

Fragmentation can affect the demographic and genetic structure of populations near the boundary of their bio-geographic range. Higher genetic differentiation among populations coupled with lower level of within population variability is expected as a consequence of reduced population size and isolation. The effects of these two factors have been rarely disentangled. Given their high gene flow, anemophilous forest trees should be more affected, in terms of loss of genetic diversity, by small population size rather than geographic isolation alone. We studied the impact of distance from the main range (a measure of isolation) and reduced population size on the within and among population components of genetic variability. We assayed 11 isozyme loci in 27 marginal populations of European beech (Fagus sylvatica L.) in Central Italy. Populations were divided in three groups with an increasing level of fragmentation. In the most fragmented group the within population genetic variability was slightly smaller and the among population differentiation significantly larger than in the other two groups. These results support the role of random genetic drift having a larger impact on the most fragmented group, while gene flow seems to balance genetic drift in the two less fragmented ones. Given that average distance from the main range is not different between the intermediate and the most fragmented group, but average population size is smaller, we can conclude that gene flow is effective, even at relatively long distances, in balancing the effect of fragmentation if population size is not too small.

Data from: Artificial selection on allometry: change in elevation but not slope

Wed, 15 Feb 2012 17:33:48 GMT

To what extent within-species (static) allometries constitute a constraint on evolution is the subject of a long-standing debate in evolutionary biology. A prerequisite for the constraint hypothesis is that static allometries are hard to change. Several studies have attempted to test this hypothesis with artificial-selection experiments, but their results remain inconclusive due to various methodological issues. Here, we present results from an experiment in which we selected independently on the slope and the elevation of the allometric relation between caudal-fin size and body size in male guppies (Poecilia reticulata). After three episodes of selection, the allometric elevation (i.e. intercept at constant slope) had diverged markedly between the lines selected to increase or decrease it, and showed a realized heritability of 50%. In contrast, the allometric slope remained unaffected by selection. These results suggest that the allometric elevation is more evolvable than the allometric slope, this latter representing a potential constraint on adaptive trait evolution. To our knowledge, this study is the first artificial-selection experiment that directly tests the evolvability of static allometric slopes.

Data from: Mitochondrial gene diversity associated with the atp9 stop codon in natural populations of wild carrot (Daucus carota ssp. carota)

Tue, 22 Nov 2011 17:51:05 GMT

Mitochondrial genomes extracted from wild populations of Daucus carota have been used as a genetic resource by breeders of cultivated carrot, yet little is known concerning the extent of their diversity in nature. Of special interest is a SNP in the putative stop codon of the mitochondrial gene atp9 that has been associated previously with male-sterile and male-fertile phenotypic variants. In this study either sequence or PCR/RFLP genotypes were obtained from the mitochondrial genes atp1, atp9 and cox1 found in D. carota individuals collected from 24 populations in the eastern U.S. More than half of the 128 individuals surveyed had a CAA or AAA, rather than TAA, genotype at the position usually thought to function as an atp9 stop codon in this species. We also found no evidence for mitochondrial RNA editing (Cytosine to Uridine) of the CAA stop codon in either floral or leaf tissue. Evidence for intra-genic recombination, as opposed the more common inter-genic recombination in plant mitochondrial genomes, in our data set is presented. Indel and SNP variants elsewhere in atp9, and in the other two genes surveyed, were non-randomly associated with the three atp9 stop codon variants, though further analysis suggested that multi-locus genotypic diversity had been enhanced by recombination. Overall the mitochondrial genetic diversity was only modestly structured among populations with an Fst of 0.34.

Data from: The response of correlated traits following cessation of fishery-induced selection

Tue, 03 Jan 2012 20:09:13 GMT

The application of evolutionary principles to the management of fisheries has gained considerable attention recently. Harvesting of fish may apply directional or disruptive selection to key life history traits and evidence for fishery-induced evolution is growing. The traits that are directly selected upon are often correlated (genetically or phenotypically) with a suite of interrelated physiological, behavioral, and morphological characters. A question that has received comparatively little attention is whether or not, after cessation of fishery-induced selection, these correlated traits revert back to previous states. Here, we empirically examine this question. In experiments with the Atlantic silverside, Menidia menidia, we applied size-selective culling for 5 generations and then maintained the lines a further 5 generations under random harvesting. We found that some traits do return to pre-harvesting levels (e.g., larval viability), some partially recover (e.g., egg volume, size at hatch), and others show no sign of change (e.g., food consumption rate, vertebral number). Such correlations among characters could, in theory, greatly accelerate or decelerate the recovery of fish populations. These results may explain why some fish stocks fail to recover after fishing pressure is relaxed.

Data from: Recent population decline and selection shape diversity of taxol-related genes

Tue, 14 Feb 2012 19:58:26 GMT

Taxanes are defensive metabolites produced by Taxus species (yews) and used in anticancer therapies. Despite their medical interest, patterns of natural diversity in taxane related genes are unknown. We examined variation at five main taxol-related genes of T. baccata in the Iberian Peninsula, a region where unique yew genetic resources are endangered. We looked at several gene features and applied complementary neutrality tests, including diversity/divergence tests, tests solely based on site-frequency spectrum and Zeng’s compound tests. To account for specific demography, microsatellite data were used to infer historical changes in population size based on an Approximate Bayesian Computation (ABC) approach. Polymorphism-divergence tests pointed to positive selection for genes TBT and TAT, and balancing selection for DBAT. In addition, neutrality tests based on site-frequency spectrum found that while a recent reduction in population size may explain most of statistics’ values, selection may still be in action in genes TBT and DBAT, at least in some populations. Molecular signatures on taxol genes suggest the action of frequent selective waves with different direction or intensity, possibly related to varying adaptive pressures produced by the host-enemy co-evolution on defense-related genes. Such natural selection processes may have produced taxane variants still undiscovered.

Data from: Plants and tortoises: mutations in the Arabidopsis jasmonate pathway increase feeding in a vertebrate folivore

Tue, 14 Feb 2012 20:10:37 GMT

Photosynthetic tissues, the major food source of many invertebrates and vertebrates, are well defended. Many defense traits in leaves are controlled via the jasmonate signalling pathway in which jasmonate acts as a hormone by binding to a receptor to activate responses that lead to increased resistance to invertebrate folivores. We predicted that mutations in jasmonate synthesis might also increase the vulnerability of leaves to vertebrate foliores and tested this hypothesis using the Eastern Hermann's tortoise (Eurotestudo boettgeri) and an Arabidopsis thaliana (Brassicaceae) allene oxide synthase (aos) mutant unable to synthesize jasmonate. Tortoises preferred the aos mutant over the wild type (WT). Based on these results we then investigated the effect of mutating jasmonate perception using a segregating population of the recesssive A. thaliana jasmonate receptor mutant coronatine insensitive1-1 (coi1-1). Genotyping of these plants after tortoise feeding revealed that the homozygous coi1-1 receptor mutant was consumed more readily than the heterozygous mutant or the WT. Therefore, the plant's ability to synthesize or perceive jasmonate reduces feeding by a vertebrate herbivore. We also tested whether or not tortoise feeding behaviour was influenced by glucosinolates, the principal defense chemicals in Arabidopsis leaves with known roles in defense against many generalist insects. However, in contrast to what has been observed with such insects, leaves in which the levels of these compounds were reduced genetically were consumed at the same rate as WT leaves.

Data from: Community assembly, species richness and nestedness of arbuscular mycorrhizal fungi in agricultural soils

Tue, 14 Feb 2012 20:46:37 GMT

Understanding how communities assemble is a central goal of ecology. This is particularly relevant for communities of arbuscular mycorrhizal fungi (AMF), because the community composition of these beneficial plant symbionts influences important ecosystem processes. Moreover, AMF may be used as sensitive indicators of ecological soil quality if they respond to environmental variation in a predictable way. Here we use a molecular profiling technique (T-RFLP of 25S rRNA gene fragments) to test which factors determine AM fungal community composition in 40 agricultural soils in the Netherlands. In particular, we test whether species richness, dominance structure and community nestedness are influenced by management type (in pairs of organically and conventionally farmed fields), and we examine the contribution of crop species (maize versus potato), soil type (sand versus clay textured soils), and habitat (plant root versus bulk soil) on AMF community characteristics. AMF richness varied from 1 to 11 taxa per field. Communities from species poor fields were found to be subsets of those in richer fields, indicating nestedness and a progressive “loss” from the species pool. AMF taxa richness and occurrence in soil and plant roots were highly correlated, and richness was related to management intensity (phosphate availability and grass cropping history together explained 34% and 50% of richness in roots and soils). Soil type together with soil chemical parameters explained only 17% of variance in AMF community structure. We synthesize these results by discussing the potential contribution of a “bottle-neck effect” on AMF communities through increased stochastic effects under environmental stress.